Publications

New Insights into the Microbial Profiles of Infected Root Canals in Traumatized Teeth.

Manoharan L, Brundin M, Rakhimova O, Chávez de Paz L, Romani Vestman N

J Clin Med 9 (12) 3877 [2020-11-28; online 2020-11-28]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]

The Human Adenovirus Type 2 Transcriptome: An Amazing Complexity of Alternatively Spliced mRNAs.

Westergren Jakobsson A, Segerman B, Wallerman O, ..., Pettersson U, Akusjärvi G

J. Virol. - (-) - [2020-11-25; online 2020-11-25]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Immobilization of sulfate and thiosulfate-reducing biomass on sand under haloalkaline conditions.

Sousa JAB, Bolgár A, Christel S, ..., Stams AJM, Plugge CM

Sci. Total Environ. 745 (-) 141017 [2020-11-25; online 2020-07-22]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genome-wide identification of Argonautes in Solanaceae with emphasis on potato.

Liao Z, Hodén KP, Singh RK, Dixelius C

Sci Rep 10 (1) 20577 [2020-11-25; online 2020-11-25]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

α-Synuclein promotes IAPP fibril formation in vitro and β-cell amyloid formation in vivo in mice.

Mucibabic M, Steneberg P, Lidh E, ..., Lindahl E, Edlund H

Sci Rep 10 (1) 20438 [2020-11-24; online 2020-11-24]

Variations among Viruses in Influent Water and Effluent Water at a Wastewater Plant over One Year as Assessed by Quantitative PCR and Metagenomics.

Wang H, Neyvaldt J, Enache L, ..., Bergstedt O, Norder H

Appl. Environ. Microbiol. 86 (24) - [2020-11-24; online 2020-11-24]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Structure dynamics of ApoA-I amyloidogenic variants in small HDL increase their ability to mediate cholesterol efflux.

Nilsson O, Lindvall M, Obici L, ..., Lagerstedt JO, Del Giudice R

J. Lipid Res. 62 (-) 100004 [2020-11-24; online 2020-11-24]

High CD45 expression of CD8+ and CD4+ T cells correlates with the size of HIV-1 reservoir in blood.

Petkov S, Bekele Y, Lakshmikanth T, ..., Brodin P, Chiodi F

Sci Rep 10 (1) 20425 [2020-11-24; online 2020-11-24]

Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Collaborative]

Inactivation of mediator complex protein 22 in podocytes results in intracellular vacuole formation, podocyte loss and premature death.

Rodriguez PQ, Unnersjö-Jess D, Zambrano SS, ..., Ebarasi L, Patrakka J

Sci Rep 10 (1) 20037 [2020-11-18; online 2020-11-18]

Integrated Microscopy Technologies Stockholm [Technology development]

Exploring autoantibody signatures in brain tissue from patients with severe mental illness.

Just D, Månberg A, Mitsios N, ..., Nilsson P, Carlström EL

Transl Psychiatry 10 (1) 401 [2020-11-18; online 2020-11-18]

Autoimmunity and Serology Profiling [Collaborative]

A complex DICER1 syndrome phenotype associated with a germline pathogenic variant affecting the RNase IIIa domain of DICER1.

Pontén E, Frisk S, Taylan F, ..., Lagerstedt-Robinson K, Nordgren A

J. Med. Genet. - (-) jmedgenet-2020-107385 [2020-11-18; online 2020-11-18]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury

Floriddia EM, Lourenço T, Zhang S, ..., Nilsson M, Castelo-Branco G

Nat Commun 11 (1) 5860 [2020-11-17; online 2020-11-17]

Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing (ISS) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Association between Aquatic Micropollutant Dissipation and River Sediment Bacterial Communities.

Coll C, Bier R, Li Z, ..., Gorokhova E, Sobek A

Environ. Sci. Technol. 54 (22) 14380-14392 [2020-11-17; online 2020-10-26]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine.

Calleja-Rodriguez A, Pan J, Funda T, ..., Abrahamsson S, Wu HX

BMC Genomics 21 (1) 796 [2020-11-16; online 2020-11-16]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

One-Pot, Metal-Free Synthesis of Dimethyl Carbonate from CO2 at Room Temperature

Khokarale SG, Bui TQ, Mikkola JP

Sustainable Chemistry 1 (3) 298-314 [2020-11-13; online 2020-11-13]

Obesity-associated microbiota contributes to mucus layer defects in genetically obese mice.

Schroeder BO, Birchenough GMH, Pradhan M, ..., Hansson GC, Bäckhed F

J. Biol. Chem. 295 (46) 15712-15726 [2020-11-13; online 2020-09-08]

Integrated Microscopy Technologies Gothenburg [Service]

A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site.

Martínez-Carranza M, Jonna VR, Lundin D, ..., Stenmark P, Hofer A

J. Biol. Chem. 295 (46) 15576-15587 [2020-11-13; online 2020-09-03]

Bioinformatics Support for Computational Resources [Service] Cryo-EM [Service] Protein Science Facility (PSF) [Service]

The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19.

Consiglio CR, Cotugno N, Sardh F, ..., Palma P, Brodin P

Cell 183 (4) 968-981.e7 [2020-11-12; online 2020-09-06]

Affinity Proteomics Stockholm [Service] Autoimmunity and Serology Profiling [Service] Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Technology development]

Identification of Pre-Diagnostic Metabolic Patterns for Glioma Using Subset Analysis of Matched Repeated Time Points.

Jonsson P, Antti H, Späth F, Melin B, Björkblom B

Cancers (Basel) 12 (11) 3349 [2020-11-12; online 2020-11-12]

Bioinformatics Support for Computational Resources [Service] Swedish Metabolomics Centre (SMC) [Service]

Development and evaluation of a deep learning based artificial intelligence for automatic identification of gold fiducial markers in an MRI-only prostate radiotherapy workflow.

Gustafsson CJ, Swärd J, Adalbjörnsson SI, Jakobsson A, Olsson LE

Phys Med Biol 65 (22) 225011 [2020-11-12; online 2020-11-12]

AIDA Data Hub [Service] Bioinformatics (NBIS) [Service]

Association of aberrant ASNS imprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL.

Watanabe A, Miyake K, Nordlund J, ..., Sugita K, Inukai T

Blood 136 (20) 2319-2333 [2020-11-12; online 2020-06-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Recurring urothelial carcinomas show genomic rearrangements incompatible with a direct relationship.

Marzouka NA, Lindgren D, Eriksson P, ..., Axelson H, Höglund M

Sci Rep 10 (1) 19539 [2020-11-11; online 2020-11-11]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Metabolomics of Interstitial Fluid, Plasma and Urine in Patients with Arterial Hypertension: New Insights into the Underlying Mechanisms.

Chachaj A, Matkowski R, Gröbner G, Szuba A, Dudka I

Diagnostics 10 (11) 936 [2020-11-11; online 2020-11-11]

Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis.

Mahmud AKMF, Nilsson K, Fahlgren A, ..., Avican K, Fällman M

mSystems 5 (6) - [2020-11-10; online 2020-11-10]

Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Targeted sequencing reveals the somatic mutation landscape in a Swedish breast cancer cohort.

Mathioudaki A, Ljungström V, Melin M, ..., Sjöblom T, Lindblad-Toh K

Sci Rep 10 (1) 19304 [2020-11-09; online 2020-11-09]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Identification of candidate genetic variants and altered protein expression in neural stem and mature neural cells support altered microtubule function to be an essential component in bipolar disorder.

Truvé K, Parris TZ, Vizlin-Hodzic D, ..., Ågren H, Funa K

Transl Psychiatry 10 (1) 390 [2020-11-09; online 2020-11-09]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Lysine-specific demethylase 1A restricts ex vivo propagation of human HSCs and is a target of UM171.

Subramaniam A, Žemaitis K, Talkhoncheh MS, ..., Zubarev RA, Larsson J

Blood 136 (19) 2151-2161 [2020-11-05; online 2020-06-26]

Bioinformatics Support for Computational Resources [Service] Chemical Proteomics [Collaborative]

Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish (Silurus glanis) Using Linked-Read Sequencing.

Ozerov MY, Flajšhans M, Noreikiene K, Vasemägi A, Gross R

G3 (Bethesda) 10 (11) 3897-3906 [2020-11-05; online 2020-11-05]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

DNA-Based Methods for Measurable Residual Disease Detection in NPM1-Mutated Acute Myeloid Leukemia; Establishment of Cut-Offs for qPCR, Digital Droplet PCR and Targeted Deep Sequencing

Pettersson L, Johansson Alm S, Almstedt A, ..., Fogelstrand L, Ehinger M

Blood 136 (Supplement 1) 6-6 [2020-11-05; online 2020-11-05]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Point-of-Care Approaches for Meningitis Diagnosis in a Low-Resource Setting (Southwestern Uganda): Observational Cohort Study Protocol of the "PI-POC" Trial.

Gaudenzi G, Kumbakumba E, Rasti R, ..., Mwanga-Amumpaire J, Alfvén T

JMIR Res Protoc 9 (11) e21430 [2020-11-04; online 2020-11-04]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells.

Sumida N, Sifakis EG, Kiani NA, ..., Göndör A, Ohlsson R

Nucleic Acids Res. 48 (19) 10867-10876 [2020-11-04; online 2020-10-15]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue.

Gyllborg D, Langseth CM, Qian X, ..., Lein ES, Nilsson M

Nucleic Acids Res. 48 (19) e112 [2020-11-04; online 2020-09-30]

Bioinformatics Support for Computational Resources [Service] In Situ Sequencing (ISS) [Technology development]

Evolution from adherent to suspension: systems biology of HEK293 cell line development.

Malm M, Saghaleyni R, Lundqvist M, ..., Nielsen J, Rockberg J

Sci Rep 10 (1) 18996 [2020-11-04; online 2020-11-04]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]

Naming the untouchable - environmental sequences and niche partitioning as taxonomical evidence in fungi.

Kalsoom Khan F, Kluting K, Tångrot J, ..., Ryberg M, Rosling A

IMA Fungus 11 (1) 23 [2020-11-03; online 2020-11-03]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

From Inquilines to Gall Inducers: Genomic Signature of a Life-Style Transition in Synergus Gall Wasps.

Gobbo E, Lartillot N, Hearn J, ..., Ide T, Ronquist F

Genome Biol Evol 12 (11) 2060-2073 [2020-11-03; online 2020-09-29]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Cross-validated Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging Quantitation Protocol for a Pharmaceutical Drug and Its Drug-Target Effects in the Brain Using Time-of-Flight and Fourier Transform Ion Cyclotron Resonance Analyzers.

Källback P, Vallianatou T, Nilsson A, ..., Svenningsson P, Andrén PE

Anal. Chem. 92 (21) 14676-14684 [2020-11-03; online 2020-10-21]

Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes.

Pértille F, Ibelli AMG, Sharif ME, ..., Guerrero-Bosagna C, Coutinho LL

Front Genet 11 (-) 508809 [2020-11-02; online 2020-11-02]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Pericyte dysfunction due to Shb gene deficiency increases B16F10 melanoma lung metastasis.

He Q, Li X, He L, ..., Betsholtz C, Welsh M

Int. J. Cancer 147 (9) 2634-2644 [2020-11-01; online 2020-05-30]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Interspecific Gene Flow and the Evolution of Specialization in Black and White Rhinoceros.

Moodley Y, Westbury MV, Russo IM, ..., Dalén L, Bruford MW

Mol. Biol. Evol. 37 (11) 3105-3117 [2020-11-01; online 2020-06-26]

NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]

Genomic epidemiology of Neisseria gonorrhoeae elucidating the gonococcal antimicrobial resistance and lineages/sublineages across Brazil, 2015-16.

Golparian D, Bazzo ML, Golfetto L, ..., Unemo M, Brazilian-GASP Network

J. Antimicrob. Chemother. 75 (11) 3163-3172 [2020-11-01; online 2020-08-14]

Clinical Genomics [Technology development] Clinical Genomics Örebro [Technology development]

Angiotensin-converting enzyme 2 (ACE2) levels in relation to risk factors for COVID-19 in two large cohorts of patients with atrial fibrillation.

Wallentin L, Lindbäck J, Eriksson N, ..., Oldgren J, Siegbahn A

Eur. Heart J. 41 (41) 4037-4046 [2020-11-01; online 2020-09-29]

Affinity Proteomics Uppsala [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The proliferative history shapes the DNA methylome of B-cell tumors and predicts clinical outcome.

Duran-Ferrer M, Clot G, Nadeu F, ..., Campo E, Martín-Subero JI

Nat Cancer 1 (11) 1066-1081 [2020-11-00; online 2020-11-02]

NGI SNP genotyping [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Sahelian pastoralism from the perspective of variants associated with lactase persistence.

Priehodová E, Austerlitz F, Čížková M, ..., Schlebusch CM, Černý V

Am. J. Phys. Anthropol. 173 (3) 423-436 [2020-11-00; online 2020-08-19]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Optimized metabarcoding with Pacific biosciences enables semi-quantitative analysis of fungal communities.

Castaño C, Berlin A, Brandström Durling M, ..., Clemmensen KE, Olson Å

New Phytol. 228 (3) - [2020-11-00; online 2020-07-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Leaf shape in Populus tremula is a complex, omnigenic trait.

Mähler N, Schiffthaler B, Robinson KM, ..., Hvidsten TR, Street NR

Ecol Evol 10 (21) 11922-11940 [2020-11-00; online 2020-10-13]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder.

Ramos J, Proven M, Halvardson J, ..., Thuresson AC, Fu D

RNA 26 (11) 1654-1666 [2020-11-00; online 2020-08-06]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Human G-MDSCs are neutrophils at distinct maturation stages promoting tumor growth in breast cancer

Mehmeti-Ajradini M, Bergenfelz C, Larsson AM, ..., Bexell D, Leandersson K

Life Sci. Alliance 3 (11) e202000893 [2020-11-00; online 2020-09-21]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Cellular Immunomonitoring [Service]

Epilepsy syndromes, etiologies, and the use of next-generation sequencing in epilepsy presenting in the first 2 years of life: A population-based study.

Stödberg T, Tomson T, Barbaro M, ..., Åmark P, Wedell A

Epilepsia 61 (11) 2486-2499 [2020-11-00; online 2020-09-23]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Divergent above- and below-ground responses of fungal functional groups to forest thinning

Collado E, Castaño C, Bonet JA, ..., Martínez de Aragón J, de-Miguel S

Soil Biology and Biochemistry 150 (-) 108010 [2020-11-00; online 2020-11-00]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Dense sampling of bird diversity increases power of comparative genomics.

Feng S, Stiller J, Deng Y, ..., Paten B, Zhang G

Nature 587 (7833) 252-257 [2020-11-00; online 2020-11-11]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Cytogenetically visible inversions are formed by multiple molecular mechanisms.

Pettersson M, Grochowski CM, Wincent J, ..., Carvalho CMB, Lindstrand A

Hum. Mutat. 41 (11) 1979-1998 [2020-11-00; online 2020-10-01]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A family-based genome-wide association study of recurrent aphthous stomatitis.

Bankvall M, Östman S, Jontell M, Torinsson Naluai Å

Oral Dis 26 (8) 1696-1705 [2020-11-00; online 2020-07-30]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A comparative genomics multitool for scientific discovery and conservation.

Zoonomia Consortium

Nature 587 (7833) 240-245 [2020-11-00; online 2020-11-11]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Origins and genetic legacy of prehistoric dogs.

Bergström A, Frantz L, Schmidt R, ..., Larson G, Skoglund P

Science 370 (6516) 557-564 [2020-10-30; online 2020-10-29]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Intra-Individual Behavioural Variability: A Trait under Genetic Control.

Henriksen R, Höglund A, Fogelholm J, ..., Dingemanse NJ, Wright D

Int J Mol Sci 21 (21) 8069 [2020-10-29; online 2020-10-29]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Impacts of thermal fluctuations on heat tolerance and its metabolomic basis in Arabidopsis thaliana, Drosophila melanogaster, and Orchesella cincta.

Noer NK, Pagter M, Bahrndorff S, Malmendal A, Kristensen TN

PLoS ONE 15 (10) e0237201 [2020-10-29; online 2020-10-29]

Horizontal Gene Transfer and Tandem Duplication Shape the Unique CAZyme Complement of the Mycoparasitic Oomycetes Pythium oligandrum and Pythium periplocum.

Liang D, Andersen CB, Vetukuri RR, Dou D, Grenville-Briggs LJ

Front Microbiol 11 (-) 581698 [2020-10-29; online 2020-10-29]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

DNA methylation in canine brains is related to domestication and dog-breed formation.

Sundman AS, Pértille F, Lehmann Coutinho L, ..., Guerrero-Bosagna C, Jensen P

PLoS ONE 15 (10) e0240787 [2020-10-29; online 2020-10-29]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Activation of RAS Signalling is Associated with Altered Cell Adhesion in Phaeochromocytoma.

Rossitti HM, Dutta RK, Larsson C, ..., Söderkvist P, Gimm O

Int J Mol Sci 21 (21) 8072 [2020-10-29; online 2020-10-29]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Linköping [Service]

Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells.

Tarbier M, Mackowiak SD, Frade J, ..., Gallant CJ, Friedländer MR

Nat Commun 11 (1) 5445 [2020-10-28; online 2020-10-28]

Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]

Microbiomes in a manganese oxide producing ecosystem in the Ytterby mine, Sweden: impact on metal mobility.

Sjöberg S, Stairs CW, Allard B, ..., Ettema TJG, Dupraz C

FEMS Microbiol. Ecol. 96 (11) - [2020-10-28; online 2020-08-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Population genomics reveals lack of greater white-fronted introgression into the Swedish lesser white-fronted goose.

Díez-Del-Molino D, von Seth J, Gyllenstrand N, ..., Sjögren-Gulve P, Dalén L

Sci Rep 10 (1) 18347 [2020-10-27; online 2020-10-27]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

ENPL-1, the Caenorhabditis elegans homolog of GRP94, promotes insulin secretion via regulation of proinsulin processing and maturation.

Podraza-Farhanieh A, Natarajan B, Raj D, Kao G, Naredi P

Development 147 (20) - [2020-10-27; online 2020-10-27]

Integrated Microscopy Technologies Gothenburg [Service]

Developmental and MAPK-responsive transcription factors drive distinct malignant subtypes and genetic dependencies in pancreatic cancer

Laise P, Turunen M, Garcia AC, ..., Olive KP, Califano A

- - (-) - [2020-10-27; online 2020-10-27]

CRISPR Functional Genomics [Service]

Coupling stabilizers open KV1-type potassium channels.

Silverå Ejneby M, Wallner B, Elinder F

Proc. Natl. Acad. Sci. U.S.A. 117 (43) 27016-27021 [2020-10-27; online 2020-10-13]

Chemical Biology Consortium Sweden (CBCS) [Service]

UvrD helicase-RNA polymerase interactions are governed by UvrD's carboxy-terminal Tudor domain.

Kawale AA, Burmann BM

Commun Biol 3 (1) 607 [2020-10-23; online 2020-10-23]

Type III ATP synthase is a symmetry-deviated dimer that induces membrane curvature through tetramerization.

Flygaard RK, Mühleip A, Tobiasson V, Amunts A

Nat Commun 11 (1) 5342 [2020-10-22; online 2020-10-22]

Cryo-EM [Service] Global Proteomics and Proteogenomics [Service]

Polycomb Repressive Complex 2-mediated histone modification H3K27me3 is associated with embryogenic potential in Norway spruce.

Nakamura M, Batista RA, Köhler C, Hennig L

J. Exp. Bot. 71 (20) 6366-6378 [2020-10-22; online 2020-09-08]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic Variants Associated with Non-Alcoholic Fatty Liver Disease Do Not Associate with Measures of Sub-Clinical Atherosclerosis: Results from the IMPROVE Study.

Castaldo L, Laguzzi F, Strawbridge RJ, ..., Mälarstig A, Gigante B

Genes 11 (11) 1243 [2020-10-22; online 2020-10-22]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Epigenetic alterations in skin homing CD4+CLA+ T cells of atopic dermatitis patients.

Acevedo N, Benfeitas R, Katayama S, ..., Söderhäll C, Scheynius A

Sci Rep 10 (1) 18020 [2020-10-22; online 2020-10-22]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training

Clarithromycin Exerts an Antibiofilm Effect against Salmonella enterica Serovar Typhimurium rdar Biofilm Formation and Transforms the Physiology towards an Apparent Oxygen-Depleted Energy and Carbon Metabolism.

Zafar M, Jahan H, Shafeeq S, ..., Römling U, Choudhary MI

Infect. Immun. 88 (11) - [2020-10-19; online 2020-10-19]

Automated identification of the mouse brain's spatial compartments from in situ sequencing data.

Partel G, Hilscher MM, Milli G, ..., Nilsson M, Wählby C

BMC Biol. 18 (1) 144 [2020-10-19; online 2020-10-19]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support for Computational Resources [Service]

A high-stringency blueprint of the human proteome.

Adhikari S, Nice EC, Deutsch EW, ..., Aebersold R, Baker MS

Nat Commun 11 (1) 5301 [2020-10-16; online 2020-10-16]

Fulvestrant-Mediated Attenuation of the Innate Immune Response Decreases ER+ Breast Cancer Growth In Vivo More Effectively than Tamoxifen.

Abrahamsson A, Rodriguez GV, Dabrosin C

Cancer Res. 80 (20) 4487-4499 [2020-10-15; online 2020-08-27]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Engineering Af1521 improves ADP-ribose binding and identification of ADP-ribosylated proteins.

Nowak K, Rosenthal F, Karlberg T, ..., Leslie Pedrioli DM, Hottiger MO

Nat Commun 11 (1) 5199 [2020-10-15; online 2020-10-15]

Discovery of USP7 small-molecule allosteric inhibitors.

Engström O, Belda O, Kullman-Magnusson M, ..., Parkes KEB, Zhao H

Bioorg. Med. Chem. Lett. 30 (20) 127471 [2020-10-15; online 2020-08-08]

The Structure of Riparian Vegetation in Agricultural Landscapes Influences Spider Communities and Aquatic-Terrestrial Linkages

Ramberg E, Burdon FJ, Sargac J, ..., Johnson RK, McKie BG

Water 12 (10) 2855 [2020-10-14; online 2020-10-14]

Analysis of translating mitoribosome reveals functional characteristics of translation in mitochondria of fungi.

Itoh Y, Naschberger A, Mortezaei N, Herrmann JM, Amunts A

Nat Commun 11 (1) 5187 [2020-10-14; online 2020-10-14]

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Novel pathogenic genomic variants leading to autosomal dominant and recessive Robinow syndrome.

Zhang C, Mazzeu JF, Eisfeldt J, ..., Sutton VR, Carvalho CMB

Am. J. Med. Genet. A - (-) - [2020-10-13; online 2020-10-13]

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The influence of common polygenic risk and gene sets on social skills group training response in autism spectrum disorder.

Li D, Choque-Olsson N, Jiao H, ..., Bölte S, Tammimies K

npj Genom. Med. 5 (1) 45 [2020-10-12; online 2020-10-12]

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TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes.

Wang J, Li B, Marques S, ..., Wei W, Pelechano V

Nucleic Acids Res. 48 (18) e104 [2020-10-09; online 2020-08-21]

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Optotracing for selective fluorescence-based detection, visualization and quantification of live S. aureus in real-time.

Butina K, Tomac A, Choong FX, ..., Löffler S, Richter-Dahlfors A

NPJ Biofilms Microbiomes 6 (1) 35 [2020-10-09; online 2020-10-09]

Integrated Microscopy Technologies Stockholm [Service]

Generation and validation of recombinant antibodies to study human aminoacyl-tRNA synthetases.

Preger C, Wigren E, Ossipova E, ..., Gräslund S, Persson H

J. Biol. Chem. 295 (41) 13981-13993 [2020-10-09; online 2020-08-14]

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An embryonic stem cell-specific heterochromatin state promotes core histone exchange in the absence of DNA accessibility.

Navarro C, Lyu J, Katsori AM, Caridha R, Elsässer SJ

Nat Commun 11 (1) 5095 [2020-10-09; online 2020-10-09]

SARS-CoV-2 exposure, symptoms and seroprevalence in healthcare workers in Sweden.

Rudberg AS, Havervall S, Månberg A, ..., Hober S, Thålin C

Nat Commun 11 (1) 5064 [2020-10-08; online 2020-10-08]

Autoimmunity and Serology Profiling [Collaborative]

Temporal changes in the vaginal microbiota in self-samples and its association with persistent HPV16 infection and CIN2.

Berggrund M, Gustavsson I, Aarnio R, ..., Olovsson M, Gyllensten U

Virol J 17 (1) 147 [2020-10-07; online 2020-10-07]

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GeneSetCluster: a tool for summarizing and integrating gene-set analysis results.

Ewing E, Planell-Picola N, Jagodic M, Gomez-Cabrero D

BMC Bioinformatics 21 (1) 443 [2020-10-07; online 2020-10-07]

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Transcriptional responses in developing lesions of European common ash (Fraxinus excelsior) reveal genes responding to infection by Hymenoscyphus fraxineus.

Sahraei SE, Cleary M, Stenlid J, Brandström Durling M, Elfstrand M

BMC Plant Biol. 20 (1) 455 [2020-10-06; online 2020-10-06]

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Key insights in the AIDA community policy on sharing of clinical imaging data for research in Sweden.

Hedlund J, Eklund A, Lundström C

Sci Data 7 (1) 331 [2020-10-06; online 2020-10-06]

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Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.

Lord E, Dussex N, Kierczak M, ..., Götherström A, Dalén L

Curr. Biol. 30 (19) 3871-3879.e7 [2020-10-05; online 2020-08-13]

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HEARTBREAK Controls Post-translational Modification of INDEHISCENT to Regulate Fruit Morphology in Capsella.

Dong Y, Majda M, Šimura J, ..., Smith RS, Østergaard L

Curr. Biol. 30 (19) 3880-3888.e5 [2020-10-05; online 2020-08-13]

Swedish Metabolomics Centre (SMC)

A latent lineage potential in resident neural stem cells enables spinal cord repair.

Llorens-Bobadilla E, Chell JM, Le Merre P, ..., Carlén M, Frisén J

Science 370 (6512) eabb8795 [2020-10-02; online 2020-10-03]

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Notch activation in the mouse mammary luminal lineage leads to ductal hyperplasia and altered partitioning of luminal cell subtypes.

Phoon YP, Chivukula IV, Tsoi YL, ..., Kuiper R, Lendahl U

Exp. Cell Res. 395 (1) 112156 [2020-10-01; online 2020-07-22]

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Large-scale targeted sequencing identifies risk genes for neurodevelopmental disorders.

Wang T, Hoekzema K, Vecchio D, ..., Xia K, Eichler EE

Nat Commun 11 (1) 4932 [2020-10-01; online 2020-10-01]

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Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens.

Schlebusch CM, Sjödin P, Breton G, ..., Soodyall H, Jakobsson M

Mol. Biol. Evol. 37 (10) 2944-2954 [2020-10-01; online 2020-07-23]

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Brain Transcriptomics of Wild and Domestic Rabbits Suggests That Changes in Dopamine Signaling and Ciliary Function Contributed to Evolution of Tameness.

Sato DX, Rafati N, Ring H, ..., Carneiro M, Andersson L

Genome Biol Evol 12 (10) 1918-1928 [2020-10-01; online 2020-08-25]

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A Repertory of Rearrangements and the Loss of an Inverted Repeat Region in Passiflora Chloroplast Genomes.

Cauz-Santos LA, da Costa ZP, Callot C, ..., van den Berg C, Vieira MLC

Genome Biol Evol 12 (10) 1841-1857 [2020-10-01; online 2020-07-30]

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Unraveling the Immune Response in Severe COVID-19.

Rodriguez L, Brodin P

J Clin Immunol 40 (7) 958-959 [2020-10-00; online 2020-08-22]

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Profiles of histidine-rich glycoprotein associate with age and risk of all-cause mortality.

Hong MG, Dodig-Crnković T, Chen X, ..., Magnusson PK, Schwenk JM

Life Sci. Alliance 3 (10) e202000817 [2020-10-00; online 2020-07-31]

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Ouabain Modulates the Functional Interaction Between Na,K-ATPase and NMDA Receptor.

Akkuratov EE, Westin L, Vazquez-Juarez E, ..., Brismar H, Aperia A

Mol Neurobiol 57 (10) 4018-4030 [2020-10-00; online 2020-07-10]

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Multi-Reader-Multi-Split Annotation of Emphysema in Computed Tomography.

Lidén M, Hjelmgren O, Vikgren J, Thunberg P

J Digit Imaging 33 (5) 1185-1193 [2020-10-00; online 2020-08-10]

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Mitigation of the replication of SARS-CoV-2 by nitric oxide in vitro.

Akaberi D, Krambrich J, Ling J, ..., Lennerstrand J, Lundkvist Å

Redox Biol 37 (-) 101734 [2020-10-00; online 2020-09-21]

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Metagenomic analysis of bacteria in stallion semen.

Al-Kass Z, Guo Y, Vinnere Pettersson O, Niazi A, Morrell JM

Animal Reproduction Science 221 (-) 106568 [2020-10-00; online 2020-08-01]

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Implications of TP53 allelic state for genome stability, clinical presentation and outcomes in myelodysplastic syndromes.

Bernard E, Nannya Y, Hasserjian RP, ..., Ogawa S, Papaemmanuil E

Nat. Med. 26 (10) 1549-1556 [2020-10-00; online 2020-08-03]

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Geographically widespread invasive meningococcal disease caused by a ciprofloxacin resistant non-groupable strain of the ST-175 clonal complex.

Willerton L, Lucidarme J, Campbell H, ..., Vogel U, Borrow R

J Infect 81 (4) 575-584 [2020-10-00; online 2020-08-25]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Genomic and drug target evaluation of 90 cardiovascular proteins in 30,931 individuals.

Folkersen L, Gustafsson S, Wang Q, ..., Ingelsson E, Mälarstig A

Nat Metab 2 (10) 1135-1148 [2020-10-00; online 2020-10-16]

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GPSeq reveals the radial organization of chromatin in the cell nucleus.

Girelli G, Custodio J, Kallas T, ..., Crosetto N, Bienko M

Nat. Biotechnol. 38 (10) 1184-1193 [2020-10-00; online 2020-05-25]

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Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling.

Lundtoft C, Pucholt P, Imgenberg-Kreuz J, ..., Rönnblom L, Hagberg N

PLoS Genet. 16 (10) e1009199 [2020-10-00; online 2020-10-26]

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Exploring the bacterial nano-universe.

Söderholm N, Singh B, Uhlin BE, Sandblad L

Curr. Opin. Struct. Biol. 64 (-) 166-173 [2020-10-00; online 2020-08-23]

Differences in structure and hibernation mechanism highlight diversification of the microsporidian ribosome.

Ehrenbolger K, Jespersen N, Sharma H, ..., Vossbrinck CR, Barandun J

PLoS Biol. 18 (10) e3000958 [2020-10-00; online 2020-10-30]

Development of a chemical probe against NUDT15.

Zhang SM, Desroses M, Hagenkort A, ..., Stenmark P, Helleday T

Nat. Chem. Biol. 16 (10) 1120-1128 [2020-10-00; online 2020-07-20]

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Association of serum anti-centromere protein F antibodies with clinical response to infliximab in patients with rheumatoid arthritis: A prospective study.

Lourido L, Ruiz-Romero C, Picchi F, ..., Nilsson P, Blanco FJ

Semin. Arthritis Rheum. 50 (5) 1101-1108 [2020-10-00; online 2020-06-30]

Autoimmunity and Serology Profiling [Collaborative]

High-fat diet and estrogen impacts the colon and its transcriptome in a sex-dependent manner.

Hases L, Archer A, Indukuri R, ..., Korach-André M, Williams C

Sci Rep 10 (1) 16160 [2020-09-30; online 2020-09-30]

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Toll-like receptors revisited; a possible role for TLR1 in lupus nephritis.

Yavuz S, Bianchi M, Kozyrev S, ..., Lindblad-Toh K, Rönnblom L

Ann. Rheum. Dis. 80 (3) 404-406 [2020-09-29; online 2020-09-29]

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Structural Basis for GTP versus ATP Selectivity in the NMP Kinase AK3.

Rogne P, Dulko-Smith B, Goodman J, ..., Sauer-Eriksson AE, Wolf-Watz M

Biochemistry 59 (38) 3570-3581 [2020-09-29; online 2020-09-11]

Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts.

Mondav R, Bertilsson S, Buck M, ..., Lindström ES, Garcia SL

mSystems 5 (5) - [2020-09-29; online 2020-09-29]

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Reconstruction of the birth of a male sex chromosome present in Atlantic herring.

Rafati N, Chen J, Herpin A, ..., Schartl M, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 117 (39) 24359-24368 [2020-09-29; online 2020-09-16]

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MAIT cell activation and dynamics associated with COVID-19 disease severity.

Parrot T, Gorin JB, Ponzetta A, ..., Strålin K, Sandberg JK

Sci Immunol 5 (51) - [2020-09-28; online 2020-09-30]

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Inducible Deletion of YAP and TAZ in Adult Mouse Smooth Muscle Causes Rapid and Lethal Colonic Pseudo-Obstruction.

Daoud F, Holmberg J, Alajbegovic A, ..., Swärd K, Albinsson S

Cellular and Molecular Gastroenterology and Hepatology 11 (2) 623-637 [2020-09-28; online 2020-09-28]

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Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription.

Pontiller B, Martínez-García S, Lundin D, Pinhassi J

Front Microbiol 11 (-) 588778 [2020-09-25; online 2020-09-25]

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Increased antibiotic efficacy and noninvasive monitoring of Staphylococcus epidermidis biofilms using per-cysteamine-substituted γ-cyclodextrin - A delivery effect validated by fluorescence microscopy.

Thomsen H, Agnes M, Uwangue O, ..., Ericson MB, Farewell A

Int J Pharm 587 (-) 119646 [2020-09-25; online 2020-07-14]

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High-Resolution Imaging of Tumor Spheroids and Organoids Enabled by Expansion Microscopy.

Edwards SJ, Carannante V, Kuhnigk K, ..., Önfelt B, Brismar H

Front Mol Biosci 7 (-) 208 [2020-09-24; online 2020-09-24]

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Therapeutic targeting of KSP in preclinical models of high-risk neuroblastoma.

Hansson K, Radke K, Aaltonen K, ..., Gisselsson D, Bexell D

Sci Transl Med 12 (562) - [2020-09-23; online 2020-09-25]

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Dental cell type atlas reveals stem and differentiated cell types in mouse and human teeth.

Krivanek J, Soldatov RA, Kastriti ME, ..., Kharchenko PV, Adameyko I

Nat Commun 11 (1) 4816 [2020-09-23; online 2020-09-23]

Sources of variation in cell-type RNA-Seq profiles.

Gustafsson J, Held F, Robinson JL, ..., Jörnsten R, Nielsen J

PLoS ONE 15 (9) e0239495 [2020-09-21; online 2020-09-21]

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Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples.

Bailey MH, Meyerson WU, Dursi LJ, ..., Ding L, PCAWG Consortium

Nat Commun 11 (1) 4748 [2020-09-21; online 2020-09-21]

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Generation of Sequencing Libraries for Structural Analysis of Bacterial 5' UTRs.

Ignatov D, Vaitkevicius K, Johansson J

STAR Protoc 1 (2) 100046 [2020-09-18; online 2020-06-06]

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Parvimonas micra as a putative non-invasive faecal biomarker for colorectal cancer.

Löwenmark T, Löfgren-Burström A, Zingmark C, ..., Edin S, Palmqvist R

Sci Rep 10 (1) 15250 [2020-09-17; online 2020-09-17]

Clinical Genomics [Collaborative] Clinical Genomics Umeå [Collaborative]

Macrocyclization of bis-indole quinolines for selective stabilization of G-quadruplex DNA structures.

Das RN, Andréasson M, Kumar R, Chorell E

Chem. Sci. 11 (38) 10529-10537 [2020-09-16; online 2020-09-16]

Presynaptic dysfunction in CASK-related neurodevelopmental disorders.

Becker M, Mastropasqua F, Reising JP, ..., Bölte S, Tammimies K

Transl Psychiatry 10 (1) 312 [2020-09-14; online 2020-09-14]

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Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne.

Liu T, Schnürer A, Björkmalm J, Willquist K, Kreuger E

Microorganisms 8 (9) 1394 [2020-09-11; online 2020-09-11]

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Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals.

Vaga S, Lee S, Ji B, ..., Engstrand L, Shoaie S

Sci Rep 10 (1) 14977 [2020-09-11; online 2020-09-11]

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A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences.

Svensson D, Rentoft M, Dahlin AM, ..., Trygg J, Johansson E

PLoS ONE 15 (9) e0237721 [2020-09-11; online 2020-09-11]

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Complete Genome Sequence of Francisella halioticida Type Strain DSM 23729 (FSC1005).

Uneklint I, Öhrman C, Karlsson L, ..., Forsman M, Sjödin A

Microbiol Resour Announc 9 (37) - [2020-09-10; online 2020-09-10]

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Integration of molecular profiles in a longitudinal wellness profiling cohort.

Tebani A, Gummesson A, Zhong W, ..., Uhlen M, Fagerberg L

Nat Commun 11 (1) 4487 [2020-09-08; online 2020-09-08]

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Profiling of Inflammatory Proteins in Plasma of HIV-1-Infected Children Receiving Antiretroviral Therapy.

Lemma M, Petkov S, Bekele Y, ..., Howe R, Chiodi F

Proteomes 8 (3) 24 [2020-09-07; online 2020-09-07]

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Genome sequence of segmented filamentous bacteria present in the human intestine.

Jonsson H, Hugerth LW, Sundh J, Lundin E, Andersson AF

Commun Biol 3 (1) 485 [2020-09-04; online 2020-09-04]

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An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction.

Hanke L, Vidakovics Perez L, Sheward DJ, ..., Murrell B, McInerney GM

Nat Commun 11 (1) 4420 [2020-09-04; online 2020-09-04]

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Bilayer-Coated Nanoparticles Reveal How Influenza Viral Entry Depends on Membrane Deformability but Not Curvature.

Villamil Giraldo AM, Kasson PM

J Phys Chem Lett 11 (17) 7190-7196 [2020-09-03; online 2020-08-19]

Toward Two-Photon Absorbing Dyes with Unusually Potentiated Nonlinear Fluorescence Response.

Benitez-Martin C, Li S, Dominguez-Alfaro A, ..., Pischel U, Andréasson J

J. Am. Chem. Soc. 142 (35) 14854-14858 [2020-09-02; online 2020-08-21]

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River biofilms adapted to anthropogenic disturbances are more resistant to WWTP inputs.

Freixa A, Perujo N, Langenheder S, Romaní AM

FEMS Microbiol. Ecol. 96 (9) - [2020-09-01; online 2020-08-09]

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Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics.

Ericson PGP, Irestedt M, Nylander JAA, ..., Joseph L, Qu Y

Syst. Biol. 69 (5) 820-829 [2020-09-01; online 2020-05-18]

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Mutations Upstream of the TBX5 and PITX1 Transcription Factor Genes Are Associated with Feathered Legs in the Domestic Chicken.

Li J, Lee M, Davis BW, ..., Siegel PB, Andersson L

Mol. Biol. Evol. 37 (9) 2477-2486 [2020-09-01; online 2020-04-29]

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Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum.

Mahajan M, Seeger C, Yee B, Andersson SGE

Genome Biol Evol 12 (9) 1528-1548 [2020-09-01; online 2020-08-08]

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Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting.

Madsen EB, Höijer I, Kvist T, Ameur A, Mikkelsen MJ

Hum. Mutat. 41 (9) 1671-1679 [2020-09-00; online 2020-06-29]

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The impact of damage-associated molecular patterns on the neurotransmitter release and gene expression in the ex vivo rat carotid body.

Mkrtchian S, Kåhlin J, Gómez-Galán M, ..., Erlandsson Harris H, Eriksson LI

Exp. Physiol. 105 (9) 1634-1647 [2020-09-00; online 2020-07-24]

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Reconstructing marine plankton food web interactions using DNA metabarcoding.

Zamora-Terol S, Novotny A, Winder M

Mol. Ecol. 29 (17) 3380-3395 [2020-09-00; online 2020-08-09]

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Linked-read sequencing enables haplotype-resolved resequencing at population scale.

Lutgen D, Ritter R, Olsen RA, ..., Suh A, Burri R

Mol Ecol Resour 20 (5) 1311-1322 [2020-09-00; online 2020-06-29]

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Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.

van der Valk T, Vezzi F, Ormestad M, Dalén L, Guschanski K

Mol Ecol Resour 20 (5) 1171-1181 [2020-09-00; online 2019-05-05]

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Hyperandrogenism and insulin resistance modulate gravid uterine and placental ferroptosis in PCOS-like rats.

Zhang Y, Hu M, Jia W, ..., Shao LR, Billig H

J Endocrinol 246 (3) 247-263 [2020-09-00; online 2020-06-27]

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Hemolytic uremic syndrome caused by Shiga toxin-producing Escherichia coli in children: incidence, risk factors, and clinical outcome.

Ylinen E, Salmenlinna S, Halkilahti J, ..., Jalanko H, Saxén H

Pediatr Nephrol 35 (9) 1749-1759 [2020-09-00; online 2020-04-22]

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Genetic comorbidity between major depression and cardio-metabolic traits, stratified by age at onset of major depression.

Hagenaars SP, Coleman JRI, Choi SW, ..., Breen G, Lewis CM

Am. J. Med. Genet. B Neuropsychiatr. Genet. 183 (6) 309-330 [2020-09-00; online 2020-07-18]

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Genetic association of gemcitabine/carboplatin-induced leukopenia and neutropenia in non-small cell lung cancer patients using whole-exome sequencing.

Svedberg A, Björn N, Sigurgeirsson B, ..., Lundeberg J, Gréen H

Lung Cancer 147 (-) 106-114 [2020-09-00; online 2020-07-12]

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Defining the proteolytic landscape during enterovirus infection.

Saeed M, Kapell S, Hertz NT, ..., Molina H, Rice CM

PLoS Pathog. 16 (9) e1008927 [2020-09-00; online 2020-09-30]

DNA methylation variation in the brain of laying hens in relation to differential behavioral patterns.

Guerrero-Bosagna C, Pértille F, Gomez Y, ..., Voelkl B, Toscano MJ

Comp Biochem Physiol Part D Genomics Proteomics 35 (-) 100700 [2020-09-00; online 2020-06-02]

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Comparative analysis of genome-wide DNA methylation in Neurospora.

Hosseini S, Meunier C, Nguyen D, Reimegård J, Johannesson H

Epigenetics 15 (9) 972-987 [2020-09-00; online 2020-03-31]

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A dynamic mutational landscape associated with an inter-regionally diverse immune response in malignant rhabdoid tumour.

Yasui H, Valind A, Karlsson J, ..., Backman T, Gisselsson D

J. Pathol. 252 (1) 22-28 [2020-09-00; online 2020-07-22]

Clinical Genomics Clinical Genomics Lund

A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells.

Dias JM, Alekseenko Z, Jeggari A, ..., Iber D, Ericson J

Sci Adv 6 (38) - [2020-09-00; online 2020-09-16]

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Sex differences in oncogenic mutational processes.

Li CH, Prokopec SD, Sun RX, ..., Boutros PC, PCAWG Consortium

Nat Commun 11 (1) 4330 [2020-08-28; online 2020-08-28]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

Prenylated Flavonoids from the Roots of Tephrosia rhodesica.

Atilaw Y, Muiva-Mutisya L, Bogaerts J, ..., Erdélyi M, Yenesew A

J. Nat. Prod. 83 (8) 2390-2398 [2020-08-28; online 2020-08-13]

Bulk-Processed Pd Nanocube–Poly(methyl methacrylate) Nanocomposites as Plasmonic Plastics for Hydrogen Sensing

Darmadi I, Stolaś A, Östergren I, ..., Müller C, Langhammer C

ACS Appl. Nano Mater. 3 (8) 8438-8445 [2020-08-28; online 2020-07-20]

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High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure.

Singh A, Nylander JAA, Schnürer A, Bongcam-Rudloff E, Müller B

Front Microbiol 11 (-) 2066 [2020-08-27; online 2020-08-27]

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Four SARS-CoV-2 Genome Sequences from Late April in Stockholm, Sweden, Reveal a Rare Mutation in the Spike Protein.

Soratto TAT, Darban H, Bjerkner A, ..., Allander T, Andersson B

Microbiol Resour Announc 9 (35) - [2020-08-27; online 2020-08-27]

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Cell-surface receptors enable perception of extracellular cytokinins.

Antoniadi I, Novák O, Gelová Z, ..., Ljung K, Turnbull C

Nat Commun 11 (1) 4284 [2020-08-27; online 2020-08-27]

µ Opioid Receptor Agonism for L-DOPA-Induced Dyskinesia in Parkinson's Disease.

Bezard E, Li Q, Hulme H, ..., Andren PE, Crossman AR

J. Neurosci. 40 (35) 6812-6819 [2020-08-26; online 2020-07-20]

Combined transcriptome and proteome profiling of the pancreatic β-cell response to palmitate unveils key pathways of β-cell lipotoxicity.

Lytrivi M, Ghaddar K, Lopes M, ..., Eizirik DL, Cnop M

BMC Genomics 21 (1) 590 [2020-08-26; online 2020-08-26]

Global Proteomics and Proteogenomics [Collaborative]

Systems-Level Immunomonitoring from Acute to Recovery Phase of Severe COVID-19.

Rodriguez L, Pekkarinen PT, Lakshmikanth T, ..., Kekäläinen E, Brodin P

Cell Reports Medicine 1 (5) 100078 [2020-08-25; online 2020-08-05]

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Whole-genome sequencing and gene network modules predict gemcitabine/carboplatin-induced myelosuppression in non-small cell lung cancer patients.

Björn N, Badam TVS, Spalinskas R, ..., Gustafsson M, Gréen H

npj Syst Biol Appl 6 (1) 25 [2020-08-24; online 2020-08-24]

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Single cell RNA sequencing identifies early diversity of sensory neurons forming via bi-potential intermediates.

Faure L, Wang Y, Kastriti ME, ..., Adameyko I, Hadjab S

Nat Commun 11 (1) 4175 [2020-08-21; online 2020-08-21]

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Natural killer cell immunotypes related to COVID-19 disease severity.

Maucourant C, Filipovic I, Ponzetta A, ..., Björkström NK, Karolinska COVID-19 Study Group

Sci Immunol 5 (50) eabd6832 [2020-08-21; online 2020-08-23]

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13q12.2 deletions in acute lymphoblastic leukemia lead to upregulation of FLT3 through enhancer hijacking.

Yang M, Safavi S, Woodward EL, ..., Nord KH, Paulsson K

Blood 136 (8) 946-956 [2020-08-20; online 2020-05-10]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Structural basis of mitochondrial translation

Aibara S, Singh V, Modelska A, Amunts A

Elife 9 (-) 1-17 [2020-08-19; online 2020-08-19]

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Rapid size change associated with intra-island evolutionary radiation in extinct Caribbean "island-shrews".

Woods R, Turvey ST, Brace S, ..., Brown MJF, Barnes I

BMC Evol. Biol. 20 (1) 106 [2020-08-18; online 2020-08-18]

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High Cysteine Membrane Proteins (HCMPs) Are Up-Regulated During Giardia-Host Cell Interactions.

Peirasmaki D, Ma'ayeh SY, Xu F, ..., Liu J, Svärd SG

Front Genet 11 (-) 913 [2020-08-18; online 2020-08-18]

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Designing custom CRISPR libraries for hypothesis-driven drug target discovery.

Iyer VS, Jiang L, Shen Y, ..., Schmierer B, Wermeling F

Computational and Structural Biotechnology Journal 18 (-) 2237-2246 [2020-08-18; online 2020-08-18]

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Association of Established Blood Pressure Loci With 10-Year Change in Blood Pressure and Their Ability to Predict Incident Hypertension.

Poveda A, Atabaki-Pasdar N, Ahmad S, ..., Renström F, Franks PW

J Am Heart Assoc 9 (16) e014513 [2020-08-18; online 2020-08-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Platelet-Specific PDGFB Ablation Impairs Tumor Vessel Integrity and Promotes Metastasis.

Zhang Y, Cedervall J, Hamidi A, ..., Dimberg A, Olsson AK

Cancer Res. 80 (16) 3345-3358 [2020-08-15; online 2020-06-25]

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Crystal structures of human PAICS reveal substrate and product binding of an emerging cancer target.

Škerlová J, Unterlass J, Göttmann M, ..., Jemth AS, Stenmark P

J. Biol. Chem. 295 (33) 11656-11668 [2020-08-14; online 2020-06-22]

Gsta4 controls apoptosis of differentiating adult oligodendrocytes during homeostasis and remyelination via the mitochondria-associated Fas-Casp8-Bid-axis.

Carlström KE, Zhu K, Ewing E, ..., Castelo-Branco G, Piehl F

Nat Commun 11 (1) 4071 [2020-08-13; online 2020-08-13]

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Variations in Plasma Membrane Topography Can Explain Heterogenous Diffusion Coefficients Obtained by Fluorescence Correlation Spectroscopy.

Gesper A, Wennmalm S, Hagemann P, ..., Happel P, Parmryd I

Front Cell Dev Biol 8 (-) 767 [2020-08-11; online 2020-08-11]

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Transcriptional mutagenesis dramatically alters genome-wide p53 transactivation landscape.

Liang S, Ezerskyte M, Wang J, Pelechano V, Dreij K

Sci Rep 10 (1) 13513 [2020-08-11; online 2020-08-11]

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Regular use of depot medroxyprogesterone acetate causes thinning of the superficial lining and apical distribution of HIV target cells in the human ectocervix.

Edfeldt G, Lajoie J, Röhl M, ..., Broliden K, Tjernlund A

J. Infect. Dis. - (-) - [2020-08-11; online 2020-08-11]

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Association of Factor V Leiden With Subsequent Atherothrombotic Events: A GENIUS-CHD Study of Individual Participant Data.

Mahmoodi BK, Tragante V, Kleber ME, ..., Asselbergs FW, Patel RS

Circulation 142 (6) 546-555 [2020-08-11; online 2020-07-13]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Mebendazole is unique among tubulin-active drugs in activating the MEK-ERK pathway.

Andersson CR, Selvin T, Blom K, ..., Nygren P, Larsson R

Sci Rep 10 (1) 13124 [2020-08-04; online 2020-08-04]

Lysophosphatidic Acid-Mediated GPR35 Signaling in CX3CR1+ Macrophages Regulates Intestinal Homeostasis.

Kaya B, Doñas C, Wuggenig P, ..., Villablanca EJ, Niess JH

Cell Rep 32 (5) 107979 [2020-08-04; online 2020-08-07]

Heterogeneous somatostatin-expressing neuron population in mouse ventral tegmental area.

Nagaeva E, Zubarev I, Bengtsson Gonzales C, ..., Augustine GJ, Korpi ER

Elife 9 (-) - [2020-08-04; online 2020-08-04]

The Relation Between Position and Chemical Composition of Bis-Indole Substituents Determines Their Interactions with G-Quadruplex DNA.

Prasad B, Das RN, Jamroskovic J, ..., Sabouri N, Chorell E

Chemistry 26 (43) 9561-9572 [2020-08-03; online 2020-07-03]

zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging.

Zhang H, Waldmann L, Manuel R, ..., Haitina T, Allalou A

Biomed. Opt. Express 11 (8) 4290-4305 [2020-08-01; online 2020-07-15]

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Optical coherence tomography for thyroid pathology: 3D analysis of tissue microstructure.

Emil Tampu I, Maintz M, Koller D, ..., Eklund A, Haj-Hosseini N

Biomed. Opt. Express 11 (8) 4130-4149 [2020-08-01; online 2020-07-09]

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Uncovering the hidden diversity of litter-decomposition mechanisms in mushroom-forming fungi.

Floudas D, Bentzer J, Ahrén D, ..., Persson P, Tunlid A

ISME J 14 (8) 2046-2059 [2020-08-00; online 2020-05-07]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

The influence of forest surroundings on the soil fungal community of black truffle (Tuber melanosporum) plantations

Oliach D, Colinas C, Castaño C, ..., Bonet JA, Oliva J

Forest Ecology and Management 469 (-) 118199 [2020-08-00; online 2020-08-00]

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The importance of the ZBED6-IGF2 axis for metabolic regulation in mouse myoblast cells.

Younis S, Naboulsi R, Wang X, ..., Welsh N, Andersson L

FASEB J. 34 (8) 10250-10266 [2020-08-00; online 2020-06-19]

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The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites.

Xu F, Jiménez-González A, Einarsson E, ..., Svärd SG, Jerlström-Hultqvist J

Microb Genom 6 (8) - [2020-08-00; online 2020-07-03]

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The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders.

Coutinho A, Günther T, Munters AR, ..., Malmström H, Jakobsson M

Am. J. Phys. Anthropol. 172 (4) 638-649 [2020-08-00; online 2020-06-04]

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Technologies for assessing vaccine responses in the very young.

Current Opinion in Immunology 65 (-) 28-31 [2020-08-00; online 2020-04-24]

SWEDEGENE-a Swedish nation-wide DNA sample collection for pharmacogenomic studies of serious adverse drug reactions.

Hallberg P, Yue QY, Eliasson E, ..., Ås J, Wadelius M

Pharmacogenomics J. 20 (4) 579-585 [2020-08-00; online 2020-01-17]

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SLC12A2 mutations cause NKCC1 deficiency with encephalopathy and impaired secretory epithelia.

Stödberg T, Magnusson M, Lesko N, ..., Stranneheim H, Wedell A

Neurol Genet 6 (4) e478 [2020-08-00; online 2020-07-02]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation.

Ottenburghs J, Honka J, Müskens GJDM, Ellegren H

Heredity (Edinb) 125 (1-2) 73-84 [2020-08-00; online 2020-05-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Preclinical safety studies of human embryonic stem cell-derived retinal pigment epithelial cells for the treatment of age-related macular degeneration.

Petrus-Reurer S, Kumar P, Padrell Sánchez S, ..., Kvanta A, Lanner F

Stem Cells Transl Med 9 (8) 936-953 [2020-08-00; online 2020-04-22]

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MrpH, a new class of metal-binding adhesin, requires zinc to mediate biofilm formation.

Jiang W, Ubhayasekera W, Breed MC, ..., Pearson MM, Knight SD

PLoS Pathog. 16 (8) e1008707 [2020-08-00; online 2020-08-11]

Management of an outbreak of postpartum Streptococcus pyogenes emm75 infections.

Trell K, Jörgensen J, Rasmussen M, Senneby E

J. Hosp. Infect. 105 (4) 752-756 [2020-08-00; online 2020-06-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Leveraging a gain-of-function allele of Caenorhabditis elegans paqr-1 to elucidate membrane homeostasis by PAQR proteins.

Busayavalasa K, Ruiz M, Devkota R, ..., Borén J, Pilon M

PLoS Genet. 16 (8) e1008975 [2020-08-00; online 2020-08-04]

Integrated Microscopy Technologies Gothenburg [Service]

Label‐free laser scanning microscopy targeting sentinel lymph node diagnostics: A feasibility study ex vivo

Kantere D, Siarov J, De Lara S, ..., Wennberg Larkö A, Ericson MB

Translational Biophotonics 2 (3) - [2020-08-00; online 2020-06-22]

Integrated Microscopy Technologies Gothenburg [Service]

Joint impact of common risk factors on incident dementia: A cohort study of the Swedish Twin Registry.

Tomata Y, Li X, Karlsson IK, ..., Pedersen NL, Hägg S

J. Intern. Med. 288 (2) 234-247 [2020-08-00; online 2020-05-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Higher host plant specialization of root-associated endophytes than mycorrhizal fungi along an arctic elevational gradient.

Abrego N, Huotari T, Tack AJM, ..., Ovaskainen O, Roslin T

Ecol Evol 10 (16) 8989-9002 [2020-08-00; online 2020-08-06]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Evolutionary genetics of canine respiratory coronavirus and recent introduction into Swedish dogs.

Wille M, Wensman JJ, Larsson S, ..., Hayer J, Malmberg M

Infection, Genetics and Evolution 82 (-) 104290 [2020-08-00; online 2020-03-20]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Determinants of genetic variation across eco-evolutionary scales in pinnipeds.

Peart CR, Tusso S, Pophaly SD, ..., Shafer ABA, Wolf JBW

Nat Ecol Evol 4 (8) 1095-1104 [2020-08-00; online 2020-06-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

CELLULOSE SYNTHASE INTERACTING 1 is required for wood mechanics and leaf morphology in aspen.

Bünder A, Sundman O, Mahboubi A, ..., Rüggeberg M, Niittylä T

Plant J. 103 (5) 1858-1868 [2020-08-00; online 2020-07-10]

Association between proteomics and obstructive sleep apnea phenotypes in a community-based cohort of women.

Ljunggren M, Theorell-Haglöw J, Freyhult E, ..., Janson C, Lindberg E

J Sleep Res 29 (4) e13041 [2020-08-00; online 2020-04-08]

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Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly.

Juottonen H, Fontaine L, Wurzbacher C, ..., Peura S, Eiler A

Environ. Microbiol. 22 (8) 3158-3171 [2020-08-00; online 2020-06-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Apparent stiffness of vimentin intermediate filaments in living cells and its relation with other cytoskeletal polymers

Smoler M, Coceano G, Testa I, Bruno L, Levi V

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1867 (8) 118726 [2020-08-00; online 2020-08-00]

Integrated Microscopy Technologies Stockholm [Service]

A robust and versatile method for production and purification of large-scale RNA samples for structural biology.

Karlsson H, Baronti L, Petzold K

RNA 26 (8) 1023-1037 [2020-08-00; online 2020-04-30]

A novel recombinant expression and purification approach for the full-length anti-apoptotic membrane protein Bcl-2.

Ådén J, Mushtaq AU, Dingeldein A, Wallgren M, Gröbner G

Protein Expression and Purification 172 (-) 105628 [2020-08-00; online 2020-03-22]

A decade of epigenetic change in aging twins: Genetic and environmental contributions to longitudinal DNA methylation.

Reynolds CA, Tan Q, Munoz E, ..., Hägg S, Pedersen NL

Aging Cell 19 (8) e13197 [2020-08-00; online 2020-07-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A 3D Cell Culture Model Identifies Wnt/β-Catenin Mediated Inhibition of p53 as a Critical Step during Human Hepatocyte Regeneration.

Oliva-Vilarnau N, Vorrink SU, Ingelman-Sundberg M, Lauschke VM

Adv Sci (Weinh) 7 (15) 2000248 [2020-08-00; online 2020-06-23]

Global Proteomics and Proteogenomics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution.

Höglund A, Strempfl K, Fogelholm J, Wright D, Henriksen R

BMC Genomics 21 (1) 518 [2020-07-29; online 2020-07-29]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

First evidence of microbial wood degradation in the coastal waters of the Antarctic.

Björdal CG, Dayton PK

Sci Rep 10 (1) 12774 [2020-07-29; online 2020-07-29]

Integrated Microscopy Technologies Gothenburg [Service]

Extracellular vesicles from human mesenchymal stem cells expedite chondrogenesis in 3D human degenerative disc cell cultures.

Hingert D, Ekström K, Aldridge J, Crescitelli R, Brisby H

Stem Cell Res Ther 11 (1) 323 [2020-07-29; online 2020-07-29]

Integrated Microscopy Technologies Gothenburg [Service]

Detection of leukemia gene fusions by targeted RNA-sequencing in routine diagnostics.

Engvall M, Cahill N, Jonsson BI, ..., Hallböök H, Cavelier L

BMC Med Genomics 13 (1) 106 [2020-07-29; online 2020-07-29]

Clinical Genomics [Technology development] Clinical Genomics Uppsala [Technology development]

Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce.

Chaudhary R, Lundén K, Dalman K, ..., Stenlid J, Elfstrand M

Sci Rep 10 (1) 12711 [2020-07-29; online 2020-07-29]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Prototypical pacemaker neurons interact with the resident microbiota.

Klimovich A, Giacomello S, Björklund Å, ..., Adameyko I, Bosch TCG

Proc. Natl. Acad. Sci. U.S.A. 117 (30) 17854-17863 [2020-07-28; online 2020-07-09]

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Early Pleistocene origin and extensive intra-species diversity of the extinct cave lion.

Stanton DWG, Alberti F, Plotnikov V, ..., Skoglund P, Dalén L

Sci Rep 10 (1) 12621 [2020-07-28; online 2020-07-28]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A Transmembrane Crenarchaeal Mannosyltransferase Is Involved in N-Glycan Biosynthesis and Displays an Unexpected Minimal Cellulose-Synthase-like Fold.

Gandini R, Reichenbach T, Spadiut O, ..., Kalyani DC, Divne C

J. Mol. Biol. 432 (16) 4658-4672 [2020-07-24; online 2020-06-19]

Recording In-Cell NMR-Spectra in Living Mammalian Cells.

Matečko-Burmann I, Burmann BM

Methods Mol. Biol. 2141 (-) 857-871 [2020-07-23; online 2020-07-23]

Multimodal Analysis of Composition and Spatial Architecture in Human Squamous Cell Carcinoma.

Ji AL, Rubin AJ, Thrane K, ..., Lundeberg J, Khavari PA

Cell 182 (2) 497-514.e22 [2020-07-23; online 2020-06-23]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Decellularization and recellularization of the ovary for bioengineering applications; studies in the mouse.

Alshaikh AB, Padma AM, Dehlin M, ..., Brännström M, Hellström M

Reprod Biol Endocrinol 18 (1) 75 [2020-07-23; online 2020-07-23]

Integrated Microscopy Technologies Gothenburg [Service]

Cell-Free Protein Synthesis of Small Intrinsically Disordered Proteins for NMR Spectroscopy.

Isaksson L, Pedersen A

Methods Mol. Biol. 2141 (-) 233-245 [2020-07-23; online 2020-07-23]

Extended-Spectrum-β-Lactamase- and Plasmid AmpC-Producing Escherichia coli Causing Community-Onset Bloodstream Infection: Association of Bacterial Clones and Virulence Genes with Septic Shock, Source of Infection, and Recurrence.

Fröding I, Hasan B, Sylvin I, ..., Nauclér P, Giske CG

Antimicrob. Agents Chemother. 64 (8) - [2020-07-22; online 2020-07-22]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Human Immune System Variation during 1 Year.

Lakshmikanth T, Muhammad SA, Olin A, ..., Uhlen M, Brodin P

Cell Rep 32 (3) 107923 [2020-07-21; online 2020-07-23]

Affinity Proteomics Stockholm [Service] Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Technology development]

Descriptive Proteome Analysis to Investigate Context-Dependent Treatment Responses to OXPHOS Inhibition in Colon Carcinoma Cells Grown as Monolayer and Multicellular Tumor Spheroids.

Steinmetz J, Senkowski W, Lengqvist J, ..., Fryknäs M, Kultima K

ACS Omega 5 (28) 17242-17254 [2020-07-21; online 2020-07-06]

Bioinformatics Support for Computational Resources [Service] Drug Discovery and Development (DDD) [Service]

Probing the retention mechanism of small hydrophilic molecules in hydrophilic interaction chromatography using saturation transfer difference nuclear magnetic resonance spectroscopy.

Shamshir A, Dinh NP, Jonsson T, Sparrman T, Irgum K

Journal of Chromatography A 1623 (-) 461130 [2020-07-19; online 2020-04-29]

Validating Signal Transducer and Activator of Transcription (STAT) Protein-Inhibitor Interactions Using Biochemical and Cellular Thermal Shift Assays.

Attarha S, Reithmeier A, Busker S, Desroses M, Page BDG

ACS Chem. Biol. 15 (7) 1842-1851 [2020-07-17; online 2020-07-02]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Unveiling the activation dynamics of a fold-switch bacterial glycosyltransferase by 19F NMR.

Liebau J, Tersa M, Trastoy B, ..., Guerin ME, Mäler L

J. Biol. Chem. 295 (29) 9868-9878 [2020-07-17; online 2020-05-20]

Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach

von der Heyde B, Emmanouilidou A, Mazzaferro E, ..., Brooke HL, den Hoed M

Sci Rep 10 (1) 11831 [2020-07-16; online 2020-07-16]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Genome Engineering Zebrafish [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]

AML displays increased CTCF occupancy associated with aberrant gene expression and transcription factor binding.

Mujahed H, Miliara S, Neddermeyer A, ..., Lennartsson A, Lehmann S

Blood 136 (3) 339-352 [2020-07-16; online 2020-04-02]

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RNA Splicing Alterations Induce a Cellular Stress Response Associated with Poor Prognosis in Acute Myeloid Leukemia.

Anande G, Deshpande NP, Mareschal S, ..., Unnikrishnan A, Pimanda JE

Clin. Cancer Res. 26 (14) 3597-3607 [2020-07-15; online 2020-03-02]

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Adding seemingly uninformative labels helps in low data regimes

Matsoukas C, Hernandez A, Liu Y, ..., Strand F, Smith K

International Conference on Machine Learning (ICML) - (-) - [2020-07-15]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Seamless integration of image and molecular analysis for spatial transcriptomics workflows.

Bergenstråhle J, Larsson L, Lundeberg J

BMC Genomics 21 (1) 482 [2020-07-14; online 2020-07-14]

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A Patient-Derived Cell Atlas Informs Precision Targeting of Glioblastoma.

Johansson P, Krona C, Kundu S, ..., Marino S, Nelander S

Cell Rep 32 (2) 107897 [2020-07-14; online 2020-07-16]

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Mapping the Interactome of the Nuclear Heparan Sulfate Proteoglycan Syndecan-1 in Mesothelioma Cells.

Kumar-Singh A, Shrinet J, Parniewska MM, ..., Dobra K, Hjerpe A

Biomolecules 10 (7) - [2020-07-11; online 2020-07-11]

Transcriptional responses in Parascaris univalens after in vitro exposure to ivermectin, pyrantel citrate and thiabendazole.

Martin F, Dube F, Karlsson Lindsjö O, ..., Bergström TF, Tydén E

Parasit Vectors 13 (1) 342 [2020-07-09; online 2020-07-09]

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SF3B1-mutant MDS as a distinct disease subtype: a proposal from the International Working Group for the Prognosis of MDS.

Malcovati L, Stevenson K, Papaemmanuil E, ..., Hellstrom-Lindberg E, Cazzola M

Blood 136 (2) 157-170 [2020-07-09; online 2020-04-30]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

Disturbance history can increase functional stability in the face of both repeated disturbances of the same type and novel disturbances.

Renes SE, Sjöstedt J, Fetzer I, Langenheder S

Sci Rep 10 (1) 11333 [2020-07-09; online 2020-07-09]

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Arachidonic acid promotes the binding of 5-lipoxygenase on nanodiscs containing 5-lipoxygenase activating protein in the absence of calcium-ions.

Kumar RB, Purhonen P, Hebert H, Jegerschöld C

PLoS ONE 15 (7) e0228607 [2020-07-09; online 2020-07-09]

Systems biology of acidophile biofilms for efficient metal extraction.

Buetti-Dinh A, Herold M, Christel S, ..., Pivkin IV, Dopson M

Sci Data 7 (1) 215 [2020-07-07; online 2020-07-07]

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Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations.

Broman E, Sun X, Stranne C, ..., Humborg C, Nascimento FJA

Front Microbiol 11 (-) 1536 [2020-07-07; online 2020-07-07]

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Discovery and population genomics of structural variation in a songbird genus.

Weissensteiner MH, Bunikis I, Catalán A, ..., Warmuth VM, Wolf JBW

Nat Commun 11 (1) 3403 [2020-07-07; online 2020-07-07]

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Clonal hematopoiesis in patients with high-grade B-cell lymphoma is associated with inferior outcome.

Amini RM, Ljungström V, Abdulla M, ..., Enblad G, Baliakas P

Am. J. Hematol. 95 (10) - [2020-07-06; online 2020-07-06]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

VEGF-B signaling impairs endothelial glucose transcytosis by decreasing membrane cholesterol content.

Moessinger C, Nilsson I, Muhl L, ..., Skogsberg J, Eriksson U

EMBO Rep. 21 (7) e49343 [2020-07-03; online 2020-05-24]

Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures.

Wallén-Mackenzie Å, Dumas S, Papathanou M, ..., König N, Björklund ÅK

Commun Biol 3 (1) 338 [2020-07-03; online 2020-07-03]

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Multiplex profiling of serum proteins in solution using barcoded antibody fragments and next generation sequencing.

Brofelth M, Ekstrand AI, Gour S, ..., Axelsson U, Borrebaeck CAK

Commun Biol 3 (1) 339 [2020-07-03; online 2020-07-03]

Clinical Genomics Clinical Genomics Lund

Diamond Blackfan anemia is mediated by hyperactive Nemo-like kinase.

Wilkes MC, Siva K, Chen J, ..., Flygare J, Sakamoto KM

Nat Commun 11 (1) 3344 [2020-07-03; online 2020-07-03]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

meQTL and ncRNA functional analyses of 102 GWAS-SNPs associated with depression implicate HACE1 and SHANK2 genes.

Ciuculete DM, Voisin S, Kular L, ..., Mwinyi J, Schiöth HB

Clin Epigenetics 12 (1) 99 [2020-07-02; online 2020-07-02]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences.

Naidoo T, Xu J, Vicente M, ..., Jakobsson M, Schlebusch CM

Genome Biol Evol 12 (7) 1031-1039 [2020-07-01; online 2020-07-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Viral antigens elicit augmented immune responses in primary Sjögren's syndrome.

Björk A, Thorlacius GE, Mofors J, ..., Kvarnström M, Wahren-Herlenius M

Rheumatology (Oxford) 59 (7) 1651-1661 [2020-07-01; online 2019-10-31]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Loqusdb: added value of an observations database of local genomic variation.

Magnusson M, Eisfeldt J, Nilsson D, ..., Wedell A, Stranneheim H

BMC Bioinformatics 21 (1) 273 [2020-07-01; online 2020-07-01]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Technology development] Clinical Genomics Stockholm [Technology development]

Genetic Associations Between Childhood Psychopathology and Adult Depression and Associated Traits in 42 998 Individuals: A Meta-analysis.

Akingbuwa WA, Hammerschlag AR, Jami ES, ..., Middeldorp CM, Bipolar Disorder and Major Depressive Disorder Working Groups of the Psychiatric Genomics Consortium

JAMA Psychiatry 77 (7) 715-728 [2020-07-01; online 2020-04-16]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Transcriptomes from German shepherd dogs reveal differences in immune activity between atopic dermatitis affected and control skin.

Tengvall K, Bergvall K, Olsson M, ..., Lindblad-Toh K, Andersson G

Immunogenetics 72 (5) 315-323 [2020-07-00; online 2020-06-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Tissue-specific isolation of Arabidopsis/plant mitochondria - IMTACT (isolation of mitochondria tagged in specific cell types).

Boussardon C, Przybyla-Toscano J, Carrie C, Keech O

Plant J. 103 (1) 459-473 [2020-07-00; online 2020-03-13]

Support systems to guide clinical decision-making in precision oncology: The Cancer Core Europe Molecular Tumor Board Portal.

Tamborero D, Dienstmann R, Rachid MH, ..., Rodon J, Lehtiö J

Nat. Med. 26 (7) 992-994 [2020-07-00; online 2020-07-08]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Stockholm [Collaborative] Global Proteomics and Proteogenomics [Technology development]

Serum Metabolites in Hand-Arm Vibration Exposed Workers.

Vihlborg P, Graff P, Hagenbjörk A, ..., Bryngelsson IL, Eriksson K

J Occup Environ Med 62 (7) 460-465 [2020-07-00; online 2020-07-31]

Proton pump inhibitors act with unprecedented potencies as inhibitors of the acetylcholine biosynthesizing enzyme-A plausible missing link for their association with incidence of dementia.

Kumar R, Kumar A, Nordberg A, Långström B, Darreh-Shori T

Alzheimers Dement 16 (7) 1031-1042 [2020-07-00; online 2020-05-08]

Proteomic analysis of follicular fluid during human ovulation.

Zakerkish F, Brännström M, Carlsohn E, ..., van der Post S, Thoroddsen A

Acta Obstet Gynecol Scand 99 (7) 917-924 [2020-07-00; online 2020-04-07]

Pre- and postnatal Lactobacillus reuteri treatment alters DNA methylation of infant T helper cells.

Forsberg A, Huoman J, Söderholm S, ..., Gustafsson M, Jenmalm MC

Pediatr Allergy Immunol 31 (5) 544-553 [2020-07-00; online 2020-04-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PHF1 fusions cause distinct gene expression and chromatin accessibility profiles in ossifying fibromyxoid tumors and mesenchymal cells.

Hofvander J, Jo VY, Fletcher CDM, ..., Magnusson L, Mertens F

Mod. Pathol. 33 (7) 1331-1340 [2020-07-00; online 2020-01-13]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Odorant receptor phylogeny confirms conserved channels for sex pheromone and host plant signals in tortricid moths.

Gonzalez F, Borrero-Echeverry F, Jósvai JK, ..., Bengtsson M, Walker WB

Ecol Evol 10 (14) 7334-7348 [2020-07-00; online 2020-06-30]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Meiofauna improve oxygenation and accelerate sulfide removal in the seasonally hypoxic seabed.

Bonaglia S, Hedberg J, Marzocchi U, ..., Glud RN, Nascimento FJA

Mar Environ Res 159 (-) 104968 [2020-07-00; online 2020-03-29]

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Inflammatory markers in women with postpartum depressive symptoms.

Bränn E, Fransson E, White RA, ..., Sundström-Poromaa I, Skalkidou A

J Neuro Res 98 (7) 1309-1321 [2020-07-00; online 2018-09-05]

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Identifying the ‘unidentified’ fungi: a global-scale long-read third-generation sequencing approach

Tedersoo L, Anslan S, Bahram M, Kõljalg U, Abarenkov K

Fungal Diversity 103 (1) 273-293 [2020-07-00; online 2020-08-08]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Growth-Inhibitory Activity of Bone Morphogenetic Protein 4 in Human Glioblastoma Cell Lines Is Heterogeneous and Dependent on Reduced SOX2 Expression.

Dalmo E, Johansson P, Niklasson M, ..., Nelander S, Westermark B

Mol Cancer Res 18 (7) 981-991 [2020-07-00; online 2020-03-31]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genomic epidemiology and antimicrobial resistance determinants of Neisseria gonorrhoeae isolates from Ukraine, 2013-2018.

Boiko I, Golparian D, Jacobsson S, ..., Shevchenko T, Unemo M

APMIS 128 (7) 465-475 [2020-07-00; online 2020-05-23]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Gastric Microbiota in a Low-Helicobacter pylori Prevalence General Population and Their Associations With Gastric Lesions.

Ndegwa N, Ploner A, Andersson AF, ..., Agreus L, Ye W

Clin Transl Gastroenterol 11 (7) e00191 [2020-07-00; online 2020-08-09]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Female-biased gene flow between two species of Darwin's finches.

Lamichhaney S, Han F, Webster MT, ..., Grant PR, Andersson L

Nat Ecol Evol 4 (7) 979-986 [2020-07-00; online 2020-05-04]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling.

Dodig-Crnković T, Hong MG, Thomas CE, ..., Uhlén M, Schwenk JM

EBioMedicine 57 (-) 102854 [2020-07-00; online 2020-07-03]

Dynamic allosteric communication pathway directing differential activation of the glucocorticoid receptor.

Köhler C, Carlström G, Gunnarsson A, ..., Edman K, Akke M

Sci Adv 6 (29) eabb5277 [2020-07-00; online 2020-07-17]

Deactivation mechanism of Cu active sites in Cu/SSZ-13 — Phosphorus poisoning and the effect of hydrothermal aging

Wang A, Xie K, Bernin D, ..., Kamasamudram K, Olsson L

Applied Catalysis B: Environmental 269 (-) 118781 [2020-07-00; online 2020-07-00]

DNA demethylation regulates gene expression in IgE-activated mouse mast cells.

Paivandy A, Grujic M, Rafati N, Pejler G

Allergy 75 (7) 1776-1780 [2020-07-00; online 2020-02-12]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii.

Zhong X, Lundberg M, Råberg L

Ecol Evol 10 (13) 6421-6434 [2020-07-00; online 2020-05-25]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Base-pair conformational switch modulates miR-34a targeting of Sirt1 mRNA.

Baronti L, Guzzetti I, Ebrahimi P, ..., Chen AA, Petzold K

Nature 583 (7814) 139-144 [2020-07-00; online 2020-05-27]

Accounting for environmental variation in co-occurrence modelling reveals the importance of positive interactions in root-associated fungal communities.

Abrego N, Roslin T, Huotari T, ..., Schmidt NM, Ovaskainen O

Mol. Ecol. 29 (14) 2736-2746 [2020-07-00; online 2020-07-04]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A framework to assess the quality and impact of bioinformatics training across ELIXIR.

Gurwitz KT, Singh Gaur P, Bellis LJ, ..., Morgan SL, Rustici G

PLoS Comput. Biol. 16 (7) e1007976 [2020-07-00; online 2020-07-23]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

A Sample Preparation Protocol for High Throughput Immunofluorescence of Suspension Cells on an Adherent Surface.

Bäckström A, Kugel L, Gnann C, ..., Lundberg E, Stadler C

J. Histochem. Cytochem. 68 (7) 473-489 [2020-07-00; online 2020-06-20]

Spatial Proteomics [Technology development]

High content drug screening for Fanconi anemia therapeutics.

Montanuy H, Camps-Fajol C, Carreras-Puigvert J, ..., Minguillón J, Surrallés J

Orphanet J Rare Dis 15 (1) 170 [2020-06-30; online 2020-06-30]

Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion.

Almeida P, Proux-Wera E, Churcher A, ..., Berlin S, Mank JE

BMC Biol. 18 (1) 78 [2020-06-30; online 2020-06-30]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells.

Onsbring H, Tice AK, Barton BT, Brown MW, Ettema TJG

BMC Genomics 21 (1) 448 [2020-06-29; online 2020-06-29]

Microbial Single Cell Genomics [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Whole genome sequencing of familial isolated oesophagus atresia uncover shared structural variants.

Klar J, Engstrand-Lilja H, Maqbool K, ..., Feuk L, Dahl N

BMC Med Genomics 13 (1) 85 [2020-06-26; online 2020-06-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Evolutionary History of the Marchantia polymorpha Complex.

Linde AM, Sawangproh W, Cronberg N, Szövényi P, Lagercrantz U

Front Plant Sci 11 (-) 829 [2020-06-26; online 2020-06-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

CAM-Delam: an in vivo approach to visualize and quantify the delamination and invasion capacity of human cancer cells.

Palaniappan TK, Šlekienė L, Jonasson AK, Gilthorpe J, Gunhaga L

Sci Rep 10 (1) 10472 [2020-06-26; online 2020-06-26]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

RNA-seq reveals altered gene expression levels in proximal tubular cell cultures compared to renal cortex but not during early glucotoxicity.

Nilsson LM, Castresana-Aguirre M, Scott L, Brismar H

Sci Rep 10 (1) 10390 [2020-06-25; online 2020-06-25]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A site-specific self-assembled light-up rotor probe for selective recognition and stabilization of c-MYC G-quadruplex DNA.

Deiana M, Chand K, Jamroskovic J, ..., Chorell E, Sabouri N

Nanoscale 12 (24) 12950-12957 [2020-06-25; online 2020-06-12]

Whole-genome sequence association analysis of blood proteins in a longitudinal wellness cohort.

Zhong W, Gummesson A, Tebani A, ..., Fagerberg L, Uhlén M

Genome Med 12 (1) 53 [2020-06-23; online 2020-06-23]

Affinity Proteomics Stockholm [Collaborative] Bioinformatics Support for Computational Resources [Service]

Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and Women.

Chapman MA, Arif M, Emanuelsson EB, ..., Mardinoglu A, Sundberg CJ

Cell Rep 31 (12) 107808 [2020-06-23; online 2020-06-25]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Amyloid precursor protein-b facilitates cell adhesion during early development in zebrafish.

Banote RK, Chebli J, Şatır TM, ..., Abramsson A, Zetterberg H

Sci Rep 10 (1) 10127 [2020-06-23; online 2020-06-23]

Genome Engineering Zebrafish [Collaborative] Integrated Microscopy Technologies Gothenburg [Service]

Altered levels of CSF proteins in patients with FTD, presymptomatic mutation carriers and non-carriers.

Remnestål J, Öijerstedt L, Ullgren A, ..., Graff C, Nilsson P

Transl Neurodegener 9 (1) 27 [2020-06-23; online 2020-06-23]

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Decreased detection of ESBL- or pAmpC-producing Escherichia coli in broiler breeders imported into Sweden.

Nilsson O, Börjesson S, Landén A, Greko C, Bengtsson B

Acta Vet. Scand. 62 (1) 33 [2020-06-22; online 2020-06-22]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Accelerated Nuclear Magnetic Resonance Spectroscopy with Deep Learning.

Qu X, Huang Y, Lu H, ..., Orekhov V, Chen Z

Angew. Chem. Int. Ed. Engl. 59 (26) 10297-10300 [2020-06-22; online 2020-04-15]

T2 and T17 cytokines alter the cargo and function of airway epithelium-derived extracellular vesicles.

Ax E, Jevnikar Z, Cvjetkovic A, ..., Rådinger M, Lässer C

Respir. Res. 21 (1) 155 [2020-06-19; online 2020-06-19]

Integrated Microscopy Technologies Gothenburg [Service]

Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation.

Tobiasson V, Amunts A

Elife 9 (-) 1-15 [2020-06-18; online 2020-06-18]

Cryo-EM [Service] Global Proteomics and Proteogenomics [Service]

Removal of H2Aub1 by ubiquitin-specific proteases 12 and 13 is required for stable Polycomb-mediated gene repression in Arabidopsis.

Kralemann LEM, Liu S, Trejo-Arellano MS, ..., Köhler C, Hennig L

Genome Biol. 21 (1) 144 [2020-06-16; online 2020-06-16]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Chanjo: Clincal grade sequence coverage analysis

Andeer R, Magnusson M, Wedell A, Stranneheim H

F1000Res 9 (-) 615 [2020-06-16; online 2020-06-16]

Clinical Genomics [Technology development] Clinical Genomics Stockholm [Technology development]

Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage.

Ciudad S, Puig E, Botzanowski T, ..., Bardiaux B, Carulla N

Nat Commun 11 (1) 3014 [2020-06-15; online 2020-06-15]

Integrated transcriptomic and genomic analysis improves prediction of complete remission and survival in elderly patients with acute myeloid leukemia.

Österroos A, Björklund M, Eriksson A, ..., Grönberg H, Lehmann S

Blood Cancer J 10 (6) 67 [2020-06-11; online 2020-06-11]

Bioinformatics Support for Computational Resources [Service]

Illuminating Genetic Mysteries of the Dead Sea Scrolls.

Anava S, Neuhof M, Gingold H, ..., Jakobsson M, Rechavi O

Cell 181 (6) 1218-1231.e27 [2020-06-11; online 2020-06-02]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Distinct pre-initiation steps in human mitochondrial translation.

Khawaja A, Itoh Y, Remes C, ..., Amunts A, Rorbach J

Nat Commun 11 (1) 2932 [2020-06-10; online 2020-06-10]

Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes.

Sakthikumar S, Roy A, Haseeb L, ..., Lindblad-Toh K, Forsberg-Nilsson K

Genome Biol. 21 (1) 127 [2020-06-09; online 2020-06-09]

Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Sales of antibiotics and occurrence of resistance in Sweden

Swedres-Svarm 19088 (-) 1-128 [2020-06-09; online 2020-06-09]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

High genomic-based predicted strain coverage among invasive meningococcal isolates when combining Bexsero and Trumenba vaccines.

Säll O, Olofsson E, Jacobsson S

Vaccine 38 (28) 4374-4378 [2020-06-09; online 2020-05-12]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

CYCLIN-B1/2 and -D1 act in opposition to coordinate cortical progenitor self-renewal and lineage commitment.

Hagey DW, Topcic D, Kee N, ..., Perlmann T, Muhr J

Nat Commun 11 (1) 2898 [2020-06-09; online 2020-06-09]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The regulation and pharmacological modulation of immune complex induced type III IFN production by plasmacytoid dendritic cells.

Hjorton K, Hagberg N, Pucholt P, Eloranta ML, Rönnblom L

Arthritis Res. Ther. 22 (1) 130 [2020-06-05; online 2020-06-05]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function.

Jhamat N, Niazi A, Guo Y, ..., Andersson G, Humblot P

BMC Genomics 21 (1) 385 [2020-06-03; online 2020-06-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Radiation Triggers a Dynamic Sequence of Transient Microglial Alterations in Juvenile Brain.

Osman AM, Sun Y, Burns TC, ..., Kele J, Blomgren K

Cell Rep 31 (9) 107699 [2020-06-02; online 2020-06-04]

Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]

Vegetation type determines spore deposition within a forest-agricultural mosaic landscape.

Redondo MA, Berlin A, Boberg J, Oliva J

FEMS Microbiol. Ecol. 96 (6) - [2020-06-01; online 2020-05-02]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Normal murine respiratory tract has its mucus concentrated in clouds based on the Muc5b mucin.

Fakih D, Rodriguez-Piñeiro AM, Trillo-Muyo S, ..., Ermund A, Hansson GC

Am J Physiol Lung Cell Mol Physiol 318 (6) L1270-L1279 [2020-06-01; online 2020-04-29]

Integrated Microscopy Technologies Gothenburg [Service]

In-plate toxicometabolomics of single zebrafish embryos.

Ribbenstedt A, Posselt M, Brunius C, Benskin JP

Mol Omics 16 (3) 185-194 [2020-06-01; online 2020-03-19]

Bioinformatics Support for Computational Resources [Service] Genome Engineering Zebrafish [Service]

Genomic analysis and antimicrobial resistance of Neisseria gonorrhoeae isolates from Vietnam in 2011 and 2015-16.

Lan PT, Golparian D, Ringlander J, ..., Van Thuong N, Unemo M

J. Antimicrob. Chemother. 75 (6) 1432-1438 [2020-06-01; online 2020-02-19]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Evolutionary Analysis of the Bacillus subtilis Genome Reveals New Genes Involved in Sporulation.

Shi L, Derouiche A, Pandit S, ..., Vlahoviček K, Mijakovic I

Mol. Biol. Evol. 37 (6) 1667-1678 [2020-06-01; online 2020-02-16]

Integrated Microscopy Technologies Gothenburg [Service]

The mating type system of the rare polypore Hapalopilus croceus

Redr D, Dahlberg A, Stenlid J, ..., Vasaitis R, Menkis A

Fungal Ecology 45 (-) 100941 [2020-06-00; online 2020-06-00]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Size-Dependent Pulmonary Impact of Thin Graphene Oxide Sheets in Mice: Toward Safe-by-Design.

Rodrigues AF, Newman L, Jasim D, ..., Kostarelos K, Bussy C

Adv Sci (Weinh) 7 (12) 1903200 [2020-06-00; online 2020-05-07]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Single-cell RNA counting at allele and isoform resolution using Smart-seq3.

Hagemann-Jensen M, Ziegenhain C, Chen P, ..., Faridani OR, Sandberg R

Nat. Biotechnol. 38 (6) 708-714 [2020-06-00; online 2020-05-04]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Predicting and elucidating the etiology of fatty liver disease: A machine learning modeling and validation study in the IMI DIRECT cohorts.

Atabaki-Pasdar N, Ohlsson M, Viñuela A, ..., Pavo I, Franks PW

PLoS Med. 17 (6) e1003149 [2020-06-00; online 2020-06-19]

Normal Testosterone but Higher Luteinizing Hormone Plasma Levels in Men With Hypersexual Disorder.

Chatzittofis A, Boström AE, Öberg KG, ..., Arver S, Jokinen J

Sex Med 8 (2) 243-250 [2020-06-00; online 2020-03-12]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

New approaches to the study of immune responses in humans.

Hum. Genet. 139 (6-7) 795-799 [2020-06-00; online 2020-02-10]

Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations.

Juras A, Makarowicz P, Chyleński M, ..., Jakobsson M, Dabert M

Am. J. Phys. Anthropol. 172 (2) 176-188 [2020-06-00; online 2020-04-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

MYO5B mutations in pheochromocytoma/paraganglioma promote cancer progression.

Tomić TT, Olausson J, Rehammar A, ..., Wassén ON, Abel F

PLoS Genet. 16 (6) e1008803 [2020-06-00; online 2020-06-08]

Clinical Genomics [Service] Clinical Genomics Gothenburg [Service]

Genome-wide CRISPR screen identifies ZIC2 as an essential gene that controls the cell fate of early mesodermal precursors to human heart progenitors.

Xu J, Zhou C, Foo KS, ..., Sahara M, Chien KR

Stem Cells 38 (6) 741-755 [2020-06-00; online 2020-03-10]

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DEqMS: A Method for Accurate Variance Estimation in Differential Protein Expression Analysis.

Zhu Y, Orre LM, Zhou Tran Y, ..., Anders S, Lehtiö J

Mol. Cell Proteomics 19 (6) 1047-1057 [2020-06-00; online 2020-03-23]

Global Proteomics and Proteogenomics [Technology development]

Benchmarking single-cell RNA-sequencing protocols for cell atlas projects.

Mereu E, Lafzi A, Moutinho C, ..., Stegle O, Heyn H

Nat. Biotechnol. 38 (6) 747-755 [2020-06-00; online 2020-04-06]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Balancing selection in Pattern Recognition Receptor signalling pathways is associated with gene function and pleiotropy in a wild rodent.

Lundberg M, Zhong X, Konrad A, Olsen RA, Råberg L

Mol. Ecol. 29 (11) 1990-2003 [2020-06-00; online 2020-06-03]

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An immune gene expression signature distinguishes central nervous system metastases from primary tumours in non-small-cell lung cancer.

Tsakonas G, Lewensohn R, Botling J, ..., Hydbring P, Ekman S

Eur. J. Cancer 132 (-) 24-34 [2020-06-00; online 2020-04-20]

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Age-of-onset information helps identify 76 genetic variants associated with allergic disease.

Ferreira MAR, Vonk JM, Baurecht H, ..., Lee Y, Koppelman GH

PLoS Genet. 16 (6) e1008725 [2020-06-00; online 2020-06-30]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Activated carbon stimulates microbial diversity and PAH biodegradation under anaerobic conditions in oil-polluted sediments.

Bonaglia S, Broman E, Brindefalk B, ..., Udekwu K, Gunnarsson JS

Chemosphere 248 (-) 126023 [2020-06-00; online 2020-01-24]

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Restoration of KMT2C/MLL3 in human colorectal cancer cells reinforces genome-wide H3K4me1 profiles and influences cell growth and gene expression.

Larsson C, Cordeddu L, Siggens L, ..., Ekwall K, Sjöblom T

Clin Epigenetics 12 (1) 74 [2020-05-29; online 2020-05-29]

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In silico Druggability Assessment of the NUDIX Hydrolase Protein Family as a Workflow for Target Prioritization.

Michel M, Homan EJ, Wiita E, ..., Helleday T, Warpman Berglund U

Front. Chem. 8 (-) 443 [2020-05-29; online 2020-05-29]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF) [Service]

Transitions in wheat endosperm metabolism upon transcriptional induction of oil accumulation by oat endosperm WRINKLED1.

Grimberg Å, Wilkinson M, Snell P, ..., Shewry P, Hofvander P

BMC Plant Biol. 20 (1) 235 [2020-05-25; online 2020-05-25]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Staphylococcus argenteus as an etiological agent of prosthetic hip joint infection: a case presentation.

Söderquist B, Wildeman P, Stenmark B, Stegger M

J Bone Jt Infect 5 (4) 172-175 [2020-05-25; online 2020-05-25]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Auxin export from proximal fruits drives arrest in temporally competent inflorescences

Ware A, Walker CH, Šimura J, ..., Wilson ZA, Bennett T

NPLANTS 6 (6) 699-707 [2020-05-25; online 2020-05-25]

Multi-ancestry GWAS of the electrocardiographic PR interval identifies 202 loci underlying cardiac conduction.

Ntalla I, Weng LC, Cartwright JH, ..., Lubitz SA, Munroe PB

Nat Commun 11 (1) 2542 [2020-05-21; online 2020-05-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Integration of whole-body [18F]FDG PET/MRI with non-targeted metabolomics can provide new insights on tissue-specific insulin resistance in type 2 diabetes.

Diamanti K, Visvanathar R, Pereira MJ, ..., Wadelius C, Ahlström H

Sci Rep 10 (1) 8343 [2020-05-20; online 2020-05-20]

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Comprehensive metabolomics analysis of prostate cancer tissue in relation to tumor aggressiveness and TMPRSS2-ERG fusion status.

Dudka I, Thysell E, Lundquist K, ..., Wikström P, Gröbner G

BMC Cancer 20 (1) 437 [2020-05-18; online 2020-05-18]

Swedish Metabolomics Centre (SMC) [Service] Swedish NMR Centre (SNC) [Collaborative]

Behavioral Characterization of dmrt3a Mutant Zebrafish Reveals Crucial Aspects of Vertebrate Locomotion through Phenotypes Related to Acceleration.

Del Pozo A, Manuel R, Iglesias Gonzalez AB, ..., Kullander K, Boije H

eNeuro 7 (3) ENEURO.0047-20.2020 [2020-05-18; online 2020-05-18]

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Single cell transcriptomics identifies stem cell-derived graft composition in a model of Parkinson's disease.

Tiklová K, Nolbrant S, Fiorenzano A, ..., Perlmann T, Parmar M

Nat Commun 11 (1) 2434 [2020-05-15; online 2020-05-15]

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Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma.

Grankvist R, Chireh A, Sandell M, ..., Daub CO, Holmin S

Sci Rep 10 (1) 8029 [2020-05-15; online 2020-05-15]

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Alterations of endometrial epithelial-mesenchymal transition and MAPK signalling components in women with PCOS are partially modulated by metformin in vitro.

Hu M, Zhang Y, Li X, ..., Shao LR, Billig H

Mol. Hum. Reprod. 26 (5) 312-326 [2020-05-15; online 2020-03-24]

Integrated Microscopy Technologies Gothenburg [Service]

Integrative genomics approach identifies molecular features associated with early-stage ovarian carcinoma histotypes.

Engqvist H, Parris TZ, Biermann J, ..., Karlsson P, Helou K

Sci Rep 10 (1) 7946 [2020-05-14; online 2020-05-14]

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Genetic and environmental influences on human height from infancy through adulthood at different levels of parental education.

Jelenkovic A, Sund R, Yokoyama Y, ..., Kaprio J, Silventoinen K

Sci Rep 10 (1) 7974 [2020-05-14; online 2020-05-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Interphase Design of Cellulose Nanocrystals/Poly(hydroxybutyrate-ran-valerate) Bionanocomposites for Mechanical and Thermal Properties Tuning.

Magnani C, Idström A, Nordstierna L, ..., Raquez JM, Lo Re G

Biomacromolecules 21 (5) 1892-1901 [2020-05-11; online 2020-03-04]

Altered Thermal and Mechanical Properties of Spruce Galactoglucomannan Films Modified with an Etherification Reaction.

Härdelin L, Bernin D, Börjesson M, Ström A, Larsson A

Biomacromolecules 21 (5) 1832-1840 [2020-05-11; online 2020-03-18]

Srebf1 Controls Midbrain Dopaminergic Neurogenesis.

Toledo EM, Yang S, Gyllborg D, ..., Linnarsson S, Arenas E

Cell Rep 31 (5) 107601 [2020-05-05; online 2020-05-07]

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High-Resolution In Situ NMR Spectroscopy of Bacterial Envelope Proteins in Outer Membrane Vesicles.

Thoma J, Burmann BM

Biochemistry 59 (17) 1656-1660 [2020-05-05; online 2020-04-06]

A progressive and complex clinical course in two family members with ERF-related craniosynostosis: a case report.

Körberg I, Nowinski D, Bondeson ML, ..., Kölby L, Stattin EL

BMC Med. Genet. 21 (1) 90 [2020-05-05; online 2020-05-05]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Lipid accumulation controls the balance between surface connection and scission of caveolae.

Hubert M, Larsson E, Vegesna NVG, ..., Moodie LW, Lundmark R

Elife 9 (-) - [2020-05-04; online 2020-05-04]

Integrated Microscopy Technologies Umeå [Collaborative] Swedish Metabolomics Centre (SMC) [Collaborative]

Rare variants in dynein heavy chain genes in two individuals with situs inversus and developmental dyslexia: a case report.

Bieder A, Einarsdottir E, Matsson H, ..., Kere J, Tapia-Páez I

BMC Med. Genet. 21 (1) 87 [2020-05-01; online 2020-05-01]

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Molecular changes during progression from nonmuscle invasive to advanced urothelial carcinoma.

Sjödahl G, Eriksson P, Patschan O, ..., Liedberg F, Höglund M

Int. J. Cancer 146 (9) 2636-2647 [2020-05-01; online 2019-11-14]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Isolation and characterization of microvesicles from mesenchymal stem cells.

Mohammadi MR, Riazifar M, Pone EJ, ..., Lotvall J, Zhao W

Methods 177 (-) 50-57 [2020-05-01; online 2019-10-25]

Integrated Microscopy Technologies Gothenburg [Service]

Extracellular vesicles from mast cells induce mesenchymal transition in airway epithelial cells.

Yin Y, Shelke GV, Lässer C, Brismar H, Lötvall J

Respir. Res. 21 (1) 101 [2020-05-01; online 2020-05-01]

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Evolution of a New Function by Fusion between Phage DNA and a Bacterial Gene.

Warsi O, Knopp M, Surkov S, Jerlström Hultqvist J, Andersson DI

Mol. Biol. Evol. 37 (5) 1329-1341 [2020-05-01; online 2020-01-25]

Differential Expression of Immune Genes between Two Closely Related Beetle Species with Different Immunocompetence following Attack by Asecodes parviclava.

Yang X, Fors L, Slotte T, ..., Wheat CW, Hambäck PA

Genome Biol Evol 12 (5) 522-534 [2020-05-01; online 2020-04-14]

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Whole-genome sequencing reveals complex chromosome rearrangement disrupting NIPBL in infant with Cornelia de Lange syndrome.

Plesser Duvdevani M, Pettersson M, Eisfeldt J, ..., Lindstrand A, Harel T

Am. J. Med. Genet. A 182 (5) 1143-1151 [2020-05-00; online 2020-03-03]

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Whole-genome sequencing of human remains to enable genealogy DNA database searches - A case report.

Tillmar A, Sjölund P, Lundqvist B, ..., Älgenäs C, Green H

Forensic Sci Int Genet 46 (-) 102233 [2020-05-00; online 2020-01-17]

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Transcriptome profiling of Ewing sarcomas - treatment resistance pathways and IGF-dependency.

Chen Y, Hesla AC, Lin Y, ..., Larsson O, Haglund F

Mol Oncol 14 (5) 1101-1117 [2020-05-00; online 2020-03-13]

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SweHLA: the high confidence HLA typing bio-resource drawn from 1000 Swedish genomes.

Nordin J, Ameur A, Lindblad-Toh K, Gyllensten U, Meadows JRS

Eur. J. Hum. Genet. 28 (5) 627-635 [2020-05-00; online 2019-12-16]

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Recurrent Fusions Between YAP1 and KMT2A in Morphologically Distinct Neoplasms Within the Spectrum of Low-grade Fibromyxoid Sarcoma and Sclerosing Epithelioid Fibrosarcoma.

Puls F, Agaimy A, Flucke U, ..., Arbajian E, Mertens F

Am. J. Surg. Pathol. 44 (5) 594-606 [2020-05-00; online 2020-01-09]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Lund [Service]

Parentage and relatedness reconstruction in Pinus sylvestris using genotyping-by-sequencing.

Hall D, Zhao W, Wennström U, Andersson Gull B, Wang XR

Heredity (Edinb) 124 (5) 633-646 [2020-05-00; online 2020-03-02]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Next-Generation Sequencing Reveals Differential Responses to Acute versus Long-Term Exposures to Graphene Oxide in Human Lung Cells.

Mukherjee SP, Gupta G, Klöditz K, ..., Kostarelos K, Fadeel B

Small 16 (21) e1907686 [2020-05-00; online 2020-03-29]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Monitoring calcium-induced epidermal differentiation in vitro using multiphoton microscopy.

Malak M, Grantham J, Ericson MB

J Biomed Opt 25 (7) 1-11 [2020-05-00; online 2020-05-11]

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In-depth plasma proteomics reveals increase in circulating PD-1 during anti-PD-1 immunotherapy in patients with metastatic cutaneous melanoma.

Babačić H, Lehtiö J, Pico de Coaña Y, Pernemalm M, Eriksson H

J Immunother Cancer 8 (1) e000204 [2020-05-00; online 2020-05-28]

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Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson's disease.

Bryois J, Skene NG, Hansen TF, ..., Hjerling-Leffler J, Sullivan PF

Nat. Genet. 52 (5) 482-493 [2020-05-00; online 2020-04-27]

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Early growth response 1 regulates hematopoietic support and proliferation in human primary bone marrow stromal cells.

Li H, Lim HC, Zacharaki D, ..., Hansson J, Scheding S

Haematologica 105 (5) 1206-1215 [2020-05-00; online 2019-08-01]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Deep sequencing of myxoinflammatory fibroblastic sarcoma.

Arbajian E, Hofvander J, Magnusson L, Mertens F

Genes Chromosomes Cancer 59 (5) 309-317 [2020-05-00; online 2020-01-31]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Comprehensive chemical proteomics for target deconvolution of the redox active drug auranofin.

Saei AA, Gullberg H, Sabatier P, ..., Arnér ESJ, Zubarev RA

Redox Biol 32 (-) 101491 [2020-05-00; online 2020-03-03]

Analysis of DNA methylation patterns in the tumor immune microenvironment of metastatic melanoma.

Mitra S, Lauss M, Cabrita R, ..., Brown KM, Jönsson G

Mol Oncol 14 (5) 933-950 [2020-05-00; online 2020-03-21]

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A molecular mechanism explaining albuminuria in kidney disease.

Butt L, Unnersjö-Jess D, Höhne M, ..., Schermer B, Benzing T

Nat Metab 2 (5) 461-474 [2020-05-00; online 2020-05-11]

Integrated Microscopy Technologies Stockholm [Collaborative]

Interactive proteogenomic exploration of response to Fusarium head blight in oat varieties with different resistance.

Willforss J, Leonova S, Tillander J, ..., Chawade A, Levander F

J Proteomics 218 (-) 103688 [2020-04-30; online 2020-02-14]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Interactions of the Lysosomotropic Detergent O-Methyl-Serine Dodecylamide Hydrochloride (MSDH) with Lipid Bilayer Membranes-Implications for Cell Toxicity.

Villamil Giraldo AM, Eriksson I, Wennmalm S, ..., Ederth T, Öllinger K

Int J Mol Sci 21 (9) 3136 [2020-04-29; online 2020-04-29]

Integrated Microscopy Technologies Stockholm [Collaborative]

Fungal Diversity in the Phyllosphere of Pinus heldreichii H. Christ—An Endemic and High-Altitude Pine of the Mediterranean Region

Lazarević J, Menkis A

Diversity 12 (5) 172 [2020-04-28; online 2020-04-28]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

DNA methylation and copy number variation profiling of T-cell lymphoblastic leukemia and lymphoma.

Haider Z, Landfors M, Golovleva I, ..., Hultdin M, Degerman S

Blood Cancer J 10 (4) 45 [2020-04-28; online 2020-04-28]

Clinical Genomics [Service] Clinical Genomics Umeå [Service]

Biodiversity between sand grains: Meiofauna composition across southern and western Sweden assessed by metabarcoding.

Atherton S, Jondelius U

Biodivers Data J 8 (-) e51813 [2020-04-27; online 2020-04-27]

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Mending Fences: Na,K-ATPase signaling via Ca2+ in the maintenance of epithelium integrity.

Aperia A, Brismar H, Uhlén P

Cell Calcium 88 (-) 102210 [2020-04-26; online 2020-04-26]

Integrated Microscopy Technologies Stockholm [Collaborative]

Low occurrence of extended-spectrum cephalosporinase producing Enterobacteriaceae and no detection of methicillin-resistant coagulase-positive staphylococci in healthy dogs in Sweden.

Börjesson S, Gunnarsson L, Landén A, Grönlund U

Acta Vet. Scand. 62 (1) 18 [2020-04-25; online 2020-04-25]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Optimization of Tetrahydroindazoles as Inhibitors of Human Dihydroorotate Dehydrogenase and Evaluation of Their Activity and In Vitro Metabolic Stability.

Popova G, Ladds MJGW, Johansson L, ..., Yngve U, Lain S

J. Med. Chem. 63 (8) 3915-3934 [2020-04-23; online 2020-04-08]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Service]

Trade-off between somatic and germline repair in a vertebrate supports the expensive germ line hypothesis.

Chen HY, Jolly C, Bublys K, Marcu D, Immler S

Proc. Natl. Acad. Sci. U.S.A. 117 (16) 8973-8979 [2020-04-21; online 2020-04-03]

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Studies of Emission Processes of Polymer Additives into Water Using Quartz Crystal Microbalance-A Case Study on Organophosphate Esters.

Xiao L, Zheng Z, Irgum K, Andersson PL

Environ. Sci. Technol. 54 (8) 4876-4885 [2020-04-21; online 2020-04-01]

Solution Conformations Explain the Chameleonic Behaviour of Macrocyclic Drugs.

Danelius E, Poongavanam V, Peintner S, ..., Erdélyi M, Kihlberg J

Chemistry 26 (23) 5231-5244 [2020-04-21; online 2020-04-06]

Molecular profiling of driver events in metastatic uveal melanoma.

Karlsson J, Nilsson LM, Mitra S, ..., Olofsson Bagge R, Nilsson JA

Nat Commun 11 (1) 1894 [2020-04-20; online 2020-04-20]

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Long-term stability of partial nitritation-anammox for treatment of municipal wastewater in a moving bed biofilm reactor pilot system.

Gustavsson DJI, Suarez C, Wilén BM, Hermansson M, Persson F

Sci. Total Environ. 714 (-) 136342 [2020-04-20; online 2020-01-07]

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Effect of Cobalt, Nickel, and Selenium/Tungsten Deficiency on Mesophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds.

Šafarič L, Yekta SS, Svensson BH, ..., Bastviken D, Björn A

Microorganisms 8 (4) 598 [2020-04-20; online 2020-04-20]

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Fungi and Oomycetes in the Irrigation Water of Forest Nurseries

Marčiulynas A, Marčiulynienė D, Lynikienė J, ..., Vaičiukynė M, Menkis A

Forests 11 (4) 459 [2020-04-18; online 2020-04-18]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Rapid Biophysical Characterization and NMR Spectroscopy Structural Analysis of Small Proteins from Bacteria and Archaea.

Kubatova N, Pyper DJ, Jonker HRA, ..., Schmitz RA, Schwalbe H

ChemBioChem 21 (8) 1178-1187 [2020-04-17; online 2020-01-21]

Genome-Scale Metabolic Modeling of Glioblastoma Reveals Promising Targets for Drug Development.

Larsson I, Uhlén M, Zhang C, Mardinoglu A

Front Genet 11 (-) 381 [2020-04-17; online 2020-04-17]

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Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs.

Bianchi M, Rafati N, Karlsson Å, ..., Lindblad-Toh K, Rosengren Pielberg G

BMC Genomics 21 (1) 307 [2020-04-16; online 2020-04-16]

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Capsid Structure of a Marine Algal Virus of the Order Picornavirales.

Munke A, Kimura K, Tomaru Y, Okamoto K

J. Virol. 94 (9) - [2020-04-16; online 2020-04-16]

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences.

Drysdale R, Cook CE, Petryszak R, ..., Durinx C, McEntyre J

Bioinformatics 36 (8) 2636-2642 [2020-04-15; online 2020-01-18]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia.

Halvorsen M, Huh R, Oskolkov N, ..., Sullivan PF, Szatkiewicz JP

Nat Commun 11 (1) 1842 [2020-04-15; online 2020-04-15]

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Effect of sample preparation techniques upon single cell chemical imaging: A practical comparison between synchrotron radiation based X-ray fluorescence (SR-XRF) and Nanoscopic Secondary Ion Mass Spectrometry (nano-SIMS).

De Samber B, De Rycke R, De Bruyne M, ..., Polerecky L, Vincze L

Anal. Chim. Acta 1106 (-) 22-32 [2020-04-15; online 2020-01-24]

Difference in virulence between Neisseria meningitidis serogroups W and Y in transgenic mice.

Eriksson L, Stenmark B, Deghmane A, ..., Mölling P, Taha M

BMC Microbiol. 20 (1) 92 [2020-04-15; online 2020-04-15]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues.

Berglund E, Saarenpää S, Jemt A, ..., Lundeberg J, Giacomello S

BMC Genomics 21 (1) 298 [2020-04-15; online 2020-04-15]

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Generation of Retinal Pigment Epithelial Cells Derived from Human Embryonic Stem Cells Lacking Human Leukocyte Antigen Class I and II.

Petrus-Reurer S, Winblad N, Kumar P, ..., Kvanta A, Lanner F

Stem Cell Reports 14 (4) 648-662 [2020-04-14; online 2020-03-19]

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MutT homologue 1 (MTH1) removes N6-methyl-dATP from the dNTP pool.

Scaletti ER, Vallin KS, Bräutigam L, ..., Stenmark P, Jemth AS

J. Biol. Chem. 295 (15) 4761-4772 [2020-04-10; online 2020-03-06]

Ex Vivo Organoid Cultures Reveal the Importance of the Tumor Microenvironment for Maintenance of Colorectal Cancer Stem Cells.

Li X, Larsson P, Ljuslinder I, ..., Edin S, Palmqvist R

Cancers (Basel) 12 (4) 923 [2020-04-10; online 2020-04-10]

Clinical Genomics [Collaborative] Clinical Genomics Umeå [Collaborative]

Hybrid Aspen Expressing a Carbohydrate Esterase Family 5 Acetyl Xylan Esterase Under Control of a Wood-Specific Promoter Shows Improved Saccharification.

Wang Z, Pawar PM, Derba-Maceluch M, ..., Jönsson LJ, Mellerowicz EJ

Front Plant Sci 11 (-) 380 [2020-04-08; online 2020-04-08]

Building blocks are synthesized on demand during the yeast cell cycle.

Campbell K, Westholm J, Kasvandik S, ..., Mormino M, Nielsen J

Proc. Natl. Acad. Sci. U.S.A. 117 (14) 7575-7583 [2020-04-07; online 2020-03-25]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

The honeybee (Apis mellifera) developmental state shapes the genetic composition of the deformed wing virus-A quasispecies during serial transmission.

Yañez O, Chávez-Galarza J, Tellgren-Roth C, ..., Neumann P, de Miranda JR

Sci Rep 10 (1) 5956 [2020-04-06; online 2020-04-06]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Draft Genome Sequence of the Urinary Catheter Isolate Enterobacter ludwigii CEB04 with High Biofilm Forming Capacity.

Shafeeq S, Wang X, Lünsdorf H, Brauner A, Römling U

Microorganisms 8 (4) 522 [2020-04-05; online 2020-04-05]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

The conifer root rot pathogens Heterobasidion irregulare and Heterobasidion occidentale employ different strategies to infect Norway spruce.

Hu Y, Elfstrand M, Stenlid J, Durling MB, Olson Å

Sci Rep 10 (1) 5884 [2020-04-03; online 2020-04-03]

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Plant resistance does not compromise parasitoid-based biocontrol of a strawberry pest.

Weber D, Egan PA, Muola A, Ericson LE, Stenberg JA

Sci Rep 10 (1) 5899 [2020-04-03; online 2020-04-03]

Guidelines for curriculum and course development in higher education and training

Tractenberg RE, Lindvall JM, Attwood T, Via A

- - (-) - [2020-04-03; online 2020-04-03]

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Genomic characterization and outcome of prosthetic joint infections caused by Staphylococcus aureus.

Wildeman P, Tevell S, Eriksson C, ..., Söderquist B, Stenmark B

Sci Rep 10 (1) 5938 [2020-04-03; online 2020-04-03]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Thermal Proteome Profiling Identifies Oxidative-Dependent Inhibition of the Transcription of Major Oncogenes as a New Therapeutic Mechanism for Select Anticancer Compounds.

Peuget S, Zhu J, Sanz G, ..., Zubarev R, Selivanova G

Cancer Res. 80 (7) 1538-1550 [2020-04-01; online 2020-02-04]

Chemical Proteomics [Collaborative]

Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures.

Mahajan M, Yee B, Hägglund E, ..., Fuerst JA, Andersson SGE

Mol. Biol. Evol. 37 (4) 1020-1040 [2020-04-01; online 2019-12-07]

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Lung developmental arrest caused by PDGF-A deletion: consequences for the adult mouse lung.

Gouveia L, Kraut S, Hadzic S, ..., Betsholtz C, Andrae J

Am J Physiol Lung Cell Mol Physiol 318 (4) L831-L843 [2020-04-01; online 2020-03-18]

Extensive Clonal Branching Shapes the Evolutionary History of High-Risk Pediatric Cancers.

Andersson N, Bakker B, Karlsson J, ..., Foijer F, Gisselsson D

Cancer Res. 80 (7) 1512-1523 [2020-04-01; online 2020-02-10]

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Effects of whole-grain wheat, rye, and lignan supplementation on cardiometabolic risk factors in men with metabolic syndrome: a randomized crossover trial.

Eriksen AK, Brunius C, Mazidi M, ..., Dicksved J, Landberg R

Am. J. Clin. Nutr. 111 (4) 864-876 [2020-04-01; online 2020-02-26]

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Development of basic building blocks for cryo-EM: the emcore and emvis software libraries.

de la Rosa-Trevín JM, Hernández Viga PA, Otón J, Lindahl E

Acta Crystallogr D Struct Biol 76 (Pt 4) 350-356 [2020-04-01; online 2020-03-31]

The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non-alcoholic fatty liver disease.

Zhang C, Bjornson E, Arif M, ..., Borén J, Mardinoglu A

Mol. Syst. Biol. 16 (4) e9495 [2020-04-00; online 2020-04-28]

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Substantial intrinsic variability in chemoradiosensitivity of newly established anaplastic thyroid cancer cell-lines.

Gretarsson S, Nygren A, Rosendahl AH, ..., Wennerberg J, Ekblad L

Acta Otolaryngol. 140 (4) 337-343 [2020-04-00; online 2020-01-10]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Simultaneous mass spectrometry imaging of multiple neuropeptides in the brain and alterations induced by experimental parkinsonism and L-DOPA therapy.

Hulme H, Fridjonsdottir E, Gunnarsdottir H, ..., Svenningsson P, Andrén PE

Neurobiol. Dis. 137 (-) 104738 [2020-04-00; online 2020-01-10]

Screening for autoantibody targets in post-vaccination narcolepsy using proteome arrays.

Lind A, Eriksson D, Akel O, ..., Elding Larsson H, Landegren N

Scand. J. Immunol. 91 (4) e12864 [2020-04-00; online 2020-02-13]

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Polymerase IV Plays a Crucial Role in Pollen Development in Capsella.

Wang Z, Butel N, Santos-González J, ..., Martinez G, Köhler C

Plant Cell 32 (4) 950-966 [2020-04-00; online 2020-01-27]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis.

Nunes L, Aasebø K, Mathot L, ..., Sjöblom T, Glimelius B

Acta Oncol 59 (4) 417-426 [2020-04-00; online 2020-01-10]

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Long-term application of Swedish sewage sludge on farmland does not cause clear changes in the soil bacterial resistome.

Rutgersson C, Ebmeyer S, Lassen SB, ..., Flach CF, Larsson DGJ

Environ Int 137 (-) 105339 [2020-04-00; online 2020-02-06]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genes and variants in hematopoiesis-related pathways are associated with gemcitabine/carboplatin-induced thrombocytopenia.

Björn N, Sigurgeirsson B, Svedberg A, ..., Lundeberg J, Gréen H

Pharmacogenomics J. 20 (2) 179-191 [2020-04-00; online 2019-10-15]

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Establishing Trypanosoma cruzi farnesyl pyrophosphate synthase as a viable target for biosensor driven fragment-based lead discovery.

Opassi G, Nordström H, Lundin A, ..., Klebe G, Danielson UH

Protein Sci. 29 (4) 991-1003 [2020-04-00; online 2020-02-07]

Cell Cycle Profiling Reveals Protein Oscillation, Phosphorylation, and Localization Dynamics.

Herr P, Boström J, Rullman E, ..., Maddalo G, Altun M

Mol. Cell Proteomics 19 (4) 608-623 [2020-04-00; online 2020-02-12]

Global Proteomics and Proteogenomics [Collaborative]

ABCB1 single-nucleotide variants and survival in patients with glioblastoma treated with radiotherapy concomitant with temozolomide.

Malmström A, Łysiak M, Åkesson L, ..., Green H, Söderkvist P

Pharmacogenomics J. 20 (2) 213-219 [2020-04-00; online 2019-10-17]

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A Multi-Omics Approach to Liver Diseases: Integration of Single Nuclei Transcriptomics with Proteomics and HiCap Bulk Data in Human Liver.

Cavalli M, Diamanti K, Pan G, ..., Komorowski J, Wadelius C

OMICS 24 (4) 180-194 [2020-04-00; online 2020-03-16]

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Transcriptome Profiling and Toxicity Following Long-Term, Low Dose Exposure of Human Lung Cells to Ni and NiO Nanoparticles-Comparison with NiCl2.

Gliga AR, Di Bucchianico S, Åkerlund E, Karlsson HL

Nanomaterials (Basel) 10 (4) 649 [2020-03-31; online 2020-03-31]

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Mutations in COL1A1/A2 and CREB3L1 are associated with oligodontia in osteogenesis imperfecta.

Andersson K, Malmgren B, Åström E, ..., Taylan F, Dahllöf G

Orphanet J Rare Dis 15 (1) 80 [2020-03-31; online 2020-03-31]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Identification of cell surface markers and establishment of monolayer differentiation to retinal pigment epithelial cells.

Plaza Reyes A, Petrus-Reurer S, Padrell Sánchez S, ..., Kvanta A, Lanner F

Nat Commun 11 (1) 1609 [2020-03-30; online 2020-03-30]

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Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans.

Cortázar-Chinarro M, Meyer-Lucht Y, Van der Valk T, ..., Laurila A, Höglund J

BMC Genet. 21 (1) 38 [2020-03-30; online 2020-03-30]

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Structural basis for the increased processivity of D-family DNA polymerases in complex with PCNA.

Madru C, Henneke G, Raia P, ..., Carroni M, Sauguet L

Nat Commun 11 (1) 1591 [2020-03-27; online 2020-03-27]

Image-Based Morphological Profiling Identifies a Lysosomotropic, Iron-Sequestering Autophagy Inhibitor.

Laraia L, Garivet G, Foley DJ, ..., Rodriguez R, Waldmann H

Angew. Chem. Int. Ed. Engl. 59 (14) 5721-5729 [2020-03-27; online 2020-01-24]

Deficits in Motor Performance, Neurotransmitters and Synaptic Plasticity in Elderly and Experimental Parkinsonian Mice Lacking GPR37.

Zhang X, Mantas I, Fridjonsdottir E, ..., Chergui K, Svenningsson P

Front Aging Neurosci 12 (-) 84 [2020-03-27; online 2020-03-27]

Towards uterus tissue engineering: a comparative study of sheep uterus decellularisation.

Tiemann TT, Padma AM, Sehic E, ..., Brännström M, Hellström M

Mol. Hum. Reprod. 26 (3) 167-178 [2020-03-26; online 2020-01-26]

Integrated Microscopy Technologies Gothenburg [Service]

An mRNA-mRNA Interaction Couples Expression of a Virulence Factor and Its Chaperone in Listeria monocytogenes.

Ignatov D, Vaitkevicius K, Durand S, ..., Condon C, Johansson J

Cell Rep 30 (12) 4027-4040.e7 [2020-03-24; online 2020-03-27]

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An atlas of human metabolism.

Robinson JL, Kocabaş P, Wang H, ..., Uhlén M, Nielsen J

Sci Signal 13 (624) - [2020-03-24; online 2020-03-24]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Marine Sediments Illuminate Chlamydiae Diversity and Evolution.

Dharamshi JE, Tamarit D, Eme L, ..., Spang A, Ettema TJG

Curr. Biol. 30 (6) 1032-1048.e7 [2020-03-23; online 2020-03-05]

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Molecular Profiling for Predictors of Radiosensitivity in Patients with Breast or Head-and-Neck Cancer.

Drobin K, Marczyk M, Halle M, ..., Schwenk JM, Haghdoost S

Cancers (Basel) 12 (3) 753 [2020-03-22; online 2020-03-22]

Non-dopaminergic Alterations in Depression-Like FSL Rats in Experimental Parkinsonism and L-DOPA Responses.

Schintu N, Zhang X, Stroth N, ..., Andrén PE, Svenningsson P

Front Pharmacol 11 (-) 304 [2020-03-20; online 2020-03-20]

Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities.

Böhm ME, Razavi M, Marathe NP, Flach CF, Larsson DGJ

Microbiome 8 (1) 41 [2020-03-20; online 2020-03-20]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Specific functions for Mediator complex subunits from different modules in the transcriptional response of Arabidopsis thaliana to abiotic stress.

Crawford T, Karamat F, Lehotai N, ..., Strand Å, Björklund S

Sci Rep 10 (1) 5073 [2020-03-19; online 2020-03-19]

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Analysis of the behaviour of confined molecules using 2H T1 nuclear magnetic relaxation dispersion

Shamshir A, Sparrman T, Westlund PO

Molecular Physics 118 (6) e1645367 [2020-03-18; online 2019-07-24]

Newborn Screening for Presymptomatic Diagnosis of Complement and Phagocyte Deficiencies.

Dezfouli M, Bergström S, Skattum L, ..., Nilsson P, Hammarström L

Front Immunol 11 (-) 455 [2020-03-17; online 2020-03-17]

Immune Profiling of Human Gut-Associated Lymphoid Tissue Identifies a Role for Isolated Lymphoid Follicles in Priming of Region-Specific Immunity.

Fenton TM, Jørgensen PB, Niss K, ..., Johansson-Lindbom B, Agace WW

Immunity 52 (3) 557-570.e6 [2020-03-17; online 2020-03-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Effects of acute sleep loss on diurnal plasma dynamics of CNS health biomarkers in young men.

Benedict C, Blennow K, Zetterberg H, Cedernaes J

Neurology 94 (11) e1181-e1189 [2020-03-17; online 2020-01-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The application of differential scanning fluorimetry in exploring bisubstrate binding to protein arginine N-methyltransferase 1.

Brown JI, Page BDG, Frankel A

Methods 175 (-) 10-23 [2020-03-15; online 2019-11-11]

Inherited DNA Repair Gene Mutations in Men with Lethal Prostate Cancer.

Rantapero T, Wahlfors T, Kähler A, ..., Schleutker J, Wiklund F

Genes 11 (3) 314 [2020-03-14; online 2020-03-14]

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Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.

Alneberg J, Bennke C, Beier S, ..., Pinhassi J, Andersson AF

Commun Biol 3 (1) 119 [2020-03-13; online 2020-03-13]

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Comparing the Performance of Microsatellites and RADseq in Population Genetic Studies: Analysis of Data for Pike (Esox lucius) and a Synthesis of Previous Studies.

Sunde J, Yıldırım Y, Tibblin P, Forsman A

Front Genet 11 (-) 218 [2020-03-13; online 2020-03-13]

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Exploiting loss of heterozygosity for allele-selective colorectal cancer chemotherapy.

Rendo V, Stoimenov I, Mateus A, ..., Cheong I, Sjöblom T

Nat Commun 11 (1) 1308 [2020-03-11; online 2020-03-11]

Bioinformatics Support for Computational Resources [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Service]

Footprints of natural selection at the mannose-6-phosphate isomerase locus in barnacles.

Nunez JCB, Flight PA, Neil KB, ..., Blomberg A, Rand DM

Proc. Natl. Acad. Sci. U.S.A. 117 (10) 5376-5385 [2020-03-10; online 2020-02-25]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]

Uncovering diversity and metabolic spectrum of animals in dead zone sediments.

Broman E, Bonaglia S, Holovachov O, ..., Hall POJ, Nascimento FJA

Commun Biol 3 (1) 106 [2020-03-06; online 2020-03-06]

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Ribonucleotide reductase inhibitors suppress SAMHD1 ara-CTPase activity enhancing cytarabine efficacy.

Rudd SG, Tsesmetzis N, Sanjiv K, ..., Helleday T, Herold N

EMBO Mol Med 12 (3) e10419 [2020-03-06; online 2020-01-17]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

An atlas of the protein-coding genes in the human, pig, and mouse brain.

Sjöstedt E, Zhong W, Fagerberg L, ..., Uhlén M, Mulder J

Science 367 (6482) eaay5947 [2020-03-06; online 2020-03-07]

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The Molecular Anatomy of Mouse Skin during Hair Growth and Rest.

Joost S, Annusver K, Jacob T, ..., Sandberg R, Kasper M

Cell Stem Cell 26 (3) 441-457.e7 [2020-03-05; online 2020-02-27]

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Stressful Beginnings with Long-Term Consequences.

Consiglio CR, Brodin P

Cell 180 (5) 820-821 [2020-03-05; online 2020-03-07]

Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Technology development]

Short-Range Order and Transport Properties in Mixtures of the Protic Ionic Liquid [C2HIm][TFSI] with Water or Imidazole.

Hasani M, Varela LM, Martinelli A

J. Phys. Chem. B 124 (9) 1767-1777 [2020-03-05; online 2020-02-20]

Genome-wide Association Analysis in Humans Links Nucleotide Metabolism to Leukocyte Telomere Length.

Li C, Stoma S, Lotta LA, ..., Langenberg C, Codd V

Am. J. Hum. Genet. 106 (3) 389-404 [2020-03-05; online 2020-02-27]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Epiphyseal Cartilage Formation Involves Differential Dynamics of Various Cellular Populations During Embryogenesis.

Zhang Y, Annusver K, Sunadome K, ..., Adameyko I, Xie M

Front Cell Dev Biol 8 (-) 122 [2020-03-05; online 2020-03-05]

Integrated Microscopy Technologies Stockholm [Service]

One-Pot Production of RNA in High Yield and Purity Through Cleaving Tandem Transcripts.

Feyrer H, Munteanu R, Baronti L, Petzold K

Molecules 25 (5) - [2020-03-04; online 2020-03-04]

Transcriptomic resources for evolutionary studies in flat periwinkles and related species.

Marques JP, Sotelo G, Galindo J, ..., Hollander J, Faria R

Sci Data 7 (1) 73 [2020-03-03; online 2020-03-03]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Oral Microbiota Profile Associates with Sugar Intake and Taste Preference Genes.

Esberg A, Haworth S, Hasslöf P, Lif Holgerson P, Johansson I

Nutrients 12 (3) 681 [2020-03-03; online 2020-03-03]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Single-cell analysis of human ovarian cortex identifies distinct cell populations but no oogonial stem cells.

Wagner M, Yoshihara M, Douagi I, ..., Lanner F, Damdimopoulou P

Nat Commun 11 (1) 1147 [2020-03-02; online 2020-03-02]

Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]

Metabolomics analyses in non-diabetic middle-aged individuals reveal metabolites impacting early glucose disturbances and insulin sensitivity.

Bos MM, Noordam R, Bennett K, ..., Surowiec I, van Heemst D

Metabolomics 16 (3) 35 [2020-03-02; online 2020-03-02]

Tumor localized agonistic anti-CD40 therapy and beyond.

Eltahir M, Persson H, Mangsbo S

Expert Opin Biol Ther 20 (3) 215-217 [2020-03-00; online 2020-01-10]

Drug Discovery and Development (DDD) [Collaborative]

The nf-core framework for community-curated bioinformatics pipelines.

Ewels PA, Peltzer A, Fillinger S, ..., Di Tommaso P, Nahnsen S

Nat. Biotechnol. 38 (3) 276-278 [2020-03-00; online 2020-02-15]

NGI Stockholm (Genomics Applications) [Technology development] NGI Stockholm (Genomics Production) [Technology development] National Genomics Infrastructure [Technology development]

Synthesis, Evaluation and Proposed Binding Pose of Substituted Spiro-Oxindole Dihydroquinazolinones as IRAP Inhibitors.

Engen K, Vanga SR, Lundbäck T, ..., Larhed M, Rosenström U

ChemistryOpen 9 (3) 325-337 [2020-03-00; online 2020-03-02]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Structure of a minimal photosystem I from the green alga Dunaliella salina.

Perez-Boerema A, Klaiman D, Caspy I, ..., Amunts A, Nelson N

NPLANTS 6 (3) 321-327 [2020-03-00; online 2020-03-02]

PIRIN2 suppresses S-type lignin accumulation in a noncell-autonomous manner in Arabidopsis xylem elements.

Zhang B, Sztojka B, Escamez S, ..., Boerjan W, Tuominen H

New Phytol. 225 (5) 1923-1935 [2020-03-00; online 2019-11-11]

Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia.

Ivanov Öfverholm I, Zachariadis V, Taylan F, ..., Nordlund J, Barbany G

Leuk. Lymphoma 61 (3) 604-613 [2020-03-00; online 2019-10-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Longitudinal changes in the frequency of mosaic chromosome Y loss in peripheral blood cells of aging men varies profoundly between individuals.

Danielsson M, Halvardson J, Davies H, ..., Dumanski JP, Forsberg LA

Eur. J. Hum. Genet. 28 (3) 349-357 [2020-03-00; online 2019-10-25]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Irreversible TrxR1 inhibitors block STAT3 activity and induce cancer cell death.

Busker S, Qian W, Haraldsson M, ..., Tamm KP, Page BDG

Sci Adv 6 (12) eaax7945 [2020-03-00; online 2020-03-20]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF) [Service]

In Situ Encapsulation of Nile Red or Doxorubicin during RAFT‐Mediated Emulsion Polymerization via Polymerization‐Induced Self‐Assembly for Biomedical Applications

Engström J, Asem H, Brismar H, ..., Malkoch M, Malmström E

Macromol. Chem. Phys. 221 (5) 1900443 [2020-03-00; online 2020-02-10]

Integrated Microscopy Technologies Stockholm [Service]

Hyena paleogenomes reveal a complex evolutionary history of cross-continental gene flow between spotted and cave hyena.

Westbury MV, Hartmann S, Barlow A, ..., Heller R, Hofreiter M

Sci Adv 6 (11) eaay0456 [2020-03-00; online 2020-03-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

High genetic risk score is associated with early disease onset, damage accrual and decreased survival in systemic lupus erythematosus.

Reid S, Alexsson A, Frodlund M, ..., Rönnblom L, Leonard D

Ann. Rheum. Dis. 79 (3) 363-369 [2020-03-00; online 2019-12-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Heritability of Caries Scores, Trajectories, and Disease Subtypes.

Haworth S, Esberg A, Lif Holgerson P, ..., Franks PW, Johansson I

J Dent Res 99 (3) 264-270 [2020-03-00; online 2020-01-06]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Functionally distinct subgroups of oligodendrocyte precursor cells integrate neural activity and execute myelin formation.

Marisca R, Hoche T, Agirre E, ..., Castelo-Branco G, Czopka T

Nat. Neurosci. 23 (3) 363-374 [2020-03-00; online 2020-02-17]

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Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.

Wang J, Street NR, Park EJ, Liu J, Ingvarsson PK

Mol. Ecol. 29 (6) 1120-1136 [2020-03-00; online 2020-03-09]

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Distinct structural modulation of photosystem I and lipid environment stabilizes its tetrameric assembly.

Chen M, Perez-Boerema A, Zhang L, ..., Li S, Amunts A

NPLANTS 6 (3) 314-320 [2020-03-00; online 2020-03-09]

Cryo-EM [Service] Global Proteomics and Proteogenomics [Service]

Discovery of Species-unique Peptide Biomarkers of Bacterial Pathogens by Tandem Mass Spectrometry-based Proteotyping.

Karlsson R, Thorsell A, Gomila M, ..., Kristiansson E, Moore ERB

Mol. Cell Proteomics 19 (3) 518-528 [2020-03-00; online 2020-01-15]

Chemical imaging of evolving amyloid plaque pathology and associated Aβ peptide aggregation in a transgenic mouse model of Alzheimer's disease.

Michno W, Wehrli P, Meier SR, ..., Blennow K, Hanrieder J

J. Neurochem. 152 (5) 602-616 [2020-03-00; online 2019-11-06]

Integrated Microscopy Technologies Gothenburg [Collaborative]

Apolipoprotein E impairs amyloid-β fibril elongation and maturation.

Islam T, Gharibyan AL, Golchin SA, ..., Olofsson L, Olofsson A

FEBS J. 287 (6) 1208-1219 [2020-03-00; online 2019-10-09]

A link between the newly described colistin resistance gene mcr-9 and clinical Enterobacteriaceae isolates carrying blaSHV-12 from horses in Sweden.

Börjesson S, Greko C, Myrenås M, ..., Nilsson O, Pedersen K

J Glob Antimicrob Resist 20 (-) 285-289 [2020-03-00; online 2019-09-05]

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PCSK6 Is a Key Protease in the Control of Smooth Muscle Cell Function in Vascular Remodeling.

Rykaczewska U, Suur BE, Röhl S, ..., Hedin U, Matic L

Circ. Res. 126 (5) 571-585 [2020-02-28; online 2020-01-02]

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Complete genome and methylome analysis of Neisseria meningitidis associated with increased serogroup Y disease.

Stenmark B, Harrison OB, Eriksson L, ..., Maiden MCJ, Mölling P

Sci Rep 10 (1) 3644 [2020-02-27; online 2020-02-27]

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The Relationship Between Polygenic Risk Scores and Cognition in Schizophrenia.

Richards AL, Pardiñas AF, Frizzati A, ..., O'Donovan MC, Walters JTR

Schizophr Bull 46 (2) 336-344 [2020-02-26; online 2019-06-18]

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Streptococcus pneumoniae Nasopharyngeal Carriage among PCV-10-Vaccinated HIV-1-Infected Children with Maintained Serological Memory in Ethiopia.

Lemma M, Bekele Y, Petkov S, ..., Howe R, Chiodi F

Pathogens 9 (3) 159 [2020-02-25; online 2020-02-25]

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Patterns of African and Asian admixture in the Afrikaner population of South Africa.

Hollfelder N, Erasmus JC, Hammaren R, ..., Greeff JM, Schlebusch CM

BMC Biol. 18 (1) 16 [2020-02-24; online 2020-02-24]

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rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression.

Pan G, Cavalli M, Carlsson B, ..., Kumar C, Wadelius C

iScience 23 (2) 100808 [2020-02-21; online 2020-01-09]

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In Vitro Regeneration of Decellularized Pig Esophagus Using Human Amniotic Stem Cells.

Nayakawde NB, Methe K, Banerjee D, ..., Premaratne GU, Olausson M

Biores Open Access 9 (1) 22-36 [2020-02-21; online 2020-02-21]

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Dominance of Mating Type A1 and Indication of Epigenetic Effects During Early Stages of Mating in Phytophthora infestans.

Tzelepis G, Hodén KP, Fogelqvist J, ..., Vetukuri RR, Dixelius C

Front Microbiol 11 (-) 252 [2020-02-21; online 2020-02-21]

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Biomolecular analyses reveal the age, sex and species identity of a near-intact Pleistocene bird carcass.

Dussex N, Stanton DWG, Sigeman H, ..., Hansson B, Dalén L

Commun Biol 3 (1) 84 [2020-02-21; online 2020-02-21]

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Backbone Cyclization and Dimerization of LL-37-Derived Peptides Enhance Antimicrobial Activity and Proteolytic Stability.

Gunasekera S, Muhammad T, Strömstedt AA, Rosengren KJ, Göransson U

Front Microbiol 11 (-) 168 [2020-02-21; online 2020-02-21]

Subtle structural alterations in G-quadruplex DNA regulate site specificity of fluorescence light-up probes.

Kumar R, Chand K, Bhowmik S, ..., Hedenström M, Chorell E

Nucleic Acids Res. 48 (3) 1108-1119 [2020-02-20; online 2020-01-09]

Primary cell wall inspired micro containers as a step towards a synthetic plant cell.

Paulraj T, Wennmalm S, Wieland DCF, ..., Cárdenas M, Svagan AJ

Nat Commun 11 (1) 958 [2020-02-19; online 2020-02-19]

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Validation of Novel Prognostic Biomarkers for Early-Stage Clear-Cell, Endometrioid and Mucinous Ovarian Carcinomas Using Immunohistochemistry.

Engqvist H, Parris TZ, Kovács A, ..., Karlsson P, Helou K

Front Oncol 10 (-) 162 [2020-02-18; online 2020-02-18]

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Managed and Unmanaged Pinus sylvestris Forest Stands Harbour Similar Diversity and Composition of the Phyllosphere and Soil Fungi.

Lynikienė J, Marčiulynienė D, Marčiulynas A, ..., Vaičiukynė M, Menkis A

Microorganisms 8 (2) 259 [2020-02-15; online 2020-02-15]

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The First Structure of an Active Mammalian dCTPase and its Complexes With Substrate Analogs and Products.

Scaletti E, Claesson M, Helleday T, Jemth AS, Stenmark P

J. Mol. Biol. 432 (4) 1126-1142 [2020-02-14; online 2020-01-15]

Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing.

Nordlund J, Marincevic-Zuniga Y, Cavelier L, ..., Lönnerholm G, Syvänen AC

Sci Rep 10 (1) 2512 [2020-02-13; online 2020-02-13]

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Using null models to compare bacterial and microeukaryotic metacommunity assembly under shifting environmental conditions.

Vass M, Székely AJ, Lindström ES, Langenheder S

Sci Rep 10 (1) 2455 [2020-02-12; online 2020-02-12]

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Quinazoline Ligands Induce Cancer Cell Death through Selective STAT3 Inhibition and G-Quadruplex Stabilization.

Jamroskovic J, Doimo M, Chand K, ..., Chorell E, Sabouri N

J. Am. Chem. Soc. 142 (6) 2876-2888 [2020-02-12; online 2020-01-28]

Subpopulations of extracellular vesicles from human metastatic melanoma tissue identified by quantitative proteomics after optimized isolation.

Crescitelli R, Lässer C, Jang SC, ..., Olofsson Bagge R, Lötvall J

J Extracell Vesicles 9 (1) 1722433 [2020-02-11; online 2020-02-11]

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Longitudinal trajectories, correlations and mortality associations of nine biological ages across 20-years follow-up.

Li X, Ploner A, Wang Y, ..., Jylhävä J, Hägg S

Elife 9 (-) - [2020-02-11; online 2020-02-11]

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Whole genome sequencing unveils genetic heterogeneity in optic nerve hypoplasia.

Dahl S, Pettersson M, Eisfeldt J, ..., Anderlid BM, Lindstrand A

PLoS ONE 15 (2) e0228622 [2020-02-10; online 2020-02-10]

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Low concentrations of the benzodiazepine drug oxazepam induce anxiolytic effects in wild-caught but not in laboratory zebrafish.

Vossen LE, Červený D, Sen Sarma O, ..., Brodin T, Winberg S

Sci. Total Environ. 703 (-) 134701 [2020-02-10; online 2019-11-01]

Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia.

Grönroos T, Mäkinen A, Laukkanen S, ..., Heinäniemi M, Lohi O

Sci Rep 10 (1) 2043 [2020-02-06; online 2020-02-06]

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Clonal competition within complex evolutionary hierarchies shapes AML over time.

Sandén C, Lilljebjörn H, Orsmark Pietras C, ..., Ågerstam H, Fioretos T

Nat Commun 11 (1) 579 [2020-02-05; online 2020-02-05]

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A chromosome-scale reference genome for Giardia intestinalis WB.

Xu F, Jex A, Svärd SG

Sci Data 7 (1) 38 [2020-02-04; online 2020-02-04]

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Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses.

Phad GE, Pushparaj P, Tran K, ..., Wyatt RT, Karlsson Hedestam GB

J. Exp. Med. 217 (2) - [2020-02-03; online 2019-11-11]

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Plasma kidney injury molecule-1 (p-KIM-1) levels and deterioration of kidney function over 16 years.

Schulz CA, Engström G, Nilsson J, ..., Melander O, Orho-Melander M

Nephrol Dial Transplant 35 (2) 265-273 [2020-02-01; online 2019-01-11]

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Glycogenin is Dispensable for Glycogen Synthesis in Human Muscle, and Glycogenin Deficiency Causes Polyglucosan Storage.

Visuttijai K, Hedberg-Oldfors C, Thomsen C, ..., Roach P, Oldfors A

J. Clin. Endocrinol. Metab. 105 (2) 557-566 [2020-02-01; online 2019-10-20]

Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies).

Wang X, Bernhardsson C, Ingvarsson PK

Genome Biol Evol 12 (2) 3803-3817 [2020-02-01; online 2020-01-21]

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Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss.

Lewis WH, Lind AE, Sendra KM, ..., Ettema TJG, Embley TM

Mol. Biol. Evol. 37 (2) 524-539 [2020-02-01; online 2019-10-28]

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The antimalarial drug amodiaquine stabilizes p53 through ribosome biogenesis stress, independently of its autophagy-inhibitory activity.

Espinoza JA, Zisi A, Kanellis DC, ..., Lindström MS, Bartek J

Cell Death Differ. 27 (2) 773-789 [2020-02-00; online 2019-07-08]

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Revealing the Regional Localization and Differential Lung Retention of Inhaled Compounds by Mass Spectrometry Imaging.

Hamm GR, Bäckström E, Brülls M, ..., Fridén M, Goodwin RJA

J Aerosol Med Pulm Drug Deliv 33 (1) 43-53 [2020-02-00; online 2019-07-31]

Plasma Lipidome and Prediction of Type 2 Diabetes in the Population-Based Malmö Diet and Cancer Cohort.

Fernandez C, Surma MA, Klose C, ..., Simons K, Melander O

Diabetes Care 43 (2) 366-373 [2020-02-00; online 2019-12-08]

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Perspective on CETSA Literature: Toward More Quantitative Data Interpretation.

Seashore-Ludlow B, Axelsson H, Lundbäck T

SLAS DISCOVERY: Advancing Life Sciences R&D 25 (2) 118-126 [2020-02-00; online 2019-10-30]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Genomic and transcriptomic features of dermatofibrosarcoma protuberans: Unusual chromosomal origin of the COL1A1-PDGFB fusion gene and synergistic effects of amplified regions in tumor development.

Köster J, Arbajian E, Viklund B, ..., Mandahl N, Mertens F

Cancer Genet 241 (-) 34-41 [2020-02-00; online 2019-12-10]

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Fast time-resolved NMR with non-uniform sampling.

Gołowicz D, Kasprzak P, Orekhov V, Kazimierczuk K

Progress in Nuclear Magnetic Resonance Spectroscopy 116 (-) 40-55 [2020-02-00; online 2019-09-25]

Exosomes influence the behavior of human mesenchymal stem cells on titanium surfaces.

Wang X, Shah FA, Vazirisani F, ..., Ekström K, Thomsen P

Biomaterials 230 (-) 119571 [2020-02-00; online 2019-10-24]

Engineering yeast phospholipid metabolism for de novo oleoylethanolamide production.

Liu Y, Liu Q, Krivoruchko A, Khoomrung S, Nielsen J

Nat. Chem. Biol. 16 (2) 197-205 [2020-02-00; online 2019-12-16]

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Dynamic architecture and regulatory implications of the miRNA network underlying the response to stress in melon.

Sanz-Carbonell A, Marques MC, Martinez G, Gomez G

RNA Biol 17 (2) 292-308 [2020-02-00; online 2019-12-10]

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Associations Between Apolipoprotein A1, High-Density Lipoprotein Cholesterol, and Urinary Cytokine Levels in Elderly Males and Females.

Fellström B, Helmersson-Karlqvist J, Lind L, ..., Ärnlöv J, Larsson A

Journal of Interferon & Cytokine Research 40 (2) 71-74 [2020-02-00; online 2019-10-10]

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Artificial intelligence for diagnosis and grading of prostate cancer in biopsies: a population-based, diagnostic study.

Ström P, Kartasalo K, Olsson H, ..., Egevad L, Eklund M

Lancet Oncol 21 (2) 222-232 [2020-02-00; online 2020-01-08]

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Analysis of the genetic variants associated with circulating levels of sgp130. Results from the IMPROVE study.

Bonomi A, Veglia F, Baldassarre D, ..., Gigante B, on behalf of the IMPROVE study group

Genes Immun. 21 (2) 100-108 [2020-02-00; online 2020-01-14]

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Painting of Fourth and the X-Linked 1.688 Satellite in D. melanogaster is Involved in Chromosome-Wide Gene Regulation.

Ekhteraei-Tousi S, Lewerentz J, Larsson J

Cells 9 (2) 323 [2020-01-30; online 2020-01-30]

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Diversity and Host Interactions Among Virulent and Temperate Baltic Sea Flavobacterium Phages.

Nilsson E, Bayfield OW, Lundin D, Antson AA, Holmfeldt K

Viruses 12 (2) 158 [2020-01-30; online 2020-01-30]

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Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants.

Garcia M, Juhos S, Larsson M, ..., Käller M, Nystedt B

F1000Res 9 (-) 63 [2020-01-29; online 2020-01-29]

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The round goby genome provides insights into mechanisms that may facilitate biological invasions.

Adrian-Kalchhauser I, Blomberg A, Larsson T, ..., Schloissnig S, Winkler S

BMC Biol. 18 (1) 11 [2020-01-28; online 2020-01-28]

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Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei.

Montoliu-Nerin M, Sánchez-García M, Bergin C, ..., Johannesson H, Rosling A

Sci Rep 10 (1) 1303 [2020-01-28; online 2020-01-28]

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Population Pharmacokinetics and Pharmacogenetics of Ethambutol in Adult Patients Coinfected with Tuberculosis and HIV.

Sundell J, Bienvenu E, Birgersson S, Äbelö A, Ashton M

Antimicrob. Agents Chemother. 64 (2) - [2020-01-27; online 2020-01-27]

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Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity.

Pillon NJ, Gabriel BM, Dollet L, ..., Krook A, Zierath JR

Nat Commun 11 (1) 470 [2020-01-24; online 2020-01-24]

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Extracellular Vesicles Released From the Skin Commensal Yeast Malassezia sympodialis Activate Human Primary Keratinocytes.

Vallhov H, Johansson C, Veerman RE, Scheynius A

Front. Cell. Infect. Microbiol. 10 (-) 6 [2020-01-24; online 2020-01-24]

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Estimating Detection Limits of Potentiometric DNA Sensors Using Surface Plasmon Resonance Analyses.

Xu X, Makaraviciute A, Abdurakhmanov E, ..., Nyholm L, Zhang Z

ACS Sens. 5 (1) 217-224 [2020-01-24; online 2019-12-23]

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CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken.

Fogelholm J, Henriksen R, Höglund A, ..., Jensen P, Wright D

Sci Rep 10 (1) 1161 [2020-01-24; online 2020-01-24]

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The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly.

Pinese M, Lacaze P, Rath EM, ..., Dinger ME, Thomas DM

Nat Commun 11 (1) 435 [2020-01-23; online 2020-01-23]

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Reverse engineering directed gene regulatory networks from transcriptomics and proteomics data of biomining bacterial communities with approximate Bayesian computation and steady-state signalling simulations.

Buetti-Dinh A, Herold M, Christel S, ..., Friedman R, Dopson M

BMC Bioinformatics 21 (1) 23 [2020-01-21; online 2020-01-21]

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Modulation of Structural Heterogeneity Controls Phytochrome Photoswitching.

Gustavsson E, Isaksson L, Persson C, ..., Orekhov V, Westenhoff S

Biophysical Journal 118 (2) 415-421 [2020-01-21; online 2019-11-26]

Transcriptome analysis of fibroblasts from schizophrenia patients reveals differential expression of schizophrenia-related genes.

Etemadikhah M, Niazi A, Wetterberg L, Feuk L

Sci Rep 10 (1) 630 [2020-01-20; online 2020-01-20]

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Loss of centromere function drives karyotype evolution in closely related Malassezia species.

Sankaranarayanan SR, Ianiri G, Coelho MA, ..., Heitman J, Sanyal K

Elife 9 (-) - [2020-01-20; online 2020-01-20]

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Genome-Based Comparison of All Species of the Genus Moorella, and Status of the Species Moorella thermoacetica and Moorella thermoautotrophica.

Redl S, Poehlein A, Esser C, ..., Dürre P, Nielsen AT

Front Microbiol 10 (-) 3070 [2020-01-17; online 2020-01-17]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A spontaneous mitonuclear epistasis converging on Rieske Fe-S protein exacerbates complex III deficiency in mice.

Purhonen J, Grigorjev V, Ekiert R, ..., Fellman V, Kallijärvi J

Nat Commun 11 (1) 322 [2020-01-16; online 2020-01-16]

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Gene regulatory response to hyposalinity in the brown seaweed Fucus vesiculosus.

Rugiu L, Panova M, Pereyra RT, Jormalainen V

BMC Genomics 21 (1) 42 [2020-01-13; online 2020-01-13]

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Development and characterization of an EMS-mutagenized wheat population and identification of salt-tolerant wheat lines.

Lethin J, Shakil SSM, Hassan S, ..., Olsson O, Aronsson H

BMC Plant Biol. 20 (1) 18 [2020-01-13; online 2020-01-13]

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Screening for bioactive secondary metabolites in Sri Lankan medicinal plants by microfractionation and targeted isolation of antimicrobial flavonoids from Derris scandens.

Mohotti S, Rajendran S, Muhammad T, ..., Hettiarachchi CM, Gunasekera S

Journal of Ethnopharmacology 246 (-) 112158 [2020-01-10; online 2019-08-14]

A regulatory role for CHD2 in myelopoiesis.

Shahin Varnoosfaderani F, Palau A, Dong W, ..., Svensson JP, Lennartsson A

Epigenetics 15 (6-7) 702-714 [2020-01-10; online 2020-01-10]

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Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure.

Shah S, Henry A, Roselli C, ..., Swerdlow DI, Lumbers RT

Nat Commun 11 (1) 163 [2020-01-09; online 2020-01-09]

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DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors.

Laan L, Klar J, Sobol M, ..., Schuster J, Dahl N

Clin Epigenetics 12 (1) 9 [2020-01-08; online 2020-01-08]

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A Light-up Logic Platform for Selective Recognition of Parallel G-Quadruplex Structures via Disaggregation-Induced Emission.

Deiana M, Chand K, Jamroskovic J, ..., Chorell E, Sabouri N

Angew. Chem. Int. Ed. Engl. 59 (2) 896-902 [2020-01-07; online 2019-11-22]

Evolutionary History, Genomic Adaptation to Toxic Diet, and Extinction of the Carolina Parakeet.

Gelabert P, Sandoval-Velasco M, Serres A, ..., Gilbert MTP, Lalueza-Fox C

Curr. Biol. 30 (1) 108-114.e5 [2020-01-06; online 2019-12-12]

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Metabolic Profiling and Compound-Class Identification Reveal Alterations in Serum Triglyceride Levels in Mice Immunized with Human Vaccine Adjuvant Alum.

Khoomrung S, Nookaew I, Sen P, ..., Harandi AM, Nielsen J

J. Proteome Res. 19 (1) 269-278 [2020-01-03; online 2019-11-01]

Integrative discovery of treatments for high-risk neuroblastoma.

Almstedt E, Elgendy R, Hekmati N, ..., Krona C, Nelander S

Nat Commun 11 (1) 71 [2020-01-03; online 2020-01-03]

The Mitogenome of Norway Spruce and a Reappraisal of Mitochondrial Recombination in Plants.

Sullivan AR, Eldfjell Y, Schiffthaler B, ..., Street NR, Wang XR

Genome Biol Evol 12 (1) 3586-3598 [2020-01-01; online 2019-11-28]

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The Genome of the Endangered Dryas Monkey Provides New Insights into the Evolutionary History of the Vervets.

van der Valk T, Gonda CM, Silegowa H, ..., Detwiler KM, Guschanski K

Mol. Biol. Evol. 37 (1) 183-194 [2020-01-01; online 2019-09-19]

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Hepatitis E virus genotype 3 strains and a plethora of other viruses detected in raw and still in tap water.

Wang H, Kjellberg I, Sikora P, ..., Bergstedt O, Norder H

Water Res. 168 (-) 115141 [2020-01-01; online 2019-09-30]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Discovery of Novel Sequences in 1,000 Swedish Genomes.

Eisfeldt J, Mårtensson G, Ameur A, Nilsson D, Lindstrand A

Mol. Biol. Evol. 37 (1) 18-30 [2020-01-01; online 2019-09-29]

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A dual-action peptide-containing hydrogel targets wound infection and inflammation.

Puthia M, Butrym M, Petrlova J, ..., Kjellström S, Schmidtchen A

Sci Transl Med 12 (524) eaax6601 [2020-01-01; online 2020-01-03]

Whole genome sequencing of apparently mutation-negative MEN1 patients.

Backman S, Bajic D, Crona J, ..., Skogseid B, Stålberg P

Eur. J. Endocrinol. 182 (1) 35-45 [2020-01-00; online 2019-10-29]

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Variable neurodevelopmental and morphological phenotypes of carriers with 12q12 duplications.

Myers L, Blyth M, Moradkhani K, ..., Anderlid BM, Tammimies K

Mol Genet Genomic Med 8 (1) e1013 [2020-01-00; online 2019-11-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease.

Haytural H, Mermelekas G, Emre C, ..., Tjernberg LO, Frykman S

Mol. Cell Proteomics 19 (1) 128-141 [2020-01-00; online 2019-11-07]

Bioinformatics Support for Computational Resources [Service] Global Proteomics and Proteogenomics [Collaborative]

Regulation of α-synuclein by chaperones in mammalian cells.

Burmann BM, Gerez JA, Matečko-Burmann I, ..., Riek R, Hiller S

Nature 577 (7788) 127-132 [2020-01-00; online 2019-12-04]

Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sjögren's syndrome.

Björk A, Richardsdotter Andersson E, Imgenberg-Kreuz J, ..., Nordmark G, Wahren-Herlenius M

RMD Open 6 (1) e000995 [2020-01-00; online 2020-01-21]

Affinity Proteomics Uppsala [Service] Bioinformatics Support for Computational Resources [Service] Clinical Biomarkers [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] PLA and Single Cell Proteomics [Service]

Probabilistic cell typing enables fine mapping of closely related cell types in situ.

Qian X, Harris KD, Hauling T, ..., Hjerling-Leffler J, Nilsson M

Nat. Methods 17 (1) 101-106 [2020-01-00; online 2019-11-18]

Bioinformatics Support for Computational Resources [Service] In Situ Sequencing (ISS) [Service]

NMR Spectroscopic Analysis to Evaluate the Quality of Insulin: Concentration, Variability, and Excipient Content.

Malmodin D, Pedersen A, Karlsson BG, Forsander G

J Diabetes Sci Technol 14 (1) 180-184 [2020-01-00; online 2019-02-19]

NIST Interlaboratory Study on Glycosylation Analysis of Monoclonal Antibodies: Comparison of Results from Diverse Analytical Methods.

De Leoz MLA, Duewer DL, Fung A, ..., Yuan H, Stein SE

Mol. Cell Proteomics 19 (1) 11-30 [2020-01-00; online 2019-10-07]

Molecular mechanisms of collateral sensitivity to the antibiotic nitrofurantoin.

Roemhild R, Linkevicius M, Andersson DI

PLoS Biol. 18 (1) e3000612 [2020-01-00; online 2020-01-27]

Metabolic response patterns in brain microdialysis fluids and serum during interstitial cisplatin treatment of high-grade glioma.

Björkblom B, Jonsson P, Tabatabaei P, ..., Bergenheim AT, Antti H

Br. J. Cancer 122 (2) 221-232 [2020-01-00; online 2019-12-10]

Identification of novel diagnostic and prognostic biomarkers for abdominal aortic aneurysm.

Memon AA, Zarrouk M, Ågren-Witteschus S, ..., Gottsäter A, Sundquist K

Eur J Prev Cardiol 27 (2) 132-142 [2020-01-00; online 2019-08-29]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

IDDomainSpotter: Compositional bias reveals domains in long disordered protein regions-Insights from transcription factors.

Millard PS, Bugge K, Marabini R, ..., Burow M, Kragelund BB

Protein Sci. 29 (1) 169-183 [2020-01-00; online 2019-11-11]

Genotypic variation in Norway spruce correlates to fungal communities in vegetative buds.

Elfstrand M, Zhou L, Baison J, ..., Stenlid J, García-Gil MR

Mol. Ecol. 29 (1) 199-213 [2020-01-00; online 2019-12-09]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Genome-wide signatures of environmental adaptation in European aspen (Populus tremula) under current and future climate conditions.

Ingvarsson PK, Bernhardsson C

Evol Appl 13 (1) 132-142 [2020-01-00; online 2019-04-02]

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Do we really know who has an MGMT methylated glioma? Results of an international survey regarding use of MGMT analyses for glioma.

Malmström A, Łysiak M, Kristensen BW, ..., Henriksson R, Söderkvist P

Neurooncol Pract 7 (1) 68-76 [2020-01-00; online 2019-09-24]

Clinical Genomics [Service] Clinical Genomics Linköping [Service]

Developmental exposure to a human relevant mixture of endocrine disruptors alters metabolism and adipogenesis in zebrafish (Danio rerio).

Mentor A, Brunström B, Mattsson A, Jönsson M

Chemosphere 238 (-) 124584 [2020-01-00; online 2019-08-13]

Circadian regulation of phosphodiesterase 6 genes in zebrafish differs between cones and rods: Implications for photopic and scotopic vision.

Abalo XM, Lagman D, Heras G, ..., Eggert J, Larhammar D

Vision Res. 166 (-) 43-51 [2020-01-00; online 2019-12-16]

Cell-of-origin determined by both gene expression profiling and immunohistochemistry is the strongest predictor of survival in patients with diffuse large B-cell lymphoma.

Abdulla M, Hollander P, Pandzic T, ..., Rosenquist R, Amini RM

Am. J. Hematol. 95 (1) 57-67 [2020-01-00; online 2019-11-07]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Association of genetic variants related to plasma fatty acids with type 2 diabetes mellitus and glycaemic traits: a Mendelian randomisation study.

Yuan S, Larsson SC

Diabetologia 63 (1) 116-123 [2020-01-00; online 2019-11-05]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Regeneration of water-deactivated Cu/SAPO-34(MO) with acids

Woo J, Bernin D, Ahari H, ..., Zammit M, Olsson L

Catal. Sci. Technol. 10 (5) 1539-1550 [2020-00-00; online 2020-00-00]

In Situ Sequencing: A High-Throughput, Multi-Targeted Gene Expression Profiling Technique for Cell Typing in Tissue Sections

Hilscher MM, Gyllborg D, Yokota C, Nilsson M

Methods Mol. Biol. 2148 (-) 313-329 [2020-00-00; online 2020-05-12]

Bioinformatics Support for Computational Resources [Service] In Situ Sequencing (ISS) [Collaborative]

An integrative toolbox to unlock the structure and dynamics of protein–surfactant complexes

Sanchez-Fernandez A, Diehl C, Houston JE, ..., Sjögren H, Wahlgren M

Nanoscale Adv. 2 (9) 4011-4023 [2020-00-00; online 2020-00-00]

A Chemical Screen Identifies a Link between Lipid Metabolism and mRNA Translation

Corman A, Kanellis DC, Häggblad M, ..., Carreras-Puigvert J, Fernandez-Capetillo O

SSRN Journal - (-) - [2020-00-00; online 2020-00-00]

Chemical Biology Consortium Sweden (CBCS) [Service]

Novel Viruses Found in Antricola Ticks Collected in Bat Caves in the Western Amazonia of Brazil.

Blomström AL, Luz HR, Öhlund P, ..., Labruna MB, Berg M

Viruses 12 (1) - [2019-12-31; online 2019-12-31]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A Comprehensive Sequencing-Based Analysis of Allelic Methylation Patterns in Hemostatic Genes in Human Liver

Olsson Lindvall M, Davila Lopez M, Klasson S, ..., Stanne TM, Jern C

Thromb. Haemost. 120 (02) 229-242 [2019-12-30; online 2019-12-30]

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Transcriptional study of appetite regulating genes in the brain of zebrafish (Danio rerio) with impaired leptin signalling.

Ahi EP, Brunel M, Tsakoumis E, Schmitz M

Sci Rep 9 (1) 20166 [2019-12-27; online 2019-12-27]

Structural and biochemical studies of the glucuronoyl esterase OtCE15A illuminate its interaction with lignocellulosic components.

Mazurkewich S, Poulsen JN, Lo Leggio L, Larsbrink J

J. Biol. Chem. 294 (52) 19978-19987 [2019-12-27; online 2019-11-18]

Identification of a C2-symmetric diol based human immunodeficiency virus protease inhibitor targeting Zika virus NS2B-NS3 protease.

Akaberi D, Chinthakindi PK, Båhlström A, ..., Lundkvist Å, Lennerstrand J

J. Biomol. Struct. Dyn. 38 (18) 1-11 [2019-12-27; online 2019-12-27]

Dynamic Chirality in the Mechanism of Action of Allosteric CD36 Modulators of Macrophage-Driven Inflammation.

Danelius E, Ohm RG, Mulumba M, ..., Erdelyi M, Lubell WD

J. Med. Chem. 62 (24) 11071-11079 [2019-12-26; online 2019-12-13]

Gene transfer across species boundaries in bryophytes: evidence from major life cycle stages in Homalothecium lutescens and H. sericeum.

Sawangproh W, Hedenäs L, Lang AS, Hansson B, Cronberg N

Ann. Bot. - (-) - [2019-12-24; online 2019-12-24]

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Inoculum Source Determines Acetate and Lactate Production during Anaerobic Digestion of Sewage Sludge and Food Waste.

Moestedt J, Westerholm M, Isaksson S, Schnürer A

Bioengineering 7 (1) 3 [2019-12-23; online 2019-12-23]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox.

Larsson P, von Seth J, Hagen IJ, ..., Stanton DWG, Dalén L

Philos. Trans. R. Soc. Lond., B, Biol. Sci. 374 (1788) 20190212 [2019-12-23; online 2019-11-04]

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Gene Expression Alterations during Development of Castration-Resistant Prostate Cancer Are Detected in Circulating Tumor Cells.

Josefsson A, Larsson K, Freyhult E, Damber J, Welén K

Cancers (Basel) 12 (1) - [2019-12-21; online 2019-12-21]

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Sequencing detects human papillomavirus in some apparently HPV-negative invasive cervical cancers.

Arroyo Mühr LS, Lagheden C, Eklund C, ..., Sundström K, Dillner J

J. Gen. Virol. - (-) - [2019-12-20; online 2019-12-20]

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Genetic Screening of Plasticity Regulating Nogo-Type Signaling Genes in Migraine.

Smedfors G, Liesecke F, Ran C, ..., Karlsson TE, Carmine Belin A

Brain Sci 10 (1) - [2019-12-20; online 2019-12-20]

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A genome-wide transcriptomic analysis of protein-coding genes in human blood cells.

Uhlen M, Karlsson MJ, Zhong W, ..., Fagerberg L, Brodin P

Science 366 (6472) - [2019-12-20; online 2019-12-21]

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Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce.

Nakamura M, Köhler C, Hennig L

BMC Genomics 20 (1) 997 [2019-12-19; online 2019-12-19]

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Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression.

Ciuculete DM, Voisin S, Kular L, ..., Mwinyi J, Schiöth HB

Epigenetics 15 (6-7) 646-663 [2019-12-19; online 2019-12-19]

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Lipid Droplet-Associated Kinase STK25 Regulates Peroxisomal Activity and Metabolic Stress Response in Steatotic Liver.

Nerstedt A, Kurhe Y, Cansby E, ..., Hoy AJ, Mahlapuu M

J. Lipid Res. - (-) - [2019-12-19; online 2019-12-19]

Levels of caspase-3 and histidine-rich glycoprotein in the embryo secretome as biomarkers of good-quality day-2 embryos and high-quality blastocysts

Kaihola H, Yaldir FG, Bohlin T, ..., Hreinsson J, Åkerud H

PLoS ONE 14 (12) e0226419 [2019-12-19; online 2019-12-19]

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Apolipoprotein B48 metabolism in chylomicrons and very low-density lipoproteins and its role in triglyceride transport in normo- and hypertriglyceridemic human subjects.

Björnson E, Packard CJ, Adiels M, ..., Taskinen MR, Borén J

J. Intern. Med. - (-) - [2019-12-17; online 2019-12-17]

A transposable element insertion is associated with an alternative life history strategy.

Woronik A, Tunström K, Perry MW, ..., Käkelä R, Wheat CW

Nat Commun 10 (1) 5757 [2019-12-17; online 2019-12-17]

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Protein profiling and network enrichment analysis in individuals before and after the onset of rheumatoid arthritis.

Brink M, Lundquist A, Alexeyenko A, Lejon K, Rantapää-Dahlqvist S

Arthritis Res. Ther. 21 (1) 288 [2019-12-16; online 2019-12-16]

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Autoregulation of RCO by Low-Affinity Binding Modulates Cytokinin Action and Shapes Leaf Diversity.

Hajheidari M, Wang Y, Bhatia N, ..., Gan X, Tsiantis M

Curr. Biol. 29 (24) 4183-4192.e6 [2019-12-16; online 2019-11-21]

NGS targeted screening of 100 Scandinavian patients with coronal synostosis.

Topa A, Rohlin A, Andersson MK, ..., Stenman G, Kölby L

Am. J. Med. Genet. A - (-) - [2019-12-14; online 2019-12-14]

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BEN-solo factors partition active chromatin to ensure proper gene activation in Drosophila.

Ueberschär M, Wang H, Zhang C, ..., Wen J, Dai Q

Nat Commun 10 (1) 5700 [2019-12-13; online 2019-12-13]

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A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.

Asp M, Giacomello S, Larsson L, ..., Sylvén C, Lundeberg J

Cell 179 (7) 1647-1660.e19 [2019-12-12; online 2019-12-14]

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Morphological analysis of Apolipoprotein E binding to Aβ Amyloid using a combination of Surface Plasmon Resonance, Immunogold Labeling and Scanning Electron Microscopy.

Islam T, Gharibyan AL, Lee CC, Olofsson A

BMC Biotechnol. 19 (1) 97 [2019-12-11; online 2019-12-11]

Cryo-EM [Technology development] Integrated Microscopy Technologies Umeå [Collaborative]

HISTONE DEACETYLASE 9 stimulates auxin-dependent thermomorphogenesis in Arabidopsis thaliana by mediating H2A.Z depletion.

van der Woude LC, Perrella G, Snoek BL, ..., Kaiserli E, van Zanten M

Proc. Natl. Acad. Sci. U.S.A. 116 (50) 25343-25354 [2019-12-10; online 2019-11-25]

The Hidden Story of Heterogeneous B-raf V600E Mutation Quantitative Protein Expression in Metastatic Melanoma-Association with Clinical Outcome and Tumor Phenotypes.

Betancourt LH, Szasz AM, Kuras M, ..., Sanchez A, Marko-Varga G

Cancers (Basel) 11 (12) - [2019-12-09; online 2019-12-09]

Comprehensive longitudinal study of epigenetic mutations in aging.

Wang Y, Karlsson R, Jylhävä J, ..., Almgren M, Hägg S

Clin Epigenetics 11 (1) 187 [2019-12-09; online 2019-12-09]

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A Gene-Environment Interaction Between Smoking and Gene polymorphisms Provides a High Risk of Two Subgroups of Sarcoidosis.

Rivera NV, Patasova K, Kullberg S, ..., Grunewald J, Padyukov L

Sci Rep 9 (1) 18633 [2019-12-09; online 2019-12-09]

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Mining the Proteome Associated with Rheumatic and Autoimmune Diseases.

Ruiz-Romero C, Lam MPY, Nilsson P, ..., Watt FE, Blanco FJ

J. Proteome Res. 18 (12) 4231-4239 [2019-12-06; online 2019-10-23]

Autoimmunity and Serology Profiling [Technology development]

Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data.

Ignjatovic V, Geyer PE, Palaniappan KK, ..., Deutsch EW, Schwenk JM

J. Proteome Res. 18 (12) 4085-4097 [2019-12-06; online 2019-10-11]

Epigenome-wide meta-analysis of blood DNA methylation and its association with subcortical volumes: findings from the ENIGMA Epigenetics Working Group.

Jia T, Chu C, Liu Y, ..., Schumann G, Desrivières S

Mol. Psychiatry - (-) - [2019-12-06; online 2019-12-06]

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Depression, GABA, and Age Correlate with Plasma Levels of Inflammatory Markers.

Bhandage AK, Cunningham JL, Jin Z, ..., Ekselius L, Birnir B

Int J Mol Sci 20 (24) 6172 [2019-12-06; online 2019-12-06]

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Cell Type-Specific Expression of Testis Elevated Genes Based on Transcriptomics and Antibody-Based Proteomics.

Pineau C, Hikmet F, Zhang C, ..., Uhlén M, Lindskog C

J. Proteome Res. 18 (12) 4215-4230 [2019-12-06; online 2019-08-29]

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Humanized Stem Cell Models of Pediatric Medulloblastoma Reveal an Oct4/mTOR Axis that Promotes Malignancy.

Čančer M, Hutter S, Holmberg KO, ..., Weishaupt H, Swartling FJ

Cell Stem Cell 25 (6) 855-870.e11 [2019-12-05; online 2019-11-27]

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GLUL Ablation Can Confer Drug Resistance to Cancer Cells via a Malate-Aspartate Shuttle-Mediated Mechanism.

Muthu M, Kumar R, Syed Khaja AS, ..., Persson JL, Nordström A

Cancers (Basel) 11 (12) 1945 [2019-12-05; online 2019-12-05]

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Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria.

Nicholls TJ, Spåhr H, Jiang S, ..., Larsson NG, Gustafsson CM

Mol. Cell 76 (5) 784-796.e6 [2019-12-05; online 2019-10-03]

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Specialized sledge dogs accompanied Inuit dispersal across the North American Arctic.

Ameen C, Feuerborn TR, Brown SK, ..., Darwent CM, Evin A

Proc. Biol. Sci. 286 (1916) 20191929 [2019-12-04; online 2019-11-27]

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Replicating associations between DNA methylation and body mass index in a longitudinal sample of older twins.

Karlsson IK, Ericsson M, Wang Y, ..., Reynolds CA, Dahl Aslan AK

Int J Obes (Lond) - (-) - [2019-12-04; online 2019-12-04]

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The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons.

Batista RA, Moreno-Romero J, Qiu Y, ..., Figueiredo DD, Köhler C

Elife 8 (-) - [2019-12-02; online 2019-12-02]

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Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait.

Vicente M, Priehodová E, Diallo I, ..., Černý V, Schlebusch CM

BMC Genomics 20 (1) 915 [2019-12-02; online 2019-12-02]

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Impact of Q-Griffithsin anti-HIV microbicide gel in non-human primates: In situ analyses of epithelial and immune cell markers in rectal mucosa.

Günaydın G, Edfeldt G, Garber DA, ..., Tjernlund A, Broliden K

Sci Rep 9 (1) 18120 [2019-12-02; online 2019-12-02]

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High throughput barcoding method for genome-scale phasing.

Redin D, Frick T, Aghelpasand H, ..., Olsen RA, Ahmadian A

Sci Rep 9 (1) 18116 [2019-12-02; online 2019-12-02]

NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]

DNA methylation profiles in chronic lymphocytic leukemia patients treated with chemoimmunotherapy.

Tsagiopoulou M, Papakonstantinou N, Moysiadis T, ..., Rosenquist R, Stamatopoulos K

Clin Epigenetics 11 (1) 177 [2019-12-02; online 2019-12-02]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Mitochondrial protein enriched extracellular vesicles discovered in human melanoma tissues can be detected in patient plasma

Jang SC, Crescitelli R, Cvjetkovic A, ..., Kalluri R, Lötvall J

J Extracell Vesicles 8 (1) 1635420 [2019-12-01; online 2019-08-27]

Glycoproteomics and MS Proteomics [Service] Integrated Microscopy Technologies Gothenburg [Service]

Endosomal signalling via exosome surface TGFβ-1

Shelke GV, Yin Y, Jang SC, ..., Nilsson JA, Lötvall J

J Extracell Vesicles 8 (1) 1650458 [2019-12-01; online 2019-09-20]

Glycoproteomics and MS Proteomics [Service] Integrated Microscopy Technologies Gothenburg [Service] Integrated Microscopy Technologies Stockholm

Arteria: An automation system for a sequencing core facility.

Dahlberg J, Hermansson J, Sturlaugsson S, ..., Hofmann O, Larsson P

Gigascience 8 (12) - [2019-12-01; online 2019-12-12]

Clinical Genomics [Technology development] Clinical Genomics Uppsala [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

iFISH is a publically available resource enabling versatile DNA FISH to study genome architecture

Gelali E, Girelli G, Matsumoto M, ..., Crosetto N, Bienko M

Nat Commun 10 (1) - [2019-12-00; online 2019-04-09]

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Zebrafish embryo as a replacement model for initial biocompatibility studies of biomaterials and drug delivery systems.

Rothenbücher TSP, Ledin J, Gibbs D, ..., Persson C, Hulsart-Billström G

Acta Biomater 100 (-) 235-243 [2019-12-00; online 2019-10-01]

Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

Franco I, Helgadottir HT, Moggio A, ..., Supek F, Eriksson M

Genome Biol. 20 (1) - [2019-12-00; online 2019-12-18]

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Voluntary exercise normalizes the proteomic landscape in muscle and brain and improves the phenotype of progeroid mice.

Ross JM, Coppotelli G, Branca RM, ..., Sinclair DA, Olson L

Aging Cell 18 (6) e13029 [2019-12-00; online 2019-09-06]

Global Proteomics and Proteogenomics [Collaborative]

Undifferentiated pleomorphic sarcomas with PRDM10 fusions have a distinct gene expression profile.

Hofvander J, Puls F, Pillay N, ..., Nilsson J, Mertens F

J. Pathol. 249 (4) 425-434 [2019-12-00; online 2019-08-27]

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Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden

Alaridah N, Hallbäck ET, Tångrot J, ..., Kaijser B, Godaly G

Sci Rep 9 (1) - [2019-12-00; online 2019-03-20]

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Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment.

Schuster J, Laan L, Klar J, ..., Birnir B, Dahl N

Neurobiol. Dis. 132 (-) 104583 [2019-12-00; online 2019-08-21]

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Towards a standardized bioinformatics infrastructure for N- and O-glycomics

Rojas-Macias MA, Mariethoz J, Andersson P, ..., Lisacek F, Karlsson NG

Nat Commun 10 (1) - [2019-12-00; online 2019-07-22]

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The potential of magnetisation transfer NMR to monitor the dissolution process of cellulose in cold alkali

Gunnarsson M, Hasani M, Bernin D

Cellulose 26 (18) 9403-9412 [2019-12-00; online 2019-09-12]

The genomic footprint of sexual conflict.

Sayadi A, Martinez Barrio A, Immonen E, ..., Nystedt B, Arnqvist G

Nat Ecol Evol 3 (12) 1725-1730 [2019-12-00; online 2019-11-18]

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The bio.tools registry of software tools and data resources for the life sciences

Ison J, Ienasescu H, Chmura P, ..., Løngreen P, Brunak S

Genome Biol. 20 (1) 164 [2019-12-00; online 2019-08-12]

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The MTH1 inhibitor TH588 is a microtubule-modulating agent that eliminates cancer cells by activating the mitotic surveillance pathway

Gul N, Karlsson J, Tängemo C, ..., Bergö MO, Lindahl P

Sci Rep 9 (1) 14667 [2019-12-00; online 2019-10-11]

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Targeted Multiple Reaction Monitoring Analysis of CSF Identifies UCHL1 and GPNMB as Candidate Biomarkers for ALS.

Zhu S, Wuolikainen A, Wu J, ..., Forsgren L, Trupp M

J. Mol. Neurosci. 69 (4) 643-657 [2019-12-00; online 2019-11-12]

Studies of liver tissue identify functional gene regulatory elements associated to gene expression, type 2 diabetes, and other metabolic diseases

Cavalli M, Baltzer N, Pan G, ..., Komorowski J, Wadelius C

Hum Genomics 13 (1) 20 [2019-12-00; online 2019-04-29]

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Structural weakening of the colonic mucus barrier is an early event in ulcerative colitis pathogenesis.

van der Post S, Jabbar KS, Birchenough G, ..., Johansson MEV, Hansson GC

Gut 68 (12) 2142-2151 [2019-12-00; online 2019-03-26]

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Single-cell study of neural stem cells derived from human iPSCs reveals distinct progenitor populations with neurogenic and gliogenic potential.

Lam M, Sanosaka T, Lundin A, ..., Okano H, Falk A

Genes Cells 24 (12) 836-847 [2019-12-00; online 2019-11-17]

Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes

Marathe NP, Berglund F, Razavi M, ..., Kristiansson E, Larsson DGJ

Microbiome 7 (1) - [2019-12-00; online 2019-06-27]

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ProTargetMiner as a proteome signature library of anticancer molecules for functional discovery

Saei AA, Beusch CM, Chernobrovkin A, ..., Végvári Á, Zubarev RA

Nat Commun 10 (1) 5715 [2019-12-00; online 2019-12-16]

Physiology, Metabolism, and Fossilization of Hot-Spring Filamentous Microbial Mats.

Dong Y, Sanford RA, Inskeep WP, ..., Fried GA, Fouke BW

Astrobiology 19 (12) 1442-1458 [2019-12-00; online 2019-04-30]

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PECTIN ACETYLESTERASE9 Affects the Transcriptome and Metabolome and Delays Aphid Feeding.

Kloth KJ, Abreu IN, Delhomme N, ..., Moritz T, Albrectsen BR

Plant Physiol. 181 (4) 1704-1720 [2019-12-00; online 2019-09-24]

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Modelling of zero-inflation improves inference of metagenomic gene count data.

Jonsson V, Österlund T, Nerman O, Kristiansson E

Stat Methods Med Res 28 (12) 3712-3728 [2019-12-00; online 2018-11-25]

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Metabolic phenotype of breast-fed infants, and infants fed standard formula or bovine MFGM supplemented formula: a randomized controlled trial

He X, Parenti M, Grip T, ..., Timby N, Slupsky CM

Sci Rep 9 (1) 339 [2019-12-00; online 2019-01-23]

Meckel syndrome: Clinical and mutation profile in six fetuses.

Radhakrishnan P, Nayak SS, Shukla A, Lindstrand A, Girisha KM

Clin. Genet. 96 (6) 560-565 [2019-12-00; online 2019-08-21]

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Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes

Diamanti K, Cavalli M, Pan G, ..., Komorowski J, Wadelius C

Sci Rep 9 (1) 9653 [2019-12-00; online 2019-07-04]

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Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members

Behra PRK, Pettersson BMF, Ramesh M, Dasgupta S, Kirsebom LA

Sci Rep 9 (1) 19259 [2019-12-00; online 2019-12-17]

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Influence of urea on methyl β-D-glucopyranoside in alkali at different temperatures

Gunnarsson M, Hasani M, Bernin D

Cellulose 26 (18) 9413-9422 [2019-12-00; online 2019-09-14]

Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers

Höglund J, Rafati N, Rask-Andersen M, ..., Ek WE, Johansson Å

Sci Rep 9 (1) - [2019-12-00; online 2019-11-14]

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Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in Saccharomyces cerevisiae

Bergman A, Hellgren J, Moritz T, ..., Nielsen J, Chen Y

Microb. Cell Fact. 18 (1) 25 [2019-12-00; online 2019-02-01]

Growth performance and nutrient removal of a Chlorella vulgaris-Rhizobium sp. co-culture during mixotrophic feed-batch cultivation in synthetic wastewater

Ferro L, Gojkovic Z, Muñoz R, Funk C

Algal Research 44 (-) 101690 [2019-12-00; online 2019-12-00]

Genomic architecture of parallel ecological divergence: Beyond a single environmental contrast.

Morales HE, Faria R, Johannesson K, ..., Westram AM, Butlin RK

Sci Adv 5 (12) eaav9963 [2019-12-00; online 2019-12-04]

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Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model

Kampfraath AA, Klasson L, Anvar SY, ..., Kraaijeveld K, Ellers J

BMC Genomics 20 (1) 106 [2019-12-00; online 2019-02-06]

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Genetic Prediction of Serum 25-Hydroxyvitamin D, Calcium, and Parathyroid Hormone Levels in Relation to Development of Type 2 Diabetes: A Mendelian Randomization Study.

Yuan S, Jiang X, Michaëlsson K, Larsson SC

Diabetes Care 42 (12) 2197-2203 [2019-12-00; online 2019-09-23]

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Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm

Moreno-Romero J, Del Toro-De León G, Yadav VK, Santos-González J, Köhler C

Genome Biol. 20 (1) - [2019-12-00; online 2019-02-21]

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Coro2b, a podocyte protein downregulated in human diabetic nephropathy, is involved in the development of protamine sulphate-induced foot process effacement

Schwarz A, Möller-Hackbarth K, Ebarasi L, ..., Lal M, Patrakka J

Sci Rep 9 (1) 8888 [2019-12-00; online 2019-06-20]

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Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing

Hård J, Al Hakim E, Kindblom M, ..., Mold JE, Frisén J

Genome Biol. 20 (1) - [2019-12-00; online 2019-04-01]

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Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast.

Wei W, Hennig BP, Wang J, ..., Steinmetz LM, Pelechano V

Genome Res. 29 (12) 1974-1984 [2019-12-00; online 2019-11-18]

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Angioimmunoblastic T-cell lymphoma and myelodysplastic syndrome with mutations in TET2, DNMT3 and CUX1 - azacitidine induces only lymphoma remission.

Tobiasson M, Pandzic T, Cavelier L, Sander B, Wahlin BE

Leuk. Lymphoma 60 (13) 3316-3319 [2019-12-00; online 2019-06-17]

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An AP2/ERF transcription factor ERF139 coordinates xylem cell expansion and secondary cell wall deposition.

Wessels B, Seyfferth C, Escamez S, ..., Felten J, Tuominen H

New Phytol. 224 (4) 1585-1599 [2019-12-00; online 2019-07-02]

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ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes

Bysani M, Agren R, Davegårdh C, ..., Bacos K, Ling C

Sci Rep 9 (1) - [2019-12-00; online 2019-05-23]

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A cell fitness selection model for neuronal survival during development

Wang Y, Wu H, Fontanet P, ..., Hadjab S, Lallemend F

Nat Commun 10 (1) - [2019-12-00; online 2019-09-12]

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A Spatiomolecular Map of the Striatum

Märtin A, Calvigioni D, Tzortzi O, ..., Wärnberg E, Meletis K

Cell Rep 29 (13) 4320-4333.e5 [2019-12-00; online 2019-12-00]

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A Mitochondrial LYR Protein Is Required for Complex I Assembly.

Ivanova A, Gill-Hille M, Huang S, ..., Whelan J, Murcha MW

Plant Physiol. 181 (4) 1632-1650 [2019-12-00; online 2019-10-10]

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Programmed DNA elimination of germline development genes in songbirds.

Kinsella CM, Ruiz-Ruano FJ, Dion-Côté AM, ..., Forstmeier W, Suh A

Nat Commun 10 (1) 5468 [2019-11-29; online 2019-11-29]

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Mucosal Metabolomic Profiling and Pathway Analysis Reveal the Metabolic Signature of Ulcerative Colitis.

Diab J, Hansen T, Goll R, ..., Florholmen J, Forsdahl G

Metabolites 9 (12) S035-S035 [2019-11-27; online 2019-11-27]

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The human secretome

Uhlén M, Karlsson MJ, Hober A, ..., Fagerberg L, Sivertsson Å

Sci. Signal. 12 (609) eaaz0274 [2019-11-26; online 2019-11-26]

The Mastery Rubric for Bioinformatics: A tool to support design and evaluation of career-spanning education and training.

Tractenberg RE, Lindvall JM, Attwood TK, Via A

PLoS ONE 14 (11) e0225256 [2019-11-26; online 2019-11-26]

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TcellSubC: An Atlas of the Subcellular Proteome of Human T Cells.

Joshi RN, Stadler C, Lehmann R, ..., Schmidt A, Vesterlund M

Front Immunol 10 (-) 2708 [2019-11-26; online 2019-11-26]

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Optimizing cultivation of Cordyceps militaris for fast growth and cordycepin overproduction using rational design of synthetic media.

Raethong N, Wang H, Nielsen J, Vongsangnak W

Computational and Structural Biotechnology Journal 18 (-) 1-8 [2019-11-26; online 2019-11-26]

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Uncovering microbial inter-domain interactions in complex communities.

Florenza J, Tamminen M, Bertilsson S

Philos. Trans. R. Soc. Lond., B, Biol. Sci. 374 (1786) 20190087 [2019-11-25; online 2019-10-07]

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MYCN-enhanced Oxidative and Glycolytic Metabolism Reveals Vulnerabilities for Targeting Neuroblastoma.

Oliynyk G, Ruiz-Pérez MV, Sainero-Alcolado L, ..., Lehtiö J, Arsenian-Henriksson M

iScience 21 (-) 188-204 [2019-11-22; online 2019-10-11]

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The Swedish Twin Registry: Content and Management as a Research Infrastructure.

Zagai U, Lichtenstein P, Pedersen NL, Magnusson PKE

Twin Res Hum Genet - (-) 1-9 [2019-11-21; online 2019-11-21]

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Evidence that genes involved in hedgehog signaling are associated with both bipolar disorder and high BMI.

Pisanu C, Williams MJ, Ciuculete DM, ..., Squassina A, Schiöth HB

Transl Psychiatry 9 (1) 315 [2019-11-21; online 2019-11-21]

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BET and Aurora Kinase A inhibitors synergize against MYCN-positive human glioblastoma cells.

Čančer M, Drews LF, Bengtsson J, ..., Weishaupt H, Swartling FJ

Cell Death Dis 10 (12) 881 [2019-11-21; online 2019-11-21]

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Interaction between Copper Chaperone Atox1 and Parkinson's Disease Protein α-Synuclein Includes Metal-Binding Sites and Occurs in Living Cells.

Horvath I, Blockhuys S, Šulskis D, ..., Burmann BM, Wittung-Stafshede P

ACS Chem Neurosci 10 (11) 4659-4668 [2019-11-20; online 2019-10-24]

Identification of Novel Putative Bacterial Feruloyl Esterases From Anaerobic Ecosystems by Use of Whole-Genome Shotgun Metagenomics and Genome Binning.

Mogodiniyai Kasmaei K, Sundh J

Front Microbiol 10 (-) 2673 [2019-11-20; online 2019-11-20]

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Fast and Efficient Fc-Specific Photoaffinity Labeling To Produce Antibody-DNA Conjugates.

Stiller C, Aghelpasand H, Frick T, ..., Ahmadian A, Karlström AE

Bioconjug. Chem. 30 (11) 2790-2798 [2019-11-20; online 2019-10-25]

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Structural Changes of Mercaptohexanol Self-Assembled Monolayers on Gold and Their Influence on Impedimetric Aptamer Sensors.

Xu X, Makaraviciute A, Kumar S, ..., Nyholm L, Zhang Z

Anal. Chem. 91 (22) 14697-14704 [2019-11-19; online 2019-11-07]

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Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen ( Populus tremula).

Apuli RP, Bernhardsson C, Schiffthaler B, ..., Street NR, Ingvarsson PK

G3 (Bethesda) - (-) - [2019-11-19; online 2019-11-19]

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Human induced pluripotent stem cells from two azoospermic patients with Klinefelter syndrome show similar X chromosome inactivation behavior to female pluripotent stem cells.

Panula S, Kurek M, Kumar P, ..., Lanner F, Stukenborg JB

Hum. Reprod. - (-) - [2019-11-19; online 2019-11-19]

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Genotype-dependent epigenetic regulation of DLGAP2 in alcohol use and dependence.

Meng W, Sjöholm LK, Kononenko O, ..., Rüegg J, Liu Y

Mol. Psychiatry - (-) - [2019-11-19; online 2019-11-19]

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Boldness in Male and Female Zebrafish ( Danio rerio) Is Dependent on Strain and Test.

Mustafa A, Roman E, Winberg S

Front. Behav. Neurosci. 13 (-) 248 [2019-11-19; online 2019-11-19]

The associations of self-rated health with cardiovascular risk proteins: a proteomics approach.

Bao X, Borné Y, Yin S, ..., Melander O, Engström G

Clin Proteomics 16 (1) 40 [2019-11-18; online 2019-11-18]

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Synthesis of Indomorphan Pseudo-Natural Product Inhibitors of Glucose Transporters GLUT-1 and -3.

Ceballos J, Schwalfenberg M, Karageorgis G, ..., Ziegler S, Waldmann H

Angew. Chem. Int. Ed. Engl. 58 (47) 17016-17025 [2019-11-18; online 2019-10-07]

Structure of a mitochondrial ATP synthase with bound native cardiolipin.

Mühleip A, McComas SE, Amunts A

Elife 8 (-) - [2019-11-18; online 2019-11-18]

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A Chemical Biology Approach to Understanding Molecular Recognition of Lipid II by Nisin(1-12): Synthesis and NMR Ensemble Analysis of Nisin(1-12) and Analogues.

Dickman R, Danelius E, Mitchell SA, ..., Erdélyi M, Tabor AB

Chemistry 25 (64) 14572-14582 [2019-11-18; online 2019-10-10]

Lithium treatment reverses irradiation-induced changes in rodent neural progenitors and rescues cognition.

Zanni G, Goto S, Fragopoulou AF, ..., Hermanson O, Blomgren K

Mol. Psychiatry - (-) - [2019-11-14; online 2019-11-14]

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Effects of the Antimicrobial Peptide LL-37 and Innate Effector Mechanisms in Colistin-Resistant Klebsiella pneumoniae With mgrB Insertions.

Al-Farsi HM, Al-Adwani S, Ahmed S, ..., Giske CG, Bergman P

Front Microbiol 10 (-) 2632 [2019-11-14; online 2019-11-14]

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Daytime melatonin levels in saliva are associated with inflammatory markers and anxiety disorders.

Sundberg I, Rasmusson AJ, Ramklint M, ..., Ekselius L, Cunningham JL

Psychoneuroendocrinology 112 (-) 104514 [2019-11-14; online 2019-11-14]

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The ALK-1/SMAD/ATOH8 axis attenuates hypoxic responses and protects against the development of pulmonary arterial hypertension.

Morikawa M, Mitani Y, Holmborn K, ..., Heldin CH, Miyazono K

Sci Signal 12 (607) eaay4430 [2019-11-12; online 2019-11-12]

Genome Engineering Zebrafish [Collaborative]

A MYC2/MYC3/MYC4-dependent transcription factor network regulates water spray-responsive gene expression and jasmonate levels.

Van Moerkercke A, Duncan O, Zander M, ..., Millar AH, Van Aken O

Proc. Natl. Acad. Sci. U.S.A. 116 (46) 23345-23356 [2019-11-12; online 2019-10-29]

On-demand virtual research environments using microservices.

Capuccini M, Larsson A, Carone M, ..., Toor S, Spjuth O

PeerJ Comput Sci 5 (-) e232 [2019-11-11; online 2019-11-11]

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Long-read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

Jamy M, Foster R, Barbera P, ..., Bass D, Burki F

Mol Ecol Resour - (-) - [2019-11-09; online 2019-11-09]

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Carnivores, competition and genetic connectivity in the Anthropocene.

Creel S, Spong G, Becker M, ..., Schiffthaler B, Chifunte C

Sci Rep 9 (1) 16339 [2019-11-08; online 2019-11-08]

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Calcium-activated chloride channel regulator 1 (CLCA1) forms non-covalent oligomers in colonic mucus and has mucin 2-processing properties.

Nyström EEL, Arike L, Ehrencrona E, Hansson GC, Johansson MEV

J. Biol. Chem. 294 (45) 17075-17089 [2019-11-08; online 2019-09-29]

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Two-step derivatization for determination of sugar phosphates in plants by combined reversed phase chromatography/tandem mass spectrometry.

Rende U, Niittylä T, Moritz T

Plant Methods 15 (1) 127 [2019-11-07; online 2019-11-07]

From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability.

Lindstrand A, Eisfeldt J, Pettersson M, ..., Lundin J, Nilsson D

Genome Med 11 (1) 68 [2019-11-07; online 2019-11-07]

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Distinct Coastal Microbiome Populations Associated With Autochthonous- and Allochthonous-Like Dissolved Organic Matter.

Broman E, Asmala E, Carstensen J, Pinhassi J, Dopson M

Front Microbiol 10 (-) 2579 [2019-11-07; online 2019-11-07]

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Comparative distribution of extended-spectrum beta-lactamase-producing Escherichia coli from urine infections and environmental waters.

Fagerström A, Mölling P, Khan FA, ..., Jass J, Söderquist B

PLoS ONE 14 (11) e0224861 [2019-11-07; online 2019-11-07]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

A Cell-Free Approach Based on Phospholipid Characterization for Determination of the Cell Specific Unbound Drug Fraction (f u,cell).

Treyer A, Walday S, Boriss H, Matsson P, Artursson P

Pharm. Res. 36 (12) 178 [2019-11-07; online 2019-11-07]

Drug Discovery and Development (DDD) [Technology development]

Linkage and exome analysis implicate multiple genes in non-syndromic intellectual disability in a large Swedish family.

Lindholm Carlström E, Halvardson J, Etemadikhah M, ..., Gustavson KH, Feuk L

BMC Med Genomics 12 (1) 156 [2019-11-06; online 2019-11-06]

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Viromics Reveal a Number of Novel RNA Viruses in Swedish Mosquitoes.

Öhlund P, Hayer J, Lundén H, Hesson JC, Blomström AL

Viruses 11 (11) - [2019-11-05; online 2019-11-05]

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Myc-dependent endothelial proliferation is controlled by phosphotyrosine 1212 in VEGF receptor-2.

Testini C, Smith RO, Jin Y, ..., Hellström M, Claesson-Welsh L

EMBO Rep. 20 (11) e47845 [2019-11-05; online 2019-09-23]

The Nlrp6 inflammasome is not required for baseline colonic inner mucus layer formation or function.

Volk JK, Nyström EEL, van der Post S, ..., Hansson GC, Birchenough GMH

J. Exp. Med. 216 (11) 2602-2618 [2019-11-04; online 2019-08-16]

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Genetic regulation of gene expression and splicing during a 10-year period of human aging.

Balliu B, Durrant M, Goede O, ..., Ingelsson E, Montgomery SB

Genome Biol. 20 (1) 230 [2019-11-04; online 2019-11-04]

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Amyloid fibrils prepared using an acetylated and methyl amidated peptide model of the α-Synuclein NAC 71-82 amino acid stretch contain an additional cross-β structure also found in prion proteins.

Näsström T, Andersson PO, Lejon C, Karlsson BCG

Sci Rep 9 (1) 15949 [2019-11-04; online 2019-11-04]

A bacterial assay for rapid screening of IAA catabolic enzymes.

Brunoni F, Collani S, Šimura J, ..., Bellini C, Ljung K

Plant Methods 15 (1) 126 [2019-11-04; online 2019-11-04]

Sulfide level in municipal sludge digesters affects microbial community response to long-chain fatty acid loads.

Shakeri Yekta S, Liu T, Axelsson Bjerg M, ..., Björn A, Schnürer A

Biotechnol Biofuels 12 (1) 259 [2019-11-02; online 2019-11-02]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Yeast Volatomes Differentially Affect Larval Feeding in an Insect Herbivore.

Ljunggren J, Borrero-Echeverry F, Chakraborty A, ..., Witzgall P, Bengtsson M

Appl. Environ. Microbiol. 85 (21) - [2019-11-01; online 2019-10-16]

Serum Parathyroid Hormone and Risk of Coronary Artery Disease: Exploring Causality Using Mendelian Randomization.

Melhus H, Michaëlsson K, Larsson SC

J. Clin. Endocrinol. Metab. 104 (11) 5595-5600 [2019-11-01; online 2019-07-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Proteome Integral Solubility Alteration: A High-Throughput Proteomics Assay for Target Deconvolution.

Gaetani M, Sabatier P, Saei AA, ..., Lundström SL, Zubarev RA

J. Proteome Res. 18 (11) 4027-4037 [2019-11-01; online 2019-10-14]

Methyl sulfonamide substituents improve the pharmacokinetic properties of bicyclic 2-pyridone based Chlamydia trachomatis inhibitors.

Kulén M, Núñez-Otero C, Cairns AG, ..., Gylfe Å, Almqvist F

Med. Chem. Commun. 10 (11) 1966-1987 [2019-11-01; online 2019-10-17]

A genomic inference of the White Plymouth Rock genealogy.

Guo Y, Lillie M, Zan Y, ..., Siegel PB, Carlborg Ö

Poult. Sci. 98 (11) 5272-5280 [2019-11-01; online 2019-07-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Tuning drug release from polyoxazoline-drug conjugates

Harris JM, Bentley MD, Moreadith RW, ..., Dizman B, Nordstierna L

European Polymer Journal 120 (-) 109241 [2019-11-00; online 2019-11-00]

Structural characterization and biological function of bivalent binding of CD2AP to intrinsically disordered domain of chikungunya virus nsP3 protein

Agback P, Dominguez F, Pustovalova Y, ..., Agback T, Frolova EI

Virology 537 (-) 130-142 [2019-11-00; online 2019-11-00]

Single-Cell Transcriptomics Uncovers Zonation of Function in the Mesenchyme during Liver Fibrosis

Dobie R, Wilson-Kanamori JR, Henderson BEP, ..., Marioni JC, Henderson NC

Cell Rep 29 (7) 1832-1847.e8 [2019-11-00; online 2019-11-00]

Eukaryotic Single Cell Genomics (ESCG) [Collaborative]

Protein Paucimannosylation Is an Enriched N-Glycosylation Signature of Human Cancers.

Chatterjee S, Lee LY, Kawahara R, ..., Palmisano G, Thaysen-Andersen M

Proteomics 19 (21-22) e1900010 [2019-11-00; online 2019-10-16]

Physical activity is associated with a large number of cardiovascular-specific proteins: Cross-sectional analyses in two independent cohorts.

Stattin K, Lind L, Elmståhl S, ..., Michaëlsson K, Byberg L

Eur J Prev Cardiol 26 (17) 1865-1873 [2019-11-00; online 2019-08-14]

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PIN-driven auxin transport emerged early in streptophyte evolution.

Skokan R, Medvecká E, Viaene T, ..., Petrášek J, Friml J

NPLANTS 5 (11) 1114-1119 [2019-11-00; online 2019-11-11]

Novel BEST1 gene mutations associated with two different forms of macular dystrophy in Tunisian families.

Chibani Z, Abid IZ, Molbaek A, ..., Feki J, Hmani-Aifa M

Clin Exp Ophthalmol 47 (8) 1063-1073 [2019-11-00; online 2019-07-24]

Clinical Genomics [Service] Clinical Genomics Linköping [Service]

Molecular pathology of the luminal class of urothelial tumors.

Bernardo C, Eriksson P, Marzouka NA, ..., Sjödahl G, Höglund M

J. Pathol. 249 (3) 308-318 [2019-11-00; online 2019-08-27]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Molecular imaging identifies age-related attenuation of acetylcholine in retrosplenial cortex in response to acetylcholinesterase inhibition.

Vallianatou T, Shariatgorji M, Nilsson A, ..., Svenningsson P, Andrén PE

Neuropsychopharmacology 44 (12) 2091-2098 [2019-11-00; online 2019-04-22]

Mice exposed to maternal androgen excess and diet-induced obesity have altered phosphorylation of catechol-O-methyltransferase in the placenta and fetal liver.

Fornes R, Manti M, Qi X, ..., Benrick A, Stener-Victorin E

Int J Obes (Lond) 43 (11) 2176-2188 [2019-11-00; online 2019-01-22]

Mesenchymal transition and increased therapy resistance of glioblastoma cells is related to astrocyte reactivity.

Niklasson M, Bergström T, Jarvius M, ..., Segerman B, Segerman A

J. Pathol. 249 (3) 295-307 [2019-11-00; online 2019-08-31]

Mass transport during coagulation of cellulose-ionic liquid solutions in different non-solvents

Hedlund A, Theliander H, Köhnke T

Cellulose 26 (16) 8525-8541 [2019-11-00; online 2019-08-19]

Leveraging European infrastructures to access 1 million human genomes by 2022.

Saunders G, Baudis M, Becker R, ..., Blomberg N, Scollen S

Nat. Rev. Genet. 20 (11) 693-701 [2019-11-00; online 2019-08-27]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Influence of blue mussel (Mytilus edulis) intake on fatty acid composition in erythrocytes and plasma phospholipids and serum metabolites in women with rheumatoid arthritis.

Lindqvist HM, Gjertsson I, Andersson S, Calder PC, Bärebring L

Prostaglandins, Leukotrienes and Essential Fatty Acids (PLEFA) 150 (-) 7-15 [2019-11-00; online 2019-08-24]

Bioinformatics Support for Computational Resources [Service] Swedish NMR Centre (SNC) [Service]

In search of causal pathways in diabetes: a study using proteomics and genotyping data from a cross-sectional study.

Beijer K, Nowak C, Sundström J, ..., Fall T, Lind L

Diabetologia 62 (11) 1998-2006 [2019-11-00; online 2019-08-24]

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Identification of two abundant Aerococcus urinae cell wall-anchored proteins.

Senneby E, Sunnerhagen T, Hallström B, ..., Karlsson C, Rasmussen M

Int. J. Med. Microbiol. 309 (7) 151325 [2019-11-00; online 2019-06-24]

Genomic analysis of Staphylococcus capitis isolated from blood cultures in neonates at a neonatal intensive care unit in Sweden.

Stenmark B, Hellmark B, Söderquist B

Eur. J. Clin. Microbiol. Infect. Dis. 38 (11) 2069-2075 [2019-11-00; online 2019-08-09]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Genetic predisposition to mosaic Y chromosome loss in blood.

Thompson DJ, Genovese G, Halvardson J, ..., Forsberg LA, Perry JRB

Nature 575 (7784) 652-657 [2019-11-00; online 2019-11-20]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic differentiation between and within ecotypes of pike (Esox lucius) in the Baltic Sea

Nordahl O, Koch‐Schmidt P, Sunde J, ..., Forsman A, Larsson P

Aquatic Conserv: Mar Freshw Ecosyst 29 (11) 1923-1935 [2019-11-00; online 2019-08-16]

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Genetic architecture of subcortical brain structures in 38,851 individuals.

Satizabal CL, Adams HHH, Hibar DP, ..., Seshadri S, Ikram MA

Nat. Genet. 51 (11) 1624-1636 [2019-11-00; online 2019-10-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Establishing arthropod community composition using metabarcoding: Surprising inconsistencies between soil samples and preservative ethanol and homogenate from Malaise trap catches.

Marquina D, Esparza-Salas R, Roslin T, Ronquist F

Mol Ecol Resour 19 (6) 1516-1530 [2019-11-00; online 2019-09-18]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Electrochemical Evaluation of a Napthalene Diimide Derivative for Potential Application in Aqueous Organic Redox Flow Batteries

Wiberg C, Owusu F, Wang E, Ahlberg E

Energy Technol. 7 (11) 1900843 [2019-11-00; online 2019-08-23]

EZH2 upregulates the PI3K/AKT pathway through IGF1R and MYC in clinically aggressive chronic lymphocytic leukaemia.

Kosalai ST, Morsy MHA, Papakonstantinou N, ..., Rosenquist R, Kanduri M

Epigenetics 14 (11) 1125-1140 [2019-11-00; online 2019-06-26]

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Diagnostic pitfalls in vitamin B6-dependent epilepsy caused by mutations in the PLPBP gene.

Jensen KV, Frid M, Stödberg T, ..., Darin N, Grønborg S

JIMD Rep 50 (1) 1-8 [2019-11-00; online 2019-09-30]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Chemical Screening Pipeline for Identification of Specific Plant Autophagy Modulators.

Dauphinee AN, Cardoso C, Dalman K, ..., Bozhkov PV, Minina EA

Plant Physiol. 181 (3) 855-866 [2019-11-00; online 2019-09-05]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Characterization of Bacterial Communities in Breeding Waters of Anopheles darlingi in Manaus in the Amazon Basin Malaria-Endemic Area.

Nilsson LKJ, de Oliveira MR, Marinotti O, ..., de Souza AQL, Terenius O

Microb. Ecol. 78 (4) 781-791 [2019-11-00; online 2019-04-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Challenges in the Multivariate Analysis of Mass Cytometry Data: The Effect of Randomization.

Papoutsoglou G, Lagani V, Schmidt A, ..., Tegnér J, Tsamardinos I

Cytometry A 95 (11) 1178-1190 [2019-11-00; online 2019-11-06]

Cellular Immunomonitoring [Service]

Assessment of genetic and non-genetic risk factors for venous thromboembolism in glioblastoma - The predictive significance of B blood group.

Heenkenda MK, Malmström A, Lysiak M, ..., Uppugunduri S, Osman A

Thromb. Res. 183 (-) 136-142 [2019-11-00; online 2019-10-22]

Clinical Genomics [Service] Clinical Genomics Linköping [Service]

A somatic mutation in CLCN2 identified in a sporadic aldosterone-producing adenoma.

Dutta RK, Arnesen T, Heie A, ..., Söderkvist P, Gimm O

Eur. J. Endocrinol. 181 (5) K37-K41 [2019-11-00; online 2019-09-07]

Clinical Genomics [Service] Clinical Genomics Linköping [Service]

A revised solid-state NMR method to assess the crystallinity of cellulose

Sparrman T, Svenningsson L, Sahlin-Sjövold K, ..., Westman G, Bernin D

Cellulose 26 (17) 8993-9003 [2019-11-00; online 2019-09-03]

A rapid and accurate method to quantify neurite outgrowth from cell and tissue cultures: Two image analytic approaches using adaptive thresholds or machine learning

Ossinger A, Bajic A, Pan S, ..., Hailer NP, Schizas N

Journal of Neuroscience Methods 331 (-) 108522 [2019-11-00; online 2019-11-00]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support for Computational Resources [Service]

The architecture of the Plasmodiophora brassicae nuclear and mitochondrial genomes.

Stjelja S, Fogelqvist J, Tellgren-Roth C, Dixelius C

Sci Rep 9 (1) 15753 [2019-10-31; online 2019-10-31]

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Associations of autozygosity with a broad range of human phenotypes.

Clark DW, Okada Y, Moore KHS, ..., Kubo M, Wilson JF

Nat Commun 10 (1) 4957 [2019-10-31; online 2019-10-31]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

High-grade progression confers poor survival in pancreatic neuroendocrine tumors.

Botling J, Lamarca A, Bajic D, ..., Skogseid B, Crona J

Neuroendocrinology - (-) - [2019-10-29; online 2019-10-29]

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CRISPR-Cas9-mediated knockout of SPRY2 in human hepatocytes leads to increased glucose uptake and lipid droplet accumulation.

Cook NL, Pjanic M, Emmerich AG, ..., Castillejo-López C, Ingelsson E

BMC Endocr Disord 19 (1) 115 [2019-10-29; online 2019-10-29]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Inhibition of translation termination by small molecules targeting ribosomal release factors.

Ge X, Oliveira A, Hjort K, ..., Sanyal S, Åqvist J

Sci Rep 9 (1) 15424 [2019-10-28; online 2019-10-28]

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Comparative analysis of obesity-related cardiometabolic and renal biomarkers in human plasma and serum.

Rajan MR, Sotak M, Barrenäs F, ..., Lange S, Börgeson E

Sci Rep 9 (1) 15385 [2019-10-28; online 2019-10-28]

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Assembly and Analysis of the Genome Sequence of the Yeast Brettanomyces naardenensis CBS 7540.

Tiukova IA, Jiang H, Dainat J, ..., Gu Z, Passoth V

Microorganisms 7 (11) - [2019-10-26; online 2019-10-26]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Detection of a High-Turnover Serotonin Circuit in the Mouse Brain Using Mass Spectrometry Imaging.

Sugiyama E, Guerrini MM, Honda K, ..., Suematsu M, Sugiura Y

iScience 20 (-) 359-372 [2019-10-25; online 2019-09-27]

Detailed Functional Characterization of a Waist-Hip Ratio Locus in 7p15.2 Defines an Enhancer Controlling Adipocyte Differentiation.

Castillejo-Lopez C, Pjanic M, Pirona AC, ..., Arner E, Ingelsson E

iScience 20 (-) 42-59 [2019-10-25; online 2019-09-10]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.

Pettersson ME, Rochus CM, Han F, ..., Folkvord A, Andersson L

Genome Res. - (-) - [2019-10-24; online 2019-10-24]

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The SH3 domains of the protein kinases ITK and LCK compete for adjacent sites on T cell-specific adapter protein.

Andersen TCB, Kristiansen PE, Huszenicza Z, ..., Andreotti AH, Spurkland A

J. Biol. Chem. 294 (42) 15480-15494 [2019-10-18; online 2019-09-04]

Puma genomes from North and South America provide insights into the genomic consequences of inbreeding.

Saremi NF, Supple MA, Byrne A, ..., Wilmers CC, Shapiro B

Nat Commun 10 (1) 4769 [2019-10-18; online 2019-10-18]

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Metal free synthesis of ethylene and propylene carbonate from alkylene halohydrin and CO2 at room temperature.

Khokarale SG, Mikkola JP

RSC Adv. 9 (58) 34023-34031 [2019-10-18; online 2019-10-22]

Lipidomics in Ulcerative Colitis Reveal Alteration in Mucosal Lipid Composition Associated With the Disease State.

Diab J, Hansen T, Goll R, ..., Florholmen J, Forsdahl G

Inflamm Bowel Dis 25 (11) 1780-1787 [2019-10-18; online 2019-05-12]

DPI Selectively Inhibits Intracellular NADPH Oxidase Activity in Human Neutrophils.

Buck A, Sanchez Klose FP, Venkatakrishnan V, ..., Christenson K, Bylund J

Immunohorizons 3 (10) 488-497 [2019-10-18; online 2019-10-18]

Considerations and Implications in the Purification of Extracellular Vesicles - A Cautionary Tale.

Lee YXF, Johansson H, Wood MJA, El Andaloussi S

Front. Neurosci. 13 (-) 1067 [2019-10-18; online 2019-10-18]

Bioinformatics Support for Computational Resources [Service] Global Proteomics and Proteogenomics [Service]

Whole-genome sequencing of synchronous thyroid carcinomas identifies aberrant DNA repair in thyroid cancer dedifferentiation

Paulsson JO, Backman S, Wang N, ..., Zedenius J, Juhlin CC

J. Pathol - (-) - [2019-10-17; online 2019-10-17]

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Microbe-host interplay in atopic dermatitis and psoriasis.

Fyhrquist N, Muirhead G, Prast-Nielsen S, ..., Andersson B, Alenius H

Nat Commun 10 (1) 4703 [2019-10-16; online 2019-10-16]

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Metagenomes and metatranscriptomes from boreal potential and actual acid sulfate soil materials.

Högfors-Rönnholm E, Lopez-Fernandez M, Christel S, ..., Engblom S, Dopson M

Sci Data 6 (1) 207 [2019-10-16; online 2019-10-16]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows.

Svensson D, Sjögren R, Sundell D, Sjödin A, Trygg J

BMC Bioinformatics 20 (1) 498 [2019-10-15; online 2019-10-15]

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Monitoring of Protein Biomarkers of Inflammation in Human Traumatic Brain Injury Using Microdialysis and Proximity Extension Assay Technology in Neurointensive Care.

Dyhrfort P, Shen Q, Clausen F, ..., Lewén A, Hillered L

J. Neurotrauma 36 (20) 2872-2885 [2019-10-15; online 2019-06-17]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Challenges for CLEM from a Light Microscopy Perspective

Anderson K, Nilsson T, Fernandez‐Rodriguez J

John Wiley & Sons Ltd 2 (-) 23-35 [2019-10-15; online 2019-09-06]

Integrated Microscopy Technologies Gothenburg [Service]

CSF levels of apolipoprotein C1 and autotaxin found to associate with neuropathic pain and fibromyalgia.

Lind AL, Just D, Mikus M, ..., Gordh T, Månberg A

J Pain Res 12 (-) 2875-2889 [2019-10-15; online 2019-10-15]

Associations Between Attention-Deficit/Hyperactivity Disorder and Various Eating Disorders: A Swedish Nationwide Population Study Using Multiple Genetically Informative Approaches.

Yao S, Kuja-Halkola R, Martin J, ..., Bulik CM, Larsson H

Biol. Psychiatry 86 (8) 577-586 [2019-10-15; online 2019-05-15]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Dynamic Nanocellulose Networks for Thermoset-like yet Recyclable Plastics with a High Melt Stiffness and Creep Resistance.

Peterson A, Östergren I, Lotsari A, ..., Boldizar A, Müller C

Biomacromolecules 20 (10) 3924-3932 [2019-10-14; online 2019-09-17]

A Fluorescent Kinase Inhibitor that Exhibits Diagnostic Changes in Emission upon Binding.

Fleming CL, Sandoz PA, Inghardt T, ..., Grøtli M, Andréasson J

Angew. Chem. Int. Ed. Engl. 58 (42) 15000-15004 [2019-10-14; online 2019-09-05]

Integrated Microscopy Technologies Gothenburg [Service]

Novel functional proteins coded by the human genome discovered in metastases of melanoma patients.

Sanchez A, Kuras M, Murillo JR, ..., Betancourt LH, Marko-Varga G

Cell Biol. Toxicol. - (-) - [2019-10-10; online 2019-10-10]

N-Trifluoromethylthiolated Sulfonimidamides and Sulfoximines: Anti-microbial, Anti-mycobacterial, and Cytotoxic Activity.

Thota N, Makam P, Rajbongshi KK, ..., Naicker T, Arvidsson PI

ACS Med Chem Lett 10 (10) 1457-1461 [2019-10-10; online 2019-09-11]

Drug Discovery and Development (DDD) [Technology development]

Correction: APR-246 reactivates mutant p53 by targeting cysteines 124 and 277.

Zhang Q, Bykov VJN, Wiman KG, Zawacka-Pankau J

Cell Death Dis 10 (10) 769 [2019-10-10; online 2019-10-10]

Chromosomal Abnormalities and Prognosis in NPM1-Mutated Acute Myeloid Leukemia: A Pooled Analysis of Individual Patient Data From Nine International Cohorts.

Angenendt L, Röllig C, Montesinos P, ..., Krug U, Schliemann C

J Clin Oncol 37 (29) 2632-2642 [2019-10-10; online 2019-08-20]

Bioinformatics Support for Computational Resources [Service]

The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon.

Malmström H, Günther T, Svensson EM, ..., Storå J, Jakobsson M

Proc. Biol. Sci. 286 (1912) 20191528 [2019-10-09; online 2019-10-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

SynQuant: an automatic tool to quantify synapses from microscopy images

Wang Y, Wang C, Ranefall P, ..., Tian L, Yu G

Bioinformatics 36 (5) 1599-1606 [2019-10-09; online 2019-10-09]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Molecular dynamics involving proton exchange of a protic ionic liquid-water mixture studied by NMR spectroscopy.

Hasani M, Nordstierna L, Martinelli A

Phys Chem Chem Phys 21 (39) 22014-22021 [2019-10-09; online 2019-09-27]

Intracrystalline Transport Barriers Affecting the Self-Diffusion of CH4 in Zeolites |Na12|-A and |Na12–K|-A

Hedin N, Rzepka P, Jasso-Salcedo AB, Church TL, Bernin D

Langmuir 35 (40) 12971-12978 [2019-10-08; online 2019-09-11]

Along the Indian Ocean coast: genomic variation in Mozambique provides new insights into the Bantu expansion.

Semo A, Gayà-Vidal M, Fortes-Lima C, ..., Schlebusch C, Rocha J

Mol. Biol. Evol. - (-) - [2019-10-08; online 2019-10-08]

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Reduced sialyl-Lewisx on salivary MUC7 from patients with burning mouth syndrome.

Acharya S, Jin C, Bylund J, ..., Carlén A, Karlsson NG

Mol Omics 15 (5) 331-339 [2019-10-07; online 2019-08-16]

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Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure.

Nascimento FJA, Dahl M, Deyanova D, ..., Creer S, Gullström M

Commun Biol 2 (-) 362 [2019-10-04; online 2019-10-04]

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Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels.

Tin A, Marten J, Halperin Kuhns VL, ..., Vitart V, Köttgen A

Nat. Genet. - (-) - [2019-10-02; online 2019-10-02]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Proteomic Analysis of Longitudinal Changes in Blood Pressure.

Lin YT, Fall T, Hammar U, ..., Engström G, Sundström J

J Clin Med 8 (10) 1585 [2019-10-02; online 2019-10-02]

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Skeletal Mineralization in Association with Type X Collagen Expression Is an Ancestral Feature for Jawed Vertebrates.

Debiais-Thibaud M, Simion P, Ventéo S, ..., Mazan S, Haitina T

Mol. Biol. Evol. 36 (10) 2265-2276 [2019-10-01; online 2019-07-05]

Bioinformatics Support for Computational Resources [Service] Genome Engineering Zebrafish [Service]

Molecular characterization of particulate organic matter in full scale anaerobic digesters: An NMR spectroscopy study.

Shakeri Yekta S, Hedenström M, Svensson BH, ..., Hertkorn N, Björn A

Sci. Total Environ. 685 (-) 1107-1115 [2019-10-01; online 2019-06-18]

Interoperable and scalable data analysis with microservices: applications in metabolomics.

Emami Khoonsari P, Moreno P, Bergmann S, ..., Kultima K, Spjuth O

Bioinformatics 35 (19) 3752-3760 [2019-10-01; online 2019-03-10]

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Industrial wastewater treatment plant enriches antibiotic resistance genes and alters the structure of microbial communities.

Bengtsson-Palme J, Milakovic M, Švecová H, ..., Grabic R, Udikovic-Kolic N

Water Res. 162 (-) 437-445 [2019-10-01; online 2019-07-04]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Extreme Differences in Recombination Rate between the Genomes of a Solitary and a Social Bee.

Jones JC, Wallberg A, Christmas MJ, Kapheim KM, Webster MT

Mol. Biol. Evol. 36 (10) 2277-2291 [2019-10-01; online 2019-05-31]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species.

Talla V, Soler L, Kawakami T, ..., Wiklund C, Backström N

Genome Biol Evol 11 (10) 2875-2886 [2019-10-01; online 2019-10-04]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Cellular uptake of self-assembled phytantriol-based hexosomes is independent of major endocytic machineries.

Rodrigues L, Schneider F, Zhang X, ..., Lundmark R, Hubert M

Journal of Colloid and Interface Science 553 (-) 820-833 [2019-10-01; online 2019-06-19]

Integrated Microscopy Technologies Umeå [Collaborative]

Upregulation of PBP1B and LpoB in cysB Mutants Confers Mecillinam (Amdinocillin) Resistance in Escherichia coli.

Thulin E, Andersson DI

Antimicrob. Agents Chemother. 63 (10) - [2019-10-00; online 2019-09-23]

Transcriptome and Proteome Profiling of Neural Induced Pluripotent Stem Cells from Individuals with Down Syndrome Disclose Dynamic Dysregulations of Key Pathways and Cellular Functions.

Sobol M, Klar J, Laan L, ..., Falk A, Dahl N

Mol Neurobiol 56 (10) 7113-7127 [2019-10-00; online 2019-04-13]

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Real time MRI to elucidate the functionality of coating films intended for modified release.

Bernin D, Marucci M, Boissier C, ..., Olsson U, Abrahmsén-Alami S

Journal of Controlled Release 311-312 (-) 117-124 [2019-10-00; online 2019-08-24]

Molecular subtypes applied to a population-based modern cystectomy series do not predict cancer-specific survival.

Kollberg P, Chebil G, Eriksson P, Sjödahl G, Liedberg F

Urol Oncol 37 (10) 791-799 [2019-10-00; online 2019-05-02]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Implantable Organic Electronic Ion Pump Enables ABA Hormone Delivery for Control of Stomata in an Intact Tobacco Plant.

Bernacka-Wojcik I, Huerta M, Tybrandt K, ..., Berggren M, Stavrinidou E

Small 15 (43) e1902189 [2019-10-00; online 2019-09-12]

High-definition spatial transcriptomics for in situ tissue profiling.

Vickovic S, Eraslan G, Salmén F, ..., Regev A, Ståhl PL

Nat. Methods 16 (10) 987-990 [2019-10-00; online 2019-09-09]

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Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats.

Schweizer M, Warmuth VM, Alaei Kakhki N, ..., Suh A, Burri R

Mol. Phylogenet. Evol. 139 (-) 106568 [2019-10-00; online 2019-07-23]

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Genetic variations in A20 DUB domain provide a genetic link to citrullination and neutrophil extracellular traps in systemic lupus erythematosus.

Odqvist L, Jevnikar Z, Riise R, ..., Collins B, Vaarala O

Ann. Rheum. Dis. 78 (10) 1363-1370 [2019-10-00; online 2019-07-12]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic basis and timing of a major mating system shift in Capsella.

Bachmann JA, Tedder A, Laenen B, ..., Castric V, Slotte T

New Phytol. 224 (1) 505-517 [2019-10-00; online 2019-08-01]

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Generation of in situ sequencing based OncoMaps to spatially resolve gene expression profiles of diagnostic and prognostic markers in breast cancer.

Svedlund J, Strell C, Qian X, ..., Sieuwerts AM, Nilsson M

EBioMedicine 48 (-) 212-223 [2019-10-00; online 2019-09-13]

In Situ Sequencing (ISS) [Technology development]

Fam83F induces p53 stabilisation and promotes its activity.

Salama M, Benitez-Riquelme D, Elabd S, ..., Davidson G, Blattner C

Cell Death Differ. 26 (10) 2125-2138 [2019-10-00; online 2019-01-28]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species.

Kurland S, Wheat CW, de la Paz Celorio Mancera M, ..., Ryman N, Laikre L

Ecol Evol 9 (19) 11448-11463 [2019-10-00; online 2019-09-26]

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Endocytic pathway of vascular cell adhesion molecule 1 in human umbilical vein endothelial cell identified in vitro by using functionalized nontoxic fluorescent quantum dots

Fu Y, Jussi J, Wang Q, ..., Yang X, Chen Y

Sensors and Actuators B: Chemical 297 (-) 126702 [2019-10-00; online 2019-10-00]

Integrated Microscopy Technologies Stockholm [Service]

Elevated IL-27 in patients with acute coronary syndrome is associated with adverse ventricular remodeling and increased risk of recurrent myocardial infarction and cardiovascular death.

Grufman H, Yndigegn T, Gonçalves I, Nilsson J, Schiopu A

Cytokine 122 (-) 154208 [2019-10-00; online 2018-02-07]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny.

Cappellini E, Welker F, Pandolfi L, ..., Lordkipanidze D, Willerslev E

Nature 574 (7776) 103-107 [2019-10-00; online 2019-09-11]

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Distribution of bacteria between different milk fractions, investigated using culture-dependent methods and molecular-based and fluorescent microscopy approaches.

Sun L, Dicksved J, Priyashantha H, Lundh Å, Johansson M

J Appl Microbiol 127 (4) 1028-1037 [2019-10-00; online 2019-07-22]

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Discovery and development of substituted thiadiazoles as inhibitors of Staphylococcus aureus Sortase A

Wehrli PM, Uzelac I, Olsson T, ..., Tietze D, Gottfries J

Bioorganic & Medicinal Chemistry 27 (19) 115043 [2019-10-00; online 2019-10-00]

Chemical Biology Consortium Sweden (CBCS) [Service] Glycoproteomics and MS Proteomics [Service] Swedish NMR Centre (SNC) [Service]

Comprehensive mapping of neurotransmitter networks by MALDI-MS imaging.

Shariatgorji M, Nilsson A, Fridjonsdottir E, ..., Odell LR, Andrén PE

Nat. Methods 16 (10) 1021-1028 [2019-10-00; online 2019-09-23]

Cell generation dynamics underlying naive T-cell homeostasis in adult humans.

Mold JE, Réu P, Olin A, ..., Brodin P, Frisén J

PLoS Biol. 17 (10) e3000383 [2019-10-00; online 2019-10-29]

Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Collaborative]

A clonal expression biomarker associates with lung cancer mortality.

Biswas D, Birkbak NJ, Rosenthal R, ..., Swanton C, TRACERx Consortium

Nat. Med. 25 (10) 1540-1548 [2019-10-00; online 2019-10-07]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Significant Changes in Metabolic Profiles after Intervention with Selenium and Coenzyme Q10 in an Elderly Population.

Alehagen U, Johansson P, Aaseth J, ..., Lundstedt-Enkel K, Lundstedt T

Biomolecules 9 (10) - [2019-09-30; online 2019-09-30]

Prognostic Impact of BRAF and KRAS Mutation in Patients with Colorectal and Appendiceal Peritoneal Metastases Scheduled for CRS and HIPEC.

Graf W, Cashin PH, Ghanipour L, ..., Terman A, Birgisson H

Ann. Surg. Oncol. - (-) - [2019-09-30; online 2019-09-30]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Interaction between VPS35 and RABG3f is necessary as a checkpoint to control fusion of late compartments with the vacuole.

Rodriguez-Furlan C, Domozych D, Qian W, ..., Raikhel NV, Hicks GR

Proc. Natl. Acad. Sci. U.S.A. - (-) - [2019-09-30; online 2019-09-30]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Clinical candidate and genistein analogue AXP107-11 has chemoenhancing functions in pancreatic adenocarcinoma through G protein-coupled estrogen receptor signaling.

Mesmar F, Dai B, Ibrahim A, ..., Fleming J, Williams C

Cancer Med - (-) - [2019-09-30; online 2019-09-30]

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Leaf metabolic signatures induced by real and simulated herbivory in black mustard (Brassica nigra).

Papazian S, Girdwood T, Wessels BA, ..., Moritz T, Albrectsen BR

Metabolomics 15 (10) 130 [2019-09-28; online 2019-09-28]

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Complete genomes of two extinct New Zealand passerines show responses to climate fluctuations but no evidence for genomic erosion prior to extinction.

Dussex N, von Seth J, Knapp M, ..., Robertson BC, Dalén L

Biol. Lett. 15 (9) 20190491 [2019-09-27; online 2019-09-04]

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Cold Atmospheric Plasma Disarms M1 Protein, an Important Streptococcal Virulence Factor.

Persson ST, Ekström S, Papareddy P, Herwald H

J Innate Immun 12 (4) 277-290 [2019-09-27; online 2019-09-27]

Translational offsetting as a mode of estrogen receptor α-dependent regulation of gene expression.

Lorent J, Kusnadi EP, van Hoef V, ..., Larsson O, Furic L

EMBO J. - (-) e101323 [2019-09-26; online 2019-09-26]

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Ethylene Signaling Is Required for Fully Functional Tension Wood in Hybrid Aspen.

Seyfferth C, Wessels BA, Gorzsás A, ..., Sundberg B, Felten J

Front Plant Sci 10 (-) 1101 [2019-09-26; online 2019-09-26]

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Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1.

Masser AE, Kang W, Roy J, ..., Friedländer MR, Andréasson C

Elife 8 (-) - [2019-09-25; online 2019-09-25]

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Predisposition to childhood acute lymphoblastic leukemia caused by a constitutional translocation disrupting ETV6.

Järviaho T, Bang B, Zachariadis V, ..., Niinimäki R, Nordgren A

Blood Adv 3 (18) 2722-2731 [2019-09-24; online 2019-09-15]

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Novel Y-Chromosome Long Non-Coding RNAs Expressed in Human Male CNS During Early Development.

Johansson MM, Pottmeier P, Suciu P, ..., Peuckert C, Jazin E

Front Genet 10 (-) 891 [2019-09-24; online 2019-09-24]

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Ataxia in Patients With Bi-Allelic NFASC Mutations and Absence of Full-Length NF186.

Kvarnung M, Shahsavani M, Taylan F, ..., Lindstrand A, Falk A

Front Genet 10 (-) 896 [2019-09-24; online 2019-09-24]

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IGEMS: The Consortium on Interplay of Genes and Environment Across Multiple Studies - An Update.

Pedersen NL, Gatz M, Finch BK, ..., Sachdev P, Whitfield KE

Twin Res Hum Genet - (-) 1-8 [2019-09-23; online 2019-09-23]

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Microwave Synthesis of Alkali‐Free Hexaniobate, Decaniobate, and Hexatantalate Polyoxometalate Ions

Rambaran MA, Pascual‐Borràs M, Ohlin CA

Eur. J. Inorg. Chem. 2019 (35) 3913-3918 [2019-09-22; online 2019-09-05]

Hypermethylation-associated downregulation of microRNA-4456 in hypersexual disorder with putative influence on oxytocin signalling: A DNA methylation analysis of miRNA genes.

Boström AE, Chatzittofis A, Ciuculete DM, ..., Schiöth HB, Jokinen J

Epigenetics - (-) 1-16 [2019-09-22; online 2019-09-22]

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The TGFB2-AS1 lncRNA Regulates TGF-β Signaling by Modulating Corepressor Activity.

Papoutsoglou P, Tsubakihara Y, Caja L, ..., Heldin CH, Moustakas A

Cell Rep 28 (12) 3182-3198.e11 [2019-09-17; online 2019-09-19]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method.

Rajan SK, Lindqvist M, Brummer RJ, Schoultz I, Repsilber D

PLoS ONE 14 (9) e0222171 [2019-09-17; online 2019-09-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Model System for the Formation of Tick-Borne Encephalitis Virus Replication Compartments without Viral RNA Replication.

Yau WL, Nguyen-Dinh V, Larsson E, ..., Överby AK, Lundmark R

J. Virol. 93 (18) - [2019-09-15; online 2019-08-28]

Bioinformatics Support for Computational Resources [Service] Cryo-EM [Service] Integrated Microscopy Technologies Umeå [Collaborative]

Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341.

Nilsson E, Li K, Fridlund J, ..., Pinhassi J, Holmfeldt K

Appl. Environ. Microbiol. 85 (18) - [2019-09-15; online 2019-08-29]

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Nestin Regulates Neurogenesis in Mice Through Notch Signaling From Astrocytes to Neural Stem Cells.

Wilhelmsson U, Lebkuechner I, Leke R, ..., Pekna M, Pekny M

Cereb. Cortex 29 (10) 4050-4066 [2019-09-13; online 2019-01-04]

Integrated Microscopy Technologies Gothenburg [Service]

Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture.

Reddy HK, Carroni M, Hajdu J, Svenda M

Elife 8 (-) - [2019-09-12; online 2019-09-12]

A Single-Stranded Oligonucleotide Inhibits Toll-Like Receptor 3 Activation and Reduces Influenza A (H1N1) Infection.

Poux C, Dondalska A, Bergenstråhle J, ..., Tregoning JS, Spetz AL

Front Immunol 10 (-) 2161 [2019-09-12; online 2019-09-12]

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Genome-wide association meta-analyses and fine-mapping elucidate pathways influencing albuminuria.

Teumer A, Li Y, Ghasemi S, ..., Pattaro C, Köttgen A

Nat Commun 10 (1) 4130 [2019-09-11; online 2019-09-11]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Correlative STED super-resolution light and electron microscopy on resin sections

Wurm CA, Schwarz H, Jans DC, ..., Humbel BM, Jakobs S

J. Phys. D: Appl. Phys. 52 (37) 374003 [2019-09-11; online 2019-07-16]

Integrated Microscopy Technologies Stockholm [Technology development]

Recurrent convergent evolution at amino acid residue 261 in fish rhodopsin.

Hill J, Enbody ED, Pettersson ME, ..., Scheerer P, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 116 (37) 18473-18478 [2019-09-10; online 2019-08-26]

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Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota.

Manoharan L, Kozlowski JA, Murdoch RW, ..., Sousa FL, Schleper C

MBio 10 (5) - [2019-09-10; online 2019-09-10]

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Evaluation of the Genetic Association Between Adult Obesity and Neuropsychiatric Disease.

Stahel P, Nahmias A, Sud SK, ..., Batterham RL, Dash S

Diabetes - (-) - [2019-09-10; online 2019-09-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Combining ERBB family and MET inhibitors is an effective therapeutic strategy in cutaneous malignant melanoma independent of BRAF/NRAS mutation status.

Das I, Wilhelm M, Höiom V, ..., Tuominen R, Egyhàzi Brage S

Cell Death Dis 10 (9) 663 [2019-09-10; online 2019-09-10]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

μLAS technology for DNA isolation coupled to Cas9-assisted targeting for sequencing and assembly of a 30 kb region in plant genome.

Milon N, Chantry-Darmon C, Satge C, ..., Bergès H, Bancaud A

Nucleic Acids Res. 47 (15) 8050-8060 [2019-09-05; online 2019-09-11]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Differential gene expression in bovine endometrial epithelial cells after challenge with LPS; specific implications for genes involved in embryo maternal interactions.

Guo Y, van Schaik T, Jhamat N, ..., Andersson G, Humblot P

PLoS ONE 14 (9) e0222081 [2019-09-05; online 2019-09-05]

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Protein prenylation restrains innate immunity by inhibiting Rac1 effector interactions.

Akula MK, Ibrahim MX, Ivarsson EG, ..., Sayin VI, Bergo MO

Nat Commun 10 (1) 3975 [2019-09-04; online 2019-09-04]

Genome Sequencing of Pleurozium schreberi: The Assembled and Annotated Draft Genome of a Pleurocarpous Feather Moss.

Pederson ERA, Warshan D, Rasmussen U

G3 (Bethesda) 9 (9) 2791-2797 [2019-09-04; online 2019-09-04]

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Associations of Smoking and Alcohol and Coffee Intake with Fracture and Bone Mineral Density: A Mendelian Randomization Study.

Yuan S, Michaëlsson K, Wan Z, Larsson SC

Calcif. Tissue Int. - (-) - [2019-09-04; online 2019-09-04]

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Genetic variance of metabolomic features and their relationship with body weight and body weight gain in Holstein cattle1

Aliakbari A, Ehsani A, Vaez Torshizi R, ..., Jensen J, Sarup P

J. Anim. Sci. 97 (9) 3832-3844 [2019-09-03; online 2019-07-05]

A novel tumor spheroid model identifies selective enhancement of radiation by an inhibitor of oxidative phosphorylation.

Karlsson H, Senkowski W, Fryknäs M, ..., Larsson R, Nygren P

Oncotarget 10 (51) 5372-5382 [2019-09-03; online 2019-09-03]

Vimentin Phosphorylation Is Required for Normal Cell Division of Immature Astrocytes.

de Pablo Y, Marasek P, Pozo-Rodrigálvarez A, ..., Pekna M, Pekny M

Cells 8 (9) 1016 [2019-09-01; online 2019-09-01]

Integrated Microscopy Technologies Gothenburg [Service]

The autoantibody response to cyclic citrullinated collagen type II peptides in rheumatoid arthritis.

Liang B, Ge C, Lönnblom E, ..., Zhao M, Holmdahl R

Rheumatology (Oxford) 58 (9) 1623-1633 [2019-09-01; online 2019-03-21]

Perturbed ovarian and uterine glucocorticoid receptor signaling accompanies the balanced regulation of mitochondrial function and NFκB-mediated inflammation under conditions of hyperandrogenism and insulin resistance.

Hu M, Zhang Y, Guo X, ..., Shao LR, Billig H

Life Sciences 232 (-) 116681 [2019-09-01; online 2019-07-23]

Integrated Microscopy Technologies Gothenburg [Service]

Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly.

Höök L, Leal L, Talla V, Backström N

Genome Biol Evol 11 (9) 2633-2652 [2019-09-01; online 2019-08-11]

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Genetic Affinities among Southern Africa Hunter-Gatherers and the Impact of Admixing Farmer and Herder Populations.

Vicente M, Jakobsson M, Ebbesen P, Schlebusch CM

Mol. Biol. Evol. 36 (9) 1849-1861 [2019-09-01; online 2019-07-10]

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Effects of allochthonous dissolved organic matter input on microbial composition and nitrogen-cycling genes at two contrasting estuarine sites.

Happel EM, Markussen T, Teikari JE, ..., Kisand V, Riemann L

FEMS Microbiol. Ecol. 95 (9) - [2019-09-01; online 2019-08-10]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast.

Tusso S, Nieuwenhuis BPS, Sedlazeck FJ, ..., Jeffares DC, Wolf JBW

Mol. Biol. Evol. 36 (9) 1975-1989 [2019-09-01; online 2019-06-22]

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Whole exome sequencing identifies novel variant underlying hereditary spastic paraplegia in consanguineous Pakistani families.

Zulfiqar S, Tariq M, Ali Z, ..., Dahl N, Baig SM

J Clin Neurosci 67 (-) 19-23 [2019-09-00; online 2019-07-04]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Targeted ultra-deep sequencing of a South African Bantu-speaking cohort to comprehensively map and characterize common and novel variants in 65 pharmacologically-related genes.

Tshabalala S, Choudhury A, Beeton-Kempen N, ..., Ramsay M, Mancama D

Pharmacogenet. Genomics 29 (7) 167-178 [2019-09-00; online 2019-06-05]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Protein kinase MST3 modulates lipid homeostasis in hepatocytes and correlates with nonalcoholic steatohepatitis in humans.

Cansby E, Kulkarni NM, Magnusson E, ..., Blüher M, Mahlapuu M

FASEB J. 33 (9) 9974-9989 [2019-09-00; online 2019-06-07]

Orthologous nuclear markers and new transcriptomes that broadly cover the phylogenetic diversity of Acanthaceae.

Morais EB, Schönenberger J, Conti E, Antonelli A, Szövényi P

Appl Plant Sci 7 (9) e11290 [2019-09-00; online 2019-09-25]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Multiplexed analysis of the secretin-like GPCR-RAMP interactome.

Lorenzen E, Dodig-Crnković T, Kotliar IB, ..., Schwenk JM, Sakmar TP

Sci Adv 5 (9) eaaw2778 [2019-09-00; online 2019-09-18]

Impact of demography on linked selection in two outcrossing Brassicaceae species.

Mattila TM, Laenen B, Horvath R, ..., Savolainen O, Slotte T

Ecol Evol 9 (17) 9532-9545 [2019-09-00; online 2019-08-13]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Global extracellular vesicle proteomic signature defines U87-MG glioma cell hypoxic status with potential implications for non-invasive diagnostics.

Indira Chandran V, Welinder C, Gonçalves de Oliveira K, ..., Marko-Varga G, Belting M

J. Neurooncol. 144 (3) 477-488 [2019-09-00; online 2019-08-14]

FLT3N676K drives acute myeloid leukemia in a xenograft model of KMT2A-MLLT3 leukemogenesis.

Hyrenius-Wittsten A, Pilheden M, Falqués-Costa A, ..., Järås M, Hagström-Andersson AK

Leukemia 33 (9) 2310-2314 [2019-09-00; online 2019-04-05]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Exploration of potential biochemical markers for persistence of patent ductus arteriosus in preterm infants at 22-27 weeks' gestation.

Olsson KW, Larsson A, Jonzon A, Sindelar R

Pediatr. Res. 86 (3) 333-338 [2019-09-00; online 2018-09-18]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL341.

Karlsson CMG, Cerro-Gálvez E, Lundin D, ..., Vila-Costa M, Pinhassi J

Microb Biotechnol 12 (5) 892-906 [2019-09-00; online 2019-07-04]

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Dimerization of 9,10-anthraquinone-2,7-Disulfonic acid (AQDS)

Wiberg C, Carney TJ, Brushett F, Ahlberg E, Wang E

Electrochimica Acta 317 (-) 478-485 [2019-09-00; online 2019-09-00]

Copy number variation and neuropsychiatric problems in females and males in the general population.

Martin J, Tammimies K, Karlsson R, ..., Lichtenstein P, Magnusson PKE

Am. J. Med. Genet. B Neuropsychiatr. Genet. 180 (6) 341-350 [2019-09-00; online 2018-10-11]

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Combining microdialysis with metabolomics to characterize the in situ composition of dissolved organic compounds in boreal forest soil

Randewig D, Marshall JD, Näsholm T, Jämtgård S

Soil Biology and Biochemistry 136 (-) 107530 [2019-09-00; online 2019-09-00]

A simultaneous assessment of organic matter and trace elements bio-accessibility in substrate and digestate from an anaerobic digestion plant.

Laera A, Shakeri Yekta S, Hedenström M, ..., Esposito G, van Hullebusch ED

Bioresour. Technol. 288 (-) 121587 [2019-09-00; online 2019-05-31]

MiDRM pol: A High-Throughput Multiplexed Amplicon Sequencing Workflow to Quantify HIV-1 Drug Resistance Mutations against Protease, Reverse Transcriptase, and Integrase Inhibitors.

Aralaguppe SG, Ambikan AT, Ashokkumar M, ..., Sönnerborg A, Neogi U

Viruses 11 (9) - [2019-08-30; online 2019-08-30]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior.

Ganna A, Verweij KJH, Nivard MG, ..., Neale BM, Zietsch BP

Science 365 (6456) - [2019-08-30; online 2019-08-31]

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Neuroticism as a predictor of frailty in old age: a genetically informative approach.

Danielsdottir HB, Jylhävä J, Hägg S, ..., Mosing MA, Lehto K

Psychosom Med - (-) - [2019-08-28; online 2019-08-28]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

DNA analysis of low- and high-density fractions defines heterogeneous subpopulations of small extracellular vesicles based on their DNA cargo and topology.

Lázaro-Ibáñez E, Lässer C, Shelke GV, ..., García-Rodríguez A, Lötvall J

J Extracell Vesicles 8 (1) 1656993 [2019-08-27; online 2019-08-27]

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Unique transcriptional and protein-expression signature in human lung tissue-resident NK cells.

Marquardt N, Kekäläinen E, Chen P, ..., Ljunggren HG, Michaëlsson J

Nat Commun 10 (1) 3841 [2019-08-26; online 2019-08-26]

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Profiling surface proteins on individual exosomes using a proximity barcoding assay.

Wu D, Yan J, Shen X, ..., Landegren U, Kamali-Moghaddam M

Nat Commun 10 (1) 3854 [2019-08-26; online 2019-08-26]

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Array-Based Profiling of Proteins and Autoantibody Repertoires in CSF.

Pin E, Sjöberg R, Andersson E, ..., Nilsson P, Månberg A

Methods Mol. Biol. 2044 (-) 303-318 [2019-08-23; online 2019-08-23]

Autoimmunity and Serology Profiling [Technology development]

The human transmembrane mucin MUC17 responds to TNFα by increased presentation at the plasma membrane.

Schneider H, Berger E, Dolan B, ..., Pelaseyed T, Hansson GC

Biochem. J. 476 (16) 2281-2295 [2019-08-22; online 2019-08-22]

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Publisher Correction: Metabolic phenotype of breast-fed infants, and infants fed standard formula or bovine MFGM supplemented formula: a randomized controlled trial.

He X, Parenti M, Grip T, ..., Timby N, Slupsky CM

Sci Rep 9 (1) 12382 [2019-08-22; online 2019-08-22]

Syntaxin 5 Is Required for the Formation and Clearance of Protein Inclusions during Proteostatic Stress.

Babazadeh R, Ahmadpour D, Jia S, ..., Liu B, Nystrom T

Cell Rep 28 (8) 2096-2110.e8 [2019-08-20; online 2019-08-23]

Integrated Microscopy Technologies Gothenburg [Service]

Separation of Isomeric O-Glycans by Ion Mobility and Liquid Chromatography-Mass Spectrometry.

Jin C, Harvey DJ, Struwe WB, Karlsson NG

Anal. Chem. 91 (16) 10604-10613 [2019-08-20; online 2019-08-01]

Glycoproteomics and MS Proteomics [Technology development]

Molecular mimicry between Anoctamin 2 and Epstein-Barr virus nuclear antigen 1 associates with multiple sclerosis risk.

Tengvall K, Huang J, Hellström C, ..., Olsson T, Kockum I

Proc. Natl. Acad. Sci. U.S.A. 116 (34) 16955-16960 [2019-08-20; online 2019-08-02]

Autoimmunity and Serology Profiling [Collaborative]

Molecular Basis and Ecological Relevance of Caulobacter Cell Filamentation in Freshwater Habitats.

Heinrich K, Leslie DJ, Morlock M, Bertilsson S, Jonas K

MBio 10 (4) - [2019-08-20; online 2019-08-20]

Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients.

Fernandes SJ, Morikawa H, Ewing E, ..., Tegnér J, Gomez-Cabrero D

Sci Rep 9 (1) 11996 [2019-08-19; online 2019-08-19]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genome-wide systematic identification of methyltransferase recognition and modification patterns.

Jensen TØ, Tellgren-Roth C, Redl S, ..., Pedersen LE, Nielsen AT

Nat Commun 10 (1) 3311 [2019-08-19; online 2019-08-19]

NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Matrisome Properties of Scaffolds Direct Fibroblasts in Idiopathic Pulmonary Fibrosis.

Elowsson Rendin L, Löfdahl A, Åhrman E, ..., Malmström J, Westergren-Thorsson G

Int J Mol Sci 20 (16) - [2019-08-17; online 2019-08-17]

Toxic Activation of an AAA+ Protease by the Antibacterial Drug Cyclomarin A.

Maurer M, Linder D, Franke KB, ..., Bukau B, Mogk A

Cell Chem Biol 26 (8) 1169-1179.e4 [2019-08-15; online 2019-06-13]

Joint and unique multiblock analysis of biological data - multiomics malaria study.

Surowiec I, Skotare T, Sjögren R, ..., Normark J, Trygg J

Faraday Discuss. 218 (0) 268-283 [2019-08-15; online 2019-05-24]

Complete Genome Sequence of Hydrocarbon-Degrading Halotolerant Acinetobacter radioresistens DD78, Isolated from the Aconcagua River Mouth in Central Chile.

Macaya CC, Méndez V, Durán RE, ..., Moore ERB, Seeger M

Microbiol Resour Announc 8 (33) - [2019-08-15; online 2019-08-15]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach.

Zan Y, Payen T, Lillie M, ..., Siegel PB, Carlborg Ö

Genet. Sel. Evol. 51 (1) 44 [2019-08-14; online 2019-08-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] Protein Science Facility (PSF) [Service]

Statistical Analysis of Community RNA Transcripts between Organic Carbon and Geogas-Fed Continental Deep Biosphere Groundwaters.

Lopez-Fernandez M, Broman E, Simone D, Bertilsson S, Dopson M

MBio 10 (4) - [2019-08-13; online 2019-08-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Nucleation of an Activating Conformational Change by a Cation-π Interaction.

Rogne P, Andersson D, Grundström C, ..., Linusson A, Wolf-Watz M

Biochemistry 58 (32) 3408-3412 [2019-08-13; online 2019-07-29]

Functional Identification of Target by Expression Proteomics (FITExP)

Gaetani M, Zubarev RA

- - (-) 257-266 [2019-08-13; online 2019-07-26]

Glycosylation influences activity, stability and immobilization of the feruloyl esterase 1a from Myceliophthora thermophila.

Bonzom C, Hüttner S, Mirgorodskaya E, ..., Verhaert RMD, Olsson L

AMB Express 9 (1) 126 [2019-08-12; online 2019-08-12]

PAK4 suppresses RELB to prevent senescence-like growth arrest in breast cancer.

Costa TDF, Zhuang T, Lorent J, ..., Defilippi P, Strömblad S

Nat Commun 10 (1) 3589 [2019-08-09; online 2019-08-09]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Lack of gene flow: Narrow and dispersed differentiation islands in a triplet of Leptidea butterfly species

Talla V, Johansson A, Dincă V, ..., Wiklund C, Backström N

Mol Ecol 28 (6) 3756-3770 [2019-08-08; online 2019-08-08]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Selective Enrichment of Phosphorylated Peptides by Monolithic Polymers Surface Imprinted with bis-Imidazolium Moieties by UV-Initiated Cryopolymerization.

Liu M, Torsetnes SB, Wierzbicka C, ..., Sellergren B, Irgum K

Anal. Chem. 91 (15) 10188-10196 [2019-08-06; online 2019-07-08]

Deciphering Isomers with a Multiple Reaction Monitoring Method for the Complete Detectable O-Glycan Repertoire of the Candidate Therapeutic, Lubricin.

Flowers SA, Lane CS, Karlsson NG

Anal. Chem. 91 (15) 9819-9827 [2019-08-06; online 2019-07-11]

Glycoproteomics and MS Proteomics [Technology development]

Classical Human Leukocyte Antigen Alleles and C4 Haplotypes Are Not Significantly Associated With Depression.

Glanville KP, Coleman JRI, Hanscombe KB, ..., O'Reilly PF, Lewis CM

Biol. Psychiatry - (-) - [2019-08-05; online 2019-08-05]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Critical Role of Dysregulated RhoB Signaling Pathway in Radioresistance of Colorectal Cancer.

Liu N, Cui W, Jiang X, ..., Wang X, Sun XF

Int. J. Radiat. Oncol. Biol. Phys. 104 (5) 1153-1164 [2019-08-01; online 2019-04-27]

Cellular Immunomonitoring [Service]

Mesenchymal stromal cell-derived nanovesicles ameliorate bacterial outer membrane vesicle-induced sepsis via IL-10.

Park KS, Svennerholm K, Shelke GV, ..., Gribonika I, Lötvall J

Stem Cell Res Ther 10 (1) 231 [2019-08-01; online 2019-08-01]

Integrated Microscopy Technologies Gothenburg [Service]

Individual Physiological Adaptations Enable Selected Bacterial Taxa To Prevail during Long-Term Incubations.

Herlemann DPR, Markert S, Meeske C, ..., Jürgens K, Schweder T

Appl. Environ. Microbiol. 85 (15) - [2019-08-01; online 2019-07-18]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Gene Flow in the Müllerian Mimicry Ring of a Poisonous Papuan Songbird Clade (Pitohui; Aves).

Garg KM, Sam K, Chattopadhyay B, ..., Ericson PGP, Rheindt FE

Genome Biol Evol 11 (8) 2332-2343 [2019-08-01; online 2019-08-17]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

sTRAIL-R2 (Soluble TNF [Tumor Necrosis Factor]-Related Apoptosis-Inducing Ligand Receptor 2) a Marker of Plaque Cell Apoptosis and Cardiovascular Events.

Gonçalves I, Singh P, Tengryd C, ..., Nilsson J, Edsfeldt A

Stroke 50 (8) 1989-1996 [2019-08-00; online 2019-07-05]

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Viral mimetic priming enhances α-synuclein-induced degeneration: Implications for Parkinson's disease.

Olsen LK, Cairns AG, Ådén J, ..., Dowd E, McKernan DP

Brain, Behavior, and Immunity 80 (-) 525-535 [2019-08-00; online 2019-04-25]

Tobacco smoking induces changes in true DNA methylation, hydroxymethylation and gene expression in bronchoalveolar lavage cells.

Ringh MV, Hagemann-Jensen M, Needhamsen M, ..., Öckinger J, Ekström TJ

EBioMedicine 46 (-) 290-304 [2019-08-00; online 2019-07-12]

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Systematic Development of Sandwich Immunoassays for the Plasma Secretome.

Häussler RS, Bendes A, Iglesias M, ..., Qundos U, Schwenk JM

Proteomics 19 (15) e1900008 [2019-08-00; online 2019-07-22]

Affinity Proteomics Stockholm [Technology development]

Substantial Heritable Variation in Recombination Rate on Multiple Scales in Honeybees and Bumblebees.

Kawakami T, Wallberg A, Olsson A, ..., Rundlöf M, Webster MT

Genetics 212 (4) 1101-1119 [2019-08-00; online 2019-05-31]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem.

Broman E, Raymond C, Sommer C, ..., Creer S, Nascimento FJA

Mol. Ecol. 28 (16) 3813-3829 [2019-08-00; online 2019-09-05]

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Role of apolipoprotein C-III overproduction in diabetic dyslipidaemia.

Adiels M, Taskinen MR, Björnson E, ..., Packard C, Borén J

Diabetes Obes Metab 21 (8) 1861-1870 [2019-08-00; online 2019-05-08]

Reply to "CRISPR screens are feasible in TP53 wild-type cells".

Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J

Mol. Syst. Biol. 15 (8) e9059 [2019-08-00; online 2019-08-30]

CRISPR Functional Genomics [Collaborative]

Post-metaphase correction of aberrant kinetochore-microtubule attachments in mammalian eggs.

Kouznetsova A, Kitajima TS, Brismar H, Höög C

EMBO Rep. 20 (8) e47905 [2019-08-00; online 2019-07-10]

Integrated Microscopy Technologies Stockholm [Collaborative]

Molecular insights into hypomineralized enamel.

Malmberg P, Norén JG, Bernin D

Eur. J. Oral Sci. 127 (4) 340-346 [2019-08-00; online 2019-04-29]

Mixture toxicity effects and uptake of titanium dioxide (TiO 2) nanoparticles and 3,3',4,4'-tetrachlorobiphenyl (PCB77) in juvenile brown trout following co-exposure via the diet.

Lammel T, Wassmur B, Mackevica A, Chen CL, Sturve J

Aquat. Toxicol. 213 (-) 105195 [2019-08-00; online 2019-05-30]

Integrated Microscopy Technologies Gothenburg [Service]

Microbial utilization of simple carbon substrates in boreal peat soils at low temperatures

Segura JH, Nilsson MB, Schleucher J, ..., Bertilsson S, Öquist MG

Soil Biology and Biochemistry 135 (-) 438-448 [2019-08-00; online 2019-08-00]

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Maintenance of High Genome Integrity over Vegetative Growth in the Fairy-Ring Mushroom Marasmius oreades

Hiltunen M, Grudzinska-Sterno M, Wallerman O, Ryberg M, Johannesson H

Current Biology 29 (16) 2758-2765.e6 [2019-08-00; online 2019-08-00]

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Linkage analysis revealed risk loci on 6p21 and 18p11.2-q11.2 in familial colon and rectal cancer, respectively.

von Holst S, Jiao X, Liu W, ..., Bryant P, Lindblom A

Eur. J. Hum. Genet. 27 (8) 1286-1295 [2019-08-00; online 2019-04-05]

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Layer formation mechanism of K-feldspar in bubbling fluidized bed combustion of phosphorus-lean and phosphorus-rich residual biomass

Wagner K, Häggström G, Skoglund N, ..., Öhman M, Hofbauer H

Applied Energy 248 (-) 545-554 [2019-08-00; online 2019-08-00]

Joint Image Deconvolution and Separation Using Mixed Dictionaries.

Siadat M, Aghazadeh N, Akbarifard F, Brismar H, Oktem O

IEEE Trans. on Image Process. 28 (8) 3936-3945 [2019-08-00; online 2019-03-06]

Integrated Microscopy Technologies Stockholm [Technology development]

Interaction of Sox2 with RNA binding proteins in mouse embryonic stem cells

Samudyata , Amaral PP, Engström PG, ..., Kouzarides T, Castelo-Branco G

Experimental Cell Research 381 (1) 129-138 [2019-08-00; online 2019-08-00]

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In-hospital metabolite changes in infective endocarditis-a longitudinal 1H NMR-based study.

Klein CF, Holle SLK, Andersen MH, ..., Iversen KK, Malmendal A

Eur. J. Clin. Microbiol. Infect. Dis. 38 (8) 1553-1560 [2019-08-00; online 2019-05-22]

Goodbye reference, hello genome graphs.

Ameur A

Nat. Biotechnol. 37 (8) 866-868 [2019-08-00; online 2019-08-04]

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Gas-Phase Collisions with Trimethylamine-N-Oxide Enable Activation-Controlled Protein Ion Charge Reduction.

Kaldmäe M, Österlund N, Lianoudaki D, ..., Marklund EG, Landreh M

J. Am. Soc. Mass Spectrom. 30 (8) 1385-1388 [2019-08-00; online 2019-07-08]

Early activating somatic PIK3CA mutations promote ectopic muscle development and upper limb overgrowth.

Frisk S, Taylan F, Blaszczyk I, ..., Laurell T, Nordgren A

Clin. Genet. 96 (2) 118-125 [2019-08-00; online 2019-05-09]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return.

Jønsson KA, Blom MPK, Marki PZ, ..., Ericson PGP, Irestedt M

Mol. Phylogenet. Evol. 137 (-) 200-209 [2019-08-00; online 2019-03-23]

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Clinical protein science in translational medicine targeting malignant melanoma.

Gil J, Betancourt LH, Pla I, ..., Malm J, Marko-Varga G

Cell Biol. Toxicol. 35 (4) 293-332 [2019-08-00; online 2019-03-21]

Circulating HER2/ErbB2 Levels Are Associated With Increased Incidence of Diabetes: A Population-Based Cohort Study.

Muhammad IF, Borné Y, Bao X, ..., Nilsson J, Engström G

Diabetes Care 42 (8) 1582-1588 [2019-08-00; online 2019-06-14]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Boreal tree species affect soil organic matter composition and saprotrophic mineralization rates

Segura JH, Nilsson MB, Sparrman T, ..., Tolu J, Öquist MG

Plant Soil 441 (1-2) 173-190 [2019-08-00; online 2019-05-24]

Bioinformatics Support for Computational Resources [Service] Swedish NMR Centre (SNC) [Collaborative]

Anti-tumor effects of PIM/PI3K/mTOR triple kinase inhibitor IBL-302 in neuroblastoma.

Mohlin S, Hansson K, Radke K, ..., von Stedingk K, Bexell D

EMBO Mol Med 11 (8) e10058 [2019-08-00; online 2019-07-16]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service] Structural Proteomics [Service]

A role for the auxin precursor anthranilic acid in root gravitropism via regulation of PIN-FORMED protein polarity and relocalisation in Arabidopsis.

Doyle SM, Rigal A, Grones P, ..., Novák O, Robert S

New Phytol. 223 (3) 1420-1432 [2019-08-00; online 2019-06-07]

Chemical Biology Consortium Sweden (CBCS) [Service] Swedish Metabolomics Centre (SMC) [Service]

31° South: The physiology of adaptation to arid conditions in a passerine bird.

Ribeiro ÂM, Puetz L, Pattinson NB, ..., Smit B, Gilbert MTP

Mol. Ecol. 28 (16) 3709-3721 [2019-08-00; online 2019-08-06]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Computational and Experimental Druggability Assessment of Human DNA Glycosylases.

Michel M, Visnes T, Homan EJ, ..., Warpman Berglund U, Helleday T

ACS Omega 4 (7) 11642-11656 [2019-07-31; online 2019-07-05]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Swedish NMR Centre (SNC) [Collaborative]

Shared and Unique Patterns of DNA Methylation in Systemic Lupus Erythematosus and Primary Sjögren's Syndrome.

Imgenberg-Kreuz J, Almlöf JC, Leonard D, ..., Sandling JK, Nordmark G

Front Immunol 10 (-) 1686 [2019-07-30; online 2019-07-30]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Multiplex plasma protein profiling identifies novel markers to discriminate patients with adenocarcinoma of the lung.

Djureinovic D, Pontén V, Landelius P, ..., Micke P, Ståhle E

BMC Cancer 19 (1) 741 [2019-07-29; online 2019-07-29]

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Impact of vitamin D and vitamin D receptor TaqI polymorphism in primary human myoblasts.

Saini A, Björkhem-Bergman L, Boström J, ..., Rullman E, Gustafsson T

Endocr Connect 8 (7) 1070-1081 [2019-07-29; online 2019-07-29]

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E3 ubiquitin-protein ligase TRIM21-mediated lysine capture by UBE2E1 reveals substrate-targeting mode of a ubiquitin-conjugating E2.

Anandapadamanaban M, Kyriakidis NC, Csizmók V, ..., Wahren-Herlenius M, Sunnerhagen M

J. Biol. Chem. 294 (30) 11404-11419 [2019-07-26; online 2019-06-03]

Combinations of Spok genes create multiple meiotic drivers in Podospora.

Vogan AA, Ament-Velásquez SL, Granger-Farbos A, ..., Saupe SJ, Johannesson H

Elife 8 (-) - [2019-07-26; online 2019-07-26]

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TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish.

Gudmundsson S, Wilbe M, Filipek-Górniok B, ..., Annerén G, Bondeson M

Sci Rep 9 (1) 10730 [2019-07-24; online 2019-07-24]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative] Genome Engineering Zebrafish [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genomic differentiation tracks earth-historic isolation in an Indo-Australasian archipelagic pitta (Pittidae; Aves) complex.

Ericson PGP, Qu Y, Rasmussen PC, ..., Rheindt FE, Irestedt M

BMC Evol. Biol. 19 (1) 151 [2019-07-24; online 2019-07-24]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

α-synuclein-lipoprotein interactions and elevated ApoE level in cerebrospinal fluid from Parkinson's disease patients.

Paslawski W, Zareba-Paslawska J, Zhang X, ..., Andrén PE, Svenningsson P

Proc. Natl. Acad. Sci. U.S.A. 116 (30) 15226-15235 [2019-07-23; online 2019-07-03]

Genetic analyses supporting colorectal, gastric, and prostate cancer syndromes.

Wallander K, Liu W, von Holst S, ..., Lindblom A, Lagerstedt-Robinson K

Genes Chromosomes Cancer - (-) - [2019-07-23; online 2019-07-23]

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Annotations, Ontologies, and Whole Slide Images - Development of an Annotated Ontology-Driven Whole Slide Image Library of Normal and Abnormal Human Tissue.

Lindman K, Rose JF, Lindvall M, Lundström C, Treanor D

J Pathol Inform 10 (-) 22 [2019-07-23; online 2019-07-23]

AIDA Data Hub [Collaborative] Bioinformatics (NBIS) [Collaborative]

Vitamin D and Phenylbutyrate Supplementation Does Not Modulate Gut Derived Immune Activation in HIV-1.

Missailidis C, Sørensen N, Ashenafi S, ..., Brighenti S, Bergman P

Nutrients 11 (7) 1675 [2019-07-21; online 2019-07-21]

Genome and plasmid diversity of Extended-Spectrum β-Lactamase-producing Escherichia coli ST131 - tracking phylogenetic trajectories with Bayesian inference.

Ny S, Sandegren L, Salemi M, Giske CG

Sci Rep 9 (1) 10291 [2019-07-16; online 2019-07-16]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

TGF-β family ligands exhibit distinct signalling dynamics that are driven by receptor localisation.

Miller DSJ, Schmierer B, Hill CS

J. Cell. Sci. 132 (14) - [2019-07-15; online 2019-07-15]

CRISPR Functional Genomics [Collaborative]

Structure-based mechanism for activation of the AAA+ GTPase McrB by the endonuclease McrC.

Nirwan N, Itoh Y, Singh P, ..., Amunts A, Saikrishnan K

Nat Commun 10 (1) 3058 [2019-07-11; online 2019-07-11]

Development, Optimization, and Validation of a High Throughput Screening Assay for Identification of Tat and Type II Secretion Inhibitors of Pseudomonas aeruginosa.

Massai F, Saleeb M, Doruk T, Elofsson M, Forsberg Å

Front. Cell. Infect. Microbiol. 9 (-) 250 [2019-07-10; online 2019-07-10]

Chemical Biology Consortium Sweden (CBCS) [Service]

Optical DNA Mapping Combined with Cas9-Targeted Resistance Gene Identification for Rapid Tracking of Resistance Plasmids in a Neonatal Intensive Care Unit Outbreak.

Bikkarolla SK, Nordberg V, Rajer F, ..., Sandegren L, Westerlund F

MBio 10 (4) - [2019-07-09; online 2019-07-09]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Systems-level immunomonitoring using self-sampled capillary blood

Josyula VS, Lakshmikanth T, Mikes J, Chen Y, Brodin P

- - (-) - [2019-07-08; online 2019-07-08]

Association between Copy Number Variation and Response to Social Skills Training in Autism Spectrum Disorder.

Tammimies K, Li D, Rabkina I, ..., Choque-Olsson N, Bölte S

Sci Rep 9 (1) 9810 [2019-07-08; online 2019-07-08]

Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]

GUESSmyLT: Software to guess the RNA-Seq library type of paired and single end read files

Wik E, Olin H, Haughey C, Klasson L, Dainat J

JOSS 4 (39) 1344 [2019-07-07; online 2019-07-07]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]

Screening a Resource of Recombinant Protein Fragments for Targeted Proteomics.

Edfors F, Forsström B, Vunk H, ..., Schwenk JM, Uhlen M

J. Proteome Res. 18 (7) 2706-2718 [2019-07-05; online 2019-06-07]

Affinity Proteomics Stockholm [Technology development]

Global gene expression analysis in etiolated and de-etiolated seedlings in conifers.

Ranade SS, Delhomme N, García-Gil MR

PLoS ONE 14 (7) e0219272 [2019-07-05; online 2019-07-05]

Bioinformatics Support for Computational Resources [Service] Cryo-EM [Service] Integrated Microscopy Technologies Umeå [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Cryo-EM structure of the activated RET signaling complex reveals the importance of its cysteine-rich domain

Bigalke JM, Aibara S, Roth R, ..., Amunts A, Sandmark J

Sci Adv 5 (7) eaau4202 [2019-07-05; online 2019-07-05]

Comparison of boreal acid sulfate soil microbial communities in oxidative and reductive environments.

Christel S, Yu C, Wu X, ..., Åström ME, Dopson M

Res. Microbiol. 170 (6-7) 288-295 [2019-07-03; online 2019-07-03]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Streptococcus pyogenes evades adaptive immunity through specific IgG glycan hydrolysis.

Naegeli A, Bratanis E, Karlsson C, ..., Malmström J, Collin M

J. Exp. Med. 216 (7) 1615-1629 [2019-07-01; online 2019-05-15]

Serum metabolite profiles of habitual diet: evaluation by 1H-nuclear magnetic resonance analysis.

Lindqvist HM, Rådjursöga M, Malmodin D, Winkvist A, Ellegård L

Am. J. Clin. Nutr. 110 (1) 53-62 [2019-07-01; online 2019-05-28]

Efficient RNA silencing suppression activity of Potato Mop-Top Virus 8K protein is driven by variability and positive selection.

Kalyandurg PB, Tahmasebi A, Vetukuri RR, ..., Grenville-Briggs LJ, Savenkov EI

Virology 535 (-) 111-121 [2019-07-01; online 2019-07-01]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Androgen Receptor Burden and Poor Response to Abiraterone or Enzalutamide in TP53 Wild-Type Metastatic Castration-Resistant Prostate Cancer.

De Laere B, Rajan P, Grönberg H, ..., Lindberg J, CORE-ARV-CTC and ProBIO Investigators

JAMA Oncol 5 (7) 1060-1062 [2019-07-01; online 2019-05-03]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Transcriptome analysis of shade avoidance and shade tolerance in conifers.

Ranade SS, Delhomme N, García-Gil MR

Planta 250 (1) 299-318 [2019-07-00; online 2019-04-26]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Transcriptional and metabolic rewiring of colorectal cancer cells expressing the oncogenic KRASG13D mutation.

Charitou T, Srihari S, Lynn MA, ..., Kolch W, Lynn DJ

Br. J. Cancer 121 (1) 37-50 [2019-07-00; online 2019-05-28]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The molecular pathogenesis of superoxide dismutase 1-linked ALS is promoted by low oxygen tension.

Keskin I, Forsgren E, Lehmann M, ..., Marklund SL, Gilthorpe JD

Acta Neuropathol. 138 (1) 85-101 [2019-07-00; online 2019-03-12]

The cholesterol transfer protein GRAMD1A regulates autophagosome biogenesis.

Laraia L, Friese A, Corkery DP, ..., Wu YW, Waldmann H

Nat. Chem. Biol. 15 (7) 710-720 [2019-07-00; online 2019-06-20]

The autoimmune targets in IPEX are dominated by gut epithelial proteins

Eriksson D, Bacchetta R, Gunnarsson HI, ..., Kämpe O, Landegren N

Journal of Allergy and Clinical Immunology 144 (1) 327-330.e8 [2019-07-00; online 2019-07-00]

TRAF6 function as a novel co-regulator of Wnt3a target genes in prostate cancer

Aripaka K, Gudey SK, Zang G, ..., von Hofsten J, Landström M

EBioMedicine 45 (-) 192-207 [2019-07-00; online 2019-07-00]

Affinity Proteomics Uppsala [Service] PLA and Single Cell Proteomics [Service]

Surface activated polyethylene separator promoting Li+ ion transport in gel polymer electrolytes and cycling stability of Li-metal anode

Qiu Z, Shi L, Wang Z, ..., Zhao Y, Yuan S

Chemical Engineering Journal 368 (-) 321-330 [2019-07-00; online 2019-07-00]

Bioinformatics Support for Computational Resources [Service] Swedish NMR Centre (SNC) [Service]

Structural basis of inhibition of the human serine hydroxymethyltransferase SHMT2 by antifolate drugs.

Scaletti E, Jemth AS, Helleday T, Stenmark P

FEBS Lett. 593 (14) 1863-1873 [2019-07-00; online 2019-06-10]

Specific amino acid substitutions in β strand S2 of FtsZ cause spiraling septation and impair assembly cooperativity in Streptomyces spp.

Sen BC, Wasserstrom S, Findlay K, ..., von Wachenfeldt C, Flärdh K

Mol. Microbiol. 112 (1) 184-198 [2019-07-00; online 2019-05-17]

Cryo-EM [Collaborative] Integrated Microscopy Technologies Umeå

Single cell analysis of autism patient with bi-allelic NRXN1-alpha deletion reveals skewed fate choice in neural progenitors and impaired neuronal functionality

Lam M, Moslem M, Bryois J, ..., Sullivan PF, Falk A

Experimental Cell Research 383 (1) 111469 [2019-07-00; online 2019-07-00]

Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

OPENER Is a Nuclear Envelope and Mitochondria Localized Protein Required for Cell Cycle Progression in Arabidopsis.

Wang W, Zhang X, Niittylä T

Plant Cell 31 (7) 1446-1465 [2019-07-00; online 2019-04-25]

Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification.

Pértille F, Da Silva VH, Johansson AM, ..., Jensen P, Guerrero-Bosagna C

Epigenetics 14 (7) 685-707 [2019-07-00; online 2019-05-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Image Analysis in Digital Pathology: Combining Automated Assessment of Ki67 Staining Quality with Calculation of Ki67 Cell Proliferation Index.

Bengtsson E, Ranefall P

Cytometry A 95 (7) 714-716 [2019-07-00; online 2018-12-03]

BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

Hemostatic Genes Exhibit a High Degree of Allele-Specific Regulation in Liver.

Olsson Lindvall M, Hansson L, Klasson S, ..., Jern C, Stanne TM

Thromb. Haemost. 119 (7) 1072-1083 [2019-07-00; online 2019-04-29]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]

Expanding the phenotypic spectrum of osteogenesis imperfecta type V including heterotopic ossification of muscle origins and attachments.

Clewemar P, Hailer NP, Hailer Y, ..., Ljunggren Ö, Stattin EL

Mol Genet Genomic Med 7 (7) e00723 [2019-07-00; online 2019-05-16]

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Epigenome-wide association study of lung function level and its change.

Imboden M, Wielscher M, Rezwan FI, ..., Jarvis D, Probst-Hensch NM

Eur. Respir. J. 54 (1) - [2019-07-00; online 2019-07-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Development of parallel reaction monitoring assays for cerebrospinal fluid proteins associated with Alzheimer's disease.

Andersson A, Remnestål J, Nellgård B, ..., Nilsson P, Fredolini C

Clin. Chim. Acta 494 (-) 79-93 [2019-07-00; online 2019-03-09]

Affinity Proteomics Stockholm [Technology development]

Confident phylogenetic identification of uncultured prokaryotes through long read amplicon sequencing of the 16S-ITS-23S rRNA operon.

Martijn J, Lind AE, Schön ME, ..., Pettersson OV, Ettema TJG

Environ. Microbiol. 21 (7) 2485-2498 [2019-07-00; online 2019-05-07]

NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Choroid plexus transcriptome and ultrastructure analysis reveals a TLR2-specific chemotaxis signature and cytoskeleton remodeling in leukocyte trafficking.

Mottahedin A, Joakim Ek C, Truvé K, Hagberg H, Mallard C

Brain, Behavior, and Immunity 79 (-) 216-227 [2019-07-00; online 2019-02-26]

Integrated Microscopy Technologies Gothenburg [Service]

BACH1 Stabilization by Antioxidants Stimulates Lung Cancer Metastasis

Wiel C, Le Gal K, Ibrahim MX, ..., Sayin VI, Bergo MO

Cell 178 (2) 330-345.e22 [2019-07-00; online 2019-07-00]

Integrated Microscopy Technologies Gothenburg [Service]

Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods.

Torabi Moghadam B, Etemadikhah M, Rajkowska G, ..., Feuk L, Carlström EL

J Psychiatr Res 114 (-) 41-47 [2019-07-00; online 2019-04-02]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

1H NMR profiling of the 6-OHDA parkinsonian rat brain reveals metabolic alterations and signs of recovery after N-acetylcysteine treatment.

Virel A, Dudka I, Laterveer R, Af Bjerkén S

Molecular and Cellular Neuroscience 98 (-) 131-139 [2019-07-00; online 2019-06-12]

Insights into the Exfoliation Process of V2O5·nH2O Nanosheet Formation Using Real-Time 51V NMR.

Etman AS, Pell AJ, Svedlindh P, ..., Sun J, Bernin D

ACS Omega 4 (6) 10899-10905 [2019-06-30; online 2019-06-24]

Influence of ABO Locus on PFA-100 Collagen-ADP Closure Time Is Not Totally Dependent on the Von Willebrand Factor. Results of a GWAS on GAIT-2 Project Phenotypes.

Pujol-Moix N, Martinez-Perez A, Sabater-Lleal M, ..., Souto JC, Soria JM

Int J Mol Sci 20 (13) - [2019-06-30; online 2019-06-30]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Allelic Variation in Taste Genes Is Associated with Taste and Diet Preferences and Dental Caries.

Eriksson L, Esberg A, Haworth S, Holgerson PL, Johansson I

Nutrients 11 (7) - [2019-06-29; online 2019-06-29]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi.

Ferrante MI, Entrambasaguas L, Johansson M, ..., Montresor M, Godhe A

Genes 10 (7) - [2019-06-28; online 2019-06-28]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Comment on 'AIRE-deficient patients harbor unique high-affinity disease-ameliorating autoantibodies'.

Landegren N, Rosen LB, Freyhult E, ..., Anderson M, Kämpe O

Elife 8 (-) - [2019-06-27; online 2019-06-27]

Autoimmunity and Serology Profiling [Service] Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Pharmacogenomics of statin-related myopathy: Meta-analysis of rare variants from whole-exome sequencing.

Floyd JS, Bloch KM, Brody JA, ..., Alfirevic A, PREDICTION-ADR Consortium and EUDRAGENE

PLoS ONE 14 (6) e0218115 [2019-06-26; online 2019-06-26]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genomic Characterization of the Emerging Pathogen Streptococcus pseudopneumoniae.

Garriss G, Nannapaneni P, Simões AS, ..., de Lencastre H, Henriques-Normark B

MBio 10 (3) - [2019-06-25; online 2019-06-25]

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Genome-wide analysis of dental caries and periodontitis combining clinical and self-reported data.

Shungin D, Haworth S, Divaris K, ..., Timpson NJ, Johansson I

Nat Commun 10 (1) 2773 [2019-06-24; online 2019-06-24]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis.

Lundmark A, Hu YOO, Huss M, ..., Andersson AF, Yucel-Lindberg T

Front. Cell. Infect. Microbiol. 9 (-) 216 [2019-06-21; online 2019-06-21]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A quantitative Streptococcus pyogenes-human protein-protein interaction map reveals localization of opsonizing antibodies.

Happonen L, Hauri S, Svensson Birkedal G, ..., Malmström L, Malmström J

Nat Commun 10 (1) 2727 [2019-06-21; online 2019-06-21]

Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden

Parducci L, Alsos IG, Unneberg P, ..., Slotte T, Wohlfarth B

Front. Ecol. Evol. 7 (-) 189 [2019-06-20; online 2019-06-20]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]

Proteomic profiling of extracellular vesicles reveals additional diagnostic biomarkers for myocardial infarction compared to plasma alone.

Gidlöf O, Evander M, Rezeli M, ..., Laurell T, Erlinge D

Sci Rep 9 (1) 8991 [2019-06-20; online 2019-06-20]

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Peptide-Loaded Cubosomes Functioning as an Antimicrobial Unit against Escherichia coli.

Boge L, Browning KL, Nordström R, ..., Ringstad L, Andersson M

ACS Appl Mater Interfaces 11 (24) 21314-21322 [2019-06-19; online 2019-06-04]

Integrated Microscopy Technologies Gothenburg [Service]

Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA.

Behra PRK, Pettersson BMF, Das S, Dasgupta S, Kirsebom LA

BMC Evol. Biol. 19 (1) 124 [2019-06-18; online 2019-06-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Ouabain-regulated phosphoproteome reveals molecular mechanisms for Na+, K+–ATPase control of cell adhesion, proliferation, and survival

Panizza E, Zhang L, Fontana JM, ..., Lehtiö J, Aperia A

The FASEB Journal - (-) fj.201900445R [2019-06-14; online 2019-06-14]

Bioinformatics Support for Computational Resources [Service] Global Proteomics and Proteogenomics [Technology development] Integrated Microscopy Technologies Stockholm [Collaborative]

Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination.

Dahlberg J, Sun L, Persson Waller K, ..., Agenäs S, Dicksved J

PLoS ONE 14 (6) e0218257 [2019-06-13; online 2019-06-13]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Improved phylogenomic sampling of free-living nematodes enhances resolution of higher-level nematode phylogeny.

Smythe AB, Holovachov O, Kocot KM

BMC Evol. Biol. 19 (1) 121 [2019-06-13; online 2019-06-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Modeling Motor Neuron Resilience in ALS Using Stem Cells.

Allodi I, Nijssen J, Benitez JA, ..., Kiehn O, Hedlund E

Stem Cell Reports 12 (6) 1329-1341 [2019-06-11; online 2019-05-09]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation.

Baião GC, Schneider DI, Miller WJ, Klasson L

BMC Genomics 20 (1) 465 [2019-06-07; online 2019-06-07]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Spatiotemporal structure of cell fate decisions in murine neural crest

Soldatov R, Kaucka M, Kastriti ME, ..., Kharchenko PV, Adameyko I

Science 364 (6444) eaas9536 [2019-06-07; online 2019-06-07]

Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing (ISS) [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles.

Fredolini C, Byström S, Sanchez-Rivera L, ..., Lehtiö J, Schwenk JM

Sci Rep 9 (1) 8324 [2019-06-06; online 2019-06-06]

Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development] Bioinformatics Support for Computational Resources [Service] Global Proteomics and Proteogenomics [Technology development]

Structural Basis for YjbH Adaptor-Mediated Recognition of Transcription Factor Spx.

Awad W, Al-Eryani Y, Ekström S, Logan DT, von Wachenfeldt C

Structure 27 (6) 923-936.e6 [2019-06-04; online 2019-04-11]

Dietary Pattern Specific Protein Biomarkers for Cardiovascular Disease: A Cross-Sectional Study in 2 Independent Cohorts.

Warensjö Lemming E, Byberg L, Stattin K, ..., Wolk A, Michaëlsson K

J Am Heart Assoc 8 (11) e011860 [2019-06-04; online 2019-06-01]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Dysregulated autophagy in muscle precursor cells from humans with type 2 diabetes.

Henriksen TI, Wigge LV, Nielsen J, ..., Sandri M, Scheele C

Sci Rep 9 (1) 8169 [2019-06-03; online 2019-06-03]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Recombinant dermatan sulfate is a potent activator of heparin cofactor II-dependent inhibition of thrombin.

Tykesson E, Maccarana M, Thorsson H, ..., Ellervik U, Westergren-Thorsson G

Glycobiology 29 (6) 446-451 [2019-06-01; online 2019-03-15]

Nitrogen dynamics of decomposing Scots pine needle litter depends on colonizing fungal species.

Baskaran P, Ekblad A, Soucémarianadin LN, ..., Schleucher J, Lindahl BD

FEMS Microbiol. Ecol. 95 (6) - [2019-06-01; online 2019-05-10]

Multiancestry Genome-Wide Association Study of Lipid Levels Incorporating Gene-Alcohol Interactions.

de Vries PS, Brown MR, Bentley AR, ..., Rao DC, Morrison AC

Am. J. Epidemiol. 188 (6) 1033-1054 [2019-06-01; online 2019-01-31]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Integrated epigenomic and transcriptomic analysis reveals TP63 as a novel player in clinically aggressive chronic lymphocytic leukemia.

Papakonstantinou N, Ntoufa S, Tsagiopoulou M, ..., Rosenquist R, Stamatopoulos K

Int. J. Cancer 144 (11) 2695-2706 [2019-06-01; online 2019-01-15]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genome-based epidemiology and antimicrobial resistance determinants of Neisseria gonorrhoeae isolates with decreased susceptibility and resistance to extended-spectrum cephalosporins in Argentina in 2011-16.

Gianecini RA, Golparian D, Zittermann S, ..., Galarza P, Gonococcal Antimicrobial Susceptibility Surveillance Programme-Argentina (GASSP-AR) Working Group

J. Antimicrob. Chemother. 74 (6) 1551-1559 [2019-06-01; online 2019-03-02]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

β-Mannosidosis caused by a novel homozygous intragenic inverted duplication in MANBA.

Blomqvist M, Smeland MF, Lindgren J, ..., Riise Stensland HMF, Asin-Cayuela J

Cold Spring Harb Mol Case Stud 5 (3) a003954 [2019-06-00; online 2019-06-03]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative] Clinical Genomics Stockholm [Service]

Unprecedented reorganization of holocentric chromosomes provides insights into the enigma of lepidopteran chromosome evolution.

Hill J, Rastas P, Hornett EA, ..., Nylin S, Wheat CW

Sci Adv 5 (6) eaau3648 [2019-06-00; online 2019-06-12]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Transcriptomic correlates of electrophysiological and morphological diversity within and across excitatory and inhibitory neuron classes.

Bomkamp C, Tripathy SJ, Bengtsson Gonzales C, ..., Craig AM, Pavlidis P

PLoS Comput. Biol. 15 (6) e1007113 [2019-06-00; online 2019-06-18]

Tracking Microscope Performance: A Workflow to Compare Point Spread Function Evaluations Over Time.

Klemm AH, Thomae AW, Wachal K, Dietzel S

Microsc Microanal 25 (3) 699-704 [2019-06-00; online 2019-02-06]

BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

The effects of male social environment on sperm phenotype and genome integrity.

Silva WTAF, Sáez-Espinosa P, Torijo-Boix S, ..., Gómez-Torres MJ, Immler S

J. Evol. Biol. 32 (6) 535-544 [2019-06-00; online 2019-03-25]

Staphylococcus aureus isolates from nares of orthopaedic patients in Sweden are mupirocin susceptible.

Magnusson C, Stegger M, Hellmark B, Stenmark B, Söderquist B

Infect Dis (Lond) 51 (6) 475-478 [2019-06-00; online 2019-04-15]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Somatic alterations detected in diagnostic prostate biopsies provide an inadequate representation of multifocal prostate cancer.

Kristiansen A, Bergström R, Delahunt B, ..., Egevad L, Lindberg J

Prostate 79 (8) 920-928 [2019-06-00; online 2019-03-25]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Single-Cell RNA Sequencing of the T Helper Cell Response to House Dust Mites Defines a Distinct Gene Expression Signature in Airway Th2 Cells

Tibbitt CA, Stark JM, Martens L, ..., Saeys Y, Coquet JM

Immunity 51 (1) 169-184.e5 [2019-06-00; online 2019-06-00]

Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Mutations in the mitochondrial tryptophanyl-tRNA synthetase cause growth retardation and progressive leukoencephalopathy.

Maffezzini C, Laine I, Dallabona C, ..., Wredenberg A, Wedell A

Mol Genet Genomic Med 7 (6) e654 [2019-06-00; online 2019-03-28]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Lipopolysaccharide-induced alteration of mitochondrial morphology induces a metabolic shift in microglia modulating the inflammatory response in vitro and in vivo.

Nair S, Sobotka KS, Joshi P, ..., Mallard C, Hagberg H

Glia 67 (6) 1047-1061 [2019-06-00; online 2019-01-13]

Integrated Microscopy Technologies Gothenburg [Service]

Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-naïve subjects.

Das J, Verma D, Gustafsson M, Lerm M

Epigenetics 14 (6) 589-601 [2019-06-00; online 2019-04-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic basis of amphibian larval development along a latitudinal gradient: Gene diversity, selection and links with phenotypic variation in transcription factor C/EBP-1.

Meyer-Lucht Y, Luquet E, Jóhannesdóttir F, ..., Höglund J, Laurila A

Mol. Ecol. 28 (11) 2786-2801 [2019-06-00; online 2019-06-07]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Gene fusion involving the insulin-like growth factor 1 receptor in an ALK-negative inflammatory myofibroblastic tumour.

Piarulli G, Puls F, Wängberg B, ..., Arbajian E, Mertens F

Histopathology 74 (7) 1098-1102 [2019-06-00; online 2019-04-24]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Lund [Service]

Further support linking the 22q11.2 microduplication to an increased risk of bladder exstrophy and highlighting LZTR1 as a candidate gene.

Lundin J, Markljung E, Baranowska Körberg I, ..., Lindstrand A, Nordenskjöld A

Mol Genet Genomic Med 7 (6) e666 [2019-06-00; online 2019-05-01]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Detecting selection signatures in three Iranian sheep breeds.

Manzari Z, Mehrabani-Yeganeh H, Nejati-Javaremi A, Moradi MH, Gholizadeh M

Anim Genet 50 (3) 298-302 [2019-06-00; online 2019-03-18]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

DSeg: A Dynamic Image Segmentation Program to Extract Backbone Patterns for Filamentous Bacteria and Hyphae Structures.

Zhang H, Söderholm N, Sandblad L, Wiklund K, Andersson M

Microsc Microanal 25 (3) 711-719 [2019-06-00; online 2019-03-21]

Crystal structure of the catalytic domain of the Weissella oryzae botulinum‐like toxin

Košenina S, Masuyer G, Zhang S, Dong M, Stenmark P

FEBS Lett 593 (12) 1403-1410 [2019-06-00; online 2019-05-31]

Bioinformatics Support for Computational Resources [Service] Protein Science Facility (PSF) [Service]

Circulating mast cell progenitors correlate with reduced lung function in allergic asthma.

Salomonsson M, Malinovschi A, Kalm-Stephens P, ..., Alving K, Hallgren J

Clin Exp Allergy 49 (6) 874-882 [2019-06-00; online 2019-03-21]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Can markers of biological age predict dependency in old age?

Jylhävä J, Jiang M, Foebel AD, Pedersen NL, Hägg S

Biogerontology 20 (3) 321-329 [2019-06-00; online 2019-01-21]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Bax to the future - A novel, high-yielding approach for purification and expression of full-length Bax protein for structural studies.

Dingeldein APG, Lindberg MJ, Ådén J, ..., Stoll R, Gröbner G

Protein Expression and Purification 158 (-) 20-26 [2019-06-00; online 2019-02-06]

Assembly mechanisms of the bacterial cytoskeletal protein FilP.

Javadi A, Söderholm N, Olofsson A, Flärdh K, Sandblad L

Life Sci. Alliance 2 (3) e201800290 [2019-06-00; online 2019-06-26]

Alterations in the metabolism of phospholipids, bile acids and branched-chain amino acids predicts development of type 2 diabetes in black South African women: a prospective cohort study.

Zeng Y, Mtintsilana A, Goedecke JH, ..., Olsson T, Chorell E

Metabolism 95 (-) 57-64 [2019-06-00; online 2019-04-04]

A targeted proteomics approach reveals a serum protein signature as diagnostic biomarker for resectable gastric cancer.

Shen Q, Polom K, Williams C, ..., Roviello F, Kamali-Moghaddam M

EBioMedicine 44 (-) 322-333 [2019-06-00; online 2019-05-28]

Affinity Proteomics Uppsala [Technology development] Bioinformatics Support for Computational Resources [Service] Clinical Biomarkers [Service] Glycoproteomics and MS Proteomics [Collaborative] PLA and Single Cell Proteomics [Technology development]

A novel RAD21 p.(Gln592del) variant expands the clinical description of Cornelia de Lange syndrome type 4 - Review of the literature.

Gudmundsson S, Annerén G, Marcos-Alcalde Í, ..., Gómez-Puertas P, Bondeson ML

Eur J Med Genet 62 (6) 103526 [2019-06-00; online 2018-08-17]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

A catalog of genetic loci associated with kidney function from analyses of a million individuals.

Wuttke M, Li Y, Li M, ..., Köttgen A, Pattaro C

Nat. Genet. 51 (6) 957-972 [2019-06-00; online 2019-05-31]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A Call for Blood—In Human Immunology

Brodin P, Duffy D, Quintana-Murci L

Immunity 50 (6) 1335-1336 [2019-06-00; online 2019-06-00]

Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Technology development]

Plasma protein profiling reveals candidate biomarkers for multiple sclerosis treatment.

Bedri SK, Nilsson OB, Fink K, ..., Grönlund H, Glaser A

PLoS ONE 14 (5) e0217208 [2019-05-29; online 2019-05-29]

A urinary extracellular vesicle microRNA biomarker discovery pipeline; from automated extracellular vesicle enrichment by acoustic trapping to microRNA sequencing.

Ku A, Ravi N, Yang M, ..., Lilja H, Ceder Y

PLoS ONE 14 (5) e0217507 [2019-05-29; online 2019-05-29]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Serum Metabolite Markers of Dementia Through Quantitative NMR Analysis: The Importance of Threonine-Linked Metabolic Pathways.

Figueira J, Adolfsson R, Nordin Adolfsson A, Nyberg L, Öhman A

J. Alzheimers Dis. 69 (3) 763-774 [2019-05-28; online 2019-05-28]

Bioinformatics Support for Computational Resources [Service] Swedish NMR Centre (SNC) [Collaborative]

A phototherapeutic fluorescent β-cyclodextrin branched polymer delivering nitric oxide.

Malanga M, Seggio M, Kirejev V, ..., Ericson MB, Sortino S

Biomater Sci 7 (6) 2272-2276 [2019-05-28; online 2019-04-30]

Integrated Microscopy Technologies Gothenburg [Service]

The viral protein corona directs viral pathogenesis and amyloid aggregation.

Ezzat K, Pernemalm M, Pålsson S, ..., Spetz AL, El Andaloussi S

Nat Commun 10 (1) 2331 [2019-05-27; online 2019-05-27]

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Barcoded Consortium Infections Resolve Cell Type-Dependent Salmonella enterica Serovar Typhimurium Entry Mechanisms.

Di Martino ML, Ek V, Hardt WD, Eriksson J, Sellin ME

MBio 10 (3) - [2019-05-21; online 2019-05-21]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Distinct glycosylation in membrane proteins within neonatal versus adult myocardial tissue.

Contessotto P, Ellis BW, Jin C, ..., Kilcoyne M, Pandit A

Matrix Biol. - (-) - [2019-05-17; online 2019-05-17]

Circulating Levels of Interferon Regulatory Factor-5 Associates With Subgroups of Systemic Lupus Erythematosus Patients.

Idborg H, Zandian A, Ossipova E, ..., Svenungsson E, Jakobsson PJ

Front Immunol 10 (-) 1029 [2019-05-17; online 2019-05-17]

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Ultrasensitive Immunoprofiling of Plasma Extracellular Vesicles Identifies Syndecan-1 as a Potential Tool for Minimally Invasive Diagnosis of Glioma.

Indira Chandran V, Welinder C, Månsson AS, ..., Sundgren PC, Belting M

Clin. Cancer Res. 25 (10) 3115-3127 [2019-05-15; online 2019-01-24]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Technology development] Structural Proteomics [Service]

Biomarkers of blood cadmium and incidence of cardiovascular events in non-smokers: results from a population-based proteomics study.

Borné Y, Fagerberg B, Sallsten G, ..., Barregard L, Engström G

Clin Proteomics 16 (1) 21 [2019-05-15; online 2019-05-15]

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Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter-gatherers in Scandinavia.

Kashuba N, Kırdök E, Damlien H, ..., Persson P, Götherström A

Commun Biol 2 (-) 185 [2019-05-15; online 2019-05-15]

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Mic60 exhibits a coordinated clustered distribution along and across yeast and mammalian mitochondria.

Stoldt S, Stephan T, Jans DC, ..., Hell SW, Jakobs S

Proc. Natl. Acad. Sci. U.S.A. 116 (20) 9853-9858 [2019-05-14; online 2019-04-26]

Integrated Microscopy Technologies Stockholm [Collaborative]

Metabolic profiling of zebrafish embryo development from blastula period to early larval stages.

Dhillon SS, Torell F, Donten M, ..., Trygg J, Lundstedt T

PLoS ONE 14 (5) e0213661 [2019-05-14; online 2019-05-14]

Genetic variation in CADM2 as a link between psychological traits and obesity.

Morris J, Bailey MES, Baldassarre D, ..., Smith DJ, Strawbridge RJ

Sci Rep 9 (1) 7339 [2019-05-14; online 2019-05-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Adult Neural Progenitor Cells Transplanted into Spinal Cord Injury Differentiate into Oligodendrocytes, Enhance Myelination, and Contribute to Recovery.

Sankavaram SR, Hakim R, Covacu R, ..., Svensson M, Brundin L

Stem Cell Reports 12 (5) 950-966 [2019-05-14; online 2019-04-25]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Automated Cell Processing for Mass Cytometry Experiments.

Mikes J, Olin A, Lakshmikanth T, Chen Y, Brodin P

Methods Mol. Biol. 1989 (-) 111-123 [2019-05-12; online 2019-05-12]

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Cardiovascular organ damage in type 2 diabetes mellitus: the role of lipids and inflammation.

Kozakova M, Morizzo C, Goncalves I, ..., Nilsson J, Palombo C

Cardiovasc Diabetol 18 (1) 61 [2019-05-10; online 2019-05-10]

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Wnt5a is a TLR2/4-ligand that induces tolerance in human myeloid cells.

Mehmeti M, Bergenfelz C, Källberg E, ..., André I, Leandersson K

Commun Biol 2 (1) 176 [2019-05-09; online 2019-05-09]

Protic Ionic Liquids Based on the Alkyl-Imidazolium Cation: Effect of the Alkyl Chain Length on Structure and Dynamics.

Abdurrokhman I, Elamin K, Danyliv O, ..., Swenson J, Martinelli A

J. Phys. Chem. B 123 (18) 4044-4054 [2019-05-09; online 2019-04-30]

Periodontal Health and Oral Microbiota in Patients with Rheumatoid Arthritis.

Eriksson K, Fei G, Lundmark A, ..., Jansson L, Yucel-Lindberg T

J Clin Med 8 (5) - [2019-05-08; online 2019-05-08]

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Shared Genetic Risk Factors Across Carbamazepine-Induced Hypersensitivity Reactions.

Nicoletti P, Barrett S, McEvoy L, ..., Alfirevic A, Pirmohamed M

Clin. Pharmacol. Ther. - (-) - [2019-05-07; online 2019-05-07]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetical Genomics of Tonic Immobility in the Chicken.

Fogelholm J, Inkabi S, Höglund A, ..., Henriksen R, Wright D

Genes 10 (5) - [2019-05-07; online 2019-05-07]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Mass Cytometry Identifies Distinct Subsets of Regulatory T Cells and Natural Killer Cells Associated With High Risk for Type 1 Diabetes.

Barcenilla H, Åkerman L, Pihl M, Ludvigsson J, Casas R

Front Immunol 10 (-) 982 [2019-05-03; online 2019-05-03]

Cellular Immunomonitoring [Service]

Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus.

Abramova A, Alm Rosenblad M, Blomberg A, Larsson TA

PLoS ONE 14 (5) e0216294 [2019-05-02; online 2019-05-02]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

SpotLight Proteomics-A IgG-Enrichment Phenotype Profiling Approach with Clinical Implications.

Lundström SL, Heyder T, Wiklundh E, ..., Grunewald J, Zubarev RA

Int J Mol Sci 20 (9) 2157 [2019-05-01; online 2019-05-01]

Software engineering for scientific big data analysis.

Grüning BA, Lampa S, Vaudel M, Blankenberg D

Gigascience 8 (5) - [2019-05-01; online 2019-05-24]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines.

Lampa S, Dahlö M, Alvarsson J, Spjuth O

Gigascience 8 (5) - [2019-05-01; online 2019-04-28]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Technology development]

Prompt apoptotic response to high glucose in SGLT-expressing renal cells.

Nilsson LM, Zhang L, Bondar A, ..., Scott L, Aperia A

Am. J. Physiol. Renal Physiol. 316 (5) F1078-F1089 [2019-05-01; online 2019-03-13]

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Identification of a non-canonical chondroitin sulfate linkage region trisaccharide.

Persson A, Nilsson J, Vorontsov E, Noborn F, Larson G

Glycobiology 29 (5) 366-371 [2019-05-01; online 2019-03-03]

How Linked Selection Shapes the Diversity Landscape in Ficedula Flycatchers

Rettelbach A, Nater A, Ellegren H

Genetics 212 (1) 277-285 [2019-05-01; online 2019-03-14]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise.

Prost S, Armstrong EE, Nylander J, ..., Ericson PGP, Irestedt M

Gigascience 8 (5) - [2019-05-01; online 2019-01-29]

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Chromosomal genome assembly of the ethanol production strain CBS 11270 indicates a highly dynamic genome structure in the yeast species Brettanomyces bruxellensis.

Tiukova IA, Pettersson ME, Hoeppner MP, ..., Söderberg J, Passoth V

PLoS ONE 14 (5) e0215077 [2019-05-01; online 2019-05-01]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Spatial proteomics: a powerful discovery tool for cell biology.

Lundberg E, Borner GHH

Nat Rev Mol Cell Biol 20 (5) 285-302 [2019-05-00; online 2019-01-20]

Pervasive hybridizations in the history of wheat relatives.

Glémin S, Scornavacca C, Dainat J, ..., David J, Ranwez V

Sci Adv 5 (5) eaav9188 [2019-05-00; online 2019-05-01]

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Parental Education and Genetics of BMI from Infancy to Old Age: A Pooled Analysis of 29 Twin Cohorts.

Silventoinen K, Jelenkovic A, Latvala A, ..., Sørensen TIA, Kaprio J

Obesity (Silver Spring) 27 (5) 855-865 [2019-05-00; online 2019-04-05]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PKCζ facilitates lymphatic metastatic spread of prostate cancer cells in a mice xenograft model

Zang G, Mu Y, Gao L, Bergh A, Landström M

Oncogene 38 (22) 4215-4231 [2019-05-00; online 2019-01-31]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Molecular orientation distribution of regenerated cellulose fibers investigated with rotor synchronized solid state NMR spectroscopy

Svenningsson L, Sparrman T, Bialik E, Bernin D, Nordstierna L

Cellulose 26 (8) 4681-4692 [2019-05-00; online 2019-04-17]

Mineralogical investigations of Jamaican hematite-rich and goethite-rich bauxites using XRD and solid state 27Al and 31P MAS NMR spectroscopy

Young NJ, Coley MD, Greenaway AM

Journal of Geochemical Exploration 200 (-) 54-76 [2019-05-00; online 2019-05-00]

Investigation of human apoB48 metabolism using a new, integrated non-steady-state model of apoB48 and apoB100 kinetics.

Björnson E, Packard CJ, Adiels M, ..., Taskinen MR, Borén J

J. Intern. Med. 285 (5) 562-577 [2019-05-00; online 2019-03-12]

Interferon signature in patients with STAT1 gain-of-function mutation is epigenetically determined.

Kaleviste E, Saare M, Leahy TR, ..., Peterson P, Kisand K

Eur. J. Immunol. 49 (5) 790-800 [2019-05-00; online 2019-03-07]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Interannual variation in seasonal diatom sedimentation reveals the importance of late winter processes and their timing for sediment signal formation

Maier DB, Diehl S, Bigler C

Limnol Oceanogr 64 (3) 1186-1199 [2019-05-00; online 2019-01-31]

Helicobacter suis infection alters glycosylation and decreases the pathogen growth inhibiting effect and binding avidity of gastric mucins.

Padra M, Adamczyk B, Flahou B, ..., Karlsson NG, Lindén SK

Mucosal Immunol 12 (3) 784-794 [2019-05-00; online 2019-03-07]

Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data.

Warmuth VM, Ellegren H

Mol Ecol Resour 19 (3) 586-596 [2019-05-00; online 2019-04-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Gene expression profile of extraocular muscles following resection strabismus surgery.

Rodríguez MA, Sandgren Hochhard K, Vicente A, Liu JX, Pedrosa Domellöf F

Exp. Eye Res. 182 (-) 182-193 [2019-05-00; online 2019-04-03]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers.

Nadachowska-Brzyska K, Burri R, Ellegren H

Mol. Ecol. 28 (9) 2290-2304 [2019-05-00; online 2019-05-29]

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FET family fusion oncoproteins target the SWI/SNF chromatin remodeling complex.

Lindén M, Thomsen C, Grundevik P, ..., Ståhlberg A, Åman P

EMBO Rep. 20 (5) - [2019-05-00; online 2019-04-08]

Exome sequencing in 51 early onset non-familial CRC cases.

Thutkawkorapin J, Lindblom A, Tham E

Mol Genet Genomic Med 7 (5) e605 [2019-05-00; online 2019-02-27]

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Endocytosis, intracellular fate, accumulation, and agglomeration of titanium dioxide (TiO 2) nanoparticles in the rainbow trout liver cell line RTL-W1.

Lammel T, Mackevica A, Johansson BR, Sturve J

Environ Sci Pollut Res 26 (15) 15354-15372 [2019-05-00; online 2019-03-31]

Integrated Microscopy Technologies Gothenburg [Service]

Elevated circulating effector memory T cells but similar levels of regulatory T cells in patients with type 2 diabetes mellitus and cardiovascular disease.

Rattik S, Engelbertsen D, Wigren M, ..., Nilsson J, Björkbacka H

Diabetes and Vascular Disease Research 16 (3) 270-280 [2019-05-00; online 2018-12-21]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Dynamic pH-induced conformational changes of the PsbO protein in the fluctuating acidity of the thylakoid lumen.

Carius AB, Rogne P, Duchoslav M, ..., Samuelsson G, Shutova T

Physiol Plantarum 166 (1) 288-299 [2019-05-00; online 2019-03-18]

Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds.

Xu L, Auer G, Peona V, ..., Irestedt M, Zhou Q

Nat Ecol Evol 3 (5) 834-844 [2019-05-00; online 2019-04-01]

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Comparisons of analysis of fatty acid methyl ester (FAME) of microalgae by chromatographic techniques

Niemi C, Lage S, Gentili FG

Algal Research 39 (-) 101449 [2019-05-00; online 2019-05-00]

Axonemal doublet microtubules can split into two complete singlets in human sperm flagellum tips.

Zabeo D, Croft JT, Höög JL

FEBS Lett. 593 (9) 892-902 [2019-05-00; online 2019-04-19]

Asthma and affective traits in adults: a genetically informative study.

Lehto K, Pedersen NL, Almqvist C, Lu Y, Brew BK

Eur. Respir. J. 53 (5) 1802142 [2019-05-00; online 2019-05-30]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

An Atlas of Vagal Sensory Neurons and Their Molecular Specialization

Kupari J, Häring M, Agirre E, Castelo-Branco G, Ernfors P

Cell Rep 27 (8) 2508-2523.e4 [2019-05-00; online 2019-05-00]

Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

AdipoR1 and AdipoR2 maintain membrane fluidity in most human cell types and independently of adiponectin.

Ruiz M, Ståhlman M, Borén J, Pilon M

J. Lipid Res. 60 (5) 995-1004 [2019-05-00; online 2019-03-19]

Integrated Microscopy Technologies Gothenburg [Service]

Invasive cervical tumors with high and low HPV titer represent molecular subgroups with different disease etiology.

Cui T, Enroth S, Ameur A, ..., Lindquist D, Gyllensten U

Carcinogenesis 40 (2) 269-278 [2019-04-29; online 2019-01-01]

NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Pyroglutamation of amyloid-βx-42 (Aβx-42) followed by Aβ1-40 deposition underlies plaque polymorphism in progressing Alzheimer's disease pathology.

Michno W, Nyström S, Wehrli P, ..., Zetterberg H, Hanrieder J

J. Biol. Chem. 294 (17) 6719-6732 [2019-04-26; online 2019-02-27]

Integrated Microscopy Technologies Gothenburg [Service]

Preeclampsia is Associated with Sex-Specific Transcriptional and Proteomic Changes in Fetal Erythroid Cells.

Masoumi Z, Maes GE, Herten K, ..., Familari M, Hansson SR

Int J Mol Sci 20 (8) - [2019-04-25; online 2019-04-25]

Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient

Helgadottir HT, Lundin P, Wallén Arzt E, ..., Graff C, Eriksson M

Hum Mol Genet 28 (16) 2675-2685 [2019-04-24; online 2019-04-24]

Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Spatial and temporal localization of immune transcripts defines hallmarks and diversity in the tuberculosis granuloma.

Carow B, Hauling T, Qian X, ..., Nilsson M, Rottenberg ME

Nat Commun 10 (1) 1823 [2019-04-23; online 2019-04-23]

In Situ Sequencing (ISS) [Collaborative]

PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination.

Falcão AM, Meijer M, Scaglione A, ..., Casaccia P, Castelo-Branco G

Cell Rep 27 (4) 1090-1102.e10 [2019-04-23; online 2019-04-25]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

EnsembleCNV: an ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data.

Zhang Z, Cheng H, Hong X, ..., Wang X, Hao K

Nucleic Acids Res. 47 (7) e39 [2019-04-23; online 2019-02-06]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Cobalt-doped hematite thin films for electrocatalytic water oxidation in highly acidic media.

Kwong WL, Lee CC, Shchukarev A, Messinger J

Chem. Commun. (Camb.) 55 (34) 5017-5020 [2019-04-23; online 2019-04-11]

Integrated Microscopy Technologies Umeå [Collaborative]

Mebendazole-induced M1 polarisation of THP-1 macrophages may involve DYRK1B inhibition.

Blom K, Rubin J, Berglund M, ..., Nygren P, Larsson R

BMC Res Notes 12 (1) 234 [2019-04-22; online 2019-04-22]

The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement

Abramova A, Lind U, Blomberg A, Rosenblad MA

Biofouling 35 (4) 416-428 [2019-04-21; online 2019-05-30]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A Genome-Wide Association Study of Bisphosphonate-Associated Atypical Femoral Fracture.

Kharazmi M, Michaëlsson K, Schilcher J, ..., Wadelius M, Hallberg P

Calcif. Tissue Int. - (-) - [2019-04-20; online 2019-04-20]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

RNA Sequencing Provides Novel Insights into the Transcriptome of Aldosterone Producing Adenomas.

Backman S, Åkerström T, Maharjan R, ..., Hellman P, Björklund P

Sci Rep 9 (1) 6269 [2019-04-18; online 2019-04-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Greedy de novo motif discovery to construct motif repositories for bacterial proteomes.

Khakzad H, Malmström J, Malmström L

BMC Bioinformatics 20 (Suppl 4) 141 [2019-04-18; online 2019-04-18]

A proton T1-nuclear magnetic resonance dispersion study of water motion in snowflakes and hexagonal ice

Westlund PO

Molecular Physics 117 (7-8) 960-967 [2019-04-18; online 2018-10-30]

The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch.

Boman J, Frankl-Vilches C, da Silva Dos Santos M, ..., Gahr M, Suh A

Genes 10 (4) - [2019-04-13; online 2019-04-13]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Neutrophil extracellular traps in the central nervous system hinder bacterial clearance during pneumococcal meningitis.

Mohanty T, Fisher J, Bakochi A, ..., Bentzer P, Linder A

Nat Commun 10 (1) 1667 [2019-04-10; online 2019-04-10]

Improved predictions of time-dependent drug-drug interactions by determination of cytosolic drug concentrations.

Filppula AM, Parvizi R, Mateus A, Baranczewski P, Artursson P

Sci Rep 9 (1) 5850 [2019-04-10; online 2019-04-10]

Drug Discovery and Development (DDD) [Technology development]

A multi-ancestry genome-wide study incorporating gene-smoking interactions identifies multiple new loci for pulse pressure and mean arterial pressure.

Sung YJ, de Las Fuentes L, Winkler TW, ..., Rao DC, Morrison AC

Hum. Mol. Genet. - (-) - [2019-04-10; online 2019-04-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

SQSTM1/p62-Directed Metabolic Reprogramming Is Essential for Normal Neurodifferentiation.

Calvo-Garrido J, Maffezzini C, Schober FA, ..., Freyer C, Wredenberg A

Stem Cell Reports 12 (4) 696-711 [2019-04-09; online 2019-02-28]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model.

Lillie M, Honaker CF, Siegel PB, Carlborg Ö

G3 (Bethesda) 9 (4) 1165-1173 [2019-04-09; online 2019-04-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The 1H NMR serum metabolomics response to a two meal challenge: a cross-over dietary intervention study in healthy human volunteers.

Rådjursöga M, Lindqvist HM, Pedersen A, ..., Ellegård L, Winkvist A

Nutr J 18 (1) 25 [2019-04-08; online 2019-04-08]

SAMURAI (Solid-phase Assisted Mutagenesis by Uracil Restriction for Accurate Integration) for antibody affinity maturation and paratope mapping.

Hu FJ, Lundqvist M, Uhlén M, Rockberg J

Nucleic Acids Res. 47 (6) e34 [2019-04-08; online 2019-02-05]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Breast cancer quantitative proteome and proteogenomic landscape.

Johansson HJ, Socciarelli F, Vacanti NM, ..., Børresen-Dale AL, Lehtiö J

Nat Commun 10 (1) 1600 [2019-04-08; online 2019-04-08]

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A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds.

Wallberg A, Bunikis I, Pettersson OV, ..., Robinson GE, Webster MT

BMC Genomics 20 (1) 275 [2019-04-08; online 2019-04-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Spatiotemporal dynamics of molecular pathology in amyotrophic lateral sclerosis.

Maniatis S, Äijö T, Vickovic S, ..., Bonneau R, Phatnani H

Science 364 (6435) 89-93 [2019-04-05; online 2019-04-06]

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Pyridine-Fused 2-Pyridones via Povarov and A 3 Reactions: Rapid Generation of Highly Functionalized Tricyclic Heterocycles Capable of Amyloid Fibril Binding.

Singh P, Adolfsson DE, Ådén J, ..., Olofsson A, Almqvist F

J. Org. Chem. 84 (7) 3887-3903 [2019-04-05; online 2019-03-20]

Cryo-EM [Service] Swedish NMR Centre (SNC) [Service]

High-Quality Library Preparation for NGS-Based Immunoglobulin Germline Gene Inference and Repertoire Expression Analysis.

Vázquez Bernat N, Corcoran M, Hardt U, ..., Martin M, Karlsson Hedestam GB

Front Immunol 10 (-) 660 [2019-04-05; online 2019-04-05]

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Exploring the Arctic Charr Intestinal Glycome: Evidence of Increased N-Glycolylneuraminic Acid Levels and Changed Host-Pathogen Interactions in Response to Inflammation.

Venkatakrishnan V, Padra JT, Sundh H, ..., Karlsson NG, Lindén SK

J. Proteome Res. 18 (4) 1760-1773 [2019-04-05; online 2019-03-19]

Osteoporosis and skeletal dysplasia caused by pathogenic variants in SGMS2.

Pekkinen M, Terhal PA, Botto LD, ..., Holthuis JC, Mäkitie O

JCI Insight 4 (7) - [2019-04-04; online 2019-04-04]

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Molecular Characterization and Comparative Genomics of Clinical Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains in Sweden.

Bai X, Zhang J, Ambikan A, ..., Xiong Y, Matussek A

Sci Rep 9 (1) 5619 [2019-04-04; online 2019-04-04]

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Genetic Architectures of Childhood- and Adult-Onset Asthma Are Partly Distinct.

Ferreira MAR, Mathur R, Vonk JM, ..., Koppelman GH, Almqvist C

Am. J. Hum. Genet. 104 (4) 665-684 [2019-04-04; online 2019-03-28]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A TetR-family transcription factor regulates fatty acid metabolism in the archaeal model organism Sulfolobus acidocaldarius.

Wang K, Sybers D, Maklad HR, ..., Lindås AC, Peeters E

Nat Commun 10 (1) 1542 [2019-04-04; online 2019-04-04]

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Silica-based diffusion probes for use in FRAP and NMR-diffusometry

Pihl M, Kolman K, Lotsari A, ..., Lorén N, Bordes R

Journal of Dispersion Science and Technology 40 (4) 555-562 [2019-04-03; online 2018-10-08]

Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia.

Yang M, Vesterlund M, Siavelis I, ..., Lehtiö J, Paulsson K

Nat Commun 10 (1) 1519 [2019-04-03; online 2019-04-03]

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Mesenchymal stem cells transplanted into spinal cord injury adopt immune cell-like characteristics.

Hakim R, Covacu R, Zachariadis V, ..., Brundin L, Svensson M

Stem Cell Res Ther 10 (1) 115 [2019-04-03; online 2019-04-03]

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A Focused DNA-Encoded Chemical Library for the Discovery of Inhibitors of NAD+-Dependent Enzymes.

Yuen LH, Dana S, Liu Y, ..., Schüler H, Franzini RM

J. Am. Chem. Soc. 141 (13) 5169-5181 [2019-04-03; online 2019-03-19]

B cell profiling in malaria reveals expansion and remodelling of CD11c+ B cell subsets.

Sundling C, Rönnberg C, Yman V, ..., Persson KE, Färnert A

JCI Insight 5 (-) - [2019-04-02; online 2019-04-02]

Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Collaborative]

Structural basis for adPEO-causing mutations in the mitochondrial TWINKLE helicase.

Peter B, Farge G, Pardo-Hernandez C, Tångefjord S, Falkenberg M

Hum. Mol. Genet. 28 (7) 1090-1099 [2019-04-01; online 2018-11-30]

Integrated Microscopy Technologies Gothenburg [Service]

The biology of the cell - insights from mass cytometry.

Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Technology development]

FEBS J. 286 (8) 1514-1522 [2019-04-00; online 2018-11-26]

Successful optimization of reconstruction parameters in structured illumination microscopy – A practical guide

Karras C, Smedh M, Förster R, ..., Fernandez-Rodriguez J, Heintzmann R

Optics Communications 436 (-) 69-75 [2019-04-00; online 2019-04-00]

Integrated Microscopy Technologies Gothenburg [Service]

Selection for longer lived sperm within ejaculate reduces reproductive ageing in offspring.

Alavioon G, Cabrera Garcia A, LeChatelier M, Maklakov AA, Immler S

Evolution Letters 3 (2) 198-206 [2019-04-00; online 2019-02-14]

Post-glacial colonization routes coincide with a life-history breakpoint along a latitudinal gradient.

Luquet E, Rödin Mörch P, Cortázar-Chinarro M, ..., Höglund J, Laurila A

J. Evol. Biol. 32 (4) 356-368 [2019-04-00; online 2019-02-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Placing RNA in context and space - methods for spatially resolved transcriptomics.

Strell C, Hilscher MM, Laxman N, ..., Yokota C, Nilsson M

FEBS J. 286 (8) 1468-1481 [2019-04-00; online 2018-03-31]

In Situ Sequencing (ISS) [Technology development]

Outbreak of Methicillin-resistant Staphylococcus aureus in a Hospital Center for Children's and Women's Health in a Swedish County.

Gideskog M, Melhus Å

APMIS 127 (4) 181-186 [2019-04-00; online 2019-03-26]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Novel fibronectin mutations and expansion of the phenotype in spondylometaphyseal dysplasia with "corner fractures".

Costantini A, Valta H, Baratang NV, ..., Mäkitie O, Campeau PM

Bone 121 (-) 163-171 [2019-04-00; online 2018-12-30]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Nitrogen utilization during germination of somatic embryos of Norway spruce: revealing the importance of supplied glutamine for nitrogen metabolism

Carlsson J, Egertsdotter U, Ganeteg U, Svennerstam H

Trees 33 (2) 383-394 [2019-04-00; online 2018-11-09]

Mutation patterns in a population-based non-small cell lung cancer cohort and prognostic impact of concomitant mutations in KRAS and TP53 or STK11.

La Fleur L, Falk-Sörqvist E, Smeds P, ..., Moens L, Botling J

Lung Cancer 130 (-) 50-58 [2019-04-00; online 2019-01-09]

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Multi-ancestry genome-wide gene-smoking interaction study of 387,272 individuals identifies new loci associated with serum lipids.

Bentley AR, Sung YJ, Brown MR, ..., Rotimi CN, Cupples LA

Nat. Genet. 51 (4) 636-648 [2019-04-00; online 2019-03-29]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Increased vascular endothelial growth factor D is associated with atrial fibrillation and ischaemic stroke.

Berntsson J, Smith JG, Johnson LSB, ..., Nilsson J, Engström G

Heart 105 (7) 553-558 [2019-04-00; online 2018-10-16]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Increase of invasive meningococcal serogroup W disease in Europe, 2013 to 2017.

Krone M, Gray S, Abad R, ..., Vogel U, Borrow R

Euro Surveill. 24 (14) - [2019-04-00; online 2019-04-11]

Clinical Genomics [Collaborative] Clinical Genomics Örebro [Collaborative]

Gain-of-function mutation of microRNA-140 in human skeletal dysplasia.

Grigelioniene G, Suzuki HI, Taylan F, ..., Sharp PA, Kobayashi T

Nat. Med. 25 (4) 583-590 [2019-04-00; online 2019-02-25]

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Dynamics of Resistance Plasmids in Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae during Postinfection Colonization.

Brolund A, Rajer F, Giske CG, ..., Titelman E, Sandegren L

Antimicrob. Agents Chemother. 63 (4) - [2019-04-00; online 2019-03-27]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Deep Learning in Image Cytometry: A Review.

Gupta A, Harrison PJ, Wieslander H, ..., Sintorn IM, Wählby C

Cytometry A 95 (4) 366-380 [2019-04-00; online 2018-12-19]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Backbone 1H, 13C, and 15N resonance assignments of BoMan26A, a β-mannanase of the glycoside hydrolase family 26 from the human gut bacterium Bacteroides ovatus.

Wernersson S, Bågenholm V, Persson C, ..., Stålbrand H, Akke M

Biomol NMR Assign 13 (1) 213-218 [2019-04-00; online 2019-02-07]

Univariate and classification analysis reveals potential diagnostic biomarkers for early stage ovarian cancer Type 1 and Type 2.

Marcišauskas S, Ulfenborg B, Kristjansdottir B, Waldemarson S, Sundfeldt K

J Proteomics 196 (-) 57-68 [2019-03-30; online 2019-01-30]

A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis

Rentoft M, Svensson D, Sjödin A, ..., Melin BS, Johansson E

PLoS ONE 14 (3) e0213350 [2019-03-27; online 2019-03-27]

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Selective auxin agonists induce specific AUX/IAA protein degradation to modulate plant development.

Vain T, Raggi S, Ferro N, ..., Pauwels L, Robert S

Proc. Natl. Acad. Sci. U.S.A. 116 (13) 6463-6472 [2019-03-26; online 2019-03-08]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Swedish Metabolomics Centre (SMC) [Service]

Improved survival prognostication of node-positive malignant melanoma patients utilizing shotgun proteomics guided by histopathological characterization and genomic data.

Betancourt LH, Pawłowski K, Eriksson J, ..., Jönsson G, Marko-Varga G

Sci Rep 9 (1) 5154 [2019-03-26; online 2019-03-26]

High Serum sCD40 and a Distinct Colonic T Cell Profile in Ulcerative Colitis Associated With Primary Sclerosing Cholangitis.

Lampinen M, Vessby J, Fredricsson A, ..., Rorsman F, Carlson M

J Crohns Colitis 13 (3) 341-350 [2019-03-26; online 2018-11-02]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Corticosteroids protect infected cells against mycobacterial killing in vitro.

Tükenmez H, Edström I, Kalsum S, ..., Elofsson M, Larsson C

Biochem. Biophys. Res. Commun. 511 (1) 117-121 [2019-03-26; online 2019-02-14]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Swedish NMR Centre (SNC) [Service]

Thickness determines microbial community structure and function in nitrifying biofilms via deterministic assembly.

Suarez C, Piculell M, Modin O, ..., Persson F, Hermansson M

Sci Rep 9 (1) 5110 [2019-03-25; online 2019-03-25]

Integrated Microscopy Technologies Gothenburg [Service]

A novel human in vitro papillomavirus type 16 positive tonsil cancer cell line with high sensitivity to radiation and cisplatin.

Forslund O, Sugiyama N, Wu C, ..., Wennerberg J, Ekblad L

BMC Cancer 19 (1) 265 [2019-03-25; online 2019-03-25]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Time-Resolved Study of Silicate Slag Formation During Combustion of Wheat Straw Pellets

Strandberg A, Skoglund N, Thyrel M, ..., Broström M, Backman R

Energy Fuels 33 (3) 2308-2318 [2019-03-21; online 2019-02-21]

Subsequent Event Risk in Individuals with Established Coronary Heart Disease: Design and Rationale of the GENIUS-CHD Consortium.

Patel R, Tragante V, Schmidt AF, ..., Hingorani AD, Asselbergs FW

Circ Genom Precis Med - (-) - [2019-03-21; online 2019-03-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Helicase/SUMO-targeted ubiquitin ligase Uls1 interacts with the Holliday junction resolvase Yen1.

Bauer SL, Chen J, Åström SU

PLoS ONE 14 (3) e0214102 [2019-03-21; online 2019-03-21]

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Association of Chromosome 9p21 with Subsequent Coronary Heart Disease Events: A GENIUS-CHD Study of Individual Participant Data.

Patel RS, Schmidt AF, Tragante V, ..., Hingorani AD, Asselbergs FW

Circ Genom Precis Med - (-) - [2019-03-21; online 2019-03-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Characterization of Double Leached Waelz Oxide for Identification of Fluoride Mineral

Sar S, Sundqvist Ökvist L, Sparrman T, Engström F, Samuelsson C

Metals 9 (3) 361 [2019-03-20; online 2019-03-20]

Current Status and Future Prospects of Clinically Exploiting Cancer-specific Metabolism-Why Is Tumor Metabolism Not More Extensively Translated into Clinical Targets and Biomarkers?

Muthu M, Nordström A

Int J Mol Sci 20 (6) 1385 [2019-03-19; online 2019-03-19]

An ABCA4 loss-of-function mutation causes a canine form of Stargardt disease

Mäkeläinen S, Gòdia M, Hellsand M, ..., Andersson G, Bergström TF

PLoS Genet. 15 (3) e1007873 [2019-03-19; online 2019-03-19]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Regulatory Diversification of INDEHISCENT in the Capsella Genus Directs Variation in Fruit Morphology.

Dong Y, Jantzen F, Stacey N, ..., Ljung K, Østergaard L

Curr. Biol. 29 (6) 1038-1046.e4 [2019-03-18; online 2019-02-28]

Pax6 and KDM5C co-occupy a subset of developmentally critical genes including Notch signaling regulators in neural progenitors

Gaudenzi G, Dethlefsen O, Walfridsson J, Hermanson O

- - (-) - [2019-03-16; online 2019-03-16]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Interaction of toluene with polar stationary phases under conditions typical of hydrophilic interaction chromatography probed by saturation transfer difference nuclear magnetic resonance spectroscopy.

Shamshir A, Dinh NP, Jonsson T, ..., Ashiq MJ, Irgum K

Journal of Chromatography A 1588 (-) 58-67 [2019-03-15; online 2018-12-13]

Extended insight into the Mycobacterium chelonae-abscessus complex through whole genome sequencing of Mycobacterium salmoniphilum outbreak and Mycobacterium salmoniphilum-like strains.

Behra PRK, Das S, Pettersson BMF, ..., Ennis DG, Kirsebom LA

Sci Rep 9 (1) 4603 [2019-03-14; online 2019-03-14]

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The Interactome of Palmitoyl-Protein Thioesterase 1 (PPT1) Affects Neuronal Morphology and Function.

Sapir T, Segal M, Grigoryan G, ..., Segal M, Reiner O

Front Cell Neurosci 13 (-) 92 [2019-03-13; online 2019-03-13]

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Surveillance of cell wall diffusion barrier integrity modulates water and solute transport in plants.

Wang P, Calvo-Polanco M, Reyt G, ..., Boursiac Y, Salt DE

Sci Rep 9 (1) 4227 [2019-03-12; online 2019-03-12]

Ancient Mitochondrial Genomes Reveal the Absence of Maternal Kinship in the Burials of Çatalhöyük People and Their Genetic Affinities.

Chyleński M, Ehler E, Somel M, ..., Juras A, Marciniak A

Genes 10 (3) - [2019-03-11; online 2019-03-11]

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In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation.

Wu C, Klaesson A, Buskas J, ..., Söderberg O, Wolf JBW

J Exp Biol 222 (Pt 5) jeb194431 [2019-03-08; online 2019-03-08]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support for Computational Resources [Service]

Polymer gels with tunable ionic Seebeck coefficient for ultra-sensitive printed thermopiles.

Zhao D, Martinelli A, Willfahrt A, ..., Fabiano S, Crispin X

Nat Commun 10 (1) 1093 [2019-03-06; online 2019-03-06]

Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development.

Cheng S, Pei Y, He L, ..., Jing N, Deng Q

Cell Rep 26 (10) 2593-2607.e3 [2019-03-05; online 2019-03-07]

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A microfluidic platform towards automated multiplexed in situ sequencing.

Maïno N, Hauling T, Cappi G, ..., Dupouy DG, Nilsson M

Sci Rep 9 (1) 3542 [2019-03-05; online 2019-03-05]

In Situ Sequencing (ISS) [Technology development]

Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida.

Stairs CW, Kokla A, Ástvaldsson Á, ..., Svärd S, Ettema TJG

BMC Biol. 17 (1) 19 [2019-03-01; online 2019-03-01]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Association of Genetic Risk Factors for Psychiatric Disorders and Traits of These Disorders in a Swedish Population Twin Sample.

Taylor MJ, Martin J, Lu Y, ..., Larsson H, Lichtenstein P

JAMA Psychiatry 76 (3) 280-289 [2019-03-01; online 2018-12-20]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Whole genome sequencing of consanguineous families reveals novel pathogenic variants in intellectual disability.

Thuresson AC, Soussi Zander C, Zhao JJ, ..., Öhrner Y, Feuk L

Clin. Genet. 95 (3) 436-439 [2019-03-00; online 2018-12-07]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The high prevalence of antibiotic heteroresistance in pathogenic bacteria is mainly caused by gene amplification.

Nicoloff H, Hjort K, Levin BR, Andersson DI

Nat Microbiol 4 (3) 504-514 [2019-03-00; online 2019-02-11]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Spontaneous calcium activity in metanephric mesenchymal cells regulates branching morphogenesis in the embryonic kidney.

Fontana JM, Khodus GR, Unnersjö-Jess D, ..., Aperia A, Brismar H

FASEB J. 33 (3) 4089-4096 [2019-03-00; online 2018-11-29]

Integrated Microscopy Technologies Stockholm [Service]

Proteomic Analysis of Endothelial Cells Exposed to Ultrasmall Nanoparticles Reveals Disruption in Paracellular and Transcellular Transport.

Kuruvilla J, Bayat N, Cristobal S

Proteomics 19 (5) e1800228 [2019-03-00; online 2019-02-25]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution.

Justice AE, Karaderi T, Highland HM, ..., North KE, Lindgren CM

Nat. Genet. 51 (3) 452-469 [2019-03-00; online 2019-02-18]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries.

Shrine N, Guyatt AL, Erzurumluoglu AM, ..., Tobin MD, Wain LV

Nat. Genet. 51 (3) 481-493 [2019-03-00; online 2019-02-25]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genome-wide meta-analysis reveals shared new loci in systemic seropositive rheumatic diseases.

Acosta-Herrera M, Kerick M, González-Serna D, ..., Mayes MD, Martin J

Ann. Rheum. Dis. 78 (3) 311-319 [2019-03-00; online 2018-12-20]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer's disease risk.

Jansen IE, Savage JE, Watanabe K, ..., Andreassen OA, Posthuma D

Nat. Genet. 51 (3) 404-413 [2019-03-00; online 2019-01-07]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Estimating the Fitness Effect of Deleterious Mutations During the Two Phases of the Life Cycle: A New Method Applied to the Root-Rot Fungus Heterobasidion parviporum.

Clergeot PH, Rode NO, Glémin S, ..., Ihrmark K, Olson Å

Genetics 211 (3) 963-976 [2019-03-00; online 2018-12-31]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Endosperm-specific transcriptome analysis by applying the INTACT system.

Del Toro-De León G, Köhler C

Plant Reprod 32 (1) 55-61 [2019-03-00; online 2018-12-26]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Chromosomal inversions associated with environmental adaptation in honeybees.

Christmas MJ, Wallberg A, Bunikis I, ..., Wallerman O, Webster MT

Mol. Ecol. 28 (6) 1358-1374 [2019-03-00; online 2018-12-21]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Asexual reproduction and growth rate: independent and plastic life history traits in Neurospora crassa.

Anderson JL, Nieuwenhuis BPS, Johannesson H

ISME J 13 (3) 780-788 [2019-03-00; online 2018-11-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A rare regulatory variant in the MEF2D gene affects gene regulation and splicing and is associated with a SLE sub-phenotype in Swedish cohorts.

Farias FHG, Dahlqvist J, Kozyrev SV, ..., Rönnblom L, Lindblad-Toh K

Eur. J. Hum. Genet. 27 (3) 432-441 [2019-03-00; online 2018-11-20]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A radical switch in clonality reveals a stem cell niche in the epiphyseal growth plate.

Newton PT, Li L, Zhou B, ..., Sävendahl L, Chagin AS

Nature 567 (7747) 234-238 [2019-03-00; online 2019-02-27]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A Phenotypic Screening Assay Identifies Modulators of Diamond Blackfan Anemia.

Siva K, Ek F, Chen J, ..., Lundbäck T, Flygare J

SLAS DISCOVERY: Advancing Life Sciences R&D 24 (3) 304-313 [2019-03-00; online 2019-02-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A High-throughput Bead-based Affinity Assay Enables Analysis of Genital Protein Signatures in Women At Risk of HIV Infection.

Månberg A, Bradley F, Qundos U, ..., Nilsson P, Broliden K

Mol. Cell Proteomics 18 (3) 461-476 [2019-03-00; online 2018-11-30]

Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction.

Das S, Frisk C, Eriksson MJ, ..., Linde C, Persson B

Sci Rep 9 (1) 3179 [2019-02-28; online 2019-02-28]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard

Andrade P, Pinho C, Pérez i de Lanuza G, ..., Andersson L, Carneiro M

Proc Natl Acad Sci USA - (-) 201820320 [2019-02-28; online 2019-02-28]

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Nanomedical Relevance of the Intermolecular Interaction Dynamics-Examples from Lysozymes and Insulins.

Zhang R, Zhang N, Mohri M, ..., Nifantiev NE, Siebert HC

ACS Omega 4 (2) 4206-4220 [2019-02-28; online 2019-02-27]

A genome-wide association study identifies new loci for factor VII and implicates factor VII in ischemic stroke etiology.

de Vries PS, Sabater-Lleal M, Huffman JE, ..., O'Donnell CJ, Smith NL

Blood 133 (9) 967-977 [2019-02-28; online 2019-01-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Population and Single-Cell Analysis of Human Cardiogenesis Reveals Unique LGR5 Ventricular Progenitors in Embryonic Outflow Tract.

Sahara M, Santoro F, Sohlmér J, ..., Gruber P, Chien KR

Dev. Cell 48 (4) 475-490.e7 [2019-02-25; online 2019-01-31]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Longitudinal effects of aging on plasma proteins levels in older adults - associations with kidney function and hemoglobin levels.

Lind L, Sundström J, Larsson A, ..., Ärnlöv J, Ingelsson E

PLoS ONE 14 (2) e0212060 [2019-02-25; online 2019-02-25]

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Recombinant Glycoprotein E of Varicella Zoster Virus Contains Glycan-Peptide Motifs That Modulate B Cell Epitopes into Discrete Immunological Signatures.

Nordén R, Nilsson J, Samuelsson E, ..., Olofsson S, Bergström T

Int J Mol Sci 20 (4) - [2019-02-22; online 2019-02-22]

A Quantitative Analysis of Colonic Mucosal Oxylipins and Endocannabinoids in Treatment-Naïve and Deep Remission Ulcerative Colitis Patients and the Potential Link With Cytokine Gene Expression.

Diab J, Al-Mahdi R, Gouveia-Figueira S, ..., Florholmen J, Forsdahl G

Inflamm Bowel Dis 25 (3) 490-497 [2019-02-21; online 2018-11-27]

Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups.

Pettersson ME, Jern P

Genes 10 (2) 162 [2019-02-20; online 2019-02-20]

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Rostania revised: testing generic delimitations in Collemataceae (Peltigerales, Lecanoromycetes).

Košuthová A, Westberg M, Tálora MAG, Wedin M

MycoKeys 47 (47) 17-33 [2019-02-20; online 2019-02-20]

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Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data.

Franco M, Jeggari A, Peuget S, ..., Selivanova G, Alexeyenko A

Sci Rep 9 (1) 2379 [2019-02-20; online 2019-02-20]

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Immune-informed mucin hydrogels evade fibrotic foreign body response in vivo

Yan H, Seignez C, Hjorth M, ..., Phillipson M, Crouzier T

- - (-) - [2019-02-19; online 2019-02-19]

High Levels of Soluble Lectinlike Oxidized Low-Density Lipoprotein Receptor-1 Are Associated With Carotid Plaque Inflammation and Increased Risk of Ischemic Stroke.

Markstad H, Edsfeldt A, Yao Mattison I, ..., Engström G, Gonçalves I

J Am Heart Assoc 8 (4) e009874 [2019-02-19; online 2019-02-13]

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Crystal Structure and Substrate Specificity of the 8-oxo-dGTP Hydrolase NUDT1 from Arabidopsis thaliana.

Jemth AS, Scaletti E, Carter M, Helleday T, Stenmark P

Biochemistry 58 (7) 887-899 [2019-02-19; online 2019-01-16]

A deep proteome and transcriptome abundance atlas of 29 healthy human tissues.

Wang D, Eraslan B, Wieland T, ..., Hahne H, Kuster B

Mol. Syst. Biol. 15 (2) e8503 [2019-02-18; online 2019-02-18]

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Genetics and epigenetics in primary Sjögren's syndrome.

Imgenberg-Kreuz J, Rasmussen A, Sivils K, Nordmark G

Rheumatology (Oxford) - (-) - [2019-02-15; online 2019-02-15]

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Fine-Tuning of Sox17 and Canonical Wnt Coordinates the Permeability Properties of the Blood-Brain Barrier.

Corada M, Orsenigo F, Bhat GP, ..., Magnusson P, Dejana E

Circ. Res. 124 (4) 511-525 [2019-02-15; online 2018-12-29]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Association of the coronary artery disease risk gene GUCY1A3 with ischaemic events after coronary intervention.

Kessler T, Wolf B, Eriksson N, ..., Kastrati A, Schunkert H

Cardiovasc. Res. - (-) - [2019-02-14; online 2019-02-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Zinc depletion does not necessarily induce ribosome hibernation in mycobacteria.

Tobiasson V, Dow A, Prisic S, Amunts A

Proc. Natl. Acad. Sci. U.S.A. 116 (7) 2395-2397 [2019-02-12; online 2019-01-25]

Metabolomic and lipidomic assessment of the metabolic syndrome in Dutch middle-aged individuals reveals novel biological signatures separating health and disease.

Surowiec I, Noordam R, Bennett K, ..., Lundstedt T, van Heemst D

Metabolomics 15 (2) 23 [2019-02-12; online 2019-02-12]

Synthesis of Sulfonimidamide-Based Amino Acid Building Blocks with Orthogonal Protecting Groups

Chinthakindi PK, Benediktsdottir A, Ibrahim A, ..., Chen Y, Sandström A

Eur. J. Org. Chem. 2019 (5) 1045-1057 [2019-02-07; online 2019-01-02]

Drug Discovery and Development (DDD) [Technology development]

Mass cytometry identifies distinct CD4+ T cell clusters distinguishing HIV-1-infected patients according to antiretroviral therapy initiation.

Bekele Y, Lakshmikanth T, Chen Y, ..., Brodin P, Chiodi F

JCI Insight 4 (3) - [2019-02-07; online 2019-02-07]

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Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding.

Verteramo ML, Stenström O, Ignjatović MM, ..., Ryde U, Akke M

J. Am. Chem. Soc. 141 (5) 2012-2026 [2019-02-06; online 2019-01-23]

Two Basidiomycete Fungi in the Cortex of Wolf Lichens.

Tuovinen V, Ekman S, Thor G, ..., Spribille T, Johannesson H

Curr. Biol. 29 (3) 476-483.e5 [2019-02-04; online 2019-01-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The genomics of major psychiatric disorders in a large pedigree from Northern Sweden.

Szatkiewicz J, Crowley JJ, Adolfsson AN, ..., Adolfsson R, Sullivan PF

Transl Psychiatry 9 (1) 60 [2019-02-04; online 2019-02-04]

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Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development

Tiklová K, Björklund ÅK, Lahti L, ..., Parmar M, Perlmann T

Nat Commun 10 (1) 581 [2019-02-04; online 2019-02-04]

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Exploring the genetics of trotting racing ability in horses using a unique Nordic horse model.

Velie BD, Lillie M, Fegraeus KJ, ..., Strand E, Lindgren G

BMC Genomics 20 (1) 104 [2019-02-04; online 2019-02-04]

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Introgression of resistance to Rhopalosiphum padi L. from wild barley into cultivated barley facilitated by doubled haploid and molecular marker techniques.

Åhman I, Bengtsson T

Theor. Appl. Genet. - (-) - [2019-02-02; online 2019-02-02]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Protein measurements in venous plasma, earlobe capillary plasma and in plasma stored on filter paper.

Siart B, de Oliveira FMS, Shen Q, ..., Kamali-Moghaddam M, Wallner B

Anal. Biochem. 566 (-) 146-150 [2019-02-01; online 2018-11-22]

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IL-6 Signaling Blockade during CD40-Mediated Immune Activation Favors Antitumor Factors by Reducing TGF-β, Collagen Type I, and PD-L1/PD-1.

Eriksson E, Milenova I, Wenthe J, ..., Alemany R, Loskog A

J. Immunol. 202 (3) 787-798 [2019-02-01; online 2019-01-07]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

GlyConnect: Glycoproteomics Goes Visual, Interactive, and Analytical.

Alocci D, Mariethoz J, Gastaldello A, ..., Packer NH, Lisacek F

J. Proteome Res. 18 (2) 664-677 [2019-02-01; online 2019-01-15]

Disentangling the genetics of lean mass.

Karasik D, Zillikens MC, Hsu YH, ..., Kiel DP, Ohlsson C

Am. J. Clin. Nutr. 109 (2) 276-287 [2019-02-01; online 2019-02-06]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Allele-Specific Methylation of SPDEF: A Novel Moderator of Psychosocial Stress and Substance Abuse.

Tay N, Macare C, Liu Y, ..., Schumann G, IMAGEN Consortium

Am J Psychiatry 176 (2) 146-155 [2019-02-01; online 2018-12-11]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Whole-genome sequencing identifies complex contributions to genetic risk by variants in genes causing monogenic systemic lupus erythematosus.

Almlöf JC, Nystedt S, Leonard D, ..., Sandling JK, Syvänen AC

Hum. Genet. 138 (2) 141-150 [2019-02-00; online 2019-02-01]

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Titanium release in peri-implantitis.

Pettersson M, Pettersson J, Johansson A, Molin Thorén M

J Oral Rehabil 46 (2) 179-188 [2019-02-00; online 2018-11-16]

Systems-level patterns emerge.

Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Technology development]

Nat. Rev. Immunol. 19 (2) 87-88 [2019-02-00; online 2019-01-04]

Structural Basis of Cross-Reactivity of Anti-Citrullinated Protein Antibodies.

Ge C, Xu B, Liang B, ..., Dobritzsch D, Holmdahl R

Arthritis & rheumatology (Hoboken, N.J.) 71 (2) 210-221 [2019-02-00; online 2019-01-04]

Spatial and temporal heterogeneity of mouse and human microglia at single-cell resolution.

Masuda T, Sankowski R, Staszewski O, ..., Stadelmann C, Prinz M

Nature 566 (7744) 388-392 [2019-02-00; online 2019-02-13]

Recognition of Amino Acid Motifs, Rather Than Specific Proteins, by Human Plasma Cell-Derived Monoclonal Antibodies to Posttranslationally Modified Proteins in Rheumatoid Arthritis.

Steen J, Forsström B, Sahlström P, ..., Klareskog L, Malmström V

Arthritis & rheumatology (Hoboken, N.J.) 71 (2) 196-209 [2019-02-00; online 2018-08-29]

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Protein profiling of fine-needle aspirates reveals subtype-associated immune signatures and involvement of chemokines in breast cancer.

Franzén B, Alexeyenko A, Kamali-Moghaddam M, ..., Landegren U, Lewensohn R

Mol Oncol 13 (2) 376-391 [2019-02-00; online 2019-01-07]

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Plasma Profiles of Inflammatory Markers Associated With Active Tuberculosis in Antiretroviral Therapy-Naive Human Immunodeficiency Virus-Positive Individuals.

Olsson O, Björkman P, Jansson M, ..., Carlsson F, Skogmar S

Open Forum Infect Dis 6 (2) ofz015 [2019-02-00; online 2019-01-31]

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Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae).

Kryvokhyzha D, Salcedo A, Eriksson MC, ..., Wright SI, Lascoux M

PLoS Genet. 15 (2) e1007949 [2019-02-00; online 2019-02-15]

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Metformin is the key factor in elevated plasma growth differentiation factor-15 levels in type 2 diabetes: A nested, case-control study.

Natali A, Nesti L, Venturi E, ..., Nilsson J, SUMMIT consortium

Diabetes Obes Metab 21 (2) 412-416 [2019-02-00; online 2018-10-02]

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Longitudinal changes in the genetic and environmental influences on the epigenetic clocks across old age: Evidence from two twin cohorts.

Jylhävä J, Hjelmborg J, Soerensen M, ..., Pedersen NL, Reynolds CA

EBioMedicine 40 (-) 710-716 [2019-02-00; online 2019-01-28]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Insights into hydrothermal aging of phosphorus-poisoned Cu-SSZ-13 for NH3-SCR

Xie K, Woo J, Bernin D, ..., Kamasamudram K, Olsson L

Applied Catalysis B: Environmental 241 (-) 205-216 [2019-02-00; online 2019-02-00]

Individual and stable autoantibody repertoires in healthy individuals.

Neiman M, Hellström C, Just D, ..., Uhlén M, Nilsson P

Autoimmunity 52 (1) 1-11 [2019-02-00; online 2019-03-05]

Autoimmunity and Serology Profiling [Collaborative]

Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences.

Karlsson Linnér R, Biroli P, Kong E, ..., Koellinger PD, Beauchamp JP

Nat. Genet. 51 (2) 245-257 [2019-02-00; online 2019-01-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Eleven loci with new reproducible genetic associations with allergic disease risk

Ferreira MAR, Vonk JM, Baurecht H, ..., Koppelman GH, Paternoster L

Journal of Allergy and Clinical Immunology 143 (2) 691-699 [2019-02-00; online 2019-02-00]

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Drug sensitivity testing on patient-derived sarcoma cells predicts patient response to treatment and identifies c-Sarc inhibitors as active drugs for translocation sarcomas.

Brodin BA, Wennerberg K, Lidbrink E, ..., Kallioniemi O, Stragliotto CL

Br. J. Cancer 120 (4) 435-443 [2019-02-00; online 2019-02-12]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements.

Eisfeldt J, Pettersson M, Vezzi F, ..., Carvalho CMB, Lindstrand A

PLoS Genet. 15 (2) e1007858 [2019-02-00; online 2019-02-08]

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Circulating proteins as predictors of cardiovascular mortality in end-stage renal disease.

Feldreich T, Nowak C, Fall T, ..., Green D, Ärnlöv J

J Nephrol 32 (1) 111-119 [2019-02-00; online 2018-11-29]

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CD99 expression is strongly associated with clinical outcome in children with B-cell precursor acute lymphoblastic leukaemia.

Chen D, Camponeschi A, Wu Q, ..., Fogelstrand L, Mårtensson IL

Br. J. Haematol. 184 (3) 418-423 [2019-02-00; online 2018-11-28]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

B cell alterations during BAFF inhibition with belimumab in SLE.

Ramsköld D, Parodis I, Lakshmikanth T, ..., Gunnarsson I, Malmström V

EBioMedicine 40 (-) 517-527 [2019-02-00; online 2018-12-26]

A Chemical Screen Identifies Compounds Limiting the Toxicity of C9ORF72 Dipeptide Repeats

Corman A, Jung B, Häggblad M, ..., Carreras-Puigvert J, Fernandez-Capetillo O

Cell Chem Biol 26 (2) 235-243.e5 [2019-02-00; online 2019-02-00]

Chemical Biology Consortium Sweden (CBCS) [Service] Spatial Proteomics [Service]

The antimicrobial protein S100A12 identified as a potential autoantigen in a subgroup of atopic dermatitis patients.

Mikus M, Johansson C, Acevedo N, Nilsson P, Scheynius A

Clin Transl Allergy 9 (-) 6 [2019-01-31; online 2019-01-31]

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Pandemrix-induced narcolepsy is associated with genes related to immunity and neuronal survival.

Hallberg P, Smedje H, Eriksson N, ..., Wadelius M, Swedegene

EBioMedicine - (-) - [2019-01-30; online 2019-01-30]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Low Molecular Mass Myocardial Hyaluronan in Human Hypertrophic Cardiomyopathy.

Lorén CE, Dahl CP, Do L, ..., Mörner S, Hellman U

Cells 8 (2) 97 [2019-01-29; online 2019-01-29]

Proline 411 biases the conformation of the intrinsically disordered plant UVR8 photoreceptor C27 domain altering the functional properties of the peptide.

Wu M, Farkas D, Eriksson LA, Strid Å

Sci Rep 9 (1) 818 [2019-01-28; online 2019-01-28]

Photoactivated Colibactin Probes Induce Cellular DNA Damage.

Moodie LWK, Hubert M, Zhou X, ..., Wanrooij S, Hedberg C

Angew. Chem. Int. Ed. Engl. 58 (5) 1417-1421 [2019-01-28; online 2018-12-27]

Genomic regions of speciation and adaptation among three species of grouse.

Kozma R, Rödin-Mörch P, Höglund J

Sci Rep 9 (1) 812 [2019-01-28; online 2019-01-28]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Peri-arterial specification of vascular mural cells from naïve mesenchyme requires Notch signaling.

Ando K, Wang W, Peng D, ..., Mochizuki N, Betsholtz C

Development 146 (2) dev165589 [2019-01-25; online 2019-01-25]

Mercury methylating microbial communities of boreal forest soils.

Xu J, Buck M, Eklöf K, ..., Bertilsson S, Bravo AG

Sci Rep 9 (1) 518 [2019-01-24; online 2019-01-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Differential Expression Patterns of Glycolytic Enzymes and Mitochondria-Dependent Apoptosis in PCOS Patients with Endometrial Hyperplasia, an Early Hallmark of Endometrial Cancer, In Vivo and the Impact of Metformin In Vitro.

Wang T, Zhang J, Hu M, ..., Shao LR, Billig H

Int. J. Biol. Sci. 15 (3) 714-725 [2019-01-24; online 2019-01-24]

Integrated Microscopy Technologies Gothenburg [Service]

Carbonic Anhydrase 6 Gene Variation influences Oral Microbiota Composition and Caries Risk in Swedish adolescents.

Esberg A, Haworth S, Brunius C, Lif Holgerson P, Johansson I

Sci Rep 9 (1) 452 [2019-01-24; online 2019-01-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The ketogenic diet influences taxonomic and functional composition of the gut microbiota in children with severe epilepsy.

Lindefeldt M, Eng A, Darban H, ..., Dahlin M, Prast-Nielsen S

NPJ Biofilms Microbiomes 5 (-) 5 [2019-01-23; online 2019-01-23]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Systems-Level Immune Monitoring by Mass Cytometry.

Lakshmikanth T, Brodin P

Methods Mol. Biol. 1913 (-) 33-48 [2019-01-23; online 2019-01-23]

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Altered human oligodendrocyte heterogeneity in multiple sclerosis

Jäkel S, Agirre E, Falcão AM, ..., Williams A, Castelo-Branco G

Nature - (-) - [2019-01-23; online 2019-01-23]

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Valorization of Humic Acids by Hydrothermal Conversion into Carbonaceous Materials: Physical and Functional Properties

Kozyatnyk I, Latham KG, Jansson S

ACS Sustainable Chem. Eng. 7 (2) 2585-2592 [2019-01-22; online 2018-12-20]

Integrated Microscopy Technologies Umeå [Service] Swedish NMR Centre (SNC) [Service]

Multi-ancestry study of blood lipid levels identifies four loci interacting with physical activity.

Kilpeläinen TO, Bentley AR, Noordam R, ..., Rao DC, Loos RJF

Nat Commun 10 (1) 376 [2019-01-22; online 2019-01-22]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Transformation of mature mouse B cells into malignant plasma cells in vitro via introduction of defined genetic elements.

Högstrand K, Lindvall JM, Sundblad A, Grandien A

Eur. J. Immunol. - (-) - [2019-01-21; online 2019-01-21]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Structure of the DP1–DP2 PolD complex bound with DNA and its implications for the evolutionary history of DNA and RNA polymerases

Raia P, Carroni M, Henry E, ..., Delarue M, Sauguet L

PLoS Biol. 17 (1) e3000122 [2019-01-18; online 2019-01-18]

Genetic and lifestyle risk factors for MRI-defined brain infarcts in a population-based setting.

Chauhan G, Adams HHH, Satizabal CL, ..., Debette S, Stroke Genetics Network (SiGN), the International Stroke Genetics Consortium (ISGC), METASTROKE, Alzheimer's Disease Genetics Consortium (ADGC), and the Neurology Working Group of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium

Neurology - (-) - [2019-01-16; online 2019-01-16]

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Complement Activation Occurs at the Surface of Platelets Activated by Streptococcal M1 Protein and This Results in Phagocytosis of Platelets.

Palm F, Sjöholm K, Malmström J, Shannon O

J. Immunol. 202 (2) 503-513 [2019-01-15; online 2018-12-12]

Transcriptomic and proteomic analyses reveal new insights into the regulation of immune pathways during adenovirus type 2 infection.

Zhao H, Chen M, Valdés A, Lind SB, Pettersson U

BMC Microbiol. 19 (1) 15 [2019-01-14; online 2019-01-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The bile salt glycocholate induces global changes in gene and protein expression and activates virulence in enterotoxigenic Escherichia coli.

Joffre E, Nicklasson M, Álvarez-Carretero S, ..., Zhu B, Sjöling Å

Sci Rep 9 (1) 108 [2019-01-14; online 2019-01-14]

Rapid determination of quaternary protein structures in complex biological samples.

Hauri S, Khakzad H, Happonen L, ..., Malmström J, Malmström L

Nat Commun 10 (1) 192 [2019-01-14; online 2019-01-14]

Targeted Analysis of Serum Proteins Encoded at Known Inflammatory Bowel Disease Risk Loci.

Drobin K, Assadi G, Hong MG, ..., D'Amato M, Halfvarson J

Inflamm Bowel Dis 25 (2) 306-316 [2019-01-10; online 2018-10-26]

Affinity Proteomics Stockholm [Collaborative] Bioinformatics Support for Computational Resources [Service] Drug Discovery and Development (DDD) [Collaborative]

Mycobacterium tuberculosis virulence inhibitors discovered by Mycobacterium marinum high-throughput screening.

Tükenmez H, Edström I, Ummanni R, ..., Elofsson M, Larsson C

Sci Rep 9 (1) 26 [2019-01-10; online 2019-01-10]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

The genetic diversity and evolution of diatom-diazotroph associations highlights traits favoring symbiont integration.

Caputo A, Nylander JAA, Foster RA

FEMS Microbiol. Lett. - (-) - [2019-01-09; online 2019-01-09]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Diplodia Tip Blight on Its Way to the North: Drivers of Disease Emergence in Northern Europe.

Brodde L, Adamson K, Julio Camarero J, ..., Özdağ Ş, Oliva J

Front Plant Sci 9 (-) 1818 [2019-01-09; online 2019-01-09]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Decreased Snow Cover Stimulates Under-Ice Primary Producers but Impairs Methanotrophic Capacity.

Garcia SL, Szekely AJ, Bergvall C, Schattenhofer M, Peura S

mSphere 4 (1) - [2019-01-09; online 2019-01-09]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Fecal pollution can explain antibiotic resistance gene abundances in anthropogenically impacted environments.

Karkman A, Pärnänen K, Larsson DGJ

Nat Commun 10 (1) 80 [2019-01-08; online 2019-01-08]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas.

van der Valk T, Díez-Del-Molino D, Marques-Bonet T, Guschanski K, Dalén L

Curr. Biol. 29 (1) 165-170.e6 [2019-01-07; online 2018-12-27]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

AXIN1 in Plasma or Serum Is a Potential New Biomarker for Endometriosis.

Ek M, Roth B, Engström G, Ohlsson B

Int J Mol Sci 20 (1) 189 [2019-01-07; online 2019-01-07]

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The Versatility of SMRT Sequencing.

Hestand MS, Ameur A

Genes 10 (1) - [2019-01-04; online 2019-01-04]

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Analysis of colony phase variation switch in Acinetobacter baumannii clinical isolates.

Ahmad I, Karah N, Nadeem A, Wai SN, Uhlin BE

PLoS ONE 14 (1) e0210082 [2019-01-04; online 2019-01-04]

Trans-ethnic kidney function association study reveals putative causal genes and effects on kidney-specific disease aetiologies.

Morris AP, Le TH, Wu H, ..., Humphreys BD, Franceschini N

Nat Commun 10 (1) 29 [2019-01-03; online 2019-01-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization.

Orre LM, Vesterlund M, Pan Y, ..., Fredlund E, Lehtiö J

Mol. Cell 73 (1) 166-182.e7 [2019-01-03; online 2019-01-05]

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Intrinsic blinking characteristics of single colloidal CdSe-CdS/ZnS core-multishell quantum dots

Fu Y, Jussi J, Elmlund L, ..., Wang Q, Brismar H

Phys. Rev. B 99 (3) - [2019-01-02; online 2019-01-02]

Integrated Microscopy Technologies Stockholm [Service]

Tracking the Epigenetic Clock Across the Human Life Course: A Meta-analysis of Longitudinal Cohort Data.

Marioni RE, Suderman M, Chen BH, ..., Deary IJ, Hägg S

J. Gerontol. A Biol. Sci. Med. Sci. 74 (1) 57-61 [2019-01-01; online 2018-05-03]

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Soil organic carbon depletion and degradation in surface soil after long-term non-growing season warming in High Arctic Svalbard.

Semenchuk PR, Krab EJ, Hedenström M, ..., Ancin-Murguzur FJ, Cooper EJ

Sci. Total Environ. 646 (-) 158-167 [2019-01-01; online 2018-07-26]

A standardized protocol for comparable analysis of GSH/GSSG by UHPLC-ESI-MSMS for human plasma.

Claeson AS, Gouveia-Figueira S, Stenlund H, Johansson AI

Journal of Chromatography B 1104 (-) 67-72 [2019-01-01; online 2018-11-10]

ZBED6 negatively regulates insulin production, neuronal differentiation, and cell aggregation in MIN6 cells.

Wang X, Jiang L, Wallerman O, ..., Welsh N, Andersson L

FASEB J. 33 (1) 88-100 [2019-01-00; online 2018-06-29]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Tissue-specific hormone profiles from woody poplar roots under bending stress.

De Zio E, Trupiano D, Karady M, ..., Ljung K, Scippa GS

Physiol Plantarum 165 (1) 101-113 [2019-01-00; online 2018-10-15]

The Iroquois homeobox proteins IRX3 and IRX5 have distinct roles in Wilms tumour development and human nephrogenesis.

Holmquist Mengelbier L, Lindell-Munther S, Yasui H, ..., Hopyan S, Gisselsson D

J. Pathol. 247 (1) 86-98 [2019-01-00; online 2018-11-29]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Single-Molecule Sequencing: Towards Clinical Applications.

Ameur A, Kloosterman WP, Hestand MS

Trends Biotechnol. 37 (1) 72-85 [2019-01-00; online 2018-08-13]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Shrunken Pore Syndrome Is Associated With Increased Levels of Atherosclerosis-Promoting Proteins.

Almén MS, Björk J, Nyman U, ..., Christensson A, Grubb A

Kidney International Reports 4 (1) 67-79 [2019-01-00; online 2018-09-13]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Near-complete phylogeny and taxonomic revision of the world's babblers (Aves: Passeriformes).

Cai T, Cibois A, Alström P, ..., Lei F, Fjeldså J

Mol. Phylogenet. Evol. 130 (-) 346-356 [2019-01-00; online 2018-10-12]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Mosaic loss of chromosome Y in leukocytes matters.

Forsberg LA, Halvardson J, Rychlicka-Buniowska E, ..., Ingelsson M, Dumanski JP

Nat. Genet. 51 (1) 4-7 [2019-01-00; online 2018-10-31]

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Introducing ribosomal tandem repeat barcoding for fungi.

Wurzbacher C, Larsson E, Bengtsson-Palme J, ..., Kagami M, Nilsson RH

Mol Ecol Resour 19 (1) 118-127 [2019-01-00; online 2018-10-24]

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Intra- and interpatient evolution of enterovirus D68 analyzed by whole-genome deep sequencing.

Dyrdak R, Mastafa M, Hodcroft EB, Neher RA, Albert J

Virus Evol 5 (1) vez007 [2019-01-00; online 2019-04-24]

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Growth differentiation factor 15 is positively associated with incidence of diabetes mellitus: the Malmö Diet and Cancer-Cardiovascular Cohort.

Bao X, Borné Y, Muhammad IF, ..., Orho-Melander M, Engström G

Diabetologia 62 (1) 78-86 [2019-01-00; online 2018-10-22]

Affinity Proteomics Stockholm [Service] Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service]

Genetic risk for neuroticism predicts emotional health depending on childhood adversity.

Lehto K, Karlsson I, Lundholm C, Pedersen NL

Psychol Med 49 (2) 260-267 [2019-01-00; online 2018-03-26]

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Exploring rare and low-frequency variants in the Saguenay-Lac-Saint-Jean population identified genes associated with asthma and allergy traits.

Morin A, Madore AM, Kwan T, ..., Pastinen T, Laprise C

Eur. J. Hum. Genet. 27 (1) 90-101 [2019-01-00; online 2018-09-11]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Effect of CTLA4-Ig (abatacept) treatment on T cells and B cells in peripheral blood of patients with polymyositis and dermatomyositis.

Tang Q, Ramsköld D, Krystufkova O, ..., Lundberg IE, Malmström V

Scand. J. Immunol. 89 (1) e12732 [2019-01-00; online 2018-12-09]

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Cryo-EM structure of the yeast respiratory supercomplex.

Rathore S, Berndtsson J, Marin-Buera L, ..., Brzezinski P, Ott M

Nat. Struct. Mol. Biol. 26 (1) 50-57 [2019-01-00; online 2018-12-31]

Complete Genome Sequence of the Marine Hydrocarbon Degrader Alcaligenes aquatilis QD168, Isolated from Crude Oil-Polluted Sediment of Quintero Bay, Central Chile.

Durán RE, Barra-Sanhueza B, Salvà-Serra F, ..., Moore ERB, Seeger M

Microbiol Resour Announc 8 (5) - [2019-01-00; online 2019-01-31]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Auxin Function in the Brown Alga Dictyota dichotoma.

Bogaert KA, Blommaert L, Ljung K, Beeckman T, De Clerck O

Plant Physiol. 179 (1) 280-299 [2019-01-00; online 2018-11-12]

An integrated transcriptome analysis in T-cell acute lymphoblastic leukemia links DNA methylation subgroups to dysregulated TAL1 and ANTP homeobox gene expression.

Haider Z, Larsson P, Landfors M, ..., Hultdin M, Degerman S

Cancer Med 8 (1) 311-324 [2019-01-00; online 2018-12-21]

Clinical Genomics [Collaborative] Clinical Genomics Umeå [Collaborative]

A Series of Analogues to the AT 2R Prototype Antagonist C38 Allow Fine Tuning of the Previously Reported Antagonist Binding Mode.

Isaksson R, Lindman J, Wannberg J, ..., Gising J, Larhed M

ChemistryOpen 8 (1) 114-125 [2019-01-00; online 2019-01-24]

Drug Discovery and Development (DDD) [Collaborative]

Understanding the mechanism of low temperature deactivation of Cu/SAPO-34 exposed to various amounts of water vapor in the NH3-SCR reaction

Woo J, Bernin D, Ahari H, ..., Zammit M, Olsson L

Catal. Sci. Technol. 9 (14) 3623-3636 [2019-00-00; online 2019-00-00]

Trophic transfer of CuO NPs and dissolved Cu from sediment to worms to fish – a proof-of-concept study

Lammel T, Thit A, Mouneyrac C, ..., Sturve J, Selck H

Environ. Sci.: Nano 6 (4) 1140-1155 [2019-00-00; online 2019-00-00]

Integrated Microscopy Technologies Gothenburg [Service]

Pelvis Segmentation Using Multi-pass U-Net and Iterative Shape Estimation

Wang C, Connolly B, de Oliveira Lopes PF, Frangi AF, Smedby Ö

- - (-) 49-57 [2019-00-00; online 2019-01-09]

AIDA Data Hub [Service] Bioinformatics (NBIS) [Service]

Efficient and catalyst free synthesis of acrylic plastic precursors: methyl propionate and methyl methacrylate synthesis through reversible CO2 capture

Khokarale SG, Mikkola JP

Green Chem. 21 (8) 2138-2147 [2019-00-00; online 2019-00-00]

Sensitive ADAR editing reporter in cancer cells enables high-throughput screening of small molecule libraries

Fritzell K, Xu LD, Otrocka M, Andréasson C, Öhman M

Nucleic Acids Res - (-) - [2018-12-22; online 2018-12-22]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Zebrafish larvae as a model system for systematic characterization of drugs and genes in dyslipidemia and atherosclerosis

Bandaru MK, Emmanouilidou A, Ranefall P, ..., Ingelsson E, den Hoed M

- - (-) - [2018-12-20; online 2018-12-20]

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PRR14L mutations are associated with chromosome 22 acquired uniparental disomy, age-related clonal hematopoiesis and myeloid neoplasia.

Chase A, Pellagatti A, Singh S, ..., Boultwood J, Cross NCP

Leukemia - (-) - [2018-12-20; online 2018-12-20]

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Targeted Delivery of Stk25 Antisense Oligonucleotides to Hepatocytes Protects Mice Against Nonalcoholic Fatty Liver Disease.

Cansby E, Nuñez-Durán E, Magnusson E, ..., Aghajan M, Mahlapuu M

Cellular and Molecular Gastroenterology and Hepatology 7 (3) 597-618 [2018-12-19; online 2018-12-19]

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Carbon's Three-Center, Four-Electron Tetrel Bond, Treated Experimentally.

Karim A, Schulz N, Andersson H, ..., Keller S, Erdélyi M

J. Am. Chem. Soc. 140 (50) 17571-17579 [2018-12-19; online 2018-12-07]

Red Fluorescent Chlamydia trachomatis Applied to Live Cell Imaging and Screening for Antibacterial Agents.

Mojica SA, Eriksson AU, Davis RA, ..., Elofsson M, Gylfe Å

Front Microbiol 9 (-) 3151 [2018-12-18; online 2018-12-18]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Rainbow Trout Maintain Intestinal Transport and Barrier Functions Following Exposure to Polystyrene Microplastics.

Ašmonaitė G, Sundh H, Asker N, Carney Almroth B

Environ. Sci. Technol. 52 (24) 14392-14401 [2018-12-18; online 2018-12-05]

Integrated Microscopy Technologies Gothenburg [Service]

A multigene typing system for human adenoviruses reveals a new genotype in a collection of Swedish clinical isolates.

Kaján GL, Lipiec A, Bartha D, Allard A, Arnberg N

PLoS ONE 13 (12) e0209038 [2018-12-14; online 2018-12-14]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals.

Elbere I, Silamikelis I, Ustinova M, ..., Schiöth HB, Klovins J

Clin Epigenetics 10 (1) 156 [2018-12-13; online 2018-12-13]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Transcriptional landscape of B cell precursor acute lymphoblastic leukemia based on an international study of 1,223 cases.

Li JF, Dai YT, Lilljebjörn H, ..., Chen SJ, Huang JY

Proc. Natl. Acad. Sci. U.S.A. 115 (50) E11711-E11720 [2018-12-11; online 2018-11-28]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Proteotyping bacteria: Characterization, differentiation and identification of pneumococcus and other species within the Mitis Group of the genus Streptococcus by tandem mass spectrometry proteomics.

Karlsson R, Gonzales-Siles L, Gomila M, ..., Kristiansson E, Moore ERB

PLoS ONE 13 (12) e0208804 [2018-12-10; online 2018-12-10]

Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project.

Omenn GS, Lane L, Overall CM, ..., Baker MS, Deutsch EW

J. Proteome Res. 17 (12) 4031-4041 [2018-12-07; online 2018-08-23]

PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud.

Peters K, Bradbury J, Bergmann S, ..., Zanetti G, Steinbeck C

Gigascience - (-) - [2018-12-07; online 2018-12-07]

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Cotranslational Folding of a Pentarepeat β-Helix Protein.

Notari L, Martínez-Carranza M, Farías-Rico JA, Stenmark P, von Heijne G

J. Mol. Biol. 430 (24) 5196-5206 [2018-12-07; online 2018-10-27]

Somatic Structural Alterations in Childhood Leukemia Can Be Backtracked in Neonatal Dried Blood Spots by Use of Whole-Genome Sequencing and Digital PCR.

Taylan F, Bang B, Öfverholm II, ..., Zachariadis V, Nordgren A

Clin. Chem. - (-) - [2018-12-05; online 2018-12-05]

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Porous Cellulose Nanofiber-Based Microcapsules for Biomolecular Sensing.

Paulraj T, Wennmalm S, Riazanova AV, ..., Crespo GA, Svagan AJ

ACS Appl Mater Interfaces 10 (48) 41146-41154 [2018-12-05; online 2018-11-26]

Integrated Microscopy Technologies Stockholm [Collaborative]

A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer.

Ni G, Simone D, Palma D, ..., Turner S, Dopson M

Front Microbiol 9 (-) 2945 [2018-12-05; online 2018-12-05]

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Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing.

Bartoschek M, Oskolkov N, Bocci M, ..., Björklund Å, Pietras K

Nat Commun 9 (1) 5150 [2018-12-04; online 2018-12-04]

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Membrane fluidity is regulated by the C. elegans transmembrane protein FLD-1 and its human homologs TLCD1/2.

Ruiz M, Bodhicharla R, Svensk E, ..., Boren J, Pilon M

Elife 7 (-) - [2018-12-04; online 2018-12-04]

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Crystal Structures and Cytotoxicity of ent-Kaurane-Type Diterpenoids from Two Aspilia Species.

Yaouba S, Valkonen A, Coghi P, ..., Erdélyi M, Yenesew A

Molecules 23 (12) 3199 [2018-12-04; online 2018-12-04]

Transcriptional and Epigenetic Changes Influencing Skeletal Muscle Metabolism in Women With Polycystic Ovary Syndrome.

Nilsson E, Benrick A, Kokosar M, ..., Ling C, Stener-Victorin E

J. Clin. Endocrinol. Metab. 103 (12) 4465-4477 [2018-12-01; online 2018-08-17]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Impact of forced fatty acid synthesis on metabolism and physiology of Saccharomyces cerevisiae.

Gossing M, Smialowska A, Nielsen J

FEMS Yeast Res. 18 (8) - [2018-12-01; online 2018-09-01]

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Whole Exome Sequencing of Patients from Multicase Families with Systemic Lupus Erythematosus Identifies Multiple Rare Variants

Delgado-Vega AM, Martínez-Bueno M, Oparina NY, ..., Kozyrev SV, Alarcón-Riquelme ME

Sci Rep 8 (1) - [2018-12-00; online 2018-06-08]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Ulvan lyase from Formosa agariphila and its applicability in depolymerisation of ulvan extracted from three different Ulva species

Konasani VR, Jin C, Karlsson NG, Albers E

Algal Research 36 (-) 106-114 [2018-12-00; online 2018-12-00]

Transancestral GWAS of alcohol dependence reveals common genetic underpinnings with psychiatric disorders

Walters RK, None , Polimanti R, ..., Edenberg HJ, Agrawal A

Nat Neurosci 21 (12) 1656-1669 [2018-12-00; online 2018-11-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The gut microbiome participates in transgenerational inheritance of low-temperature responses in Drosophila melanogaster.

Zare A, Johansson AM, Karlsson E, Delhomme N, Stenberg P

FEBS Lett. 592 (24) 4078-4086 [2018-12-00; online 2018-11-15]

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The Mutant p53-Targeting Compound APR-246 Induces ROS-Modulating Genes in Breast Cancer Cells.

Synnott NC, Madden SF, Bykov VJN, ..., Wiman KG, Duffy MJ

Transl Oncol 11 (6) 1343-1349 [2018-12-00; online 2018-09-06]

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Targeting PFKFB3 radiosensitizes cancer cells and suppresses homologous recombination

Gustafsson NMS, Färnegårdh K, Bonagas N, ..., Olin T, Helleday T

Nat Commun 9 (1) - [2018-12-00; online 2018-09-24]

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T-cell transcriptomics from peripheral blood highlights differences between polymyositis and dermatomyositis patients

Houtman M, Ekholm L, Hesselberg E, ..., Lundberg IE, Padyukov L

Arthritis Res. Ther. 20 (1) - [2018-12-00; online 2018-08-29]

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Structure of a functional obligate complex III 2IV2 respiratory supercomplex from Mycobacterium smegmatis.

Wiseman B, Nitharwal RG, Fedotovskaya O, ..., Brzezinski P, Högbom M

Nat. Struct. Mol. Biol. 25 (12) 1128-1136 [2018-12-00; online 2018-12-05]

Stereocilin gene variants associated with episodic vertigo: expansion of the DFNB16 phenotype.

Frykholm C, Klar J, Tomanovic T, Ameur A, Dahl N

Eur. J. Hum. Genet. 26 (12) 1871-1874 [2018-12-00; online 2018-09-24]

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Somatic mutagenesis in satellite cells associates with human skeletal muscle aging

Franco I, Johansson A, Olsson K, ..., Fischer H, Eriksson M

Nat Commun 9 (1) - [2018-12-00; online 2018-02-23]

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Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens: evidence from high-throughput sequencing

Onuț-Brännström I, Benjamin M, Scofield DG, ..., Lindström ES, Johannesson H

Sci Rep 8 (1) - [2018-12-00; online 2018-03-13]

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RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells

Gliga AR, Di Bucchianico S, Lindvall J, Fadeel B, Karlsson HL

Sci Rep 8 (1) - [2018-12-00; online 2018-04-27]

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Publisher Correction: A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage

Ladds MJGW, van Leeuwen IMM, Drummond CJ, ..., McCormack E, Laín S

Nat Commun 9 (1) - [2018-12-00; online 2018-05-22]

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Protein Profiling in Serum and Cerebrospinal Fluid Following Complex Surgery on the Thoracic Aorta Identifies Biological Markers of Neurologic Injury.

Lindblom RPF, Shen Q, Axén S, ..., Kamali-Moghaddam M, Thelin S

J. of Cardiovasc. Trans. Res. 11 (6) 503-516 [2018-12-00; online 2018-10-26]

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Oxidatively stressed mitochondria-mimicking membranes: A molecular insight into their organization during apoptosis.

Dingeldein APG, Sparrman T, Gröbner G

Biochimica et Biophysica Acta (BBA) - Biomembranes 1860 (12) 2644-2654 [2018-12-00; online 2018-10-05]

Molecular Investigation of the Ciliate Spirostomum semivirescens, with First Transcriptome and New Geographical Records

Hines HN, Onsbring H, Ettema TJG, Esteban GF

Protist 169 (6) 875-886 [2018-12-00; online 2018-12-00]

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Linking FOXO3, NCOA3, and TCF7L2 to Ras pathway phenotypes through a genome-wide forward genetic screen in human colorectal cancer cells

Kundu S, Ali MA, Handin N, ..., Hellström M, Sjöblom T

Genome Med 10 (1) - [2018-12-00; online 2018-01-04]

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Intramolecular 13C analysis of tree rings provides multiple plant ecophysiology signals covering decades

Wieloch T, Ehlers I, Yu J, ..., Gessler A, Schleucher J

Sci Rep 8 (1) - [2018-12-00; online 2018-03-22]

Individual Genetic Variation Might Predict Acute Skin Reactions in Women Undergoing Adjuvant Breast Cancer Radiotherapy.

Oliva D, Nilsson M, Strandéus M, ..., Laytragoon-Lewin N, Lewin F

Anticancer Res. 38 (12) 6763-6770 [2018-12-00; online 2018-12-07]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Image-Based Detection of Patient-Specific Drug-Induced Cell-Cycle Effects in Glioblastoma.

Matuszewski DJ, Wählby C, Krona C, Nelander S, Sintorn IM

SLAS DISCOVERY: Advancing Life Sciences R&D 23 (10) 1030-1039 [2018-12-00; online 2018-08-03]

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High-efficient bacterial production of human ApoA-I amyloidogenic variants.

Del Giudice R, Lagerstedt JO

Protein Sci. 27 (12) 2101-2109 [2018-12-00; online 2018-10-07]

Genomic screening in rare disorders: New mutations and phenotypes, highlighting ALG14 as a novel cause of severe intellectual disability.

Kvarnung M, Taylan F, Nilsson D, ..., Nordgren A, Lundberg ES

Clin. Genet. 94 (6) 528-537 [2018-12-00; online 2018-10-15]

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Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes

Alneberg J, Karlsson CMG, Divne AM, ..., Andersson AF, Pinhassi J

Microbiome 6 (1) - [2018-12-00; online 2018-09-28]

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Genome sequencing and conservation genomics in the Scandinavian wolverine population

Ekblom R, Brechlin B, Persson J, ..., Flagstad Ø, Ellegren H

Conservation Biology 32 (6) 1301-1312 [2018-12-00; online 2018-09-07]

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Genetic characterization of a novel picorna-like virus in Culex spp. mosquitoes from Mozambique

Cholleti H, Hayer J, Fafetine J, Berg M, Blomström AL

Virol J 15 (1) - [2018-12-00; online 2018-04-18]

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Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms

De Wit P, Durland E, Ventura A, Langdon CJ

BMC Genomics 19 (1) - [2018-12-00; online 2018-02-22]

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GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes

Franceschini N, None , Giambartolomei C, ..., Casas JP, O’Donnell CJ

Nat Commun 9 (1) - [2018-12-00; online 2018-12-03]

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Extracellular nanovesicles released from the commensal yeast Malassezia sympodialis are enriched in allergens and interact with cells in human skin

Johansson HJ, Vallhov H, Holm T, ..., Lehtiö J, Scheynius A

Sci Rep 8 (1) - [2018-12-00; online 2018-06-15]

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Exploring benzimidazole resistance in Haemonchus contortus by next generation sequencing and droplet digital PCR

Baltrušis P, Halvarsson P, Höglund J

International Journal for Parasitology: Drugs and Drug Resistance 8 (3) 411-419 [2018-12-00; online 2018-12-00]

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Epigenetics and early domestication: differences in hypothalamic DNA methylation between red junglefowl divergently selected for high or low fear of humans

Bélteky J, Agnvall B, Bektic L, ..., Jensen P, Guerrero-Bosagna C

Genet. Sel. Evol. 50 (1) - [2018-12-00; online 2018-04-02]

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Eleven percent intact PGM3 in a severely immunodeficient patient with a novel splice-site mutation, a case report

Lundin KE, Wang Q, Hamasy A, ..., Ekwall O, Smith CIE

BMC Pediatr 18 (1) 285 [2018-12-00; online 2018-08-29]

Clinical Genomics [Collaborative] Clinical Genomics Stockholm [Collaborative]

Effects of predation stress and food ration on perch gut microbiota

Zha Y, Eiler A, Johansson F, Svanbäck R

Microbiome 6 (1) - [2018-12-00; online 2018-02-06]

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EMBLmyGFF3: a converter facilitating genome annotation submission to European Nucleotide Archive

Norling M, Jareborg N, Dainat J

BMC Res Notes 11 (1) - [2018-12-00; online 2018-08-13]

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Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements

Svedberg J, Hosseini S, Chen J, ..., Lascoux M, Johannesson H

Nat Commun 9 (1) - [2018-12-00; online 2018-10-12]

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Comprehensive analysis of CTNNB1 in adrenocortical carcinomas: Identification of novel mutations and correlation to survival

Maharjan R, Backman S, Åkerström T, Hellman P, Björklund P

Sci Rep 8 (1) 8610 [2018-12-00; online 2018-06-05]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction

Bornelöv S, Seroussi E, Yosefi S, ..., Andersson L, Friedman-Einat M

BMC Genomics 19 (1) - [2018-12-00; online 2018-04-26]

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Anti-Rift Valley fever virus activity in vitro, pre-clinical pharmacokinetics and oral bioavailability of benzavir-2, a broad-acting antiviral compound

Islam MK, Strand M, Saleeb M, ..., Elofsson M, Evander M

Sci Rep 8 (1) - [2018-12-00; online 2018-01-31]

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Analysis of porcine body size variation using re-sequencing data of miniature and large pigs

Reimer C, Rubin CJ, Sharifi AR, ..., Schlather M, Simianer H

BMC Genomics 19 (1) - [2018-12-00; online 2018-09-19]

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Aberrant splicing and defective mRNA production induced by somatic spliceosome mutations in myelodysplasia

Shiozawa Y, Malcovati L, Gallì A, ..., Ogawa S, Cazzola M

Nat Commun 9 (1) - [2018-12-00; online 2018-09-07]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

A randomized controlled cross-over trial investigating the effect of anti-inflammatory diet on disease activity and quality of life in rheumatoid arthritis: the Anti-inflammatory Diet In Rheumatoid Arthritis (ADIRA) study protocol

Winkvist A, Bärebring L, Gjertsson I, Ellegård L, Lindqvist HM

Nutr J 17 (1) - [2018-12-00; online 2018-04-20]

A novel ulvan lyase family with broad-spectrum activity from the ulvan utilisation loci of Formosa agariphila KMM 3901

Konasani VR, Jin C, Karlsson NG, Albers E

Sci Rep 8 (1) - [2018-12-00; online 2018-10-02]

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A novel derivative of the fungal antimicrobial peptide plectasin is active against Mycobacterium tuberculosis.

Tenland E, Krishnan N, Rönnholm A, ..., Robertson BD, Godaly G

Tuberculosis 113 (-) 231-238 [2018-12-00; online 2018-10-30]

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A major locus controls local adaptation and adaptive life history variation in a perennial plant

Wang J, Ding J, Tan B, ..., Street NR, Ingvarsson PK

Genome Biol. 19 (1) - [2018-12-00; online 2018-06-04]

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A drug screening assay on cancer cells chronically adapted to acidosis

Pellegrini P, Serviss JT, Lundbäck T, ..., Linder S, De Milito A

Cancer Cell Int 18 (1) - [2018-12-00; online 2018-09-25]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons

Södersten E, Toskas K, Rraklli V, ..., Perlmann T, Holmberg J

Nat Commun 9 (1) - [2018-12-00; online 2018-03-26]

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Using High Content Imaging to Quantify Target Engagement in Adherent Cells.

Axelsson H, Almqvist H, Seashore-Ludlow B

J Vis Exp - (141) - [2018-11-29; online 2018-11-29]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

The Human Salivary Antimicrobial Peptide Profile according to the Oral Microbiota in Health, Periodontitis and Smoking.

Grant M, Kilsgård O, Åkerman S, ..., Malmström J, Jönsson D

J Innate Immun 11 (5) 432-444 [2018-11-28; online 2018-11-28]

RollFISH achieves robust quantification of single-molecule RNA biomarkers in paraffin-embedded tumor tissue samples.

Wu C, Simonetti M, Rossell C, ..., Crosetto N, Nilsson M

Commun Biol 1 (-) 209 [2018-11-28; online 2018-11-28]

Advanced FISH Technologies [Technology development] In Situ Sequencing (ISS) [Technology development]

Metabolic control of PPAR activity by aldehyde dehydrogenase regulates invasive cell behavior and predicts survival in hepatocellular and renal clear cell carcinoma.

Andrejeva D, Kugler JM, Nguyen HT, ..., Loya AC, Cohen SM

BMC Cancer 18 (1) 1180 [2018-11-28; online 2018-11-28]

Folding pathway of an Ig domain is conserved on and off the ribosome.

Tian P, Steward A, Kudva R, ..., Clarke J, Best RB

Proc. Natl. Acad. Sci. U.S.A. 115 (48) E11284-E11293 [2018-11-27; online 2018-11-09]

Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers.

Lopez-Fernandez M, Åström M, Bertilsson S, Dopson M

Front Microbiol 9 (-) 2880 [2018-11-27; online 2018-11-27]

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The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding.

Kudva R, Tian P, Pardo-Avila F, ..., Bernstein HD, von Heijne G

Elife 7 (-) - [2018-11-26; online 2018-11-26]

Out in the Cold: Identification of Genomic Regions Associated With Cold Tolerance in the Biocontrol Fungus Clonostachys rosea Through Genome-Wide Association Mapping.

Broberg M, Dubey M, Sun MH, ..., Brandström Durling M, Karlsson M

Front Microbiol 9 (-) 2844 [2018-11-22; online 2018-11-22]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis.

Mayrhofer M, De Laere B, Whitington T, ..., Grönberg H, Lindberg J

Genome Med 10 (1) 85 [2018-11-21; online 2018-05-11]

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Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere

Lopez-Fernandez M, Simone D, Wu X, ..., Bertilsson S, Dopson M

MBio 9 (6) - [2018-11-20; online 2018-11-20]

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Quantitative Interpretation of Intracellular Drug Binding and Kinetics Using the Cellular Thermal Shift Assay

Seashore-Ludlow B, Axelsson H, Almqvist H, ..., Jonsson M, Lundbäck T

Biochemistry - (-) - [2018-11-19; online 2018-11-19]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Genome-Wide Association Studies of Estimated Fatty Acid Desaturase Activity in Serum and Adipose Tissue in Elderly Individuals: Associations with Insulin Sensitivity

Marklund M, Morris A, Mahajan A, ..., Lind L, Risérus U

Nutrients 10 (11) 1791 [2018-11-17; online 2018-11-17]

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Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation.

Visnes T, Cázares-Körner A, Hao W, ..., Boldogh I, Helleday T

Science 362 (6416) 834-839 [2018-11-16; online 2018-11-18]

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MutT homologue 1 (MTH1) catalyzes the hydrolysis of mutagenic O6-methyl-dGTP.

Jemth AS, Gustafsson R, Bräutigam L, ..., Stenmark P, Helleday T

Nucleic Acids Res. 46 (20) 10888-10904 [2018-11-16; online 2018-10-12]

Expression profiling and in situ screening of circular RNAs in human tissues.

Zaghlool A, Ameur A, Wu C, ..., Nilsson M, Feuk L

Sci Rep 8 (1) 16953 [2018-11-16; online 2018-11-16]

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Diazotrophs and N2-Fixation Associated With Particles in Coastal Estuarine Waters.

Pedersen JN, Bombar D, Paerl RW, Riemann L

Front Microbiol 9 (-) 2759 [2018-11-16; online 2018-11-16]

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Diet-dependent gene expression highlights the importance of Cytochrome P450 in detoxification of algal secondary metabolites in a marine isopod.

De Wit P, Yamada K, Panova M, André C, Johannesson K

Sci Rep 8 (1) 16824 [2018-11-14; online 2018-11-14]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Comparative Analysis of the Nodule Transcriptomes of Ceanothus thyrsiflorus (Rhamnaceae, Rosales) and Datisca glomerata (Datiscaceae, Cucurbitales).

Salgado MG, van Velzen R, Nguyen TV, ..., Lundin D, Pawlowski K

Front Plant Sci 9 (-) 1629 [2018-11-14; online 2018-11-14]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Satiety Factors Oleoylethanolamide, Stearoylethanolamide, and Palmitoylethanolamide in Mother's Milk Are Strongly Associated with Infant Weight at Four Months of Age-Data from the Odense Child Cohort.

Bruun S, Gouveia-Figueira S, Domellöf M, ..., Fowler CJ, Zachariassen G

Nutrients 10 (11) 1747 [2018-11-13; online 2018-11-13]

Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies

Akhter S, Kretzschmar WW, Nordal V, ..., Emanuelsson O, Sundström JF

Front Plant Sci 9 (-) - [2018-11-13; online 2018-11-13]

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Parallel plumage colour evolution and introgressive hybridization in wheatears.

Schweizer M, Warmuth V, Alaei Kakhki N, ..., Suh A, Burri R

J. Evol. Biol. - (-) - [2018-11-12; online 2018-11-12]

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Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis

Falcão AM, van Bruggen D, Marques S, ..., Guerreiro-Cacais AO, Castelo-Branco G

Nat Med - (-) - [2018-11-12; online 2018-11-12]

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New tools for automated high-resolution cryo-EM structure determination in RELION-3

Zivanov J, Nakane T, Forsberg BO, ..., Lindahl E, Scheres SH

Elife 7 (-) - [2018-11-09; online 2018-11-09]

Affinity to cellulose is a shared property among coiled-coil domains of intermediate filaments and prokaryotic intermediate filament-like proteins.

Söderholm N, Javadi A, Flores IS, Flärdh K, Sandblad L

Sci Rep 8 (1) 16524 [2018-11-08; online 2018-11-08]

Markers of Basement Membrane Remodeling Are Associated With Higher Mortality in Patients With Known Atherosclerosis.

Holm Nielsen S, Tengryd C, Edsfeldt A, ..., Nilsson J, Goncalves I

J Am Heart Assoc 7 (21) e009193 [2018-11-06; online 2019-01-05]

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Vandermonde Factorization of Hankel Matrix for Complex Exponential Signal Recovery—Application in Fast NMR Spectroscopy

Ying J, Cai JF, Guo D, ..., Chen Z, Qu X

IEEE Trans. Signal Process. 66 (21) 5520-5533 [2018-11-01; online 2018-11-01]

Structures of two fimbrial adhesins, AtfE and UcaD, from the uropathogen Proteus mirabilis.

Jiang W, Ubhayasekera W, Pearson MM, Knight SD

Acta Crystallogr D Struct Biol 74 (Pt 11) 1053-1062 [2018-11-01; online 2018-10-29]

Computational and Statistical Analysis of Array-Based DNA Methylation Data.

Nordlund J, Bäcklin C, Raine A

Methods Mol. Biol. 1878 (-) 173-191 [2018-11-01; online 2018-11-01]

NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

VEGF receptor-2/neuropilin 1 trans-complex formation between endothelial and tumor cells is an independent predictor of pancreatic cancer survival

Morin E, Sjöberg E, Tjomsland V, ..., Sjöblom T, Claesson-Welsh L

J. Pathol 246 (3) 311-322 [2018-11-00; online 2018-09-04]

Affinity Proteomics Uppsala [Service] Bioinformatics Support for Computational Resources [Service] PLA and Single Cell Proteomics [Service]

Upregulated BMP-Smad signaling activity in the glucuronyl C5-epimerase knock out MEF cells

Batool T, Fang J, Jansson V, ..., Moustakas A, Li JP

Cellular Signalling - (-) - [2018-11-00; online 2018-11-00]

Affinity Proteomics Uppsala [Collaborative] PLA and Single Cell Proteomics [Collaborative]

Uncovering the regional localization of inhaled salmeterol retention in the lung.

Bäckström E, Hamm G, Nilsson A, ..., Goodwin RJA, Fridén M

Drug Deliv 25 (1) 838-845 [2018-11-00; online 2018-03-29]

Serum, plasma and erythrocyte membrane lipidomes in infants fed formula supplemented with bovine milk fat globule membranes.

Grip T, Dyrlund TS, Ahonen L, ..., Orešič M, Timby N

Pediatr. Res. 84 (5) 726-732 [2018-11-00; online 2018-08-04]

Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization.

Nazaryan-Petersen L, Eisfeldt J, Pettersson M, ..., Tümer Z, Lindstrand A

PLoS Genet. 14 (11) e1007780 [2018-11-00; online 2018-11-12]

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Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays.

Giacomello S, Lundeberg J

Nat Protoc 13 (11) 2425-2446 [2018-11-00; online 2018-10-26]

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One-view breast tomosynthesis versus two-view mammography in the Malmö Breast Tomosynthesis Screening Trial (MBTST): a prospective, population-based, diagnostic accuracy study

Zackrisson S, Lång K, Rosso A, ..., Tingberg A, Andersson I

The Lancet Oncology 19 (11) 1493-1503 [2018-11-00; online 2018-11-00]

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Notch signaling promotes a HIF2α-driven hypoxic response in multiple tumor cell types.

Mutvei AP, Landor SK, Fox R, ..., Jin S, Lendahl U

Oncogene 37 (46) 6083-6095 [2018-11-00; online 2018-07-11]

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Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens.

Srinivas V, Lebrette H, Lundin D, ..., Sjöberg BM, Högbom M

Nature 563 (7731) 416-420 [2018-11-00; online 2018-10-31]

Global Proteomics and Proteogenomics [Collaborative]

LMO7 and LIMCH1 interact with LRIG proteins in lung cancer, with prognostic implications for early-stage disease.

Karlsson T, Kvarnbrink S, Holmlund C, ..., Johansson M, Hedman H

Lung Cancer 125 (-) 174-184 [2018-11-00; online 2018-09-24]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Isomeric Separation and Recognition of Anionic and Zwitterionic N-glycans from Royal Jelly Glycoproteins.

Hykollari A, Malzl D, Eckmair B, ..., Wilson IBH, Paschinger K

Mol. Cell Proteomics 17 (11) 2177-2196 [2018-11-00; online 2018-08-13]

Glycomics@ExPASy: Bridging the Gap.

Mariethoz J, Alocci D, Gastaldello A, ..., Packer NH, Lisacek F

Mol. Cell Proteomics 17 (11) 2164-2176 [2018-11-00; online 2018-08-10]

Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle

Lind AE, Lewis WH, Spang A, ..., Embley TM, Ettema TJG

ISME J 12 (11) 2655-2667 [2018-11-00; online 2018-07-10]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders

Ligthart S, Vaez A, Võsa U, ..., Frayling TM, Slagboom EP

The American Journal of Human Genetics 103 (5) 691-706 [2018-11-00; online 2018-11-00]

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Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps.

Mahajan A, Taliun D, Thurner M, ..., Boehnke M, McCarthy MI

Nat. Genet. 50 (11) 1505-1513 [2018-11-00; online 2018-10-08]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Detection of autoantibodies against cancer-testis antigens in non-small cell lung cancer.

Djureinovic D, Dodig-Crnković T, Hellström C, ..., Schwenk JM, Micke P

Lung Cancer 125 (-) 157-163 [2018-11-00; online 2018-09-17]

Autoimmunity and Serology Profiling [Service] Bioinformatics Support for Computational Resources [Service]

Convergent evolution of 11p allelic loss in multifocal Wilms tumors arising in WT1 mutation carriers.

Valind A, Wessman S, Pal N, ..., Sandstedt B, Gisselsson D

Pediatr Blood Cancer 65 (11) e27301 [2018-11-00; online 2018-07-03]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections.

Salmén F, Ståhl PL, Mollbrink A, ..., Frisén J, Lundeberg J

Nat Protoc 13 (11) 2501-2534 [2018-11-00; online 2018-10-26]

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Gene-level associations in suicide attempter families show overrepresentation of synaptic genes and genes differentially expressed in brain development

Sokolowski M, Wasserman J, Wasserman D

Am. J. Med. Genet. - (-) - [2018-10-31; online 2018-10-31]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Copper Chaperone Atox1 Interacts with Cell Cycle Proteins.

Matson Dzebo M, Blockhuys S, Valenzuela S, ..., Esbjörner EK, Wittung-Stafshede P

Computational and Structural Biotechnology Journal 16 (-) 443-449 [2018-10-31; online 2018-10-31]

SMAD4 Is Essential for Human Cardiac Mesodermal Precursor Cell Formation.

Xu J, Gruber PJ, Chien KR

Stem Cells - (-) - [2018-10-30; online 2018-10-30]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Quantitative proteomic characterization of the lung extracellular matrix in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis.

Åhrman E, Hallgren O, Malmström L, ..., Westergren-Thorsson G, Malmström J

J Proteomics 189 (-) 23-33 [2018-10-30; online 2018-03-01]

E. coli HMS174(DE3) is a sustainable alternative to BL21(DE3).

Hausjell J, Weissensteiner J, Molitor C, Halbwirth H, Spadiut O

Microb. Cell Fact. 17 (1) 169 [2018-10-30; online 2018-10-30]

Cigarette smoking affects microRNAs and inflammatory biomarkers in healthy individuals and an association to single nucleotide polymorphisms is indicated

Andersson BÅ, Sayardoust S, Löfgren S, Rutqvist LE, Laytragoon-Lewin N

Biomarkers - (-) 1-17 [2018-10-30; online 2018-10-30]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen

Lin YC, Wang J, Delhomme N, ..., Ingvarsson PK, Street NR

Proc Natl Acad Sci USA - (-) 201801437 [2018-10-29; online 2018-10-29]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Targeting autophagy by small molecule inhibitors of vacuolar protein sorting 34 (Vps34) improves the sensitivity of breast cancer cells to Sunitinib.

Dyczynski M, Yu Y, Otrocka M, ..., De Milito A, Pokrovskaja Tamm K

Cancer Lett. 435 (-) 32-43 [2018-10-28; online 2018-07-25]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Single-cell RNA-seq analysis reveals the platinum resistance gene COX7B and the surrogate marker CD63.

Tanaka N, Katayama S, Reddy A, ..., Oya M, Uhlén P

Cancer Med - (-) - [2018-10-26; online 2018-10-26]

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Single-Stranded Nucleic Acids Regulate TLR3/4/7 Activation through Interference with Clathrin-Mediated Endocytosis.

Järver P, Dondalska A, Poux C, ..., LeGrand R, Spetz AL

Sci Rep 8 (1) 15841 [2018-10-26; online 2018-10-26]

Global Proteomics and Proteogenomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Role of OmpA1 and OmpA2 in Aggregatibacter actinomycetemcomitans and Aggregatibacter aphrophilus serum resistance.

Lindholm M, Min Aung K, Nyunt Wai S, Oscarsson J

Journal of Oral Microbiology 11 (1) 1536192 [2018-10-26; online 2018-10-26]

STAT3 differential scanning fluorimetry and differential scanning light scattering assays: Addressing a missing link in the characterization of STAT3 inhibitor interactions.

Desroses M, Busker S, Astorga-Wells J, ..., Grandér D, Page BDG

Journal of Pharmaceutical and Biomedical Analysis 160 (-) 80-88 [2018-10-25; online 2018-07-17]

Chemical Proteomics [Collaborative] Protein Science Facility (PSF) [Service]

Detection of post-translational modifications using solid-phase proximity ligation assay.

Oliveira FMS, Mereiter S, Lönn P, ..., Reis CA, Kamali-Moghaddam M

N Biotechnol 45 (-) 51-59 [2018-10-25; online 2017-10-31]

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Combination of phage and Gram-positive bacterial display of human antibody repertoires enables isolation of functional high affinity binders.

Hu FJ, Volk AL, Persson H, ..., Uhlen M, Rockberg J

N Biotechnol 45 (-) 80-88 [2018-10-25; online 2017-08-01]

Drug Discovery and Development (DDD) [Technology development]

Amplification of the Melanocortin-1 Receptor in Nephrotic Syndrome Identifies a Target for Podocyte Cytoskeleton Stabilization.

Bergwall L, Wallentin H, Elvin J, ..., Nyström J, Buvall L

Sci Rep 8 (1) 15731 [2018-10-24; online 2018-10-24]

XLSY: Extra-Large NMR Spectroscopy

Pustovalova Y, Mayzel M, Orekhov VY

Angew. Chem. Int. Ed. 57 (43) 14043-14045 [2018-10-22; online 2018-10-01]

Swedish NMR Centre (SNC) [Technology development]

Role of Thiol Reactivity for Targeting Mutant p53.

Zhang Q, Bergman J, Wiman KG, Bykov VJN

Cell Chem Biol 25 (10) 1219-1230.e3 [2018-10-18; online 2018-07-26]

Identification of Potential Plasma Biomarkers for Abdominal Aortic Aneurysm Using Tandem Mass Tag Quantitative Proteomics.

Henriksson AE, Lindqvist M, Sihlbom C, Bergström J, Bylund D

Proteomes 6 (4) - [2018-10-18; online 2018-10-18]

Looking for a Treatment for Hailey-Hailey Disease: The Importance of Being Consistent in Case Reports.

Micaroni M

J Cutan Med Surg 22 (6) 660 [2018-10-17; online 2018-10-17]

Integrated Microscopy Technologies Gothenburg [Service]

Halogen Bond Asymmetry in Solution.

Lindblad S, Mehmeti K, Veiga AX, ..., Gräfenstein J, Erdélyi M

J. Am. Chem. Soc. 140 (41) 13503-13513 [2018-10-17; online 2018-10-04]

Single-Cell Transcriptomics of Traced Epidermal and Hair Follicle Stem Cells Reveals Rapid Adaptations during Wound Healing.

Joost S, Jacob T, Sun X, ..., Sur I, Kasper M

Cell Rep 25 (3) 585-597.e7 [2018-10-16; online 2018-10-18]

Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma

Thrane K, Eriksson H, Maaskola J, Hansson J, Lundeberg J

Cancer Res 78 (20) 5970-5979 [2018-10-15; online 2018-10-15]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival.

Engqvist H, Parris TZ, Rönnerman EW, ..., Karlsson P, Helou K

Oncotarget 9 (80) 35162-35180 [2018-10-12; online 2018-10-12]

Bioinformatics (NBIS) [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Service]

Dynamics of a Perturbed Microbial Community during Thermophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds

Šafarič L, Shakeri Yekta S, Liu T, ..., Bastviken D, Björn A

Microorganisms 6 (4) 105 [2018-10-11; online 2018-10-11]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

BabA-mediated adherence of pediatric ulcerogenic H. pylori strains to gastric mucins at neutral and acidic pH.

Quintana-Hayashi MP, Rocha R, Padra M, ..., Oleastro M, Lindén SK

Virulence 9 (1) 1699-1717 [2018-10-10; online 2018-10-10]

De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data.

Ameur A, Che H, Martin M, ..., Feuk L, Gyllensten U

Genes 9 (10) 486 [2018-10-09; online 2018-10-09]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Chorea, psychosis, acanthocytosis, and prolonged survival associated with

Paucar M, Pajak A, Freyer C, ..., Wredenberg A, Svenningsson P

Neurology 91 (15) 710-712 [2018-10-09; online 2018-09-14]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

An orthotopic glioblastoma animal model suitable for high-throughput screenings.

Pudelko L, Edwards S, Balan M, ..., Helleday T, Bräutigam L

Neuro-oncology 20 (11) 1475-1484 [2018-10-09; online 2018-05-12]

Integrated Microscopy Technologies Stockholm [Collaborative]

The Xerobranching Response Represses Lateral Root Formation When Roots Are Not in Contact with Water.

Orman-Ligeza B, Morris EC, Parizot B, ..., Beeckman T, Draye X

Curr. Biol. 28 (19) 3165-3173.e5 [2018-10-08; online 2018-09-27]

Enhanced validation of antibodies for research applications.

Edfors F, Hober A, Linderbäck K, ..., Forsström B, Uhlen M

Nat Commun 9 (1) 4130 [2018-10-08; online 2018-10-08]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A Recurrent De Novo Heterozygous COG4 Substitution Leads to Saul-Wilson Syndrome, Disrupted Vesicular Trafficking, and Altered Proteoglycan Glycosylation.

Ferreira CR, Xia ZJ, Clément A, ..., Gahl WA, Freeze HH

Am. J. Hum. Genet. 103 (4) 553-567 [2018-10-04; online 2018-10-06]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

NormalyzerDE: Online tool for improved normalization of omics expression data and high-sensitivity differential expression analysis.

Willforss J, Chawade A, Levander F

J. Proteome Res. - (-) - [2018-10-02; online 2018-10-02]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Hepatitis E Virus Genotype 3 Genomes from RNA-Positive but Serologically Negative Plasma Donors Have CUG as the Start Codon for ORF3.

Norder H, Galli C, Magnil E, ..., Nyström K, Magnius LO

Intervirology 61 (2) 96-103 [2018-10-02; online 2018-10-02]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

A systems-approach reveals human nestin is an endothelial-enriched, angiogenesis-independent intermediate filament protein.

Dusart P, Fagerberg L, Perisic L, ..., Odeberg J, Butler LM

Sci Rep 8 (1) 14668 [2018-10-02; online 2018-10-02]

Development and Validation of a Novel RNA Sequencing-Based Prognostic Score for Acute Myeloid Leukemia.

Wang M, Lindberg J, Klevebring D, ..., Grönberg H, Rantalainen M

J. Natl. Cancer Inst. 110 (10) 1094-1101 [2018-10-01; online 2018-03-06]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It

Bolívar P, Mugal CF, Rossi M, ..., Dutoit L, Ellegren H

- 35 (10) 2475-2486 [2018-10-01; online 2018-08-02]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Using Scipion for stream image processing at Cryo-EM facilities

Gómez-Blanco J, de la Rosa-Trevín JM, Marabini R, ..., Conesa P, Carazo JM

Journal of Structural Biology - (-) - [2018-10-00; online 2018-10-00]

Use of Vascular Assessments and Novel Biomarkers to Predict Cardiovascular Events in Type 2 Diabetes: The SUMMIT VIP Study.

Shore AC, Colhoun HM, Natali A, ..., Nilsson J, SUMMIT Consortium

Diabetes Care 41 (10) 2212-2219 [2018-10-00; online 2018-07-30]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Rapid Increase in Carriage Rates of Enterobacteriaceae Producing Extended-Spectrum β-Lactamases in Healthy Preschool Children, Sweden

Kaarme J, Riedel H, Schaal W, ..., Nevéus T, Melhus Å

Emerg. Infect. Dis. 24 (10) 1874-1881 [2018-10-00; online 2018-10-00]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor.

Wang H, Marcišauskas S, Sánchez BJ, ..., Nielsen J, Kerkhoven EJ

PLoS Comput. Biol. 14 (10) e1006541 [2018-10-00; online 2018-10-18]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Plasma levels of the proprotein convertase furin and incidence of diabetes and mortality.

Fernandez C, Rysä J, Almgren P, ..., Ruskoaho H, Melander O

J. Intern. Med. 284 (4) 377-387 [2018-10-00; online 2018-07-02]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Partial genomic survival of cave bears in living brown bears.

Barlow A, Cahill JA, Hartmann S, ..., Shapiro B, Hofreiter M

Nat Ecol Evol 2 (10) 1563-1570 [2018-10-00; online 2018-08-27]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia.

Gunnarsson R, Dilorenzo S, Lundin-Ström KB, ..., Isaksson A, Johansson B

Leukemia 32 (10) 2117-2125 [2018-10-00; online 2018-03-12]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Ibrutinib induces rapid down-regulation of inflammatory markers and altered transcription of chronic lymphocytic leukaemia-related genes in blood and lymph nodes.

Palma M, Krstic A, Peña Perez L, ..., Månsson R, Smith CIE

Br. J. Haematol. 183 (2) 212-224 [2018-10-00; online 2018-08-20]

Affinity Proteomics Uppsala [Collaborative] PLA and Single Cell Proteomics [Collaborative]

Genome-wide binding of transcription factor ZEB1 in triple-negative breast cancer cells.

Maturi V, Enroth S, Heldin CH, Moustakas A

J. Cell. Physiol. 233 (10) 7113-7127 [2018-10-00; online 2018-05-10]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Genetic architecture of traits associated with reproductive barriers in Silene: Coupling, sex chromosomes and variation.

Liu X, Karrenberg S

Mol. Ecol. 27 (19) 3889-3904 [2018-10-00; online 2018-04-29]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits.

Evangelou E, Warren HR, Mosen-Ansorena D, ..., Caulfield MJ, Million Veteran Program

Nat. Genet. 50 (10) 1412-1425 [2018-10-00; online 2018-09-17]

Bioinformatics Support for Computational Resources [Service]

Exploring photoinactivation of microbial biofilms using laser scanning microscopy and confined 2-photon excitation.

Thomsen H, Graf FE, Farewell A, Ericson MB

J. Biophotonics 11 (10) e201800018 [2018-10-00; online 2018-06-19]

Integrated Microscopy Technologies Gothenburg [Service]

Deep learning is combined with massive-scale citizen science to improve large-scale image classification

Sullivan DP, Winsnes CF, Åkesson L, ..., Szantner A, Lundberg E

Nat Biotechnol 36 (9) 820-828 [2018-10-00; online 2018-10-01]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Spatial Proteomics [Collaborative]

Backbone 1H, 13C, and 15N resonance assignments of the ligand binding domain of the human wildtype glucocorticoid receptor and the F602S mutant variant

Köhler C, Carlström G, Tångefjord S, ..., Edman K, Akke M

Biomol NMR Assign 12 (2) 263-268 [2018-10-00; online 2018-04-17]

Associations of Circulating Protein Levels With Lipid Fractions in the General Population.

Figarska SM, Gustafsson S, Sundström J, ..., Lind L, Ingelsson E

Arterioscler. Thromb. Vasc. Biol. 38 (10) 2505-2518 [2018-10-00; online 2018-10-26]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads.

Krzewińska M, Kılınç GM, Juras A, ..., Storå J, Götherström A

Sci Adv 4 (10) eaat4457 [2018-10-00; online 2018-10-03]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Alu-Alu mediated intragenic duplications in IFT81 and MATN3 are associated with skeletal dysplasias.

Pettersson M, Vaz R, Hammarsjö A, ..., Grigelioniene G, Lindstrand A

Hum. Mutat. 39 (10) 1456-1467 [2018-10-00; online 2018-08-22]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?

Poongavanam V, Danelius E, Peintner S, ..., Ermondi G, Kihlberg J

ACS Omega 3 (9) 11742-11757 [2018-09-30; online 2018-09-24]

Interferon-α enhances the IL-12-induced STAT4 activation selectively in carriers of the STAT4 SLE risk allele rs7574865[T].

Hagberg N, Rönnblom L

Ann. Rheum. Dis. - (-) - [2018-09-29; online 2018-09-29]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells.

Ni G, Canizales S, Broman E, ..., Sleutels T, Dopson M

Front Microbiol 9 (-) 2308 [2018-09-28; online 2018-09-28]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Male sex and the pattern of recurrent myeloid mutations are strong independent predictors of blood transfusion intensity in patients with myelodysplastic syndromes

Rydén J, Edgren G, Karimi M, ..., Hellström-Lindberg E, Höglund P

Leukemia - (-) - [2018-09-28; online 2018-09-28]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins

Wang Y, Karlsson R, Lampa E, ..., Pedersen NL, Hägg S

Epigenetics - (-) - [2018-09-28; online 2018-09-28]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Structural and biochemical characterization of the Cutibacterium acnes exo-β-1,4-mannosidase that targets the N-glycan core of host glycoproteins

Reichenbach T, Kalyani D, Gandini R, ..., Aspeborg H, Divne C

PLoS ONE 13 (9) e0204703 [2018-09-27; online 2018-09-27]

Bioinformatics Support for Computational Resources [Service] Protein Science Facility (PSF) [Service]

High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia.

Ritter CD, Zizka A, Roger F, ..., Nilsson RH, Antonelli A

PeerJ 6 (-) e5661 [2018-09-25; online 2018-09-25]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genotyping of Phytophthora infestans in eastern-Africa reveals a dominating invasive European lineage

Njoroge AW, Andersson B, Lees AK, ..., Yuen J, Pelle R

Phytopathology - (-) - [2018-09-25; online 2018-09-25]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

NMR Determination of the Binding Constant of Ionic Species: A Caveat.

Schulz N, Schindler S, Huber SM, Erdelyi M

J. Org. Chem. 83 (18) 10881-10886 [2018-09-21; online 2018-08-23]

Methanogens and Iron-Reducing Bacteria: the Overlooked Members of Mercury-Methylating Microbial Communities in Boreal Lakes

Bravo AG, Peura S, Buck M, ..., Björn E, Bertilsson S

Appl Environ Microbiol 84 (23) - [2018-09-21; online 2018-11-15]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Characterization of different fat depots in NAFLD using inflammation-associated proteome, lipidome and metabolome.

Lovric A, Granér M, Bjornson E, ..., Mardinoglu A, Boren J

Sci Rep 8 (1) 14200 [2018-09-21; online 2018-09-21]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Impact of spliceosome mutations on RNA splicing in myelodysplasia: dysregulated genes/pathways and clinical associations

Pellagatti A, Armstrong RN, Steeples V, ..., Smith S, Boultwood J

Blood 132 (12) 1225-1240 [2018-09-20; online 2018-06-21]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

SWI/SNF interacts with cleavage and polyadenylation factors and facilitates pre-mRNA 3' end processing.

Yu S, Jordán-Pla A, Gañez-Zapater A, ..., Östlund Farrants AK, Visa N

Nucleic Acids Res. 46 (16) 8557-8573 [2018-09-19; online 2018-06-04]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Loss of zebrafish ctnnd2b results in disorganised forebrain neuron clusters

Hofmeister W, Vaz R, Edwards S, Dueñas Rey A, Lindstrand A

- - (-) - [2018-09-18; online 2018-09-18]

Integrated Microscopy Technologies Stockholm

14-3-3 proteins activate Pseudomonas exotoxins-S and -T by chaperoning a hydrophobic surface.

Karlberg T, Hornyak P, Pinto AF, ..., Björkegren C, Schüler H

Nat Commun 9 (1) 3785 [2018-09-17; online 2018-09-17]

Bioinformatics Support for Computational Resources [Service] Protein Science Facility (PSF) [Service]

Structural and Functional Characterization of the BcsG Subunit of the Cellulose Synthase in Salmonella typhimurium.

Sun L, Vella P, Schnell R, ..., Schneider G, Römling U

J. Mol. Biol. 430 (18 Pt B) 3170-3189 [2018-09-14; online 2018-07-12]

TP53 outperforms other androgen receptor biomarkers to predict abiraterone or enzalutamide outcome in metastatic castration-resistant prostate cancer.

De Laere B, Oeyen S, Mayrhofer M, ..., Lindberg J, Dirix LY

Clin. Cancer Res. - (-) - [2018-09-12; online 2018-09-12]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system.

Petitpré C, Wu H, Sharma A, ..., Hadjab S, Lallemend F

Nat Commun 9 (1) 3691 [2018-09-12; online 2018-09-12]

Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Continuous Immune Cell Differentiation Inferred From Single-Cell Measurements Following Allogeneic Stem Cell Transplantation.

Chen Y, Lakshmikanth T, Olin A, ..., Remberger M, Brodin P

Front Mol Biosci 5 (-) 81 [2018-09-12; online 2018-09-12]

Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Technology development]

How Does the Sweet Violet (Viola odorata L.) Fight Pathogens and Pests - Cyclotides as a Comprehensive Plant Host Defense System.

Slazak B, Kapusta M, Strömstedt AA, ..., Kuta E, Göransson U

Front Plant Sci 9 (-) 1296 [2018-09-11; online 2018-09-11]

The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant

Graells T, Ishak H, Larsson M, Guy L

FEMS Microbiol. Ecol. - (-) - [2018-09-10; online 2018-09-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town.

Krzewińska M, Kjellström A, Günther T, ..., Storå J, Götherström A

Curr. Biol. 28 (17) 2730-2738.e10 [2018-09-10; online 2018-08-23]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Contribution of allelic imbalance to colorectal cancer.

Palin K, Pitkänen E, Turunen M, ..., Taipale J, Aaltonen LA

Nat Commun 9 (1) 3664 [2018-09-10; online 2018-09-10]

Bioinformatics Support for Computational Resources [Service] CRISPR Functional Genomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Neuroblastoma with flat genomic profile: a question of representativity?

Valind A, Öra I, Mertens F, Gisselsson D

BMJ Case Reports 2018 (-) bcr-2018-225568 [2018-09-08; online 2018-09-08]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Higher Energy Collisional Dissociation Mass Spectrometry of Sulfated O-Linked Oligosaccharides.

Issa SMA, Vitiazeva V, Hayes CA, Karlsson NG

J. Proteome Res. 17 (9) 3259-3267 [2018-09-07; online 2018-08-13]

Glycoproteomics and MS Proteomics [Technology development]

Attached stratified mucus separates bacteria from the epithelial cells in COPD lungs.

Fernández-Blanco JA, Fakih D, Arike L, ..., Ermund A, Hansson GC

JCI Insight 3 (17) - [2018-09-06; online 2018-09-06]

Integrated Microscopy Technologies Gothenburg [Service]

The Thomsen-Friedenreich Antigen: A Highly Sensitive and Specific Predictor of Microsatellite Instability in Gastric Cancer.

Mereiter S, Polom K, Williams C, ..., Magalhães A, Reis CA

J Clin Med 7 (9) - [2018-09-05; online 2018-09-05]

A New Species of the γ-Proteobacterium Francisella, F. adeliensis Sp. Nov., Endocytobiont in an Antarctic Marine Ciliate and Potential Evolutionary Forerunner of Pathogenic Species

Vallesi A, Sjödin A, Petrelli D, ..., Gutiérrez G, Villalobo E

Microb Ecol 77 (3) 587-596 [2018-09-05; online 2018-09-05]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Neuronal Expression of Opioid Gene is Controlled by Dual Epigenetic and Transcriptional Mechanism in Human Brain.

Bazov I, Sarkisyan D, Kononenko O, ..., Yakovleva T, Bakalkin G

Cereb. Cortex 28 (9) 3129-3142 [2018-09-01; online 2017-10-03]

Bioinformatics Support for Computational Resources [Service] Fluorescence Tissue Profiling [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Interactions between monomeric CCTδ and p150 Glued: A novel function for CCTδ at the cell periphery distinct from the protein folding activity of the molecular chaperone CCT.

Echbarthi M, Vallin J, Grantham J

Exp. Cell Res. 370 (1) 137-149 [2018-09-01; online 2018-06-18]

Integrated Microscopy Technologies Gothenburg [Service]

Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.

Vetukuri RR, Tripathy S, Malar C M, ..., Grenville-Briggs LJ, Whisson SC

Genome Biol Evol 10 (9) 2432-2442 [2018-09-01; online 2018-09-01]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids

Narrowe AB, Spang A, Stairs CW, ..., Miller CS, Ettema TJG

Genome Biol Evol 10 (9) 2380-2393 [2018-09-01; online 2018-08-27]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The molecular genetic basis of herbivory between butterflies and their host plants.

Nallu S, Hill JA, Don K, ..., Wheat CW, Kronforst MR

Nat Ecol Evol 2 (9) 1418-1427 [2018-09-00; online 2018-08-03]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The downfall of TBA-354 - a possible explanation for its neurotoxicity via mass spectrometric imaging.

Ntshangase S, Shobo A, Kruger HG, ..., Govender T, Baijnath S

Xenobiotica 48 (9) 938-944 [2018-09-00; online 2017-10-13]

Drug Discovery and Development (DDD) [Collaborative]

The Protozoan Parasite Toxoplasma gondii Selectively Reprograms the Host Cell Translatome.

Leroux LP, Lorent J, Graber TE, ..., Larsson O, Jaramillo M

Infect. Immun. 86 (9) - [2018-09-00; online 2018-08-22]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome

Dutoit L, Mugal CF, Bolívar P, ..., Gustafsson L, Ellegren H

Mol Ecol 27 (18) 3572-3581 [2018-09-00; online 2018-09-04]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Screening for Inhibitors of Acetaldehyde Dehydrogenase (AdhE) from Enterohemorrhagic Escherichia coli (EHEC).

Zetterström CE, Uusitalo P, Qian W, ..., Grundström C, Elofsson M

SLAS DISCOVERY: Advancing Life Sciences R&D 23 (8) 815-822 [2018-09-00; online 2018-04-09]

Chemical Biology Consortium Sweden (CBCS) [Service]

STK25 regulates oxidative capacity and metabolic efficiency in adipose tissue.

Sütt S, Cansby E, Paul A, ..., Enerbäck S, Mahlapuu M

J Endocrinol 238 (3) 187-202 [2018-09-00; online 2018-05-24]

Integrated Microscopy Technologies Gothenburg [Service]

Phylogenetic relationships of rollers (Coraciidae) based on complete mitochondrial genomes and fifteen nuclear genes.

Johansson US, Irestedt M, Qu Y, Ericson PGP

Mol. Phylogenet. Evol. 126 (-) 17-22 [2018-09-00; online 2018-04-06]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Membrane Fluidity Is Regulated Cell Nonautonomously by Caenorhabditiselegans PAQR-2 and Its Mammalian Homolog AdipoR2.

Bodhicharla R, Devkota R, Ruiz M, Pilon M

Genetics 210 (1) 189-201 [2018-09-00; online 2018-07-11]

Integrated Microscopy Technologies Gothenburg [Service]

Lack of thinning effects over inter-annual changes in soil fungal community and diversity in a Mediterranean pine forest

Castaño C, Alday JG, Lindahl BD, ..., Pera J, Bonet JA

Forest Ecology and Management 424 (-) 420-427 [2018-09-00; online 2018-09-00]

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Genome Sequence Resource for the Oomycete Taro Pathogen Phytophthora colocasiae.

Vetukuri RR, Kushwaha SK, Sen D, ..., Lamour KH, Grenville-Briggs LJ

Mol. Plant Microbe Interact. 31 (9) 903-905 [2018-09-00; online 2018-08-03]

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Formation of a Secretion-Competent Protein Complex by a Dynamic Wrap-around Binding Mechanism

Gupta AA, Reinartz I, Karunanithy G, ..., Schug A, Wolf-Watz M

Journal of Molecular Biology 430 (18) 3157-3169 [2018-09-00; online 2018-09-00]

FADD (Fas-Associated Protein With Death Domain), Caspase-3, and Caspase-8 and Incidence of Ischemic Stroke.

Muhammad IF, Borné Y, Melander O, ..., Söderholm M, Engström G

Stroke 49 (9) 2224-2226 [2018-09-00; online 2018-10-26]

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Ein Fall von Pankreaskarzinom

Löhr JM, Kordes M, Gustafsson-Liljefors M, ..., Permert J, Jäger D

Forum 33 (4) 232-235 [2018-09-00; online 2018-08-14]

Clinical Genomics [Collaborative] Clinical Genomics Stockholm [Collaborative]

Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing.

Höijer I, Tsai YC, Clark TA, ..., Gyllensten U, Ameur A

Hum. Mutat. 39 (9) 1262-1272 [2018-09-00; online 2018-07-12]

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Broad spectrum developmental role of Brachypodium AUX1.

van der Schuren A, Voiniciuc C, Bragg J, ..., Pauly M, Hardtke CS

New Phytol. 219 (4) 1216-1223 [2018-09-00; online 2018-06-27]

Autosomal Recessive Osteogenesis Imperfecta Caused by a Novel Homozygous COL1A2 Mutation

Costantini A, Tournis S, Kämpe A, ..., Doulgeraki A, Mäkitie O

Calcif Tissue Int 103 (3) 353-358 [2018-09-00; online 2018-03-23]

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Autoantibody profiling reveals four protein candidate autoantigens associated with systemic lupus erythematosus.

Frostegård J, Hellström C, Nilsson P, Frostegård AG, Ajeganova S

Lupus 27 (10) 1670-1678 [2018-09-00; online 2018-07-24]

A fine-needle aspiration-based protein signature discriminates benign from malignant breast lesions

Franzén B, Kamali-Moghaddam M, Alexeyenko A, ..., Landegren U, Lewensohn R

Mol Oncol 12 (9) 1415-1428 [2018-09-00; online 2018-08-09]

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The endoplasmic reticulum-resident collagen chaperone Hsp47 interacts with and promotes the secretion of decorin, fibromodulin, and lumican.

Ishikawa Y, Rubin K, Bächinger HP, Kalamajski S

J. Biol. Chem. 293 (35) 13707-13716 [2018-08-31; online 2018-07-12]

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Sequentially acting SOX proteins orchestrate astrocyte‐ and oligodendrocyte‐specific gene expression

Klum S, Zaouter C, Alekseenko Z, ..., Muhr J, Bergsland M

EMBO Rep. - (-) e46635 [2018-08-30; online 2018-08-30]

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A glutaredoxin domain fused to the radical-generating subunit of ribonucleotide reductase (RNR) functions as an efficient RNR reductant.

Rozman Grinberg I, Lundin D, Sahlin M, ..., Hofer A, Sjöberg BM

J. Biol. Chem. - (-) - [2018-08-30; online 2018-08-30]

Patient-derived xenograft models reveal intratumor heterogeneity and temporal stability in neuroblastoma

Braekeveldt N, von Stedingk K, Fransson S, ..., Påhlman S, Bexell D

Cancer Res - (-) canres.0527.2018 [2018-08-28; online 2018-08-28]

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Metabolic reprogramming of acute lymphoblastic leukemia cells in response to glucocorticoid treatment.

Dyczynski M, Vesterlund M, Björklund AC, ..., Tamm KP, Nilsson R

Cell Death Dis 9 (9) 846 [2018-08-28; online 2018-08-28]

Global Proteomics and Proteogenomics [Collaborative]

Life history of Parnips and the evolutionary origin of gall wasps

Ronquist F, Nylander JAA, Vårdal H, Nieves-Aldrey JL

JHR 65 (-) 91-110 [2018-08-27; online 2018-08-27]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Exploratory Profiling of Urine MicroRNAs in the dy Mouse Model of LAMA2-CMD: Relation to Disease Progression.2J/dy2J

Moreira Soares Oliveira B, Gawlik KI, Durbeej M, Holmberg J

PLoS Curr 10 (-) - [2018-08-27; online 2018-08-27]

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A Protein-Based Encapsulation System with Calcium-Controlled Cargo Loading and Detachment

Lizatović R, Assent M, Barendregt A, ..., Wennmalm S, André I

Angew. Chem. Int. Ed. 57 (35) 11334-11338 [2018-08-27; online 2018-07-30]

Integrated Microscopy Technologies Stockholm [Collaborative]

Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis.

Tan DJX, Chattopadhyay B, Garg KM, ..., Irestedt M, Rheindt FE

Sci Rep 8 (1) 12804 [2018-08-24; online 2018-08-24]

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Reduced expression of PROX1 transitions glioblastoma cells into a mesenchymal gene expression subtype

Goudarzi KM, Espinoza JA, Guo M, ..., Lindström MS, Hägerstrand D

Cancer Res - (-) canres.0320.2018 [2018-08-22; online 2018-08-22]

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Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types.

He L, Vanlandewijck M, Mäe MA, ..., Lendahl U, Betsholtz C

Sci Data 5 (1) 180160 [2018-08-21; online 2018-08-21]

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Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum.

Liao Z, Kjellin J, Hoeppner MP, Grabherr M, Söderbom F

RNA Biol 15 (7) 937-954 [2018-08-21; online 2018-08-21]

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Diversity of Interneurons in the Dorsal Striatum Revealed by Single-Cell RNA Sequencing and PatchSeq.

Muñoz-Manchado AB, Bengtsson Gonzales C, Zeisel A, ..., Linnarsson S, Hjerling-Leffler J

Cell Rep 24 (8) 2179-2190.e7 [2018-08-21; online 2018-08-23]

Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.

Marques S, van Bruggen D, Vanichkina DP, ..., Taft RJ, Castelo-Branco G

Dev. Cell 46 (4) 504-517.e7 [2018-08-20; online 2018-08-02]

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The structure-activity relationship of the salicylimide derived inhibitors of UDP-sugar producing pyrophosphorylases.

Decker D, Öberg C, Kleczkowski LA

Plant Signal Behav 13 (8) e1507406 [2018-08-20; online 2018-08-20]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Transthyretin Interferes with Aβ Amyloid Formation by Redirecting Oligomeric Nuclei into Non-Amyloid Aggregates.

Nilsson L, Pamrén A, Islam T, ..., Gharibyan AL, Olofsson A

J. Mol. Biol. 430 (17) 2722-2733 [2018-08-17; online 2018-06-08]

Sulfonimidamides: Synthesis and Applications in Preparative Organic Chemistry

Nandi GC, Arvidsson PI

Adv. Synth. Catal. 360 (16) 2976-3001 [2018-08-17; online 2018-05-25]

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Pharmacokinetic Properties of the Nephrotoxin Orellanine in Rats.

Najar D, Haraldsson B, Thorsell A, ..., Nyström J, Ebefors K

Toxins (Basel) 10 (8) - [2018-08-17; online 2018-08-17]

BtsCI and BseGI display sequence preference in the nucleotides flanking the recognition sequence

Rosa J, Fernandez-Gonzalez E, Ducani C, Högberg B

PLoS ONE 13 (8) e0202057 [2018-08-17; online 2018-08-17]

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Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake

Peura S, Buck M, Aalto SL, ..., Nykänen H, Eiler A

MBio 9 (4) - [2018-08-14; online 2018-08-14]

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Reduction in White Blood Cell, Neutrophil and Red Blood Cell counts Related to Gender, HLA and Islet Autoantibodies in Swedish TEDDY Children at Increased Risk for Type 1 Diabetes

Salami F, Lee HS, Freyhult E, ..., Lernmark Å, Törn C

Diabetes - (-) db180355 [2018-08-13; online 2018-08-13]

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Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing

Das S, Pettersson F, Behra PRK, ..., Ennis DG, Kirsebom L

Sci. Rep. 8 (1) - [2018-08-13; online 2018-08-13]

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Nutritional Metabolomics: Postprandial Response of Meals Relating to Vegan, Lacto-Ovo Vegetarian, and Omnivore Diets.

Rådjursöga M, Lindqvist HM, Pedersen A, ..., Ellegård L, Winkvist A

Nutrients 10 (8) 1063 [2018-08-10; online 2018-08-10]

Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.

Hu YOO, Ndegwa N, Alneberg J, ..., Fagerberg J, Andersson AF

Sci Rep 8 (1) 11907 [2018-08-09; online 2018-08-09]

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SURGE complex of Plasmodium falciparum in the rhoptry-neck (SURFIN4.2-RON4-GLURP) contributes to merozoite invasion.

Quintana MDP, Ch'ng JH, Zandian A, ..., Chan S, Wahlgren M

PLoS ONE 13 (8) e0201669 [2018-08-09; online 2018-08-09]

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Molecular Architecture of the Mouse Nervous System.

Zeisel A, Hochgerner H, Lönnerberg P, ..., Marklund U, Linnarsson S

Cell 174 (4) 999-1014.e22 [2018-08-09; online 2018-08-11]

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Biermann J, Parris TZ, Nemes S, ..., Karlsson P, Helou K

Breast Cancer Res. 20 (1) 96 [2018-08-09; online 2018-08-09]

Thermodynamics of Hg(II) Bonding to Thiol Groups in Suwannee River Natural Organic Matter Resolved by Competitive Ligand Exchange, Hg LIII-Edge EXAFS and 1H NMR Spectroscopy

Song Y, Jiang T, Liem-Nguyen V, ..., Björn E, Skyllberg U

Environ. Sci. Technol. 52 (15) 8292-8301 [2018-08-07; online 2018-07-07]

Proteomic Biomarkers for Incident Aortic Stenosis Requiring Valvular Replacement.

Ljungberg J, Janiec M, Bergdahl IA, ..., Fall T, Söderberg S

Circulation 138 (6) 590-599 [2018-08-07; online 2018-03-01]

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Modeling the structural implications of an alternatively spliced Exoc3l2, a paralog of the tunneling nanotube-forming M-Sec

O’Callaghan P, Zarb Y, Noborn F, Kreuger J

PLoS ONE 13 (8) e0201557 [2018-08-07; online 2018-08-07]

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Huntingtin Aggregation Impairs Autophagy, Leading to Argonaute-2 Accumulation and Global MicroRNA Dysregulation.

Pircs K, Petri R, Madsen S, ..., Barker RA, Jakobsson J

Cell Rep 24 (6) 1397-1406 [2018-08-07; online 2018-08-09]

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A genetic map of ostrich Z chromosome and the role of inversions in avian sex chromosome evolution.

Papoli Yazdi H, Ellegren H

Genome Biol Evol - (-) - [2018-08-07; online 2018-08-07]

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Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing.

Nascimento FJA, Lallias D, Bik HM, Creer S

Sci Rep 8 (1) 11737 [2018-08-06; online 2018-08-06]

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Biaryl sulfonamide motifs up- or down-regulate ion channel activity by activating voltage sensors.

Liin SI, Lund PE, Larsson JE, ..., Wallner B, Elinder F

J. Gen. Physiol. 150 (8) 1215-1230 [2018-08-06; online 2018-07-12]

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Substrate-Induced Response in Biogas Process Performance and Microbial Community Relates Back to Inoculum Source

Liu T, Sun L, Nordberg Å, Schnürer A

Microorganisms 6 (3) 80 [2018-08-05; online 2018-08-05]

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Impact in Plasma Metabolome as Effect of Lifestyle Intervention for Weight-Loss Reveals Metabolic Benefits in Metabolically Healthy Obese Women.

Almanza-Aguilera E, Brunius C, Bernal-Lopez MR, ..., Landberg R, Andres-Lacueva C

J. Proteome Res. 17 (8) 2600-2610 [2018-08-03; online 2018-06-28]

Contrasting distribution patterns between aquatic and terrestrial Phytophthora species along a climatic gradient are linked to functional traits

Redondo MA, Boberg J, Stenlid J, Oliva J

ISME J - (-) - [2018-08-02; online 2018-08-02]

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Sulfonyl Fluorides (SFs): More Than Click Reagents?

Chinthakindi PK, Arvidsson PI

Eur. J. Org. Chem. 2018 (27-28) 3648-3666 [2018-08-01; online 2018-07-06]

Drug Discovery and Development (DDD) [Technology development]

Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling

Lopez-Fernandez M, Broman E, Turner S, ..., Bertilsson S, Dopson M

FEMS Microbiol. Ecol. 94 (8) - [2018-08-01; online 2018-06-19]

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CD93 promotes β1 integrin activation and fibronectin fibrillogenesis during tumor angiogenesis.

Lugano R, Vemuri K, Yu D, ..., Dejana E, Dimberg A

J. Clin. Invest. 128 (8) 3280-3297 [2018-08-01; online 2018-06-25]

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Stereotypic Immune System Development in Newborn Children

Olin A, Henckel E, Chen Y, ..., Bohlin K, Brodin P

Cell 174 (5) 1277-1292.e14 [2018-08-00; online 2018-08-00]

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Sex-specific manifestation of genetic risk for attention deficit hyperactivity disorder in the general population.

Martin J, Taylor MJ, Rydell M, ..., Thapar A, Lichtenstein P

J Child Psychol Psychiatry 59 (8) 908-916 [2018-08-00; online 2018-02-16]

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Scanning electron microscopy as a tool for evaluating morphology of amyloid structures formed on surface plasmon resonance chips.

Bra Nnstro M K, Gharibyan AL, Islam T, ..., Pamren A, Olofsson A

Data Brief 19 (-) 1166-1170 [2018-08-00; online 2018-05-26]

RNA velocity of single cells.

La Manno G, Soldatov R, Zeisel A, ..., Linnarsson S, Kharchenko PV

Nature 560 (7719) 494-498 [2018-08-00; online 2018-08-08]

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Proteome‐wide analysis of phospho‐regulated PDZ domain interactions

Sundell GN, Arnold R, Ali M, ..., Chi CN, Ivarsson Y

Mol. Syst. Biol. 14 (8) e8129 [2018-08-00; online 2018-08-20]

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PrgB promotes aggregation, biofilm formation, and conjugation through DNA binding and compaction.

Schmitt A, Jiang K, Camacho MI, ..., Christie PJ, Berntsson RP

Mol. Microbiol. 109 (3) 291-305 [2018-08-00; online 2018-07-31]

Prenatal arsenic exposure is associated with increased plasma IGFBP3 concentrations in 9-year-old children partly via changes in DNA methylation.

Gliga AR, Engström K, Kippler M, ..., Raqib R, Broberg K

Arch. Toxicol. 92 (8) 2487-2500 [2018-08-00; online 2018-06-08]

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Plasma Protein Profiling Reveal Osteoprotegerin as a Marker of Prognostic Impact for Colorectal Cancer

Birgisson H, Tsimogiannis K, Freyhult E, Kamali-Moghaddam M

Transl Oncol 11 (4) 1034-1043 [2018-08-00; online 2018-08-00]

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Novel Multiomics Profiling of Human Carotid Atherosclerotic Plaques and Plasma Reveals Biliverdin Reductase B as a Marker of Intraplaque Hemorrhage.

Matic LP, Jesus Iglesias M, Vesterlund M, ..., Odeberg J, Hedin U

JACC Basic Transl Sci 3 (4) 464-480 [2018-08-00; online 2018-08-01]

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Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals.

Lee JJ, Wedow R, Okbay A, ..., Benjamin DJ, Cesarini D

Nat. Genet. 50 (8) 1112-1121 [2018-08-00; online 2018-07-23]

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Epigenetics in pediatric acute lymphoblastic leukemia.

Nordlund J, Syvänen AC

Semin. Cancer Biol. 51 (-) 129-138 [2018-08-00; online 2017-09-05]

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Effect of the paste-anode interface under impressed current cathodic protection in concrete structures

Zhang EQ, Tang L, Bernin D, Jansson H

Materials and Corrosion 69 (8) 1104-1116 [2018-08-00; online 2018-03-06]

Detailed analysis of the plasma extracellular vesicle proteome after separation from lipoproteins

Karimi N, Cvjetkovic A, Jang SC, ..., Lötvall J, Lässer C

Cell. Mol. Life Sci. 75 (15) 2873-2886 [2018-08-00; online 2018-02-13]

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Delineating closely related dinoflagellate lineages using phylotranscriptomics.

Annenkova NV, Ahrén D, Logares R, Kremp A, Rengefors K

J. Phycol. 54 (4) 571-576 [2018-08-00; online 2018-06-13]

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Data on the nucleotide composition of the first codons encoding the complementary determining region 3 (CDR3) in immunoglobulin heavy chains.

Thörnqvist L, Ohlin M

Data Brief 19 (-) 337-352 [2018-08-00; online 2018-05-04]

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Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change.

Markussen T, Happel EM, Teikari JE, ..., Middelboe M, Kisand V

Environ. Microbiol. 20 (8) 3083-3099 [2018-08-00; online 2018-09-19]

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Comprehensive RNA sequencing analysis in serum and muscle reveals novel small RNA signatures with biomarker potential for Duchenne Muscular Dystrophy

Coenen-Stass AML, Sork H, Gatto S, ..., Wood MJA, Roberts TC

Mol Ther Nucleic Acids - (-) - [2018-08-00; online 2018-08-00]

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Characterization of an activating R1353H insulin-like growth factor 1 receptor variant in a male with extreme tall height.

Lin Y, van Duyvenvoorde HA, Liu H, ..., Wit JM, Larsson O

Eur. J. Endocrinol. 179 (2) 85-95 [2018-08-00; online 2018-05-22]

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Characterization of Swedish Campylobacter coli clade 2 and clade 3 water isolates.

Nilsson A, Skarp A, Johansson C, ..., Engstrand L, Rautelin H

Microbiologyopen 7 (4) e00583 [2018-08-00; online 2018-02-09]

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An imidazole based H-Phe-Phe-NH 2 peptidomimetic with anti-allodynic effect in spared nerve injury mice

Skogh A, Lesniak A, Sköld C, ..., Hallberg M, Sandström A

Bioorganic & Medicinal Chemistry Letters 28 (14) 2446-2450 [2018-08-00; online 2018-08-00]

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Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans

Cedernaes J, Schönke M, Westholm JO, ..., Zierath JR, Benedict C

Sci Adv 4 (8) eaar8590 [2018-08-00; online 2018-08-22]

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A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.

Jerlström Hultqvist J, Warsi O, Söderholm A, ..., Selmer M, Andersson DI

Nat Ecol Evol 2 (8) 1321-1330 [2018-08-00; online 2018-05-28]

BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea.

Alneberg J, Sundh J, Bennke C, ..., Labrenz M, Andersson AF

Sci Data 5 (-) 180146 [2018-07-31; online 2018-07-31]

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Regulation of Neuronal Na,K-ATPase by Extracellular Scaffolding Proteins.

Liebmann T, Fritz N, Kruusmägi M, ..., Aperia A, Brismar H

Int J Mol Sci 19 (8) 2214 [2018-07-29; online 2018-07-29]

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ClpB mutants of Francisella tularensis subspecies holarctica and tularensis are defective for type VI secretion and intracellular replication.

Alam A, Golovliov I, Javed E, Sjöstedt A

Sci Rep 8 (1) 11324 [2018-07-27; online 2018-07-27]

Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat.

Sigeman H, Ponnikas S, Videvall E, ..., Naurin S, Hansson B

Genes 9 (8) 373 [2018-07-26; online 2018-07-26]

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Glyco-engineered cell line and computational docking studies reveals enterotoxigenic Escherichia coli CFA/I fimbriae bind to Lewis a glycans.

Mottram L, Liu J, Chavan S, ..., Svennerholm AM, Holgersson J

Sci Rep 8 (1) 11250 [2018-07-26; online 2018-07-26]

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Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea.

Berner C, Bertos-Fortis M, Pinhassi J, Legrand C

Front Microbiol 9 (-) 1562 [2018-07-25; online 2018-07-25]

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A patient-derived xenograft pre-clinical trial reveals treatment responses and a resistance mechanism to karonudib in metastatic melanoma.

Einarsdottir BO, Karlsson J, Söderberg EMV, ..., Helleday T, Nilsson JA

Cell Death Dis 9 (8) 810 [2018-07-24; online 2018-07-24]

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The psoriasis risk allele HLA-Cw0602 shows evidence of association with chronic or recurrent streptococcal tonsillitis.

Haapasalo K, Koskinen LLE, Suvilehto J, ..., Jokiranta TS, Saavalainen P

Infect. Immun. - (-) - [2018-07-23; online 2018-07-23]

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Mebendazole stimulates CD14+ myeloid cells to enhance T-cell activation and tumour cell killing.

Rubin J, Mansoori S, Blom K, ..., Nygren P, Larsson R

Oncotarget 9 (56) 30805-30813 [2018-07-20; online 2018-07-20]

Effective Assignment of α2,3/α2,6-Sialic Acid Isomers by LC-MS/MS-Based Glycoproteomics.

Pett C, Nasir W, Sihlbom C, ..., Nilsson J, Westerlind U

Angew. Chem. Int. Ed. Engl. 57 (30) 9320-9324 [2018-07-20; online 2018-06-20]

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Characterisation of the Virome of Tonsils from Conventional Pigs and from Specific Pathogen-Free Pigs

Blomström AL, Ye X, Fossum C, Wallgren P, Berg M

Viruses 10 (7) 382 [2018-07-20; online 2018-07-20]

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Disruption of a GATA1-binding motif upstream of XG/PBDX abolishes Xga expression and resolves the Xg blood group system.

Möller M, Lee YQ, Vidovic K, ..., Storry JR, Olsson ML

Blood 132 (3) 334-338 [2018-07-19; online 2018-05-10]

Structural basis for endotoxin neutralisation and anti-inflammatory activity of thrombin-derived C-terminal peptides.

Saravanan R, Holdbrook DA, Petrlova J, ..., Malmsten M, Schmidtchen A

Nat Commun 9 (1) 2762 [2018-07-17; online 2018-07-17]

Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure.

Broman E, Li L, Fridlund J, ..., Legrand C, Dopson M

Microb. Ecol. - (-) - [2018-07-17; online 2018-07-17]

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Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome.

Sork H, Corso G, Krjutskov K, ..., Mäger I, El Andaloussi S

Sci Rep 8 (1) 10813 [2018-07-17; online 2018-07-17]

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Molecular profiles of oxyphilic and chief cell parathyroid adenoma.

Lu M, Kjellin H, Fotouhi O, ..., Lehtiö J, Larsson C

Mol. Cell. Endocrinol. 470 (-) 84-95 [2018-07-15; online 2017-10-03]

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Andermann T, Cano Á, Zizka A, Bacon C, Antonelli A

PeerJ 6 (-) e5175 [2018-07-13; online 2018-07-13]

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Microdeletion of 7p12.1p13, including IKZF1, causes intellectual impairment, overgrowth, and susceptibility to leukaemia.

Järviaho T, Zachariadis V, Tesi B, ..., Harila-Saari A, Nordgren A

Br. J. Haematol. - (-) - [2018-07-13; online 2018-07-13]

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Bacterial Outer Membrane Vesicles Induce Vitronectin Release Into the Bronchoalveolar Space Conferring Protection From Complement-Mediated Killing.

Paulsson M, Che KF, Ahl J, ..., Lindén A, Riesbeck K

Front Microbiol 9 (-) 1559 [2018-07-13; online 2018-07-13]

Untargeted 1H NMR-Based Metabolomics Analysis of Urine and Serum Profiles after Consumption of Lentils, Chickpeas, and Beans: An Extended Meal Study To Discover Dietary Biomarkers of Pulses.

Madrid-Gambin F, Brunius C, Garcia-Aloy M, ..., Landberg R, Andres-Lacueva C

J. Agric. Food Chem. 66 (27) 6997-7005 [2018-07-11; online 2018-07-02]

Gastrointestinal microbiota contributes to the development of murine transfusion-related acute lung injury.

Kapur R, Kim M, Rebetz J, ..., Speck ER, Semple JW

Blood Adv 2 (13) 1651-1663 [2018-07-10; online 2018-07-12]

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Autoantibody profiling in intraocular fluid of patients with uveitis.

Ten Berge JC, Schreurs MW, van Rosmalen J, Rothova A

Exp. Eye Res. 176 (-) 141-146 [2018-07-10; online 2018-07-10]

Metabolic Profiling of Multiorgan Samples: Evaluation of MODY5/RCAD Mutant Mice.

Torell F, Bennett K, Cereghini S, ..., Trygg J, Lundstedt T

J. Proteome Res. 17 (7) 2293-2306 [2018-07-06; online 2018-06-15]

Primary glioblastoma cells for precision medicine: a quantitative portrait of genomic (in)stability during the first 30 passages.

Baskaran S, Mayrhofer M, Kultima HG, ..., Isaksson A, Nelander S

Neuro-oncology 20 (8) 1080-1091 [2018-07-05; online 2018-02-21]

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Multimodal Chemical Imaging of Amyloid Plaque Polymorphism Reveals Aβ Aggregation Dependent Anionic Lipid Accumulations and Metabolism.

Michno W, Kaya I, Nyström S, ..., Zetterberg H, Hanrieder J

Anal. Chem. 90 (13) 8130-8138 [2018-07-03; online 2018-06-19]

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Enteric Species F Human Adenoviruses use Laminin-Binding Integrins as Co-Receptors for Infection of Ht-29 Cells.

Rajan A, Persson BD, Frängsmyr L, ..., Gall J, Arnberg N

Sci Rep 8 (1) 10019 [2018-07-03; online 2018-07-03]

Human Immunodeficiency Virus-Infected Women Have High Numbers of CD103-CD8+ T Cells Residing Close to the Basal Membrane of the Ectocervical Epithelium.

Gibbs A, Buggert M, Edfeldt G, ..., Broliden K, Tjernlund A

J. Infect. Dis. 218 (3) 453-465 [2018-07-02; online 2017-12-23]

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EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.

Jeggari A, Alekseenko Z, Petrov I, ..., Ericson J, Alexeyenko A

Nucleic Acids Res. 46 (W1) W163-W170 [2018-07-02; online 2018-06-13]

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A synthetic diphosphoinositol phosphate analogue of inositol trisphosphate.

Riley AM, Unterlass J, Konieczny V, ..., Helleday T, Potter BVL

Med. Chem. Commun. 9 (7) 1105-1113 [2018-07-01; online 2018-06-04]

The mycoparasitic fungus Clonostachys rosea responds with both common and specific gene expression during interspecific interactions with fungal prey

Nygren K, Dubey M, Zapparata A, ..., Jensen DF, Karlsson M

Evol Appl 11 (6) 931-949 [2018-07-00; online 2018-03-14]

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The STAT4 SLE risk allele rs7574865[T] is associated with increased IL-12-induced IFN-γ production in T cells from patients with SLE.

Hagberg N, Joelsson M, Leonard D, ..., Bryceson YT, Rönnblom L

Ann. Rheum. Dis. 77 (7) 1070-1077 [2018-07-00; online 2018-02-23]

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Porosity measurements in suspension plasma sprayed YSZ coatings using NMR cryoporometry and X-ray microscopy

Klement U, Ekberg J, Creci S, Kelly ST

J Coat Technol Res 15 (4) 753-757 [2018-07-00; online 2018-03-13]

OLMα2 Cells Bidirectionally Modulate Learning

Siwani S, França ASC, Mikulovic S, ..., Tort ABL, Kullander K

Neuron 99 (2) 404-412.e3 [2018-07-00; online 2018-07-00]

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Novel gene variants associated with cardiovascular disease in systemic lupus erythematosus and rheumatoid arthritis.

Leonard D, Svenungsson E, Dahlqvist J, ..., Criswell LA, Rönnblom L

Ann. Rheum. Dis. 77 (7) 1063-1069 [2018-07-00; online 2018-03-07]

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Multiplexed fluorescence microscopy reveals heterogeneity among stromal cells in mouse bone marrow sections

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Cytometry 93 (9) 876-888 [2018-07-00; online 2018-08-14]

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Increased Neuronal Differentiation of Neural Progenitor Cells Derived from Phosphovimentin-Deficient Mice.

Chen M, Puschmann TB, Marasek P, ..., Wilhelmsson U, Pekny M

Mol Neurobiol 55 (7) 5478-5489 [2018-07-00; online 2017-09-27]

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Identification of inhibitors of Tartrate-resistant acid phosphatase (TRAP/ACP5) activity by small-molecule screening.

Reithmeier A, Lundbäck T, Haraldsson M, ..., Gustavsson AL, Andersson G

Chem Biol Drug Des 92 (1) 1255-1271 [2018-07-00; online 2018-03-30]

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Genotype-Phenotype Correlation of PLOD2 Skeletal Dysplasias Using Structural Information.

Tham E, Grigelionis G, Hammarsjö A, Grigelioniene G

J. Bone Miner. Res. 33 (7) 1377-1378 [2018-07-00; online 2018-06-07]

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Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence.

Savage JE, Jansen PR, Stringer S, ..., Wright MJ, Posthuma D

Nat. Genet. 50 (7) 912-919 [2018-07-00; online 2018-06-25]

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Detection of novel syntrophic acetate-oxidizing bacteria from biogas processes by continuous acetate enrichment approaches.

Westerholm M, Müller B, Singh A, Karlsson Lindsjö O, Schnürer A

Microb Biotechnol 11 (4) 680-693 [2018-07-00; online 2017-12-04]

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Complete genome sequence of the marine Rhodococcus sp. H-CA8f isolated from Comau fjord in Northern Patagonia, Chile.

Undabarrena A, Salvà-Serra F, Jaén-Luchoro D, ..., Seeger M, Cámara B

Marine Genomics 40 (-) 13-17 [2018-07-00; online 2018-02-15]

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Calcium-activated Chloride Channel Regulator 1 (CLCA1) Controls Mucus Expansion in Colon by Proteolytic Activity.

Nyström EEL, Birchenough GMH, van der Post S, ..., Hansson GC, Johansson MEV

EBioMedicine 33 (-) 134-143 [2018-07-00; online 2018-06-07]

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CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response.

Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J

Nat. Med. 24 (7) 927-930 [2018-07-00; online 2018-06-11]

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Bioconda: sustainable and comprehensive software distribution for the life sciences

Grüning B, Dale R, Sjödin A, ..., Valieris R, Köster J

Nat Methods 15 (7) 475-476 [2018-07-00; online 2018-07-02]

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Assessment of titanium dioxide nanoparticle toxicity in the rainbow trout (Onchorynchus mykiss) liver and gill cell lines RTL-W1 and RTgill-W1 under particular consideration of nanoparticle stability and interference with fluorometric assays

Lammel T, Sturve J

NanoImpact 11 (-) 1-19 [2018-07-00; online 2018-07-00]

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A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility.

Wei B, Jolma A, Sahu B, ..., Taipale M, Taipale J

Nat. Biotechnol. 36 (6) 521-529 [2018-07-00; online 2018-05-21]

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A heterogeneous response of liver and skeletal muscle fat to the combination of a Paleolithic diet and exercise in obese individuals with type 2 diabetes: a randomised controlled trial

Otten J, Stomby A, Waling M, ..., Hauksson J, Olsson T

Diabetologia 61 (7) 1548-1559 [2018-07-00; online 2018-04-26]

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A freshwater diatom challenged by Zn: Biochemical, physiological and metabolomic responses of Tabellaria flocculosa(Roth) Kützing.

Gonçalves S, Kahlert M, Almeida SFP, Figueira E

Environ Pollut 238 (-) 959-971 [2018-07-00; online 2018-04-28]

LC-MS/MS characterization of xyloside-primed glycosaminoglycans with cytotoxic properties reveals structural diversity and novel glycan modifications.

Persson A, Gomez Toledo A, Vorontsov E, ..., Nilsson J, Larson G

J. Biol. Chem. 293 (26) 10202-10219 [2018-06-29; online 2018-05-08]

Model Communities Hint at Promiscuous Metabolic Linkages between Ubiquitous Free-Living Freshwater Bacteria.

Garcia SL, Buck M, Hamilton JJ, ..., McMahon KD, Eiler A

mSphere 3 (3) - [2018-06-27; online 2018-05-30]

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Confined photo-release of nitric oxide with simultaneous two-photon fluorescence tracking in a cellular system.

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Sci Rep 8 (1) 9753 [2018-06-27; online 2018-06-27]

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appreci8: a pipeline for precise variant calling integrating 8 tools

Sandmann S, Karimi M, de Graaf AO, ..., Jansen JH, Dugas M

- - (-) - [2018-06-26; online 2018-06-26]

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The contribution of common genetic risk variants for ADHD to a general factor of childhood psychopathology.

Brikell I, Larsson H, Lu Y, ..., Lichtenstein P, Martin J

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The Properties of Amyloid-β Fibrils Are Determined by their Path of Formation.

Brännström K, Islam T, Gharibyan AL, ..., Pamrén A, Olofsson A

J. Mol. Biol. 430 (13) 1940-1949 [2018-06-22; online 2018-05-09]

In Vitro Evolution of Antibodies Inspired by In Vivo Evolution

Persson H, Kirik U, Thörnqvist L, ..., Levander F, Ohlin M

Front Immunol 9 (-) - [2018-06-21; online 2018-06-21]

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Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity

Berglund E, Maaskola J, Schultz N, ..., Helleday T, Lundeberg J

Nat Commun 9 (1) 2419 [2018-06-20; online 2018-06-20]

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Simultaneous determination of ribonucleoside and deoxyribonucleoside triphosphates in biological samples by hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry.

Kong Z, Jia S, Chabes AL, ..., Moritz T, Chabes A

Nucleic Acids Res. 46 (11) e66 [2018-06-20; online 2018-03-20]

Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks.

De Vadder F, Grasset E, Mannerås Holm L, ..., Olofsson LE, Bäckhed F

Proc. Natl. Acad. Sci. U.S.A. 115 (25) 6458-6463 [2018-06-19; online 2018-06-04]

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Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics.

Lundmark A, Gerasimcik N, Båge T, ..., Lundeberg J, Yucel-Lindberg T

Sci Rep 8 (1) 9370 [2018-06-19; online 2018-06-19]

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Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries.

Feitosa MF, Kraja AT, Chasman DI, ..., Province MA, Levy D

PLoS ONE 13 (6) e0198166 [2018-06-18; online 2018-06-18]

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Poly(alkylidenimine) Dendrimers Functionalized with the Organometallic Moiety [Ru(η⁵-C₅H₅)(PPh₃)₂]⁺ as Promising Drugs Against Cisplatin-Resistant Cancer Cells and Human Mesenchymal Stem Cells.

Gouveia M, Figueira J, Jardim MG, ..., Rissanen K, Rodrigues J

Molecules 23 (6) 1471 [2018-06-17; online 2018-06-17]

Stabilized Cyclic Peptides as Scavengers of Autoantibodies: Neutralization of Anticitrullinated Protein/Peptide Antibodies in Rheumatoid Arthritis

Gunasekera S, Fernandes-Cerqueira C, Wennmalm S, ..., Jakobsson PJ, Göransson U

ACS Chem. Biol. 13 (6) 1525-1535 [2018-06-15; online 2018-04-09]

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Plant Hormonomics: Multiple Phytohormone Profiling by Targeted Metabolomics

Šimura J, Antoniadi I, Široká J, ..., Ljung K, Novák O

Plant Physiol. 177 (2) 476-489 [2018-06-13; online 2018-04-27]

Investigating Holocene human population history in North Asia using ancient mitogenomes.

Kılınç GM, Kashuba N, Yaka R, ..., Storå J, Götherström A

Sci Rep 8 (1) 8969 [2018-06-12; online 2018-06-12]

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Multi-ethnic genome-wide association study for atrial fibrillation.

Roselli C, Chaffin MD, Weng LC, ..., Lunetta KL, Ellinor PT

Nat. Genet. 50 (9) 1225-1233 [2018-06-11; online 2018-06-11]

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Modular ssDNA binding and inhibition of telomerase activity by designer PPR proteins.

Spåhr H, Chia T, Lingford JP, ..., Filipovska A, Rackham O

Nat Commun 9 (1) 2212 [2018-06-07; online 2018-06-07]

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Cárdenas CA, González-Aravena M, Font A, ..., Malmberg M, Bongcam-Rudloff E

PeerJ 6 (-) e4935 [2018-06-07; online 2018-06-07]

Higher Concentrations of BCAAs and 3-HIB Are Associated with Insulin Resistance in the Transition from Gestational Diabetes to Type 2 Diabetes.

Andersson-Hall U, Gustavsson C, Pedersen A, ..., Joelsson L, Holmäng A

Journal of Diabetes Research 2018 (-) 4207067 [2018-06-05; online 2018-06-05]

Four evolutionary trajectories underlie genetic intratumoral variation in childhood cancer

Karlsson J, Valind A, Holmquist Mengelbier L, ..., Bexell D, Gisselsson D

Nat Genet 50 (7) 944-950 [2018-06-04; online 2018-06-04]

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Active and inactive β1 integrins segregate into distinct nanoclusters in focal adhesions.

Spiess M, Hernandez-Varas P, Oddone A, ..., Lakadamyali M, Strömblad S

J. Cell Biol. 217 (6) 1929-1940 [2018-06-04; online 2018-04-09]

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Presence of Aedes and Anopheles mosquito larvae is correlated to bacteria found in domestic water-storage containers

Nilsson LKJ, Sharma A, Bhatnagar RK, Bertilsson S, Terenius O

FEMS Microbiol. Ecol. 94 (6) - [2018-06-01; online 2018-03-29]

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Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum

Schmidt R, Durling MB, de Jager V, ..., Karlsson M, Garbeva P

FEMS Microbiol. Ecol. 94 (6) - [2018-06-01; online 2018-04-30]

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γ-glutamyl transpeptidase deficiency caused by a large homozygous intragenic deletion in GGT1.

Darin N, Leckström K, Sikora P, ..., Almén G, Asin-Cayuela J

Eur. J. Hum. Genet. 26 (6) 808-817 [2018-06-00; online 2018-02-26]

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Topology of membrane proteins — predictions, limitations and variations

Tsirigos KD, Govindarajan S, Bassot C, ..., Shu N, Elofsson A

Current Opinion in Structural Biology 50 (-) 9-17 [2018-06-00; online 2018-06-00]

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Testis transcriptome alterations in zebrafish (Danio rerio) with reduced fertility due to developmental exposure to 17α-ethinyl estradiol

Porseryd T, Reyhanian Caspillo N, Volkova K, ..., Olsson PE, Porsch-Hällström I

General and Comparative Endocrinology 262 (-) 44-58 [2018-06-00; online 2018-06-00]

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Streptococcus pyogenes Infection and the Human Proteome with a Special Focus on the Immunoglobulin G-cleaving Enzyme IdeS.

Karlsson CAQ, Järnum S, Winstedt L, ..., Linder A, Malmström JA

Mol. Cell Proteomics 17 (6) 1097-1111 [2018-06-00; online 2018-03-06]

Paternally expressed imprinted genes associate with hybridization barriers in Capsella

Lafon-Placette C, Hatorangan MR, Steige KA, ..., Slotte T, Köhler C

NPLANTS 4 (6) 352-357 [2018-06-00; online 2018-05-28]

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Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell types.

Häring M, Zeisel A, Hochgerner H, ..., Linnarsson S, Ernfors P

Nat. Neurosci. 21 (6) 869-880 [2018-06-00; online 2018-04-23]

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Neuronal Aβ42 is enriched in small vesicles at the presynaptic side of synapses.

Yu Y, Jans DC, Winblad B, Tjernberg LO, Schedin-Weiss S

Life Sci. Alliance 1 (3) e201800028 [2018-06-00; online 2018-06-14]

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Mechanistic study of hydrothermally aged Cu/SSZ-13 catalysts for ammonia-SCR

Leistner K, Kumar A, Kamasamudram K, Olsson L

Catalysis Today 307 (-) 55-64 [2018-06-00; online 2018-06-00]

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Liquid Norbornadiene Photoswitches for Solar Energy Storage

Dreos A, Wang Z, Udmark J, ..., Nielsen MB, Moth-Poulsen K

Adv. Energy Mater. 8 (18) 1703401 [2018-06-00; online 2018-03-25]

Genomewide binding of transcription factor Snail1 in triple-negative breast cancer cells

Maturi V, Morén A, Enroth S, Heldin CH, Moustakas A

Mol Oncol 12 (7) 1153-1174 [2018-06-00; online 2018-05-21]

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Expression of ribosomal and actin network proteins and immunochemotherapy resistance in diffuse large B cell lymphoma patients

Bram Ednersson S, Stenson M, Stern M, ..., Hasselblom S, Andersson PO

Br J Haematol 181 (6) 770-781 [2018-06-00; online 2018-05-16]

Glycoproteomics and MS Proteomics [Service] Integrated Microscopy Technologies Gothenburg [Service]

PubMed

Development and Utility of a Birth Defects Surveillance Toolkit.

Flores AL, Turay K, Valencia D, ..., Groisman B, Mastroiacovo P

J Glob Health Perspect 0 (-) - [2018-06-00; online 2018-06-14]

Bioinformatics Support for Computational Resources [Service]

Design, synthesis and evaluation of potent and selective inhibitors of mono-(ADP-ribosyl)transferases PARP10 and PARP14

Holechek J, Lease R, Thorsell AG, ..., Schüler H, Ferraris D

Bioorganic & Medicinal Chemistry Letters 28 (11) 2050-2054 [2018-06-00; online 2018-06-00]

Bioinformatics Support for Computational Resources [Service] Protein Science Facility (PSF) [Service]

Cracking the Sugar Code by Mass Spectrometry : An Invited Perspective in Honor of Dr. Catherine E. Costello, Recipient of the 2017 ASMS Distinguished Contribution Award.

Mirgorodskaya E, Karlsson NG, Sihlbom C, Larson G, Nilsson CL

J. Am. Soc. Mass Spectrom. 29 (6) 1065-1074 [2018-06-00; online 2018-04-11]

Circadian clock components control daily growth activities by modulating cytokinin levels and cell division-associated gene expression in Populus trees.

Edwards KD, Takata N, Johansson M, ..., Ljung K, Eriksson ME

Plant Cell Environ. 41 (6) 1468-1482 [2018-06-00; online 2018-04-15]

Assessing Cu impacts on freshwater diatoms: biochemical and metabolomic responses of Tabellaria flocculosa (Roth) Kützing

Gonçalves S, Kahlert M, Almeida SFP, Figueira E

Science of The Total Environment 625 (-) 1234-1246 [2018-06-00; online 2018-06-00]

Bioinformatics Support for Computational Resources [Service] Swedish Metabolomics Centre (SMC) [Service]

A novel ECEL1 mutation expands the phenotype of distal arthrogryposis multiplex congenita type 5D to include pretibial vertical skin creases.

Stattin EL, Johansson J, Gudmundsson S, ..., Bondeson ML, Wilbe M

Am. J. Med. Genet. A 176 (6) 1405-1410 [2018-06-00; online 2018-04-16]

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PubMed

A genome scan for quantitative trait loci affecting average daily gain and Kleiber ratio in Baluchi Sheep.

Pasandideh M, Rahimi-Mianji G, Gholizadeh M

J. Genet. 97 (2) 493-503 [2018-06-00; online 2018-06-23]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Equilibrative nucleoside transporter 1 gene polymorphisms and clinical outcomes following acute coronary syndromes: findings from the PLATelet inhibition and patient Outcomes (PLATO) study.

Parker WAE, Eriksson N, Becker RC, ..., Storey RF, PLATO Investigators

Platelets - (-) 1-10 [2018-05-31; online 2018-05-31]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces).

Blåhed IM, Königsson H, Ericsson G, Spong G

PLoS ONE 13 (5) e0197364 [2018-05-30; online 2018-05-30]

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Common genetic variation in the autoimmune regulator (AIRE) locus is associated with autoimmune Addison's disease in Sweden.

Eriksson D, Bianchi M, Landegren N, ..., Rosengren Pielberg G, Kämpe O

Sci Rep 8 (1) 8395 [2018-05-30; online 2018-05-30]

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Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function.

Davies G, Lam M, Harris SE, ..., Lencz T, Deary IJ

Nat Commun 9 (1) 2098 [2018-05-29; online 2018-05-29]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Diminished CXCR5 expression in peripheral blood of patients with Sjögren's syndrome may relate to both genotype and salivary gland homing

Aqrawi LA, Ivanchenko M, Björk A, ..., Skarstein K, Wahren-Herlenius M

Clin Exp Immunol 192 (3) 259-270 [2018-05-25; online 2018-03-24]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Kynurenine pathway is altered in patients with SLE and associated with severe fatigue.

Åkesson K, Pettersson S, Ståhl S, ..., Svenungsson E, Idborg H

Lupus Sci Med 5 (1) e000254 [2018-05-23; online 2018-05-23]

SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma.

Jordán-Pla A, Yu S, Waldholm J, ..., Östlund Farrants AK, Visa N

BMC Genomics 19 (1) 367 [2018-05-18; online 2018-05-18]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells.

Guzzi N, Cieśla M, Ngoc PCT, ..., Hsieh AC, Bellodi C

Cell 173 (5) 1204-1216.e26 [2018-05-17; online 2018-04-05]

Quantitation of Endogenous Metabolites in Mouse Tumors Using Mass-Spectrometry Imaging.

Swales JG, Dexter A, Hamm G, ..., Critchlow SE, Goodwin RJA

Anal. Chem. 90 (10) 6051-6058 [2018-05-15; online 2018-04-26]

Inflammatory biomarker profiling in classical orthostatic hypotension: Insights from the SYSTEMA cohort.

Johansson M, Ricci F, Aung N, ..., Melander O, Fedorowski A

Int. J. Cardiol. 259 (-) 192-197 [2018-05-15; online 2018-03-27]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

A mass spectrometry imaging approach for investigating how drug-drug interactions influence drug blood-brain barrier permeability.

Vallianatou T, Strittmatter N, Nilsson A, ..., Goodwin RJA, Andrén PE

Neuroimage 172 (-) 808-816 [2018-05-15; online 2018-01-10]

A genome-wide association study of IgM antibody against phosphorylcholine: shared genetics and phenotypic relationship to chronic lymphocytic leukemia.

Chen X, Gustafsson S, Whitington T, ..., Frostegård J, Magnusson PKE

Hum. Mol. Genet. 27 (10) 1809-1818 [2018-05-15; online 2018-03-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Transcriptomic analysis of the harvested endothelial cells in a swine model of mechanical thrombectomy.

Jaff N, Grankvist R, Muhl L, ..., Eriksson U, Holmin S

Neuroradiology - (-) - [2018-05-14; online 2018-05-14]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Soil microclimate changes affect soil fungal communities in a Mediterranean pine forest

Castaño C, Lindahl BD, Alday JG, ..., Pera J, Bonet JA

New Phytol - (-) - [2018-05-14; online 2018-05-14]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Habitual coffee consumption and cognitive function: a Mendelian randomization meta-analysis in up to 415,530 participants.

Zhou A, Taylor AE, Karhunen V, ..., Llewellyn DJ, Hyppönen E

Sci Rep 8 (1) 7526 [2018-05-14; online 2018-05-14]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Impact of Dynamically Exposed Polarity on Permeability and Solubility of Chameleonic Drugs Beyond the Rule of 5

Rossi Sebastiano M, Doak BC, Backlund M, ..., Matsson P, Kihlberg J

J. Med. Chem. 61 (9) 4189-4202 [2018-05-10; online 2018-04-02]

Chemical Biology Consortium Sweden (CBCS) [Service] Drug Discovery and Development (DDD) [Service]

Humanizing Miniature Hearts through 4-Flow Cannulation Perfusion Decellularization and Recellularization.

Nguyen DT, O'Hara M, Graneli C, ..., Althage M, Heydarkhan-Hagvall S

Sci Rep 8 (1) 7458 [2018-05-10; online 2018-05-10]

Integrated Microscopy Technologies Gothenburg [Service]

Modulation of gene transcription and epigenetics of colon carcinoma cells by bacterial membrane vesicles.

Vdovikova S, Gilfillan S, Wang S, ..., Wai SN, Hurtado A

Sci Rep 8 (1) 7434 [2018-05-09; online 2018-05-09]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma.

Parris TZ, Rönnerman EW, Engqvist H, ..., Karlsson P, Helou K

Oncotarget 9 (35) 24140-24154 [2018-05-08; online 2018-05-08]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genome-wide association meta-analysis of circulating odd-numbered chain saturated fatty acids: Results from the CHARGE Consortium.

de Oliveira Otto MC, Lemaitre RN, Sun Q, ..., Siscovick DS, Mozaffarian D

PLoS ONE 13 (5) e0196951 [2018-05-08; online 2018-05-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3.

Schmidt A, Marabita F, Kiani NA, ..., Lahesmaa R, Tegnér J

BMC Biol. 16 (1) 47 [2018-05-07; online 2018-05-07]

Global Proteomics and Proteogenomics [Collaborative]

Ligation of free HMGB1 to TLR2 in the absence of ligand is negatively regulated by the C-terminal tail domain.

Aucott H, Sowinska A, Harris HE, Lundback P

Mol. Med. 24 (1) 19 [2018-05-04; online 2018-05-04]

The GTPase domain of gamma-tubulin is required for normal mitochondrial function and spatial organization.

Lindström L, Li T, Malycheva D, ..., Rosselló CA, Alvarado-Kristensson M

Commun Biol 1 (1) 37 [2018-05-03; online 2018-05-03]

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The structure of the N-terminal module of the cell wall hydrolase RipA and its role in regulating catalytic activity.

Steiner EM, Lyngsø J, Guy JE, ..., Schneider G, Schnell R

Proteins - (-) - [2018-05-02; online 2018-05-02]

Multiplexed Antigen Bead Arrays for the Assessment of Antibody Selectivity and Epitope Mapping.

Ayoglu B, Nilsson P, Schwenk JM

Methods Mol. Biol. 1785 (-) 239-248 [2018-05-02; online 2018-05-02]

Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development]

High-Density Antigen Microarrays for the Assessment of Antibody Selectivity and Off-Target Binding.

Sjöberg R, Andersson E, Hellström C, ..., Nilsson P, Ayoglu B

Methods Mol. Biol. 1785 (-) 231-238 [2018-05-02; online 2018-05-02]

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O6-methylguanine–induced transcriptional mutagenesis reduces p53 tumor-suppressor function

Ezerskyte M, Paredes JA, Malvezzi S, ..., Scicchitano DA, Dreij K

Proc. Natl. Acad. Sci. U.S.A. 115 (18) 4731-4736 [2018-05-01; online 2018-04-17]

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Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World's Rarest Hyena Species, the Brown Hyena.

Westbury MV, Hartmann S, Barlow A, ..., Dalén L, Hofreiter M

Mol. Biol. Evol. 35 (5) 1225-1237 [2018-05-01; online 2018-03-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

BAP1 induces cell death via interaction with 14-3-3 in neuroblastoma.

Sime W, Niu Q, Abassi Y, ..., Fu H, Massoumi R

Cell Death Dis 9 (5) 458 [2018-05-01; online 2018-05-01]

Array profiling reveals contribution of Cthrc1 to growth of the denervated rat urinary bladder.

Zhu B, Ekman M, Svensson D, ..., Uvelius B, Swärd K

Am. J. Physiol. Renal Physiol. 314 (5) F893-F905 [2018-05-01; online 2018-01-10]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Uterine progesterone signaling is a target for metformin therapy in PCOS-like rats.

Hu M, Zhang Y, Feng J, ..., Shao LR, Billig H

J Endocrinol 237 (2) 123-137 [2018-05-00; online 2018-03-13]

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Transcription profiling of peripheral B cells in antibody-positive primary Sjögren's syndrome reveals upregulated expression of CX3CR1 and a type I and type II interferon signature.

Imgenberg-Kreuz J, Sandling JK, Björk A, ..., Syvänen AC, Nordmark G

Scand. J. Immunol. 87 (5) e12662 [2018-05-00; online 2018-04-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Sulfasalazine-Induced Agranulocytosis Is Associated With the Human Leukocyte Antigen Locus.

Wadelius M, Eriksson N, Kreutz R, ..., Hallberg P, EuDAC

Clin. Pharmacol. Ther. 103 (5) 843-853 [2018-05-00; online 2017-09-28]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Pretreatment of anaerobic digester samples by hydrochloric acid for solution-state 1 H and 13 C NMR spectroscopic characterization of organic matter

Shakeri Yekta S, Hedenström M, Stehr JE, ..., Hertkorn N, Björn A

Chemosphere 199 (-) 201-209 [2018-05-00; online 2018-05-00]

Potentials and pitfalls of inverse fluorescence correlation spectroscopy

Wennmalm S

Methods 140-141 (-) 23-31 [2018-05-00; online 2018-05-00]

Integrated Microscopy Technologies Stockholm [Technology development]

Molecular barcoding of viral vectors enables mapping and optimization of mRNAtrans-splicing

Davidsson M, Díaz-Fernández P, Torroba M, ..., Lundberg C, Björklund T

RNA 24 (5) 673-687 [2018-05-00; online 2018-01-31]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Mitochondrial Translation Efficiency Controls Cytoplasmic Protein Homeostasis

Suhm T, Kaimal JM, Dawitz H, ..., Andréasson C, Ott M

Cell Metabolism - (-) - [2018-05-00; online 2018-05-00]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]

Microenvironmental control of breast cancer subtype elicited through paracrine platelet-derived growth factor-CC signaling.

Roswall P, Bocci M, Bartoschek M, ..., Eriksson U, Pietras K

Nat. Med. 24 (4) 463-473 [2018-05-00; online 2018-03-12]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Increasing sorghum yields by seed treatment with an aqueous extract of the plant Eclipta alba may involve a dual mechanism of hydropriming and suppression of fungal pathogens

Zida PE, Néya BJ, Stokholm MS, ..., Sérémé P, Lund OS

Crop Protection 107 (-) 48-55 [2018-05-00; online 2018-05-00]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Identification of novel diagnostic biomarkers for deep venous thrombosis.

Memon AA, Sundquist K, PirouziFard M, ..., Sundquist J, Zöller B

Br. J. Haematol. 181 (3) 378-385 [2018-05-00; online 2018-04-19]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies

Pent M, Hiltunen M, Põldmaa K, ..., Ryberg M, Bahram M

Environ Microbiol 20 (5) 1641-1650 [2018-05-00; online 2018-03-25]

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Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.

Wray NR, Ripke S, Mattheisen M, ..., Sullivan PF, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium

Nat. Genet. 50 (5) 668-681 [2018-05-00; online 2018-04-26]

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Fatal demyelinating disease is induced by monocyte-derived macrophages in the absence of TGF-β signaling

Lund H, Pieber M, Parsa R, ..., Zhang XM, Harris RA

Nat. Immunol. 19 (5) 1-7 [2018-05-00; online 2018-04-16]

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Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen.

Felten J, Vahala J, Love J, ..., Mellerowicz EJ, Sundberg B

New Phytol. 218 (3) 999-1014 [2018-05-00; online 2018-03-12]

Cryo-EM [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Editorial and Review: 29th ASMS Sanibel Conference on Mass Spectrometry-Peptidomics: Bridging the Gap between Proteomics and Metabolomics by MS.

Li L, Andrén PE, Sweedler JV

J. Am. Soc. Mass Spectrom. 29 (5) 801-806 [2018-05-00; online 2018-04-07]

Darkened Leaves Use Different Metabolic Strategies for Senescence and Survival.

Law SR, Chrobok D, Juvany M, ..., Gardeström P, Keech O

Plant Physiol. 177 (1) 132-150 [2018-05-00; online 2018-03-09]

DNA methylation mapping identifies gene regulatory effects in patients with systemic lupus erythematosus.

Imgenberg-Kreuz J, Carlsson Almlöf J, Leonard D, ..., Syvänen AC, Sandling JK

Ann. Rheum. Dis. 77 (5) 736-743 [2018-05-00; online 2018-02-01]

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Combined BET bromodomain and CDK2 inhibition in MYC-driven medulloblastoma.

Bolin S, Borgenvik A, Persson CU, ..., Weishaupt H, Swartling FJ

Oncogene 37 (21) 2850-2862 [2018-05-00; online 2018-03-07]

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Abstract 472: Identifying and Characterizing Causal Genes in GWAS-identified Loci for Triglyceride Levels Using High-throughput, Image-based Screens in Zebrafish Larvae

von der Heyde B, Masiero M, Emmanouilidou A, Klingström T, den Hoed M

Arterioscler. Thromb. Vasc. Biol. 38 (Suppl_1) - [2018-05-00; online 2018-05-00]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Ultra-rapid auxin metabolite profiling for high-throughput mutant screening in Arabidopsis.

Pencík A, Casanova-Sáez R, Pilarová V, ..., Ljung K, Novák O

J. Exp. Bot. 69 (10) 2569-2579 [2018-04-27; online 2018-03-08]

Rebooting Human Immunology.

Davis MM, Brodin P

Annu. Rev. Immunol. 36 (-) 843-864 [2018-04-26; online 2018-02-28]

Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas.

van der Valk T, Sandoval-Castellanos E, Caillaud D, ..., Dalén L, Guschanski K

Sci Rep 8 (1) 6551 [2018-04-25; online 2018-04-25]

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Quantification of endogenous and exogenous protein expressions of Na,K-ATPase with super-resolution PALM/STORM imaging.

Bernhem K, Blom H, Brismar H

PLoS ONE 13 (4) e0195825 [2018-04-25; online 2018-04-25]

Bioinformatics Support for Computational Resources [Service] Integrated Microscopy Technologies Stockholm [Technology development]

Experimental validation of predicted cancer genes using FRET

Guala D, Bernhem K, Blal HA, ..., Brismar H, Sonnhammer ELL

Methods Appl. Fluoresc. 6 (3) 035007 [2018-04-25; online 2018-04-25]

Bioinformatics Support for Computational Resources [Service] Integrated Microscopy Technologies Stockholm [Collaborative]

Repeated evolution of self-compatibility for reproductive assurance.

Nieuwenhuis BPS, Tusso S, Bjerling P, ..., Wolf JBW, Immler S

Nat Commun 9 (1) 1639 [2018-04-24; online 2018-04-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Genome-Guided Analysis of Clostridium ultunense and Comparative Genomics Reveal Different Strategies for Acetate Oxidation and Energy Conservation in Syntrophic Acetate-Oxidising Bacteria

Manzoor S, Schnürer A, Bongcam-Rudloff E, Müller B

Genes 9 (4) 225 [2018-04-23; online 2018-04-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Autophagic flux blockage by accumulation of weakly basic tenovins leads to elimination of B-Raf mutant tumour cells that survive vemurafenib

Ladds MJGW, Pastor-Fernández A, Popova G, ..., Bhatia R, Laín S

PLoS ONE 13 (4) e0195956 [2018-04-23; online 2018-04-23]

Human erythrocyte-derived nanovesicles can readily be loaded with doxorubicin and act as anticancer agents.

Dubois L, None , Löf L, ..., Ronquist G, Ronquist KG

Cancer Res Front 4 (1) 13-26 [2018-04-20; online 2018-04-20]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Full Mitogenomes in the Critically Endangered Kākāpō Reveal Major Post-Glacial and Anthropogenic Effects on Neutral Genetic Diversity.

Dussex N, von Seth J, Robertson BC, Dalén L

Genes 9 (4) 220 [2018-04-19; online 2018-04-19]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A GWAS meta-analysis from 5 population-based cohorts implicates ion channel genes in the pathogenesis of irritable bowel syndrome.

Bonfiglio F, Henström M, Nag A, ..., Zhernakova A, D'Amato M

Neurogastroenterol. Motil. - (-) e13358 [2018-04-19; online 2018-04-19]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic and Environmental Contributions to the Covariation Between Cardiometabolic Traits.

Chen X, Kuja-Halkola R, Chang Z, ..., Pedersen NL, Magnusson PKE

J Am Heart Assoc 7 (9) - [2018-04-18; online 2018-04-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer.

La Fleur L, Boura VF, Alexeyenko A, ..., Karlsson MCI, Botling J

Int. J. Cancer - (-) - [2018-04-18; online 2018-04-18]

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Data quality of whole genome bisulfite sequencing on Illumina platforms.

Raine A, Liljedahl U, Nordlund J

PLoS ONE 13 (4) e0195972 [2018-04-18; online 2018-04-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

Complete Remission with Reduction of High-Risk Clones following Haploidentical NK-Cell Therapy against MDS and AML

Björklund AT, Carlsten M, Sohlberg E, ..., Ljunggren HG, Malmberg KJ

Clin. Cancer Res. 24 (8) 1834-1844 [2018-04-15; online 2018-02-14]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia.

Danielsson F, Fasterius E, Sullivan D, ..., Williams C, Lundberg E

Oncotarget 9 (28) 19730-19744 [2018-04-13; online 2018-04-13]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Granule-stored MUC5B mucins are packed by the non-covalent formation of N-terminal head-to-head tetramers.

Trillo-Muyo S, Nilsson HE, Recktenwald CV, ..., Hebert H, Hansson GC

J. Biol. Chem. 293 (15) 5746-5754 [2018-04-13; online 2018-02-13]

Integrated Microscopy Technologies Gothenburg [Service]

Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate.

Giri J, Bhosale R, Huang G, ..., Swarup R, Bennett MJ

Nat Commun 9 (1) 1408 [2018-04-12; online 2018-04-12]

Crystal Structure of Botulinum Neurotoxin A2 in Complex with the Human Protein Receptor SV2C Reveals Plasticity in Receptor Binding.

Gustafsson R, Zhang S, Masuyer G, Dong M, Stenmark P

Toxins (Basel) 10 (4) - [2018-04-12; online 2018-04-12]

A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate.

Bhosale R, Giri J, Pandey BK, ..., Bennett MJ, Swarup R

Nat Commun 9 (1) 1409 [2018-04-12; online 2018-04-12]

Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima.

Morgunova E, Yin Y, Das PK, ..., Nilsson L, Taipale J

Elife 7 (-) - [2018-04-11; online 2018-04-11]

Bioinformatics Support for Computational Resources [Service] Protein Science Facility (PSF) [Service]

Expression levels of long non-coding RNAs are prognostic for AML outcome.

Mer AS, Lindberg J, Nilsson C, ..., Lehmann S, Rantalainen M

J Hematol Oncol 11 (1) 52 [2018-04-07; online 2018-04-07]

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Allele-selective RUNX1 binding regulates P1 blood group status by transcriptional control of A4GALT.

Westman JS, Stenfelt L, Vidovic K, ..., Kjellström S, Olsson ML

Blood 131 (14) 1611-1616 [2018-04-05; online 2018-02-08]

Female-specific Association Between Variants on Chromosome 9 and Self-reported Diagnosis of Irritable Bowel Syndrome.

Bonfiglio F, Zheng T, Garcia-Etxebarria K, ..., Zhernakova A, D'Amato M

Gastroenterology - (-) - [2018-04-04; online 2018-04-04]

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Abundant fish protein inhibits α-synuclein amyloid formation.

Werner T, Kumar R, Horvath I, Scheers N, Wittung-Stafshede P

Sci Rep 8 (1) 5465 [2018-04-03; online 2018-04-03]

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Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor

Perez Boerema A, Aibara S, Paul B, ..., Lindahl E, Amunts A

NPLANTS 4 (4) 212-217 [2018-04-02; online 2018-04-02]

An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics.

Gelali E, Custodio J, Girelli G, ..., Crosetto N, Bienko M

Methods Mol. Biol. 1766 (-) 303-333 [2018-04-02; online 2018-04-02]

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Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce.

Jokipii-Lukkari S, Delhomme N, Schiffthaler B, ..., Street NR, Tuominen H

Plant Physiol. 176 (4) 2851-2870 [2018-04-00; online 2018-02-27]

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The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines. Correction

Hofving T, Arvidsson Y, Almobarak B, ..., Johanson V, Nilsson O

Endocr Relat Cancer 25 (4) X1-X2 [2018-04-00; online 2018-04-00]

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The functional 3'-end of immunoglobulin heavy chain variable (IGHV) genes.

Thörnqvist L, Ohlin M

Mol. Immunol. 96 (-) 61-68 [2018-04-00; online 2018-02-28]

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Structural and functional studies of Spr1654: an essential aminotransferase in teichoic acid biosynthesis in

Han X, Sun R, Sandalova T, Achour A

Open Biol 8 (4) - [2018-04-00; online 2018-04-20]

Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes.

Mahajan A, Wessel J, Willems SM, ..., Rotter JI, McCarthy MI

Nat. Genet. 50 (4) 559-571 [2018-04-00; online 2018-04-09]

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RNA Sequencing of Stentor Cell Fragments Reveals Transcriptional Changes during Cellular Regeneration

Onsbring H, Jamy M, Ettema TJG

Current Biology 28 (8) 1281-1288.e3 [2018-04-00; online 2018-04-00]

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Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes.

Malik R, Chauhan G, Traylor M, ..., Debette S, Dichgans M

Nat. Genet. 50 (4) 524-537 [2018-04-00; online 2018-03-12]

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Modulation of saturation and chain length of fatty acids in Saccharomyces cerevisiae for production of cocoa butter-like lipids

Bergenholm D, Gossing M, Wei Y, Siewers V, Nielsen J

Biotechnol. Bioeng. 115 (4) 932-942 [2018-04-00; online 2018-01-24]

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Long Non-Coding RNAs Associated with Metabolic Traits in Human White Adipose Tissue.

Gao H, Kerr A, Jiao H, ..., Dahlman I, Arner P

EBioMedicine 30 (-) 248-260 [2018-04-00; online 2018-03-15]

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Know your farmer: Ancient origins and multiple independent domestications of ambrosia beetle fungal cultivars

Vanderpool D, Bracewell RR, McCutcheon JP

Mol Ecol 27 (8) 2077-2094 [2018-04-00; online 2017-11-23]

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Identification of Potential MR-Derived Biomarkers for Tumor Tissue Response to 177Lu-Octreotate Therapy in an Animal Model of Small Intestine Neuroendocrine Tumor.

Montelius M, Spetz J, Jalnefjord O, ..., Ljungberg M, Forssell-Aronsson E

Transl Oncol 11 (2) 193-204 [2018-04-00; online 2018-01-11]

Identification of Poly(ADP-Ribose) Polymerase Macrodomain Inhibitors Using an AlphaScreen Protocol

Ekblad T, Verheugd P, Lindgren AE, ..., Elofsson M, Schüler H

SLAS DISCOVERY: Advancing Life Sciences R&D 23 (4) 353-362 [2018-04-00; online 2018-01-09]

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GABA Regulates Release of Inflammatory Cytokines From Peripheral Blood Mononuclear Cells and CD4 + T Cells and Is Immunosuppressive in Type 1 Diabetes

Bhandage AK, Jin Z, Korol SV, ..., Kamali-Moghaddam M, Birnir B

EBioMedicine 30 (-) 283-294 [2018-04-00; online 2018-04-00]

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Effects of fixation on electrophysiology and structure of human jejunal villi.

Casselbrant A, Helander HF

Microsc Res Tech 81 (4) 376-383 [2018-04-00; online 2018-01-11]

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Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments.

Wang H, Sikora P, Rutgersson C, ..., Larsson DGJ, Norder H

International Journal of Hygiene and Environmental Health 221 (3) 479-488 [2018-04-00; online 2018-02-01]

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Confocal super-resolution imaging of the glomerular filtration barrier enabled by tissue expansion

Unnersjö-Jess D, Scott L, Sevilla SZ, ..., Blom H, Brismar H

Kidney International 93 (4) 1008-1013 [2018-04-00; online 2018-04-00]

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An in vitro evaluation of browser and grazer fermentation efficiency and microbiota using European moose spring and summer foods

Krizsan SJ, Mateos-Rivera A, Bertilsson S, ..., Gidlund H, Huhtanen P

Ecol Evol 8 (8) 4183-4196 [2018-04-00; online 2018-03-31]

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Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes.

Klaesson A, Grannas K, Ebai T, ..., Söderberg O, Landegren U

Sci Rep 8 (1) 5400 [2018-03-29; online 2018-03-29]

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Evaluation of the ISL1 gene in the pathogenesis of bladder exstrophy in a Swedish cohort.

Arkani S, Cao J, Lundin J, ..., Matsson H, Nordenskjöld A

Hum Genome Var 5 (-) 18009 [2018-03-29; online 2018-03-29]

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Strong impact on plasma protein profiles by precentrifugation delay but not by repeated freeze-thaw cycles, as analyzed using multiplex proximity extension assays.

Shen Q, Björkesten J, Galli J, ..., Tybring G, Landegren U

Clin. Chem. Lab. Med. 56 (4) 582-594 [2018-03-28; online 2017-10-19]

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Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia.

Valdiosera C, Günther T, Vera-Rodríguez JC, ..., Smith CI, Jakobsson M

Proc. Natl. Acad. Sci. U.S.A. 115 (13) 3428-3433 [2018-03-27; online 2018-03-12]

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Changes in methylation within the STK32B promoter are associated with an increased risk for generalized anxiety disorder in adolescents.

Ciuculete DM, Boström AE, Tuunainen AK, ..., Mwinyi J, Schiöth HB

J Psychiatr Res 102 (-) 44-51 [2018-03-26; online 2018-03-26]

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AMYCNE: Confident copy number assessment using whole genome sequencing data.

Eisfeldt J, Nilsson D, Andersson-Assarsson JC, Lindstrand A

PLoS ONE 13 (3) e0189710 [2018-03-26; online 2018-03-26]

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Protein Expression in Tonsillar and Base of Tongue Cancer and in Relation to Human Papillomavirus (HPV) and Clinical Outcome.

Ramqvist T, Näsman A, Franzén B, ..., Dalianis T, Munck-Wikland E

Int J Mol Sci 19 (4) 978 [2018-03-25; online 2018-03-25]

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Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb

Rasmussen PU, Hugerth LW, Blanchet FG, ..., Lindahl BD, Tack AJM

New Phytol - (-) - [2018-03-24; online 2018-03-24]

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A Meta-Analysis of Genome-Wide Association Studies of Growth Differentiation Factor-15 Concentration in Blood.

Jiang J, Thalamuthu A, Ho JE, ..., Sachdev PS, Mather KA

Front Genet 9 (-) 97 [2018-03-23; online 2018-03-23]

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Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury.

Dias DO, Kim H, Holl D, ..., Göritz C, Frisén J

Cell 173 (1) 153-165.e22 [2018-03-22; online 2018-03-01]

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Peptide ion channel toxins from the bootlace worm, the longest animal on Earth.

Jacobsson E, Andersson HS, Strand M, ..., Tytgat J, Göransson U

Sci Rep 8 (1) 4596 [2018-03-22; online 2018-03-22]

Introduction of Intrinsic Kinetics of Protein-Ligand Interactions and Their Implications for Drug Design.

Linkuvienė V, Talibov VO, Danielson UH, Matulis D

J. Med. Chem. 61 (6) 2292-2302 [2018-03-22; online 2018-03-02]

Molecular mechanism of ATP versus GTP selectivity of adenylate kinase

Rogne P, Rosselin M, Grundström C, ..., Sauer UH, Wolf-Watz M

Proc Natl Acad Sci USA 115 (12) 3012-3017 [2018-03-20; online 2018-03-05]

A Space Efficient Direct Access Data Compression Approach for Mass Spectrometry Imaging.

Källback P, Nilsson A, Shariatgorji M, Andrén PE

Anal. Chem. 90 (6) 3676-3682 [2018-03-20; online 2018-03-08]

Myopathy With SQSTM1 and TIA1 Variants: Clinical and Pathological Features.

Niu Z, Pontifex CS, Berini S, ..., Pfeffer G, Milone M

Front Neurol 9 (-) 147 [2018-03-19; online 2018-03-19]

ILF2 and ILF3 are autoantigens in canine systemic autoimmune disease.

Bremer HD, Landegren N, Sjöberg R, ..., Kämpe O, Hansson-Hamlin H

Sci Rep 8 (1) 4852 [2018-03-19; online 2018-03-19]

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Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics.

Ardui S, Ameur A, Vermeesch JR, Hestand MS

Nucleic Acids Res. 46 (5) 2159-2168 [2018-03-16; online 2018-02-06]

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Recurrent, low-frequency coding variants contributing to colorectal cancer in the Swedish population.

Jiao X, Liu W, Mahdessian H, ..., Dunlop M, Lindblom A

PLoS ONE 13 (3) e0193547 [2018-03-16; online 2018-03-16]

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A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage.

Ladds MJGW, van Leeuwen IMM, Drummond CJ, ..., McCormack E, Laín S

Nat Commun 9 (1) 1107 [2018-03-16; online 2018-03-16]

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Protein profiling in serum after traumatic brain injury in rats reveals potential injury markers.

Thelin EP, Just D, Frostell A, ..., Nilsson P, Bellander BM

Behav. Brain Res. 340 (-) 71-80 [2018-03-15; online 2016-08-31]

Clinical Presentation of a Complex Neurodevelopmental Disorder Caused by Mutations in ADNP.

Van Dijck A, Vulto-van Silfhout AT, Cappuyns E, ..., Vandeweyer G, Kooy RF

Biol. Psychiatry - (-) - [2018-03-15; online 2018-03-15]

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Transcriptional stimulation of rate-limiting components of the autophagic pathway improves plant fitness.

Minina EA, Moschou PN, Vetukuri RR, ..., Hofius D, Bozhkov PV

J. Exp. Bot. 69 (6) 1415-1432 [2018-03-14; online 2018-01-25]

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Seyfferth C, Wessels B, Jokipii-Lukkari S, ..., Felten J, Tuominen H

Front Plant Sci 9 (-) 272 [2018-03-14; online 2018-03-14]

High-resolution detection of chromosomal rearrangements in leukemias through mate pair whole genome sequencing.

Tran AN, Taylan F, Zachariadis V, ..., Nilsson D, Barbany G

PLoS ONE 13 (3) e0193928 [2018-03-12; online 2018-03-12]

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Increased thermal stability of nanocellulose composites by functionalization of the sulfate groups on cellulose nanocrystals with azetidinium ions

Börjesson M, Sahlin K, Bernin D, Westman G

J. Appl. Polym. Sci. 135 (10) 45963 [2018-03-10; online 2017-11-08]

Clinical Value of RNA Sequencing-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network-Breast Initiative.

Brueffer C, Vallon-Christersson J, Grabau D, ..., Borg Å, Saal LH

JCO Precision Oncology 2 (2) 1-18 [2018-03-09; online 2018-03-09]

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Biological annotation of genetic loci associated with intelligence in a meta-analysis of 87,740 individuals.

Coleman JRI, Bryois J, Gaspar HA, ..., Posthuma D, Breen G

Mol. Psychiatry - (-) - [2018-03-08; online 2018-03-08]

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The Interaction Modes of Haloimidazolium Salts in Solution.

Schulz N, Sokkar P, Engelage E, ..., Sanchez-Garcia E, Huber SM

Chemistry 24 (14) 3464-3473 [2018-03-07; online 2017-12-28]

Genome-wide analysis yields new loci associating with aortic valve stenosis.

Helgadottir A, Thorleifsson G, Gretarsdottir S, ..., Holm H, Stefansson K

Nat Commun 9 (1) 987 [2018-03-07; online 2018-03-07]

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Global analysis of A-to-I RNA editing reveals association with common disease variants

Franzén O, Ermel R, Sukhavasi K, ..., Schadt EE, Björkegren JLM

PeerJ 6 (-) e4466 [2018-03-06; online 2018-03-06]

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CEP128 Localizes to the Subdistal Appendages of the Mother Centriole and Regulates TGF-β/BMP Signaling at the Primary Cilium.

Mönnich M, Borgeskov L, Breslin L, ..., Larsen LA, Pedersen LB

Cell Rep 22 (10) 2584-2592 [2018-03-06; online 2018-03-08]

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An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans.

Mardinoglu A, Wu H, Bjornson E, ..., Taskinen MR, Borén J

Cell Metab. 27 (3) 559-571.e5 [2018-03-06; online 2018-02-15]

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The Immunogenicity of a Proline-Substituted Altered Peptide Ligand toward the Cancer-Associated TEIPP Neoepitope Trh4 Is Unrelated to Complex Stability.

Hafstrand I, Doorduijn EM, Sun R, ..., van Hall T, Achour A

J. Immunol. - (-) - [2018-03-05; online 2018-03-05]

DNA methylation holds prognostic information in relapsed precursor B-cell acute lymphoblastic leukemia.

Borssén M, Nordlund J, Haider Z, ..., Lönnerholm G, Degerman S

Clin Epigenetics 10 (-) 31 [2018-03-05; online 2018-03-05]

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Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death.

Reza SH, Delhomme N, Street NR, ..., Minina EA, Bozhkov PV

PLoS ONE 13 (3) e0192945 [2018-03-02; online 2018-03-02]

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NMR Study of Rcf2 Reveals an Unusual Dimeric Topology in Detergent Micelles.

Zhou S, Pettersson P, Brzezinski P, Ädelroth P, Mäler L

ChemBioChem 19 (5) 444-447 [2018-03-02; online 2018-01-25]

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.

Zhu Y, Orre LM, Johansson HJ, ..., Branca RMM, Lehtiö J

Nat Commun 9 (1) 903 [2018-03-02; online 2018-03-02]

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Striatal Tyrosine Hydroxylase Is Stimulated via TAAR1 by 3-Iodothyronamine, But Not by Tyramine or β-Phenylethylamine.

Zhang X, Mantas I, Alvarsson A, ..., Chergui K, Svenningsson P

Front Pharmacol 9 (-) 166 [2018-03-01; online 2018-03-01]

Sexual dimorphism in the width of the mouse synaptonemal complex

Agostinho A, Kouznetsova A, Hernández-Hernández A, ..., Brismar H, Höög C

J Cell Sci 131 (5) jcs212548 [2018-03-01; online 2018-02-02]

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Impact of genetic risk loci for multiple sclerosis on expression of proximal genes in patients.

James T, Lindén M, Morikawa H, ..., Gomez-Cabrero D, Kockum I

Hum. Mol. Genet. 27 (5) 912-928 [2018-03-01; online 2018-01-13]

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Genomic signatures of 60 years of bidirectional selection for 8-week body weight in chickens

Lillie M, Sheng ZY, Honaker CF, ..., Siegel PB, Carlborg Ö

Poult. Sci. 97 (3) 781-790 [2018-03-01; online 2017-12-20]

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Genetic variants influencing phenotypic variance heterogeneity.

Ek WE, Rask-Andersen M, Karlsson T, ..., Gyllensten U, Johansson Å

Hum. Mol. Genet. 27 (5) 799-810 [2018-03-01; online 2018-01-13]

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A Large-Scale Multi-ancestry Genome-wide Study Accounting for Smoking Behavior Identifies Multiple Significant Loci for Blood Pressure.

Sung YJ, Winkler TW, de Las Fuentes L, ..., Rao DC, Chasman DI

Am. J. Hum. Genet. 102 (3) 375-400 [2018-03-01; online 2018-02-15]

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The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines.

Hofving T, Arvidsson Y, Almobarak B, ..., Johanson V, Nilsson O

Endocr. Relat. Cancer 25 (3) 367-380 [2018-03-00; online 2018-02-16]

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The fungus that came in from the cold: dry rot’s pre-adapted ability to invade buildings

Balasundaram SV, Hess J, Durling MB, ..., Eastwood DC, Skrede I

ISME J 12 (3) 791-801 [2018-03-00; online 2018-01-05]

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Relicts of the lost arc: High-throughput sequencing of the Eutrichomyias rowleyi (Aves: Passeriformes) holotype uncovers an ancient biogeographic link between the Philippines and Fiji.

Jønsson KA, Blom MPK, Päckert M, Ericson PGP, Irestedt M

Mol. Phylogenet. Evol. 120 (-) 28-32 [2018-03-00; online 2017-12-02]

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Proteomic Profiling for Cardiovascular Biomarker Discovery in Orthostatic Hypotension.

Johansson M, Ricci F, Aung N, ..., Melander O, Fedorowski A

Hypertension 71 (3) 465-472 [2018-03-00; online 2018-01-02]

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Nubbin isoform antagonism governs Drosophila intestinal immune homeostasis.

Lindberg BG, Tang X, Dantoft W, ..., Lindvall JM, Engström Y

PLoS Pathog. 14 (3) e1006936 [2018-03-00; online 2018-03-02]

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Molecularly imprinted polymers synthesized via template immobilization on fumed silica nanoparticles for the enrichment of phosphopeptides.

Duarte M, Subedi P, Yilmaz E, ..., Laurell T, Ekström S

J. Mol. Recognit. 31 (3) - [2018-03-00; online 2017-10-12]

Lipids Shape the Electron Acceptor-Binding Site of the Peripheral Membrane Protein Dihydroorotate Dehydrogenase

Costeira-Paulo J, Gault J, Popova G, ..., Marklund EG, Landreh M

Cell Chem Biol 25 (3) 309-317.e4 [2018-03-00; online 2018-03-00]

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Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases

Bravo AG, Zopfi J, Buck M, ..., Poté J, Cosio C

ISME J 12 (3) 802-812 [2018-03-00; online 2018-01-10]

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Galectin-3 levels relate in children to total body fat, abdominal fat, body fat distribution, and cardiac size.

Dencker M, Arvidsson D, Karlsson MK, ..., Andersen LB, Thorsson O

Eur J Pediatr 177 (3) 461-467 [2018-03-00; online 2018-01-11]

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Fungal community shifts underpin declining mycelial production and turnover across a Pinus sylvestris chronosequence

Hagenbo A, Kyaschenko J, Clemmensen KE, Lindahl BD, Fransson P

J Ecol 106 (2) 490-501 [2018-03-00; online 2018-02-13]

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Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste

Marathe NP, Janzon A, Kotsakis SD, ..., Kristiansson E, Larsson DGJ

Environment International 112 (-) 279-286 [2018-03-00; online 2018-03-00]

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First de novo whole genome sequencing and assembly of the pink-footed goose.

Pujolar JM, Dalén L, Olsen RA, Hansen MM, Madsen J

Genomics 110 (2) 75-79 [2018-03-00; online 2017-08-30]

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Cleaner fish escape salmon farms and hybridize with local wrasse populations

Faust E, Halvorsen KT, Andersen P, Knutsen H, André C

R. Soc. open sci. 5 (3) 171752 [2018-03-00; online 2018-03-21]

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Cardiovascular disease in systemic lupus erythematosus is associated with increased levels of biomarkers reflecting receptor-activated apoptosis.

Wigren M, Svenungsson E, Mattisson IY, ..., Fredrikson GN, Nilsson J

Atherosclerosis 270 (-) 1-7 [2018-03-00; online 2018-01-17]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Affinity of charcoals for different forms of radioactive organic iodine

Aneheim E, Bernin D, Foreman MRS

Nuclear Engineering and Design 328 (-) 228-240 [2018-03-00; online 2018-03-00]

Current applications of antibody microarrays.

Chen Z, Dodig-Crnković T, Schwenk JM, Tao SC

Clin Proteomics 15 (-) 7 [2018-02-28; online 2018-02-28]

Yale School of Public Health Symposium on tissue imaging mass spectrometry: illuminating phenotypic heterogeneity and drug disposition at the molecular level.

Charkoftaki G, Rattray NJW, Andrén PE, ..., Johnson CH, Vasiliou V

Hum Genomics 12 (1) 10 [2018-02-27; online 2018-02-27]

The ZBED6–IGF2 axis has a major effect on growth of skeletal muscle and internal organs in placental mammals

Younis S, Schönke M, Massart J, ..., Zierath JR, Andersson L

Proc Natl Acad Sci USA 115 (9) E2048-E2057 [2018-02-27; online 2018-02-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Brain Tissue Sample Stabilization and Extraction Strategies for Neuropeptidomics.

Fridjonsdottir E, Nilsson A, Wadensten H, Andrén PE

Methods Mol. Biol. 1719 (-) 41-49 [2018-02-25; online 2018-02-25]

Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella

Bachmann JA, Tedder A, Laenen B, Steige KA, Slotte T

G3 (Bethesda) 8 (4) 1327-1333 [2018-02-23; online 2018-02-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Disruption of Accumbens and Thalamic White Matter Connectivity Revealed by Diffusion Tensor Tractography in Young Men with Genetic Risk for Obesity

Olivo G, Latini F, Wiemerslage L, Larsson EM, Schiöth HB

Front Hum Neurosci 12 (-) - [2018-02-22; online 2018-02-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A molecular atlas of cell types and zonation in the brain vasculature.

Vanlandewijck M, He L, Mäe MA, ..., Lendahl U, Betsholtz C

Nature 554 (7693) 475-480 [2018-02-22; online 2018-02-14]

Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

In Situ Target Engagement Studies in Adherent Cells

Axelsson H, Almqvist H, Otrocka M, ..., Lundbäck T, Seashore-Ludlow B

ACS Chem. Biol. - (-) - [2018-02-21; online 2018-02-21]

Bioinformatics Support for Computational Resources [Service] Chemical Biology Consortium Sweden (CBCS) [Technology development]

Structural and Biophysical Characterization of Human EXTL3: Domain Organization, Glycosylation, and Solution Structure.

Awad W, Kjellström S, Svensson Birkedal G, Mani K, Logan DT

Biochemistry 57 (7) 1166-1177 [2018-02-20; online 2018-02-05]

Antibodies in children with malaria to PfEMP1, RIFIN and SURFIN expressed at the Plasmodium falciparum parasitized red blood cell surface.

Quintana MDP, Ch'ng JH, Moll K, ..., Qundos U, Wahlgren M

Sci Rep 8 (1) 3262 [2018-02-19; online 2018-02-19]

Autoimmunity and Serology Profiling [Service] Bioinformatics Support for Computational Resources [Service]

Two novel colorectal cancer risk loci in the region on chromosome 9q22.32

Thutkawkorapin J, Mahdessian H, Barber T, ..., Jiao X, Lindblom A

Oncotarget 9 (13) - [2018-02-16; online 2018-01-30]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Mesenchymal stem cell-derived exosomes have altered microRNA profiles and induce osteogenic differentiation depending on the stage of differentiation.

Wang X, Omar O, Vazirisani F, Thomsen P, Ekström K

PLoS ONE 13 (2) e0193059 [2018-02-15; online 2018-02-15]

Integrated Microscopy Technologies Gothenburg [Service]

Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions.

Tang J, Tanoli ZU, Ravikumar B, ..., Wennerberg K, Aittokallio T

Cell Chem Biol 25 (2) 224-229.e2 [2018-02-15; online 2017-12-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Irreversible inhibition of cytosolic thioredoxin reductase 1 as a mechanistic basis for anticancer therapy.

Stafford WC, Peng X, Olofsson MH, ..., Linder S, Arnér ESJ

Sci Transl Med 10 (428) - [2018-02-14; online 2018-02-16]

Affinity proteomic profiling of plasma for proteins associated to area-based mammographic breast density.

Byström S, Eklund M, Hong MG, ..., Schwenk JM, Gabrielson M

Breast Cancer Res. 20 (1) 14 [2018-02-14; online 2018-02-14]

Affinity Proteomics Stockholm [Collaborative] Bioinformatics Support for Computational Resources [Service]

Educated natural killer cells show dynamic movement of the activating receptor NKp46 and confinement of the inhibitory receptor Ly49A

Staaf E, Hedde PN, Bagawath Singh S, ..., Gratton E, Johansson S

Sci. Signal. 11 (517) eaai9200 [2018-02-13; online 2018-02-13]

Integrated Microscopy Technologies Stockholm [Service]

Dispersed Uniform Nanoparticles from a Macroscopic Organosilica Powder.

Church TL, Bernin D, Garcia-Bennett AE, Hedin N

Langmuir 34 (6) 2274-2281 [2018-02-13; online 2018-02-05]

Advancing the immunoaffinity platform AFFIRM to targeted measurements of proteins in serum in the pg/ml range.

Säll A, Corbee D, Vikström S, ..., Persson H, Waldemarson S

PLoS ONE 13 (2) e0189116 [2018-02-13; online 2018-02-13]

Drug Discovery and Development (DDD) [Technology development]

Proteomic analyses identify prognostic biomarkers for pancreatic ductal adenocarcinoma.

Hu D, Ansari D, Pawłowski K, ..., Marko-Varga G, Andersson R

Oncotarget 9 (11) 9789-9807 [2018-02-09; online 2018-01-03]

The DNA Methylome of the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius

Couturier M, Lindås AC

Front Microbiol 9 (-) - [2018-02-08; online 2018-02-08]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A novel monoclonal antibody targeting carboxymethyllysine, an advanced glycation end product in atherosclerosis and pancreatic cancer.

Wendel U, Persson N, Risinger C, ..., Jansson B, Blixt O

PLoS ONE 13 (2) e0191872 [2018-02-08; online 2018-02-08]

Vascular Endothelial Growth Factor D, Pulmonary Congestion, and Incidence of Heart Failure.

Borné Y, Gränsbo K, Nilsson J, ..., Smith JG, Engström G

J. Am. Coll. Cardiol. 71 (5) 580-582 [2018-02-06; online 2018-02-07]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

MYCN-amplified neuroblastoma maintains an aggressive and undifferentiated phenotype by deregulation of estrogen and NGF signaling.

Dzieran J, Rodriguez Garcia A, Westermark UK, ..., Lehtiö J, Arsenian-Henriksson M

Proc. Natl. Acad. Sci. U.S.A. 115 (6) E1229-E1238 [2018-02-06; online 2018-01-26]

Global Proteomics and Proteogenomics [Collaborative]

Kynurenic Acid and Gpr35 Regulate Adipose Tissue Energy Homeostasis and Inflammation.

Agudelo LZ, Ferreira DMS, Cervenka I, ..., Berggren PO, Ruas JL

Cell Metab. 27 (2) 378-392.e5 [2018-02-06; online 2018-02-08]

Bioinformatics Support for Computational Resources [Service] Cellular Immunomonitoring [Collaborative]

Human NUDT22 Is a UDP-Glucose/Galactose Hydrolase Exhibiting a Unique Structural Fold.

Carter M, Jemth AS, Carreras-Puigvert J, ..., Helleday T, Stenmark P

Structure 26 (2) 295-303.e6 [2018-02-06; online 2018-02-08]

Crystal Structures and Inhibitor Interactions of Mouse and Dog MTH1 Reveal Species-Specific Differences in Affinity.

Narwal M, Jemth AS, Gustafsson R, ..., Helleday T, Stenmark P

Biochemistry 57 (5) 593-603 [2018-02-06; online 2018-01-16]

Ten steps to get started in Genome Assembly and Annotation

Dominguez Del Angel V, Hjerde E, Sterck L, ..., Binzer-Panchal M, Lantz H

F1000Res 7 (-) 148 [2018-02-05; online 2018-02-05]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Technology development] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Interferon γ treatment increases endocannabinoid and related N-acylethanolamine levels in T84 human colon carcinoma cells

Alhouayek M, Rankin L, Gouveia-Figueira S, Fowler CJ

British Journal of Pharmacology - (-) - [2018-02-05; online 2018-02-05]

CheckQC: Quick quality control of Illumina sequencing runs

Åslin M, Brandt M, Dahlberg J

JOSS 3 (22) 556 [2018-02-05; online 2018-02-05]

NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

A Common Peptidolytic Mechanism for Targeting Peptide Degradation in Mitochondria and Chloroplasts.

Kmiec B, Branca RMM, Murcha MW, ..., Glaser E, Teixeira PF

Mol Plant 11 (2) 342-345 [2018-02-05; online 2017-11-26]

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [Service]

Mechanism of Peptide Binding and Cleavage by the Human Mitochondrial Peptidase Neurolysin.

Teixeira PF, Masuyer G, Pinho CM, ..., Stenmark P, Glaser E

J. Mol. Biol. 430 (3) 348-362 [2018-02-02; online 2017-11-26]

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service]

Novel ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit.

Rozman Grinberg I, Lundin D, Hasan M, ..., Logan DT, Sjöberg BM

Elife 7 (-) - [2018-02-01; online 2018-02-01]

Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilum T.

Christel S, Herold M, Bellenberg S, ..., Poetsch A, Dopson M

Appl. Environ. Microbiol. 84 (3) e02091-17 [2018-02-01; online 2018-01-17]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Isolated myelosarcoma is characterized by recurrent NFE2 mutations and concurrent preleukemic clones in the bone marrow.

Lazarevic V, Orsmark-Pietras C, Lilljebjörn H, ..., Juliusson G, Fioretos T

Blood 131 (5) 577-581 [2018-02-01; online 2017-11-30]

Clinical Genomics [Collaborative] Clinical Genomics Lund [Collaborative]

Human Adenovirus Infection Causes Cellular E3 Ubiquitin Ligase MKRN1 Degradation Involving the Viral Core Protein pVII.

Inturi R, Mun K, Singethan K, Schreiner S, Punga T

J. Virol. 92 (3) - [2018-02-01; online 2018-01-17]

Affinity Proteomics Uppsala [Service] PLA and Single Cell Proteomics [Service]

De novo mutations implicate novel genes in systemic lupus erythematosus.

Pullabhatla V, Roberts AL, Lewis MJ, ..., Syvänen AC, Vyse TJ

Hum. Mol. Genet. 27 (3) 421-429 [2018-02-01; online 2017-11-28]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

U-CAN: a prospective longitudinal collection of biomaterials and clinical information from adult cancer patients in Sweden.

Glimelius B, Melin B, Enblad G, ..., Palmqvist R, Sjöblom T

Acta Oncol 57 (2) 187-194 [2018-02-00; online 2017-06-20]

Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis

Borges F, Parent JS, van Ex F, ..., Köhler C, Martienssen RA

Nat Genet 50 (2) 186-192 [2018-02-00; online 2018-01-15]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana.

McDonald MC, Ahren D, Simpfendorfer S, Milgate A, Solomon PS

Mol. Plant Pathol. 19 (2) 432-439 [2018-02-00; online 2017-03-12]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

The Influence of Heat Treatments on the Porosity of Suspension Plasma-Sprayed Yttria-Stabilized Zirconia Coatings

Ekberg J, Ganvir A, Klement U, Creci S, Nordstierna L

J Therm Spray Tech 27 (3) 391-401 [2018-02-00; online 2018-01-04]

Targeted proteomic analysis of habitual coffee consumption.

Cornelis MC, Gustafsson S, Ärnlöv J, ..., Lind L, Ingelsson E

J. Intern. Med. 283 (2) 200-211 [2018-02-00; online 2017-11-16]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

T cells are influenced by a long non-coding RNA in the autoimmune associated PTPN2 locus

Houtman M, Shchetynsky K, Chemin K, ..., Malmström V, Padyukov L

Journal of Autoimmunity 90 (-) 28-38 [2018-02-00; online 2018-02-00]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Small molecule PGC-1α1 protein stabilizers induce adipocyte Ucp1 expression and uncoupled mitochondrial respiration

Pettersson-Klein AT, Izadi M, Ferreira DMS, ..., Griffin PR, Ruas JL

Mol Metab - (-) - [2018-02-00; online 2018-02-00]

Bioinformatics Support for Computational Resources [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Service]

Slow evolution of sex-biased genes in the reproductive tissue of the dioecious plant Salix viminalis

Darolti I, Wright AE, Pucholt P, Berlin S, Mank JE

Mol Ecol 27 (3) 694-708 [2018-02-00; online 2018-01-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Red meat intake in chronic kidney disease patients: Two sides of the coin

Mafra D, Borges NA, Cardozo LFMdF, ..., Lindholm B, Stenvinkel P

Nutrition 46 (-) 26-32 [2018-02-00; online 2018-02-00]

Bioinformatics Support for Computational Resources [Service] Swedish Metabolomics Centre (SMC) [Service]

Quantitative image analysis of protein expression and colocalisation in skin sections

Zhang H, Ericsson M, Virtanen M, ..., Vahlquist A, Törmä H

Exp Dermatol 27 (2) 196-199 [2018-02-00; online 2018-01-09]

BioImage Informatics [Service] Bioinformatics (NBIS) [Service]

Probing the activity of a recombinant Zn2+ -transporting P-type ATPase.

Ravishankar H, Barth A, Andersson M

Biopolymers 109 (2) - [2018-02-00; online 2017-11-23]

Paternal easiRNAs regulate parental genome dosage in Arabidopsis

Martinez G, Wolff P, Wang Z, ..., Slotkin RK, Köhler C

Nat Genet 50 (2) 193-198 [2018-02-00; online 2018-01-15]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Megakaryocytes harbour the del(5q) abnormality despite complete clinical and cytogenetic remission induced by lenalidomide treatment

Scharenberg C, Jansson M, Saft L, Hellström-Lindberg E

Br J Haematol 180 (4) 526-533 [2018-02-00; online 2018-01-29]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

Life after tree death: Does restored dead wood host different fungal communities to natural woody substrates?

Pasanen H, Junninen K, Boberg J, ..., Stenlid J, Kouki J

Forest Ecology and Management 409 (-) 863-871 [2018-02-00; online 2018-02-00]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

In situ protein detection with enhanced specificity using DNA-conjugated antibodies and proximity ligation.

Zieba A, Ponten F, Uhlén M, Landegren U

Mod. Pathol. 31 (2) 253-263 [2018-02-00; online 2017-09-22]

Affinity Proteomics Uppsala [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] PLA and Single Cell Proteomics [Technology development] Tissue Profiling [Collaborative]

Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation.

Leal L, Talla V, Källman T, ..., Vila R, Backström N

Mol. Ecol. 27 (4) 935-948 [2018-02-00; online 2018-02-26]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Formation of mercury methylation hotspots as a consequence of forestry operations

Eklöf K, Bishop K, Bertilsson S, ..., Kronberg RM, Bravo AG

Science of The Total Environment 613-614 (-) 1069-1078 [2018-02-00; online 2018-02-00]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Establishment of Photosynthesis through Chloroplast Development Is Controlled by Two Distinct Regulatory Phases.

Dubreuil C, Jin X, Barajas-López JD, ..., Small I, Strand Å

Plant Physiol. 176 (2) 1199-1214 [2018-02-00; online 2017-06-16]

Dispersal timing determines the importance of priority effects in bacterial communities

Svoboda P, Lindström ES, Ahmed Osman O, Langenheder S

ISME J 12 (2) 644-646 [2018-02-00; online 2017-10-20]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Copy Number Variation Analysis of 100 Twin Pairs Enriched for Neurodevelopmental Disorders.

Stamouli S, Anderlid BM, Willfors C, ..., Tammimies K, Bölte S

Twin Res Hum Genet 21 (1) 1-11 [2018-02-00; online 2018-01-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing.

Hochgerner H, Zeisel A, Lönnerberg P, Linnarsson S

Nat. Neurosci. 21 (2) 290-299 [2018-02-00; online 2018-01-15]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Bacterial secretion of D-arginine controls environmental microbial biodiversity.

Alvarez L, Aliashkevich A, de Pedro MA, Cava F

ISME J 12 (2) 438-450 [2018-02-00; online 2017-10-13]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA

Ahmed E, Parducci L, Unneberg P, ..., Slotte T, Wohlfarth B

Quaternary Science Reviews 181 (-) 19-29 [2018-02-00; online 2018-02-00]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Activating FGFR1 Mutations in Sporadic Pheochromocytomas.

Welander J, Łysiak M, Brauckhoff M, ..., Söderkvist P, Gimm O

World J Surg 42 (2) 482-489 [2018-02-00; online 2017-11-22]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A convenient transesterification method for synthesis of AT2 receptor ligands with improved stability in human liver microsomes

Wannberg J, Isaksson R, Bremberg U, ..., Hallberg M, Larhed M

Bioorganic & Medicinal Chemistry Letters 28 (3) 519-522 [2018-02-00; online 2018-02-00]

Drug Discovery and Development (DDD) [Collaborative]

A DNA methylation biomarker of alcohol consumption.

Liu C, Marioni RE, Hedman ÅK, ..., Ingelsson E, Levy D

Mol. Psychiatry 23 (2) 422-433 [2018-02-00; online 2016-11-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Pulmonary fibrosis in vivo displays increased p21 expression reduced by 5-HT2B receptor antagonists in vitro - a potential pathway affecting proliferation.

Löfdahl A, Rydell-Törmänen K, Larsson-Callerfelt A, Wenglén C, Westergren-Thorsson G

Sci Rep 8 (1) 1927 [2018-01-31; online 2018-01-31]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

A Single Bout of Electroacupuncture Remodels Epigenetic and Transcriptional Changes in Adipose Tissue in Polycystic Ovary Syndrome.

Kokosar M, Benrick A, Perfilyev A, ..., Ling C, Stener-Victorin E

Sci Rep 8 (1) 1878 [2018-01-30; online 2018-01-30]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Metabolome dynamics of diapause in the butterfly Pieris napi: distinguishing maintenance, termination and post-diapause phases.

Lehmann P, Pruisscher P, Koštál V, ..., Wheat CW, Gotthard K

J Exp Biol 221 (Pt 2) - [2018-01-25; online 2018-01-25]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Innate immune alterations are elicited in microglial cells before plaque deposition in the Alzheimer's disease mouse model 5xFAD.

Boza-Serrano A, Yang Y, Paulus A, Deierborg T

Sci Rep 8 (1) 1550 [2018-01-24; online 2018-01-24]

In Situ Analyses Directly in Diarrheal Stool Reveal Large Variations in Bacterial Load and Active Toxin Expression of Enterotoxigenic Escherichia coli and Vibrio cholerae

Begum YA, Rydberg HA, Thorell K, ..., Qadri F, Sjöling Å

mSphere 3 (1) e00517-17 [2018-01-24; online 2018-01-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Genetical genomics of growth in a chicken model.

Johnsson M, Henriksen R, Höglund A, ..., Jensen P, Wright D

BMC Genomics 19 (1) 72 [2018-01-23; online 2018-01-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina.

Laenen B, Tedder A, Nowak MD, ..., Coupland G, Slotte T

Proc. Natl. Acad. Sci. U.S.A. 115 (4) 816-821 [2018-01-23; online 2018-01-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Targeted NUDT5 inhibitors block hormone signaling in breast cancer cells.

Page BDG, Valerie NCK, Wright RHG, ..., Beato M, Helleday T

Nat Commun 9 (1) 250 [2018-01-17; online 2018-01-17]

Bioinformatics Support for Computational Resources [Service] Drug Discovery and Development (DDD) [Service] Protein Science Facility (PSF) [Service]

Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels.

Jiang X, O'Reilly PF, Aschard H, ..., Kraft P, Kiel DP

Nat Commun 9 (1) 260 [2018-01-17; online 2018-01-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Alpha-actinin of the chlorarchiniophyte Bigelowiella natans.

Backman L

PeerJ 6 (-) e4288 [2018-01-17; online 2018-01-17]

Spotty Carotid Plaques Are Associated with Inflammation and the Occurrence of Cerebrovascular Symptoms.

Halak S, Östling G, Edsfeldt A, ..., Gonçalves I, Asciutto G

Cerebrovasc Dis Extra 8 (1) 16-25 [2018-01-15; online 2018-01-15]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D

Jenjaroenpun P, Wongsurawat T, Pereira R, ..., Nielsen J, Nookaew I

Nucleic Acids Res - (-) - [2018-01-13; online 2018-01-13]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Rapid hybrid speciation in Darwin’s finches

Lamichhaney S, Han F, Webster MT, ..., Grant BR, Grant PR

Science 359 (6372) 224-228 [2018-01-12; online 2017-11-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Meta-analysis of exome array data identifies six novel genetic loci for lung function.

Jackson VE, Latourelle JC, Wain LV, ..., Tobin MD, London SJ

Wellcome Open Res 3 (-) 4 [2018-01-12; online 2018-01-12]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Identification of shared genetic variants between schizophrenia and lung cancer.

Zuber V, Jönsson EG, Frei O, ..., Mills IG, Andreassen OA

Sci Rep 8 (1) 674 [2018-01-12; online 2018-01-12]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Global Acetylome of the Human Pathogen Vibrio cholerae V52 Reveals Lysine Acetylation of Major Transcriptional Regulators.

Jers C, Ravikumar V, Lezyk M, ..., Wai SN, Mijakovic I

Front. Cell. Infect. Microbiol. 7 (-) 537 [2018-01-11; online 2018-01-11]

Splicing of platelet resident pre-mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications.

Nassa G, Giurato G, Cimmino G, ..., Weisz A, Tarallo R

Sci Rep 8 (1) 498 [2018-01-11; online 2018-01-11]

Global Proteomics and Proteogenomics [Collaborative]

Sample handling of gastric tissue and O-glycan alterations in paired gastric cancer and non-tumorigenic tissues.

Adamczyk B, Jin C, Polom K, ..., Roviello F, Karlsson NG

Sci Rep 8 (1) 242 [2018-01-10; online 2018-01-10]

Glycoproteomics and MS Proteomics [Technology development]

Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration.

Schroeder BO, Birchenough GMH, Ståhlman M, ..., Hansson GC, Bäckhed F

Cell Host Microbe 23 (1) 27-40.e7 [2018-01-10; online 2017-12-21]

Integrated Microscopy Technologies Gothenburg [Service]

A protein interaction network centered on leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) regulates growth factor receptors

Faraz M, Herdenberg C, Holmlund C, Henriksson R, Hedman H

J. Biol. Chem. - (-) jbc.M117.807487 [2018-01-09; online 2018-01-09]

Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]

Discovering viral genomes in human metagenomic data by predicting unknown protein families.

Barrientos-Somarribas M, Messina DN, Pou C, ..., Andersson B, Sonnhammer ELL

Sci Rep 8 (1) 28 [2018-01-08; online 2018-01-08]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Comprehensive Mass Spectrometric Survey of Streptococcus pyogenes Subcellular Proteomes.

Wilk L, Happonen L, Malmström J, Herwald H

J. Proteome Res. 17 (1) 600-617 [2018-01-05; online 2017-12-04]

The ATPase activity of Asna1/TRC40 is required for pancreatic progenitor cell survival.

Norlin S, Parekh V, Edlund H

Development 145 (1) dev154468 [2018-01-03; online 2018-01-03]

Evaluating vacquinol-1 in rats carrying glioblastoma models RG2 and NS1

Ahlstedt J, Förnvik K, Zolfaghari S, ..., Salford LG, Redebrandt HN

Oncotarget - (-) - [2018-01-03; online 2018-01-03]

Bioinformatics Support for Computational Resources [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum.

Fogelqvist J, Tzelepis G, Bejai S, ..., Schwelm A, Dixelius C

BMC Genomics 19 (1) 14 [2018-01-03; online 2018-01-03]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees.

Obudulu O, Mähler N, Skotare T, ..., Trygg J, Tuominen H

BMC Genomics 19 (1) 11 [2018-01-03; online 2018-01-03]

Differential impact of RB status on E2F1 reprogramming in human cancer.

McNair C, Xu K, Mandigo AC, ..., Brown M, Knudsen KE

J. Clin. Invest. 128 (1) 341-358 [2018-01-02; online 2017-12-04]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Angiopoietin-1 deficiency increases renal capillary rarefaction and tubulointerstitial fibrosis in mice

Loganathan K, Salem Said E, Winterrowd E, ..., Quaggin SE, Jeansson M

PLoS ONE 13 (1) e0189433 [2018-01-02; online 2018-01-02]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy

Bernhem K, Brismar H

Bioinformatics 34 (1) 137-138 [2018-01-01; online 2017-09-04]

Bioinformatics Support for Computational Resources [Service] Integrated Microscopy Technologies Stockholm [Technology development]

Metabolism and Whole-Body Fat Oxidation Following Postexercise Carbohydrate or Protein Intake.

Andersson-Hall U, Pettersson S, Edin F, ..., Malmodin D, Madsen K

International Journal of Sport Nutrition and Exercise Metabolism 28 (1) 37-45 [2018-01-01; online 2018-01-17]

Metabolic and functional phenotypic profiling of Drosophila melanogaster reveals reduced sex differentiation under stressful environmental conditions

Ørsted M, Malmendal A, Muñoz J, Kristensen TN

Biol J Linn Soc Lond 123 (1) 155-162 [2018-01-01; online 2017-10-31]

Cytokine Autoantibody Screening in the Swedish Addison Registry Identifies Patients With Undiagnosed APS1

Eriksson D, Dalin F, Eriksson GN, ..., Munoz KD, None

J. Clin. Endocrinol. Metab. 103 (1) 179-186 [2018-01-01; online 2017-10-20]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique

Cholleti H, Hayer J, Mulandane FC, ..., Berg M, Blomström AL

Infect Ecol Epidemiol 8 (1) 1478585 [2018-01-00; online 2018-05-28]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive.

Low GW, Chattopadhyay B, Garg KM, ..., Wu S, Rheindt FE

Heredity (Edinb) 120 (2) 138-153 [2018-01-00; online 2017-12-11]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.

Salvatore M, Shu N, Elofsson A

Protein Sci. 27 (1) 195-201 [2018-01-00; online 2017-10-24]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]

Surface treatment of cellulose nanocrystals (CNC): effects on dispersion rheology

Sahlin K, Forsgren L, Moberg T, ..., Rigdahl M, Westman G

Cellulose 25 (1) 331-345 [2018-01-00; online 2017-11-28]

Solid and fluid segments within the same molecule of stratum corneum ceramide lipid.

Pham QD, Mojumdar EH, Gooris GS, ..., Sparr E, Topgaard D

Quart. Rev. Biophys. 51 (-) e7 [2018-01-00; online 2018-01-01]

Single-molecule DNA sequencing of acute myeloid leukemia and myelodysplastic syndromes with multiple TP53 alterations.

Lodé L, Ameur A, Coste T, ..., Lavabre-Bertrand T, Soussi T

Haematologica 103 (1) e13-e16 [2018-01-00; online 2017-10-27]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity.

Turcot V, Lu Y, Highland HM, ..., MAGIC Investigators , Understanding Society Scientific Group

Nat. Genet. 50 (1) 26-41 [2018-01-00; online 2017-12-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation.

Günther T, Malmström H, Svensson EM, ..., Götherström A, Jakobsson M

PLoS Biol. 16 (1) e2003703 [2018-01-00; online 2018-01-09]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Perspectives on NMR studies of CO2 adsorption

Bernin D, Hedin N

Current Opinion in Colloid & Interface Science 33 (-) 53-62 [2018-01-00; online 2018-01-00]

Normalization of mass spectrometry data (NOMAD).

Murie C, Sandri B, Sandberg AS, ..., Wendt C, Larsson O

Adv Biol Regul 67 (-) 128-133 [2018-01-00; online 2017-11-20]

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service]

Natural product inspired library synthesis - Identification of 2,3-diarylbenzofuran and 2,3-dihydrobenzofuran based inhibitors of Chlamydia trachomatis

Saleeb M, Mojica S, Eriksson AU, ..., Gylfe Å, Elofsson M

European Journal of Medicinal Chemistry 143 (-) 1077-1089 [2018-01-00; online 2018-01-00]

Bioinformatics Support for Computational Resources [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Minimizing inequality in access to precision medicine in breast cancer by real-time population-based molecular analysis in the SCAN-B initiative.

Rydén L, Loman N, Larsson C, ..., Saal LH, Borg Å

Br J Surg 105 (2) e158-e168 [2018-01-00; online 2018-01-18]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Lund [Collaborative]

MicroRNA expression profiles in non‑epithelial ovarian tumors.

Chang RK, Li X, Mu N, ..., Larsson C, Lui WO

Int. J. Oncol. 52 (1) 55-66 [2018-01-00; online 2017-11-10]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Leucocyte recruitment and molecular fortification of keratinocytes triggered by streptococcal M1 protein.

Persson ST, Hauri S, Malmström J, Herwald H

Cell. Microbiol. 20 (1) - [2018-01-00; online 2017-10-19]

Homozygosity for a missense variant in COMP gene associated with severe pseudoachondroplasia

Tariq M, Khan TN, Lundin L, ..., Dahl N, Klar J

Clin Genet 93 (1) 182-186 [2018-01-00; online 2017-11-21]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Herpesvirus deconjugases inhibit the IFN response by promoting TRIM25 autoubiquitination and functional inactivation of the RIG-I signalosome.

Gupta S, Ylä-Anttila P, Callegari S, ..., Delecluse HJ, Masucci MG

PLoS Pathog. 14 (1) e1006852 [2018-01-00; online 2018-01-22]

Genomic consequences of intensive inbreeding in an isolated wolf population

Kardos M, Åkesson M, Fountain T, ..., Wikenros C, Ellegren H

Nat Ecol Evol 2 (1) 124-131 [2018-01-00; online 2017-11-20]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Exome sequencing reveals NAA15 and PUF60 as candidate genes associated with intellectual disability.

Zhao JJ, Halvardson J, Zander CS, ..., Thuresson AC, Feuk L

Am. J. Med. Genet. B Neuropsychiatr. Genet. 177 (1) 10-20 [2018-01-00; online 2017-10-09]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Epigenetic Changes in the CRH Gene are Related to Severity of Suicide Attempt and a General Psychiatric Risk Score in Adolescents.

Jokinen J, Boström AE, Dadfar A, ..., Åsberg M, Schiöth HB

EBioMedicine 27 (-) 123-133 [2018-01-00; online 2017-12-18]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest-tundra ecotone

Vowles T, Lindwall F, Ekblad A, ..., Ryberg M, Björk RG

Ecol Evol 8 (2) 1019-1030 [2018-01-00; online 2017-12-14]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Clofazimine protects against Mycobacterium tuberculosis dissemination in the central nervous system following aerosol challenge in a murine model.

Baijnath S, Moodley C, Ngcobo B, ..., Pym A, Govender T

International Journal of Antimicrobial Agents 51 (1) 77-81 [2018-01-00; online 2017-08-24]

Drug Discovery and Development (DDD) [Collaborative]

Circulating proteins as predictors of incident heart failure in the elderly.

Stenemo M, Nowak C, Byberg L, ..., Fall T, Ärnlöv J

Eur. J. Heart Fail. 20 (1) 55-62 [2018-01-00; online 2017-10-02]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Characterization of gamma-tubulin filaments in mammalian cells.

Lindström L, Alvarado-Kristensson M

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1865 (1) 158-171 [2018-01-00; online 2017-10-16]

Integrated Microscopy Technologies Gothenburg [Service]

Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes

Suh A, Smeds L, Ellegren H

Mol Ecol 27 (1) 99-111 [2018-01-00; online 2017-12-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Whole Slide Image Registration for the Study of Tumor Heterogeneity

Solorzano L, Almeida GM, Mesquita B, ..., Oliveira C, Wählby C

- - (-) 95-102 [2018-00-00; online 2018-09-14]

BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

The CO2capturing ability of cellulose dissolved in NaOH(aq) at low temperature

Gunnarsson M, Bernin D, Östlund Å, Hasani M

Green Chem. 20 (14) 3279-3286 [2018-00-00; online 2018-00-00]

The CO2 capturing ability of cellulose dissolved in NaOH(aq) at low temperature

Gunnarsson M, Bernin D, Östlund Å, Hasani M

Green Chem. 20 (14) 3279-3286 [2018-00-00; online 2018-00-00]

Synthesis of novel 1,2,4-thiadiazinane 1,1-dioxides via three component SuFEx type reaction

Khumalo MF, Akpan ED, Chinthakindi PK, ..., Naicker T, Arvidsson PI

RSC Adv. 8 (65) 37503-37507 [2018-00-00; online 2018-00-00]

Drug Discovery and Development (DDD) [Technology development]

Phylogeny, species delimitation and revision of Pleioluma (Sapotaceae) in New Caledonia, a frequently gynodioecious genus

Swenson U, Nylander JAA, Munzinger J

Aust. Systematic Bot. 31 (2) 120 [2018-00-00; online 2018-00-00]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Orange is the new white: rapid curing of an ethylene-glycidyl methacrylate copolymer with a Ti-bisphenolate type catalyst

Mauri M, Svenningsson L, Hjertberg T, ..., Prieto O, Müller C

Polym. Chem. 9 (13) 1710-1718 [2018-00-00; online 2018-00-00]

Optimising methods for the recovery and quantification of di- and tripeptides in soil

Jämtgård S, Robinson N, Moritz T, Colgrave ML, Schmidt S

Soil Res. 56 (4) 404 [2018-00-00; online 2018-00-00]

Improved Reconstruction of Low Intensity Magnetic Resonance Spectroscopy With Weighted Low Rank Hankel Matrix Completion

Guo D, Qu X

IEEE Access 6 (-) 4933-4940 [2018-00-00; online 2018-00-00]

High-fidelity spectroscopy reconstruction in accelerated NMR

Qu X, Qiu T, Guo D, ..., Orekhov V, Chen Z

Chem. Commun. 54 (78) 10958-10961 [2018-00-00; online 2018-00-00]

Swedish NMR Centre (SNC) [Technology development]

High purity and viability cell separation of a bacterivorous jakobid flagellate based on a steep velocity gradient induced soft inertial force

Deng P, Fu CJ, Wu Z

RSC Adv. 8 (62) 35512-35520 [2018-00-00; online 2018-00-00]

Microbial Single Cell Genomics [Service]

Efficient C–C coupling of bio-based furanics and carbonyl compounds to liquid hydrocarbon precursors over lignosulfonate derived acidic carbocatalysts

Konwar LJ, Samikannu A, Mäki-Arvela P, Mikkola JP

Catal. Sci. Technol. 8 (9) 2449-2459 [2018-00-00; online 2018-00-00]

Effect of various structure directing agents (SDAs) on low-temperature deactivation of Cu/SAPO-34 during NH3-SCR reaction

Woo J, Leistner K, Bernin D, ..., Zammit M, Olsson L

Catal. Sci. Technol. 8 (12) 3090-3106 [2018-00-00; online 2018-00-00]

Effect of various structure directing agents (SDAs) on low-temperature deactivation of Cu/SAPO-34 during NH3-SCR reaction

Woo J, Leistner K, Bernin D, ..., Zammit M, Olsson L

Catal. Sci. Technol. 8 (12) 3090-3106 [2018-00-00; online 2018-00-00]

Bioinformatics Support for Computational Resources [Service] Swedish NMR Centre (SNC) [Service]

An unexpected re-arrangement of the antibiotic carbapenem core to new 1,4-diazepin-5-one scaffolds

Peters BK, Razuwika R, Samipillai M, ..., Govender T, Naicker T

RSC Adv. 8 (1) 190-193 [2018-00-00; online 2018-00-00]

Drug Discovery and Development (DDD) [Collaborative]

InSiDDe: A Server for Designing Artificial Disordered Proteins.

Schramm A, Lieutaud P, Gianni S, Longhi S, Bignon C

Int J Mol Sci 19 (1) - [2017-12-29; online 2017-12-29]

Targeted copy number screening highlights an intragenic deletion of WDR63 as the likely cause of human occipital encephalocele and abnormal CNS development in zebrafish.

Hofmeister W, Pettersson M, Kurtoglu D, ..., Gustavsson P, Lindstrand A

Hum. Mutat. - (-) - [2017-12-28; online 2017-12-28]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Methylation-based estimated biological age and cardiovascular disease

Lind L, Ingelsson E, Sundström J, Siegbahn A, Lampa E

Eur J Clin Invest - (-) e12872 [2017-12-27; online 2017-12-27]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Chemical and microbiological evaluation of novel chemical treatment methods for acid sulfate soils.

Högfors-Rönnholm E, Christel S, Dalhem K, ..., Österholm P, Dopson M

Sci. Total Environ. 625 (-) 39-49 [2017-12-26; online 2017-12-26]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Reading and editing the Pleurodeles waltl genome reveals novel features of tetrapod regeneration.

Elewa A, Wang H, Talavera-López C, ..., Andersson B, Simon A

Nat Commun 8 (1) 2286 [2017-12-22; online 2017-12-22]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Low Concentrations of Vitamin C Reduce the Synthesis of Extracellular Polymers and Destabilize Bacterial Biofilms.

Pandit S, Ravikumar V, Abdel-Haleem AM, ..., Westerlund F, Mijakovic I

Front Microbiol 8 (-) 2599 [2017-12-22; online 2017-12-22]

Common founder effects of hereditary hemochromatosis, Wilson´s disease, the long QT syndrome and autosomal recessive deafness caused by two novel mutations in the WHRN and TMC1 genes.

Olsson KS, Wålinder O, Jansson U, ..., Raha-Chowdhury R, Williams R

Hereditas 154 (1) 16 [2017-12-19; online 2017-12-19]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

A family-based genome-wide association study of chronic rhinosinusitis with nasal polyps implicates several genes in the disease pathogenesis

Bohman A, Juodakis J, Oscarsson M, ..., Bende M, Torinsson Naluai Å

PLoS ONE 12 (12) e0185244 [2017-12-18; online 2017-12-18]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A chemical screen identifies trifluoperazine as an inhibitor of glioblastoma growth.

Pinheiro T, Otrocka M, Seashore-Ludlow B, ..., Simon A, Kirkham M

Biochem. Biophys. Res. Commun. 494 (3-4) 477-483 [2017-12-16; online 2017-10-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Targeting tumor cells based on Phosphodiesterase 3A expression.

Nazir M, Senkowski W, Nyberg F, ..., Larsson R, Fryknäs M

Exp. Cell Res. 361 (2) 308-315 [2017-12-15; online 2017-10-26]

Discovery of the fourth mobile sulfonamide resistance gene.

Razavi M, Marathe NP, Gillings MR, ..., Kristiansson E, Joakim Larsson DG

Microbiome 5 (1) 160 [2017-12-15; online 2017-12-15]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Cancer risk susceptibility loci in a Swedish population.

Liu W, Jiao X, Thutkawkorapin J, Mahdessian H, Lindblom A

Oncotarget 8 (66) 110300-110310 [2017-12-15; online 2017-11-25]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Gene expression and risk of leukemic transformation in myelodysplasia.

Shiozawa Y, Malcovati L, Gallì A, ..., Cazzola M, Ogawa S

Blood 130 (24) 2642-2653 [2017-12-14; online 2017-11-02]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

CELSR2 is a candidate susceptibility gene in idiopathic scoliosis

Einarsdottir E, Grauers A, Wang J, ..., Kere J, Gerdhem P

PLoS ONE 12 (12) e0189591 [2017-12-14; online 2017-12-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Transcriptomics and Targeted Proteomics Analysis to Gain Insights Into the Immune-control Mechanisms of HIV-1 Infected Elite Controllers.

Zhang W, Ambikan AT, Sperk M, ..., Sönnerborg A, Neogi U

EBioMedicine - (-) - [2017-12-12; online 2017-12-12]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Comparative cell cycle transcriptomics reveals synchronization of developmental transcription factor networks in cancer cells

Boström J, Sramkova Z, Salašová A, ..., Altun M, Andäng M

PLoS ONE 12 (12) e0188772 [2017-12-11; online 2017-12-11]

Characterization of the Giardia intestinalis secretome during interaction with human intestinal epithelial cells: The impact on host cells

Ma’ayeh SY, Liu J, Peirasmaki D, ..., Bergquist J, Svärd SG

PLoS Negl Trop Dis 11 (12) e0006120 [2017-12-11; online 2017-12-11]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Genomic and phenotypic characteristics of Swedish C. jejuni water isolates.

Nilsson A, Johansson C, Skarp A, ..., Engstrand L, Rautelin H

PLoS ONE 12 (12) e0189222 [2017-12-07; online 2017-12-07]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

A Unique ISR Program Determines Cellular Responses to Chronic Stress.

Guan BJ, van Hoef V, Jobava R, ..., Larsson O, Hatzoglou M

Mol. Cell 68 (5) 885-900.e6 [2017-12-07; online 2017-12-09]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Magnesium induces preconditioning of the neonatal brain via profound mitochondrial protection

Koning G, Leverin AL, Nair S, ..., Mallard C, Hagberg H

J Cereb Blood Flow Metab 39 (6) 1038-1055 [2017-12-05; online 2017-12-05]

Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff ( Phylloscopus collybita abietinus/P. tristis).

Talla V, Kalsoom F, Shipilina D, Marova I, Backström N

G3 (Bethesda) 7 (12) 3983-3998 [2017-12-04; online 2017-12-04]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Human Plasma Proteome Draft of 2017: Building on the Human Plasma PeptideAtlas from Mass Spectrometry and Complementary Assays.

Schwenk JM, Omenn GS, Sun Z, ..., Moritz RL, Deutsch EW

J. Proteome Res. 16 (12) 4299-4310 [2017-12-01; online 2017-10-10]

Metabolome and transcriptome profiling reveal new insights into somatic embryo germination in Norway spruce (Picea abies).

Dobrowolska I, Businge E, Abreu IN, Moritz T, Egertsdotter U

Tree Physiol 37 (12) 1752-1766 [2017-12-01; online 2017-10-07]

Towards repositioning of quinacrine for treatment of acute myeloid leukemia - Promising synergies and in vivo effects.

Eriksson A, Chantzi E, Fryknäs M, ..., Höglund M, Larsson R

Leuk Res 63 (-) 41-46 [2017-12-00; online 2017-10-28]

The oxylipin and endocannabidome responses in acute phase Plasmodium falciparum malaria in children

Surowiec I, Gouveia-Figueira S, Orikiiriza J, ..., Normark J, Trygg J

Malar. J. 16 (1) - [2017-12-00; online 2017-09-08]

The dynamic dimer structure of the chaperone Trigger Factor

Morgado L, Burmann BM, Sharpe T, Mazur A, Hiller S

Nat Commun 8 (1) - [2017-12-00; online 2017-12-08]

Structural basis for dolichylphosphate mannose biosynthesis

Gandini R, Reichenbach T, Tan TC, Divne C

Nat Commun 8 (1) - [2017-12-00; online 2017-07-25]

Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology.

Ferreira MA, Vonk JM, Baurecht H, ..., Koppelman GH, Paternoster L

Nat. Genet. 49 (12) 1752-1757 [2017-12-00; online 2017-10-30]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Rho-kinase inhibitor Y-27632 and hypoxia synergistically enhance chondrocytic phenotype and modify S100 protein profiles in human chondrosarcoma cells

Piltti J, Bygdell J, Fernández-Echevarría C, Marcellino D, Lammi MJ

Sci Rep 7 (1) - [2017-12-00; online 2017-06-16]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study

Berghoff BA, Karlsson T, Källman T, Wagner EGH, Grabherr MG

BioData Mining 10 (1) - [2017-12-00; online 2017-09-05]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Plasma stem cell factor levels are associated with risk of cardiovascular disease and death.

Björkbacka H, Yao Mattisson I, Wigren M, ..., Engström G, Nilsson J

J. Intern. Med. 282 (6) 508-521 [2017-12-00; online 2017-09-21]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Overexpression of PaNAC03, a stress induced NAC gene family transcription factor in Norway spruce leads to reduced flavonol biosynthesis and aberrant embryo development

Dalman K, Wind JJ, Nemesio-Gorriz M, ..., Ezcurra I, Elfstrand M

BMC Plant Biol. 17 (1) - [2017-12-00; online 2017-01-06]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Novel risk genes for systemic lupus erythematosus predicted by random forest classification

Almlöf JC, Alexsson A, Imgenberg-Kreuz J, ..., Sandling JK, Syvänen AC

Sci Rep 7 (1) - [2017-12-00; online 2017-07-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma

Lauss M, Donia M, Harbst K, ..., Svane IM, Jönsson G

Nat Commun 8 (1) - [2017-12-00; online 2017-11-23]

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Multiple genotypes within aecial clusters in Puccinia graminis and Puccinia coronata: improved understanding of the biology of cereal rust fungi

Berlin A, Samils B, Andersson B

Fungal Biol Biotechnol 4 (1) - [2017-12-00; online 2017-05-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size.

Pečnerová P, Palkopoulou E, Wheat CW, ..., Díez-Del-Molino D, Dalén L

Evolution Letters 1 (6) 292-303 [2017-12-00; online 2017-11-28]

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Mechanistic Insights into Autoinhibition of the Oncogenic Chromatin Remodeler ALC1

Lehmann LC, Hewitt G, Aibara S, ..., Boulton SJ, Deindl S

Molecular Cell 68 (5) 847-859.e7 [2017-12-00; online 2017-12-00]

Cryo-EM [Service] Protein Science Facility (PSF) [Service]

Mapping of leptin and its syntenic genes to chicken chromosome 1p

Seroussi E, Pitel F, Leroux S, ..., Anderson L, Friedman-Einat M

BMC Genet. 18 (1) - [2017-12-00; online 2017-08-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

MALDIViz: A Comprehensive Informatics Tool for MALDI-MS Data Visualization and Analysis.

Jagadeesan KK, Ekström S

SLAS DISCOVERY: Advancing Life Sciences R&D 22 (10) 1246-1252 [2017-12-00; online 2017-08-21]

Low-dose γ-secretase inhibition increases secretion of Aβ peptides and intracellular oligomeric Aβ.

Agholme L, Clarin M, Gkanatsiou E, ..., Portelius E, Zetterberg H

Molecular and Cellular Neuroscience 85 (-) 211-219 [2017-12-00; online 2017-11-08]

Integrated Microscopy Technologies Gothenburg [Service]

Large-scale suppression of recombination predates genomic rearrangements in Neurospora tetrasperma

Sun Y, Svedberg J, Hiltunen M, Corcoran P, Johannesson H

Nat Commun 8 (1) - [2017-12-00; online 2017-10-26]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Influence of pulsed and continuous substrate inputs on freshwater bacterial community composition and functioning in bioreactors

Ricão Canelhas M, Andersson M, Eiler A, Lindström ES, Bertilsson S

Environ Microbiol 19 (12) 5078-5087 [2017-12-00; online 2017-12-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Inflammatory infiltrates in parathyroid tumors.

Haglund F, Hallström BM, Nilsson IL, ..., Juhlin CC, Larsson C

Eur. J. Endocrinol. 177 (6) 445-453 [2017-12-00; online 2017-08-30]

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Increasing the permeability of Escherichia coli using MAC13243

Muheim C, Götzke H, Eriksson AU, ..., Nørholm MHH, Daley DO

Sci Rep 7 (1) - [2017-12-00; online 2017-12-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Identification and description of three families with familial Alzheimer disease that segregate variants in the SORL1 gene

Thonberg H, Chiang HH, Lilius L, ..., Rönnbäck A, Graff C

Acta Neuropathol Commun 5 (1) - [2017-12-00; online 2017-06-09]

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Highly sensitive and specific protein detection via combined capillary isoelectric focusing and proximity ligation

Padhan N, Yan J, Boge A, ..., Claesson-Welsh L, Landegren U

Sci Rep 7 (1) - [2017-12-00; online 2017-05-04]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

High levels of cerebrospinal fluid chemokines point to the presence of neuroinflammation in peripheral neuropathic pain: a cross-sectional study of 2 cohorts of patients compared with healthy controls.

Bäckryd E, Lind AL, Thulin M, ..., Gerdle B, Gordh T

Pain 158 (12) 2487-2495 [2017-12-00; online 2017-09-21]

Affinity Proteomics Stockholm [Service] Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service]

Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens

Lillie M, Sheng Z, Honaker CF, ..., Siegel PB, Carlborg Ö

BMC Genomics 18 (1) - [2017-12-00; online 2017-01-18]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic- and Lifestyle-dependent Dental Caries Defined by the Acidic Proline-rich Protein Genes PRH1 and PRH2

Strömberg N, Esberg A, Sheng N, ..., Danielsson K, Källestål C

EBioMedicine 26 (-) 38-46 [2017-12-00; online 2017-12-00]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Filter Plate-Based Screening of MIP SPE Materials for Capture of the Biomarker Pro-Gastrin-Releasing Peptide.

Jagadeesan KK, Rossetti C, Abdel Qader A, ..., Laurell T, Ekström S

SLAS DISCOVERY: Advancing Life Sciences R&D 22 (10) 1253-1261 [2017-12-00; online 2017-01-31]

Elevated Markers of Death Receptor-Activated Apoptosis are Associated with Increased Risk for Development of Diabetes and Cardiovascular Disease.

Mattisson IY, Björkbacka H, Wigren M, ..., Almgren P, Nilsson J

EBioMedicine 26 (-) 187-197 [2017-12-00; online 2017-11-24]

Affinity Proteomics Stockholm [Service] Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service]

Draft genome of the brown-rot fungus Fomitopsis pinicola GR9-4

Kancherla RP, Durling MB, Stenlid J, Högberg N

Data Brief 15 (-) 496-500 [2017-12-00; online 2017-12-00]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Development of an efficient route for combined recycling of PET and cotton from mixed fabrics

Palme A, Peterson A, de la Motte H, Theliander H, Brelid H

Text Cloth Sustain 3 (1) - [2017-12-00; online 2017-02-22]

Detection of QTL for greasy fleece weight in sheep using a 50 K single nucleotide polymorphism chip

Ebrahimi F, Gholizadeh M, Rahimi-Mianji G, Farhadi A

Trop Anim Health Prod 49 (8) 1657-1662 [2017-12-00; online 2017-08-11]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost

Bornelöv S, Seroussi E, Yosefi S, ..., Friedman-Einat M, Andersson L

Genome Biol. 18 (1) - [2017-12-00; online 2017-06-14]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Comparison of laccase-catalyzed cross-linking of organosolv lignin and lignosulfonates

Gillgren T, Hedenström M, Jönsson LJ

International Journal of Biological Macromolecules 105 (-) 438-446 [2017-12-00; online 2017-12-00]

Combined genome and transcriptome sequencing to investigate the plant cell wall degrading enzyme system in the thermophilic fungus Malbranchea cinnamomea

Hüttner S, Nguyen TT, Granchi Z, ..., Thanh VN, Olsson L

Biotechnol Biofuels 10 (1) - [2017-12-00; online 2017-11-13]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Brassinosteroid signaling-dependent root responses to prolonged elevated ambient temperature

Martins S, Montiel-Jorda A, Cayrel A, ..., Ljung K, Vert G

Nat Commun 8 (1) - [2017-12-00; online 2017-08-21]

Automated Training of Deep Convolutional Neural Networks for Cell Segmentation

Sadanandan SK, Ranefall P, Le Guyader S, Wählby C

Sci Rep 7 (1) - [2017-12-00; online 2017-08-10]

BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

Autoantibodies against aldehyde-modified collagen type IV are associated with risk of development of myocardial infarction.

Vallejo J, Dunér P, Fredrikson GN, Nilsson J, Bengtsson E

J. Intern. Med. 282 (6) 496-507 [2017-12-00; online 2017-09-25]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

An essential regulatory function of the DnaK chaperone dictates the decision between proliferation and maintenance in Caulobacter crescentus.

Schramm FD, Heinrich K, Thüring M, Bernhardt J, Jonas K

PLoS Genet. 13 (12) e1007148 [2017-12-00; online 2017-12-27]

Agonist-induced dimer dissociation as a macromolecular step in G protein-coupled receptor signaling

Petersen J, Wright SC, Rodríguez D, ..., Carlsson J, Schulte G

Nat Commun 8 (1) - [2017-12-00; online 2017-08-09]

Fluorescence Correlation Spectroscopy [Collaborative] Integrated Microscopy Technologies Stockholm [Service]

A female Viking warrior confirmed by genomics.

Hedenstierna-Jonson C, Kjellström A, Zachrisson T, ..., Götherström A, Storå J

Am. J. Phys. Anthropol. 164 (4) 853-860 [2017-12-00; online 2017-09-08]

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A comprehensive structural, biochemical and biological profiling of the human NUDIX hydrolase family

Carreras-Puigvert J, Zitnik M, Jemth AS, ..., Zupan B, Helleday T

Nat Commun 8 (1) - [2017-12-00; online 2017-11-16]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] Drug Discovery and Development (DDD) [Collaborative] Protein Science Facility (PSF) [Service]

A short feature vector for image matching: The Log-Polar Magnitude feature descriptor.

Matuszewski DJ, Hast A, Wählby C, Sintorn IM

PLoS ONE 12 (11) e0188496 [2017-11-30; online 2017-11-30]

BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

Intra-tumor heterogeneity in breast cancer has limited impact on transcriptomic-based molecular profiling.

Karthik GM, Rantalainen M, Stålhammar G, ..., Bergh J, Hartman J

BMC Cancer 17 (1) 802 [2017-11-29; online 2017-11-29]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Evidence that circulating proteins are more promising than miRNAs for identification of patients with squamous cell carcinoma of the tongue.

Boldrup L, Troiano G, Gu X, ..., Wang L, Nylander K

Oncotarget 8 (61) 103437-103448 [2017-11-28; online 2017-09-30]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Bliss and Loewe interaction analyses of clinically relevant drug combinations in human colon cancer cell lines reveal complex patterns of synergy and antagonism.

Kashif M, Andersson C, Mansoori S, ..., Nygren P, Gustafsson MG

Oncotarget 8 (61) 103952-103967 [2017-11-28; online 2017-10-19]

STRT-seq-2i: dual-index 5' single cell and nucleus RNA-seq on an addressable microwell array.

Hochgerner H, Lönnerberg P, Hodge R, ..., Zeisel A, Linnarsson S

Sci Rep 7 (1) 16327 [2017-11-27; online 2017-11-27]

Cellular Immunomonitoring [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Regulatory coiled-coil domains promote head-to-head assemblies of AAA+ chaperones essential for tunable activity control.

Carroni M, Franke KB, Maurer M, ..., Bukau B, Mogk A

Elife 6 (-) - [2017-11-22; online 2017-11-22]

Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth.

Pečnerová P, Díez-Del-Molino D, Dussex N, ..., Vartanyan S, Dalén L

Curr. Biol. 27 (22) 3505-3510.e3 [2017-11-20; online 2017-11-02]

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Dog ownership and the risk of cardiovascular disease and death - a nationwide cohort study.

Mubanga M, Byberg L, Nowak C, ..., Ingelsson E, Fall T

Sci Rep 7 (1) 15821 [2017-11-17; online 2017-11-17]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Combined transcriptome and translatome analyses reveal a role for tryptophan-dependent auxin biosynthesis in the control of DOG1-dependent seed dormancy

Bai B, Novák O, Ljung K, Hanson J, Bentsink L

New Phytol - (-) - [2017-11-15; online 2017-11-15]

Novel KIAA0753 mutations extend the phenotype of skeletal ciliopathies.

Hammarsjö A, Wang Z, Vaz R, ..., Grigelioniene G, Ikegawa S

Sci Rep 7 (1) 15585 [2017-11-14; online 2017-11-14]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Diffusion in Ionic Liquid–Cellulose Solutions during Coagulation in Water: Mass Transport and Coagulation Rate Measurements

Hedlund A, Köhnke T, Theliander H

Macromolecules 50 (21) 8707-8719 [2017-11-14; online 2017-10-17]

Female mice lacking Pald1 exhibit endothelial cell apoptosis and emphysema.

Egaña I, Kaito H, Nitzsche A, ..., Hellström M, German Mouse Clinic Consortium

Sci Rep 7 (1) 15453 [2017-11-13; online 2017-11-13]

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Collaborative]

Antibody Heavy Chain Variable Domains of Different Germline Gene Origins Diversify through Different Paths

Kirik U, Persson H, Levander F, Greiff L, Ohlin M

Front Immunol 8 (-) - [2017-11-13; online 2017-11-13]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Drug Discovery and Development (DDD) [Collaborative]

Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer.

Jabs V, Edlund K, König H, ..., Hengstler JG, Micke P

PLoS ONE 12 (11) e0187246 [2017-11-07; online 2017-11-07]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Adipocyte Expression of SLC19A1 Links DNA Hypermethylation to Adipose Tissue Inflammation and Insulin Resistance

Petrus P, Bialesova L, Checa A, ..., Gao H, Rydén M

- - (-) - [2017-11-07; online 2017-11-07]

Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans.

Rodríguez-Varela R, Günther T, Krzewińska M, ..., Götherström A, Girdland-Flink L

Curr. Biol. 27 (21) 3396-3402.e5 [2017-11-06; online 2017-10-26]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago.

Schlebusch CM, Malmström H, Günther T, ..., Lombard M, Jakobsson M

Science 358 (6363) 652-655 [2017-11-03; online 2017-09-28]

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RNA-Seq de novo assembly and differential transcriptome analysis of the nematode Ascaridia galli in relation to in vivo exposure to flubendazole

Martis MM, Tarbiat B, Tydén E, Jansson DS, Höglund J

PLoS ONE 12 (11) e0185182 [2017-11-03; online 2017-11-03]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Unique case of cerebrotendinous xanthomatosis revisited: All the mutations responsible for this disease are present in the CYP27A1 gene.

Jiao H, Olin M, Hansson M, ..., Angelin B, Björkhem I

J. Intern. Med. - (-) - [2017-11-02; online 2017-11-02]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics.

Marathe NP, Pal C, Gaikwad SS, ..., Kristiansson E, Larsson DGJ

Water Res. 124 (-) 388-397 [2017-11-01; online 2017-07-25]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Highly HIV-exposed HIV uninfected Kenyan female sex workers display a thick ectocervical epithelium

Röhl M, Lajoie J, Tjernlund A, ..., Fowke KR, Broliden K

HIV&Hepatitis Nordic Conference, Stockholm, 2017-09-27-29 - (-) - [2017-11-01]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Cryo-EM reconstruction of the chlororibosome to 3.2 Å resolution within 24 h

Forsberg BO, Aibara S, Kimanius D, ..., Lindahl E, Amunts A

Int Union Crystallogr J IUCr J Int Union Cryst J IUCrJ 4 (6) 723-727 [2017-11-01; online 2017-09-22]

Whole mitochondrial genome capture from faecal samples and museum-preserved specimens.

van der Valk T, Lona Durazo F, Dalén L, Guschanski K

Mol Ecol Resour 17 (6) e111-e121 [2017-11-00; online 2017-08-03]

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Type B Response Regulators Act As Central Integrators in Transcriptional Control of the Auxin Biosynthesis Enzyme TAA1

Yan Z, Liu X, Ljung K, ..., Wang M, Tao Y

Plant Physiol. 175 (3) 1438-1454 [2017-11-00; online 2017-09-20]

SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.

Ameur A, Dahlberg J, Olason P, ..., Magnusson PK, Gyllensten U

Eur. J. Hum. Genet. 25 (11) 1253-1260 [2017-11-00; online 2017-08-23]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]

Registration free automatic identification of gold fiducial markers in MRI target delineation images for prostate radiotherapy.

Gustafsson C, Korhonen J, Persson E, ..., Nyholm T, Olsson LE

Med Phys 44 (11) 5563-5574 [2017-11-00; online 2017-09-11]

AIDA Data Hub [Service] Bioinformatics (NBIS) [Service]

Rare X Chromosome Abnormalities in Systemic Lupus Erythematosus and Sjögren's Syndrome.

Sharma R, Harris VM, Cavett J, ..., Sivils KL, Scofield RH

Arthritis & rheumatology (Hoboken, N.J.) 69 (11) 2187-2192 [2017-11-00; online 2017-10-12]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Quantitative high-content/high-throughput microscopy analysis of lipid droplets in subject-specific adipogenesis models.

Bombrun M, Gao H, Ranefall P, ..., Arner P, Wählby C

Cytometry A 91 (11) 1068-1077 [2017-11-00; online 2017-10-14]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Proteomic Analysis of Phytophthora infestans Reveals the Importance of Cell Wall Proteins in Pathogenicity

Resjö S, Brus M, Ali A, ..., Grenville-Briggs L, Andreasson E

Mol Cell Proteomics 16 (11) 1958-1971 [2017-11-00; online 2017-09-21]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.

Svartström O, Alneberg J, Terrapon N, ..., Aspeborg H, Andersson AF

ISME J 11 (11) 2538-2551 [2017-11-00; online 2017-07-21]

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Integrative studies implicate matrix metalloproteinase-12 as a culprit gene for large-artery atherosclerotic stroke

Mahdessian H, Perisic Matic L, Lengquist M, ..., Mälarstig A, None

J Intern Med 282 (5) 429-444 [2017-11-00; online 2017-08-28]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

High abundance and expression of transposases in bacteria from the Baltic Sea.

Vigil-Stenman T, Ininbergs K, Bergman B, Ekman M

ISME J 11 (11) 2611-2623 [2017-11-00; online 2017-07-21]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genotype-based recall to study metabolic effects of genetic variation: a pilot study of PPARG Pro12Ala carriers.

Kamble PG, Gustafsson S, Pereira MJ, ..., Eriksson JW, Ingelsson E

Ups. J. Med. Sci. 122 (4) 234-242 [2017-11-00; online 2018-01-05]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Demographic inference from whole-genome and RAD sequencing data suggests alternating human impacts on goose populations since the last ice age.

Pujolar JM, Dalén L, Hansen MM, Madsen J

Mol. Ecol. 26 (22) 6270-6283 [2017-11-00; online 2017-11-03]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans

Scott RA, Scott LJ, Mägi R, ..., McCarthy MI, Prokopenko I

Diabetes 66 (11) 2888-2902 [2017-11-00; online 2017-05-31]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A novel approach using long-read sequencing and ddPCR to investigate gonadal mosaicism and estimate recurrence risk in two families with developmental disorders.

Wilbe M, Gudmundsson S, Johansson J, ..., Frykholm C, Bondeson ML

Prenat. Diagn. 37 (11) 1146-1154 [2017-11-00; online 2017-10-17]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]

A nonsense mutation in CEP55 defines a new locus for a Meckel-like syndrome, an autosomal recessive lethal fetal ciliopathy.

Bondeson ML, Ericson K, Gudmundsson S, ..., Frykholm C, Wilbe M

Clin. Genet. 92 (5) 510-516 [2017-11-00; online 2017-05-03]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]

Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions

Hubalek V, Buck M, Tan B, ..., Bertilsson S, Eiler A

mSystems 2 (5) e00038-17 [2017-10-31; online 2017-10-31]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Orellanine specifically targets renal clear cell carcinoma.

Buvall L, Hedman H, Khramova A, ..., Haraldsson B, Nyström J

Oncotarget 8 (53) 91085-91098 [2017-10-31; online 2017-07-25]

Institutional profile: the national Swedish academic drug discovery & development platform at SciLifeLab.

Arvidsson PI, Sandberg K, Sakariassen KS

Future Sci. OA 3(2), FSO176 (2) - [2017-10-30; online 2017-04-07]

Drug Discovery and Development (DDD) [Technology development]

Exome-wide association study of plasma lipids in >300,000 individuals.

Liu DJ, Peloso GM, Yu H, ..., Willer CJ, Kathiresan S

Nat. Genet. - (-) - [2017-10-30; online 2017-10-30]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Microbial mineralization of cellulose in frozen soils.

Segura JH, Nilsson MB, Haei M, ..., Schleucher J, Öquist MG

Nat Commun 8 (1) 1154 [2017-10-27; online 2017-10-27]

Combined x-ray crystallography and computational modeling approach to investigate the Hsp90 C-terminal peptide binding to FKBP51.

Kumar R, Moche M, Winblad B, Pavlov PF

Sci Rep 7 (1) 14288 [2017-10-27; online 2017-10-27]

Thiol-ene-epoxy thermoset for low-temperature bonding to biofunctionalized microarray surfaces.

Zhou XC, Sjöberg R, Druet A, ..., Haraldsson T, Carlborg CF

Lab Chip 17 (21) 3672-3681 [2017-10-25; online 2017-10-05]

Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development]

Efficient protein production by yeast requires global tuning of metabolism.

Huang M, Bao J, Hallström BM, Petranovic D, Nielsen J

Nat Commun 8 (1) 1131 [2017-10-25; online 2017-10-25]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Crystal structures of OrfX2 and P47 from a Botulinum neurotoxin OrfX type gene cluster.

Gustafsson R, Berntsson RP, Martínez-Carranza M, ..., Johnson EA, Stenmark P

FEBS Lett. - (-) - [2017-10-25; online 2017-10-25]

Polysome-profiling in small tissue samples.

Liang S, Bellato HM, Lorent J, ..., Hajj GNM, Larsson O

Nucleic Acids Res. - (-) - [2017-10-23; online 2017-10-23]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Below-ground organic matter accumulation along a boreal forest fertility gradient relates to guild interaction within fungal communities

Kyaschenko J, Clemmensen KE, Karltun E, Lindahl BD

Ecol Lett - (-) - [2017-10-22; online 2017-10-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Proteomic analysis of cell cycle progression in asynchronous cultures, including mitotic subphases, using PRIMMUS.

Ly T, Whigham A, Clarke R, ..., Wadsworth P, Lamond AI

Elife 6 (-) - [2017-10-20; online 2017-10-20]

Effects of long-term low oxygen tension in human chondrosarcoma cells

Piltti J, Bygdell J, Qu C, Lammi MJ

J. Cell. Biochem. - (-) - [2017-10-18; online 2017-10-18]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Zebrafish larvae as a model system for high-throughput, image-based screens in diabetes and insulin resistance

Emmanouilidou A, Ranefall P, Bandaru M, ..., Ingelsson E, den Hoed M

ASHG 2017 Annual Meeting - The American Society of Human Genetics - (-) - [2017-10-17; online 2017-10-17]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Zebrafish larvae as a model system for high-throughput, image-based genetic screens in cardiometabolic diseases

den Hoed M, Emmanouilidou A, Bandaru M, ..., Larsson A, Ingelsson E

ASHG 2017 Annual Meeting - The American Society of Human Genetics - (-) - [2017-10-17; online 2017-10-17]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Large-scale validation of zebrafish larvae as a model system for genetic screens in dyslipidaemia, atherosclerosis and coronary artery disease

Bandaru M, Emmanouilidou A, Ranefall P, ..., Ingelsson E, den Hoed M

ASHG 2017 Annual Meeting - The American Society of Human Genetics - (-) - [2017-10-17; online 2017-10-17]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Glycoproteomics and MS Proteomics [Technology development]

Glycoforest 1.0.

Horlacher O, Jin C, Alocci D, ..., Karlsson NG, Lisacek F

Anal. Chem. 89 (20) 10932-10940 [2017-10-17; online 2017-09-25]

Glioblastoma and glioblastoma stem cells are dependent on functional MTH1.

Pudelko L, Rouhi P, Sanjiv K, ..., Helleday T, Bräutigam L

Oncotarget 8 (49) 84671-84684 [2017-10-17; online 2017-07-20]

Integrated Microscopy Technologies Stockholm [Collaborative]

Extracellular vesicles from human pancreatic islets suppress human islet amyloid polypeptide amyloid formation.

Ribeiro D, Horvath I, Heath N, ..., Forslöw A, Wittung-Stafshede P

Proc. Natl. Acad. Sci. U.S.A. 114 (42) 11127-11132 [2017-10-17; online 2017-10-02]

Integrated Microscopy Technologies Gothenburg [Service]

RANK rewires energy homeostasis in lung cancer cells and drives primary lung cancer.

Rao S, Sigl V, Wimmer RA, ..., Dougall W, Penninger JM

Genes Dev. 31 (20) 2099-2112 [2017-10-15; online 2017-11-08]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Delivery of cyclodextrin polymers to bacterial biofilms - An exploratory study using rhodamine labelled cyclodextrins and multiphoton microscopy.

Thomsen H, Benkovics G, Fenyvesi É, ..., Malanga M, Ericson MB

Int J Pharm 531 (2) 650-657 [2017-10-15; online 2017-06-06]

Integrated Microscopy Technologies Gothenburg [Service]

Solid-phase extraction of the alcohol abuse biomarker phosphatidylethanol using newly synthesized polymeric sorbent materials containing quaternary heterocyclic groups.

Duarte M, Jagadeesan KK, Billing J, ..., Laurell T, Ekström S

Journal of Chromatography A 1519 (-) 1-8 [2017-10-13; online 2017-08-25]

Proteolytic signatures define unique thrombin-derived peptides present in human wound fluid in vivo.

Saravanan R, Adav SS, Choong YK, ..., Sze SK, Schmidtchen A

Sci Rep 7 (1) 13136 [2017-10-13; online 2017-10-13]

Lubricin binds cartilage proteins, cartilage oligomeric matrix protein, fibronectin and collagen II at the cartilage surface.

Flowers SA, Zieba A, Örnros J, ..., Kamali-Moghaddam M, Karlsson NG

Sci Rep 7 (1) 13149 [2017-10-13; online 2017-10-13]

Affinity Proteomics Uppsala [Collaborative] Glycoproteomics and MS Proteomics [Collaborative] PLA and Single Cell Proteomics [Collaborative]

Entirely enzymatic nanofabrication of DNA–protein conjugates

Bernardinelli G, Högberg B

Nucleic Acids Res 45 (18) e160-e160 [2017-10-13; online 2017-08-16]

De novo design and synthesis of a 30-cistron translation-factor module

Shepherd TR, Du L, Liljeruhm J, ..., Yomo T, Forster AC

Nucleic Acids Res 45 (18) 10895-10905 [2017-10-13; online 2017-09-04]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Spatial detection of fetal marker genes expressed at low level in adult human heart tissue.

Asp M, Salmén F, Ståhl PL, ..., Linde C, Lundeberg J

Sci Rep 7 (1) 12941 [2017-10-11; online 2017-10-11]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments.

Broman E, Sachpazidou V, Dopson M, Hylander S

Proc. Biol. Sci. 284 (1864) - [2017-10-11; online 2017-10-06]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Chemical Proteomics for Target Discovery of Head-to-Tail Cyclized Mini-Proteins

Hellinger R, Thell K, Vasileva M, ..., Becker CW, Gruber CW

Front. Chem. 5 (-) - [2017-10-11; online 2017-10-11]

CRISPR/Cas9 screening using unique molecular identifiers.

Schmierer B, Botla SK, Zhang J, ..., Kivioja T, Taipale J

Mol. Syst. Biol. 13 (10) 945 [2017-10-09; online 2017-10-09]

CRISPR Functional Genomics [Technology development]

Subphenotypes of inflammatory bowel disease are characterized by specific serum protein profiles.

Andersson E, Bergemalm D, Kruse R, ..., Repsilber D, Halfvarson J

PLoS ONE 12 (10) e0186142 [2017-10-05; online 2017-10-05]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Late presenting atypical severe combined immunodeficiency (SCID) associated with a novel missense mutation in DCLRE1C.

Sundin M, Uhlin M, Gaballa A, ..., Marits P, Nilsson J

Pediatr Allergy Immunol - (-) - [2017-10-05; online 2017-10-05]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development.

Guo J, Grow EJ, Yi C, ..., Hotaling JM, Cairns BR

Cell Stem Cell 21 (4) 533-546.e6 [2017-10-05; online 2017-10-07]

Motivating students with authentic science experiences: changes in motivation for school science

Hellgren JM, Lindberg S

Research in Science & Technological Education 35 (4) 409-426 [2017-10-02; online 2017-05-03]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Identification and characterization of the novel colonization factor CS30 based on whole genome sequencing in enterotoxigenic Escherichia coli (ETEC).

von Mentzer A, Tobias J, Wiklund G, ..., Sjöling Å, Svennerholm AM

Sci Rep 7 (1) 12514 [2017-10-02; online 2017-10-02]

The Evolution of Dark Matter in the Mitogenome of Seed Beetles

Sayadi A, Immonen E, Tellgren-Roth C, Arnqvist G

Genome Biol Evol 9 (10) 2697-2706 [2017-10-01; online 2017-09-27]

Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]

Shaping the Tumor Stroma and Sparking Immune Activation by CD40 and 4-1BB Signaling Induced by an Armed Oncolytic Virus

Eriksson E, Milenova I, Wenthe J, ..., Alemany R, Loskog A

Clin. Cancer Res. 23 (19) 5846-5857 [2017-10-01; online 2017-05-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies.

Talla V, Suh A, Kalsoom F, ..., Wiklund C, Backström N

Genome Biol Evol 9 (10) 2491-2505 [2017-10-01; online 2017-10-06]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Profiling of in vitro activities of urea-based inhibitors against cysteine synthases from Mycobacterium tuberculosis.

Brunner K, Steiner EM, Reshma RS, ..., Schnell R, Schneider G

Bioorg. Med. Chem. Lett. 27 (19) 4582-4587 [2017-10-01; online 2017-08-19]

Chemical Biology Consortium Sweden (CBCS) [Service] Protein Science Facility (PSF) [Service]

GlyTouCan: an accessible glycan structure repository.

Tiemeyer M, Aoki K, Paulson J, ..., Narimatsu H, Aoki-Kinoshita KF

Glycobiology 27 (10) 915-919 [2017-10-01; online 2017-09-20]

DNA methylation profiles in red blood cells of adult hens correlate with their rearing conditions

Pértille F, Brantsæter M, Nordgreen J, ..., Jensen P, Guerrero-Bosagna C

J Exp Biol 220 (19) 3579-3587 [2017-10-01; online 2017-08-07]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A MIR4646 associated methylation locus is hypomethylated in adolescent depression.

Boström AE, Ciuculete DM, Attwood M, ..., Mwinyi J, Schiöth HB

J Affect Disord 220 (-) 117-128 [2017-10-01; online 2017-05-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Validation of risk stratification models in acute myeloid leukemia using sequencing-based molecular profiling.

Wang M, Lindberg J, Klevebring D, ..., Lehmann S, Grönberg H

Leukemia 31 (10) 2029-2036 [2017-10-00; online 2017-02-07]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Tumor SHB gene expression affects disease characteristics in human acute myeloid leukemia.

Jamalpour M, Li X, Cavelier L, ..., Höglund M, Welsh M

Tumour Biol. 39 (10) 1010428317720643 [2017-10-00; online 2017-10-07]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Tumor Necrosis Factor Receptor 1 and 2 Are Associated With Risk of Intracerebral Hemorrhage.

Svensson EH, Söderholm M, Abul-Kasim K, Engström G

Stroke 48 (10) 2710-2715 [2017-10-00; online 2017-08-22]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Transcriptomic and Proteomic Profiling Provides Insight into Mesangial Cell Function in IgA Nephropathy.

Liu P, Lassén E, Nair V, ..., Ebefors K, Nyström J

J. Am. Soc. Nephrol. 28 (10) 2961-2972 [2017-10-00; online 2017-06-23]

The evolutionary history of the DMRT3 ‘Gait keeper’ haplotype

Staiger EA, Almén MS, Promerová M, ..., Rubin CJ, Andersson L

Anim Genet 48 (5) 551-559 [2017-10-00; online 2017-07-25]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The cagE gene sequence as a diagnostic marker to identify JP2 and non-JP2 highly leukotoxic Aggregatibacter actinomycetemcomitans serotype b strains.

Johansson A, Claesson R, Höglund Åberg C, Haubek D, Oscarsson J

J. Periodont. Res. 52 (5) 903-912 [2017-10-00; online 2017-04-10]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Structures of the human mitochondrial ribosome in native states of assembly

Brown A, Rathore S, Kimanius D, ..., Amunts A, Ramakrishnan V

Nat Struct Mol Biol 24 (10) 866-869 [2017-10-00; online 2017-09-11]

Spheroid Segmentation Using Multiscale Deep Adversarial Networks

Sadanandan SK, Karlsson J, Wahlby C

The IEEE International Conference on Computer Vision (ICCV), 2017 - (-) 36-41 [2017-10-00; online 2017-10-00]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Reduced cell surface levels of GPI-linked markers in a new case with PIGG loss of function.

Zhao JJ, Halvardson J, Knaus A, ..., Thuresson AC, Feuk L

Hum. Mutat. 38 (10) 1394-1401 [2017-10-00; online 2017-06-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Quantitative interactions between the biocontrol fungus Phlebiopsis gigantea, the forest pathogen Heterobasidion annosum and the fungal community inhabiting Norway spruce stumps

Oliva J, Messal M, Wendt L, Elfstrand M

Forest Ecology and Management 402 (-) 253-264 [2017-10-00; online 2017-10-00]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Protective Effect of Intravitreal Administration of Exosomes Derived from Mesenchymal Stem Cells on Retinal Ischemia.

Moisseiev E, Anderson JD, Oltjen S, ..., Nolta JA, Park SS

Current Eye Research 42 (10) 1358-1367 [2017-10-00; online 2017-06-21]

Novel genetic loci associated HLA-B*08:01 positive myasthenia gravis

Varade J, Wang N, Lim CK, ..., Xu X, Hammarström L

Journal of Autoimmunity - (-) - [2017-10-00; online 2017-10-00]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

NorWood: a gene expression resource for evo-devo studies of conifer wood development.

Jokipii-Lukkari S, Sundell D, Nilsson O, ..., Street NR, Tuominen H

New Phytol. 216 (2) 482-494 [2017-10-00; online 2017-02-10]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

N-Acylated Derivatives of Sulfamethoxazole Block Chlamydia Fatty Acid Synthesis and Interact with FabF.

Mojica SA, Salin O, Bastidas RJ, ..., Elofsson M, Gylfe Å

Antimicrob. Agents Chemother. 61 (10) e00716-17 [2017-10-00; online 2017-09-22]

Multivariate strategy for the sample selection and integration of multi-batch data in metabolomics

Surowiec I, Johansson E, Torell F, ..., Jakobsson PJ, Trygg J

Metabolomics 13 (10) - [2017-10-00; online 2017-08-24]

Swedish Metabolomics Centre (SMC) [Technology development]

Hormonal contraceptive use affects HIV susceptibility: mechanisms revealed by image analysis

Edfeldt G , Lajoie J , Röhl M , Tjernlund A

Scand J Immunol 86 (4) 249-350 [2017-10-00; online 2017-09-27]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

GDF-15 and TRAIL-R2 are powerful predictors of long-term mortality in patients with acute myocardial infarction.

Skau E, Henriksen E, Wagner P, ..., Siegbahn A, Leppert J

Eur J Prev Cardiol 24 (15) 1576-1583 [2017-10-00; online 2017-08-01]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Eosinophil Cationic Protein, Carotid Plaque, and Incidence of Stroke.

Sundström J, Söderholm M, Borné Y, ..., Orho-Melander M, Engström G

Stroke 48 (10) 2686-2692 [2017-10-00; online 2017-09-13]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Deep Convolutional Neural Networks for Detecting Cellular Changes Due to Malignancy

Forslid G, Wieslander H, Bengtsson E, ..., Stark CR, Sadanandan SK

The IEEE International Conference on Computer Vision (ICCV), 2017 - (-) - [2017-10-00; online 2017-10-00]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny

Rydin C, Wikström N, Bremer B

Am. J. Bot. 104 (10) 1522-1532 [2017-10-00; online 2017-10-18]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Comprehensive analysis of NMR data using advanced line shape fitting

Niklasson M, Otten R, Ahlner A, ..., Petzold K, Lundström P

J Biomol NMR 69 (2) 93-99 [2017-10-00; online 2017-10-17]

Cetuximab sensitivity of head and neck squamous cell carcinoma xenografts is associated with treatment-induced reduction in EGFR, pEGFR, and pSrc.

Jedlinski A, Garvin S, Johansson A, ..., Ponten F, Roberg K

J. Oral Pathol. Med. 46 (9) 717-724 [2017-10-00; online 2017-01-28]

Breast cancer in young women and prognosis: How important are proliferation markers?

Fredholm H, Magnusson K, Lindström LS, ..., Frisell J, Fredriksson I

Eur. J. Cancer 84 (-) 278-289 [2017-10-00; online 2017-08-29]

Bioinformatory-assisted analysis of next-generation sequencing data for precision medicine in pancreatic cancer.

Malgerud L, Lindberg J, Wirta V, ..., Grönberg H, Löhr JM

Mol Oncol 11 (10) 1413-1429 [2017-10-00; online 2017-08-08]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Artificial Selection Response due to Polygenic Adaptation from a Multilocus, Multiallelic Genetic Architecture

Zan Y, Sheng Z, Lillie M, ..., Siegel PB, Carlborg Ö

- 34 (10) 2678-2689 [2017-10-00; online 2017-07-11]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Antibody Affinity Against 2009 A/H1N1 Influenza and Pandemrix Vaccine Nucleoproteins Differs Between Childhood Narcolepsy Patients and Controls.

Lind A, Freyhult E, Ramelius A, ..., Elding Larsson H, Lernmark Å

Viral Immunol. 30 (8) 590-600 [2017-10-00; online 2017-08-10]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Alterations of c-di-GMP turnover proteins modulate semi-constitutive rdar biofilm formation in commensal and uropathogenic Escherichia coli.

Cimdins A, Simm R, Li F, ..., Brauner A, Römling U

Microbiologyopen 6 (5) - [2017-10-00; online 2017-09-15]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Identification of the PAK4 interactome reveals PAK4 phosphorylation of N-WASP and promotion of Arp2/3-dependent actin polymerization.

Zhao M, Spiess M, Johansson HJ, ..., Lehtiö J, Strömblad S

Oncotarget 8 (44) 77061-77074 [2017-09-29; online 2017-08-18]

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service]

A Drosophila female pheromone elicits species-specific long-range attraction via an olfactory channel with dual specificity for sex and food.

Lebreton S, Borrero-Echeverry F, Gonzalez F, ..., Becher PG, Witzgall P

BMC Biol. 15 (1) 88 [2017-09-29; online 2017-09-29]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus

Matzov D, Aibara S, Basu A, ..., Amunts A, Yonath AE

Nat Commun 8 (1) 723 [2017-09-28; online 2017-09-28]

Identification of a novel proinsulin-associated SNP and demonstration that proinsulin is unlikely to be a causal factor in subclinical vascular remodelling using Mendelian randomisation.

Strawbridge RJ, Silveira A, Hoed MD, ..., Hamsten A, IMPROVE study group

Atherosclerosis 266 (-) 196-204 [2017-09-28; online 2017-09-28]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Epidemiological characterization of a nosocomial outbreak of extended spectrum β-lactamase Escherichia coli ST-131 confirms the clinical value of core genome multilocus sequence typing

Woksepp H, Ryberg A, Berglind L, Schön T, Söderman J

APMIS - (-) - [2017-09-28; online 2017-09-28]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Validating Missing Proteins in Human Sperm Cells by Targeted Mass-Spectrometry- and Antibody-based Methods.

Carapito C, Duek P, Macron C, ..., Lane L, Pineau C

J. Proteome Res. - (-) - [2017-09-26; online 2017-09-26]

Novel spirocyclic systems via multicomponent aza-Diels-Alder reaction.

Llona-Minguez S, Throup A, Steiner E, ..., Jenmalm-Jensen A, Helleday T

Org. Biomol. Chem. 15 (37) 7758-7764 [2017-09-26; online 2017-09-12]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Anti-mycobacterial activity correlates with altered DNA methylation pattern in immune cells from BCG-vaccinated subjects.

Verma D, Parasa VR, Raffetseder J, ..., Netea M, Lerm M

Sci Rep 7 (1) 12305 [2017-09-26; online 2017-09-26]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic risk scores and family history as predictors of schizophrenia in Nordic registers.

Lu Y, Pouget JG, Andreassen OA, ..., Werge T, Sullivan PF

Psychol Med - (-) 1-9 [2017-09-25; online 2017-09-25]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The human protein atlas: A spatial map of the human proteome.

Thul PJ, Lindskog C

Protein Sci. - (-) - [2017-09-23; online 2017-09-23]

The regulation of hydroxysteroid 17β-dehydrogenase type 1 and 2 gene expression in breast cancer cell lines by estradiol, dihydrotestosterone, microRNAs, and genes related to breast cancer.

Hilborn E, Stål O, Alexeyenko A, Jansson A

Oncotarget 8 (37) 62183-62194 [2017-09-22; online 2017-07-10]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

New oncogenic subtypes in pediatric B-cell precursor acute lymphoblastic leukemia.

Lilljebjörn H, Fioretos T

Blood 130 (12) 1395-1401 [2017-09-21; online 2017-08-04]

Clinical Genomics [Collaborative] Clinical Genomics Lund [Collaborative]

Cu/Zn Superoxide Dismutase Forms Amyloid Fibrils under Near-Physiological Quiescent Conditions: The Roles of Disulfide Bonds and Effects of Denaturant.

Khan MAI, Respondek M, Kjellström S, ..., Linse S, Akke M

ACS Chem Neurosci 8 (9) 2019-2026 [2017-09-20; online 2017-06-20]

Major transcriptional changes observed in the Fulani, an ethnic group less susceptible to malaria.

Quin JE, Bujila I, Chérif M, ..., Nebie I, Östlund Farrants AK

Elife 6 (-) - [2017-09-19; online 2017-09-19]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The complete genome sequence of human adenovirus 84, a highly recombinant new Human mastadenovirus D type with a unique fiber gene.

Kaján GL, Kajon AE, Pinto AC, Bartha D, Arnberg N

Virus Res. 242 (-) 79-84 [2017-09-18; online 2017-09-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Tartrate-resistant acid phosphatase (TRAP/ACP5) promotes metastasis-related properties via TGFβ2/TβR and CD44 in MDA-MB-231 breast cancer cells.

Reithmeier A, Panizza E, Krumpel M, ..., Ek-Rylander B, Andersson G

BMC Cancer 17 (1) 650 [2017-09-15; online 2017-09-15]

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service]

Metabolic profiles from two different breakfast meals characterized by 1H NMR-based metabolomics.

Rådjursöga M, Karlsson GB, Lindqvist HM, ..., Ellegård L, Winkvist A

Food Chem 231 (-) 267-274 [2017-09-15; online 2017-03-27]

Effects of tumour necrosis factor α upon the metabolism of the endocannabinoid anandamide in prostate cancer cells.

Karlsson J, Gouveia-Figueira S, Alhouayek M, Fowler CJ

PLoS ONE 12 (9) e0185011 [2017-09-14; online 2017-09-14]

Correction to Piperazin-1-ylpyridazine Derivatives Are a Novel Class of Human dCTP Pyrophosphatase 1 Inhibitors.

Llona-Minguez S, Höglund A, Ghassemian A, ..., Scobie M, Helleday T

J. Med. Chem. 60 (17) 7614 [2017-09-14; online 2017-09-01]

Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth.

Yu NY, Bieder A, Raman A, ..., Daub CO, Kere J

Sci Rep 7 (1) 11458 [2017-09-13; online 2017-09-13]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Mass Cytometry Identifies Distinct Lung CD4+ T Cell Patterns in Löfgren's Syndrome and Non-Löfgren's Syndrome Sarcoidosis.

Kaiser Y, Lakshmikanth T, Chen Y, ..., Achour A, Grunewald J

Front Immunol 8 (-) 1130 [2017-09-12; online 2017-09-12]

Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis

Wheeler E, Leong A, Liu CT, ..., None , None

PLoS Med. 14 (9) e1002383 [2017-09-12; online 2017-09-12]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Deficiency in Calcium-Binding Protein S100A4 Impairs the Adjuvant Action of Cholera Toxin.

Sun JB, Holmgren J, Larena M, ..., Bresnick AR, Xiang Z

Front Immunol 8 (-) 1119 [2017-09-11; online 2017-09-11]

Integrated Microscopy Technologies Gothenburg [Service]

Copper chaperone ATOX1 regulates pluripotency factor OCT4 in preimplantation mouse embryos.

Celauro E, Mukaj A, Fierro-González JC, Wittung-Stafshede P

Biochem. Biophys. Res. Commun. 491 (1) 147-153 [2017-09-09; online 2017-07-12]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Impact of N-methylation of the substance P 1-7 amide on anti-allodynic effect in mice after peripheral administration.

Skogh A, Lesniak A, Gaugaz FZ, ..., Hallberg M, Sandström A

Eur J Pharm Sci 109 (-) 533-540 [2017-09-05; online 2017-09-05]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Service]

Capturing LTA 4 hydrolase in action: Insights to the chemistry and dynamics of chemotactic LTB4 synthesis.

Stsiapanava A, Samuelsson B, Haeggström JZ

Proc. Natl. Acad. Sci. U.S.A. 114 (36) 9689-9694 [2017-09-05; online 2017-08-21]

Auxin minimum triggers the developmental switch from cell division to cell differentiation in the Arabidopsis root.

Di Mambro R, De Ruvo M, Pacifici E, ..., Grieneisen VA, Sabatini S

Proc. Natl. Acad. Sci. U.S.A. 114 (36) E7641-E7649 [2017-09-05; online 2017-08-22]

Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition.

Amlinger L, Hoekzema M, Wagner EGH, Koskiniemi S, Lundgren M

Sci Rep 7 (1) 10392 [2017-09-04; online 2017-09-04]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing.

Hugerth LW, Andersson AF

Front Microbiol 8 (-) 1561 [2017-09-04; online 2017-09-04]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The U2AF1S34F mutation induces lineage-specific splicing alterations in myelodysplastic syndromes.

Yip BH, Steeples V, Repapi E, ..., Pellagatti A, Boultwood J

J. Clin. Invest. 127 (9) 3557 [2017-09-01; online 2017-09-01]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

The TLR2 Antagonist Staphylococcal Superantigen-Like Protein 3 Acts as a Virulence Factor to Promote Bacterial Pathogenicity in vivo.

Koymans KJ, Goldmann O, Karlsson CAQ, ..., van Strijp JAG, Medina E

J Innate Immun 9 (6) 561-573 [2017-09-01; online 2017-09-01]

The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves.

Evkaikina AI, Berke L, Romanova MA, ..., Pawlowski K, Voitsekhovskaja OV

Genome Biol Evol 9 (9) 2444-2460 [2017-09-01; online 2017-09-29]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Retention of seed trees fails to lifeboat ectomycorrhizal fungal diversity in harvested Scots pine forests.

Varenius K, Lindahl BD, Dahlberg A

FEMS Microbiol. Ecol. 93 (9) - [2017-09-01; online 2017-09-29]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Multifocus structured illumination microscopy for fast volumetric super-resolution imaging

Abrahamsson S, Blom H, Agostinho A, ..., Heintzmann R, Brismar H

Biomed. Opt. Express 8 (9) 4135 [2017-09-01; online 2017-08-17]

Integrated Microscopy Technologies Stockholm [Technology development]

Genome Characterization of Oleaginous Aspergillus oryzae BCC7051: A Potential Fungal-Based Platform for Lipid Production.

Thammarongtham C, Nookaew I, Vorapreeda T, ..., Jeennor S, Laoteng K

Curr. Microbiol. - (-) - [2017-09-01; online 2017-09-01]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog

Montero-Mendieta S, Grabherr M, Lantz H, ..., Webster MT, Vilà C

PeerJ 5 (-) e3702 [2017-09-01; online 2017-09-01]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The relative contribution of DNA methylation and genetic variants on protein biomarkers for human diseases.

Ahsan M, Ek WE, Rask-Andersen M, ..., Gyllensten U, Johansson Å

PLoS Genet. 13 (9) e1007005 [2017-09-00; online 2017-09-15]

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The adiponectin receptor AdipoR2 and its Caenorhabditis elegans homolog PAQR-2 prevent membrane rigidification by exogenous saturated fatty acids.

Devkota R, Svensk E, Ruiz M, ..., Borén J, Pilon M

PLoS Genet. 13 (9) e1007004 [2017-09-00; online 2017-09-08]

Integrated Microscopy Technologies Gothenburg [Service]

The Abl-1 Kinase is Dispensable for NK Cell Inhibitory Signalling and is not Involved in Murine NK Cell Education.

Ganesan S, Luu TT, Chambers BJ, ..., Kadri N, Höglund P

Scand. J. Immunol. 86 (3) 135-142 [2017-09-00; online 2017-06-13]

Serotonin, ATRX, and DAXX Expression in Pituitary Adenomas: Markers in the Differential Diagnosis of Neuroendocrine Tumors of the Sellar Region.

Casar-Borota O, Botling J, Granberg D, ..., Pontén F, Trouillas J

Am. J. Surg. Pathol. 41 (9) 1238-1246 [2017-09-00; online 2017-07-19]

Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO2-acidified sea water

Bailey A, De Wit P, Thor P, ..., Thompson C, Hop H

Ecol Evol 7 (18) 7145-7160 [2017-09-00; online 2017-08-02]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Proteomics in Hypothermia as Adjunctive Therapy in Patients with ST-Segment Elevation Myocardial Infarction: A CHILL-MI Substudy.

Mohammad MA, Noc M, Lang I, ..., Metzler B, Erlinge D

Ther Hypothermia Temp Manag 7 (3) 152-161 [2017-09-00; online 2017-03-02]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Measurement of protein backbone 13CO and 15N relaxation dispersion at high resolution

Mayzel M, Ahlner A, Lundström P, Orekhov VY

J Biomol NMR 69 (1) 1-12 [2017-09-00; online 2017-09-01]

Genome scale metabolic modeling of cancer.

Nilsson A, Nielsen J

Metab. Eng. 43 (Pt B) 103-112 [2017-09-00; online 2016-11-04]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Enhanced Secondary- and Hormone Metabolism in Leaves of Arbuscular Mycorrhizal Medicago truncatula

Adolfsson L, Nziengui H, Abreu IN, ..., Schoefs B, Spetea C

Plant Physiol. 175 (1) 392-411 [2017-09-00; online 2017-07-11]

Effect of food intake on 92 neurological biomarkers in plasma.

Dencker M, Björgell O, Hlebowicz J

Brain Behav 7 (9) e00747 [2017-09-00; online 2017-08-01]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Cartilage oligomeric matrix protein neoepitope in the synovial fluid of horses with acute lameness: A new biomarker for the early stages of osteoarthritis.

Skiöldebrand E, Ekman S, Mattsson Hultén L, ..., Sihlbom C, Rüetschi U

Equine Vet. J. 49 (5) 662-667 [2017-09-00; online 2017-02-28]

Cartilage oligomeric matrix protein forms protein complexes with synovial lubricin via non-covalent and covalent interactions.

Flowers SA, Kalamajski S, Ali L, ..., Karlsson NG, Jin C

Osteoarthr. Cartil. 25 (9) 1496-1504 [2017-09-00; online 2017-04-01]

Analytically Sensitive Protein Detection in Microtiter Plates by Proximity Ligation with Rolling Circle Amplification

Ebai T, Souza de Oliveira FM, Löf L, ..., Landegren U, Kamali-Moghaddam M

Clinical Chemistry 63 (9) 1497-1505 [2017-09-00; online 2017-06-30]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

A CRISPR-Cas9 Generated MDCK Cell Line Expressing Human MDR1 Without Endogenous Canine MDR1 (cABCB1): An Improved Tool for Drug Efflux Studies.

Karlgren M, Simoff I, Backlund M, ..., Oswald S, Artursson P

J Pharm Sci 106 (9) 2909-2913 [2017-09-00; online 2017-04-24]

Bioinformatics Support for Computational Resources [Service] Chemical Biology Consortium Sweden (CBCS) [Technology development] Drug Discovery and Development (DDD) [Technology development] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Silencing FLI or targeting CD13/ANPEP lead to dephosphorylation of EPHA2, a mediator of BRAF inhibitor resistance, and induce growth arrest or apoptosis in melanoma cells.

Azimi A, Tuominen R, Costa Svedman F, ..., Hansson J, Egyhazi Brage S

Cell Death Dis 8 (8) e3029 [2017-08-31; online 2017-08-31]

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Neuroblastoma patient-derived xenograft cells cultured in stem-cell promoting medium retain tumorigenic and metastatic capacities but differentiate in serum.

Persson CU, von Stedingk K, Bexell D, ..., Påhlman S, Wigerup C

Sci Rep 7 (1) 10274 [2017-08-31; online 2017-08-31]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A genomic exploration identifies mechanisms that may explain adverse cardiovascular effects of COX-2 inhibitors.

Brænne I, Willenborg C, Tragante V, ..., Erdmann J, Schunkert H

Sci Rep 7 (1) 10252 [2017-08-31; online 2017-08-31]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Importance of N- and C-terminal residues of substance P 1-7 for alleviating allodynia in mice after peripheral administration.

Skogh A, Lesniak A, Gaugaz FZ, ..., Hallberg M, Sandström A

Eur J Pharm Sci 106 (-) 345-351 [2017-08-30; online 2017-06-03]

Drug Discovery and Development (DDD) [Collaborative]

Synthetic lethality between androgen receptor signalling and the PARP pathway in prostate cancer.

Asim M, Tarish F, Zecchini HI, ..., Neal D, Helleday T

Nat Commun 8 (1) 374 [2017-08-29; online 2017-08-29]

Advanced FISH Technologies [Collaborative]

Mass Cytometry and Topological Data Analysis Reveal Immune Parameters Associated with Complications after Allogeneic Stem Cell Transplantation.

Lakshmikanth T, Olin A, Chen Y, ..., Omazic B, Brodin P

Cell Rep 20 (9) 2238-2250 [2017-08-29; online 2017-08-31]

Quantitative proteomic characterization of lung-MSC and bone marrow-MSC using DIA-mass spectrometry.

Rolandsson Enes S, Åhrman E, Palani A, ..., Malmström J, Westergren-Thorsson G

Sci Rep 7 (1) 9316 [2017-08-24; online 2017-08-24]

Nitrogen uptake and assimilation in proliferating embryogenic cultures of Norway spruce-Investigating the specific role of glutamine.

Carlsson J, Svennerstam H, Moritz T, Egertsdotter U, Ganeteg U

PLoS ONE 12 (8) e0181785 [2017-08-24; online 2017-08-24]

Identification of NCAN as a candidate gene for developmental dyslexia.

Einarsdottir E, Peyrard-Janvid M, Darki F, ..., Leinonen E, Kere J

Sci Rep 7 (1) 9294 [2017-08-24; online 2017-08-24]

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Clonal Evolution of Autoreactive Germinal Centers.

Degn SE, van der Poel CE, Firl DJ, ..., Victora GD, Carroll MC

Cell 170 (5) 913-926.e19 [2017-08-24; online 2017-08-26]

Cerium oxide nanoparticles inhibit differentiation of neural stem cells.

Gliga AR, Edoff K, Caputo F, ..., Ceccatelli S, Fadeel B

Sci Rep 7 (1) 9284 [2017-08-24; online 2017-08-24]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Integrated Microscopy Technologies Stockholm [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Mitochondrial genome of the North African Sahara Honeybee, Apis mellifera sahariensis (Hymenoptera: Apidae).

Haddad N, Adjlane N, Loucif-Ayad W, ..., Al-Nakeeb K, Sicheritz-Ponten T

Mitochondrial DNA Part B 2 (2) 548-549 [2017-08-22; online 2017-08-22]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genomic correlates of glatiramer acetate adverse cardiovascular effects lead to a novel locus mediating coronary risk

Brænne I, Zeng L, Willenborg C, ..., None , None

PLoS ONE 12 (8) e0182999 [2017-08-22; online 2017-08-22]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A specific antibody to detect transcription factor T-Pit: a reliable marker of corticotroph cell differentiation and a tool to improve the classification of pituitary neuroendocrine tumours.

Sjöstedt E, Bollerslev J, Mulder J, ..., Pontén F, Casar-Borota O

Acta Neuropathol. - (-) - [2017-08-19; online 2017-08-19]

Identification of bacterial biofilm and the Staphylococcus aureus derived protease, staphopain, on the skin surface of patients with atopic dermatitis.

Sonesson A, Przybyszewska K, Eriksson S, ..., Potempa J, Schmidtchen A

Sci Rep 7 (1) 8689 [2017-08-18; online 2017-08-18]

A pathology atlas of the human cancer transcriptome.

Uhlen M, Zhang C, Lee S, ..., Mardinoglu A, Ponten F

Science 357 (6352) eaan2507 [2017-08-18; online 2017-08-19]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Technology development]

SF3B1-initiating mutations in MDS-RSs target lymphomyeloid hematopoietic stem cells

Mortera-Blanco T, Dimitriou M, Woll PS, ..., Jacobsen SEW, Hellström-Lindberg E

Blood 130 (7) 881-890 [2017-08-17; online 2017-06-20]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

Tea and coffee consumption in relation to DNA methylation in four European cohorts.

Ek WE, Tobi EW, Ahsan M, ..., Johansson Å, Epigenome-Wide Association Study Consortium

Hum. Mol. Genet. 26 (16) 3221-3231 [2017-08-15; online 2017-05-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

SubCons: a new ensemble method for improved human subcellular localization predictions.

Salvatore M, Warholm P, Shu N, Basile W, Elofsson A

Bioinformatics 33 (16) 2464-2470 [2017-08-15; online 2017-04-14]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Diverse heterocyclic scaffolds as dCTP pyrophosphatase 1 inhibitors. Part 1: Triazoles, triazolopyrimidines, triazinoindoles, quinoline hydrazones and arylpiperazines.

Llona-Minguez S, Häggblad M, Martens U, ..., Scobie M, Helleday T

Bioorg. Med. Chem. Lett. 27 (16) 3897-3904 [2017-08-15; online 2017-06-16]

Drug Discovery and Development (DDD) [Collaborative]

Circulating GDF-15 levels predict future secondary manifestations of cardiovascular disease explicitly in women but not men with atherosclerosis.

Gohar A, Gonçalves I, Vrijenhoek J, ..., Björkbacka H, de Jager SCA

Int. J. Cardiol. 241 (-) 430-436 [2017-08-15; online 2017-03-22]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles.

Marincevic-Zuniga Y, Dahlberg J, Nilsson S, ..., Nordlund J, Syvänen AC

J Hematol Oncol 10 (1) 148 [2017-08-14; online 2017-08-14]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Sydney Heart Bank: improving translational research while eliminating or reducing the use of animal models of human heart disease.

Dos Remedios CG, Lal SP, Li A, ..., Linke W, van der Velden J

Biophys Rev - (-) - [2017-08-14; online 2017-08-14]

Mucin-Inspired Lubrication on Hydrophobic Surfaces

Käsdorf BT, Weber F, Petrou G, ..., Crouzier T, Lieleg O

Biomacromolecules 18 (8) 2454-2462 [2017-08-14; online 2017-07-03]

Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian.

Cortázar-Chinarro M, Lattenkamp EZ, Meyer-Lucht Y, ..., Laurila A, Höglund J

BMC Evol. Biol. 17 (1) 189 [2017-08-14; online 2017-08-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

High RBM3 expression is associated with an improved survival and oxaliplatin response in patients with metastatic colorectal cancer.

Siesing C, Sorbye H, Dragomir A, ..., Glimelius B, Eberhard J

PLoS ONE 12 (8) e0182512 [2017-08-11; online 2017-08-11]

Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life

Spang A, Caceres EF, Ettema TJG

Science 357 (6351) eaaf3883 [2017-08-11; online 2017-08-10]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.

Broman E, Sjöstedt J, Pinhassi J, Dopson M

Microbiome 5 (1) 96 [2017-08-09; online 2017-08-09]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Rho-associated kinase is a therapeutic target in neuroblastoma.

Dyberg C, Fransson S, Andonova T, ..., Johnsen JI, Wickström M

Proc. Natl. Acad. Sci. U.S.A. 114 (32) E6603-E6612 [2017-08-08; online 2017-07-24]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Use of Proteomics To Investigate Kidney Function Decline over 5 Years.

Carlsson AC, Ingelsson E, Sundström J, ..., Lind L, Ärnlöv J

Clin J Am Soc Nephrol 12 (8) 1226-1235 [2017-08-07; online 2017-07-21]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

PLS3 Deletions Lead to Severe Spinal Osteoporosis and Disturbed Bone Matrix Mineralization.

Kämpe AJ, Costantini A, Levy-Shraga Y, ..., Grasemann C, Mäkitie O

J. Bone Miner. Res. - (-) - [2017-08-04; online 2017-08-04]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Membrane trafficking under the microscope, what new imaging technologies have brought to light

Fernandez-Rodriguez J, Nilsson T

CRC Press 1st Edition (-) - [2017-08-01]

Integrated Microscopy Technologies Gothenburg [Service]

Diverse heterocyclic scaffolds as dCTP pyrophosphatase 1 inhibitors. Part 2: Pyridone- and pyrimidinone-derived systems.

Llona-Minguez S, Häggblad M, Martens U, ..., Scobie M, Helleday T

Bioorg. Med. Chem. Lett. 27 (15) 3219-3225 [2017-08-01; online 2017-06-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Service]

Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing

Corcoll N, Österlund T, Sinclair L, ..., Backhaus T, Eriksson KM

FEMS Microbiol. Lett. 364 (14) - [2017-08-01; online 2017-06-29]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds

Kawakami T, Mugal CF, Suh A, ..., Smeds L, Ellegren H

Mol Ecol 26 (16) 4158-4172 [2017-08-00; online 2017-07-05]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The structure of the tetanus toxin reveals pH-mediated domain dynamics.

Masuyer G, Conrad J, Stenmark P

EMBO Rep. 18 (8) 1306-1317 [2017-08-00; online 2017-06-23]

The anticancer effect of mebendazole may be due to M1 monocyte/macrophage activation via ERK1/2 and TLR8-dependent inflammasome activation.

Blom K, Senkowski W, Jarvius M, ..., Nygren P, Larsson R

Immunopharmacol Immunotoxicol 39 (4) 199-210 [2017-08-00; online 2017-05-04]

Switchable ionic liquids enable efficient nanofibrillation of wood pulp

Berglund L, Anugwom I, Hedenström M, ..., Mikkola JP, Oksman K

Cellulose 24 (8) 3265-3279 [2017-08-00; online 2017-06-06]

Structural pathway of regulated substrate transfer and threading through an Hsp100 disaggregase.

Deville C, Carroni M, Franke KB, ..., Mogk A, Saibil HR

Sci Adv 3 (8) e1701726 [2017-08-00; online 2017-08-04]

Site-specific gene expression analysis of implant-near cells in a soft tissue infection model - Application of laser microdissection to study biomaterial-associated infection.

Svensson S, Trobos M, Omar O, Thomsen P

J. Biomed. Mater. Res. 105 (8) 2210-2217 [2017-08-00; online 2017-05-10]

Integrated Microscopy Technologies Gothenburg [Service]

Regional genetic differentiation in the blue mussel from the Baltic Sea area

Larsson J, Lind EE, Corell H, ..., Smolarz K, Lönn M

Estuarine, Coastal and Shelf Science 195 (-) 98-109 [2017-08-00; online 2017-08-00]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Rates of gene flow in a freshwater snail and the evolution of phenotypic plasticity

Hollander J, Ahlgren J, Brönmark C

Biol J Linn Soc Lond 121 (4) 764-770 [2017-08-00; online 2017-06-01]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds

Wurzbacher C, Nilsson RH, Rautio M, Peura S

ISME J 11 (8) 1938-1941 [2017-08-00; online 2017-04-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Objective automated quantification of fluorescence signal in histological sections of rat lens

Talebizadeh N, Hagström NZ, Yu Z, ..., Söderberg P, Wählby C

Cytometry 91 (8) 815-821 [2017-08-00; online 2017-05-11]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations.

Hollfelder N, Schlebusch CM, Günther T, ..., Hassan HY, Jakobsson M

PLoS Genet. 13 (8) e1006976 [2017-08-00; online 2017-08-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Molecular composition and distribution of gap junctions in the sensory epithelium of the human cochlea-a super-resolution structured illumination microscopy (SR-SIM) study.

Liu W, Li H, Edin F, ..., Pfaller K, Rask-Andersen H

Ups. J. Med. Sci. 122 (3) 160-170 [2017-08-00; online 2017-05-17]

Integrated Microscopy Technologies Stockholm [Service]

Low-Frequency Synonymous Coding Variation in CYP2R1 Has Large Effects on Vitamin D Levels and Risk of Multiple Sclerosis

Manousaki D, Dudding T, Haworth S, ..., Timpson NJ, Richards JB

The American Journal of Human Genetics 101 (2) 227-238 [2017-08-00; online 2017-08-00]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Low temperature, autotrophic microbial denitrification using thiosulfate or thiocyanate as electron donor.

Broman E, Jawad A, Wu X, ..., Sundkvist JE, Dopson M

Biodegradation 28 (4) 287-301 [2017-08-00; online 2017-06-02]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Investigation of calcium-dependent activity and conformational dynamics of zebra fish 12-lipoxygenase

Mittal M, Hasan M, Balagunaseelan N, ..., Haeggström JZ, Rinaldo-Matthis A

Biochimica et Biophysica Acta (BBA) - General Subjects 1861 (8) 2099-2111 [2017-08-00; online 2017-08-00]

Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa

Vijay N, Weissensteiner M, Burri R, ..., Ellegren H, Wolf JBW

Mol Ecol 26 (16) 4284-4295 [2017-08-00; online 2017-06-27]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genome-Wide Association Study of Angioedema Induced by Ace Inhibitors or Arbs in Sweden

Wadelius M, Eriksson N, Johansson C, ..., Magnusson PKE, Hallberg P

Clinical Therapeutics 39 (8) e76 [2017-08-00; online 2017-08-00]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks

Lundberg M, Liedvogel M, Larson K, ..., Åkesson S, Bensch S

Evolution Letters 1 (3) 155-168 [2017-08-00; online 2017-06-16]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Gene Expression Profiling of Large Cell Lung Cancer Links Transcriptional Phenotypes to the New Histological WHO 2015 Classification

Karlsson A, Brunnström H, Micke P, ..., Planck M, Staaf J

Journal of Thoracic Oncology 12 (8) 1257-1267 [2017-08-00; online 2017-08-00]

Clinical Genomics [Service] Clinical Genomics Lund [Service] Clinical Genomics Uppsala [Collaborative]

Dual herbivore attack and herbivore density affect metabolic profiles of Brassica nigra leaves

Ponzio C, Papazian S, Albrectsen BR, Dicke M, Gols R

Plant, Cell & Environment 40 (8) 1356-1367 [2017-08-00; online 2017-02-24]

Differences in genetic and environmental variation in adult BMI by sex, age, time period, and region: an individual-based pooled analysis of 40 twin cohorts

Silventoinen K, Jelenkovic A, Sund R, ..., Sørensen TI, Kaprio J

Am J Clin Nutr 106 (2) 457-466 [2017-08-00; online 2017-07-05]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Data on haplotype-supported immunoglobulin germline gene inference.

Kirik U, Greiff L, Levander F, Ohlin M

Data Brief 13 (-) 620-640 [2017-08-00; online 2017-06-27]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Comprehensive Profiling of the Androgen Receptor in Liquid Biopsies from Castration-resistant Prostate Cancer Reveals Novel Intra-AR Structural Variation and Splice Variant Expression Patterns.

De Laere B, van Dam PJ, Whitington T, ..., Grönberg H, Lindberg J

Eur. Urol. 72 (2) 192-200 [2017-08-00; online 2017-01-16]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

CKM Glu83Gly Is Associated With Blunted Creatine Kinase Variation, but Not With Myalgia.

Siddiqui MK, Veluchamy A, Maroteau C, ..., Palmer CNA, PREDICTION-ADR Consortium

Circ Cardiovasc Genet 10 (4) e001737 [2017-08-00; online 2017-08-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Bioinformatic processing of RAD‐seq data dramatically impacts downstream population genetic inference

Shafer ABA, Peart CR, Tusso S, ..., Wheat CW, Wolf JBW

Methods Ecol Evol 8 (8) 907-917 [2017-08-00; online 2016-11-28]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Aeromonas salmonicida Growth in Response to Atlantic Salmon Mucins Differs between Epithelial Sites, Is Governed by Sialylated and N-Acetylhexosamine-Containing O-Glycans, and Is Affected by Ca2.

Padra JT, Sundh H, Sundell K, ..., Karlsson NG, Lindén SK

Infect. Immun. 85 (8) - [2017-08-00; online 2017-07-19]

A MUTYH germline mutation is associated with small intestinal neuroendocrine tumors.

Dumanski JP, Rasi C, Björklund P, ..., Hellman P, Tiensuu Janson E

Endocr. Relat. Cancer 24 (8) 427-443 [2017-08-00; online 2017-06-20]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Dual action of bacteriocin PLNC8 αβ through inhibition of Porphyromonas gingivalis infection and promotion of cell proliferation.

Bengtsson T, Zhang B, Selegård R, ..., Aili D, Khalaf H

Pathog Dis 75 (5) - [2017-07-31; online 2017-06-13]

Solution NMR structure of the TRIM21 B-box2 and identification of residues involved in its interaction with the RING domain

Wallenhammar A, Anandapadamanaban M, Lemak A, ..., Wallner B, Sunnerhagen M

PLoS ONE 12 (7) e0181551 [2017-07-28; online 2017-07-28]

Isoflavones and Rotenoids from the Leaves of Millettia oblata ssp. teitensis

Deyou T, Marco M, Heydenreich M, ..., Yenesew A, Erdélyi M

J. Nat. Prod. 80 (7) 2060-2066 [2017-07-28; online 2017-06-30]

Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules.

Redin D, Borgström E, He M, ..., Käller M, Ahmadian A

Nucleic Acids Res. 45 (13) e125 [2017-07-27; online 2017-05-20]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PLS3 sequencing in childhood-onset primary osteoporosis identifies two novel disease-causing variants.

Kämpe AJ, Costantini A, Mäkitie RE, ..., Jiao H, Mäkitie O

Osteoporos Int - (-) - [2017-07-26; online 2017-07-26]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Biophysical characterization of the calmodulin-like domain of Plasmodium falciparum calcium dependent protein kinase 3

Andresen C, Niklasson M, Cassman Eklöf S, Wallner B, Lundström P

PLoS ONE 12 (7) e0181721 [2017-07-26; online 2017-07-26]

Protein Science Facility (PSF) [Service] Swedish NMR Centre (SNC) [Service]

About structural changes of lignin during kraft cooking and the kinetics of delignification

Mattsson C, Hasani M, Dang B, Mayzel M, Theliander H

Holzforschung 71 (7-8) 545-553 [2017-07-26; online 2017-07-26]

Untargeted screening for novel autoantibodies with prognostic value in first-episode psychosis.

Zandian A, Wingård L, Nilsson H, ..., Nilsson P, Persson MAA

Transl Psychiatry 7 (7) e1177 [2017-07-25; online 2017-07-25]

Autoimmunity and Serology Profiling [Collaborative] Tissue Profiling [Collaborative]

Recent increased identification and transmission of HIV-1 unique recombinant forms in Sweden.

Neogi U, Siddik AB, Kalaghatgi P, ..., Marrone G, Sönnerborg A

Sci Rep 7 (1) 6371 [2017-07-25; online 2017-07-25]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Prediction of intracellular exposure bridges the gap between target- and cell-based drug discovery

Mateus A, Gordon LJ, Wayne GJ, ..., Hann MM, Artursson P

Proc Natl Acad Sci USA 114 (30) E6231-E6239 [2017-07-25; online 2017-07-12]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Mass Spectrometry Imaging proves differential absorption profiles of well-characterised permeability markers along the crypt-villus axis.

Nilsson A, Peric A, Strimfors M, ..., Andrén PE, Hilgendorf C

Sci Rep 7 (1) 6352 [2017-07-25; online 2017-07-25]

Haploid selection within a single ejaculate increases offspring fitness

Alavioon G, Hotzy C, Nakhro K, ..., Maklakov AA, Immler S

Proc Natl Acad Sci USA 114 (30) 8053-8058 [2017-07-25; online 2017-07-11]

Genome Engineering Zebrafish [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Continuous immunotypes describe human immune variation and predict diverse responses.

Kaczorowski KJ, Shekhar K, Nkulikiyimfura D, ..., Chakraborty AK, Brodin P

Proc. Natl. Acad. Sci. U.S.A. 114 (30) E6097-E6106 [2017-07-25; online 2017-07-10]

Combined epigenetic and differentiation-based treatment inhibits neuroblastoma tumor growth and links HIF2α to tumor suppression.

Westerlund I, Shi Y, Toskas K, ..., Schlisio S, Holmberg J

Proc. Natl. Acad. Sci. U.S.A. 114 (30) E6137-E6146 [2017-07-25; online 2017-07-10]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Novel Blood Pressure Locus and Gene Discovery Using Genome-Wide Association Study and Expression Data Sets From Blood and the Kidney.

Wain LV, Vaez A, Jansen R, ..., Caulfield MJ, Ehret GB

Hypertension 70 (3) e4-e19 [2017-07-24; online 2017-07-24]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Large meta-analysis of genome-wide association studies identifies five loci for lean body mass.

Zillikens MC, Demissie S, Hsu YH, ..., Ohlsson C, Kiel DP

Nat Commun 8 (1) 80 [2017-07-19; online 2017-07-19]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Tuning Metabolome Coverage in Reversed Phase LC-MS Metabolomics of MeOH Extracted Samples Using the Reconstitution Solvent Composition.

Lindahl A, Sääf S, Lehtiö J, Nordström A

Anal. Chem. 89 (14) 7356-7364 [2017-07-18; online 2017-06-28]

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [Technology development]

Targeted sequencing of tonsillar and base of tongue cancer and human papillomavirus positive unknown primary of the head and neck reveals prognostic effects of mutated FGFR3

Bersani C, Sivars L, Haeggblom L, ..., Ramqvist T, Dalianis T

Oncotarget - (-) - [2017-07-18; online 2017-02-09]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Transcriptional profiling of the rat nucleus accumbens after modest or high alcohol exposure.

Morud J, Ashouri A, Larsson E, Ericson M, Söderpalm B

PLoS ONE 12 (7) e0181084 [2017-07-17; online 2017-07-17]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Transancestral mapping and genetic load in systemic lupus erythematosus.

Langefeld CD, Ainsworth HC, Cunninghame Graham DS, ..., Gaffney PM, Vyse TJ

Nat Commun 8 (-) 16021 [2017-07-17; online 2017-07-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial-mesenchymal transition.

Larsson C, Ali MA, Pandzic T, ..., He L, Sjöblom T

BMC Cancer 17 (1) 487 [2017-07-17; online 2017-07-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Association analyses based on false discovery rate implicate new loci for coronary artery disease

Nelson CP, Goel A, Butterworth AS, ..., Watkins H, Deloukas P

Nat Genet 49 (9) 1385-1391 [2017-07-17; online 2017-07-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity.

Lind U, Järvå M, Alm Rosenblad M, ..., Hedfalk K, Blomberg A

PLoS ONE 12 (7) e0181192 [2017-07-17; online 2017-07-17]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Moderate Expression of SEC16 Increases Protein Secretion by Saccharomyces cerevisiae.

Bao J, Huang M, Petranovic D, Nielsen J

Appl. Environ. Microbiol. 83 (14) - [2017-07-15; online 2017-06-30]

Integrated Microscopy Technologies Gothenburg [Service]

Does antifouling paint select for antibiotic resistance?

Flach CF, Pal C, Svensson CJ, ..., Tysklind M, Larsson DG

Sci. Total Environ. 590-591 (-) 461-468 [2017-07-15; online 2017-03-08]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Prediction and modeling of pre-analytical sampling errors as a strategy to improve plasma NMR metabolomics data

Brunius C, Pedersen A, Malmodin D, ..., Tybring G, Landberg R

Bioinformatics - (-) - [2017-07-14; online 2017-07-14]

Lipid Driven Nanodomains in Giant Lipid Vesicles are Fluid and Disordered.

Koukalová A, Amaro M, Aydogan G, ..., Hof M, Šachl R

Sci Rep 7 (1) 5460 [2017-07-14; online 2017-07-14]

A TRPV1-to-secretagogin regulatory axis controls pancreatic β-cell survival by modulating protein turnover.

Malenczyk K, Girach F, Szodorai E, ..., Groop L, Harkany T

EMBO J. 36 (14) 2107-2125 [2017-07-14; online 2017-06-21]

Lansoprazole-sulfide, pharmacokinetics of this promising anti-tuberculous agent

Mdanda S, Baijnath S, Shobo A, ..., Naicker T, Govender T

Biomedical Chromatography - (-) e4035 [2017-07-13; online 2017-07-13]

Drug Discovery and Development (DDD) [Collaborative]

Genotype–covariate interaction effects and the heritability of adult body mass index

Robinson MR, English G, Moser G, ..., Cesarini D, Visscher PM

Nat Genet 49 (8) 1174-1181 [2017-07-10; online 2017-07-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Multipotent peripheral glial cells generate neuroendocrine cells of the adrenal medulla.

Furlan A, Dyachuk V, Kastriti ME, ..., Ernfors P, Adameyko I

Science 357 (6346) - [2017-07-07; online 2017-07-08]

Anti-citrullinated protein antibodies cause arthritis by cross-reactivity to joint cartilage.

Ge C, Tong D, Liang B, ..., Dobritzsch D, Holmdahl R

JCI Insight 2 (13) - [2017-07-06; online 2017-07-06]

Autoimmunity and Serology Profiling [Service] Protein Science Facility (PSF) [Service]

High-Density Serum/Plasma Reverse Phase Protein Arrays.

Hellström C, Dodig-Crnković T, Hong MG, ..., Nilsson P, Sjöberg R

Methods Mol. Biol. 1619 (-) 229-238 [2017-07-05; online 2017-07-05]

Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development]

Detection of Extracellular Vesicles Using Proximity Ligation Assay with Flow Cytometry Readout-ExoPLA.

Löf L, Arngården L, Ebai T, ..., Söderberg O, Kamali-Moghaddam M

Curr Protoc Cytom 81 (-) 4.8.1-4.8.10 [2017-07-05; online 2017-07-05]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Bead-Based and Multiplexed Immunoassays for Protein Profiling via Sequential Affinity Capture.

Birgersson E, Schwenk JM, Ayoglu B

Methods Mol. Biol. 1619 (-) 45-54 [2017-07-05; online 2017-07-05]

Affinity Proteomics Stockholm [Technology development]

Paternal personality and social status influence offspring activity in zebrafish.

Zajitschek S, Herbert-Read JE, Abbasi NM, Zajitschek F, Immler S

BMC Evol. Biol. 17 (1) 157 [2017-07-03; online 2017-07-03]

Niche-mediated depletion of the normal hematopoietic stem cell reservoir by Flt3-ITD-induced myeloproliferation.

Mead AJ, Neo WH, Barkas N, ..., Nerlov C, Jacobsen SEW

J. Exp. Med. 214 (7) 2005-2021 [2017-07-03; online 2017-06-21]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Mineral Type Structures Soil Microbial Communities

Ahmed E, Hugerth LW, Logue JB, ..., Andersson AF, Holmström SJM

Geomicrobiology Journal 34 (6) 538-545 [2017-07-03; online 2016-11-22]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Isoelectric point-based fractionation by HiRIEF coupled to LC-MS allows for in-depth quantitative analysis of the phosphoproteome.

Panizza E, Branca RMM, Oliviusson P, Orre LM, Lehtiö J

Sci Rep 7 (1) 4513 [2017-07-03; online 2017-07-03]

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service]

Structure-metabolism-relationships in the microsomal clearance of piperazin-1-ylpyridazines.

Llona-Minguez S, Ghassemian A, Baranczewski P, ..., Scobie M, Helleday T

Med. Chem. Commun. 8 (7) 1553-1560 [2017-07-01; online 2017-07-04]

Drug Discovery and Development (DDD) [Collaborative]

Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae).

Sullivan AR, Schiffthaler B, Thompson SL, Street NR, Wang XR

Mol. Biol. Evol. 34 (7) 1689-1701 [2017-07-01; online 2017-04-07]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genetics of phenotypic plasticity and biomass traits in hybrid willows across contrasting environments and years

Berlin S, Hallingbäck HR, Beyer F, ..., Weih M, Rönnberg-Wästljung AC

- 120 (1) 87-100 [2017-07-01; online 2017-04-25]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Epitope mapping of a new anti-Tn antibody detecting gastric cancer cells.

Persson N, Stuhr-Hansen N, Risinger C, ..., Jansson B, Blixt O

Glycobiology 27 (7) 635-645 [2017-07-01; online 2017-04-19]

Wholegrain oat diet changes the expression of genes associated with intestinal bile acid transport.

Andersson KE, Chawade A, Thuresson N, ..., Olsson O, Hellstrand P

Mol Nutr Food Res 61 (7) - [2017-07-00; online 2017-03-30]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Three-dimensional structures and functional studies of two GH43 arabinofuranosidases from Weissella sp. strain 142 and Lactobacillus brevis.

Linares-Pastén JA, Falck P, Albasri K, ..., Logan DT, Karlsson EN

FEBS J. 284 (13) 2019-2036 [2017-07-00; online 2017-06-18]

Stability of Proteins in Dried Blood Spot Biobanks

Björkesten J, Enroth S, Shen Q, ..., Kamali-Moghaddam M, Landegren U

Mol Cell Proteomics 16 (7) 1286-1296 [2017-07-00; online 2017-05-13]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Relations between lipoprotein(a) concentrations, LPA genetic variants, and the risk of mortality in patients with established coronary heart disease: a molecular and genetic association study

Zewinger S, Kleber ME, Tragante V, ..., März W, Speer T

The Lancet Diabetes & Endocrinology 5 (7) 534-543 [2017-07-00; online 2017-07-00]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Reaching the limits of prognostication in non-small cell lung cancer: an optimized biomarker panel fails to outperform clinical parameters.

Grinberg M, Djureinovic D, Brunnström HR, ..., Rahnenführer J, Micke P

Mod. Pathol. 30 (7) 964-977 [2017-07-00; online 2017-03-10]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative] Tissue Profiling [Collaborative]

Primary familial brain calcification linked to deletion of 5' noncoding region of SLC20A2.

Pasanen P, Mäkinen J, Myllykangas L, ..., Pöyhönen M, Baumann P

Acta Neurol. Scand. 136 (1) 59-63 [2017-07-00; online 2016-10-10]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery.

Kirik U, Greiff L, Levander F, Ohlin M

Mol. Immunol. 87 (-) 12-22 [2017-07-00; online 2017-04-04]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Integrative Genomics Identifies the Molecular Basis of Resistance to Azacitidine Therapy in Myelodysplastic Syndromes

Unnikrishnan A, Papaemmanuil E, Beck D, ..., Campbell PJ, Pimanda JE

Cell Rep 20 (3) 572-585 [2017-07-00; online 2017-07-00]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

Genomewide analysis of admixture and adaptation in the Africanized honeybee.

Nelson RM, Wallberg A, Simões ZLP, Lawson DJ, Webster MT

Mol. Ecol. 26 (14) 3603-3617 [2017-07-00; online 2017-04-24]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence.

Sniekers S, Stringer S, Watanabe K, ..., van Duijn CM, Posthuma D

Nat. Genet. 49 (7) 1107-1112 [2017-07-00; online 2017-05-22]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

EGR2 mutations define a new clinically aggressive subgroup of chronic lymphocytic leukemia

Young E, Noerenberg D, Mansouri L, ..., Rosenquist R, Damm F

Leukemia 31 (7) 1547-1554 [2017-07-00; online 2017-01-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Design and synthesis of potent inhibitors of the mono(ADP-ribosyl)transferase, PARP14

Upton K, Meyers M, Thorsell AG, ..., Schüler H, Ferraris D

Bioorganic & Medicinal Chemistry Letters 27 (13) 2907-2911 [2017-07-00; online 2017-07-00]

D-methionine interferes with non-typeable Haemophilus influenzae peptidoglycan synthesis during growth and biofilm formation.

Dawe H, Berger E, Sihlbom C, ..., Faust SN, Allan RN

Microbiology (Reading, Engl.) 163 (7) 1093-1104 [2017-07-00; online 2017-07-21]

Close Encounters – Probing Proximal Proteins in Live or Fixed Cells

Lönn P, Landegren U

Trends in Biochemical Sciences 42 (7) 504-515 [2017-07-00; online 2017-07-00]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Blood transcriptomes and de novo identification of candidate loci for mating success in lekking great snipe (Gallinago media)

Höglund J, Wang B, Saether SA, ..., Kålås JA, Ekblom R

Mol Ecol 26 (13) 3458-3471 [2017-07-00; online 2017-04-28]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A Low-Frequency Inactivating AKT2 Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk.

Manning A, Highland HM, Gasser J, ..., Gloyn AL, Lindgren CM

Diabetes 66 (7) 2019-2032 [2017-07-00; online 2017-03-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.

Hernandez-Castro LE, Paterno M, Villacís AG, ..., Grijalva MJ, Llewellyn MS

PLoS Negl Trop Dis 11 (7) e0005710 [2017-07-00; online 2017-07-19]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

Feng C, Pettersson M, Lamichhaney S, ..., Folkvord A, Andersson L

Elife 6 (-) - [2017-06-30; online 2017-06-30]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The wolf reference genome sequence (Canis lupus lupus) and its implications for Canis spp. population genomics.

Gopalakrishnan S, Samaniego Castruita JA, Sinding MS, ..., Dalén L, Gilbert MTP

BMC Genomics 18 (1) 495 [2017-06-29; online 2017-06-29]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

New Promises of Chemical Proteomics for Drug Development

Gaetani M, Zubarev RA

Novel Approaches in Drug Designing & Development 2 (1) 555579 [2017-06-27]

Halogen Bonding: A Powerful Tool for Modulation of Peptide Conformation

Danelius E, Andersson H, Jarvoll P, ..., Gräfenstein J, Erdélyi M

Biochemistry 56 (25) 3265-3272 [2017-06-27; online 2017-06-12]

Identification of a Sjögren's syndrome susceptibility locus at OAS1 that influences isoform switching, protein expression, and responsiveness to type I interferons

Li H, Reksten TR, Ice JA, ..., Sivils KL, None

PLoS Genet. 13 (6) e1006820 [2017-06-22; online 2017-06-22]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Functional metabolomics as a tool to analyze Mediator function and structure in plants.

Davoine C, Abreu IN, Khajeh K, ..., Moritz T, Björklund S

PLoS ONE 12 (6) e0179640 [2017-06-22; online 2017-06-22]

Identifying Bird Remains Using Ancient DNA Barcoding.

Dalén L, Lagerholm VK, Nylander JAA, ..., Irestedt M, Stewart JR

Genes 8 (6) 169 [2017-06-21; online 2017-06-21]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Identification of novel small molecules that inhibit STAT3-dependent transcription and function.

Kolosenko I, Yu Y, Busker S, ..., Page BDG, Grander D

PLoS ONE 12 (6) e0178844 [2017-06-21; online 2017-06-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Systems Biology of Metabolism.

Nielsen J

Annu. Rev. Biochem. 86 (1) 245-275 [2017-06-20; online 2017-03-08]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica.

Kerkhoven EJ, Kim YM, Wei S, ..., Metz TO, Nielsen J

MBio 8 (3) - [2017-06-20; online 2017-06-20]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Global Kinetic Mechanism of Microsomal Glutathione Transferase 1 and Insights into Dynamic Enzyme Activation.

Spahiu L, Ålander J, Ottosson-Wadlund A, ..., Armstrong RN, Morgenstern R

Biochemistry 56 (24) 3089-3098 [2017-06-20; online 2017-06-09]

Drug Discovery and Development (DDD) [Collaborative]

Combining Flow and Mass Cytometry in the Search for Biomarkers in Chronic Graft-versus-Host Disease.

Stikvoort A, Chen Y, Rådestad E, ..., Brodin P, Uhlin M

Front Immunol 8 (-) 717 [2017-06-19; online 2017-06-19]

Establishment of photosynthesis is controlled by two distinct regulatory phases

Dubreuil C, Jin X, Barajas-López JdD, ..., Small ID, Strand A

Plant Physiol. - (-) pp.00435.2017 [2017-06-16; online 2017-06-16]

Cryo-EM [Service] Swedish Metabolomics Centre (SMC) [Service]

Protein expression in tension wood formation monitored at high tissue resolution in Populus

Bygdell J, Srivastava V, Obudulu O, ..., Mellerowicz EJ, Wingsle G

- 68 (13) 3405-3417 [2017-06-15; online 2017-06-13]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Microbial Community Structure in a Serpentine-Hosted Abiotic Gas Seepage at the Chimaera Ophiolite, Turkey.

Neubeck A, Sun L, Müller B, ..., Broman C, Schnürer A

Appl. Environ. Microbiol. 83 (12) - [2017-06-15; online 2017-05-31]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Stimulated Emission Depletion Microscopy.

Blom H, Widengren J

Chem. Rev. 117 (11) 7377-7427 [2017-06-14; online 2017-03-06]

Integrated Microscopy Technologies Stockholm [Technology development]

Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions

Shungin D, Deng WQ, Varga TV, ..., Franks PW, None

PLoS Genet. 13 (6) e1006812 [2017-06-14; online 2017-06-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic loci associated with heart rate variability and their effects on cardiac disease risk.

Nolte IM, Munoz ML, Tragante V, ..., Snieder H, de Geus EJC

Nat Commun 8 (-) 15805 [2017-06-14; online 2017-06-14]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Structural basis for ligand binding to an enzyme by a conformational selection pathway.

Kovermann M, Grundström C, Sauer-Eriksson AE, Sauer UH, Wolf-Watz M

Proc. Natl. Acad. Sci. U.S.A. 114 (24) 6298-6303 [2017-06-13; online 2017-05-30]

Four simple recommendations to encourage best practices in research software

Jiménez RC, Kuzak M, Alhamdoosh M, ..., Watson-Haigh NS, Crouch S

F1000Res 6 (-) 876 [2017-06-13; online 2017-06-13]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

A community proposal to integrate proteomics activities in ELIXIR

Vizcaíno JA, Walzer M, Jiménez RC, ..., Martens L, Kohlbacher O

F1000Res 6 (-) 875 [2017-06-13; online 2017-06-13]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Alterations of anti-inflammatory lipids in plasma from women with chronic widespread pain - a case control study.

Stensson N, Ghafouri B, Gerdle B, Ghafouri N

Lipids Health Dis 16 (1) 112 [2017-06-12; online 2017-06-12]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Functional and Compositional Stability of Bacterial Metacommunities in Response to Salinity Changes

Berga M, Zha Y, Székely AJ, Langenheder S

Front Microbiol 8 (-) - [2017-06-08; online 2017-06-08]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

SNX10 gene mutation leading to osteopetrosis with dysfunctional osteoclasts.

Stattin EL, Henning P, Klar J, ..., Wikström J, Lerner UH

Sci Rep 7 (1) 3012 [2017-06-07; online 2017-06-07]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Fast and general tests of genetic interaction for genome-wide association studies

Frånberg M, Strawbridge RJ, Hamsten A, ..., Sennblad B, None

PLoS Comput. Biol. 13 (6) e1005556 [2017-06-06; online 2017-06-06]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Effect of food intake on 92 biomarkers for cardiovascular disease.

Dencker M, Gårdinger Y, Björgell O, Hlebowicz J

PLoS ONE 12 (6) e0178656 [2017-06-06; online 2017-06-06]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Mass spectrometry imaging identifies palmitoylcarnitine as an immunological mediator during Salmonella Typhimurium infection.

Hulme HE, Meikle LM, Wessel H, ..., Burchmore R, Wall DM

Sci Rep 7 (1) 2786 [2017-06-05; online 2017-06-05]

Mast Cell Infiltration in Human Brain Metastases Modulates the Microenvironment and Contributes to the Metastatic Potential.

Roy A, Libard S, Weishaupt H, ..., Alafuzoff I, Tchougounova E

Front Oncol 7 (-) 115 [2017-06-02; online 2017-06-02]

Large-Scale Identification of Common Trait and Disease Variants Affecting Gene Expression.

Hauberg ME, Zhang W, Giambartolomei C, ..., Björkegren JLM, Roussos P

Am. J. Hum. Genet. 100 (6) 885-894 [2017-06-01; online 2017-05-25]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Injury Leads to the Appearance of Cells with Characteristics of Both Microglia and Astrocytes in Mouse and Human Brain.

Wilhelmsson U, Andersson D, de Pablo Y, ..., Pekny M, Pekna M

Cereb. Cortex 27 (6) 3360-3377 [2017-06-01; online 2017-04-12]

Fluorescence Tissue Profiling [Collaborative] Integrated Microscopy Technologies Gothenburg [Service]

Genome Sequence of Roseovarius mucosus Strain SMR3, Isolated from a Culture of the Diatom Skeletonema marinoi.

Töpel M, Pinder MIM, Johansson ON, ..., Godhe A, Clarke AK

Genome Announc 5 (22) - [2017-06-01; online 2017-06-01]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Coordinated nitrogen and carbon remobilization for nitrate assimilation in leaf, sheath and root and associated cytokinin signals during early regrowth of Lolium perenne.

Roche J, Turnbull MH, Guo Q, ..., Jameson PE, Love J

Ann. Bot. 119 (8) 1353-1364 [2017-06-01; online 2017-03-24]

Typing and Characterization of Bacteria Using Bottom-up Tandem Mass Spectrometry Proteomics.

Boulund F, Karlsson R, Gonzales-Siles L, ..., Moore ERB, Kristiansson E

Mol. Cell Proteomics 16 (6) 1052-1063 [2017-06-00; online 2017-04-18]

Tumoral cubilin is a predictive marker for treatment of renal cancer patients with sunitinib and sorafenib.

Niinivirta M, Enblad G, Edqvist PH, ..., Dragomir A, Ullenhag GJ

J. Cancer Res. Clin. Oncol. 143 (6) 961-970 [2017-06-00; online 2017-03-04]

The transcriptome of the avian malaria parasite Plasmodium ashfordi displays host-specific gene expression.

Videvall E, Cornwallis CK, Ahrén D, ..., Valkiūnas G, Hellgren O

Mol. Ecol. 26 (11) 2939-2958 [2017-06-00; online 2017-04-08]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

The effects of thawing on the plasma metabolome: evaluating differences between thawed plasma and multi-organ samples

Torell F, Bennett K, Rännar S, ..., Lundstedt T, Trygg J

Metabolomics 13 (6) - [2017-06-00; online 2017-04-17]

Synthetic approaches to radiochemical probes for imaging of bacterial infections

Dutta J, Naicker T, Ebenhan T, ..., Arvidsson PI, Govender T

European Journal of Medicinal Chemistry 133 (-) 287-308 [2017-06-00; online 2017-06-00]

Drug Discovery and Development (DDD) [Collaborative]

Separating the effects of forage source and field microbiota on silage fermentation quality and aerobic stability

Mogodiniyai Kasmaei K, Dicksved J, Spörndly R, Udén P

Grass Forage Sci 72 (2) 281-289 [2017-06-00; online 2016-06-06]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

On the bridge over the translational valley of death: interview with Per I Arvidsson.

Arvidsson PI

Future Science OA 3 (2) FSO183 [2017-06-00; online 2017-04-10]

Drug Discovery and Development (DDD) [Technology development]

No evidence for MHC class II-based non-random mating at the gametic haplotype in Atlantic salmon

Promerová M, Alavioon G, Tusso S, Burri R, Immler S

Heredity 118 (6) 563-567 [2017-06-00; online 2017-01-18]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Methylation of HPA axis related genes in men with hypersexual disorder

Jokinen J, Boström AE, Chatzittofis A, ..., Arver S, Schiöth HB

Psychoneuroendocrinology 80 (-) 67-73 [2017-06-00; online 2017-06-00]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Metabolite quantification by NMR and LC-MS/MS reveals differences between unstimulated, stimulated, and pure parotid saliva

Figueira J, Gouveia-Figueira S, Öhman C, ..., Nording ML, Öhman A

Journal of Pharmaceutical and Biomedical Analysis 140 (-) 295-300 [2017-06-00; online 2017-06-00]

Swedish Metabolomics Centre (SMC) [Service] Swedish NMR Centre (SNC) [Collaborative]

Lower inflammatory markers in women with antenatal depression brings the M1/M2 balance into focus from a new direction

Edvinsson Å, Bränn E, Hellgren C, ..., Cunningham JL, Sundström-Poromaa I

Psychoneuroendocrinology 80 (-) 15-25 [2017-06-00; online 2017-06-00]

Affinity Proteomics Uppsala [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Collaborative]

Levels of oxylipins, endocannabinoids and related lipids in plasma before and after low-level exposure to acrolein in healthy individuals and individuals with chemical intolerance

Claeson AS, Gouveia-Figueira S, Häggström J, Fowler CJ, Nording ML

Prostaglandins, Leukotrienes and Essential Fatty Acids (PLEFA) 121 (-) 60-67 [2017-06-00; online 2017-06-00]

Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation.

Christophersen IE, Rienstra M, Roselli C, ..., Ellinor PT, AFGen Consortium

Nat. Genet. 49 (6) 946-952 [2017-06-00; online 2017-04-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Identification and characterization of inhibitors of UDP-glucose and UDP-sugar pyrophosphorylases for in vivo studies.

Decker D, Öberg C, Kleczkowski LA

Plant J. 90 (6) 1093-1107 [2017-06-00; online 2017-04-13]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

Han F, Lamichhaney S, Grant BR, ..., Andersson L, Webster MT

Genome Res. 27 (6) 1004-1015 [2017-06-00; online 2017-04-25]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Draft genome of the oomycete pathogen Phytophthora cactorum strain LV007 isolated from European beech (Fagus sylvatica).

Grenville-Briggs LJ, Kushwaha SK, Cleary MR, ..., Chawade A, Vetukuri RR

Genom Data 12 (-) 155-156 [2017-06-00; online 2017-05-12]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Downregulation of RWA genes in hybrid aspen affects xylan acetylation and wood saccharification.

Pawar PM, Ratke C, Balasubramanian VK, ..., Jönsson LJ, Mellerowicz EJ

New Phytol. 214 (4) 1491-1505 [2017-06-00; online 2017-03-03]

Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons

Comte J, Berga M, Severin I, Logue JB, Lindström ES

Environ Microbiol 19 (6) 2391-2404 [2017-06-00; online 2017-05-05]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Chemisorption of air CO2 on cellulose: an overlooked feature of the cellulose/NaOH(aq) dissolution system

Gunnarsson M, Theliander H, Hasani M

Cellulose 24 (6) 2427-2436 [2017-06-00; online 2017-04-12]

An automated method measures variability in P-glycoprotein and ABCG2 densities across brain regions and brain matter.

Kannan P, Schain M, Kretzschmar WW, ..., Hall MD, Mulder J

J. Cereb. Blood Flow Metab. - (-) 271678X16660984 [2017-06-00; online 2016-08-05]

Fluorescence Tissue Profiling [Technology development]

Affinity Proteomics Exploration of Melanoma Identifies Proteins in Serum with Associations to T-Stage and Recurrence.

Byström S, Fredolini C, Edqvist PH, ..., Pontén F, Schwenk JM

Transl Oncol 10 (3) 385-395 [2017-06-00; online 2017-04-20]

Affinity Proteomics Stockholm [Collaborative] Tissue Profiling [Collaborative]

A missense variant in ITPR1 provides evidence for autosomal recessive SCA29 with asymptomatic cerebellar hypoplasia in carriers

Klar J, Ali Z, Farooq M, ..., Baig SM, Dahl N

Eur J Hum Genet 25 (7) 848-853 [2017-06-00; online 2017-05-10]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A DNA methylation site within the KLF13 gene is associated with orexigenic processes based on neural responses and ghrelin levels.

Wiemerslage L, Islam R, van der Kamp C, ..., Benedict C, Schiöth HB

Int J Obes (Lond) 41 (6) 990-994 [2017-06-00; online 2017-02-14]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

High-affinity recognition of the human C-reactive protein independent of phosphocholine.

Yang J, Gustavsson AL, Haraldsson M, ..., Norberg T, Baltzer L

Org. Biomol. Chem. 15 (21) 4644-4654 [2017-05-31; online 2017-05-18]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Swedish NMR Centre (SNC) [Service]

Expression of CD226 is associated to but not required for NK cell education.

Wagner AK, Kadri N, Snäll J, ..., Kärre K, Chambers BJ

Nat Commun 8 (-) 15627 [2017-05-31; online 2017-05-31]

Genetic susceptibility to cardiovascular disease and risk of dementia.

Karlsson IK, Ploner A, Song C, ..., Pedersen NL, Hägg S

Transl Psychiatry 7 (5) e1142 [2017-05-30; online 2017-05-30]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A subcellular map of the human proteome.

Thul PJ, Åkesson L, Wiking M, ..., Uhlén M, Lundberg E

Science 356 (6340) - [2017-05-26; online 2017-05-11]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Spatial Proteomics [Collaborative]

Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes.

Väremo L, Henriksen TI, Scheele C, ..., Pedersen BK, Nielsen J

Genome Med 9 (1) 47 [2017-05-25; online 2017-05-25]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Piperazin-1-ylpyridazine Derivatives Are a Novel Class of Human dCTP Pyrophosphatase 1 Inhibitors.

Llona-Minguez S, Höglund A, Ghassemian A, ..., Scobie M, Helleday T

J. Med. Chem. 60 (10) 4279-4292 [2017-05-25; online 2017-05-16]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Collaborative] Protein Science Facility (PSF) [Service]

Draft Genome Sequence of the Mycoparasitic Oomycete Pythium oligandrum Strain CBS 530.74.

Kushwaha SK, Vetukuri RR, Grenville-Briggs LJ

Genome Announc 5 (21) - [2017-05-25; online 2017-05-25]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Apoptotic Bax at Oxidatively Stressed Mitochondrial Membranes: Lipid Dynamics and Permeabilization.

Dingeldein APG, Pokorná Š, Lidman M, ..., Hof M, Gröbner G

Biophysical Journal 112 (10) 2147-2158 [2017-05-23; online 2017-05-26]

Neuroproteomic Profiling of Cerebrospinal Fluid (CSF) by Multiplexed Affinity Arrays.

Häggmark-Månberg A, Nilsson P, Schwenk JM

Methods Mol. Biol. 1598 (-) 247-254 [2017-05-17; online 2017-05-17]

Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development]

ProQ3D: improved model quality assessments using deep learning.

Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A

Bioinformatics 33 (10) 1578-1580 [2017-05-15; online 2017-01-06]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Whole blood gene expression in adolescent chronic fatigue syndrome: an exploratory cross-sectional study suggesting altered B cell differentiation and survival.

Nguyen CB, Alsøe L, Lindvall JM, ..., Nilsen H, Wyller VB

J Transl Med 15 (1) 102 [2017-05-11; online 2017-05-11]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Genome Sequence of a Bovine Rhinitis B Virus Identified in Cattle in Sweden

Blomström AL, Oma V, Khatri M, ..., Berg M, Myrmel M

Genome Announc 5 (19) e00172-17 [2017-05-11; online 2017-05-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data.

Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A

F1000Res 6 (-) 664 [2017-05-10; online 2017-05-10]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Reproducible diagnostic metabolites in plasma from typhoid fever patients in Asia and Africa

Näsström E, Parry CM, Vu Thieu NT, ..., Antti H, Baker S

Elife 6 (-) - [2017-05-09; online 2017-05-09]

Influence of Glycosylation on Interfacial Properties of Recombinant Mucins: Adsorption, Surface Forces, and Friction.

An J, Jin C, Dėdinaitė A, ..., Karlsson NG, Claesson PM

Langmuir 33 (18) 4386-4395 [2017-05-09; online 2017-04-26]

Spatially resolved transcriptome profiling in model plant species.

Giacomello S, Salmén F, Terebieniec BK, ..., Street NR, Lundeberg J

NPLANTS 3 (-) 17061 [2017-05-08; online 2017-05-08]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Regulation of PfEMP1-VAR2CSA translation by a Plasmodium translation-enhancing factor.

Chan S, Frasch A, Mandava CS, ..., Sanyal S, Wahlgren M

Nat Microbiol 2 (-) 17068 [2017-05-08; online 2017-05-08]

Bioinformatics Support for Computational Resources [Service] Global Proteomics and Proteogenomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Screening and Validation of Novel Biomarkers in Osteoarticular Pathologies by Comprehensive Combination of Protein Array Technologies.

Sierra-Sánchez Á, Garrido-Martín D, Lourido L, ..., Blanco F, Fuentes M

J. Proteome Res. 16 (5) 1890-1899 [2017-05-05; online 2017-04-17]

Autoimmunity and Serology Profiling [Collaborative]

QTL mapping of stress related gene expression in a cross between domesticated chickens and ancestral red junglefowl.

Fallahsharoudi A, de Kock N, Johnsson M, ..., Wright D, Jensen P

Mol. Cell. Endocrinol. 446 (-) 52-58 [2017-05-05; online 2017-02-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Impact of cytosine methylation on DNA binding specificities of human transcription factors

Yin Y, Morgunova E, Jolma A, ..., Vinson C, Taipale J

Science 356 (6337) eaaj2239 [2017-05-05; online 2017-05-04]

Regulating plant physiology with organic electronics

Poxson DJ, Karady M, Gabrielsson R, ..., Simon DT, Berggren M

Proc Natl Acad Sci USA 114 (18) 4597-4602 [2017-05-02; online 2017-04-18]

PDE2A2 regulates mitochondria morphology and apoptotic cell death via local modulation of cAMP/PKA signalling.

Monterisi S, Lobo MJ, Livie C, ..., Micaroni M, Zaccolo M

Elife 6 (-) - [2017-05-02; online 2017-05-02]

Integrated Microscopy Technologies Gothenburg [Service]

Mechanistic characterization of a copper containing thiosemicarbazone with potent antitumor activity.

Karlsson H, Fryknäs M, Strese S, ..., Larsson R, Nygren P

Oncotarget 8 (18) 30217-30234 [2017-05-02; online 2017-04-19]

Glioblastoma Cell Malignancy and Drug Sensitivity Are Affected by the Cell of Origin.

Jiang Y, Marinescu VD, Xie Y, ..., Nelander S, Uhrbom L

Cell Rep 19 (5) 1080-1081 [2017-05-02; online 2017-05-04]

Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees.

Wallberg A, Schöning C, Webster MT, Hasselmann M

PLoS Genet. 13 (5) e1006792 [2017-05-00; online 2017-05-25]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.

Engström K, Wojdacz TK, Marabita F, ..., Vahter M, Broberg K

Arch. Toxicol. 91 (5) 2067-2078 [2017-05-00; online 2016-11-12]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]

Three-dimensional functional human neuronal networks in uncompressed low-density electrospun fiber scaffolds.

Jakobsson A, Ottosson M, Zalis MC, ..., Johansson UE, Johansson F

Nanomedicine 13 (4) 1563-1573 [2017-05-00; online 2017-01-05]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

The effect of temperature and substrate quality on the carbon use efficiency of saprotrophic decomposition

Öquist MG, Erhagen B, Haei M, ..., Schleucher J, Nilsson MB

Plant Soil 414 (1-2) 113-125 [2017-05-00; online 2016-11-26]

The chloroplast genome of Ephedra foeminea (Ephedraceae, Gnetales), an entomophilous gymnosperm endemic to the Mediterranean area.

Hou C, Wikström N, Rydin C

Mitochondrial DNA A DNA Mapp Seq Anal 28 (3) 330-331 [2017-05-00; online 2015-12-29]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Structural Diversity of Human Gastric Mucin Glycans.

Jin C, Kenny DT, Skoog EC, ..., Lindén SK, Karlsson NG

Mol. Cell Proteomics 16 (5) 743-758 [2017-05-00; online 2017-05-04]

Affinity Proteomics Uppsala [Service] Glycoproteomics and MS Proteomics [Service] PLA and Single Cell Proteomics [Service]

Loss of chromosome Y (LOY) in blood cells is associated with increased risk for disease and mortality in aging men

Forsberg LA

Hum Genet 136 (5) 657-663 [2017-05-00; online 2017-04-19]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Inflammatory markers in late pregnancy in association with postpartum depression-A nested case-control study.

Bränn E, Papadopoulos F, Fransson E, ..., Sundström-Poromaa I, Skalkidou A

Psychoneuroendocrinology 79 (-) 146-159 [2017-05-00; online 2017-02-28]

Affinity Proteomics Uppsala [Collaborative] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Collaborative]

Induction of functional dopamine neurons from human astrocytes in vitro and mouse astrocytes in a Parkinson's disease model.

Rivetti di Val Cervo P, Romanov RA, Spigolon G, ..., Fisone G, Arenas E

Nat. Biotechnol. 35 (5) 444-452 [2017-05-00; online 2017-04-10]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Immune Biomarkers on the Radar—Comprehensive “Immunograms” for Multimodal Treatment Prediction

Botling J, Sandelin M

Journal of Thoracic Oncology 12 (5) 770-772 [2017-05-00; online 2017-05-00]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

High levels of the AR-V7 Splice Variant and Co-Amplification of the Golgi Protein Coding YIPF6 in AR Amplified Prostate Cancer Bone Metastases.

Djusberg E, Jernberg E, Thysell E, ..., Brattsand M, Wikström P

Prostate 77 (6) 625-638 [2017-05-00; online 2017-02-01]

Genomic repertoire of the Woeseiaceae/JTB255, cosmopolitan and abundant core members of microbial communities in marine sediments.

Mußmann M, Pjevac P, Krüger K, Dyksma S

ISME J 11 (5) 1276-1281 [2017-05-00; online 2017-01-06]

Microbial Single Cell Genomics [Service]

Further evidence for specific IFIH1 mutation as a cause of Singleton-Merten syndrome with phenotypic heterogeneity.

Pettersson M, Bergendal B, Norderyd J, ..., Nordgren A, Lindstrand A

Am. J. Med. Genet. A 173 (5) 1396-1399 [2017-05-00; online 2017-03-20]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

FADD, Caspase-3, and Caspase-8 and Incidence of Coronary Events.

Xue L, Borné Y, Mattisson IY, ..., Nilsson J, Engström G

Arterioscler. Thromb. Vasc. Biol. 37 (5) 983-989 [2017-05-00; online 2017-03-16]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Contrasting patterns of cytokinins between years in senescing aspen leaves

Edlund E, Novak O, Karady M, Ljung K, Jansson S

Plant, Cell & Environment 40 (5) 622-634 [2017-05-00; online 2017-03-27]

Comparative genomics and expression levels of hydrophobins from eight mycorrhizal genomes.

Rineau F, Lmalem H, Ahren D, ..., Martin F, Colpaert JV

Mycorrhiza 27 (4) 383-396 [2017-05-00; online 2017-01-09]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications.

Weissensteiner MH, Pang AWC, Bunikis I, ..., Suh A, Wolf JBW

Genome Res. 27 (5) 697-708 [2017-05-00; online 2017-03-30]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]

Brodie vs Hummers graphite oxides for preparation of multi-layered materials

Talyzin AV, Mercier G, Klechikov A, ..., Opitz A, Moons E

Carbon 115 (-) 430-440 [2017-05-00; online 2017-05-00]

Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations

Wang M, Uebbing S, Ellegren H

Genome Biol Evol 9 (5) 1266-1279 [2017-05-00; online 2017-05-01]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Absolute Quantification of Protein and mRNA Abundances Demonstrate Variability in Gene-Specific Translation Efficiency in Yeast

Lahtvee PJ, Sánchez BJ, Smialowska A, ..., Gatto F, Nielsen J

Cell Syst 4 (5) 495-504.e5 [2017-05-00; online 2017-05-00]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

A Preliminary Report: Radical Surgery and Stem Cell Transplantation for the Treatment of Patients With Pancreatic Cancer.

Omazic B, Ayoglu B, Löhr M, ..., Maeurer MJ, Ringden O

J. Immunother. 40 (4) 132-139 [2017-05-00; online 2017-03-25]

Affinity Proteomics Stockholm [Collaborative] Autoimmunity and Serology Profiling [Collaborative]

Mitochondrial genome divergence between beluga whales in Baffin Bay and the Sea of Okhotsk.

Skovrind M, Samaniego Castruita JA, Heide-Jørgensen MP, Dalén L, Lorenzen E

Mitochondrial DNA Part B 2 (1) 257-258 [2017-04-28; online 2017-04-28]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genetic Profile of Ductal Adenocarcinoma of the Prostate.

Seipel AH, Whitington T, Delahunt B, ..., Lindberg J, Egevad L

Hum. Pathol. - (-) - [2017-04-27; online 2017-04-27]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Does the sex of one's co-twin affect height and BMI in adulthood? A study of dizygotic adult twins from 31 cohorts.

Bogl LH, Jelenkovic A, Vuoksimaa E, ..., Silventoinen K, Kaprio J

Biol Sex Differ 8 (-) 14 [2017-04-27; online 2017-04-27]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genome-wide meta-analysis of 241,258 adults accounting for smoking behaviour identifies novel loci for obesity traits

Justice AE, Winkler TW, Feitosa MF, ..., North KE, Cupples LA

Nat Commun 8 (-) 14977 [2017-04-26; online 2017-04-26]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Corrigendum: MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool.

Gad H, Koolmeister T, Jemth AS, ..., Scobie M, Ulrika Warpman Berglund &Thomas Helleday

Nature 544 (7651) 508 [2017-04-26; online 2017-04-28]

Correlation of histopathologic characteristics to protein expression and function in malignant melanoma.

Welinder C, Pawłowski K, Szasz AM, ..., Wieslander E, Marko-Varga G

PLoS ONE 12 (4) e0176167 [2017-04-26; online 2017-04-26]

Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean

Lamichhaney S, Fuentes-Pardo AP, Rafati N, ..., Ruzzante DE, Andersson L

Proc Natl Acad Sci USA 114 (17) E3452-E3461 [2017-04-25; online 2017-04-07]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease.

Tobiasson M, Abdulkadir H, Lennartsson A, ..., Hellström-Lindberg E, Ungerstedt J

Oncotarget 8 (17) 28812-28825 [2017-04-25; online 2017-04-22]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk

Day FR, Thompson DJ, Helgason H, ..., Ong KK, Perry JRB

Nat Genet 49 (6) 834-841 [2017-04-24; online 2017-04-24]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Influence of Hydroxyapatite Nanoparticle Morphology on Embryonic Development in a Zebrafish Exposure Model.

Pujari-Palmer S, Lu X, Karlsson Ott M

Nanomaterials (Basel) 7 (4) - [2017-04-22; online 2017-04-22]

Respiratory chain complex III deficiency due to mutated BCS1L: a novel phenotype with encephalomyopathy, partially phenocopied in a Bcs1l mutant mouse model.

Tegelberg S, Tomašić N, Kallijärvi J, ..., Eklund EA, Fellman V

Orphanet J Rare Dis 12 (1) 73 [2017-04-20; online 2017-04-20]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Persistent Effects of Developmental Exposure to 17α-Ethinylestradiol on the Zebrafish (Danio rerio) Brain Transcriptome and Behavior

Porseryd T, Volkova K, Reyhanian Caspillo N, ..., Dinnetz P, Porsh Hällström I

Front. Behav. Neurosci. 11 (-) - [2017-04-20; online 2017-04-20]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

In muro deacetylation of xylan affects lignin properties and improves saccharification of aspen wood.

Pawar PM, Derba-Maceluch M, Chong SL, ..., Jönsson LJ, Mellerowicz EJ

Biotechnol Biofuels 10 (1) 98 [2017-04-20; online 2017-04-20]

Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms.

Tesi B, Davidsson J, Voss M, ..., Cammenga J, Bryceson YT

Blood 129 (16) 2266-2279 [2017-04-20; online 2017-02-15]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Adenovirus-mediated CD40L gene transfer increases Teffector/Tregulatory cell ratio and upregulates death receptors in metastatic melanoma patients.

Schiza A, Wenthe J, Mangsbo S, ..., Loskog A, Ullenhag G

J Transl Med 15 (1) 79 [2017-04-20; online 2017-04-20]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Synthesis and characterization of poly-3-((2,5-hydroquinone)vinyl)-1H-pyrrole: investigation on backbone/pendant interactions in a conducting redox polymer.

Huang H, Karlsson C, Strømme M, Gogoll A, Sjödin M

Phys Chem Chem Phys 19 (16) 10427-10435 [2017-04-19; online 2017-04-06]

Histology-Compatible MALDI Mass Spectrometry Based Imaging of Neuronal Lipids for Subsequent Immunofluorescent Staining.

Kaya I, Michno W, Brinet D, ..., Zetterberg H, Hanrieder J

Anal. Chem. 89 (8) 4685-4694 [2017-04-18; online 2017-04-06]

Integrated Microscopy Technologies Gothenburg [Service]

Conversion of Glycerol to 3-Hydroxypropanoic Acid by Genetically Engineered Bacillus subtilis.

Kalantari A, Chen T, Ji B, ..., Goelzer A, Mijakovic I

Front Microbiol 8 (-) 638 [2017-04-18; online 2017-04-18]

Oriented clonal cell dynamics enables accurate growth and shaping of vertebrate cartilage

Kaucka M, Zikmund T, Tesarova M, ..., Fried K, Adameyko I

Elife 6 (-) - [2017-04-17; online 2017-04-17]

Integrated Microscopy Technologies Stockholm [Collaborative]

Anaerobic Methanotrophic Archaea of the ANME-2d Cluster Are Active in a Low-sulfate, Iron-rich Freshwater Sediment.

Weber HS, Habicht KS, Thamdrup B

Front Microbiol 8 (-) 619 [2017-04-12; online 2017-04-12]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Adaptation to infectious disease exposure in indigenous Southern African populations.

Owers KA, Sjödin P, Schlebusch CM, ..., Soodyall H, Jakobsson M

Proc. Biol. Sci. 284 (1852) 20170226 [2017-04-12; online 2017-04-07]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

SnoN Stabilizes the SMAD3/SMAD4 Protein Complex

Walldén K, Nyman T, Hällberg BM

Sci Rep 7 (-) 46370 [2017-04-11; online 2017-04-11]

Serglycin as a potential biomarker for glioma: association of serglycin expression, extent of mast cell recruitment and glioblastoma progression.

Roy A, Attarha S, Weishaupt H, ..., Pontén F, Tchougounova E

Oncotarget 8 (15) 24815-24827 [2017-04-11; online 2017-04-28]

Multi-label prediction of subcellular localization in confocal images using deep neural networks

Winsnes CF, Sullivan DP, Smith K, Lundberg E

Molecular Biology of the Cell 27 (-) - [2017-04-10; online 2017-04-10]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Large-scale genome-wide analysis identifies genetic variants associated with cardiac structure and function

Wild PS, Felix JF, Schillert A, ..., Vasan RS, Dörr M

J Clin Invest. 127 (5) 1798-1812 [2017-04-10; online 2017-04-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing.

Raine A, Manlig E, Wahlberg P, Syvänen AC, Nordlund J

Nucleic Acids Res. 45 (6) e36 [2017-04-07; online 2016-12-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana

Reimegård J, Kundu S, Pendle A, ..., Sundström JF, Emanuelsson O

Nucleic Acids Res 45 (6) 3253-3265 [2017-04-07; online 2017-02-08]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Draft Genome Sequences of Six Strains of Streptococcus pneumoniae from Serotypes 5, 6A, 6B, 18C, 19A, and 23F.

Jakobsson HE, Salvà-Serra F, Thorell K, ..., Kristiansson E, Moore ER

Genome Announc 5 (14) - [2017-04-06; online 2017-04-06]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Complete Genome Sequences of the Xylose-Fermenting Candida intermedia Strains CBS 141442 and PYCC 4715

Moreno AD, Tellgren-Roth C, Soler L, ..., Olsson L, Geijer C

Genome Announc 5 (14) e00138-17 [2017-04-06; online 2017-04-06]

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dUTPase inhibition augments replication defects of 5-Fluorouracil.

Hagenkort A, Paulin CBJ, Desroses M, ..., Scobie M, Helleday T

Oncotarget 8 (14) 23713-23726 [2017-04-04; online 2017-04-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Flow Cytometric Measurement of Blood Cells with BCR-ABL1 Fusion Protein in Chronic Myeloid Leukemia.

Löf L, Arngården L, Olsson-Strömberg U, ..., Landegren U, Kamali-Moghaddam M

Sci Rep 7 (1) 623 [2017-04-04; online 2017-04-04]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Sulfonimidamides in Medicinal and Agricultural Chemistry

Chinthakindi PK, Naicker T, Thota N, ..., Kruger HG, Arvidsson PI

Angew. Chem. Int. Ed. 56 (15) 4100-4109 [2017-04-03; online 2017-02-23]

Drug Discovery and Development (DDD) [Technology development]

Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species.

Nielsen JC, Grijseels S, Prigent S, ..., Workman M, Nielsen J

Nat Microbiol 2 (-) 17044 [2017-04-03; online 2017-04-03]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Total body fat, abdominal fat, body fat distribution and surrogate markers for health related to adipocyte fatty acid-binding protein (FABP4) in children.

Dencker M, Danielson A, Karlsson MK, ..., Andersen LB, Thorsson O

J Pediatr Endocrinol Metab 30 (4) 375-382 [2017-04-01; online 2017-01-14]

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Somatic Ephrin Receptor Mutations Are Associated with Metastasis in Primary Colorectal Cancer.

Mathot L, Kundu S, Ljungström V, ..., Nilsson M, Sjöblom T

Cancer Res. 77 (7) 1730-1740 [2017-04-01; online 2017-01-20]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Membrane-Depolarizing Channel Blockers Induce Selective Glioma Cell Death by Impairing Nutrient Transport and Unfolded Protein/Amino Acid Responses.

Niklasson M, Maddalo G, Sramkova Z, ..., Enger PØ, Andäng M

Cancer Res. 77 (7) 1741-1752 [2017-04-01; online 2017-01-13]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Interactions of Freshwater Cyanobacteria with Bacterial Antagonists

Osman OA, Beier S, Grabherr M, Bertilsson S

Appl. Environ. Microbiol. 83 (7) e02634-16 [2017-04-01; online 2017-01-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Identification and quantification of even and odd chained 5-n alkylresorcinols, branched chain-alkylresorcinols and methylalkylresorcinols in Quinoa (Chenopodium quinoa).

Ross AB, Svelander C, Karlsson G, Savolainen OI

Food Chem 220 (-) 344-351 [2017-04-01; online 2016-10-05]

Green listed—a CRISPR screen tool

Panda SK, Boddul SV, Jiménez-Andrade GY, ..., Fernandez-Ricaud L, Wermeling F

Bioinformatics 33 (7) 1099-1100 [2017-04-01; online 2016-12-19]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Discrimination of pancreatic cancer and pancreatitis by LC-MS metabolomics.

Lindahl A, Heuchel R, Forshed J, ..., Löhr M, Nordström A

Metabolomics 13 (5) 61 [2017-04-01; online 2017-04-01]

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [Service]

Whole-Genome Bisulfite Sequencing of Human Pancreatic Islets Reveals Novel Differentially Methylated Regions in Type 2 Diabetes Pathogenesis

Volkov P, Bacos K, Ofori JK, ..., Rönn T, Ling C

Diabetes 66 (4) 1074-1085 [2017-04-00; online 2017-01-04]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The minimum information required for a glycomics experiment (MIRAGE) project: improving the standards for reporting glycan microarray-based data.

Liu Y, McBride R, Stoll M, ..., Feizi T, Smith DF

Glycobiology 27 (4) 280-284 [2017-04-00; online 2016-11-22]

The anti-inflammatory compound palmitoylethanolamide inhibits prostaglandin and hydroxyeicosatetraenoic acid production by a macrophage cell line

Gabrielsson L, Gouveia-Figueira S, Häggström J, Alhouayek M, Fowler CJ

Pharmacol Res Perspect 5 (2) e00300 [2017-04-00; online 2017-02-27]

Shift in fungal communities and associated enzyme activities along an age gradient of managed Pinus sylvestris stands

Kyaschenko J, Clemmensen KE, Hagenbo A, Karltun E, Lindahl BD

ISME J 11 (4) 863-874 [2017-04-00; online 2017-01-13]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Porosity investigation of yttria-stabilized zirconia topcoats using NMR cryoporometry

Ekberg J, Nordstierna L, Klement U

Surface and Coatings Technology 315 (-) 468-474 [2017-04-00; online 2017-04-00]

Neonatal Cord Blood Oxylipins and Exposure to Particulate Matter in the Early-Life Environment: An ENVIRONAGE Birth Cohort Study.

Martens DS, Gouveia S, Madhloum N, ..., Nording M, Nawrot TS

Environ. Health Perspect. 125 (4) 691-698 [2017-04-00; online 2016-11-05]

Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease.

Folkersen L, Fauman E, Sabater-Lleal M, ..., Hamsten A, Mälarstig A

PLoS Genet. 13 (4) e1006706 [2017-04-00; online 2017-04-03]

Affinity Proteomics Uppsala [Service] Bioinformatics Support for Computational Resources [Service] Clinical Biomarkers [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] PLA and Single Cell Proteomics [Service]

Lipid response patterns in acute phase paediatric Plasmodium falciparum malaria

Orikiiriza J, Surowiec I, Lindquist E, ..., Trygg J, Normark J

Metabolomics 13 (4) - [2017-04-00; online 2017-02-23]

Intranasal C3a treatment ameliorates cognitive impairment in a mouse model of neonatal hypoxic-ischemic brain injury.

Morán J, Stokowska A, Walker FR, ..., Hagberg H, Pekna M

Exp. Neurol. 290 (-) 74-84 [2017-04-00; online 2017-01-04]

Integrated Microscopy Technologies Gothenburg [Service]

Induction of Apoptosis in Intestinal Toxicity to a Histone Deacetylase Inhibitor in a Phase I Study with Pelvic Radiotherapy.

Kalanxhi E, Risberg K, Barua IS, ..., Flatmark K, Ree AH

Cancer Res Treat 49 (2) 374-386 [2017-04-00; online 2016-08-05]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.

Davies H, Glodzik D, Morganella S, ..., Stratton MR, Nik-Zainal S

Nat. Med. 23 (4) 517-525 [2017-04-00; online 2017-03-13]

Clinical Genomics [Collaborative] Clinical Genomics Lund [Collaborative]

Genomic analysis reveals the presence of a class D beta-lactamase with broad substrate specificity in animal bite associated Capnocytophaga species.

Zangenah S, Andersson AF, Özenci V, Bergman P

Eur. J. Clin. Microbiol. Infect. Dis. 36 (4) 657-662 [2017-04-00; online 2016-12-03]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Gene co-expression network connectivity is an important determinant of selective constraint.

Mähler N, Wang J, Terebieniec BK, ..., Street NR, Hvidsten TR

PLoS Genet. 13 (4) e1006402 [2017-04-00; online 2017-04-13]

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Frequent low-level mutations of protein kinase D2 in angiolipoma

Hofvander J, Arbajian E, Stenkula KG, ..., Hornick JL, Mertens F

J. Pathol 241 (5) 578-582 [2017-04-00; online 2017-02-27]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

FZD10-Gα13 signalling axis points to a role of FZD10 in CNS angiogenesis.

Hot B, Valnohova J, Arthofer E, ..., Mulder J, Schulte G

Cell. Signal. 32 (-) 93-103 [2017-04-00; online 2017-01-24]

Epigenome-wide DNA methylation study of IgE concentration in relation to self-reported allergies.

Ek WE, Ahsan M, Rask-Andersen M, ..., Gyllensten U, Johansson Å

Epigenomics 9 (4) 407-418 [2017-04-00; online 2017-03-21]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Effects of dietary inclusion of the yeasts Saccharomyces cerevisiae and Wickerhamomyces anomalus on gut microbiota of rainbow trout

Huyben D, Nyman A, Vidaković A, ..., Dicksved J, Lundh T

Aquaculture 473 (-) 528-537 [2017-04-00; online 2017-04-00]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Editorial for the special issue on "Golgi-related human disorders".

Micaroni M

Tissue and Cell 49 (2 Pt A) 131-132 [2017-04-00; online 2017-03-28]

Integrated Microscopy Technologies Gothenburg [Service]

Combined immunodeficiency and hypoglycemia associated with mutations in hypoxia upregulated 1.

Haapaniemi EM, Fogarty CL, Keskitalo S, ..., Seppänen M, Kere J

J. Allergy Clin. Immunol. 139 (4) 1391-1393.e11 [2017-04-00; online 2016-12-04]

Bioinformatics Support for Computational Resources [Service]

Cardiometabolic biomarkers are predictors of readmission and death in patients hospitalized for acute dyspnea.

Lund N, Gränsbo K, Wernersson C, Melander O

The American Journal of Emergency Medicine 35 (4) 610-614 [2017-04-00; online 2016-12-22]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

An assessment of the importance of exposure routes to the uptake and internal localisation of fluorescent nanoparticles in zebrafish (Danio rerio), using light sheet microscopy.

Skjolding LM, Ašmonaitė G, Jølck RI, ..., Baun A, Sturve J

Nanotoxicology 11 (3) 351-359 [2017-04-00; online 2017-03-29]

Integrated Microscopy Technologies Gothenburg [Service]

A Large Inversion Involving GNAS Exon A/B and All Exons Encoding Gsα Is Associated With Autosomal Dominant Pseudohypoparathyroidism Type Ib (PHP1B).

Grigelioniene G, Nevalainen PI, Reyes M, ..., Mäkitie O, Jüppner H

J. Bone Miner. Res. 32 (4) 776-783 [2017-04-00; online 2017-02-24]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology

Viļuma A, Mikko S, Hahn D, ..., Andersson G, Bergström TF

Sci Rep 7 (-) 45518 [2017-03-31; online 2017-03-31]

Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Improvement of identification methods for honeybee specific Lactic Acid Bacteria; future approaches.

Lamei S, Hu YO, Olofsson TC, ..., Forsgren E, Vásquez A

PLoS ONE 12 (3) e0174614 [2017-03-27; online 2017-03-27]

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Light-sensing via hydrogen peroxide and a peroxiredoxin.

Bodvard K, Peeters K, Roger F, ..., Käll M, Molin M

Nat Commun 8 (1) 14791 [2017-03-24; online 2017-03-24]

Integrated Microscopy Technologies Gothenburg [Service]

Potential for hydrogen-oxidizing chemolithoautotrophic and diazotrophic populations to initiate biofilm formation in oligotrophic, deep terrestrial subsurface waters.

Wu X, Pedersen K, Edlund J, ..., Bertilsson S, Dopson M

Microbiome 5 (1) 37 [2017-03-23; online 2017-03-23]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

NEArender: an R package for functional interpretation of 'omics' data via network enrichment analysis.

Jeggari A, Alexeyenko A

BMC Bioinformatics 18 (Suppl 5) 118 [2017-03-23; online 2017-03-23]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Draft Genome Sequence of the Mycoparasitic Oomycete Pythium periplocum Strain CBS 532.74.

Kushwaha SK, Vetukuri RR, Grenville-Briggs LJ

Genome Announc 5 (12) - [2017-03-23; online 2017-03-23]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis.

Chang D, Knapp M, Enk J, ..., Hofreiter M, Shapiro B

Sci Rep 7 (-) 44585 [2017-03-22; online 2017-03-22]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Atrophin controls developmental signaling pathways via interactions with Trithorax-like

Yeung K, Boija A, Karlsson E, ..., Mannervik M, McNeill H

Elife 6 (-) - [2017-03-22; online 2017-03-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Quantification of HER2 and estrogen receptor heterogeneity in breast cancer by single-molecule RNA fluorescence in situ hybridization.

Annaratone L, Simonetti M, Wernersson E, ..., Sapino A, Crosetto N

Oncotarget 8 (12) 18680-18698 [2017-03-21; online 2017-04-21]

Advanced FISH Technologies [Collaborative]

Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.

Zhu Y, Engström PG, Tellgren-Roth C, ..., Scheynius A, Lehtiö J

Nucleic Acids Res. 45 (5) 2629-2643 [2017-03-17; online 2017-01-20]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Proteomics Mass spectrometry [Technology development] Global Proteomics and Proteogenomics [Technology development] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c.

Pan G, Ameur A, Enroth S, ..., Gyllensten U, Wadelius C

Nucleic Acids Res. 45 (5) 2408-2422 [2017-03-17; online 2016-12-10]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Technology development]

Chromosome and Megaplasmid Sequences of Borrelia anserina (Sakharoff 1891), the Agent of Avian Spirochetosis and Type Species of the Genus

Elbir H, Sitlani P, Bergström S, Barbour AG

Genome Announc 5 (11) e00018-17 [2017-03-16; online 2017-03-16]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Altered expression of maize PLASTOCHRON1 enhances biomass and seed yield by extending cell division duration

Sun X, Cahill J, Van Hautegem T, ..., Inzé D, Nelissen H

Nat Commun 8 (-) 14752 [2017-03-16; online 2017-03-16]

Revertant mosaicism repairs skin lesions in a patient with keratitis-ichthyosis-deafness syndrome by second-site mutations in connexin 26.

Gudmundsson S, Wilbe M, Ekvall S, ..., Törmä H, Bondeson ML

Hum. Mol. Genet. 26 (6) 1070-1077 [2017-03-15; online 2017-02-06]

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Endocytic turnover of Rab8 controls cell polarization.

Vidal-Quadras M, Holst MR, Francis MK, ..., Martín-Belmonte F, Lundmark R

J. Cell. Sci. 130 (6) 1147-1157 [2017-03-15; online 2017-01-30]

Integrated Microscopy Technologies Gothenburg [Service]

Microbial community assembly and evolution in subseafloor sediment

Starnawski P, Bataillon T, Ettema TJG, ..., Schramm A, Kjeldsen KU

Proc Natl Acad Sci USA 114 (11) 2940-2945 [2017-03-14; online 2017-02-27]

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Identification of Triazolothiadiazoles as Potent Inhibitors of the dCTP Pyrophosphatase 1.

Llona-Minguez S, Höglund A, Wiita E, ..., Scobie M, Helleday T

J. Med. Chem. 60 (5) 2148-2154 [2017-03-09; online 2017-02-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Service]

Discovery of circulating proteins associated to knee radiographic osteoarthritis.

Lourido L, Ayoglu B, Fernández-Tajes J, ..., Nilsson P, Blanco FJ

Sci Rep 7 (1) 137 [2017-03-09; online 2017-03-09]

Peptide Functionalized Gold Nanoparticles as a Stimuli Responsive Contrast Medium in Multiphoton Microscopy.

Borglin J, Selegård R, Aili D, Ericson MB

Nano Lett. 17 (3) 2102-2108 [2017-03-08; online 2017-02-23]

Integrated Microscopy Technologies Gothenburg [Service]

Life-Saving Degeneracy in the Human Immune System.

Cell Host Microbe 21 (3) 309-310 [2017-03-08; online 2017-03-11]

Diverse origin of mitochondrial lineages in Iron Age Black Sea Scythians.

Juras A, Krzewińska M, Nikitin AG, ..., Dabert M, Götherström A

Sci Rep 7 (-) 43950 [2017-03-07; online 2017-03-07]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Structure determination of a major facilitator peptide transporter: Inward facing PepTSt from Streptococcus thermophilus crystallized in space group P3121.

Quistgaard EM, Martinez Molledo M, Löw C

PLoS ONE 12 (3) e0173126 [2017-03-06; online 2017-03-06]

Postnatal development of the small intestinal mucosa drives age-dependent, regio-selective susceptibility to Escherichia coli K1 infection.

Birchenough GM, Dalgakiran F, Witcomb LA, ..., Hansson GC, Taylor PW

Sci Rep 7 (1) 83 [2017-03-06; online 2017-03-06]

Integrated Microscopy Technologies Gothenburg [Service]

Method to Visualize and Analyze Membrane Interacting Proteins by Transmission Electron Microscopy

B. Kumar R, Zhu L, Hebert H, Jegerschöld C

J Vis Exp - (121) - [2017-03-05; online 2017-03-05]

Antibody Validation by Immunoprecipitation Followed by Mass Spectrometry Analysis.

Persson H, Preger C, Marcon E, Lengqvist J, Gräslund S

Methods Mol. Biol. 1575 (-) 175-187 [2017-03-04; online 2017-03-04]

Whole-Proteome Peptide Microarrays for Profiling Autoantibody Repertoires within Multiple Sclerosis and Narcolepsy.

Zandian A, Forsström B, Häggmark-Månberg A, ..., Nilsson P, Ayoglu B

J. Proteome Res. 16 (3) 1300-1314 [2017-03-03; online 2017-02-09]

Autoimmunity and Serology Profiling [Technology development]

Evidence of both systemic inflammation and neuroinflammation in fibromyalgia patients, as assessed by a multiplex protein panel applied to the cerebrospinal fluid and to plasma.

Bäckryd E, Tanum L, Lind AL, Larsson A, Gordh T

J Pain Res 10 (-) 515-525 [2017-03-03; online 2017-03-03]

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Toward a Self-Updating Platform for Estimating Rates of Speciation and Migration, Ages, and Relationships of Taxa.

Antonelli A, Hettling H, Condamine FL, ..., Oxelman B, Vos RA

Syst. Biol. 66 (2) 152-166 [2017-03-01; online 2016-09-13]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

SpeciesGeoCoder: Fast Categorization of Species Occurrences for Analyses of Biodiversity, Biogeography, Ecology, and Evolution.

Töpel M, Zizka A, Calió MF, ..., Silvestro D, Antonelli A

Syst. Biol. 66 (2) 145-151 [2017-03-01; online 2016-08-04]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Mating Changes Sexually Dimorphic Gene Expression in the Seed Beetle Callosobruchus maculatus.

Immonen E, Sayadi A, Bayram H, Arnqvist G

Genome Biol Evol 9 (3) 677-699 [2017-03-01; online 2017-04-10]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Complete mitochondrial genome of the Oriental Hornet, Vespa orientalis F. (Hymenoptera: Vespidae).

Haddad NJ, Al-Nakeeb K, Petersen B, ..., Blom N, Sicheritz-Pontén T

Mitochondrial DNA Part B 2 (1) 139-140 [2017-03-01; online 2017-03-01]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Use of a proximity extension assay proteomics chip to discover new biomarkers associated with albuminuria.

Carlsson AC, Sundström J, Carrero JJ, ..., Lind L, Ärnlöv J

Eur J Prev Cardiol 24 (4) 340-348 [2017-03-00; online 2016-10-28]

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Tracing Cellular Origin of Human Exosomes Using Multiplex Proximity Extension Assays

Larssen P, Wik L, Czarnewski P, ..., Gabrielsson S, Kamali-Moghaddam M

Mol Cell Proteomics 16 (3) 502-511 [2017-03-00; online 2017-01-22]

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Towards a whole-genome sequence for rye (Secale cereale L.).

Bauer E, Schmutzer T, Barilar I, ..., Schön CC, Scholz U

Plant J. 89 (5) 853-869 [2017-03-00; online 2016-11-27]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Strain improvement of Pichia kudriavzevii TY13 for raised phytase production and reduced phosphate repression.

Qvirist L, Vorontsov E, Veide Vilg J, Andlid T

Microb Biotechnol 10 (2) 341-353 [2017-03-00; online 2016-10-28]

Stool frequency is associated with gut microbiota composition.

Hadizadeh F, Walter S, Belheouane M, ..., Franke A, D'Amato M

Gut 66 (3) 559-560 [2017-03-00; online 2016-05-20]

Clinical Genomics [Collaborative] Clinical Genomics Stockholm [Collaborative]

Signs of ongoing inflammation in female patients with chronic widespread pain: A multivariate, explorative, cross-sectional study of blood samples.

Gerdle B, Ghafouri B, Ghafouri N, Bäckryd E, Gordh T

Medicine 96 (9) e6130 [2017-03-00; online 2017-03-02]

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Reducing VEGF-B Signaling Ameliorates Renal Lipotoxicity and Protects against Diabetic Kidney Disease

Falkevall A, Mehlem A, Palombo I, ..., Nash A, Eriksson U

Cell Metabolism 25 (3) 713-726 [2017-03-00; online 2017-03-00]

Phylogenetic analysis of Monascus and new species from honey, pollen and nests of stingless bees

Barbosa RN, Leong SL, Vinnere-Pettersson O, ..., Oliveira NT, Houbraken J

Studies in Mycology 86 (-) 29-51 [2017-03-00; online 2017-03-00]

NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Overexpression of protein kinase STK25 in mice exacerbates ectopic lipid accumulation, mitochondrial dysfunction and insulin resistance in skeletal muscle.

Chursa U, Nuñez-Durán E, Cansby E, ..., Sihlbom C, Mahlapuu M

Diabetologia 60 (3) 553-567 [2017-03-00; online 2016-12-16]

Metapopulation theory identifies biogeographical patterns among core and satellite marine bacteria scaling from tens to thousands of kilometers.

Lindh MV, Sjöstedt J, Ekstam B, ..., Legrand C, Pinhassi J

Environ. Microbiol. 19 (3) 1222-1236 [2017-03-00; online 2017-02-06]

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Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in Ficedula Flycatcher Genome Sequences

Kardos M, Qvarnström A, Ellegren H

Genetics 205 (3) 1319-1334 [2017-03-00; online 2017-01-18]

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High GC content causes orphan proteins to be intrinsically disordered.

Basile W, Sachenkova O, Light S, Elofsson A

PLoS Comput. Biol. 13 (3) e1005375 [2017-03-00; online 2017-03-29]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Genomic Variation in IbA10G2 and Other Patient-Derived Cryptosporidium hominis Subtypes.

Sikora P, Andersson S, Winiecka-Krusnell J, ..., Beser J, Arrighi RB

J. Clin. Microbiol. 55 (3) 844-858 [2017-03-00; online 2016-12-21]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Discovery of new biomarkers for atrial fibrillation using a custom-made proteomics chip.

Lind L, Sundström J, Stenemo M, Hagström E, Ärnlöv J

Heart 103 (5) 377-382 [2017-03-00; online 2016-09-08]

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Development of [(11)C]/[(3)H]THK-5351 - A potential novel carbon-11 tau imaging PET radioligand.

Stepanov V, Svedberg M, Jia Z, ..., Nordberg A, Halldin C

Nucl. Med. Biol. 46 (-) 50-53 [2017-03-00; online 2016-12-26]

Damaged reward areas in human alcoholics: neuronal proportion decline and astrocyte activation.

Sarkisyan D, Bazov I, Watanabe H, ..., Yakovleva T, Bakalkin G

Acta Neuropathol. 133 (3) 485-487 [2017-03-00; online 2017-01-17]

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DNA methylation profiling of pediatric B-cell lymphoblastic leukemia with KMT2A rearrangement identifies hypomethylation at enhancer sites.

Bergmann AK, Castellano G, Alten J, ..., Schrappe M, Siebert R

Pediatr Blood Cancer 64 (3) - [2017-03-00; online 2016-10-27]

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Binding and processing of β-lactam antibiotics by the transpeptidase LdtMt2fromMycobacterium tuberculosis

Steiner EM, Schneider G, Schnell R

FEBS J 284 (5) 725-741 [2017-03-00; online 2017-02-08]

Antibody-encoding repertoires of bone marrow and peripheral blood—a focus on IgE

Levin M, Levander F, Palmason R, Greiff L, Ohlin M

Journal of Allergy and Clinical Immunology 139 (3) 1026-1030 [2017-03-00; online 2017-03-00]

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Anaesthetic-induced cardioprotection in an experimental model of the Takotsubo syndrome - isoflurane vs. propofol.

Oras J, Redfors B, Ali A, ..., Omerovic E, Ricksten SE

Acta Anaesthesiol Scand 61 (3) 309-321 [2017-03-00; online 2017-01-22]

Amino acid transporter mutants of Arabidopsis provides evidence that a non-mycorrhizal plant acquires organic nitrogen from agricultural soil.

Ganeteg U, Ahmad I, Jämtgård S, ..., Schmidt S, Näsholm T

Plant Cell Environ. 40 (3) 413-423 [2017-03-00; online 2016-12-13]

A genetic risk score is significantly associated with statin therapy response in the elderly population.

Ciuculete DM, Bandstein M, Benedict C, ..., Schiöth HB, Mwinyi J

Clin. Genet. 91 (3) 379-385 [2017-03-00; online 2016-12-13]

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Assessing the Ability of Spectroscopic Methods to Determine the Difference in the Folding Propensities of Highly Similar β-Hairpins

Andersson H, Danelius E, Jarvoll P, ..., Brath U, Erdélyi M

ACS Omega 2 (2) 508-516 [2017-02-28; online 2017-02-13]

Measuring true localization accuracy in super resolution microscopy with DNA-origami nanostructures

Reuss M, Fördős F, Blom H, ..., Högberg B, Brismar H

New J. Phys. 19 (2) 025013 [2017-02-27; online 2017-02-27]

Integrated Microscopy Technologies Stockholm [Technology development]

Flavonoids fromErythrina schliebenii

Nyandoro SS, Munissi JJE, Kombo M, ..., Rissanen K, Erdélyi M

J. Nat. Prod. 80 (2) 377-383 [2017-02-24; online 2017-01-23]

Evaluating Variant Calling Tools for Non-Matched Next-Generation Sequencing Data.

Sandmann S, de Graaf AO, Karimi M, ..., Jansen JH, Dugas M

Sci Rep 7 (-) 43169 [2017-02-24; online 2017-02-24]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Epitopes of anti-RIFIN antibodies and characterization of rif-expressing Plasmodium falciparum parasites by RNA sequencing.

Ch'ng JH, Sirel M, Zandian A, ..., Qundos U, Wahlgren M

Sci Rep 7 (-) 43190 [2017-02-24; online 2017-02-24]

Characterization of the Ruler Protein Interaction Interface on the Substrate Specificity Switch Protein in the Yersinia Type III Secretion System.

Ho O, Rogne P, Edgren T, ..., Login FH, Wolf-Watz M

J. Biol. Chem. 292 (8) 3299-3311 [2017-02-24; online 2016-12-30]

Protein Science Facility (PSF) [Service] Swedish NMR Centre (SNC) [Service]

Structural Basis for Potency and Promiscuity in Poly(ADP-ribose) Polymerase (PARP) and Tankyrase Inhibitors

Thorsell AG, Ekblad T, Karlberg T, ..., Cohen MS, Schüler H

J. Med. Chem. 60 (4) 1262-1271 [2017-02-23; online 2016-12-21]

Intracellular drug bioavailability: a new predictor of system dependent drug disposition.

Mateus A, Treyer A, Wegler C, ..., Matsson P, Artursson P

Sci Rep 7 (-) 43047 [2017-02-22; online 2017-02-22]

Defining the human copper proteome and analysis of its expression variation in cancers.

Blockhuys S, Celauro E, Hildesjö C, ..., Fierro-González JC, Wittung-Stafshede P

Metallomics 9 (2) 112-123 [2017-02-22; online 2016-12-13]

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Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

Dutoit L, Vijay N, Mugal CF, ..., Wolf J, Ellegren H

Proc. R. Soc. B 284 (1849) 20162756 [2017-02-22; online 2017-02-15]

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Clonal reversal of ageing-associated stem cell lineage bias via a pluripotent intermediate.

Wahlestedt M, Erlandsson E, Kristiansen T, ..., Martin-Gonzalez J, Bryder D

Nat Commun 8 (-) 14533 [2017-02-22; online 2017-02-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

RhoA knockout fibroblasts lose tumor-inhibitory capacity in vitro and promote tumor growth in vivo.

Alkasalias T, Alexeyenko A, Hennig K, ..., Gad AK, Pavlova T

Proc. Natl. Acad. Sci. U.S.A. 114 (8) E1413-E1421 [2017-02-21; online 2017-02-07]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Spatial Proteomics [Collaborative]

Three Chalconoids and a Pterocarpene from the Roots of Tephrosia aequilata.

Atilaw Y, Duffy S, Heydenreich M, ..., Erdélyi M, Yenesew A

Molecules 22 (2) 318 [2017-02-20; online 2017-02-20]

Methane Production in Dairy Cows Correlates with Rumen Methanogenic and Bacterial Community Structure.

Danielsson R, Dicksved J, Sun L, ..., Schnürer A, Bertilsson J

Front Microbiol 8 (-) 226 [2017-02-17; online 2017-02-17]

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The mitochondrial genome sequences of the round goby and the sand goby reveal patterns of recent evolution in gobiid fish.

Adrian-Kalchhauser I, Svensson O, Kutschera VE, ..., Blomberg A, Burkhardt-Holm P

BMC Genomics 18 (1) 177 [2017-02-16; online 2017-02-16]

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Comparison of whole genome amplification techniques for human single cell exome sequencing.

Borgström E, Paterlini M, Mold JE, Frisen J, Lundeberg J

PLoS ONE 12 (2) e0171566 [2017-02-16; online 2017-02-16]

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Genome-wide Association for Major Depression Through Age at Onset Stratification: Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium.

Power RA, Tansey KE, Buttenschøn HN, ..., Breen G, Lewis CM

Biol. Psychiatry 81 (4) 325-335 [2017-02-15; online 2016-08-16]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios

Juottonen H, Eiler A, Biasi C, ..., Yrjälä K, Fritze H

Appl. Environ. Microbiol. 83 (4) e02533-16 [2017-02-15; online 2016-12-02]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Delineating Amyloid Plaque Associated Neuronal Sphingolipids in Transgenic Alzheimer's Disease Mice (tgArcSwe) Using MALDI Imaging Mass Spectrometry.

Kaya I, Brinet D, Michno W, ..., Blennow K, Hanrieder J

ACS Chem Neurosci 8 (2) 347-355 [2017-02-15; online 2017-01-10]

Integrated Microscopy Technologies Gothenburg [Service]

Crystal Structure of the Emerging Cancer Target MTHFD2 in Complex with a Substrate-Based Inhibitor.

Gustafsson R, Jemth AS, Gustafsson NM, ..., Helleday T, Stenmark P

Cancer Res. 77 (4) 937-948 [2017-02-15; online 2016-11-29]

Drug Discovery and Development (DDD) [Collaborative]

Driver GW, Huang Y, Laaksonen A, ..., Wang YL, Westlund PO

Phys Chem Chem Phys 19 (7) 4975-4988 [2017-02-15; online 2017-01-12]

The Baltic Sea Virome: Diversity and Transcriptional Activity of DNA and RNA Viruses.

Zeigler Allen L, McCrow JP, Ininbergs K, ..., Bergman B, Venter JC

mSystems 2 (1) - [2017-02-14; online 2017-02-14]

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Longitudinal analysis of hepatic transcriptome and serum metabolome demonstrates altered lipid metabolism following the onset of hyperglycemia in spontaneously diabetic biobreeding rats.

Regnell SE, Hessner MJ, Jia S, ..., La Torre D, Lernmark Å

PLoS ONE 12 (2) e0171372 [2017-02-13; online 2017-02-13]

A novel RNA sequencing data analysis method for cell line authentication.

Fasterius E, Raso C, Kennedy S, ..., Uhlén M, Al-Khalili Szigyarto C

PLoS ONE 12 (2) e0171435 [2017-02-13; online 2017-02-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genetic and Functional Study of L-Type Amino Acid Transporter 1 in Schizophrenia.

Comasco E, Vumma R, Toffoletto S, ..., Jönsson EG, Venizelos N

Neuropsychobiology 74 (2) 96-103 [2017-02-11; online 2017-02-11]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Detection of Somatic Mutations in Gastroenteropancreatic Neuroendocrine Tumors Using Targeted Deep Sequencing

BACKMAN S, NORLÉN O, ERIKSSON B, ..., STÅLBERG P, CRONA J

AR 37 (2) 705-712 [2017-02-10; online 2017-02-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

microRNAs with AAGUGC seed motif constitute an integral part of an oncogenic signaling network.

Zhou Y, Frings O, Branca RM, ..., Agami R, Orre LM

Oncogene 36 (6) 731-745 [2017-02-09; online 2016-08-01]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Rare and low-frequency coding variants alter human adult height.

Marouli E, Graff M, Medina-Gomez C, ..., Deloukas P, Lettre G

Nature 542 (7640) 186-190 [2017-02-09; online 2017-02-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

IL-8 predicts early mortality in patients with acute hypercapnic respiratory failure treated with noninvasive positive pressure ventilation.

Jónsdóttir B, Jaworowski Å, San Miguel C, Melander O

BMC Pulm Med 17 (1) 35 [2017-02-08; online 2017-02-08]

Affinity Proteomics Stockholm [Service] Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service]

SpotLight Proteomics: uncovering the hidden blood proteome improves diagnostic power of proteomics.

Lundström SL, Zhang B, Rutishauser D, Aarsland D, Zubarev RA

Sci Rep 7 (-) 41929 [2017-02-07; online 2017-02-07]

MASTL is essential for anaphase entry of proliferating primordial germ cells and establishment of female germ cells in mice.

Risal S, Zhang J, Adhikari D, ..., Kaldis P, Liu K

Cell Discov 3 (1) 16052 [2017-02-07; online 2017-02-07]

Integrated Microscopy Technologies Gothenburg [Service]

The Arabidopsis bZIP11 transcription factor links low-energy signalling to auxin-mediated control of primary root growth

Weiste C, Pedrotti L, Selvanayagam J, ..., Hanson J, Dröge-Laser W

PLoS Genet. 13 (2) e1006607 [2017-02-03; online 2017-02-03]

Seasonal Variation in Abundance and Diversity of Bacterial Methanotrophs in Five Temperate Lakes

Samad MS, Bertilsson S

Front Microbiol 8 (-) - [2017-02-03; online 2017-02-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Posttranscriptional Regulation in Adenovirus Infected Cells.

Zhao H, Konzer A, Mi J, ..., Pettersson U, Lind SB

J. Proteome Res. 16 (2) 872-888 [2017-02-03; online 2016-12-13]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Photochemically Induced Aryl Azide Rearrangement: Solution NMR Spectroscopic Identification of the Rearrangement Product

Andersson H, Gräfenstein J, Isobe M, Erdélyi M, Sydnes MO

J. Org. Chem. 82 (3) 1812-1816 [2017-02-03; online 2017-01-23]

A Synthesis of “Dual Warhead” β-Aryl Ethenesulfonyl Fluorides and One-Pot Reaction to β-Sultams

Chinthakindi PK, Govender KB, Kumar AS, ..., Naicker T, Arvidsson PI

Org. Lett. 19 (3) 480-483 [2017-02-03; online 2017-01-11]

Drug Discovery and Development (DDD) [Technology development]

The Human Adrenal Gland Proteome Defined by Transcriptomics and Antibody-Based Profiling.

Bergman J, Botling J, Fagerberg L, ..., Uhlén M, Pontén F

Endocrinology 158 (2) 239-251 [2017-02-01; online 2016-12-03]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Technology development]

Metabolic and functional characterization of effects of developmental temperature in Drosophila melanogaster.

Schou MF, Kristensen TN, Pedersen A, ..., Loeschcke V, Malmendal A

Am. J. Physiol. Regul. Integr. Comp. Physiol. 312 (2) R211-R222 [2017-02-01; online 2016-12-09]

Genome-wide association study with additional genetic and post-transcriptional analyses reveals novel regulators of plasma factor XI levels.

Sennblad B, Basu S, Mazur J, ..., Trégouët DA, Sabater-Lleal M

Hum. Mol. Genet. 26 (3) 637-649 [2017-02-01; online 2017-01-06]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Dysregulated fatty acid metabolism in coronary ectasia: An extended lipidomic analysis.

Boles U, Pinto RC, David S, Abdullah AS, Henein MY

Int. J. Cardiol. 228 (-) 303-308 [2017-02-01; online 2016-11-11]

Design, synthesis and in vitro biological evaluation of oligopeptides targeting E. coli type I signal peptidase (LepB).

De Rosa M, Lu L, Zamaratski E, ..., Mowbray SL, Karlén A

Bioorg. Med. Chem. 25 (3) 897-911 [2017-02-01; online 2016-12-07]

Causal Effect of Genetic Variants Associated With Body Mass Index on Multiple Sclerosis Susceptibility.

Gianfrancesco MA, Glymour MM, Walter S, ..., Alfredsson L, Barcellos LF

Am. J. Epidemiol. 185 (3) 162-171 [2017-02-01; online 2017-01-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Whole-Genome Sequencing of Cytogenetically Balanced Chromosome Translocations Identifies Potentially Pathological Gene Disruptions and Highlights the Importance of Microhomology in the Mechanism of Formation.

Nilsson D, Pettersson M, Gustavsson P, ..., Carvalho CMB, Lindstrand A

Hum. Mutat. 38 (2) 180-192 [2017-02-00; online 2016-12-05]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The in silico identification and characterization of a bread wheat/Triticum militinae introgression line.

Abrouk M, Balcárková B, Šimková H, ..., Doležel J, Valárik M

Plant Biotechnol. J. 15 (2) 249-256 [2017-02-00; online 2016-08-12]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Targeting SAMHD1 with the Vpx protein to improve cytarabine therapy for hematological malignancies.

Herold N, Rudd SG, Ljungblad L, ..., Helleday T, Schaller T

Nat. Med. 23 (2) 256-263 [2017-02-00; online 2017-01-09]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF) [Service]

PCSK9 genetic variants and risk of type 2 diabetes: a mendelian randomisation study.

Schmidt AF, Swerdlow DI, Holmes MV, ..., UCLEB consortium , Sattar N

Lancet Diabetes Endocrinol 5 (2) 97-105 [2017-02-00; online 2016-12-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Opioid precursor protein isoform is targeted to the cell nuclei in the human brain.

Kononenko O, Bazov I, Watanabe H, ..., Yakovleva T, Bakalkin G

Biochimica et Biophysica Acta (BBA) - General Subjects 1861 (2) 246-255 [2017-02-00; online 2016-11-10]

Novel seminal fluid proteins in the seed beetle Callosobruchus maculatus identified by a proteomic and transcriptomic approach.

Bayram H, Sayadi A, Goenaga J, Immonen E, Arnqvist G

Insect Mol. Biol. 26 (1) 58-73 [2017-02-00; online 2016-10-24]

Bioinformatics Support for Computational Resources [Service] Mass Spectrometry-based Proteomics, Uppsala [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Molecular interrogation of hypothalamic organization reveals distinct dopamine neuronal subtypes.

Romanov RA, Zeisel A, Bakker J, ..., Horvath TL, Harkany T

Nat. Neurosci. 20 (2) 176-188 [2017-02-00; online 2016-12-19]

Meta-omic analyses of Baltic Sea cyanobacteria: diversity, community structure and salt acclimation.

Celepli N, Sundh J, Ekman M, ..., Bergman B, Ininbergs K

Environ. Microbiol. 19 (2) 673-686 [2017-02-00; online 2017-01-27]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy

Dalin MG, Engström PG, Ivarsson EG, ..., Andersson B, Bergo MO

International Journal of Cardiology 228 (-) 742-748 [2017-02-00; online 2017-02-00]

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Identification of new TRIP12 variants and detailed clinical evaluation of individuals with non-syndromic intellectual disability with or without autism.

Bramswig NC, Lüdecke HJ, Pettersson M, ..., Kleefstra T, Wieczorek D

Hum. Genet. 136 (2) 179-192 [2017-02-00; online 2016-11-15]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genetic and Targeted eQTL Mapping Reveals Strong Candidate Genes Modulating the Stress Response During Chicken Domestication

Fallahsharoudi A, de Kock N, Johnsson M, ..., Wright D, Jensen P

G3 (Bethesda) 7 (2) 497-504 [2017-02-00; online 2016-12-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Evolution of bird genomes-a transposon's-eye view.

Kapusta A, Suh A

Ann. N. Y. Acad. Sci. 1389 (1) 164-185 [2017-02-00; online 2016-12-20]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Evidence for three genetic loci involved in both anorexia nervosa risk and variation of body mass index.

Hinney A, Kesselmeier M, Jall S, ..., Müller TD, Hebebrand J

Mol. Psychiatry 22 (2) 192-201 [2017-02-00; online 2016-05-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Effects of microbe- and mussel-based diets on the gut microbiota in Arctic charr ( Salvelinus alpinus )

Nyman A, Huyben D, Lundh T, Dicksved J

Aquaculture Reports 5 (-) 34-40 [2017-02-00; online 2017-02-00]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Distinct global binding patterns of the Wilms tumor gene 1 (WT1) -KTS and +KTS isoforms in leukemic cells.

Ullmark T, Järvstråt L, Sandén C, ..., Nilsson B, Gullberg U

Haematologica 102 (2) 336-345 [2017-02-00; online 2016-09-09]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Defense Responses in Aspen with Altered Pectin Methylesterase Activity Reveal the Hormonal Inducers of Tyloses

Leśniewska J, Öhman D, Krzesłowska M, ..., Moritz T, Mellerowicz EJ

Plant Physiol. 173 (2) 1409-1419 [2017-02-00; online 2016-12-06]

Complement peptide C3a stimulates neural plasticity after experimental brain ischaemia.

Stokowska A, Atkins AL, Morán J, ..., Dragunow M, Pekna M

Brain 140 (2) 353-369 [2017-02-00; online 2016-12-12]

Integrated Microscopy Technologies Gothenburg [Service]

Characterization of Glycan Structures of Chondroitin Sulfate-Glycopeptides Facilitated by Sodium Ion-Pairing and Positive Mode LC-MS/MS.

Nilsson J, Noborn F, Gomez Toledo A, ..., Sihlbom C, Larson G

J. Am. Soc. Mass Spectrom. 28 (2) 229-241 [2017-02-00; online 2016-11-21]

Glycoproteomics and MS Proteomics [Technology development]

Associations of defect mismatch repair genes with prognosis and heredity in sporadic colorectal cancer.

Ghanipour L, Jirström K, Sundström M, Glimelius B, Birgisson H

Eur J Surg Oncol 43 (2) 311-321 [2017-02-00; online 2016-11-12]

Activation of myeloid and endothelial cells by CD40L gene therapy supports T-cell expansion and migration into the tumor microenvironment

Eriksson E, Moreno R, Milenova I, ..., Alemany R, Loskog A

Gene Ther 24 (2) 92-103 [2017-02-00; online 2016-12-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A meta-analysis of reflux genome-wide association studies in 6750 Northern Europeans from the general population.

Bonfiglio F, Hysi PG, Ek W, ..., Schmidt PT, D'Amato M

Neurogastroenterol. Motil. 29 (2) - [2017-02-00; online 2016-08-04]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Towards encoded particles for highly multiplexed colorimetric point of care autoantibody detection.

Svedberg G, Jeong Y, Na H, ..., Gantelius J, Svahn HA

Lab Chip 17 (3) 549-556 [2017-01-31; online 2017-01-20]

Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora.

Steige KA, Laenen B, Reimegård J, Scofield DG, Slotte T

Proc. Natl. Acad. Sci. U.S.A. 114 (5) 1087-1092 [2017-01-31; online 2017-01-17]

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Copper chaperone Atox1 plays role in breast cancer cell migration.

Blockhuys S, Wittung-Stafshede P

Biochem. Biophys. Res. Commun. 483 (1) 301-304 [2017-01-29; online 2016-12-24]

Integrated Microscopy Technologies Gothenburg [Service]

Polyoxygenated Cyclohexenes and Other Constituents of Cleistochlamys kirkii Leaves

Nyandoro SS, Munissi JJE, Gruhonjic A, ..., Rissanen K, Erdélyi M

J. Nat. Prod. 80 (1) 114-125 [2017-01-27; online 2016-12-21]

Draft Genome Sequences of Semiconstitutive Red, Dry, and Rough Biofilm-Forming Commensal and Uropathogenic Escherichia coli Isolates.

Cimdins A, Lüthje P, Li F, ..., Brauner A, Römling U

Genome Announc 5 (4) - [2017-01-26; online 2017-01-26]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Cell Cycle and Cell Size Dependent Gene Expression Reveals Distinct Subpopulations at Single-Cell Level.

Dolatabadi S, Candia J, Akrap N, ..., Åman P, Ståhlberg A

Front Genet 8 (-) 1 [2017-01-25; online 2017-01-25]

Integrated Microscopy Technologies Gothenburg [Service]

In vitro and in vivo anti-leukemic activity of the peptidase-potentiated alkylator melflufen in acute myeloid leukemia.

Strese S, Hassan SB, Velander E, ..., Larsson R, Gullbo J

Oncotarget 8 (4) 6341-6352 [2017-01-24; online 2016-12-16]

Early onset of inflammation during ontogeny of bipolar disorder: the NLRP2 inflammasome gene distinctly differentiates between patients and healthy controls in the transition between iPS cell and neural stem cell stages

Vizlin-Hodzic D, Zhai Q, Illes S, ..., Ågren H, Funa K

Transl Psychiatry 7 (1) e1010 [2017-01-24; online 2017-01-24]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Vimentin Levels and Serine 71 Phosphorylation in the Control of Cell-Matrix Adhesions, Migration Speed, and Shape of Transformed Human Fibroblasts

Terriac E, Coceano G, Mavajian Z, ..., Lautenschläger F, Gad A

Cells 6 (1) 2 [2017-01-22; online 2017-01-22]

Integrated Microscopy Technologies Stockholm [Service]

Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci.

Jones GT, Tromp G, Kuivaniemi H, ..., Samani NJ, Bown MJ

Circ. Res. 120 (2) 341-353 [2017-01-20; online 2016-12-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Novel genetic loci associated with hippocampal volume.

Hibar DP, Adams HH, Jahanshad N, ..., Thompson PM, Ikram MA

Nat Commun 8 (-) 13624 [2017-01-18; online 2017-01-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Perivascular PDGFR-β is an independent marker for prognosis in renal cell carcinoma.

Frödin M, Mezheyeuski A, Corvigno S, ..., Johansson M, Östman A

Br. J. Cancer 116 (2) 195-201 [2017-01-17; online 2016-12-09]

A methylome-wide mQTL analysis reveals associations of methylation sites with GAD1 and HDAC3 SNPs and a general psychiatric risk score.

Ciuculete DM, Boström AE, Voisin S, ..., Mwinyi J, Schiöth HB

Transl Psychiatry 7 (1) e1002 [2017-01-17; online 2017-01-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

NLK-mediated phosphorylation of HDAC1 negatively regulates Wnt signaling.

Masoumi KC, Daams R, Sime W, ..., Levander F, Massoumi R

Mol. Biol. Cell 28 (2) 346-355 [2017-01-15; online 2016-11-30]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III inStreptococcus pyogenes

Le Rhun A, Lécrivain AL, Reimegård J, ..., Della Beffa C, Charpentier E

Nucleic Acids Res - (-) gkw1316 [2017-01-12; online 2017-01-12]

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Asgard archaea illuminate the origin of eukaryotic cellular complexity

Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, ..., Spang A, Ettema TJG

Nature 541 (7637) 353-358 [2017-01-11; online 2017-01-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Proteomic analysis of enterotoxigenic Escherichia coli (ETEC) in neutral and alkaline conditions.

Gonzales-Siles L, Karlsson R, Kenny D, Karlsson A, Sjöling Å

BMC Microbiol. 17 (1) 11 [2017-01-07; online 2017-01-07]

Identification of a Novel Autoimmune Peptide Epitope of Prostein in Prostate Cancer.

Pin E, Henjes F, Hong MG, ..., Nilsson P, Schwenk JM

J. Proteome Res. 16 (1) 204-216 [2017-01-06; online 2016-10-05]

Autoimmunity and Serology Profiling [Collaborative]

Antibody Validation in Bioimaging Applications Based on Endogenous Expression of Tagged Proteins.

Skogs M, Stadler C, Schutten R, ..., Uhlén M, Lundberg E

J. Proteome Res. 16 (1) 147-155 [2017-01-06; online 2016-10-12]

Spatial Proteomics [Technology development]

Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages.

Kee N, Volakakis N, Kirkeby A, ..., Parmar M, Perlmann T

Cell Stem Cell 20 (1) 29-40 [2017-01-05; online 2016-10-27]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Proteomic analyses of limbic regions in neonatal male, female and androgen receptor knockout mice.

Zettergren A, Karlsson S, Studer E, ..., Sihlbom C, Westberg L

BMC Neurosci 18 (1) 9 [2017-01-05; online 2017-01-05]

Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus

Odhams CA, Cortini A, Chen L, ..., Vyse TJ, Cunninghame Graham DS

Hum. Mol. Genet. - (-) ddw417 [2017-01-05; online 2017-01-05]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Imputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Loci.

Brandt M, Ahsan M, Honaker CF, Siegel PB, Carlborg Ö

G3 (Bethesda) 7 (1) 119-128 [2017-01-05; online 2017-01-05]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A systematic search strategy identifies cubilin as independent prognostic marker for renal cell carcinoma.

Gremel G, Djureinovic D, Niinivirta M, ..., Stewart GD, Pontén F

BMC Cancer 17 (1) 9 [2017-01-04; online 2017-01-04]

Profile of upregulated inflammatory proteins in sera of Myasthenia Gravis patients.

Molin CJ, Westerberg E, Punga AR

Sci Rep 7 (1) 39716 [2017-01-03; online 2017-01-03]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Small Molecule Microarray Based Discovery of PARP14 Inhibitors

Peng B, Thorsell AG, Karlberg T, Schüler H, Yao SQ

Angew. Chem. Int. Ed. 56 (1) 248-253 [2017-01-02; online 2016-12-05]

Epigenetic changes as prognostic predictors in endometrial carcinomas.

Farkas SA, Sorbe BG, Nilsson TK

Epigenetics 12 (1) 19-26 [2017-01-02; online 2016-11-23]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Comprehensive RNA sequencing of healthy human endometrium at two time points of the menstrual cycle.

Sigurgeirsson B, Åmark H, Jemt A, ..., Lundeberg J, Gidlöf S

Biol. Reprod. 96 (1) 24-33 [2017-01-01; online 2017-04-11]

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cis-Cinnamic Acid Is a Novel, Natural Auxin Efflux Inhibitor That Promotes Lateral Root Formation

Steenackers W, Klíma P, Quareshy M, ..., Boerjan W, Vanholme B

Plant Physiol. 173 (1) 552-565 [2017-01-00; online 2016-11-11]

VAV1 regulates experimental autoimmune arthritis and is associated with anti-CCP negative rheumatoid arthritis.

Guerreiro-Cacais AO, Norin U, Gyllenberg A, ..., Kockum I, Padyukov L

Genes Immun. 18 (1) 48-56 [2017-01-00; online 2017-01-05]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

SHADE AVOIDANCE 4 Is Required for Proper Auxin Distribution in the Hypocotyl

Ge Y, Yan F, Zourelidou M, ..., Schwechheimer C, Tao Y

Plant Physiol. 173 (1) 788-800 [2017-01-00; online 2016-11-21]

Rye B chromosomes encode a functional Argonaute-like protein with in vitro slicer activities similar to its A chromosome paralog.

Ma W, Gabriel TS, Martis MM, ..., Banaei-Moghaddam AM, Houben A

New Phytol. 213 (2) 916-928 [2017-01-00; online 2016-07-29]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

P1.02-063 Mutation Profiling by Targeted Next-Generation Sequencing of an Unselected NSCLC Cohort

La Fleur L, Falk-Sorqvist E, Smeds P, ..., Moens L, Botling J

Journal of Thoracic Oncology 12 (1) S526-S527 [2017-01-00; online 2017-01-00]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Multiethnic genome-wide meta-analysis of ectopic fat depots identifies loci associated with adipocyte development and differentiation.

Chu AY, Deng X, Fisher VA, ..., Steinhauser ML, Fox CS

Nat. Genet. 49 (1) 125-130 [2017-01-00; online 2016-12-06]

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Meta-GWAS Accuracy and Power (MetaGAP) Calculator Shows that Hiding Heritability Is Partially Due to Imperfect Genetic Correlations across Studies.

de Vlaming R, Okbay A, Rietveld CA, ..., Thurik AR, Koellinger PD

PLoS Genet. 13 (1) e1006495 [2017-01-00; online 2017-01-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Investigating kinship of Neolithic post-LBK human remains from Krusza Zamkowa, Poland using ancient DNA.

Juras A, Chyleński M, Krenz-Niedbała M, ..., Jakobsson M, Dabert M

Forensic Sci Int Genet 26 (-) 30-39 [2017-01-00; online 2016-10-14]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Identification of two distinct mesenchymal stromal cell populations in human malignant glioma.

Svensson A, Ramos-Moreno T, Eberstål S, Scheding S, Bengzon J

J. Neurooncol. 131 (2) 245-254 [2017-01-00; online 2016-10-18]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

Human immune system variation.

Brodin P, Davis MM

Nat. Rev. Immunol. 17 (1) 21-29 [2017-01-00; online 2016-12-05]

Genetic and methylation variation in the CYP2B6 gene is related to circulating p,p'-dde levels in a population-based sample.

Lind L, Ng E, Ingelsson E, ..., Morris AP, Lind PM

Environ Int 98 (-) 212-218 [2017-01-00; online 2016-11-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Expression of possible targets for new proteasome inhibitors in diffuse large B-cell lymphoma.

Delforoush M, Berglund M, Edqvist PH, ..., Gullbo J, Enblad G

Eur. J. Haematol. 98 (1) 52-56 [2017-01-00; online 2016-07-12]

Expression of Transient Receptor Potential Channels in the Purified Human Pancreatic β-Cells.

Marabita F, Islam MS

Pancreas 46 (1) 97-101 [2017-01-00; online 2016-07-29]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Evolutionary engineering reveals divergent paths when yeast is adapted to different acidic environments.

Fletcher E, Feizi A, Bisschops MMM, ..., Siewers V, Nielsen J

Metab. Eng. 39 (-) 19-28 [2017-01-00; online 2016-11-02]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Epigenetic Patterns in Blood Associated With Lipid Traits Predict Incident Coronary Heart Disease Events and Are Enriched for Results From Genome-Wide Association Studies.

Hedman ÅK, Mendelson MM, Marioni RE, ..., Levy D, Ingelsson E

Circ Cardiovasc Genet 10 (1) - [2017-01-00; online 2017-02-19]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Emerging microbiota during cold storage and temperature abuse of ready-to-eat salad

Söderqvist K, Ahmed Osman O, Wolff C, ..., Vågsholm I, Boqvist S

Infect Ecol Epidemiol 7 (1) 1328963 [2017-01-00; online 2017-06-06]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Elevated levels of circulating CDH5 and FABP1 in association with human drug-induced liver injury.

Mikus M, Drobin K, Gry M, ..., Nilsson P, Schuppe-Koistinen I

Liver Int. 37 (1) 132-140 [2017-01-00; online 2016-05-26]

Deep Fish: Deep Learning–Based Classification of Zebrafish Deformation for High-Throughput Screening

Ishaq O, Sadanandan SK, Wählby C

SLAS DISCOVERY: Advancing Life Sciences R&D 22 (1) 102-107 [2017-01-00; online 2016-09-26]

BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

Contribution of different dispersal sources to the metabolic response of lake bacterioplankton following a salinity change.

Comte J, Langenheder S, Berga M, Lindström ES

Environ. Microbiol. 19 (1) 251-260 [2017-01-00; online 2016-11-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects.

Marshall CR, Howrigan DP, Merico D, ..., Sebat J, CNV and Schizophrenia Working Groups of the Psychiatric Genomics Consortium

Nat. Genet. 49 (1) 27-35 [2017-01-00; online 2016-11-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Both maternal and offspring Elovl2 genotypes determine systemic DHA levels in perinatal mice.

Pauter AM, Trattner S, Gonzalez-Bengtsson A, ..., Dethlefsen O, Jacobsson A

J. Lipid Res. 58 (1) 111-123 [2017-01-00; online 2016-11-20]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach.

Mendelson MM, Marioni RE, Joehanes R, ..., Levy D, Deary IJ

PLoS Med. 14 (1) e1002215 [2017-01-00; online 2017-01-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A multi-step peptidolytic cascade for amino acid recovery in chloroplasts.

Teixeira PF, Kmiec B, Branca RM, ..., Lehtiö J, Glaser E

Nat. Chem. Biol. 13 (1) 15-17 [2017-01-00; online 2016-10-31]

Clinical Proteomics Mass spectrometry [Collaborative] Global Proteomics and Proteogenomics [Collaborative] Swedish Metabolomics Centre (SMC) [Service]

A combined large-scale meta-analysis identifies COG6 as a novel shared risk locus for rheumatoid arthritis and systemic lupus erythematosus.

Márquez A, Vidal-Bralo L, Rodríguez-Rodríguez L, ..., Alarcón-Riquelme ME, Martín J

Ann. Rheum. Dis. 76 (1) 286-294 [2017-01-00; online 2016-05-20]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The 15N NMR chemical shift in the characterization of weak halogen bonding in solution

Hakkert SB, Gräfenstein J, Erdelyi M

Faraday Discuss. 203 (-) 333-346 [2017-00-00; online 2017-00-00]

Synthesis of phenanthridine spiropyrans and studies of their effects on G-quadruplex DNA

Livendahl M, Jamroskovic J, Hedenström M, ..., Sabouri N, Chorell E

Org. Biomol. Chem. 15 (15) 3265-3275 [2017-00-00; online 2017-00-00]

Lysozyme's lectin-like characteristics facilitates its immune defense function

Zhang R, Wu L, Eckert T, ..., Nifantiev NE, Siebert HC

Quart. Rev. Biophys. 50 (-) - [2017-00-00; online 2017-05-30]

Low Rank Enhanced Matrix Recovery of Hybrid Time and Frequency Data in Fast Magnetic Resonance Spectroscopy

Lu H, Zhang X, Qiu T, ..., Chen Z, Qu X

IEEE Trans. Biomed. Eng. - (-) 1-1 [2017-00-00; online 2017-00-00]

Favored surface-limited oxidation of cellulose with Oxone® in water

Ruan CQ, Strømme M, Mihranyan A, Lindh J

RSC Adv. 7 (64) 40600-40607 [2017-00-00; online 2017-00-00]

Differential Neuroprotective Effects of Interleukin-1 Receptor Antagonist on Spinal Cord Neurons after Excitotoxic Injury

Schizas N, Perry S, Andersson B, ..., Kullander K, Hailer NP

Neuroimmunomodulation 24 (4-5) 220-230 [2017-00-00; online 2018-01-26]

BioImage Informatics [Service] Bioinformatics (NBIS) [Service]

Decoding Gene Expression in 2D and 3D

Bombrun M, Ranefall P, Lindblad J, ..., Nilsson M, Wählby C

Scandinavian Conference on Image Analysis 2017 - (-) 257-268 [2017-00-00; online 2017-05-19]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

Achieving enhanced ionic mobility in nanoporous silica by controlled surface interactions

Garaga MN, Aguilera L, Yaghini N, ..., Persson M, Martinelli A

Phys. Chem. Chem. Phys. 19 (8) 5727-5736 [2017-00-00; online 2017-00-00]

A Fast Low Rank Hankel Matrix Factorization Reconstruction Method for Non-Uniformly Sampled Magnetic Resonance Spectroscopy

Guo D, Lu H, Qu X

IEEE Access 5 (-) 16033-16039 [2017-00-00; online 2017-00-00]

124 CHANGES IN GENE EXPRESSION FOLLOWING EXPOSURE OF BOVINE ENDOMETRIAL EPITHELIAL CELLS (bEEC) TO ESCHERICHIA COLI LPS; THEIR POSSIBLE EFFECT ON IMPLANTATION

Guo Y, Jahmat N, Van Shaik T, ..., Andersson G, Humblot P

Reprod. Fertil. Dev. 29 (1) 170 [2017-00-00; online 2017-00-00]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Zebrafish (Danio rerio) behaviour is largely unaffected by elevated pCO2.

Vossen LE, Jutfelt F, Cocco A, Thörnqvist P, Winberg S

Conserv Physiol 4 (1) cow065 [2016-12-29; online 2016-12-29]

Identification of Compounds that Selectively Stabilize Specific G-Quadruplex Structures by Using a Thioflavin T-Displacement Assay as a Tool.

Jamroskovic J, Livendahl M, Eriksson J, Chorell E, Sabouri N

Chemistry 22 (52) 18932-18943 [2016-12-23; online 2016-11-20]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Single-Nucleotide Polymorphisms and Cancer Risk, Tumor Recurrence, or Survival of Head and Neck Cancer Patients.

Laytragoon-Lewin N, Cederblad L, Andersson BÅ, ..., Löfgren S, Lewin F

Oncology 92 (3) 161-169 [2016-12-21; online 2016-12-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Identification of a Differentially Expressed TIR-NBS-LRR Gene in a Major QTL Associated to Leaf Rust Resistance in Salix.

Martin T, Rönnberg-Wästljung AC, Stenlid J, Samils B

PLoS ONE 11 (12) e0168776 [2016-12-21; online 2016-12-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A Combinatory Antibody-Antigen Microarray Assay for High-Content Screening of Single-Chain Fragment Variable Clones from Recombinant Libraries.

Persson N, Jansson B, Stuhr-Hansen N, ..., Danielsson L, Blixt O

PLoS ONE 11 (12) e0168761 [2016-12-21; online 2016-12-21]

Spontaneous Vesiculation and pH-Induced Disassembly of a Lysosomotropic Detergent: Impacts on Lysosomotropism and Lysosomal Delivery.

Villamil Giraldo AM, Fyrner T, Wennmalm S, ..., Öllinger K, Ederth T

Langmuir 32 (50) 13566-13575 [2016-12-20; online 2016-12-13]

Fluorescence Correlation Spectroscopy [Collaborative] Integrated Microscopy Technologies Stockholm

Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity.

Corcoran MM, Phad GE, Néstor VB, ..., Martin M, Karlsson Hedestam GB

Nat Commun 7 (-) 13642 [2016-12-20; online 2016-12-20]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Human IgM Antibodies to Malondialdehyde Conjugated With Albumin Are Negatively Associated With Cardiovascular Disease Among 60-Year-Olds.

Thiagarajan D, Frostegård AG, Singh S, ..., Lundström SL, Frostegård J

J Am Heart Assoc 5 (12) - [2016-12-20; online 2016-12-20]

Chemical Proteomics [Collaborative]

Regio- and Stereoselective Alkylation of Pyridine-N-oxides: Synthesis of Substituted Piperidines and Pyridines

Barange DK, Johnson MT, Cairns AG, Olsson R, Almqvist F

Org. Lett. 18 (24) 6228-6231 [2016-12-16; online 2016-11-28]

Transposon Mutagenesis Reveals Fludarabine Resistance Mechanisms in Chronic Lymphocytic Leukemia.

Pandzic T, Larsson J, He L, ..., Sjöblom T, Hellström M

Clin. Cancer Res. 22 (24) 6217-6227 [2016-12-15; online 2016-03-10]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Novel SACS mutations associated with intellectual disability, epilepsy and widespread supratentorial abnormalities.

Ali Z, Klar J, Jameel M, ..., Baig S, Dahl N

J. Neurol. Sci. 371 (-) 105-111 [2016-12-15; online 2016-11-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Ionization of Cellobiose in Aqueous Alkali and the Mechanism of Cellulose Dissolution.

Bialik E, Stenqvist B, Fang Y, ..., Lund M, Bernin D

J Phys Chem Lett 7 (24) 5044-5048 [2016-12-15; online 2016-11-29]

Genome-wide association study of caffeine metabolites provides new insights to caffeine metabolism and dietary caffeine-consumption behavior.

Cornelis MC, Kacprowski T, Menni C, ..., Grabe HJ, Ingelsson E

Hum. Mol. Genet. 25 (24) 5472-5482 [2016-12-15; online 2016-10-06]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic Variants in CHIA and CHI3L1 Are Associated with the IgE Response to the Ascaris Resistance Marker ABA-1 and the Birch Pollen Allergen Bet v 1.

Acevedo N, Bornacelly A, Mercado D, ..., Scheynius A, Caraballo L

PLoS ONE 11 (12) e0167453 [2016-12-15; online 2016-12-15]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Service]

Disentangling genetic and epigenetic determinants of ultrafast adaptation.

Gjuvsland AB, Zörgö E, Samy JK, ..., Omholt SW, Warringer J

Mol. Syst. Biol. 12 (12) 892 [2016-12-15; online 2016-12-15]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Aspen phenylpropanoid genes’ expression levels correlate with genets’ tannin richness and vary both in responses to soil nitrogen and associations with phenolic profiles

Decker VHG, Bandau F, Gundale MJ, Cole CT, Albrectsen BR

Tree Physiol - (-) - [2016-12-15; online 2016-12-15]

The protein phosphatase 2A regulatory subunit PR70 is a gonosomal melanoma tumor suppressor gene.

van Kempen LC, Redpath M, Elchebly M, ..., Feunteun J, Spatz A

Sci Transl Med 8 (369) 369ra177 [2016-12-14; online 2016-12-16]

TRPM8 polymorphisms associated with increased risk of IBS-C and IBS-M.

Henström M, Hadizadeh F, Beyder A, ..., Farrugia G, D'Amato M

Gut - (-) - [2016-12-14; online 2016-12-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The In Vitro Stability of Circulating Tumour DNA.

Henao Diaz E, Yachnin J, Grönberg H, Lindberg J

PLoS ONE 11 (12) e0168153 [2016-12-13; online 2016-12-13]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Clonal Variation in Drug and Radiation Response among Glioma-Initiating Cells Is Linked to Proneural-Mesenchymal Transition.

Segerman A, Niklasson M, Haglund C, ..., Segerman B, Westermark B

Cell Rep 17 (11) 2994-3009 [2016-12-13; online 2016-12-16]

Drug Discovery and Development (DDD) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Serum Autoantibody Profiling of Patients with Paraneoplastic and Non-Paraneoplastic Autoimmune Retinopathy.

Ten Berge JC, van Rosmalen J, Vermeer J, ..., Rothova A, Schreurs MW

PLoS ONE 11 (12) e0167909 [2016-12-08; online 2016-12-08]

Autoimmunity and Serology Profiling [Collaborative] Tissue Profiling [Collaborative]

PDGFB, a new candidate plasma biomarker for venous thromboembolism: results from the VEREMA affinity proteomics study.

Bruzelius M, Iglesias MJ, Hong MG, ..., Trégouët DA, Odeberg J

Blood 128 (23) e59-e66 [2016-12-08; online 2016-10-14]

Frequent NFKBIE deletions are associated with poor outcome in primary mediastinal B-cell lymphoma.

Mansouri L, Noerenberg D, Young E, ..., Rosenquist R, Damm F

Blood 128 (23) 2666-2670 [2016-12-08; online 2016-09-26]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

An oxygen-sensitive toxin-antitoxin system.

Marimon O, Teixeira JM, Cordeiro TN, ..., Wood TK, Pons M

Nat Commun 7 (-) 13634 [2016-12-08; online 2016-12-08]

Iron chelators target both proliferating and quiescent cancer cells.

Fryknäs M, Zhang X, Bremberg U, ..., Linder S, Larsson R

Sci Rep 6 (-) 38343 [2016-12-07; online 2016-12-07]

Cluster Flow: A user-friendly bioinformatics workflow tool.

Ewels P, Krueger F, Käller M, Andrews S

F1000Res 5 (-) 2824 [2016-12-06; online 2016-12-06]

NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]

A genetic risk score composed of rheumatoid arthritis risk alleles, HLA-DRB1 haplotypes, and response to TNFi therapy - results from a Swedish cohort study.

Jiang X, Askling J, Saevarsdottir S, ..., Viatte S, Frisell T

Arthritis Res. Ther. 18 (1) 288 [2016-12-03; online 2016-12-03]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Viral Metagenomic Analysis Displays the Co-Infection Situation in Healthy and PMWS Affected Pigs.

Blomström AL, Fossum C, Wallgren P, Berg M

PLoS ONE 11 (12) e0166863 [2016-12-01; online 2016-12-01]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Quantitative and Selective Analysis of Feline Growth Related Proteins Using Parallel Reaction Monitoring High Resolution Mass Spectrometry.

Sundberg M, Strage EM, Bergquist J, Holst BS, Ramström M

PLoS ONE 11 (12) e0167138 [2016-12-01; online 2016-12-01]

Mass Spectrometry-based Proteomics, Uppsala [Technology development]

Elucidating selection processes for antibiotic resistance in sewage treatment plants using metagenomics.

Bengtsson-Palme J, Hammarén R, Pal C, ..., Tysklind M, Larsson DG

Sci. Total Environ. 572 (-) 697-712 [2016-12-01; online 2016-08-21]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Validation and development of MTH1 inhibitors for treatment of cancer.

Warpman Berglund U, Sanjiv K, Gad H, ..., Scobie M, Helleday T

Ann. Oncol. 27 (12) 2275-2283 [2016-12-00; online 2016-11-08]

Advanced Mass Spectrometry Proteomics [Collaborative] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Chemical Proteomics [Service] Clinical Proteomics Mass spectrometry [Collaborative] Drug Discovery and Development (DDD) [Collaborative]

Using 2D NMR to characterize the structure of the low and high molecular weight fractions of bio-oil obtained from LignoBoost™ kraft lignin depolymerized in subcritical water

Mattsson C, Andersson SI, Belkheiri T, ..., Vamling L, Theliander H

Biomass and Bioenergy 95 (-) 364-377 [2016-12-00; online 2016-12-00]

The disappearing San of southeastern Africa and their genetic affinities.

Schlebusch CM, Prins F, Lombard M, Jakobsson M, Soodyall H

Hum. Genet. 135 (12) 1365-1373 [2016-12-00; online 2016-09-20]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots.

Santuari L, Sanchez-Perez GF, Luijten M, ..., Scheres B, Heidstra R

Plant Cell 28 (12) 2937-2951 [2016-12-00; online 2016-12-05]

Structural and conformational determinants of macrocycle cell permeability

Over B, Matsson P, Tyrchan C, ..., Duvall JR, Kihlberg J

Nat Chem Biol 12 (12) 1065-1074 [2016-12-00; online 2016-10-17]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Spatial subsidies in spider diets vary with shoreline structure: Complementary evidence from molecular diet analysis and stable isotopes.

Hambäck PA, Weingartner E, Dalén L, Wirta H, Roslin T

Ecol Evol 6 (23) 8431-8439 [2016-12-00; online 2016-10-26]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Regulation of amino-acid metabolism controls flux to lipid accumulation in Yarrowia lipolytica

Kerkhoven EJ, Pomraning KR, Baker SE, Nielsen J

npj Syst Biol Appl 2 (1) - [2016-12-00; online 2016-03-03]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Preclinical PET imaging of EGFR levels: pairing a targeting with a non-targeting Sel-tagged Affibody-based tracer to estimate the specific uptake.

Cheng Q, Wållberg H, Grafström J, ..., Ståhl S, Sel-tag imaging project

EJNMMI Res 6 (1) 58 [2016-12-00; online 2016-07-07]

Affinity Proteomics Uppsala [Service] PLA and Single Cell Proteomics [Service]

Novel genetic loci underlying human intracranial volume identified through genome-wide association.

Adams HH, Hibar DP, Chouraki V, ..., Ikram MA, Thompson PM

Nat. Neurosci. 19 (12) 1569-1582 [2016-12-00; online 2016-11-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Genome-wide analysis identifies 12 loci influencing human reproductive behavior.

Barban N, Jansen R, de Vlaming R, ..., Snieder H, Mills MC

Nat. Genet. 48 (12) 1462-1472 [2016-12-00; online 2016-11-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Extended exome sequencing identifies BACH2 as a novel major risk locus for Addison's disease.

Eriksson D, Bianchi M, Landegren N, ..., Kämpe O, Pielberg GR

J. Intern. Med. 280 (6) 595-608 [2016-12-00; online 2016-11-02]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Evolutionary History of the Nesophontidae, the Last Unplaced Recent Mammal Family.

Brace S, Thomas JA, Dalén L, ..., Barnes I, Turvey ST

Mol. Biol. Evol. 33 (12) 3095-3103 [2016-12-00; online 2016-09-15]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Early Perspective: Microplate Applications of the Cellular Thermal Shift Assay (CETSA)

Seashore-Ludlow B, Lundbäck T

J Biomol Screen 21 (10) 1019-1033 [2016-12-00; online 2016-07-20]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Distribution and expression of microbial rhodopsins in the Baltic Sea and adjacent waters.

Brindefalk B, Ekman M, Ininbergs K, ..., Pinhassi J, Bergman B

Environ. Microbiol. 18 (12) 4442-4455 [2016-12-00; online 2016-06-17]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Dissecting the Metabolic Role of Mitochondria during Developmental Leaf Senescence.

Chrobok D, Law SR, Brouwer B, ..., Gardeström P, Keech O

Plant Physiol. 172 (4) 2132-2153 [2016-12-00; online 2016-10-21]

Coetzeea brasiliensis gen. nov., sp. nov. isolated from larvae of Anopheles darlingi.

Kämpfer P, Glaeser SP, Marinotti O, ..., Busse HJ, Terenius O

Int. J. Syst. Evol. Microbiol. 66 (12) 5211-5217 [2016-12-00; online 2016-09-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

CSF profiling of the human brain enriched proteome reveals associations of neuromodulin and neurogranin to Alzheimer's disease.

Remnestål J, Just D, Mitsios N, ..., Nilsson P, Häggmark-Månberg A

Proteomics Clin Appl 10 (12) 1242-1253 [2016-12-00; online 2016-10-10]

Affinity Proteomics Stockholm [Collaborative] Fluorescence Tissue Profiling [Collaborative]

Application of amide hydrogen/deuterium exchange mass spectrometry for epitope mapping in human cystatin C.

Prądzińska M, Behrendt I, Astorga-Wells J, ..., Rodziewicz-Motowidło S, Czaplewska P

Amino Acids 48 (12) 2809-2820 [2016-12-00; online 2016-08-29]

Advanced Mass Spectrometry Proteomics [Collaborative] Chemical Proteomics [Collaborative]

A high-throughput functional genomics workflow based on CRISPR/Cas9-mediated targeted mutagenesis in zebrafish.

Varshney GK, Carrington B, Pei W, ..., Sood R, Burgess SM

Nat Protoc 11 (12) 2357-2375 [2016-12-00; online 2016-10-27]

Genome Engineering Zebrafish [Technology development]

Identification and Characterization of Novel Compounds Blocking Shiga Toxin Expression in Escherichia coli O157:H7.

Huerta-Uribe A, Marjenberg ZR, Yamaguchi N, ..., Gally DL, Roe AJ

Front Microbiol 7 (-) 1930 [2016-11-30; online 2016-11-30]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A stromal cell population in the large intestine identified by tissue factor expression that is lost during colorectal cancer progression.

Eriksson O, Asplund A, Hegde G, ..., Pontén F, Siegbahn A

Thromb. Haemost. 116 (6) 1050-1059 [2016-11-30; online 2016-09-22]

Identification of Shared and Unique Serum Lipid Profiles in Diabetes Mellitus and Myocardial Infarction.

Kjellqvist S, Klose C, Surma MA, ..., Melander O, Fernandez C

J Am Heart Assoc 5 (12) e004503 [2016-11-29; online 2016-11-29]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

DNA methylation patterns associated with oxidative stress in an ageing population.

Hedman ÅK, Zilmer M, Sundström J, Lind L, Ingelsson E

BMC Med Genomics 9 (1) 72 [2016-11-25; online 2016-11-25]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Towards agile large-scale predictive modelling in drug discovery with flow-based programming design principles.

Lampa S, Alvarsson J, Spjuth O

J Cheminform 8 (-) 67 [2016-11-24; online 2016-11-24]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Phylogenetic Signals of Salinity and Season in Bacterial Community Composition Across the Salinity Gradient of the Baltic Sea.

Herlemann DP, Lundin D, Andersson AF, Labrenz M, Jürgens K

Front Microbiol 7 (-) 1883 [2016-11-24; online 2016-11-24]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Abnormal primary and permanent dentitions with ectodermal symptoms predict WNT10A deficiency.

Bergendal B, Norderyd J, Zhou X, Klar J, Dahl N

BMC Med. Genet. 17 (1) 88 [2016-11-24; online 2016-11-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.

Hefzi H, Ang KS, Hanscho M, ..., Lee DY, Lewis NE

Cell Syst 3 (5) 434-443.e8 [2016-11-23; online 2016-11-25]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The great spruce bark beetle (Dendroctonus micans Kug.) (Coleoptera: Scolytidae) in Lithuania: occurrence, phenology, morphology and communities of associated fungi.

Menkis A, Lynikienė J, Marčiulynas A, Gedminas A, Povilaitienė A

Bull. Entomol. Res. - (-) 1-8 [2016-11-22; online 2016-11-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A novel process of viral vector barcoding and library preparation enables high-diversity library generation and recombination-free paired-end sequencing.

Davidsson M, Diaz-Fernandez P, Schwich OD, ..., Wang G, Björklund T

Sci Rep 6 (-) 37563 [2016-11-22; online 2016-11-22]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A microarray whole-genome gene expression dataset in a rat model of inflammatory corneal angiogenesis.

Mukwaya A, Lindvall JM, Xeroudaki M, ..., Jensen LD, Lagali N

Sci Data 3 (-) 160103 [2016-11-22; online 2016-11-22]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

The endosomal transcriptional regulator RNF11 integrates degradation and transport of EGFR.

Scharaw S, Iskar M, Ori A, ..., Bork P, Pepperkok R

J. Cell Biol. 215 (4) 543-558 [2016-11-21; online 2016-11-08]

Functional variants in the sucrase-isomaltase gene associate with increased risk of irritable bowel syndrome.

Henström M, Diekmann L, Bonfiglio F, ..., Naim HY, D'Amato M

Gut - (-) - [2016-11-21; online 2016-11-21]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Stockholm [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

ANLN is a prognostic biomarker independent of Ki-67 and essential for cell cycle progression in primary breast cancer.

Magnusson K, Gremel G, Rydén L, ..., Jirström K, Pontén F

BMC Cancer 16 (1) 904 [2016-11-18; online 2016-11-18]

Novel genetic loci associated with long-term deterioration in blood lipid concentrations and coronary artery disease in European adults.

Varga TV, Kurbasic A, Aine M, ..., Renström F, Franks PW

Int J Epidemiol - (-) - [2016-11-17; online 2016-11-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Large-Scale Gene Expression Profiling Platform for Identification of Context-Dependent Drug Responses in Multicellular Tumor Spheroids.

Senkowski W, Jarvius M, Rubin J, ..., Larsson R, Fryknäs M

Cell Chem Biol 23 (11) 1428-1438 [2016-11-17; online 2016-10-27]

Drug Discovery and Development (DDD) [Service] Tissue Profiling [Service]

Complete Genome Sequence of an African Swine Fever Virus Isolate from Sardinia, Italy.

Granberg F, Torresi C, Oggiano A, ..., De Mia GM, Belák S

Genome Announc 4 (6) - [2016-11-17; online 2016-11-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

An automated approach to prepare tissue-derived spatially barcoded RNA-sequencing libraries.

Jemt A, Salmén F, Lundmark A, ..., Yucel-Lindberg T, Lundeberg J

Sci Rep 6 (-) 37137 [2016-11-16; online 2016-11-16]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Periostin is identified as a putative metastatic marker in breast cancer-derived exosomes.

Vardaki I, Ceder S, Rutishauser D, ..., Foukakis T, Panaretakis T

Oncotarget 7 (46) 74966-74978 [2016-11-15; online 2016-09-03]

Advanced Mass Spectrometry Proteomics [Collaborative]

Nuclear Magnetic Resonance Structure and Mutational Analysis of the Lactococcin A Immunity Protein.

Kristiansen PE, Persson C, Fuochi V, ..., Nissen-Meyer J, Oppegård C

Biochemistry 55 (45) 6250-6257 [2016-11-15; online 2016-11-03]

Hyperelastic Nanocellulose-Reinforced Hydrogel of High Water Content for Ophthalmic Applications.

Tummala GK, Joffre T, Lopes VR, ..., Griffith M, Mihranyan A

ACS Biomater. Sci. Eng. 2 (11) 2072-2079 [2016-11-14; online 2016-10-18]

Functional and Structural Characterization of a Novel HLA-DRB1*04:01-Restricted α-Enolase T Cell Epitope in Rheumatoid Arthritis.

Gerstner C, Dubnovitsky A, Sandin C, ..., Achour A, Malmström V

Front Immunol 7 (-) 494 [2016-11-14; online 2016-11-14]

Chemical Proteomics [Service]

Study on genetic stability in human urothelial cells in vitro.

Chamorro CI, Zeiai S, Reinfeldt Engberg G, ..., Nordenskjöld A, Fossum M

J Tissue Eng Regen Med - (-) - [2016-11-12; online 2016-11-12]

Bioinformatics and Expression Analysis (BEA) [Service]

Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease.

Matsson H, Söderhäll C, Einarsdottir E, ..., Lundbäck B, Klar J

BMC Pulm Med 16 (1) 146 [2016-11-11; online 2016-11-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

DcR3, TFF3, and Midkine Are Novel Serum Biomarkers in Small Intestinal Neuroendocrine Tumors.

Edfeldt K, Daskalakis K, Bäcklin C, ..., Hellman P, Stålberg P

Neuroendocrinology 105 (2) 170-181 [2016-11-09; online 2016-11-09]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Catalytic Formation of Disulfide Bonds in Peptides by Molecularly Imprinted Microgels at Oil/Water Interfaces.

Shen X, Huang C, Shinde S, ..., Fritz E, Sellergren B

ACS Appl Mater Interfaces 8 (44) 30484-30491 [2016-11-09; online 2016-10-26]

Targeting SOX9 for degradation to inhibit chemoresistance, metastatic spread, and recurrence.

Suryo Rahmanto A, Swartling FJ, Sangfelt O

Mol Cell Oncol 4 (1) e1252871 [2016-11-08; online 2016-11-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

PROX1 is a novel pathway-specific prognostic biomarker for high-grade astrocytomas; results from independent glioblastoma cohorts stratified by age and IDH mutation status.

Roodakker KR, Elsir T, Edqvist PD, ..., Malmström A, Smits A

Oncotarget 7 (45) 72431-72442 [2016-11-08; online 2016-09-15]

Flexibility is important for inhibition of the MDM2/p53 protein-protein interaction by cyclic β-hairpins.

Danelius E, Pettersson M, Bred M, ..., Grøtli M, Erdelyi M

Org. Biomol. Chem. 14 (44) 10386-10393 [2016-11-08; online 2016-10-13]

Case-specific potentiation of glioblastoma drugs by pterostilbene.

Schmidt L, Baskaran S, Johansson P, ..., Krona C, Nelander S

Oncotarget 7 (45) 73200-73215 [2016-11-08; online 2016-10-01]

Drug Discovery and Development (DDD) [Collaborative]

A metagenomic analysis displays the diverse microbial community of a vermicomposting system in Uganda.

Blomström AL, Lalander C, Komakech AJ, Vinnerås B, Boqvist S

Infect Ecol Epidemiol 6 (-) 32453 [2016-11-08; online 2016-11-08]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

The Arabidopsis TOR Kinase Specifically Regulates the Expression of Nuclear Genes Coding for Plastidic Ribosomal Proteins and the Phosphorylation of the Cytosolic Ribosomal Protein S6.

Dobrenel T, Mancera-Martínez E, Forzani C, ..., Hanson J, Meyer C

Front Plant Sci 7 (-) 1611 [2016-11-07; online 2016-11-07]

Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update.

Vandenbrouck Y, Lane L, Carapito C, ..., Garin J, Pineau C

J. Proteome Res. 15 (11) 3998-4019 [2016-11-04; online 2016-08-23]

Periodontal Ehlers-Danlos Syndrome Is Caused by Mutations in C1R and C1S, which Encode Subcomponents C1r and C1s of Complement.

Kapferer-Seebacher I, Pepin M, Werner R, ..., Byers PH, Zschocke J

Am. J. Hum. Genet. 99 (5) 1005-1014 [2016-11-03; online 2016-10-18]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

WhatsHap: fast and accurate read-based phasing

Martin M, Patterson M, Garg S, ..., Schöenhuth A, Marschall T

bioRxiv - (-) - [2016-11-02; online 2016-11-02]

Bioinformatics (NBIS) [Technology development] Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Image analysis-derived metrics of histomorphological complexity predicts prognosis and treatment response in stage II-III colon cancer.

Mezheyeuski A, Hrynchyk I, Karlberg M, ..., Glimelius B, Östman A

Sci Rep 6 (-) 36149 [2016-11-02; online 2016-11-02]

Combined Solution- and Magic Angle Spinning NMR Reveals Regions of Distinct Dynamics in Amyloid β Protofibrils

Lendel C, Sparrman T, Mayzel M, ..., Karlsson G, Härd T

ChemistrySelect 1 (18) 5850-5853 [2016-11-01; online 2016-11-11]

Tryptophan Metabolism Along the Kynurenine Pathway Downstream of Toll-like Receptor Stimulation in Peripheral Monocytes.

Orhan F, Bhat M, Sandberg K, ..., Erhardt S, Schwieler L

Scand. J. Immunol. 84 (5) 262-271 [2016-11-00; online 2016-10-27]

Drug Discovery and Development (DDD) [Collaborative]

The tight junction gene Claudin-1 is associated with atopic dermatitis among Ethiopians.

Asad S, Winge MC, Wahlgren CF, ..., Taylan F, Bradley M

J Eur Acad Dermatol Venereol 30 (11) 1939-1941 [2016-11-00; online 2016-10-25]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

The H3 chaperone function of NASP is conserved in Arabidopsis.

Maksimov V, Nakamura M, Wildhaber T, ..., Bergquist J, Hennig L

Plant J. 88 (3) 425-436 [2016-11-00; online 2016-09-15]

Mass Spectrometry-based Proteomics, Uppsala [Collaborative]

Mass spectrometric analysis of synaptosomal membrane preparations for the determination of brain receptors, transporters and channels.

Sialana FJ, Gulyassy P, Májek P, ..., Bennett KL, Lubec G

Proteomics 16 (22) 2911-2920 [2016-11-00; online 2016-10-21]

Long-term outcome in young women with breast cancer: a population-based study.

Fredholm H, Magnusson K, Lindström LS, ..., Frisell J, Fredriksson I

Breast Cancer Res. Treat. 160 (1) 131-143 [2016-11-00; online 2016-09-13]

Long-term effects of tree harvesting on ectomycorrhizal fungal communities in boreal Scots pine forests

Varenius K, Kårén O, Lindahl B, Dahlberg A

Forest Ecology and Management 380 (-) 41-49 [2016-11-00; online 2016-11-00]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Isolation and characterization of autoantibodies against human cystatin C.

Prądzińska M, Behrendt I, Spodzieja M, ..., Macur K, Czaplewska P

Amino Acids 48 (11) 2501-2518 [2016-11-00; online 2016-06-08]

Advanced Mass Spectrometry Proteomics [Collaborative] Chemical Proteomics [Collaborative]

Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia.

Teppo S, Laukkanen S, Liuksiala T, ..., Heinäniemi M, Lohi O

Genome Res. 26 (11) 1468-1477 [2016-11-00; online 2016-09-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Genome-wide DNA methylation analysis in multiple tissues in primary Sjögren's syndrome reveals regulatory effects at interferon-induced genes.

Imgenberg-Kreuz J, Sandling JK, Almlöf JC, ..., Syvänen AC, Nordmark G

Ann. Rheum. Dis. 75 (11) 2029-2036 [2016-11-00; online 2016-02-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Extension of diffuse low-grade gliomas beyond radiological borders as shown by the coregistration of histopathological and magnetic resonance imaging data.

Zetterling M, Roodakker KR, Berntsson SG, ..., Larsson EM, Smits A

J. Neurosurg. 125 (5) 1155-1166 [2016-11-00; online 2016-02-26]

Effects of cigarette smoking on cardiovascular-related protein profiles in two community-based cohort studies.

Huang B, Svensson P, Ärnlöv J, ..., Lind L, Ingelsson E

Atherosclerosis 254 (-) 52-58 [2016-11-00; online 2016-09-15]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps.

Iotchkova V, Huang J, Morris JA, ..., Auer PL, Soranzo N

Nat. Genet. 48 (11) 1303-1312 [2016-11-00; online 2016-10-28]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Deletion of FtsH11 protease has impact on chloroplast structure and function in Arabidopsis thaliana when grown under continuous light.

Wagner R, von Sydow L, Aigner H, ..., Clarke A, Funk C

Plant Cell Environ. 39 (11) 2530-2544 [2016-11-00; online 2016-08-02]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Common variants at PVT1, ATG13-AMBRA1, AHI1 and CLEC16A are associated with selective IgA deficiency.

Bronson PG, Chang D, Bhangale T, ..., Graham RR, Behrens TW

Nat. Genet. 48 (11) 1425-1429 [2016-11-00; online 2016-10-28]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Central Metabolic Responses to Ozone and Herbivory Affect Photosynthesis and Stomatal Closure.

Papazian S, Khaling E, Bonnet C, ..., Blande JD, Albrectsen BR

Plant Physiol. 172 (3) 2057-2078 [2016-11-00; online 2016-10-21]

Acidithiobacillus ferrivorans SS3 presents little RNA transcript response related to cold stress during growth at 8 °C suggesting it is a eurypsychrophile.

Christel S, Fridlund J, Watkin EL, Dopson M

Extremophiles 20 (6) 903-913 [2016-11-00; online 2016-10-25]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A ribonucleotide reductase inhibitor with deoxyribonucleoside-reversible cytotoxicity.

Crona M, Codó P, Jonna VR, ..., Fernandes AP, Tholander F

Mol Oncol 10 (9) 1375-1386 [2016-11-00; online 2016-07-26]

A novel high mobility group box 1 neutralizing chimeric antibody attenuates drug-induced liver injury and postinjury inflammation in mice.

Lundbäck P, Lea JD, Sowinska A, ..., Antoine DJ, Erlandsson Harris H

Hepatology 64 (5) 1699-1710 [2016-11-00; online 2016-09-01]

Rawcopy: Improved copy number analysis with Affymetrix arrays.

Mayrhofer M, Viklund B, Isaksson A

Sci Rep 6 (-) 36158 [2016-10-31; online 2016-10-31]

Array and Analysis Facility [Technology development]

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex.

Vijay N, Bossu CM, Poelstra JW, ..., Kryukov AP, Wolf JB

Nat Commun 7 (1) 13195 [2016-10-31; online 2016-10-31]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Rapid Newcastle Disease Virus Detection Based on Loop-Mediated Isothermal Amplification and Optomagnetic Readout

Tian B, Ma J, Zardán Gómez de la Torre T, ..., Svedlindh P, Strömberg M

ACS Sens. 1 (10) 1228-1234 [2016-10-28; online 2016-09-26]

Discovery of Selective Inhibitors Targeting Acetylcholinesterase 1 from Disease-Transmitting Mosquitoes.

Engdahl C, Knutsson S, Ekström F, Linusson A

J. Med. Chem. 59 (20) 9409-9421 [2016-10-27; online 2016-09-07]

Chemical Biology Consortium Sweden (CBCS) [Service]

Introduction and persistence of tularemia in Bulgaria.

Myrtennäs K, Marinov K, Johansson A, ..., Byström M, Forsman M

Infect Ecol Epidemiol 6 (-) 32838 [2016-10-26; online 2016-10-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Relation between Established Glioma Risk Variants and DNA Methylation in the Tumor.

Dahlin AM, Wibom C, Ghasimi S, ..., Andersson U, Melin B

PLoS ONE 11 (10) e0163067 [2016-10-25; online 2016-10-25]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Mesenchymal state of intimal cells may explain higher propensity to ascending aortic aneurysm in bicuspid aortic valves.

Maleki S, Kjellqvist S, Paloschi V, ..., Eriksson P, Björck HM

Sci Rep 6 (-) 35712 [2016-10-25; online 2016-10-25]

Clinical Proteomics Mass spectrometry [Collaborative] Global Proteomics and Proteogenomics [Collaborative]

Identification of mutations, gene expression changes and fusion transcripts by whole transcriptome RNAseq in docetaxel resistant prostate cancer cells.

Ma Y, Miao Y, Peng Z, ..., Nilsson S, Li C

Springerplus 5 (1) 1861 [2016-10-24; online 2016-10-24]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Auxotrophy-based High Throughput Screening assay for the identification of Bacillus subtilis stringent response inhibitors.

Andresen L, Varik V, Tozawa Y, ..., Tenson T, Hauryliuk V

Sci Rep 6 (-) 35824 [2016-10-24; online 2016-10-24]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic.

Baltar F, Lundin D, Palovaara J, ..., Herndl GJ, Pinhassi J

Front Microbiol 7 (-) 1670 [2016-10-21; online 2016-10-21]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Over Expression of NANOS3 and DAZL in Human Embryonic Stem Cells.

Panula S, Reda A, Stukenborg JB, ..., Reijo Pera RA, Hovatta O

PLoS ONE 11 (10) e0165268 [2016-10-21; online 2016-10-21]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Failure to Genotype: A Cautionary Note on an Elusive loxP Sequence.

Kreuger J, O'Callaghan P

PLoS ONE 11 (10) e0165012 [2016-10-21; online 2016-10-21]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Computational pan-genomics: status, promises and challenges.

Computational Pan-Genomics Consortium

Brief. Bioinformatics - (-) - [2016-10-21; online 2016-10-21]

Bioinformatics (NBIS) [Technology development] Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Integrative analysis of human omics data using biomolecular networks.

Robinson JL, Nielsen J

Mol Biosyst 12 (10) 2953-2964 [2016-10-20; online 2016-08-12]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Gene-specific correlation of RNA and protein levels in human cells and tissues.

Edfors F, Danielsson F, Hallström BM, ..., Forsström B, Uhlén M

Mol. Syst. Biol. 12 (10) 883 [2016-10-20; online 2016-10-20]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]

(13)C NMR assignments of regenerated cellulose from solid-state 2D NMR spectroscopy.

Idström A, Schantz S, Sundberg J, ..., Gatenholm P, Nordstierna L

Carbohydr Polym 151 (-) 480-487 [2016-10-20; online 2016-05-31]

The Transcriptome of Rhabdomyosarcoma Cells Infected with Cytolytic and Non-Cytolytic Variants of Coxsackievirus B2 Ohio-1.

Sävneby A, Luthman J, Nordenskjöld F, Andersson B, Lindberg AM

PLoS ONE 11 (10) e0164548 [2016-10-19; online 2016-10-19]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Aryl Sulfonamide Inhibitors of Insulin-Regulated Aminopeptidase Enhance Spine Density in Primary Hippocampal Neuron Cultures.

Diwakarla S, Nylander E, Grönbladh A, ..., Chai SY, Hallberg M

ACS Chem Neurosci 7 (10) 1383-1392 [2016-10-19; online 2016-08-08]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Collaborative]

Metabolite and Lipid Profiling of Biobank Plasma Samples Collected Prior to Onset of Rheumatoid Arthritis.

Surowiec I, Ärlestig L, Rantapää-Dahlqvist S, Trygg J

PLoS ONE 11 (10) e0164196 [2016-10-18; online 2016-10-18]

Analysis of the Distribution of CD103 on CD8 T Cells in Blood and Genital Mucosa of HIVinfected Female Sex Workers

Gibbs A, Buggert M, Ranefall P, ..., Broliden K, Tjernlund A

Conference on HIV Research for Prevention (HIV R4P), 2016, October 17–20, Chicago - (-) - [2016-10-17]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

High-Throughput Analysis of the Plasma N-Glycome by UHPLC.

Adamczyk B, Stöckmann H, O'Flaherty R, Karlsson NG, Rudd PM

Methods Mol. Biol. 1503 (-) 97-108 [2016-10-16; online 2016-10-16]

Glycoproteomics and MS Proteomics [Technology development]

Databases and Associated Tools for Glycomics and Glycoproteomics.

Lisacek F, Mariethoz J, Alocci D, ..., Jin C, Karlsson NG

Methods Mol. Biol. 1503 (-) 235-264 [2016-10-16; online 2016-10-16]

Reconstructing a hydrogen-driven microbial metabolic network in Opalinus Clay rock.

Bagnoud A, Chourey K, Hettich RL, ..., Schwyn B, Bernier-Latmani R

Nat Commun 7 (-) 12770 [2016-10-14; online 2016-10-14]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Penicillium arizonense, a new, genome sequenced fungal species, reveals a high chemical diversity in secreted metabolites.

Grijseels S, Nielsen JC, Randelovic M, ..., Workman M, Frisvad JC

Sci Rep 6 (-) 35112 [2016-10-14; online 2016-10-14]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Massive and parallel expression profiling using microarrayed single-cell sequencing.

Vickovic S, Ståhl PL, Salmén F, ..., Frisén J, Lundeberg J

Nat Commun 7 (-) 13182 [2016-10-14; online 2016-10-14]

Advanced FISH Technologies Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Differential selection on pollen and pistil traits in relation to pollen competition in the context of a sexual conflict over timing of stigma receptivity.

Lankinen Å, Strandh M

AoB Plants 8 (-) - [2016-10-13; online 2016-08-27]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

No Association of Coronary Artery Disease with X-Chromosomal Variants in Comprehensive International Meta-Analysis.

Loley C, Alver M, Assimes TL, ..., Erdmann J, König IR

Sci Rep 6 (-) 35278 [2016-10-12; online 2016-10-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Complete genome sequence of Methanoculleus bourgensis strain MAB1, the syntrophic partner of mesophilic acetate-oxidising bacteria (SAOB).

Manzoor S, Schnürer A, Bongcam-Rudloff E, Müller B

Stand Genomic Sci 11 (-) 80 [2016-10-12; online 2016-10-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Virome characterisation from Guthrie cards in children who later developed acute lymphoblastic leukaemia.

Bogdanovic G, Pou C, Barrientos-Somarribas M, ..., Andersson B, Gustafsson B

Br. J. Cancer 115 (8) 1008-1014 [2016-10-11; online 2016-08-24]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes.

Segerstolpe Å, Palasantza A, Eliasson P, ..., Ämmälä C, Sandberg R

Cell Metab. 24 (4) 593-607 [2016-10-11; online 2016-09-22]

Analysis of the brain mural cell transcriptome.

He L, Vanlandewijck M, Raschperger E, ..., Keller A, Betsholtz C

Sci Rep 6 (-) 35108 [2016-10-11; online 2016-10-11]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Demographic Development of the First Farmers in Anatolia.

Kılınç GM, Omrak A, Özer F, ..., Jakobsson M, Götherström A

Curr. Biol. 26 (19) 2659-2666 [2016-10-10; online 2016-08-04]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Supersaturation of poorly soluble drugs induced by mesoporous magnesium carbonate.

Zhang P, Zardán Gómez de la Torre T, Welch K, Bergström C, Strømme M

Eur J Pharm Sci 93 (-) 468-474 [2016-10-10; online 2016-08-31]

BioMaterial Interactions (BioMat) [Service]

The structure and diversity of human, animal and environmental resistomes.

Pal C, Bengtsson-Palme J, Kristiansson E, Larsson DG

Microbiome 4 (1) 54 [2016-10-07; online 2016-10-07]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Multidimensional Normalization to Minimize Plate Effects of Suspension Bead Array Data.

Hong MG, Lee W, Nilsson P, Pawitan Y, Schwenk JM

J. Proteome Res. 15 (10) 3473-3480 [2016-10-07; online 2016-08-30]

Affinity Proteomics Stockholm [Technology development]

Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis.

Hammond M, Homa F, Andersson-Svahn H, Ettema TJ, Joensson HN

Microbiome 4 (1) 52 [2016-10-06; online 2016-10-06]

Bioinformatics Support for Computational Resources [Service] Microbial Single Cell Genomics [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Molecular Diversity of Midbrain Development in Mouse, Human, and Stem Cells.

La Manno G, Gyllborg D, Codeluppi S, ..., Arenas E, Linnarsson S

Cell 167 (2) 566-580.e19 [2016-10-06; online 2016-10-08]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

ProQ3: Improved model quality assessments using Rosetta energy terms.

Uziela K, Shu N, Wallner B, Elofsson A

Sci Rep 6 (-) 33509 [2016-10-04; online 2016-10-04]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Scaffolding protein IQGAP1: an insulin-dependent link between caveolae and the cytoskeleton in primary human adipocytes?

Jufvas A, Rajan MR, Jo nsson C, Stralfors P, Turkina MV

Biochemical Journal 473 (19) 3177-3188 [2016-10-01; online 2016-07-25]

Affinity Proteomics Uppsala [Service] PLA and Single Cell Proteomics [Service]

MultiQC: summarize analysis results for multiple tools and samples in a single report.

Ewels P, Magnusson M, Lundin S, Käller M

Bioinformatics 32 (19) 3047-3048 [2016-10-01; online 2016-06-16]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Technology development] NGI Stockholm (Genomics Production) [Technology development] National Genomics Infrastructure [Technology development]

Estrogen Receptor α Promotes Breast Cancer by Reprogramming Choline Metabolism.

Jia M, Andreassen T, Jensen L, ..., Moestue SA, Dahlman-Wright K

Cancer Res. 76 (19) 5634-5646 [2016-10-01; online 2016-07-28]

Whole-Exome Sequencing Suggests LAMB3 as a Susceptibility Gene for Morbid Obesity.

Jiao H, Kulyté A, Näslund E, ..., Arner P, Dahlman I

Diabetes 65 (10) 2980-2989 [2016-10-00; online 2016-07-20]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Various Antibody Clones of Napsin A, Thyroid Transcription Factor 1, and p40 and Comparisons With Cytokeratin 5 and p63 in Histopathologic Diagnostics of Non-Small Cell Lung Carcinoma.

Tran L, Mattsson JS, Nodin B, ..., Micke P, Brunnström H

Appl. Immunohistochem. Mol. Morphol. 24 (9) 648-659 [2016-10-00; online 2016-10-18]

Urea-Dependent Adenylate Kinase Activation following Redistribution of Structural States

Rogne P, Wolf-Watz M

Biophysical Journal 111 (7) 1385-1395 [2016-10-00; online 2016-10-00]

Trans-ancestry meta-analyses identify rare and common variants associated with blood pressure and hypertension.

Surendran P, Drenos F, Young R, ..., Howson JM, Munroe PB

Nat. Genet. 48 (10) 1151-1161 [2016-10-00; online 2016-09-13]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Towards integration of population and comparative genomics in forest trees.

Ingvarsson PK, Hvidsten TR, Street NR

New Phytol. 212 (2) 338-344 [2016-10-00; online 2016-08-31]

NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The genetics of blood pressure regulation and its target organs from association studies in 342,415 individuals.

Ehret GB, Ferreira T, Chasman DI, ..., Newton-Cheh C, Munroe PB

Nat. Genet. 48 (10) 1171-1184 [2016-10-00; online 2016-09-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

The Allelochemical MDCA Inhibits Lignification and Affects Auxin Homeostasis.

Steenackers W, Cesarino I, Klíma P, ..., Boerjan W, Vanholme B

Plant Physiol. 172 (2) 874-888 [2016-10-00; online 2016-08-09]

Soluble CD93 Is Involved in Metabolic Dysregulation but Does Not Influence Carotid Intima-Media Thickness.

Strawbridge RJ, Hilding A, Silveira A, ..., Bäcklund A, IMPROVE Study Group

Diabetes 65 (10) 2888-2899 [2016-10-00; online 2016-09-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Sodium pump organization in dendritic spines.

Blom H, Bernhem K, Brismar H

Neurophotonics 3 (4) 041803 [2016-10-00; online 2016-05-14]

Integrated Microscopy Technologies Stockholm [Technology development]

Serum thioredoxin reductase is highly increased in mice with hepatocellular carcinoma and its activity is restrained by several mechanisms.

Zhang L, Cheng Q, Zhang L, ..., Arnér ES, Zhang J

Free Radic. Biol. Med. 99 (-) 426-435 [2016-10-00; online 2016-08-28]

Mass Spectrometry-based Proteomics, Uppsala [Service]

Polygenic associations of neurodevelopmental genes in suicide attempt.

Sokolowski M, Wasserman J, Wasserman D

Mol. Psychiatry 21 (10) 1381-1390 [2016-10-00; online 2015-12-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Personality Polygenes, Positive Affect, and Life Satisfaction.

Weiss A, Baselmans BM, Hofer E, ..., Bartels M, Luciano M

Twin Res Hum Genet 19 (5) 407-417 [2016-10-00; online 2016-08-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Open for collaboration: an academic platform for drug discovery and development at SciLifeLab.

Arvidsson PI, Sandberg K, Forsberg-Nilsson K

Drug Discov. Today 21 (10) 1690-1698 [2016-10-00; online 2016-07-05]

Drug Discovery and Development (DDD) [Technology development]

Non-targeted metabolomics combined with genetic analyses identifies bile acid synthesis and phospholipid metabolism as being associated with incident type 2 diabetes.

Fall T, Salihovic S, Brandmaier S, ..., Ingelsson E, Lind L

Diabetologia 59 (10) 2114-2124 [2016-10-00; online 2016-07-14]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Mutations in HECW2 are associated with intellectual disability and epilepsy.

Halvardson J, Zhao JJ, Zaghlool A, ..., Thuresson AC, Feuk L

J. Med. Genet. 53 (10) 697-704 [2016-10-00; online 2016-06-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Metabolomic Quality Assessment of EDTA Plasma and Serum Samples.

Malm L, Tybring G, Moritz T, Landin B, Galli J

Biopreserv Biobank 14 (5) 416-423 [2016-10-00; online 2016-06-27]

Genome-Wide Association Study of the Modified Stumvoll Insulin Sensitivity Index Identifies BCL2 and FAM19A2 as Novel Insulin Sensitivity Loci.

Walford GA, Gustafsson S, Rybin D, ..., Ingelsson E, Florez JC

Diabetes 65 (10) 3200-3211 [2016-10-00; online 2016-07-16]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic rescue in a severely inbred wolf population.

Åkesson M, Liberg O, Sand H, ..., Bensch S, Flagstad Ø

Mol. Ecol. 25 (19) 4745-4756 [2016-10-00; online 2016-08-09]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Generation and analyses of human synthetic antibody libraries and their application for protein microarrays.

Säll A, Walle M, Wingren C, ..., Borrebaeck CAK, Persson H

Protein Eng. Des. Sel. 29 (10) 427-437 [2016-10-00; online 2016-09-01]

Drug Discovery and Development (DDD) [Technology development] Protein Science Facility (PSF) [Collaborative]

Expression of Interferon-Stimulated Genes in Insulitic Pancreatic Islets of Patients Recently Diagnosed With Type 1 Diabetes.

Lundberg M, Krogvold L, Kuric E, Dahl-Jørgensen K, Skog O

Diabetes 65 (10) 3104-3110 [2016-10-00; online 2016-07-17]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Elevated Basal Insulin Secretion in Type 2 Diabetes Caused by Reduced Plasma Membrane Cholesterol.

Nagaraj V, Kazim AS, Helgeson J, ..., Zhang E, Renström E

Mol. Endocrinol. 30 (10) 1059-1069 [2016-10-00; online 2016-08-18]

Fluorescence Correlation Spectroscopy [Collaborative] Integrated Microscopy Technologies Stockholm

Effects of multiple dimensions of bacterial diversity on functioning, stability and multifunctionality.

Roger F, Bertilsson S, Langenheder S, Osman OA, Gamfeldt L

Ecology 97 (10) 2716-2728 [2016-10-00; online 2016-09-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Effect of Insulin Resistance on Monounsaturated Fatty Acid Levels: A Multi-cohort Non-targeted Metabolomics and Mendelian Randomization Study.

Nowak C, Salihovic S, Ganna A, ..., Ingelsson E, Fall T

PLoS Genet. 12 (10) e1006379 [2016-10-00; online 2016-10-21]

Affinity Proteomics Uppsala [Service] Bioinformatics Support for Computational Resources [Service] Clinical Biomarkers [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] PLA and Single Cell Proteomics [Service]

Direct acquisition of organic N by white clover even in the presence of inorganic N

Czaban W, Jämtgård S, Näsholm T, ..., Nicolaisen M, Fomsgaard IS

Plant Soil 407 (1-2) 91-107 [2016-10-00; online 2016-04-15]

DNA methylome analysis of acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands.

Wahlberg P, Lundmark A, Nordlund J, ..., Lönnerholm G, Syvänen AC

Epigenomics 8 (10) 1367-1387 [2016-10-00; online 2016-08-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield.

Hubalek V, Wu X, Eiler A, ..., Bertilsson S, Ionescu D

ISME J 10 (10) 2447-2458 [2016-10-00; online 2016-03-30]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Clonality of erythromycin resistance in Francisella tularensis.

Karlsson E, Golovliov I, Lärkeryd A, ..., Forsman M, Johansson A

J. Antimicrob. Chemother. 71 (10) 2815-2823 [2016-10-00; online 2016-06-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Biophysics in drug discovery: impact, challenges and opportunities.

Renaud JP, Chung CW, Danielson UH, ..., Hubbard RE, Nar H

Nat Rev Drug Discov 15 (10) 679-698 [2016-10-00; online 2016-08-16]

Drug Discovery and Development (DDD) [Technology development]

Autoantibodies Targeting a Collecting Duct–Specific Water Channel in Tubulointerstitial Nephritis

Landegren N, Pourmousa Lindberg M, Skov J, ..., Fenton RA, Kämpe O

J. Am. Soc. Nephrol. 27 (10) 3220-3228 [2016-10-00; online 2016-03-16]

Affinity Proteomics Uppsala [Service] PLA and Single Cell Proteomics [Service]

Abstracts of the HIV Research for Prevention Meeting, HIVR4P, 17-20 October, 2016, Chicago, USA

AIDS Research and Human Retroviruses 32 (S1) 1-409 [2016-10-00; online 2016-10-00]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

A proposal for validation of antibodies.

Uhlen M, Bandrowski A, Carr S, ..., Snyder M, Yamamoto T

Nat. Methods 13 (10) 823-827 [2016-10-00; online 2016-09-05]

The domesticated brain: genetics of brain mass and brain structure in an avian species.

Henriksen R, Johnsson M, Andersson L, Jensen P, Wright D

Sci Rep 6 (1) 34031 [2016-09-30; online 2016-09-30]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Feralisation targets different genomic loci to domestication in the chicken.

Johnsson M, Gering E, Willis P, ..., Friberg U, Wright D

Nat Commun 7 (-) 12950 [2016-09-30; online 2016-09-30]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Genomic Regions Associated With Interspecies Communication in Dogs Contain Genes Related to Human Social Disorders.

Persson ME, Wright D, Roth LS, Batakis P, Jensen P

Sci Rep 6 (-) 33439 [2016-09-29; online 2016-09-29]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Detecting individual extracellular vesicles using a multicolor in situ proximity ligation assay with flow cytometric readout.

Löf L, Ebai T, Dubois L, ..., Landegren U, Kamali-Moghaddam M

Sci Rep 6 (1) 34358 [2016-09-29; online 2016-09-29]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Aberrant activation of the PI3K/mTOR pathway promotes resistance to sorafenib in AML.

Lindblad O, Cordero E, Puissant A, ..., Rönnstrand L, Kazi JU

Oncogene 35 (39) 5119-5131 [2016-09-29; online 2016-03-22]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Discovery of Novel Viruses in Mosquitoes from the Zambezi Valley of Mozambique.

Cholleti H, Hayer J, Abilio AP, ..., Berg M, Blomström AL

PLoS ONE 11 (9) e0162751 [2016-09-28; online 2016-09-28]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Analysis of Body-wide Unfractionated Tissue Data to Identify a Core Human Endothelial Transcriptome.

Butler LM, Hallström BM, Fagerberg L, ..., Renné T, Odeberg J

Cell Syst 3 (3) 287-301.e3 [2016-09-28; online 2016-09-15]

Loss of ncm(5) and mcm(5) wobble uridine side chains results in an altered metabolic profile.

Karlsborn T, Mahmud AK, Tükenmez H, Byström AS

Metabolomics 12 (12) 177 [2016-09-27; online 2016-09-27]

Dynamic regulation of auxin oxidase and conjugating enzymes AtDAO1 and GH3 modulates auxin homeostasis.

Mellor N, Band LR, Pěnčík A, ..., Bennett MJ, Owen MR

Proc. Natl. Acad. Sci. U.S.A. 113 (39) 11022-11027 [2016-09-27; online 2016-09-20]

Dioxygenase-encoding AtDAO1 gene controls IAA oxidation and homeostasis in Arabidopsis.

Porco S, Pěnčík A, Rashed A, ..., Bennett MJ, Ljung K

Proc. Natl. Acad. Sci. U.S.A. 113 (39) 11016-11021 [2016-09-27; online 2016-09-22]

Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes.

Lindqvist CM, Lundmark A, Nordlund J, ..., Berglund EC, Syvänen AC

Oncotarget 7 (39) 64071-64088 [2016-09-27; online 2016-09-04]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome.

Dutoit L, Burri R, Nater A, Mugal CF, Ellegren H

Mol Ecol Resour 17 (4) 586-597 [2016-09-26; online 2016-09-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Exploration of high-density protein microarrays for antibody validation and autoimmunity profiling.

Sjöberg R, Mattsson C, Andersson E, ..., Ayoglu B, Nilsson P

N Biotechnol 33 (5 Pt A) 582-592 [2016-09-25; online 2015-09-30]

Autoimmunity and Serology Profiling [Technology development]

Overlap in serum metabolic profiles between non-related diseases: Implications for LC-MS metabolomics biomarker discovery.

Lindahl A, Forshed J, Nordström A

Biochem. Biophys. Res. Commun. 478 (3) 1472-1477 [2016-09-23; online 2016-08-28]

Naphthalene Derivatives from the Roots of Pentas parvifolia and Pentas bussei.

Abdissa N, Pan F, Gruhonjic A, ..., Yenesew A, Erdélyi M

J. Nat. Prod. 79 (9) 2181-2187 [2016-09-23; online 2016-08-12]

Molecular insights into substrate recognition and catalytic mechanism of the chaperone and FKBP peptidyl-prolyl isomerase SlyD.

Quistgaard EM, Weininger U, Ural-Blimke Y, ..., Akke M, Löw C

BMC Biol. 14 (1) 82 [2016-09-23; online 2016-09-23]

Genetic Spectrum of Idiopathic Restrictive Cardiomyopathy Uncovered by Next-Generation Sequencing.

Kostareva A, Kiselev A, Gudkova A, ..., Sejersen T, Shlyakhto E

PLoS ONE 11 (9) e0163362 [2016-09-23; online 2016-09-23]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Combinatorial identification of DNA methylation patterns over age in the human brain.

Torabi Moghadam B, Dabrowski M, Kaminska B, Grabherr MG, Komorowski J

BMC Bioinformatics 17 (1) 393 [2016-09-23; online 2016-09-23]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

The Oncolytic Efficacy and in Vivo Pharmacokinetics of [2-(4-Chlorophenyl)quinolin-4-yl](piperidine-2-yl)methanol (Vacquinol-1) Are Governed by Distinct Stereochemical Features.

Hammarström LG, Harmel RK, Granath M, ..., Lehmann F, Ernfors P

J. Med. Chem. 59 (18) 8577-8592 [2016-09-22; online 2016-09-09]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Collaborative]

Multiplexed, targeted profiling of single-cell proteomes and transcriptomes in a single reaction.

Genshaft AS, Li S, Gallant CJ, ..., Landegren U, Shalek AK

Genome Biol. 17 (1) 188 [2016-09-19; online 2016-09-19]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Linkage between Fitness of Yeast Cells and Adenylate Kinase Catalysis

Tükenmez H, Magnussen HM, Kovermann M, Byström A, Wolf-Watz M

PLoS ONE 11 (9) e0163115 [2016-09-19; online 2016-09-19]

Investigation of rare and low-frequency variants using high-throughput sequencing with pooled DNA samples.

Wang J, Skoog T, Einarsdottir E, ..., Kere J, Jiao H

Sci Rep 6 (-) 33256 [2016-09-16; online 2016-09-16]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genome-wide association analysis reveals variants on chromosome 19 that contribute to childhood risk of chronic otitis media with effusion.

Einarsdottir E, Hafrén L, Leinonen E, ..., Kere J, Mattila PS

Sci Rep 6 (-) 33240 [2016-09-16; online 2016-09-16]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

NUDT15 Hydrolyzes 6-Thio-DeoxyGTP to Mediate the Anticancer Efficacy of 6-Thioguanine.

Valerie NC, Hagenkort A, Page BD, ..., Jemth AS, Helleday T

Cancer Res. 76 (18) 5501-5511 [2016-09-15; online 2016-08-16]

Epigenome-wide association study reveals differential DNA methylation in individuals with a history of myocardial infarction

Rask-Andersen M, Martinsson D, Ahsan M, ..., Gyllensten U, Johansson Å

Hum. Mol. Genet. - (-) ddw302 [2016-09-15; online 2016-09-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells.

Morin A, Kwan T, Ge B, ..., Lathrop MG, Pastinen T

BMC Med Genomics 9 (1) 59 [2016-09-13; online 2016-09-13]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Associations Between Macrophage Colony-Stimulating Factor and Monocyte Chemotactic Protein 1 in Plasma and First-Time Coronary Events: A Nested Case-Control Study.

Schiopu A, Bengtsson E, Gonçalves I, ..., Fredrikson GN, Björkbacka H

J Am Heart Assoc 5 (9) e002851 [2016-09-13; online 2016-09-13]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

The infectious particle of insect-borne totivirus-like Omono River virus has raised ridges and lacks fibre complexes.

Okamoto K, Miyazaki N, Larsson DS, ..., Murata K, Hajdu J

Sci Rep 6 (-) 33170 [2016-09-12; online 2016-09-12]

Mass Spectrometry-based Proteomics, Uppsala [Service]

Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.

Ferreira PG, Oti M, Barann M, ..., Guigó R, Sammeth M

Sci Rep 6 (-) 32406 [2016-09-12; online 2016-09-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Limited clonal relatedness between gut IgA plasma cells and memory B cells after oral immunization.

Bemark M, Hazanov H, Strömberg A, ..., Mehr R, Lycke NY

Nat Commun 7 (-) 12698 [2016-09-06; online 2016-09-06]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative]

Design and Synthesis of 2,2'-Diindolylmethanes to Selectively Target Certain G-Quadruplex DNA Structures.

Livendahl M, Jamroskovic J, Ivanova S, ..., Sabouri N, Chorell E

Chemistry 22 (37) 13004-13009 [2016-09-05; online 2016-07-20]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Association between renin and atherosclerotic burden in subjects with and without type 2 diabetes.

Gonçalves I, Edsfeldt A, Colhoun HM, ..., Nilsson J, SUMMIT consortium

BMC Cardiovasc Disord 16 (1) 171 [2016-09-05; online 2016-09-05]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Trans-ethnic Fine Mapping Highlights Kidney-Function Genes Linked to Salt Sensitivity.

Mahajan A, Rodan AR, Le TH, ..., Morris AP, Franceschini N

Am. J. Hum. Genet. 99 (3) 636-646 [2016-09-01; online 2016-09-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The BR domain of PsrP interacts with extracellular DNA to promote bacterial aggregation; structural insights into pneumococcal biofilm formation.

Schulte T, Mikaelsson C, Beaussart A, ..., Nygren PÅ, Achour A

Sci Rep 6 (-) 32371 [2016-09-01; online 2016-09-01]

Absence of the Autophagy Adaptor SQSTM1/p62 Causes Childhood-Onset Neurodegeneration with Ataxia, Dystonia, and Gaze Palsy.

Haack TB, Ignatius E, Calvo-Garrido J, ..., Carroll CJ, Klopstock T

Am. J. Hum. Genet. 99 (3) 735-743 [2016-09-01; online 2016-08-23]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A novel variant in MYLK causes thoracic aortic dissections: genotypic and phenotypic description.

Hannuksela M, Stattin EL, Klar J, ..., Sörensen K, Carlberg B

BMC Med. Genet. 17 (1) 61 [2016-09-01; online 2016-09-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Tissue microarray profiling in human heart failure.

Lal S, Nguyen L, Tezone R, ..., Li A, Dos Remedios C

Proteomics 16 (17) 2319-2326 [2016-09-00; online 2016-08-11]

The peroxisome proliferator-activated receptor α agonist, AZD4619, induces alanine aminotransferase-1 gene and protein expression in human, but not in rat hepatocytes: Correlation with serum ALT levels.

Thulin P, Bamberg K, Buler M, Dahl B, Glinghammar B

Int. J. Mol. Med. 38 (3) 961-968 [2016-09-00; online 2016-07-20]

Drug Discovery and Development (DDD) [Collaborative]

The distribution of α-kleisin during meiosis in the holocentromeric plant Luzula elegans.

Ma W, Schubert V, Martis MM, ..., Cheng Z, Houben A

Chromosome Res. 24 (3) 393-405 [2016-09-00; online 2016-06-14]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

The crystal structure of the major pneumococcal autolysin LytA in complex with a large peptidoglycan fragment reveals the pivotal role of glycans for lytic activity.

Sandalova T, Lee M, Henriques-Normark B, ..., Mellroth P, Achour A

Mol. Microbiol. 101 (6) 954-967 [2016-09-00; online 2016-07-05]

The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts.

Lindholm ME, Giacomello S, Werne Solnestam B, ..., Kjellqvist S, Sundberg CJ

PLoS Genet. 12 (9) e1006294 [2016-09-00; online 2016-09-22]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Repeated LPS Injection Induces Distinct Changes in the Kynurenine Pathway in Mice.

Larsson MK, Faka A, Bhat M, ..., Schwieler L, Erhardt S

Neurochem. Res. 41 (9) 2243-2255 [2016-09-00; online 2016-05-10]

Drug Discovery and Development (DDD) [Collaborative]

Protein profiles of CCL5, HPGDS, and NPSR1 in plasma reveal association with childhood asthma.

Hamsten C, Häggmark A, Grundström J, ..., Nilsson P, van Hage M

Allergy 71 (9) 1357-1361 [2016-09-00; online 2016-05-25]

Affinity Proteomics Stockholm [Collaborative] Tissue Profiling [Collaborative]

Phenotypic Modulation of Smooth Muscle Cells in Atherosclerosis Is Associated With Downregulation of LMOD1, SYNPO2, PDLIM7, PLN, and SYNM.

Perisic Matic L, Rykaczewska U, Razuvaev A, ..., Hamsten A, Hedin U

Arterioscler. Thromb. Vasc. Biol. 36 (9) 1947-1961 [2016-09-00; online 2016-07-28]

Clinical Proteomics Mass spectrometry [Collaborative] Global Proteomics and Proteogenomics [Collaborative]

Mass spectrometry data from a quantitative analysis of protein expression in gills of immuno-challenged blue mussels (Mytilus edulis).

Hörnaeus K, Guillemant J, Mi J, ..., Bergquist J, Lind SB

Data Brief 8 (-) 470-473 [2016-09-00; online 2016-06-03]

Mass Spectrometry-based Proteomics, Uppsala [Collaborative]

Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry.

Al-Eryani Y, Ib Rasmussen M, Kjellström S, ..., Emanuelsson C, von Wachenfeldt C

Proteins 84 (9) 1234-1245 [2016-09-00; online 2016-06-15]

Epigenome-wide analysis of DNA methylation reveals a rectal cancer-specific epigenomic signature.

Vymetalkova V, Vodicka P, Pardini B, ..., Nilsson TK, Farkas SA

Epigenomics 8 (9) 1193-1207 [2016-09-00; online 2016-08-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Endarterectomy patients with elevated levels of circulating IL-16 have fewer cardiovascular events during follow-up.

Grönberg C, Asciutto G, Persson A, ..., Gonçalves I, Björkbacka H

Cytokine 85 (-) 137-139 [2016-09-00; online 2016-06-22]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Electricity generation from an inorganic sulfur compound containing mining wastewater by acidophilic microorganisms.

Ni G, Christel S, Roman P, ..., Bijmans MF, Dopson M

Res. Microbiol. 167 (7) 568-575 [2016-09-00; online 2016-05-08]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Direct estimate of the rate of germline mutation in a bird.

Smeds L, Qvarnström A, Ellegren H

Genome Res. 26 (9) 1211-1218 [2016-09-00; online 2016-07-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Detailed gene dose analysis reveals recurrent focal gene deletions in pediatric B-cell precursor acute lymphoblastic leukemia.

Ivanov Öfverholm I, Tran AN, Olsson L, ..., Nordgren A, Barbany G

Leuk. Lymphoma 57 (9) 2161-2170 [2016-09-00; online 2016-04-20]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Data on the expression of cellular lncRNAs in human adenovirus infected cells.

Chen M, Zhao H, Lind SB, Pettersson U

Data Brief 8 (-) 1263-1279 [2016-09-00; online 2016-08-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Clinical impact of recurrently mutated genes on lymphoma diagnostics: state-of-the-art and beyond.

Rosenquist R, Rosenwald A, Du MQ, ..., Stamatopoulos K, European Research Initiative on CLL (ERIC) and the European Association for Haematopathology (EAHP)

Haematologica 101 (9) 1002-1009 [2016-09-00; online 2016-09-02]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Bacterial associations reveal spatial population dynamics in Anopheles gambiae mosquitoes

Buck M, Nilsson LKJ, Brunius C, ..., Hopkins R, Terenius O

Sci Rep 6 (1) - [2016-09-00; online 2016-03-10]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Autoantibody targets in vaccine-associated narcolepsy.

Häggmark-Månberg A, Zandian A, Forsström B, ..., Olsson T, Nilsson P

Autoimmunity 49 (6) 421-433 [2016-09-00; online 2016-05-20]

Autoimmunity and Serology Profiling [Collaborative]

Approach for Identifying Human Leukocyte Antigen (HLA)-DR Bound Peptides from Scarce Clinical Samples.

Heyder T, Kohler M, Tarasova NK, ..., Grunewald J, Ytterberg AJ

Mol. Cell Proteomics 15 (9) 3017-3029 [2016-09-00; online 2016-07-24]

Advanced Mass Spectrometry Proteomics [Collaborative]

Advancing the global proteome survey platform by using an oriented single chain antibody fragment immobilization approach

Säll A, Persson H, Ohlin M, Borrebaeck CAK, Wingren C

New Biotechnology 33 (5) 503-513 [2016-09-00; online 2016-09-00]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

ATM mutations in major stereotyped subsets of chronic lymphocytic leukemia: enrichment in subset #2 is associated with markedly short telomeres.

Navrkalova V, Young E, Baliakas P, ..., Rosenquist R, Trbusek M

Haematologica 101 (9) e369-e373 [2016-09-00; online 2016-08-02]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

A genetic variant in proximity to the gene LYPLAL1 is associated with lower hunger feelings and increased weight loss following Roux-en-Y gastric bypass surgery.

Bandstein M, Mwinyi J, Ernst B, ..., Schultes B, Schiöth HB

Scand. J. Gastroenterol. 51 (9) 1050-1055 [2016-09-00; online 2016-05-18]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A Role for the Chromatin-Remodeling Factor BAZ1A in Neurodevelopment.

Zaghlool A, Halvardson J, Zhao JJ, ..., Thuresson AC, Feuk L

Hum. Mutat. 37 (9) 964-975 [2016-09-00; online 2016-07-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A Rickettsiales symbiont of amoebae with ancient features.

Schulz F, Martijn J, Wascher F, ..., Ettema TJ, Horn M

Environ. Microbiol. 18 (8) 2326-2342 [2016-09-00; online 2015-04-25]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A Genetic Risk Score Is Associated with Weight Loss Following Roux-en Y Gastric Bypass Surgery.

Bandstein M, Voisin S, Nilsson EK, ..., Mwinyi J, Schiöth HB

Obes Surg 26 (9) 2183-2189 [2016-09-00; online 2016-02-03]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Adipose Transcriptional Response to Insulin Is Determined by Obesity, Not Insulin Sensitivity.

Rydén M, Hrydziuszko O, Mileti E, ..., Daub CO, Arner P

Cell Rep 16 (9) 2317-2326 [2016-08-30; online 2016-08-23]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Cystatin C and Cardiovascular Disease: A Mendelian Randomization Study.

van der Laan SW, Fall T, Soumaré A, ..., Holmes MV, Asselbergs FW

J. Am. Coll. Cardiol. 68 (9) 934-945 [2016-08-30; online 2016-08-27]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Phosphorylation of Leukotriene C4 Synthase at Serine 36 Impairs Catalytic Activity.

Ahmad S, Ytterberg AJ, Thulasingam M, ..., Rinaldo-Matthis A, Haeggström JZ

J. Biol. Chem. 291 (35) 18410-18418 [2016-08-26; online 2016-06-30]

Advanced Mass Spectrometry Proteomics [Collaborative]

One-night sleep deprivation induces changes in the DNA methylation and serum activity indices of stearoyl-CoA desaturase in young healthy men.

Skuladottir GV, Nilsson EK, Mwinyi J, Schiöth HB

Lipids Health Dis 15 (1) 137 [2016-08-26; online 2016-08-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Factors regulating capillary remodeling in a reversible model of inflammatory corneal angiogenesis.

Mukwaya A, Peebo B, Xeroudaki M, ..., Jensen L, Lagali N

Sci Rep 6 (1) 32137 [2016-08-26; online 2016-08-26]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Enantioselective Organocatalyzed Transformations of β-Ketoesters.

Govender T, Arvidsson PI, Maguire GE, Kruger HG, Naicker T

Chem. Rev. 116 (16) 9375-9437 [2016-08-24; online 2016-07-28]

Drug Discovery and Development (DDD) [Collaborative]

Oxidation and cyclization of casbene in the biosynthesis of Euphorbia factors from mature seeds of Euphorbia lathyris L.

Luo D, Callari R, Hamberger B, ..., Staerk D, Hamberger B

Proc. Natl. Acad. Sci. U.S.A. 113 (34) E5082-E5089 [2016-08-23; online 2016-08-11]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Identification of Multiple QTLs Linked to Neuropathology in the Engrailed-1 Heterozygous Mouse Model of Parkinson's Disease.

Kurowska Z, Jewett M, Brattås PL, ..., Brundin P, Swanberg M

Sci Rep 6 (-) 31701 [2016-08-23; online 2016-08-23]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Effects of wastewater treatment plant effluent inputs on planktonic metabolic rates and microbial community composition in the Baltic Sea

Vaquer-Sunyer R, Reader HE, Muthusamy S, ..., Conley DJ, Kritzberg ES

Biogeosciences 13 (16) 4751-4765 [2016-08-23; online 2016-08-23]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression.

Ivanov M, Kals M, Lauschke V, ..., Milani L, Ingelman-Sundberg M

Nucleic Acids Res. 44 (14) 6756-6769 [2016-08-19; online 2016-04-29]

Bioinformatics Support for Computational Resources [Service] Clinical Proteomics Mass spectrometry [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases.

Franzén O, Ermel R, Cohain A, ..., Schadt EE, Björkegren JL

Science 353 (6301) 827-830 [2016-08-19; online 2016-08-20]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Structural origin of proton mobility in a protic ionic liquid/imidazole mixture: insights from computational and experimental results.

Yaghini N, Gómez-González V, Varela LM, Martinelli A

Phys Chem Chem Phys 18 (33) 23195-23206 [2016-08-17; online 2016-08-09]

Multifunctional Hyaluronic Acid and Chondroitin Sulfate Nanoparticles: Impact of Glycosaminoglycan Presentation on Receptor Mediated Cellular Uptake and Immune Activation.

Oommen OP, Duehrkop C, Nilsson B, Hilborn J, Varghese OP

ACS Appl Mater Interfaces 8 (32) 20614-20624 [2016-08-17; online 2016-07-29]

Cinobufagin Modulates Human Innate Immune Responses and Triggers Antibacterial Activity.

Xie S, Spelmink L, Codemo M, ..., Henriques-Normark B, Olliver M

PLoS ONE 11 (8) e0160734 [2016-08-16; online 2016-08-16]

Mass Spectrometry-based Proteomics, Uppsala [Service]

Chondroitin sulfate derived theranostic nanoparticles for targeted drug delivery.

Varghese OP, Liu J, Sundaram K, Hilborn J, Oommen OP

Biomater Sci 4 (9) 1310-1313 [2016-08-16; online 2016-07-20]

Cellular Barcoding Links B-1a B Cell Potential to a Fetal Hematopoietic Stem Cell State at the Single-Cell Level.

Kristiansen TA, Jaensson Gyllenbäck E, Zriwil A, ..., Bryder D, Yuan J

Immunity 45 (2) 346-357 [2016-08-16; online 2016-08-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Metastasis Stimulation by Hypoxia and Acidosis-Induced Extracellular Lipid Uptake Is Mediated by Proteoglycan-Dependent Endocytosis.

Menard JA, Christianson HC, Kucharzewska P, ..., Johansson MC, Belting M

Cancer Res. 76 (16) 4828-4840 [2016-08-15; online 2016-05-19]

Substituent Effects on the [N-I-N](+) Halogen Bond.

Carlsson AC, Mehmeti K, Uhrbom M, ..., Rissanen K, Erdélyi M

J. Am. Chem. Soc. 138 (31) 9853-9863 [2016-08-10; online 2016-06-17]

Large-scale ligand-based predictive modelling using support vector machines.

Alvarsson J, Lampa S, Schaal W, ..., Wikberg JE, Spjuth O

J Cheminform 8 (-) 39 [2016-08-10; online 2016-08-10]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius.

Liu H, Wang K, Lindås AC, Peeters E

BMC Genomics 17 (-) 569 [2016-08-08; online 2016-08-08]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Stromal Hedgehog signalling is downregulated in colon cancer and its restoration restrains tumour growth.

Gerling M, Büller NV, Kirn LM, ..., van den Brink GR, Toftgård R

Nat Commun 7 (-) 12321 [2016-08-05; online 2016-08-05]

Bioinformatics and Expression Analysis (BEA) [Service]

Inconsistent results in the analysis of ALK rearrangements in non-small cell lung cancer.

Mattsson JS, Brunnström H, Jabs V, ..., Micke P, Svensson MA

BMC Cancer 16 (-) 603 [2016-08-05; online 2016-08-05]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service] Tissue Profiling [Collaborative]

The genetic architecture of type 2 diabetes.

Fuchsberger C, Flannick J, Teslovich TM, ..., Altshuler D, McCarthy MI

Nature 536 (7614) 41-47 [2016-08-04; online 2016-07-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Rapid and specific hypomethylation of enhancers in endothelial cells during adaptation to cell culturing.

Magnusson M, Larsson P, Lu EX, ..., Carén H, Jern S

Epigenetics 11 (8) 614-624 [2016-08-02; online 2016-06-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Mutation-Induced Population Shift in the MexR Conformational Ensemble Disengages DNA Binding: A Novel Mechanism for MarR Family Derepression.

Anandapadamanaban M, Pilstål R, Andresen C, ..., Wallner B, Sunnerhagen M

Structure 24 (8) 1311-1321 [2016-08-02; online 2016-07-14]

Compounds from the marine sponge Cribrochalina vasculum offer a way to target IGF-1R mediated signaling in tumor cells

Zovko A, Novak M, Hååg P, ..., Lewensohn R, Viktorsson K

Oncotarget 7 (31) 50258-50276 [2016-08-02; online 2016-07-01]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

ω-3 Polyunsaturated Fatty Acid Biomarkers and Coronary Heart Disease: Pooling Project of 19 Cohort Studies.

Del Gobbo LC, Imamura F, Aslibekyan S, ..., Mozaffarian D, Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Fatty Acids and Outcomes Research Consortium (FORCe)

JAMA Intern Med 176 (8) 1155-1166 [2016-08-01; online 2016-07-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Simultaneous imaging of multiple neurotransmitters and neuroactive substances in the brain by desorption electrospray ionization mass spectrometry.

Shariatgorji M, Strittmatter N, Nilsson A, ..., Goodwin RJ, Andren PE

Neuroimage 136 (-) 129-138 [2016-08-01; online 2016-05-04]

Profilin connects actin assembly with microtubule dynamics.

Nejedla M, Sadi S, Sulimenko V, ..., Aspenström P, Karlsson R

Mol. Biol. Cell 27 (15) 2381-2393 [2016-08-01; online 2016-06-17]

Integrated Microscopy Technologies Stockholm [Collaborative]

On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1.

Xu F, Jerlström-Hultqvist J, Kolisko M, ..., Svärd SG, Andersson JO

BMC Biol. 14 (-) 62 [2016-08-01; online 2016-08-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

MetLab: An In Silico Experimental Design, Simulation and Analysis Tool for Viral Metagenomics Studies.

Norling M, Karlsson-Lindsjö OE, Gourlé H, Bongcam-Rudloff E, Hayer J

PLoS ONE 11 (8) e0160334 [2016-08-01; online 2016-08-01]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Kinetic investigation of human 5-lipoxygenase with arachidonic acid.

Mittal M, Kumar RB, Balagunaseelan N, ..., Haeggström JZ, Rinaldo-Matthis A

Bioorg. Med. Chem. Lett. 26 (15) 3547-3551 [2016-08-01; online 2016-06-11]

Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria.

Eiler A, Mondav R, Sinclair L, ..., Woyke T, Bertilsson S

ISME J 10 (8) 1902-1914 [2016-08-00; online 2016-01-19]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training Microbial Single Cell Genomics [Collaborative]

Transcriptomic analysis reveals how a lack of potassium ions increases Sulfolobus acidocaldarius sensitivity to pH changes.

Buetti-Dinh A, Dethlefsen O, Friedman R, Dopson M

Microbiology (Reading, Engl.) 162 (8) 1422-1434 [2016-08-00; online 2016-05-28]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Spondyloocular Syndrome: Novel Mutations in XYLT2 Gene and Expansion of the Phenotypic Spectrum.

Taylan F, Costantini A, Coles N, ..., Tüysüz B, Mäkitie O

J. Bone Miner. Res. 31 (8) 1577-1585 [2016-08-00; online 2016-03-19]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Serum nuclear magnetic resonance-based metabolomics and outcome in diffuse large B-cell lymphoma patients - a pilot study.

Stenson M, Pedersen A, Hasselblom S, ..., Pinto R, Andersson PO

Leuk. Lymphoma 57 (8) 1814-1822 [2016-08-00; online 2016-02-17]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Swedish NMR Centre (SNC) [Collaborative]

SATB2 is expressed in Merkel cell carcinoma.

Fukuhara M, Agnarsdóttir M, Edqvist PH, Coter A, Ponten F

Arch. Dermatol. Res. 308 (6) 449-454 [2016-08-00; online 2016-06-04]

Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin.

Langenheder S, Comte J, Zha Y, ..., Eiler A, Lindström ES

Environ Microbiol Rep 8 (4) 479-485 [2016-08-00; online 2016-03-02]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Rapid Evolution of Genomic Imprinting in Two Species of the Brassicaceae.

Hatorangan MR, Laenen B, Steige KA, Slotte T, Köhler C

Plant Cell 28 (8) 1815-1827 [2016-08-00; online 2016-07-29]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Postprandial alterations in whole-blood DNA methylation are mediated by changes in white blood cell composition.

Rask-Andersen M, Bringeland N, Nilsson EK, ..., Benedict C, Schiöth HB

Am. J. Clin. Nutr. 104 (2) 518-525 [2016-08-00; online 2016-07-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Phytophthora infestans Argonaute 1 binds microRNA and small RNAs from effector genes and transposable elements.

Åsman AK, Fogelqvist J, Vetukuri RR, Dixelius C

New Phytol. 211 (3) 993-1007 [2016-08-00; online 2016-03-25]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Novel regulatory variant detected on the VKORC1 haplotype that is associated with warfarin dose.

Cavalli M, Pan G, Nord H, ..., Wadelius C, Wadelius M

Pharmacogenomics 17 (12) 1305-1314 [2016-08-00; online 2016-02-06]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Neuroprotective potential of Linezolid: a quantitative and distribution study via mass spectrometry.

Baijnath S, Shobo A, Bester LA, ..., Naicker T, Govender T

J. Mol. Histol. 47 (4) 429-435 [2016-08-00; online 2016-06-22]

Drug Discovery and Development (DDD) [Collaborative]

Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine.

Gormley P, Anttila V, Winsvold BS, ..., Nyholt DR, Palotie A

Nat. Genet. 48 (8) 856-866 [2016-08-00; online 2016-06-21]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Intra-tumour IgA1 is common in cancer and is correlated with poor prognosis in bladder cancer.

Welinder C, Jirström K, Lehn S, ..., Danielsson L, Jansson B

Heliyon 2 (8) e00143 [2016-08-00; online 2016-08-16]

In quest for the optimal delignification of lignocellulosic biomass using hydrated, SO2 switched DBU MEASIL switchable ionic liquid

Anugwom I, Rujana L, Wärnå J, Hedenström M, Mikkola JP

Chemical Engineering Journal 297 (-) 256-264 [2016-08-00; online 2016-08-00]

Impact of ocean acidification on antimicrobial activity in gills of the blue mussel (Mytilus edulis).

Hernroth B, Baden S, Tassidis H, ..., Bergström Lind S, Bergquist J

Fish Shellfish Immunol. 55 (-) 452-459 [2016-08-00; online 2016-06-08]

Mass Spectrometry-based Proteomics, Uppsala [Collaborative]

Genome-wide association meta-analysis in Chinese and European individuals identifies ten new loci associated with systemic lupus erythematosus.

Morris DL, Sheng Y, Zhang Y, ..., Cui Y, Vyse TJ

Nat. Genet. 48 (8) 940-946 [2016-08-00; online 2016-07-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic determinants of warfarin maintenance dose and time in therapeutic treatment range: a RE-LY genomics substudy.

Eriksson N, Wallentin L, Berglund L, ..., Yusuf S, Wadelius M

Pharmacogenomics 17 (13) 1425-1439 [2016-08-00; online 2016-08-04]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Genetic and environmental effects on body mass index from infancy to the onset of adulthood: an individual-based pooled analysis of 45 twin cohorts participating in the COllaborative project of Development of Anthropometrical measures in Twins (CODATwins) study.

Silventoinen K, Jelenkovic A, Sund R, ..., Boomsma DI, Kaprio J

Am. J. Clin. Nutr. 104 (2) 371-379 [2016-08-00; online 2016-07-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Developmental exposure to progestins causes male bias and precocious puberty in zebrafish (Danio rerio).

Svensson J, Mustafa A, Fick J, Schmitz M, Brunström B

Aquat. Toxicol. 177 (-) 316-323 [2016-08-00; online 2016-06-14]

Assessing the taxonomic status of Osmoderma cristinae (Coleoptera: Scarabaeidae), endemic to Sicily, by genetic, morphological and pheromonal analyses

Zauli A, Carpaneto GM, Chiari S, ..., Bologna MA, Svensson GP

J Zool Syst Evol Res 54 (3) 206-214 [2016-08-00; online 2016-02-12]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Analysis of neural crest-derived clones reveals novel aspects of facial development.

Kaucka M, Ivashkin E, Gyllborg D, ..., Hellander A, Adameyko I

Sci Adv 2 (8) e1600060 [2016-08-00; online 2016-08-03]

Integrated Microscopy Technologies Stockholm [Collaborative]

Adaptation to different types of stress converge on mitochondrial metabolism

Lahtvee PJ, Kumar R, Hallström BM, Nielsen J

Mol. Biol. Cell 27 (15) 2505-2514 [2016-08-00; online 2016-08-00]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A novel splicing mutation in the IQSEC2 gene that modulates the phenotype severity in a family with intellectual disability.

Madrigal I, Alvarez-Mora MI, Rosell J, ..., Syvänen AC, Mila M

Eur. J. Hum. Genet. 24 (8) 1117-1123 [2016-08-00; online 2016-01-07]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

A new class of fatty acid allene oxide formed by the DOX-P450 fusion proteins of human and plant pathogenic fungi, C. immitis and Z. tritici.

Oliw EH, Aragó M, Chen Y, Jernerén F

J. Lipid Res. 57 (8) 1518-1528 [2016-08-00; online 2016-06-11]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Inhibitors of the Cysteine Synthase CysM with Antibacterial Potency against Dormant Mycobacterium tuberculosis.

Brunner K, Maric S, Reshma RS, ..., Schnell R, Schneider G

J. Med. Chem. 59 (14) 6848-6859 [2016-07-28; online 2016-07-13]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF) [Service]

Delineating the conformational flexibility of trisaccharides from NMR spectroscopy experiments and computer simulations.

Yang M, Angles d'Ortoli T, Säwén E, ..., Widmalm G, MacKerell AD

Phys Chem Chem Phys 18 (28) 18776-18794 [2016-07-28; online 2016-06-27]

The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus.

Sayadi A, Immonen E, Bayram H, Arnqvist G

PLoS ONE 11 (7) e0158565 [2016-07-21; online 2016-07-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Short Chain Fatty Acids (SCFA) Reprogram Gene Expression in Human Malignant Epithelial and Lymphoid Cells.

Astakhova L, Ngara M, Babich O, ..., Ernberg I, Matskova L

PLoS ONE 11 (7) e0154102 [2016-07-21; online 2016-07-21]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Metabolic Profiling of Systemic Lupus Erythematosus and Comparison with Primary Sjögren's Syndrome and Systemic Sclerosis.

Bengtsson AA, Trygg J, Wuttge DM, ..., Rännar S, Lundstedt T

PLoS ONE 11 (7) e0159384 [2016-07-21; online 2016-07-21]

Systematic Analysis Reveals that Cancer Mutations Converge on Deregulated Metabolism of Arachidonate and Xenobiotics.

Gatto F, Schulze A, Nielsen J

Cell Rep 16 (3) 878-895 [2016-07-19; online 2016-07-12]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Horizontal Cells, the Odd Ones Out in the Retina, Give Insights into Development and Disease.

Boije H, Shirazi Fard S, Edqvist PH, Hallböök F

Front Neuroanat 10 (-) 77 [2016-07-19; online 2016-07-19]

DNA Content in Extracellular Vesicles Isolated from Porcine Coronary Venous Blood Directly after Myocardial Ischemic Preconditioning.

Svennerholm K, Rodsand P, Hellman U, ..., Ronquist G, Haney M

PLoS ONE 11 (7) e0159105 [2016-07-19; online 2016-07-19]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Peroxisome Proliferator-activated Receptor γ Coactivator-1 α Isoforms Selectively Regulate Multiple Splicing Events on Target Genes.

Martínez-Redondo V, Jannig PR, Correia JC, ..., Dahlman-Wright K, Ruas JL

J. Biol. Chem. 291 (29) 15169-15184 [2016-07-15; online 2016-05-28]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Direct imaging of elemental distributions in tissue sections by laser ablation mass spectrometry.

Shariatgorji M, Nilsson A, Bonta M, ..., Limbeck A, Andrén PE

Methods 104 (-) 86-92 [2016-07-15; online 2016-06-02]

Abstract 2688: A forward genetics screen of murine brain tumors identifies novel candidate genes involved in gliomagenesis

Cancer M, Weishaupt H, Rosen G, ..., Ameur A, Swartling FJ

Cancer Res 76 (14 Supplement) 2688-2688 [2016-07-15; online 2016-07-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Abstract 2473: Combined BET-bromodomain and CDK2 inhibition in MYC-driven medulloblastoma

Bolin S, Borgenvik A, Persson C, ..., Weishaupt H, Swartling FJ

Cancer Res 76 (14 Supplement) 2473-2473 [2016-07-15; online 2016-07-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification.

Reischauer S, Stone OA, Villasenor A, ..., Andersson O, Stainier DY

Nature 535 (7611) 294-298 [2016-07-14; online 2016-07-15]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A C2HC zinc finger is essential for the RING-E2 interaction of the ubiquitin ligase RNF125.

Bijlmakers MJ, Teixeira JM, Boer R, ..., Pons M, Crosas B

Sci Rep 6 (-) 29232 [2016-07-14; online 2016-07-14]

Rosette-Disrupting Effect of an Anti-Plasmodial Compound for the Potential Treatment of Plasmodium falciparum Malaria Complications.

Ch'ng JH, Moll K, Quintana Mdel P, ..., Eriksson AB, Wahlgren M

Sci Rep 6 (-) 29317 [2016-07-11; online 2016-07-11]

Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci.

Miller CL, Pjanic M, Wang T, ..., Björkegren JL, Quertermous T

Nat Commun 7 (-) 12092 [2016-07-08; online 2016-07-08]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Dysregulated signaling hubs of liver lipid metabolism reveal hepatocellular carcinoma pathogenesis.

Lee S, Mardinoglu A, Zhang C, Lee D, Nielsen J

Nucleic Acids Res. 44 (12) 5529-5539 [2016-07-08; online 2016-05-25]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Profiling cancer testis antigens in non-small-cell lung cancer.

Djureinovic D, Hallström BM, Horie M, ..., Uhlén M, Micke P

JCI Insight 1 (10) e86837 [2016-07-07; online 2016-07-07]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]

Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies.

Rafati N, Andersson LS, Mikko S, ..., Lindgren G, Rubin CJ

G3 (Bethesda) 6 (7) 2213-2223 [2016-07-07; online 2016-07-07]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Exome sequencing in pooled DNA samples to identify maternal pre-eclampsia risk variants.

Kaartokallio T, Wang J, Heinonen S, ..., Kere J, Laivuori H

Sci Rep 6 (-) 29085 [2016-07-07; online 2016-07-07]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Diversity and Expression of Bacterial Metacaspases in an Aquatic Ecosystem.

Asplund-Samuelsson J, Sundh J, Dupont CL, ..., Ininbergs K, Ekman M

Front Microbiol 7 (-) 1043 [2016-07-06; online 2016-07-06]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Survival-associated heterogeneity of marker-defined perivascular cells in colorectal cancer.

Mezheyeuski A, Bradic Lindh M, Guren TK, ..., Sorbye H, Östman A

Oncotarget 7 (27) 41948-41958 [2016-07-05; online 2016-06-02]

Fluorescence Tissue Profiling [Collaborative] Tissue Profiling [Collaborative]

Pooled analysis of genome-wide association studies of cervical intraepithelial neoplasia 3 (CIN3) identifies a new susceptibility locus.

Chen D, Enroth S, Liu H, ..., Xu S, Gyllensten U

Oncotarget 7 (27) 42216-42224 [2016-07-05; online 2016-06-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc.

Jeong C, Ozga AT, Witonsky DB, ..., Di Rienzo A, Warinner C

Proc. Natl. Acad. Sci. U.S.A. 113 (27) 7485-7490 [2016-07-05; online 2016-06-20]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.

Ståhl PL, Salmén F, Vickovic S, ..., Lundeberg J, Frisén J

Science 353 (6294) 78-82 [2016-07-01; online 2016-07-02]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Fluorescence Tissue Profiling [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]

The epidermis coordinates auxin-induced stem growth in response to shade.

Procko C, Burko Y, Jaillais Y, ..., Long JA, Chory J

Genes Dev. 30 (13) 1529-1541 [2016-07-01; online 2016-07-13]

Genome-wide association study identifies multiple susceptibility loci for multiple myeloma.

Mitchell JS, Li N, Weinhold N, ..., Nilsson B, Houlston RS

Nat Commun 7 (-) 12050 [2016-07-01; online 2016-07-01]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Establishing a Proteomics-Based Monocyte Assay To Assess Differential Innate Immune Activation Responses.

Tarasova NK, Ytterberg AJ, Lundberg K, ..., Harris RA, Zubarev RA

J. Proteome Res. 15 (7) 2337-2345 [2016-07-01; online 2016-06-03]

Advanced Mass Spectrometry Proteomics [Collaborative] Chemical Proteomics [Technology development]

Dinosaur: A Refined Open-Source Peptide MS Feature Detector.

Teleman J, Chawade A, Sandin M, Levander F, Malmström J

J. Proteome Res. 15 (7) 2143-2151 [2016-07-01; online 2016-05-26]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Whole genome duplication in coast redwood (Sequoia sempervirens) and its implications for explaining the rarity of polyploidy in conifers.

Scott AD, Stenz NW, Ingvarsson PK, Baum DA

New Phytol. 211 (1) 186-193 [2016-07-00; online 2016-03-22]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens.

Wang J, Street NR, Scofield DG, Ingvarsson PK

Mol. Biol. Evol. 33 (7) 1754-1767 [2016-07-00; online 2016-03-18]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The role of germline alterations in the DNA damage response genes BRIP1 and BRCA2 in melanoma susceptibility.

Tuominen R, Engström PG, Helgadottir H, ..., Hansson J, Höiom V

Genes Chromosomes Cancer 55 (7) 601-611 [2016-07-00; online 2016-04-14]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The genetic landscape of paediatric de novo acute myeloid leukaemia as defined by single nucleotide polymorphism array and exon sequencing of 100 candidate genes.

Olsson L, Zettermark S, Biloglav A, ..., Paulsson K, Johansson B

Br. J. Haematol. 174 (2) 292-301 [2016-07-00; online 2016-03-31]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The Human Protein Atlas - an important resource for basic and clinical research.

Lindskog C

Expert Rev Proteomics 13 (7) 627-629 [2016-07-00; online 2016-06-22]

Super-resolution structured illumination fluorescence microscopy of the lateral wall of the cochlea: the Connexin26/30 proteins are separately expressed in man.

Liu W, Edin F, Blom H, ..., Laurell G, Rask-Andersen H

Cell Tissue Res. 365 (1) 13-27 [2016-07-00; online 2016-03-05]

Integrated Microscopy Technologies Stockholm [Collaborative]

Prevention of apoptosis averts glomerular tubular disconnection and podocyte loss in proteinuric kidney disease.

Burlaka I, Nilsson LM, Scott L, ..., Brismar H, Aperia A

Kidney Int. 90 (1) 135-148 [2016-07-00; online 2016-05-25]

Integrated Microscopy Technologies Stockholm [Collaborative]

Multi-platform metabolomics assays for human lung lavage fluids in an air pollution exposure study.

Surowiec I, Karimpour M, Gouveia-Figueira S, ..., Trygg J, Nording ML

Anal Bioanal Chem 408 (17) 4751-4764 [2016-07-00; online 2016-04-25]

Increasing the power of genome wide association studies in natural populations using repeated measures - evaluation and implementation.

Rönnegård L, McFarlane SE, Husby A, ..., Ellegren H, Qvarnström A

Methods Ecol Evol 7 (7) 792-799 [2016-07-00; online 2016-02-05]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Identification of Inhibitors of Pseudomonas aeruginosa Exotoxin-S ADP-Ribosyltransferase Activity.

Pinto AF, Ebrahimi M, Saleeb M, ..., Elofsson M, Schüler H

J Biomol Screen 21 (6) 590-595 [2016-07-00; online 2016-02-05]

Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells.

Hagey DW, Zaouter C, Combeau G, ..., Huss M, Muhr J

Genome Res. 26 (7) 908-917 [2016-07-00; online 2016-05-02]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Combined structural, biochemical and cellular evidence demonstrates that both FGDF motifs in alphavirus nsP3 are required for efficient replication.

Schulte T, Liu L, Panas MD, ..., Achour A, McInerney GM

Open Biol 6 (7) - [2016-07-00; online 2016-07-08]

An Integrative Genomic Analysis of Formalin Fixed Paraffin-Embedded Archived Serous Ovarian Carcinoma Comparing Long-term and Short-term Survivors.

Stålberg K, Crona J, Razmara M, ..., Skogseid B, Stålberg P

Int. J. Gynecol. Cancer 26 (6) 1027-1032 [2016-07-00; online 2016-05-14]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them.

Humble E, Martinez-Barrio A, Forcada J, ..., Wolf JB, Hoffman JI

Mol Ecol Resour 16 (4) 909-921 [2016-07-00; online 2015-12-20]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.

Körber I, Katayama S, Einarsdottir E, ..., Lehesjoki AE, Joensuu T

PLoS ONE 11 (6) e0158195 [2016-06-29; online 2016-06-29]

Bioinformatics and Expression Analysis (BEA) [Service]

Conserved 33-kb haplotype in the MHC class III region regulates chronic arthritis.

Yau AC, Tuncel J, Haag S, ..., Padyukov L, Holmdahl R

Proc. Natl. Acad. Sci. U.S.A. 113 (26) E3716-E3724 [2016-06-28; online 2016-06-16]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PRECOG: a tool for automated extraction and visualization of fitness components in microbial growth phenomics.

Fernandez-Ricaud L, Kourtchenko O, Zackrisson M, Warringer J, Blomberg A

BMC Bioinformatics 17 (-) 249 [2016-06-23; online 2016-06-23]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Genetic and environmental influences on height from infancy to early adulthood: An individual-based pooled analysis of 45 twin cohorts.

Jelenkovic A, Sund R, Hur YM, ..., Kaprio J, Silventoinen K

Sci Rep 6 (-) 28496 [2016-06-23; online 2016-06-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes.

Troell K, Hallström B, Divne AM, ..., Beser J, Bertilsson S

BMC Genomics 17 (-) 471 [2016-06-23; online 2016-06-23]

Bioinformatics Support for Computational Resources [Service] Microbial Single Cell Genomics [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The Aquaporin Splice Variant NbXIP1;1α Is Permeable to Boric Acid and Is Phosphorylated in the N-terminal Domain.

Ampah-Korsah H, Anderberg HI, Engfors A, ..., Kjellbom P, Johanson U

Front Plant Sci 7 (-) 862 [2016-06-16; online 2016-06-16]

Effects of Fluoxetine on Human Embryo Development.

Kaihola H, Yaldir FG, Hreinsson J, ..., Åkerud H, Sundström-Poromaa I

Front Cell Neurosci 10 (-) 160 [2016-06-16; online 2016-06-16]

Mass Spectrometry-based Proteomics, Uppsala [Collaborative]

Draft Genome Sequence of Moraxella catarrhalis Type Strain CCUG 353T.

Jakobsson HE, Salvà-Serra F, Thorell K, ..., Kristiansson E, Moore ERB

Genome Announc 4 (3) e00552-16 [2016-06-16; online 2016-06-16]

Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative] Clinical Genomics Stockholm [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Read-based phasing of related individuals.

Garg S, Martin M, Marschall T

Bioinformatics 32 (12) i234-i242 [2016-06-15; online 2016-06-17]

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Parental epigenetic asymmetry of PRC2-mediated histone modifications in the Arabidopsis endosperm.

Moreno-Romero J, Jiang H, Santos-González J, Köhler C

EMBO J. 35 (12) 1298-1311 [2016-06-15; online 2016-04-27]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Tumor acidosis enhances cytotoxic effects and autophagy inhibition by salinomycin on cancer cell lines and cancer stem cells.

Pellegrini P, Dyczynski M, Sbrana FV, ..., Kharaziha P, De Milito A

Oncotarget 7 (24) 35703-35723 [2016-06-14; online 2016-06-02]

Chemical Biology Consortium Sweden (CBCS) [Service]

Evolution and expression of the phosphodiesterase 6 genes unveils vertebrate novelty to control photosensitivity.

Lagman D, Franzén IE, Eggert J, Larhammar D, Abalo XM

BMC Evol. Biol. 16 (1) 124 [2016-06-13; online 2016-06-13]

Genome Engineering Zebrafish [Technology development]

Structural Analysis of a Complex between Small Ubiquitin-like Modifier 1 (SUMO1) and the ZZ Domain of CREB-binding Protein (CBP/p300) Reveals a New Interaction Surface on SUMO.

Diehl C, Akke M, Bekker-Jensen S, ..., Streicher W, Wikström M

J. Biol. Chem. 291 (24) 12658-12672 [2016-06-10; online 2016-04-25]

Regulation of Bone Morphogenetic Protein Signaling by ADP-ribosylation

Watanabe Y, Papoutsoglou P, Maturi V, ..., Heldin CH, Moustakas A

J. Biol. Chem. 291 (24) 12706-12723 [2016-06-10; online 2016-04-21]

Affinity Proteomics Uppsala [Service] PLA and Single Cell Proteomics [Service]

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system.

Marques S, Zeisel A, Codeluppi S, ..., Linnarsson S, Castelo-Branco G

Science 352 (6291) 1326-1329 [2016-06-10; online 2016-06-11]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Recommendations on e-infrastructures for next-generation sequencing.

Spjuth O, Bongcam-Rudloff E, Dahlberg J, ..., Vezzi F, Korpelainen E

Gigascience 5 (-) 26 [2016-06-07; online 2016-06-07]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

Identification of ETV6-RUNX1-like and DUX4-rearranged subtypes in paediatric B-cell precursor acute lymphoblastic leukaemia.

Lilljebjörn H, Henningsson R, Hyrenius-Wittsten A, ..., Fontes M, Fioretos T

Nat Commun 7 (-) 11790 [2016-06-06; online 2016-06-06]

Clinical Genomics [Collaborative] Clinical Genomics Lund [Collaborative]

Elevated levels of FN1 and CCL2 in bronchoalveolar lavage fluid from sarcoidosis patients.

Hamsten C, Wiklundh E, Grönlund H, ..., Grunewald J, Häggmark-Månberg A

Respir. Res. 17 (1) 69 [2016-06-04; online 2016-06-04]

Guidance Molecule SEMA3A Restricts Tumor Growth by Differentially Regulating the Proliferation of Tumor-Associated Macrophages.

Wallerius M, Wallmann T, Bartish M, ..., Andersson J, Rolny C

Cancer Res. 76 (11) 3166-3178 [2016-06-01; online 2016-04-06]

Aerobic exercise augments muscle transcriptome profile of resistance exercise.

Lundberg TR, Fernandez-Gonzalo R, Tesch PA, Rullman E, Gustafsson T

Am. J. Physiol. Regul. Integr. Comp. Physiol. 310 (11) R1279-R1287 [2016-06-01; online 2016-04-13]

Bioinformatics and Expression Analysis (BEA) [Service]

The oxidized phospholipid PazePC promotes permeabilization of mitochondrial membranes by Bax.

Lidman M, Pokorná Š, Dingeldein AP, ..., Hof M, Gröbner G

Biochim. Biophys. Acta 1858 (6) 1288-1297 [2016-06-00; online 2016-03-04]

Somatic, positive and negative domains of the Center for Epidemiological Studies Depression (CES-D) scale: a meta-analysis of genome-wide association studies.

Demirkan A, Lahti J, Direk N, ..., van Duijn CM, Räikkönen K

Psychol Med 46 (8) 1613-1623 [2016-06-00; online 2016-03-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Single Chain Antibodies as Tools to Study transforming growth factor-β-Regulated SMAD Proteins in Proximity Ligation-Based Pharmacological Screens.

Blokzijl A, Zieba A, Hust M, ..., Dübel S, Landegren U

Mol. Cell Proteomics 15 (6) 1848-1856 [2016-06-00; online 2016-03-02]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Scolytus multistriatus associated with Dutch elm disease on the island of Gotland: phenology and communities of vectored fungi

Menkis A, Östbrant IL, Davydenko K, ..., Balalaikins M, Vasaitis R

Mycol Progress 15 (6) - [2016-06-00; online 2016-05-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Mosaic Loss of Chromosome Y in Blood Is Associated with Alzheimer Disease

Dumanski JP, Lambert JC, Rasi C, ..., Lind L, Forsberg LA

The American Journal of Human Genetics 98 (6) 1208-1219 [2016-06-00; online 2016-06-00]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

High density of REC8 constrains sister chromatid axes and prevents illegitimate synaptonemal complex formation.

Agostinho A, Manneberg O, van Schendel R, ..., Brismar H, Höög C

EMBO Rep. 17 (6) 901-913 [2016-06-00; online 2016-05-14]

Integrated Microscopy Technologies Stockholm [Collaborative]

Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses.

Okbay A, Baselmans BM, De Neve JE, ..., Bartels M, Cesarini D

Nat. Genet. 48 (6) 624-633 [2016-06-00; online 2016-04-19]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic variants associated with antithyroid drug-induced agranulocytosis: a genome-wide association study in a European population.

Hallberg P, Eriksson N, Ibañez L, ..., Wadelius M, EuDAC collaborators

Lancet Diabetes Endocrinol 4 (6) 507-516 [2016-06-00; online 2016-05-10]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

GPR44 is a pancreatic protein restricted to the human beta cell.

Hellström-Lindahl E, Danielsson A, Ponten F, ..., Johansson L, Eriksson O

Acta Diabetol 53 (3) 413-421 [2016-06-00; online 2015-10-14]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]

Epigenomics of Total Acute Sleep Deprivation in Relation to Genome-Wide DNA Methylation Profiles and RNA Expression.

Nilsson EK, Boström AE, Mwinyi J, Schiöth HB

OMICS 20 (6) 334-342 [2016-06-00; online 2016-06-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Epigenome-wide DNA methylation patterns associated with fatigue in primary Sjögren's syndrome.

Brække Norheim K, Imgenberg-Kreuz J, Jonsdottir K, ..., Nordmark G, Omdal R

Rheumatology (Oxford) 55 (6) 1074-1082 [2016-06-00; online 2016-03-12]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Disruptive selection without genome-wide evolution across a migratory divide.

von Rönn JA, Shafer AB, Wolf JB

Mol. Ecol. 25 (11) 2529-2541 [2016-06-00; online 2016-01-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Detection of Biomarkers with Solid-Phase Proximity Ligation Assay in Patients with Colorectal Cancer

Ghanipour L, Darmanis S, Landegren U, ..., Påhlman L, Birgisson H

Transl Oncol 9 (3) 251-255 [2016-06-00; online 2016-06-00]

Affinity Proteomics Uppsala [Collaborative] PLA and Single Cell Proteomics [Collaborative] Tissue Profiling [Service]

Coxsackievirus counters the host innate immune response by blocking type III interferon expression.

Lind K, Svedin E, Domsgen E, ..., Moll M, Flodström-Tullberg M

J. Gen. Virol. 97 (6) 1-12 [2016-06-00; online 2016-03-02]

Common and Rare Genetic Variation in CCR2, CCR5, or CX3CR1 and Risk of Atherosclerotic Coronary Heart Disease and Glucometabolic Traits.

Golbus JR, Stitziel NO, Zhao W, ..., Reilly MP, CARDIoGRAMplusC4D, Myocardial Infarction Genetics (MIGen), Exome Sequencing Project and Early-Onset Myocardial Infarction (ESP EOMI), and the Pakistan Risk of Myocardial Infarction Study (PROMIS) Consortia*

Circ Cardiovasc Genet 9 (3) 250-258 [2016-06-00; online 2016-03-26]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Allele-specific transcription factor binding in liver and cervix cells unveils many likely drivers of GWAS signals.

Cavalli M, Pan G, Nord H, ..., Wallerman O, Wadelius C

Genomics 107 (6) 248-254 [2016-06-00; online 2016-04-30]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Variants within the SP110 nuclear body protein modify risk of canine degenerative myelopathy.

Ivansson EL, Megquier K, Kozyrev SV, ..., Coates JR, Lindblad-Toh K

Proc. Natl. Acad. Sci. U.S.A. 113 (22) E3091-E3100 [2016-05-31; online 2016-05-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The POU/Oct Transcription Factor Pdm1/nub Is Necessary for a Beneficial Gut Microbiota and Normal Lifespan of Drosophila.

Dantoft W, Lundin D, Esfahani SS, Engström Y

J Innate Immun 8 (4) 412-426 [2016-05-28; online 2016-05-28]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Thermotolerant yeasts selected by adaptive evolution express heat stress response at 30 °C.

Caspeta L, Chen Y, Nielsen J

Sci Rep 6 (-) 27003 [2016-05-27; online 2016-05-27]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Genome-wide association study identifies 74 loci associated with educational attainment.

Okbay A, Beauchamp JP, Fontana MA, ..., Cesarini D, Benjamin DJ

Nature 533 (7604) 539-542 [2016-05-26; online 2016-05-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Targeting Serglycin Prevents Metastasis in Murine Mammary Carcinoma.

Roy A, Femel J, Huijbers EJ, ..., Olsson AK, Åbrink M

PLoS ONE 11 (5) e0156151 [2016-05-25; online 2016-05-25]

Array and Analysis Facility [Service]

New technologies for DNA analysis--a review of the READNA Project.

McGinn S, Bauer D, Brefort T, ..., Willcocks JP, Gut IG

N Biotechnol 33 (3) 311-330 [2016-05-25; online 2015-10-26]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Glycosaminoglycan Profiling in Patients' Plasma and Urine Predicts the Occurrence of Metastatic Clear Cell Renal Cell Carcinoma.

Gatto F, Volpi N, Nilsson H, ..., Basso U, Nielsen J

Cell Rep 15 (8) 1822-1836 [2016-05-24; online 2016-05-18]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Chroman-4-one and chromone based somatostatin β-turn mimetics.

Fridén-Saxin M, Seifert T, Malo M, ..., Grøtli M, Luthman K

Eur J Med Chem 114 (-) 59-64 [2016-05-23; online 2016-02-21]

Metagenomic Analysis of the Indian Ocean Picocyanobacterial Community: Structure, Potential Function and Evolution.

Díez B, Nylander JA, Ininbergs K, ..., Rusch DB, Bergman B

PLoS ONE 11 (5) e0155757 [2016-05-19; online 2016-05-19]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A Population Shift between Sparsely Populated Folding Intermediates Determines Amyloidogenicity.

Karamanos TK, Pashley CL, Kalverda AP, ..., Orekhov VY, Radford SE

J. Am. Chem. Soc. 138 (19) 6271-6280 [2016-05-18; online 2016-05-06]

Pseudomonas aeruginosa elastase cleaves a C-terminal peptide from human thrombin that inhibits host inflammatory responses.

van der Plas MJ, Bhongir RK, Kjellström S, ..., Mörgelin M, Schmidtchen A

Nat Commun 7 (-) 11567 [2016-05-16; online 2016-05-16]

Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities.

Zha Y, Berga M, Comte J, Langenheder S

PLoS ONE 11 (5) e0155239 [2016-05-16; online 2016-05-16]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Multiplexed MALDI-MS arrays for screening of MIP solid phase extraction materials.

Jagadeesan KK, Wierzbicka C, Laurell T, ..., Shinde S, Ekström S

Journal of Chromatography B 1021 (-) 213-220 [2016-05-15; online 2015-10-30]

Minimal selective concentrations of tetracycline in complex aquatic bacterial biofilms.

Lundström SV, Östman M, Bengtsson-Palme J, ..., Flach CF, Larsson DG

Sci. Total Environ. 553 (-) 587-595 [2016-05-15; online 2016-03-05]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Microwell-Based Live Cell Imaging of NK Cell Dynamics to Assess Heterogeneity in Motility and Cytotoxic Response.

Vanherberghen B, Frisk T, Forslund E, ..., Guldevall K, Önfelt B

Methods Mol. Biol. 1441 (-) 87-106 [2016-05-15; online 2016-05-15]

Integrated Microscopy Technologies Stockholm [Technology development]

Inclusion of dyad-repeat pattern improves topology prediction of transmembrane β-barrel proteins.

Hayat S, Peters C, Shu N, Tsirigos KD, Elofsson A

Bioinformatics 32 (10) 1571-1573 [2016-05-15; online 2016-01-23]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)

Nilsson RH, Alm Rosenblad M, Martín MP, ..., Wurzbacher C, Abarenkov K

MycoKeys 13 (-) 21-33 [2016-05-13; online 2016-05-13]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

A combined computational and structural model of the full-length human prolactin receptor.

Bugge K, Papaleo E, Haxholm GW, ..., Lindorff-Larsen K, Kragelund BB

Nat Commun 7 (-) 11578 [2016-05-13; online 2016-05-13]

Diversity of Pico- to Mesoplankton along the 2000 km Salinity Gradient of the Baltic Sea.

Hu YO, Karlson B, Charvet S, Andersson AF

Front Microbiol 7 (-) 679 [2016-05-12; online 2016-05-12]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Inflammatory Serum Protein Profiling of Patients with Lumbar Radicular Pain One Year after Disc Herniation.

Moen A, Lind AL, Thulin M, ..., Gjerstad J, Gordh T

Int J Inflam 2016 (-) 3874964 [2016-05-11; online 2016-05-11]

Affinity Proteomics Uppsala [Collaborative] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Collaborative]

Divergent non-heme iron enzymes in the nogalamycin biosynthetic pathway.

Siitonen V, Selvaraj B, Niiranen L, ..., Schneider G, Metsä-Ketelä M

Proc. Natl. Acad. Sci. U.S.A. 113 (19) 5251-5256 [2016-05-10; online 2016-04-25]

Determining breast cancer histological grade from RNA-sequencing data.

Wang M, Klevebring D, Lindberg J, ..., Grönberg H, Rantalainen M

Breast Cancer Res. 18 (1) 48 [2016-05-10; online 2016-05-10]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Unscrambling Cyanobacteria Community Dynamics Related to Environmental Factors.

Bertos-Fortis M, Farnelid HM, Lindh MV, ..., Pinhassi J, Legrand C

Front Microbiol 7 (-) 625 [2016-05-09; online 2016-05-09]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Asp-ase Activity of the Opossum Granzyme B Supports the Role of Granzyme B as Part of Anti-Viral Immunity Already during Early Mammalian Evolution.

Fu Z, Thorpe M, Akula S, Hellman L

PLoS ONE 11 (5) e0154886 [2016-05-06; online 2016-05-06]

Mass Spectrometry-based Proteomics, Uppsala [Service]

The Effects of High Steady State Auxin Levels on Root Cell Elongation in Brachypodium.

Pacheco-Villalobos D, Díaz-Moreno SM, van der Schuren A, ..., Bulone V, Hardtke CS

Plant Cell - (-) - [2016-05-05; online 2016-05-05]

Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth.

Pečnerová P, Díez-Del-Molino D, Vartanyan S, Dalén L

Sci Rep 6 (-) 25274 [2016-05-04; online 2016-05-04]

Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.

Martinez Barrio A, Lamichhaney S, Fan G, ..., Xu X, Andersson L

Elife 5 (-) - [2016-05-03; online 2016-05-03]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Sister Chromatid Cohesion Establishment Factor ESCO1 Operates by Substrate-Assisted Catalysis.

Kouznetsova E, Kanno T, Karlberg T, ..., Sjögren C, Schüler H

Structure 24 (5) 789-796 [2016-05-03; online 2016-04-21]

Schizophrenia and subsequent neighborhood deprivation: revisiting the social drift hypothesis using population, twin and molecular genetic data.

Sariaslan A, Fazel S, D'Onofrio BM, ..., Kuja-Halkola R, Lichtenstein P

Transl Psychiatry 6 (-) e796 [2016-05-03; online 2016-05-03]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Epigenetic silencing of miR-26A1 in chronic lymphocytic leukemia and mantle cell lymphoma: Impact on EZH2 expression.

Kopparapu PK, Bhoi S, Mansouri L, ..., Rosenquist R, Kanduri M

Epigenetics 11 (5) 335-343 [2016-05-03; online 2016-04-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

mRNA GPR162 changes are associated with decreased food intake in rat, and its human genetic variants with impairments in glucose homeostasis in two Swedish cohorts.

Caruso V, Sreedharan S, Carlini VP, ..., Fredriksson R, Schiöth HB

Gene 581 (2) 139-145 [2016-05-01; online 2016-02-02]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

High-Density Genetic Mapping Identifies New Susceptibility Variants in Sarcoidosis Phenotypes and Shows Genomic-driven Phenotypic Differences.

Rivera NV, Ronninger M, Shchetynsky K, ..., Padyukov L, Grunewald J

Am. J. Respir. Crit. Care Med. 193 (9) 1008-1022 [2016-05-01; online 2015-12-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Evidence for Genetic Overlap Between Schizophrenia and Age at First Birth in Women.

Mehta D, Tropf FC, Gratten J, ..., Weiser M, Wu JQ

JAMA Psychiatry 73 (5) 497-505 [2016-05-01; online 2016-03-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

nanoCAGE reveals 5' UTR features that define specific modes of translation of functionally related MTOR-sensitive mRNAs.

Gandin V, Masvidal L, Hulea L, ..., Larsson O, Topisirovic I

Genome Res. 26 (5) 636-648 [2016-05-00; online 2016-03-18]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Whole-genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations.

Kardos M, Husby A, McFarlane SE, Qvarnström A, Ellegren H

Mol Ecol Resour 16 (3) 727-741 [2016-05-00; online 2015-12-10]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development-Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus.

Truvé K, Dickinson P, Xiong A, ..., Bannasch D, Lindblad-Toh K

PLoS Genet. 12 (5) e1006000 [2016-05-00; online 2016-05-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Synchronous genetic turnovers across Western Eurasia in Late Pleistocene collared lemmings.

Palkopoulou E, Baca M, Abramson NI, ..., Stankovic A, Dalén L

Glob Chang Biol 22 (5) 1710-1721 [2016-05-00; online 2016-02-27]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Regulating retrotransposon activity through the use of alternative transcription start sites.

Persson J, Steglich B, Smialowska A, ..., Nielsen O, Ekwall K

EMBO Rep. 17 (5) 753-768 [2016-05-00; online 2016-02-22]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Bioinformatics and Expression Analysis (BEA) [Service]

Reduced mitochondrial malate dehydrogenase activity has a strong effect on photorespiratory metabolism as revealed by 13C labelling.

Lindén P, Keech O, Stenlund H, Gardeström P, Moritz T

J. Exp. Bot. 67 (10) 3123-3135 [2016-05-00; online 2016-02-19]

Molecular Characterization of Three Canine Models of Human Rare Bone Diseases: Caffey, van den Ende-Gupta, and Raine Syndromes.

Hytönen MK, Arumilli M, Lappalainen AK, ..., Drögemüller C, Lohi H

PLoS Genet. 12 (5) e1006037 [2016-05-00; online 2016-05-17]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.

Wu X, Holmfeldt K, Hubalek V, ..., Bertilsson S, Dopson M

ISME J 10 (5) 1192-1203 [2016-05-00; online 2015-10-21]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Metabolomics study of fatigue in patients with rheumatoid arthritis naïve to biological treatment.

Surowiec I, Gjesdal CG, Jonsson G, ..., Trygg J, Omdal R

Rheumatol. Int. 36 (5) 703-711 [2016-05-00; online 2016-01-25]

High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree.

Smeds L, Mugal CF, Qvarnström A, Ellegren H

PLoS Genet. 12 (5) e1006044 [2016-05-00; online 2016-05-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic risk variants in the CDKN2A/B, RTEL1 and EGFR genes are associated with somatic biomarkers in glioma.

Ghasimi S, Wibom C, Dahlin AM, ..., Andersson U, Melin B

J. Neurooncol. 127 (3) 483-492 [2016-05-00; online 2016-02-04]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic loci on chromosome 5 are associated with circulating levels of interleukin-5 and eosinophil count in a European population with high risk for cardiovascular disease.

McLeod O, Silveira A, Valdes-Marquez E, ..., Strawbridge RJ, IMPROVE Study Group

Cytokine 81 (-) 1-9 [2016-05-00; online 2016-01-29]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Functionalized silk assembled from a recombinant spider silk fusion protein (Z-4RepCT) produced in the methylotrophic yeast Pichia pastoris.

Jansson R, Lau CH, Ishida T, ..., Sandgren M, Hedhammar M

Biotechnol J 11 (5) 687-699 [2016-05-00; online 2016-03-04]

Mass Spectrometry-based Proteomics, Uppsala [Collaborative]

Divergence in gene expression within and between two closely related flycatcher species.

Uebbing S, Künstner A, Mäkinen H, ..., Searle SM, Ellegren H

Mol. Ecol. 25 (9) 2015-2028 [2016-05-00; online 2016-03-02]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Distinct temporal changes in host cell lncRNA expression during the course of an adenovirus infection.

Zhao H, Chen M, Lind SB, Pettersson U

Virology 492 (-) 242-250 [2016-05-00; online 2016-03-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Displacement of US-1 clonal lineage by a new lineage ofPhytophthora infestanson potato in Kenya and Uganda

Njoroge AW, Tusiime G, Forbes GA, Yuen JE

Plant Pathol 65 (4) 587-592 [2016-05-00; online 2015-09-16]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Details in the catalytic mechanism of mammalian thioredoxin reductase 1 revealed using point mutations and juglone-coupled enzyme activities.

Xu J, Cheng Q, Arnér ES

Free Radic. Biol. Med. 94 (-) 110-120 [2016-05-00; online 2016-02-17]

Mass Spectrometry-based Proteomics, Uppsala [Service]

DNA-metabarcoding uncovers the diversity of soil-inhabiting fungi in the tropical island of Puerto Rico

Urbina H, Scofield DG, Cafaro M, Rosling A

Mycoscience 57 (3) 217-227 [2016-05-00; online 2016-05-00]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Biotin and Thiamine Responsive Basal Ganglia Disease--A vital differential diagnosis in infants with severe encephalopathy.

Ygberg S, Naess K, Eriksson M, ..., Wedell A, Wickström R

Eur. J. Paediatr. Neurol. 20 (3) 457-461 [2016-05-00; online 2016-03-16]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Association mapping in Salix viminalis L. (Salicaceae) - identification of candidate genes associated with growth and phenology.

Hallingbäck HR, Fogelqvist J, Powers SJ, ..., Berlin S, Rönnberg-Wästljung AC

Glob Change Biol Bioenergy 8 (3) 670-685 [2016-05-00; online 2015-07-29]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Antigen arrays for profiling autoantibody repertoires.

Ayoglu B, Schwenk JM, Nilsson P

Bioanalysis 8 (10) 1105-1126 [2016-05-00; online 2016-04-22]

Autoimmunity and Serology Profiling [Technology development]

An obesity-associated risk allele within the FTO gene affects human brain activity for areas important for emotion, impulse control and reward in response to food images.

Wiemerslage L, Nilsson EK, Solstrand Dahlberg L, ..., Brooks SJ, Schiöth HB

Eur. J. Neurosci. 43 (9) 1173-1180 [2016-05-00; online 2016-01-23]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression.

Cavalli M, Pan G, Nord H, ..., Lindblad Toh K, Wadelius C

Hum. Genet. 135 (5) 485-497 [2016-05-00; online 2016-03-20]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A Systematic Characterization of Aquaporin-9 Expression in Human Normal and Pathological Tissues.

Lindskog C, Asplund A, Catrina A, Nielsen S, Rützler M

J. Histochem. Cytochem. 64 (5) 287-300 [2016-05-00; online 2016-03-29]

TOR Signaling and Nutrient Sensing.

Dobrenel T, Caldana C, Hanson J, ..., Veit B, Meyer C

Annu Rev Plant Biol 67 (-) 261-285 [2016-04-29; online 2016-02-26]

The Bee Microbiome: Impact on Bee Health and Model for Evolution and Ecology of Host-Microbe Interactions.

Engel P, Kwong WK, McFrederick Q, ..., vanEngelsdorp D, Dainat B

MBio 7 (2) e02164-e02115 [2016-04-26; online 2016-04-26]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Elevated Levels of SOX10 in Serum from Vitiligo and Melanoma Patients, Analyzed by Proximity Ligation Assay

Blokzijl A, Chen LE, Gustafsdottir SM, ..., Kamali-Moghaddam M, Hedstrand H

PLoS ONE 11 (4) e0154214 [2016-04-25; online 2016-04-25]

Affinity Proteomics Uppsala [Collaborative] PLA and Single Cell Proteomics [Collaborative]

Longitudinal genome-wide methylation study of Roux-en-Y gastric bypass patients reveals novel CpG sites associated with essential hypertension.

Boström AE, Mwinyi J, Voisin S, ..., Zhang K, Schiöth HB

BMC Med Genomics 9 (-) 20 [2016-04-22; online 2016-04-22]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A beak size locus in Darwin's finches facilitated character displacement during a drought.

Lamichhaney S, Han F, Berglund J, ..., Grant PR, Andersson L

Science 352 (6284) 470-474 [2016-04-22; online 2016-04-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Spatio-Temporal Interdependence of Bacteria and Phytoplankton during a Baltic Sea Spring Bloom.

Bunse C, Bertos-Fortis M, Sassenhagen I, ..., Pinhassi J, Legrand C

Front Microbiol 7 (-) 517 [2016-04-21; online 2016-04-21]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Associations between a locus downstream DRD1 gene and cerebrospinal fluid dopamine metabolite concentrations in psychosis.

Andreou D, Söderman E, Axelsson T, ..., Agartz I, Jönsson EG

Neurosci. Lett. 619 (-) 126-130 [2016-04-21; online 2016-03-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Hypoxia regulates global membrane protein endocytosis through caveolin-1 in cancer cells.

Bourseau-Guilmain E, Menard JA, Lindqvist E, ..., Welinder C, Belting M

Nat Commun 7 (-) 11371 [2016-04-20; online 2016-04-20]

msIQuant--Quantitation Software for Mass Spectrometry Imaging Enabling Fast Access, Visualization, and Analysis of Large Data Sets.

Källback P, Nilsson A, Shariatgorji M, Andrén PE

Anal. Chem. 88 (8) 4346-4353 [2016-04-19; online 2016-04-05]

Mutations in histone modulators are associated with prolonged survival during azacitidine therapy.

Tobiasson M, McLornan DP, Karimi M, ..., Mufti GJ, Hellström-Lindberg E

Oncotarget 7 (16) 22103-22115 [2016-04-19; online 2016-03-10]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

EPH/ephrin profile and EPHB2 expression predicts patient survival in breast cancer.

Husa AM, Magić Ž, Larsson M, Fornander T, Pérez-Tenorio G

Oncotarget 7 (16) 21362-21380 [2016-04-19; online 2016-02-13]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Improved topology prediction using the terminal hydrophobic helices rule.

Peters C, Tsirigos KD, Shu N, Elofsson A

Bioinformatics 32 (8) 1158-1162 [2016-04-15; online 2015-12-09]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Cytosolic splice isoform of Hsp70 nucleotide exchange factor Fes1 is required for the degradation of misfolded proteins in yeast.

Gowda NK, Kaimal JM, Masser AE, ..., Friedländer MR, Andréasson C

Mol. Biol. Cell 27 (8) 1210-1219 [2016-04-15; online 2016-02-26]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A role for PDGF-C/PDGFRα signaling in the formation of the meningeal basement membranes surrounding the cerebral cortex.

Andrae J, Gouveia L, Gallini R, ..., Eriksson U, Betsholtz C

Biol Open 5 (4) 461-474 [2016-04-15; online 2016-04-15]

Bioinformatics and Expression Analysis (BEA) [Service]

Using an Inbred Horse Breed in a High Density Genome-Wide Scan for Genetic Risk Factors of Insect Bite Hypersensitivity (IBH).

Velie BD, Shrestha M, Franҫois L, ..., Buys N, Lindgren G

PLoS ONE 11 (4) e0152966 [2016-04-12; online 2016-04-12]

Array and Analysis Facility [Service]

Immunostimulatory AdCD40L gene therapy combined with low-dose cyclophosphamide in metastatic melanoma patients.

Loskog A, Maleka A, Mangsbo S, ..., Tötterman TH, Ullenhag G

Br. J. Cancer 114 (8) 872-880 [2016-04-12; online 2016-03-31]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Tissue and Serum miRNA Profile in Locally Advanced Breast Cancer (LABC) in Response to Neo-Adjuvant Chemotherapy (NAC) Treatment.

Al-Khanbashi M, Caramuta S, Alajmi AM, ..., Lui WO, Al-Moundhri MS

PLoS ONE 11 (4) e0152032 [2016-04-11; online 2016-04-11]

Bioinformatics and Expression Analysis (BEA) [Service]

The Mycobacterium phlei Genome: Expectations and Surprises.

Das S, Pettersson BM, Behra PR, ..., Bhattacharya A, Kirsebom LA

Genome Biol Evol 8 (4) 975-985 [2016-04-08; online 2016-03-05]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Identification and Characterization of IgdE, a Novel IgG-degrading Protease of Streptococcus suis with Unique Specificity for Porcine IgG.

Spoerry C, Seele J, Valentin-Weigand P, Baums CG, von Pawel-Rammingen U

J. Biol. Chem. 291 (15) 7915-7925 [2016-04-08; online 2016-02-11]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Modifications of the 7-Hydroxyl Group of the Transthyretin Ligand Luteolin Provide Mechanistic Insights into Its Binding Properties and High Plasma Specificity.

Nilsson L, Larsson A, Begum A, ..., Sauer-Eriksson AE, Olofsson A

PLoS ONE 11 (4) e0153112 [2016-04-06; online 2016-04-06]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Microchip Screening Platform for Single Cell Assessment of NK Cell Cytotoxicity.

Guldevall K, Brandt L, Forslund E, ..., Uhlin M, Önfelt B

Front Immunol 7 (-) 119 [2016-04-05; online 2016-04-05]

Integrated Microscopy Technologies Stockholm [Technology development]

Markers of fibroblast-rich tumor stroma and perivascular cells in serous ovarian cancer: Inter- and intra-patient heterogeneity and impact on survival.

Corvigno S, Wisman GB, Mezheyeuski A, ..., Östman A, Dahlstrand H

Oncotarget 7 (14) 18573-18584 [2016-04-05; online 2016-02-27]

Transcriptomics resources of human tissues and organs.

Uhlén M, Hallström BM, Lindskog C, ..., Pontén F, Nielsen J

Mol. Syst. Biol. 12 (4) 862 [2016-04-04; online 2016-04-04]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Technology development] Tissue Profiling [Collaborative]

Label-Free Fluctuation Spectroscopy Based on Coherent Anti-Stokes Raman Scattering from Bulk Water Molecules.

Rabasovic MD, Sisamakis E, Wennmalm S, Widengren J

Chemphyschem 17 (7) 1025-1033 [2016-04-04; online 2016-01-29]

Fluorescence Correlation Spectroscopy [Technology development] Integrated Microscopy Technologies Stockholm

Structural Studies of Lipopolysaccharide-defective Mutants from Brucella melitensis Identify a Core Oligosaccharide Critical in Virulence.

Fontana C, Conde-Álvarez R, Ståhle J, ..., Moriyón I, Widmalm G

J. Biol. Chem. 291 (14) 7727-7741 [2016-04-01; online 2016-02-11]

Sex-dependent expression of anti-Müllerian hormone (amh) and amh receptor 2 during sex organ differentiation and characterization of the Müllerian duct development in Xenopus tropicalis.

Jansson E, Mattsson A, Goldstone J, Berg C

Gen. Comp. Endocrinol. 229 (-) 132-144 [2016-04-01; online 2016-03-19]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Na+-K+-ATPase, a new class of plasma membrane receptors.

Aperia A, Akkuratov EE, Fontana JM, Brismar H

Am. J. Physiol., Cell Physiol. 310 (7) C491-C495 [2016-04-01; online 2016-01-23]

Integrated Microscopy Technologies Stockholm [Collaborative]

Genome-wide association and Mendelian randomization study of NT-proBNP in patients with acute coronary syndrome.

Johansson Å, Eriksson N, Lindholm D, ..., Wallentin L, PLATO Investigators

Hum. Mol. Genet. 25 (7) 1447-1456 [2016-04-01; online 2016-02-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array.

Marzouka NA, Nordlund J, Bäcklin CL, ..., Syvänen AC, Carlsson Almlöf J

Bioinformatics 32 (7) 1080-1082 [2016-04-01; online 2015-11-09]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]

Whole-body fat oxidation increases more by prior exercise than overnight fasting in elite endurance athletes.

Andersson Hall U, Edin F, Pedersen A, Madsen K

Appl Physiol Nutr Metab 41 (4) 430-437 [2016-04-00; online 2015-12-17]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Swedish NMR Centre (SNC) [Collaborative]

Solution structure of the calmodulin-like C-terminal domain of Entamoeba α-actinin2.

Karlsson G, Persson C, Mayzel M, Hedenström M, Backman L

Proteins 84 (4) 461-466 [2016-04-00; online 2016-02-05]

Single-cell transcriptome analysis of endometrial tissue.

Krjutškov K, Katayama S, Saare M, ..., Salumets A, Kere J

Hum. Reprod. 31 (4) 844-853 [2016-04-00; online 2016-02-13]

Bioinformatics and Expression Analysis (BEA) [Service]

Replacement of the European wheat yellow rust population by new races from the centre of diversity in the near-Himalayan region

Hovmøller MS, Walter S, Bayles RA, ..., Ali S, de Vallavieille-Pope C

Plant Pathol 65 (3) 402-411 [2016-04-00; online 2015-07-20]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Reduced oxidative stress in primary human cells by antioxidant released from nanoporous alumina.

Pujari-Palmer S, Pujari-Palmer M, Karlsson Ott M

J. Biomed. Mater. Res. Part B Appl. Biomater. 104 (3) 568-575 [2016-04-00; online 2015-05-09]

RNA transcript sequencing reveals inorganic sulfur compound oxidation pathways in the acidophile Acidithiobacillus ferrivorans.

Christel S, Fridlund J, Buetti-Dinh A, ..., Watkin EL, Dopson M

FEMS Microbiol. Lett. 363 (7) - [2016-04-00; online 2016-03-10]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PGC-1α Coordinates Mitochondrial Respiratory Capacity and Muscular Fatty Acid Uptake via Regulation of VEGF-B.

Mehlem A, Palombo I, Wang X, ..., Eriksson U, Falkevall A

Diabetes 65 (4) 861-873 [2016-04-00; online 2016-01-30]

One CNV Discordance in NRXN1 Observed Upon Genome-wide Screening in 38 Pairs of Adult Healthy Monozygotic Twins.

Magnusson PK, Lee D, Chen X, ..., Feuk L, Pawitan Y

Twin Res Hum Genet 19 (2) 97-103 [2016-04-00; online 2016-02-22]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Novel technologies applied to the nucleotide sequencing and comparative sequence analysis of the genomes of infectious agents in veterinary medicine.

Granberg F, Bálint Á, Belák S

Rev. - Off. Int. Epizoot. 35 (1) 25-42 [2016-04-00; online 2016-05-25]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Novel mode of inhibition by D-tagatose 6-phosphate through a Heyns rearrangement in the active site of transaldolase B variants.

Stellmacher L, Sandalova T, Schneider S, ..., Sprenger GA, Samland AK

Acta Crystallogr D Struct Biol 72 (Pt 4) 467-476 [2016-04-00; online 2016-03-24]

Neuroproteomic profiling of human body fluids.

Häggmark A, Schwenk JM, Nilsson P

Proteomics Clin Appl 10 (4) 485-502 [2016-04-00; online 2015-10-12]

Autoimmunity and Serology Profiling [Technology development]

Multiplexed protein profiling by sequential affinity capture.

Ayoglu B, Birgersson E, Mezger A, ..., Nilsson P, Schwenk JM

Proteomics 16 (8) 1251-1256 [2016-04-00; online 2016-03-31]

Affinity Proteomics Stockholm [Technology development]

Multi-platform mass spectrometry analysis of the CSF and plasma metabolomes of rigorously matched amyotrophic lateral sclerosis, Parkinson's disease and control subjects.

Wuolikainen A, Jonsson P, Ahnlund M, ..., Andersen PM, Trupp M

Mol Biosyst 12 (4) 1287-1298 [2016-04-00; online 2016-02-18]

Identification of Drug-Like Inhibitors of Insulin-Regulated Aminopeptidase Through Small-Molecule Screening.

Engen K, Rosenström U, Axelsson H, ..., Lundbäck T, Larhed M

Assay Drug Dev Technol 14 (3) 180-193 [2016-04-00; online 2016-04-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Service]

High-Throughput Screening Using a Whole-Cell Virus Replication Reporter Gene Assay to Identify Inhibitory Compounds against Rift Valley Fever Virus Infection.

Islam MK, Baudin M, Eriksson J, ..., Ahlm C, Evander M

J Biomol Screen 21 (4) 354-362 [2016-04-00; online 2016-01-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Global gray-level thresholding based on object size.

Ranefall P, Wählby C

Cytometry A 89 (4) 385-390 [2016-04-00; online 2016-01-23]

BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

Global genome splicing analysis reveals an increased number of alternatively spliced genes with aging.

Rodríguez SA, Grochová D, McKenna T, ..., Erdos MR, Eriksson M

Aging Cell 15 (2) 267-278 [2016-04-00; online 2015-12-22]

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Gene regulatory mechanisms underpinning prostate cancer susceptibility.

Whitington T, Gao P, Song W, ..., Wei GH, Wiklund F

Nat. Genet. 48 (4) 387-397 [2016-04-00; online 2016-03-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Fish from Head to Tail: The 9th European Zebrafish Meeting in Oslo.

Griffiths G, Müller F, Ledin J, ..., Press CM, Aleström P

Zebrafish 13 (2) 132-137 [2016-04-00; online 2016-02-09]

Genome Engineering Zebrafish [Collaborative]

Fatal acquisition of vanD gene during vancomycin treatment of septicaemia caused by Enterococcus faecium.

Starlander G, Tellgren-Roth C, Melhus Å

J. Hosp. Infect. 92 (4) 409-410 [2016-04-00; online 2016-02-16]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Engineering a thermostable Halothermothrix orenii β-glucosidase for improved galacto-oligosaccharide synthesis.

Hassan N, Geiger B, Gandini R, ..., Divne C, Tan TC

Appl. Microbiol. Biotechnol. 100 (8) 3533-3543 [2016-04-00; online 2015-12-02]

Effect of PTPN22 Gene Variant R620W on Type I Interferon Production Stimulated by Different Toll-like Receptor 7 Agonists: Comment on the Article by Wang et al.

Berggren O, Rönnblom L, Eloranta ML

Arthritis & rheumatology (Hoboken, N.J.) 68 (4) 1045 [2016-04-00; online 2016-01-11]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Digital image analysis outperforms manual biomarker assessment in breast cancer.

Stålhammar G, Fuentes Martinez N, Lippert M, ..., Grunkin M, Hartman J

Mod. Pathol. 29 (4) 318-329 [2016-04-00; online 2016-02-27]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

DeMix-Q: Quantification-Centered Data Processing Workflow.

Zhang B, Käll L, Zubarev RA

Mol. Cell Proteomics 15 (4) 1467-1478 [2016-04-00; online 2016-01-04]

Connective Auxin Transport in the Shoot Facilitates Communication between Shoot Apices.

Bennett T, Hines G, van Rongen M, ..., Ljung K, Leyser O

PLoS Biol. 14 (4) e1002446 [2016-04-00; online 2016-04-27]

Binding to and Inhibition of Insulin-Regulated Aminopeptidase by Macrocyclic Disulfides Enhances Spine Density.

Diwakarla S, Nylander E, Grönbladh A, ..., Chai SY, Hallberg M

Mol. Pharmacol. 89 (4) 413-424 [2016-04-00; online 2016-01-16]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

An Ouzo emulsion of toluene in water characterized by NMR diffusometry and static multiple light scattering

Tehrani-Bagha AR, Viladot A, Holmberg K, Nordstierna L

Colloids and Surfaces A: Physicochemical and Engineering Aspects 494 (-) 81-86 [2016-04-00; online 2016-04-00]

Adaptive major histocompatibility complex (MHC) and neutral genetic variation in two native Baltic Sea fishes (perch Perca fluviatilis and zander Sander lucioperca) with comparisons to an introduced and disease susceptible population in Australia (P. fluviatilis): assessing the risk of disease epidemics.

Faulks LK, Östman Ö

J. Fish Biol. 88 (4) 1564-1583 [2016-04-00; online 2016-03-05]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A saposin-lipoprotein nanoparticle system for membrane proteins.

Frauenfeld J, Löving R, Armache JP, ..., Cheng Y, Nordlund P

Nat. Methods 13 (4) 345-351 [2016-04-00; online 2016-03-07]

Super-resolution microscopy reveals γ-secretase at both sides of the neuronal synapse.

Schedin-Weiss S, Caesar I, Winblad B, Blom H, Tjernberg LO

Acta Neuropathol Commun 4 (-) 29 [2016-03-31; online 2016-03-31]

Integrated Microscopy Technologies Stockholm [Collaborative]

A Facile Synthesis of NODASA-Functionalized Peptide

Naicker T, Albericio F, Dutta J, ..., Kruger H, Govender T

Synlett 27 (11) 1685-1688 [2016-03-30; online 2016-03-30]

Drug Discovery and Development (DDD) [Collaborative]

Pseudomonas aeruginosa N-3-oxo-dodecanoyl-homoserine Lactone Elicits Changes in Cell Volume, Morphology, and AQP9 Characteristics in Macrophages

Holm A, Magnusson KE, Vikström E

Front. Cell. Infect. Microbiol. 6 (-) - [2016-03-24; online 2016-03-24]

Integrated Microscopy Technologies Stockholm [Service]

Draft Genome Sequence of Streptococcus gordonii Type Strain CCUG 33482T.

Salvà-Serra F, Jakobsson HE, Thorell K, ..., Kristiansson E, Moore ER

Genome Announc 4 (2) e00175-16 [2016-03-24; online 2016-03-24]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Gothenburg [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

CETSA screening identifies known and novel thymidylate synthase inhibitors and slow intracellular activation of 5-fluorouracil.

Almqvist H, Axelsson H, Jafari R, ..., Lundbäck T, Nordlund P

Nat Commun 7 (-) 11040 [2016-03-24; online 2016-03-24]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF) [Service]

VEGFR2 pY949 signalling regulates adherens junction integrity and metastatic spread.

Li X, Padhan N, Sjöström EO, ..., Jansson L, Claesson-Welsh L

Nat Commun 7 (-) 11017 [2016-03-23; online 2016-03-23]

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The chemosensory receptors of codling moth Cydia pomonella-expression in larvae and adults.

Walker WB, Gonzalez F, Garczynski SF, Witzgall P

Sci Rep 6 (-) 23518 [2016-03-23; online 2016-03-23]

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System-wide Clinical Proteomics of Breast Cancer Reveals Global Remodeling of Tissue Homeostasis.

Pozniak Y, Balint-Lahat N, Rudolph JD, ..., Barshack I, Geiger T

Cell Syst 2 (3) 172-184 [2016-03-23; online 2016-03-03]

Metagenomic analysis of bloodstream infections in patients with acute leukemia and therapy-induced neutropenia.

Gyarmati P, Kjellander C, Aust C, ..., Öhrmalm L, Giske CG

Sci Rep 6 (-) 23532 [2016-03-21; online 2016-03-21]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Local auxin metabolism regulates environment-induced hypocotyl elongation

Zheng Z, Guo Y, Novák O, ..., Noel JP, Chory J

NPLANTS 2 (4) 16025 [2016-03-21; online 2016-03-21]

On-Water Synthesis of Biaryl Sulfonyl Fluorides.

Chinthakindi PK, Kruger HG, Govender T, Naicker T, Arvidsson PI

J. Org. Chem. 81 (6) 2618-2623 [2016-03-18; online 2016-02-24]

Drug Discovery and Development (DDD) [Collaborative]

PopulationProfiler: A Tool for Population Analysis and Visualization of Image-Based Cell Screening Data.

Matuszewski DJ, Wählby C, Puigvert JC, Sintorn IM

PLoS ONE 11 (3) e0151554 [2016-03-17; online 2016-03-17]

BioImage Informatics [Service] Bioinformatics (NBIS) [Service]

Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave, Northern Sweden.

Zepeda Mendoza ML, Lundberg J, Ivarsson M, ..., Sallstedt T, Dalen L

PLoS ONE 11 (3) e0151577 [2016-03-17; online 2016-03-17]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

In Situ Staining and Laser Capture Microdissection of Lymph Node Residing SIV Gag-Specific CD8+ T cells--A Tool to Interrogate a Functional Immune Response Ex Vivo.

Tjernlund A, Burgener A, Lindvall JM, ..., McElrath MJ, Corey L

PLoS ONE 11 (3) e0149907 [2016-03-17; online 2016-03-17]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

The role of transposable elements for gene expression in Capsella hybrids and allopolyploids

Steige K, Reimegård J, Rebernig CA, ..., Scofield DG, Slotte T

bioRxiv - (-) - [2016-03-16; online 2016-03-16]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

The Intestinal Eukaryotic Virome in Healthy and Diarrhoeic Neonatal Piglets.

Karlsson OE, Larsson J, Hayer J, Berg M, Jacobson M

PLoS ONE 11 (3) e0151481 [2016-03-16; online 2016-03-16]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

The FAIR Guiding Principles for scientific data management and stewardship.

Wilkinson MD, Dumontier M, Aalbersberg IJ, ..., Zhao J, Mons B

Sci Data 3 (-) 160018 [2016-03-15; online 2016-03-15]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Transition from Bioinert to Bioactive Material by Tailoring the Biological Cell Response to Carboxylated Nanocellulose.

Hua K, Rocha I, Zhang P, ..., Mihranyan A, Ferraz N

Biomacromolecules 17 (3) 1224-1233 [2016-03-14; online 2016-03-01]

Luminescent Nanocellulose Platform: From Controlled Graft Block Copolymerization to Biomarker Sensing.

Navarro JR, Wennmalm S, Godfrey J, Breitholtz M, Edlund U

Biomacromolecules 17 (3) 1101-1109 [2016-03-14; online 2016-01-21]

Fluorescence Correlation Spectroscopy [Collaborative] Integrated Microscopy Technologies Stockholm

Thiazolino 2-Pyridone Amide Inhibitors of Chlamydia trachomatis Infectivity.

Good JA, Silver J, Núñez-Otero C, ..., Bergström S, Almqvist F

J. Med. Chem. 59 (5) 2094-2108 [2016-03-10; online 2016-02-22]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Kinetically Selective Inhibitors of Human Carbonic Anhydrase Isozymes I, II, VII, IX, XII, and XIII.

Talibov VO, Linkuvienė V, Matulis D, Danielson UH

J. Med. Chem. 59 (5) 2083-2093 [2016-03-10; online 2016-01-26]

Drug Discovery and Development (DDD) [Collaborative]

Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly.

Celorio-Mancera Mde L, Wheat CW, Huss M, ..., Nylin S, Janz N

BMC Evol. Biol. 16 (-) 59 [2016-03-08; online 2016-03-08]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Service]

Crystal Structures of Type-II Inositol Polyphosphate 5-Phosphatase INPP5B with Synthetic Inositol Polyphosphate Surrogates Reveal New Mechanistic Insights for the Inositol 5-Phosphatase Family.

Mills SJ, Silvander C, Cozier G, ..., Nordlund P, Potter BV

Biochemistry 55 (9) 1384-1397 [2016-03-08; online 2016-02-29]

Whole genome sequencing identifies a novel species of the genus Capnocytophaga isolated from dog and cat bite wounds in humans.

Zangenah S, Abbasi N, Andersson AF, Bergman P

Sci Rep 6 (-) 22919 [2016-03-07; online 2016-03-07]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Multifunctional Antioxidants: Regenerable Radical-Trapping and Hydroperoxide-Decomposing Ebselenols.

Kumar S, Yan J, Poon JF, ..., Engman L, Kumar S

Angew. Chem. Int. Ed. Engl. 55 (11) 3729-3733 [2016-03-07; online 2016-02-16]

Monitoring polydispersity by NMR diffusometry with tailored norm regularisation and moving-frame processing.

Urbańczyk M, Bernin D, Czuroń A, Kazimierczuk K

Analyst 141 (5) 1745-1752 [2016-03-07; online 2016-01-30]

Swedish NMR Centre (SNC) [Technology development]

Mechanistic investigation of the on-surface enzymatic digestion (oSED) protein adsorption detection method using targeted mass spectrometry.

Undin T, Dahlin A, Hörnaeus K, Bergquist J, Lind SB

Analyst 141 (5) 1714-1720 [2016-03-07; online 2016-02-13]

Mass Spectrometry-based Proteomics, Uppsala [Collaborative]

Local coordination and dynamics of a protic ammonium based ionic liquid immobilized in nano-porous silica micro-particles probed by Raman and NMR spectroscopy.

Garaga MN, Persson M, Yaghini N, Martinelli A

Soft Matter 12 (9) 2583-2592 [2016-03-07; online 2016-02-03]

Lesion Size Is Exacerbated in Hypoxic Rats Whereas Hypoxia-Inducible Factor-1 Alpha and Vascular Endothelial Growth Factor Increase in Injured Normoxic Rats: A Prospective Cohort Study of Secondary Hypoxia in Focal Traumatic Brain Injury.

Thelin EP, Frostell A, Mulder J, ..., Morganti-Kossmann MC, Bellander BM

Front Neurol 7 (-) 23 [2016-03-07; online 2016-03-07]

Analysis of the Cerebrospinal Fluid Proteome in Alzheimer's Disease.

Khoonsari PE, Häggmark A, Lönnberg M, ..., Kultima K, Shevchenko G

PLoS ONE 11 (3) e0150672 [2016-03-07; online 2016-03-07]

Disruption of POGZ Is Associated with Intellectual Disability and Autism Spectrum Disorders.

Stessman HA, Willemsen MH, Fenckova M, ..., Eichler EE, Kleefstra T

Am. J. Hum. Genet. 98 (3) 541-552 [2016-03-03; online 2016-03-05]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Systematic analysis of overall survival and interactions between tumor mutations and drug treatment.

Gatto F, Nielsen J

J Hematol Oncol 9 (-) 15 [2016-03-02; online 2016-03-02]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2.

Prezza N, Vezzi F, Käller M, Policriti A

BMC Bioinformatics 17 Suppl 4 (-) 69 [2016-03-02; online 2016-03-02]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Service]

Cells release subpopulations of exosomes with distinct molecular and biological properties.

Willms E, Johansson HJ, Mäger I, ..., Wood MJ, Vader P

Sci Rep 6 (-) 22519 [2016-03-02; online 2016-03-02]

Clinical Proteomics Mass spectrometry [Technology development]

Visible-Light-Mediated Photocatalytic Difunctionalization of Olefins by Radical Acylarylation and Tandem Acylation/Semipinacol Rearrangement.

Bergonzini G, Cassani C, Lorimer-Olsson H, Hörberg J, Wallentin CJ

Chemistry 22 (10) 3292-3295 [2016-03-01; online 2016-02-02]

The MHC Class I Cancer-Associated Neoepitope Trh4 Linked with Impaired Peptide Processing Induces a Unique Noncanonical TCR Conformer.

Hafstrand I, Doorduijn EM, Duru AD, ..., van Hall T, Achour A

J. Immunol. 196 (5) 2327-2334 [2016-03-01; online 2016-01-22]

mRNA and microRNA transcriptomics analyses in a murine model of dystrophin loss and therapeutic restoration.

Roberts TC, Blomberg KE, Smith CI, El Andaloussi S, Wood MJ

Genom Data 7 (-) 88-89 [2016-03-00; online 2015-12-02]

Bioinformatics and Expression Analysis (BEA) [Service]

The transcriptional coregulator MAML1 affects DNA methylation and gene expression patterns in human embryonic kidney cells.

Putnik M, Brodin D, Wojdacz TK, ..., Dahlman-Wright K, Wallberg AE

Mol. Biol. Rep. 43 (3) 141-150 [2016-03-00; online 2016-02-08]

Bioinformatics and Expression Analysis (BEA) [Service]

The structure and catalytic mechanism of human sphingomyelin phosphodiesterase like 3a--an acid sphingomyelinase homologue with a novel nucleotide hydrolase activity.

Lim SM, Yeung K, Trésaugues L, Ling TH, Nordlund P

FEBS J. 283 (6) 1107-1123 [2016-03-00; online 2016-02-05]

The influence of population structure on gene expression and flowering time variation in the ubiquitous weed Capsella bursa-pastoris (Brassicaceae).

Kryvokhyzha D, Holm K, Chen J, ..., Lagercrantz U, Lascoux M

Mol. Ecol. 25 (5) 1106-1121 [2016-03-00; online 2016-01-23]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

T-cell receptor-HLA-DRB1 associations suggest specific antigens in pulmonary sarcoidosis.

Grunewald J, Kaiser Y, Ostadkarampour M, ..., Ronninger M, Eklund A

Eur. Respir. J. 47 (3) 898-909 [2016-03-00; online 2015-11-19]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]

Reclassification of Wolbachia persica as Francisella persica comb. nov. and emended description of the family Francisellaceae.

Larson MA, Nalbantoglu U, Sayood K, ..., Sjöstedt A, Hinrichs SH

Int. J. Syst. Evol. Microbiol. 66 (3) 1200-1205 [2016-03-00; online 2016-01-10]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Rat Prostate Tumor Cells Progress in the Bone Microenvironment to a Highly Aggressive Phenotype.

Bergström SH, Rudolfsson SH, Bergh A

Neoplasia 18 (3) 152-161 [2016-03-00; online 2016-03-20]

Rapid and straightforward transesterification of sulfonyl carbamates

Isaksson R, Kumpiņa I, Larhed M, Wannberg J

Tetrahedron Letters 57 (13) 1476-1478 [2016-03-00; online 2016-03-00]

Drug Discovery and Development (DDD) [Collaborative]

Quantitative Auxin Metabolite Profiling Using Stable Isotope Dilution UHPLC-MS/MS.

Novák O, Pěnčík A, Blahoušek O, Ljung K

Curr Protoc Plant Biol 1 (2) 419-430 [2016-03-00; online 2016-03-01]

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers.

Nadachowska-Brzyska K, Burri R, Smeds L, Ellegren H

Mol. Ecol. 25 (5) 1058-1072 [2016-03-00; online 2016-01-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Oncogene-Induced Senescence in Pituitary Adenomas--an Immunohistochemical Study.

Manojlovic-Gacic E, Skender-Gazibara M, Popovic V, ..., Pontén F, Casar-Borota O

Endocr. Pathol. 27 (1) 1-11 [2016-03-00; online 2015-11-18]

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.

Wang J, Street NR, Scofield DG, Ingvarsson PK

Genetics 202 (3) 1185-1200 [2016-03-00; online 2016-01-02]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Meta-analysis of Genome-Wide Association Studies for Extraversion: Findings from the Genetics of Personality Consortium.

van den Berg SM, de Moor MH, Verweij KJ, ..., Martin NG, Boomsma DI

Behav. Genet. 46 (2) 170-182 [2016-03-00; online 2015-09-13]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Innovation in the prognostication of chronic lymphocytic leukemia: how far beyond TP53 gene analysis can we go?

Pospisilova S, Sutton LA, Malcikova J, ..., Ghia P, European Research Initiative on CLL (ERIC)

Haematologica 101 (3) 263-265 [2016-03-00; online 2016-03-02]

Clinical Genomics [Service] Clinical Genomics Uppsala [Service]

Immune Adaptation to Environmental Influence: The Case of NK Cells and HCMV.

Rölle A, Brodin P

Trends Immunol. 37 (3) 233-243 [2016-03-00; online 2016-02-09]

Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof of concept.

Franke B, Stein JL, Ripke S, ..., Medland SE, Sullivan PF

Nat. Neurosci. 19 (3) 420-431 [2016-03-00; online 2016-02-09]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Estimation of copy number aberrations: Comparison of exome sequencing data with SNP microarrays identifies homozygous deletions of 19q13.2 and CIC in neuroblastoma.

Fransson S, Östensson M, Djos A, ..., Kogner P, Martinsson T

Int. J. Oncol. 48 (3) 1103-1116 [2016-03-00; online 2016-01-23]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Ectomycorrhizal fungi decompose soil organic matter using oxidative mechanisms adapted from saprotrophic ancestors.

Shah F, Nicolás C, Bentzer J, ..., Persson P, Tunlid A

New Phytol. 209 (4) 1705-1719 [2016-03-00; online 2015-11-04]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Coordinated Changes in Gene Expression Throughout Encystation of Giardia intestinalis.

Einarsson E, Troell K, Hoeppner MP, ..., Ribacke U, Svärd SG

PLoS Negl Trop Dis 10 (3) e0004571 [2016-03-00; online 2016-03-25]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Comprehensive Proteomic Analysis of Mesenchymal Stem Cell Exosomes Reveals Modulation of Angiogenesis via Nuclear Factor-KappaB Signaling.

Anderson JD, Johansson HJ, Graham CS, ..., Lehtiö J, Nolta JA

Stem Cells 34 (3) 601-613 [2016-03-00; online 2016-02-19]

Clinical Proteomics Mass spectrometry [Collaborative] Global Proteomics and Proteogenomics [Collaborative]

Characterization of genetic variation in TLR8 in relation to allergic rhinitis.

Henmyr V, Lind-Halldén C, Carlberg D, ..., Säll T, Cardell LO

Allergy 71 (3) 333-341 [2016-03-00; online 2015-11-12]

Biochemical Conversion of Torrefied Norway Spruce After Pretreatment with Acid or Ionic Liquid

Normark M, Pommer L, Gräsvik J, ..., Winestrand S, Jönsson LJ

Bioenerg. Res. 9 (1) 355-368 [2016-03-00; online 2015-11-26]

Altered DNA methylation of glycolytic and lipogenic genes in liver from obese and type 2 diabetic patients.

Kirchner H, Sinha I, Gao H, ..., Dahlman-Wright K, Zierath JR

Mol Metab 5 (3) 171-183 [2016-03-00; online 2016-01-02]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Bacterial community composition and fhs profiles of low- and high-ammonia biogas digesters reveal novel syntrophic acetate-oxidising bacteria.

Müller B, Sun L, Westerholm M, Schnürer A

Biotechnol Biofuels 9 (-) 48 [2016-02-27; online 2016-02-27]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Mechanistic Modeling of Pitavastatin Disposition in Sandwich-Cultured Human Hepatocytes: A Proteomics-Informed Bottom-Up Approach

Vildhede A, Mateus A, Khan EK, ..., Artursson P, Kjellsson MC

Drug Metab. Dispos. 44 (4) 505-516 [2016-02-26; online 2016-02-03]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Whole-exome sequencing in relapsing chronic lymphocytic leukemia: clinical impact of recurrent RPS15 mutations.

Ljungström V, Cortese D, Young E, ..., Sjöblom T, Rosenquist R

Blood 127 (8) 1007-1016 [2016-02-25; online 2015-12-18]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Bioelectric and Morphological Response of Liquid-Covered Human Airway Epithelial Calu-3 Cell Monolayer to Periodic Deposition of Colloidal 3-Mercaptopropionic-Acid Coated CdSe-CdS/ZnS Core-Multishell Quantum Dots.

Turdalieva A, Solandt J, Shambetova N, ..., Zelenina M, Fu Y

PLoS ONE 11 (2) e0149915 [2016-02-25; online 2016-02-25]

Integrated Microscopy Technologies Stockholm [Collaborative]

Association between plasma concentrations of linoleic acid-derived oxylipins and the perceived pain scores in an exploratory study in women with chronic neck pain.

Hellström F, Gouveia-Figueira S, Nording ML, Björklund M, Fowler CJ

BMC Musculoskelet Disord 17 (-) 103 [2016-02-25; online 2016-02-25]

A Multiplex Protein Panel Applied to Cerebrospinal Fluid Reveals Three New Biomarker Candidates in ALS but None in Neuropathic Pain Patients

Lind AL, Wu D, Freyhult E, ..., Landegren U, Kamali-Moghaddam M

PLoS ONE 11 (2) e0149821 [2016-02-25; online 2016-02-25]

Affinity Proteomics Uppsala [Technology development] Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] PLA and Single Cell Proteomics [Technology development]

Efficient Isotope Editing of Proteins for Site-Directed Vibrational Spectroscopy.

Peuker S, Andersson H, Gustavsson E, ..., Erdelyi M, Westenhoff S

J. Am. Chem. Soc. 138 (7) 2312-2318 [2016-02-24; online 2016-02-10]

An Efficient Protecting-Group-Free Synthesis of Vinylic Sulfoximines via Horner–Wadsworth–Emmons Reaction

Naicker T, Arvidsson P, Chinthakindi P, ..., Govender T, Kruger H

Synlett 27 (09) 1423-1427 [2016-02-24; online 2016-02-24]

Drug Discovery and Development (DDD) [Collaborative]

Anoctamin 2 identified as an autoimmune target in multiple sclerosis.

Ayoglu B, Mitsios N, Kockum I, ..., Olsson T, Nilsson P

Proc. Natl. Acad. Sci. U.S.A. 113 (8) 2188-2193 [2016-02-23; online 2016-02-09]

Autoimmunity and Serology Profiling [Collaborative] Fluorescence Tissue Profiling [Collaborative]

Microwave Promoted Transcarbamylation Reaction of Sulfonylcarbamates under Continuous-Flow Conditions

Kumpiņa I, Isaksson R, Sävmarker J, Wannberg J, Larhed M

Org. Process Res. Dev. 20 (2) 440-445 [2016-02-19; online 2016-01-05]

Drug Discovery and Development (DDD) [Collaborative]

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea.

Olsen JL, Rouzé P, Verhelst B, ..., Reusch TB, Van de Peer Y

Nature 530 (7590) 331-335 [2016-02-18; online 2016-01-28]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Quantitative proteomics reveals protein profiles underlying major transitions in aspen wood development.

Obudulu O, Bygdell J, Sundberg B, ..., Trygg J, Wingsle G

BMC Genomics 17 (-) 119 [2016-02-18; online 2016-02-18]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Swedish Metabolomics Centre (SMC) [Service]

Postprandial metabolomics: A pilot mass spectrometry and NMR study of the human plasma metabolome in response to a challenge meal.

Karimpour M, Surowiec I, Wu J, ..., Zivkovic AM, Nording ML

Anal. Chim. Acta 908 (-) 121-131 [2016-02-18; online 2016-01-31]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Swedish Metabolomics Centre (SMC) [Service]

GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information.

Edsgärd D, Iglesias MJ, Reilly SJ, ..., Odeberg J, Emanuelsson O

Sci Rep 6 (-) 21134 [2016-02-18; online 2016-02-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Resting-State Brain and the FTO Obesity Risk Allele: Default Mode, Sensorimotor, and Salience Network Connectivity Underlying Different Somatosensory Integration and Reward Processing between Genotypes.

Olivo G, Wiemerslage L, Nilsson EK, ..., Brooks SJ, Schiöth HB

Front Hum Neurosci 10 (-) 52 [2016-02-17; online 2016-02-17]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Species identification of Swedish mosquitoes through DNA metabarcoding

Lilja T, Nylander JAA, Troell K, Lindström A

JOURNAL OF THE EUROPEAN MOSQUITO CONTROL ASSOCIATION 35 (-) 1-9 [2016-02-16; online 2016-02-16]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Genomic comparison of Escherichia coli serotype O103:H2 isolates with and without verotoxin genes: implications for risk assessment of strains commonly found in ruminant reservoirs.

Söderlund R, Hurel J, Jinnerot T, ..., Eriksson E, Bongcam-Rudloff E

Infect Ecol Epidemiol 6 (-) 30246 [2016-02-16; online 2016-02-16]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea.

Baker BJ, Saw JH, Lind AE, ..., Teske AP, Ettema TJG

Nat Microbiol 1 (-) 16002 [2016-02-15; online 2016-02-15]

Microbial Single Cell Genomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genome-wide DNA methylation study identifies genes associated with the cardiovascular biomarker GDF-15.

Ek WE, Hedman ÅK, Enroth S, ..., Lind L, Johansson Å

Hum. Mol. Genet. 25 (4) 817-827 [2016-02-15; online 2015-12-19]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Exome sequencing in one family with gastric- and rectal cancer.

Thutkawkorapin J, Picelli S, Kontham V, ..., Nilsson D, Lindblom A

BMC Genet. 17 (-) 41 [2016-02-13; online 2016-02-13]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Stockholm [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Discovery of the First Potent and Selective Inhibitors of Human dCTP Pyrophosphatase 1.

Llona-Minguez S, Höglund A, Jacques SA, ..., Scobie M, Helleday T

J. Med. Chem. 59 (3) 1140-1148 [2016-02-11; online 2016-01-27]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Collaborative] Protein Science Facility (PSF) [Service]

Aurora kinase inhibitor nanoparticles target tumors with favorable therapeutic index in vivo.

Ashton S, Song YH, Nolan J, ..., Jewsbury PJ, Barry ST

Sci Transl Med 8 (325) 325ra17 [2016-02-10; online 2016-02-13]

Genome-wide profiling of histone H3 lysine 27 and lysine 4 trimethylation in multiple myeloma reveals the importance of Polycomb gene targeting and highlights EZH2 as a potential therapeutic target.

Agarwal P, Alzrigat M, Párraga AA, ..., Kalushkova A, Jernberg-Wiklund H

Oncotarget 7 (6) 6809-6823 [2016-02-09; online 2016-01-13]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Stereoselective synthesis towards unnatural proline based amino acids

S.Makhathini S, Das SK, Singh T, ..., Govender T, Naicker T

ARKIVOC 2016 (3) 134-144 [2016-02-07; online 2016-02-07]

Drug Discovery and Development (DDD) [Collaborative]

Targeted Proteomics Approach for Precision Plant Breeding.

Chawade A, Alexandersson E, Bengtsson T, Andreasson E, Levander F

J. Proteome Res. 15 (2) 638-646 [2016-02-05; online 2015-12-26]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Systems Proteomics View of the Endogenous Human Claudin Protein Family.

Liu F, Koval M, Ranganathan S, ..., Kelleher NL, Baker MS

J. Proteome Res. 15 (2) 339-359 [2016-02-05; online 2016-01-12]

Structure and Interactions of a Dimeric Variant of sHIP, a Novel Virulence Determinant of Streptococcus pyogenes.

Diehl C, Wisniewska M, Frick IM, ..., Malmström J, Wikström M

Front Microbiol 7 (-) 95 [2016-02-05; online 2016-02-05]

Elucidating the Molecular Composition of Cartilage by Proteomics.

Hsueh MF, Khabut A, Kjellström S, Önnerfjord P, Kraus VB

J. Proteome Res. 15 (2) 374-388 [2016-02-05; online 2016-01-15]

Xenacoelomorpha is the sister group to Nephrozoa.

Cannon JT, Vellutini BC, Smith J, ..., Jondelius U, Hejnol A

Nature 530 (7588) 89-93 [2016-02-04; online 2016-02-06]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Proteome-wide survey of the autoimmune target repertoire in autoimmune polyendocrine syndrome type 1

Landegren N, Sharon D, Freyhult E, ..., Snyder M, Kämpe O

Sci Rep 6 (1) 20104 [2016-02-01; online 2016-02-01]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Tissue Profiling [Collaborative]

New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk

Lu Y, Day FR, Gustafsson S, ..., Kilpeläinen TO, Loos RJF

Nat Commun 7 (1) 10495 [2016-02-01; online 2016-02-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels.

Kilpeläinen TO, Carli JF, Skowronski AA, ..., Leibel RL, Loos RJ

Nat Commun 7 (-) 10494 [2016-02-01; online 2016-02-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Cellular High-Energy Cavitation Trauma - Description of a Novel In Vitro Trauma Model in Three Different Cell Types.

Cao Y, Risling M, Malm E, ..., Bolling MF, Sköld MK

Front Neurol 7 (-) 10 [2016-02-01; online 2016-02-01]

Bioinformatics and Expression Analysis (BEA) [Service]

Worldwide population structure of the wheat rust fungus Puccinia striiformis in the past.

Thach T, Ali S, de Vallavieille-Pope C, Justesen AF, Hovmøller MS

Fungal Genet. Biol. 87 (-) 1-8 [2016-02-00; online 2016-01-03]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Transcriptome profiling of immune tissues reveals habitat-specific gene expression between lake and river sticklebacks.

Huang Y, Chain FJ, Panchal M, ..., Milinski M, Feulner PG

Mol. Ecol. 25 (4) 943-958 [2016-02-00; online 2016-01-11]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Tissue sample stability: thawing effect on multi-organ samples

Torell F, Bennett K, Cereghini S, ..., Trygg J, Lundstedt T

Metabolomics 12 (2) - [2016-02-00; online 2015-12-31]

The Role of Lipids in Regulation of Programmed Cell Death

Lidman M, Dingeldein A, Pokorná Š, ..., Hof M, Gröbner G

Biophysical Journal 110 (3) 473a [2016-02-00; online 2016-02-00]

The C repressor of the P2 bacteriophage.

Massad T, Papadopolos E, Stenmark P, Damberg P

J. Biomol. NMR 64 (2) 175-180 [2016-02-00; online 2015-12-22]

Six Novel Loci Associated with Circulating VEGF Levels Identified by a Meta-analysis of Genome-Wide Association Studies.

Choi SH, Ruggiero D, Sorice R, ..., Seshadri S, Ciullo M

PLoS Genet. 12 (2) e1005874 [2016-02-00; online 2016-02-24]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Segmentation and Track-Analysis in Time-Lapse Imaging of Bacteria

Sadanandan SK, Baltekin O, Magnusson KEG, ..., Elf J, Wahlby C

IEEE J. Sel. Top. Signal Process. 10 (1) 174-184 [2016-02-00; online 2016-02-00]

BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

Replacement of two amino acids of 9R-dioxygenase-allene oxide synthase of Aspergillus niger inverts the chirality of the hydroperoxide and the allene oxide.

Sooman L, Wennman A, Hamberg M, Hoffmann I, Oliw EH

Biochim. Biophys. Acta 1861 (2) 108-118 [2016-02-00; online 2015-11-26]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses.

Imsland F, McGowan K, Rubin CJ, ..., Barsh GS, Andersson L

Nat. Genet. 48 (2) 152-158 [2016-02-00; online 2015-12-23]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Numerous Genes in Loci Associated With Body Fat Distribution Are Linked to Adipose Function.

Dahlman I, Rydén M, Brodin D, ..., Strawbridge RJ, Arner P

Diabetes 65 (2) 433-437 [2016-02-00; online 2016-01-23]

Bioinformatics and Expression Analysis (BEA) [Service]

Genome-Wide Association Analysis of Young-Onset Stroke Identifies a Locus on Chromosome 10q25 Near HABP2.

Cheng YC, Stanne TM, Giese AK, ..., Saleheen D, Mitchell BD

Stroke 47 (2) 307-316 [2016-02-00; online 2016-01-07]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Fuzzy regions in an intrinsically disordered protein impair protein-protein interactions.

Gruet A, Dosnon M, Blocquel D, ..., Longhi S, Bignon C

FEBS J. 283 (4) 576-594 [2016-02-00; online 2016-01-12]

Exemplifying the Screening Power of Mass Spectrometry Imaging over Label-Based Technologies for Simultaneous Monitoring of Drug and Metabolite Distributions in Tissue Sections.

Goodwin RJA, Nilsson A, Mackay CL, ..., Andrén PE, Iverson SL

J Biomol Screen 21 (2) 187-193 [2016-02-00; online 2015-12-23]

Spatial Mass Spectrometry

Ex Vivo Assessment of Drug Activity in Patient Tumor Cells as a Basis for Tailored Cancer Therapy.

Blom K, Nygren P, Alvarsson J, Larsson R, Andersson CR

J Lab Autom 21 (1) 178-187 [2016-02-00; online 2015-08-05]

Epigenetic profiling in CD4+ and CD8+ T cells from Graves' disease patients reveals changes in genes associated with T cell receptor signaling.

Limbach M, Saare M, Tserel L, ..., Milani L, Peterson P

J. Autoimmun. 67 (-) 46-56 [2016-02-00; online 2015-10-16]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Dynamical and Structural Alterations withing Lipid-Protein Assemblies Control Apoptotic Pore Formation - A Solid State NMR Study

Dingeldein APG, Lidman M, Sparrman T, Gröbner G

Biophysical Journal 110 (3) 59a-60a [2016-02-00; online 2016-02-00]

Direct Measurement of Intracellular Compound Concentration by RapidFire Mass Spectrometry Offers Insights into Cell Permeability

Gordon LJ, Allen M, Artursson P, ..., Wayne GJ, West A

J Biomol Screen 21 (2) 156-164 [2016-02-00; online 2015-09-03]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Diffusion-Controlled Drug Release From the Mesoporous Magnesium Carbonate Upsalite(®).

Zhang P, Zardán Gómez de la Torre T, Forsgren J, Bergström CA, Strømme M

J Pharm Sci 105 (2) 657-663 [2016-02-00; online 2015-06-20]

Decreased levels of stem cell factor in subjects with incident coronary events.

Wigren M, Rattik S, Hultman K, ..., Gonçalves I, Nilsson J

J. Intern. Med. 279 (2) 180-191 [2016-02-00; online 2015-10-14]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Crystal structure of the flavoenzyme PA4991 from Pseudomonas aeruginosa.

Jacewicz A, Schnell R, Lindqvist Y, Schneider G

Acta Crystallogr F Struct Biol Commun 72 (Pt 2) 105-111 [2016-02-00; online 2016-01-22]

Complete Knockout of Endogenous Mdr1 ( Abcb1 ) in MDCK Cells by CRISPR-Cas9

Simoff I, Karlgren M, Backlund M, ..., Matsson P, Artursson P

Journal of Pharmaceutical Sciences 105 (2) 1017-1021 [2016-02-00; online 2016-02-00]

Chemical Biology Consortium Sweden (CBCS) [Technology development] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Biobanking multifocal breast carcinomas: sample adequacy with regard to histology and DNA content.

Pekar G, Davies H, Lukacs AP, ..., Dumanski J, Tot T

Histopathology 68 (3) 411-421 [2016-02-00; online 2015-06-18]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Association analysis of copy numbers of FC-gamma receptor genes for rheumatoid arthritis and other immune-mediated phenotypes.

Franke L, el Bannoudi H, Jansen DT, ..., Toes RE, Zhernakova A

Eur. J. Hum. Genet. 24 (2) 263-270 [2016-02-00; online 2015-05-15]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Are freshwater bacterioplankton indifferent to variable types of amino acid substrates?

Ricão Canelhas M, Eiler A, Bertilsson S

FEMS Microbiol. Ecol. 92 (2) - [2016-02-00; online 2016-01-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Analysis of hepatitis C NS5A resistance associated polymorphisms using ultra deep single molecule real time (SMRT) sequencing.

Bergfors A, Leenheer D, Bergqvist A, Ameur A, Lennerstrand J

Antiviral Res. 126 (-) 81-89 [2016-02-00; online 2015-12-19]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Analyses of the ash dieback pathogen,Hymenoscyphus fraxineus, suggest role of tree species diversity on colonization and population structure differentiation

Nguyen DT, Cleary MR, Enderle R, Berlin A, Stenlid J

For. Path. 46 (1) 82-84 [2016-02-00; online 2015-10-28]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A novel phenotype in N-glycosylation disorders: Gillessen-Kaesbach–Nishimura skeletal dysplasia due to pathogenic variants in ALG9

Tham E, Eklund EA, Hammarsjö A, ..., Nishimura G, Grigelioniene G

Eur J Hum Genet 24 (2) 198-207 [2016-02-00; online 2015-05-13]

Clinical Genomics Clinical Genomics Stockholm

The Story of a Hitchhiker: Population Genetic Patterns in the Invasive Barnacle Balanus(Amphibalanus) improvisus Darwin 1854.

Wrange AL, Charrier G, Thonig A, ..., Jonsson PR, André C

PLoS ONE 11 (1) e0147082 [2016-01-28; online 2016-01-28]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

High levels of cathepsin D and cystatin B are associated with increased risk of coronary events.

Gonçalves I, Hultman K, Dunér P, ..., Nilsson J, Bengtsson E

Open Heart 3 (1) e000353 [2016-01-27; online 2016-01-27]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

High Plasma Levels of Galectin-3 Are Associated with Increased Risk for Stroke after Carotid Endarterectomy.

Edsfeldt A, Bengtsson E, Asciutto G, ..., Nilsson J, Goncalves I

Cerebrovasc Dis 41 (3-4) 199-203 [2016-01-27; online 2016-01-27]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Genomic sequencing of a dyslexia susceptibility haplotype encompassing ROBO1.

Massinen S, Wang J, Laivuori K, ..., Jiao H, Kere J

J Neurodev Disord 8 (-) 4 [2016-01-27; online 2016-01-27]

Bioinformatics Support for Computational Resources [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A dynamic Asp-Arg interaction is essential for catalysis in microsomal prostaglandin E2 synthase.

Brock JS, Hamberg M, Balagunaseelan N, ..., Rinaldo-Matthis A, Haeggström JZ

Proc. Natl. Acad. Sci. U.S.A. 113 (4) 972-977 [2016-01-26; online 2016-01-11]

Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool.

Omrak A, Günther T, Valdiosera C, ..., Jakobsson M, Götherström A

Curr. Biol. 26 (2) 270-275 [2016-01-25; online 2015-12-31]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Metabolites in Blood for Prediction of Bacteremic Sepsis in the Emergency Room.

Kauppi AM, Edin A, Ziegler I, ..., Strålin K, Johansson A

PLoS ONE 11 (1) e0147670 [2016-01-22; online 2016-01-22]

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

Pattaro C, Teumer A, Gorski M, ..., Kao WH, Fox CS

Nat Commun 7 (1) 10023 [2016-01-21; online 2016-01-21]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Backbone Assignment of the MALT1 Paracaspase by Solution NMR.

Unnerståle S, Nowakowski M, Baraznenok V, ..., Orekhov V, Agback T

PLoS ONE 11 (1) e0146496 [2016-01-20; online 2016-01-20]

Reconstructing ecosystem functions of the active microbial community of the Baltic Sea oxygen depleted sediments.

Thureborn P, Franzetti A, Lundin D, Sjöling S

PeerJ 4 (-) e1593 [2016-01-19; online 2016-01-19]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Geographical distribution of genetic diversity in Secale landrace and wild accessions.

Hagenblad J, Oliveira HR, Forsberg NE, Leino MW

BMC Plant Biol. 16 (-) 23 [2016-01-19; online 2016-01-19]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic Determinants of Thrombin Generation and Their Relation to Venous Thrombosis: Results from the GAIT-2 Project.

Martin-Fernandez L, Ziyatdinov A, Carrasco M, ..., Souto JC, Soria JM

PLoS ONE 11 (1) e0146922 [2016-01-19; online 2016-01-19]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Chondroitin sulfate coated gold nanoparticles: a new strategy to resolve multidrug resistance and thromboinflammation.

Gurav D, Varghese OP, Hamad OA, ..., Hilborn J, Oommen OP

Chem. Commun. (Camb.) 52 (5) 966-969 [2016-01-18; online 2015-11-21]

Using Whole-Exome Sequencing to Identify Genetic Markers for Carboplatin and Gemcitabine-Induced Toxicities.

Gréen H, Hasmats J, Kupershmidt I, ..., Peterson C, Lundeberg J

Clin. Cancer Res. 22 (2) 366-373 [2016-01-15; online 2015-09-16]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Phytoconstituents with Radical Scavenging and Cytotoxic Activities from Diospyros shimbaensis

Aronsson P, Munissi J, Gruhonjic A, ..., Nyandoro S, Erdelyi M

Diseases 4 (1) 3 [2016-01-15; online 2016-01-15]

A meta-analysis of 120 246 individuals identifies 18 new loci for fibrinogen concentration.

de Vries PS, Chasman DI, Sabater-Lleal M, ..., Strachan DP, Dehghan A

Hum. Mol. Genet. 25 (2) 358-370 [2016-01-15; online 2015-11-10]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Cryptochromes Interact Directly with PIFs to Control Plant Growth in Limiting Blue Light.

Pedmale UV, Huang SS, Zander M, ..., Ecker JR, Chory J

Cell 164 (1-2) 233-245 [2016-01-14; online 2016-01-05]

The protein kinase LKB1 negatively regulates bone morphogenetic protein receptor signaling.

Raja E, Tzavlaki K, Vuilleumier R, ..., Heldin CH, Moustakas A

Oncotarget 7 (2) 1120-1143 [2016-01-12; online 2015-12-25]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Spatial sexual dimorphism of X and Y homolog gene expression in the human central nervous system during early male development.

Johansson MM, Lundin E, Qian X, ..., Nilsson M, Jazin E

Biol Sex Differ 7 (-) 5 [2016-01-12; online 2016-01-12]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Simultaneous Multiplexed Measurement of RNA and Proteins in Single Cells.

Darmanis S, Gallant CJ, Marinescu VD, ..., Westermark B, Landegren U

Cell Rep 14 (2) 380-389 [2016-01-12; online 2016-01-11]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Genome-wide identification of Wig-1 mRNA targets by RIP-Seq analysis.

Bersani C, Huss M, Giacomello S, ..., Lui WO, Wiman KG

Oncotarget 7 (2) 1895-1911 [2016-01-12; online 2015-12-18]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

BMP Sustains Embryonic Stem Cell Self-Renewal through Distinct Functions of Different Krüppel-like Factors.

Morikawa M, Koinuma D, Mizutani A, ..., Heldin CH, Miyazono K

Stem Cell Reports 6 (1) 64-73 [2016-01-12; online 2016-01-16]

Genome Engineering Zebrafish [Collaborative]

Serum Trimethylamine-N-Oxide Is Strongly Related to Renal Function and Predicts Outcome in Chronic Kidney Disease.

Missailidis C, Hällqvist J, Qureshi AR, ..., Stenvinkel P, Bergman P

PLoS ONE 11 (1) e0141738 [2016-01-11; online 2016-01-11]

Whole-Genome Sequencing of a Canine Family Trio Reveals a FAM83G Variant Associated with Hereditary Footpad Hyperkeratosis.

Sayyab S, Viluma A, Bergvall K, ..., Andersson G, Bergström TF

G3 (Bethesda) 6 (3) 521-527 [2016-01-08; online 2016-01-08]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

The 5300-year-old Helicobacter pylori genome of the Iceman.

Maixner F, Krause-Kyora B, Turaev D, ..., Rattei T, Zink A

Science 351 (6269) 162-165 [2016-01-08; online 2016-01-09]

Clinical Genomics [Collaborative] Clinical Genomics Stockholm [Collaborative]

Identifying Novel Gene Variants in Coronary Artery Disease and Shared Genes With Several Cardiovascular Risk Factors.

LeBlanc M, Zuber V, Andreassen BK, ..., Dale AM, Andreassen OA

Circ. Res. 118 (1) 83-94 [2016-01-08; online 2015-10-22]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

PGSB PlantsDB: updates to the database framework for comparative plant genome research.

Spannagl M, Nussbaumer T, Bader KC, ..., Gundlach H, Mayer KF

Nucleic Acids Res. 44 (D1) D1141-D1147 [2016-01-04; online 2015-11-04]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Characterization and Expression of the Zebrafish qki Paralogs.

Radomska KJ, Sager J, Farnsworth B, ..., Jazin E, Emilsson LS

PLoS ONE 11 (1) e0146155 [2016-01-04; online 2016-01-04]

CRISPRz: a database of zebrafish validated sgRNAs.

Varshney GK, Zhang S, Pei W, ..., Sood R, Burgess SM

Nucleic Acids Res. 44 (D1) D822-D826 [2016-01-04; online 2015-10-04]

Genome Engineering Zebrafish [Technology development]

Protein Detection Using the Multiplexed Proximity Extension Assay (PEA) from Plasma and Vaginal Fluid Applied to the Indicating FTA Elute Micro Card™.

Berggrund M, Ekman D, Gustavsson I, ..., Enroth S, Gyllensten U

Journal of Circulating Biomarkers 5 (-) 9 [2016-01-01; online 2016-01-01]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Ionic liquid mediated technology for synthesis of cellulose acetates using different co-solvents.

Jogunola O, Eta V, Hedenström M, ..., Salmi T, Mikkola JP

Carbohydr Polym 135 (-) 341-348 [2016-01-01; online 2015-09-02]

Changes in the drug release pattern of fresh and set simvastatin-loaded brushite cement.

Mestres G, Kugiejko K, Pastorino D, ..., Ginebra MP, Persson C

Mater Sci Eng C Mater Biol Appl 58 (-) 88-96 [2016-01-01; online 2015-08-14]

The WD40 Domain Protein MSI1 Functions in a Histone Deacetylase Complex to Fine-Tune Abscisic Acid Signaling.

Mehdi S, Derkacheva M, Ramström M, ..., Bergquist J, Hennig L

Plant Cell 28 (1) 42-54 [2016-01-00; online 2015-12-24]

Mass Spectrometry-based Proteomics, Uppsala [Collaborative]

Super-resolution stimulated emission depletion imaging of slit diaphragm proteins in optically cleared kidney tissue.

Unnersjö-Jess D, Scott L, Blom H, Brismar H

Kidney Int. 89 (1) 243-247 [2016-01-00; online 2015-10-08]

Integrated Microscopy Technologies Stockholm [Technology development]

Structural genomic changes underlie alternative reproductive strategies in the ruff (Philomachus pugnax).

Lamichhaney S, Fan G, Widemo F, ..., Liu X, Andersson L

Nat. Genet. 48 (1) 84-88 [2016-01-00; online 2015-11-17]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Protein Biomarkers for Insulin Resistance and Type 2 Diabetes Risk in Two Large Community Cohorts.

Nowak C, Sundström J, Gustafsson S, ..., Ingelsson E, Fall T

Diabetes 65 (1) 276-284 [2016-01-00; online 2015-09-29]

Affinity Proteomics Uppsala [Service] Bioinformatics Support for Computational Resources [Service] Clinical Biomarkers NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] PLA and Single Cell Proteomics [Service]

Pathogenenic variant in the COL2A1 gene is associated with Spondyloepiphyseal dysplasia type Stanescu.

Hammarsjö A, Nordgren A, Lagerstedt-Robinson K, ..., Nishimura G, Grigelioniene G

Am. J. Med. Genet. A 170A (1) 266-269 [2016-01-00; online 2015-10-01]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Service] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

PAX5-ESRRB is a recurrent fusion gene in B-cell precursor pediatric acute lymphoblastic leukemia.

Marincevic-Zuniga Y, Zachariadis V, Cavelier L, ..., Syvänen AC, Nordlund J

Haematologica 101 (1) e20-e23 [2016-01-00; online 2015-10-22]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Oxylipins, endocannabinoids, and related compounds in human milk: Levels and effects of storage conditions.

Wu J, Gouveia-Figueira S, Domellöf M, Zivkovic AM, Nording ML

Prostaglandins Other Lipid Mediat. 122 (-) 28-36 [2016-01-00; online 2015-12-15]

Mutations in FLVCR2 associated with Fowler syndrome and survival beyond infancy.

Kvarnung M, Taylan F, Nilsson D, ..., Nordgren A, Syk Lundberg E

Clin. Genet. 89 (1) 99-103 [2016-01-00; online 2015-02-14]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Increased lanosterol turnover: a metabolic burden for daunorubicin-resistant leukemia cells.

Stäubert C, Krakowsky R, Bhuiyan H, ..., Broom O, Nordström A

Med. Oncol. 33 (1) 6 [2016-01-00; online 2015-12-23]

G×E Interaction Influences Trajectories of Hand Grip Strength.

Petersen I, Pedersen NL, Rantanen T, ..., Krueger RF, Reynolds C

Behav. Genet. 46 (1) 20-30 [2016-01-00; online 2015-09-01]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic heterogeneity in rhabdomyosarcoma revealed by SNP array analysis.

Walther C, Mayrhofer M, Nilsson J, ..., Gisselsson D, Mertens F

Genes Chromosomes Cancer 55 (1) 3-15 [2016-01-00; online 2015-10-20]

Array and Analysis Facility [Collaborative]

Gene-Environment Interplay in Physical, Psychological, and Cognitive Domains in Mid to Late Adulthood: Is APOE a Variability Gene?

Reynolds CA, Gatz M, Christensen K, ..., Pedersen NL, Interplay of Genes and Environment across Multiple Studies (IGEMS) consortium

Behav. Genet. 46 (1) 4-19 [2016-01-00; online 2015-11-06]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

GREM1 and POLE variants in hereditary colorectal cancer syndromes.

Rohlin A, Eiengård F, Lundstam U, ..., Björk J, Nordling M

Genes Chromosomes Cancer 55 (1) 95-106 [2016-01-00; online 2015-10-23]

Fat intake and breast milk fatty acid composition in farming and nonfarming women and allergy development in the offspring.

Jonsson K, Barman M, Moberg S, ..., Wold AE, Sandberg AS

Pediatr. Res. 79 (1-1) 114-123 [2016-01-00; online 2015-09-21]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

F11 is associated with recurrent VTE in women. A prospective cohort study.

Bruzelius M, Ljungqvist M, Bottai M, ..., Lärfars G, Odeberg J

Thromb. Haemost. 115 (2) 406-414 [2016-01-00; online 2015-10-02]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Exome and genome sequencing: a revolution for the discovery and diagnosis of monogenic disorders.

Stranneheim H, Wedell A

J. Intern. Med. 279 (1) 3-15 [2016-01-00; online 2015-08-08]

Clinical Genomics [Service] Clinical Genomics Stockholm [Service]

Development of single-tube nested real-time PCR assays with long internally quenched probes for detection of norovirus genogroup II.

Xia H, Gravelsina S, Öhrmalm C, Ottoson J, Blomberg J

BioTechniques 60 (1) 28-34 [2016-01-00; online 2016-01-01]

NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Composition of human faecal microbiota in resistance to Campylobacter infection.

Kampmann C, Dicksved J, Engstrand L, Rautelin H

Clin. Microbiol. Infect. 22 (1) 61.e1-61.e8 [2016-01-00; online 2015-09-16]

Clinical Genomics [Collaborative] Clinical Genomics Stockholm [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

An Immunochip-based interaction study of contrasting interaction effects with smoking in ACPA-positive versus ACPA-negative rheumatoid arthritis.

Jiang X, Källberg H, Chen Z, ..., Padyukov L, Alfredsson L

Rheumatology (Oxford) 55 (1) 149-155 [2016-01-00; online 2015-08-15]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Adaptive radiation of Darwin's finches revisited using whole genome sequencing.

Almén MS, Lamichhaney S, Berglund J, ..., Webster MT, Andersson L

Bioessays 38 (1) 14-20 [2016-01-00; online 2015-11-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Overexpression of Trypanosoma rangeli trypanothione reductase increases parasite survival under oxidative stress

BELTRAME-BOTELHO IT, STOCO PH, STEINDEL M, ..., GADELHA FR, GRISARD EC

Parasitology Open 2 (-) - [2016-00-00; online 2016-11-14]

NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Organocatalyzed Mannich reactions on minocycline: Towards novel tetracycline antibiotics

CHIWUNZE TE, Azumah R, Ramtahal M, ..., Govender T, Naicker T

S.Afr.j.chem. 69 (-) - [2016-00-00; online 2016-00-00]

Drug Discovery and Development (DDD) [Collaborative]

NMR analysis of the human saliva metabolome distinguishes dementia patients from matched controls

Figueira J, Jonsson P, Nordin Adolfsson A, ..., Nyberg L, Öhman A

Mol. BioSyst. 12 (8) 2562-2571 [2016-00-00; online 2016-00-00]

Feature Augmented Deep Neural Networks for Segmentation of Cells

Sadanandan SK, Ranefall P, Wählby C

- - (-) 231-243 [2016-00-00; online 2016-09-18]

BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development]

Bridging Histology and Bioinformatics—Computational Analysis of Spatially Resolved Transcriptomics

Mignardi M, Ishaq O, Qian X, Wahlby C

Proc. IEEE - (-) 1-12 [2016-00-00; online 2016-00-00]

BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative]

The Urinary Bladder Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling.

Habuka M, Fagerberg L, Hallström BM, ..., Yamamoto T, Uhlen M

PLoS ONE 10 (12) e0145301 [2015-12-22; online 2015-12-22]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Collaborative]

Sequence and gene expression evolution of paralogous genes in willows.

Harikrishnan SL, Pucholt P, Berlin S

Sci Rep 5 (-) 18662 [2015-12-22; online 2015-12-22]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Transcriptome analysis reveals mucin 4 to be highly associated with periodontitis and identifies pleckstrin as a link to systemic diseases.

Lundmark A, Davanian H, Båge T, ..., Lundeberg J, Yucel-Lindberg T

Sci Rep 5 (-) 18475 [2015-12-21; online 2015-12-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genome-wide genetic homogeneity between sexes and populations for human height and body mass index.

Yang J, Bakshi A, Zhu Z, ..., Ingelsson E, Visscher PM

Hum. Mol. Genet. 24 (25) 7445-7449 [2015-12-20; online 2015-10-22]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Exploring water as building bricks in enzyme engineering.

Hendil-Forssell P, Martinelle M, Syrén PO

Chem. Commun. (Camb.) 51 (97) 17221-17224 [2015-12-18; online 2015-10-02]

A significant risk locus on 19q13 for bipolar disorder identified using a combined genome-wide linkage and copy number variation analysis.

Lekman M, Karlsson R, Graae L, Hössjer O, Kockum I

BioData Mining 8 (-) 42 [2015-12-18; online 2015-12-18]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Powerful Populations Respond to Viruses and Vaccines.

Immunity 43 (6) 1035-1037 [2015-12-15; online 2015-12-20]

Metagenome-assembled genomes uncover a global brackish microbiome.

Hugerth LW, Larsson J, Alneberg J, ..., Pinhassi J, Andersson AF

Genome Biol. 16 (-) 279 [2015-12-14; online 2015-12-14]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Metagenome-Based Metabolic Reconstruction Reveals the Ecophysiological Function of Epsilonproteobacteria in a Hydrocarbon-Contaminated Sulfidic Aquifer.

Keller AH, Schleinitz KM, Starke R, ..., Vogt C, Kleinsteuber S

Front Microbiol 6 (-) 1396 [2015-12-10; online 2015-12-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

High levels of WNT-5A in human glioma correlate with increased presence of tumor-associated microglia/monocytes.

Dijksterhuis JP, Arthofer E, Marinescu VD, ..., Mulder J, Schulte G

Exp. Cell Res. 339 (2) 280-288 [2015-12-10; online 2015-10-25]

Pleiotrophin promotes vascular abnormalization in gliomas and correlates with poor survival in patients with astrocytomas.

Zhang L, Kundu S, Feenstra T, ..., Dieterich LC, Dimberg A

Sci Signal 8 (406) ra125 [2015-12-08; online 2015-12-08]

Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation.

Soler Artigas M, Wain LV, Miller S, ..., Hall IP, Tobin MD

Nat Commun 6 (-) 8658 [2015-12-04; online 2015-12-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken.

Johnsson M, Jonsson KB, Andersson L, Jensen P, Wright D

G3 (Bethesda) 6 (2) 311-319 [2015-12-04; online 2015-12-04]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Structural insights into the DNA-binding specificity of E2F family transcription factors.

Morgunova E, Yin Y, Jolma A, ..., Nilsson L, Taipale J

Nat Commun 6 (1) 10050 [2015-12-03; online 2015-12-03]

Karolinska High Throughput Center (KHTC) Protein Science Facility (PSF)

Population structure and genetic diversity in the nannandrous moss Homalothecium lutescens: does the dwarf male system facilitate gene flow?

Rosengren F, Hansson B, Cronberg N

BMC Evol. Biol. 15 (-) 270 [2015-12-03; online 2015-12-03]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Within-species divergence in the seminal fluid proteome and its effect on male and female reproduction in a beetle.

Goenaga J, Yamane T, Rönn J, Arnqvist G

BMC Evol. Biol. 15 (-) 266 [2015-12-02; online 2015-12-02]

A Combination of Culture Conditions and Gene Expression Analysis Can Be Used to Investigate and Predict hES Cell Differentiation Potential towards Male Gonadal Cells.

Kjartansdóttir KR, Reda A, Panula S, ..., Hovatta O, Stukenborg JB

PLoS ONE 10 (12) e0144029 [2015-12-02; online 2015-12-02]

Protein profiling reveals consequences of lifestyle choices on predicted biological aging.

Enroth S, Enroth SB, Johansson Å, Gyllensten U

Sci Rep 5 (1) 17282 [2015-12-01; online 2015-12-01]

Affinity Proteomics Uppsala [Technology development] Clinical Biomarkers PLA and Single Cell Proteomics [Service]

Multi-level omics analysis in a murine model of dystrophin loss and therapeutic restoration.

Roberts TC, Johansson HJ, McClorey G, ..., El Andaloussi S, Wood MJ

Hum. Mol. Genet. 24 (23) 6756-6768 [2015-12-01; online 2015-09-20]

Metabolic Profiling of Chicken Embryos Exposed to Perfluorooctanoic Acid (PFOA) and Agonists to Peroxisome Proliferator-Activated Receptors.

Mattsson A, Kärrman A, Pinto R, Brunström B

PLoS ONE 10 (12) e0143780 [2015-12-01; online 2015-12-01]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Highly Sensitive FRET-FCS Detects Amyloid β-Peptide Oligomers in Solution at Physiological Concentrations.

Wennmalm S, Chmyrov V, Widengren J, Tjernberg L

Anal. Chem. 87 (23) 11700-11705 [2015-12-01; online 2015-10-23]

Fluorescence Correlation Spectroscopy [Collaborative] Integrated Microscopy Technologies Stockholm

Gene-based meta-analysis of genome-wide association studies implicates new loci involved in obesity.

Hägg S, Ganna A, Van Der Laan SW, ..., Pawitan Y, Ingelsson E

Hum. Mol. Genet. 24 (23) 6849-6860 [2015-12-01; online 2015-09-18]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella.

Kovatcheva-Datchary P, Nilsson A, Akrami R, ..., Björck I, Bäckhed F

Cell Metab. 22 (6) 971-982 [2015-12-01; online 2015-11-11]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The body mass index (BMI) is significantly correlated with levels of cytokines and chemokines in cerebrospinal fluid.

Larsson A, Carlsson L, Lind AL, ..., Kamali-Moghaddam M, Thulin M

Cytokine 76 (2) 514-518 [2015-12-00; online 2015-07-15]

Affinity Proteomics Uppsala [Collaborative] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Collaborative]

The Plant Genome Integrative Explorer Resource: PlantGenIE.org.

Sundell D, Mannapperuma C, Netotea S, ..., Hvidsten TR, Street NR

New Phytol. 208 (4) 1149-1156 [2015-12-00; online 2015-07-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

Hurst LD, Ghanbarian AT, Forrest AR, FANTOM consortium , Huminiecki L

PLoS Biol. 13 (12) e1002315 [2015-12-00; online 2015-12-18]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Susceptibility to infections, without concomitant hyper-IgE, reported in 1976, is caused by hypomorphic mutation in the phosphoglucomutase 3 (PGM3) gene.

Lundin KE, Hamasy A, Backe PH, ..., Stenmark S, Smith CI

Clin. Immunol. 161 (2) 366-372 [2015-12-00; online 2015-10-19]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Selenium metabolism to the trimethylselenonium ion (TMSe) varies markedly because of polymorphisms in the indolethylamine N-methyltransferase gene.

Kuehnelt D, Engström K, Skröder H, ..., Broberg K, Vahter M

Am. J. Clin. Nutr. 102 (6) 1406-1415 [2015-12-00; online 2015-11-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Phenotypic expansion of visceral myopathy associated with ACTG2 tandem base substitution.

Klar J, Raykova D, Gustafson E, ..., Wanders A, Dahl N

Eur. J. Hum. Genet. 23 (12) 1679-1683 [2015-12-00; online 2015-03-18]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Oral microbiota in patients with atherosclerosis.

Fåk F, Tremaroli V, Bergström G, Bäckhed F

Atherosclerosis 243 (2) 573-578 [2015-12-00; online 2015-11-05]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Nanocellulose from green algae modulates the in vitro inflammatory response of monocytes/macrophages

Hua K, Strømme M, Mihranyan A, Ferraz N

Cellulose 22 (6) 3673-3688 [2015-12-00; online 2015-10-03]

Multi-ancestry genome-wide association study of 21,000 cases and 95,000 controls identifies new risk loci for atopic dermatitis.

Paternoster L, Standl M, Waage J, ..., Weidinger S, EArly Genetics and Lifecourse Epidemiology (EAGLE) Eczema Consortium

Nat. Genet. 47 (12) 1449-1456 [2015-12-00; online 2015-10-21]

Identification of proteins from human permanent erupted enamel.

Castiblanco GA, Rutishauser D, Ilag LL, ..., Castellanos JE, Mejía W

Eur. J. Oral Sci. 123 (6) 390-395 [2015-12-00; online 2015-10-04]

Hormone Replacement Therapy Associated White Blood Cell DNA Methylation and Gene Expression are Associated With Within-Pair Differences of Body Adiposity and Bone Mass.

Bahl A, Pöllänen E, Ismail K, ..., Kovanen V, Ollikainen M

Twin Res Hum Genet 18 (6) 647-661 [2015-12-00; online 2015-12-19]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.

Gaulton KJ, Ferreira T, Lee Y, ..., Morris AP, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium

Nat. Genet. 47 (12) 1415-1425 [2015-12-00; online 2015-11-09]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus.

Bentham J, Morris DL, Cunninghame Graham DS, ..., Alarcón-Riquelme ME, Vyse TJ

Nat. Genet. 47 (12) 1457-1464 [2015-12-00; online 2015-10-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Freshwater protists do not go with the flow: population structure in Gonyostomum semen independent of connectivity among lakes.

Sassenhagen I, Sefbom J, Säll T, Godhe A, Rengefors K

Environ. Microbiol. 17 (12) 5063-5072 [2015-12-00; online 2015-07-18]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Experiences with workflows for automating data-intensive bioinformatics

Spjuth O, Bongcam-Rudloff E, Hernández GC, ..., Siretskiy A, Vassilev D

Biol. Direct 10 (1) - [2015-12-00; online 2015-08-19]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Emmprin Expression Predicts Response and Survival following Cisplatin Containing Chemotherapy for Bladder Cancer: A Validation Study.

Hemdan T, Malmström PU, Jahnson S, Segersten U

J. Urol. 194 (6) 1575-1581 [2015-12-00; online 2015-06-30]

Discovery of New Risk Markers for Ischemic Stroke Using a Novel Targeted Proteomics Chip.

Lind L, Siegbahn A, Lindahl B, ..., Sundström J, Ärnlöv J

Stroke 46 (12) 3340-3347 [2015-12-00; online 2015-11-05]

Affinity Proteomics Uppsala [Technology development] Clinical Biomarkers PLA and Single Cell Proteomics [Service]

Characterization of human organ donors testing positive for type 1 diabetes-associated autoantibodies.

Wiberg A, Granstam A, Ingvast S, ..., Korsgren O, Skog O

Clin. Exp. Immunol. 182 (3) 278-288 [2015-12-00; online 2015-08-28]

Captured metagenomics: large-scale targeting of genes based on 'sequence capture' reveals functional diversity in soils.

Manoharan L, Kushwaha SK, Hedlund K, Ahrén D

DNA Res. 22 (6) 451-460 [2015-12-00; online 2015-10-23]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Bioenergetic cues shift FXR splicing towards FXRα2 to modulate hepatic lipolysis and fatty acid metabolism.

Correia JC, Massart J, de Boer JF, ..., Groen AK, Ruas JL

Mol Metab 4 (12) 891-902 [2015-12-00; online 2015-09-26]

Bacterial diversity along a 2600 km river continuum.

Savio D, Sinclair L, Ijaz UZ, ..., Farnleitner AH, Eiler A

Environ. Microbiol. 17 (12) 4994-5007 [2015-12-00; online 2015-04-30]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Associations between circulating proteins and corresponding genes expressed in coronary thrombi in patients with acute myocardial infarction.

Helseth R, Weiss TW, Opstad TB, ..., Arnesen H, Seljeflot S

Thromb. Res. 136 (6) 1240-1244 [2015-12-00; online 2015-10-08]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Amelioration of the Fitness Costs of Antibiotic Resistance Due To Reduced Outer Membrane Permeability by Upregulation of Alternative Porins.

Knopp M, Andersson DI

Mol. Biol. Evol. 32 (12) 3252-3263 [2015-12-00; online 2015-09-12]

De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.

Olsen RA, Bunikis I, Tiukova I, ..., Käller M, Vezzi F

Gigascience 4 (-) 56 [2015-11-26; online 2015-11-26]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genome-Wide Association Study Identifies That the ABO Blood Group System Influences Interleukin-10 Levels and the Risk of Clinical Events in Patients with Acute Coronary Syndrome.

Johansson Å, Alfredsson J, Eriksson N, Wallentin L, Siegbahn A

PLoS ONE 10 (11) e0142518 [2015-11-24; online 2015-11-24]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel.

Zubair S, Fischer A, Liljander A, ..., Bongcam-Rudloff E, Jores J

Stand Genomic Sci 10 (-) 109 [2015-11-20; online 2015-11-20]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Combinations of Genetic Data Present in Bipolar Patients, but Absent in Control Persons.

Mellerup E, Andreassen OA, Bennike B, ..., Werge T, Moeller GL

PLoS ONE 10 (11) e0143432 [2015-11-20; online 2015-11-20]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes.

Le Rhun A, Beer YY, Reimegård J, Chylinski K, Charpentier E

RNA Biol 13 (2) 177-195 [2015-11-19; online 2015-11-19]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

DNA-dependent formation of transcription factor pairs alters their binding specificity.

Jolma A, Yin Y, Nitta KR, ..., Morgunova E, Taipale J

Nature 527 (7578) 384-388 [2015-11-19; online 2015-11-10]

Karolinska High Throughput Center (KHTC) Protein Science Facility (PSF)

A Conserved Odorant Receptor Detects the Same 1-Indanone Analogs in a Tortricid and a Noctuid Moth

Gonzalez F, Bengtsson JM, Walker WB, ..., Ignell R, Bengtsson M

Front. Ecol. Evol. 3 (-) - [2015-11-19; online 2015-11-19]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring.

Kvastad L, Werne Solnestam B, Johansson E, ..., Latta D, Lundeberg J

Sci Rep 5 (-) 16519 [2015-11-12; online 2015-11-12]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3.

Manzoor S, Müller B, Niazi A, Schnürer A, Bongcam-Rudloff E

Stand Genomic Sci 10 (-) 99 [2015-11-11; online 2015-11-11]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Normalization of Host Intestinal Mucus Layers Requires Long-Term Microbial Colonization.

Johansson ME, Jakobsson HE, Holmén-Larsson J, ..., Bäckhed F, Hansson GC

Cell Host Microbe 18 (5) 582-592 [2015-11-11; online 2015-11-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Immunocapture strategies in translational proteomics.

Fredolini C, Byström S, Pin E, ..., Nilsson P, Schwenk JM

Expert Rev Proteomics 13 (1) 83-98 [2015-11-11; online 2015-11-11]

Affinity Proteomics Stockholm [Technology development]

Effect of genetic and environmental factors on protein biomarkers for common non-communicable disease and use of personally normalized plasma protein profiles (PNPPP).

Enroth S, Bosdotter Enroth S, Johansson Å, Gyllensten U

Biomarkers 20 (6-7) 355-364 [2015-11-09; online 2015-11-09]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure PLA and Single Cell Proteomics [Service]

Meta-analysis identifies seven susceptibility loci involved in the atopic march.

Marenholz I, Esparza-Gordillo J, Rüschendorf F, ..., Henderson AJ, Lee YA

Nat Commun 6 (-) 8804 [2015-11-06; online 2015-11-06]

Intra-mitochondrial Methylation Deficiency Due to Mutations in SLC25A26.

Kishita Y, Pajak A, Bolar NA, ..., Okazaki Y, Wedell A

Am. J. Hum. Genet. 97 (5) 761-768 [2015-11-05; online 2015-11-03]

Clinical Genomics Clinical Genomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

In search for symmetries in the metabolism of cancer.

Gatto F, Nielsen J

Wiley Interdiscip Rev Syst Biol Med 8 (1) 23-35 [2015-11-05; online 2015-11-05]

Bioinformatics (NBIS) [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Dominant Genetic Variation and Missing Heritability for Human Complex Traits: Insights from Twin versus Genome-wide Common SNP Models.

Chen X, Kuja-Halkola R, Rahman I, ..., Pedersen NL, Magnusson PK

Am. J. Hum. Genet. 97 (5) 708-714 [2015-11-05; online 2015-11-07]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Quantitative proteogenomics of human pathogens using DIA-MS.

Malmström L, Bakochi A, Svensson G, ..., Karlsson C, Malmström J

J Proteomics 129 (-) 98-107 [2015-11-03; online 2015-09-19]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Elevated expression of the C-type lectin CD93 in the glioblastoma vasculature regulates cytoskeletal rearrangements that enhance vessel function and reduce host survival.

Langenkamp E, Zhang L, Lugano R, ..., Smits A, Dimberg A

Cancer Res. 75 (21) 4504-4516 [2015-11-01; online 2015-09-11]

Variant Profiling of Candidate Genes in Pancreatic Ductal Adenocarcinoma.

Huang J, Löhr JM, Nilsson M, ..., Zheng Z, Ye W

Clin. Chem. 61 (11) 1408-1416 [2015-11-00; online 2015-09-16]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The Role of FTO and Vitamin D for the Weight Loss Effect of Roux-en-Y Gastric Bypass Surgery in Obese Patients.

Bandstein M, Schultes B, Ernst B, ..., Schiöth HB, Benedict C

Obes Surg 25 (11) 2071-2077 [2015-11-00; online 2015-03-01]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The Human Endometrium-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling.

Zieba A, Sjöstedt E, Olovsson M, ..., Uhlen M, Ponten F

OMICS 19 (11) 659-668 [2015-11-00; online 2015-10-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Technology development]

Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution.

Martijn J, Schulz F, Zaremba-Niedzwiedzka K, ..., Guy L, Ettema TJ

ISME J 9 (11) 2373-2385 [2015-11-00; online 2015-04-07]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data.

Nater A, Burri R, Kawakami T, Smeds L, Ellegren H

Syst. Biol. 64 (6) 1000-1017 [2015-11-00; online 2015-07-19]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Rescue of primary ubiquinone deficiency due to a novel COQ7 defect using 2,4-dihydroxybensoic acid.

Freyer C, Stranneheim H, Naess K, ..., Wredenberg A, Wedell A

J. Med. Genet. 52 (11) 779-783 [2015-11-00; online 2015-06-19]

Clinical Genomics Clinical Genomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Population genetic differentiation of height and body mass index across Europe.

Robinson MR, Hemani G, Medina-Gomez C, ..., Yang J, Visscher PM

Nat. Genet. 47 (11) 1357-1362 [2015-11-00; online 2015-09-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Mutation in CEP63 co-segregating with developmental dyslexia in a Swedish family.

Einarsdottir E, Svensson I, Darki F, ..., Kere J, Matsson H

Hum. Genet. 134 (11-12) 1239-1248 [2015-11-00; online 2015-09-25]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers.

Burri R, Nater A, Kawakami T, ..., Török J, Ellegren H

Genome Res. 25 (11) 1656-1665 [2015-11-00; online 2015-09-09]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Inactivation of the Deg protease family in the cyanobacterium Synechocystis sp. PCC 6803 has impact on the outer cell layers.

Cheregi O, Miranda H, Gröbner G, Funk C

Journal of Photochemistry and Photobiology B: Biology 152 (Pt B) 383-394 [2015-11-00; online 2015-05-22]

Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata Née)

Sork VL, Smouse PE, Grivet D, Scofield DG

Evol Ecol 29 (6) 927-945 [2015-11-00; online 2015-11-12]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

High-Throughput Sequencing Reveals Drastic Changes in Fungal Communities in the Phyllosphere of Norway Spruce (Picea abies) Following Invasion of the Spruce Bud Scale (Physokermes piceae).

Menkis A, Marčiulynas A, Gedminas A, Lynikienė J, Povilaitienė A

Microb. Ecol. 70 (4) 904-911 [2015-11-00; online 2015-06-10]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Herring and Beef Meals Lead to Differences in Plasma 2-Aminoadipic Acid, β-Alanine, 4-Hydroxyproline, Cetoleic Acid, and Docosahexaenoic Acid Concentrations in Overweight Men.

Ross AB, Svelander C, Undeland I, Pinto R, Sandberg AS

J. Nutr. 145 (11) 2456-2463 [2015-11-00; online 2015-09-25]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples.

Moens LN, Falk-Sörqvist E, Ljungström V, ..., Nilsson M, Botling J

J Mol Diagn 17 (6) 729-739 [2015-11-00; online 2015-09-03]

Clinical Genomics Clinical Genomics Uppsala NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin.

Wu G, Zhao H, Li C, ..., Nagarajan N, Dawson TL

PLoS Genet. 11 (11) e1005614 [2015-11-00; online 2015-11-05]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Fibroblast Growth Factor 23 and Incidence of Subarachnoid Hemorrhage: Nested Case-Control Study.

Söderholm M, Engström G

Stroke 46 (11) 3260-3262 [2015-11-00; online 2015-09-22]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Exploring the genetics of irritable bowel syndrome: a GWA study in the general population and replication in multinational case-control cohorts.

Ek WE, Reznichenko A, Ripke S, ..., Wouters MM, D'Amato M

Gut 64 (11) 1774-1782 [2015-11-00; online 2014-09-23]

Mutation Analysis Facility (MAF) NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Early Exposure to Dogs and Farm Animals and the Risk of Childhood Asthma.

Fall T, Lundholm C, Örtqvist AK, ..., Ingelsson E, Almqvist C

JAMA Pediatr 169 (11) e153219 [2015-11-00; online 2015-11-02]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Assessing the consistency of public human tissue RNA-seq data sets.

Danielsson F, James T, Gomez-Cabrero D, Huss M

Brief. Bioinformatics 16 (6) 941-949 [2015-11-00; online 2015-04-02]

Bioinformatics (NBIS) [Technology development] Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Assessing the Barley Genome Zipper and Genomic Resources for Breeding Purposes.

Silvar C, Martis MM, Nussbaumer T, ..., Ordon F, Perovic D

Plant Genome 8 (3) eplantgenome2015.06.0045 [2015-11-00; online 2015-11-01]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities.

Sanli K, Bengtsson-Palme J, Nilsson RH, ..., Blanck H, Eriksson KM

Front Microbiol 6 (-) 1192 [2015-10-30; online 2015-10-30]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India.

Johnning A, Kristiansson E, Angelin M, ..., Johansson A, Larsson DG

BMC Microbiol. 15 (-) 235 [2015-10-24; online 2015-10-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Nurr1 and Retinoid X Receptor Ligands Stimulate Ret Signaling in Dopamine Neurons and Can Alleviate α-Synuclein Disrupted Gene Expression.

Volakakis N, Tiklova K, Decressac M, ..., Björklund A, Perlmann T

J. Neurosci. 35 (42) 14370-14385 [2015-10-21; online 2015-10-23]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetic Polymorphisms in Vitamin D Metabolism and Signaling Genes and Risk of Breast Cancer: A Nested Case-Control Study.

Clendenen TV, Ge W, Koenig KL, ..., Sund M, Zeleniuch-Jacquotte A

PLoS ONE 10 (10) e0140478 [2015-10-21; online 2015-10-21]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Structure-activity relationships for lipoprotein lipase agonists that lower plasma triglycerides in vivo.

Caraballo R, Larsson M, Nilsson SK, ..., Enquist P, Elofsson M

Eur J Med Chem 103 (-) 191-209 [2015-10-20; online 2015-09-12]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Membrane vesicle-mediated release of bacterial RNA.

Sjöström AE, Sandblad L, Uhlin BE, Wai SN

Sci Rep 5 (-) 15329 [2015-10-20; online 2015-10-20]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans.

Dumesic PA, Rosenblad MA, Samuelsson T, ..., Yates JR, Madhani HD

Nucleic Acids Res. 43 (18) 9017-9027 [2015-10-15; online 2015-08-16]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Mutation in NRAS in familial Noonan syndrome--case report and review of the literature.

Ekvall S, Wilbe M, Dahlgren J, ..., Annerén G, Bondeson ML

BMC Med. Genet. 16 (-) 95 [2015-10-14; online 2015-10-14]

Clinical Genomics Clinical Genomics Uppsala

The folate-coupled enzyme MTHFD2 is a nuclear protein and promotes cell proliferation.

Gustafsson Sheppard N, Jarl L, Mahadessian D, ..., Jain M, Nilsson R

Sci Rep 5 (-) 15029 [2015-10-13; online 2015-10-13]

Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes.

Pucholt P, Sjödin P, Weih M, Rönnberg-Wästljung AC, Berlin S

BMC Plant Biol. 15 (-) 244 [2015-10-12; online 2015-10-12]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Brachyspira suanatina sp. nov., an enteropathogenic intestinal spirochaete isolated from pigs and mallards: genomic and phenotypic characteristics.

Mushtaq M, Zubair S, Råsbäck T, Bongcam-Rudloff E, Jansson DS

BMC Microbiol. 15 (-) 208 [2015-10-12; online 2015-10-12]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers.

Voisin S, Almén MS, Zheleznyakova GY, ..., Rask-Andersen M, Schiöth HB

Genome Med 7 (-) 103 [2015-10-08; online 2015-10-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Growth of Chitinophaga pinensis on Plant Cell Wall Glycans and Characterisation of a Glycoside Hydrolase Family 27 β-l-Arabinopyranosidase Implicated in Arabinogalactan Utilisation.

McKee LS, Brumer H

PLoS ONE 10 (10) e0139932 [2015-10-08; online 2015-10-08]

Evaluation of whole-genome sequencing of four Chinese crested dogs for variant detection using the ion proton system.

Viluma A, Sayyab S, Mikko S, Andersson G, Bergström TF

Canine Genet Epidemiol 2 (-) 16 [2015-10-08; online 2015-10-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Comparative Sigma Factor-mRNA Levels in Mycobacterium marinum under Stress Conditions and during Host Infection.

Pettersson BM, Das S, Behra PR, ..., Ennis DG, Kirsebom LA

PLoS ONE 10 (10) e0139823 [2015-10-07; online 2015-10-07]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling.

Caesar R, Tremaroli V, Kovatcheva-Datchary P, Cani PD, Bäckhed F

Cell Metab. 22 (4) 658-668 [2015-10-06; online 2015-09-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment.

Sheng Z, Pettersson ME, Honaker CF, Siegel PB, Carlborg Ö

Genome Biol. 16 (-) 219 [2015-10-01; online 2015-10-01]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Spatiotemporal Heterogeneity Characterizes the Genetic Landscape of Pheochromocytoma and Defines Early Events in Tumorigenesis.

Crona J, Backman S, Maharjan R, ..., Hellman P, Björklund P

Clin. Cancer Res. 21 (19) 4451-4460 [2015-10-01; online 2015-05-21]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Homozygous loss-of-function variants in European cosmopolitan and isolate populations.

Kaiser VB, Svinti V, Prendergast JG, ..., Semple CA, Wilson JF

Hum. Mol. Genet. 24 (19) 5464-5474 [2015-10-01; online 2015-07-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Candidate gene analysis and exome sequencing confirm LBX1 as a susceptibility gene for idiopathic scoliosis.

Grauers A, Wang J, Einarsdottir E, ..., Kere J, Gerdhem P

Spine J 15 (10) 2239-2246 [2015-10-01; online 2015-05-20]

Mutation Analysis Facility (MAF) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Trimeric microsomal glutathione transferase 2 displays one third of the sites reactivity.

Ahmad S, Thulasingam M, Palombo I, ..., Haeggström JZ, Rinaldo-Matthis A

Biochim. Biophys. Acta 1854 (10 Pt A) 1365-1371 [2015-10-00; online 2015-06-13]

Transcriptome Profiling Reveals Degree of Variability in Induced Pluripotent Stem Cell Lines: Impact for Human Disease Modeling.

Schuster J, Halvardson J, Pilar Lorenzo L, ..., Feuk L, Dahl N

Cell Reprogram 17 (5) 327-337 [2015-10-00; online 2015-09-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The use of gene arrays and corresponding connectivity mapping (Cmap) to identify novel anti-ageing ingredients.

Gillbro JM, Merinville E, Olsson M, ..., Visdal-Johnsen L, Mavon A

Int J Cosmet Sci 37 Suppl 1 (-) 9-14 [2015-10-00; online 2015-06-27]

The effects of age and gender on plasma levels of 63 cytokines.

Larsson A, Carlsson L, Gordh T, ..., Thulin M, Kamali-Moghaddam M

J. Immunol. Methods 425 (-) 58-61 [2015-10-00; online 2015-06-14]

Affinity Proteomics Uppsala [Collaborative] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Collaborative]

The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study.

Winkler TW, Justice AE, Graff M, ..., Kutalik Z, Loos RJ

PLoS Genet. 11 (10) e1005378 [2015-10-00; online 2015-10-01]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents.

Bengtsson-Palme J, Angelin M, Huss M, ..., Larsson DGJ, Johansson A

Antimicrob. Agents Chemother. 59 (10) 6551-6560 [2015-10-00; online 2015-08-12]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

The Human Glioblastoma Cell Culture Resource: Validated Cell Models Representing All Molecular Subtypes.

Xie Y, Bergström T, Jiang Y, ..., Forsberg-Nilsson K, Uhrbom L

EBioMedicine 2 (10) 1351-1363 [2015-10-00; online 2015-08-15]

Signatures of post-zygotic structural genetic aberrations in the cells of histologically normal breast tissue that can predispose to sporadic breast cancer.

Forsberg LA, Rasi C, Pekar G, ..., Tot T, Dumanski JP

Genome Res. 25 (10) 1521-1535 [2015-10-00; online 2015-10-03]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Quantitative Mass Spectrometry Reveals Partial Translational Regulation for Dosage Compensation in Chicken.

Uebbing S, Konzer A, Xu L, ..., Bergquist J, Ellegren H

Mol. Biol. Evol. 32 (10) 2716-2725 [2015-10-00; online 2015-06-26]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Profound parental bias associated with chromosome 14 acquired uniparental disomy indicates targeting of an imprinted locus.

Chase A, Leung W, Tapper W, ..., Dumanski JP, Cross NC

Leukemia 29 (10) 2069-2074 [2015-10-00; online 2015-06-27]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Positive Modulation of the Glycine Receptor by Means of Glycine Receptor-Binding Aptamers.

Shalaly ND, Aneiros E, Blank M, ..., Andersson CV, Sandberg K

J Biomol Screen 20 (9) 1112-1123 [2015-10-00; online 2015-06-12]

Drug Discovery and Development (DDD) [Collaborative]

Isolation of novel IncA/C and IncN fluoroquinolone resistance plasmids from an antibiotic-polluted lake.

Flach CF, Johnning A, Nilsson I, ..., Kristiansson E, Larsson DG

J. Antimicrob. Chemother. 70 (10) 2709-2717 [2015-10-00; online 2015-07-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index.

Yang J, Bakshi A, Zhu Z, ..., Goddard ME, Visscher PM

Nat. Genet. 47 (10) 1114-1120 [2015-10-00; online 2015-09-01]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Dibenzocyclooctadiene lignans from Schisandra spp. selectively inhibit the growth of the intracellular bacteria Chlamydia pneumoniae and Chlamydia trachomatis.

Hakala E, Hanski L, Uvell H, ..., Elofsson M, Vuorela PM

J. Antibiot. 68 (10) 609-614 [2015-10-00; online 2015-05-07]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Cytostatic Effect of Repeated Exposure to Simvastatin: A Mechanism for Chronic Myotoxicity Revealed by the Use of Mesodermal Progenitors Derived from Human Pluripotent Stem Cells.

Peric D, Barragan I, Giraud-Triboult K, ..., Laustriat D, Peschanski M

Stem Cells 33 (10) 2936-2948 [2015-10-00; online 2015-07-18]

Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella.

Steige KA, Reimegård J, Koenig D, Scofield DG, Slotte T

Mol. Biol. Evol. 32 (10) 2501-2514 [2015-10-00; online 2015-08-28]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

BCG Skin Infection Triggers IL-1R-MyD88-Dependent Migration of EpCAMlow CD11bhigh Skin Dendritic cells to Draining Lymph Node During CD4+ T-Cell Priming.

Bollampalli VP, Harumi Yamashiro L, Feng X, ..., Nylén S, Rothfuchs AG

PLoS Pathog. 11 (10) e1005206 [2015-10-00; online 2015-10-06]

Integrated Microscopy Technologies Stockholm [Service]

Acid-Base Catalyst Discriminates between a Fructose 6-Phosphate Aldolase and a Transaldolase

Stellmacher L, Sandalova T, Leptihn S, ..., Sprenger GA, Samland AK

ChemCatChem 7 (19) 3140-3151 [2015-10-00; online 2015-08-06]

A comprehensive 1,000 Genomes-based genome-wide association meta-analysis of coronary artery disease.

Nikpay M, Goel A, Won HH, ..., Farrall M, CARDIoGRAMplusC4D Consortium

Nat. Genet. 47 (10) 1121-1130 [2015-10-00; online 2015-09-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A New Method for Detecting Associations with Rare Copy-Number Variants.

Tzeng JY, Magnusson PK, Sullivan PF, Swedish Schizophrenia Consortium , Szatkiewicz JP

PLoS Genet. 11 (10) e1005403 [2015-10-00; online 2015-10-02]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Cerebrospinal fluid monoamine metabolite concentrations as intermediate phenotypes between glutamate-related genes and psychosis.

Andreou D, Söderman E, Axelsson T, ..., Agartz I, Jönsson EG

Psychiatry Res 229 (1-2) 497-504 [2015-09-30; online 2015-07-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Virtual Screening for Transition State Analogue Inhibitors of IRAP Based on Quantum Mechanically Derived Reaction Coordinates

Svensson F, Engen K, Lundbäck T, Larhed M, Sköld C

J. Chem. Inf. Model. 55 (9) 1984-1993 [2015-09-28; online 2015-09-28]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).

Delhomme N, Sundström G, Zamani N, ..., Grabherr MG, Street NR

PLoS ONE 10 (9) e0139080 [2015-09-28; online 2015-09-28]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis.

Dmitriev AA, Rosenberg EE, Krasnov GS, ..., Senchenko VN, Kashuba VI

Dis. Markers 2015 (-) 241301 [2015-09-28; online 2015-09-28]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes.

Saw JH, Spang A, Zaremba-Niedzwiedzka K, ..., Guy L, Ettema TJG

Philos. Trans. R. Soc. Lond., B, Biol. Sci. 370 (1678) 20140328 [2015-09-26; online 2015-09-02]

Microbial Single Cell Genomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The genomes of three stocks comprising the most widely utilized live sporozoite Theileria parva vaccine exhibit very different degrees and patterns of sequence divergence.

Norling M, Bishop RP, Pelle R, ..., Daubenberger CA, Silva JC

BMC Genomics 16 (-) 729 [2015-09-24; online 2015-09-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques.

Günther T, Valdiosera C, Malmström H, ..., Götherström A, Jakobsson M

Proc. Natl. Acad. Sci. U.S.A. 112 (38) 11917-11922 [2015-09-22; online 2015-09-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Gene expression profiling of pre-eclamptic placentae by RNA sequencing.

Kaartokallio T, Cervera A, Kyllönen A, ..., Laivuori H, FINNPEC Core Investigator Group

Sci Rep 5 (-) 14107 [2015-09-21; online 2015-09-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Draft genome sequence of 'Treponema phagedenis' strain V1, isolated from bovine digital dermatitis.

Mushtaq M, Manzoor S, Pringle M, Rosander A, Bongcam-Rudloff E

Stand Genomic Sci 10 (-) 67 [2015-09-21; online 2015-09-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Dormant phages of Helicobacter pylori reveal distinct populations in Europe.

Vale FF, Vadivelu J, Oleastro M, ..., Mégraud F, Lehours P

Sci Rep 5 (-) 14333 [2015-09-21; online 2015-09-21]

Clinical Genomics [Collaborative] Clinical Genomics Stockholm [Collaborative]

PARP1- and CTCF-Mediated Interactions between Active and Repressed Chromatin at the Lamina Promote Oscillating Transcription.

Zhao H, Sifakis EG, Sumida N, ..., Imreh MP, Göndör A

Mol. Cell 59 (6) 984-997 [2015-09-17; online 2015-08-27]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetic and morphological evidence for introgression between three species of willows.

Fogelqvist J, Verkhozina AV, Katyshev AI, ..., Lascoux M, Berlin S

BMC Evol. Biol. 15 (-) 193 [2015-09-16; online 2015-09-16]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

WNT3 involvement in human bladder exstrophy and cloaca development in zebrafish.

Baranowska Körberg I, Hofmeister W, Markljung E, ..., Lindstrand A, Nordenskjöld A

Hum. Mol. Genet. 24 (18) 5069-5078 [2015-09-15; online 2015-06-25]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

HLA class I is most tightly linked to levels of tapasin compared with other antigen-processing proteins in glioblastoma.

Thuring C, Follin E, Geironson L, ..., Buus S, Paulsson KM

Br. J. Cancer 113 (6) 952-962 [2015-09-15; online 2015-08-28]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Glioma-derived plasminogen activator inhibitor-1 (PAI-1) regulates the recruitment of LRP1 positive mast cells.

Roy A, Coum A, Marinescu VD, ..., Pontén F, Tchougounova E

Oncotarget 6 (27) 23647-23661 [2015-09-15; online 2015-07-15]

Genetics and Prognostication in Splenic Marginal Zone Lymphoma: Revelations from Deep Sequencing.

Parry M, Rose-Zerilli MJ, Ljungström V, ..., Oscier D, Strefford JC

Clin. Cancer Res. 21 (18) 4174-4183 [2015-09-15; online 2015-03-18]

Clinical Genomics Clinical Genomics Uppsala

Comprehensive analysis of microRNA expression in regionalized human neural progenitor cells reveals microRNA-10 as a caudalizing factor.

Jönsson ME, Nelander Wahlestedt J, Åkerblom M, ..., Jakobsson J, Parmar M

Development 142 (18) 3166-3177 [2015-09-15; online 2015-09-24]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Surface Chemistry of Nanocellulose Fibers Directs Monocyte/Macrophage Response.

Hua K, Ålander E, Lindström T, ..., Strømme M, Ferraz N

Biomacromolecules 16 (9) 2787-2795 [2015-09-14; online 2015-08-08]

Determination of obesity associated gene variants related to TMEM18 through ultra-deep targeted re-sequencing in a case-control cohort for pediatric obesity.

Rask-Andersen M, Sällman Almén M, Jacobsson JA, ..., Fredriksson R, Schiöth HB

Genet Res (Camb) 97 (-) e16 [2015-09-14; online 2015-09-14]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Rare and low-frequency variants and their association with plasma levels of fibrinogen, FVII, FVIII, and vWF.

Huffman JE, de Vries PS, Morrison AC, ..., O'Donnell CJ, Smith NL

Blood 126 (11) e19-e29 [2015-09-10; online 2015-06-25]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The epigenetic signature of subcutaneous fat cells is linked to altered expression of genes implicated in lipid metabolism in obese women.

Arner P, Sinha I, Thorell A, ..., Dahlman-Wright K, Dahlman I

Clin Epigenetics 7 (-) 93 [2015-09-08; online 2015-09-08]

Tandem Benzophenone Amino Pyridines, Potent and Selective Inhibitors of Human Leukotriene C4 Synthase

Kleinschmidt TK, Haraldsson M, Basavarajappa D, ..., Lindbom L, Haeggstrom JZ

Journal of Pharmacology and Experimental Therapeutics 355 (1) 108-116 [2015-09-08; online 2015-08-17]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Paternally expressed imprinted genes establish postzygotic hybridization barriers in Arabidopsis thaliana.

Wolff P, Jiang H, Wang G, Santos-González J, Köhler C

Elife 4 (-) - [2015-09-07; online 2015-09-07]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.

Horvatovich P, Lundberg EK, Chen YJ, ..., Paik YK, Hancock WS

J. Proteome Res. 14 (9) 3415-3431 [2015-09-04; online 2015-07-23]

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification.

Omenn GS, Lane L, Lundberg EK, ..., Nesvizhskii AI, Deutsch EW

J. Proteome Res. 14 (9) 3452-3460 [2015-09-04; online 2015-07-15]

High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases.

Nätt D, Johansson I, Faresjö T, Ludvigsson J, Thorsell A

Clin Epigenetics 7 (-) 91 [2015-09-04; online 2015-09-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Pseudomonas aeruginosa lasI/rhlI quorum sensing genes promote phagocytosis and aquaporin 9 redistribution to the leading and trailing regions in macrophages.

Holm A, Karlsson T, Vikström E

Front Microbiol 6 (-) 915 [2015-09-03; online 2015-09-03]

Integrated Microscopy Technologies Stockholm [Service]

Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures.

Stödberg T, McTague A, Ruiz AJ, ..., Wedell A, Kurian MA

Nat Commun 6 (-) 8038 [2015-09-03; online 2015-09-03]

Clinical Genomics Clinical Genomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Transplanted Bone Marrow-Derived Cells Contribute to Human Adipogenesis.

Rydén M, Uzunel M, Hård JL, ..., Mattsson J, Arner P

Cell Metab. 22 (3) 408-417 [2015-09-01; online 2015-07-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

An Exopolysaccharide-Deficient Mutant of Lactobacillus rhamnosus GG Efficiently Displays a Protective Llama Antibody Fragment against Rotavirus on Its Surface.

Álvarez B, Krogh-Andersen K, Tellgren-Roth C, ..., Hammarström L, Marcotte H

Appl. Environ. Microbiol. 81 (17) 5784-5793 [2015-09-01; online 2015-06-21]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Widespread non-additive and interaction effects within HLA loci modulate the risk of autoimmune diseases.

Lenz TL, Deutsch AJ, Han B, ..., de Bakker PI, Raychaudhuri S

Nat. Genet. 47 (9) 1085-1090 [2015-09-00; online 2015-08-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Whole exome sequencing identifies LRP1 as a pathogenic gene in autosomal recessive keratosis pilaris atrophicans.

Klar J, Schuster J, Khan TN, ..., Baig SM, Dahl N

J. Med. Genet. 52 (9) 599-606 [2015-09-00; online 2015-07-05]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Use of a proximity extension assay proteomics chip to discover new biomarkers for human atherosclerosis.

Lind L, Ärnlöv J, Lindahl B, ..., Sundström J, Ingelsson E

Atherosclerosis 242 (1) 205-210 [2015-09-00; online 2015-07-14]

Affinity Proteomics Uppsala [Technology development] Clinical Biomarkers PLA and Single Cell Proteomics [Service]

Transcriptomics of colour patterning and coloration shifts in crows.

Poelstra JW, Vijay N, Hoeppner MP, Wolf JB

Mol. Ecol. 24 (18) 4617-4628 [2015-09-00; online 2015-08-25]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Towards a stereoselective synthesis of α,α-disubstituted proline analogues

Das SK, Bhatt N, Mujahid M, ..., Naicker T, Govender T

Tetrahedron Letters 56 (37) 5172-5174 [2015-09-00; online 2015-09-00]

Drug Discovery and Development (DDD) [Collaborative]

Synthesis of enantiopure angiotensin II type 2 receptor [AT2R] antagonist EMA401

Wakchaure PB, Bremberg U, Wannberg J, Larhed M

Tetrahedron 71 (38) 6881-6887 [2015-09-00; online 2015-09-00]

Shared immunological targets in the lungs and joints of patients with rheumatoid arthritis: identification and validation.

Ytterberg AJ, Joshua V, Reynisdottir G, ..., Klareskog L, Catrina AI

Ann. Rheum. Dis. 74 (9) 1772-1777 [2015-09-00; online 2014-05-13]

Polymorphisms in the FK506 binding protein 5 gene are associated with attention deficit hyperactivity disorder and diurnal cortisol levels.

Isaksson J, Allen M, Nilsson KW, Lindblad F

Acta Paediatr. 104 (9) 910-915 [2015-09-00; online 2015-06-03]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Half-of-the-Sites Reactivity of the Castor Δ9-18:0-Acyl Carrier Protein Desaturase.

Liu Q, Chai J, Moche M, ..., Lindqvist Y, Shanklin J

Plant Physiol. 169 (1) 432-441 [2015-09-00; online 2015-08-01]

Exome sequencing followed by genotyping suggests SYPL2 as a susceptibility gene for morbid obesity.

Jiao H, Arner P, Gerdhem P, ..., Kere J, Dahlman I

Eur. J. Hum. Genet. 23 (9) 1216-1222 [2015-09-00; online 2014-11-20]

Mutation Analysis Facility (MAF) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Design, Synthesis and Inhibitory Activity of Photoswitchable RET Kinase Inhibitors

Ferreira R, Nilsson JR, Solano C, Andréasson J, Grøtli M

Sci Rep 5 (1) - [2015-09-00; online 2015-05-06]

Chemical Biology Consortium Sweden (CBCS) [Service]

Auxotrophy and intrapopulation complementary in the 'interactome' of a cultivated freshwater model community.

Garcia SL, Buck M, McMahon KD, ..., Eiler A, Warnecke F

Mol. Ecol. 24 (17) 4449-4459 [2015-09-00; online 2015-07-17]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Analysis of the genetic architecture of susceptibility to cervical cancer indicates that common SNPs explain a large proportion of the heritability.

Chen D, Cui T, Ek WE, ..., Wang H, Gyllensten U

Carcinogenesis 36 (9) 992-998 [2015-09-00; online 2015-06-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Altered serotonin (5-HT) 1D and 2A receptor expression may contribute to defective insulin and glucagon secretion in human type 2 diabetes.

Bennet H, Balhuizen A, Medina A, ..., Wierup N, Fex M

Peptides 71 (-) 113-120 [2015-09-00; online 2015-07-25]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Acute Sleep Loss Induces Tissue-Specific Epigenetic and Transcriptional Alterations to Circadian Clock Genes in Men.

Cedernaes J, Osler ME, Voisin S, ..., Schiöth HB, Benedict C

J. Clin. Endocrinol. Metab. 100 (9) E1255-E1261 [2015-09-00; online 2015-07-15]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Molecular profiling of prostate cancer derived exosomes may reveal a predictive signature for response to docetaxel.

Kharaziha P, Chioureas D, Rutishauser D, ..., Nilsson S, Panaretakis T

Oncotarget 6 (25) 21740-21754 [2015-08-28; online 2015-04-07]

BEX1 acts as a tumor suppressor in acute myeloid leukemia.

Lindblad O, Li T, Su X, ..., Rönnstrand L, Kazi JU

Oncotarget 6 (25) 21395-21405 [2015-08-28; online 2015-06-06]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast.

Huang M, Bai Y, Sjostrom SL, ..., Andersson-Svahn H, Nielsen J

Proc. Natl. Acad. Sci. U.S.A. 112 (34) E4689-E4696 [2015-08-25; online 2015-08-12]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica.

Gkarmiri K, Finlay RD, Alström S, ..., Cubeta MA, Högberg N

BMC Genomics 16 (-) 630 [2015-08-22; online 2015-08-22]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Structure of the Glycosyltransferase Ktr4p from Saccharomyces cerevisiae.

Possner DD, Claesson M, Guy JE

PLoS ONE 10 (8) e0136239 [2015-08-21; online 2015-08-21]

Personality and intelligence: persistence, not self-directedness, cooperativeness or self-transcendence, is related to twins' cognitive abilities.

Mousavi F, Rozsa S, Nilsson T, ..., Anckarsäter H, Garcia D

PeerJ 3 (-) e1195 [2015-08-20; online 2015-08-20]

In Vitro and In Vivo Response to Low-Modulus PMMA-Based Bone Cement.

Carlsson E, Mestres G, Treerattrakoon K, ..., Larsson S, Persson C

Biomed Res Int 2015 (-) 594284 [2015-08-20; online 2015-08-20]

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.

Yu NY, Hallström BM, Fagerberg L, ..., Uhlén M, Daub CO

Nucleic Acids Res. 43 (14) 6787-6798 [2015-08-18; online 2015-06-27]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Collaborative]

The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution.

Zuccolo A, Scofield DG, De Paoli E, Morgante M

Gene 568 (1) 89-99 [2015-08-15; online 2015-05-20]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Genome-wide association study of toxic metals and trace elements reveals novel associations.

Ng E, Lind PM, Lindgren C, ..., Morris A, Lind L

Hum. Mol. Genet. 24 (16) 4739-4745 [2015-08-15; online 2015-05-31]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Gene × dietary pattern interactions in obesity: analysis of up to 68 317 adults of European ancestry.

Nettleton JA, Follis JL, Ngwa JS, ..., Loos RJ, Franks PW

Hum. Mol. Genet. 24 (16) 4728-4738 [2015-08-15; online 2015-05-23]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Sex-Specific Effects of Adiponectin on Carotid Intima-Media Thickness and Incident Cardiovascular Disease.

Persson J, Strawbridge RJ, McLeod O, ..., Hamsten A, IMPROVE Study Group

J Am Heart Assoc 4 (8) e001853 [2015-08-14; online 2015-08-14]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Whole Exome- and mRNA-Sequencing of an AT/RT Case Reveals Few Somatic Mutations and Several Deregulated Signalling Pathways in the Context of SMARCB1 Deficiency.

Sandgren J, Holm S, Marino AM, ..., Nistér M, Díaz de Ståhl T

Biomed Res Int 2015 (-) 862039 [2015-08-12; online 2015-08-12]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Adaptive mutations in sugar metabolism restore growth on glucose in a pyruvate decarboxylase negative yeast strain.

Zhang Y, Liu G, Engqvist MK, ..., Siewers V, Nielsen J

Microb. Cell Fact. 14 (-) 116 [2015-08-08; online 2015-08-08]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Microstructural White Matter Properties Mediate the Association between APOE and Perceptual Speed in Very Old Persons without Dementia.

Laukka EJ, Lövdén M, Kalpouzos G, ..., Fratiglioni L, Bäckman L

PLoS ONE 10 (8) e0134766 [2015-08-07; online 2015-08-07]

Effect of a Bromo Substituent on the Glutathione Peroxidase Activity of a Pyridoxine-like Diselenide.

Singh VP, Poon JF, Butcher RJ, ..., Ott MK, Engman L

J. Org. Chem. 80 (15) 7385-7395 [2015-08-07; online 2015-07-03]

Comprehensive genomic profiles of small cell lung cancer

George J, Lim JS, Jang SJ, ..., Sage J, Thomas RK

Nature 524 (7563) 47-53 [2015-08-06; online 2015-07-13]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation.

Tremaroli V, Karlsson F, Werling M, ..., Nielsen J, Bäckhed F

Cell Metab. 22 (2) 228-238 [2015-08-04; online 2015-08-06]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Crystal structure, biochemical and cellular activities demonstrate separate functions of MTH1 and MTH2.

Carter M, Jemth AS, Hagenkort A, ..., Helleday T, Stenmark P

Nat Commun 6 (-) 7871 [2015-08-04; online 2015-08-04]

MicroRNA-132 enhances transition from inflammation to proliferation during wound healing.

Li D, Wang A, Liu X, ..., Ståhle M, Landén NX

J. Clin. Invest. 125 (8) 3008-3026 [2015-08-03; online 2015-06-30]

Identifying and Assessing Interesting Subgroups in a Heterogeneous Population.

Lee W, Alexeyenko A, Pernemalm M, ..., Lehtiö J, Pawitan Y

Biomed Res Int 2015 (-) 462549 [2015-08-03; online 2015-08-03]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Heat differentiated complement factor profiling.

Hamsten C, Skattum L, Truedsson L, ..., Nilsson P, Neiman M

J Proteomics 126 (-) 155-162 [2015-08-03; online 2015-06-07]

Affinity Proteomics Stockholm [Technology development]

Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution.

Sahlén P, Abdullayev I, Ramsköld D, ..., Lundeberg J, Sandberg R

Genome Biol. 16 (-) 156 [2015-08-03; online 2015-08-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer.

O'Hurley G, Busch C, Fagerberg L, ..., Uhlén M, Pontén F

PLoS ONE 10 (8) e0133449 [2015-08-03; online 2015-08-03]

Affinity Proteomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling [Technology development]

Effect of genetic variations on ticagrelor plasma levels and clinical outcomes.

Varenhorst C, Eriksson N, Johansson Å, ..., Wallentin L, PLATO Investigators

Eur. Heart J. 36 (29) 1901-1912 [2015-08-01; online 2015-05-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Whole-exome sequencing of Ethiopian patients with ichthyosis vulgaris and atopic dermatitis.

Taylan F, Nilsson D, Asad S, ..., Nordenskjöld M, Bradley M

J. Allergy Clin. Immunol. 136 (2) 507-9.e19 [2015-08-00; online 2015-03-31]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Representation of selected-reaction monitoring data in the mzQuantML data standard.

Qi D, Lawless C, Teleman J, ..., Hubbard S, Jones AR

Proteomics 15 (15) 2592-2596 [2015-08-00; online 2015-04-18]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Prevalence of polymorphisms with significant resistance to NS5A inhibitors in treatment-naive patients with hepatitis C virus genotypes 1a and 3a in Sweden.

Lindström I, Kjellin M, Palanisamy N, ..., Lannergard A, Lennerstrand J

Infect Dis (Lond) 47 (8) 555-562 [2015-08-00; online 2015-04-09]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Manganese lipoxygenase of F. oxysporum and the structural basis for biosynthesis of distinct 11-hydroperoxy stereoisomers.

Wennman A, Magnuson A, Hamberg M, Oliw EH

J. Lipid Res. 56 (8) 1606-1615 [2015-08-00; online 2015-06-27]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Inbreeding Affects Gene Expression Differently in Two Self-Incompatible Arabidopsis lyrata Populations with Similar Levels of Inbreeding Depression.

Menzel M, Sletvold N, Ågren J, Hansson B

Mol. Biol. Evol. 32 (8) 2036-2047 [2015-08-00; online 2015-04-10]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Association of the LINGO2-related SNP rs10968576 with body mass in a cohort of elderly Swedes.

Rask-Andersen M, Almén MS, Lind L, Schiöth HB

Mol. Genet. Genomics 290 (4) 1485-1491 [2015-08-00; online 2015-02-26]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A prezygotic transmission distorter acting equally in female and male zebra finches Taeniopygia guttata.

Knief U, Schielzeth H, Ellegren H, Kempenaers B, Forstmeier W

Mol. Ecol. 24 (15) 3846-3859 [2015-08-00; online 2015-06-20]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Bioinformatic Challenges in Clinical Diagnostic Application of Targeted Next Generation Sequencing: Experience from Pheochromocytoma.

Crona J, Ljungström V, Welin S, ..., Hellman P, Björklund P

PLoS ONE 10 (7) e0133210 [2015-07-31; online 2015-07-31]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Identification of New Potential Interaction Partners for Human Cytoplasmic Copper Chaperone Atox1: Roles in Gene Regulation?

Öhrvik H, Wittung-Stafshede P

Int J Mol Sci 16 (8) 16728-16739 [2015-07-23; online 2015-07-23]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Directional dominance on stature and cognition in diverse human populations.

Joshi PK, Esko T, Mattsson H, ..., Polašek O, Wilson JF

Nature 523 (7561) 459-462 [2015-07-23; online 2015-07-02]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio.

Clausson C, Arngården L, Ishaq O, ..., Wählby C, Söderberg O

Sci Rep 5 (-) 12317 [2015-07-23; online 2015-07-23]

BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development] Integrated Microscopy Technologies Stockholm [Collaborative]

lobChIP: from cells to sequencing ready ChIP libraries in a single day.

Wallerman O, Nord H, Bysani M, Borghini L, Wadelius C

Epigenetics Chromatin 8 (-) 25 [2015-07-21; online 2015-07-21]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Two new loci and gene sets related to sex determination and cancer progression are associated with susceptibility to testicular germ cell tumor.

Kristiansen W, Karlsson R, Rounge TB, ..., Grotmol T, Wiklund F

Hum. Mol. Genet. 24 (14) 4138-4146 [2015-07-15; online 2015-04-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Predisposition to Childhood Otitis Media and Genetic Polymorphisms within the Toll-Like Receptor 4 (TLR4) Locus.

Hafrén L, Einarsdottir E, Kentala E, ..., Kere J, Mattila PS

PLoS ONE 10 (7) e0132551 [2015-07-15; online 2015-07-15]

Evaluation of the protein biomarkers and the analgesic response to systemic methylene blue in patients with refractory neuropathic pain: a double-blind, controlled study.

Miclescu AA, Svahn M, Gordh TE

J Pain Res 8 (-) 387-397 [2015-07-15; online 2015-07-15]

Affinity Proteomics Uppsala [Technology development] Clinical Biomarkers PLA and Single Cell Proteomics [Service]

Distinguishing Mast Cell Progenitors from Mature Mast Cells in Mice.

Dahlin JS, Ding Z, Hallgren J

Stem Cells Dev. 24 (14) 1703-1711 [2015-07-15; online 2015-03-10]

Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems.

Osman A, Hitzler WE, Ameur A, Provost P

PLoS ONE 10 (7) e0133070 [2015-07-14; online 2015-07-14]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes.

Peura S, Sinclair L, Bertilsson S, Eiler A

Sci Rep 5 (-) 12102 [2015-07-10; online 2015-07-10]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

SF3B1 mutation identifies a distinct subset of myelodysplastic syndrome with ring sideroblasts.

Malcovati L, Karimi M, Papaemmanuil E, ..., Cazzola M, Hellström Lindberg E

Blood 126 (2) 233-241 [2015-07-09; online 2015-05-10]

Clinical Genomics Clinical Genomics Uppsala NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress.

Wallace-Salinas V, Brink DP, Ahrén D, Gorwa-Grauslund MF

BMC Genomics 16 (-) 514 [2015-07-09; online 2015-07-09]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Identification of large variation in pfcrt, pfmdr-1 and pfubp-1 markers in Plasmodium falciparum isolates from Ethiopia and Tanzania.

Golassa L, Kamugisha E, Ishengoma DS, ..., Choy A, Swedberg G

Malar. J. 14 (-) 264 [2015-07-08; online 2015-07-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation.

Tan TC, Kracher D, Gandini R, ..., Ludwig R, Divne C

Nat Commun 6 (-) 7542 [2015-07-07; online 2015-07-07]

Scaffolding of a bacterial genome using MinION nanopore sequencing.

Karlsson E, Lärkeryd A, Sjödin A, Forsman M, Stenberg P

Sci Rep 5 (-) 11996 [2015-07-07; online 2015-07-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genome Characterization, Prevalence and Distribution of a Macula-Like Virus from Apis mellifera and Varroa destructor.

de Miranda JR, Cornman RS, Evans JD, ..., Neumann P, Gauthier L

Viruses 7 (7) 3586-3602 [2015-07-06; online 2015-07-06]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Foxf2 Is Required for Brain Pericyte Differentiation and Development and Maintenance of the Blood-Brain Barrier.

Reyahi A, Nik AM, Ghiami M, ..., Johansson BR, Carlsson P

Dev. Cell 34 (1) 19-32 [2015-07-06; online 2015-06-25]

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides.

Tsirigos KD, Peters C, Shu N, Käll L, Elofsson A

Nucleic Acids Res. 43 (W1) W401-W407 [2015-07-01; online 2015-05-15]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Using Genetic Variants to Assess the Relationship Between Circulating Lipids and Type 2 Diabetes.

Fall T, Xie W, Poon W, ..., Frayling TM, Ingelsson E

Diabetes 64 (7) 2676-2684 [2015-07-00; online 2015-05-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

UV irradiation responses in Giardia intestinalis.

Einarsson E, Svärd SG, Troell K

Exp. Parasitol. 154 (-) 25-32 [2015-07-00; online 2015-04-01]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Toward Rare Blood Cell Preservation for RNA Sequencing.

Vickovic S, Ahmadian A, Lewensohn R, Lundeberg J

J Mol Diagn 17 (4) 352-359 [2015-07-00; online 2015-05-16]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Proteomics for the detection of indirect markers of steroids treatment in bovine muscle.

Stella R, Biancotto G, Arrigoni G, ..., Angeletti R, James P

Proteomics 15 (13) 2332-2341 [2015-07-00; online 2015-03-12]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Potential role of milk fat globule membrane in modulating plasma lipoproteins, gene expression, and cholesterol metabolism in humans: a randomized study.

Rosqvist F, Smedman A, Lindmark-Månsson H, ..., Dahlman I, Risérus U

Am. J. Clin. Nutr. 102 (1) 20-30 [2015-07-00; online 2015-05-29]

Polymorphisms in DCDC2 and S100B associate with developmental dyslexia.

Matsson H, Huss M, Persson H, ..., Peyrard-Janvid M, Kere J

J. Hum. Genet. 60 (7) 399-401 [2015-07-00; online 2015-04-17]

Mutation Analysis Facility (MAF) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Meta-analysis of Genome-wide Association Studies for Neuroticism, and the Polygenic Association With Major Depressive Disorder.

Genetics of Personality Consortium , de Moor MH, van den Berg SM, ..., Martin NG, Boomsma DI

JAMA Psychiatry 72 (7) 642-650 [2015-07-00; online 2015-05-21]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Identifying glycoside hydrolase family 18 genes in the mycoparasitic fungal species Clonostachys rosea.

Tzelepis G, Dubey M, Jensen DF, Karlsson M

Microbiology (Reading, Engl.) 161 (7) 1407-1419 [2015-07-00; online 2015-04-18]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

HHEX_23 AA Genotype Exacerbates Effect of Diabetes on Dementia and Alzheimer Disease: A Population-Based Longitudinal Study.

Xu WL, Pedersen NL, Keller L, ..., Bäckman L, Fratiglioni L

PLoS Med. 12 (7) e1001853 [2015-07-00; online 2015-07-14]

Global Multilocus Sequence Type Analysis of Chlamydia trachomatis Strains from 16 Countries.

Herrmann B, Isaksson J, Ryberg M, ..., Gravningen K, Bruisten S

J. Clin. Microbiol. 53 (7) 2172-2179 [2015-07-00; online 2015-05-01]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Genome-wide association study of plasma levels of polychlorinated biphenyls disclose an association with the CYP2B6 gene in a population-based sample.

Ng E, Salihovic S, Lind PM, ..., Morris AP, Lind L

Environ. Res. 140 (-) 95-101 [2015-07-00; online 2015-04-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genome-wide association study identifies new susceptibility loci for cutaneous lupus erythematosus.

Kunz M, König IR, Schillert A, ..., Kuhn A, Ibrahim SM

Exp. Dermatol. 24 (7) 510-515 [2015-07-00; online 2015-04-02]

Function of Isolated Pancreatic Islets From Patients at Onset of Type 1 Diabetes: Insulin Secretion Can Be Restored After Some Days in a Nondiabetogenic Environment In Vitro: Results From the DiViD Study.

Krogvold L, Skog O, Sundström G, ..., Korsgren O, Dahl-Jørgensen K

Diabetes 64 (7) 2506-2512 [2015-07-00; online 2015-02-14]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Epigenetic activation of a cryptic TBC1D16 transcript enhances melanoma progression by targeting EGFR.

Vizoso M, Ferreira HJ, Lopez-Serra P, ..., Marais R, Esteller M

Nat. Med. 21 (7) 741-750 [2015-07-00; online 2015-06-01]

Elevated Plasma Levels of MMP-12 Are Associated With Atherosclerotic Burden and Symptomatic Cardiovascular Disease in Subjects With Type 2 Diabetes.

Goncalves I, Bengtsson E, Colhoun HM, ..., Nilsson J, SUMMIT Consortium

Arterioscler. Thromb. Vasc. Biol. 35 (7) 1723-1731 [2015-07-00; online 2015-05-07]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation.

Horikoshi M, Mӓgi R, van de Bunt M, ..., Morris AP, ENGAGE Consortium

PLoS Genet. 11 (7) e1005230 [2015-07-00; online 2015-07-01]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Detection of leukemia-associated mutations in peripheral blood DNA of hematologically normal elderly individuals.

Score J, Chase A, Forsberg LA, ..., Gale RE, Cross NC

Leukemia 29 (7) 1600-1602 [2015-07-00; online 2015-01-30]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

CTCF/cohesin-binding sites are frequently mutated in cancer.

Katainen R, Dave K, Pitkänen E, ..., Taipale J, Aaltonen LA

Nat. Genet. 47 (7) 818-821 [2015-07-00; online 2015-06-09]

Structural Basis for the Specificity of Human NUDT16 and Its Regulation by Inosine Monophosphate

Trésaugues L, Lundbäck T, Welin M, ..., Gräslund S, Nordlund P

PLoS ONE 10 (6) e0131507 [2015-06-29; online 2015-06-29]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF)

High BRAF Mutation Frequency and Marked Survival Differences in Subgroups According to KRAS/BRAF Mutation Status and Tumor Tissue Availability in a Prospective Population-Based Metastatic Colorectal Cancer Cohort.

Sorbye H, Dragomir A, Sundström M, ..., Qvortrup C, Glimelius B

PLoS ONE 10 (6) e0131046 [2015-06-29; online 2015-06-29]

The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling.

Lindskog C, Linné J, Fagerberg L, ..., Pontén F, Uhlén M

BMC Genomics 16 (-) 475 [2015-06-25; online 2015-06-25]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Tissue Profiling [Collaborative]

Ebf1 heterozygosity results in increased DNA damage in pro-B cells and their synergistic transformation by Pax5 haploinsufficiency.

Prasad MA, Ungerbäck J, Åhsberg J, ..., Hagman J, Sigvardsson M

Blood 125 (26) 4052-4059 [2015-06-25; online 2015-04-02]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Structure of the nuclease subunit of human mitochondrial RNase P.

Reinhard L, Sridhara S, Hällberg BM

Nucleic Acids Res. 43 (11) 5664-5672 [2015-06-23; online 2015-05-09]

The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases.

Schwelm A, Fogelqvist J, Knaust A, ..., Ludwig-Müller J, Dixelius C

Sci Rep 5 (-) 11153 [2015-06-18; online 2015-06-18]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Dynamics of Cell Generation and Turnover in the Human Heart.

Bergmann O, Zdunek S, Felker A, ..., Druid H, Frisén J

Cell 161 (7) 1566-1575 [2015-06-18; online 2015-06-16]

Integrated Microscopy Technologies Stockholm [Service]

Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth.

Alexeyenko A, Alkasalias T, Pavlova T, ..., Guven H, Klein G

J. Exp. Clin. Cancer Res. 34 (-) 62 [2015-06-18; online 2015-06-18]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Transglutaminase 4 as a prostate autoantigen in male subfertility

Landegren N, Sharon D, Shum AK, ..., Snyder M, Kämpe O

Sci. Transl. Med. 7 (292) 292ra101 [2015-06-17; online 2015-06-17]

Affinity Proteomics Uppsala [Service] Autoimmunity and Serology Profiling [Service] Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training PLA and Single Cell Proteomics

Elevated Serum GAD65 and GAD65-GADA Immune Complexes in Stiff Person Syndrome.

Gu Urban GJ, Friedman M, Ren P, ..., Landegren U, Kamali-Moghaddam M

Sci Rep 5 (1) 11196 [2015-06-16; online 2015-06-16]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Characterization of Three Mycobacterium spp. with Potential Use in Bioremediation by Genome Sequencing and Comparative Genomics.

Das S, Pettersson BM, Behra PR, ..., Bhattacharya A, Kirsebom LA

Genome Biol Evol 7 (7) 1871-1886 [2015-06-16; online 2015-06-16]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Whiteboard: a framework for the programmatic visualization of complex biological analyses.

Sundström G, Zamani N, Grabherr MG, Mauceli E

Bioinformatics 31 (12) 2054-2055 [2015-06-15; online 2015-02-11]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

IFN-α production by plasmacytoid dendritic cell associations with polymorphisms in gene loci related to autoimmune and inflammatory diseases.

Berggren O, Alexsson A, Morris DL, ..., Rönnblom L, Eloranta ML

Hum. Mol. Genet. 24 (12) 3571-3581 [2015-06-15; online 2015-03-18]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex.

Sjöstedt E, Fagerberg L, Hallström BM, ..., Uhlén M, Mulder J

PLoS ONE 10 (6) e0130028 [2015-06-15; online 2015-06-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Collaborative]

Contribution of common non-synonymous variants in PCSK1 to body mass index variation and risk of obesity: a systematic review and meta-analysis with evidence from up to 331 175 individuals.

Nead KT, Li A, Wehner MR, ..., Anand SS, Meyre D

Hum. Mol. Genet. 24 (12) 3582-3594 [2015-06-15; online 2015-03-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Proximity-dependent initiation of hybridization chain reaction.

Koos B, Cane G, Grannas K, ..., Kamali-Moghaddam M, Söderberg O

Nat Commun 6 (-) 7294 [2015-06-12; online 2015-06-12]

Affinity Proteomics Uppsala [Service] PLA and Single Cell Proteomics [Service]

Phasing of single DNA molecules by massively parallel barcoding.

Borgström E, Redin D, Lundin S, ..., Andersson AF, Ahmadian A

Nat Commun 6 (-) 7173 [2015-06-09; online 2015-06-09]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Functional Identification of Target by Expression Proteomics (FITExP) reveals protein targets and highlights mechanisms of action of small molecule drugs.

Chernobrovkin A, Marin-Vicente C, Visa N, Zubarev RA

Sci Rep 5 (-) 11176 [2015-06-08; online 2015-06-08]

Advanced Mass Spectrometry Proteomics Chemical Proteomics [Technology development]

Evolutionary analysis of the female-specific avian W chromosome.

Smeds L, Warmuth V, Bolivar P, ..., Török J, Ellegren H

Nat Commun 6 (-) 7330 [2015-06-04; online 2015-06-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data.

Siretskiy A, Sundqvist T, Voznesenskiy M, Spjuth O

Gigascience 4 (-) 26 [2015-06-04; online 2015-06-04]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Processing of protein ADP-ribosylation by Nudix hydrolases.

Palazzo L, Thomas B, Jemth AS, ..., Helleday T, Ahel I

Biochem. J. 468 (2) 293-301 [2015-06-01; online 2015-03-20]

Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia.

Mansouri L, Sutton LA, Ljungström V, ..., Nilsson M, Rosenquist R

J. Exp. Med. 212 (6) 833-843 [2015-06-01; online 2015-05-18]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds.

Skoglund P, Ersmark E, Palkopoulou E, Dalén L

Curr. Biol. 25 (11) 1515-1519 [2015-06-01; online 2015-05-26]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Zebrafish: A possible tool to evaluate bioactive ions.

Montazerolghaem M, Nyström L, Engqvist H, Karlsson Ott M

Acta Biomater 19 (-) 10-14 [2015-06-00; online 2015-03-17]

Whole-genome Linkage Analysis and Sequence Analysis of Candidate Loci in Familial Breast Cancer.

PubMed

Marikkannu R, Aravidis C, Rantala J, ..., Nilsson D, Lindblom A

Anticancer Res. 35 (6) 3155-3165 [2015-06-00; online 2015-05-31]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Tumor vessel up-regulation of INSR revealed by single-cell expression analysis of the tyrosine kinome and phosphatome in human cancers.

Kiflemariam S, Ljungström V, Pontén F, Sjöblom T

Am. J. Pathol. 185 (6) 1600-1609 [2015-06-00; online 2015-04-10]

Three-Dimensional Cell Culture-Based Screening Identifies the Anthelmintic Drug Nitazoxanide as a Candidate for Treatment of Colorectal Cancer.

Senkowski W, Zhang X, Olofsson MH, ..., Larsson R, Fryknäs M

Mol Cancer Ther 14 (6) 1504-1516 [2015-06-00; online 2015-04-24]

The potential clinical impact of the tissue-based map of the human proteome.

Lindskog C

Expert Rev Proteomics 12 (3) 213-215 [2015-06-00; online 2015-04-30]

The impact of low-frequency and rare variants on lipid levels.

Surakka I, Horikoshi M, Mägi R, ..., Ripatti S, ENGAGE Consortium

Nat. Genet. 47 (6) 589-597 [2015-06-00; online 2015-05-12]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Single locus sex determination and female heterogamety in the basket willow (Salix viminalis L.).

Pucholt P, Rönnberg-Wästljung AC, Berlin S

Heredity (Edinb) 114 (6) 575-583 [2015-06-00; online 2015-02-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Non-reciprocal Interspecies Hybridization Barriers in the Capsella Genus Are Established in the Endosperm.

Rebernig CA, Lafon-Placette C, Hatorangan MR, Slotte T, Köhler C

PLoS Genet. 11 (6) e1005295 [2015-06-00; online 2015-06-18]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

NLRC4 Inflammasome Is an Important Regulator of Interleukin-18 Levels in Patients With Acute Coronary Syndromes: Genome-Wide Association Study in the PLATelet inhibition and patient Outcomes Trial (PLATO).

Johansson Å, Eriksson N, Becker RC, ..., Siegbahn A, PLATO Investigators

Circ Cardiovasc Genet 8 (3) 498-506 [2015-06-00; online 2015-03-10]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Multiple Changes of Gene Expression and Function Reveal Genomic and Phenotypic Complexity in SLE-like Disease.

Wilbe M, Kozyrev SV, Farias FH, ..., Hansson-Hamlin H, Lindblad-Toh K

PLoS Genet. 11 (6) e1005248 [2015-06-00; online 2015-06-09]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring.

Ininbergs K, Bergman B, Larsson J, Ekman M

Ambio 44 Suppl 3 (-) 439-450 [2015-06-00; online 2015-05-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Loss of ASRGL1 expression is an independent biomarker for disease-specific survival in endometrioid endometrial carcinoma.

Edqvist PH, Huvila J, Forsström B, ..., Pontén F, Auranen A

Gynecol. Oncol. 137 (3) 529-537 [2015-06-00; online 2015-04-07]

Human adaptation to arsenic-rich environments.

Schlebusch CM, Gattepaille LM, Engström K, ..., Jakobsson M, Broberg K

Mol. Biol. Evol. 32 (6) 1544-1555 [2015-06-00; online 2015-03-03]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

High-throughput mutational screening adds clinically important information in myelodysplastic syndromes and secondary or therapy-related acute myeloid leukemia.

Karimi M, Nilsson C, Dimitriou M, ..., Kere J, Hellström-Lindberg E

Haematologica 100 (6) e223-e225 [2015-06-00; online 2015-03-15]

Mutation Analysis Facility (MAF) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Hemophagocytic lymphohistiocytosis in 2 patients with underlying IFN-γ receptor deficiency

Tesi B, Sieni E, Neves C, ..., Azzari C, Bryceson YT

Journal of Allergy and Clinical Immunology 135 (6) 1638-1641.e5 [2015-06-00; online 2015-06-00]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Exome sequencing of contralateral breast cancer identifies metastatic disease.

Klevebring D, Lindberg J, Rockberg J, ..., Sandberg M, Czene K

Breast Cancer Res. Treat. 151 (2) 319-324 [2015-06-00; online 2015-04-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Exome Sequencing and CNV Analysis on Chromosome 18 in Small Intestinal Neuroendocrine Tumors: Ruling Out a Suspect?

Delgado Verdugo A, Crona J, Maharjan R, ..., Westin G, Björklund P

Horm. Metab. Res. 47 (6) 452-455 [2015-06-00; online 2014-10-30]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Effect of host plant and immune challenge on the levels of chemosensory and odorant-binding proteins in caterpillar salivary glands.

Celorio-Mancera Mde L, Ytterberg AJ, Rutishauser D, Janz N, Zubarev RA

Insect Biochem. Mol. Biol. 61 (-) 34-45 [2015-06-00; online 2015-04-29]

Differential Gene Regulation in Fibroblasts in Co-culture with Keratinocytes and Head and Neck SCC Cells.

PubMed

Hakelius M, Saiepour D, Göransson H, ..., Gerdin B, Nowinski D

Anticancer Res. 35 (6) 3253-3265 [2015-06-00; online 2015-05-31]

Consequences of increased terrestrial dissolved organic matter and temperature on bacterioplankton community composition during a Baltic Sea mesocosm experiment.

Lindh MV, Lefébure R, Degerman R, ..., Andersson A, Pinhassi J

Ambio 44 Suppl 3 (-) 402-412 [2015-06-00; online 2015-05-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

CETSA: a target engagement assay with potential to transform drug discovery

Jensen AJ, Molina DM, Lundbäck T

Future Medicinal Chemistry 7 (8) 975-978 [2015-06-00; online 2015-06-00]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin.

Svensson JP, Shukla M, Menendez-Benito V, ..., Allshire RC, Ekwall K

Genome Res. 25 (6) 872-883 [2015-06-00; online 2015-03-18]

Circulating microRNA expression pattern separates patients with anti-neutrophil cytoplasmic antibody associated vasculitis from healthy controls.

PubMed

Skoglund C, Carlsen AL, Weiner M, ..., Heegaard NH, Segelmark M

Clin. Exp. Rheumatol. 33 (2 Suppl 89) S-64-71 [2015-05-26; online 2015-05-26]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Phylogeny, evolution and classification of gall wasps: the plot thickens.

Ronquist F, Nieves-Aldrey JL, Buffington ML, ..., Liljeblad J, Nylander JA

PLoS ONE 10 (5) e0123301 [2015-05-20; online 2015-05-20]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth.

Palkopoulou E, Mallick S, Skoglund P, ..., Reich D, Dalén L

Curr. Biol. 25 (10) 1395-1400 [2015-05-18; online 2015-04-23]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

CGGBP1 mitigates cytosine methylation at repetitive DNA sequences.

Agarwal P, Collier P, Fritz MH, ..., Westermark B, Singh U

BMC Genomics 16 (-) 390 [2015-05-16; online 2015-05-16]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Phylogeographical pattern of Francisella tularensis in a nationwide outbreak of tularaemia in Norway, 2011.

Afset JE, Larssen KW, Bergh K, ..., Johansson A, Forsman M

Euro Surveill. 20 (19) 9-14 [2015-05-14; online 2015-05-14]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Complex archaea that bridge the gap between prokaryotes and eukaryotes.

Spang A, Saw JH, Jørgensen SL, ..., Guy L, Ettema TJ

Nature 521 (7551) 173-179 [2015-05-14; online 2015-05-07]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.

Rivas MA, Pirinen M, Conrad DF, ..., Lappalainen T, MacArthur DG

Science 348 (6235) 666-669 [2015-05-08; online 2015-05-09]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Complement inhibitor CD55 governs the integrity of membrane rafts in pancreatic beta cells, but plays no role in insulin secretion.

Nagaraj V, King B, Storm P, ..., Blom AM, Renström E

Biochem. Biophys. Res. Commun. 460 (3) 518-524 [2015-05-08; online 2015-03-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait.

Husby A, Kawakami T, Rönnegård L, ..., Ellegren H, Qvarnström A

Proc. Biol. Sci. 282 (1806) 20150156 [2015-05-07; online 2015-04-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Intestinal dysbiosis in children with short bowel syndrome is associated with impaired outcome.

Engstrand Lilja H, Wefer H, Nyström N, Finkel Y, Engstrand L

Microbiome 3 (-) 18 [2015-05-04; online 2015-05-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Tracking the origin of metastatic prostate cancer.

Lindberg J, Kristiansen A, Wiklund P, Grönberg H, Egevad L

Eur. Urol. 67 (5) 819-822 [2015-05-00; online 2014-09-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The role of genetic factors for hearing deterioration across 20 years: a twin study.

Bogo R, Farah A, Johnson AC, ..., Svartengren M, Skjönsberg Å

J. Gerontol. A Biol. Sci. Med. Sci. 70 (5) 647-653 [2015-05-00; online 2015-02-11]

Plant-mediated gene silencing restricts growth of the potato late blight pathogen Phytophthora infestans.

Jahan SN, Åsman AK, Corcoran P, ..., Vetukuri RR, Dixelius C

J. Exp. Bot. 66 (9) 2785-2794 [2015-05-00; online 2015-03-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

NOTA: a potent metallo-β-lactamase inhibitor.

Somboro AM, Tiwari D, Bester LA, ..., Naicker T, Essack SY

J. Antimicrob. Chemother. 70 (5) 1594-1596 [2015-05-00; online 2015-01-06]

Drug Discovery and Development (DDD) [Collaborative]

Mixed ancestry and admixture in Kauai's feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs.

Gering E, Johnsson M, Willis P, Getty T, Wright D

Mol. Ecol. 24 (9) 2112-2124 [2015-05-00; online 2015-02-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption.

Coffee and Caffeine Genetics Consortium , Cornelis MC, Byrne EM, ..., van Dam RM, Chasman DI

Mol. Psychiatry 20 (5) 647-656 [2015-05-00; online 2014-10-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic regulation of bone metabolism in the chicken: similarities and differences to Mammalian systems.

Johnsson M, Jonsson KB, Andersson L, Jensen P, Wright D

PLoS Genet. 11 (5) e1005250 [2015-05-00; online 2015-05-29]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Dietary fat quality impacts genome-wide DNA methylation patterns in a cross-sectional study of Greek preadolescents.

Voisin S, Almén MS, Moschonis G, ..., Manios Y, Schiöth HB

Eur. J. Hum. Genet. 23 (5) 654-662 [2015-05-00; online 2014-07-31]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PubMed

Diagnostic urinary proteome profile for immunoglobulin a nephropathy.

Samavat S, Kalantari S, Nafar M, ..., Parvin M, Zubarev RA

Iran J Kidney Dis 9 (3) 239-248 [2015-05-00; online 2015-05-10]

Cu(OAc)2-Catalysed Oxidative Dual C-H/N-H Activation of Terminal Alkynes andN-Deprotected Sulfonimidamides: An Easy Access toN-Alkynylated Sulfonimidamides

Nandi GC, Kota SR, Naicker T, ..., Kruger HG, Arvidsson PI

Eur. J. Org. Chem. 2015 (13) 2861-2867 [2015-05-00; online 2015-03-17]

Drug Discovery and Development (DDD) [Technology development]

Cooperative genetic changes in pediatric B-cell precursor acute lymphoblastic leukemia with deletions or mutations of IKZF1.

Olsson L, Albitar F, Castor A, ..., Paulsson K, Johansson B

Genes Chromosomes Cancer 54 (5) 315-325 [2015-05-00; online 2015-03-03]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Autosomal recessive mutations in the COL2A1 gene cause severe spondyloepiphyseal dysplasia.

Tham E, Nishimura G, Geiberger S, ..., Nordenskjöld M, Grigelioniene G

Clin. Genet. 87 (5) 496-498 [2015-05-00; online 2014-07-26]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Age- and sex-specific causal effects of adiposity on cardiovascular risk factors.

Fall T, Hägg S, Ploner A, ..., Ingelsson E, ENGAGE Consortium

Diabetes 64 (5) 1841-1852 [2015-05-00; online 2015-02-26]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Nanoparticle-stabilized microbubbles for multimodal imaging and drug delivery.

Mørch Ý, Hansen R, Berg S, ..., de Lange Davies C, Stenstad PM

Contrast Media Mol Imaging 10 (5) 356-366 [2015-04-30; online 2015-04-30]

Integrated Microscopy Technologies Stockholm [Collaborative]

Deep sequencing and SNP array analyses of pediatric T-cell acute lymphoblastic leukemia reveal NOTCH1 mutations in minor subclones and a high incidence of uniparental isodisomies affecting CDKN2A.

Karrman K, Castor A, Behrendtz M, ..., Paulsson K, Johansson B

J Hematol Oncol 8 (-) 42 [2015-04-24; online 2015-04-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetically determined height and coronary artery disease.

Nelson CP, Hamby SE, Saleheen D, ..., Samani NJ, CARDIoGRAM+C4D Consortium

N. Engl. J. Med. 372 (17) 1608-1618 [2015-04-23; online 2015-04-09]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Circulating carnosine dipeptidase 1 associates with weight loss and poor prognosis in gastrointestinal cancer.

Arner P, Henjes F, Schwenk JM, ..., Nilsson P, Rydén M

PLoS ONE 10 (4) e0123566 [2015-04-21; online 2015-04-21]

Affinity Proteomics Stockholm

Polymorphisms in chloroquine resistance-associated genes in Plasmodium vivax in Ethiopia.

Golassa L, Erko B, Baliraine FN, Aseffa A, Swedberg G

Malar. J. 14 (-) 164 [2015-04-16; online 2015-04-16]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Combination effects of AHR agonists and Wnt/β-catenin modulators in zebrafish embryos: Implications for physiological and toxicological AHR functions.

Wincent E, Stegeman JJ, Jönsson ME

Toxicol. Appl. Pharmacol. 284 (2) 163-179 [2015-04-15; online 2015-02-21]

AP-1-mediated chromatin looping regulates ZEB2 transcription: new insights into TNFα-induced epithelial-mesenchymal transition in triple-negative breast cancer.

Qiao Y, Shiue CN, Zhu J, ..., Zhao C, Dahlman-Wright K

Oncotarget 6 (10) 7804-7814 [2015-04-10; online 2015-03-13]

Common genetic variants influence human subcortical brain structures.

Hibar DP, Stein JL, Renteria ME, ..., Thompson PM, Medland SE

Nature 520 (7546) 224-229 [2015-04-09; online 2015-01-22]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Inter-relationships between the metrics of instrumental meat color and microbial growth during aerobic storage of beef at 4°C

Li S, Zamaratskaia G, Roos S, ..., Borch E, Johansson M

Acta Agriculturae Scandinavica, Section A - Animal Science 65 (2) 97-106 [2015-04-03; online 2015-09-00]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities.

Lindh MV, Figueroa D, Sjöstedt J, ..., Legrand C, Pinhassi J

Front Microbiol 6 (-) 223 [2015-04-01; online 2015-04-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A prognosis based classification of undifferentiated uterine sarcomas: identification of mitotic index, hormone receptors and YWHAE-FAM22 translocation status as predictors of survival.

Gremel G, Liew M, Hamzei F, ..., Pontén F, Carlson JW

Int. J. Cancer 136 (7) 1608-1618 [2015-04-01; online 2014-08-19]

Using genetics to test the causal relationship of total adiposity and periodontitis: Mendelian randomization analyses in the Gene-Lifestyle Interactions and Dental Endpoints (GLIDE) Consortium.

Shungin D, Cornelis MC, Divaris K, ..., Johansson I, Franks PW

Int J Epidemiol 44 (2) 638-650 [2015-04-00; online 2015-06-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Oseltamivir-resistant influenza A (H1N1) virus strain with an H274Y mutation in neuraminidase persists without drug pressure in infected mallards.

Gillman A, Muradrasoli S, Söderström H, ..., Olsen B, Järhult JD

Appl. Environ. Microbiol. 81 (7) 2378-2383 [2015-04-00; online 2015-01-27]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Mixture effects of levonorgestrel and ethinylestradiol: estrogenic biomarkers and hormone receptor mRNA expression during sexual programming.

Säfholm M, Jansson E, Fick J, Berg C

Aquat. Toxicol. 161 (-) 146-153 [2015-04-00; online 2015-02-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Is the adiposity-associated FTO gene variant related to all-cause mortality independent of adiposity? Meta-analysis of data from 169,551 Caucasian adults.

Zimmermann E, Ängquist LH, Mirza SS, ..., Sonestedt E, Sørensen TIA

Obes Rev 16 (4) 327-340 [2015-04-00; online 2015-03-05]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Is label-free LC-MS/MS ready for biomarker discovery?

Sandin M, Chawade A, Levander F

Proteomics Clin Appl 9 (3-4) 289-294 [2015-04-00; online 2015-02-07]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Immunohistochemistry-based prognostic biomarkers in NSCLC: novel findings on the road to clinical use?

Lindskog C, Edlund K, Mattsson JS, Micke P

Expert Rev. Mol. Diagn. 15 (4) 471-490 [2015-04-00; online 2015-01-19]

Identification and validation of N-acetyltransferase 2 as an insulin sensitivity gene.

Knowles JW, Xie W, Zhang Z, ..., Walker M, Quertermous T

J. Clin. Invest. 125 (4) 1739-1751 [2015-04-00; online 2015-03-23]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

GWAS-identified loci for coronary heart disease are associated with intima-media thickness and plaque presence at the carotid artery bulb.

den Hoed M, Strawbridge RJ, Almgren P, ..., Melander O, Lind L

Atherosclerosis 239 (2) 304-310 [2015-04-00; online 2015-02-16]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Functional anti-CD94/NKG2A and anti-CD94/NKG2C autoantibodies in patients with systemic lupus erythematosus.

Hagberg N, Theorell J, Hjorton K, ..., Bryceson YT, Rönnblom L

Arthritis & rheumatology (Hoboken, N.J.) 67 (4) 1000-1011 [2015-04-00; online 2014-12-17]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Fluctuating expression of microRNAs in adenovirus infected cells.

Zhao H, Chen M, Tellgren-Roth C, Pettersson U

Virology 478 (-) 99-111 [2015-04-00; online 2015-03-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Duffy antigen receptor genetic variant and the association with Interleukin 8 levels.

Moreno Velásquez I, Kumar J, Björkbacka H, ..., de Faire U, Gigante B

Cytokine 72 (2) 178-184 [2015-04-00; online 2015-01-31]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Birth weight as an independent predictor of ADHD symptoms: a within-twin pair analysis.

Pettersson E, Sjölander A, Almqvist C, ..., Lichtenstein P, Larsson H

J Child Psychol Psychiatry 56 (4) 453-459 [2015-04-00; online 2014-07-22]

Adiposity as a cause of cardiovascular disease: a Mendelian randomization study.

Hägg S, Fall T, Ploner A, ..., Ingelsson E, European Network for Genetic and Genomic Epidemiology Consortium

Int J Epidemiol 44 (2) 578-586 [2015-04-00; online 2015-05-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Methylation levels of SLC23A2 and NCOR2 genes correlate with spinal muscular atrophy severity.

Zheleznyakova GY, Nilsson EK, Kiselev AV, ..., Baranov VS, Schiöth HB

PLoS ONE 10 (3) e0121964 [2015-03-30; online 2015-03-30]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Site-specific programming of the host epithelial transcriptome by the gut microbiota.

Sommer F, Nookaew I, Sommer N, Fogelstrand P, Bäckhed F

Genome Biol. 16 (-) 62 [2015-03-28; online 2015-03-28]

Array and Analysis Facility Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Modulation of genetic associations with serum urate levels by body-mass-index in humans.

Huffman JE, Albrecht E, Teumer A, ..., Köttgen A, Vitart V

PLoS ONE 10 (3) e0119752 [2015-03-26; online 2015-03-26]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Age-associated DNA methylation changes in immune genes, histone modifiers and chromatin remodeling factors within 5 years after birth in human blood leukocytes.

Acevedo N, Reinius LE, Vitezic M, ..., Greco D, Kere J

Clin Epigenetics 7 (-) 34 [2015-03-26; online 2015-03-26]

Discovery of molecular markers to discriminate corneal endothelial cells in the human body.

Yoshihara M, Ohmiya H, Hara S, ..., Tsujikawa M, Nishida K

PLoS ONE 10 (3) e0117581 [2015-03-25; online 2015-03-25]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Crystal structures of the kinase domain of the sulfate-activating complex in Mycobacterium tuberculosis.

Poyraz Ö, Brunner K, Lohkamp B, ..., Schnell R, Schneider G

PLoS ONE 10 (3) e0121494 [2015-03-25; online 2015-03-25]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF)

Low elastin content of carotid plaques is associated with increased risk of ipsilateral stroke.

Asciutto G, Dias NV, Edsfeldt A, ..., Nilsson J, Gonçalves I

PLoS ONE 10 (3) e0121086 [2015-03-24; online 2015-03-24]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Complete genome sequence of Borrelia afzelii K78 and comparative genome analysis.

Schüler W, Bunikis I, Weber-Lehman J, ..., Bergström S, Lundberg U

PLoS ONE 10 (3) e0120548 [2015-03-23; online 2015-03-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Structural basis for lack of ADP-ribosyltransferase activity in poly(ADP-ribose) polymerase-13/zinc finger antiviral protein.

Karlberg T, Klepsch M, Thorsell AG, ..., Linusson A, Schüler H

J. Biol. Chem. 290 (12) 7336-7344 [2015-03-20; online 2015-01-31]

Complete Genome Sequence of Francisella guangzhouensis Strain 08HL01032T, Isolated from Air-Conditioning Systems in China.

Svensson D, Öhrman C, Bäckman S, ..., Forsman M, Sjödin A

Genome Announc 3 (2) - [2015-03-19; online 2015-03-19]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Comparative proteomic analysis of hyphae and germinating cysts of Phytophthora pisi and Phytophthora sojae.

Hosseini S, Resjö S, Liu Y, ..., Andreasson E, Karlsson M

J Proteomics 117 (-) 24-40 [2015-03-18; online 2015-01-24]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis.

Vigil-Stenman T, Larsson J, Nylander JA, Bergman B

BMC Genomics 16 (-) 193 [2015-03-17; online 2015-03-17]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution.

Nitta KR, Jolma A, Yin Y, ..., Furlong EE, Taipale J

Elife 4 (-) - [2015-03-17; online 2015-03-17]

Analysis of the role of interleukin 6 receptor haplotypes in the regulation of circulating levels of inflammatory biomarkers and risk of coronary heart disease.

Gigante B, Strawbridge RJ, Velasquez IM, ..., Humphries SE, de Faire U

PLoS ONE 10 (3) e0119980 [2015-03-17; online 2015-03-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

SLC10A4 is a vesicular amine-associated transporter modulating dopamine homeostasis.

Larhammar M, Patra K, Blunder M, ..., Wallén-Mackenzie Å, Kullander K

Biol. Psychiatry 77 (6) 526-536 [2015-03-15; online 2014-09-02]

Integrated Microscopy Technologies Stockholm [Collaborative]

Microsatellite instability and mutations in BRAF and KRAS are significant predictors of disseminated disease in colon cancer.

Birgisson H, Edlund K, Wallin U, ..., Glimelius B, Sundström M

BMC Cancer 15 (-) 125 [2015-03-14; online 2015-03-14]

Variations of gastric corpus microbiota are associated with early esophageal squamous cell carcinoma and squamous dysplasia.

Nasrollahzadeh D, Malekzadeh R, Ploner A, ..., Dawsey SM, Ye W

Sci Rep 5 (-) 8820 [2015-03-06; online 2015-03-06]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris.

Douglas GM, Gos G, Steige KA, ..., Slotte T, Wright SI

Proc. Natl. Acad. Sci. U.S.A. 112 (9) 2806-2811 [2015-03-03; online 2015-02-19]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Proteomic profiling reveals autoimmune targets in sarcoidosis.

Häggmark A, Hamsten C, Wiklundh E, ..., Grunewald J, Nilsson P

Am. J. Respir. Crit. Care Med. 191 (5) 574-583 [2015-03-01; online 2015-01-22]

Autoimmunity and Serology Profiling [Collaborative] Tissue Profiling [Collaborative]

The H1-receptor antagonist cetirizine ameliorates high-fat diet-induced glucose intolerance in male C57BL/6 mice, but not diabetes outcome in female non-obese diabetic (NOD) mice.

Anvari E, Wang X, Sandler S, Welsh N

Ups. J. Med. Sci. 120 (1) 40-46 [2015-03-00; online 2014-10-08]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The Fun30 chromatin remodeler Fft3 controls nuclear organization and chromatin structure of insulators and subtelomeres in fission yeast.

Steglich B, Strålfors A, Khorosjutina O, ..., Javerzat JP, Ekwall K

PLoS Genet. 11 (3) e1005101 [2015-03-00; online 2015-03-23]

Bioinformatics and Expression Analysis (BEA) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Targeted next-generation sequencing in chronic lymphocytic leukemia: a high-throughput yet tailored approach will facilitate implementation in a clinical setting.

Sutton LA, Ljungström V, Mansouri L, ..., Stamatopoulos K, Rosenquist R

Haematologica 100 (3) 370-376 [2015-03-00; online 2014-12-07]

Clinical Genomics Clinical Genomics Uppsala

Structural characterization of substrate and inhibitor binding to farnesyl pyrophosphate synthase from Pseudomonas aeruginosa.

Schmidberger JW, Schnell R, Schneider G

Acta Crystallogr. D Biol. Crystallogr. 71 (Pt 3) 721-731 [2015-03-00; online 2015-02-26]

Preclinical characterization of acyl sulfonimidamides: potential carboxylic acid bioisosteres with tunable properties.

Borhade SR, Svensson R, Brandt P, ..., Arvidsson PI, Sandström A

ChemMedChem 10 (3) 455-460 [2015-03-00; online 2015-01-30]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

MuSK: a new target for lethal fetal akinesia deformation sequence (FADS).

Wilbe M, Ekvall S, Eurenius K, ..., Annerén G, Bondeson ML

J. Med. Genet. 52 (3) 195-202 [2015-03-00; online 2015-01-22]

Clinical Genomics Clinical Genomics Uppsala NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

High-resolution crystal structure of a polyextreme GH43 glycosidase from Halothermothrix orenii with α-L-arabinofuranosidase activity.

Hassan N, Kori LD, Gandini R, ..., Divne C, Tan TC

Acta Crystallogr F Struct Biol Commun 71 (Pt 3) 338-345 [2015-03-00; online 2015-02-19]

High-density genotyping of immune loci in Koreans and Europeans identifies eight new rheumatoid arthritis risk loci.

Kim K, Bang SY, Lee HS, ..., Plenge RM, Bae SC

Ann. Rheum. Dis. 74 (3) e13 [2015-03-00; online 2014-02-14]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genomewide association study of body weight traits in Baluchi sheep.

Gholizadeh M, Rahimi-Mianji G, Nejati-Javaremi A

J. Genet. 94 (1) 143-146 [2015-03-00; online 2015-04-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

FGF2 as a potential prognostic biomarker for proneural glioma patients.

Sooman L, Freyhult E, Jaiswal A, ..., Bergqvist M, Ekman S

Acta Oncol 54 (3) 385-394 [2015-03-00; online 2014-09-30]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training Tissue Profiling

Evaluation of human papillomavirus DNA detection in samples obtained for routine Chlamydia trachomatis screening.

Söderlund-Strand A, Wikström A, Dillner J

J. Clin. Virol. 64 (-) 88-91 [2015-03-00; online 2015-01-13]

Effects of ecological engineered oxygenation on the bacterial community structure in an anoxic fjord in western Sweden.

Forth M, Liljebladh B, Stigebrandt A, Hall PO, Treusch AH

ISME J 9 (3) 656-669 [2015-03-00; online 2014-09-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Detection of cell aggregation and altered cell viability by automated label-free video microscopy: a promising alternative to endpoint viability assays in high-throughput screening.

Aftab O, Fryknäs M, Hammerling U, Larsson R, Gustafsson MG

J Biomol Screen 20 (3) 372-381 [2015-03-00; online 2014-12-17]

Amplification-free sequencing of cell-free DNA for prenatal non-invasive diagnosis of chromosomal aberrations.

Karlsson K, Sahlin E, Iwarsson E, ..., Nordenskjöld M, Linnarsson S

Genomics 105 (3) 150-158 [2015-03-00; online 2014-12-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A genomic duplication is associated with ectopic eomesodermin expression in the embryonic chicken comb and two duplex-comb phenotypes.

Dorshorst B, Harun-Or-Rashid M, Bagherpoor AJ, ..., Hallböök F, Andersson L

PLoS Genet. 11 (3) e1004947 [2015-03-00; online 2015-03-19]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics.

Kushwaha SK, Manoharan L, Meerupati T, Hedlund K, Ahrén D

BMC Bioinformatics 16 (-) 65 [2015-02-28; online 2015-02-28]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Roux-en Y gastric bypass surgery induces genome-wide promoter-specific changes in DNA methylation in whole blood of obese patients.

Nilsson EK, Ernst B, Voisin S, ..., Schultes B, Schiöth HB

PLoS ONE 10 (2) e0115186 [2015-02-24; online 2015-02-24]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The roles of SNF2/SWI2 nucleosome remodeling enzymes in blood cell differentiation and leukemia.

Prasad P, Lennartsson A, Ekwall K

Biomed Res Int 2015 (-) 347571 [2015-02-19; online 2015-02-19]

Evolution of Darwin's finches and their beaks revealed by genome sequencing.

Lamichhaney S, Berglund J, Almén MS, ..., Webster MT, Andersson L

Nature 518 (7539) 371-375 [2015-02-19; online 2015-02-18]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia.

Nordlund J, Bäcklin CL, Zachariadis V, ..., Forestier E, Syvänen AC

Clin Epigenetics 7 (-) 11 [2015-02-17; online 2015-02-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

New genetic loci link adipose and insulin biology to body fat distribution.

Shungin D, Winkler TW, Croteau-Chonka DC, ..., Lindgren CM, Mohlke KL

Nature 518 (7538) 187-196 [2015-02-12; online 2015-02-13]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic studies of body mass index yield new insights for obesity biology.

Locke AE, Kahali B, Berndt SI, ..., Loos RJF, Speliotes EK

Nature 518 (7538) 197-206 [2015-02-12; online 2015-02-13]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing.

Cavelier L, Ameur A, Häggqvist S, ..., Olsson-Strömberg U, Hermanson M

BMC Cancer 15 (-) 45 [2015-02-12; online 2015-02-12]

Bioinformatics Support for Computational Resources [Service] Clinical Genomics Clinical Genomics Uppsala NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Data processing has major impact on the outcome of quantitative label-free LC-MS analysis.

Chawade A, Sandin M, Teleman J, Malmström J, Levander F

J. Proteome Res. 14 (2) 676-687 [2015-02-06; online 2014-11-20]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Microbial community composition and diversity via 16S rRNA gene amplicons: evaluating the illumina platform.

Sinclair L, Osman OA, Bertilsson S, Eiler A

PLoS ONE 10 (2) e0116955 [2015-02-03; online 2015-02-03]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Risk of childhood asthma is associated with CpG-site polymorphisms, regional DNA methylation and mRNA levels at the GSDMB/ORMDL3 locus.

Acevedo N, Reinius LE, Greco D, ..., Kere J, Söderhäll C

Hum. Mol. Genet. 24 (3) 875-890 [2015-02-01; online 2014-09-27]

Bioinformatics and Expression Analysis (BEA) Mutation Analysis Facility (MAF)

Transcriptional responses of the bacterial antagonist Serratia plymuthica to the fungal phytopathogen Rhizoctonia solani.

Neupane S, Finlay RD, Alström S, Elfstrand M, Högberg N

Environ Microbiol Rep 7 (1) 123-127 [2015-02-00; online 2014-08-21]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The composition of the gut microbiota shapes the colon mucus barrier.

Jakobsson HE, Rodríguez-Piñeiro AM, Schütte A, ..., Hansson GC, Johansson ME

EMBO Rep. 16 (2) 164-177 [2015-02-00; online 2014-12-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The GH receptor exon 3 deleted/full-length polymorphism is associated with central adiposity in the general population.

Glad CA, Carlsson LM, Melander O, ..., Svensson PA, Johannsson G

Eur. J. Endocrinol. 172 (2) 123-128 [2015-02-00; online 2014-11-14]

Proposal of Thorsellia kenyensis sp. nov. and Thorsellia kandunguensis sp. nov., isolated from larvae of Anopheles arabiensis, as members of the family Thorselliaceae fam. nov.

Kämpfer P, Glaeser SP, Nilsson LKJ, ..., Busse H, Terenius O

Int. J. Syst. Evol. Microbiol. 65 (Pt 2) 444-451 [2015-02-00; online 2014-11-12]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Predicting venous thrombosis in women using a combination of genetic markers and clinical risk factors.

Bruzelius M, Bottai M, Sabater-Lleal M, ..., Hamsten A, Odeberg J

J. Thromb. Haemost. 13 (2) 219-227 [2015-02-00; online 2014-12-05]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Novel high-throughput screening method for identification of fungal dimorphism blockers.

Stylianou M, Uvell H, Lopes JP, ..., Elofsson M, Urban CF

J Biomol Screen 20 (2) 285-291 [2015-02-00; online 2014-10-05]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Multi-omic data analysis using Galaxy.

Boekel J, Chilton JM, Cooke IR, ..., Moerland PD, Griffin TJ

Nat. Biotechnol. 33 (2) 137-139 [2015-02-00; online 2015-02-07]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training Clinical Proteomics Mass spectrometry

Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date.

Leong SL, Lantz H, Pettersson OV, ..., Tellgren-Roth C, Schnürer J

Environ. Microbiol. 17 (2) 496-513 [2015-02-00; online 2014-08-22]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling.

Edqvist PH, Fagerberg L, Hallström BM, ..., Uhlén M, Pontén F

J. Histochem. Cytochem. 63 (2) 129-141 [2015-02-00; online 2014-11-19]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Technology development]

Environmental and genetic factors in the development of anticitrullinated protein antibodies (ACPAs) and ACPA-positive rheumatoid arthritis: an epidemiological investigation in twins.

Hensvold AH, Magnusson PK, Joshua V, ..., Klareskog L, Catrina AI

Ann. Rheum. Dis. 74 (2) 375-380 [2015-02-00; online 2013-11-28]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

CTNND2-a candidate gene for reading problems and mild intellectual disability.

Hofmeister W, Nilsson D, Topa A, ..., Syk Lundberg E, Lindstrand A

J. Med. Genet. 52 (2) 111-122 [2015-02-00; online 2014-12-05]

Clinical Genomics Clinical Genomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Biochemical and structural characterization of a thermostable β-glucosidase from Halothermothrix orenii for galacto-oligosaccharide synthesis.

Hassan N, Nguyen TH, Intanon M, ..., Divne C, Tan TC

Appl. Microbiol. Biotechnol. 99 (4) 1731-1744 [2015-02-00; online 2014-09-01]

Associations between the 17q21 region and allergic rhinitis in 5 birth cohorts.

Fuertes E, Söderhäll C, Acevedo N, ..., Carlsten C, Melén E

J. Allergy Clin. Immunol. 135 (2) 573-576 [2015-02-00; online 2014-09-30]

Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility.

Wessel J, Chu AY, Willems SM, ..., Scott RA, Goodarzi MO

Nat Commun 6 (-) 5897 [2015-01-29; online 2015-01-29]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Prognostic impact of COX-2 in non-small cell lung cancer: a comprehensive compartment-specific evaluation of tumor and stromal cell expression.

Mattsson JS, Bergman B, Grinberg M, ..., Micke P, Gulyas M

Cancer Lett. 356 (2 Pt B) 837-845 [2015-01-28; online 2014-10-31]

Endonuclease specificity and sequence dependence of type IIS restriction enzymes.

Lundin S, Jemt A, Terje-Hegge F, ..., Lexow P, Lundeberg J

PLoS ONE 10 (1) e0117059 [2015-01-28; online 2015-01-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Next-generation sequencing reveals low-dose effects of cationic dendrimers in primary human bronchial epithelial cells.

Feliu N, Kohonen P, Ji J, ..., Nyström A, Fadeel B

ACS Nano 9 (1) 146-163 [2015-01-27; online 2014-12-23]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Intratumoral genome diversity parallels progression and predicts outcome in pediatric cancer.

Mengelbier LH, Karlsson J, Lindgren D, ..., Mayrhofer M, Gisselsson D

Nat Commun 6 (-) 6125 [2015-01-27; online 2015-01-27]

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

TGF-β1-Induced Epithelial-Mesenchymal Transition Promotes Monocyte/Macrophage Properties in Breast Cancer Cells.

Johansson J, Tabor V, Wikell A, Jalkanen S, Fuxe J

Front Oncol 5 (-) 3 [2015-01-26; online 2015-01-26]

Proteomics. Tissue-based map of the human proteome.

Uhlén M, Fagerberg L, Hallström BM, ..., Nielsen J, Pontén F

Science 347 (6220) 1260419 [2015-01-23; online 2015-01-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling [Technology development]

Biological interpretation of genome-wide association studies using predicted gene functions.

Pers TH, Karjalainen JM, Chan Y, ..., Hirschhorn JN, Franke L

Nat Commun 6 (-) 5890 [2015-01-19; online 2015-01-19]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Drug-induced mRNA signatures are enriched for the minority of genes that are highly heritable.

Gao T, Brodin P, Davis MM, Jojic V

Pac Symp Biocomput - (-) 395-406 [2015-01-17; online 2015-01-17]

Variation in the human immune system is largely driven by non-heritable influences.

Brodin P, Jojic V, Gao T, ..., Maecker HT, Davis MM

Cell 160 (1-2) 37-47 [2015-01-15; online 2015-01-17]

Transcription-coupled recruitment of human CHD1 and CHD2 influences chromatin accessibility and histone H3 and H3.3 occupancy at active chromatin regions.

Siggens L, Cordeddu L, Rönnerblad M, Lennartsson A, Ekwall K

Epigenetics Chromatin 8 (1) 4 [2015-01-15; online 2015-01-15]

The statistical geometry of transcriptome divergence in cell-type evolution and cancer.

Liang C, FANTOM Consortium , Forrest AR, Wagner GP

Nat Commun 6 (-) 6066 [2015-01-14; online 2015-01-14]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Comparison of heritability of Cystatin C- and creatinine-based estimates of kidney function and their relation to heritability of cardiovascular disease.

Arpegård J, Viktorin A, Chang Z, ..., Magnusson PK, Svensson P

J Am Heart Assoc 4 (1) e001467 [2015-01-14; online 2015-01-14]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The higher frequency of IgA deficiency among Swedish twins is not explained by HLA haplotypes.

Frankowiack M, Kovanen RM, Repasky GA, ..., Pedersen NL, Hammarström L

Genes Immun. 16 (3) 199-205 [2015-01-08; online 2015-01-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea.

Karlsson M, Durling MB, Choi J, ..., Lee YH, Jensen DF

Genome Biol Evol 7 (2) 465-480 [2015-01-08; online 2015-01-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Defects of CRB2 cause steroid-resistant nephrotic syndrome.

Ebarasi L, Ashraf S, Bierzynska A, ..., Hildebrandt F, Majumdar A

Am. J. Hum. Genet. 96 (1) 153-161 [2015-01-08; online 2015-01-06]

A genetic study on C5-TRAF1 and progression of joint damage in rheumatoid arthritis.

van Steenbergen HW, Rodríguez-Rodríguez L, Berglin E, ..., Rantapää-Dahlqvist S, van der Helm-van Mil AH

Arthritis Res. Ther. 17 (-) 1 [2015-01-08; online 2015-01-08]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Parallel protein detection by solid-phase proximity ligation assay with real-time PCR or sequencing.

Ebai T, Kamali-Moghaddam M, Landegren U

Curr Protoc Mol Biol 109 (-) 20.10.1-20.1025 [2015-01-05; online 2015-01-05]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Mutagenesis. Smoking is associated with mosaic loss of chromosome Y.

Dumanski JP, Rasi C, Lönn M, ..., Ingelsson E, Forsberg LA

Science 347 (6217) 81-83 [2015-01-02; online 2014-12-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A secretagogin locus of the mammalian hypothalamus controls stress hormone release.

Romanov RA, Alpár A, Zhang MD, ..., Hökfelt T, Harkany T

EMBO J. 34 (1) 36-54 [2015-01-02; online 2014-11-27]

The mutational landscape in pediatric acute lymphoblastic leukemia deciphered by whole genome sequencing.

Lindqvist CM, Nordlund J, Ekman D, ..., Syvänen AC, Berglund EC

Hum. Mutat. 36 (1) 118-128 [2015-01-00; online 2014-10-31]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling.

Gremel G, Wanders A, Cedernaes J, ..., Uhlén M, Pontén F

J. Gastroenterol. 50 (1) 46-57 [2015-01-00; online 2014-05-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling

The Biobanking Analysis Resource Catalogue (BARCdb): a new research tool for the analysis of biobank samples.

Galli J, Oelrich J, Taussig MJ, ..., Ortega-Paino E, Landegren U

Nucleic Acids Res. 43 (Database issue) D1158-D1162 [2015-01-00; online 2014-10-23]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Synthesis of Vinyl- and Aryl-Acyl Sulfonimidamides Through Pd-Catalyzed Carbonylation Using Mo(CO)6as ex situ CO Source

Wakchaure PB, Borhade SR, Sandström A, Arvidsson PI

Eur. J. Org. Chem. 2015 (1) 213-219 [2015-01-00; online 2014-11-19]

Drug Discovery and Development (DDD) [Technology development]

Scavenging effect of Trolox released from brushite cements.

Mestres G, Santos CF, Engman L, Persson C, Ott MK

Acta Biomater 11 (-) 459-466 [2015-01-00; online 2014-09-16]

Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis.

Avican K, Fahlgren A, Huss M, ..., Dersch P, Fällman M

PLoS Pathog. 11 (1) e1004600 [2015-01-00; online 2015-01-15]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Phenotypic plasticity and differentiation in an invasive freshwater microalga

Sassenhagen I, Wilken S, Godhe A, Rengefors K

Harmful Algae 41 (-) 38-45 [2015-01-00; online 2015-01-00]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Methylated RASSF1A in malignant peripheral nerve sheath tumors identifies neurofibromatosis type 1 patients with inferior prognosis.

Danielsen SA, Lind GE, Kolberg M, ..., Picci P, Lothe RA

Neuro-oncology 17 (1) 63-69 [2015-01-00; online 2014-07-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Lessons and implications from association studies and post-GWAS analyses of cervical cancer.

Chen D, Gyllensten U

Trends Genet. 31 (1) 41-54 [2015-01-00; online 2014-12-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Identification and functional characterization of G6PC2 coding variants influencing glycemic traits define an effector transcript at the G6PC2-ABCB11 locus.

Mahajan A, Sim X, Ng HJ, ..., Gloyn AL, T2D-GENES consortium and GoT2D consortium

PLoS Genet. 11 (1) e1004876 [2015-01-00; online 2015-01-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

High plasma levels of heparin-binding epidermal growth factor are associated with a more stable plaque phenotype and reduced incidence of coronary events.

Rattik S, Wigren M, Björkbacka H, ..., Gonçalves I, Nilsson J

Arterioscler. Thromb. Vasc. Biol. 35 (1) 222-228 [2015-01-00; online 2014-10-30]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Healthy Nordic diet downregulates the expression of genes involved in inflammation in subcutaneous adipose tissue in individuals with features of the metabolic syndrome.

Kolehmainen M, Ulven SM, Paananen J, ..., Arner P, Dahlman I

Am. J. Clin. Nutr. 101 (1) 228-239 [2015-01-00; online 2014-12-21]

Expression of human leukocyte antigen class I in endocrine and exocrine pancreatic tissue at onset of type 1 diabetes.

Skog O, Korsgren S, Wiberg A, ..., Korsgren O, Dahl-Jørgensen K

Am. J. Pathol. 185 (1) 129-138 [2015-01-00; online 2014-12-20]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Combining an amyloid-beta (Aβ) cleaving enzyme inhibitor with a γ-secretase modulator results in an additive reduction of Aβ production.

Strömberg K, Eketjäll S, Georgievska B, ..., Cowburn RF, Dabrowski M

FEBS J. 282 (1) 65-73 [2015-01-00; online 2014-11-07]

Drug Discovery and Development (DDD) [Collaborative]

Body composition and bone mineral density in women with Cushing's syndrome in remission and the association with common genetic variants influencing glucocorticoid sensitivity.

Ragnarsson O, Glad CA, Bergthorsdottir R, ..., Wängberg B, Johannsson G

Eur. J. Endocrinol. 172 (1) 1-10 [2015-01-00; online 2014-11-26]

Applied Enantioselective Aminocatalysis: α-Heteroatom Functionalization Reactions on the Carbapenem (β-Lactam Antibiotic) Core

Cele ZED, Arvidsson PI, Kruger HG, Govender T, Naicker T

Eur. J. Org. Chem. 2015 (3) 638-646 [2015-01-00; online 2014-12-11]

Drug Discovery and Development (DDD) [Collaborative]

A Machine Learning Approach to Explain Drug Selectivity to Soluble and Membrane Protein Targets.

Freyhult E, Gustafsson MG, Strömbergsson H

Mol Inform 34 (1) 44-52 [2015-01-00; online 2015-01-08]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

The effect of N-methylation of amino acids (Ac-X-OMe) on solubility and conformation: a DFT study

Md. Abdur Rauf S, Arvidsson PI, Albericio F, ..., Kruger HG, Honarparvar B

Org. Biomol. Chem. 13 (39) 9993-10006 [2015-00-00; online 2015-00-00]

Drug Discovery and Development (DDD) [Collaborative]

Pd-catalyzed C–N coupling of vinylbromides and sulfonimidamides: a facile synthesis of N′-vinylsulfonimidamides

Nandi GC, Kota SR, Wakchaure PB, ..., Naicker T, Arvidsson PI

RSC Adv. 5 (76) 62084-62090 [2015-00-00; online 2015-00-00]

Drug Discovery and Development (DDD) [Technology development]

Cytotoxicity, in Vivo Skin Irritation and Acute Systemic Toxicity of the Mesoporous Magnesium Carbonate Upsalite®

Frykstrand S, Forsgren J, Zhang P, Strømme M, Ferraz N

JBNB 06 (04) 257-266 [2015-00-00; online 2015-00-00]

Anti-Obesity Effects and Metabolism in DIO Mice of a Novel Hybrid Lipid with Lauric and Lipoic Acid

Madawala SR

J Obes Weight Loss Ther 05 (02) - [2015-00-00; online 2015-00-00]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

A novel cytosolic NADH:quinone oxidoreductase fromMethanothermobacter marburgensis

Ullmann E, Tan TC, Gundinger T, ..., Divne C, Spadiut O

Biosci. Rep. 34 (6) 893-904 [2014-12-23; online 2014-12-23]

Inhibitory Activity of the Isoflavone Biochanin A on Intracellular Bacteria of Genus Chlamydia and Initial Development of a Buccal Formulation

Hanski L, Genina N, Uvell H, ..., Sandler N, Vuorela PM

PLoS ONE 9 (12) e115115 [2014-12-16; online 2014-12-16]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Exploration and pharmacokinetic profiling of phenylalanine based carbamates as novel substance p 1-7 analogues.

Fransson R, Nordvall G, Bylund J, ..., Hallberg M, Sandström A

ACS Med Chem Lett 5 (12) 1272-1277 [2014-12-11; online 2014-10-29]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Sensitive detection of aggregated prion protein via proximity ligation.

Hammond M, Wik L, Deslys JP, ..., Landegren U, Kamali-Moghaddam M

Prion 8 (3) 261-265 [2014-12-09; online 2014-12-09]

Affinity Proteomics Uppsala [Technology development] Clinical Biomarkers PLA and Single Cell Proteomics [Technology development]

Inhibition of tumor cell proliferation and motility by fibroblasts is both contact and soluble factor dependent.

Alkasalias T, Flaberg E, Kashuba V, ..., Klein G, Guven H

Proc. Natl. Acad. Sci. U.S.A. 111 (48) 17188-17193 [2014-12-02; online 2014-11-19]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Vinylated linear P2 pyrimidinyloxyphenylglycine based inhibitors of the HCV NS3/4A protease and corresponding macrocycles.

Lampa A, Alogheli H, Ehrenberg AE, ..., Karlén A, Sandström A

Bioorg. Med. Chem. 22 (23) 6595-6615 [2014-12-01; online 2014-12-03]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Both Lewis and secretor status mediate susceptibility to rotavirus infections in a rotavirus genotype-dependent manner.

Nordgren J, Sharma S, Bucardo F, ..., Larson G, Svensson L

Clin. Infect. Dis. 59 (11) 1567-1573 [2014-12-01; online 2014-08-07]

An outbreak of respiratory tularemia caused by diverse clones of Francisella tularensis.

Johansson A, Lärkeryd A, Widerström M, ..., Forsman M, Larsson P

Clin. Infect. Dis. 59 (11) 1546-1553 [2014-12-01; online 2014-08-05]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The lung-specific proteome defined by integration of transcriptomics and antibody-based profiling.

Lindskog C, Fagerberg L, Hallström B, ..., Pontén F, Micke P

FASEB J. 28 (12) 5184-5196 [2014-12-00; online 2014-08-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Collaborative]

Studies of plant colonisation by closely related Bacillus amyloliquefaciens biocontrol agents using strain specific quantitative PCR assays.

Johansson AH, Bejai S, Niazi A, ..., Bongcam-Rudloff E, Meijer J

Antonie Van Leeuwenhoek 106 (6) 1247-1257 [2014-12-00; online 2014-10-09]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Serotonin receptor gene (5HT-2A) polymorphism is associated with provoked vestibulodynia and comorbid symptoms of pain.

Heddini U, Bohm-Starke N, Grönbladh A, ..., Nilsson KW, Johannesson U

J Sex Med 11 (12) 3064-3071 [2014-12-00; online 2014-09-02]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Peritoneal carcinomatosis from small intestinal neuroendocrine tumors: Clinical course and genetic profiling.

Norlén O, Edfeldt K, Akerstrom G, ..., Bjorklund P, Stalberg P

Surgery 156 (6) 1512-21; discussion 1521-2 [2014-12-00; online 2014-11-11]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Large-scale metabolomic profiling identifies novel biomarkers for incident coronary heart disease.

Ganna A, Salihovic S, Sundström J, ..., Fall T, Ingelsson E

PLoS Genet. 10 (12) e1004801 [2014-12-00; online 2014-12-11]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] PLA and Single Cell Proteomics [Service]

Intragenic duplication--a novel causative mechanism for SATB2-associated syndrome.

Liedén A, Kvarnung M, Nilssson D, Sahlin E, Lundberg ES

Am. J. Med. Genet. A 164A (12) 3083-3087 [2014-12-00; online 2014-09-25]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Insights into conifer giga-genomes.

De La Torre AR, Birol I, Bousquet J, ..., Zerbe P, Bohlmann J

Plant Physiol. 166 (4) 1724-1732 [2014-12-00; online 2014-10-29]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Inhibition of Insulin-Regulated Aminopeptidase (IRAP) by Arylsulfonamides.

Borhade SR, Rosenström U, Sävmarker J, ..., Larhed M, Hallberg M

ChemistryOpen 3 (6) 256-263 [2014-12-00; online 2014-11-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Collaborative]

Gene expression associated with intersterility in Heterobasidion

Van der Nest MA, Olson Å, Karlsson M, ..., Wingfield BD, Stenlid J

Fungal Genetics and Biology 73 (-) 104-119 [2014-12-00; online 2014-12-00]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Evaluation of efficacy of a new MEK inhibitor, RO4987655, in human tumor xenografts by [(18)F] FDG-PET imaging combined with proteomic approaches.

Tegnebratt T, Ruge E, Bader S, ..., Tessier J, Stone-Elander S

EJNMMI Res 4 (1) 34 [2014-12-00; online 2014-09-09]

Efficient application of next-generation sequencing for the diagnosis of rare genetic syndromes.

Madrigal I, Alvarez-Mora MI, Karlberg O, ..., Syvänen AC, Milà M

J. Clin. Pathol. 67 (12) 1099-1103 [2014-12-00; online 2014-10-02]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Donor or recipient origin of posttransplant lymphoproliferative disorders following solid organ transplantation.

Kinch A, Cavelier L, Bengtsson M, ..., Sundström C, Pauksens K

Am. J. Transplant. 14 (12) 2838-2845 [2014-12-00; online 2014-10-10]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Common genetic variants highlight the role of insulin resistance and body fat distribution in type 2 diabetes, independent of obesity.

Scott RA, Fall T, Pasko D, ..., Langenberg C, Wareham NJ

Diabetes 63 (12) 4378-4387 [2014-12-00; online 2014-06-19]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Applying polygenic risk scores to postpartum depression.

Byrne EM, Carrillo-Roa T, Penninx BW, ..., Meltzer-Brody S, Wray NR

Arch Womens Ment Health 17 (6) 519-528 [2014-12-00; online 2014-07-19]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

High opsin diversity in a non-visual infaunal brittle star.

Delroisse J, Ullrich-Lüter E, Ortega-Martinez O, ..., Mallefet J, Flammang P

BMC Genomics 15 (-) 1035 [2014-11-28; online 2014-11-28]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Complete Genome Sequence of Francisella endociliophora Strain FSC1006, Isolated from a Laboratory Culture of the Marine Ciliate Euplotes raikovi.

Sjödin A, Ohrman C, Bäckman S, ..., Stenberg P, Thelaus J

Genome Announc 2 (6) - [2014-11-26; online 2014-11-26]

Bioinformatics Support for Computational Resources [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

1p36 deletion is a marker for tumour dissemination in microsatellite stable stage II-III colon cancer.

Mayrhofer M, Kultima HG, Birgisson H, ..., Glimelius B, Isaksson A

BMC Cancer 14 (-) 872 [2014-11-24; online 2014-11-24]

The Eph tyrosine kinase receptors EphB2 and EphA2 are novel proteolytic substrates of tissue factor/coagulation factor VIIa.

Eriksson O, Ramström M, Hörnaeus K, ..., Mokhtari D, Siegbahn A

J. Biol. Chem. 289 (47) 32379-32391 [2014-11-21; online 2014-10-05]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Microwave Heated Flow Synthesis of Spiro-oxindole Dihydroquinazolinone Based IRAP Inhibitors

Engen K, Sävmarker J, Rosenström U, ..., Jenmalm-Jensen A, Larhed M

Org. Process Res. Dev. 18 (11) 1582-1588 [2014-11-21; online 2014-10-16]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Growth differentiation factor 15, a marker of oxidative stress and inflammation, for risk assessment in patients with atrial fibrillation: insights from the Apixaban for Reduction in Stroke and Other Thromboembolic Events in Atrial Fibrillation (ARISTOTLE) trial.

Wallentin L, Hijazi Z, Andersson U, ..., Siegbahn A, ARISTOTLE Investigators

Circulation 130 (21) 1847-1858 [2014-11-18; online 2014-10-07]

Affinity Proteomics Uppsala [Technology development] Clinical Biomarkers PLA and Single Cell Proteomics [Service]

Metagenomic approaches to disclose disease-associated pathogens: detection of viral pathogens in honeybees.

Granberg F, Karlsson OE, Belák S

Methods Mol. Biol. 1247 (-) 491-511 [2014-11-17; online 2014-11-17]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Pathway analysis of cervical cancer genome-wide association study highlights the MHC region and pathways involved in response to infection.

Chen D, Enroth S, Ivansson E, Gyllensten U

Hum. Mol. Genet. 23 (22) 6047-6060 [2014-11-15; online 2014-06-18]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Leachability and desorption of PCBs from soil and their dependency on pH and dissolved organic matter.

Badea SL, Mustafa M, Lundstedt S, Tysklind M

Sci. Total Environ. 499 (-) 220-227 [2014-11-15; online 2014-09-07]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes

Smeds L, Kawakami T, Burri R, ..., Uebbing S, Ellegren H

Nat Commun 5 (-) 5448 [2014-11-07; online 2014-11-07]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Defining the human adipose tissue proteome to reveal metabolic alterations in obesity.

Mardinoglu A, Kampf C, Asplund A, ..., Uhlen M, Nielsen J

J. Proteome Res. 13 (11) 5106-5119 [2014-11-07; online 2014-09-16]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling

Analysis of autoantibody profiles in osteoarthritis using comprehensive protein array concepts.

Henjes F, Lourido L, Ruiz-Romero C, ..., Nilsson P, Fuentes M

J. Proteome Res. 13 (11) 5218-5229 [2014-11-07; online 2014-10-09]

Autoimmunity and Serology Profiling [Collaborative]

Affinity proteomic profiling of plasma, cerebrospinal fluid, and brain tissue within multiple sclerosis.

Byström S, Ayoglu B, Häggmark A, ..., Nilsson P, Schwenk JM

J. Proteome Res. 13 (11) 4607-4619 [2014-11-07; online 2014-09-19]

Affinity Proteomics Stockholm [Collaborative] Fluorescence Tissue Profiling

Multimodal fluorescence microscopy of prion strain specific PrP deposits stained by thiophene-based amyloid ligands.

Magnusson K, Simon R, Sjölander D, ..., Hammarström P, Nilsson KP

Prion 8 (4) 319-329 [2014-11-01; online 2014-11-01]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Aberrantly activated claudin 6 and 18.2 as potential therapy targets in non-small-cell lung cancer.

Micke P, Mattsson JS, Edlund K, ..., Sahin U, Türeci O

Int. J. Cancer 135 (9) 2206-2214 [2014-11-01; online 2014-04-09]

Replicability and robustness of genome-wide-association studies for behavioral traits.

Rietveld CA, Conley D, Eriksson N, ..., Koellinger PD, Social Science Genetics Association Consortium

Psychol Sci 25 (11) 1975-1986 [2014-11-00; online 2014-10-06]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Parallel barcoding of antibodies for DNA-assisted proteomics.

Dezfouli M, Vickovic S, Iglesias MJ, Schwenk JM, Ahmadian A

Proteomics 14 (21-22) 2432-2436 [2014-11-00; online 2014-09-30]

Affinity Proteomics Stockholm [Technology development] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Integration of genome-wide of Stat3 binding and epigenetic modification mapping with transcriptome reveals novel Stat3 target genes in glioma cells.

Kruczyk M, Przanowski P, Dabrowski M, ..., Kaminska B, Komorowski J

Biochim. Biophys. Acta 1839 (11) 1341-1350 [2014-11-00; online 2014-08-12]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Human isolates of Listeria monocytogenes in Sweden during half a century (1958-2010).

Lopez-Valladares G, Tham W, Parihar VS, ..., Henriques-Normark B, Danielsson-Tham ML

Epidemiol. Infect. 142 (11) 2251-2260 [2014-11-00; online 2014-02-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Fat mass and obesity-associated gene (FTO) is linked to higher plasma levels of the hunger hormone ghrelin and lower serum levels of the satiety hormone leptin in older adults.

Benedict C, Axelsson T, Söderberg S, ..., Lind L, Schiöth HB

Diabetes 63 (11) 3955-3959 [2014-11-00; online 2014-06-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Evolution reveals a glutathione-dependent mechanism of 3-hydroxypropionic acid tolerance.

Kildegaard KR, Hallström BM, Blicher TH, ..., Nielsen J, Borodina I

Metab. Eng. 26 (-) 57-66 [2014-11-00; online 2014-09-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array.

Kawakami T, Backström N, Burri R, ..., Qvarnström A, Ellegren H

Mol Ecol Resour 14 (6) 1248-1260 [2014-11-00; online 2014-05-03]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Defining the role of common variation in the genomic and biological architecture of adult human height.

Wood AR, Esko T, Yang J, ..., Hirschhorn JN, Frayling TM

Nat. Genet. 46 (11) 1173-1186 [2014-11-00; online 2014-10-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Defining the human gallbladder proteome by transcriptomics and affinity proteomics.

Kampf C, Mardinoglu A, Fagerberg L, ..., Pontén F, Uhlen M

Proteomics 14 (21-22) 2498-2507 [2014-11-00; online 2014-09-02]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling

Cesarean delivery and hematopoietic stem cell epigenetics in the newborn infant: implications for future health?

Almgren M, Schlinzig T, Gomez-Cabrero D, ..., Norman M, Ekström TJ

Am. J. Obstet. Gynecol. 211 (5) 502.e1-502.e8 [2014-11-00; online 2014-07-06]

Binning metagenomic contigs by coverage and composition.

Alneberg J, Bjarnason BS, de Bruijn I, ..., Andersson AF, Quince C

Nat. Methods 11 (11) 1144-1146 [2014-11-00; online 2014-09-15]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Bcl-2 maintains the mitochondrial membrane potential, but fails to affect production of reactive oxygen species and endoplasmic reticulum stress, in sodium palmitate-induced β-cell death.

Wang X, Welsh N

Ups. J. Med. Sci. 119 (4) 306-315 [2014-11-00; online 2014-10-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Antibody validation of immunohistochemistry for biomarker discovery: recommendations of a consortium of academic and pharmaceutical based histopathology researchers.

Howat WJ, Lewis A, Jones P, ..., Womack C, Warford A

Methods 70 (1) 34-38 [2014-11-00; online 2014-02-15]

Abolished InsP3R2 function inhibits sweat secretion in both humans and mice.

Klar J, Hisatsune C, Baig SM, ..., Mikoshiba K, Dahl N

J. Clin. Invest. 124 (11) 4773-4780 [2014-11-00; online 2014-10-20]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Melanoma patient-derived xenografts accurately model the disease and develop fast enough to guide treatment decisions.

Einarsdottir BO, Bagge RO, Bhadury J, ..., Ny L, Nilsson JA

Oncotarget 5 (20) 9609-9618 [2014-10-30; online 2014-09-18]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Populus tremula (European aspen) shows no evidence of sexual dimorphism.

Robinson KM, Delhomme N, Mähler N, ..., Jansson S, Street NR

BMC Plant Biol. 14 (-) 276 [2014-10-16; online 2014-10-16]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs.

Adoue V, Schiavi A, Light N, ..., Syvänen A, Pastinen T

Mol. Syst. Biol. 10 (-) 754 [2014-10-16; online 2014-10-16]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Identification of 33 candidate oncogenes by screening for base-specific mutations.

Tuupanen S, Hänninen UA, Kondelin J, ..., Pitkänen E, Aaltonen LA

Br. J. Cancer 111 (8) 1657-1662 [2014-10-14; online 2014-08-15]

Human genetic evidence for involvement of CD137 in atherosclerosis.

Söderström LÅ, Gertow K, Folkersen L, ..., Hansson GK, Olofsson PS

Mol. Med. 20 (-) 456-465 [2014-10-14; online 2014-07-18]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Inter- and intratumoral heterogeneity of BCL2 correlates with IgH expression and prognosis in follicular lymphoma.

Barreca A, Martinengo C, Annaratone L, ..., van Oudenaarden A, Chiarle R

Blood Cancer J 4 (-) e249 [2014-10-10; online 2014-10-10]

Advanced FISH Technologies [Collaborative]

Gene and protein expression and cellular localisation of cytochrome P450 enzymes of the 1A, 2A, 2C, 2D and 2E subfamilies in equine intestine and liver.

Tydén E, Tjälve H, Larsson P

Acta Vet. Scand. 56 (-) 69 [2014-10-08; online 2014-10-08]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects.

Ameur A, Bunikis I, Enroth S, Gyllensten U

Database (Oxford) 2014 (-) - [2014-10-03; online 2014-10-03]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Biofuels. Altered sterol composition renders yeast thermotolerant.

Caspeta L, Chen Y, Ghiaci P, ..., Petranovic D, Nielsen J

Science 346 (6205) 75-78 [2014-10-03; online 2014-10-02]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Parent-of-origin-specific allelic associations among 106 genomic loci for age at menarche.

Perry JR, Day F, Elks CE, ..., Murabito JM, Ong KK

Nature 514 (7520) 92-97 [2014-10-02; online 2014-07-23]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Acetate availability and utilization supports the growth of mutant sub-populations on aging bacterial colonies.

Bergman JM, Wrande M, Hughes D

PLoS ONE 9 (10) e109255 [2014-10-02; online 2014-10-02]

Uneven distribution of human papillomavirus 16 in cervical carcinoma in situ and squamous cell carcinoma in older females: A retrospective database study.

Andersson S, Mints M, Gyllensten U, ..., Lambe M, Wilander E

Oncol Lett 8 (4) 1528-1532 [2014-10-00; online 2014-09-10]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing.

Lindholm ME, Huss M, Solnestam BW, ..., Lundeberg J, Sundberg CJ

FASEB J. 28 (10) 4571-4581 [2014-10-00; online 2014-07-11]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

The DMRT3 'Gait keeper' mutation affects performance of Nordic and Standardbred trotters.

Jäderkvist K, Andersson LS, Johansson AM, ..., Andersson L, Lindgren G

J. Anim. Sci. 92 (10) 4279-4286 [2014-10-00; online 2014-08-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Signals that regulate the oncogenic fate of neural stem cells and progenitors.

Swartling FJ, Bolin S, Phillips JJ, Persson AI

Exp. Neurol. 260 (-) 56-68 [2014-10-00; online 2013-02-05]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

NPSR1 polymorphisms influence recurrent abdominal pain in children: a population-based study.

Henström M, Zucchelli M, Söderhäll C, ..., Olén O, D'Amato M

Neurogastroenterol. Motil. 26 (10) 1417-1425 [2014-10-00; online 2014-08-05]

Medium from γ-irradiated Escherichia coli bacteria stimulates a unique immune response in Drosophila cells.

Lindberg BG, Oldenvi S, Steiner H

Dev. Comp. Immunol. 46 (2) 392-400 [2014-10-00; online 2014-06-04]

In situ sequencing identifies TMPRSS2-ERG fusion transcripts, somatic point mutations and gene expression levels in prostate cancers.

Kiflemariam S, Mignardi M, Ali MA, ..., Nilsson M, Sjöblom T

J. Pathol. 234 (2) 253-261 [2014-10-00; online 2014-08-04]

HemR is an OmpR/PhoB-like response regulator from Leptospira, which simultaneously effects transcriptional activation and repression of key haem metabolism genes.

Morero NR, Botti H, Nitta KR, ..., Picardeau M, Buschiazzo A

Mol. Microbiol. 94 (2) 340-352 [2014-10-00; online 2014-08-26]

Evidence for autosomal recessive inheritance in SPG3A caused by homozygosity for a novel ATL1 missense mutation.

Khan TN, Klar J, Tariq M, ..., Baig SM, Dahl N

Eur. J. Hum. Genet. 22 (10) 1180-1184 [2014-10-00; online 2014-01-30]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Epoxy alcohol synthase of the rice blast fungus represents a novel subfamily of dioxygenase-cytochrome P450 fusion enzymes.

Hoffmann I, Jernerén F, Oliw EH

J. Lipid Res. 55 (10) 2113-2123 [2014-10-00; online 2014-08-15]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Design of a general-purpose European compound screening library for EU-OPENSCREEN.

Horvath D, Lisurek M, Rupp B, ..., Quintana J, Frank R

ChemMedChem 9 (10) 2309-2326 [2014-10-00; online 2014-07-15]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Controversies inASSAY and Drug Development Technologies: A Focus on Assessing Irreproducibility

Glickman JF, Lundbäck T, Napper AD, ..., Zaman GJR, Osada H

ASSAY and Drug Development Technologies 12 (8) 443-451 [2014-10-00; online 2014-10-00]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Analyses of historical and current populations of black grouse in Central Europe reveal strong effects of genetic drift and loss of genetic diversity

Segelbacher G, Strand TM, Quintela M, ..., Koelewijn HP, Höglund J

Conserv Genet 15 (5) 1183-1195 [2014-10-00; online 2014-04-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A worldwide survey of genome sequence variation provides insight into the evolutionary history of the honeybee Apis mellifera.

Wallberg A, Han F, Wellhagen G, ..., Pirk CW, Webster MT

Nat. Genet. 46 (10) 1081-1088 [2014-10-00; online 2014-08-26]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Human cytomegalovirus tegument protein pp65 is detected in all intra- and extra-axial brain tumours independent of the tumour type or grade.

Libard S, Popova SN, Amini RM, ..., Ponten F, Alafuzoff I

PLoS ONE 9 (9) e108861 [2014-09-30; online 2014-09-30]

The Chironomus tentans genome sequence and the organization of the Balbiani ring genes.

Kutsenko A, Svensson T, Nystedt B, ..., Visa N, Wieslander L

BMC Genomics 15 (-) 819 [2014-09-27; online 2014-09-27]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Plasmidome interchange between Clostridium botulinum, Clostridium novyi and Clostridium haemolyticum converts strains of independent lineages into distinctly different pathogens.

Skarin H, Segerman B

PLoS ONE 9 (9) e107777 [2014-09-25; online 2014-09-25]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Oncoprotein stabilization in brain tumors.

Hede SM, Savov V, Weishaupt H, Sangfelt O, Swartling FJ

Oncogene 33 (39) 4709-4721 [2014-09-25; online 2013-10-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Glial origin of mesenchymal stem cells in a tooth model system.

Kaukua N, Shahidi MK, Konstantinidou C, ..., Fried K, Adameyko I

Nature 513 (7519) 551-554 [2014-09-25; online 2014-08-01]

Integrated Microscopy Technologies Stockholm [Collaborative]

Evidence that breast cancer risk at the 2q35 locus is mediated through IGFBP5 regulation.

Ghoussaini M, Edwards SL, Michailidou K, ..., Dunning AM, Australian Ovarian Cancer Management Group

Nat Commun 4 (1) 4999 [2014-09-23; online 2014-09-23]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Common genetic variants associated with cognitive performance identified using the proxy-phenotype method.

Rietveld CA, Esko T, Davies G, ..., Cesarini D, Koellinger PD

Proc. Natl. Acad. Sci. U.S.A. 111 (38) 13790-13794 [2014-09-23; online 2014-09-08]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Histidine-rich glycoprotein uptake and turnover is mediated by mononuclear phagocytes.

Tugues S, Roche F, Noguer O, ..., Tolmachev V, Claesson-Welsh L

PLoS ONE 9 (9) e107483 [2014-09-22; online 2014-09-22]

Distinguishing between driver and passenger mutations in individual cancer genomes by network enrichment analysis.

Merid SK, Goranskaya D, Alexeyenko A

BMC Bioinformatics 15 (-) 308 [2014-09-19; online 2014-09-19]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

A universal approach to prepare reagents for DNA-assisted protein analysis.

Yan J, Gu GJ, Jost C, ..., Landegren U, Kamali-Moghaddam M

PLoS ONE 9 (9) e108061 [2014-09-18; online 2014-09-18]

Affinity Proteomics Uppsala [Technology development] Clinical Biomarkers PLA and Single Cell Proteomics [Technology development]

Characterization of stem-like cells in mucoepidermoid tracheal paediatric tumor.

Lim ML, Ooi BN, Jungebluth P, ..., Ahrlund-Richter L, Macchiarini P

PLoS ONE 9 (9) e107712 [2014-09-17; online 2014-09-17]

Structural and functional characterization of ochratoxinase, a novel mycotoxin-degrading enzyme.

Dobritzsch D, Wang H, Schneider G, Yu S

Biochem. J. 462 (3) 441-452 [2014-09-15; online 2014-06-21]

The DEK oncoprotein binds to highly and ubiquitously expressed genes with a dual role in their transcriptional regulation.

Sandén C, Järvstråt L, Lennartsson A, ..., Nilsson B, Gullberg U

Mol. Cancer 13 (-) 215 [2014-09-12; online 2014-09-12]

Bioinformatics and Expression Analysis (BEA) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genome-wide analysis reveals DNA methylation markers that vary with both age and obesity.

Almén MS, Nilsson EK, Jacobsson JA, ..., Fredriksson R, Schiöth HB

Gene 548 (1) 61-67 [2014-09-10; online 2014-07-11]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The prognostic value and therapeutic target role of stathmin-1 in urinary bladder cancer.

Hemdan T, Lindén M, Lind SB, ..., Malmström PU, Segersten U

Br. J. Cancer 111 (6) 1180-1187 [2014-09-09; online 2014-07-29]

The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera.

Ahola V, Lehtonen R, Somervuo P, ..., Frilander MJ, Hanski I

Nat Commun 5 (-) 4737 [2014-09-05; online 2014-09-05]

Neu-Laxova syndrome is a heterogeneous metabolic disorder caused by defects in enzymes of the L-serine biosynthesis pathway.

Acuna-Hidalgo R, Schanze D, Kariminejad A, ..., Hoischen A, Zenker M

Am. J. Hum. Genet. 95 (3) 285-293 [2014-09-04; online 2014-08-26]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Abstract of the 35th Scandinavian Congress of Rheumatology, September 20-23, 2014, Stockholm, Sweden.

Scand J Rheumatol Suppl 43 (127) 1-97 [2014-09-04; online 2014-09-04]

Predictive urinary biomarkers for steroid-resistant and steroid-sensitive focal segmental glomerulosclerosis using high resolution mass spectrometry and multivariate statistical analysis.

Kalantari S, Nafar M, Rutishauser D, ..., Yang H, Zubarev RA

BMC Nephrol 15 (-) 141 [2014-09-02; online 2014-09-02]

Metagenomics reveals that detoxification systems are underrepresented in marine bacterial communities.

Bengtsson-Palme J, Alm Rosenblad M, Molin M, Blomberg A

BMC Genomics 15 (-) 749 [2014-09-01; online 2014-09-01]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

An integrative analysis of the tumorigenic role of TAZ in human non-small cell lung cancer.

Noguchi S, Saito A, Horie M, ..., Micke P, Nagase T

Clin. Cancer Res. 20 (17) 4660-4672 [2014-09-01; online 2014-06-22]

Sexual structures and recombination of the wheat rust fungus Puccinia striiformis on Berberis vulgaris.

Rodriguez-Algaba J, Walter S, Sørensen CK, Hovmøller MS, Justesen AF

Fungal Genet. Biol. 70 (-) 77-85 [2014-09-00; online 2014-07-22]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Recurrent GATA1 mutations in Diamond-Blackfan anaemia.

Klar J, Khalfallah A, Arzoo PS, Gazda HT, Dahl N

Br. J. Haematol. 166 (6) 949-951 [2014-09-00; online 2014-04-29]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics

Eiler A, Zaremba‐Niedzwiedzka K, Martínez‐García M, ..., Andersson SGE, Bertilsson S

Environ Microbiol 16 (9) 2682-2698 [2014-09-00; online 2013-11-12]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Picocyanobacteria containing a novel pigment gene cluster dominate the brackish water Baltic Sea.

Larsson J, Celepli N, Ininbergs K, ..., Bergman B, Ekman M

ISME J 8 (9) 1892-1903 [2014-09-00; online 2014-03-14]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Interactive effects of KIBRA and CLSTN2 polymorphisms on episodic memory in old-age unipolar depression.

Pantzar A, Laukka EJ, Atti AR, ..., Fratiglioni L, Bäckman L

Neuropsychologia 62 (-) 137-142 [2014-09-00; online 2014-08-01]

Identification of three novel FGF16 mutations in X-linked recessive fusion of the fourth and fifth metacarpals and possible correlation with heart disease.

Laurell T, Nilsson D, Hofmeister W, ..., Grigelioniene G, Nordgren A

Mol Genet Genomic Med 2 (5) 402-411 [2014-09-00; online 2014-05-14]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Hypomethylated pollen bypasses the interploidy hybridization barrier in Arabidopsis.

Schatlowski N, Wolff P, Santos-González J, ..., Tamaru H, Köhler C

Plant Cell 26 (9) 3556-3568 [2014-09-00; online 2014-09-12]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genome of the avirulent human-infective trypanosome--Trypanosoma rangeli.

Stoco PH, Wagner G, Talavera-Lopez C, ..., de Vasconcelos AT, Grisard EC

PLoS Negl Trop Dis 8 (9) e3176 [2014-09-00; online 2014-09-18]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Do the same genes underlie parallel phenotypic divergence in different Littorina saxatilis populations?

Westram AM, Galindo J, Alm Rosenblad M, ..., Panova M, Butlin RK

Mol. Ecol. 23 (18) 4603-4616 [2014-09-00; online 2014-08-13]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Cu(OAc)2 promoted Chan–Evans–Lam C–N cross coupling reactions on the N- and N′-nitrogen atoms of sulfonimidamides with aryl boronic acids

Nandi GC, Kota SR, Govender T, Kruger HG, Arvidsson PI

Tetrahedron 70 (35) 5428-5433 [2014-09-00; online 2014-09-00]

Drug Discovery and Development (DDD) [Technology development]

Splicing in the human brain.

Zaghlool A, Ameur A, Cavelier L, Feuk L

Int. Rev. Neurobiol. 116 (-) 95-125 [2014-08-31; online 2014-08-31]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Structural basis for regulation of the human acetyl-CoA thioesterase 12 and interactions with the steroidogenic acute regulatory protein-related lipid transfer (START) domain.

Swarbrick CM, Roman N, Cowieson N, ..., Lehtiö L, Forwood JK

J. Biol. Chem. 289 (35) 24263-24274 [2014-08-29; online 2014-07-09]

Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication.

Carneiro M, Rubin CJ, Di Palma F, ..., Lindblad-Toh K, Andersson L

Science 345 (6200) 1074-1079 [2014-08-29; online 2014-08-30]

Bioinformatics Support for Computational Resources NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Deep amplicon sequencing of preselected isolates of Parascaris equorum in β-tubulin codons associated with benzimidazole resistance in other nematodes.

Tydén E, Dahlberg J, Karlberg O, Höglund J

Parasit Vectors 7 (-) 410 [2014-08-29; online 2014-08-29]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The Arthonialean challenge: Restructuring Arthoniaceae

Frisch A, Thor G, Ertz D, Grube M

Taxon 63 (4) 727-744 [2014-08-28; online 2014-08-28]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

A multicentre hospital outbreak in Sweden caused by introduction of a vanB2 transposon into a stably maintained pRUM-plasmid in an Enterococcus faecium ST192 clone.

Sivertsen A, Billström H, Melefors Ö, ..., Sundsfjord A, Hegstad K

PLoS ONE 9 (8) e103274 [2014-08-25; online 2014-08-25]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Strong effects of genetic and lifestyle factors on biomarker variation and use of personalized cutoffs.

Enroth S, Johansson A, Enroth SB, Gyllensten U

Nat Commun 5 (1) 4684 [2014-08-22; online 2014-08-22]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Small RNA sequence analysis of adenovirus VA RNA-derived miRNAs reveals an unexpected serotype-specific difference in structure and abundance.

Kamel W, Segerman B, Punga T, Akusjärvi G

PLoS ONE 9 (8) e105746 [2014-08-21; online 2014-08-21]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Missing genes, multiple ORFs, and C-to-U type RNA editing in Acrasis kona (Heterolobosea, Excavata) mitochondrial DNA.

Fu CJ, Sheikh S, Miao W, Andersson SG, Baldauf SL

Genome Biol Evol 6 (9) 2240-2257 [2014-08-21; online 2014-08-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Winter bloom of a rare betaproteobacterium in the Arctic Ocean.

Alonso-Sáez L, Zeder M, Harding T, ..., Bertilsson S, Pedrós-Alió C

Front Microbiol 5 (-) 425 [2014-08-20; online 2014-08-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Meta-analysis in more than 17,900 cases of ischemic stroke reveals a novel association at 12q24.12.

Kilarski LL, Achterberg S, Devan WJ, ..., Bevan S, GARNET Collaborative Research Group WTCCC2ASGCtMCatISGC

Neurology 83 (8) 678-685 [2014-08-19; online 2014-07-16]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Tandem RNA chimeras contribute to transcriptome diversity in human population and are associated with intronic genetic variants.

Greger L, Su J, Rung J, ..., Dermitzakis ET, Brazma A

PLoS ONE 9 (8) e104567 [2014-08-18; online 2014-08-18]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Species and gene divergence in Littorina snails detected by array comparative genomic hybridization.

Panova M, Johansson T, Canbäck B, ..., Tunlid A, André C

BMC Genomics 15 (-) 687 [2014-08-18; online 2014-08-18]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Evaluation of exome sequencing to estimate tumor burden in plasma.

Klevebring D, Neiman M, Sundling S, ..., Grönberg H, Lindberg J

PLoS ONE 9 (8) e104417 [2014-08-18; online 2014-08-18]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

BESST--efficient scaffolding of large fragmented assemblies.

Sahlin K, Vezzi F, Nystedt B, Lundeberg J, Arvestad L

BMC Bioinformatics 15 (-) 281 [2014-08-15; online 2014-08-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genome analysis of Bacillus amyloliquefaciens Subsp. plantarum UCMB5113: a rhizobacterium that improves plant growth and stress management.

Niazi A, Manzoor S, Asari S, ..., Meijer J, Bongcam-Rudloff E

PLoS ONE 9 (8) e104651 [2014-08-13; online 2014-08-13]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The cellular thermal shift assay for evaluating drug target interactions in cells

Jafari R, Almqvist H, Axelsson H, ..., Nordlund P, Molina DM

Nat Protoc 9 (9) 2100-2122 [2014-08-07; online 2014-08-07]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Common genetic determinants of lung function, subclinical atherosclerosis and risk of coronary artery disease.

Sabater-Lleal M, Mälarstig A, Folkersen L, ..., Tobin MD, Hamsten A

PLoS ONE 9 (8) e104082 [2014-08-05; online 2014-08-05]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Differences in gene expression between mouse and human for dynamically regulated genes in early embryo.

Madissoon E, Töhönen V, Vesterlund L, ..., Hovatta O, Kere J

PLoS ONE 9 (8) e102949 [2014-08-04; online 2014-08-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

IgA measurements in over 12 000 Swedish twins reveal sex differential heritability and regulatory locus near CD30L.

Viktorin A, Frankowiack M, Padyukov L, ..., Hammarström L, Magnusson PK

Hum. Mol. Genet. 23 (15) 4177-4184 [2014-08-01; online 2014-03-27]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Exome sequencing reveals frequent inactivating mutations in ARID1A, ARID1B, ARID2 and ARID4A in microsatellite unstable colorectal cancer.

Cajuso T, Hänninen UA, Kondelin J, ..., Kilpivaara O, Vahteristo P

Int. J. Cancer 135 (3) 611-623 [2014-08-01; online 2014-01-03]

Analysis of candidate genes for lineage-specific expression changes in humans and primates.

Lindskog C, Kuhlwilm M, Davierwala A, ..., Pääbo S, Pontén F

J. Proteome Res. 13 (8) 3596-3606 [2014-08-01; online 2014-07-15]

The human carotid body releases acetylcholine, ATP and cytokines during hypoxia.

Kåhlin J, Mkrtchian S, Ebberyd A, ..., Fagerlund MJ, Eriksson LI

Exp. Physiol. 99 (8) 1089-1098 [2014-08-00; online 2014-06-03]

Systematic investigation of contribution of genetic variation in the HLA-DP region to cervical cancer susceptibility.

Chen D, Gyllensten U

Carcinogenesis 35 (8) 1765-1769 [2014-08-00; online 2014-04-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Selectivity mechanism of a bacterial homolog of the human drug-peptide transporters PepT1 and PepT2.

Guettou F, Quistgaard EM, Raba M, ..., Löw C, Nordlund P

Nat. Struct. Mol. Biol. 21 (8) 728-731 [2014-08-00; online 2014-07-30]

Plasma profiling reveals three proteins associated to amyotrophic lateral sclerosis.

Häggmark A, Mikus M, Mohsenchian A, ..., Kuźma-Kozakiewicz M, Nilsson P

Ann Clin Transl Neurol 1 (8) 544-553 [2014-08-00; online 2014-07-14]

Multifactorial analysis of changes in body mass index across the adult life course: a study with 65 years of follow-up.

Dahl AK, Reynolds CA, Fall T, Magnusson PK, Pedersen NL

Int J Obes (Lond) 38 (8) 1133-1141 [2014-08-00; online 2013-11-07]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Mechanisms of mRNA export.

Björk P, Wieslander L

Semin. Cell Dev. Biol. 32 (-) 47-54 [2014-08-00; online 2014-05-13]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Influence of coronary artery disease-associated genetic variants on risk of venous thromboembolism.

Bruzelius M, Strawbridge RJ, Trégouët D, ..., Odeberg J, Hamsten A

Thromb. Res. 134 (2) 426-432 [2014-08-00; online 2014-04-22]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

High risk of tobacco-related cancers in CDKN2A mutation-positive melanoma families.

Helgadottir H, Höiom V, Jönsson G, ..., Olsson H, Hansson J

J. Med. Genet. 51 (8) 545-552 [2014-08-00; online 2014-06-18]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetic variation in the CYP1A1 gene is related to circulating PCB118 levels in a population-based sample.

Lind L, Penell J, Syvänen AC, ..., van Bavel B, Lind PM

Environ. Res. 133 (-) 135-140 [2014-08-00; online 2014-06-14]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic association study of QT interval highlights role for calcium signaling pathways in myocardial repolarization.

Arking DE, Pulit SL, Crotti L, ..., de Bakker PIW, Newton-Cheh C

Nat. Genet. 46 (8) 826-836 [2014-08-00; online 2014-06-24]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Fusions involving protein kinase C and membrane-associated proteins in benign fibrous histiocytoma.

Płaszczyca A, Nilsson J, Magnusson L, ..., Nord KH, Mertens F

Int. J. Biochem. Cell Biol. 53 (-) 475-481 [2014-08-00; online 2014-04-08]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Distinct roles of Candida albicans-specific genes in host-pathogen interactions.

Wilson D, Mayer FL, Miramón P, ..., Jacobsen ID, Hube B

Eukaryotic Cell 13 (8) 977-989 [2014-08-00; online 2014-03-13]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Differential methylation in CN-AML preferentially targets non-CGI regions and is dictated by DNMT3A mutational status and associated with predominant hypomethylation of HOX genes.

Qu Y, Lennartsson A, Gaidzik VI, ..., Döhner K, Lehmann S

Epigenetics 9 (8) 1108-1119 [2014-08-00; online 2014-05-29]

Bioinformatics and Expression Analysis (BEA) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

DegePrime, a program for degenerate primer design for broad-taxonomic-range PCR in microbial ecology studies.

Hugerth LW, Wefer HA, Lundin S, ..., Engstrand L, Andersson AF

Appl. Environ. Microbiol. 80 (16) 5116-5123 [2014-08-00; online 2014-06-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Cluster of infections caused by methicillin-resistant Staphylococcus pseudintermedius in humans in a tertiary hospital.

Starlander G, Börjesson S, Grönlund-Andersson U, Tellgren-Roth C, Melhus A

J. Clin. Microbiol. 52 (8) 3118-3120 [2014-08-00; online 2014-05-30]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution.

Kawakami T, Smeds L, Backström N, ..., Olason P, Ellegren H

Mol. Ecol. 23 (16) 4035-4058 [2014-08-00; online 2014-05-28]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Nuclease-assisted suppression of human DNA background in sepsis.

Song Y, Giske CG, Gille-Johnson P, ..., Lundeberg J, Gyarmati P

PLoS ONE 9 (7) e103610 [2014-07-30; online 2014-07-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Polymorphisms in genes implicated in dopamine, serotonin and noradrenalin metabolism suggest association with cerebrospinal fluid monoamine metabolite concentrations in psychosis.

Andreou D, Söderman E, Axelsson T, ..., Agartz I, Jönsson EG

Behav Brain Funct 10 (-) 26 [2014-07-29; online 2014-07-29]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Analysis of stranded information using an automated procedure for strand specific RNA sequencing.

Sigurgeirsson B, Emanuelsson O, Lundeberg J

BMC Genomics 15 (-) 631 [2014-07-28; online 2014-07-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Identification of a small molecule that stabilizes lipoprotein lipase in vitro and lowers triglycerides in vivo.

Larsson M, Caraballo R, Ericsson M, ..., Nilsson SK, Olivecrona G

Biochem. Biophys. Res. Commun. 450 (2) 1063-1069 [2014-07-25; online 2014-07-02]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Biological insights from 108 schizophrenia-associated genetic loci.

Schizophrenia Working Group of the Psychiatric Genomics Consortium

Nature 511 (7510) 421-427 [2014-07-24; online 2014-07-22]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A Picea abies linkage map based on SNP markers identifies QTLs for four aspects of resistance to Heterobasidion parviporum infection.

Lind M, Källman T, Chen J, ..., Lascoux M, Stenlid J

PLoS ONE 9 (7) e101049 [2014-07-18; online 2014-07-18]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Single nucleotide polymorphisms with cis-regulatory effects on long non-coding transcripts in human primary monocytes.

Almlöf JC, Lundmark P, Lundmark A, ..., Ouwehand WH, Syvänen AC

PLoS ONE 9 (7) e102612 [2014-07-15; online 2014-07-15]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genome-wide profiling of AP-1-regulated transcription provides insights into the invasiveness of triple-negative breast cancer.

Zhao C, Qiao Y, Jonsson P, ..., Williams C, Dahlman-Wright K

Cancer Res. 74 (14) 3983-3994 [2014-07-15; online 2014-05-17]

Comparative structural analysis of the putative mono-ADP-ribosyltransferases of the ARTD/PARP family.

Pinto AF, Schüler H

Curr. Top. Microbiol. Immunol. 384 (-) 153-166 [2014-07-13; online 2014-07-13]

Peroxiredoxin-1 protects estrogen receptor α from oxidative stress-induced suppression and is a protein biomarker of favorable prognosis in breast cancer.

O'Leary PC, Terrile M, Bajor M, ..., Zagozdzon R, Gallagher WM

Breast Cancer Res. 16 (4) R79 [2014-07-10; online 2014-07-10]

Structural and biochemical characterization of human PR70 in isolation and in complex with the scaffolding subunit of protein phosphatase 2A.

Dovega R, Tsutakawa S, Quistgaard EM, ..., Löw C, Nordlund P

PLoS ONE 9 (7) e101846 [2014-07-09; online 2014-07-09]

The archaeal legacy of eukaryotes: a phylogenomic perspective.

Guy L, Saw JH, Ettema TJ

Cold Spring Harb Perspect Biol 6 (10) a016022 [2014-07-03; online 2014-07-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Transcriptome analysis reveals signature of adaptation to landscape fragmentation.

Somervuo P, Kvist J, Ikonen S, ..., Ahola V, Hanski I

PLoS ONE 9 (7) e101467 [2014-07-02; online 2014-07-02]

Large-scale genome-wide association studies and meta-analyses of longitudinal change in adult lung function.

Tang W, Kowgier M, Loth DW, ..., Hall IP, Cassano PA

PLoS ONE 9 (7) e100776 [2014-07-01; online 2014-07-01]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

l-Proline organocatalyzed Michael synthesis of monobactam and carbapenem β-lactam cores

Khanyase S, Naicker T, Maguire GEM, ..., Arvidsson PI, Govender T

Tetrahedron: Asymmetry 25 (13-14) 969-973 [2014-07-00; online 2014-07-00]

Drug Discovery and Development (DDD) [Collaborative]

The human liver-specific proteome defined by transcriptomics and antibody-based profiling.

Kampf C, Mardinoglu A, Fagerberg L, ..., Nielsen J, Uhlen M

FASEB J. 28 (7) 2901-2914 [2014-07-00; online 2014-03-22]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling

Structural basis for PTPA interaction with the invariant C-terminal tail of PP2A.

Löw C, Quistgaard EM, Kovermann M, ..., Balbach J, Nordlund P

Biol. Chem. 395 (7-8) 881-889 [2014-07-00; online 2014-07-09]

Screening for inhibition of Vibrio cholerae VipA-VipB interaction identifies small-molecule compounds active against type VI secretion.

Sun K, Bröms J, Lavander M, ..., Elofsson M, Sjöstedt A

Antimicrob. Agents Chemother. 58 (7) 4123-4130 [2014-07-00; online 2014-05-07]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Polymorphism of the cystatin C gene in patients with acute coronary syndromes: Results from the PLATelet inhibition and patient Outcomes study.

Akerblom A, Eriksson N, Wallentin L, ..., James SK, PLATO Investigators

Am. Heart J. 168 (1) 96-102.e2 [2014-07-00; online 2014-04-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Novel approach identifies SNPs in SLC2A10 and KCNK9 with evidence for parent-of-origin effect on body mass index.

Hoggart CJ, Venturini G, Mangino M, ..., Loos RJ, Kutalik Z

PLoS Genet. 10 (7) e1004508 [2014-07-00; online 2014-07-31]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

MiR-146a negatively regulates TLR2-induced inflammatory responses in keratinocytes.

Meisgen F, Xu Landén N, Wang A, ..., Breton L, Pivarcsi A

J. Invest. Dermatol. 134 (7) 1931-1940 [2014-07-00; online 2014-03-29]

Management intensity at field and landscape levels affects the structure of generalist predator communities.

Rusch A, Birkhofer K, Bommarco R, Smith HG, Ekbom B

Oecologia 175 (3) 971-983 [2014-07-00; online 2014-05-09]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Hepatic uptake of atorvastatin: influence of variability in transporter expression on uptake clearance and drug-drug interactions.

Vildhede A, Karlgren M, Svedberg EK, ..., Norén A, Artursson P

Drug Metab. Dispos. 42 (7) 1210-1218 [2014-07-00; online 2014-05-05]

Chemical Biology Consortium Sweden (CBCS) [Service]

Harmonization of Neuroticism and Extraversion phenotypes across inventories and cohorts in the Genetics of Personality Consortium: an application of Item Response Theory.

van den Berg SM, de Moor MH, McGue M, ..., Martin NG, Boomsma DI

Behav. Genet. 44 (4) 295-313 [2014-07-00; online 2014-05-15]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Haplotypes of the inducible nitric oxide synthase gene are strongly associated with exhaled nitric oxide levels in adults: a population-based study.

Dahgam S, Modig L, Torinsson Naluai Å, Olin AC, Nyberg F

J. Med. Genet. 51 (7) 449-454 [2014-07-00; online 2014-04-15]

Genome-wide association analysis identifies six new loci associated with forced vital capacity.

Loth DW, Soler Artigas M, Gharib SA, ..., Tobin MD, London SJ

Nat. Genet. 46 (7) 669-677 [2014-07-00; online 2014-06-15]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genome wide association identifies common variants at the SERPINA6/SERPINA1 locus influencing plasma cortisol and corticosteroid binding globulin.

Bolton JL, Hayward C, Direk N, ..., Walker BR, CORtisol NETwork (CORNET) Consortium

PLoS Genet. 10 (7) e1004474 [2014-07-00; online 2014-07-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic variants in CDC42 and NXPH1 as susceptibility factors for constipation and diarrhoea predominant irritable bowel syndrome.

Wouters MM, Lambrechts D, Knapp M, ..., D'Amato M, Boeckxstaens G

Gut 63 (7) 1103-1111 [2014-07-00; online 2013-09-18]

Characterization of an experimental vaccine for bovine respiratory syncytial virus.

Hägglund S, Hu K, Blodörn K, ..., Valarcher JF, Eléouët JF

Clin. Vaccine Immunol. 21 (7) 997-1004 [2014-07-00; online 2014-05-16]

CXCR4 Antagonists: A Screening Strategy for Identification of Functionally Selective Ligands.

Castaldo C, Benicchi T, Otrocka M, ..., Varrone M, Porcari V

J Biomol Screen 19 (6) 859-869 [2014-07-00; online 2014-03-14]

Chemical Biology Consortium Sweden (CBCS) [Service]

Autosomal dominant brachyolmia in a large Swedish family: phenotypic spectrum and natural course.

Grigelioniene G, Geiberger S, Horemuzova E, ..., Nordgren A, Mäkitie O

Am. J. Med. Genet. A 164A (7) 1635-1641 [2014-07-00; online 2014-03-29]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Affinity proteomics within rare diseases: a BIO-NMD study for blood biomarkers of muscular dystrophies.

Ayoglu B, Chaouch A, Lochmüller H, ..., Nilsson P, Al-Khalili Szigyarto C

EMBO Mol Med 6 (7) 918-936 [2014-07-00; online 2014-06-13]

'Geoarchaeote NAG1' is a deeply rooting lineage of the archaeal order Thermoproteales rather than a new phylum.

Guy L, Spang A, Saw JH, Ettema TJ

ISME J 8 (7) 1353-1357 [2014-07-00; online 2014-02-14]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A universal genomic coordinate translator for comparative genomics.

Zamani N, Sundström G, Meadows JR, ..., Haas BJ, Grabherr MG

BMC Bioinformatics 15 (-) 227 [2014-06-30; online 2014-06-30]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Large tilts in transmembrane helices can be induced during tertiary structure formation.

Virkki M, Boekel C, Illergård K, ..., von Heijne G, Nilsson I

J. Mol. Biol. 426 (13) 2529-2538 [2014-06-26; online 2014-04-30]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Exome sequencing circumvents missing clinical data and identifies a BSCL2 mutation in congenital lipodystrophy.

Schuster J, Khan TN, Tariq M, ..., Baig SM, Klar J

BMC Med. Genet. 15 (-) 71 [2014-06-24; online 2014-06-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Short-term variation in sperm competition causes sperm-mediated epigenetic effects on early offspring performance in the zebrafish.

Zajitschek S, Hotzy C, Zajitschek F, Immler S

Proc. Biol. Sci. 281 (1785) 20140422 [2014-06-22; online 2014-05-03]

The genomic landscape underlying phenotypic integrity in the face of gene flow in crows

Poelstra JW, Vijay N, Bossu CM, ..., Grabherr MG, Wolf JBW

Science 344 (6190) 1410-1414 [2014-06-20; online 2014-06-19]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Myelodysplastic syndromes are propagated by rare and distinct human cancer stem cells in vivo.

Woll PS, Kjällquist U, Chowdhury O, ..., Linnarsson S, Jacobsen SE

Cancer Cell 25 (6) 794-808 [2014-06-16; online 2014-05-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Complete genome sequence of a plant associated bacterium Bacillus amyloliquefaciens subsp. plantarum UCMB5033.

Niazi A, Manzoor S, Bejai S, Meijer J, Bongcam-Rudloff E

Stand Genomic Sci 9 (3) 718-725 [2014-06-15; online 2014-02-15]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Tyrosine phosphorylation profiling via in situ proximity ligation assay.

Elfineh L, Classon C, Asplund A, ..., Kamali-Moghaddam M, Lind SB

BMC Cancer 14 (-) 435 [2014-06-13; online 2014-06-13]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria.

Ekblom R, Smeds L, Ellegren H

BMC Genomics 15 (-) 467 [2014-06-12; online 2014-06-12]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Mapping-by-sequencing accelerates forward genetics in barley.

Mascher M, Jost M, Kuon JE, ..., Graner A, Stein N

Genome Biol. 15 (6) R78 [2014-06-10; online 2014-06-10]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Normalyzer: a tool for rapid evaluation of normalization methods for omics data sets.

Chawade A, Alexandersson E, Levander F

J. Proteome Res. 13 (6) 3114-3120 [2014-06-06; online 2014-04-29]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Efficient de novo assembly of large and complex genomes by massively parallel sequencing of Fosmid pools.

Alexeyenko A, Nystedt B, Vezzi F, ..., Wu CC, Lundeberg J

BMC Genomics 15 (-) 439 [2014-06-06; online 2014-06-06]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Scanning inverse fluorescence correlation spectroscopy.

Bergstrand J, Rönnlund D, Widengren J, Wennmalm S

Opt Express 22 (11) 13073-13090 [2014-06-02; online 2014-06-13]

Fluorescence Correlation Spectroscopy [Technology development] Integrated Microscopy Technologies Stockholm

Crystal structure of human CRMP-4: correction of intensities for lattice-translocation disorder

Ponnusamy R, Lebedev AA, Pahlow S, Lohkamp B

Acta Crystallogr. D Biol. Crystallogr. 70 (6) 1680-1694 [2014-06-01; online 2014-05-30]

p53 protein expression independently predicts outcome in patients with lower-risk myelodysplastic syndromes with del(5q).

Saft L, Karimi M, Ghaderi M, ..., MacBeth KJ, Hellström-Lindberg E

Haematologica 99 (6) 1041-1049 [2014-06-00; online 2014-04-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

microRNA-34b/c on chromosome 11q23 is aberrantly methylated in chronic lymphocytic leukemia.

Deneberg S, Kanduri M, Ali D, ..., Lennartsson A, Lehmann S

Epigenetics 9 (6) 910-917 [2014-06-00; online 2014-04-02]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The human testis-specific proteome defined by transcriptomics and antibody-based profiling.

Djureinovic D, Fagerberg L, Hallström B, ..., Uhlén M, Pontén F

Mol. Hum. Reprod. 20 (6) 476-488 [2014-06-00; online 2014-03-07]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling

The benefits of staying active in old age: physical activity counteracts the negative influence of PICALM, BIN1, and CLU risk alleles on episodic memory functioning.

Ferencz B, Laukka EJ, Welmer AK, ..., Lövdén M, Bäckman L

Psychol Aging 29 (2) 440-449 [2014-06-00; online 2014-03-26]

The age and genomic integrity of neurons after cortical stroke in humans.

Huttner HB, Bergmann O, Salehpour M, ..., Lundeberg J, Frisén J

Nat. Neurosci. 17 (6) 801-803 [2014-06-00; online 2014-04-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The HLA locus contains novel foetal susceptibility alleles for congenital heart block with significant paternal influence.

Meisgen S, Östberg T, Salomonsson S, ..., Kockum I, Wahren-Herlenius M

J. Intern. Med. 275 (6) 640-651 [2014-06-00; online 2013-12-21]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

SpliceVista, a tool for splice variant identification and visualization in shotgun proteomics data.

Zhu Y, Hultin-Rosenberg L, Forshed J, ..., Orre LM, Lehtiö J

Mol. Cell Proteomics 13 (6) 1552-1562 [2014-06-00; online 2014-04-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Simultaneous uptake of lignocellulose-based monosaccharides by Escherichia coli.

Jarmander J, Hallström BM, Larsson G

Biotechnol. Bioeng. 111 (6) 1108-1115 [2014-06-00; online 2014-01-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Recurrent activating mutation in PRKACA in cortisol-producing adrenal tumors.

Goh G, Scholl UI, Healy JM, ..., Carling T, Lifton RP

Nat. Genet. 46 (6) 613-617 [2014-06-00; online 2014-04-22]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Recurrent EWSR1-CREB3L1 gene fusions in sclerosing epithelioid fibrosarcoma.

Arbajian E, Puls F, Magnusson L, ..., Kindblom LG, Mertens F

Am. J. Surg. Pathol. 38 (6) 801-808 [2014-06-00; online 2014-01-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Proteome-wide epitope mapping of antibodies using ultra-dense peptide arrays.

Forsström B, Axnäs BB, Stengele K, ..., Rockberg J, Uhlen M

Mol. Cell Proteomics 13 (6) 1585-1597 [2014-06-00; online 2014-04-08]

Autoimmunity and Serology Profiling [Technology development]

Old but not (so) degenerated--slow evolution of largely homomorphic sex chromosomes in ratites.

Yazdi HP, Ellegren H

Mol. Biol. Evol. 31 (6) 1444-1453 [2014-06-00; online 2014-03-13]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Numerical compression schemes for proteomics mass spectrometry data.

Teleman J, Dowsey AW, Gonzalez-Galarza FF, ..., Deutsch EW, Levander F

Mol. Cell Proteomics 13 (6) 1537-1542 [2014-06-00; online 2014-03-29]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Nucleosome regulatory dynamics in response to TGFβ.

Enroth S, Andersson R, Bysani M, ..., Komorowski J, Wadelius C

Nucleic Acids Res. 42 (11) 6921-6934 [2014-06-00; online 2014-04-29]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Mosaic loss of chromosome Y in peripheral blood is associated with shorter survival and higher risk of cancer.

Forsberg LA, Rasi C, Malmqvist N, ..., Lind L, Dumanski JP

Nat. Genet. 46 (6) 624-628 [2014-06-00; online 2014-04-30]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Impact of type 2 diabetes susceptibility variants on quantitative glycemic traits reveals mechanistic heterogeneity.

Dimas AS, Lagou V, Barker A, ..., Prokopenko I, MAGIC Investigators

Diabetes 63 (6) 2158-2171 [2014-06-00; online 2013-12-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Immunoproteomics using polyclonal antibodies and stable isotope-labeled affinity-purified recombinant proteins.

Edfors F, Boström T, Forsström B, ..., Mann M, Uhlen M

Mol. Cell Proteomics 13 (6) 1611-1624 [2014-06-00; online 2014-04-12]

Immunomodulatory activity of commonly used drugs on Fc-receptor-mediated human natural killer cell activation.

Theorell J, Gustavsson AL, Tesi B, ..., Lundbäck T, Bryceson YT

Cancer Immunol. Immunother. 63 (6) 627-641 [2014-06-00; online 2014-03-30]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Identification of a large protein network involved in epigenetic transmission in replicating DNA of embryonic stem cells.

Aranda S, Rutishauser D, Ernfors P

Nucleic Acids Res. 42 (11) 6972-6986 [2014-06-00; online 2014-05-24]

Genetic factors may play a prominent role in the development of coronary heart disease dependent on important environmental factors.

Song C, Chang Z, Magnusson PK, Ingelsson E, Pedersen NL

J. Intern. Med. 275 (6) 631-639 [2014-06-00; online 2013-12-18]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetic associations to germinal centre formation in primary Sjogren's syndrome.

Reksten TR, Johnsen SJ, Jonsson MV, ..., Jonsson R, Nordmark G

Ann. Rheum. Dis. 73 (6) 1253-1258 [2014-06-00; online 2013-04-23]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Garbage in, garbage out: a critical evaluation of strategies used for validation of immunohistochemical biomarkers.

O'Hurley G, Sjöstedt E, Rahman A, ..., Gallagher WM, Lindskog C

Mol Oncol 8 (4) 783-798 [2014-06-00; online 2014-04-15]

Diversity and abundance of aromatic catabolic genes in lake sediments in response to temperature change.

Osman OA, Gudasz C, Bertilsson S

FEMS Microbiol. Ecol. 88 (3) 468-481 [2014-06-00; online 2014-03-07]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Decreased decorin expression in the tumor microenvironment.

Bozoky B, Savchenko A, Guven H, ..., Klein G, Szekely L

Cancer Med 3 (3) 485-491 [2014-06-00; online 2014-03-19]

Identification of candidate risk gene variations by whole-genome sequence analysis of four rat strains commonly used in inflammation research.

Bäckdahl L, Ekman D, Jagodic M, Olsson T, Holmdahl R

BMC Genomics 15 (-) 391 [2014-05-21; online 2014-05-21]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genetic architecture of main effect QTL for heading date in European winter wheat.

Zanke C, Ling J, Plieske J, ..., Ganal MW, Röder MS

Front Plant Sci 5 (-) 217 [2014-05-20; online 2014-05-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers.

Skoglund P, Malmström H, Omrak A, ..., Götherström A, Jakobsson M

Science 344 (6185) 747-750 [2014-05-16; online 2014-04-24]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Structure and inhibition of mouse leukotriene C4 synthase.

Niegowski D, Kleinschmidt T, Ahmad S, ..., Rinaldo-Matthis A, Haeggström JZ

PLoS ONE 9 (5) e96763 [2014-05-08; online 2014-05-08]

Chemical Biology Consortium Sweden (CBCS) [Service] Protein Science Facility (PSF)

Genetic variation in the CYP2B6 gene is related to circulating 2,2',4,4'-tetrabromodiphenyl ether (BDE-47) concentrations: an observational population-based study.

Penell J, Lind L, Fall T, ..., Ingelsson E, Lind PM

Environ Health 13 (1) 34 [2014-05-08; online 2014-05-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Responsibility and cooperativeness are constrained, not determined.

Garcia D, Stråge A, Lundström S, ..., Kerekes N, Anckarsäter H

Front Psychol 5 (-) 308 [2014-05-07; online 2014-05-07]

Structural basis for phosphoinositide substrate recognition, catalysis, and membrane interactions in human inositol polyphosphate 5-phosphatases.

Trésaugues L, Silvander C, Flodin S, ..., Berglund H, Nordlund P

Structure 22 (5) 744-755 [2014-05-06; online 2014-04-08]

Bead arrays for antibody and complement profiling reveal joint contribution of antibody isotypes to C3 deposition.

Ayoglu B, Szarka E, Huber K, ..., Nilsson P, Papp K

PLoS ONE 9 (5) e96403 [2014-05-05; online 2014-05-05]

Affinity Proteomics Stockholm [Collaborative] Autoimmunity and Serology Profiling [Technology development]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Besingi W, Johansson A

Hum. Mol. Genet. 23 (9) 2290-2297 [2014-05-01; online 2013-12-18]

DNA mismatch repair gene MSH6 implicated in determining age at natural menopause.

Perry JR, Hsu YH, Chasman DI, ..., Karasik D, Murray A

Hum. Mol. Genet. 23 (9) 2490-2497 [2014-05-01; online 2013-12-19]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

miR-20b regulates expression of proteinase-activated receptor-1 (PAR-1) thrombin receptor in melanoma cells.

Saleiban A, Faxälv L, Claesson K, Jönsson JI, Osman A

Pigment Cell Melanoma Res 27 (3) 431-441 [2014-05-00; online 2014-02-06]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

The role of pleiotropy and linkage in genes affecting a sexual ornament and bone allocation in the chicken.

Johnsson M, Rubin CJ, Höglund A, ..., Jensen P, Wright D

Mol. Ecol. 23 (9) 2275-2286 [2014-05-00; online 2014-03-25]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The role of SATB2 as a diagnostic marker for tumors of colorectal origin: Results of a pathology-based clinical prospective study.

Dragomir A, de Wit M, Johansson C, Uhlen M, Pontén F

Am. J. Clin. Pathol. 141 (5) 630-638 [2014-05-00; online 2014-04-10]

The RING-Finger E3 Ubiquitin Ligase COP1 SUPPRESSOR1 Negatively Regulates COP1 Abundance in Maintaining COP1 Homeostasis in Dark-Grown Arabidopsis Seedlings.

Xu D, Lin F, Jiang Y, ..., Holm M, Deng XW

Plant Cell 26 (5) 1981-1991 [2014-05-00; online 2014-05-16]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The H1-receptor antagonist cetirizine protects partially against cytokine- and hydrogen peroxide-induced β-TC6 cell death in vitro.

Anvari E, Fred RG, Welsh N

Pancreas 43 (4) 624-629 [2014-05-00; online 2014-04-11]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Somatic cells with a heavy mitochondrial DNA mutational load render induced pluripotent stem cells with distinct differentiation defects.

Wahlestedt M, Ameur A, Moraghebi R, ..., Woods NB, Bryder D

Stem Cells 32 (5) 1173-1182 [2014-05-00; online 2014-01-22]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Single cell genomics of deep ocean bacteria

Zhao W, Andersson SGE

Trends Microbiol. 22 (5) 233-234 [2014-05-00; online 2014-05-00]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Quality control and conduct of genome-wide association meta-analyses.

Winkler TW, Day FR, Croteau-Chonka DC, ..., Loos RJ, Genetic Investigation of Anthropometric Traits (GIANT) Consortium

Nat Protoc 9 (5) 1192-1212 [2014-05-00; online 2014-04-24]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Protein biomarker validation via proximity ligation assays.

Blokzijl A, Nong R, Darmanis S, ..., Landegren U, Kamali-Moghaddam M

Biochim. Biophys. Acta 1844 (5) 933-939 [2014-05-00; online 2013-08-13]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

PTPN6 expression is epigenetically regulated and influences survival and response to chemotherapy in high-grade gliomas.

Sooman L, Ekman S, Tsakonas G, ..., Gullbo J, Lennartsson J

Tumour Biol. 35 (5) 4479-4488 [2014-05-00; online 2014-02-11]

N-acylated derivatives of sulfamethoxazole and sulfafurazole inhibit intracellular growth of Chlamydia trachomatis.

Marwaha S, Uvell H, Salin O, ..., Elofsson M, Gylfe A

Antimicrob. Agents Chemother. 58 (5) 2968-2971 [2014-05-00; online 2014-02-26]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Impact of soil transfer between test fields on fungal diversity and wood durability

Råberg U, Terziev N, Daniel G

International Wood Products Journal 5 (2) 83-91 [2014-05-00; online 2013-12-19]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genetic influences on political ideologies: twin analyses of 19 measures of political ideologies from five democracies and genome-wide findings from three populations.

Hatemi PK, Medland SE, Klemmensen R, ..., Eaves LJ, Martin NG

Behav. Genet. 44 (3) 282-294 [2014-05-00; online 2014-02-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

GRM1 is upregulated through gene fusion and promoter swapping in chondromyxoid fibroma.

Nord KH, Lilljebjörn H, Vezzi F, ..., Hogendoorn PC, Szuhai K

Nat. Genet. 46 (5) 474-477 [2014-05-00; online 2014-03-25]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A new look at adenovirus splicing.

Zhao H, Chen M, Pettersson U

Virology 456-457 (-) 329-341 [2014-05-00; online 2014-04-25]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Fish oil and krill oil supplementations differentially regulate lipid catabolic and synthetic pathways in mice.

Tillander V, Bjørndal B, Burri L, ..., Berge RK, Alexson SE

Nutr Metab (Lond) 11 (-) 20 [2014-04-27; online 2014-04-27]

The complete genome of Blastobotrys (Arxula) adeninivorans LS3 - a yeast of biotechnological interest.

Kunze G, Gaillardin C, Czernicka M, ..., Scholz U, Neuvéglise C

Biotechnol Biofuels 7 (-) 66 [2014-04-24; online 2014-04-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis.

Prasad P, Rönnerblad M, Arner E, ..., Ekwall K, FANTOM consortium

Blood 123 (17) e46-e57 [2014-04-24; online 2014-03-29]

Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation.

Rönnerblad M, Andersson R, Olofsson T, ..., Lennartsson A, FANTOM consortium

Blood 123 (17) e79-e89 [2014-04-24; online 2014-03-29]

Bioinformatics and Expression Analysis (BEA) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Seasonal pattern of lesion development in diseased Fraxinus excelsior infected by Hymenoscyphus pseudoalbidus.

Bengtsson SB, Barklund P, von Brömssen C, Stenlid J

PLoS ONE 9 (4) e76429 [2014-04-23; online 2014-04-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Systematic design of 18S rRNA gene primers for determining eukaryotic diversity in microbial consortia.

Hugerth LW, Muller EE, Hu YO, ..., Wilmes P, Andersson AF

PLoS ONE 9 (4) e95567 [2014-04-22; online 2014-04-22]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Oppositional defiant- and conduct disorder-like problems: neurodevelopmental predictors and genetic background in boys and girls, in a nationwide twin study.

Kerekes N, Lundström S, Chang Z, ..., Nilsson T, Anckarsäter H

PeerJ 2 (-) e359 [2014-04-22; online 2014-04-22]

Erysipelothrix rhusiopathiae contamination in the poultry house environment during erysipelas outbreaks in organic laying hen flocks.

Eriksson H, Bagge E, Båverud V, Fellström C, Jansson DS

Avian Pathol. 43 (3) 231-237 [2014-04-22; online 2014-03-26]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Elucidating the interactions between the human gut microbiota and its host through metabolic modeling.

Shoaie S, Nielsen J

Front Genet 5 (-) 86 [2014-04-22; online 2014-04-22]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A Drosophila immune response against Ras-induced overgrowth.

Hauling T, Krautz R, Markus R, ..., Kucerova L, Theopold U

Biol Open 3 (4) 250-260 [2014-04-15; online 2014-03-25]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Clinical and genetic features of pediatric acute lymphoblastic leukemia in Down syndrome in the Nordic countries.

Lundin C, Forestier E, Klarskov Andersen M, ..., Swedish Cytogenetic Leukemia Study Group (SCLSG) , NOPHO Leukemia Cytogenetic Study Group (NLCSG)

J Hematol Oncol 7 (-) 32 [2014-04-11; online 2014-04-11]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Vulnerability of glioblastoma cells to catastrophic vacuolization and death induced by a small molecule.

Kitambi SS, Toledo EM, Usoskin D, ..., Hammarström LGJ, Ernfors P

Cell 157 (2) 313-328 [2014-04-10; online 2014-03-25]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

MTH1 inhibition eradicates cancer by preventing sanitation of the dNTP pool.

Gad H, Koolmeister T, Jemth A, ..., Berglund UW, Helleday T

Nature 508 (7495) 215-221 [2014-04-10; online 2014-04-02]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Collaborative] Protein Science Facility (PSF)

A high-throughput cell-based method to predict the unbound drug fraction in the brain.

Mateus A, Matsson P, Artursson P

J. Med. Chem. 57 (7) 3005-3010 [2014-04-10; online 2014-03-20]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

ZBED6 modulates the transcription of myogenic genes in mouse myoblast cells.

Jiang L, Wallerman O, Younis S, ..., Andersson G, Andersson L

PLoS ONE 9 (4) e94187 [2014-04-08; online 2014-04-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Autosomal recessive transmission of a rare KRT74 variant causes hair and nail ectodermal dysplasia: allelism with dominant woolly hair/hypotrichosis.

Raykova D, Klar J, Azhar A, ..., Baig SM, Dahl N

PLoS ONE 9 (4) e93607 [2014-04-08; online 2014-04-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

RNA- and antibody-based profiling of the human proteome with focus on chromosome 19.

Stadler C, Fagerberg L, Sivertsson Å, ..., Lundberg E, Uhlén M

J. Proteome Res. 13 (4) 2019-2027 [2014-04-04; online 2014-03-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics

Quantitative label-free phosphoproteomics of six different life stages of the late blight pathogen Phytophthora infestans reveals abundant phosphorylation of members of the CRN effector family.

Resjö S, Ali A, Meijer HJ, ..., Govers F, Andreasson E

J. Proteome Res. 13 (4) 1848-1859 [2014-04-04; online 2014-03-05]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Genome-scale metabolic reconstructions of Bifidobacterium adolescentis L2-32 and Faecalibacterium prausnitzii A2-165 and their interaction.

El-Semman IE, Karlsson FH, Shoaie S, ..., Soliman TH, Nielsen J

BMC Syst Biol 8 (-) 41 [2014-04-03; online 2014-04-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Fine mapping seronegative and seropositive rheumatoid arthritis to shared and distinct HLA alleles by adjusting for the effects of heterogeneity.

Han B, Diogo D, Eyre S, ..., de Bakker PI, Raychaudhuri S

Am. J. Hum. Genet. 94 (4) 522-532 [2014-04-03; online 2014-03-20]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Rask-Andersen M, Philippot G, Moschonis G, ..., Fredriksson R, Schiöth HB

PLoS ONE 9 (4) e93193 [2014-04-02; online 2014-04-02]

WNT5A-mediated β-catenin-independent signalling is a novel regulator of cancer cell metabolism.

Sherwood V, Chaurasiya SK, Ekström EJ, ..., James P, Andersson T

Carcinogenesis 35 (4) 784-794 [2014-04-00; online 2013-12-03]

Temporal profiling of cytokine-induced genes in pancreatic β-cells by meta-analysis and network inference.

Lopes M, Kutlu B, Miani M, ..., Bontempi G, Eizirik DL

Genomics 103 (4) 264-275 [2014-04-00; online 2014-01-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Organocatalytic Mannich Reactions on a Carbapenem Core - Synthesis of Mannich Bases and Bicyclic Diazanonanes

Cele ZED, Pawar SA, Naicker T, ..., Kruger HG, Govender T

Eur. J. Org. Chem. 2014 (11) 2253-2260 [2014-04-00; online 2014-02-06]

Drug Discovery and Development (DDD) [Collaborative]

Loss-of-function mutations in SLC30A8 protect against type 2 diabetes.

Flannick J, Thorleifsson G, Beer NL, ..., Stefansson K, Altshuler D

Nat. Genet. 46 (4) 357-363 [2014-04-00; online 2014-03-02]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Investigation of molecular alterations of AKT-3 in triple-negative breast cancer.

O'Hurley G, Daly E, O'Grady A, ..., Kay EW, Gallagher WM

Histopathology 64 (5) 660-670 [2014-04-00; online 2013-10-22]

Disassembly of the divisome in Escherichia coli: evidence that FtsZ dissociates before compartmentalization.

Söderström B, Skoog K, Blom H, ..., von Heijne G, Daley DO

Mol. Microbiol. 92 (1) 1-9 [2014-04-00; online 2014-02-20]

Integrated Microscopy Technologies Stockholm [Service]

DNA methylation changes in genes frequently mutated in sporadic colorectal cancer and in the DNA repair and Wnt/β-catenin signaling pathway genes.

Farkas SA, Vymetalkova V, Vodickova L, Vodicka P, Nilsson TK

Epigenomics 6 (2) 179-191 [2014-04-00; online 2014-05-09]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Affinity proteomics reveals elevated muscle proteins in plasma of children with cerebral malaria.

Bachmann J, Burté F, Pramana S, ..., Fernandez-Reyes D, Nilsson P

PLoS Pathog. 10 (4) e1004038 [2014-04-00; online 2014-04-17]

A novel SERPINE1-FOSB fusion gene results in transcriptional up-regulation of FOSB in pseudomyogenic haemangioendothelioma.

Walther C, Tayebwa J, Lilljebjörn H, ..., Fletcher CD, Mertens F

J. Pathol. 232 (5) 534-540 [2014-04-00; online 2014-01-29]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A central role for GRB10 in regulation of islet function in man.

Prokopenko I, Poon W, Mägi R, ..., Groop L, Lyssenko V

PLoS Genet. 10 (4) e1004235 [2014-04-00; online 2014-04-03]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Syntheses and biological evaluation of 2-amino-3-acyl-tetrahydrobenzothiophene derivatives; antibacterial agents with antivirulence activity.

Dang HT, Chorell E, Uvell H, ..., Hultgren SJ, Almqvist F

Org. Biomol. Chem. 12 (12) 1942-1956 [2014-03-28; online 2014-02-17]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A replication study of GWAS findings in migraine identifies association in a Swedish case-control sample.

Ran C, Graae L, Magnusson PK, ..., Olson L, Belin AC

BMC Med. Genet. 15 (-) 38 [2014-03-28; online 2014-03-28]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Impact of stereospecific intramolecular hydrogen bonding on cell permeability and physicochemical properties.

Over B, McCarren P, Artursson P, ..., Duvall JR, Kihlberg J

J. Med. Chem. 57 (6) 2746-2754 [2014-03-27; online 2014-02-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

High prevalence of pfcrt-CVIET haplotype in isolates from asymptomatic and symptomatic patients in south-central Oromia, Ethiopia.

Golassa L, Enweji N, Erko B, Aseffa A, Swedberg G

Malar. J. 13 (-) 120 [2014-03-27; online 2014-03-27]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Design, synthesis, crystallographic studies, and preliminary biological appraisal of new substituted triazolo[4,3-b]pyridazin-8-amine derivatives as tankyrase inhibitors.

Liscio P, Carotti A, Asciutti S, ..., Pellicciari R, Camaioni E

J. Med. Chem. 57 (6) 2807-2812 [2014-03-27; online 2014-02-18]

Visualization of angiogenesis during cancer development in the polyoma middle T breast cancer model: molecular imaging with (R)-[11C]PAQ.

Samén E, Lu L, Mulder J, ..., Rundqvist H, Stone-Elander S

EJNMMI Res 4 (1) 17 [2014-03-26; online 2014-03-26]

The novel diagnostic biomarkers for focal segmental glomerulosclerosis.

Nafar M, Kalantari S, Samavat S, ..., Rutishuser D, Zubarev RA

Int J Nephrol 2014 (-) 574261 [2014-03-26; online 2014-03-26]

Nanoscopic spine localization of Norbin, an mGluR5 accessory protein.

Westin L, Reuss M, Lindskog M, Aperia A, Brismar H

BMC Neurosci 15 (-) 45 [2014-03-26; online 2014-03-26]

Integrated Microscopy Technologies Stockholm [Technology development]

Neuronal calcium-binding proteins 1/2 localize to dorsal root ganglia and excitatory spinal neurons and are regulated by nerve injury.

Zhang MD, Tortoriello G, Hsueh B, ..., Harkany T, Hökfelt TG

Proc. Natl. Acad. Sci. U.S.A. 111 (12) E1149-E1158 [2014-03-25; online 2014-03-13]

An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge.

Brownstein CA, Beggs AH, Homer N, ..., Kohane IS, Margulies DM

Genome Biol. 15 (3) R53 [2014-03-25; online 2014-03-25]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Draft Genome Sequence of Pseudomonas aeruginosa SG17M, an Environmental Isolate Belonging to Clone C, Prevalent in Patients and Aquatic Habitats.

Lee C, Peters V, Melefors O, Römling U

Genome Announc 2 (2) - [2014-03-20; online 2014-03-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Identification of anticancer drugs for hepatocellular carcinoma through personalized genome-scale metabolic modeling.

Agren R, Mardinoglu A, Asplund A, ..., Uhlen M, Nielsen J

Mol. Syst. Biol. 10 (-) 721 [2014-03-19; online 2014-03-19]

Comprehensive profiling of the vaginal microbiome in HIV positive women using massive parallel semiconductor sequencing.

Ameur A, Meiring TL, Bunikis I, ..., Williamson AL, Gyllensten U

Sci Rep 4 (-) 4398 [2014-03-18; online 2014-03-18]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Binding of Pro-Gly-Pro at the active site of leukotriene A4 hydrolase/aminopeptidase and development of an epoxide hydrolase selective inhibitor.

Stsiapanava A, Olsson U, Wan M, ..., Rinaldo-Matthis A, Haeggström JZ

Proc. Natl. Acad. Sci. U.S.A. 111 (11) 4227-4232 [2014-03-18; online 2014-03-05]

Advanced Mass Spectrometry Proteomics Protein Science Facility (PSF)

Genetic characterization of a novel Iflavirus associated with vomiting disease in the Chinese oak silkmoth Antheraea pernyi.

Geng P, Li W, Lin L, ..., An L, Terenius O

PLoS ONE 9 (3) e92107 [2014-03-17; online 2014-03-17]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Sequencing degraded RNA addressed by 3' tag counting.

Sigurgeirsson B, Emanuelsson O, Lundeberg J

PLoS ONE 9 (3) e91851 [2014-03-14; online 2014-03-14]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Novel Peptidomimetic Hepatitis C Virus NS3/4A Protease Inhibitors Spanning the P2-P1' Region.

Lampa AK, Bergman SM, Gustafsson SS, ..., Karlén A, Sandström A

ACS Med Chem Lett 5 (3) 249-254 [2014-03-13; online 2013-08-02]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Achiral pyrazinone-based inhibitors of the hepatitis C virus NS3 protease and drug-resistant variants with elongated substituents directed toward the S2 pocket.

Gising J, Belfrage AK, Alogheli H, ..., Larhed M, Sandström A

J. Med. Chem. 57 (5) 1790-1801 [2014-03-13; online 2013-03-23]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Epitope-specific antibody response is controlled by immunoglobulin V(H) polymorphisms.

Raposo B, Dobritzsch D, Ge C, ..., Schneider G, Holmdahl R

J. Exp. Med. 211 (3) 405-411 [2014-03-10; online 2014-02-19]

A chromosome-centric analysis of antibodies directed toward the human proteome using Antibodypedia.

Alm T, von Feilitzen K, Lundberg E, Sivertsson Å, Uhlén M

J. Proteome Res. 13 (3) 1669-1676 [2014-03-07; online 2014-02-19]

Whole genome sequencing of the black grouse (Tetrao tetrix): reference guided assembly suggests faster-Z and MHC evolution.

Wang B, Ekblom R, Bunikis I, Siitari H, Höglund J

BMC Genomics 15 (-) 180 [2014-03-06; online 2014-03-06]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

ZapE is a novel cell division protein interacting with FtsZ and modulating the Z-ring dynamics.

Marteyn BS, Karimova G, Fenton AK, ..., Sansonetti PJ, Tang CM

MBio 5 (2) e00022-e00014 [2014-03-04; online 2014-03-04]

Molecular- and organelle-based predictive paradigm underlying recovery by left ventricular assist device support.

Liem DA, Nsair A, Setty SP, ..., Ping P, Deng MC

Circ Heart Fail 7 (2) 359-366 [2014-03-01; online 2014-03-20]

A study of embryonic stem cell-related proteins in human astrocytomas: identification of Nanog as a predictor of survival.

Elsir T, Edqvist PH, Carlson J, ..., Nistér M, Smits A

Int. J. Cancer 134 (5) 1123-1131 [2014-03-01; online 2013-09-17]

Urinary prognostic biomarkers in patients with focal segmental glomerulosclerosis.

Kalantari S, Nafar M, Samavat S, ..., Rutishauser D, Zubarev R

Nephrourol Mon 6 (2) e16806 [2014-03-00; online 2014-03-09]

The Dictyostelium discoideum RNA-dependent RNA polymerase RrpC silences the centromeric retrotransposon DIRS-1 post-transcriptionally and is required for the spreading of RNA silencing signals.

Wiegand S, Meier D, Seehafer C, ..., Söderbom F, Hammann C

Nucleic Acids Res. 42 (5) 3330-3345 [2014-03-00; online 2013-12-27]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Purification, stability, and immunogenicity analyses of five bluetongue virus proteins for use in development of a subunit vaccine that allows differentiation of infected from vaccinated animals.

Anderson J, Bréard E, Lövgren Bengtsson K, ..., Valarcher JF, Hägglund S

Clin. Vaccine Immunol. 21 (3) 443-452 [2014-03-00; online 2014-01-24]

On the biogeography of Centipeda: a species-tree diffusion approach.

Nylinder S, Lemey P, De Bruyn M, ..., Walsh N, Anderberg AA

Syst. Biol. 63 (2) 178-191 [2014-03-00; online 2013-12-18]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

MAX mutations status in Swedish patients with pheochromocytoma and paraganglioma tumours.

Crona J, Maharjan R, Delgado Verdugo A, ..., Hellman P, Björklund P

Fam. Cancer 13 (1) 121-125 [2014-03-00; online 2013-06-08]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Investigation of a putative melanoma susceptibility locus at chromosome 3q29.

Tuominen R, Jönsson G, Enerbäck C, ..., Hansson J, Höiom V

Cancer Genet 207 (3) 70-74 [2014-03-00; online 2014-02-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.

DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium , Asian Genetic Epidemiology Network Type 2 Diabetes (AGEN-T2D) Consortium , South Asian Type 2 Diabetes (SAT2D) Consortium , ..., McCarthy MI, Morris AP

Nat. Genet. 46 (3) 234-244 [2014-03-00; online 2014-02-11]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Feasibility of targeted next-generation sequencing of the TP53 and ATM genes in chronic lymphocytic leukemia.

Mansouri L, Sutton LA, Ljungström V, ..., Nilsson M, Rosenquist R

Leukemia 28 (3) 694-696 [2014-03-00; online 2013-10-31]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Detection of enterovirus in the islet cells of patients with type 1 diabetes: what do we learn from immunohistochemistry?

Hansson SF, Korsgren S, Pontén F, Korsgren O

Diabetologia 57 (3) 645-646 [2014-03-00; online 2013-12-20]

Centromeric histone H2B monoubiquitination promotes noncoding transcription and chromatin integrity.

Sadeghi L, Siggens L, Svensson JP, Ekwall K

Nat. Struct. Mol. Biol. 21 (3) 236-243 [2014-03-00; online 2014-02-18]

Cancer death is related to high palmitoleic acid in serum and to polymorphisms in the SCD-1 gene in healthy Swedish men.

Byberg L, Kilander L, Warensjö Lemming E, Michaëlsson K, Vessby B

Am. J. Clin. Nutr. 99 (3) 551-558 [2014-03-00; online 2013-12-26]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Antibody performance in western blot applications is context-dependent.

Algenäs C, Agaton C, Fagerberg L, ..., Ottosson Takanen J, Hober S

Biotechnol J 9 (3) 435-445 [2014-03-00; online 2014-01-10]

Analysis of plasma from prostate cancer patients links decreased carnosine dipeptidase 1 levels to lymph node metastasis

Qundos U, Johannesson H, Fredolini C, ..., Nilsson P, Schwenk JM

Translational Proteomics 2 (-) 14-24 [2014-03-00; online 2014-03-00]

Robust isolation of malignant plasma cells in multiple myeloma

Frigyesi I, Adolfsson J, Ali M, ..., Hansson M, Nilsson B

Blood 123 (9) 1336-1340 [2014-02-27; online 2014-02-27]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Functional tradeoffs underpin salinity-driven divergence in microbial community composition.

Dupont CL, Larsson J, Yooseph S, ..., Venter JC, Bergman B

PLoS ONE 9 (2) e89549 [2014-02-27; online 2014-02-27]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Crystal structures of leukotriene C4 synthase in complex with product analogs: implications for the enzyme mechanism.

Niegowski D, Kleinschmidt T, Olsson U, ..., Rinaldo-Matthis A, Haeggström JZ

J. Biol. Chem. 289 (8) 5199-5207 [2014-02-21; online 2013-12-25]

Genetics of rheumatoid arthritis contributes to biology and drug discovery.

Okada Y, Wu D, Trynka G, ..., Yamamoto K, Plenge RM

Nature 506 (7488) 376-381 [2014-02-20; online 2013-12-25]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

An alternative root for the eukaryote tree of life.

He D, Fiz-Palacios O, Fu CJ, ..., Tsai CC, Baldauf SL

Curr. Biol. 24 (4) 465-470 [2014-02-17; online 2014-02-11]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Integrative genome and transcriptome analyses reveal two distinct types of ring chromosome in soft tissue sarcomas.

Nord KH, Macchia G, Tayebwa J, ..., Mandahl N, Mertens F

Hum. Mol. Genet. 23 (4) 878-888 [2014-02-15; online 2013-09-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

BET bromodomain inhibition of MYC-amplified medulloblastoma.

Bandopadhayay P, Bergthold G, Nguyen B, ..., Beroukhim R, Cho YJ

Clin. Cancer Res. 20 (4) 912-925 [2014-02-15; online 2013-12-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Microevolution during an Anthrax outbreak leading to clonal heterogeneity and penicillin resistance.

Ågren J, Finn M, Bengtsson B, Segerman B

PLoS ONE 9 (2) e89112 [2014-02-13; online 2014-02-13]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Structural and functional insights into peptidoglycan access for the lytic amidase LytA of Streptococcus pneumoniae.

Mellroth P, Sandalova T, Kikhney A, ..., Henriques-Normark B, Achour A

MBio 5 (1) e01120-e01113 [2014-02-11; online 2014-02-11]

Sequential pH-driven dimerization and stabilization of the N-terminal domain enables rapid spider silk formation.

Kronqvist N, Otikovs M, Chmyrov V, ..., Jaudzems K, Johansson J

Nat Commun 5 (-) 3254 [2014-02-11; online 2014-02-11]

Fluorescence Correlation Spectroscopy [Collaborative] Integrated Microscopy Technologies Stockholm

Prognostic polypeptide blood plasma biomarkers of Alzheimer's disease progression.

Yang H, Lyutvinskiy Y, Herukka SK, ..., Rutishauser D, Zubarev RA

J. Alzheimers Dis. 40 (3) 659-666 [2014-02-08; online 2014-02-08]

Identification of novel downstream molecules of tissue factor activation by comparative proteomic analysis.

Kask L, Jorsback A, Winkvist M, ..., Bergquist J, Siegbahn A

J. Proteome Res. 13 (2) 477-488 [2014-02-07; online 2013-12-11]

Affinity Proteomics Uppsala [Technology development] Clinical Biomarkers PLA and Single Cell Proteomics [Service]

Visual detection of DNA on paper chips.

Song Y, Gyarmati P, Araújo AC, ..., Brumer H, Ståhl PL

Anal. Chem. 86 (3) 1575-1582 [2014-02-04; online 2014-01-17]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Removal of total organic carbon from sewage wastewater using poly(ethylenimine)-functionalized magnetic nanoparticles.

Lakshmanan R, Sanchez-Dominguez M, Matutes-Aquino JA, Wennmalm S, Kuttuva Rajarao G

Langmuir 30 (4) 1036-1044 [2014-02-04; online 2014-01-17]

Fluorescence Correlation Spectroscopy [Collaborative] Integrated Microscopy Technologies Stockholm

Intraclonal variations among Streptococcus pneumoniae isolates influence the likelihood of invasive disease in children.

Browall S, Norman M, Tångrot J, ..., Normark S, Henriques-Normark B

J. Infect. Dis. 209 (3) 377-388 [2014-02-01; online 2013-09-07]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

WNT10A mutations account for ¼ of population-based isolated oligodontia and show phenotypic correlations.

Arzoo PS, Klar J, Bergendal B, Norderyd J, Dahl N

Am. J. Med. Genet. A 164A (2) 353-359 [2014-02-00; online 2014-01-23]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The genome of Spironucleus salmonicida highlights a fish pathogen adapted to fluctuating environments.

Xu F, Jerlström-Hultqvist J, Einarsson E, ..., Svärd SG, Andersson JO

PLoS Genet. 10 (2) e1004053 [2014-02-00; online 2014-02-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Subtyping of gliomas of various WHO grades by the application of immunohistochemistry.

Popova SN, Bergqvist M, Dimberg A, ..., Sooman L, Alafuzoff I

Histopathology 64 (3) 365-379 [2014-02-00; online 2014-01-15]

Rearrangements of chromosome bands 15q12-q21 are secondary to HMGA2 deregulation in conventional lipoma.

Macchia G, Nord KH, D'Alessandro G, ..., Storlazzi CT, Mertens F

Oncol. Rep. 31 (2) 807-811 [2014-02-00; online 2013-12-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Product formation controlled by substrate dynamics in leukotriene A4 hydrolase.

Stsiapanava A, Tholander F, Kumar RB, ..., Haeggström JZ, Rinaldo-Matthis A

Biochim. Biophys. Acta 1844 (2) 439-446 [2014-02-00; online 2013-12-18]

Lipid mediator profiles differ between lung compartments in asthmatic and healthy humans.

Larsson N, Lundström SL, Pinto R, ..., Wheelock CE, Nording ML

Eur. Respir. J. 43 (2) 453-463 [2014-02-00; online 2013-09-17]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Global DNA methylation patterns through an array-based approach in small intestinal neuroendocrine tumors.

Verdugo AD, Crona J, Starker L, ..., Hellman P, Björklund P

Endocr. Relat. Cancer 21 (1) L5-L7 [2014-02-00; online 2013-11-07]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Glioma-derived macrophage migration inhibitory factor (MIF) promotes mast cell recruitment in a STAT5-dependent manner.

Põlajeva J, Bergström T, Edqvist PH, ..., Forsberg Nilsson K, Tchougounova E

Mol Oncol 8 (1) 50-58 [2014-02-00; online 2013-10-05]

Collecting and preserving biological samples from challenging environments for DNA analysis.

Buś MM, Allen M

Biopreserv Biobank 12 (1) 17-22 [2014-02-00; online 2014-03-14]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Analysis of the human tissue-specific expression by genome-wide integration of transcriptomics and antibody-based proteomics.

Fagerberg L, Hallström BM, Oksvold P, ..., Ponten F, Uhlén M

Mol. Cell Proteomics 13 (2) 397-406 [2014-02-00; online 2013-12-07]

Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling

A prostate cancer susceptibility allele at 6q22 increases RFX6 expression by modulating HOXB13 chromatin binding.

Huang Q, Whitington T, Gao P, ..., Taipale J, Wei GH

Nat. Genet. 46 (2) 126-135 [2014-02-00; online 2014-01-07]

A possible genetic association with chronic fatigue in primary Sjögren's syndrome: a candidate gene study.

Norheim KB, Le Hellard S, Nordmark G, ..., Jonsson R, Omdal R

Rheumatol. Int. 34 (2) 191-197 [2014-02-00; online 2013-09-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

2′-(Z)-Cinnamoylsalicortin: A novel salicinoid isolated from Populus tremula

Keefover-Ring K, Carlsson M, Albrectsen BR

Phytochemistry Letters 7 (-) 212-216 [2014-02-00; online 2014-02-00]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Increased alpha-9 human papillomavirus species viral load in human immunodeficiency virus positive women.

Mbulawa ZZ, Johnson LF, Marais DJ, ..., Gyllensten U, Williamson AL

BMC Infect. Dis. 14 (-) 51 [2014-01-31; online 2014-01-31]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Trypanosoma cruzi Clone Dm28c Draft Genome Sequence.

Grisard EC, Teixeira SM, de Almeida LG, ..., Andersson B, de Vasconcelos AT

Genome Announc 2 (1) - [2014-01-30; online 2014-01-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Aspirin degradation in surface-charged TEMPO-oxidized mesoporous crystalline nanocellulose.

Carlsson DO, Hua K, Forsgren J, Mihranyan A

Int J Pharm 461 (1-2) 74-81 [2014-01-30; online 2013-12-03]

Mycobacteria bypass mucosal NF-kB signalling to induce an epithelial anti-inflammatory IL-22 and IL-10 response.

Lutay N, Håkansson G, Alaridah N, ..., Westergren-Thorsson G, Godaly G

PLoS ONE 9 (1) e86466 [2014-01-28; online 2014-01-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Isolation and characterization of anti-adenoviral secondary metabolites from marine actinobacteria.

Strand M, Carlsson M, Uvell H, ..., Wadell G, Almqvist F

Mar Drugs 12 (2) 799-821 [2014-01-28; online 2014-01-28]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Metabolic enzyme expression highlights a key role for MTHFD2 and the mitochondrial folate pathway in cancer.

Nilsson R, Jain M, Madhusudhan N, ..., Asplund A, Mootha VK

Nat Commun 5 (-) 3128 [2014-01-24; online 2014-01-24]

BDNF polymorphisms are linked to poorer working memory performance, reduced cerebellar and hippocampal volumes and differences in prefrontal cortex in a Swedish elderly population.

Brooks SJ, Nilsson EK, Jacobsson JA, ..., Lind L, Schiöth HB

PLoS ONE 9 (1) e82707 [2014-01-23; online 2014-01-23]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Integrative genetic characterization and phenotype correlations in pheochromocytoma and paraganglioma tumours.

Crona J, Nordling M, Maharjan R, ..., Hellman P, Björklund P

PLoS ONE 9 (1) e86756 [2014-01-22; online 2014-01-22]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Structural basis for binding of fluorinated glucose and galactose to Trametes multicolor pyranose 2-oxidase variants with improved galactose conversion.

Tan TC, Spadiut O, Gandini R, Haltrich D, Divne C

PLoS ONE 9 (1) e86736 [2014-01-21; online 2014-01-21]

Eight New Genomes and Synthetic Controls Increase the Accessibility of Rapid Melt-MAMA SNP Typing of Coxiella burnetii

Karlsson E, Macellaro A, Byström M, ..., Sjödin A, Myrtennäs K

PLoS ONE 9 (1) e85417 [2014-01-21; online 2014-01-21]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Host-specificity and dynamics in bacterial communities associated with Bloom-forming freshwater phytoplankton.

Bagatini IL, Eiler A, Bertilsson S, ..., Tessarolli LP, Vieira AAH

PLoS ONE 9 (1) e85950 [2014-01-20; online 2014-01-20]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

FuseFISH: robust detection of transcribed gene fusions in single cells.

Semrau S, Crosetto N, Bienko M, ..., Chiarle R, van Oudenaarden A

Cell Rep 6 (1) 18-23 [2014-01-16; online 2013-12-27]

Advanced FISH Technologies [Technology development]

Transmission of hepatitis C virus among intravenous drug users in the Uppsala region of Sweden.

Danielsson A, Palanisamy N, Golbob S, ..., Sylvan S, Lennerstrand J

Infect Ecol Epidemiol 4 (-) - [2014-01-15; online 2014-01-15]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The basic keratin 10-binding domain of the virulence-associated pneumococcal serine-rich protein PsrP adopts a novel MSCRAMM fold.

Schulte T, Löfling J, Mikaelsson C, ..., Henriques-Normark B, Achour A

Open Biol 4 (-) 130090 [2014-01-15; online 2014-01-15]

Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease.

Mardinoglu A, Agren R, Kampf C, ..., Uhlen M, Nielsen J

Nat Commun 5 (-) 3083 [2014-01-15; online 2014-01-15]

Dating the diversification of the major lineages of Passeriformes (Aves).

Ericson PG, Klopfstein S, Irestedt M, Nguyen JM, Nylander JA

BMC Evol. Biol. 14 (-) 8 [2014-01-15; online 2014-01-15]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

An N-Terminal Missense Mutation in STX11 Causative of FHL4 Abrogates Syntaxin-11 Binding to Munc18-2.

Müller ML, Chiang SC, Meeths M, ..., Naqvi A, Bryceson YT

Front Immunol 4 (-) 515 [2014-01-14; online 2014-01-14]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Draft Genome Sequence of Saccharopolyspora rectivirgula.

Pettersson BM, Behra PR, Manduva S, ..., Bhattacharya A, Kirsebom LA

Genome Announc 2 (1) - [2014-01-09; online 2014-01-09]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Assessment of whole genome amplification for sequence capture and massively parallel sequencing.

Hasmats J, Gréen H, Orear C, ..., Käller M, Lundeberg J

PLoS ONE 9 (1) e84785 [2014-01-07; online 2014-01-07]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins.

Lane L, Bairoch A, Beavis RC, ..., Lundberg E, Omenn GS

J. Proteome Res. 13 (1) 15-20 [2014-01-03; online 2013-12-25]

Dominant mutations in GRHL3 cause Van der Woude Syndrome and disrupt oral periderm development.

Peyrard-Janvid M, Leslie EJ, Kousa YA, ..., Kere J, Schutte BC

Am. J. Hum. Genet. 94 (1) 23-32 [2014-01-02; online 2013-12-24]

RipD (Rv1566c) from Mycobacterium tuberculosis: adaptation of an NlpC/p60 domain to a non-catalytic peptidoglycan-binding function.

Böth D, Steiner EM, Izumi A, Schneider G, Schnell R

Biochem. J. 457 (1) 33-41 [2014-01-01; online 2013-10-11]

Why time matters: codon evolution and the temporal dynamics of dN/dS.

Mugal CF, Wolf JB, Kaj I

Mol. Biol. Evol. 31 (1) 212-231 [2014-01-00; online 2013-10-17]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The maintenance of mitochondrial genetic variation by negative frequency-dependent selection.

Kazancıoğlu E, Arnqvist G

Ecol. Lett. 17 (1) 22-27 [2014-01-00; online 2013-10-19]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

SNPs within the GH-signaling pathway are associated with the early IGF1 response to GH replacement therapy in GHD adults.

Glad CA, Barbosa EJ, Filipsson Nyström H, ..., Svensson PA, Johannsson G

Eur. J. Endocrinol. 170 (1) 101-107 [2014-01-00; online 2013-10-12]

Protein biomarkers in vernix with potential to predict the development of atopic eczema in early childhood.

Holm T, Rutishauser D, Kai-Larsen Y, ..., Alm J, Scheynius A

Allergy 69 (1) 104-112 [2014-01-00; online 2013-11-12]

Polymorphisms in the dopamine receptor 2 gene region influence improvements during working memory training in children and adolescents.

Söderqvist S, Matsson H, Peyrard-Janvid M, Kere J, Klingberg T

J Cogn Neurosci 26 (1) 54-62 [2014-01-00; online 2013-09-05]

Magnetic bead assisted labeling of antibodies at nanogram scale.

Dezfouli M, Vickovic S, Iglesias MJ, ..., Schwenk JM, Ahmadian A

Proteomics 14 (1) 14-18 [2014-01-00; online 2013-12-07]

Affinity Proteomics Stockholm [Technology development] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics.

Branca RM, Orre LM, Johansson HJ, ..., Käll L, Lehtiö J

Nat. Methods 11 (1) 59-62 [2014-01-00; online 2013-11-17]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Different mutations in PDE4D associated with developmental disorders with mirror phenotypes.

Lindstrand A, Grigelioniene G, Nilsson D, ..., Mäkitie O, Nordgren A

J. Med. Genet. 51 (1) 45-54 [2014-01-00; online 2013-11-10]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Detection of the human endogenous retrovirus ERV3-encoded Env-protein in human tissues using antibody-based proteomics.

Fei C, Atterby C, Edqvist PH, ..., Larsson E, Ryan FP

J R Soc Med 107 (1) 22-29 [2014-01-00; online 2013-11-23]

Data processing methods and quality control strategies for label-free LC-MS protein quantification.

Sandin M, Teleman J, Malmström J, Levander F

Biochim. Biophys. Acta 1844 (1 Pt A) 29-41 [2014-01-00; online 2013-04-10]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

A systematic analysis of commonly used antibodies in cancer diagnostics.

Gremel G, Bergman J, Djureinovic D, ..., Micke P, Pontén F

Histopathology 64 (2) 293-305 [2014-01-00; online 2013-12-18]

A population-based assessment of germline HOXB13 G84E mutation and prostate cancer risk.

Karlsson R, Aly M, Clements M, ..., Grönberg H, Wiklund F

Eur. Urol. 65 (1) 169-176 [2014-01-00; online 2012-07-20]

Translational study between structure and biological response of nanocellulose from wood and green algae

Hua K, Carlsson DO, Ålander E, ..., Mihranyan A, Ferraz N

RSC Adv. 4 (6) 2892-2903 [2014-00-00; online 2014-00-00]

Proline N-oxides: modulators of the 3D conformation of linear peptides through “NO-turns”

Farahani MD, Honarparvar B, Albericio F, ..., Arvidsson PI, Kruger HG

Org. Biomol. Chem. 12 (25) 4479 [2014-00-00; online 2014-00-00]

Drug Discovery and Development (DDD) [Collaborative]

Photocatalysis induces bioactivity of an organic polymer based material

Cai Y, Strømme M, Zhang P, Engqvist H, Welch K

RSC Adv. 4 (101) 57715-57723 [2014-00-00; online 2014-00-00]

Disinfection Kinetics and Contribution of Reactive Oxygen Species When Eliminating Bacteria with TiO2 Induced Photocatalysis

Cai Y, Strømme M, Welch K

JBNB 05 (03) 200-209 [2014-00-00; online 2014-00-00]

A luminescence-based assay of UDP-sugar producing pyrophosphorylases

Decker D, Lindberg S, Eriksson J, Kleczkowski LA

Anal. Methods 6 (1) 57-61 [2014-00-00; online 2014-00-00]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Structure-activity relationships of synthetic cordycepin analogues as experimental therapeutics for African trypanosomiasis.

Vodnala SK, Lundbäck T, Yeheskieli E, ..., Hammarström LG, Rottenberg ME

J. Med. Chem. 56 (24) 9861-9873 [2013-12-27; online 2013-12-10]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Association of STAT4 polymorphism with severe renal insufficiency in lupus nephritis.

Bolin K, Sandling JK, Zickert A, ..., Gunnarsson I, Nordmark G

PLoS ONE 8 (12) e84450 [2013-12-27; online 2013-12-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Profiling post-centrifugation delay of serum and plasma with antibody bead arrays.

Qundos U, Hong M, Tybring G, ..., Nilsson P, Schwenk JM

J Proteomics 95 (-) 46-54 [2013-12-16; online 2013-05-02]

Automated quality control system for LC-SRM setups.

Teleman J, Waldemarson S, Malmström J, Levander F

J Proteomics 95 (-) 77-83 [2013-12-16; online 2013-04-16]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Combining genetic mapping with genome-wide expression in experimental autoimmune encephalomyelitis highlights a gene network enriched for T cell functions and candidate genes regulating autoimmunity.

Thessen Hedreul M, Möller S, Stridh P, ..., Olsson T, Jagodic M

Hum. Mol. Genet. 22 (24) 4952-4966 [2013-12-15; online 2013-07-29]

Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B.

Karlsson EK, Sigurdsson S, Ivansson E, ..., Breen M, Lindblad-Toh K

Genome Biol. 14 (12) R132 [2013-12-12; online 2013-12-12]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Chemical probes to study ADP-ribosylation: synthesis and biochemical evaluation of inhibitors of the human ADP-ribosyltransferase ARTD3/PARP3.

Lindgren AE, Karlberg T, Ekblad T, ..., Schüler H, Elofsson M

J. Med. Chem. 56 (23) 9556-9568 [2013-12-12; online 2013-11-06]

Linkage analysis in familial non-Lynch syndrome colorectal cancer families from Sweden.

Kontham V, von Holst S, Lindblom A

PLoS ONE 8 (12) e83936 [2013-12-11; online 2013-12-11]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Utilizing twins as controls for non-twin case-materials in genome wide association studies.

Ganna A, Ortega-Alonso A, Havulinna A, ..., Hultman CM, Magnusson PKE

PLoS ONE 8 (12) e83101 [2013-12-10; online 2013-12-10]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Statistical molecular design: a tool to follow up hits from small-molecule screening.

Lindgren AE, Larsson A, Linusson A, Elofsson M

Methods Mol. Biol. 1056 (-) 169-188 [2013-12-07; online 2013-12-07]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Urinary prognostic biomarkers and classification of IgA nephropathy by high resolution mass spectrometry coupled with liquid chromatography.

Kalantari S, Rutishauser D, Samavat S, ..., Rezaei-Tavirani M, Zubarev RA

PLoS ONE 8 (12) e80830 [2013-12-05; online 2013-12-05]

Accurate detection of subclonal single nucleotide variants in whole genome amplified and pooled cancer samples using HaloPlex target enrichment.

Berglund EC, Lindqvist CM, Hayat S, ..., Lönnerholm G, Syvänen AC

BMC Genomics 14 (-) 856 [2013-12-05; online 2013-12-05]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The resveratrol tetramer (-)-hopeaphenol inhibits type III secretion in the gram-negative pathogens Yersinia pseudotuberculosis and Pseudomonas aeruginosa.

Zetterström CE, Hasselgren J, Salin O, ..., Sundin C, Elofsson M

PLoS ONE 8 (12) e81969 [2013-12-04; online 2013-12-04]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Integrated molecular portrait of non-small cell lung cancers.

Lazar V, Suo C, Orear C, ..., Hansson J, Pawitan Y

BMC Med Genomics 6 (-) 53 [2013-12-03; online 2013-12-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A genome-wide association study of atopic dermatitis identifies loci with overlapping effects on asthma and psoriasis.

Weidinger S, Willis-Owen SA, Kamatani Y, ..., Irvine AD, Moffatt MF

Hum. Mol. Genet. 22 (23) 4841-4856 [2013-12-01; online 2013-07-28]

Using transcriptomics to improve butanol tolerance of Synechocystis sp. strain PCC 6803.

Anfelt J, Hallström B, Nielsen J, Uhlén M, Hudson EP

Appl. Environ. Microbiol. 79 (23) 7419-7427 [2013-12-00; online 2013-09-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The association between plasma homocysteine and coronary heart disease is modified by the MTHFR 677C>T polymorphism.

Mehlig K, Leander K, de Faire U, ..., Lissner L, Thelle D

Heart 99 (23) 1761-1765 [2013-12-00; online 2013-09-10]

Selectivity analysis of single binder assays used in plasma protein profiling.

Neiman M, Fredolini C, Johansson H, ..., Nilsson P, Schwenk JM

Proteomics 13 (23-24) 3406-3410 [2013-12-00; online 2013-10-24]

Affinity Proteomics Stockholm [Technology development]

Protein expansion is primarily due to indels in intrinsically disordered regions.

Light S, Sagit R, Sachenkova O, Ekman D, Elofsson A

Mol. Biol. Evol. 30 (12) 2645-2653 [2013-12-00; online 2013-09-17]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

High expression of glycolytic and pigment proteins is associated with worse clinical outcome in stage III melanoma.

Falkenius J, Lundeberg J, Johansson H, ..., Hansson J, Egyhazi Brage S

Melanoma Res. 23 (6) 452-460 [2013-12-00; online 2013-10-17]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetic variation at the IGF1 locus shows association with post-stroke outcome and to circulating IGF1.

Aberg ND, Olsson S, Aberg D, ..., Isgaard J, Jern C

Eur. J. Endocrinol. 169 (6) 759-765 [2013-12-00; online 2013-10-21]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Evaluation of real-time immunohistochemistry and interaction map as an alternative objective assessment of HER2 expression in human breast cancer tissue.

Gedda L, Björkelund H, Lebel L, ..., Malmqvist M, Andersson K

Appl. Immunohistochem. Mol. Morphol. 21 (6) 497-505 [2013-12-00; online 2013-03-05]

Distinct loci in the CHRNA5/CHRNA3/CHRNB4 gene cluster are associated with onset of regular smoking.

Stephens SH, Hartz SM, Hoft NR, ..., Bierut LJ, Ehringer MA

Genet. Epidemiol. 37 (8) 846-859 [2013-12-00; online 2013-11-05]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

DNA damage leads to progressive replicative decline but extends the life span of long-lived mutant animals.

Lans H, Lindvall JM, Thijssen K, ..., Nilsen H, Vermeulen W

Cell Death Differ. 20 (12) 1709-1718 [2013-12-00; online 2013-09-10]

Single-cell genomics reveal low recombination frequencies in freshwater bacteria of the SAR11 clade.

Zaremba-Niedzwiedzka K, Viklund J, Zhao W, ..., Stepanauskas R, Andersson SG

Genome Biol. 14 (11) R130 [2013-11-28; online 2013-11-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Identification of candidate serum proteins for classifying well-differentiated small intestinal neuroendocrine tumors.

Darmanis S, Cui T, Drobin K, ..., Schwenk JM, Giandomenico V

PLoS ONE 8 (11) e81712 [2013-11-25; online 2013-11-25]

Germline genetic contributions to risk for esophageal adenocarcinoma, Barrett's esophagus, and gastroesophageal reflux.

Ek WE, Levine DM, D'Amato M, ..., MacGregor S, BEACON study investigators

J. Natl. Cancer Inst. 105 (22) 1711-1718 [2013-11-20; online 2013-10-29]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Rule-based models of the interplay between genetic and environmental factors in childhood allergy.

Bornelöv S, Sääf A, Melén E, ..., Pershagen G, Komorowski J

PLoS ONE 8 (11) e80080 [2013-11-19; online 2013-11-19]

De novo SNP discovery in the Scandinavian brown bear (Ursus arctos).

Norman AJ, Street NR, Spong G

PLoS ONE 8 (11) e81012 [2013-11-18; online 2013-11-18]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

miR-128 regulates non-myocyte hyperplasia, deposition of extracellular matrix and Islet1 expression during newt cardiac regeneration.

Witman N, Heigwer J, Thaler B, Lui WO, Morrison JI

Dev. Biol. 383 (2) 253-263 [2013-11-15; online 2013-09-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Substrate specificity and oligomerization of human GMP synthetase.

Welin M, Lehtiö L, Johansson A, ..., Gräslund S, Nordlund P

J. Mol. Biol. 425 (22) 4323-4333 [2013-11-15; online 2013-07-03]

Early B-cell factor 1 regulates the expansion of B-cell progenitors in a dose-dependent manner.

Åhsberg J, Ungerbäck J, Strid T, ..., Qian H, Sigvardsson M

J. Biol. Chem. 288 (46) 33449-33461 [2013-11-15; online 2013-09-27]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Discovery of an allosteric inhibitor binding site in 3-Oxo-acyl-ACP reductase from Pseudomonas aeruginosa.

Cukier CD, Hope AG, Elamin AA, ..., Gray DW, Schneider G

ACS Chem. Biol. 8 (11) 2518-2527 [2013-11-15; online 2013-09-11]

Polymer–Pendant Interactions in Poly(pyrrol-3-ylhydroquinone): A Solution for the Use of Conducting Polymers at Stable Conditions

Karlsson C, Huang H, Strømme M, Gogoll A, Sjödin M

J. Phys. Chem. C 117 (45) 23558-23567 [2013-11-14; online 2013-11-05]

Efficient cellular fractionation improves RNA sequencing analysis of mature and nascent transcripts from human tissues.

Zaghlool A, Ameur A, Nyberg L, ..., Cavelier L, Feuk L

BMC Biotechnol. 13 (-) 99 [2013-11-13; online 2013-11-13]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Disturbance induced decoupling between host genetics and composition of the associated microbiome.

Wegner KM, Volkenborn N, Peter H, Eiler A

BMC Microbiol. 13 (-) 252 [2013-11-09; online 2013-11-09]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

ChIP-seq in steatohepatitis and normal liver tissue identifies candidate disease mechanisms related to progression to cancer.

Bysani M, Wallerman O, Bornelöv S, ..., Komorowski J, Wadelius C

BMC Med Genomics 6 (-) 50 [2013-11-08; online 2013-11-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Inference of the genetic architecture underlying BMI and height with the use of 20,240 sibling pairs.

Hemani G, Yang J, Vinkhuyzen A, ..., Martin NG, Visscher PM

Am. J. Hum. Genet. 93 (5) 865-875 [2013-11-07; online 2013-10-31]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Identification of candidate genes and mutations in QTL regions for chicken growth using bioinformatic analysis of NGS and SNP-chip data.

Ahsan M, Li X, Lundberg AE, ..., Carlborg O, Marklund S

Front Genet 4 (-) 226 [2013-11-05; online 2013-11-05]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

In vitro and in vivo evaluation of osteoporosis therapeutic peptide PTH 1-34 loaded pegylated chitosan nanoparticles.

Narayanan D, Anitha A, Jayakumar R, Chennazhi KP

Mol. Pharm. 10 (11) 4159-4167 [2013-11-04; online 2013-09-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Combined in vitro-in vivo approach to assess the hepatobiliary disposition of a novel oral thrombin inhibitor.

Matsson EM, Eriksson UG, Palm JE, ..., Schützer K, Lennernäs H

Mol. Pharm. 10 (11) 4252-4262 [2013-11-04; online 2013-10-02]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

7,8- and 5,8-Linoleate diol synthases support the heterolytic scission of oxygen-oxygen bonds by different amide residues.

Hoffmann I, Oliw EH

Arch. Biochem. Biophys. 539 (1) 87-91 [2013-11-01; online 2013-09-26]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Wobble decoding by the Escherichia coli selenocysteine insertion machinery.

Xu J, Croitoru V, Rutishauser D, Cheng Q, Arnér ES

Nucleic Acids Res. 41 (21) 9800-9811 [2013-11-00; online 2013-08-29]

Variants at multiple loci implicated in both innate and adaptive immune responses are associated with Sjögren's syndrome.

Lessard CJ, Li H, Adrianto I, ..., Harley JB, Sivils KL

Nat. Genet. 45 (11) 1284-1292 [2013-11-00; online 2013-10-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.

't Hoen PA, Friedländer MR, Almlöf J, ..., Dermitzakis ET, Lappalainen T

Nat. Biotechnol. 31 (11) 1015-1022 [2013-11-00; online 2013-09-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Metal-mediated crystallization of the xylose transporter XylE from Escherichia coli in three different crystal forms.

Quistgaard EM, Löw C, Moberg P, Nordlund P

J. Struct. Biol. 184 (2) 375-378 [2013-11-00; online 2013-09-26]

Genomic mechanisms accounting for the adaptation to parasitism in nematode-trapping fungi.

Meerupati T, Andersson KM, Friman E, ..., Tunlid A, Ahrén D

PLoS Genet. 9 (11) e1003909 [2013-11-00; online 2013-11-14]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Genome-wide DNA methylation assay reveals novel candidate biomarker genes in cervical cancer.

Farkas SA, Milutin-Gašperov N, Grce M, Nilsson TK

Epigenetics 8 (11) 1213-1225 [2013-11-00; online 2013-09-14]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Discovery and refinement of loci associated with lipid levels.

Global Lipids Genetics Consortium N, Willer CJ, Schmidt EM, ..., Ingelsson E, Abecasis GR

Nat. Genet. 45 (11) 1274-1283 [2013-11-00; online 2013-10-08]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Comparative drug pair screening across multiple glioblastoma cell lines reveals novel drug-drug interactions.

Schmidt L, Kling T, Monsefi N, ..., Gerlee P, Nelander S

Neuro-oncology 15 (11) 1469-1478 [2013-11-00; online 2013-10-06]

Drug Discovery and Development (DDD) [Collaborative]

Common variants associated with plasma triglycerides and risk for coronary artery disease.

Do R, Willer CJ, Schmidt EM, ..., Neale BM, Kathiresan S

Nat. Genet. 45 (11) 1345-1352 [2013-11-00; online 2013-10-08]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Association of genes in the NF-κB pathway with antibody-positive primary Sjögren's syndrome.

Nordmark G, Wang C, Vasaitis L, ..., Syvänen AC, UK Primary Sjögren’s Syndrome Registry

Scand. J. Immunol. 78 (5) 447-454 [2013-11-00; online 2013-08-16]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Antibodies biotinylated using a synthetic Z-domain from protein A provide stringent in situ protein detection.

Andersson S, Konrad A, Ashok N, ..., Hober S, Asplund A

J. Histochem. Cytochem. 61 (11) 773-784 [2013-11-00; online 2013-08-08]

In situ Protein Detection for Companion Diagnostics.

Gremel G, Grannas K, Sutton LA, Pontén F, Zieba A

Front Oncol 3 (-) 271 [2013-10-31; online 2013-10-31]

Proteins of novel lactic acid bacteria from Apis mellifera mellifera: an insight into the production of known extra-cellular proteins during microbial stress.

Butler È, Alsterfjord M, Olofsson TC, ..., Malmström J, Vásquez A

BMC Microbiol. 13 (-) 235 [2013-10-22; online 2013-10-22]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Nanobody mediated crystallization of an archeal mechanosensitive channel.

Löw C, Yau YH, Pardon E, ..., Steyaert J, Nordlund P

PLoS ONE 8 (10) e77984 [2013-10-21; online 2013-10-21]

Eleven candidate susceptibility genes for common familial colorectal cancer.

Gylfe AE, Katainen R, Kondelin J, ..., Karhu A, Aaltonen LA

PLoS Genet. 9 (10) e1003876 [2013-10-17; online 2013-10-17]

Transcriptome signatures in Helicobacter pylori-infected mucosa identifies acidic mammalian chitinase loss as a corpus atrophy marker.

Nookaew I, Thorell K, Worah K, ..., Nielsen J, Lundin SB

BMC Med Genomics 6 (-) 41 [2013-10-11; online 2013-10-11]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Divergent structure-activity relationships of structurally similar acetylcholinesterase inhibitors.

Andersson CD, Forsgren N, Akfur C, ..., Ekström F, Linusson A

J. Med. Chem. 56 (19) 7615-7624 [2013-10-10; online 2013-08-30]

Chemical Biology Consortium Sweden (CBCS) [Service]

Chemical fragmentation for massively parallel sequencing library preparation.

Gyarmati P, Song Y, Hällman J, Käller M

J. Biotechnol. 168 (1) 95-100 [2013-10-10; online 2013-09-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Molecular characterization of the α-subunit of Na⁺/K⁺ ATPase from the euryhaline barnacle Balanus improvisus reveals multiple genes and differential expression of alternative splice variants.

Lind U, Alm Rosenblad M, Wrange AL, ..., Havenhand J, Blomberg A

PLoS ONE 8 (10) e77069 [2013-10-09; online 2013-10-09]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Brain proteomics supports the role of glutamate metabolism and suggests other metabolic alterations in protein l-isoaspartyl methyltransferase (PIMT)-knockout mice.

Yang H, Lowenson JD, Clarke S, Zubarev RA

J. Proteome Res. 12 (10) 4566-4576 [2013-10-04; online 2013-08-21]

Aneuploidy in neuroblastoma tumors is not associated with inactivating point mutations in the STAG2 gene.

Djos A, Fransson S, Kogner P, Martinsson T

BMC Med. Genet. 14 (-) 102 [2013-10-02; online 2013-10-02]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Transcription factor ZBED6 affects gene expression, proliferation, and cell death in pancreatic beta cells.

Wang X, Jiang L, Wallerman O, ..., Andersson L, Welsh N

Proc. Natl. Acad. Sci. U.S.A. 110 (40) 15997-16002 [2013-10-01; online 2013-09-16]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Structural diversity of signal recognition particle RNAs in plastids.

Rosenblad MA, Träger C, Schünemann D

Plant Signal Behav 8 (10) doi: 10.4161/psb.26848 [2013-10-00; online 2014-02-05]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Recent advances in crayfish hematopoietic stem cell culture: a model for studies of hemocyte differentiation and immunity.

Söderhäll I

Cytotechnology 65 (5) 691-695 [2013-10-00; online 2013-05-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Profiling of atherosclerotic lesions by gene and tissue microarrays reveals PCSK6 as a novel protease in unstable carotid atherosclerosis.

Perisic L, Hedin E, Razuvaev A, ..., Odeberg J, Hedin U

Arterioscler. Thromb. Vasc. Biol. 33 (10) 2432-2443 [2013-10-00; online 2013-08-03]

Heart research advances using database search engines, Human Protein Atlas and the Sydney Heart Bank.

Li A, Estigoy C, Raftery M, ..., Lal S, Dos Remedios CG

Heart Lung Circ 22 (10) 819-826 [2013-10-00; online 2013-07-17]

Determining indicator taxa across spatial and seasonal gradients in the Columbia River coastal margin.

Fortunato CS, Eiler A, Herfort L, ..., Peterson TD, Crump BC

ISME J 7 (10) 1899-1911 [2013-10-00; online 2013-05-31]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Comprehensive genetic analysis identifies a pathognomonic NAB2/STAT6 fusion gene, nonrandom secondary genomic imbalances, and a characteristic gene expression profile in solitary fibrous tumor.

Mohajeri A, Tayebwa J, Collin A, ..., Nord KH, Mertens F

Genes Chromosomes Cancer 52 (10) 873-886 [2013-10-00; online 2013-06-14]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Transcriptome and genome sequencing uncovers functional variation in humans.

Lappalainen T, Sammeth M, Friedländer MR, ..., Estivill X, Dermitzakis ET

Nature 501 (7468) 506-511 [2013-09-26; online 2013-09-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

FHOD1, a formin upregulated in epithelial-mesenchymal transition, participates in cancer cell migration and invasion.

Gardberg M, Kaipio K, Lehtinen L, ..., Koivisto M, Carpén O

PLoS ONE 8 (9) e74923 [2013-09-26; online 2013-09-26]

Genetic variants of coagulation factor XI show association with ischemic stroke up to 70 years of age.

Hanson E, Nilsson S, Jood K, ..., Melander O, Jern C

PLoS ONE 8 (9) e75286 [2013-09-25; online 2013-09-25]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Spinal deformity in aged zebrafish is accompanied by degenerative changes to their vertebrae that resemble osteoarthritis.

Hayes AJ, Reynolds S, Nowell MA, ..., Caterson B, Hammond CL

PLoS ONE 8 (9) e75787 [2013-09-24; online 2013-09-24]

Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia.

Nordlund J, Bäcklin CL, Wahlberg P, ..., Lönnerholm G, Syvänen AC

Genome Biol. 14 (9) r105 [2013-09-24; online 2013-09-24]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Equine multiple congenital ocular anomalies and silver coat colour result from the pleiotropic effects of mutant PMEL.

Andersson LS, Wilbe M, Viluma A, ..., Ewart S, Lindgren G

PLoS ONE 8 (9) e75639 [2013-09-23; online 2013-09-23]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A metagenomics transect into the deepest point of the Baltic Sea reveals clear stratification of microbial functional capacities.

Thureborn P, Lundin D, Plathan J, ..., Sjöberg BM, Sjöling S

PLoS ONE 8 (9) e74983 [2013-09-23; online 2013-09-23]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Ebsulfur is a benzisothiazolone cytocidal inhibitor targeting the trypanothione reductase of Trypanosoma brucei.

Lu J, Vodnala SK, Gustavsson AL, ..., Rottenberg ME, Holmgren A

J. Biol. Chem. 288 (38) 27456-27468 [2013-09-20; online 2013-07-29]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Hydrogenosomes in the diplomonad Spironucleus salmonicida.

Jerlström-Hultqvist J, Einarsson E, Xu F, ..., Andersson JO, Svärd SG

Nat Commun 4 (-) 2493 [2013-09-18; online 2013-09-18]

Multiethnic meta-analysis of genome-wide association studies in >100 000 subjects identifies 23 fibrinogen-associated Loci but no strong evidence of a causal association between circulating fibrinogen and cardiovascular disease.

Sabater-Lleal M, Huang J, Chasman D, ..., Hamsten A, O'Donnell CJ

Circulation 128 (12) 1310-1324 [2013-09-17; online 2013-08-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Blood plasma IgG Fc glycans are significantly altered in Alzheimer's disease and progressive mild cognitive impairment.

Lundström SL, Yang H, Lyutvinskiy Y, ..., Soininen H, Zubarev RA

J. Alzheimers Dis. 38 (3) 567-579 [2013-09-14; online 2013-09-14]

Deep resequencing of GWAS loci identifies rare variants in CARD9, IL23R and RNF186 that are associated with ulcerative colitis.

Beaudoin M, Goyette P, Boucher G, ..., Daly MJ, Rioux JD

PLoS Genet. 9 (9) e1003723 [2013-09-12; online 2013-09-12]

A tosyl-activated magnetic bead cellulose as solid support for sensitive protein detection.

Yan J, Horák D, Lenfeld J, Hammond M, Kamali-Moghaddam M

J. Biotechnol. 167 (3) 235-240 [2013-09-10; online 2013-07-03]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

The Oct1 homolog Nubbin is a repressor of NF-κB-dependent immune gene expression that increases the tolerance to gut microbiota.

Dantoft W, Davis MM, Lindvall JM, ..., Beskow A, Engström Y

BMC Biol. 11 (-) 99 [2013-09-06; online 2013-09-06]

Post-zygotic and inter-individual structural genetic variation in a presumptive enhancer element of the locus between the IL10Rβ and IFNAR1 genes.

Razzaghian HR, Forsberg LA, Prakash KR, ..., Absher D, Dumanski JP

PLoS ONE 8 (9) e67752 [2013-09-04; online 2013-09-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Structural insights into substrate recognition in proton-dependent oligopeptide transporters.

Guettou F, Quistgaard EM, Trésaugues L, ..., Nordlund P, Löw C

EMBO Rep. 14 (9) 804-810 [2013-09-00; online 2013-07-23]

Role of individual MARK isoforms in phosphorylation of tau at Ser²⁶² in Alzheimer's disease.

Gu GJ, Lund H, Wu D, ..., Sunnemark D, Kamali-Moghaddam M

Neuromolecular Med. 15 (3) 458-469 [2013-09-00; online 2013-05-12]

Affinity Proteomics Uppsala [Technology development] Clinical Biomarkers PLA and Single Cell Proteomics

Progesterone receptor negativity is an independent risk factor for relapse in patients with early stage endometrioid endometrial adenocarcinoma.

Huvila J, Talve L, Carpén O, ..., Grénman S, Auranen A

Gynecol. Oncol. 130 (3) 463-469 [2013-09-00; online 2013-06-20]

Phylogeography of willow grouse (Lagopus lagopus) in the Arctic: taxonomic discordance as inferred from molecular data

Höglund J, Wang B, Axelsson T, Quintela M

Biol J Linn Soc Lond 110 (1) 77-90 [2013-09-00; online 2013-05-22]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Multilocus genetic risk scores for coronary heart disease prediction.

Ganna A, Magnusson PKE, Pedersen NL, ..., Hamsten A, Ingelsson E

Arterioscler. Thromb. Vasc. Biol. 33 (9) 2267-2272 [2013-09-00; online 2013-05-21]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Identification of candidate oncogenes in human colorectal cancers with microsatellite instability.

Gylfe AE, Kondelin J, Turunen M, ..., Vahteristo P, Aaltonen LA

Gastroenterology 145 (3) 540-3.e22 [2013-09-00; online 2013-05-21]

High modal number and triple trisomies are highly correlated favorable factors in childhood B-cell precursor high hyperdiploid acute lymphoblastic leukemia treated according to the NOPHO ALL 1992/2000 protocols.

Paulsson K, Forestier E, Andersen MK, ..., Swedish Cytogenetic Leukemia Study Group (SCLSG) , NOPHO Leukemia Cytogenetic Study Group (NLCSG)

Haematologica 98 (9) 1424-1432 [2013-09-00; online 2013-05-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Glutamatergic GRIN2B and polyaminergic ODC1 genes in suicide attempts: associations and gene-environment interactions with childhood/adolescent physical assault.

Sokolowski M, Ben-Efraim YJ, Wasserman J, Wasserman D

Mol. Psychiatry 18 (9) 985-992 [2013-09-00; online 2012-08-02]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Global DNA hypermethylation is associated with high serum levels of persistent organic pollutants in an elderly population.

Lind L, Penell J, Luttropp K, ..., Ingelsson E, Lind PM

Environ Int 59 (-) 456-461 [2013-09-00; online 2013-08-13]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genome-wide analysis shows association of epigenetic changes in regulators of Rab and Rho GTPases with spinal muscular atrophy severity.

Zheleznyakova GY, Voisin S, Kiselev AV, ..., Baranov VS, Schiöth HB

Eur. J. Hum. Genet. 21 (9) 988-993 [2013-09-00; online 2013-01-10]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genetic relationship between five psychiatric disorders estimated from genome-wide SNPs.

Cross-Disorder Group of the Psychiatric Genomics Consortium N, Lee SH, Ripke S, ..., Wray NR, International Inflammatory Bowel Disease Genetics Consortium (IIBDGC) N

Nat. Genet. 45 (9) 984-994 [2013-09-00; online 2013-08-13]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genes identified in Asian SLE GWASs are also associated with SLE in Caucasian populations.

Wang C, Ahlford A, Järvinen TM, ..., Syvänen AC, Sandling JK

Eur. J. Hum. Genet. 21 (9) 994-999 [2013-09-00; online 2012-12-20]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Autoantibody profiling in multiple sclerosis using arrays of human protein fragments.

Ayoglu B, Häggmark A, Khademi M, ..., Schwenk JM, Nilsson P

Mol. Cell Proteomics 12 (9) 2657-2672 [2013-09-00; online 2013-06-05]

Autoimmunity and Serology Profiling [Technology development]

Comparison of the nodule vs. root transcriptome of the actinorhizal plant Datisca glomerata: actinorhizal nodules contain a specific class of defensins.

Demina IV, Persson T, Santos P, Plaszczyca M, Pawlowski K

PLoS ONE 8 (8) e72442 [2013-08-29; online 2013-08-29]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genome-wide transcriptional analysis of Drosophila larvae infected by entomopathogenic nematodes shows involvement of complement, recognition and extracellular matrix proteins.

Arefin B, Kucerova L, Dobes P, ..., Zurovec M, Theopold U

J Innate Immun 6 (2) 192-204 [2013-08-27; online 2013-08-27]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Structure-Guided Design of Novel Thiazolidine Inhibitors ofO-Acetyl Serine Sulfhydrylase from Mycobacterium tuberculosis

Poyraz Ö, Jeankumar VU, Saxena S, ..., Sriram D, Schneider G

J. Med. Chem. 56 (16) 6457-6466 [2013-08-22; online 2013-08-22]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Svartström O, Mushtaq M, Pringle M, Segerman B

PLoS ONE 8 (8) e71281 [2013-08-19; online 2013-08-19]

Automated serial extraction of DNA and RNA from biobanked tissue specimens.

Mathot L, Wallin M, Sjöblom T

BMC Biotechnol. 13 (-) 66 [2013-08-19; online 2013-08-19]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PARP inhibitor with selectivity toward ADP-ribosyltransferase ARTD3/PARP3.

Lindgren AE, Karlberg T, Thorsell AG, ..., Elofsson M, Schüler H

ACS Chem. Biol. 8 (8) 1698-1703 [2013-08-16; online 2013-06-08]

Transcription factor binding in human cells occurs in dense clusters formed around cohesin anchor sites.

Yan J, Enge M, Whitington T, ..., Taipale M, Taipale J

Cell 154 (4) 801-813 [2013-08-15; online 2013-08-21]

Bioinformatics and Expression Analysis (BEA) Karolinska High Throughput Center (KHTC)

The STK33-linked SNP rs4929949 is associated with obesity and BMI in two independent cohorts of Swedish and Greek children.

Rask-Andersen M, Moschonis G, Chrousos GP, ..., Fredriksson R, Schiöth HB

PLoS ONE 8 (8) e71353 [2013-08-15; online 2013-08-15]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Investigation of six testicular germ cell tumor susceptibility genes suggests a parent-of-origin effect in SPRY4.

Karlsson R, Andreassen KE, Kristiansen W, ..., Grotmol T, Wiklund F

Hum. Mol. Genet. 22 (16) 3373-3380 [2013-08-15; online 2013-05-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Structural and biophysical characterization of the cytoplasmic domains of human BAP29 and BAP31.

Quistgaard EM, Löw C, Moberg P, ..., Maddi K, Nordlund P

PLoS ONE 8 (8) e71111 [2013-08-13; online 2013-08-13]

Advanced Mass Spectrometry Proteomics Protein Science Facility (PSF)

Meta-analysis of gene-level associations for rare variants based on single-variant statistics.

Hu Y, Berndt SI, Gustafsson S, ..., Ingelsson E, Lin D

Am. J. Hum. Genet. 93 (2) 236-248 [2013-08-08; online 2013-07-31]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Temperament and character in the Child and Adolescent Twin Study in Sweden (CATSS): comparison to the general population, and genetic structure analysis.

Garcia D, Lundström S, Brändström S, ..., Nilsson T, Anckarsäter H

PLoS ONE 8 (8) e70475 [2013-08-05; online 2013-08-05]

An Integratedin VitroModel for Simultaneous Assessment of Drug Uptake, Metabolism, and Efflux

Neve EPA, Artursson P, Ingelman-Sundberg M, Karlgren M

Mol. Pharmaceutics 10 (8) 3152-3163 [2013-08-05; online 2013-08-05]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Improved production of membrane proteins in Escherichia coli by selective codon substitutions.

Nørholm MH, Toddo S, Virkki MT, ..., von Heijne G, Daley DO

FEBS Lett. 587 (15) 2352-2358 [2013-08-02; online 2013-06-19]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Identification of adenovirus-encoded small RNAs by deep RNA sequencing.

Zhao H, Chen M, Pettersson U

Virology 442 (2) 148-155 [2013-08-01; online 2013-05-11]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Chronic airway-induced allergy in mice modifies gene expression in the brain toward insulin resistance and inflammatory responses.

Sarlus H, Wang X, Cedazo-Minguez A, Schultzberg M, Oprica M

J Neuroinflammation 10 (-) 99 [2013-08-01; online 2013-08-01]

Tumour expression of bladder cancer-associated urinary proteins.

Lindén M, Segersten U, Runeson M, ..., Lind SB, Malmström PU

BJU Int. 112 (3) 407-415 [2013-08-00; online 2013-03-09]

Synergistic interactions between camptothecin and EGFR or RAC1 inhibitors and between imatinib and Notch signaling or RAC1 inhibitors in glioblastoma cell lines.

Sooman L, Ekman S, Andersson C, ..., Lennartsson J, Gullbo J

Cancer Chemother. Pharmacol. 72 (2) 329-340 [2013-08-00; online 2013-06-06]

Proteome of the nematode-trapping cells of the fungus Monacrosporium haptotylum.

Andersson KM, Meerupati T, Levander F, ..., Ahrén D, Tunlid A

Appl. Environ. Microbiol. 79 (16) 4993-5004 [2013-08-00; online 2013-06-19]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Molecular identification and phylogenic analysis by sequencing the rDNA of copper-tolerant soft-rot Phialophora spp.

Karunasekera H, Daniel G

International Biodeterioration & Biodegradation 82 (-) 45-52 [2013-08-00; online 2013-08-00]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

In silico instrumental response correction improves precision of label-free proteomics and accuracy of proteomics-based predictive models.

Lyutvinskiy Y, Yang H, Rutishauser D, Zubarev RA

Mol. Cell Proteomics 12 (8) 2324-2331 [2013-08-00; online 2013-04-17]

High-resolution structure of TBP with TAF1 reveals anchoring patterns in transcriptional regulation.

Anandapadamanaban M, Andresen C, Helander S, ..., Moche M, Sunnerhagen M

Nat. Struct. Mol. Biol. 20 (8) 1008-1014 [2013-08-00; online 2013-07-16]

Genetic variation in the dimethylarginine dimethylaminohydrolase 1 gene (DDAH1) is related to asymmetric dimethylarginine (ADMA) levels, but not to endothelium-dependent vasodilation.

Lind L, Ingelsson E, Kumar J, ..., Axelsson T, Teerlink T

Vasc Med 18 (4) 192-199 [2013-08-00; online 2013-07-31]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Expression of chondroitin/dermatan sulfate glycosyltransferases during early zebrafish development.

Filipek-Górniok B, Holmborn K, Haitina T, ..., Kreuger J, Ledin J

Dev. Dyn. 242 (8) 964-975 [2013-08-00; online 2013-06-18]

Design of a highly selective and potent class of non-planar estrogen receptor β agonists.

Sundén H, Ma JN, Hansen LK, ..., Burstein ES, Olsson R

ChemMedChem 8 (8) 1283-1294 [2013-08-00; online 2013-06-19]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Antibody-based profiling of cerebrospinal fluid within multiple sclerosis.

Häggmark A, Byström S, Ayoglu B, ..., Schwenk JM, Nilsson P

Proteomics 13 (15) 2256-2267 [2013-08-00; online 2013-05-23]

A novel intellectual disability syndrome caused by GPI anchor deficiency due to homozygous mutations in PIGT.

Kvarnung M, Nilsson D, Lindstrand A, ..., Nordenskjöld M, Nordgren A

J. Med. Genet. 50 (8) 521-528 [2013-08-00; online 2013-05-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

New viruses in veterinary medicine, detected by metagenomic approaches.

Belák S, Karlsson OE, Blomström AL, Berg M, Granberg F

Vet. Microbiol. 165 (1-2) 95-101 [2013-07-26; online 2013-02-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Gene × physical activity interactions in obesity: combined analysis of 111,421 individuals of European ancestry.

Ahmad S, Rukh G, Varga TV, ..., Orho-Melander M, Franks PW

PLoS Genet. 9 (7) e1003607 [2013-07-25; online 2013-07-25]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

NCR3/NKp30 contributes to pathogenesis in primary Sjogren's syndrome.

Rusakiewicz S, Nocturne G, Lazure T, ..., Zitvogel L, Mariette X

Sci Transl Med 5 (195) 195ra96 [2013-07-24; online 2013-07-26]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Retinoic acid receptor alpha is associated with tamoxifen resistance in breast cancer.

Johansson HJ, Sanchez BC, Mundt F, ..., Linderholm BK, Lehtiö J

Nat Commun 4 (-) 2175 [2013-07-23; online 2013-07-23]

Drug Discovery and Development (DDD) [Collaborative]

Genetic variants in hormone-related genes and risk of breast cancer.

Clendenen T, Zeleniuch-Jacquotte A, Wirgin I, ..., Shore RE, Chen Y

PLoS ONE 8 (7) e69367 [2013-07-23; online 2013-07-23]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

SNP in TXNRD2 associated with radiation-induced fibrosis: a study of genetic variation in reactive oxygen species metabolism and signaling.

Edvardsen H, Landmark-Høyvik H, Reinertsen KV, ..., Fosså SD, Kristensen VN

Int. J. Radiat. Oncol. Biol. Phys. 86 (4) 791-799 [2013-07-15; online 2013-04-20]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Novel signatures of cancer-associated fibroblasts.

Bozóky B, Savchenko A, Csermely P, ..., Székely L, Klein G

Int. J. Cancer 133 (2) 286-293 [2013-07-15; online 2013-01-16]

Prevalence, comorbidity and heritability of hoarding symptoms in adolescence: a population based twin study in 15-year olds.

Ivanov VZ, Mataix-Cols D, Serlachius E, ..., Långström N, Rück C

PLoS ONE 8 (7) e69140 [2013-07-10; online 2013-07-10]

Amyloid-β protofibrils: size, morphology and synaptotoxicity of an engineered mimic.

Dubnovitsky A, Sandberg A, Rahman MM, ..., Lendel C, Härd T

PLoS ONE 8 (7) e66101 [2013-07-02; online 2013-07-02]

Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity.

Cousminer DL, Berry DJ, Timpson NJ, ..., Widén E, Early Growth Genetics (EGG) Consortium

Hum. Mol. Genet. 22 (13) 2735-2747 [2013-07-01; online 2013-02-27]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Somatic mutations in H-RAS in sporadic pheochromocytoma and paraganglioma identified by exome sequencing.

Crona J, Delgado Verdugo A, Maharjan R, ..., Hellman P, Björklund P

J. Clin. Endocrinol. Metab. 98 (7) E1266-E1271 [2013-07-00; online 2013-05-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Response of Acidithiobacillus caldus toward suboptimal pH conditions.

Mangold S, Rao Jonna V, Dopson M

Extremophiles 17 (4) 689-696 [2013-07-00; online 2013-05-29]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Republished: Non-heritable genetics of human disease: spotlight on post-zygotic genetic variation acquired during lifetime.

Forsberg LA, Absher D, Dumanski JP

Postgrad Med J 89 (1053) 417-426 [2013-07-00; online 2013-06-20]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Massive functional mapping of a 5'-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing.

Holmqvist E, Reimegård J, Wagner EG

Nucleic Acids Res. 41 (12) e122 [2013-07-00; online 2013-04-24]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Implications of baseline polymorphisms for potential resistance to NS3 protease inhibitors in Hepatitis C virus genotypes 1a, 2b and 3a.

Palanisamy N, Danielsson A, Kokkula C, ..., Duberg AS, Lennerstrand J

Antiviral Res. 99 (1) 12-17 [2013-07-00; online 2013-05-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Family-based study of HTR2A in suicide attempts: observed gene, gene × environment and parent-of-origin associations.

Ben-Efraim YJ, Wasserman D, Wasserman J, Sokolowski M

Mol. Psychiatry 18 (7) 758-766 [2013-07-00; online 2012-07-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Family-based study of AVPR1B association and interaction with stressful life events on depression and anxiety in suicide attempts.

Ben-Efraim YJ, Wasserman D, Wasserman J, Sokolowski M

Neuropsychopharmacology 38 (8) 1504-1511 [2013-07-00; online 2013-02-21]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Estrogen receptor β expression induces changes in the microRNA pool in human colon cancer cells.

Edvardsson K, Nguyen-Vu T, Kalasekar SM, ..., Gustafsson JÅ, Williams C

Carcinogenesis 34 (7) 1431-1441 [2013-07-00; online 2013-02-26]

Enzymatic production of 'monoclonal stoichiometric' single-stranded DNA oligonucleotides.

Ducani C, Kaul C, Moche M, Shih WM, Högberg B

Nat. Methods 10 (7) 647-652 [2013-07-00; online 2013-06-04]

Computational Prospecting for Drug–Transporter Interactions

Matsson P, Artursson P

Clin Pharmacol Ther 94 (1) 30-32 [2013-07-00; online 2013-04-02]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Clinical depression, antidepressant use and risk of future cardiovascular disease.

Rahman I, Humphreys K, Bennet AM, ..., Pedersen NL, Magnusson PK

Eur. J. Epidemiol. 28 (7) 589-595 [2013-07-00; online 2013-07-09]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Cenani-Lenz syndrome restricted to limb and kidney anomalies associated with a novel LRP4 missense mutation.

Khan TN, Klar J, Ali Z, ..., Baig SM, Dahl N

Eur J Med Genet 56 (7) 371-374 [2013-07-00; online 2013-05-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

CDK-mediated activation of the SCF(FBXO) (28) ubiquitin ligase promotes MYC-driven transcription and tumourigenesis and predicts poor survival in breast cancer.

Cepeda D, Ng HF, Sharifi HR, ..., Larsson LG, Sangfelt O

EMBO Mol Med 5 (7) 1067-1086 [2013-07-00; online 2013-06-19]

Active nitrogen-fixing heterotrophic bacteria at and below the chemocline of the central Baltic Sea.

Farnelid H, Bentzon-Tilia M, Andersson AF, ..., Jürgens K, Riemann L

ISME J 7 (7) 1413-1423 [2013-07-00; online 2013-03-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Unbiased approach for virus detection in skin lesions.

Bzhalava D, Johansson H, Ekström J, ..., Forslund O, Dillner J

PLoS ONE 8 (6) e65953 [2013-06-28; online 2013-06-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Continuous Aging of the Human DNA Methylome Throughout the Human Lifespan.

Johansson A, Enroth S, Gyllensten U

PLoS ONE 8 (6) e67378 [2013-06-27; online 2013-06-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Constrained H-Phe-Phe-NH2 analogues with high affinity to the substance P 1-7 binding site and with improved metabolic stability and cell permeability.

Fransson R, Sköld C, Kratz JM, ..., Hallberg M, Sandström A

J. Med. Chem. 56 (12) 4953-4965 [2013-06-27; online 2013-06-06]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

The crystal structure of the lumenal domain of Erv41p, a protein involved in transport between the endoplasmic reticulum and Golgi apparatus.

Biterova EI, Svärd M, Possner DD, Guy JE

J. Mol. Biol. 425 (12) 2208-2218 [2013-06-26; online 2013-03-26]

The role of adiposity in cardiometabolic traits: a Mendelian randomization analysis.

Fall T, Hägg S, Mägi R, ..., Prokopenko I, European Network for Genetic and Genomic Epidemiology (ENGAGE) consortium N

PLoS Med. 10 (6) e1001474 [2013-06-25; online 2013-06-25]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data.

Lampa S, Dahlö M, Olason PI, Hagberg J, Spjuth O

Gigascience 2 (1) 9 [2013-06-25; online 2013-06-25]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Substrate Channel Flexibility in Pseudomonas aeruginosa MurB Accommodates Two Distinct Substrates.

Chen MW, Lohkamp B, Schnell R, Lescar J, Schneider G

PLoS ONE 8 (6) e66936 [2013-06-21; online 2013-06-21]

GWAS of 126,559 individuals identifies genetic variants associated with educational attainment.

Rietveld CA, Medland SE, Derringer J, ..., Cesarini D, Koellinger PD

Science 340 (6139) 1467-1471 [2013-06-21; online 2013-06-01]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Vandetanib combined with a p38 MAPK inhibitor synergistically reduces glioblastoma cell survival.

Sooman L, Lennartsson J, Gullbo J, ..., Blomquist E, Ekman S

Med. Oncol. 30 (3) 638 [2013-06-20; online 2013-06-20]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training Tissue Profiling

Behavioural and Brain Gene Expression Profiling in Pigs during Tail Biting Outbreaks - Evidence of a Tail Biting Resistant Phenotype.

Brunberg E, Jensen P, Isaksson A, Keeling LJ

PLoS ONE 8 (6) e66513 [2013-06-18; online 2013-06-18]

Stable isotope labeling methods in protein profiling.

Lengqvist J, Sandberg A

Methods Mol. Biol. 1023 (-) 21-51 [2013-06-15; online 2013-06-15]

Protein quantification by peptide quality control (PQPQ) of shotgun proteomics data.

Forshed J

Methods Mol. Biol. 1023 (-) 149-158 [2013-06-15; online 2013-06-15]

Narrow-range peptide isoelectric focusing as peptide prefractionation method prior to tandem mass spectrometry analysis.

Pernemalm M

Methods Mol. Biol. 1023 (-) 3-11 [2013-06-15; online 2013-06-15]

Highly multiplexed antibody suspension bead arrays for plasma protein profiling.

Drobin K, Nilsson P, Schwenk JM

Methods Mol. Biol. 1023 (-) 137-145 [2013-06-15; online 2013-06-15]

Affinity Proteomics Stockholm [Technology development]

Comprehensive analysis of MHC ligands in clinical material by immunoaffinity-mass spectrometry.

Kasuga K

Methods Mol. Biol. 1023 (-) 203-218 [2013-06-15; online 2013-06-15]

Molecular genetics and subjective well-being.

Rietveld CA, Cesarini D, Benjamin DJ, ..., Krueger RF, Bartels M

Proc. Natl. Acad. Sci. U.S.A. 110 (24) 9692-9697 [2013-06-11; online 2013-05-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The prognostic relevance of tumour-infiltrating plasma cells and immunoglobulin kappa C indicates an important role of the humoral immune response in non-small cell lung cancer.

Lohr M, Edlund K, Botling J, ..., Rahnenführer J, Micke P

Cancer Lett. 333 (2) 222-228 [2013-06-10; online 2013-02-02]

Contribution of antibody-based protein profiling to the human Chromosome-centric Proteome Project (C-HPP).

Fagerberg L, Oksvold P, Skogs M, ..., von Feilitzen K, Uhlén M

J. Proteome Res. 12 (6) 2439-2448 [2013-06-07; online 2013-01-02]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling

Promoter DNA methylation pattern identifies prognostic subgroups in childhood T-cell acute lymphoblastic leukemia.

Borssén M, Palmqvist L, Karrman K, ..., Roos G, Degerman S

PLoS ONE 8 (6) e65373 [2013-06-06; online 2013-06-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Rapid Measurement of Intracellular Unbound Drug Concentrations

Mateus A, Matsson P, Artursson P

Mol. Pharmaceutics 10 (6) 2467-2478 [2013-06-03; online 2013-06-03]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Next-generation sequencing in the clinical genetic screening of patients with pheochromocytoma and paraganglioma.

Crona J, Verdugo AD, Granberg D, ..., Hellman P, Björklund P

Endocr Connect 2 (2) 104-111 [2013-06-01; online 2013-05-28]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The value of selected in vitro and in silico methods to predict acute oral toxicity in a regulatory context: results from the European Project ACuteTox.

Prieto P, Kinsner-Ovaskainen A, Stanzel S, ..., Zurbano MJ, Kopp-Schneider A

Toxicol In Vitro 27 (4) 1357-1376 [2013-06-00; online 2012-08-28]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

The impact of splicing on protein domain architecture.

Light S, Elofsson A

Curr. Opin. Struct. Biol. 23 (3) 451-458 [2013-06-00; online 2013-04-09]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Structural basis for substrate transport in the GLUT-homology family of monosaccharide transporters.

Quistgaard EM, Löw C, Moberg P, Trésaugues L, Nordlund P

Nat. Struct. Mol. Biol. 20 (6) 766-768 [2013-06-00; online 2013-04-30]

Structural and dynamic insights into substrate binding and catalysis of human lipocalin prostaglandin D synthase.

Lim SM, Chen D, Teo H, ..., Pervushin K, Nordlund P

J. Lipid Res. 54 (6) 1630-1643 [2013-06-00; online 2013-03-26]

Stepping-stone expansion and habitat loss explain a peculiar genetic structure and distribution of a forest insect.

Cassel-Lundhagen A, Ronnås C, Battisti A, Wallén J, Larsson S

Mol. Ecol. 22 (12) 3362-3375 [2013-06-00; online 2013-05-31]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Sortilin receptor 1 predicts longitudinal cognitive change.

Reynolds CA, Zavala C, Gatz M, ..., Prince JA, Pedersen NL

Neurobiol. Aging 34 (6) 1710.e11-1710.e18 [2013-06-00; online 2013-01-16]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Solid-phase proximity ligation assays for individual or parallel protein analyses with readout via real-time PCR or sequencing.

Nong RY, Wu D, Yan J, ..., Landegren U, Darmanis S

Nat Protoc 8 (6) 1234-1248 [2013-06-00; online 2013-05-30]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits.

Randall JC, Winkler TW, Kutalik Z, ..., North KE, Heid IM

PLoS Genet. 9 (6) e1003500 [2013-06-00; online 2013-06-06]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Prevalence of extended-spectrum beta-lactamase-producing Enterobacteriaceae in healthy Swedish preschool children.

Kaarme J, Molin Y, Olsen B, Melhus A

Acta Paediatr. 102 (6) 655-660 [2013-06-00; online 2013-02-20]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Parallel visualization of multiple protein complexes in individual cells in tumor tissue.

Leuchowius KJ, Clausson CM, Grannas K, ..., Landegren U, Söderberg O

Mol. Cell Proteomics 12 (6) 1563-1571 [2013-06-00; online 2013-02-26]

Affinity Proteomics Uppsala [Technology development] NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure PLA and Single Cell Proteomics

No association of primary Sjögren's syndrome with Fcγ receptor gene variants.

Haldorsen K, Appel S, Le Hellard S, ..., Jonsson R, Bolstad AI

Genes Immun. 14 (4) 234-237 [2013-06-00; online 2013-04-05]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse.

Geiger T, Velic A, Macek B, ..., Cox J, Mann M

Mol. Cell Proteomics 12 (6) 1709-1722 [2013-06-00; online 2013-02-26]

Identification of heart rate-associated loci and their effects on cardiac conduction and rhythm disorders.

den Hoed M, Eijgelsheim M, Esko T, ..., Samani NJ, Loos RJF

Nat. Genet. 45 (6) 621-631 [2013-06-00; online 2013-04-16]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Gambogic acid is cytotoxic to cancer cells through inhibition of the ubiquitin-proteasome system.

Felth J, Lesiak-Mieczkowska K, D'Arcy P, ..., Fryknäs M, Rickardson L

Invest New Drugs 31 (3) 587-598 [2013-06-00; online 2012-11-28]

Exome sequencing in diagnostic evaluation of colorectal cancer predisposition in young patients.

Tanskanen T, Gylfe AE, Katainen R, ..., Vahteristo P, Aaltonen LA

Scand. J. Gastroenterol. 48 (6) 672-678 [2013-06-00; online 2013-04-03]

Coronary heart disease in systemic lupus erythematosus is associated with interferon regulatory factor-8 gene variants.

Leonard D, Svenungsson E, Sandling JK, ..., Syvänen AC, Rönnblom L

Circ Cardiovasc Genet 6 (3) 255-263 [2013-06-00; online 2013-05-11]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Contribution of IKBKE and IFIH1 gene variants to SLE susceptibility.

Wang C, Ahlford A, Laxman N, ..., Rönnblom L, Syvänen AC

Genes Immun. 14 (4) 217-222 [2013-06-00; online 2013-03-29]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Circadian regulation of melanization and prokineticin homologues is conserved in the brain of freshwater crayfish and zebrafish.

Noonin C, Watthanasurorot A, Winberg S, Söderhäll I

Dev. Comp. Immunol. 40 (2) 218-226 [2013-06-00; online 2013-03-19]

Genome Engineering Zebrafish NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A significant fraction of 21-nucleotide small RNA originates from phased degradation of resistance genes in several perennial species.

Källman T, Chen J, Gyllenstrand N, Lagercrantz U

Plant Physiol. 162 (2) 741-754 [2013-06-00; online 2013-04-13]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The Norway spruce genome sequence and conifer genome evolution.

Nystedt B, Street NR, Wetterbom A, ..., Lundeberg J, Jansson S

Nature 497 (7451) 579-584 [2013-05-30; online 2013-05-22]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support for Computational Resources Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Metagenomic de novo assembly of an aquatic representative of the verrucomicrobial class Spartobacteria.

Herlemann DP, Lundin D, Labrenz M, ..., Aspeborg H, Andersson AF

MBio 4 (3) e00569-e00512 [2013-05-28; online 2013-05-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Dynamic gradients of an intermediate filament-like cytoskeleton are recruited by a polarity landmark during apical growth.

Fuchino K, Bagchi S, Cantlay S, ..., Flärdh K, Ausmees N

Proc. Natl. Acad. Sci. U.S.A. 110 (21) E1889-E1897 [2013-05-21; online 2013-05-04]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

A texture based pattern recognition approach to distinguish melanoma from non-melanoma cells in histopathological tissue microarray sections.

Rexhepaj E, Agnarsdóttir M, Bergman J, ..., Lundberg E, Ponten F

PLoS ONE 8 (5) e62070 [2013-05-17; online 2013-05-17]

Adaptive mutations and replacements of virulence traits in the Escherichia coli O104:H4 outbreak population.

Guy L, Jernberg C, Arvén Norling J, ..., Engstrand L, Andersson SGE

PLoS ONE 8 (5) e63027 [2013-05-10; online 2013-05-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Age dependence of tumor genetics in unfavorable neuroblastoma: arrayCGH profiles of 34 consecutive cases, using a Swedish 25-year neuroblastoma cohort for validation.

Cetinkaya C, Martinsson T, Sandgren J, ..., Díaz de Ståhl T, Hedborg F

BMC Cancer 13 (-) 231 [2013-05-09; online 2013-05-09]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genome-wide association study of susceptibility loci for cervical cancer.

Chen D, Juko-Pecirep I, Hammer J, ..., Wilander E, Gyllensten U

J. Natl. Cancer Inst. 105 (9) 624-633 [2013-05-01; online 2013-03-12]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Active transcriptomic and proteomic reprogramming in the C. elegans nucleotide excision repair mutant xpa-1.

Arczewska KD, Tomazella GG, Lindvall JM, ..., Thiede B, Nilsen H

Nucleic Acids Res. 41 (10) 5368-5381 [2013-05-01; online 2013-04-13]

Variation in genes in the endothelin pathway and endothelium-dependent and endothelium-independent vasodilation in an elderly population.

Lind L, Syvänen AC, Axelsson T, ..., Hägg S, Larsson A

Acta Physiol (Oxf) 208 (1) 88-94 [2013-05-00; online 2013-01-23]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The combined effects of single-nucleotide polymorphisms, tobacco products, and ethanol on normal resting blood mononuclear cells.

Cederblad L, Thunberg U, Engström M, ..., Rutqvist LE, Laytragoon-Lewin N

Nicotine Tob. Res. 15 (5) 890-895 [2013-05-00; online 2012-10-09]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The adenovirus VA RNA-derived miRNAs are not essential for lytic virus growth in tissue culture cells.

Kamel W, Segerman B, Öberg D, Punga T, Akusjärvi G

Nucleic Acids Res. 41 (9) 4802-4812 [2013-05-00; online 2013-03-26]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Membrane protein shaving with thermolysin can be used to evaluate topology predictors.

Bendz M, Skwark M, Nilsson D, ..., Käll L, Elofsson A

Proteomics 13 (9) 1467-1480 [2013-05-00; online 2013-03-21]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Long indels are disordered: a study of disorder and indels in homologous eukaryotic proteins.

Light S, Sagit R, Ekman D, Elofsson A

Biochim. Biophys. Acta 1834 (5) 890-897 [2013-05-00; online 2013-01-22]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Identification of acetate-oxidizing bacteria in a coastal marine surface sediment by RNA-stable isotope probing in anoxic slurries and intact cores.

Vandieken V, Thamdrup B

FEMS Microbiol. Ecol. 84 (2) 373-386 [2013-05-00; online 2013-01-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Identification of a functional apolipoprotein E promoter polymorphism regulating plasma apolipoprotein E concentration.

Mannila MN, Mahdessian H, Franco-Cereceda A, ..., Hamsten A, van 't Hooft FM

Arterioscler. Thromb. Vasc. Biol. 33 (5) 1063-1069 [2013-05-00; online 2013-02-23]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Identification and expression of stressosomal proteins in Mycobacterium marinum under various growth and stress conditions.

Pettersson BMF, Nitharwal RG, Das S, ..., Bhattacharya A, Kirsebom LA

FEMS Microbiol. Lett. 342 (2) 98-105 [2013-05-00; online 2013-03-14]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture.

Berndt SI, Gustafsson S, Mägi R, ..., Loos RJF, Ingelsson E

Nat. Genet. 45 (5) 501-512 [2013-05-00; online 2013-04-09]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genome-wide analysis in German shepherd dogs reveals association of a locus on CFA 27 with atopic dermatitis.

Tengvall K, Kierczak M, Bergvall K, ..., Hedhammar Å, Lindblad-Toh K

PLoS Genet. 9 (5) e1003475 [2013-05-00; online 2013-05-09]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic determinants of mortality. Can findings from genome-wide association studies explain variation in human mortality?

Ganna A, Rivadeneira F, Hofman A, ..., Ingelsson E, Tiemeier H

Hum. Genet. 132 (5) 553-561 [2013-05-00; online 2013-01-29]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Comprehensive analysis of copy number variation in monozygotic twins discordant for bipolar disorder or schizophrenia.

Bloom RJ, Kähler AK, Collins AL, ..., Hultman C, Sullivan PF

Schizophr. Res. 146 (1-3) 289-290 [2013-05-00; online 2013-03-20]

An adaptive alignment algorithm for quality-controlled label-free LC-MS.

Sandin M, Ali A, Hansson K, ..., Resjö S, Levander F

Mol. Cell Proteomics 12 (5) 1407-1420 [2013-05-00; online 2013-01-12]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

A phylogeny of the highly diverse cup-fungus family Pyronemataceae (Pezizomycetes, Ascomycota) clarifies relationships and evolution of selected life history traits.

Hansen K, Perry BA, Dranginis AW, Pfister DH

Mol. Phylogenet. Evol. 67 (2) 311-335 [2013-05-00; online 2013-02-14]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

SoxB1-driven transcriptional network underlies neural-specific interpretation of morphogen signals.

Oosterveen T, Kurdija S, Ensterö M, ..., Muhr J, Ericson J

Proc. Natl. Acad. Sci. U.S.A. 110 (18) 7330-7335 [2013-04-30; online 2013-04-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Employment of complementary dissociation techniques for body fluid characterization and biomarker discovery.

Good DM, Rutishauser D

Methods Mol. Biol. 1002 (-) 223-232 [2013-04-30; online 2013-04-30]

Majority of differentially expressed genes are down-regulated during malignant transformation in a four-stage model.

Danielsson F, Skogs M, Huss M, ..., Uhlén M, Lundberg E

Proc. Natl. Acad. Sci. U.S.A. 110 (17) 6853-6858 [2013-04-23; online 2013-04-10]

Expression of fusion proteins of Aspergillus terreus reveals a novel allene oxide synthase.

Hoffmann I, Jernerén F, Oliw EH

J. Biol. Chem. 288 (16) 11459-11469 [2013-04-19; online 2013-03-13]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Renal sensory and sympathetic nerves reinnervate the kidney in a similar time-dependent fashion after renal denervation in rats.

Mulder J, Hökfelt T, Knuepfer MM, Kopp UC

Am. J. Physiol. Regul. Integr. Comp. Physiol. 304 (8) R675-R682 [2013-04-15; online 2013-02-15]

Eating problems and overlap with ADHD and autism spectrum disorders in a nationwide twin study of 9- and 12-year-old children.

Råstam M, Täljemark J, Tajnia A, ..., Anckarsäter H, Kerekes N

ScientificWorldJournal 2013 (-) 315429 [2013-04-15; online 2013-04-15]

Viral Metagenomics – New applications for the broad-range detection of viromes in veterinary and public health settings

Karlsson OE, Norling M, Granberg F, Belák S, Bongcam-Rudloff E

EMBnet j. 19 (A) 21 [2013-04-08; online 2013-04-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Metagenomics sample preparation and sequencing.

Karlsson OE, Norling M, Bongcam-Rudloff E

EMBnet j. 19 (A) 55 [2013-04-08; online 2013-04-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Ion Torrent sequencing and pipeline assembly of the first genome sequence of a mesophilic syntrophic acetate oxidizing bacterium (SAOB)

Manzoor S, Bongcam-Rudloff E, Schnürer A, Müller B

EMBnet j. 19 (A) 60 [2013-04-08; online 2013-04-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

European H16N3 gull influenza virus attaches to the human respiratory tract and eye.

Lindskog C, Ellström P, Olsen B, ..., Kuiken T, Jourdain E

PLoS ONE 8 (4) e60757 [2013-04-08; online 2013-04-08]

The molecular genetic architecture of self-employment.

van der Loos MJHM, Rietveld CA, Eklund N, ..., Hofman A, Thurik AR

PLoS ONE 8 (4) e60542 [2013-04-04; online 2013-04-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

β-thymosins and hemocyte homeostasis in a crustacean.

Saelee N, Noonin C, Nupan B, ..., Söderhäll K, Söderhäll I

PLoS ONE 8 (4) e60974 [2013-04-02; online 2013-04-02]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Systematic antibody generation and validation via tissue microarray technology leading to identification of a novel protein prognostic panel in breast cancer.

O Leary PC, Penny SA, Dolan RT, ..., Jirström K, Gallagher WM

BMC Cancer 13 (-) 175 [2013-04-02; online 2013-04-02]

Interaction between retinoid acid receptor-related orphan receptor alpha (RORA) and neuropeptide S receptor 1 (NPSR1) in asthma.

Acevedo N, Sääf A, Söderhäll C, ..., Kere J, Pulkkinen V

PLoS ONE 8 (4) e60111 [2013-04-02; online 2013-04-02]

Genetic determinants of dabigatran plasma levels and their relation to bleeding.

Paré G, Eriksson N, Lehr T, ..., Yusuf S, Wallentin L

Circulation 127 (13) 1404-1412 [2013-04-02; online 2013-03-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

RNA-binding protein QKI regulates Glial fibrillary acidic protein expression in human astrocytes.

Radomska KJ, Halvardson J, Reinius B, ..., Feuk L, Jazin E

Hum. Mol. Genet. 22 (7) 1373-1382 [2013-04-01; online 2013-01-15]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Welander distal myopathy caused by an ancient founder mutation in TIA1 associated with perturbed splicing.

Klar J, Sobol M, Melberg A, ..., Casar-Borota O, Dahl N

Hum. Mutat. 34 (4) 572-577 [2013-04-00; online 2013-01-26]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The transporter ABCB7 is a mediator of the phenotype of acquired refractory anemia with ring sideroblasts.

Nikpour M, Scharenberg C, Liu A, ..., Grandien A, Hellström-Lindberg E

Leukemia 27 (4) 889-896 [2013-04-00; online 2012-10-17]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The mitochondrial and autosomal mutation landscapes of prostate cancer.

Lindberg J, Mills IG, Klevebring D, ..., Egevad L, Grönberg H

Eur. Urol. 63 (4) 702-708 [2013-04-00; online 2012-12-26]

Karolinska High Throughput Center (KHTC) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Modelling the effects of dispersal mechanisms and hydrodynamic regimes upon the structure of microbial communities within fluvial biofilms.

Woodcock S, Besemer K, Battin TJ, Curtis TP, Sloan WT

Environ. Microbiol. 15 (4) 1216-1225 [2013-04-00; online 2012-12-18]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Lack of dosage compensation accompanies the arrested stage of sex chromosome evolution in ostriches.

Adolfsson S, Ellegren H

Mol. Biol. Evol. 30 (4) 806-810 [2013-04-00; online 2013-01-19]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Immunofluorescence and fluorescent-protein tagging show high correlation for protein localization in mammalian cells.

Stadler C, Rexhepaj E, Singan VR, ..., Simpson JC, Lundberg E

Nat. Methods 10 (4) 315-323 [2013-04-00; online 2013-02-26]

Identification of seven loci affecting mean telomere length and their association with disease.

Codd V, Nelson CP, Albrecht E, ..., van der Harst P, Samani NJ

Nat. Genet. 45 (4) 422-7, 427e1-2 [2013-04-00; online 2013-03-29]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Hereditary uveal melanoma: a report of a germline mutation in BAP1.

Höiom V, Edsgärd D, Helgadottir H, ..., Emanuelsson O, Hansson J

Genes Chromosomes Cancer 52 (4) 378-384 [2013-04-00; online 2013-01-23]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Degradation of Scots pine and beech wood exposed in four test fields used for testing of wood preservatives

Råberg U, Terziev N, Daniel G

International Biodeterioration & Biodegradation 79 (-) 20-27 [2013-04-00; online 2013-04-00]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Comparative genomics of Wolbachia and the bacterial species concept.

Ellegaard KM, Klasson L, Näslund K, Bourtzis K, Andersson SG

PLoS Genet. 9 (4) e1003381 [2013-04-00; online 2013-04-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Automated classification of immunostaining patterns in breast tissue from the human protein atlas.

Swamidoss IN, Kårsnäs A, Uhlmann V, ..., Wählby C, Strand R

J Pathol Inform 4 (Suppl) S14 [2013-03-30; online 2013-03-30]

BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development] Tissue Profiling

Genetic variants from lipid-related pathways and risk for incident myocardial infarction.

Song C, Pedersen NL, Reynolds CA, ..., Prince JA, Ingelsson E

PLoS ONE 8 (3) e60454 [2013-03-29; online 2013-03-29]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

Franzén O, Jerlström-Hultqvist J, Einarsson E, ..., Andersson B, Svärd SG

PLoS Comput. Biol. 9 (3) e1003000 [2013-03-28; online 2013-03-28]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Optimizing Solubility and Permeability of a Biopharmaceutics Classification System (BCS) Class 4 Antibiotic Drug Using Lipophilic Fragments Disturbing the Crystal Lattice

Tehler U, Fagerberg JH, Svensson R, ..., Artursson P, Bergström CAS

J. Med. Chem. 56 (6) 2690-2694 [2013-03-28; online 2013-03-28]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Patchwork: allele-specific copy number analysis of whole-genome sequenced tumor tissue.

Mayrhofer M, DiLorenzo S, Isaksson A

Genome Biol. 14 (3) R24 [2013-03-25; online 2013-03-25]

Offshoots of the ESF functional genomics programme.

Landegren U

N Biotechnol 30 (3) 296-298 [2013-03-25; online 2013-01-09]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

The genomic signature of dog domestication reveals adaptation to a starch-rich diet.

Axelsson E, Ratnakumar A, Arendt M, ..., Hedhammar A, Lindblad-Toh K

Nature 495 (7441) 360-364 [2013-03-21; online 2013-01-29]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Integration of clinical data with a genome-scale metabolic model of the human adipocyte.

Mardinoglu A, Agren R, Kampf C, ..., Uhlen M, Nielsen J

Mol. Syst. Biol. 9 (-) 649 [2013-03-21; online 2013-03-21]

Genome Sequence of a Plant-Associated Bacterium, Bacillus amyloliquefaciens Strain UCMB5036.

Manzoor S, Niazi A, Bejai S, Meijer J, Bongcam-Rudloff E

Genome Announc 1 (2) e0011113 [2013-03-21; online 2013-03-21]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Identification of genetic variants influencing the human plasma proteome.

Johansson Å, Enroth S, Palmblad M, ..., Bergquist J, Gyllensten U

Proc. Natl. Acad. Sci. U.S.A. 110 (12) 4673-4678 [2013-03-19; online 2013-03-15]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Identification and verification of microRNAs by high-throughput sequencing.

Hällman J, Avesson L, Reimegård J, Käller M, Söderbom F

Methods Mol. Biol. 983 (-) 125-138 [2013-03-16; online 2013-03-16]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

DNA topoisomerase III localizes to centromeres and affects centromeric CENP-A levels in fission yeast.

Norman-Axelsson U, Durand-Dubief M, Prasad P, Ekwall K

PLoS Genet. 9 (3) e1003371 [2013-03-14; online 2013-03-14]

Transcriptome of the alternative ethanol production strain Dekkera bruxellensis CBS 11270 in sugar limited, low oxygen cultivation.

Tiukova IA, Petterson ME, Tellgren-Roth C, ..., Pettersson OV, Passoth V

PLoS ONE 8 (3) e58455 [2013-03-13; online 2013-03-13]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The HUPO proteomics standards initiative- mass spectrometry controlled vocabulary.

Mayer G, Montecchi-Palazzi L, Ovelleiro D, ..., Eisenacher M, HUPO-PSI Group

Database (Oxford) 2013 (-) bat009 [2013-03-12; online 2013-03-12]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Gene rearrangements in hormone receptor negative breast cancers revealed by mate pair sequencing.

Jiao X, Hooper SD, Djureinovic T, ..., Botling J, Sjöblom T

BMC Genomics 14 (-) 165 [2013-03-12; online 2013-03-12]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Hierarchical molecular tagging to resolve long continuous sequences by massively parallel sequencing.

Lundin S, Gruselius J, Nystedt B, ..., Käller M, Lundeberg J

Sci Rep 3 (-) 1186 [2013-03-09; online 2013-03-09]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Recognition of mono-ADP-ribosylated ARTD10 substrates by ARTD8 macrodomains.

Forst AH, Karlberg T, Herzog N, ..., Schüler H, Lüscher B

Structure 21 (3) 462-475 [2013-03-05; online 2013-03-12]

TagGD: fast and accurate software for DNA Tag generation and demultiplexing.

Costea PI, Lundeberg J, Akan P

PLoS ONE 8 (3) e57521 [2013-03-04; online 2013-03-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The genetic structure of the Lithuanian wolf population

Baltrūnaitė L, Balčiauskas L, Åkesson M

Open Life Sci 8 (5) 440-447 [2013-03-01; online 2013-03-01]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The effect of substrate and operational parameters on the abundance of sulphate-reducing bacteria in industrial anaerobic biogas digesters.

Moestedt J, Nilsson Påledal S, Schnürer A

Bioresour. Technol. 132 (-) 327-332 [2013-03-00; online 2013-02-19]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Structure of LdtMt2, an L,D-transpeptidase from Mycobacterium tuberculosis.

Böth D, Steiner EM, Stadler D, ..., Schnell R, Schneider G

Acta Crystallogr. D Biol. Crystallogr. 69 (Pt 3) 432-441 [2013-03-00; online 2013-02-16]

Secretion of two novel enzymes, manganese 9S-lipoxygenase and epoxy alcohol synthase, by the rice pathogen Magnaporthe salvinii.

Wennman A, Oliw EH

J. Lipid Res. 54 (3) 762-775 [2013-03-00; online 2012-12-13]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Oral rehydration solution with glycerol to dairy calves: Effects on fluid balance, metabolism, and intestinal microbiota

Omazic AW, Tråvén M, Roos S, Mellgren E, Holtenius K

Acta Agriculturae Scandinavica, Section A - Animal Science 63 (1) 47-56 [2013-03-00; online 2013-03-00]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Higher magnesium intake is associated with lower fasting glucose and insulin, with no evidence of interaction with select genetic loci, in a meta-analysis of 15 CHARGE Consortium Studies.

Hruby A, Ngwa JS, Renström F, ..., McKeown NM, Nettleton JA

J. Nutr. 143 (3) 345-353 [2013-03-00; online 2013-01-25]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic effects on old-age cognitive functioning: a population-based study.

Laukka EJ, Lövdén M, Herlitz A, ..., Fratiglioni L, Bäckman L

Psychol Aging 28 (1) 262-274 [2013-03-00; online 2013-01-02]

Genetic determinants of plasma β₂-glycoprotein I levels: a genome-wide association study in extended pedigrees from Spain.

Athanasiadis G, Sabater-Lleal M, Buil A, ..., Hamsten A, Soria JM

J. Thromb. Haemost. 11 (3) 521-528 [2013-03-00; online 2013-01-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Fine-mapping of restless legs locus 4 (RLS4) identifies a haplotype over the SPATS2L and KCTD18 genes.

Pichler I, Schwienbacher C, Zanon A, ..., Hicks AA, Pramstaller PP

J. Mol. Neurosci. 49 (3) 600-605 [2013-03-00; online 2012-10-12]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Determination of the obesity-associated gene variants within the entire FTO gene by ultra-deep targeted sequencing in obese and lean children.

Sällman Almén M, Rask-Andersen M, Jacobsson JA, ..., Fredriksson R, Schiöth HB

Int J Obes (Lond) 37 (3) 424-431 [2013-03-00; online 2012-04-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Brain gene expression differences are associated with abnormal tail biting behavior in pigs.

Brunberg E, Jensen P, Isaksson A, Keeling LJ

Genes Brain Behav. 12 (2) 275-281 [2013-03-00; online 2012-11-14]

Astakine 2--the dark knight linking melatonin to circadian regulation in crustaceans.

Watthanasurorot A, Saelee N, Phongdara A, ..., Söderhäll K, Söderhäll I

PLoS Genet. 9 (3) e1003361 [2013-03-00; online 2013-03-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A modified Glenn shunt improves haemodynamics in acute right ventricular failure in an experimental model.

Vikholm P, Schiller P, Johansson J, Hellgren L

Eur J Cardiothorac Surg 43 (3) 612-618 [2013-03-00; online 2012-07-05]

A genome-wide assessment of variability in human serum metabolism.

Hong MG, Karlsson R, Magnusson PK, ..., Wiklund F, Prince JA

Hum. Mutat. 34 (3) 515-524 [2013-03-00; online 2013-01-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A gene transfer agent and a dynamic repertoire of secretion systems hold the keys to the explosive radiation of the emerging pathogen Bartonella.

Guy L, Nystedt B, Toft C, ..., Eriksson AS, Andersson SG

PLoS Genet. 9 (3) e1003393 [2013-03-00; online 2013-03-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Metagenomic detection of viral pathogens in Spanish honeybees: co-infection by Aphid Lethal Paralysis, Israel Acute Paralysis and Lake Sinai Viruses.

Granberg F, Vicente-Rubiano M, Rubio-Guerri C, ..., Belák S, Sánchez-Vizcaíno JM

PLoS ONE 8 (2) e57459 [2013-02-27; online 2013-02-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Origin and evolution of medium chain alcohol dehydrogenases.

Jörnvall H, Hedlund J, Bergman T, ..., Cederlund E, Persson B

Chem. Biol. Interact. 202 (1-3) 91-96 [2013-02-25; online 2012-12-04]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Classification and nomenclature of the superfamily of short-chain dehydrogenases/reductases (SDRs).

Persson B, Kallberg Y

Chem. Biol. Interact. 202 (1-3) 111-115 [2013-02-25; online 2012-12-04]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Evolution of sperm structure and energetics in passerine birds.

Rowe M, Laskemoen T, Johnsen A, Lifjeld JT

Proc. Biol. Sci. 280 (1753) 20122616 [2013-02-22; online 2013-01-04]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Imatinib ameliorates neuroinflammation in a rat model of multiple sclerosis by enhancing blood-brain barrier integrity and by modulating the peripheral immune response.

Adzemovic MV, Adzemovic MZ, Zeitelhofer M, ..., Olsson T, Nilsson I

PLoS ONE 8 (2) e56586 [2013-02-20; online 2013-02-20]

The synthetic progestin levonorgestrel is a potent androgen in the three-spined stickleback (Gasterosteus aculeatus).

Svensson J, Fick J, Brandt I, Brunström B

Environ. Sci. Technol. 47 (4) 2043-2051 [2013-02-19; online 2013-02-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

STC1 expression by cancer-associated fibroblasts drives metastasis of colorectal cancer.

Peña C, Céspedes MV, Lindh MB, ..., Augsten M, Ostman A

Cancer Res. 73 (4) 1287-1297 [2013-02-15; online 2012-12-18]

Coastal bacterioplankton community dynamics in response to a natural disturbance.

Yeo SK, Huggett MJ, Eiler A, Rappé MS

PLoS ONE 8 (2) e56207 [2013-02-07; online 2013-02-07]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Causal relationship between obesity and vitamin D status: bi-directional Mendelian randomization analysis of multiple cohorts.

Vimaleswaran KS, Berry DJ, Lu C, ..., Hingorani AD, Hyppönen E

PLoS Med. 10 (2) e1001383 [2013-02-05; online 2013-02-05]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

FANTOM: Functional and taxonomic analysis of metagenomes.

Sanli K, Karlsson FH, Nookaew I, Nielsen J

BMC Bioinformatics 14 (-) 38 [2013-02-01; online 2013-02-01]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

The phylogeographic pattern of Francisella tularensis in Sweden indicates a Scandinavian origin of Eurosiberian tularaemia.

Karlsson E, Svensson K, Lindgren P, ..., Forsman M, Johansson A

Environ. Microbiol. 15 (2) 634-645 [2013-02-00; online 2012-12-16]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The Swedish Twin Registry: establishment of a biobank and other recent developments.

Magnusson PKE, Almqvist C, Rahman I, ..., Pedersen NL, Lichtenstein P

Twin Res Hum Genet 16 (1) 317-329 [2013-02-00; online 2012-11-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Sequence variation in mitochondrialATPsynthase subunit 6 & 8and nuclear genesITS1andITS2in 17 cyprinid species

Demandt MH

J. Appl. Ichthyol. 29 (1) 278-280 [2013-02-00; online 2012-06-22]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Population pharmacokinetic modeling and deconvolution of enantioselective absorption of eflornithine in the rat

Johansson CC, Gennemark P, Artursson P, ..., Ashton M, Jansson-Löfmark R

J Pharmacokinet Pharmacodyn 40 (1) 117-128 [2013-02-00; online 2013-01-10]

Chemical Biology Consortium Sweden (CBCS) [Service]

Olfactory receptor 51E1 protein as a potential novel tissue biomarker for small intestine neuroendocrine carcinomas.

Cui T, Tsolakis AV, Li S, ..., Öberg K, Giandomenico V

Eur. J. Endocrinol. 168 (2) 253-261 [2013-02-00; online 2012-11-28]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

In vitro and in vivo activities of 2-aminopyrazines and 2-aminopyridines in experimental models of human African trypanosomiasis.

Vodnala SK, Lundbäck T, Sjöberg B, ..., Rottenberg ME, Hammarström LGJ

Antimicrob. Agents Chemother. 57 (2) 1012-1018 [2013-02-00; online 2012-12-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Genome-wide association analyses identify 18 new loci associated with serum urate concentrations.

Köttgen A, Albrecht E, Teumer A, ..., Bochud M, Gieger C

Nat. Genet. 45 (2) 145-154 [2013-02-00; online 2012-12-25]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

First insights into the syntrophic acetate-oxidizing bacteria--a genetic study.

Müller B, Sun L, Schnürer A

Microbiologyopen 2 (1) 35-53 [2013-02-00; online 2012-12-15]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Exome sequencing of prostate cancer supports the hypothesis of independent tumour origins.

Lindberg J, Klevebring D, Liu W, ..., Egevad L, Grönberg H

Eur. Urol. 63 (2) 347-353 [2013-02-00; online 2012-04-17]

Karolinska High Throughput Center (KHTC) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis.

Liu Y, Aryee MJ, Padyukov L, ..., Ekström TJ, Feinberg AP

Nat. Biotechnol. 31 (2) 142-147 [2013-02-00; online 2013-01-22]

Early-phase GVHD gene expression profile in target versus non-target tissues: kidney, a possible target?

Sadeghi B, Al-Chaqmaqchi H, Al-Hashmi S, ..., Moshfegh A, Hassan M

Bone Marrow Transplant. 48 (2) 284-293 [2013-02-00; online 2012-07-25]

Early cone setting in Picea abies acrocona is associated with increased transcriptional activity of a MADS box transcription factor.

Uddenberg D, Reimegård J, Clapham D, ..., Emanuelsson O, Sundström JF

Plant Physiol. 161 (2) 813-823 [2013-02-00; online 2012-12-12]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

An MBL-like protein may interfere with the activation of the proPO-system, an important innate immune reaction in invertebrates.

Wu C, Charoensapsri W, Nakamura S, ..., Söderhäll I, Söderhäll K

Immunobiology 218 (2) 159-168 [2013-02-00; online 2012-03-31]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Adipose tissue resting energy expenditure and expression of genes involved in mitochondrial function are higher in women than in men.

Nookaew I, Svensson PA, Jacobson P, ..., Nielsen J, Carlsson LM

J. Clin. Endocrinol. Metab. 98 (2) E370-E378 [2013-02-00; online 2012-12-25]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

A versatile genome-scale PCR-based pipeline for high-definition DNA FISH.

Bienko M, Crosetto N, Teytelman L, ..., Itzkovitz S, van Oudenaarden A

Nat. Methods 10 (2) 122-124 [2013-02-00; online 2012-12-23]

Advanced FISH Technologies [Technology development]

A gene-centric study of common carotid artery remodelling.

Harrison SC, Zabaneh D, Asselbergs FW, ..., Hamsten A, Humphries SE

Atherosclerosis 226 (2) 440-446 [2013-02-00; online 2012-12-19]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Workshop on laboratory protocol standards for the Molecular Methods Database.

Klingström T, Soldatova L, Stevens R, ..., Landegren U, Bongcam-Rudloff E

N Biotechnol 30 (2) 109-113 [2013-01-25; online 2012-06-02]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Protein tag-mediated conjugation of oligonucleotides to recombinant affinity binders for proximity ligation.

Gu GJ, Friedman M, Jost C, ..., Landegren U, Söderberg O

N Biotechnol 30 (2) 144-152 [2013-01-25; online 2012-06-06]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Multiplex protein detection with DNA readout via mass spectrometry.

Flanigon J, Kamali-Moghaddam M, Burbulis I, ..., Landegren U, Cantor C

N Biotechnol 30 (2) 153-158 [2013-01-25; online 2012-12-04]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

DNA methylation in the Neuropeptide S Receptor 1 (NPSR1) promoter in relation to asthma and environmental factors.

Reinius LE, Gref A, Sääf A, ..., Söderhäll C, Kere J

PLoS ONE 8 (1) e53877 [2013-01-23; online 2013-01-23]

Unveiling distribution patterns of freshwater phytoplankton by a next generation sequencing based approach.

Eiler A, Drakare S, Bertilsson S, ..., Znachor P, Lindström ES

PLoS ONE 8 (1) e53516 [2013-01-22; online 2013-01-22]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genomic insights into the atopic eczema-associated skin commensal yeast Malassezia sympodialis.

Gioti A, Nystedt B, Li W, ..., Heitman J, Scheynius A

MBio 4 (1) e00572-e00512 [2013-01-22; online 2013-01-22]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

DNA-binding specificities of human transcription factors.

Jolma A, Yan J, Whitington T, ..., Kivioja T, Taipale J

Cell 152 (1-2) 327-339 [2013-01-17; online 2013-01-22]

A genome-wide association study identifies genomic regions for virulence in the non-model organism Heterobasidion annosum s.s.

Dalman K, Himmelstrand K, Olson Å, ..., Brandström-Durling M, Stenlid J

PLoS ONE 8 (1) e53525 [2013-01-16; online 2013-01-16]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Meta-analysis investigating associations between healthy diet and fasting glucose and insulin levels and modification by loci associated with glucose homeostasis in data from 15 cohorts.

Nettleton JA, Hivert MF, Lemaitre RN, ..., Meigs JB, Franks PW

Am. J. Epidemiol. 177 (2) 103-115 [2013-01-15; online 2012-12-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data.

Teschendorff AE, Marabita F, Lechner M, ..., Gomez-Cabrero D, Beck S

Bioinformatics 29 (2) 189-196 [2013-01-15; online 2012-11-24]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Gene expression deregulation in postnatal skeletal muscle of TK2 deficient mice reveals a lower pool of proliferating myogenic progenitor cells.

Paredes JA, Zhou X, Höglund S, Karlsson A

PLoS ONE 8 (1) e53698 [2013-01-14; online 2013-01-14]

Exome RNA sequencing reveals rare and novel alternative transcripts.

Halvardson J, Zaghlool A, Feuk L

Nucleic Acids Res. 41 (1) e6 [2013-01-07; online 2012-08-31]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

RNA deep sequencing as a tool for selection of cell lines for systematic subcellular localization of all human proteins.

Danielsson F, Wiking M, Mahdessian D, ..., Uhlén M, Lundberg E

J. Proteome Res. 12 (1) 299-307 [2013-01-04; online 2012-12-12]

A chromosome-centric human proteome project (C-HPP) to characterize the sets of proteins encoded in chromosome 17.

Liu S, Im H, Bairoch A, ..., Beavis RC, Hancock WS

J. Proteome Res. 12 (1) 45-57 [2013-01-04; online 2012-12-25]

Biomarker discovery in non-small cell lung cancer: integrating gene expression profiling, meta-analysis, and tissue microarray validation.

Botling J, Edlund K, Lohr M, ..., Hengstler JG, Micke P

Clin. Cancer Res. 19 (1) 194-204 [2013-01-01; online 2012-10-02]

Array and Analysis Facility Tissue Profiling

Proceedings of the 15th International Congress on Circumpolar Health

International Journal of Circumpolar Health 72 (1) 22447 [2013-01-00; online 2013-08-05]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Non-heritable genetics of human disease: spotlight on post-zygotic genetic variation acquired during lifetime.

Forsberg LA, Absher D, Dumanski JP

J. Med. Genet. 50 (1) 1-10 [2013-01-00; online 2012-11-23]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Large-scale association analysis identifies new risk loci for coronary artery disease.

CARDIoGRAMplusC4D Consortium N, Deloukas P, Kanoni S, ..., Schunkert H, Samani NJ

Nat. Genet. 45 (1) 25-33 [2013-01-00; online 2012-12-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genome-wide profiling of target genes for the systemic lupus erythematosus-associated transcription factors IRF5 and STAT4.

Wang C, Sandling JK, Hagberg N, ..., Eloranta ML, Syvänen AC

Ann. Rheum. Dis. 72 (1) 96-103 [2013-01-00; online 2012-06-26]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

First Genome Sequence of a Syntrophic Acetate-Oxidizing Bacterium, Tepidanaerobacter acetatoxydans Strain Re1.

Manzoor S, Bongcam-Rudloff E, Schnürer A, Müller B

Genome Announc 1 (1) - [2013-01-00; online 2013-02-21]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

450K-array analysis of chronic lymphocytic leukemia cells reveals global DNA methylation to be relatively stable over time and similar in resting and proliferative compartments.

Cahill N, Bergh AC, Kanduri M, ..., Rosén A, Rosenquist R

Leukemia 27 (1) 150-158 [2013-01-00; online 2012-08-28]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The A-CD analogue of 16β,17α-estriol is a potent and highly selective estrogen receptor β agonist

Sauvée C, Schäfer A, Sundén H, ..., Burstein ES, Olsson R

Med. Chem. Commun. 4 (11) 1439 [2013-00-00; online 2013-00-00]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Nanoscale elucidation of Na,K-ATPase isoforms in dendritic spines

Liebmann T, Blom H, Aperia A, Brismar H

Optical Nanoscopy Opt Nanoscopy 2 (1) 6 [2013-00-00; online 2013-00-00]

Integrated Microscopy Technologies Stockholm [Technology development]

Powerful identification of cis-regulatory SNPs in human primary monocytes using allele-specific gene expression.

Almlöf JC, Lundmark P, Lundmark A, ..., Cambien F, Syvänen A

PLoS ONE 7 (12) e52260 [2012-12-26; online 2012-12-26]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Genomic diversity of the 2011 European outbreaks of Escherichia coli O104:H4.

Guy L, Jernberg C, Ivarsson S, ..., Engstrand L, Andersson SG

Proc. Natl. Acad. Sci. U.S.A. 109 (52) E3627-E3628 [2012-12-26; online 2012-12-19]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genome-wide sequencing for the identification of rearrangements associated with Tourette syndrome and obsessive-compulsive disorder.

Hooper SD, Johansson AC, Tellgren-Roth C, ..., Cavelier L, Feuk L

BMC Med. Genet. 13 (-) 123 [2012-12-19; online 2012-12-19]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Integration of genome-wide association studies with biological knowledge identifies six novel genes related to kidney function.

Chasman DI, Fuchsberger C, Pattaro C, ..., Fox CS, Köttgen A

Hum. Mol. Genet. 21 (24) 5329-5343 [2012-12-15; online 2012-09-11]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Chemical Biology Consortium Sweden (CBCS) [Service]

Berg L, Niemiec MS, Qian W, ..., Ekström F, Linusson A

Angew. Chem. Int. Ed. Engl. 51 (51) 12716-12720 [2012-12-14; online 2012-11-20]

Evidence for small RNAs homologous to effector-encoding genes and transposable elements in the oomycete Phytophthora infestans.

Vetukuri RR, Åsman AKM, Tellgren-Roth C, ..., Whisson SC, Dixelius C

PLoS ONE 7 (12) e51399 [2012-12-14; online 2012-12-14]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Novel missense mutation in the RSPO4 gene in congenital hyponychia and evidence for a polymorphic initiation codon (p.M1I).

Khan TN, Klar J, Nawaz S, ..., Baig SM, Dahl N

BMC Med. Genet. 13 (-) 120 [2012-12-13; online 2012-12-13]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Mice lacking a Myc enhancer that includes human SNP rs6983267 are resistant to intestinal tumors.

Sur IK, Hallikas O, Vähärautio A, ..., Aaltonen LA, Taipale J

Science 338 (6112) 1360-1363 [2012-12-07; online 2012-11-03]

EGFR gene variants are associated with specific somatic aberrations in glioma.

Wibom C, Ghasimi S, Van Loo P, ..., Rydén P, Melin B

PLoS ONE 7 (12) e47929 [2012-12-07; online 2012-12-07]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Symptomatic atherosclerosis is associated with an altered gut metagenome.

Karlsson FH, Fåk F, Nookaew I, ..., Bäckhed F, Nielsen J

Nat Commun 3 (-) 1245 [2012-12-06; online 2012-12-06]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genome-wide association study for circulating levels of PAI-1 provides novel insights into its regulation.

Huang J, Sabater-Lleal M, Asselbergs FW, ..., O'Donnell CJ, Hamsten A

Blood 120 (24) 4873-4881 [2012-12-06; online 2012-09-20]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Interferometry and Fluorescence Detection for Simultaneous Analysis of Labeled and Unlabeled Nanoparticles in Solution

Wennmalm S, Widengren J

J. Am. Chem. Soc. 134 (48) 19516-19519 [2012-12-05; online 2012-11-16]

Fluorescence Correlation Spectroscopy [Service]

Distinct transcriptional control in major immunogenetic subsets of chronic lymphocytic leukemia exhibiting subset-biased global DNA methylation profiles.

Kanduri M, Marincevic M, Halldórsdóttir AM, ..., Stamatopoulos K, Rosenquist R

Epigenetics 7 (12) 1435-1442 [2012-12-01; online 2012-11-17]

Transcription factor PROX1: its role in development and cancer.

Elsir T, Smits A, Lindström MS, Nistér M

Cancer Metastasis Rev. 31 (3-4) 793-805 [2012-12-00; online 2012-06-27]

The impact of intronic single nucleotide polymorphisms and ethnic diversity for studies on the obesity gene FTO.

Jacobsson JA, Schiöth HB, Fredriksson R

Obes Rev 13 (12) 1096-1109 [2012-12-00; online 2012-08-31]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

PCR-based multiparametric assays in single cells.

Darmanis S, Gallant C, Landegren U

Clin. Chem. 58 (12) 1618-1619 [2012-12-00; online 2012-10-17]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism and age at onset of schizophrenia: no consistent evidence for an association in the Nordic population.

Saetre P, Grove J, Børglum AD, ..., Terenius L, Jönsson EG

Am. J. Med. Genet. B Neuropsychiatr. Genet. 159B (8) 981-986 [2012-12-00; online 2012-10-19]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Integration of genetics into a systems model of electrocardiographic traits using HumanCVD BeadChip.

Gaunt TR, Shah S, Nelson CP, ..., Kumari M, Day IN

Circ Cardiovasc Genet 5 (6) 630-638 [2012-12-00; online 2012-11-10]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Insights into p53 transcriptional function via genome-wide chromatin occupancy and gene expression analysis.

Nikulenkov F, Spinnler C, Li H, ..., Taipale J, Selivanova G

Cell Death Differ. 19 (12) 1992-2002 [2012-12-00; online 2012-07-14]

Identification of the BCAR1-CFDP1-TMEM170A locus as a determinant of carotid intima-media thickness and coronary artery disease risk.

Gertow K, Sennblad B, Strawbridge RJ, ..., Humphries SE, Hamsten A

Circ Cardiovasc Genet 5 (6) 656-665 [2012-12-00; online 2012-11-16]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

High-resolution mapping of linear antibody epitopes using ultrahigh-density peptide microarrays.

Buus S, Rockberg J, Forsström B, ..., Uhlen M, Schafer-Nielsen C

Mol. Cell Proteomics 11 (12) 1790-1800 [2012-12-00; online 2012-09-18]

High-density genetic mapping identifies new susceptibility loci for rheumatoid arthritis.

Eyre S, Bowes J, Diogo D, ..., Gregersen PK, Worthington J

Nat. Genet. 44 (12) 1336-1340 [2012-12-00; online 2012-11-13]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genome sequence of Francisella tularensis subspecies holarctica strain FSC200, isolated from a child with tularemia.

Svensson K, Sjödin A, Byström M, ..., Larsson P, Johansson A

J. Bacteriol. 194 (24) 6965-6966 [2012-12-00; online 2012-12-05]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Evolution from the prokaryotic to the higher plant chloroplast signal recognition particle: the signal recognition particle RNA is conserved in plastids of a wide range of photosynthetic organisms.

Träger C, Rosenblad MA, Ziehe D, ..., Aronsson H, Schünemann D

Plant Cell 24 (12) 4819-4836 [2012-12-00; online 2012-12-28]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Epitope-specificity of recombinant antibodies reveals promiscuous peptide-binding properties.

Olsson N, Wallin S, James P, Borrebaeck CA, Wingren C

Protein Sci. 21 (12) 1897-1910 [2012-12-00; online 2012-10-05]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

A genome-wide association study of monozygotic twin-pairs suggests a locus related to variability of serum high-density lipoprotein cholesterol.

Surakka I, Whitfield JB, Perola M, ..., Peltonen L, GenomEUtwin Project N

Twin Res Hum Genet 15 (6) 691-699 [2012-12-00; online 2012-10-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Automated analysis and reannotation of subcellular locations in confocal images from the Human Protein Atlas.

Li J, Newberg JY, Uhlén M, Lundberg E, Murphy RF

PLoS ONE 7 (11) e50514 [2012-11-30; online 2012-11-30]

The genomic landscape of species divergence in Ficedula flycatchers.

Ellegren H, Smeds L, Burri R, ..., Uebbing S, Wolf JB

Nature 491 (7426) 756-760 [2012-11-29; online 2012-10-30]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Estimating microtubule distributions from 2D immunofluorescence microscopy images reveals differences among human cultured cell lines.

Li J, Shariff A, Wiking M, ..., Rohde GK, Murphy RF

PLoS ONE 7 (11) e50292 [2012-11-28; online 2012-11-28]

Strong signatures of selection in the domestic pig genome.

Rubin C, Megens H, Martinez Barrio A, ..., Groenen MAM, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 109 (48) 19529-19536 [2012-11-27; online 2012-11-16]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Sequence based analysis of U-2973, a cell line established from a double-hit B-cell lymphoma with concurrent MYC and BCL2 rearrangements.

Hooper SD, Jiao X, Sundström E, ..., Sjöblom T, Cavelier L

BMC Res Notes 5 (-) 648 [2012-11-22; online 2012-11-22]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The plant short-chain dehydrogenase (SDR) superfamily: genome-wide inventory and diversification patterns.

Moummou H, Kallberg Y, Tonfack LB, Persson B, van der Rest B

BMC Plant Biol. 12 (-) 219 [2012-11-20; online 2012-11-20]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Population-scale sequencing reveals genetic differentiation due to local adaptation in Atlantic herring.

Lamichhaney S, Martinez Barrio A, Rafati N, ..., Ryman N, Andersson L

Proc. Natl. Acad. Sci. U.S.A. 109 (47) 19345-19350 [2012-11-20; online 2012-11-09]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Polymorphisms in peptidylarginine deiminase associate with rheumatoid arthritis in diverse Asian populations: evidence from MyEIRA study and meta-analysis.

Too CL, Murad S, Dhaliwal JS, ..., Klareskog L, Padyukov L

Arthritis Res. Ther. 14 (6) R250 [2012-11-19; online 2012-11-19]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Comprehensive analysis of the genome transcriptome and proteome landscapes of three tumor cell lines.

Akan P, Alexeyenko A, Costea PI, ..., Uhlén M, Lundeberg J

Genome Med 4 (11) 86 [2012-11-18; online 2012-11-18]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics

CD99 is a novel prognostic stromal marker in non-small cell lung cancer.

Edlund K, Lindskog C, Saito A, ..., Ostman A, Micke P

Int. J. Cancer 131 (10) 2264-2273 [2012-11-15; online 2012-03-07]

Array and Analysis Facility Tissue Profiling

Genetic variants and associations of 25-hydroxyvitamin D concentrations with major clinical outcomes.

Levin GP, Robinson-Cohen C, de Boer IH, ..., Siscovick D, Kestenbaum B

JAMA 308 (18) 1898-1905 [2012-11-14; online 2012-11-15]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Library preparation and multiplex capture for massive parallel sequencing applications made efficient and easy.

Neiman M, Sundling S, Grönberg H, ..., Lindberg J, Klevebring D

PLoS ONE 7 (11) e48616 [2012-11-05; online 2012-11-05]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A 2nd generation linkage map of Heterobasidion annosum s.l. based on in silico anchoring of AFLP markers.

Lind M, van der Nest M, Olson Å, Brandström-Durling M, Stenlid J

PLoS ONE 7 (11) e48347 [2012-11-05; online 2012-11-05]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms.

Chen J, Uebbing S, Gyllenstrand N, ..., Lascoux M, Källman T

BMC Genomics 13 (-) 589 [2012-11-02; online 2012-11-02]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.

Nookaew I, Papini M, Pornputtapong N, ..., Uhlén M, Nielsen J

Nucleic Acids Res. 40 (20) 10084-10097 [2012-11-01; online 2012-09-12]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Unexpected T-cell recognition of an altered peptide ligand is driven by reversed thermodynamics.

Allerbring EB, Duru AD, Uchtenhagen H, ..., Nygren PÅ, Achour A

Eur. J. Immunol. 42 (11) 2990-3000 [2012-11-00; online 2012-07-28]

Transcriptional profiling of human glioblastoma vessels indicates a key role of VEGF-A and TGFβ2 in vascular abnormalization.

Dieterich LC, Mellberg S, Langenkamp E, ..., Alafuzoff I, Dimberg A

J. Pathol. 228 (3) 378-390 [2012-11-00; online 2012-07-13]

Array and Analysis Facility Tissue Profiling

TPX2 and AURKA promote 20q amplicon-driven colorectal adenoma to carcinoma progression.

Sillars-Hardebol AH, Carvalho B, Tijssen M, ..., Fijneman RJ, Meijer GA

Gut 61 (11) 1568-1575 [2012-11-00; online 2011-12-31]

Reclassification of the Candida haemulonii complex as Candida haemulonii (C. haemulonii group I), C. duobushaemulonii sp. nov. (C. haemulonii group II), and C. haemulonii var. vulnera var. nov.: three multiresistant human pathogenic yeasts.

Cendejas-Bueno E, Kolecka A, Alastruey-Izquierdo A, ..., Gómez-López A, Boekhout T

J. Clin. Microbiol. 50 (11) 3641-3651 [2012-11-00; online 2012-09-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

2-[4,5-Difluoro-2-(2-fluorobenzoylamino)-benzoylamino]benzoic acid, an antiviral compound with activity against acyclovir-resistant isolates of herpes simplex virus types 1 and 2.

Strand M, Islam K, Edlund K, ..., Elofsson M, Wadell G

Antimicrob. Agents Chemother. 56 (11) 5735-5743 [2012-11-00; online 2012-08-22]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Human cord blood derived immature basophils show dual characteristics, expressing both basophil and eosinophil associated proteins.

Grundström J, Reimer JM, Magnusson SE, ..., Wernersson S, Hellman L

PLoS ONE 7 (10) e48308 [2012-10-31; online 2012-10-31]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs.

Solnestam BW, Stranneheim H, Hällman J, ..., Lundeberg J, Akan P

BMC Genomics 13 (-) 574 [2012-10-30; online 2012-10-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics

Secretagogin is expressed in sensory CGRP neurons and in spinal cord of mouse and complements other calcium-binding proteins, with a note on rat and human.

Shi TJ, Xiang Q, Zhang MD, ..., Harkany T, Hökfelt T

Mol Pain 8 (-) 80 [2012-10-29; online 2012-10-29]

Strategy for minimizing between-study variation of large-scale phenotypic experiments using multivariate analysis.

Pinto RC, Gerber L, Eliasson M, Sundberg B, Trygg J

Anal. Chem. 84 (20) 8675-8681 [2012-10-16; online 2012-09-18]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Chromosome 1p13 genetic variants antagonize the risk of myocardial infarction associated with high ApoB serum levels.

Gigante B, Leander K, Vikström M, Ye S, de Faire U

BMC Cardiovasc Disord 12 (-) 90 [2012-10-16; online 2012-10-16]

A novel mutation in the Lipase H gene underlies autosomal recessive hypotrichosis and woolly hair.

Tariq M, Azhar A, Baig SM, Dahl N, Klar J

Sci Rep 2 (-) 730 [2012-10-12; online 2012-10-12]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The Pseudomonas aeruginosa N-acylhomoserine lactone quorum sensing molecules target IQGAP1 and modulate epithelial cell migration.

Karlsson T, Turkina MV, Yakymenko O, Magnusson K, Vikström E

PLoS Pathog. 8 (10) e1002953 [2012-10-11; online 2012-10-11]

Integrated Microscopy Technologies Stockholm [Service]

Multiply-primed rolling circle amplification of human papillomavirus using sequence-specific primers.

Marincevic-Zuniga Y, Gustavsson I, Gyllensten U

Virology 432 (1) 57-62 [2012-10-10; online 2012-06-29]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Scheffersomyces stipitis: a comparative systems biology study with the Crabtree positive yeast Saccharomyces cerevisiae.

Papini M, Nookaew I, Uhlén M, Nielsen J

Microb. Cell Fact. 11 (-) 136 [2012-10-09; online 2012-10-09]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Proteomic analysis reveals drug accessible cell surface N-glycoproteins of primary and established glioblastoma cell lines.

Bock T, Moest H, Omasits U, ..., Frei K, Wollscheid B

J. Proteome Res. 11 (10) 4885-4893 [2012-10-05; online 2012-08-23]

Multiplex epitope mapping using bacterial surface display reveals both linear and conformational epitopes.

Hudson EP, Uhlen M, Rockberg J

Sci Rep 2 (-) 706 [2012-10-04; online 2012-10-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

PubMed

The science of librarianship. University of Wales at Aberystwyth, July 31, 1917.

Osler W

J Med Libr Assoc 100 (4 Suppl) A [2012-10-00; online 2013-03-21]

Clinical Genomics [Service] Clinical Genomics Linköping [Service]

Selected polymorphisms in sex hormone-related genes, circulating sex hormones and risk of endometrial cancer.

Lundin E, Wirgin I, Lukanova A, ..., Shore RE, Zeleniuch-Jacquotte A

Cancer Epidemiol 36 (5) 445-452 [2012-10-00; online 2012-05-29]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

MicroRNAs in Amoebozoa: deep sequencing of the small RNA population in the social amoeba Dictyostelium discoideum reveals developmentally regulated microRNAs.

Avesson L, Reimegård J, Wagner EGH, Söderbom F

RNA 18 (10) 1771-1782 [2012-10-00; online 2012-08-10]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Mapping QTL affecting a systemic sclerosis-like disorder in a cross between UCD-200 and red jungle fowl chickens.

Ek W, Sahlqvist AS, Crooks L, ..., Kämpe O, Kerje S

Dev. Comp. Immunol. 38 (2) 352-359 [2012-10-00; online 2012-07-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Lack of association between the regulator of G-protein signaling 4 (RGS4) rs951436 polymorphism and schizophrenia.

Jönsson EG, Saetre P, Nyholm H, ..., Agartz I, Terenius L

Psychiatr. Genet. 22 (5) 263-264 [2012-10-00; online 2011-12-14]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

High-resolution insights into binding of unfolded polypeptides by the PPIase chaperone SlpA.

Quistgaard EM, Nordlund P, Löw C

FASEB J. 26 (10) 4003-4013 [2012-10-00; online 2012-06-28]

Genetic variation in Puccinia graminis collected from oats, rye, and barberry.

Berlin A, Djurle A, Samils B, Yuen J

Phytopathology 102 (10) 1006-1012 [2012-10-00; online 2012-06-28]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PubMed

Evaluating the effectiveness of clinical medical librarian programs: a systematic review of the literature. J Med Libr Assoc 92(1) January 2004.

Wagner KC, Byrd GD

J Med Libr Assoc 100 (4 Suppl) J [2012-10-00; online 2013-03-21]

Clinical Genomics [Service] Clinical Genomics Lund [Service]

D-amino acid oxidase activator gene (DAOA) variation affects cerebrospinal fluid homovanillic acid concentrations in healthy Caucasians.

Andreou D, Saetre P, Werge T, ..., Terenius L, Jönsson EG

Eur Arch Psychiatry Clin Neurosci 262 (7) 549-556 [2012-10-00; online 2012-03-29]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Consistent mutation status within histologically heterogeneous lung cancer lesions.

Mattsson JS, Imgenberg-Kreuz J, Edlund K, Botling J, Micke P

Histopathology 61 (4) 744-748 [2012-10-00; online 2012-03-31]

Chemosensory proteins, major salivary factors in caterpillar mandibular glands.

Celorio-Mancera Mde L, Sundmalm SM, Vogel H, ..., Zubarev RA, Janz N

Insect Biochem. Mol. Biol. 42 (10) 796-805 [2012-10-00; online 2012-08-14]

On the roles and regulation of chondroitin sulfate and heparan sulfate in zebrafish pharyngeal cartilage morphogenesis.

Holmborn K, Habicher J, Kasza Z, ..., Kreuger J, Ledin J

J. Biol. Chem. 287 (40) 33905-33916 [2012-09-28; online 2012-08-06]

Genome-wide and locus specific alterations in CDC73/HRPT2-mutated parathyroid tumors.

Sulaiman L, Haglund F, Hashemi J, ..., Larsson C, Juhlin CC

PLoS ONE 7 (9) e46325 [2012-09-28; online 2012-09-28]

Gene expression profiles in paired gingival biopsies from periodontitis-affected and healthy tissues revealed by massively parallel sequencing.

Davanian H, Stranneheim H, Båge T, ..., Lundeberg J, Yucel-Lindberg T

PLoS ONE 7 (9) e46440 [2012-09-28; online 2012-09-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Microscopic particles in two fractions of fresh cerebrospinal fluid in twins with schizophrenia or bipolar disorder and in healthy controls.

Johansson V, Nybom R, Wetterberg L, ..., Ekman CJ, Landén M

PLoS ONE 7 (9) e45994 [2012-09-25; online 2012-09-25]

Elevated MARK2-dependent phosphorylation of Tau in Alzheimer's disease.

Gu GJ, Wu D, Lund H, ..., Landegren U, Kamali-Moghaddam M

J. Alzheimers Dis. 33 (3) 699-713 [2012-09-25; online 2012-09-25]

Affinity Proteomics Uppsala [Technology development] Clinical Biomarkers PLA and Single Cell Proteomics

Comprehensive exploration of the effects of miRNA SNPs on monocyte gene expression.

Greliche N, Zeller T, Wild PS, ..., Blankenberg S, Trégouët DA

PLoS ONE 7 (9) e45863 [2012-09-21; online 2012-09-21]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Role of sepsis in the development of limb muscle weakness in a porcine intensive care unit model.

Aare S, Radell P, Eriksson LI, ..., Hoffman EP, Larsson L

Physiol. Genomics 44 (18) 865-877 [2012-09-18; online 2012-08-02]

Molecular tools for companion diagnostics.

Zieba A, Grannas K, Söderberg O, ..., Nilsson M, Landegren U

N Biotechnol 29 (6) 634-640 [2012-09-15; online 2012-05-24]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Catalytic convergence of manganese and iron lipoxygenases by replacement of a single amino acid.

Wennman A, Jernerén F, Hamberg M, Oliw EH

J. Biol. Chem. 287 (38) 31757-31765 [2012-09-14; online 2012-07-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Discovery of Ligands for ADP-Ribosyltransferases via Docking-Based Virtual Screening

Andersson CD, Karlberg T, Ekblad T, ..., Schüler H, Linusson A

J. Med. Chem. 55 (17) 7706-7718 [2012-09-13; online 2012-09-13]

Chemical Biology Consortium Sweden (CBCS) [Service] Protein Science Facility (PSF)

Loss-of-heterozygosity on chromosome 19q in early-stage serous ovarian cancer is associated with recurrent disease.

Skirnisdottir I, Mayrhofer M, Rydåker M, Akerud H, Isaksson A

BMC Cancer 12 (-) 407 [2012-09-12; online 2012-09-12]

GCH1-polymorphism and pain sensitivity among women with provoked vestibulodynia.

Heddini U, Bohm-Starke N, Grönbladh A, ..., Nilsson KW, Johannesson U

Mol Pain 8 (-) 68 [2012-09-12; online 2012-09-12]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Evolutionary conservation of the ribosomal biogenesis factor Rbm19/Mrd1: implications for function.

Kallberg Y, Segerstolpe Å, Lackmann F, Persson B, Wieslander L

PLoS ONE 7 (9) e43786 [2012-09-12; online 2012-09-12]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

A tool to facilitate clinical biomarker studies--a tissue dictionary based on the Human Protein Atlas.

Kampf C, Bergman J, Oksvold P, ..., Uhlén M, Ponten F

BMC Med 10 (-) 103 [2012-09-12; online 2012-09-12]

Identification of candidate SNPs for drug induced toxicity from differentially expressed genes in associated tissues.

Hasmats J, Kupershmidt I, Rodríguez-Antona C, ..., Lundeberg J, Green H

Gene 506 (1) 62-68 [2012-09-10; online 2012-07-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences

Nilsson RH, Tedersoo L, Abarenkov K, ..., Larsson E, Kõljalg U

MycoKeys 4 (-) 37-63 [2012-09-05; online 2012-09-05]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Improved gap size estimation for scaffolding algorithms.

Sahlin K, Street N, Lundeberg J, Arvestad L

Bioinformatics 28 (17) 2215-2222 [2012-09-01; online 2012-08-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The evolution of filamin-a protein domain repeat perspective.

Light S, Sagit R, Ithychanda SS, Qin J, Elofsson A

J. Struct. Biol. 179 (3) 289-298 [2012-09-00; online 2012-03-15]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Stepping stones in DNA sequencing.

Stranneheim H, Lundeberg J

Biotechnol J 7 (9) 1063-1073 [2012-09-00; online 2012-08-08]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes.

Morris AP, Voight BF, Teslovich TM, ..., McCarthy MI, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium

Nat. Genet. 44 (9) 981-990 [2012-09-00; online 2012-08-14]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Large-scale association analyses identify new loci influencing glycemic traits and provide insight into the underlying biological pathways.

Scott RA, Lagou V, Welch RP, ..., Prokopenko I, Barroso I

Nat. Genet. 44 (9) 991-1005 [2012-09-00; online 2012-08-14]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Global transcriptional response to ISCOM-Matrix adjuvant at the site of administration and in the draining lymph node early after intramuscular injection in pigs.

Ahlberg V, Lövgren Bengtsson K, Wallgren P, Fossum C

Dev. Comp. Immunol. 38 (1) 17-26 [2012-09-00; online 2012-03-20]

Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice.

Andersson LS, Larhammar M, Memic F, ..., Andersson L, Kullander K

Nature 488 (7413) 642-646 [2012-08-30; online 2012-08-31]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A sexual ornament in chickens is affected by pleiotropic alleles at HAO1 and BMP2, selected during domestication.

Johnsson M, Gustafson I, Rubin C, ..., Jensen P, Wright D

PLoS Genet. 8 (8) e1002914 [2012-08-30; online 2012-08-30]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Validation of whole genome amplification for analysis of the p53 tumor suppressor gene in limited amounts of tumor samples.

Hasmats J, Green H, Solnestam BW, ..., Bjursell M, Lundeberg J

Biochem. Biophys. Res. Commun. 425 (2) 379-383 [2012-08-24; online 2012-07-31]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

MicroRNA-125b down-regulates matrix metallopeptidase 13 and inhibits cutaneous squamous cell carcinoma cell proliferation, migration, and invasion.

Xu N, Zhang L, Meisgen F, ..., Sonkoly E, Pivarcsi A

J. Biol. Chem. 287 (35) 29899-29908 [2012-08-24; online 2012-07-12]

Use of allele-specific FAIRE to determine functional regulatory polymorphism using large-scale genotyping arrays.

Smith AJ, Howard P, Shah S, ..., Talmud PJ, Humphries SE

PLoS Genet. 8 (8) e1002908 [2012-08-16; online 2012-08-16]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Expression analysis in multiple muscle groups and serum reveals complexity in the microRNA transcriptome of the mdx mouse with implications for therapy.

Roberts TC, Blomberg KE, McClorey G, ..., Smith CI, Wood MJ

Mol Ther Nucleic Acids 1 (-) e39 [2012-08-14; online 2012-08-14]

Evidence of association between interferon regulatory factor 5 gene polymorphisms and asthma.

Wang C, Rose-Zerilli MJ, Koppelman GH, ..., Syvänen AC, Dideberg V

Gene 504 (2) 220-225 [2012-08-10; online 2012-05-23]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Proteomic screen reveals Fbw7 as a modulator of the NF-κB pathway.

Arabi A, Ullah K, Branca RM, ..., Lehtiö J, Sangfelt O

Nat Commun 3 (-) 976 [2012-08-07; online 2012-08-07]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Platelet-derived growth factor over-expression in retinal progenitors results in abnormal retinal vessel formation.

Edqvist PH, Niklasson M, Vidal-Sanz M, Hallböök F, Forsberg-Nilsson K

PLoS ONE 7 (8) e42488 [2012-08-03; online 2012-08-03]

Erlin-2 is associated with active γ-secretase in brain and affects amyloid β-peptide production.

Teranishi Y, Hur JY, Gu GJ, ..., Frykman S, Tjernberg LO

Biochem. Biophys. Res. Commun. 424 (3) 476-481 [2012-08-03; online 2012-07-10]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Loss of cancer drug activity in colon cancer HCT-116 cells during spheroid formation in a new 3-D spheroid cell culture system.

Karlsson H, Fryknäs M, Larsson R, Nygren P

Exp. Cell Res. 318 (13) 1577-1585 [2012-08-01; online 2012-04-11]

Unraveling assembly of stream biofilm communities.

Besemer K, Peter H, Logue JB, ..., Tranvik LJ, Battin TJ

ISME J 6 (8) 1459-1468 [2012-08-00; online 2012-01-13]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The novel tyrosine kinase inhibitor AKN-028 has significant antileukemic activity in cell lines and primary cultures of acute myeloid leukemia

Eriksson A, Hermanson M, Wickström M, ..., Parrow V, Höglund M

Blood Cancer J 2 (8) e81 [2012-08-00; online 2012-08-00]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Quantitative proteomics targeting classes of motif-containing peptides using immunoaffinity-based mass spectrometry.

Olsson N, James P, Borrebaeck CA, Wingren C

Mol. Cell Proteomics 11 (8) 342-354 [2012-08-00; online 2012-05-01]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

QTL and quantitative genetic analysis of beak morphology reveals patterns of standing genetic variation in an Estrildid finch.

Knief U, Schielzeth H, Kempenaers B, Ellegren H, Forstmeier W

Mol. Ecol. 21 (15) 3704-3717 [2012-08-00; online 2012-06-15]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Polymorphisms in sh2b1 and spns1 loci are associated with triglyceride levels in a healthy population in northern Sweden.

Västermark Å, Jacobsson JA, Johansson Å, ..., Gyllensten U, Schiöth HB

J. Genet. 91 (2) 237-240 [2012-08-00; online 2012-09-04]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Long noncoding RNA-mediated maintenance of DNA methylation and transcriptional gene silencing.

Mohammad F, Pandey GK, Mondal T, ..., Gyllensten U, Kanduri C

Development 139 (15) 2792-2803 [2012-08-00; online 2012-06-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Intractable epilepsy of infancy due to homozygous mutation in the EFHC1 gene.

Berger I, Dor T, Halvardson J, ..., Feuk L, Elpeleg O

Epilepsia 53 (8) 1436-1440 [2012-08-00; online 2012-06-12]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Impact of common variation in bone-related genes on type 2 diabetes and related traits.

Billings LK, Hsu YH, Ackerman RJ, ..., Kiel DP, Florez JC

Diabetes 61 (8) 2176-2186 [2012-08-00; online 2012-06-16]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Evidence-based approach to assess passive diffusion and carrier-mediated drug transport

Di L, Artursson P, Avdeef A, ..., Lennernäs H, Sugano K

Drug Discovery Today 17 (15-16) 905-912 [2012-08-00; online 2012-08-00]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Design, synthesis and evaluation of triazole functionalized ring-fused 2-pyridones as antibacterial agents.

Bengtsson C, Lindgren AEG, Uvell H, Almqvist F

Eur J Med Chem 54 (-) 637-646 [2012-08-00; online 2012-07-04]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Compensatory mutations in agrC partly restore fitness in vitro to peptide deformylase inhibitor-resistant Staphylococcus aureus.

Zorzet A, Andersen JM, Nilsson AI, Møller NF, Andersson DI

J. Antimicrob. Chemother. 67 (8) 1835-1842 [2012-08-00; online 2012-05-12]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A-to-I editing of microRNAs in the mammalian brain increases during development.

Ekdahl Y, Farahani HS, Behm M, Lagergren J, Öhman M

Genome Res. 22 (8) 1477-1487 [2012-08-00; online 2012-05-31]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

A genome-wide association study identifies KNG1 as a genetic determinant of plasma factor XI Level and activated partial thromboplastin time.

Sabater-Lleal M, Martinez-Perez A, Buil A, ..., Hamsten A, Soria JM

Arterioscler. Thromb. Vasc. Biol. 32 (8) 2008-2016 [2012-08-00; online 2012-06-16]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Polyploidy and the evolution of complex traits.

Huminiecki L, Conant GC

Int J Evol Biol 2012 (-) 292068 [2012-07-30; online 2012-07-30]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility.

Reinius LE, Acevedo N, Joerink M, ..., Scheynius A, Kere J

PLoS ONE 7 (7) e41361 [2012-07-25; online 2012-07-25]

The presence of tumor associated macrophages in tumor stroma as a prognostic marker for breast cancer patients.

Medrek C, Pontén F, Jirström K, Leandersson K

BMC Cancer 12 (-) 306 [2012-07-23; online 2012-07-23]

Functional analysis of two PLA2G2A variants associated with secretory phospholipase A2-IIA levels.

Exeter HJ, Folkersen L, Palmen J, ..., Humphries SE, Talmud PJ

PLoS ONE 7 (7) e41139 [2012-07-17; online 2012-07-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Small molecule screening for inhibitors of the YopH phosphatase of Yersinia pseudotuberculosis.

Eriksson J, Grundström C, Sauer-Eriksson AE, ..., Wolf-Watz H, Elofsson M

Adv. Exp. Med. Biol. 954 (-) 357-363 [2012-07-12; online 2012-07-12]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Profiling cellular protein complexes by proximity ligation with dual tag microarray readout.

Hammond M, Nong RY, Ericsson O, Pardali K, Landegren U

PLoS ONE 7 (7) e40405 [2012-07-10; online 2012-07-10]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Automated selected reaction monitoring software for accurate label-free protein quantification.

Teleman J, Karlsson C, Waldemarson S, ..., Malmström J, Levander F

J. Proteome Res. 11 (7) 3766-3773 [2012-07-06; online 2012-06-05]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Ethanol effects on apparent solubility of poorly soluble drugs in simulated intestinal fluid.

Fagerberg JH, Al-Tikriti Y, Ragnarsson G, Bergström CAS

Mol. Pharm. 9 (7) 1942-1952 [2012-07-02; online 2012-06-02]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Polymorphisms and variants in the prion protein sequence of European moose (Alces alces), reindeer (Rangifer tarandus), roe deer (Capreolus capreolus) and fallow deer (Dama dama) in Scandinavia.

Wik L, Mikko S, Klingeborn M, ..., Simonsson M, Linné T

Prion 6 (3) 256-260 [2012-07-01; online 2012-03-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The role of obesity-related genetic loci in insulin sensitivity.

Fall T, Arnlöv J, Berne C, Ingelsson E

Diabet. Med. 29 (7) e62-e66 [2012-07-00; online 2012-03-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Pain sensitivity and opioid analgesia: a pharmacogenomic twin study.

Angst MS, Phillips NG, Drover DR, ..., Lazzeroni LC, Clark JD

Pain 153 (7) 1397-1409 [2012-07-00; online 2012-03-27]

Next generation RNA-sequencing in prognostic subsets of chronic lymphocytic leukemia.

Mansouri L, Gunnarsson R, Sutton LA, ..., Gyllensten U, Rosenquist R

Am. J. Hematol. 87 (7) 737-740 [2012-07-00; online 2012-06-03]

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Intercellular variation in signaling through the TGF-β pathway and its relation to cell density and cell cycle phase.

Zieba A, Pardali K, Söderberg O, ..., Heldin CH, Landegren U

Mol. Cell Proteomics 11 (7) M111.013482 [2012-07-00; online 2012-03-24]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Ichthyin/NIPAL4 localizes to keratins and desmosomes in epidermis and Ichthyin mutations affect epidermal lipid metabolism.

Dahlqvist J, Westermark GT, Vahlquist A, Dahl N

Arch. Dermatol. Res. 304 (5) 377-386 [2012-07-00; online 2012-01-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Heterozygosity-fitness correlations in zebra finches: microsatellite markers can be better than their reputation.

Forstmeier W, Schielzeth H, Mueller JC, Ellegren H, Kempenaers B

Mol. Ecol. 21 (13) 3237-3249 [2012-07-00; online 2012-05-05]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Effects of redox modulation by inhibition of thioredoxin reductase on radiosensitivity and gene expression.

Selenius M, Hedman M, Brodin D, ..., Björnstedt M, Fernandes AP

J. Cell. Mol. Med. 16 (7) 1593-1605 [2012-07-00; online 2011-10-19]

Aversive and reinforcing opioid effects: a pharmacogenomic twin study.

Angst MS, Lazzeroni LC, Phillips NG, ..., Swan GE, Clark JD

Anesthesiology 117 (1) 22-37 [2012-07-00; online 2012-06-21]

Antibodies for profiling the human proteome-The Human Protein Atlas as a resource for cancer research.

Asplund A, Edqvist PH, Schwenk JM, Pontén F

Proteomics 12 (13) 2067-2077 [2012-07-00; online 2012-05-25]

Affinity Proteomics Stockholm [Technology development] Tissue Profiling

1012 Synergistic Effects of PI3K or P38 MAPK Inhibition in Combination With Vandetanib Treatment in Glioblastoma Cells

Sooman L, Ekman S, Andersson C, ..., Lennartsson J, Gullbo J

European Journal of Cancer 48 (-) S244 [2012-07-00; online 2012-07-00]

Preferential genome targeting of the CBP co-activator by Rel and Smad proteins in early Drosophila melanogaster embryos.

Holmqvist P, Boija A, Philip P, ..., Stenberg P, Mannervik M

PLoS Genet. 8 (6) e1002769 [2012-06-21; online 2012-06-21]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Geographic differences in genetic susceptibility to IgA nephropathy: GWAS replication study and geospatial risk analysis.

Kiryluk K, Li Y, Sanna-Cherchi S, ..., Lifton RP, Gharavi AG

PLoS Genet. 8 (6) e1002765 [2012-06-21; online 2012-06-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Visualising individual sequence-specific protein-DNA interactions in situ.

Weibrecht I, Gavrilovic M, Lindbom L, ..., Wählby C, Söderberg O

N Biotechnol 29 (5) 589-598 [2012-06-15; online 2011-09-13]

Affinity Proteomics Uppsala [Collaborative] BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] PLA and Single Cell Proteomics

Validation of affinity reagents using antigen microarrays.

Sjöberg R, Sundberg M, Gundberg A, ..., Uhlén M, Nilsson P

N Biotechnol 29 (5) 555-563 [2012-06-15; online 2011-12-03]

Autoimmunity and Serology Profiling [Technology development]

Local contamination in relation to population genetic diversity and resilience of an arctic marine amphipod.

Bach L, Dahllöf I

Aquat. Toxicol. 114-115 (-) 58-66 [2012-06-15; online 2012-03-17]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Classification of protein profiles from antibody microarrays using heat and detergent treatment.

Häggmark A, Neiman M, Drobin K, ..., Nilsson P, Schwenk JM

N Biotechnol 29 (5) 564-570 [2012-06-15; online 2011-10-26]

Affinity Proteomics Stockholm [Technology development]

Data-driven unbiased curation of the TP53 tumor suppressor gene mutation database and validation by ultradeep sequencing of human tumors.

Edlund K, Larsson O, Ameur A, ..., Botling J, Soussi T

Proc. Natl. Acad. Sci. U.S.A. 109 (24) 9551-9556 [2012-06-12; online 2012-05-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Integrative approach to pain genetics identifies pain sensitivity loci across diseases.

Ruau D, Dudley JT, Chen R, ..., Butte AJ, Angst MS

PLoS Comput. Biol. 8 (6) e1002538 [2012-06-07; online 2012-06-07]

Which sequencing depth is sufficient to describe patterns in bacterial α- and β-diversity?

Lundin D, Severin I, Logue JB, ..., Andersson AF, Lindström ES

Environ Microbiol Rep 4 (3) 367-372 [2012-06-00; online 2012-04-23]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

The Rose-comb mutation in chickens constitutes a structural rearrangement causing both altered comb morphology and defective sperm motility.

Imsland F, Feng C, Boije H, ..., Li N, Andersson L

PLoS Genet. 8 (6) e1002775 [2012-06-00; online 2012-06-28]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Selection-driven gene loss in bacteria.

Koskiniemi S, Sun S, Berg OG, Andersson DI

PLoS Genet. 8 (6) e1002787 [2012-06-00; online 2012-06-28]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Freshwater bacterioplankton richness in oligotrophic lakes depends on nutrient availability rather than on species-area relationships.

Logue JB, Langenheder S, Andersson AF, ..., Lanzén A, Lindström ES

ISME J 6 (6) 1127-1136 [2012-06-00; online 2011-12-16]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Digital gene expression profiling of primary acute lymphoblastic leukemia cells.

Nordlund J, Kiialainen A, Karlberg O, ..., Lönnerholm G, Syvänen AC

Leukemia 26 (6) 1218-1227 [2012-06-00; online 2011-12-16]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Common and low-frequency genetic variants in the PCSK9 locus influence circulating PCSK9 levels.

Chernogubova E, Strawbridge R, Mahdessian H, ..., Hamsten A, van 't Hooft FM

Arterioscler. Thromb. Vasc. Biol. 32 (6) 1526-1534 [2012-06-00; online 2012-03-31]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Association between genetic variants in the tumour necrosis factor/lymphotoxin α/lymphotoxin β locus and primary Sjogren's syndrome in Scandinavian samples.

Bolstad AI, Le Hellard S, Kristjansdottir G, ..., Nordmark G, Jonsson R

Ann. Rheum. Dis. 71 (6) 981-988 [2012-06-00; online 2012-02-02]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Accelerated proliferation and differential global gene expression in pancreatic islets of five-week-old heterozygous Men1 mice: Men1 is a haploinsufficient suppressor.

Lejonklou MH, Barbu A, Stålberg P, Skogseid B

Endocrinology 153 (6) 2588-2598 [2012-06-00; online 2012-04-12]

A novel variant in plakophilin-2 gene detected in a family with arrhythmogenic right ventricular cardiomyopathy.

Ostrowska Dahlgren B, Allen M, Lindström AC, Bjerke M, Blomström-Lundqvist C

J Interv Card Electrophysiol 34 (1) 11-18 [2012-06-00; online 2011-12-16]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A non-peptide receptor inhibitor with selectivity for one of the neutrophil formyl peptide receptors, FPR 1

Çevik-Aras H, Kalderén C, Jenmalm Jensen A, ..., Dahlgren C, Forsman H

Biochemical Pharmacology 83 (12) 1655-1662 [2012-06-00; online 2012-06-00]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Production of tissue microarrays, immunohistochemistry staining and digitalization within the human protein atlas.

Kampf C, Olsson I, Ryberg U, Sjöstedt E, Pontén F

J Vis Exp - (63) - [2012-05-31; online 2012-05-31]

Evidence for a negative association between schizophrenia and a polymorphism in the insulin receptor substrate-3 (IRS-3) gene.

Melkersson K, Persson B

Neuro Endocrinol. Lett. 33 (3) 321-330 [2012-05-29; online 2012-05-29]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Classification of Inhibitors of Hepatic Organic Anion Transporting Polypeptides (OATPs): Influence of Protein Expression on Drug–Drug Interactions

Karlgren M, Vildhede A, Norinder U, ..., Haglund U, Artursson P

J. Med. Chem. 55 (10) 4740-4763 [2012-05-24; online 2012-05-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

The MAP2K5-linked SNP rs2241423 is associated with BMI and obesity in two cohorts of Swedish and Greek children.

Rask-Andersen M, Jacobsson JA, Moschonis G, ..., Fredriksson R, Schiöth HB

BMC Med. Genet. 13 (-) 36 [2012-05-17; online 2012-05-17]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Novel pancreatic beta cell-specific proteins: antibody-based proteomics for identification of new biomarker candidates.

Lindskog C, Korsgren O, Pontén F, ..., Johansson L, Danielsson A

J Proteomics 75 (9) 2611-2620 [2012-05-17; online 2012-04-03]

GABA-A channel subunit expression in human glioma correlates with tumor histology and clinical outcome.

Smits A, Jin Z, Elsir T, ..., Aronica E, Birnir B

PLoS ONE 7 (5) e37041 [2012-05-17; online 2012-05-17]

Association between a genetic variant in the serotonin transporter gene (SLC6A4) and suicidal behavior in patients with schizophrenia.

Lindholm Carlström E, Saetre P, Rosengren A, ..., Terenius L, Jönsson EG

Behav Brain Funct 8 (-) 24 [2012-05-17; online 2012-05-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

MAGI1 copy number variation in bipolar affective disorder and schizophrenia.

Karlsson R, Graae L, Lekman M, ..., Belin AC, Paddock S

Biol. Psychiatry 71 (10) 922-930 [2012-05-15; online 2012-03-03]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Derivatives of 8-hydroxyquinoline--antibacterial agents that target intra- and extracellular Gram-negative pathogens.

Enquist P, Gylfe A, Hägglund U, ..., Sundin C, Elofsson M

Bioorg. Med. Chem. Lett. 22 (10) 3550-3553 [2012-05-15; online 2012-04-25]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A genome-wide approach accounting for body mass index identifies genetic variants influencing fasting glycemic traits and insulin resistance.

Manning AK, Hivert MF, Scott RA, ..., Meigs JB, Langenberg C

Nat. Genet. 44 (6) 659-669 [2012-05-13; online 2012-05-13]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genome-wide association for abdominal subcutaneous and visceral adipose reveals a novel locus for visceral fat in women.

Fox CS, Liu Y, White CC, ..., Cupples LA, Borecki IB

PLoS Genet. 8 (5) e1002695 [2012-05-10; online 2012-05-10]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Prediction of ischemic events on the basis of transcriptomic and genomic profiling in patients undergoing carotid endarterectomy.

Folkersen L, Persson J, Ekstrand J, ..., Hedin U, Paulsson-Berne G

Mol. Med. 18 (-) 669-675 [2012-05-09; online 2012-03-01]

Bioinformatics and Expression Analysis (BEA) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Multimodel pathway enrichment methods for functional evaluation of expression regulation.

Kirik U, Cifani P, Albrekt AS, ..., Heyden A, Levander F

J. Proteome Res. 11 (5) 2955-2967 [2012-05-04; online 2012-04-05]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Genetic adaptation of fatty-acid metabolism: a human-specific haplotype increasing the biosynthesis of long-chain omega-3 and omega-6 fatty acids.

Ameur A, Enroth S, Johansson A, ..., Campbell H, Gyllensten U

Am. J. Hum. Genet. 90 (5) 809-820 [2012-05-04; online 2012-04-12]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Differential evolutionary wiring of the tyrosine kinase Btk.

Nawaz HM, Kylsten P, Hamada N, ..., Smith CI, Lindvall JM

PLoS ONE 7 (5) e35640 [2012-05-04; online 2012-05-04]

A comprehensive analysis of human gene expression profiles identifies stromal immunoglobulin κ C as a compatible prognostic marker in human solid tumors.

Schmidt M, Hellwig B, Hammad S, ..., Rahnenführer J, Hengstler JG

Clin. Cancer Res. 18 (9) 2695-2703 [2012-05-01; online 2012-02-22]

Transgenerational effects of early experience on behavioral, hormonal and gene expression responses to acute stress in the precocial chicken.

Goerlich VC, Nätt D, Elfwing M, Macdonald B, Jensen P

Horm Behav 61 (5) 711-718 [2012-05-00; online 2012-04-03]

No interactions between previously associated 2-hour glucose gene variants and physical activity or BMI on 2-hour glucose levels.

Scott RA, Chu AY, Grarup N, ..., Wareham NJ, Langenberg C

Diabetes 61 (5) 1291-1296 [2012-05-00; online 2012-03-15]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A novel mutation in lysophosphatidic acid receptor 6 gene in autosomal recessive hypotrichosis and evidence for a founder effect.

Azhar A, Tariq M, Baig SM, Dahl N, Klar J

Eur J Dermatol 22 (4) 464-466 [2012-04-26; online 2012-04-26]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Common SNPs explain some of the variation in the personality dimensions of neuroticism and extraversion.

Vinkhuyzen AA, Pedersen NL, Yang J, ..., Visscher PM, Wray NR

Transl Psychiatry 2 (-) e102 [2012-04-17; online 2012-04-17]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Synthesis, biological evaluation, and structure-activity relationships of 2-[2-(benzoylamino)benzoylamino]benzoic acid analogues as inhibitors of adenovirus replication.

Öberg CT, Strand M, Andersson EK, ..., Wadell G, Elofsson M

J. Med. Chem. 55 (7) 3170-3181 [2012-04-12; online 2012-03-01]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

DNA methylation analysis of bone marrow cells at diagnosis of acute lymphoblastic leukemia and at remission.

Nordlund J, Milani L, Lundmark A, Lönnerholm G, Syvänen AC

PLoS ONE 7 (4) e34513 [2012-04-06; online 2012-04-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Systematic validation of antibody binding and protein subcellular localization using siRNA and confocal microscopy.

Stadler C, Hjelmare M, Neumann B, ..., Uhlén M, Lundberg E

J Proteomics 75 (7) 2236-2251 [2012-04-03; online 2012-03-01]

Tumor-mast cell interactions: induction of pro-tumorigenic genes and anti-tumorigenic 4-1BB in MCs in response to Lewis Lung Carcinoma.

Wensman H, Kamgari N, Johansson A, ..., Rönnberg E, Pejler G

Mol. Immunol. 50 (4) 210-219 [2012-04-00; online 2012-02-22]

The plastid redox insensitive 2 mutant of Arabidopsis is impaired in PEP activity and high light-dependent plastid redox signalling to the nucleus.

Kindgren P, Kremnev D, Blanco NE, ..., Small I, Strand A

Plant J. 70 (2) 279-291 [2012-04-00; online 2012-01-04]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Proteinase production in Pseudomonas fluorescens ON2 is affected by carbon sources and allows surface-attached but not planktonic cells to utilize protein for growth in lake water.

Nicolaisen MH, Worm J, Jørgensen NOG, Middelboe M, Nybroe O

FEMS Microbiol. Ecol. 80 (1) 168-178 [2012-04-00; online 2012-01-10]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Prevalence of Rickettsia spp., Anaplasma phagocytophilum, and Coxiella burnetii in adult Ixodes ricinus ticks from 29 study areas in central and southern Sweden.

Wallménius K, Pettersson JH, Jaenson TGT, Nilsson K

Ticks Tick Borne Dis 3 (2) 100-106 [2012-04-00; online 2012-01-09]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Mutational analysis of human glutathione transferase A2-2 identifies structural elements supporting high activity with the prodrug azathioprine.

Modén O, Zhang W, Mannervik B

Protein Eng. Des. Sel. 25 (4) 189-197 [2012-04-00; online 2012-02-16]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Mantle cell lymphoma displays a homogenous methylation profile: a comparative analysis with chronic lymphocytic leukemia.

Halldórsdóttir AM, Kanduri M, Marincevic M, ..., Ehrencrona H, Rosenquist R

Am. J. Hematol. 87 (4) 361-367 [2012-04-00; online 2012-03-01]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Manipulating the genetic code for membrane protein production: what have we learnt so far?

Nørholm MH, Light S, Virkki MT, ..., von Heijne G, Daley DO

Biochim. Biophys. Acta 1818 (4) 1091-1096 [2012-04-00; online 2011-09-03]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Can weed hosts increase aggressiveness of Phytophthora infestans on potato?

Grönberg L, Andersson B, Yuen J

Phytopathology 102 (4) 429-433 [2012-04-00; online 2011-12-22]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The interleukin-6 receptor as a target for prevention of coronary heart disease: a mendelian randomisation analysis.

Interleukin-6 Receptor Mendelian Randomisation Analysis (IL6R MR) Consortium , Swerdlow DI, Holmes MV, ..., Hingorani AD, Casas JP

Lancet 379 (9822) 1214-1224 [2012-03-31; online 2012-03-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Interleukin-6 receptor pathways in coronary heart disease: a collaborative meta-analysis of 82 studies.

IL6R Genetics Consortium Emerging Risk Factors Collaboration , Sarwar N, Butterworth AS, ..., Harari O, Danesh J

Lancet 379 (9822) 1205-1213 [2012-03-31; online 2012-03-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Novel loci for adiponectin levels and their influence on type 2 diabetes and metabolic traits: a multi-ethnic meta-analysis of 45,891 individuals.

Dastani Z, Hivert MF, Timpson N, ..., Rader DJ, Kathiresan S

PLoS Genet. 8 (3) e1002607 [2012-03-29; online 2012-03-29]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genome-wide association and functional follow-up reveals new loci for kidney function.

Pattaro C, Köttgen A, Teumer A, ..., Kao WH, Fox CS

PLoS Genet. 8 (3) e1002584 [2012-03-29; online 2012-03-29]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Toward the single-hour high-quality genome.

Ståhl PL, Lundeberg J

Annu. Rev. Biochem. 81 (-) 359-378 [2012-03-20; online 2012-03-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The transcriptome of the adenovirus infected cell.

Zhao H, Dahlö M, Isaksson A, Syvänen AC, Pettersson U

Virology 424 (2) 115-128 [2012-03-15; online 2012-01-13]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Neurobeachin, a regulator of synaptic protein targeting, is associated with body fat mass and feeding behavior in mice and body-mass index in humans.

Olszewski PK, Rozman J, Jacobsson JA, ..., Schiöth HB, Kilimann MW

PLoS Genet. 8 (3) e1002568 [2012-03-15; online 2012-03-15]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Inflammation-associated nitrotyrosination affects TCR recognition through reduced stability and alteration of the molecular surface of the MHC complex.

Madhurantakam C, Duru AD, Sandalova T, Webb JR, Achour A

PLoS ONE 7 (3) e32805 [2012-03-14; online 2012-03-14]

Antibiotic-induced change of bacterial communities associated with the copepod Nitocra spinipes.

Edlund A, Ek K, Breitholtz M, Gorokhova E

PLoS ONE 7 (3) e33107 [2012-03-12; online 2012-03-12]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Infantile cerebellar-retinal degeneration associated with a mutation in mitochondrial aconitase, ACO2.

Spiegel R, Pines O, Ta-Shma A, ..., Feuk L, Elpeleg O

Am. J. Hum. Genet. 90 (3) 518-523 [2012-03-09; online 2012-03-13]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Scalable in situ hybridization on tissue arrays for validation of novel cancer and tissue-specific biomarkers.

Kiflemariam S, Andersson S, Asplund A, Pontén F, Sjöblom T

PLoS ONE 7 (3) e32927 [2012-03-08; online 2012-03-08]

Ecosystem effects of materials proposed for thin‑layer capping of contaminated sediments

Näslund J, Samuelsson G, Gunnarsson J, ..., Cornelissen G, Schaanning M

Mar. Ecol. Prog. Ser. 449 (-) 27-40 [2012-03-08; online 2012-03-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Variation in the oxytocin receptor gene is associated with pair-bonding and social behavior.

Walum H, Lichtenstein P, Neiderhiser JM, ..., Larsson H, Westberg L

Biol. Psychiatry 71 (5) 419-426 [2012-03-01; online 2011-10-22]

Can silencing of transposons contribute to variation in effector gene expression in Phytophthora infestans?

Whisson S, Vetukuri R, Avrova A, Dixelius C

Mob Genet Elements 2 (2) 110-114 [2012-03-01; online 2012-08-31]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Systematic analysis of protein pools, isoforms, and modifications affecting turnover and subcellular localization.

Ahmad Y, Boisvert FM, Lundberg E, Uhlen M, Lamond AI

Mol. Cell Proteomics 11 (3) M111.013680 [2012-03-00; online 2011-10-18]

Signaling pathways involved in the regulation of TNFα-induced toll-like receptor 2 expression in human gingival fibroblasts.

Davanian H, Båge T, Lindberg J, ..., Sällberg Chen M, Yucel-Lindberg T

Cytokine 57 (3) 406-416 [2012-03-00; online 2012-01-10]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Phenotypic variation within a clonal lineage of Phytophthora infestans infecting both tomato and potato in Nicaragua.

Blandón-Díaz JU, Widmark A, Hannukkala A, ..., Högberg N, Yuen JE

Phytopathology 102 (3) 323-330 [2012-03-00; online 2011-11-17]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Oral contraceptive and progestin-only use correlates to tissue tumor marker expression in women with cervical intraepithelial neoplasia.

Samir R, Asplund A, Tot T, Pekar G, Hellberg D

Contraception 85 (3) 288-293 [2012-03-00; online 2011-11-10]

Novel amplifications in pediatric medulloblastoma identified by genome-wide copy number profiling.

Nord H, Pfeifer S, Nilsson P, ..., Nistér M, Díaz de Ståhl T

J. Neurooncol. 107 (1) 37-49 [2012-03-00; online 2011-10-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Microarray profiling of diaphyseal bone of rats suffering from hypervitaminosis A.

Lind T, Hu L, Lind PM, ..., Jacobson A, Melhus H

Calcif. Tissue Int. 90 (3) 219-229 [2012-03-00; online 2012-01-05]

Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens.

Dengjel J, Høyer-Hansen M, Nielsen MO, ..., Jäättelä M, Andersen JS

Mol. Cell Proteomics 11 (3) M111.014035 [2012-03-00; online 2012-02-06]

Genome-wide and gene-based association implicates FRMD6 in alzheimer disease

Hong MG, Reynolds CA, Feldman AL, ..., Pedersen NL, Prince JA

Human Mutation 33 (3) 521-529 [2012-03-00; online 2012-01-23]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genome wide analysis reveals association of a FTO gene variant with epigenetic changes.

Almén MS, Jacobsson JA, Moschonis G, ..., Fredriksson R, Schiöth HB

Genomics 99 (3) 132-137 [2012-03-00; online 2012-01-12]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Characterization of MRFAP1 turnover and interactions downstream of the NEDD8 pathway.

Larance M, Kirkwood KJ, Xirodimas DP, ..., Uhlen M, Lamond AI

Mol. Cell Proteomics 11 (3) M111.014407 [2012-03-00; online 2011-10-29]

Antibody-based protein profiling of the human chromosome 21.

Uhlén M, Oksvold P, Älgenäs C, ..., Kondo T, Sivertsson Å

Mol. Cell Proteomics 11 (3) M111.013458 [2012-03-00; online 2011-11-02]

A Protein Epitope Signature Tag (PrEST) library allows SILAC-based absolute quantification and multiplexed determination of protein copy numbers in cell lines.

Zeiler M, Straube WL, Lundberg E, Uhlen M, Mann M

Mol. Cell Proteomics 11 (3) O111.009613 [2012-03-00; online 2011-10-04]

A dimerized single-chain variable fragment system for the assessment of neutralizing activity of phage display-selected antibody fragments specific for cytomegalovirus.

Carlsson F, Trilling M, Perez F, Ohlin M

J. Immunol. Methods 376 (1-2) 69-78 [2012-02-28; online 2011-12-14]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Combined chromatin and expression analysis reveals specific regulatory mechanisms within cytokine genes in the macrophage early immune response.

Iglesias MJ, Jesus Iglesias M, Reilly SJ, ..., Hamsten A, Odeberg J

PLoS ONE 7 (2) e32306 [2012-02-27; online 2012-02-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Coexpression network analysis in abdominal and gluteal adipose tissue reveals regulatory genetic loci for metabolic syndrome and related phenotypes.

Min JL, Nicholson G, Halgrimsdottir I, ..., Lindgren CM, Zondervan KT

PLoS Genet. 8 (2) e1002505 [2012-02-23; online 2012-02-23]

Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion.

Schnell R, Oehlmann W, Sandalova T, ..., Singh M, Schneider G

PLoS ONE 7 (2) e31133 [2012-02-16; online 2012-02-16]

Genome-wide association study identifies novel loci associated with circulating phospho- and sphingolipid concentrations.

Demirkan A, van Duijn CM, Ugocsai P, ..., Schmitz G, EUROSPAN consortium

PLoS Genet. 8 (2) e1002490 [2012-02-16; online 2012-02-16]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Syntheses of pseudoceramines A-D and a new synthesis of spermatinamine, bromotyrosine natural products from marine sponges.

Hillgren JM, Oberg CT, Elofsson M

Org. Biomol. Chem. 10 (6) 1246-1254 [2012-02-14; online 2011-12-20]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

High-resolution structure of a BRICHOS domain and its implications for anti-amyloid chaperone activity on lung surfactant protein C.

Willander H, Askarieh G, Landreh M, ..., Knight SD, Johansson J

Proc. Natl. Acad. Sci. U.S.A. 109 (7) 2325-2329 [2012-02-14; online 2012-02-07]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Forsberg LA, Rasi C, Razzaghian HR, ..., Absher D, Dumanski JP

Am. J. Hum. Genet. 90 (2) 217-228 [2012-02-10; online 2012-02-07]

Genetic and environmental contributions to weight, height, and BMI from birth to 19 years of age: an international study of over 12,000 twin pairs.

Dubois L, Ohm Kyvik K, Girard M, ..., Lichtenstein P, Martin NG

PLoS ONE 7 (2) e30153 [2012-02-08; online 2012-02-08]

Heritable genome-wide variation of gene expression and promoter methylation between wild and domesticated chickens.

Nätt D, Rubin CJ, Wright D, ..., Andersson L, Jensen P

BMC Genomics 13 (-) 59 [2012-02-04; online 2012-02-04]

Characterization of the lipid droplet proteome of a clonal insulin-producing β-cell line (INS-1 832/13).

Larsson S, Resjö S, Gomez MF, James P, Holm C

J. Proteome Res. 11 (2) 1264-1273 [2012-02-03; online 2012-01-25]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Sequential closure of the cytoplasm and then the periplasm during cell division in Escherichia coli.

Skoog K, Söderström B, Widengren J, von Heijne G, Daley DO

J. Bacteriol. 194 (3) 584-586 [2012-02-00; online 2011-11-22]

Integrated Microscopy Technologies Stockholm [Collaborative]

Low diversity of the gut microbiota in infants with atopic eczema.

Abrahamsson TR, Jakobsson HE, Andersson AF, ..., Engstrand L, Jenmalm MC

J. Allergy Clin. Immunol. 129 (2) 434-40, 440.e1-2 [2012-02-00; online 2011-12-14]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

In vitro and in silico strategies to identify OATP1B1 inhibitors and predict clinical drug-drug interactions.

Karlgren M, Ahlin G, Bergström CA, ..., Palm J, Artursson P

Pharm. Res. 29 (2) 411-426 [2012-02-00; online 2011-08-23]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Can balancing selection on MHC loci counteract genetic drift in small fragmented populations of black grouse?

Strand TM, Segelbacher G, Quintela M, ..., Axelsson T, Höglund J

Ecol Evol 2 (2) 341-353 [2012-02-00; online 2012-03-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

BCL2L1 has a functional role in colorectal cancer and its protein expression is associated with chromosome 20q gain.

Sillars-Hardebol AH, Carvalho B, Beliën JA, ..., Fijneman RJ, Meijer GA

J. Pathol. 226 (3) 442-450 [2012-02-00; online 2011-10-20]

Association of TMEM18 variants with BMI and waist circumference in children and correlation of mRNA expression in the PFC with body weight in rats.

Rask-Andersen M, Jacobsson JA, Moschonis G, ..., Fredriksson R, Schiöth HB

Eur. J. Hum. Genet. 20 (2) 192-197 [2012-02-00; online 2011-09-29]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Mutations in CTC1, encoding conserved telomere maintenance component 1, cause Coats plus.

Anderson BH, Kasher PR, Mayer J, ..., Rice GI, Crow YJ

Nat. Genet. 44 (3) 338-342 [2012-01-22; online 2012-01-22]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Meta-analyses identify 13 loci associated with age at menopause and highlight DNA repair and immune pathways.

Stolk L, Perry JR, Chasman DI, ..., Visser JA, Lunetta KL

Nat. Genet. 44 (3) 260-268 [2012-01-22; online 2012-01-22]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Non-bullous congentital ichthyosiform erythroderma associated with homozygosity for a novel missense mutation in an ATP binding domain of ABCA12.

Nawaz S, Tariq M, Ahmad I, ..., Dahl N, Klar J

Eur J Dermatol 22 (2) 178-181 [2012-01-20; online 2012-01-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A strand specific high resolution normalization method for chip-sequencing data employing multiple experimental control measurements.

Enroth S, Andersson CR, Andersson R, ..., Gustafsson MG, Komorowski J

Algorithms Mol Biol 7 (1) 2 [2012-01-16; online 2012-01-16]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Long-range DNA looping and gene expression analyses identify DEXI as an autoimmune disease candidate gene.

Davison LJ, Wallace C, Cooper JD, ..., Syvannen AC, Tennstedt S

Hum. Mol. Genet. 21 (2) 322-333 [2012-01-15; online 2011-10-13]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Deregulation of the A-to-I RNA editing mechanism in psychiatric disorders.

Silberberg G, Lundin D, Navon R, Öhman M

Hum. Mol. Genet. 21 (2) 311-321 [2012-01-15; online 2011-10-11]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Contribution of TMC6 and TMC8 (EVER1 and EVER2) variants to cervical cancer susceptibility.

Castro FA, Ivansson EL, Schmitt M, ..., Gyllensten UB, Pawlita M

Int. J. Cancer 130 (2) 349-355 [2012-01-15; online 2011-03-10]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Structural genetic variation in the context of somatic mosaicism.

Dumanski JP, Piotrowski A

Methods Mol. Biol. 838 (-) 249-272 [2012-01-10; online 2012-01-10]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Differential expression patterns of conserved miRNAs and isomiRs during Atlantic halibut development.

Bizuayehu TT, Lanes CFC, Furmanek T, ..., Johansen SD, Babiak I

BMC Genomics 13 (-) 11 [2012-01-10; online 2012-01-10]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Combinations of histone modifications mark exon inclusion levels.

Enroth S, Bornelöv S, Wadelius C, Komorowski J

PLoS ONE 7 (1) e29911 [2012-01-05; online 2012-01-05]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A genome-wide association search for type 2 diabetes genes in African Americans.

Palmer ND, McDonough CW, Hicks PJ, ..., Mooser V, Sladek R

PLoS ONE 7 (1) e29202 [2012-01-04; online 2012-01-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

siRNA silencing of proteasome maturation protein (POMP) activates the unfolded protein response and constitutes a model for KLICK genodermatosis.

Dahlqvist J, Törmä H, Badhai J, Dahl N

PLoS ONE 7 (1) e29471 [2012-01-03; online 2012-01-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Lymphoblastoid cell line with B1 cell characteristics established from a chronic lymphocytic leukemia clone by in vitro EBV infection.

Rosén A, Bergh AC, Gogok P, ..., Rosenquist R, Klein E

Oncoimmunology 1 (1) 18-27 [2012-01-01; online 2012-06-22]

Sequencing of high-complexity DNA pools for identification of nucleotide and structural variants in regions associated with complex traits.

Zaboli G, Ameur A, Igl W, ..., Gyllensten U, EUROSPAN Consortium

Eur. J. Hum. Genet. 20 (1) 77-83 [2012-01-00; online 2011-08-03]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

QTL linkage mapping of zebra finch beak color shows an oligogenic control of a sexually selected trait.

Schielzeth H, Kempenaers B, Ellegren H, Forstmeier W

Evolution 66 (1) 18-30 [2012-01-00; online 2011-09-20]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

QTL linkage mapping of wing length in zebra finch using genome-wide single nucleotide polymorphisms markers.

Schielzeth H, Forstmeier W, Kempenaers B, Ellegren H

Mol. Ecol. 21 (2) 329-339 [2012-01-00; online 2011-11-25]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Kynurenine 3-monooxygenase polymorphisms: relevance for kynurenic acid synthesis in patients with schizophrenia and healthy controls.

Holtze M, Saetre P, Engberg G, ..., Schalling M, Erhardt S

J Psychiatry Neurosci 37 (1) 53-57 [2012-01-00; online 2011-06-23]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton.

Martinez-Garcia M, Swan BK, Poulton NJ, ..., Sieracki ME, Stepanauskas R

ISME J 6 (1) 113-123 [2012-01-00; online 2011-07-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetic variants near the MGAT1 gene are associated with body weight, BMI and fatty acid metabolism among adults and children.

Jacobsson JA, Rask-Andersen M, Risérus U, ..., Schiöth HB, Fredriksson R

Int J Obes (Lond) 36 (1) 119-129 [2012-01-00; online 2011-02-10]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Biosensor Based Protein Profiling on Reverse Phase Serum Microarray

Sjöberg R, Hammarström L, Nilsson P

JPB 05 (08) - [2012-00-00; online 2012-00-00]

Autoimmunity and Serology Profiling [Technology development]

A Complex Genomic Rearrangement Involving the Endothelin 3 Locus Causes Dermal Hyperpigmentation in the Chicken

Dorshorst B, Molin AM, Rubin CJ, ..., Ashwell C, Andersson L

PLoS Genet. 7 (12) e1002412 [2011-12-22; online 2011-12-22]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Mechanisms underlying the sparing of masticatory versus limb muscle function in an experimental critical illness model.

Aare S, Ochala J, Norman HS, ..., Hoffman EP, Larsson L

Physiol. Genomics 43 (24) 1334-1350 [2011-12-16; online 2011-10-20]

Polymorphisms in B3GAT1, SLC9A9 and MGAT5 are associated with variation within the human plasma N-glycome of 3533 European adults.

Huffman JE, Knezevic A, Vitart V, ..., Wright AF, Lauc G

Hum. Mol. Genet. 20 (24) 5000-5011 [2011-12-15; online 2011-09-13]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Identification of immunogenic proteins in Treponema phagedenis-like strain V1 from digital dermatitis lesions by phage display.

Rosander A, Guss B, Frykberg L, ..., Näslund K, Pringle M

Vet. Microbiol. 153 (3-4) 315-322 [2011-12-15; online 2011-07-19]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PubMed

Association between body mass index and insulin receptor substrate-4 (IRS-4) gene polymorphisms in patients with schizophrenia.

Melkersson K, Persson B

Neuro Endocrinol. Lett. 32 (5) 634-640 [2011-12-15; online 2011-12-15]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The inner nuclear membrane proteins Man1 and Ima1 link to two different types of chromatin at the nuclear periphery in S. pombe.

Steglich B, Filion GJ, van Steensel B, Ekwall K

Nucleus 3 (1) 77-87 [2011-12-14; online 2011-12-14]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Muscle wasting and the temporal gene expression pattern in a novel rat intensive care unit model.

Llano-Diez M, Gustafson AM, Olsson C, Goransson H, Larsson L

BMC Genomics 12 (-) 602 [2011-12-13; online 2011-12-13]

Blood pressure loci identified with a gene-centric array.

Johnson T, Gaunt TR, Newhouse SJ, ..., Caulfield MJ, Munroe PB

Am. J. Hum. Genet. 89 (6) 688-700 [2011-12-09; online 2011-11-22]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Common variants of the BRCA1 wild-type allele modify the risk of breast cancer in BRCA1 mutation carriers.

Cox DG, Simard J, Sinnett D, ..., Sinilnikova OM, Consortium of Investigators of Modifiers of BRCA1/2

Hum. Mol. Genet. 20 (23) 4732-4747 [2011-12-01; online 2011-09-06]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Salt-inducible kinase 1 influences Na(+),K(+)-ATPase activity in vascular smooth muscle cells and associates with variations in blood pressure.

Popov S, Silveira A, Wågsäter D, ..., Melander O, Bertorello AM

J. Hypertens. 29 (12) 2395-2403 [2011-12-00; online 2011-11-03]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Pathway-based analysis of genetic susceptibility to cervical cancer in situ: HLA-DPB1 affects risk in Swedish women.

Ivansson EL, Juko-Pecirep I, Erlich HA, Gyllensten UB

Genes Immun. 12 (8) 605-614 [2011-12-00; online 2011-07-01]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

High nuclear RBM3 expression is associated with an improved prognosis in colorectal cancer.

Hjelm B, Brennan DJ, Zendehrokh N, ..., Jirström K, Uhlen M

Proteomics Clin Appl 5 (11-12) 624-635 [2011-12-00; online 2011-10-01]

Targeting acetylcholinesterase: identification of chemical leads by high throughput screening, structure determination and molecular modeling.

Berg L, Andersson CD, Artursson E, ..., Linusson A, Ekström F

PLoS ONE 6 (11) e26039 [2011-11-30; online 2011-11-30]

Chemical Biology Consortium Sweden (CBCS) [Service]

Next-generation sequencing technologies and applications for human genetic history and forensics.

Berglund EC, Kiialainen A, Syvänen AC

Investig Genet 2 (-) 23 [2011-11-24; online 2011-11-24]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Counting absolute numbers of molecules using unique molecular identifiers.

Kivioja T, Vähärautio A, Karlsson K, ..., Linnarsson S, Taipale J

Nat. Methods 9 (1) 72-74 [2011-11-20; online 2011-11-20]

Variance decomposition of protein profiles from antibody arrays using a longitudinal twin model.

Kato BS, Nicholson G, Neiman M, ..., Spector TD, Schwenk JM

Proteome Sci 9 (-) 73 [2011-11-17; online 2011-11-17]

Prognostic DNA methylation patterns in cytogenetically normal acute myeloid leukemia are predefined by stem cell chromatin marks.

Deneberg S, Guardiola P, Lennartsson A, ..., Döhner K, Lehmann S

Blood 118 (20) 5573-5582 [2011-11-17; online 2011-10-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genome sequencing reveals a phage in Helicobacter pylori.

Lehours P, Vale FF, Bjursell MK, ..., Engstrand L, Andersson AF

MBio 2 (6) - [2011-11-15; online 2011-11-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1.

Bown MJ, Jones GT, Harrison SC, ..., Deloukas P, Samani NJ

Am. J. Hum. Genet. 89 (5) 619-627 [2011-11-11; online 2011-11-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain.

Ameur A, Zaghlool A, Halvardson J, ..., Cavelier L, Feuk L

Nat. Struct. Mol. Biol. 18 (12) 1435-1440 [2011-11-06; online 2011-11-06]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Inhibition of proteasome deubiquitinating activity as a new cancer therapy.

D'Arcy P, Brnjic S, Olofsson MH, ..., Larsson R, Linder S

Nat. Med. 17 (12) 1636-1640 [2011-11-06; online 2011-11-06]

Plasma profiling reveals human fibulin-1 as candidate marker for renal impairment.

Neiman M, Hedberg JJ, Dönnes PR, ..., Schwenk JM, Nilsson P

J. Proteome Res. 10 (11) 4925-4934 [2011-11-04; online 2011-09-29]

SWI/SNF regulates the alternative processing of a specific subset of pre-mRNAs in Drosophila melanogaster.

Waldholm J, Wang Z, Brodin D, ..., Farrants AK, Visa N

BMC Mol. Biol. 12 (-) 46 [2011-11-02; online 2011-11-02]

Hypothalamic mitochondrial dysfunction associated with anorexia in the anx/anx mouse.

Lindfors C, Nilsson IA, Garcia-Roves PM, ..., Schalling M, Johansen JE

Proc. Natl. Acad. Sci. U.S.A. 108 (44) 18108-18113 [2011-11-01; online 2011-10-26]

Abundant class of non-coding RNA regulates development in the social amoeba Dictyostelium discoideum.

Avesson L, Schumacher HT, Fechter P, ..., Hellman U, Söderbom F

RNA Biol 8 (6) 1094-1104 [2011-11-01; online 2011-09-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Western blotting via proximity ligation for high performance protein analysis.

Liu Y, Gu J, Hagner-McWhirter Å, ..., Ivansson D, Landegren U

Mol. Cell Proteomics 10 (11) O111.011031 [2011-11-00; online 2011-08-02]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

The Human Protein Atlas as a proteomic resource for biomarker discovery.

Pontén F, Schwenk JM, Asplund A, Edqvist PH

J. Intern. Med. 270 (5) 428-446 [2011-11-00; online 2011-08-03]

Affinity Proteomics Stockholm [Technology development] Tissue Profiling

Targeted enrichment of genomic DNA regions for next-generation sequencing.

Mertes F, Elsharawy A, Sauer S, ..., Lehrach H, Brookes AJ

Brief Funct Genomics 10 (6) 374-386 [2011-11-00; online 2011-11-26]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Generation of monospecific antibodies based on affinity capture of polyclonal antibodies.

Hjelm B, Forsström B, Igel U, ..., Johansson C, Uhlén M

Protein Sci. 20 (11) 1824-1835 [2011-11-00; online 2011-09-08]

Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development] Spatial Proteomics

Gene copy number aberrations are associated with survival in histologic subgroups of non-small cell lung cancer.

Micke P, Edlund K, Holmberg L, ..., Isaksson A, Botling J

J Thorac Oncol 6 (11) 1833-1840 [2011-11-00; online 2011-10-21]

Increasing the dynamic range of in situ PLA.

Clausson C, Allalou A, Weibrecht I, ..., Wählby C, Söderberg O

Nat. Methods 8 (11) 892-893 [2011-10-28; online 2011-10-28]

Affinity Proteomics Uppsala [Collaborative] BioImage Informatics [Collaborative] Bioinformatics (NBIS) [Collaborative] PLA and Single Cell Proteomics

Allele-specific copy number analysis of tumor samples with aneuploidy and tumor heterogeneity.

Rasmussen M, Sundström M, Göransson Kultima H, ..., Glimelius B, Isaksson A

Genome Biol. 12 (10) R108 [2011-10-24; online 2011-10-24]

Genome-wide association study identifies loci influencing concentrations of liver enzymes in plasma.

Chambers JC, Zhang W, Sehmi J, ..., Elliott P, Kooner JS

Nat. Genet. 43 (11) 1131-1138 [2011-10-16; online 2011-10-16]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

MED12, the mediator complex subunit 12 gene, is mutated at high frequency in uterine leiomyomas.

Mäkinen N, Mehine M, Tolvanen J, ..., Vahteristo P, Aaltonen LA

Science 334 (6053) 252-255 [2011-10-14; online 2011-08-27]

Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease.

Rivas MA, Beaudoin M, Gardet A, ..., Xavier RJ, Daly MJ

Nat. Genet. 43 (11) 1066-1073 [2011-10-09; online 2011-10-09]

Pseudoceramines A-D, new antibacterial bromotyrosine alkaloids from the marine sponge Pseudoceratina sp.

Yin S, Davis RA, Shelper T, ..., Sundin C, Quinn RJ

Org. Biomol. Chem. 9 (19) 6755-6760 [2011-10-07; online 2011-08-19]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Adenosine kinase deficiency disrupts the methionine cycle and causes hypermethioninemia, encephalopathy, and abnormal liver function.

Bjursell MK, Blom HJ, Cayuela JA, ..., Lundeberg J, Wedell A

Am. J. Hum. Genet. 89 (4) 507-515 [2011-10-07; online 2011-10-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Tracking Phytophthora infestans with SSR markers within and between seasons - a field study in Sweden

Widmark AK, Andersson B, Sandström M, Yuen JE

Plant Pathol 60 (5) 938-945 [2011-10-00; online 2011-03-16]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

No evidence for an association between genetic variation at the SERPINI1 locus and ischemic stroke.

Tjärnlund-Wolf A, Olsson S, Jood K, Blomstrand C, Jern C

J. Neurol. 258 (10) 1885-1887 [2011-10-00; online 2011-04-14]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Histone modifications influence mediator interactions with chromatin.

Zhu X, Zhang Y, Bjornsdottir G, ..., Gustafsson CM, Myers LC

Nucleic Acids Res. 39 (19) 8342-8354 [2011-10-00; online 2011-07-12]

High-risk HPV infection and CIN grade correlates to the expression of c-myc, CD4+, FHIT, E-cadherin, Ki-67, and p16INK4a.

Samir R, Asplund A, Tot T, Pekar G, Hellberg D

J Low Genit Tract Dis 15 (4) 280-286 [2011-10-00; online 2011-05-12]

Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes.

Strawbridge RJ, Dupuis J, Prokopenko I, ..., Hamsten A, Florez JC

Diabetes 60 (10) 2624-2634 [2011-10-00; online 2011-08-30]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic variation in complement component C3 shows association with ischaemic stroke.

Olsson S, Stokowska A, Holmegaard L, ..., Pekna M, Jern C

Eur. J. Neurol. 18 (10) 1272-1274 [2011-10-00; online 2011-03-19]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Evidence for involvement of Dicer-like, Argonaute and histone deacetylase proteins in gene silencing in Phytophthora infestans.

Vetukuri RR, Avrova AO, Grenville-Briggs LJ, ..., Whisson SC, Dixelius C

Mol. Plant Pathol. 12 (8) 772-785 [2011-10-00; online 2011-07-06]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Early transcriptional regulation by C-peptide in freshly isolated rat proximal tubular cells.

Lindahl E, Nordquist L, Müller P, ..., Palm F, Jörnvall H

Diabetes Metab. Res. Rev. 27 (7) 697-704 [2011-10-00; online 2011-05-28]

The Lin28/let-7 axis regulates glucose metabolism.

Zhu H, Shyh-Chang N, Segrè AV, ..., Altshuler D, Daley GQ

Cell 147 (1) 81-94 [2011-09-30; online 2011-10-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

ProteinSeq: high-performance proteomic analyses by proximity ligation and next generation sequencing.

Darmanis S, Nong RY, Vänelid J, ..., Kamali-Moghaddam M, Landegren U

PLoS ONE 6 (9) e25583 [2011-09-29; online 2011-09-29]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

High RBM3 expression in prostate cancer independently predicts a reduced risk of biochemical recurrence and disease progression.

Jonsson L, Gaber A, Ulmert D, ..., Bjartell A, Jirström K

Diagn Pathol 6 (-) 91 [2011-09-28; online 2011-09-28]

Genome-wide association study identifies six new loci influencing pulse pressure and mean arterial pressure.

Wain LV, Verwoert GC, O'Reilly PF, ..., Elliott P, van Duijn CM

Nat. Genet. 43 (10) 1005-1011 [2011-09-11; online 2011-09-11]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Engineering GST M2-2 for high activity with indene 1,2-oxide and indication of an H-site residue sustaining catalytic promiscuity.

Norrgård MA, Mannervik B

J. Mol. Biol. 412 (1) 111-120 [2011-09-09; online 2011-08-09]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Large-scale protein profiling in human cell lines using antibody-based proteomics.

Fagerberg L, Strömberg S, El-Obeid A, ..., Ponten F, Asplund A

J. Proteome Res. 10 (9) 4066-4075 [2011-09-02; online 2011-07-06]

Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport.

Phirke P, Efimenko E, Mohan S, ..., Leroux MR, Swoboda P

Dev. Biol. 357 (1) 235-247 [2011-09-01; online 2011-07-12]

Variants in STAT5B associate with serum TC and LDL-C levels.

Kornfeld JW, Isaacs A, Vitart V, ..., Pramstaller PP, Hicks AA

J. Clin. Endocrinol. Metab. 96 (9) E1496-E1501 [2011-09-00; online 2011-07-15]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Total zinc intake may modify the glucose-raising effect of a zinc transporter (SLC30A8) variant: a 14-cohort meta-analysis.

Kanoni S, Nettleton JA, Hivert MF, ..., Franks PW, Dedoussis GV

Diabetes 60 (9) 2407-2416 [2011-09-00; online 2011-08-04]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Structural features determining the intestinal epithelial permeability and efflux of novel HIV-1 protease inhibitors.

Lazorova L, Hubatsch I, Ekegren JK, ..., Larhed M, Artursson P

J Pharm Sci 100 (9) 3763-3772 [2011-09-00; online 2011-04-15]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Large-scale gene-centric analysis identifies novel variants for coronary artery disease.

IBC 50K CAD Consortium N

PLoS Genet. 7 (9) e1002260 [2011-09-00; online 2011-09-22]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genomic and clinical characteristics of six patients with partially overlapping interstitial deletions at 10p12p11.

Wentzel C, Rajcan-Separovic E, Ruivenkamp CA, ..., Giurgea I, Thuresson AC

Eur. J. Hum. Genet. 19 (9) 959-964 [2011-09-00; online 2011-04-28]

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Dystrobrevin-binding protein 1 gene (DTNBP1) variants associated with cerebrospinal fluid homovanillic acid and 5-hydroxyindoleacetic acid concentrations in healthy volunteers.

Andreou D, Saetre P, Kähler AK, ..., Terenius L, Jönsson EG

Eur Neuropsychopharmacol 21 (9) 700-704 [2011-09-00; online 2011-02-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Combinations of SNPs related to signal transduction in bipolar disorder.

Koefoed P, Andreassen OA, Bennike B, ..., Werge T, Mellerup E

PLoS ONE 6 (8) e23812 [2011-08-29; online 2011-08-29]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Identification of Bacterial Target Proteins for the Salicylidene Acylhydrazide Class of Virulence-blocking Compounds

Wang D, Zetterström CE, Gabrielsen M, ..., Elofsson M, Roe AJ

J. Biol. Chem. 286 (34) 29922-29931 [2011-08-26; online 2011-07-01]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Changes in the acetogenic population in a mesophilic anaerobic digester in response to increasing ammonia concentration.

Westerholm M, Müller B, Arthurson V, Schnürer A

Microbes Environ. 26 (4) 347-353 [2011-08-24; online 2011-08-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Identification of cis- and trans-acting genetic variants explaining up to half the variation in circulating vascular endothelial growth factor levels.

Debette S, Visvikis-Siest S, Chen MH, ..., Vasan RS, Seshadri S

Circ. Res. 109 (5) 554-563 [2011-08-19; online 2011-07-16]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Characterization of a 8q21.11 microdeletion syndrome associated with intellectual disability and a recognizable phenotype.

Palomares M, Delicado A, Mansilla E, ..., Hennekam RC, Lapunzina P

Am. J. Hum. Genet. 89 (2) 295-301 [2011-08-12; online 2011-08-02]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis.

International Multiple Sclerosis Genetics Consortium N, Wellcome Trust Case Control Consortium 2 N, Sawcer S, ..., Donnelly P, Compston A

Nature 476 (7359) 214-219 [2011-08-10; online 2011-08-10]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Functional and prognostic relevance of the homeobox protein MSX2 in malignant melanoma.

Gremel G, Ryan D, Rafferty M, ..., Ponten F, Gallagher WM

Br. J. Cancer 105 (4) 565-574 [2011-08-09; online 2011-07-07]

Mapping the subcellular protein distribution in three human cell lines.

Fagerberg L, Stadler C, Skogs M, ..., Uhlén M, Lundberg E

J. Proteome Res. 10 (8) 3766-3777 [2011-08-05; online 2011-06-17]

The genetic structure of the Swedish population.

Humphreys K, Grankvist A, Leu M, ..., Palmgren J, Magnusson PK

PLoS ONE 6 (8) e22547 [2011-08-04; online 2011-08-04]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer.

Håfström T, Jansson DS, Segerman B

BMC Genomics 12 (-) 395 [2011-08-04; online 2011-08-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Influence of the COMT genotype on working memory and brain activity changes during development.

Dumontheil I, Roggeman C, Ziermans T, ..., Kere J, Klingberg T

Biol. Psychiatry 70 (3) 222-229 [2011-08-01; online 2011-04-26]

The short non-coding transcriptome of the protozoan parasite Trypanosoma cruzi.

Franzén O, Arner E, Ferella M, ..., Andersson B, Daub CO

PLoS Negl Trop Dis 5 (8) e1283 [2011-08-00; online 2011-08-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

RBM3-regulated genes promote DNA integrity and affect clinical outcome in epithelial ovarian cancer.

Ehlén Å, Nodin B, Rexhepaj E, ..., Brennan DJ, Jirström K

Transl Oncol 4 (4) 212-221 [2011-08-00; online 2011-08-01]

Lack of association between two dopamine D2 receptor gene polymorphisms and schizophrenia.

Caprini S, Saetre P, Melle I, ..., Terenius L, Jönsson EG

Psychiatr. Genet. 21 (4) 214-215 [2011-08-00; online 2011-06-30]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Lack of association between genetic variations in the KALRN region and ischemic stroke.

Olsson S, Jood K, Melander O, ..., Lindgren A, Jern C

Clin. Biochem. 44 (12) 1018-1020 [2011-08-00; online 2011-06-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Hyphae-colonizing Burkholderia sp.--a new source of biological control agents against sheath blight disease (Rhizoctonia solani AG1-IA) in rice.

Cuong ND, Nicolaisen MH, Sørensen J, Olsson S

Microb. Ecol. 62 (2) 425-434 [2011-08-00; online 2011-03-03]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Gene-environment interactions between CRHR1 variants and physical assault in suicide attempts.

Ben-Efraim YJ, Wasserman D, Wasserman J, Sokolowski M

Genes Brain Behav. 10 (6) 663-672 [2011-08-00; online 2011-05-25]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Evaluation of Fanconi anaemia genes FANCA, FANCC and FANCL in cervical cancer susceptibility.

Juko-Pecirep I, Ivansson EL, Gyllensten UB

Gynecol. Oncol. 122 (2) 377-381 [2011-08-00; online 2011-05-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Correlation between LRIG1 and LRIG2 expressions and expression of 11 tumor markers, with special reference to tumor suppressors, in CIN and normal cervical epithelium.

Lindström AK, Asplund A, Hellberg D

Gynecol. Oncol. 122 (2) 372-376 [2011-08-00; online 2011-06-03]

Array-based genomic screening at diagnosis and during follow-up in chronic lymphocytic leukemia.

Gunnarsson R, Mansouri L, Isaksson A, ..., Juliusson G, Rosenquist R

Haematologica 96 (8) 1161-1169 [2011-08-00; online 2011-05-07]

Array and Analysis Facility NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Antimicrobial susceptibility of Brachyspira spp. isolated from commercial laying hens and free-living wild mallards (Anas platyrhynchos).

Jansson DS, Pringle M

Avian Pathol. 40 (4) 387-393 [2011-08-00; online 2011-08-05]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation.

Mild M, Hedskog C, Jernberg J, Albert J

PLoS ONE 6 (7) e22741 [2011-07-25; online 2011-07-25]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Structural alterations from multiple displacement amplification of a human genome revealed by mate-pair sequencing.

Jiao X, Rosenlund M, Hooper SD, ..., Mangion J, Sjöblom T

PLoS ONE 6 (7) e22250 [2011-07-22; online 2011-07-22]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Low RBM3 protein expression correlates with tumour progression and poor prognosis in malignant melanoma: an analysis of 215 cases from the Malmö Diet and Cancer Study.

Jonsson L, Bergman J, Nodin B, ..., Uhlén M, Jirström K

J Transl Med 9 (-) 114 [2011-07-21; online 2011-07-21]

The use of genome-wide eQTL associations in lymphoblastoid cell lines to identify novel genetic pathways involved in complex traits.

Min JL, Taylor JM, Richards JB, ..., Spector TD, Zondervan KT

PLoS ONE 6 (7) e22070 [2011-07-15; online 2011-07-15]

Scalable transcriptome preparation for massive parallel sequencing.

Stranneheim H, Werne B, Sherwood E, Lundeberg J

PLoS ONE 6 (7) e21910 [2011-07-07; online 2011-07-07]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Identification of noncoding transcripts from within CENP-A chromatin at fission yeast centromeres.

Choi ES, Strålfors A, Castillo AG, ..., Ekwall K, Allshire RC

J. Biol. Chem. 286 (26) 23600-23607 [2011-07-01; online 2011-05-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Species sorting and neutral processes are both important during the initial assembly of bacterial communities.

Langenheder S, Székely AJ

ISME J 5 (7) 1086-1094 [2011-07-00; online 2011-01-29]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

SATB2 in combination with cytokeratin 20 identifies over 95% of all colorectal carcinomas.

Magnusson K, de Wit M, Brennan DJ, ..., Jirström K, Pontén F

Am. J. Surg. Pathol. 35 (7) 937-948 [2011-07-00; online 2011-06-17]

Replication and explorations of high-order epistasis using a large advanced intercross line pedigree.

Pettersson M, Besnier F, Siegel PB, Carlborg O

PLoS Genet. 7 (7) e1002180 [2011-07-00; online 2011-07-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Prostasomal DNA characterization and transfer into human sperm.

Ronquist GK, Larsson A, Ronquist G, ..., Carlsson L, Stavreus-Evers A

Mol. Reprod. Dev. 78 (7) 467-476 [2011-07-00; online 2011-06-04]

Potential association of muscarinic receptor 3 gene variants with primary Sjogren's syndrome.

Appel S, Le Hellard S, Bruland O, ..., Wahren-Herlenius M, Jonsson R

Ann. Rheum. Dis. 70 (7) 1327-1329 [2011-07-00; online 2011-04-01]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic architecture of circulating lipid levels.

Demirkan A, Amin N, Isaacs A, ..., van Duijn CM, ENGAGE CONSORTIUM

Eur. J. Hum. Genet. 19 (7) 813-819 [2011-07-00; online 2011-03-30]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Concomitant autoimmunity in myasthenia gravis--lack of association with IgA deficiency.

Ramanujam R, Piehl F, Pirskanen R, Gregersen PK, Hammarström L

J. Neuroimmunol. 236 (1-2) 118-122 [2011-07-00; online 2011-06-15]

Genome wide association study identifies KCNMA1 contributing to human obesity.

Jiao H, Arner P, Hoffstedt J, ..., Clement K, Dahlman I

BMC Med Genomics 4 (-) 51 [2011-06-28; online 2011-06-28]

Bioinformatics and Expression Analysis (BEA) Mutation Analysis Facility (MAF) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile.

Kilpeläinen TO, Zillikens MC, Stančákova A, ..., Laakso M, Loos RJ

Nat. Genet. 43 (8) 753-760 [2011-06-26; online 2011-06-26]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Specific syndecan-1 domains regulate mesenchymal tumor cell adhesion, motility and migration.

Zong F, Fthenou E, Mundt F, ..., Hjerpe A, Dobra K

PLoS ONE 6 (6) e14816 [2011-06-23; online 2011-06-23]

Translational database selection and multiplexed sequence capture for up front filtering of reliable breast cancer biomarker candidates.

Ståhl PL, Bjursell MK, Mahdessian H, ..., Jirström K, Lundeberg J

PLoS ONE 6 (6) e20794 [2011-06-15; online 2011-06-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

KIT pathway alterations in mucosal melanomas of the vulva and other sites.

Omholt K, Grafström E, Kanter-Lewensohn L, Hansson J, Ragnarsson-Olding BK

Clin. Cancer Res. 17 (12) 3933-3942 [2011-06-15; online 2011-06-18]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The fat mass and obesity gene is linked to reduced verbal fluency in overweight and obese elderly men.

Benedict C, Jacobsson JA, Rönnemaa E, ..., Kilander L, Schiöth HB

Neurobiol. Aging 32 (6) 1159.e1-1159.e5 [2011-06-00; online 2011-04-05]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Tepidanaerobacter acetatoxydans sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from two ammonium-enriched mesophilic methanogenic processes.

Westerholm M, Roos S, Schnürer A

Syst. Appl. Microbiol. 34 (4) 260-266 [2011-06-00; online 2011-04-19]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genetic association and gene expression analysis identify FGFR1 as a new susceptibility gene for human obesity.

Jiao H, Arner P, Dickson SL, ..., Clement K, Dahlman I

J. Clin. Endocrinol. Metab. 96 (6) E962-E966 [2011-06-00; online 2011-03-25]

Bioinformatics and Expression Analysis (BEA) Mutation Analysis Facility (MAF) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Feather pecking behavior in laying hens: hypothalamic gene expression in birds performing and receiving pecks.

Brunberg E, Jensen P, Isaksson A, Keeling L

Poult. Sci. 90 (6) 1145-1152 [2011-06-00; online 2011-05-21]

Cytochrome P450 1A, 1B, and 1C mRNA induction patterns in three-spined stickleback exposed to a transient and a persistent inducer.

Gao K, Brandt I, Goldstone JV, Jönsson ME

Comp. Biochem. Physiol. C Toxicol. Pharmacol. 154 (1) 42-55 [2011-06-00; online 2011-03-01]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Co-occurring SHOC2 and PTPN11 mutations in a patient with severe/complex Noonan syndrome-like phenotype.

Ekvall S, Hagenäs L, Allanson J, Annerén G, Bondeson ML

Am. J. Med. Genet. A 155A (6) 1217-1224 [2011-06-00; online 2011-05-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

(R,S)-dichlorprop herbicide in agricultural soil induces proliferation and expression of multiple dioxygenase-encoding genes in the indigenous microbial community.

Paulin MM, Nicolaisen MH, Sørensen J

Environ. Microbiol. 13 (6) 1513-1523 [2011-06-00; online 2011-03-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Detailed analysis of variants in FTO in association with body composition in a cohort of 70-year-olds suggests a weakened effect among elderly.

Jacobsson JA, Almén MS, Benedict C, ..., Lind L, Schiöth HB

PLoS ONE 6 (5) e20158 [2011-05-27; online 2011-05-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Multiple recognition assay reveals prostasomes as promising plasma biomarkers for prostate cancer.

Tavoosidana G, Ronquist G, Darmanis S, ..., Landegren UD, Kamali-Moghaddam M

Proc. Natl. Acad. Sci. U.S.A. 108 (21) 8809-8814 [2011-05-24; online 2011-05-11]

Affinity Proteomics Uppsala [Technology development] Clinical Biomarkers PLA and Single Cell Proteomics

Sequence and generation of mature ribosomal RNA transcripts in Dictyostelium discoideum.

Boesler C, Kruse J, Söderbom F, Hammann C

J. Biol. Chem. 286 (20) 17693-17703 [2011-05-20; online 2011-04-02]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Cardio-facio-cutaneous syndrome: does genotype predict phenotype?

Allanson JE, Annerén G, Aoki Y, ..., Verloes A, Zenker M

Am J Med Genet C Semin Med Genet 157C (2) 129-135 [2011-05-15; online 2011-04-16]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

A roadmap to generate renewable protein binders to the human proteome.

Colwill K, Renewable Protein Binder Working Group , Gräslund S

Nat. Methods 8 (7) 551-558 [2011-05-15; online 2011-05-15]

Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development]

Experimental evidence supports a sex-specific selective sieve in mitochondrial genome evolution.

Innocenti P, Morrow EH, Dowling DK

Science 332 (6031) 845-848 [2011-05-13; online 2011-05-14]

Cys-X scanning for expansion of active-site residues and modulation of catalytic functions in a glutathione transferase.

Norrgård MA, Hellman U, Mannervik B

J. Biol. Chem. 286 (19) 16871-16878 [2011-05-13; online 2011-04-02]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Methods for Analysis of Transcription Factor DNA-Binding Specificity In Vitro.

Jolma A, Taipale J

Subcell. Biochem. 52 (-) 155-173 [2011-05-11; online 2011-05-11]

Growth differentiation factor 15: a prognostic marker for recurrence in colorectal cancer.

Wallin U, Glimelius B, Jirström K, ..., Påhlman L, Birgisson H

Br. J. Cancer 104 (10) 1619-1627 [2011-05-10; online 2011-04-07]

Melanoma cells produce multiple laminin isoforms and strongly migrate on α5 laminin(s) via several integrin receptors.

Oikawa Y, Hansson J, Sasaki T, ..., Tryggvason K, Patarroyo M

Exp. Cell Res. 317 (8) 1119-1133 [2011-05-01; online 2011-01-05]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Characterization of NPY Y2 receptor protein expression in the mouse brain. II. Coexistence with NPY, the Y1 receptor, and other neurotransmitter-related molecules.

Stanić D, Mulder J, Watanabe M, Hökfelt T

J. Comp. Neurol. 519 (7) 1219-1257 [2011-05-01; online 2011-04-01]

The 12q14 microdeletion syndrome: six new cases confirming the role of HMGA2 in growth.

Lynch SA, Foulds N, Thuresson AC, ..., Ennis S, Sharkey F

Eur. J. Hum. Genet. 19 (5) 534-539 [2011-05-00; online 2011-01-27]

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Parental criticism and externalizing behavior problems in adolescents: the role of environment and genotype-environment correlation.

Narusyte J, Neiderhiser JM, Andershed AK, ..., Ganiban J, Lichtenstein P

J Abnorm Psychol 120 (2) 365-376 [2011-05-00; online 2011-02-02]

Directional genetic selection by pulp mill effluent on multiple natural populations of three-spined stickleback (Gasterosteus aculeatus).

Lind EE, Grahn M

Ecotoxicology 20 (3) 503-512 [2011-05-00; online 2011-04-02]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Nitrogenase gene amplicons from global marine surface waters are dominated by genes of non-cyanobacteria.

Farnelid H, Andersson AF, Bertilsson S, ..., Hagström Å, Riemann L

PLoS ONE 6 (4) e19223 [2011-04-29; online 2011-04-29]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Large scale library generation for high throughput sequencing.

Borgström E, Lundin S, Lundeberg J

PLoS ONE 6 (4) e19119 [2011-04-27; online 2011-04-27]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Structure and assembly-disassembly properties of wild-type transthyretin amyloid protofibrils observed with atomic force microscopy.

Pires RH, Saraiva MJ, Damas AM, Kellermayer MS

J. Mol. Recognit. 24 (3) 467-476 [2011-04-20; online 2011-04-20]

Novel asymmetrically localizing components of human centrosomes identified by complementary proteomics methods.

Jakobsen L, Vanselow K, Skogs M, ..., Hyman AA, Andersen JS

EMBO J. 30 (8) 1520-1535 [2011-04-20; online 2011-03-15]

Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements.

Skarin H, Håfström T, Westerberg J, Segerman B

BMC Genomics 12 (-) 185 [2011-04-12; online 2011-04-12]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Utilizing twins concordance rates to infer the predisposition to myasthenia gravis.

Ramanujam R, Pirskanen R, Ramanujam S, Hammarström L

Twin Res Hum Genet 14 (2) 129-136 [2011-04-00; online 2011-03-24]

Synthesis and application of a bromomethyl substituted scaffold to be used for efficient optimization of anti-virulence activity.

Chorell E, Bengtsson C, Sainte-Luce Banchelin T, ..., Hultgren SJ, Almqvist F

Eur J Med Chem 46 (4) 1103-1116 [2011-04-00; online 2011-01-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Kynurenine 3-monooxygenase (KMO) polymorphisms in schizophrenia: An association study

Holtze M, Saetre P, Erhardt S, ..., Jönsson EG, Schalling M

Schizophr. Res. 127 (1-3) 270-272 [2011-04-00; online 2011-04-00]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A candidate gene study of the type I interferon pathway implicates IKBKE and IL8 as risk loci for SLE.

Sandling JK, Garnier S, Sigurdsson S, ..., Rönnblom L, Syvänen AC

Eur. J. Hum. Genet. 19 (4) 479-484 [2011-04-00; online 2010-12-24]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

FATP4 missense and nonsense mutations cause similar features in Ichthyosis Prematurity Syndrome.

Sobol M, Dahl N, Klar J

BMC Res Notes 4 (-) 90 [2011-03-30; online 2011-03-30]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Human oral, gut, and plaque microbiota in patients with atherosclerosis.

Koren O, Spor A, Felin J, ..., Ley RE, Bäckhed F

Proc. Natl. Acad. Sci. U.S.A. 108 Suppl 1 (-) 4592-4598 [2011-03-15; online 2010-10-13]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Molecular characterization of acquired tolerance of tumor cells to picropodophyllin (PPP).

Hashemi J, Worrall C, Vasilcanu D, ..., Larsson O, Larsson C

PLoS ONE 6 (3) e14757 [2011-03-14; online 2011-03-14]

An assessment of CETP sequence variation in relation to cognitive decline and dementia risk.

PubMed

Reynolds CA, Gatz M, Pedersen NL, Prince JA

Int J Mol Epidemiol Genet 2 (2) 122-129 [2011-03-10; online 2011-03-10]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Decoding a substantial set of samples in parallel by massive sequencing.

Neiman M, Lundin S, Savolainen P, Ahmadian A

PLoS ONE 6 (3) e17785 [2011-03-09; online 2011-03-09]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease.

Coronary Artery Disease (C4D) Genetics Consortium

Nat. Genet. 43 (4) 339-344 [2011-03-06; online 2011-03-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Antibody suspension bead arrays.

Schwenk JM, Nilsson P

Methods Mol. Biol. 723 (-) 29-36 [2011-03-04; online 2011-03-04]

Affinity Proteomics Stockholm [Technology development]

Bioinformatic tools for using whole genome sequencing as a rapid high resolution diagnostic typing tool when tracing bioterror organisms in the food and feed chain.

Segerman B, De Medici D, Ehling Schulz M, ..., Van Rotterdam B, Knutsson R

Int. J. Food Microbiol. 145 Suppl 1 (-) S167-S176 [2011-03-01; online 2010-09-10]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Ultra-deep sequencing of mouse mitochondrial DNA: mutational patterns and their origins.

Ameur A, Stewart JB, Freyer C, ..., Larsson NG, Gyllensten U

PLoS Genet. 7 (3) e1002028 [2011-03-00; online 2011-03-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Systematic antibody and antigen-based proteomic profiling with microarrays.

Ayoglu B, Häggmark A, Neiman M, ..., Schwenk JM, Nilsson P

Expert Rev. Mol. Diagn. 11 (2) 219-234 [2011-03-00; online 2011-03-17]

Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development]

Genome-wide association analysis identifies variants associated with nonalcoholic fatty liver disease that have distinct effects on metabolic traits.

Speliotes EK, Yerges-Armstrong LM, Wu J, ..., Borecki IB, GOLD Consortium

PLoS Genet. 7 (3) e1001324 [2011-03-00; online 2011-03-10]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

CUBN is a gene locus for albuminuria.

Böger CA, Chen MH, Tin A, ..., Fox CS, Kao WH

J. Am. Soc. Nephrol. 22 (3) 555-570 [2011-03-00; online 2011-03-01]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Association of EBF1, FAM167A(C8orf13)-BLK and TNFSF4 gene variants with primary Sjögren's syndrome.

Nordmark G, Kristjansdottir G, Theander E, ..., Jonsson R, Syvänen AC

Genes Immun. 12 (2) 100-109 [2011-03-00; online 2010-09-23]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A novel unstable duplication upstream of HAS2 predisposes to a breed-defining skin phenotype and a periodic fever syndrome in Chinese Shar-Pei dogs.

Olsson M, Meadows JRS, Truvé K, ..., Tintle L, Lindblad-Toh K

PLoS Genet. 7 (3) e1001332 [2011-03-00; online 2011-03-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Expression of 5,8-LDS of Aspergillus fumigatus and its dioxygenase domain. A comparison with 7,8-LDS, 10-dioxygenase, and cyclooxygenase.

Hoffmann I, Jernerén F, Garscha U, Oliw EH

Arch. Biochem. Biophys. 506 (2) 216-222 [2011-02-15; online 2010-12-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Identification of epigenetically regulated genes that predict patient outcome in neuroblastoma.

Carén H, Djos A, Nethander M, ..., Nilsson S, Martinsson T

BMC Cancer 11 (-) 66 [2011-02-11; online 2011-02-11]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Performance of microarray and liquid based capture methods for target enrichment for massively parallel sequencing and SNP discovery.

Kiialainen A, Karlberg O, Ahlford A, ..., Lindblad-Toh K, Syvänen AC

PLoS ONE 6 (2) e16486 [2011-02-09; online 2011-02-09]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic association of sequence variants near AGER/NOTCH4 and dementia.

Bennet AM, Reynolds CA, Eriksson UK, ..., Pedersen NL, Prince JA

J. Alzheimers Dis. 24 (3) 475-484 [2011-02-08; online 2011-02-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The Swedish new variant of Chlamydia trachomatis.

Unemo M, Clarke IN

Curr. Opin. Infect. Dis. 24 (1) 62-69 [2011-02-00; online 2010-12-16]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Sun-induced nonsynonymous p53 mutations are extensively accumulated and tolerated in normal appearing human skin.

Ståhl PL, Stranneheim H, Asplund A, ..., Pontén F, Lundeberg J

J. Invest. Dermatol. 131 (2) 504-508 [2011-02-00; online 2010-10-15]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Reactive astrocytes and Wnt/β-catenin signaling link nigrostriatal injury to repair in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine model of Parkinson's disease.

L'Episcopo F, Tirolo C, Testa N, ..., Pluchino S, Marchetti B

Neurobiol. Dis. 41 (2) 508-527 [2011-02-00; online 2010-11-09]

High-resolution genomic screening in mantle cell lymphoma--specific changes correlate with genomic complexity, the proliferation signature and survival.

Halldórsdóttir AM, Sander B, Göransson H, ..., Rosenquist R, Ehrencrona H

Genes Chromosomes Cancer 50 (2) 113-121 [2011-02-00; online 2010-12-01]

Array and Analysis Facility NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetic variation on chromosome 9p21 shows association with the ischaemic stroke subtype large-vessel disease in a Swedish sample aged ≤ 70.

Olsson S, Jood K, Blomstrand C, Jern C

Eur. J. Neurol. 18 (2) 365-367 [2011-02-00; online 2010-05-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

GAD1 is a biomarker for benign and malignant prostatic tissue.

Jaraj SJ, Augsten M, Häggarth L, ..., Ostman A, Egevad L

Scand. J. Urol. Nephrol. 45 (1) 39-45 [2011-02-00; online 2010-11-26]

Diagnostic biomarkers of prostate cancer.

Häggarth L, Hägglöf C, Jaraj SJ, ..., Ostman A, Egevad L

Scand. J. Urol. Nephrol. 45 (1) 60-67 [2011-02-00; online 2010-11-03]

Common pathogenetic mechanism involving human chromosome 18 in familial and sporadic ileal carcinoid tumors.

Cunningham JL, Díaz de Ståhl T, Sjöblom T, ..., Dumanski JP, Janson ET

Genes Chromosomes Cancer 50 (2) 82-94 [2011-02-00; online 2010-11-26]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Tumor-specific HMG-CoA reductase expression in primary premenopausal breast cancer predicts response to tamoxifen.

Brennan DJ, Laursen H, O'Connor DP, ..., Rydén L, Jirström K

Breast Cancer Res. 13 (1) R12 [2011-01-31; online 2011-01-31]

HRG inhibits tumor growth and metastasis by inducing macrophage polarization and vessel normalization through downregulation of PlGF.

Rolny C, Mazzone M, Tugues S, ..., Claesson-Welsh L, Carmeliet P

Cancer Cell 19 (1) 31-44 [2011-01-18; online 2011-01-11]

Fine mapping and replication of QTL in outbred chicken advanced intercross lines.

Besnier F, Wahlberg P, Rönnegård L, ..., Siegel PB, Carlborg O

Genet. Sel. Evol. 43 (1) 3 [2011-01-17; online 2011-01-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

New CYP1 genes in the frog Xenopus (Silurana) tropicalis: induction patterns and effects of AHR agonists during development.

Jönsson ME, Berg C, Goldstone JV, Stegeman JJ

Toxicol. Appl. Pharmacol. 250 (2) 170-183 [2011-01-15; online 2010-10-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

A systems biology model of the regulatory network in Populus leaves reveals interacting regulators and conserved regulation.

Street NR, Jansson S, Hvidsten TR

BMC Plant Biol. 11 (-) 13 [2011-01-13; online 2011-01-13]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Vitamin D receptor genotypes, ultraviolet radiation exposure, and risk of non-Hodgkin lymphoma.

Smedby KE, Eloranta S, Duvefelt K, ..., Hjalgrim H, Chang ET

Am. J. Epidemiol. 173 (1) 48-54 [2011-01-01; online 2010-11-16]

Targeted resequencing of candidate genes using selector probes.

Johansson H, Isaksson M, Sörqvist EF, ..., Ericsson O, Nilsson M

Nucleic Acids Res. 39 (2) e8 [2011-01-00; online 2010-11-08]

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Structure and etiology of co-occurring internalizing and externalizing disorders in adolescents.

Cosgrove VE, Rhee SH, Gelhorn HL, ..., Young SE, Hewitt JK

J Abnorm Child Psychol 39 (1) 109-123 [2011-01-00; online 2010-08-05]

Meta-analysis of the association between variants in SORL1 and Alzheimer disease.

Reitz C, Cheng R, Rogaeva E, ..., Mayeux R, Genetic and Environmental Risk in Alzheimer Disease 1 Consortium

Arch. Neurol. 68 (1) 99-106 [2011-01-00; online 2011-01-12]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Mechanisms of blast induced brain injuries, experimental studies in rats.

Risling M, Plantman S, Angeria M, ..., Arborelius U, Davidsson J

Neuroimage 54 Suppl 1 (-) S89-S97 [2011-01-00; online 2010-05-25]

Tryptophan hydroxylase gene 1 (TPH1) variants associated with cerebrospinal fluid 5-hydroxyindole acetic acid and homovanillic acid concentrations in healthy volunteers.

Andreou D, Saetre P, Werge T, ..., Terenius L, Jönsson EG

Psychiatry Res 180 (2-3) 63-67 [2010-12-30; online 2010-06-29]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Defining the transcriptome and proteome in three functionally different human cell lines.

Lundberg E, Fagerberg L, Klevebring D, ..., Mann M, Uhlen M

Mol. Syst. Biol. 6 (-) 450 [2010-12-21; online 2010-12-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics

Unbalanced translocation 9;16 in two children with dysmorphic features, and severe developmental delay: Evidence of cross-over within derivative chromosome 9 in patient #1.

Zambrano RM, Wohler E, Annerén G, ..., Cutting GR, Batista DA

Eur J Med Genet 54 (2) 189-193 [2010-12-07; online 2010-12-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Analysis of transcript and protein overlap in a human osteosarcoma cell line.

Klevebring D, Fagerberg L, Lundberg E, ..., Uhlén M, Lundeberg J

BMC Genomics 11 (-) 684 [2010-12-02; online 2010-12-02]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure Spatial Proteomics

Associations of gene sequence variation and serum levels of C-reactive protein and interleukin-6 with Alzheimer's disease and dementia.

Eriksson UK, Pedersen NL, Reynolds CA, ..., Dickman PW, Bennet AM

J. Alzheimers Dis. 23 (2) 361-369 [2010-12-01; online 2010-12-01]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Towards a knowledge-based Human Protein Atlas.

Uhlen M, Oksvold P, Fagerberg L, ..., Björling L, Ponten F

Nat. Biotechnol. 28 (12) 1248-1250 [2010-12-00; online 2010-12-09]

Thirty new loci for age at menarche identified by a meta-analysis of genome-wide association studies.

Elks CE, Perry JR, Sulem P, ..., Ong KK, Murray A

Nat. Genet. 42 (12) 1077-1085 [2010-12-00; online 2010-11-26]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The genetic architecture of domestication in the chicken: effects of pleiotropy and linkage.

Wright D, Rubin CJ, Martinez Barrio A, ..., Jensen P, Andersson L

Mol. Ecol. 19 (23) 5140-5156 [2010-12-00; online 2010-11-03]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

SOX10 expression in superficial spreading and nodular malignant melanomas.

Agnarsdóttir M, Sooman L, Bolander A, ..., Uhlen M, Hedstrand H

Melanoma Res. 20 (6) 468-478 [2010-12-00; online 2010-10-05]

SNPs in genes coding for ROS metabolism and signalling in association with docetaxel clearance.

Edvardsen H, Brunsvig PF, Solvang H, ..., Aamdal S, Kristensen VN

Pharmacogenomics J. 10 (6) 513-523 [2010-12-00; online 2010-02-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Interactions of dietary whole-grain intake with fasting glucose- and insulin-related genetic loci in individuals of European descent: a meta-analysis of 14 cohort studies.

Nettleton JA, McKeown NM, Kanoni S, ..., Franks PW, Meigs JB

Diabetes Care 33 (12) 2684-2691 [2010-12-00; online 2010-08-10]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

High frequency of p16(INK4A) promoter methylation in NRAS-mutated cutaneous melanoma.

Jonsson A, Tuominen R, Grafström E, Hansson J, Egyhazi S

J. Invest. Dermatol. 130 (12) 2809-2817 [2010-12-00; online 2010-08-13]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Distinct gene expression profiles in subsets of chronic lymphocytic leukemia expressing stereotyped IGHV4-34 B-cell receptors.

Marincevic M, Mansouri M, Kanduri M, ..., Stamatopoulos K, Rosenquist R

Haematologica 95 (12) 2072-2079 [2010-12-00; online 2010-08-31]

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Common variants at 10 genomic loci influence hemoglobin A₁(C) levels via glycemic and nonglycemic pathways.

Soranzo N, Sanna S, Wheeler E, ..., Barroso I, Meigs JB

Diabetes 59 (12) 3229-3239 [2010-12-00; online 2010-09-21]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A pyrosequencing study in twins shows that gastrointestinal microbial profiles vary with inflammatory bowel disease phenotypes.

Willing BP, Dicksved J, Halfvarson J, ..., Jansson JK, Engstrand L

Gastroenterology 139 (6) 1844-1854.e1 [2010-12-00; online 2010-09-08]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A high-density scan of the Z chromosome in Ficedula flycatchers reveals candidate loci for diversifying selection.

Backström N, Lindell J, Zhang Y, ..., Saetre GP, Ellegren H

Evolution 64 (12) 3461-3475 [2010-12-00; online 2010-07-16]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Keller L, Xu W, Wang HX, ..., Fratiglioni L, Graff C

J. Alzheimers Dis. 23 (3) 461-469 [2010-11-26; online 2010-11-26]

SNP detection and prediction of variability between chicken lines using genome resequencing of DNA pools.

Marklund S, Carlborg O

BMC Genomics 11 (-) 665 [2010-11-25; online 2010-11-25]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Gene expression profiling and chromatin immunoprecipitation identify DBN1, SETMAR and HIG2 as direct targets of SOX11 in mantle cell lymphoma.

Wang X, Björklund S, Wasik AM, ..., Christensson B, Sander B

PLoS ONE 5 (11) e14085 [2010-11-22; online 2010-11-22]

Toward next generation plasma profiling via heat-induced epitope retrieval and array-based assays.

Schwenk JM, Igel U, Neiman M, ..., Nilsson P, Uhlen M

Mol. Cell Proteomics 9 (11) 2497-2507 [2010-11-00; online 2010-08-05]

Affinity Proteomics Stockholm [Technology development]

Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution.

Heid IM, Jackson AU, Randall JC, ..., Mohlke KL, Lindgren CM

Nat. Genet. 42 (11) 949-960 [2010-11-00; online 2010-10-12]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Meiofauna reduces bacterial mineralization of naphthalene in marine sediment.

Näslund J, Nascimento FJ, Gunnarsson JS

ISME J 4 (11) 1421-1430 [2010-11-00; online 2010-05-14]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Creation of an antibody-based subcellular protein atlas.

Lundberg E, Uhlén M

Proteomics 10 (22) 3984-3996 [2010-11-00; online 2010-07-22]

Common variants in the ATP2B1 gene are associated with susceptibility to hypertension: the Japanese Millennium Genome Project.

Tabara Y, Kohara K, Kita Y, ..., Ueshima H, Miki T

Hypertension 56 (5) 973-980 [2010-11-00; online 2010-10-06]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Four novel Loci (19q13, 6q24, 12q24, and 5q14) influence the microcirculation in vivo.

Ikram MK, Sim X, Xueling S, ..., Vingerling JR, Wong TY

PLoS Genet. 6 (10) e1001184 [2010-10-28; online 2010-10-28]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Sensitive detection of Aβ protofibrils by proximity ligation--relevance for Alzheimer's disease.

Kamali-Moghaddam M, Pettersson FE, Wu D, ..., Lannfelt L, Landegren U

BMC Neurosci 11 (-) 124 [2010-10-05; online 2010-10-05]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Association analysis of PALB2 and BRCA2 in bipolar disorder and schizophrenia in a scandinavian case-control sample.

Tesli M, Athanasiu L, Mattingsdal M, ..., Djurovic S, Andreassen OA

Am. J. Med. Genet. B Neuropsychiatr. Genet. 153B (7) 1276-1282 [2010-10-05; online 2010-09-28]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

An exploratory model for G x E interaction on hippocampal volume in schizophrenia; obstetric complications and hypoxia-related genes.

Haukvik UK, Saetre P, McNeil T, ..., Jönsson EG, Agartz I

Prog. Neuropsychopharmacol. Biol. Psychiatry 34 (7) 1259-1265 [2010-10-01; online 2010-07-20]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Somatic mosaicism for chromosome X and Y aneuploidies in monozygotic twins heterozygous for sickle cell disease mutation.

Razzaghian HR, Shahi MH, Forsberg LA, ..., Westerman MP, Dumanski JP

Am. J. Med. Genet. A 152A (10) 2595-2598 [2010-10-00; online 2010-08-25]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Lycosid spiders and alternative food: Feeding behavior and implications for biological control

Kuusk AK, Ekbom B

Biological Control 55 (1) 20-26 [2010-10-00; online 2010-10-00]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Linkage to 20p13 including the ANGPT4 gene in families with mixed Alzheimer's disease and vascular dementia.

Sillén A, Brohede J, Lilius L, ..., Winblad B, Graff C

J. Hum. Genet. 55 (10) 649-655 [2010-10-00; online 2010-07-03]

Brain gene expression in relation to fearfulness in female red junglefowl (Gallus gallus).

Jöngren M, Westander J, Nätt D, Jensen P

Genes Brain Behav. 9 (7) 751-758 [2010-10-00; online 2010-07-06]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

A chromatin-remodeling protein is a component of fission yeast mediator.

Khorosjutina O, Wanrooij PH, Walfridsson J, ..., Ekwall K, Gustafsson CM

J. Biol. Chem. 285 (39) 29729-29737 [2010-09-24; online 2010-07-14]

A trans-acting locus regulates an anti-viral expression network and type 1 diabetes risk.

Heinig M, Petretto E, Wallace C, ..., Hubner N, Cook SA

Nature 467 (7314) 460-464 [2010-09-23; online 2010-09-10]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Pleiotropy in the presence of allelic heterogeneity: alternative genetic models for the influence of APOE on serum LDL, CSF amyloid-β42, and dementia.

Bennet AM, Reynolds CA, Gatz M, ..., Pedersen NL, Prince JA

J. Alzheimers Dis. 22 (1) 129-134 [2010-09-18; online 2010-09-18]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Trisomy and triploidy are sources of embryo mortality in the zebra finch.

Forstmeier W, Ellegren H

Proc. Biol. Sci. 277 (1694) 2655-2660 [2010-09-07; online 2010-05-07]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Small-molecule screening using a whole-cell viral replication reporter gene assay identifies 2-{[2-(benzoylamino)benzoyl]amino}-benzoic acid as a novel antiadenoviral compound.

Andersson EK, Strand M, Edlund K, ..., Mei Y, Wadell G

Antimicrob. Agents Chemother. 54 (9) 3871-3877 [2010-09-00; online 2010-06-30]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Profiling protein expression and interactions: proximity ligation as a tool for personalized medicine.

Blokzijl A, Friedman M, Pontén F, Landegren U

J. Intern. Med. 268 (3) 232-245 [2010-09-00; online 2010-08-11]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Production of ectomycorrhizal mycelium peaks during canopy closure in Norway spruce forests.

Wallander H, Johansson U, Sterkenburg E, Brandström Durling M, Lindahl BD

New Phytol. 187 (4) 1124-1134 [2010-09-00; online 2010-06-22]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

High-density screening reveals a different spectrum of genomic aberrations in chronic lymphocytic leukemia patients with 'stereotyped' IGHV3-21 and IGHV4-34 B-cell receptors.

Marincevic M, Cahill N, Gunnarsson R, ..., Stamatopoulos K, Rosenquist R

Haematologica 95 (9) 1519-1525 [2010-09-00; online 2010-04-28]

Association of IFIH1 and other autoimmunity risk alleles with selective IgA deficiency.

Ferreira RC, Pan-Hammarström Q, Graham RR, ..., Behrens TW, Hammarström L

Nat. Genet. 42 (9) 777-780 [2010-09-00; online 2010-08-10]

Expression of the RNA-binding protein RBM3 is associated with a favourable prognosis and cisplatin sensitivity in epithelial ovarian cancer.

Ehlén A, Brennan DJ, Nodin B, ..., Pontén F, Jirström K

J Transl Med 8 (-) 78 [2010-08-20; online 2010-08-20]

Familial cutaneous melanoma.

Hansson J

Adv. Exp. Med. Biol. 685 (-) 134-145 [2010-08-07; online 2010-08-07]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Biological, clinical and population relevance of 95 loci for blood lipids.

Teslovich TM, Musunuru K, Smith AV, ..., Boehnke M, Kathiresan S

Nature 466 (7307) 707-713 [2010-08-05; online 2010-08-06]

NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Topoisomerase I amplification in melanoma is associated with more advanced tumours and poor prognosis.

Ryan D, Rafferty M, Hegarty S, ..., Dervan PA, Gallagher WM

Pigment Cell Melanoma Res 23 (4) 542-553 [2010-08-00; online 2010-05-15]

The role of IL-1beta in reduced IL-7 production by stromal and epithelial cells: a model for impaired T-cell numbers in the gut during HIV-1 infection.

Thang PH, Ruffin N, Brodin D, ..., Vivar N, Chiodi F

J. Intern. Med. 268 (2) 181-193 [2010-08-00; online 2010-05-26]

Sex-linked barring in chickens is controlled by the CDKN2A /B tumour suppressor locus.

Hellström AR, Sundström E, Gunnarsson U, ..., Kerje S, Andersson L

Pigment Cell Melanoma Res 23 (4) 521-530 [2010-08-00; online 2010-03-29]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

No evidence for Z-chromosome rearrangements between the pied flycatcher and the collared flycatcher as judged by gene-based comparative genetic maps.

Backström N, Palkopoulou E, Qvarnström A, Ellegren H

Mol. Ecol. 19 (16) 3394-3405 [2010-08-00; online 2010-07-31]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Niemann-Pick C1 modulates hepatic triglyceride metabolism and its genetic variation contributes to serum triglyceride levels.

Uronen RL, Lundmark P, Orho-Melander M, ..., Syvänen AC, Ikonen E

Arterioscler. Thromb. Vasc. Biol. 30 (8) 1614-1620 [2010-08-00; online 2010-05-22]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genome-wide association study identifies a sequence variant within the DAB2IP gene conferring susceptibility to abdominal aortic aneurysm.

Gretarsdottir S, Baas AF, Thorleifsson G, ..., Thorsteinsdottir U, Stefansson K

Nat. Genet. 42 (8) 692-697 [2010-08-00; online 2010-07-14]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Association of genetic risk variants with expression of proximal genes identifies novel susceptibility genes for cardiovascular disease.

Folkersen L, van't Hooft F, Chernogubova E, ..., Eriksson P, BiKE and ASAP study groups

Circ Cardiovasc Genet 3 (4) 365-373 [2010-08-00; online 2010-06-22]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Identification of novel exons and transcribed regions by chimpanzee transcriptome sequencing.

Wetterbom A, Ameur A, Feuk L, Gyllensten U, Cavelier L

Genome Biol. 11 (7) R78 [2010-07-23; online 2010-07-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

A functional polymorphism in the HMGCR promoter affects transcriptional activity but not the risk for Alzheimer disease in Swedish populations.

Keller L, Murphy C, Wang HX, ..., Graff C, Meaney S

Brain Res. 1344 (-) 185-191 [2010-07-16; online 2010-05-11]

Induction patterns of new CYP1 genes in environmentally exposed rainbow trout.

Jönsson ME, Gao K, Olsson JA, Goldstone JV, Brandt I

Aquat. Toxicol. 98 (4) 311-321 [2010-07-15; online 2010-04-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Different SNP combinations in the GCH1 gene and use of labor analgesia.

Dabo F, Grönbladh A, Nyberg F, Sundström-Poromaa I, Akerud H

Mol Pain 6 (-) 41 [2010-07-15; online 2010-07-15]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Topoisomerase I regulates open chromatin and controls gene expression in vivo.

Durand-Dubief M, Persson J, Norman U, Hartsuiker E, Ekwall K

EMBO J. 29 (13) 2126-2134 [2010-07-07; online 2010-06-08]

Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo.

Wei GH, Badis G, Berger MF, ..., Bulyk ML, Taipale J

EMBO J. 29 (13) 2147-2160 [2010-07-07; online 2010-06-03]

Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.

Hedskog C, Mild M, Jernberg J, ..., Andersson B, Albert J

PLoS ONE 5 (7) e11345 [2010-07-07; online 2010-07-07]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Classification of DNA sequences using Bloom filters.

Stranneheim H, Käller M, Allander T, ..., Arvestad L, Lundeberg J

Bioinformatics 26 (13) 1595-1600 [2010-07-01; online 2010-05-18]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Tissue factor pathway inhibitor-2 is induced by fluid shear stress in vascular smooth muscle cells and affects cell proliferation and survival.

Ekstrand J, Razuvaev A, Folkersen L, Roy J, Hedin U

J. Vasc. Surg. 52 (1) 167-175 [2010-07-00; online 2010-06-12]

Subcellular distribution and expression of prenylated Rab acceptor 1 domain family, member 2 (PRAF2) in malignant glioma: Influence on cell survival and migration.

Borsics T, Lundberg E, Geerts D, ..., Wester K, Bachmann AS

Cancer Sci. 101 (7) 1624-1631 [2010-07-00; online 2010-03-19]

Revolutionizing membrane protein overexpression in bacteria.

Schlegel S, Klepsch M, Gialama D, ..., Slotboom DJ, de Gier JW

Microb Biotechnol 3 (4) 403-411 [2010-07-00; online 2009-09-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Ontogenetic complexity of sexual dimorphism and sex-specific selection.

Mank JE, Nam K, Brunström B, Ellegren H

Mol. Biol. Evol. 27 (7) 1570-1578 [2010-07-00; online 2010-02-10]

Gene expression analysis in hypoplastic lungs in the nitrofen model of congenital diaphragmatic hernia.

Burgos CM, Uggla AR, Fagerström-Billai F, ..., Frenckner B, Nord M

J. Pediatr. Surg. 45 (7) 1445-1454 [2010-07-00; online 2010-07-20]

Characterization of the RNA content of chromatin.

Mondal T, Rasmussen M, Pandey GK, Isaksson A, Kanduri C

Genome Res. 20 (7) 899-907 [2010-07-00; online 2010-04-21]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic evidence of multiple loci in dystocia--difficult labour.

Algovik M, Kivinen K, Peterson H, Westgren M, Kere J

BMC Med. Genet. 11 (-) 105 [2010-06-30; online 2010-06-30]

HIV-1 exposed uninfected men who have sex with men have increased levels of salivary CC-chemokines associated with sexual behavior.

Hasselrot K, Bratt G, Duvefelt K, ..., Sandström E, Broliden K

AIDS 24 (10) 1569-1575 [2010-06-19; online 2010-06-16]

Genome-wide mapping of estrogen receptor-beta-binding regions reveals extensive cross-talk with transcription factor activator protein-1.

Zhao C, Gao H, Liu Y, ..., Gustafsson JA, Dahlman-Wright K

Cancer Res. 70 (12) 5174-5183 [2010-06-15; online 2010-05-27]

Interstitial Deletions at 6q14.1-q15 Associated with Obesity, Developmental Delay and a Distinct Clinical Phenotype.

Wentzel C, Lynch SA, Stattin EL, ..., Annerén G, Thuresson AC

Mol Syndromol 1 (2) 75-81 [2010-06-09; online 2010-06-09]

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Analysis of oestrogen regulation of alpha-, beta- and gamma-secretase gene and protein expression in cultured human neuronal and glial cells.

Nord LC, Sundqvist J, Andersson E, Fried G

Neurodegener Dis 7 (6) 349-364 [2010-06-04; online 2010-06-04]

Genetic diversity and differentiation among Lagopus lagopus populations in Scandinavia and Scotland: evolutionary significant units confirmed by SNP markers.

Quintela M, Berlin S, Wang B, Höglund J

Mol. Ecol. 19 (12) 2380-2393 [2010-06-01; online 2010-07-20]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Tissue tumor marker expression in smokers, including serum cotinine concentrations, in women with cervical intraepithelial neoplasia or normal squamous cervical epithelium.

Samir R, Asplund A, Tot T, Pekar G, Hellberg D

Am. J. Obstet. Gynecol. 202 (6) 579.e1-579.e7 [2010-06-00; online 2010-01-12]

Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities.

Jolma A, Kivioja T, Toivonen J, ..., Ukkonen E, Taipale J

Genome Res. 20 (6) 861-873 [2010-06-00; online 2010-04-10]

Karolinska High Throughput Center (KHTC) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Improving Bayesian credibility intervals for classifier error rates using maximum entropy empirical priors.

Gustafsson MG, Wallman M, Wickenberg Bolin U, ..., Andersson CR, Isaksson A

Artif Intell Med 49 (2) 93-104 [2010-06-00; online 2010-03-30]

Genetics of HPA-axis, depression and suicidality.

Wasserman D, Wasserman J, Sokolowski M

Eur. Psychiatry 25 (5) 278-280 [2010-06-00; online 2010-05-07]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic analysis of metabolic traits in an intercross between body weight-selected chicken lines.

Ek W, Strömstedt L, Wahlberg P, ..., Andersson L, Carlborg O

Physiol. Genomics 42 (1) 20-22 [2010-06-00; online 2010-03-25]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

PubMed

Antibody-based proteomics for discovery and exploration of proteins expressed in pancreatic islets.

Lindskog C, Asplund A, Engkvist M, ..., Korsgren O, Ponten F

Discov Med 9 (49) 565-578 [2010-06-00; online 2010-07-01]

Alpha terpineol: a potential anticancer agent which acts through suppressing NF-kappaB signalling.

PubMed

Hassan SB, Gali-Muhtasib H, Göransson H, Larsson R

Anticancer Res. 30 (6) 1911-1919 [2010-06-00; online 2010-07-24]

A variant near the interleukin-6 gene is associated with fat mass in Caucasian men.

Andersson N, Strandberg L, Nilsson S, ..., Jansson JO, Osteoporotic Fractures in Men MrOS Research Group

Int J Obes (Lond) 34 (6) 1011-1019 [2010-06-00; online 2010-02-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Molecular make-up of the glomerular filtration barrier.

Patrakka J, Tryggvason K

Biochem. Biophys. Res. Commun. 396 (1) 164-169 [2010-05-21; online 2010-05-25]

Analysis of lipid pathway genes indicates association of sequence variation near SREBF1/TOM1L2/ATPAF2 with dementia risk.

Reynolds CA, Hong MG, Eriksson UK, ..., Pedersen NL, Prince JA

Hum. Mol. Genet. 19 (10) 2068-2078 [2010-05-15; online 2010-02-20]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Adipose tissue pathways involved in weight loss of cancer cachexia.

Dahlman I, Mejhert N, Linder K, ..., Rydén M, Arner P

Br. J. Cancer 102 (10) 1541-1548 [2010-05-11; online 2010-04-22]

Genetic risk factors in lupus nephritis and IgA nephropathy--no support of an overlap.

Vuong MT, Gunnarsson I, Lundberg S, ..., Jacobson SH, Padyukov L

PLoS ONE 5 (5) e10559 [2010-05-10; online 2010-05-10]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Chd1 remodelers maintain open chromatin and regulate the epigenetics of differentiation.

Persson J, Ekwall K

Exp. Cell Res. 316 (8) 1316-1323 [2010-05-01; online 2010-03-10]

Variation in STAT4 is associated with systemic lupus erythematosus in a Finnish family cohort.

Hellquist A, Sandling JK, Zucchelli M, ..., Syvänen AC, Kere J

Ann. Rheum. Dis. 69 (5) 883-886 [2010-05-00; online 2009-09-01]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The impact of RNA standardization and heterogeneous gene expression on the results of cDNA array of human breast carcinoma.

Khoshnoud R, He Q, Sylván M, ..., Rutqvist L, Skog S

Int. J. Mol. Med. 25 (5) 735-741 [2010-05-00; online 2010-04-08]

Mapping of the fibroblast growth factors in human white adipose tissue.

Mejhert N, Galitzky J, Pettersson AT, ..., Arner P, Rydén M

J. Clin. Endocrinol. Metab. 95 (5) 2451-2457 [2010-05-00; online 2010-03-17]

Gene-specific and global methylation patterns predict outcome in patients with acute myeloid leukemia.

Deneberg S, Grövdal M, Karimi M, ..., Hellström-Lindberg E, Lehmann S

Leukemia 24 (5) 932-941 [2010-05-00; online 2010-03-20]

Detailed physiologic characterization reveals diverse mechanisms for novel genetic Loci regulating glucose and insulin metabolism in humans.

Ingelsson E, Langenberg C, Hivert MF, ..., Florez JC, MAGIC investigators

Diabetes 59 (5) 1266-1275 [2010-05-00; online 2010-02-27]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Abundance and expression of enantioselective rdpA and sdpA dioxygenase genes during degradation of the racemic herbicide (R,S)-2-(2,4-dichlorophenoxy)propionate in soil.

Paulin MM, Nicolaisen MH, Sørensen J

Appl. Environ. Microbiol. 76 (9) 2873-2883 [2010-05-00; online 2010-03-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

A STAT4 risk allele is associated with ischaemic cerebrovascular events and anti-phospholipid antibodies in systemic lupus erythematosus.

Svenungsson E, Gustafsson J, Leonard D, ..., Syvänen AC, Rönnblom L

Ann. Rheum. Dis. 69 (5) 834-840 [2010-05-00; online 2009-09-19]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A single fixation protocol for proteome-wide immunofluorescence localization studies.

Stadler C, Skogs M, Brismar H, Uhlén M, Lundberg E

J Proteomics 73 (6) 1067-1078 [2010-04-18; online 2009-11-10]

Increased throughput by parallelization of library preparation for massive sequencing.

Lundin S, Stranneheim H, Pettersson E, Klevebring D, Lundeberg J

PLoS ONE 5 (4) e10029 [2010-04-06; online 2010-04-06]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Tumour-specific HMG-CoAR is an independent predictor of recurrence free survival in epithelial ovarian cancer.

Brennan DJ, Brändstedt J, Rexhepaj E, ..., O'Herlihy C, Jirstrom K

BMC Cancer 10 (-) 125 [2010-04-01; online 2010-04-01]

The recombination landscape of the zebra finch Taeniopygia guttata genome.

Backström N, Forstmeier W, Schielzeth H, ..., Kempenaers B, Ellegren H

Genome Res. 20 (4) 485-495 [2010-04-00; online 2010-03-31]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Reaction mechanism of 5,8-linoleate diol synthase, 10R-dioxygenase, and 8,11-hydroperoxide isomerase of Aspergillus clavatus.

Jernerén F, Garscha U, Hoffmann I, Hamberg M, Oliw EH

Biochim. Biophys. Acta 1801 (4) 503-507 [2010-04-00; online 2010-01-05]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

PubMed

Increased serum progesterone and estradiol correlate to increased COX-2 tissue expression in cervical intraepithelial neoplasia.

Samir R, Tot T, Asplund A, Pekar G, Hellberg D

Anticancer Res. 30 (4) 1217-1222 [2010-04-00; online 2010-06-10]

ELMOD2, a candidate gene for idiopathic pulmonary fibrosis, regulates antiviral responses.

Pulkkinen V, Bruce S, Rintahaka J, ..., Matikainen S, Kere J

FASEB J. 24 (4) 1167-1177 [2010-04-00; online 2009-12-08]

Copy number variation, chromosome rearrangement, and their association with recombination during avian evolution.

Völker M, Backström N, Skinner BM, ..., Ellegren H, Griffin DK

Genome Res. 20 (4) 503-511 [2010-04-00; online 2010-03-31]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Novel associations of multiple genetic loci with plasma levels of factor VII, factor VIII, and von Willebrand factor: The CHARGE (Cohorts for Heart and Aging Research in Genome Epidemiology) Consortium.

Smith NL, Chen MH, Dehghan A, ..., Tang W, O'Donnell CJ

Circulation 121 (12) 1382-1392 [2010-03-30; online 2010-03-17]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Whole-genome resequencing reveals loci under selection during chicken domestication.

Rubin C, Zody MC, Eriksson J, ..., Lindblad-Toh K, Andersson L

Nature 464 (7288) 587-591 [2010-03-25; online 2010-03-12]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

In-depth transcriptome analysis reveals novel TARs and prevalent antisense transcription in human cell lines.

Klevebring D, Bjursell M, Emanuelsson O, Lundeberg J

PLoS ONE 5 (3) e9762 [2010-03-25; online 2010-03-25]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genome-wide characterisation of the Gcn5 histone acetyltransferase in budding yeast during stress adaptation reveals evolutionarily conserved and diverged roles.

Xue-Franzén Y, Johnsson A, Brodin D, ..., Bürglin TR, Wright AP

BMC Genomics 11 (-) 200 [2010-03-25; online 2010-03-25]

Short-term antibiotic treatment has differing long-term impacts on the human throat and gut microbiome.

Jakobsson HE, Jernberg C, Andersson AF, ..., Jansson JK, Engstrand L

PLoS ONE 5 (3) e9836 [2010-03-24; online 2010-03-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Sustained inflammation due to nuclear factor-kappa B activation in irradiated human arteries.

Halle M, Gabrielsen A, Paulsson-Berne G, ..., Farnebo F, Tornvall P

J. Am. Coll. Cardiol. 55 (12) 1227-1236 [2010-03-23; online 2010-03-20]

Investigation of gene dosage imbalances in patients with Noonan syndrome using multiplex ligation-dependent probe amplification analysis.

Nyström AM, Ekvall S, Thuresson AC, ..., Annerén G, Bondeson ML

Eur J Med Genet 53 (3) 117-121 [2010-03-17; online 2010-03-17]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Global and unbiased detection of splice junctions from RNA-seq data.

Ameur A, Wetterbom A, Feuk L, Gyllensten U

Genome Biol. 11 (3) R34 [2010-03-17; online 2010-03-17]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The sexually antagonistic genes of Drosophila melanogaster.

Innocenti P, Morrow EH

PLoS Biol. 8 (3) e1000335 [2010-03-16; online 2010-03-16]

The tryptophan hydroxylase 1 (TPH1) gene, schizophrenia susceptibility, and suicidal behavior: a multi-centre case-control study and meta-analysis.

Saetre P, Lundmark P, Wang A, ..., Terenius L, Jönsson EG

Am. J. Med. Genet. B Neuropsychiatr. Genet. 153B (2) 387-396 [2010-03-05; online 2009-06-16]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Association between methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism and age of onset in schizophrenia.

Vares M, Saetre P, Deng H, ..., Terenius L, Jönsson EG

Am. J. Med. Genet. B Neuropsychiatr. Genet. 153B (2) 610-618 [2010-03-05; online 2009-09-12]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The impact of tissue fixatives on morphology and antibody-based protein profiling in tissues and cells.

Paavilainen L, Edvinsson A, Asplund A, ..., Pontén F, Wester K

J. Histochem. Cytochem. 58 (3) 237-246 [2010-03-00; online 2009-11-11]

Comparative genomics based on massive parallel transcriptome sequencing reveals patterns of substitution and selection across 10 bird species.

Künstner A, Wolf JB, Backström N, ..., Warren WC, Ellegren H

Mol. Ecol. 19 Suppl 1 (Suppl 1) 266-276 [2010-03-00; online 2010-04-02]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Appearance of Cxcl10-expressing cell clusters is common for traumatic brain injury and neurodegenerative disorders.

Israelsson C, Bengtsson H, Lobell A, ..., Hillered L, Ebendal T

Eur. J. Neurosci. 31 (5) 852-863 [2010-03-00; online 2010-04-09]

Molecular profiling using tissue microarrays as a tool to identify predictive biomarkers in laryngeal cancer treated with radiotherapy.

PubMed

Holgersson G, Ekman S, Reizenstein J, ..., Hellström K, Bergström S

Cancer Genomics Proteomics 7 (1) 1-7 [2010-02-26; online 2010-02-26]

Gene-specific FACS sorting method for target selection in high-throughput amplicon sequencing.

Sandberg J, Neiman M, Ahmadian A, Lundeberg J

BMC Genomics 11 (-) 140 [2010-02-26; online 2010-02-26]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

High-density linkage mapping and evolution of paralogs and orthologs in Salix and Populus.

Berlin S, Lagercrantz U, von Arnold S, Ost T, Rönnberg-Wästljung AC

BMC Genomics 11 (-) 129 [2010-02-23; online 2010-02-23]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Coffee consumption and CYP1A2 genotype in relation to bone mineral density of the proximal femur in elderly men and women: a cohort study.

Hallström H, Melhus H, Glynn A, ..., Syvänen AC, Michaëlsson K

Nutr Metab (Lond) 7 (-) 12 [2010-02-22; online 2010-02-22]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

DNA methylation for subtype classification and prediction of treatment outcome in patients with childhood acute lymphoblastic leukemia.

Milani L, Lundmark A, Kiialainen A, ..., Lönnerholm G, Syvänen AC

Blood 115 (6) 1214-1225 [2010-02-11; online 2009-11-25]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

SUMOylation mediates the nuclear translocation and signaling of the IGF-1 receptor.

Sehat B, Tofigh A, Lin Y, ..., Lagergren J, Larsson O

Sci Signal 3 (108) ra10 [2010-02-09; online 2010-02-09]

NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Sequence variation in SORL1 and dementia risk in Swedes.

Reynolds CA, Hong MG, Eriksson UK, ..., Bennet AM, Prince JA

Neurogenetics 11 (1) 139-142 [2010-02-00; online 2009-08-05]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Sensitive plasma protein analysis by microparticle-based proximity ligation assays.

Darmanis S, Nong RY, Hammond M, ..., Landegren U, Kamali-Moghaddam M

Mol. Cell Proteomics 9 (2) 327-335 [2010-02-00; online 2009-12-04]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae.

Lantermann AB, Straub T, Strålfors A, ..., Ekwall K, Korber P

Nat. Struct. Mol. Biol. 17 (2) 251-257 [2010-02-00; online 2010-01-31]

New genetic loci implicated in fasting glucose homeostasis and their impact on type 2 diabetes risk.

Dupuis J, Langenberg C, Prokopenko I, ..., Florez JC, Barroso I

Nat. Genet. 42 (2) 105-116 [2010-02-00; online 2010-01-19]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Infection of mast cells with live streptococci causes a toll-like receptor 2- and cell-cell contact-dependent cytokine and chemokine response.

Rönnberg E, Guss B, Pejler G

Infect. Immun. 78 (2) 854-864 [2010-02-00; online 2009-11-26]

Global gene expression analysis of rodent motor neurons following spinal cord injury associates molecular mechanisms with development of postinjury spasticity.

Wienecke J, Westerdahl AC, Hultborn H, Kiehn O, Ryge J

J. Neurophysiol. 103 (2) 761-778 [2010-02-00; online 2009-11-27]

Genetic variation in GIPR influences the glucose and insulin responses to an oral glucose challenge.

Saxena R, Hivert MF, Langenberg C, ..., Wareham NJ, Watanabe RM

Nat. Genet. 42 (2) 142-148 [2010-02-00; online 2010-01-19]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genetic variants and disease-associated factors contribute to enhanced interferon regulatory factor 5 expression in blood cells of patients with systemic lupus erythematosus.

Feng D, Stone RC, Eloranta ML, ..., Rönnblom L, Barnes BJ

Arthritis Rheum. 62 (2) 562-573 [2010-02-00; online 2010-01-30]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Connective tissue growth factor is expressed in malignant cells of Hodgkin lymphoma but not in other mature B-cell lymphomas.

Birgersdotter A, Baumforth KR, Wei W, ..., Porwit A, Ernberg I

Am. J. Clin. Pathol. 133 (2) 271-280 [2010-02-00; online 2010-01-23]

Comparative protein profiling of serum and plasma using an antibody suspension bead array approach.

Schwenk JM, Igel U, Kato BS, ..., Uhlén M, Nilsson P

Proteomics 10 (3) 532-540 [2010-02-00; online 2009-12-03]

Affinity Proteomics Stockholm [Technology development]

Coexisting NRAS and BRAF mutations in primary familial melanomas with specific CDKN2A germline alterations.

Jovanovic B, Egyhazi S, Eskandarpour M, ..., Hayward NK, Hansson J

J. Invest. Dermatol. 130 (2) 618-620 [2010-02-00; online 2009-09-18]

NGI Short read [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure [Service]

Genetic and biochemical studies of SNPs of the mitochondrial A beta-degrading protease, hPreP.

Pinho CM, Björk BF, Alikhani N, ..., Glaser E, Graff C

Neurosci. Lett. 469 (2) 204-208 [2010-01-22; online 2009-12-08]

Differential genome-wide array-based methylation profiles in prognostic subsets of chronic lymphocytic leukemia.

Kanduri M, Cahill N, Göransson H, ..., Isaksson A, Rosenquist R

Blood 115 (2) 296-305 [2010-01-14; online 2009-11-10]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Association study of PDE4B gene variants in Scandinavian schizophrenia and bipolar disorder multicenter case-control samples.

Kähler AK, Otnaess MK, Wirgenes KV, ..., Andreassen OA, Djurovic S

Am. J. Med. Genet. B Neuropsychiatr. Genet. 153B (1) 86-96 [2010-01-05; online 2009-04-08]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

A computational screen for site selective A-to-I editing detects novel sites in neuron specific Hu proteins.

Ensterö M, Akerborg O, Lundin D, ..., Ohman M, Lagergren J

BMC Bioinformatics 11 (-) 6 [2010-01-04; online 2010-01-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The 2009 Nobel conference on the role of genetics in promoting suicide prevention and the mental health of the population.

Wasserman D, Terenius L, Wasserman J, Sokolowski M

Mol. Psychiatry 15 (1) 12-17 [2010-01-00; online 2009-12-24]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Large but not small copy-number alterations correlate to high-risk genomic aberrations and survival in chronic lymphocytic leukemia: a high-resolution genomic screening of newly diagnosed patients.

Gunnarsson R, Isaksson A, Mansouri M, ..., Juliusson G, Rosenquist R

Leukemia 24 (1) 211-215 [2010-01-00; online 2009-09-11]

Characterization of the cytotoxic properties of the benzimidazole fungicides, benomyl and carbendazim, in human tumour cell lines and primary cultures of patient tumour cells.

Laryea D, Gullbo J, Isaksson A, Larsson R, Nygren P

Anticancer Drugs 21 (1) 33-42 [2010-01-00; online 2009-09-30]

Association of polymorphisms in the SLIT2 axonal guidance gene with anger in suicide attempters.

Sokolowski M, Wasserman J, Wasserman D

Mol. Psychiatry 15 (1) 10-11 [2010-01-00; online 2009-12-24]

NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Tissue-Specific Protein Expression in Human Cells, Tissues and Organs

Marcus G, Oksvold P, Pontén F, Uhlén M

JPB 03 (10) - [2010-00-00; online 2010-00-00]

So what's a little free fluid?

Marx JA

Acad Emerg Med 7 (4) 383-384 [2000-04-00; online 2000-05-11]

Kinetics of c-phycocyanin reaction with hypochlorite.

Romay C, Gonzalez R, Pizarro M, Lissi E

J Protein Chem 19 (2) 151-155 [2000-02-00; online 2000-08-17]

Relationship between antibiotic feeding in animals and emergence of bacterial resistance in man.

Pohl P

J. Antimicrob. Chemother. 3 Suppl C (-) 67-72 [1977-11-00; online 1977-11-01]

The oxylog [proceedings].

PubMed

Humphrey SJ, Wolff HS

J Physiol 267 (1) 12P [1977-05-00; online 1977-05-01]