Publications 2020

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 Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] 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 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 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]

Structural Proteomics [Collaborative]

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 Compute and Storage [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]

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 Compute and Storage [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 Compute and Storage [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]

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 Compute and Storage [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 Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]

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 Compute and Storage [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]

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 Compute and Storage [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]

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 Compute and Storage [Service] Bioinformatics Long-term Support WABI [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 Compute and Storage [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 Compute and Storage [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 Compute and Storage [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 Compute and Storage [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 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 Compute and Storage [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 Compute and Storage [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 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 Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] 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 Compute and Storage [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]

Spatial Mass Spectrometry [Technology development]

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 Compute and Storage [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 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 Compute and Storage [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 Compute and Storage [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 Compute and Storage [Service] 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]

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]

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

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 Compute and Storage [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 Compute and Storage [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 Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [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 Compute and Storage [Service] Bioinformatics Support and Infrastructure 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]

Global Proteomics and Proteogenomics [Service]

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 Compute and Storage [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]

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]

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

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]

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

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

Autoimmunity and Serology Profiling [Service] Drug Discovery and Development (DDD) [Collaborative]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

AIDA Data Hub [Technology development]

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]

Bioinformatics Compute and Storage [Service] 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]

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]

Eukaryotic Single Cell Genomics (ESCG) [Service] Integrated Microscopy Technologies Stockholm [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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

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]

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

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]

Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]

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]

Affinity Proteomics Stockholm [Collaborative] Autoimmunity and Serology Profiling [Service] Bioinformatics Compute and Storage [Service]

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]

Integrated Microscopy Technologies Stockholm [Technology development]

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]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Service] Drug Discovery and Development (DDD) [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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]

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]

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]

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

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]

Integrated Microscopy Technologies Stockholm [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

Cryo-EM [Collaborative]

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]

Chemical Biology Consortium Sweden (CBCS) [Collaborative] Protein Science Facility (PSF) [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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]

Affinity Proteomics Stockholm [Service]

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]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Integrated Microscopy Technologies Stockholm [Technology development]

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]

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]

Eukaryotic Single Cell Genomics (ESCG) [Service]

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]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

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]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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 Umeå [Collaborative]

Transcriptome analysis of EPO and GFP HEK293 Cell-lines Reveal Shifts in Energy and ER Capacity Support Improved Erythropoietin Production in HEK293F Cells

Saghaleyni R, Malm M, Zrimec J, ..., Robinson JL, Rockberg J

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Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [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]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Affinity Proteomics Stockholm [Collaborative] Autoimmunity and Serology Profiling [Collaborative] Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Cellular Immunomonitoring [Collaborative] Swedish Metabolomics Centre (SMC) [Collaborative]

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]

Affinity Proteomics Stockholm [Service]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

Bioinformatics Compute and Storage [Service] Protein Science Facility (PSF) [Service]

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]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Bioinformatics Compute and Storage [Service] Cryo-EM [Service] Integrated Microscopy Technologies Umeå [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]

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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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]

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

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]

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

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]

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

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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 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]

Bioinformatics Compute and Storage [Service] 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]

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]

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]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Affinity Proteomics Stockholm [Service] Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]

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]

Affinity Proteomics Stockholm [Service] Bioinformatics Compute and Storage [Service]

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]

Structural basis of mitochondrial translation.

Aibara S, Singh V, Modelska A, Amunts A

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

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

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]

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

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]

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

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]

Bioinformatics Compute and Storage [Service] CRISPR Functional Genomics [Collaborative]

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]

PLA and Single Cell Proteomics [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Integrated Microscopy Technologies Stockholm [Collaborative]

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]

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

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]

BioImage Informatics [Service]

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]

Drug Discovery and Development (DDD) [Service]

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]

Eukaryotic Single Cell Genomics (ESCG) [Service]

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]

BioImage Informatics [Technology development] Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]

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 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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Technologies for assessing vaccine responses in the very young.

Brodin P

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

Cellular Immunomonitoring [Technology development]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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 Compute and Storage [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]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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 Compute and Storage [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 2020-04-19]

Integrated Microscopy Technologies Stockholm [Service]

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

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

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]

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 Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]

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 Compute and Storage [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 Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] 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]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

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]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Service]

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]

Global Proteomics and Proteogenomics [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

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 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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service]

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 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 Compute and Storage [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 Compute and Storage [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]

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 Compute and Storage [Service] 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 Compute and Storage [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 Compute and Storage [Service] 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]

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.

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Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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Bioinformatics Compute and Storage [Service] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

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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.

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Mol Cancer Res 18 (7) 981-991 [2020-07-00; online 2020-03-31]

Bioinformatics Compute and Storage [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.

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APMIS 128 (7) 465-475 [2020-07-00; online 2020-05-23]

Gastric Microbiota in a Low-Helicobacter pylori Prevalence General Population and Their Associations With Gastric Lesions.

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Bioinformatics Compute and Storage [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.

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Nat Ecol Evol 4 (7) 979-986 [2020-07-00; online 2020-05-04]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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EBioMedicine 57 (-) 102854 [2020-07-00; online 2020-07-03]

Dynamic allosteric communication pathway directing differential activation of the glucocorticoid receptor.

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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

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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

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

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Zhong X, Lundberg M, Råberg L

Ecol Evol 10 (13) 6421-6434 [2020-07-00; online 2020-05-25]

Bioinformatics Compute and Storage [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.

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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.

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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.

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PLoS Comput. Biol. 16 (7) e1007976 [2020-07-00; online 2020-07-23]

Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

A Sample Preparation Protocol for High Throughput Immunofluorescence of Suspension Cells on an Adherent Surface.

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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.

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Orphanet J Rare Dis 15 (1) 170 [2020-06-30; online 2020-06-30]

Drug Discovery and Development (DDD)

Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion.

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BMC Biol. 18 (1) 78 [2020-06-30; online 2020-06-30]

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.

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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.

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BMC Med Genomics 13 (1) 85 [2020-06-26; online 2020-06-26]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Evolutionary History of the Marchantia polymorpha Complex.

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Front Plant Sci 11 (-) 829 [2020-06-26; online 2020-06-26]

Bioinformatics Compute and Storage [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.

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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.

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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.

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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 Compute and Storage [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 Compute and Storage [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.

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Sci Rep 10 (1) 10127 [2020-06-23; online 2020-06-23]

Genome Engineering Zebrafish [Collaborative]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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 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]

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 Compute and Storage [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.

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Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [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]

High genomic-based predicted strain coverage among invasive meningococcal isolates when combining Bexsero and Trumenba vaccines.

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Vaccine 38 (28) 4374-4378 [2020-06-09; online 2020-05-12]

CYCLIN-B1/2 and -D1 act in opposition to coordinate cortical progenitor self-renewal and lineage commitment.

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Nat Commun 11 (1) 2898 [2020-06-09; online 2020-06-09]

Bioinformatics Compute and Storage [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.

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Arthritis Res. Ther. 22 (1) 130 [2020-06-05; online 2020-06-05]

Bioinformatics Compute and Storage [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.

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BMC Genomics 21 (1) 385 [2020-06-03; online 2020-06-03]

Bioinformatics Compute and Storage [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 Compute and Storage [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

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 Compute and Storage [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]

The mating type system of the rare polypore Hapalopilus croceus

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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.

Brodin P

Hum. Genet. 139 (6-7) 795-799 [2020-06-00; online 2020-02-10]

Cellular Immunomonitoring [Technology development]

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 Compute and Storage [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 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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [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 [2020-06-00; online 2020-05-25]

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]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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]

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]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]

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]

BioImage Informatics [Service] Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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 [2020-05-13; online 2020-05-13]

Bioinformatics Compute and Storage [Service] In Situ Sequencing (ISS) [Collaborative]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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 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]

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

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]

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]

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Yin Y, Shelke GV, Lässer C, Brismar H, Lötvall J

Respir. Res. 21 (1) 101 [2020-05-01; online 2020-05-01]

Integrated Microscopy Technologies Stockholm [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

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 Compute and Storage [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]

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]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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]

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]

Drug Discovery and Development (DDD)

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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 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 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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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]

Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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 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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service] Systems Biology [Collaborative]

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]

Cryo-EM [Collaborative]

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]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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 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 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 Compute and Storage [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 Compute and Storage [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]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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

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Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

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]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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]

Global Proteomics and Proteogenomics [Service]

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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Cryo-EM [Technology development]

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]

Affinity Proteomics Stockholm [Service] Bioinformatics Compute and Storage [Service]

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]

Spatial Mass Spectrometry [Technology development]

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]

Autoimmunity and Serology Profiling [Service] Bioinformatics Compute and Storage [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

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]

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]

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]

Drug Discovery and Development (DDD)

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]

Bioinformatics Compute and Storage [Service] Clinical Genomics Linköping [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

Cryo-EM [Collaborative]

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]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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 Support, Infrastructure and Training [Technology development] Systems Biology [Technology development]

Marine Sediments Illuminate Chlamydiae Diversity and Evolution.

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Curr. Biol. 30 (6) 1032-1048.e7 [2020-03-23; online 2020-03-05]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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

Inherited DNA Repair Gene Mutations in Men with Lethal Prostate Cancer.

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Genes 11 (3) 314 [2020-03-14; online 2020-03-14]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Ecosystem-wide metagenomic binning enables prediction of ecological niches from genomes.

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Commun Biol 3 (1) 119 [2020-03-13; online 2020-03-13]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Exploiting loss of heterozygosity for allele-selective colorectal cancer chemotherapy.

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Nat Commun 11 (1) 1308 [2020-03-11; online 2020-03-11]

Bioinformatics Compute and Storage [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 Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Uncovering diversity and metabolic spectrum of animals in dead zone sediments.

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Commun Biol 3 (1) 106 [2020-03-06; online 2020-03-06]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Ribonucleotide reductase inhibitors suppress SAMHD1 ara-CTPase activity enhancing cytarabine efficacy.

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EMBO Mol Med 12 (3) e10419 [2020-03-06; online 2020-01-17]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The Molecular Anatomy of Mouse Skin during Hair Growth and Rest.

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Cell Stem Cell 26 (3) 441-457.e7 [2020-03-05; online 2020-02-27]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Stressful Beginnings with Long-Term Consequences.

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Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]

Short-Range Order and Transport Properties in Mixtures of the Protic Ionic Liquid [C2HIm][TFSI] with Water or Imidazole.

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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.

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

Transcriptomic resources for evolutionary studies in flat periwinkles and related species.

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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.

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Nutrients 12 (3) 681 [2020-03-03; online 2020-03-03]

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

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Nat Commun 11 (1) 1147 [2020-03-02; online 2020-03-02]

Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]

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Metabolomics 16 (3) 35 [2020-03-02; online 2020-03-02]

Tumor localized agonistic anti-CD40 therapy and beyond.

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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.

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ChemistryOpen 9 (3) 325-337 [2020-03-00; online 2020-03-02]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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Bioinformatics Compute and Storage [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.

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Eur. J. Hum. Genet. 28 (3) 349-357 [2020-03-00; online 2019-10-25]

Bioinformatics Compute and Storage [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]

In Situ Encapsulation of Nile Red or Doxorubicin during RAFT‐Mediated Emulsion Polymerization via Polymerization‐Induced Self‐Assembly for Biomedical Applications

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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.

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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

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Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

Heritability of Caries Scores, Trajectories, and Disease Subtypes.

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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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Glycoproteomics [Collaborative]

Apolipoprotein E impairs amyloid-β fibril elongation and maturation.

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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.

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J Glob Antimicrob Resist 20 (-) 285-289 [2020-03-00; online 2019-09-05]

Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]

PCSK6 Is a Key Protease in the Control of Smooth Muscle Cell Function in Vascular Remodeling.

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Circ. Res. 126 (5) 571-585 [2020-02-28; online 2020-01-02]

Global Proteomics and Proteogenomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

Clinical Genomics Örebro [Technology development]

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]

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

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]

Clinical Genomics Stockholm

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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.

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Front Microbiol 11 (-) 168 [2020-02-21; online 2020-02-21]

Achieving symptom relief in patients with Myalgic encephalomyelitis by targeting the neuro-immune interface and inducing disease tolerance

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Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Collaborative]

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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]

Integrated Microscopy Technologies Stockholm [Collaborative]

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]

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

The First Structure of an Active Mammalian dCTPase and its Complexes With Substrate Analogs and Products.

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J. Mol. Biol. 432 (4) 1126-1142 [2020-02-14; online 2020-01-15]

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Sci Rep 10 (1) 2512 [2020-02-13; online 2020-02-13]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Quinazoline Ligands Induce Cancer Cell Death through Selective STAT3 Inhibition and G-Quadruplex Stabilization.

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Elife 9 (-) - [2020-02-11; online 2020-02-11]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Low concentrations of the benzodiazepine drug oxazepam induce anxiolytic effects in wild-caught but not in laboratory zebrafish.

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Sci Rep 10 (1) 2043 [2020-02-06; online 2020-02-06]

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

Clonal competition within complex evolutionary hierarchies shapes AML over time.

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Nat Commun 11 (1) 579 [2020-02-05; online 2020-02-05]

Clinical Genomics Lund

A chromosome-scale reference genome for Giardia intestinalis WB.

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

Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses.

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Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Plasma kidney injury molecule-1 (p-KIM-1) levels and deterioration of kidney function over 16 years.

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

Glycogenin is Dispensable for Glycogen Synthesis in Human Muscle, and Glycogenin Deficiency Causes Polyglucosan Storage.

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Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies).

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Genome Biol Evol 12 (2) 3803-3817 [2020-02-01; online 2020-01-21]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Convergent Evolution of Hydrogenosomes from Mitochondria by Gene Transfer and Loss.

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

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Chemical Biology Consortium Sweden (CBCS) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund

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.

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Biomaterials 230 (-) 119571 [2020-02-00; online 2019-10-24]

Engineering yeast phospholipid metabolism for de novo oleoylethanolamide production.

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Nat. Chem. Biol. 16 (2) 197-205 [2020-02-00; online 2019-12-16]

Integrated Microscopy Technologies Gothenburg [Service]

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]

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

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]

BioImage Informatics [Service] Bioinformatics Compute and Storage [Service]

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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development] Clinical Genomics Stockholm [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Microbial Single Cell Genomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

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]

Bioinformatics Compute and Storage [Service] Integrated Microscopy Technologies Stockholm [Service]

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]

Drug Discovery and Development (DDD) [Technology development]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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

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]

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]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] CRISPR Functional Genomics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

DAF-16/FOXO requires Protein Phosphatase 4 to initiate transcription of stress resistance and longevity promoting genes.

Sen I, Zhou X, Chernobrovkin A, ..., Zubarev RA, Riedel CG

Nat Commun 11 (1) 138 [2020-01-09; online 2020-01-09]

Bioinformatics Compute and Storage [Service] Chemical Proteomics [Service]

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]

Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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]

Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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 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]

Bioinformatics Compute and Storage [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 [Collaborative]

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]

Structural Proteomics [Collaborative]

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]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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 Compute and Storage [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 Compute and Storage [Service] Global Proteomics and Proteogenomics [Collaborative]

Tailoring subtractive cell biopanning to identify diffuse gastric adenocarcinoma-associated antigens via human scFv antibodies.

Mehdipour T, Tohidkia MR, Ata Saei A, ..., Zubarev RA, Nouri M

Immunology 159 (1) 96-108 [2020-01-00; online 2019-11-08]

Chemical Proteomics [Service]

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]

Bioinformatics Compute and Storage [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 Compute and Storage [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]

Glycoproteomics [Collaborative]

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]

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]

Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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 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 Compute and Storage [Service] 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 Compute and Storage [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]

Swedish NMR Centre (SNC)

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]