Publications 2018

PRR14L mutations are associated with chromosome 22 acquired uniparental disomy, age-related clonal hematopoiesis and myeloid neoplasia.

Chase A, Pellagatti A, Singh S, ..., Boultwood J, Cross NCP

Leukemia - (-) - [2018-12-20; online 2018-12-20]

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

Targeted Delivery of Stk25 Antisense Oligonucleotides to Hepatocytes Protects Mice Against Nonalcoholic Fatty Liver Disease.

Cansby E, Nuñez-Durán E, Magnusson E, ..., Aghajan M, Mahlapuu M

Cellular and Molecular Gastroenterology and Hepatology 7 (3) 597-618 [2018-12-19; online 2018-12-19]

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

Carbon's Three-Center, Four-Electron Tetrel Bond, Treated Experimentally.

Karim A, Schulz N, Andersson H, ..., Keller S, Erdélyi M

J. Am. Chem. Soc. 140 (50) 17571-17579 [2018-12-19; online 2018-12-07]

Red Fluorescent Chlamydia trachomatis Applied to Live Cell Imaging and Screening for Antibacterial Agents.

Mojica SA, Eriksson AU, Davis RA, ..., Elofsson M, Gylfe Å

Front Microbiol 9 (-) 3151 [2018-12-18; online 2018-12-18]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Rainbow Trout Maintain Intestinal Transport and Barrier Functions Following Exposure to Polystyrene Microplastics.

Ašmonaitė G, Sundh H, Asker N, Carney Almroth B

Environ. Sci. Technol. 52 (24) 14392-14401 [2018-12-18; online 2018-12-05]

Integrated Microscopy Technologies Gothenburg [Service]

A multigene typing system for human adenoviruses reveals a new genotype in a collection of Swedish clinical isolates.

Kaján GL, Lipiec A, Bartha D, Allard A, Arnberg N

PLoS ONE 13 (12) e0209038 [2018-12-14; online 2018-12-14]

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

Significantly altered peripheral blood cell DNA methylation profile as a result of immediate effect of metformin use in healthy individuals.

Elbere I, Silamikelis I, Ustinova M, ..., Schiöth HB, Klovins J

Clin Epigenetics 10 (1) 156 [2018-12-13; online 2018-12-13]

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

Proteome Integral Stability Alteration assay dramatically increases throughput and sensitivity in profiling factor-induced proteome changes

Gaetani M, Sabatier P, Saei AA, ..., Lundstrom S, Zubarev RA

- - (-) - [2018-12-13; online 2018-12-13]

Chemical Proteomics [Technology development]

Transcriptional landscape of B cell precursor acute lymphoblastic leukemia based on an international study of 1,223 cases.

Li JF, Dai YT, Lilljebjörn H, ..., Chen SJ, Huang JY

Proc. Natl. Acad. Sci. U.S.A. 115 (50) E11711-E11720 [2018-12-11; online 2018-11-28]

Proteotyping bacteria: Characterization, differentiation and identification of pneumococcus and other species within the Mitis Group of the genus Streptococcus by tandem mass spectrometry proteomics.

Karlsson R, Gonzales-Siles L, Gomila M, ..., Kristiansson E, Moore ERB

PLoS ONE 13 (12) e0208804 [2018-12-10; online 2018-12-10]

Progress on Identifying and Characterizing the Human Proteome: 2018 Metrics from the HUPO Human Proteome Project.

Omenn GS, Lane L, Overall CM, ..., Baker MS, Deutsch EW

J. Proteome Res. 17 (12) 4031-4041 [2018-12-07; online 2018-08-23]

Affinity Proteomics Stockholm [Collaborative]

PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud.

Peters K, Bradbury J, Bergmann S, ..., Zanetti G, Steinbeck C

Gigascience - (-) - [2018-12-07; online 2018-12-07]

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

Cotranslational Folding of a Pentarepeat β-Helix Protein.

Notari L, Martínez-Carranza M, Farías-Rico JA, Stenmark P, von Heijne G

J. Mol. Biol. 430 (24) 5196-5206 [2018-12-07; online 2018-10-27]

Somatic Structural Alterations in Childhood Leukemia Can Be Backtracked in Neonatal Dried Blood Spots by Use of Whole-Genome Sequencing and Digital PCR.

Taylan F, Bang B, Öfverholm II, ..., Zachariadis V, Nordgren A

Clin. Chem. - (-) - [2018-12-05; online 2018-12-05]

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

Porous Cellulose Nanofiber-Based Microcapsules for Biomolecular Sensing.

Paulraj T, Wennmalm S, Riazanova AV, ..., Crespo GA, Svagan AJ

ACS Appl Mater Interfaces 10 (48) 41146-41154 [2018-12-05; online 2018-11-26]

Integrated Microscopy Technologies Stockholm [Collaborative]

A Novel Inorganic Sulfur Compound Metabolizing Ferroplasma-Like Population Is Suggested to Mediate Extracellular Electron Transfer.

Ni G, Simone D, Palma D, ..., Turner S, Dopson M

Front Microbiol 9 (-) 2945 [2018-12-05; online 2018-12-05]

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

Spatially and functionally distinct subclasses of breast cancer-associated fibroblasts revealed by single cell RNA sequencing.

Bartoschek M, Oskolkov N, Bocci M, ..., Björklund Å, Pietras K

Nat Commun 9 (1) 5150 [2018-12-04; online 2018-12-04]

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

Membrane fluidity is regulated by the C. elegans transmembrane protein FLD-1 and its human homologs TLCD1/2.

Ruiz M, Bodhicharla R, Svensk E, ..., Boren J, Pilon M

Elife 7 (-) - [2018-12-04; online 2018-12-04]

Integrated Microscopy Technologies Gothenburg [Service]

Crystal Structures and Cytotoxicity of ent-Kaurane-Type Diterpenoids from Two Aspilia Species.

Yaouba S, Valkonen A, Coghi P, ..., Erdélyi M, Yenesew A

Molecules 23 (12) 3199 [2018-12-04; online 2018-12-04]

Transcriptional and Epigenetic Changes Influencing Skeletal Muscle Metabolism in Women With Polycystic Ovary Syndrome.

Nilsson E, Benrick A, Kokosar M, ..., Ling C, Stener-Victorin E

J. Clin. Endocrinol. Metab. 103 (12) 4465-4477 [2018-12-01; online 2018-08-17]

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

Impact of forced fatty acid synthesis on metabolism and physiology of Saccharomyces cerevisiae.

Gossing M, Smialowska A, Nielsen J

FEMS Yeast Res. 18 (8) - [2018-12-01; online 2018-09-01]

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

Whole Exome Sequencing of Patients from Multicase Families with Systemic Lupus Erythematosus Identifies Multiple Rare Variants

Delgado-Vega AM, Martínez-Bueno M, Oparina NY, ..., Kozyrev SV, Alarcón-Riquelme ME

Sci Rep 8 (1) - [2018-12-00; online 2018-06-08]

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

Ulvan lyase from Formosa agariphila and its applicability in depolymerisation of ulvan extracted from three different Ulva species

Konasani VR, Jin C, Karlsson NG, Albers E

Algal Research 36 (-) 106-114 [2018-12-00; online 2018-12-00]

Transancestral GWAS of alcohol dependence reveals common genetic underpinnings with psychiatric disorders

Walters RK, None , Polimanti R, ..., Edenberg HJ, Agrawal A

Nat Neurosci 21 (12) 1656-1669 [2018-12-00; online 2018-11-26]

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

The gut microbiome participates in transgenerational inheritance of low-temperature responses in Drosophila melanogaster.

Zare A, Johansson AM, Karlsson E, Delhomme N, Stenberg P

FEBS Lett. 592 (24) 4078-4086 [2018-12-00; online 2018-11-15]

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

The Mutant p53-Targeting Compound APR-246 Induces ROS-Modulating Genes in Breast Cancer Cells.

Synnott NC, Madden SF, Bykov VJN, ..., Wiman KG, Duffy MJ

Transl Oncol 11 (6) 1343-1349 [2018-12-00; online 2018-09-06]

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

Targeting PFKFB3 radiosensitizes cancer cells and suppresses homologous recombination

Gustafsson NMS, Färnegårdh K, Bonagas N, ..., Olin T, Helleday T

Nat Commun 9 (1) - [2018-12-00; online 2018-09-24]

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

T-cell transcriptomics from peripheral blood highlights differences between polymyositis and dermatomyositis patients

Houtman M, Ekholm L, Hesselberg E, ..., Lundberg IE, Padyukov L

Arthritis Res. Ther. 20 (1) - [2018-12-00; online 2018-08-29]

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

Structure of a functional obligate complex III 2IV2 respiratory supercomplex from Mycobacterium smegmatis.

Wiseman B, Nitharwal RG, Fedotovskaya O, ..., Brzezinski P, Högbom M

Nat. Struct. Mol. Biol. 25 (12) 1128-1136 [2018-12-00; online 2018-12-05]

Stereocilin gene variants associated with episodic vertigo: expansion of the DFNB16 phenotype.

Frykholm C, Klar J, Tomanovic T, Ameur A, Dahl N

Eur. J. Hum. Genet. 26 (12) 1871-1874 [2018-12-00; online 2018-09-24]

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

Somatic mutagenesis in satellite cells associates with human skeletal muscle aging

Franco I, Johansson A, Olsson K, ..., Fischer H, Eriksson M

Nat Commun 9 (1) - [2018-12-00; online 2018-02-23]

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]

Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens: evidence from high-throughput sequencing

Onuț-Brännström I, Benjamin M, Scofield DG, ..., Lindström ES, Johannesson H

Sci Rep 8 (1) - [2018-12-00; online 2018-03-13]

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

RNA-sequencing reveals long-term effects of silver nanoparticles on human lung cells

Gliga AR, Di Bucchianico S, Lindvall J, Fadeel B, Karlsson HL

Sci Rep 8 (1) - [2018-12-00; online 2018-04-27]

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]

Publisher Correction: A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage

Ladds MJGW, van Leeuwen IMM, Drummond CJ, ..., McCormack E, Laín S

Nat Commun 9 (1) - [2018-12-00; online 2018-05-22]

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

Protein Profiling in Serum and Cerebrospinal Fluid Following Complex Surgery on the Thoracic Aorta Identifies Biological Markers of Neurologic Injury.

Lindblom RPF, Shen Q, Axén S, ..., Kamali-Moghaddam M, Thelin S

J. of Cardiovasc. Trans. Res. 11 (6) 503-516 [2018-12-00; online 2018-10-26]

Bioinformatics Compute and Storage [Service] PLA and Single Cell Proteomics [Collaborative]

Oxidatively stressed mitochondria-mimicking membranes: A molecular insight into their organization during apoptosis.

Dingeldein APG, Sparrman T, Gröbner G

Biochimica et Biophysica Acta (BBA) - Biomembranes 1860 (12) 2644-2654 [2018-12-00; online 2018-10-05]

Molecular Investigation of the Ciliate Spirostomum semivirescens, with First Transcriptome and New Geographical Records

Hines HN, Onsbring H, Ettema TJG, Esteban GF

Protist 169 (6) 875-886 [2018-12-00; online 2018-12-00]

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

Linking FOXO3, NCOA3, and TCF7L2 to Ras pathway phenotypes through a genome-wide forward genetic screen in human colorectal cancer cells

Kundu S, Ali MA, Handin N, ..., Hellström M, Sjöblom T

Genome Med 10 (1) - [2018-12-00; online 2018-01-04]

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

Intramolecular 13C analysis of tree rings provides multiple plant ecophysiology signals covering decades

Wieloch T, Ehlers I, Yu J, ..., Gessler A, Schleucher J

Sci Rep 8 (1) - [2018-12-00; online 2018-03-22]

Individual Genetic Variation Might Predict Acute Skin Reactions in Women Undergoing Adjuvant Breast Cancer Radiotherapy.

Oliva D, Nilsson M, Strandéus M, ..., Laytragoon-Lewin N, Lewin F

Anticancer Res. 38 (12) 6763-6770 [2018-12-00; online 2018-12-07]

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

High-efficient bacterial production of human ApoA-I amyloidogenic variants.

Del Giudice R, Lagerstedt JO

Protein Sci. 27 (12) 2101-2109 [2018-12-00; online 2018-10-07]

Genomic screening in rare disorders: New mutations and phenotypes, highlighting ALG14 as a novel cause of severe intellectual disability.

Kvarnung M, Taylan F, Nilsson D, ..., Nordgren A, Lundberg ES

Clin. Genet. 94 (6) 528-537 [2018-12-00; online 2018-10-15]

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

Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes

Alneberg J, Karlsson CMG, Divne AM, ..., Andersson AF, Pinhassi J

Microbiome 6 (1) - [2018-12-00; online 2018-09-28]

Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genome sequencing and conservation genomics in the Scandinavian wolverine population

Ekblom R, Brechlin B, Persson J, ..., Flagstad Ø, Ellegren H

Conservation Biology 32 (6) 1301-1312 [2018-12-00; online 2018-09-07]

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

Genetic characterization of a novel picorna-like virus in Culex spp. mosquitoes from Mozambique

Cholleti H, Hayer J, Fafetine J, Berg M, Blomström AL

Virol J 15 (1) - [2018-12-00; online 2018-04-18]

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

Gene expression correlated with delay in shell formation in larval Pacific oysters (Crassostrea gigas) exposed to experimental ocean acidification provides insights into shell formation mechanisms

De Wit P, Durland E, Ventura A, Langdon CJ

BMC Genomics 19 (1) - [2018-12-00; online 2018-02-22]

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

GWAS and colocalization analyses implicate carotid intima-media thickness and carotid plaque loci in cardiovascular outcomes

Franceschini N, None , Giambartolomei C, ..., Casas JP, O’Donnell CJ

Nat Commun 9 (1) - [2018-12-00; online 2018-12-03]

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

Extracellular nanovesicles released from the commensal yeast Malassezia sympodialis are enriched in allergens and interact with cells in human skin

Johansson HJ, Vallhov H, Holm T, ..., Lehtiö J, Scheynius A

Sci Rep 8 (1) - [2018-12-00; online 2018-06-15]

Bioinformatics Compute and Storage [Service] Cryo-EM [Service] Global Proteomics and Proteogenomics [Collaborative] Integrated Microscopy Technologies Stockholm [Collaborative]

Exploring benzimidazole resistance in Haemonchus contortus by next generation sequencing and droplet digital PCR

Baltrušis P, Halvarsson P, Höglund J

International Journal for Parasitology: Drugs and Drug Resistance 8 (3) 411-419 [2018-12-00; online 2018-12-00]

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

Epigenetics and early domestication: differences in hypothalamic DNA methylation between red junglefowl divergently selected for high or low fear of humans

Bélteky J, Agnvall B, Bektic L, ..., Jensen P, Guerrero-Bosagna C

Genet. Sel. Evol. 50 (1) - [2018-12-00; online 2018-04-02]

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

Effects of predation stress and food ration on perch gut microbiota

Zha Y, Eiler A, Johansson F, Svanbäck R

Microbiome 6 (1) - [2018-12-00; online 2018-02-06]

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

EMBLmyGFF3: a converter facilitating genome annotation submission to European Nucleotide Archive

Norling M, Jareborg N, Dainat J

BMC Res Notes 11 (1) - [2018-12-00; online 2018-08-13]

Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements

Svedberg J, Hosseini S, Chen J, ..., Lascoux M, Johannesson H

Nat Commun 9 (1) - [2018-12-00; online 2018-10-12]

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

Comprehensive analysis of CTNNB1 in adrenocortical carcinomas: Identification of novel mutations and correlation to survival

Maharjan R, Backman S, Åkerström T, Hellman P, Björklund P

Sci Rep 8 (1) 8610 [2018-12-00; online 2018-06-05]

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

Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction

Bornelöv S, Seroussi E, Yosefi S, ..., Andersson L, Friedman-Einat M

BMC Genomics 19 (1) - [2018-12-00; online 2018-04-26]

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

Anti-Rift Valley fever virus activity in vitro, pre-clinical pharmacokinetics and oral bioavailability of benzavir-2, a broad-acting antiviral compound

Islam MK, Strand M, Saleeb M, ..., Elofsson M, Evander M

Sci Rep 8 (1) - [2018-12-00; online 2018-01-31]

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

Analysis of porcine body size variation using re-sequencing data of miniature and large pigs

Reimer C, Rubin CJ, Sharifi AR, ..., Schlather M, Simianer H

BMC Genomics 19 (1) - [2018-12-00; online 2018-09-19]

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

Aberrant splicing and defective mRNA production induced by somatic spliceosome mutations in myelodysplasia

Shiozawa Y, Malcovati L, Gallì A, ..., Ogawa S, Cazzola M

Nat Commun 9 (1) - [2018-12-00; online 2018-09-07]

A randomized controlled cross-over trial investigating the effect of anti-inflammatory diet on disease activity and quality of life in rheumatoid arthritis: the Anti-inflammatory Diet In Rheumatoid Arthritis (ADIRA) study protocol

Winkvist A, Bärebring L, Gjertsson I, Ellegård L, Lindqvist HM

Nutr J 17 (1) - [2018-12-00; online 2018-04-20]

A novel ulvan lyase family with broad-spectrum activity from the ulvan utilisation loci of Formosa agariphila KMM 3901

Konasani VR, Jin C, Karlsson NG, Albers E

Sci Rep 8 (1) - [2018-12-00; online 2018-10-02]

Glycoproteomics [Service] Swedish NMR Centre (SNC) [Service]

A novel derivative of the fungal antimicrobial peptide plectasin is active against Mycobacterium tuberculosis

Tenland E, Krishnan N, Rönnholm A, ..., Robertson BD, Godaly G

Tuberculosis 113 (-) 231-238 [2018-12-00; online 2018-12-00]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A major locus controls local adaptation and adaptive life history variation in a perennial plant

Wang J, Ding J, Tan B, ..., Street NR, Ingvarsson PK

Genome Biol. 19 (1) - [2018-12-00; online 2018-06-04]

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]

A drug screening assay on cancer cells chronically adapted to acidosis

Pellegrini P, Serviss JT, Lundbäck T, ..., Linder S, De Milito A

Cancer Cell Int 18 (1) - [2018-12-00; online 2018-09-25]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A comprehensive map coupling histone modifications with gene regulation in adult dopaminergic and serotonergic neurons

Södersten E, Toskas K, Rraklli V, ..., Perlmann T, Holmberg J

Nat Commun 9 (1) - [2018-12-00; online 2018-03-26]

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]

Using High Content Imaging to Quantify Target Engagement in Adherent Cells.

Axelsson H, Almqvist H, Seashore-Ludlow B

J Vis Exp - (141) - [2018-11-29; online 2018-11-29]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

The Human Salivary Antimicrobial Peptide Profile according to the Oral Microbiota in Health, Periodontitis and Smoking.

Grant M, Kilsgård O, Åkerman S, ..., Malmström J, Jönsson D

J Innate Immun 11 (5) 432-444 [2018-11-28; online 2018-11-28]

Structural Proteomics [Collaborative]

RollFISH achieves robust quantification of single-molecule RNA biomarkers in paraffin-embedded tumor tissue samples.

Wu C, Simonetti M, Rossell C, ..., Crosetto N, Nilsson M

Commun Biol 1 (-) 209 [2018-11-28; online 2018-11-28]

Advanced FISH Technologies [Technology development] In Situ Sequencing (ISS) [Technology development]

Metabolic control of PPAR activity by aldehyde dehydrogenase regulates invasive cell behavior and predicts survival in hepatocellular and renal clear cell carcinoma.

Andrejeva D, Kugler JM, Nguyen HT, ..., Loya AC, Cohen SM

BMC Cancer 18 (1) 1180 [2018-11-28; online 2018-11-28]

Folding pathway of an Ig domain is conserved on and off the ribosome.

Tian P, Steward A, Kudva R, ..., Clarke J, Best RB

Proc. Natl. Acad. Sci. U.S.A. 115 (48) E11284-E11293 [2018-11-27; online 2018-11-09]

Depth and Dissolved Organic Carbon Shape Microbial Communities in Surface Influenced but Not Ancient Saline Terrestrial Aquifers.

Lopez-Fernandez M, Åström M, Bertilsson S, Dopson M

Front Microbiol 9 (-) 2880 [2018-11-27; online 2018-11-27]

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

The shape of the bacterial ribosome exit tunnel affects cotranslational protein folding.

Kudva R, Tian P, Pardo-Avila F, ..., Bernstein HD, von Heijne G

Elife 7 (-) - [2018-11-26; online 2018-11-26]

Out in the Cold: Identification of Genomic Regions Associated With Cold Tolerance in the Biocontrol Fungus Clonostachys rosea Through Genome-Wide Association Mapping.

Broberg M, Dubey M, Sun MH, ..., Brandström Durling M, Karlsson M

Front Microbiol 9 (-) 2844 [2018-11-22; online 2018-11-22]

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

Cell-free DNA profiling of metastatic prostate cancer reveals microsatellite instability, structural rearrangements and clonal hematopoiesis.

Mayrhofer M, De Laere B, Whitington T, ..., Grönberg H, Lindberg J

Genome Med 10 (1) 85 [2018-11-21; online 2018-05-11]

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

Metatranscriptomes Reveal That All Three Domains of Life Are Active but Are Dominated by Bacteria in the Fennoscandian Crystalline Granitic Continental Deep Biosphere

Lopez-Fernandez M, Simone D, Wu X, ..., Bertilsson S, Dopson M

MBio 9 (6) - [2018-11-20; online 2018-11-20]

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]

Quantitative Interpretation of Intracellular Drug Binding and Kinetics Using the Cellular Thermal Shift Assay

Seashore-Ludlow B, Axelsson H, Almqvist H, ..., Jonsson M, Lundbäck T

Biochemistry - (-) - [2018-11-19; online 2018-11-19]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Genome-Wide Association Studies of Estimated Fatty Acid Desaturase Activity in Serum and Adipose Tissue in Elderly Individuals: Associations with Insulin Sensitivity

Marklund M, Morris A, Mahajan A, ..., Lind L, Risérus U

Nutrients 10 (11) 1791 [2018-11-17; online 2018-11-17]

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

Small-molecule inhibitor of OGG1 suppresses proinflammatory gene expression and inflammation.

Visnes T, Cázares-Körner A, Hao W, ..., Boldogh I, Helleday T

Science 362 (6416) 834-839 [2018-11-16; online 2018-11-18]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Chemical Proteomics [Collaborative] Drug Discovery and Development (DDD) [Service] Protein Science Facility (PSF) [Service]

MutT homologue 1 (MTH1) catalyzes the hydrolysis of mutagenic O6-methyl-dGTP.

Jemth AS, Gustafsson R, Bräutigam L, ..., Stenmark P, Helleday T

Nucleic Acids Res. 46 (20) 10888-10904 [2018-11-16; online 2018-10-12]

Expression profiling and in situ screening of circular RNAs in human tissues.

Zaghlool A, Ameur A, Wu C, ..., Nilsson M, Feuk L

Sci Rep 8 (1) 16953 [2018-11-16; online 2018-11-16]

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

Diazotrophs and N2-Fixation Associated With Particles in Coastal Estuarine Waters.

Pedersen JN, Bombar D, Paerl RW, Riemann L

Front Microbiol 9 (-) 2759 [2018-11-16; online 2018-11-16]

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

Diet-dependent gene expression highlights the importance of Cytochrome P450 in detoxification of algal secondary metabolites in a marine isopod.

De Wit P, Yamada K, Panova M, André C, Johannesson K

Sci Rep 8 (1) 16824 [2018-11-14; online 2018-11-14]

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

Comparative Analysis of the Nodule Transcriptomes of Ceanothus thyrsiflorus (Rhamnaceae, Rosales) and Datisca glomerata (Datiscaceae, Cucurbitales).

Salgado MG, van Velzen R, Nguyen TV, ..., Lundin D, Pawlowski K

Front Plant Sci 9 (-) 1629 [2018-11-14; online 2018-11-14]

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

Satiety Factors Oleoylethanolamide, Stearoylethanolamide, and Palmitoylethanolamide in Mother's Milk Are Strongly Associated with Infant Weight at Four Months of Age-Data from the Odense Child Cohort.

Bruun S, Gouveia-Figueira S, Domellöf M, ..., Fowler CJ, Zachariassen G

Nutrients 10 (11) 1747 [2018-11-13; online 2018-11-13]

Integrative Analysis of Three RNA Sequencing Methods Identifies Mutually Exclusive Exons of MADS-Box Isoforms During Early Bud Development in Picea abies

Akhter S, Kretzschmar WW, Nordal V, ..., Emanuelsson O, Sundström JF

Front Plant Sci 9 (-) - [2018-11-13; online 2018-11-13]

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

Parallel plumage colour evolution and introgressive hybridization in wheatears.

Schweizer M, Warmuth V, Alaei Kakhki N, ..., Suh A, Burri R

J. Evol. Biol. - (-) - [2018-11-12; online 2018-11-12]

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

Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis

Falcão AM, van Bruggen D, Marques S, ..., Guerreiro-Cacais AO, Castelo-Branco G

Nat Med - (-) - [2018-11-12; online 2018-11-12]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

New tools for automated high-resolution cryo-EM structure determination in RELION-3

Zivanov J, Nakane T, Forsberg BO, ..., Lindahl E, Scheres SH

Elife 7 (-) - [2018-11-09; online 2018-11-09]

Cryo-EM [Technology development]

Affinity to cellulose is a shared property among coiled-coil domains of intermediate filaments and prokaryotic intermediate filament-like proteins.

Söderholm N, Javadi A, Flores IS, Flärdh K, Sandblad L

Sci Rep 8 (1) 16524 [2018-11-08; online 2018-11-08]

Markers of Basement Membrane Remodeling Are Associated With Higher Mortality in Patients With Known Atherosclerosis.

Holm Nielsen S, Tengryd C, Edsfeldt A, ..., Nilsson J, Goncalves I

J Am Heart Assoc 7 (21) e009193 [2018-11-06; online 2019-01-05]

Affinity Proteomics Stockholm [Service] Clinical Biomarkers [Service]

Vandermonde Factorization of Hankel Matrix for Complex Exponential Signal Recovery—Application in Fast NMR Spectroscopy

Ying J, Cai JF, Guo D, ..., Chen Z, Qu X

IEEE Trans. Signal Process. 66 (21) 5520-5533 [2018-11-01; online 2018-11-01]

Computational and Statistical Analysis of Array-Based DNA Methylation Data.

Nordlund J, Bäcklin C, Raine A

Methods Mol. Biol. 1878 (-) 173-191 [2018-11-01; online 2018-11-01]

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

VEGF receptor-2/neuropilin 1 trans-complex formation between endothelial and tumor cells is an independent predictor of pancreatic cancer survival

Morin E, Sjöberg E, Tjomsland V, ..., Sjöblom T, Claesson-Welsh L

J. Pathol 246 (3) 311-322 [2018-11-00; online 2018-09-04]

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

Upregulated BMP-Smad signaling activity in the glucuronyl C5-epimerase knock out MEF cells

Batool T, Fang J, Jansson V, ..., Moustakas A, Li JP

Cellular Signalling - (-) - [2018-11-00; online 2018-11-00]

PLA and Single Cell Proteomics [Collaborative]

Uncovering the regional localization of inhaled salmeterol retention in the lung.

Bäckström E, Hamm G, Nilsson A, ..., Goodwin RJA, Fridén M

Drug Deliv 25 (1) 838-845 [2018-11-00; online 2018-03-29]

Spatial Mass Spectrometry [Service]

Replicative and non-replicative mechanisms in the formation of clustered CNVs are indicated by whole genome characterization.

Nazaryan-Petersen L, Eisfeldt J, Pettersson M, ..., Tümer Z, Lindstrand A

PLoS Genet. 14 (11) e1007780 [2018-11-00; online 2018-11-12]

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

Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays.

Giacomello S, Lundeberg J

Nat Protoc 13 (11) 2425-2446 [2018-11-00; online 2018-10-26]

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

One-view breast tomosynthesis versus two-view mammography in the Malmö Breast Tomosynthesis Screening Trial (MBTST): a prospective, population-based, diagnostic accuracy study

Zackrisson S, Lång K, Rosso A, ..., Tingberg A, Andersson I

The Lancet Oncology 19 (11) 1493-1503 [2018-11-00; online 2018-11-00]

AIDA Data Hub [Service]

Metal-free ribonucleotide reduction powered by a DOPA radical in Mycoplasma pathogens.

Srinivas V, Lebrette H, Lundin D, ..., Sjöberg BM, Högbom M

Nature 563 (7731) 416-420 [2018-11-00; online 2018-10-31]

Global Proteomics and Proteogenomics [Collaborative]

LMO7 and LIMCH1 interact with LRIG proteins in lung cancer, with prognostic implications for early-stage disease.

Karlsson T, Kvarnbrink S, Holmlund C, ..., Johansson M, Hedman H

Lung Cancer 125 (-) 174-184 [2018-11-00; online 2018-09-24]

Clinical Genomics Uppsala [Collaborative]

Isomeric Separation and Recognition of Anionic and Zwitterionic N-glycans from Royal Jelly Glycoproteins.

Hykollari A, Malzl D, Eckmair B, ..., Wilson IBH, Paschinger K

Mol. Cell Proteomics 17 (11) 2177-2196 [2018-11-00; online 2018-08-13]

Glycomics@ExPASy: Bridging the Gap.

Mariethoz J, Alocci D, Gastaldello A, ..., Packer NH, Lisacek F

Mol. Cell Proteomics 17 (11) 2164-2176 [2018-11-00; online 2018-08-10]

Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle

Lind AE, Lewis WH, Spang A, ..., Embley TM, Ettema TJG

ISME J 12 (11) 2655-2667 [2018-11-00; online 2018-07-10]

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

Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders

Ligthart S, Vaez A, Võsa U, ..., Frayling TM, Slagboom EP

The American Journal of Human Genetics 103 (5) 691-706 [2018-11-00; online 2018-11-00]

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

Fine-mapping type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps.

Mahajan A, Taliun D, Thurner M, ..., Boehnke M, McCarthy MI

Nat. Genet. 50 (11) 1505-1513 [2018-11-00; online 2018-10-08]

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

Detection of autoantibodies against cancer-testis antigens in non-small cell lung cancer.

Djureinovic D, Dodig-Crnković T, Hellström C, ..., Schwenk JM, Micke P

Lung Cancer 125 (-) 157-163 [2018-11-00; online 2018-09-17]

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

Convergent evolution of 11p allelic loss in multifocal Wilms tumors arising in WT1 mutation carriers.

Valind A, Wessman S, Pal N, ..., Sandstedt B, Gisselsson D

Pediatr Blood Cancer 65 (11) e27301 [2018-11-00; online 2018-07-03]

Barcoded solid-phase RNA capture for Spatial Transcriptomics profiling in mammalian tissue sections.

Salmén F, Ståhl PL, Mollbrink A, ..., Frisén J, Lundeberg J

Nat Protoc 13 (11) 2501-2534 [2018-11-00; online 2018-10-26]

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

Gene-level associations in suicide attempter families show overrepresentation of synaptic genes and genes differentially expressed in brain development

Sokolowski M, Wasserman J, Wasserman D

Am. J. Med. Genet. - (-) - [2018-10-31; online 2018-10-31]

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

Copper Chaperone Atox1 Interacts with Cell Cycle Proteins.

Matson Dzebo M, Blockhuys S, Valenzuela S, ..., Esbjörner EK, Wittung-Stafshede P

Computational and Structural Biotechnology Journal 16 (-) 443-449 [2018-10-31; online 2018-10-31]

SMAD4 Is Essential for Human Cardiac Mesodermal Precursor Cell Formation.

Xu J, Gruber PJ, Chien KR

Stem Cells - (-) - [2018-10-30; online 2018-10-30]

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

Quantitative proteomic characterization of the lung extracellular matrix in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis.

Åhrman E, Hallgren O, Malmström L, ..., Westergren-Thorsson G, Malmström J

J Proteomics 189 (-) 23-33 [2018-10-30; online 2018-03-01]

Structural Proteomics [Collaborative]

Cigarette smoking affects microRNAs and inflammatory biomarkers in healthy individuals and an association to single nucleotide polymorphisms is indicated

Andersson BÅ, Sayardoust S, Löfgren S, Rutqvist LE, Laytragoon-Lewin N

Biomarkers - (-) 1-17 [2018-10-30; online 2018-10-30]

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

Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen

Lin YC, Wang J, Delhomme N, ..., Ingvarsson PK, Street NR

Proc Natl Acad Sci USA - (-) 201801437 [2018-10-29; online 2018-10-29]

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

Single-cell RNA-seq analysis reveals the platinum resistance gene COX7B and the surrogate marker CD63.

Tanaka N, Katayama S, Reddy A, ..., Oya M, Uhlén P

Cancer Med - (-) - [2018-10-26; online 2018-10-26]

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]

Single-Stranded Nucleic Acids Regulate TLR3/4/7 Activation through Interference with Clathrin-Mediated Endocytosis.

Järver P, Dondalska A, Poux C, ..., LeGrand R, Spetz AL

Sci Rep 8 (1) 15841 [2018-10-26; online 2018-10-26]

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

Role of OmpA1 and OmpA2 in Aggregatibacter actinomycetemcomitans and Aggregatibacter aphrophilus serum resistance.

Lindholm M, Min Aung K, Nyunt Wai S, Oscarsson J

Journal of Oral Microbiology 11 (1) 1536192 [2018-10-26; online 2018-10-26]

STAT3 differential scanning fluorimetry and differential scanning light scattering assays: Addressing a missing link in the characterization of STAT3 inhibitor interactions.

Desroses M, Busker S, Astorga-Wells J, ..., Grandér D, Page BDG

Journal of Pharmaceutical and Biomedical Analysis 160 (-) 80-88 [2018-10-25; online 2018-07-17]

Chemical Proteomics [Collaborative] Protein Science Facility (PSF) [Service]

Detection of post-translational modifications using solid-phase proximity ligation assay.

Oliveira FMS, Mereiter S, Lönn P, ..., Reis CA, Kamali-Moghaddam M

N Biotechnol 45 (-) 51-59 [2018-10-25; online 2017-10-31]

Glycoproteomics [Technology development] PLA and Single Cell Proteomics [Technology development]

Combination of phage and Gram-positive bacterial display of human antibody repertoires enables isolation of functional high affinity binders.

Hu FJ, Volk AL, Persson H, ..., Uhlen M, Rockberg J

N Biotechnol 45 (-) 80-88 [2018-10-25; online 2017-08-01]

Drug Discovery and Development (DDD) [Technology development]

Amplification of the Melanocortin-1 Receptor in Nephrotic Syndrome Identifies a Target for Podocyte Cytoskeleton Stabilization.

Bergwall L, Wallentin H, Elvin J, ..., Nyström J, Buvall L

Sci Rep 8 (1) 15731 [2018-10-24; online 2018-10-24]

XLSY: Extra-Large NMR Spectroscopy

Pustovalova Y, Mayzel M, Orekhov VY

Angew. Chem. Int. Ed. 57 (43) 14043-14045 [2018-10-22; online 2018-10-01]

Swedish NMR Centre (SNC) [Technology development]

Identification of Potential Plasma Biomarkers for Abdominal Aortic Aneurysm Using Tandem Mass Tag Quantitative Proteomics.

Henriksson AE, Lindqvist M, Sihlbom C, Bergström J, Bylund D

Proteomes 6 (4) - [2018-10-18; online 2018-10-18]

Looking for a Treatment for Hailey-Hailey Disease: The Importance of Being Consistent in Case Reports.

Micaroni M

J Cutan Med Surg 22 (6) 660 [2018-10-17; online 2018-10-17]

Integrated Microscopy Technologies Gothenburg [Service]

Halogen Bond Asymmetry in Solution.

Lindblad S, Mehmeti K, Veiga AX, ..., Gräfenstein J, Erdélyi M

J. Am. Chem. Soc. 140 (41) 13503-13513 [2018-10-17; online 2018-10-04]

Single-Cell Transcriptomics of Traced Epidermal and Hair Follicle Stem Cells Reveals Rapid Adaptations during Wound Healing.

Joost S, Jacob T, Sun X, ..., Sur I, Kasper M

Cell Rep 25 (3) 585-597.e7 [2018-10-16; online 2018-10-18]

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

Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma.

Thrane K, Eriksson H, Maaskola J, Hansson J, Lundeberg J

Cancer Res. 78 (20) 5970-5979 [2018-10-15; online 2018-08-28]

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

Transcriptomic and genomic profiling of early-stage ovarian carcinomas associated with histotype and overall survival.

Engqvist H, Parris TZ, Rönnerman EW, ..., Karlsson P, Helou K

Oncotarget 9 (80) 35162-35180 [2018-10-12; online 2018-10-12]

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

Dynamics of a Perturbed Microbial Community during Thermophilic Anaerobic Digestion of Chemically Defined Soluble Organic Compounds

Šafarič L, Shakeri Yekta S, Liu T, ..., Bastviken D, Björn A

Microorganisms 6 (4) 105 [2018-10-11; online 2018-10-11]

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

BabA-mediated adherence of pediatric ulcerogenic H. pylori strains to gastric mucins at neutral and acidic pH.

Quintana-Hayashi MP, Rocha R, Padra M, ..., Oleastro M, Lindén SK

Virulence 9 (1) 1699-1717 [2018-10-10; online 2018-10-10]

De Novo Assembly of Two Swedish Genomes Reveals Missing Segments from the Human GRCh38 Reference and Improves Variant Calling of Population-Scale Sequencing Data.

Ameur A, Che H, Martin M, ..., Feuk L, Gyllensten U

Genes 9 (10) 486 [2018-10-09; online 2018-10-09]

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

Chorea, psychosis, acanthocytosis, and prolonged survival associated with

Paucar M, Pajak A, Freyer C, ..., Wredenberg A, Svenningsson P

Neurology 91 (15) 710-712 [2018-10-09; online 2018-09-14]

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

An orthotopic glioblastoma animal model suitable for high-throughput screenings.

Pudelko L, Edwards S, Balan M, ..., Helleday T, Bräutigam L

Neuro-oncology 20 (11) 1475-1484 [2018-10-09; online 2018-05-12]

Integrated Microscopy Technologies Stockholm [Collaborative]

The Xerobranching Response Represses Lateral Root Formation When Roots Are Not in Contact with Water.

Orman-Ligeza B, Morris EC, Parizot B, ..., Beeckman T, Draye X

Curr. Biol. 28 (19) 3165-3173.e5 [2018-10-08; online 2018-09-27]

Enhanced validation of antibodies for research applications.

Edfors F, Hober A, Linderbäck K, ..., Forsström B, Uhlen M

Nat Commun 9 (1) 4130 [2018-10-08; online 2018-10-08]

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

A Recurrent De Novo Heterozygous COG4 Substitution Leads to Saul-Wilson Syndrome, Disrupted Vesicular Trafficking, and Altered Proteoglycan Glycosylation.

Ferreira CR, Xia ZJ, Clément A, ..., Gahl WA, Freeze HH

Am. J. Hum. Genet. 103 (4) 553-567 [2018-10-04; online 2018-10-06]

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

NormalyzerDE: Online tool for improved normalization of omics expression data and high-sensitivity differential expression analysis.

Willforss J, Chawade A, Levander F

J. Proteome Res. - (-) - [2018-10-02; online 2018-10-02]

Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Hepatitis E Virus Genotype 3 Genomes from RNA-Positive but Serologically Negative Plasma Donors Have CUG as the Start Codon for ORF3.

Norder H, Galli C, Magnil E, ..., Nyström K, Magnius LO

Intervirology 61 (2) 96-103 [2018-10-02; online 2018-10-02]

Clinical Genomics Gothenburg [Collaborative]

A systems-approach reveals human nestin is an endothelial-enriched, angiogenesis-independent intermediate filament protein.

Dusart P, Fagerberg L, Perisic L, ..., Odeberg J, Butler LM

Sci Rep 8 (1) 14668 [2018-10-02; online 2018-10-02]

Spatial Proteomics [Service]

Development and Validation of a Novel RNA Sequencing-Based Prognostic Score for Acute Myeloid Leukemia.

Wang M, Lindberg J, Klevebring D, ..., Grönberg H, Rantalainen M

J. Natl. Cancer Inst. 110 (10) 1094-1101 [2018-10-01; online 2018-03-06]

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

Biased Inference of Selection Due to GC-Biased Gene Conversion and the Rate of Protein Evolution in Flycatchers When Accounting for It

Bolívar P, Mugal CF, Rossi M, ..., Dutoit L, Ellegren H

- 35 (10) 2475-2486 [2018-10-01; online 2018-08-02]

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

Using Scipion for stream image processing at Cryo-EM facilities

Gómez-Blanco J, de la Rosa-Trevín JM, Marabini R, ..., Conesa P, Carazo JM

Journal of Structural Biology - (-) - [2018-10-00; online 2018-10-00]

Cryo-EM [Technology development]

Use of Vascular Assessments and Novel Biomarkers to Predict Cardiovascular Events in Type 2 Diabetes: The SUMMIT VIP Study.

Shore AC, Colhoun HM, Natali A, ..., Nilsson J, SUMMIT Consortium

Diabetes Care 41 (10) 2212-2219 [2018-10-00; online 2018-07-30]

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

Targeting autophagy by small molecule inhibitors of vacuolar protein sorting 34 (Vps34) improves the sensitivity of breast cancer cells to Sunitinib

Dyczynski M, Yu Y, Otrocka M, ..., De Milito A, Pokrovskaja Tamm K

Cancer Letters 435 (-) 32-43 [2018-10-00; online 2018-10-00]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Rapid Increase in Carriage Rates of Enterobacteriaceae Producing Extended-Spectrum β-Lactamases in Healthy Preschool Children, Sweden

Kaarme J, Riedel H, Schaal W, ..., Nevéus T, Melhus Å

Emerg. Infect. Dis. 24 (10) 1874-1881 [2018-10-00; online 2018-10-00]

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

RAVEN 2.0: A versatile toolbox for metabolic network reconstruction and a case study on Streptomyces coelicolor.

Wang H, Marcišauskas S, Sánchez BJ, ..., Nielsen J, Kerkhoven EJ

PLoS Comput. Biol. 14 (10) e1006541 [2018-10-00; online 2018-10-18]

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

Plasma levels of the proprotein convertase furin and incidence of diabetes and mortality.

Fernandez C, Rysä J, Almgren P, ..., Ruskoaho H, Melander O

J. Intern. Med. 284 (4) 377-387 [2018-10-00; online 2018-07-02]

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

Partial genomic survival of cave bears in living brown bears.

Barlow A, Cahill JA, Hartmann S, ..., Shapiro B, Hofreiter M

Nat Ecol Evol 2 (10) 1563-1570 [2018-10-00; online 2018-08-27]

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

Mutation, methylation, and gene expression profiles in dup(1q)-positive pediatric B-cell precursor acute lymphoblastic leukemia.

Gunnarsson R, Dilorenzo S, Lundin-Ström KB, ..., Isaksson A, Johansson B

Leukemia 32 (10) 2117-2125 [2018-10-00; online 2018-03-12]

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

Ibrutinib induces rapid down-regulation of inflammatory markers and altered transcription of chronic lymphocytic leukaemia-related genes in blood and lymph nodes.

Palma M, Krstic A, Peña Perez L, ..., Månsson R, Smith CIE

Br. J. Haematol. 183 (2) 212-224 [2018-10-00; online 2018-08-20]

PLA and Single Cell Proteomics [Collaborative]

Genome-wide binding of transcription factor ZEB1 in triple-negative breast cancer cells.

Maturi V, Enroth S, Heldin CH, Moustakas A

J. Cell. Physiol. 233 (10) 7113-7127 [2018-10-00; online 2018-05-10]

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

Genetic architecture of traits associated with reproductive barriers in Silene: Coupling, sex chromosomes and variation.

Liu X, Karrenberg S

Mol. Ecol. 27 (19) 3889-3904 [2018-10-00; online 2018-04-29]

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

Genetic analysis of over 1 million people identifies 535 new loci associated with blood pressure traits.

Evangelou E, Warren HR, Mosen-Ansorena D, ..., Caulfield MJ, Million Veteran Program

Nat. Genet. 50 (10) 1412-1425 [2018-10-00; online 2018-09-17]

Bioinformatics Compute and Storage [Service]

Exploring photoinactivation of microbial biofilms using laser scanning microscopy and confined 2-photon excitation.

Thomsen H, Graf FE, Farewell A, Ericson MB

J. Biophotonics 11 (10) e201800018 [2018-10-00; online 2018-06-19]

Integrated Microscopy Technologies Gothenburg [Service]

Deep learning is combined with massive-scale citizen science to improve large-scale image classification.

Sullivan DP, Winsnes CF, Åkesson L, ..., Szantner A, Lundberg E

Nat. Biotechnol. 36 (9) 820-828 [2018-10-00; online 2018-08-20]

BioImage Informatics [Collaborative] Spatial Proteomics [Collaborative]

Backbone 1H, 13C, and 15N resonance assignments of the ligand binding domain of the human wildtype glucocorticoid receptor and the F602S mutant variant

Köhler C, Carlström G, Tångefjord S, ..., Edman K, Akke M

Biomol NMR Assign 12 (2) 263-268 [2018-10-00; online 2018-04-17]

Associations of Circulating Protein Levels With Lipid Fractions in the General Population.

Figarska SM, Gustafsson S, Sundström J, ..., Lind L, Ingelsson E

Arterioscler. Thromb. Vasc. Biol. 38 (10) 2505-2518 [2018-10-00; online 2018-10-26]

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

Ancient genomes suggest the eastern Pontic-Caspian steppe as the source of western Iron Age nomads.

Krzewińska M, Kılınç GM, Juras A, ..., Storå J, Götherström A

Sci Adv 4 (10) eaat4457 [2018-10-00; online 2018-10-03]

Bioinformatics 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]

Alu-Alu mediated intragenic duplications in IFT81 and MATN3 are associated with skeletal dysplasias.

Pettersson M, Vaz R, Hammarsjö A, ..., Grigelioniene G, Lindstrand A

Hum. Mutat. 39 (10) 1456-1467 [2018-10-00; online 2018-08-22]

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

Conformational Sampling of Macrocyclic Drugs in Different Environments: Can We Find the Relevant Conformations?

Poongavanam V, Danelius E, Peintner S, ..., Ermondi G, Kihlberg J

ACS Omega 3 (9) 11742-11757 [2018-09-30; online 2018-09-24]

Interferon-α enhances the IL-12-induced STAT4 activation selectively in carriers of the STAT4 SLE risk allele rs7574865[T].

Hagberg N, Rönnblom L

Ann. Rheum. Dis. - (-) - [2018-09-29; online 2018-09-29]

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

Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells.

Ni G, Canizales S, Broman E, ..., Sleutels T, Dopson M

Front Microbiol 9 (-) 2308 [2018-09-28; online 2018-09-28]

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

Male sex and the pattern of recurrent myeloid mutations are strong independent predictors of blood transfusion intensity in patients with myelodysplastic syndromes

Rydén J, Edgren G, Karimi M, ..., Hellström-Lindberg E, Höglund P

Leukemia - (-) - [2018-09-28; online 2018-09-28]

Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins

Wang Y, Karlsson R, Lampa E, ..., Pedersen NL, Hägg S

Epigenetics - (-) - [2018-09-28; online 2018-09-28]

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

Structural and biochemical characterization of the Cutibacterium acnes exo-β-1,4-mannosidase that targets the N-glycan core of host glycoproteins

Reichenbach T, Kalyani D, Gandini R, ..., Aspeborg H, Divne C

PLoS ONE 13 (9) e0204703 [2018-09-27; online 2018-09-27]

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

High-throughput metabarcoding reveals the effect of physicochemical soil properties on soil and litter biodiversity and community turnover across Amazonia.

Ritter CD, Zizka A, Roger F, ..., Nilsson RH, Antonelli A

PeerJ 6 (-) e5661 [2018-09-25; online 2018-09-25]

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

Genotyping of Phytophthora infestans in eastern-Africa reveals a dominating invasive European lineage

Njoroge AW, Andersson B, Lees AK, ..., Yuen J, Pelle R

Phytopathology - (-) - [2018-09-25; online 2018-09-25]

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

NMR Determination of the Binding Constant of Ionic Species: A Caveat

Schulz N, Schindler S, Huber SM, Erdelyi M

J. Org. Chem. 83 (18) 10881-10886 [2018-09-21; online 2018-08-15]

Methanogens and Iron-Reducing Bacteria: the Overlooked Members of Mercury-Methylating Microbial Communities in Boreal Lakes

Bravo AG, Peura S, Buck M, ..., Björn E, Bertilsson S

Appl Environ Microbiol 84 (23) - [2018-09-21; online 2018-11-15]

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

Characterization of different fat depots in NAFLD using inflammation-associated proteome, lipidome and metabolome.

Lovric A, Granér M, Bjornson E, ..., Mardinoglu A, Boren J

Sci Rep 8 (1) 14200 [2018-09-21; online 2018-09-21]

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

Impact of spliceosome mutations on RNA splicing in myelodysplasia: dysregulated genes/pathways and clinical associations

Pellagatti A, Armstrong RN, Steeples V, ..., Smith S, Boultwood J

Blood 132 (12) 1225-1240 [2018-09-20; online 2018-06-21]

SWI/SNF interacts with cleavage and polyadenylation factors and facilitates pre-mRNA 3' end processing.

Yu S, Jordán-Pla A, Gañez-Zapater A, ..., Östlund Farrants AK, Visa N

Nucleic Acids Res. 46 (16) 8557-8573 [2018-09-19; online 2018-06-04]

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

Loss of zebrafish ctnnd2b results in disorganised forebrain neuron clusters

Hofmeister W, Vaz R, Edwards S, Dueñas Rey A, Lindstrand A

- - (-) - [2018-09-18; online 2018-09-18]

Integrated Microscopy Technologies Stockholm

14-3-3 proteins activate Pseudomonas exotoxins-S and -T by chaperoning a hydrophobic surface.

Karlberg T, Hornyak P, Pinto AF, ..., Björkegren C, Schüler H

Nat Commun 9 (1) 3785 [2018-09-17; online 2018-09-17]

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

Structural and Functional Characterization of the BcsG Subunit of the Cellulose Synthase in Salmonella typhimurium.

Sun L, Vella P, Schnell R, ..., Schneider G, Römling U

J. Mol. Biol. 430 (18 Pt B) 3170-3189 [2018-09-14; online 2018-07-12]

TP53 outperforms other androgen receptor biomarkers to predict abiraterone or enzalutamide outcome in metastatic castration-resistant prostate cancer.

De Laere B, Oeyen S, Mayrhofer M, ..., Lindberg J, Dirix LY

Clin. Cancer Res. - (-) - [2018-09-12; online 2018-09-12]

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

Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system.

Petitpré C, Wu H, Sharma A, ..., Hadjab S, Lallemend F

Nat Commun 9 (1) 3691 [2018-09-12; online 2018-09-12]

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

Continuous Immune Cell Differentiation Inferred From Single-Cell Measurements Following Allogeneic Stem Cell Transplantation.

Chen Y, Lakshmikanth T, Olin A, ..., Remberger M, Brodin P

Front Mol Biosci 5 (-) 81 [2018-09-12; online 2018-09-12]

Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Technology development]

How Does the Sweet Violet (Viola odorata L.) Fight Pathogens and Pests - Cyclotides as a Comprehensive Plant Host Defense System.

Slazak B, Kapusta M, Strömstedt AA, ..., Kuta E, Göransson U

Front Plant Sci 9 (-) 1296 [2018-09-11; online 2018-09-11]

The all-intracellular order Legionellales is unexpectedly diverse, globally distributed and lowly abundant

Graells T, Ishak H, Larsson M, Guy L

FEMS Microbiol. Ecol. - (-) - [2018-09-10; online 2018-09-10]

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

Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town.

Krzewińska M, Kjellström A, Günther T, ..., Storå J, Götherström A

Curr. Biol. 28 (17) 2730-2738.e10 [2018-09-10; online 2018-08-23]

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

Contribution of allelic imbalance to colorectal cancer.

Palin K, Pitkänen E, Turunen M, ..., Taipale J, Aaltonen LA

Nat Commun 9 (1) 3664 [2018-09-10; online 2018-09-10]

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

Neuroblastoma with flat genomic profile: a question of representativity?

Valind A, Öra I, Mertens F, Gisselsson D

BMJ Case Reports 2018 (-) bcr-2018-225568 [2018-09-08; online 2018-09-08]

Higher Energy Collisional Dissociation Mass Spectrometry of Sulfated O-Linked Oligosaccharides.

Issa SMA, Vitiazeva V, Hayes CA, Karlsson NG

J. Proteome Res. 17 (9) 3259-3267 [2018-09-07; online 2018-08-13]

Glycoproteomics [Technology development]

Attached stratified mucus separates bacteria from the epithelial cells in COPD lungs.

Fernández-Blanco JA, Fakih D, Arike L, ..., Ermund A, Hansson GC

JCI Insight 3 (17) - [2018-09-06; online 2018-09-06]

Integrated Microscopy Technologies Gothenburg [Service]

The Thomsen-Friedenreich Antigen: A Highly Sensitive and Specific Predictor of Microsatellite Instability in Gastric Cancer.

Mereiter S, Polom K, Williams C, ..., Magalhães A, Reis CA

J Clin Med 7 (9) - [2018-09-05; online 2018-09-05]

A New Species of the γ-Proteobacterium Francisella, F. adeliensis Sp. Nov., Endocytobiont in an Antarctic Marine Ciliate and Potential Evolutionary Forerunner of Pathogenic Species

Vallesi A, Sjödin A, Petrelli D, ..., Gutiérrez G, Villalobo E

Microb Ecol 77 (3) 587-596 [2018-09-05; online 2018-09-05]

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

Neuronal Expression of Opioid Gene is Controlled by Dual Epigenetic and Transcriptional Mechanism in Human Brain.

Bazov I, Sarkisyan D, Kononenko O, ..., Yakovleva T, Bakalkin G

Cereb. Cortex 28 (9) 3129-3142 [2018-09-01; online 2017-10-03]

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

Interactions between monomeric CCTδ and p150 Glued: A novel function for CCTδ at the cell periphery distinct from the protein folding activity of the molecular chaperone CCT.

Echbarthi M, Vallin J, Grantham J

Exp. Cell Res. 370 (1) 137-149 [2018-09-01; online 2018-06-18]

Integrated Microscopy Technologies Gothenburg [Service]

Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.

Vetukuri RR, Tripathy S, Malar C M, ..., Grenville-Briggs LJ, Whisson SC

Genome Biol Evol 10 (9) 2432-2442 [2018-09-01; online 2018-09-01]

Bioinformatics 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]

Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids

Narrowe AB, Spang A, Stairs CW, ..., Miller CS, Ettema TJG

Genome Biol Evol 10 (9) 2380-2393 [2018-09-01; online 2018-08-27]

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

The molecular genetic basis of herbivory between butterflies and their host plants.

Nallu S, Hill JA, Don K, ..., Wheat CW, Kronforst MR

Nat Ecol Evol 2 (9) 1418-1427 [2018-09-00; online 2018-08-03]

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

The downfall of TBA-354 - a possible explanation for its neurotoxicity via mass spectrometric imaging.

Ntshangase S, Shobo A, Kruger HG, ..., Govender T, Baijnath S

Xenobiotica 48 (9) 938-944 [2018-09-00; online 2017-10-13]

Drug Discovery and Development (DDD) [Collaborative]

The Protozoan Parasite Toxoplasma gondii Selectively Reprograms the Host Cell Translatome.

Leroux LP, Lorent J, Graber TE, ..., Larsson O, Jaramillo M

Infect. Immun. 86 (9) - [2018-09-00; online 2018-08-22]

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

Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome

Dutoit L, Mugal CF, Bolívar P, ..., Gustafsson L, Ellegren H

Mol Ecol 27 (18) 3572-3581 [2018-09-00; online 2018-09-04]

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

Screening for Inhibitors of Acetaldehyde Dehydrogenase (AdhE) from Enterohemorrhagic Escherichia coli (EHEC).

Zetterström CE, Uusitalo P, Qian W, ..., Grundström C, Elofsson M

SLAS DISCOVERY: Advancing Life Sciences R&D 23 (8) 815-822 [2018-09-00; online 2018-04-09]

Chemical Biology Consortium Sweden (CBCS) [Service]

STK25 regulates oxidative capacity and metabolic efficiency in adipose tissue.

Sütt S, Cansby E, Paul A, ..., Enerbäck S, Mahlapuu M

J Endocrinol 238 (3) 187-202 [2018-09-00; online 2018-05-24]

Integrated Microscopy Technologies Gothenburg [Service]

Phylogenetic relationships of rollers (Coraciidae) based on complete mitochondrial genomes and fifteen nuclear genes.

Johansson US, Irestedt M, Qu Y, Ericson PGP

Mol. Phylogenet. Evol. 126 (-) 17-22 [2018-09-00; online 2018-04-06]

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

Membrane Fluidity Is Regulated Cell Nonautonomously by Caenorhabditiselegans PAQR-2 and Its Mammalian Homolog AdipoR2.

Bodhicharla R, Devkota R, Ruiz M, Pilon M

Genetics 210 (1) 189-201 [2018-09-00; online 2018-07-11]

Integrated Microscopy Technologies Gothenburg [Service]

Lack of thinning effects over inter-annual changes in soil fungal community and diversity in a Mediterranean pine forest

Castaño C, Alday JG, Lindahl BD, ..., Pera J, Bonet JA

Forest Ecology and Management 424 (-) 420-427 [2018-09-00; online 2018-09-00]

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

Genome Sequence Resource for the Oomycete Taro Pathogen Phytophthora colocasiae.

Vetukuri RR, Kushwaha SK, Sen D, ..., Lamour KH, Grenville-Briggs LJ

Mol. Plant Microbe Interact. 31 (9) 903-905 [2018-09-00; online 2018-08-03]

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

Formation of a Secretion-Competent Protein Complex by a Dynamic Wrap-around Binding Mechanism

Gupta AA, Reinartz I, Karunanithy G, ..., Schug A, Wolf-Watz M

Journal of Molecular Biology 430 (18) 3157-3169 [2018-09-00; online 2018-09-00]

FADD (Fas-Associated Protein With Death Domain), Caspase-3, and Caspase-8 and Incidence of Ischemic Stroke.

Muhammad IF, Borné Y, Melander O, ..., Söderholm M, Engström G

Stroke 49 (9) 2224-2226 [2018-09-00; online 2018-10-26]

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

Ein Fall von Pankreaskarzinom

Löhr JM, Kordes M, Gustafsson-Liljefors M, ..., Permert J, Jäger D

Forum 33 (4) 232-235 [2018-09-00; online 2018-08-14]

Clinical Genomics Stockholm [Collaborative]

Detailed analysis of HTT repeat elements in human blood using targeted amplification-free long-read sequencing.

Höijer I, Tsai YC, Clark TA, ..., Gyllensten U, Ameur A

Hum. Mutat. 39 (9) 1262-1272 [2018-09-00; online 2018-07-12]

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

Broad spectrum developmental role of Brachypodium AUX1.

van der Schuren A, Voiniciuc C, Bragg J, ..., Pauly M, Hardtke CS

New Phytol. 219 (4) 1216-1223 [2018-09-00; online 2018-06-27]

Autosomal Recessive Osteogenesis Imperfecta Caused by a Novel Homozygous COL1A2 Mutation

Costantini A, Tournis S, Kämpe A, ..., Doulgeraki A, Mäkitie O

Calcif Tissue Int 103 (3) 353-358 [2018-09-00; online 2018-03-23]

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]

Autoantibody profiling reveals four protein candidate autoantigens associated with systemic lupus erythematosus.

Frostegård J, Hellström C, Nilsson P, Frostegård AG, Ajeganova S

Lupus 27 (10) 1670-1678 [2018-09-00; online 2018-07-24]

Autoimmunity and Serology Profiling [Service]

A fine-needle aspiration-based protein signature discriminates benign from malignant breast lesions

Franzén B, Kamali-Moghaddam M, Alexeyenko A, ..., Landegren U, Lewensohn R

Mol Oncol 12 (9) 1415-1428 [2018-09-00; online 2018-08-09]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Technology development]

The endoplasmic reticulum-resident collagen chaperone Hsp47 interacts with and promotes the secretion of decorin, fibromodulin, and lumican.

Ishikawa Y, Rubin K, Bächinger HP, Kalamajski S

J. Biol. Chem. 293 (35) 13707-13716 [2018-08-31; online 2018-07-12]

PLA and Single Cell Proteomics [Service]

Sequentially acting SOX proteins orchestrate astrocyte‐ and oligodendrocyte‐specific gene expression

Klum S, Zaouter C, Alekseenko Z, ..., Muhr J, Bergsland M

EMBO Rep. - (-) e46635 [2018-08-30; online 2018-08-30]

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

A glutaredoxin domain fused to the radical-generating subunit of ribonucleotide reductase (RNR) functions as an efficient RNR reductant.

Rozman Grinberg I, Lundin D, Sahlin M, ..., Hofer A, Sjöberg BM

J. Biol. Chem. - (-) - [2018-08-30; online 2018-08-30]

Eleven percent intact PGM3 in a severely immunodeficient patient with a novel splice-site mutation, a case report.

Lundin KE, Wang Q, Hamasy A, ..., Ekwall O, Smith CIE

BMC Pediatr 18 (1) 285 [2018-08-29; online 2018-08-29]

Clinical Genomics Stockholm [Collaborative]

Patient-derived xenograft models reveal intratumor heterogeneity and temporal stability in neuroblastoma

Braekeveldt N, von Stedingk K, Fransson S, ..., Påhlman S, Bexell D

Cancer Res - (-) canres.0527.2018 [2018-08-28; online 2018-08-28]

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

Metabolic reprogramming of acute lymphoblastic leukemia cells in response to glucocorticoid treatment.

Dyczynski M, Vesterlund M, Björklund AC, ..., Tamm KP, Nilsson R

Cell Death Dis 9 (9) 846 [2018-08-28; online 2018-08-28]

Global Proteomics and Proteogenomics [Collaborative]

Life history of Parnips and the evolutionary origin of gall wasps

Ronquist F, Nylander JAA, Vårdal H, Nieves-Aldrey JL

JHR 65 (-) 91-110 [2018-08-27; online 2018-08-27]

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

Exploratory Profiling of Urine MicroRNAs in the dy Mouse Model of LAMA2-CMD: Relation to Disease Progression.2J/dy2J

Moreira Soares Oliveira B, Gawlik KI, Durbeej M, Holmberg J

PLoS Curr 10 (-) - [2018-08-27; online 2018-08-27]

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

A Protein-Based Encapsulation System with Calcium-Controlled Cargo Loading and Detachment

Lizatović R, Assent M, Barendregt A, ..., Wennmalm S, André I

Angew. Chem. Int. Ed. 57 (35) 11334-11338 [2018-08-27; online 2018-07-30]

Integrated Microscopy Technologies Stockholm [Collaborative]

Novel genome and genome-wide SNPs reveal early fragmentation effects in an edge-tolerant songbird population across an urbanized tropical metropolis.

Tan DJX, Chattopadhyay B, Garg KM, ..., Irestedt M, Rheindt FE

Sci Rep 8 (1) 12804 [2018-08-24; online 2018-08-24]

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

Stereotypic Immune System Development in Newborn Children.

Olin A, Henckel E, Chen Y, ..., Bohlin K, Brodin P

Cell 174 (5) 1277-1292.e14 [2018-08-23; online 2018-08-25]

Affinity Proteomics Stockholm [Service] Bioinformatics Compute and Storage [Service] Cellular Immunomonitoring [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Reduced expression of PROX1 transitions glioblastoma cells into a mesenchymal gene expression subtype

Goudarzi KM, Espinoza JA, Guo M, ..., Lindström MS, Hägerstrand D

Cancer Res - (-) canres.0320.2018 [2018-08-22; online 2018-08-22]

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

Single-cell RNA sequencing of mouse brain and lung vascular and vessel-associated cell types.

He L, Vanlandewijck M, Mäe MA, ..., Lendahl U, Betsholtz C

Sci Data 5 (1) 180160 [2018-08-21; online 2018-08-21]

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]

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum.

Liao Z, Kjellin J, Hoeppner MP, Grabherr M, Söderbom F

RNA Biol 15 (7) 937-954 [2018-08-21; online 2018-08-21]

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

Diversity of Interneurons in the Dorsal Striatum Revealed by Single-Cell RNA Sequencing and PatchSeq.

Muñoz-Manchado AB, Bengtsson Gonzales C, Zeisel A, ..., Linnarsson S, Hjerling-Leffler J

Cell Rep 24 (8) 2179-2190.e7 [2018-08-21; online 2018-08-23]

Eukaryotic Single Cell Genomics (ESCG) [Service]

Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.

Marques S, van Bruggen D, Vanichkina DP, ..., Taft RJ, Castelo-Branco G

Dev. Cell 46 (4) 504-517.e7 [2018-08-20; online 2018-08-02]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]

The structure-activity relationship of the salicylimide derived inhibitors of UDP-sugar producing pyrophosphorylases.

Decker D, Öberg C, Kleczkowski LA

Plant Signal Behav 13 (8) e1507406 [2018-08-20; online 2018-08-20]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Transthyretin Interferes with Aβ Amyloid Formation by Redirecting Oligomeric Nuclei into Non-Amyloid Aggregates.

Nilsson L, Pamrén A, Islam T, ..., Gharibyan AL, Olofsson A

J. Mol. Biol. 430 (17) 2722-2733 [2018-08-17; online 2018-06-08]

Sulfonimidamides: Synthesis and Applications in Preparative Organic Chemistry

Nandi GC, Arvidsson PI

Adv. Synth. Catal. 360 (16) 2976-3001 [2018-08-17; online 2018-05-25]

Drug Discovery and Development (DDD) [Technology development]

Pharmacokinetic Properties of the Nephrotoxin Orellanine in Rats.

Najar D, Haraldsson B, Thorsell A, ..., Nyström J, Ebefors K

Toxins (Basel) 10 (8) - [2018-08-17; online 2018-08-17]

BtsCI and BseGI display sequence preference in the nucleotides flanking the recognition sequence

Rosa J, Fernandez-Gonzalez E, Ducani C, Högberg B

PLoS ONE 13 (8) e0202057 [2018-08-17; online 2018-08-17]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Protein Science Facility (PSF) [Service]

Novel Autotrophic Organisms Contribute Significantly to the Internal Carbon Cycling Potential of a Boreal Lake

Peura S, Buck M, Aalto SL, ..., Nykänen H, Eiler A

MBio 9 (4) - [2018-08-14; online 2018-08-14]

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

Reduction in White Blood Cell, Neutrophil and Red Blood Cell counts Related to Gender, HLA and Islet Autoantibodies in Swedish TEDDY Children at Increased Risk for Type 1 Diabetes

Salami F, Lee HS, Freyhult E, ..., Lernmark Å, Törn C

Diabetes - (-) db180355 [2018-08-13; online 2018-08-13]

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

Extensive genomic diversity among Mycobacterium marinum strains revealed by whole genome sequencing

Das S, Pettersson F, Behra PRK, ..., Ennis DG, Kirsebom L

Sci. Rep. 8 (1) - [2018-08-13; online 2018-08-13]

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

Nutritional Metabolomics: Postprandial Response of Meals Relating to Vegan, Lacto-Ovo Vegetarian, and Omnivore Diets

Rådjursöga M, Lindqvist H, Pedersen A, ..., Ellegård L, Winkvist A

Nutrients 10 (8) 1063 [2018-08-10; online 2018-08-10]

Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.

Hu YOO, Ndegwa N, Alneberg J, ..., Fagerberg J, Andersson AF

Sci Rep 8 (1) 11907 [2018-08-09; online 2018-08-09]

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

SURGE complex of Plasmodium falciparum in the rhoptry-neck (SURFIN4.2-RON4-GLURP) contributes to merozoite invasion.

Quintana MDP, Ch'ng JH, Zandian A, ..., Chan S, Wahlgren M

PLoS ONE 13 (8) e0201669 [2018-08-09; online 2018-08-09]

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

Molecular Architecture of the Mouse Nervous System.

Zeisel A, Hochgerner H, Lönnerberg P, ..., Marklund U, Linnarsson S

Cell 174 (4) 999-1014.e22 [2018-08-09; online 2018-08-11]

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

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

Biermann J, Parris TZ, Nemes S, ..., Karlsson P, Helou K

Breast Cancer Res. 20 (1) 96 [2018-08-09; online 2018-08-09]

Thermodynamics of Hg(II) Bonding to Thiol Groups in Suwannee River Natural Organic Matter Resolved by Competitive Ligand Exchange, Hg LIII-Edge EXAFS and 1H NMR Spectroscopy

Song Y, Jiang T, Liem-Nguyen V, ..., Björn E, Skyllberg U

Environ. Sci. Technol. 52 (15) 8292-8301 [2018-08-07; online 2018-07-07]

Proteomic Biomarkers for Incident Aortic Stenosis Requiring Valvular Replacement.

Ljungberg J, Janiec M, Bergdahl IA, ..., Fall T, Söderberg S

Circulation 138 (6) 590-599 [2018-08-07; online 2018-03-01]

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

Modeling the structural implications of an alternatively spliced Exoc3l2, a paralog of the tunneling nanotube-forming M-Sec

O’Callaghan P, Zarb Y, Noborn F, Kreuger J

PLoS ONE 13 (8) e0201557 [2018-08-07; online 2018-08-07]

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

Huntingtin Aggregation Impairs Autophagy, Leading to Argonaute-2 Accumulation and Global MicroRNA Dysregulation.

Pircs K, Petri R, Madsen S, ..., Barker RA, Jakobsson J

Cell Rep 24 (6) 1397-1406 [2018-08-07; online 2018-08-09]

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

A genetic map of ostrich Z chromosome and the role of inversions in avian sex chromosome evolution.

Papoli Yazdi H, Ellegren H

Genome Biol Evol - (-) - [2018-08-07; online 2018-08-07]

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

Sample size effects on the assessment of eukaryotic diversity and community structure in aquatic sediments using high-throughput sequencing.

Nascimento FJA, Lallias D, Bik HM, Creer S

Sci Rep 8 (1) 11737 [2018-08-06; online 2018-08-06]

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

Biaryl sulfonamide motifs up- or down-regulate ion channel activity by activating voltage sensors.

Liin SI, Lund PE, Larsson JE, ..., Wallner B, Elinder F

J. Gen. Physiol. 150 (8) 1215-1230 [2018-08-06; online 2018-07-12]

Chemical Biology Consortium Sweden (CBCS) [Service]

Substrate-Induced Response in Biogas Process Performance and Microbial Community Relates Back to Inoculum Source

Liu T, Sun L, Nordberg Å, Schnürer A

Microorganisms 6 (3) 80 [2018-08-05; online 2018-08-05]

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

Impact in Plasma Metabolome as Effect of Lifestyle Intervention for Weight-Loss Reveals Metabolic Benefits in Metabolically Healthy Obese Women

Almanza-Aguilera E, Brunius C, Bernal-Lopez MR, ..., Landberg R, Andres-Lacueva C

J. Proteome Res. 17 (8) 2600-2610 [2018-08-03; online 2018-06-07]

Image-Based Detection of Patient-Specific Drug-Induced Cell-Cycle Effects in Glioblastoma

Matuszewski DJ, Wählby C, Krona C, Nelander S, Sintorn IM

SLAS DISCOVERY: Advancing Life Sciences R&D - (-) 247255521879141 [2018-08-03; online 2018-08-03]

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

Contrasting distribution patterns between aquatic and terrestrial Phytophthora species along a climatic gradient are linked to functional traits

Redondo MA, Boberg J, Stenlid J, Oliva J

ISME J - (-) - [2018-08-02; online 2018-08-02]

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

Sulfonyl Fluorides (SFs): More Than Click Reagents?

Chinthakindi PK, Arvidsson PI

Eur. J. Org. Chem. 2018 (27-28) 3648-3666 [2018-08-01; online 2018-07-06]

Drug Discovery and Development (DDD) [Technology development]

Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling

Lopez-Fernandez M, Broman E, Turner S, ..., Bertilsson S, Dopson M

FEMS Microbiol. Ecol. 94 (8) - [2018-08-01; online 2018-06-19]

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

CD93 promotes β1 integrin activation and fibronectin fibrillogenesis during tumor angiogenesis.

Lugano R, Vemuri K, Yu D, ..., Dejana E, Dimberg A

J. Clin. Invest. 128 (8) 3280-3297 [2018-08-01; online 2018-06-25]

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

Sex-specific manifestation of genetic risk for attention deficit hyperactivity disorder in the general population.

Martin J, Taylor MJ, Rydell M, ..., Thapar A, Lichtenstein P

J Child Psychol Psychiatry 59 (8) 908-916 [2018-08-00; online 2018-02-16]

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

Scanning electron microscopy as a tool for evaluating morphology of amyloid structures formed on surface plasmon resonance chips.

Bra Nnstro M K, Gharibyan AL, Islam T, ..., Pamren A, Olofsson A

Data Brief 19 (-) 1166-1170 [2018-08-00; online 2018-05-26]

Cryo-EM [Technology development]

RNA velocity of single cells.

La Manno G, Soldatov R, Zeisel A, ..., Linnarsson S, Kharchenko PV

Nature 560 (7719) 494-498 [2018-08-00; online 2018-08-08]

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

Proteome‐wide analysis of phospho‐regulated PDZ domain interactions

Sundell GN, Arnold R, Ali M, ..., Chi CN, Ivarsson Y

Mol. Syst. Biol. 14 (8) e8129 [2018-08-00; online 2018-08-20]

Drug Discovery and Development (DDD) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Prenatal arsenic exposure is associated with increased plasma IGFBP3 concentrations in 9-year-old children partly via changes in DNA methylation.

Gliga AR, Engström K, Kippler M, ..., Raqib R, Broberg K

Arch. Toxicol. 92 (8) 2487-2500 [2018-08-00; online 2018-06-08]

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

Plasma Protein Profiling Reveal Osteoprotegerin as a Marker of Prognostic Impact for Colorectal Cancer

Birgisson H, Tsimogiannis K, Freyhult E, Kamali-Moghaddam M

Transl Oncol 11 (4) 1034-1043 [2018-08-00; online 2018-08-00]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Novel Multiomics Profiling of Human Carotid Atherosclerotic Plaques and Plasma Reveals Biliverdin Reductase B as a Marker of Intraplaque Hemorrhage.

Matic LP, Jesus Iglesias M, Vesterlund M, ..., Odeberg J, Hedin U

JACC Basic Transl Sci 3 (4) 464-480 [2018-08-00; online 2018-08-01]

Affinity Proteomics Stockholm [Collaborative] Bioinformatics Compute and Storage [Service] Global Proteomics and Proteogenomics [Collaborative]

Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals.

Lee JJ, Wedow R, Okbay A, ..., Benjamin DJ, Cesarini D

Nat. Genet. 50 (8) 1112-1121 [2018-08-00; online 2018-07-23]

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

Epigenetics in pediatric acute lymphoblastic leukemia.

Nordlund J, Syvänen AC

Semin. Cancer Biol. 51 (-) 129-138 [2018-08-00; online 2017-09-05]

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

Effect of the paste-anode interface under impressed current cathodic protection in concrete structures

Zhang EQ, Tang L, Bernin D, Jansson H

Materials and Corrosion 69 (8) 1104-1116 [2018-08-00; online 2018-03-06]

Detailed analysis of the plasma extracellular vesicle proteome after separation from lipoproteins

Karimi N, Cvjetkovic A, Jang SC, ..., Lötvall J, Lässer C

Cell. Mol. Life Sci. 75 (15) 2873-2886 [2018-08-00; online 2018-02-13]

Glycoproteomics [Service] Integrated Microscopy Technologies Gothenburg [Service]

Delineating closely related dinoflagellate lineages using phylotranscriptomics.

Annenkova NV, Ahrén D, Logares R, Kremp A, Rengefors K

J. Phycol. 54 (4) 571-576 [2018-08-00; online 2018-06-13]

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

Data on the nucleotide composition of the first codons encoding the complementary determining region 3 (CDR3) in immunoglobulin heavy chains.

Thörnqvist L, Ohlin M

Data Brief 19 (-) 337-352 [2018-08-00; online 2018-05-04]

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

Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change.

Markussen T, Happel EM, Teikari JE, ..., Middelboe M, Kisand V

Environ. Microbiol. 20 (8) 3083-3099 [2018-08-00; online 2018-09-19]

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

Comprehensive RNA sequencing analysis in serum and muscle reveals novel small RNA signatures with biomarker potential for Duchenne Muscular Dystrophy

Coenen-Stass AML, Sork H, Gatto S, ..., Wood MJA, Roberts TC

Mol Ther Nucleic Acids - (-) - [2018-08-00; online 2018-08-00]

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]

Characterization of an activating R1353H insulin-like growth factor 1 receptor variant in a male with extreme tall height.

Lin Y, van Duyvenvoorde HA, Liu H, ..., Wit JM, Larsson O

Eur. J. Endocrinol. 179 (2) 85-95 [2018-08-00; online 2018-05-22]

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

Characterization of Swedish Campylobacter coli clade 2 and clade 3 water isolates.

Nilsson A, Skarp A, Johansson C, ..., Engstrand L, Rautelin H

Microbiologyopen 7 (4) e00583 [2018-08-00; online 2018-02-09]

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

An imidazole based H-Phe-Phe-NH 2 peptidomimetic with anti-allodynic effect in spared nerve injury mice

Skogh A, Lesniak A, Sköld C, ..., Hallberg M, Sandström A

Bioorganic & Medicinal Chemistry Letters 28 (14) 2446-2450 [2018-08-00; online 2018-08-00]

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

Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans

Cedernaes J, Schönke M, Westholm JO, ..., Zierath JR, Benedict C

Sci Adv 4 (8) eaar8590 [2018-08-00; online 2018-08-22]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] Swedish Metabolomics Centre (SMC) [Service]

A bacteriophage enzyme induces bacterial metabolic perturbation that confers a novel promiscuous function.

Jerlström Hultqvist J, Warsi O, Söderholm A, ..., Selmer M, Andersson DI

Nat Ecol Evol 2 (8) 1321-1330 [2018-08-00; online 2018-05-28]

BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea.

Alneberg J, Sundh J, Bennke C, ..., Labrenz M, Andersson AF

Sci Data 5 (-) 180146 [2018-07-31; online 2018-07-31]

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

Regulation of Neuronal Na,K-ATPase by Extracellular Scaffolding Proteins

Liebmann T, Fritz N, Kruusmägi M, ..., Aperia A, Brismar H

Int J Mol Sci 19 (8) 2214 [2018-07-29; online 2018-07-29]

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

ClpB mutants of Francisella tularensis subspecies holarctica and tularensis are defective for type VI secretion and intracellular replication.

Alam A, Golovliov I, Javed E, Sjöstedt A

Sci Rep 8 (1) 11324 [2018-07-27; online 2018-07-27]

Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat.

Sigeman H, Ponnikas S, Videvall E, ..., Naurin S, Hansson B

Genes 9 (8) 373 [2018-07-26; online 2018-07-26]

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

Glyco-engineered cell line and computational docking studies reveals enterotoxigenic Escherichia coli CFA/I fimbriae bind to Lewis a glycans.

Mottram L, Liu J, Chavan S, ..., Svennerholm AM, Holgersson J

Sci Rep 8 (1) 11250 [2018-07-26; online 2018-07-26]

Integrated Microscopy Technologies Gothenburg [Service]

Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea.

Berner C, Bertos-Fortis M, Pinhassi J, Legrand C

Front Microbiol 9 (-) 1562 [2018-07-25; online 2018-07-25]

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

A patient-derived xenograft pre-clinical trial reveals treatment responses and a resistance mechanism to karonudib in metastatic melanoma.

Einarsdottir BO, Karlsson J, Söderberg EMV, ..., Helleday T, Nilsson JA

Cell Death Dis 9 (8) 810 [2018-07-24; online 2018-07-24]

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

The psoriasis risk allele HLA-Cw0602 shows evidence of association with chronic or recurrent streptococcal tonsillitis.

Haapasalo K, Koskinen LLE, Suvilehto J, ..., Jokiranta TS, Saavalainen P

Infect. Immun. - (-) - [2018-07-23; online 2018-07-23]

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

Mebendazole stimulates CD14+ myeloid cells to enhance T-cell activation and tumour cell killing.

Rubin J, Mansoori S, Blom K, ..., Nygren P, Larsson R

Oncotarget 9 (56) 30805-30813 [2018-07-20; online 2018-07-20]

Drug Discovery and Development (DDD) [Service]

Effective Assignment of α2,3/α2,6-Sialic Acid Isomers by LC-MS/MS-Based Glycoproteomics.

Pett C, Nasir W, Sihlbom C, ..., Nilsson J, Westerlind U

Angew. Chem. Int. Ed. Engl. 57 (30) 9320-9324 [2018-07-20; online 2018-06-20]

Glycoproteomics [Technology development]

Characterisation of the Virome of Tonsils from Conventional Pigs and from Specific Pathogen-Free Pigs

Blomström AL, Ye X, Fossum C, Wallgren P, Berg M

Viruses 10 (7) 382 [2018-07-20; online 2018-07-20]

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

Disruption of a GATA1-binding motif upstream of XG/PBDX abolishes Xga expression and resolves the Xg blood group system.

Möller M, Lee YQ, Vidovic K, ..., Storry JR, Olsson ML

Blood 132 (3) 334-338 [2018-07-19; online 2018-05-10]

Structural Proteomics [Collaborative]

Structural basis for endotoxin neutralisation and anti-inflammatory activity of thrombin-derived C-terminal peptides.

Saravanan R, Holdbrook DA, Petrlova J, ..., Malmsten M, Schmidtchen A

Nat Commun 9 (1) 2762 [2018-07-17; online 2018-07-17]

Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure.

Broman E, Li L, Fridlund J, ..., Legrand C, Dopson M

Microb. Ecol. - (-) - [2018-07-17; online 2018-07-17]

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

Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome.

Sork H, Corso G, Krjutskov K, ..., Mäger I, El Andaloussi S

Sci Rep 8 (1) 10813 [2018-07-17; online 2018-07-17]

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

Molecular profiles of oxyphilic and chief cell parathyroid adenoma.

Lu M, Kjellin H, Fotouhi O, ..., Lehtiö J, Larsson C

Mol. Cell. Endocrinol. 470 (-) 84-95 [2018-07-15; online 2017-10-03]

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service]

SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments

Andermann T, Cano Á, Zizka A, Bacon C, Antonelli A

PeerJ 6 (-) e5175 [2018-07-13; online 2018-07-13]

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]

Microdeletion of 7p12.1p13, including IKZF1, causes intellectual impairment, overgrowth, and susceptibility to leukaemia.

Järviaho T, Zachariadis V, Tesi B, ..., Harila-Saari A, Nordgren A

Br. J. Haematol. - (-) - [2018-07-13; online 2018-07-13]

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

Bacterial Outer Membrane Vesicles Induce Vitronectin Release Into the Bronchoalveolar Space Conferring Protection From Complement-Mediated Killing.

Paulsson M, Che KF, Ahl J, ..., Lindén A, Riesbeck K

Front Microbiol 9 (-) 1559 [2018-07-13; online 2018-07-13]

Untargeted 1H NMR-Based Metabolomics Analysis of Urine and Serum Profiles after Consumption of Lentils, Chickpeas, and Beans: An Extended Meal Study To Discover Dietary Biomarkers of Pulses

Madrid-Gambin F, Brunius C, Garcia-Aloy M, ..., Landberg R, Andres-Lacueva C

J. Agric. Food Chem. 66 (27) 6997-7005 [2018-07-11; online 2018-06-19]

Notch signaling promotes a HIF2α-driven hypoxic response in multiple tumor cell types.

Mutvei AP, Landor SK, Fox R, ..., Jin S, Lendahl U

Oncogene - (-) - [2018-07-11; online 2018-07-11]

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

Gastrointestinal microbiota contributes to the development of murine transfusion-related acute lung injury.

Kapur R, Kim M, Rebetz J, ..., Speck ER, Semple JW

Blood Adv 2 (13) 1651-1663 [2018-07-10; online 2018-07-12]

Autoantibody profiling in intraocular fluid of patients with uveitis.

Ten Berge JC, Schreurs MW, van Rosmalen J, Rothova A

Exp. Eye Res. 176 (-) 141-146 [2018-07-10; online 2018-07-10]

Autoimmunity and Serology Profiling [Service]

Metabolic Profiling of Multiorgan Samples: Evaluation of MODY5/RCAD Mutant Mice.

Torell F, Bennett K, Cereghini S, ..., Trygg J, Lundstedt T

J. Proteome Res. 17 (7) 2293-2306 [2018-07-06; online 2018-06-15]

Primary glioblastoma cells for precision medicine: a quantitative portrait of genomic (in)stability during the first 30 passages.

Baskaran S, Mayrhofer M, Kultima HG, ..., Isaksson A, Nelander S

Neuro-oncology 20 (8) 1080-1091 [2018-07-05; online 2018-02-21]

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

Multimodal Chemical Imaging of Amyloid Plaque Polymorphism Reveals Aβ Aggregation Dependent Anionic Lipid Accumulations and Metabolism.

Michno W, Kaya I, Nyström S, ..., Zetterberg H, Hanrieder J

Anal. Chem. 90 (13) 8130-8138 [2018-07-03; online 2018-06-19]

Integrated Microscopy Technologies Gothenburg [Service]

Enteric Species F Human Adenoviruses use Laminin-Binding Integrins as Co-Receptors for Infection of Ht-29 Cells.

Rajan A, Persson BD, Frängsmyr L, ..., Gall J, Arnberg N

Sci Rep 8 (1) 10019 [2018-07-03; online 2018-07-03]

Human Immunodeficiency Virus-Infected Women Have High Numbers of CD103-CD8+ T Cells Residing Close to the Basal Membrane of the Ectocervical Epithelium.

Gibbs A, Buggert M, Edfeldt G, ..., Broliden K, Tjernlund A

J. Infect. Dis. 218 (3) 453-465 [2018-07-02; online 2017-12-23]

BioImage Informatics [Collaborative]

EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.

Jeggari A, Alekseenko Z, Petrov I, ..., Ericson J, Alexeyenko A

Nucleic Acids Res. 46 (W1) W163-W170 [2018-07-02; online 2018-06-13]

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]

The mycoparasitic fungus Clonostachys rosea responds with both common and specific gene expression during interspecific interactions with fungal prey

Nygren K, Dubey M, Zapparata A, ..., Jensen DF, Karlsson M

Evol Appl 11 (6) 931-949 [2018-07-00; online 2018-03-14]

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

The STAT4 SLE risk allele rs7574865[T] is associated with increased IL-12-induced IFN-γ production in T cells from patients with SLE.

Hagberg N, Joelsson M, Leonard D, ..., Bryceson YT, Rönnblom L

Ann. Rheum. Dis. 77 (7) 1070-1077 [2018-07-00; online 2018-02-23]

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

Porosity measurements in suspension plasma sprayed YSZ coatings using NMR cryoporometry and X-ray microscopy

Klement U, Ekberg J, Creci S, Kelly ST

J Coat Technol Res 15 (4) 753-757 [2018-07-00; online 2018-03-13]

OLMα2 Cells Bidirectionally Modulate Learning

Siwani S, França ASC, Mikulovic S, ..., Tort ABL, Kullander K

Neuron 99 (2) 404-412.e3 [2018-07-00; online 2018-07-00]

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

Novel gene variants associated with cardiovascular disease in systemic lupus erythematosus and rheumatoid arthritis.

Leonard D, Svenungsson E, Dahlqvist J, ..., Criswell LA, Rönnblom L

Ann. Rheum. Dis. 77 (7) 1063-1069 [2018-07-00; online 2018-03-07]

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

Multiplexed fluorescence microscopy reveals heterogeneity among stromal cells in mouse bone marrow sections

Holzwarth K, Köhler R, Philipsen L, ..., Niesner RA, Hauser AE

Cytometry 93 (9) 876-888 [2018-07-00; online 2018-08-14]

BioImage Informatics [Collaborative]

Increased Neuronal Differentiation of Neural Progenitor Cells Derived from Phosphovimentin-Deficient Mice.

Chen M, Puschmann TB, Marasek P, ..., Wilhelmsson U, Pekny M

Mol Neurobiol 55 (7) 5478-5489 [2018-07-00; online 2017-09-27]

Integrated Microscopy Technologies Gothenburg [Service]

Identification of inhibitors of Tartrate-resistant acid phosphatase (TRAP/ACP5) activity by small-molecule screening.

Reithmeier A, Lundbäck T, Haraldsson M, ..., Gustavsson AL, Andersson G

Chem Biol Drug Des 92 (1) 1255-1271 [2018-07-00; online 2018-03-30]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Genotype-Phenotype Correlation of PLOD2 Skeletal Dysplasias Using Structural Information.

Tham E, Grigelionis G, Hammarsjö A, Grigelioniene G

J. Bone Miner. Res. 33 (7) 1377-1378 [2018-07-00; online 2018-06-07]

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

Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence.

Savage JE, Jansen PR, Stringer S, ..., Wright MJ, Posthuma D

Nat. Genet. 50 (7) 912-919 [2018-07-00; online 2018-06-25]

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

Detection of novel syntrophic acetate-oxidizing bacteria from biogas processes by continuous acetate enrichment approaches.

Westerholm M, Müller B, Singh A, Karlsson Lindsjö O, Schnürer A

Microb Biotechnol 11 (4) 680-693 [2018-07-00; online 2017-12-04]

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

Complete genome sequence of the marine Rhodococcus sp. H-CA8f isolated from Comau fjord in Northern Patagonia, Chile.

Undabarrena A, Salvà-Serra F, Jaén-Luchoro D, ..., Seeger M, Cámara B

Marine Genomics 40 (-) 13-17 [2018-07-00; online 2018-02-15]

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

Calcium-activated Chloride Channel Regulator 1 (CLCA1) Controls Mucus Expansion in Colon by Proteolytic Activity.

Nyström EEL, Birchenough GMH, van der Post S, ..., Hansson GC, Johansson MEV

EBioMedicine 33 (-) 134-143 [2018-07-00; online 2018-06-07]

Integrated Microscopy Technologies Gothenburg [Service]

CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response.

Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J

Nat. Med. 24 (7) 927-930 [2018-07-00; online 2018-06-11]

CRISPR Functional Genomics [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Protein Science Facility (PSF) [Service]

Bioconda: sustainable and comprehensive software distribution for the life sciences

Grüning B, Dale R, Sjödin A, ..., Valieris R, Köster J

Nat Methods 15 (7) 475-476 [2018-07-00; online 2018-07-02]

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

Assessment of titanium dioxide nanoparticle toxicity in the rainbow trout (Onchorynchus mykiss) liver and gill cell lines RTL-W1 and RTgill-W1 under particular consideration of nanoparticle stability and interference with fluorometric assays

Lammel T, Sturve J

NanoImpact 11 (-) 1-19 [2018-07-00; online 2018-07-00]

Integrated Microscopy Technologies Gothenburg [Service]

A protein activity assay to measure global transcription factor activity reveals determinants of chromatin accessibility.

Wei B, Jolma A, Sahu B, ..., Taipale M, Taipale J

Nat. Biotechnol. 36 (6) 521-529 [2018-07-00; online 2018-05-21]

Global Proteomics and Proteogenomics [Collaborative]

A heterogeneous response of liver and skeletal muscle fat to the combination of a Paleolithic diet and exercise in obese individuals with type 2 diabetes: a randomised controlled trial

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Diabetologia 61 (7) 1548-1559 [2018-07-00; online 2018-04-26]

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

LC-MS/MS characterization of xyloside-primed glycosaminoglycans with cytotoxic properties reveals structural diversity and novel glycan modifications.

Persson A, Gomez Toledo A, Vorontsov E, ..., Nilsson J, Larson G

J. Biol. Chem. 293 (26) 10202-10219 [2018-06-29; online 2018-05-08]

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Garcia SL, Buck M, Hamilton JJ, ..., McMahon KD, Eiler A

mSphere 3 (3) - [2018-06-27; online 2018-05-30]

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

Confined photo-release of nitric oxide with simultaneous two-photon fluorescence tracking in a cellular system.

Thomsen H, Marino N, Conoci S, Sortino S, Ericson MB

Sci Rep 8 (1) 9753 [2018-06-27; online 2018-06-27]

Integrated Microscopy Technologies Gothenburg [Service]

appreci8: a pipeline for precise variant calling integrating 8 tools

Sandmann S, Karimi M, de Graaf AO, ..., Jansen JH, Dugas M

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The contribution of common genetic risk variants for ADHD to a general factor of childhood psychopathology.

Brikell I, Larsson H, Lu Y, ..., Lichtenstein P, Martin J

Mol. Psychiatry - (-) - [2018-06-22; online 2018-06-22]

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

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J. Mol. Biol. 430 (13) 1940-1949 [2018-06-22; online 2018-05-09]

In Vitro Evolution of Antibodies Inspired by In Vivo Evolution

Persson H, Kirik U, Thörnqvist L, ..., Levander F, Ohlin M

Front Immunol 9 (-) - [2018-06-21; online 2018-06-21]

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

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity.

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Nat Commun 9 (1) 2419 [2018-06-20; online 2018-06-20]

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

Simultaneous determination of ribonucleoside and deoxyribonucleoside triphosphates in biological samples by hydrophilic interaction liquid chromatography coupled with tandem mass spectrometry.

Kong Z, Jia S, Chabes AL, ..., Moritz T, Chabes A

Nucleic Acids Res. 46 (11) e66 [2018-06-20; online 2018-03-20]

Gut microbiota regulates maturation of the adult enteric nervous system via enteric serotonin networks.

De Vadder F, Grasset E, Mannerås Holm L, ..., Olofsson LE, Bäckhed F

Proc. Natl. Acad. Sci. U.S.A. 115 (25) 6458-6463 [2018-06-19; online 2018-06-04]

Integrated Microscopy Technologies Gothenburg [Service]

Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics.

Lundmark A, Gerasimcik N, Båge T, ..., Lundeberg J, Yucel-Lindberg T

Sci Rep 8 (1) 9370 [2018-06-19; online 2018-06-19]

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

Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries.

Feitosa MF, Kraja AT, Chasman DI, ..., Province MA, Levy D

PLoS ONE 13 (6) e0198166 [2018-06-18; online 2018-06-18]

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

Poly(alkylidenimine) Dendrimers Functionalized with the Organometallic Moiety [Ru(η⁵-C₅H₅)(PPh₃)₂]⁺ as Promising Drugs Against Cisplatin-Resistant Cancer Cells and Human Mesenchymal Stem Cells.

Gouveia M, Figueira J, Jardim MG, ..., Rissanen K, Rodrigues J

Molecules 23 (6) 1471 [2018-06-17; online 2018-06-17]

Stabilized Cyclic Peptides as Scavengers of Autoantibodies: Neutralization of Anticitrullinated Protein/Peptide Antibodies in Rheumatoid Arthritis

Gunasekera S, Fernandes-Cerqueira C, Wennmalm S, ..., Jakobsson PJ, Göransson U

ACS Chem. Biol. 13 (6) 1525-1535 [2018-06-15; online 2018-04-09]

Bioinformatics Compute and Storage [Service] Integrated Microscopy Technologies Stockholm [Collaborative] Swedish NMR Centre (SNC) [Service]

Plant Hormonomics: Multiple Phytohormone Profiling by Targeted Metabolomics

Šimura J, Antoniadi I, Široká J, ..., Ljung K, Novák O

Plant Physiol. 177 (2) 476-489 [2018-06-13; online 2018-04-27]

Investigating Holocene human population history in North Asia using ancient mitogenomes.

Kılınç GM, Kashuba N, Yaka R, ..., Storå J, Götherström A

Sci Rep 8 (1) 8969 [2018-06-12; online 2018-06-12]

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

Multi-ethnic genome-wide association study for atrial fibrillation.

Roselli C, Chaffin MD, Weng LC, ..., Lunetta KL, Ellinor PT

Nat. Genet. 50 (9) 1225-1233 [2018-06-11; online 2018-06-11]

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

Modular ssDNA binding and inhibition of telomerase activity by designer PPR proteins.

Spåhr H, Chia T, Lingford JP, ..., Filipovska A, Rackham O

Nat Commun 9 (1) 2212 [2018-06-07; online 2018-06-07]

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

Cárdenas CA, González-Aravena M, Font A, ..., Malmberg M, Bongcam-Rudloff E

PeerJ 6 (-) e4935 [2018-06-07; online 2018-06-07]

Higher Concentrations of BCAAs and 3-HIB Are Associated with Insulin Resistance in the Transition from Gestational Diabetes to Type 2 Diabetes

Andersson-Hall U, Gustavsson C, Pedersen A, ..., Joelsson L, Holmäng A

Journal of Diabetes Research 2018 (-) 1-12 [2018-06-05; online 2018-06-05]

Four evolutionary trajectories underlie genetic intratumoral variation in childhood cancer

Karlsson J, Valind A, Holmquist Mengelbier L, ..., Bexell D, Gisselsson D

Nat Genet 50 (7) 944-950 [2018-06-04; online 2018-06-04]

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

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Spiess M, Hernandez-Varas P, Oddone A, ..., Lakadamyali M, Strömblad S

J. Cell Biol. 217 (6) 1929-1940 [2018-06-04; online 2018-04-09]

Integrated Microscopy Technologies Stockholm [Collaborative]

Presence of Aedes and Anopheles mosquito larvae is correlated to bacteria found in domestic water-storage containers

Nilsson LKJ, Sharma A, Bhatnagar RK, Bertilsson S, Terenius O

FEMS Microbiol. Ecol. 94 (6) - [2018-06-01; online 2018-03-29]

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

Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum

Schmidt R, Durling MB, de Jager V, ..., Karlsson M, Garbeva P

FEMS Microbiol. Ecol. 94 (6) - [2018-06-01; online 2018-04-30]

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

γ-glutamyl transpeptidase deficiency caused by a large homozygous intragenic deletion in GGT1.

Darin N, Leckström K, Sikora P, ..., Almén G, Asin-Cayuela J

Eur. J. Hum. Genet. 26 (6) 808-817 [2018-06-00; online 2018-02-26]

Clinical Genomics Gothenburg [Collaborative] Clinical Genomics Stockholm [Service]

Topology of membrane proteins — predictions, limitations and variations

Tsirigos KD, Govindarajan S, Bassot C, ..., Shu N, Elofsson A

Current Opinion in Structural Biology 50 (-) 9-17 [2018-06-00; online 2018-06-00]

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

Testis transcriptome alterations in zebrafish (Danio rerio) with reduced fertility due to developmental exposure to 17α-ethinyl estradiol

Porseryd T, Reyhanian Caspillo N, Volkova K, ..., Olsson PE, Porsch-Hällström I

General and Comparative Endocrinology 262 (-) 44-58 [2018-06-00; online 2018-06-00]

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

Streptococcus pyogenes Infection and the Human Proteome with a Special Focus on the Immunoglobulin G-cleaving Enzyme IdeS.

Karlsson CAQ, Järnum S, Winstedt L, ..., Linder A, Malmström JA

Mol. Cell Proteomics 17 (6) 1097-1111 [2018-06-00; online 2018-03-06]

Structural Proteomics [Technology development]

Paternally expressed imprinted genes associate with hybridization barriers in Capsella

Lafon-Placette C, Hatorangan MR, Steige KA, ..., Slotte T, Köhler C

NPLANTS 4 (6) 352-357 [2018-06-00; online 2018-05-28]

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

Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell types.

Häring M, Zeisel A, Hochgerner H, ..., Linnarsson S, Ernfors P

Nat. Neurosci. 21 (6) 869-880 [2018-06-00; online 2018-04-23]

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

Neuronal Aβ42 is enriched in small vesicles at the presynaptic side of synapses

Yu Y, Jans DC, Winblad B, Tjernberg LO, Schedin-Weiss S

Life Sci. Alliance 1 (3) e201800028 [2018-06-00; online 2018-06-14]

Integrated Microscopy Technologies Stockholm [Collaborative]

Mechanistic study of hydrothermally aged Cu/SSZ-13 catalysts for ammonia-SCR

Leistner K, Kumar A, Kamasamudram K, Olsson L

Catalysis Today 307 (-) 55-64 [2018-06-00; online 2018-06-00]

Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Service]

Liquid Norbornadiene Photoswitches for Solar Energy Storage

Dreos A, Wang Z, Udmark J, ..., Nielsen MB, Moth-Poulsen K

Adv. Energy Mater. 8 (18) 1703401 [2018-06-00; online 2018-03-25]

Genomewide binding of transcription factor Snail1 in triple-negative breast cancer cells

Maturi V, Morén A, Enroth S, Heldin CH, Moustakas A

Mol Oncol 12 (7) 1153-1174 [2018-06-00; online 2018-05-21]

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

Expression of ribosomal and actin network proteins and immunochemotherapy resistance in diffuse large B cell lymphoma patients

Bram Ednersson S, Stenson M, Stern M, ..., Hasselblom S, Andersson PO

Br J Haematol 181 (6) 770-781 [2018-06-00; online 2018-05-16]

Glycoproteomics [Service] Integrated Microscopy Technologies Gothenburg [Service]

Diminished CXCR5 expression in peripheral blood of patients with Sjögren's syndrome may relate to both genotype and salivary gland homing.

Aqrawi LA, Ivanchenko M, Björk A, ..., Skarstein K, Wahren-Herlenius M

Clin. Exp. Immunol. 192 (3) 259-270 [2018-06-00; online 2018-03-24]

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

PubMed

Development and Utility of a Birth Defects Surveillance Toolkit.

Flores AL, Turay K, Valencia D, ..., Groisman B, Mastroiacovo P

J Glob Health Perspect 0 (-) - [2018-06-00; online 2018-06-14]

Bioinformatics Compute and Storage [Service]

Design, synthesis and evaluation of potent and selective inhibitors of mono-(ADP-ribosyl)transferases PARP10 and PARP14

Holechek J, Lease R, Thorsell AG, ..., Schüler H, Ferraris D

Bioorganic & Medicinal Chemistry Letters 28 (11) 2050-2054 [2018-06-00; online 2018-06-00]

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

Cracking the Sugar Code by Mass Spectrometry : An Invited Perspective in Honor of Dr. Catherine E. Costello, Recipient of the 2017 ASMS Distinguished Contribution Award.

Mirgorodskaya E, Karlsson NG, Sihlbom C, Larson G, Nilsson CL

J. Am. Soc. Mass Spectrom. 29 (6) 1065-1074 [2018-06-00; online 2018-04-11]

Circadian clock components control daily growth activities by modulating cytokinin levels and cell division-associated gene expression in Populus trees.

Edwards KD, Takata N, Johansson M, ..., Ljung K, Eriksson ME

Plant Cell Environ. 41 (6) 1468-1482 [2018-06-00; online 2018-04-15]

Assessing Cu impacts on freshwater diatoms: biochemical and metabolomic responses of Tabellaria flocculosa (Roth) Kützing

Gonçalves S, Kahlert M, Almeida SFP, Figueira E

Science of The Total Environment 625 (-) 1234-1246 [2018-06-00; online 2018-06-00]

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

A novel ECEL1 mutation expands the phenotype of distal arthrogryposis multiplex congenita type 5D to include pretibial vertical skin creases.

Stattin EL, Johansson J, Gudmundsson S, ..., Bondeson ML, Wilbe M

Am. J. Med. Genet. A 176 (6) 1405-1410 [2018-06-00; online 2018-04-16]

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

PubMed

A genome scan for quantitative trait loci affecting average daily gain and Kleiber ratio in Baluchi Sheep.

Pasandideh M, Rahimi-Mianji G, Gholizadeh M

J. Genet. 97 (2) 493-503 [2018-06-00; online 2018-06-23]

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

Equilibrative nucleoside transporter 1 gene polymorphisms and clinical outcomes following acute coronary syndromes: findings from the PLATelet inhibition and patient Outcomes (PLATO) study.

Parker WAE, Eriksson N, Becker RC, ..., Storey RF, PLATO Investigators

Platelets - (-) 1-10 [2018-05-31; online 2018-05-31]

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

Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces).

Blåhed IM, Königsson H, Ericsson G, Spong G

PLoS ONE 13 (5) e0197364 [2018-05-30; online 2018-05-30]

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

Common genetic variation in the autoimmune regulator (AIRE) locus is associated with autoimmune Addison's disease in Sweden.

Eriksson D, Bianchi M, Landegren N, ..., Rosengren Pielberg G, Kämpe O

Sci Rep 8 (1) 8395 [2018-05-30; online 2018-05-30]

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

Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function.

Davies G, Lam M, Harris SE, ..., Lencz T, Deary IJ

Nat Commun 9 (1) 2098 [2018-05-29; online 2018-05-29]

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

Kynurenine pathway is altered in patients with SLE and associated with severe fatigue.

Åkesson K, Pettersson S, Ståhl S, ..., Svenungsson E, Idborg H

Lupus Sci Med 5 (1) e000254 [2018-05-23; online 2018-05-23]

SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma.

Jordán-Pla A, Yu S, Waldholm J, ..., Östlund Farrants AK, Visa N

BMC Genomics 19 (1) 367 [2018-05-18; online 2018-05-18]

Bioinformatics 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]

Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells.

Guzzi N, Cieśla M, Ngoc PCT, ..., Hsieh AC, Bellodi C

Cell 173 (5) 1204-1216.e26 [2018-05-17; online 2018-04-05]

Quantitation of Endogenous Metabolites in Mouse Tumors Using Mass-Spectrometry Imaging.

Swales JG, Dexter A, Hamm G, ..., Critchlow SE, Goodwin RJA

Anal. Chem. 90 (10) 6051-6058 [2018-05-15; online 2018-04-26]

Inflammatory biomarker profiling in classical orthostatic hypotension: Insights from the SYSTEMA cohort.

Johansson M, Ricci F, Aung N, ..., Melander O, Fedorowski A

Int. J. Cardiol. 259 (-) 192-197 [2018-05-15; online 2018-03-27]

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

A mass spectrometry imaging approach for investigating how drug-drug interactions influence drug blood-brain barrier permeability.

Vallianatou T, Strittmatter N, Nilsson A, ..., Goodwin RJA, Andrén PE

Neuroimage 172 (-) 808-816 [2018-05-15; online 2018-01-10]

A genome-wide association study of IgM antibody against phosphorylcholine: shared genetics and phenotypic relationship to chronic lymphocytic leukemia.

Chen X, Gustafsson S, Whitington T, ..., Frostegård J, Magnusson PKE

Hum. Mol. Genet. 27 (10) 1809-1818 [2018-05-15; online 2018-03-17]

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

Transcriptomic analysis of the harvested endothelial cells in a swine model of mechanical thrombectomy.

Jaff N, Grankvist R, Muhl L, ..., Eriksson U, Holmin S

Neuroradiology - (-) - [2018-05-14; online 2018-05-14]

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

Soil microclimate changes affect soil fungal communities in a Mediterranean pine forest

Castaño C, Lindahl BD, Alday JG, ..., Pera J, Bonet JA

New Phytol - (-) - [2018-05-14; online 2018-05-14]

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

Habitual coffee consumption and cognitive function: a Mendelian randomization meta-analysis in up to 415,530 participants.

Zhou A, Taylor AE, Karhunen V, ..., Llewellyn DJ, Hyppönen E

Sci Rep 8 (1) 7526 [2018-05-14; online 2018-05-14]

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

Impact of Dynamically Exposed Polarity on Permeability and Solubility of Chameleonic Drugs Beyond the Rule of 5

Rossi Sebastiano M, Doak BC, Backlund M, ..., Matsson P, Kihlberg J

J. Med. Chem. 61 (9) 4189-4202 [2018-05-10; online 2018-04-02]

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

Humanizing Miniature Hearts through 4-Flow Cannulation Perfusion Decellularization and Recellularization.

Nguyen DT, O'Hara M, Graneli C, ..., Althage M, Heydarkhan-Hagvall S

Sci Rep 8 (1) 7458 [2018-05-10; online 2018-05-10]

Integrated Microscopy Technologies Gothenburg [Service]

Modulation of gene transcription and epigenetics of colon carcinoma cells by bacterial membrane vesicles.

Vdovikova S, Gilfillan S, Wang S, ..., Wai SN, Hurtado A

Sci Rep 8 (1) 7434 [2018-05-09; online 2018-05-09]

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

Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma.

Parris TZ, Rönnerman EW, Engqvist H, ..., Karlsson P, Helou K

Oncotarget 9 (35) 24140-24154 [2018-05-08; online 2018-05-08]

Bioinformatics 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]

Genome-wide association meta-analysis of circulating odd-numbered chain saturated fatty acids: Results from the CHARGE Consortium.

de Oliveira Otto MC, Lemaitre RN, Sun Q, ..., Siscovick DS, Mozaffarian D

PLoS ONE 13 (5) e0196951 [2018-05-08; online 2018-05-08]

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

Time-resolved transcriptome and proteome landscape of human regulatory T cell (Treg) differentiation reveals novel regulators of FOXP3.

Schmidt A, Marabita F, Kiani NA, ..., Lahesmaa R, Tegnér J

BMC Biol. 16 (1) 47 [2018-05-07; online 2018-05-07]

Global Proteomics and Proteogenomics [Collaborative]

The GTPase domain of gamma-tubulin is required for normal mitochondrial function and spatial organization.

Lindström L, Li T, Malycheva D, ..., Rosselló CA, Alvarado-Kristensson M

Commun Biol 1 (1) 37 [2018-05-03; online 2018-05-03]

Integrated Microscopy Technologies Gothenburg [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

The structure of the N-terminal module of the cell wall hydrolase RipA and its role in regulating catalytic activity.

Steiner EM, Lyngsø J, Guy JE, ..., Schneider G, Schnell R

Proteins - (-) - [2018-05-02; online 2018-05-02]

Multiplexed Antigen Bead Arrays for the Assessment of Antibody Selectivity and Epitope Mapping.

Ayoglu B, Nilsson P, Schwenk JM

Methods Mol. Biol. 1785 (-) 239-248 [2018-05-02; online 2018-05-02]

Affinity Proteomics Stockholm [Technology development] Autoimmunity and Serology Profiling [Technology development]

High-Density Antigen Microarrays for the Assessment of Antibody Selectivity and Off-Target Binding.

Sjöberg R, Andersson E, Hellström C, ..., Nilsson P, Ayoglu B

Methods Mol. Biol. 1785 (-) 231-238 [2018-05-02; online 2018-05-02]

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

O6-methylguanine–induced transcriptional mutagenesis reduces p53 tumor-suppressor function

Ezerskyte M, Paredes JA, Malvezzi S, ..., Scicchitano DA, Dreij K

Proc. Natl. Acad. Sci. U.S.A. 115 (18) 4731-4736 [2018-05-01; online 2018-04-17]

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] National Genomics Infrastructure [Service]

Extended and Continuous Decline in Effective Population Size Results in Low Genomic Diversity in the World's Rarest Hyena Species, the Brown Hyena.

Westbury MV, Hartmann S, Barlow A, ..., Dalén L, Hofreiter M

Mol. Biol. Evol. 35 (5) 1225-1237 [2018-05-01; online 2018-03-13]

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

BAP1 induces cell death via interaction with 14-3-3 in neuroblastoma.

Sime W, Niu Q, Abassi Y, ..., Fu H, Massoumi R

Cell Death Dis 9 (5) 458 [2018-05-01; online 2018-05-01]

Array profiling reveals contribution of Cthrc1 to growth of the denervated rat urinary bladder.

Zhu B, Ekman M, Svensson D, ..., Uvelius B, Swärd K

Am. J. Physiol. Renal Physiol. 314 (5) F893-F905 [2018-05-01; online 2018-01-10]

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

Uterine progesterone signaling is a target for metformin therapy in PCOS-like rats.

Hu M, Zhang Y, Feng J, ..., Shao LR, Billig H

J Endocrinol 237 (2) 123-137 [2018-05-00; online 2018-03-13]

Integrated Microscopy Technologies Gothenburg [Service]

Transcription profiling of peripheral B cells in antibody-positive primary Sjögren's syndrome reveals upregulated expression of CX3CR1 and a type I and type II interferon signature.

Imgenberg-Kreuz J, Sandling JK, Björk A, ..., Syvänen AC, Nordmark G

Scand. J. Immunol. 87 (5) e12662 [2018-05-00; online 2018-04-15]

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

Sulfasalazine-Induced Agranulocytosis Is Associated With the Human Leukocyte Antigen Locus.

Wadelius M, Eriksson N, Kreutz R, ..., Hallberg P, EuDAC

Clin. Pharmacol. Ther. 103 (5) 843-853 [2018-05-00; online 2017-09-28]

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

Pretreatment of anaerobic digester samples by hydrochloric acid for solution-state 1 H and 13 C NMR spectroscopic characterization of organic matter

Shakeri Yekta S, Hedenström M, Stehr JE, ..., Hertkorn N, Björn A

Chemosphere 199 (-) 201-209 [2018-05-00; online 2018-05-00]

Potentials and pitfalls of inverse fluorescence correlation spectroscopy

Wennmalm S

Methods 140-141 (-) 23-31 [2018-05-00; online 2018-05-00]

Integrated Microscopy Technologies Stockholm [Technology development]

Molecular barcoding of viral vectors enables mapping and optimization of mRNAtrans-splicing

Davidsson M, Díaz-Fernández P, Torroba M, ..., Lundberg C, Björklund T

RNA 24 (5) 673-687 [2018-05-00; online 2018-01-31]

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

Mitochondrial Translation Efficiency Controls Cytoplasmic Protein Homeostasis

Suhm T, Kaimal JM, Dawitz H, ..., Andréasson C, Ott M

Cell Metabolism - (-) - [2018-05-00; online 2018-05-00]

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

Microenvironmental control of breast cancer subtype elicited through paracrine platelet-derived growth factor-CC signaling.

Roswall P, Bocci M, Bartoschek M, ..., Eriksson U, Pietras K

Nat. Med. 24 (4) 463-473 [2018-05-00; online 2018-03-12]

Increasing sorghum yields by seed treatment with an aqueous extract of the plant Eclipta alba may involve a dual mechanism of hydropriming and suppression of fungal pathogens

Zida PE, Néya BJ, Stokholm MS, ..., Sérémé P, Lund OS

Crop Protection 107 (-) 48-55 [2018-05-00; online 2018-05-00]

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

Identification of novel diagnostic biomarkers for deep venous thrombosis.

Memon AA, Sundquist K, PirouziFard M, ..., Sundquist J, Zöller B

Br. J. Haematol. 181 (3) 378-385 [2018-05-00; online 2018-04-19]

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

Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies

Pent M, Hiltunen M, Põldmaa K, ..., Ryberg M, Bahram M

Environ Microbiol 20 (5) 1641-1650 [2018-05-00; online 2018-03-25]

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

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.

Wray NR, Ripke S, Mattheisen M, ..., Sullivan PF, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium

Nat. Genet. 50 (5) 668-681 [2018-05-00; online 2018-04-26]

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

Fatal demyelinating disease is induced by monocyte-derived macrophages in the absence of TGF-β signaling.

Lund H, Pieber M, Parsa R, ..., Zhang XM, Harris RA

Nat. Immunol. 19 (5) 1-7 [2018-05-00; online 2018-04-16]

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

Ethylene signaling induces gelatinous layers with typical features of tension wood in hybrid aspen.

Felten J, Vahala J, Love J, ..., Mellerowicz EJ, Sundberg B

New Phytol. 218 (3) 999-1014 [2018-05-00; online 2018-03-12]

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

Editorial and Review: 29th ASMS Sanibel Conference on Mass Spectrometry-Peptidomics: Bridging the Gap between Proteomics and Metabolomics by MS.

Li L, Andrén PE, Sweedler JV

J. Am. Soc. Mass Spectrom. 29 (5) 801-806 [2018-05-00; online 2018-04-07]

Darkened Leaves Use Different Metabolic Strategies for Senescence and Survival.

Law SR, Chrobok D, Juvany M, ..., Gardeström P, Keech O

Plant Physiol. 177 (1) 132-150 [2018-05-00; online 2018-03-09]

DNA methylation mapping identifies gene regulatory effects in patients with systemic lupus erythematosus.

Imgenberg-Kreuz J, Carlsson Almlöf J, Leonard D, ..., Syvänen AC, Sandling JK

Ann. Rheum. Dis. 77 (5) 736-743 [2018-05-00; online 2018-02-01]

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

Combined BET bromodomain and CDK2 inhibition in MYC-driven medulloblastoma.

Bolin S, Borgenvik A, Persson CU, ..., Weishaupt H, Swartling FJ

Oncogene 37 (21) 2850-2862 [2018-05-00; online 2018-03-07]

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

Ultra-rapid auxin metabolite profiling for high-throughput mutant screening in Arabidopsis.

Pencík A, Casanova-Sáez R, Pilarová V, ..., Ljung K, Novák O

J. Exp. Bot. 69 (10) 2569-2579 [2018-04-27; online 2018-03-08]

Rebooting Human Immunology.

Davis MM, Brodin P

Annu. Rev. Immunol. 36 (-) 843-864 [2018-04-26; online 2018-02-28]

Cellular Immunomonitoring [Collaborative]

Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas.

van der Valk T, Sandoval-Castellanos E, Caillaud D, ..., Dalén L, Guschanski K

Sci Rep 8 (1) 6551 [2018-04-25; online 2018-04-25]

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

Quantification of endogenous and exogenous protein expressions of Na,K-ATPase with super-resolution PALM/STORM imaging.

Bernhem K, Blom H, Brismar H

PLoS ONE 13 (4) e0195825 [2018-04-25; online 2018-04-25]

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

Experimental validation of predicted cancer genes using FRET

Guala D, Bernhem K, Blal HA, ..., Brismar H, Sonnhammer ELL

Methods Appl. Fluoresc. 6 (3) 035007 [2018-04-25; online 2018-04-25]

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

Repeated evolution of self-compatibility for reproductive assurance.

Nieuwenhuis BPS, Tusso S, Bjerling P, ..., Wolf JBW, Immler S

Nat Commun 9 (1) 1639 [2018-04-24; online 2018-04-24]

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

Genome-Guided Analysis of Clostridium ultunense and Comparative Genomics Reveal Different Strategies for Acetate Oxidation and Energy Conservation in Syntrophic Acetate-Oxidising Bacteria

Manzoor S, Schnürer A, Bongcam-Rudloff E, Müller B

Genes 9 (4) 225 [2018-04-23; online 2018-04-23]

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

Autophagic flux blockage by accumulation of weakly basic tenovins leads to elimination of B-Raf mutant tumour cells that survive vemurafenib

Ladds MJGW, Pastor-Fernández A, Popova G, ..., Bhatia R, Laín S

PLoS ONE 13 (4) e0195956 [2018-04-23; online 2018-04-23]

Drug Discovery and Development (DDD) [Service]

Human erythrocyte-derived nanovesicles can readily be loaded with doxorubicin and act as anticancer agents.

Dubois L, None , Löf L, ..., Ronquist G, Ronquist KG

Cancer Res Front 4 (1) 13-26 [2018-04-20; online 2018-04-20]

PLA and Single Cell Proteomics [Technology development]

Full Mitogenomes in the Critically Endangered Kākāpō Reveal Major Post-Glacial and Anthropogenic Effects on Neutral Genetic Diversity.

Dussex N, von Seth J, Robertson BC, Dalén L

Genes 9 (4) - [2018-04-19; online 2018-04-19]

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

Eleven loci with new reproducible genetic associations with allergic disease risk.

Ferreira MAR, Vonk JM, Baurecht H, ..., Koppelman GH, Paternoster L

J. Allergy Clin. Immunol. - (-) - [2018-04-19; online 2018-04-19]

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

A GWAS meta-analysis from 5 population-based cohorts implicates ion channel genes in the pathogenesis of irritable bowel syndrome.

Bonfiglio F, Henström M, Nag A, ..., Zhernakova A, D'Amato M

Neurogastroenterol. Motil. - (-) e13358 [2018-04-19; online 2018-04-19]

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

Genetic and Environmental Contributions to the Covariation Between Cardiometabolic Traits.

Chen X, Kuja-Halkola R, Chang Z, ..., Pedersen NL, Magnusson PKE

J Am Heart Assoc 7 (9) - [2018-04-18; online 2018-04-18]

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

Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer.

La Fleur L, Boura VF, Alexeyenko A, ..., Karlsson MCI, Botling J

Int. J. Cancer - (-) - [2018-04-18; online 2018-04-18]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics Uppsala [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Data quality of whole genome bisulfite sequencing on Illumina platforms.

Raine A, Liljedahl U, Nordlund J

PLoS ONE 13 (4) e0195972 [2018-04-18; online 2018-04-18]

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

Complete Remission with Reduction of High-Risk Clones following Haploidentical NK-Cell Therapy against MDS and AML

Björklund AT, Carlsten M, Sohlberg E, ..., Ljunggren HG, Malmberg KJ

Clin. Cancer Res. 24 (8) 1834-1844 [2018-04-15; online 2018-02-14]

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

Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia.

Danielsson F, Fasterius E, Sullivan D, ..., Williams C, Lundberg E

Oncotarget 9 (28) 19730-19744 [2018-04-13; online 2018-04-13]

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

Granule-stored MUC5B mucins are packed by the non-covalent formation of N-terminal head-to-head tetramers.

Trillo-Muyo S, Nilsson HE, Recktenwald CV, ..., Hebert H, Hansson GC

J. Biol. Chem. 293 (15) 5746-5754 [2018-04-13; online 2018-02-13]

Integrated Microscopy Technologies Gothenburg [Service]

Rice auxin influx carrier OsAUX1 facilitates root hair elongation in response to low external phosphate.

Giri J, Bhosale R, Huang G, ..., Swarup R, Bennett MJ

Nat Commun 9 (1) 1408 [2018-04-12; online 2018-04-12]

Crystal Structure of Botulinum Neurotoxin A2 in Complex with the Human Protein Receptor SV2C Reveals Plasticity in Receptor Binding.

Gustafsson R, Zhang S, Masuyer G, Dong M, Stenmark P

Toxins (Basel) 10 (4) - [2018-04-12; online 2018-04-12]

A mechanistic framework for auxin dependent Arabidopsis root hair elongation to low external phosphate.

Bhosale R, Giri J, Pandey BK, ..., Bennett MJ, Swarup R

Nat Commun 9 (1) 1409 [2018-04-12; online 2018-04-12]

Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima.

Morgunova E, Yin Y, Das PK, ..., Nilsson L, Taipale J

Elife 7 (-) - [2018-04-11; online 2018-04-11]

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

Expression levels of long non-coding RNAs are prognostic for AML outcome.

Mer AS, Lindberg J, Nilsson C, ..., Lehmann S, Rantalainen M

J Hematol Oncol 11 (1) 52 [2018-04-07; online 2018-04-07]

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

Allele-selective RUNX1 binding regulates P1 blood group status by transcriptional control of A4GALT.

Westman JS, Stenfelt L, Vidovic K, ..., Kjellström S, Olsson ML

Blood 131 (14) 1611-1616 [2018-04-05; online 2018-02-08]

Female-specific Association Between Variants on Chromosome 9 and Self-reported Diagnosis of Irritable Bowel Syndrome.

Bonfiglio F, Zheng T, Garcia-Etxebarria K, ..., Zhernakova A, D'Amato M

Gastroenterology - (-) - [2018-04-04; online 2018-04-04]

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

Abundant fish protein inhibits α-synuclein amyloid formation.

Werner T, Kumar R, Horvath I, Scheers N, Wittung-Stafshede P

Sci Rep 8 (1) 5465 [2018-04-03; online 2018-04-03]

Integrated Microscopy Technologies Gothenburg [Service]

An Application-Directed, Versatile DNA FISH Platform for Research and Diagnostics.

Gelali E, Custodio J, Girelli G, ..., Crosetto N, Bienko M

Methods Mol. Biol. 1766 (-) 303-333 [2018-04-02; online 2018-04-02]

Advanced FISH Technologies [Technology development]

Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce.

Jokipii-Lukkari S, Delhomme N, Schiffthaler B, ..., Street NR, Tuominen H

Plant Physiol. 176 (4) 2851-2870 [2018-04-00; online 2018-02-27]

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

The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines. Correction

Hofving T, Arvidsson Y, Almobarak B, ..., Johanson V, Nilsson O

Endocr Relat Cancer 25 (4) X1-X2 [2018-04-00; online 2018-04-00]

Integrated Microscopy Technologies Gothenburg [Service]

The functional 3'-end of immunoglobulin heavy chain variable (IGHV) genes.

Thörnqvist L, Ohlin M

Mol. Immunol. 96 (-) 61-68 [2018-04-00; online 2018-02-28]

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

Structure of the chloroplast ribosome with chl-RRF and hibernation-promoting factor.

Perez Boerema A, Aibara S, Paul B, ..., Lindahl E, Amunts A

NPLANTS 4 (4) 212-217 [2018-04-00; online 2018-04-02]

Structural and functional studies of Spr1654: an essential aminotransferase in teichoic acid biosynthesis in

Han X, Sun R, Sandalova T, Achour A

Open Biol 8 (4) - [2018-04-00; online 2018-04-20]

Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes.

Mahajan A, Wessel J, Willems SM, ..., Rotter JI, McCarthy MI

Nat. Genet. 50 (4) 559-571 [2018-04-00; online 2018-04-09]

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

RNA Sequencing of Stentor Cell Fragments Reveals Transcriptional Changes during Cellular Regeneration

Onsbring H, Jamy M, Ettema TJG

Current Biology 28 (8) 1281-1288.e3 [2018-04-00; online 2018-04-00]

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

Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes.

Malik R, Chauhan G, Traylor M, ..., MEGASTROKE Consortium , MEGASTROKE Consortium:

Nat. Genet. 50 (4) 524-537 [2018-04-00; online 2018-03-12]

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

Modulation of saturation and chain length of fatty acids in Saccharomyces cerevisiae for production of cocoa butter-like lipids

Bergenholm D, Gossing M, Wei Y, Siewers V, Nielsen J

Biotechnol. Bioeng. 115 (4) 932-942 [2018-04-00; online 2018-01-24]

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

Long Non-Coding RNAs Associated with Metabolic Traits in Human White Adipose Tissue.

Gao H, Kerr A, Jiao H, ..., Dahlman I, Arner P

EBioMedicine 30 (-) 248-260 [2018-04-00; online 2018-03-15]

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

Know your farmer: Ancient origins and multiple independent domestications of ambrosia beetle fungal cultivars

Vanderpool D, Bracewell RR, McCutcheon JP

Mol Ecol 27 (8) 2077-2094 [2018-04-00; online 2017-11-23]

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

Identification of Potential MR-Derived Biomarkers for Tumor Tissue Response to 177Lu-Octreotate Therapy in an Animal Model of Small Intestine Neuroendocrine Tumor.

Montelius M, Spetz J, Jalnefjord O, ..., Ljungberg M, Forssell-Aronsson E

Transl Oncol 11 (2) 193-204 [2018-04-00; online 2018-01-11]

Identification of Poly(ADP-Ribose) Polymerase Macrodomain Inhibitors Using an AlphaScreen Protocol

Ekblad T, Verheugd P, Lindgren AE, ..., Elofsson M, Schüler H

SLAS DISCOVERY: Advancing Life Sciences R&D 23 (4) 353-362 [2018-04-00; online 2018-01-09]

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

GABA Regulates Release of Inflammatory Cytokines From Peripheral Blood Mononuclear Cells and CD4 + T Cells and Is Immunosuppressive in Type 1 Diabetes

Bhandage AK, Jin Z, Korol SV, ..., Kamali-Moghaddam M, Birnir B

EBioMedicine 30 (-) 283-294 [2018-04-00; online 2018-04-00]

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

Effects of fixation on electrophysiology and structure of human jejunal villi.

Casselbrant A, Helander HF

Microsc Res Tech 81 (4) 376-383 [2018-04-00; online 2018-01-11]

Integrated Microscopy Technologies Gothenburg [Service]

Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments.

Wang H, Sikora P, Rutgersson C, ..., Larsson DGJ, Norder H

International Journal of Hygiene and Environmental Health 221 (3) 479-488 [2018-04-00; online 2018-02-01]

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

Confocal super-resolution imaging of the glomerular filtration barrier enabled by tissue expansion

Unnersjö-Jess D, Scott L, Sevilla SZ, ..., Blom H, Brismar H

Kidney International 93 (4) 1008-1013 [2018-04-00; online 2018-04-00]

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

An in vitro evaluation of browser and grazer fermentation efficiency and microbiota using European moose spring and summer foods

Krizsan SJ, Mateos-Rivera A, Bertilsson S, ..., Gidlund H, Huhtanen P

Ecol Evol 8 (8) 4183-4196 [2018-04-00; online 2018-03-31]

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

Improved efficiency of in situ protein analysis by proximity ligation using UnFold probes.

Klaesson A, Grannas K, Ebai T, ..., Söderberg O, Landegren U

Sci Rep 8 (1) 5400 [2018-03-29; online 2018-03-29]

PLA and Single Cell Proteomics [Technology development]

Evaluation of the ISL1 gene in the pathogenesis of bladder exstrophy in a Swedish cohort.

Arkani S, Cao J, Lundin J, ..., Matsson H, Nordenskjöld A

Hum Genome Var 5 (-) 18009 [2018-03-29; online 2018-03-29]

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]

Strong impact on plasma protein profiles by precentrifugation delay but not by repeated freeze-thaw cycles, as analyzed using multiplex proximity extension assays.

Shen Q, Björkesten J, Galli J, ..., Tybring G, Landegren U

Clin. Chem. Lab. Med. 56 (4) 582-594 [2018-03-28; online 2017-10-19]

PLA and Single Cell Proteomics [Technology development]

Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia.

Valdiosera C, Günther T, Vera-Rodríguez JC, ..., Smith CI, Jakobsson M

Proc. Natl. Acad. Sci. U.S.A. 115 (13) 3428-3433 [2018-03-27; online 2018-03-12]

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

Changes in methylation within the STK32B promoter are associated with an increased risk for generalized anxiety disorder in adolescents.

Ciuculete DM, Boström AE, Tuunainen AK, ..., Mwinyi J, Schiöth HB

J Psychiatr Res 102 (-) 44-51 [2018-03-26; online 2018-03-26]

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

AMYCNE: Confident copy number assessment using whole genome sequencing data.

Eisfeldt J, Nilsson D, Andersson-Assarsson JC, Lindstrand A

PLoS ONE 13 (3) e0189710 [2018-03-26; online 2018-03-26]

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

Protein Expression in Tonsillar and Base of Tongue Cancer and in Relation to Human Papillomavirus (HPV) and Clinical Outcome.

Ramqvist T, Näsman A, Franzén B, ..., Dalianis T, Munck-Wikland E

Int J Mol Sci 19 (4) 978 [2018-03-25; online 2018-03-25]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Biomarkers [Service] PLA and Single Cell Proteomics [Service]

Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb

Rasmussen PU, Hugerth LW, Blanchet FG, ..., Lindahl BD, Tack AJM

New Phytol - (-) - [2018-03-24; online 2018-03-24]

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

A Meta-Analysis of Genome-Wide Association Studies of Growth Differentiation Factor-15 Concentration in Blood.

Jiang J, Thalamuthu A, Ho JE, ..., Sachdev PS, Mather KA

Front Genet 9 (-) 97 [2018-03-23; online 2018-03-23]

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

Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury.

Dias DO, Kim H, Holl D, ..., Göritz C, Frisén J

Cell 173 (1) 153-165.e22 [2018-03-22; online 2018-03-01]

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

Peptide ion channel toxins from the bootlace worm, the longest animal on Earth.

Jacobsson E, Andersson HS, Strand M, ..., Tytgat J, Göransson U

Sci Rep 8 (1) 4596 [2018-03-22; online 2018-03-22]

Introduction of Intrinsic Kinetics of Protein-Ligand Interactions and Their Implications for Drug Design.

Linkuvienė V, Talibov VO, Danielson UH, Matulis D

J. Med. Chem. 61 (6) 2292-2302 [2018-03-22; online 2018-03-02]

Drug Discovery and Development (DDD) [Service]

Molecular mechanism of ATP versus GTP selectivity of adenylate kinase

Rogne P, Rosselin M, Grundström C, ..., Sauer UH, Wolf-Watz M

Proc Natl Acad Sci USA 115 (12) 3012-3017 [2018-03-20; online 2018-03-05]

A Space Efficient Direct Access Data Compression Approach for Mass Spectrometry Imaging.

Källback P, Nilsson A, Shariatgorji M, Andrén PE

Anal. Chem. 90 (6) 3676-3682 [2018-03-20; online 2018-03-08]

Myopathy With SQSTM1 and TIA1 Variants: Clinical and Pathological Features.

Niu Z, Pontifex CS, Berini S, ..., Pfeffer G, Milone M

Front Neurol 9 (-) 147 [2018-03-19; online 2018-03-19]

Spatial Proteomics [Service]

ILF2 and ILF3 are autoantigens in canine systemic autoimmune disease.

Bremer HD, Landegren N, Sjöberg R, ..., Kämpe O, Hansson-Hamlin H

Sci Rep 8 (1) 4852 [2018-03-19; online 2018-03-19]

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

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics.

Ardui S, Ameur A, Vermeesch JR, Hestand MS

Nucleic Acids Res. 46 (5) 2159-2168 [2018-03-16; online 2018-02-06]

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

Recurrent, low-frequency coding variants contributing to colorectal cancer in the Swedish population.

Jiao X, Liu W, Mahdessian H, ..., Dunlop M, Lindblom A

PLoS ONE 13 (3) e0193547 [2018-03-16; online 2018-03-16]

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

A DHODH inhibitor increases p53 synthesis and enhances tumor cell killing by p53 degradation blockage.

Ladds MJGW, van Leeuwen IMM, Drummond CJ, ..., McCormack E, Laín S

Nat Commun 9 (1) 1107 [2018-03-16; online 2018-03-16]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Collaborative] Protein Science Facility (PSF) [Service]

Protein profiling in serum after traumatic brain injury in rats reveals potential injury markers.

Thelin EP, Just D, Frostell A, ..., Nilsson P, Bellander BM

Behav. Brain Res. 340 (-) 71-80 [2018-03-15; online 2016-08-31]

Affinity Proteomics Stockholm [Collaborative]

Clinical Presentation of a Complex Neurodevelopmental Disorder Caused by Mutations in ADNP.

Van Dijck A, Vulto-van Silfhout AT, Cappuyns E, ..., Vandeweyer G, Kooy RF

Biol. Psychiatry - (-) - [2018-03-15; online 2018-03-15]

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

Transcriptional stimulation of rate-limiting components of the autophagic pathway improves plant fitness.

Minina EA, Moschou PN, Vetukuri RR, ..., Hofius D, Bozhkov PV

J. Exp. Bot. 69 (6) 1415-1432 [2018-03-14; online 2018-01-25]

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

Seyfferth C, Wessels B, Jokipii-Lukkari S, ..., Felten J, Tuominen H

Front Plant Sci 9 (-) 272 [2018-03-14; online 2018-03-14]

High-resolution detection of chromosomal rearrangements in leukemias through mate pair whole genome sequencing.

Tran AN, Taylan F, Zachariadis V, ..., Nilsson D, Barbany G

PLoS ONE 13 (3) e0193928 [2018-03-12; online 2018-03-12]

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

Increased thermal stability of nanocellulose composites by functionalization of the sulfate groups on cellulose nanocrystals with azetidinium ions

Börjesson M, Sahlin K, Bernin D, Westman G

J. Appl. Polym. Sci. 135 (10) 45963 [2018-03-10; online 2017-11-08]

Clinical Value of RNA Sequencing-Based Classifiers for Prediction of the Five Conventional Breast Cancer Biomarkers: A Report From the Population-Based Multicenter Sweden Cancerome Analysis Network-Breast Initiative.

Brueffer C, Vallon-Christersson J, Grabau D, ..., Borg Å, Saal LH

JCO Precision Oncology 2 (2) 1-18 [2018-03-09; online 2018-03-09]

Biological annotation of genetic loci associated with intelligence in a meta-analysis of 87,740 individuals.

Coleman JRI, Bryois J, Gaspar HA, ..., Posthuma D, Breen G

Mol. Psychiatry - (-) - [2018-03-08; online 2018-03-08]

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

Genome-wide analysis yields new loci associating with aortic valve stenosis.

Helgadottir A, Thorleifsson G, Gretarsdottir S, ..., Holm H, Stefansson K

Nat Commun 9 (1) 987 [2018-03-07; online 2018-03-07]

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

Global analysis of A-to-I RNA editing reveals association with common disease variants

Franzén O, Ermel R, Sukhavasi K, ..., Schadt EE, Björkegren JLM

PeerJ 6 (-) e4466 [2018-03-06; online 2018-03-06]

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

CEP128 Localizes to the Subdistal Appendages of the Mother Centriole and Regulates TGF-β/BMP Signaling at the Primary Cilium.

Mönnich M, Borgeskov L, Breslin L, ..., Larsen LA, Pedersen LB

Cell Rep 22 (10) 2584-2592 [2018-03-06; online 2018-03-08]

Integrated Microscopy Technologies Stockholm [Service] Spatial Proteomics [Collaborative]

An Integrated Understanding of the Rapid Metabolic Benefits of a Carbohydrate-Restricted Diet on Hepatic Steatosis in Humans.

Mardinoglu A, Wu H, Bjornson E, ..., Taskinen MR, Borén J

Cell Metab. 27 (3) 559-571.e5 [2018-03-06; online 2018-02-15]

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

The Immunogenicity of a Proline-Substituted Altered Peptide Ligand toward the Cancer-Associated TEIPP Neoepitope Trh4 Is Unrelated to Complex Stability.

Hafstrand I, Doorduijn EM, Sun R, ..., van Hall T, Achour A

J. Immunol. - (-) - [2018-03-05; online 2018-03-05]

DNA methylation holds prognostic information in relapsed precursor B-cell acute lymphoblastic leukemia.

Borssén M, Nordlund J, Haider Z, ..., Lönnerholm G, Degerman S

Clin Epigenetics 10 (-) 31 [2018-03-05; online 2018-03-05]

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

Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death.

Reza SH, Delhomme N, Street NR, ..., Minina EA, Bozhkov PV

PLoS ONE 13 (3) e0192945 [2018-03-02; online 2018-03-02]

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

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow.

Zhu Y, Orre LM, Johansson HJ, ..., Branca RMM, Lehtiö J

Nat Commun 9 (1) 903 [2018-03-02; online 2018-03-02]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Global Proteomics and Proteogenomics [Technology development]

Striatal Tyrosine Hydroxylase Is Stimulated via TAAR1 by 3-Iodothyronamine, But Not by Tyramine or β-Phenylethylamine.

Zhang X, Mantas I, Alvarsson A, ..., Chergui K, Svenningsson P

Front Pharmacol 9 (-) 166 [2018-03-01; online 2018-03-01]

Sexual dimorphism in the width of the mouse synaptonemal complex

Agostinho A, Kouznetsova A, Hernández-Hernández A, ..., Brismar H, Höög C

J Cell Sci 131 (5) jcs212548 [2018-03-01; online 2018-02-02]

Integrated Microscopy Technologies Stockholm [Collaborative]

Impact of genetic risk loci for multiple sclerosis on expression of proximal genes in patients.

James T, Lindén M, Morikawa H, ..., Gomez-Cabrero D, Kockum I

Hum. Mol. Genet. 27 (5) 912-928 [2018-03-01; online 2018-01-13]

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

Genomic signatures of 60 years of bidirectional selection for 8-week body weight in chickens

Lillie M, Sheng ZY, Honaker CF, ..., Siegel PB, Carlborg Ö

Poult. Sci. 97 (3) 781-790 [2018-03-01; online 2017-12-20]

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

Genetic variants influencing phenotypic variance heterogeneity.

Ek WE, Rask-Andersen M, Karlsson T, ..., Gyllensten U, Johansson Å

Hum. Mol. Genet. 27 (5) 799-810 [2018-03-01; online 2018-01-13]

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

A Large-Scale Multi-ancestry Genome-wide Study Accounting for Smoking Behavior Identifies Multiple Significant Loci for Blood Pressure.

Sung YJ, Winkler TW, de Las Fuentes L, ..., Rao DC, Chasman DI

Am. J. Hum. Genet. 102 (3) 375-400 [2018-03-01; online 2018-02-15]

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

The neuroendocrine phenotype, genomic profile and therapeutic sensitivity of GEPNET cell lines.

Hofving T, Arvidsson Y, Almobarak B, ..., Johanson V, Nilsson O

Endocr. Relat. Cancer 25 (3) 367-380 [2018-03-00; online 2018-02-16]

Integrated Microscopy Technologies Gothenburg [Service]

The fungus that came in from the cold: dry rot’s pre-adapted ability to invade buildings

Balasundaram SV, Hess J, Durling MB, ..., Eastwood DC, Skrede I

ISME J 12 (3) 791-801 [2018-03-00; online 2018-01-05]

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

Relicts of the lost arc: High-throughput sequencing of the Eutrichomyias rowleyi (Aves: Passeriformes) holotype uncovers an ancient biogeographic link between the Philippines and Fiji.

Jønsson KA, Blom MPK, Päckert M, Ericson PGP, Irestedt M

Mol. Phylogenet. Evol. 120 (-) 28-32 [2018-03-00; online 2017-12-02]

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

Proteomic Profiling for Cardiovascular Biomarker Discovery in Orthostatic Hypotension.

Johansson M, Ricci F, Aung N, ..., Melander O, Fedorowski A

Hypertension 71 (3) 465-472 [2018-03-00; online 2018-01-02]

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

Nubbin isoform antagonism governs Drosophila intestinal immune homeostasis.

Lindberg BG, Tang X, Dantoft W, ..., Lindvall JM, Engström Y

PLoS Pathog. 14 (3) e1006936 [2018-03-00; online 2018-03-02]

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

Molecularly imprinted polymers synthesized via template immobilization on fumed silica nanoparticles for the enrichment of phosphopeptides.

Duarte M, Subedi P, Yilmaz E, ..., Laurell T, Ekström S

J. Mol. Recognit. 31 (3) - [2018-03-00; online 2017-10-12]

Lipids Shape the Electron Acceptor-Binding Site of the Peripheral Membrane Protein Dihydroorotate Dehydrogenase

Costeira-Paulo J, Gault J, Popova G, ..., Marklund EG, Landreh M

Cell Chem Biol 25 (3) 309-317.e4 [2018-03-00; online 2018-03-00]

Drug Discovery and Development (DDD) [Collaborative]

Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases

Bravo AG, Zopfi J, Buck M, ..., Poté J, Cosio C

ISME J 12 (3) 802-812 [2018-03-00; online 2018-01-10]

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

Galectin-3 levels relate in children to total body fat, abdominal fat, body fat distribution, and cardiac size.

Dencker M, Arvidsson D, Karlsson MK, ..., Andersen LB, Thorsson O

Eur J Pediatr 177 (3) 461-467 [2018-03-00; online 2018-01-11]

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

Fungal community shifts underpin declining mycelial production and turnover across a Pinus sylvestris chronosequence

Hagenbo A, Kyaschenko J, Clemmensen KE, Lindahl BD, Fransson P

J Ecol 106 (2) 490-501 [2018-03-00; online 2018-02-13]

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

Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste

Marathe NP, Janzon A, Kotsakis SD, ..., Kristiansson E, Larsson DGJ

Environment International 112 (-) 279-286 [2018-03-00; online 2018-03-00]

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

First de novo whole genome sequencing and assembly of the pink-footed goose.

Pujolar JM, Dalén L, Olsen RA, Hansen MM, Madsen J

Genomics 110 (2) 75-79 [2018-03-00; online 2017-08-30]

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

Cleaner fish escape salmon farms and hybridize with local wrasse populations

Faust E, Halvorsen KT, Andersen P, Knutsen H, André C

R. Soc. open sci. 5 (3) 171752 [2018-03-00; online 2018-03-21]

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

Cardiovascular disease in systemic lupus erythematosus is associated with increased levels of biomarkers reflecting receptor-activated apoptosis.

Wigren M, Svenungsson E, Mattisson IY, ..., Fredrikson GN, Nilsson J

Atherosclerosis 270 (-) 1-7 [2018-03-00; online 2018-01-17]

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

Affinity of charcoals for different forms of radioactive organic iodine

Aneheim E, Bernin D, Foreman MRS

Nuclear Engineering and Design 328 (-) 228-240 [2018-03-00; online 2018-03-00]

Current applications of antibody microarrays.

Chen Z, Dodig-Crnković T, Schwenk JM, Tao SC

Clin Proteomics 15 (-) 7 [2018-02-28; online 2018-02-28]

Affinity Proteomics Stockholm [Collaborative]

Yale School of Public Health Symposium on tissue imaging mass spectrometry: illuminating phenotypic heterogeneity and drug disposition at the molecular level.

Charkoftaki G, Rattray NJW, Andrén PE, ..., Johnson CH, Vasiliou V

Hum Genomics 12 (1) 10 [2018-02-27; online 2018-02-27]

The ZBED6–IGF2 axis has a major effect on growth of skeletal muscle and internal organs in placental mammals

Younis S, Schönke M, Massart J, ..., Zierath JR, Andersson L

Proc Natl Acad Sci USA 115 (9) E2048-E2057 [2018-02-27; online 2018-02-12]

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

Brain Tissue Sample Stabilization and Extraction Strategies for Neuropeptidomics.

Fridjonsdottir E, Nilsson A, Wadensten H, Andrén PE

Methods Mol. Biol. 1719 (-) 41-49 [2018-02-25; online 2018-02-25]

Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella

Bachmann JA, Tedder A, Laenen B, Steige KA, Slotte T

G3 (Bethesda) 8 (4) 1327-1333 [2018-02-23; online 2018-02-23]

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

Disruption of Accumbens and Thalamic White Matter Connectivity Revealed by Diffusion Tensor Tractography in Young Men with Genetic Risk for Obesity

Olivo G, Latini F, Wiemerslage L, Larsson EM, Schiöth HB

Front Hum Neurosci 12 (-) - [2018-02-22; online 2018-02-22]

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

A molecular atlas of cell types and zonation in the brain vasculature.

Vanlandewijck M, He L, Mäe MA, ..., Lendahl U, Betsholtz C

Nature 554 (7693) 475-480 [2018-02-22; online 2018-02-14]

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

In Situ Target Engagement Studies in Adherent Cells

Axelsson H, Almqvist H, Otrocka M, ..., Lundbäck T, Seashore-Ludlow B

ACS Chem. Biol. - (-) - [2018-02-21; online 2018-02-21]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Technology development]

Structural and Biophysical Characterization of Human EXTL3: Domain Organization, Glycosylation, and Solution Structure.

Awad W, Kjellström S, Svensson Birkedal G, Mani K, Logan DT

Biochemistry 57 (7) 1166-1177 [2018-02-20; online 2018-02-05]

Antibodies in children with malaria to PfEMP1, RIFIN and SURFIN expressed at the Plasmodium falciparum parasitized red blood cell surface.

Quintana MDP, Ch'ng JH, Moll K, ..., Qundos U, Wahlgren M

Sci Rep 8 (1) 3262 [2018-02-19; online 2018-02-19]

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

Two novel colorectal cancer risk loci in the region on chromosome 9q22.32

Thutkawkorapin J, Mahdessian H, Barber T, ..., Jiao X, Lindblom A

Oncotarget 9 (13) - [2018-02-16; online 2018-01-30]

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

Mesenchymal stem cell-derived exosomes have altered microRNA profiles and induce osteogenic differentiation depending on the stage of differentiation.

Wang X, Omar O, Vazirisani F, Thomsen P, Ekström K

PLoS ONE 13 (2) e0193059 [2018-02-15; online 2018-02-15]

Integrated Microscopy Technologies Gothenburg [Service]

Drug Target Commons: A Community Effort to Build a Consensus Knowledge Base for Drug-Target Interactions.

Tang J, Tanoli ZU, Ravikumar B, ..., Wennerberg K, Aittokallio T

Cell Chem Biol 25 (2) 224-229.e2 [2018-02-15; online 2017-12-21]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Irreversible inhibition of cytosolic thioredoxin reductase 1 as a mechanistic basis for anticancer therapy.

Stafford WC, Peng X, Olofsson MH, ..., Linder S, Arnér ESJ

Sci Transl Med 10 (428) - [2018-02-14; online 2018-02-16]

Affinity proteomic profiling of plasma for proteins associated to area-based mammographic breast density.

Byström S, Eklund M, Hong MG, ..., Schwenk JM, Gabrielson M

Breast Cancer Res. 20 (1) 14 [2018-02-14; online 2018-02-14]

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

Educated natural killer cells show dynamic movement of the activating receptor NKp46 and confinement of the inhibitory receptor Ly49A

Staaf E, Hedde PN, Bagawath Singh S, ..., Gratton E, Johansson S

Sci. Signal. 11 (517) eaai9200 [2018-02-13; online 2018-02-13]

Integrated Microscopy Technologies Stockholm [Service]

Dispersed Uniform Nanoparticles from a Macroscopic Organosilica Powder

Church TL, Bernin D, Garcia-Bennett AE, Hedin N

Langmuir 34 (6) 2274-2281 [2018-02-13; online 2018-02-05]

Advancing the immunoaffinity platform AFFIRM to targeted measurements of proteins in serum in the pg/ml range.

Säll A, Corbee D, Vikström S, ..., Persson H, Waldemarson S

PLoS ONE 13 (2) e0189116 [2018-02-13; online 2018-02-13]

Drug Discovery and Development (DDD) [Technology development]

Proteomic analyses identify prognostic biomarkers for pancreatic ductal adenocarcinoma.

Hu D, Ansari D, Pawłowski K, ..., Marko-Varga G, Andersson R

Oncotarget 9 (11) 9789-9807 [2018-02-09; online 2018-01-03]

The DNA Methylome of the Hyperthermoacidophilic Crenarchaeon Sulfolobus acidocaldarius

Couturier M, Lindås AC

Front Microbiol 9 (-) - [2018-02-08; online 2018-02-08]

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

A novel monoclonal antibody targeting carboxymethyllysine, an advanced glycation end product in atherosclerosis and pancreatic cancer.

Wendel U, Persson N, Risinger C, ..., Jansson B, Blixt O

PLoS ONE 13 (2) e0191872 [2018-02-08; online 2018-02-08]

Vascular Endothelial Growth Factor D, Pulmonary Congestion, and Incidence of Heart Failure.

Borné Y, Gränsbo K, Nilsson J, ..., Smith JG, Engström G

J. Am. Coll. Cardiol. 71 (5) 580-582 [2018-02-06; online 2018-02-07]

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

MYCN-amplified neuroblastoma maintains an aggressive and undifferentiated phenotype by deregulation of estrogen and NGF signaling.

Dzieran J, Rodriguez Garcia A, Westermark UK, ..., Lehtiö J, Arsenian-Henriksson M

Proc. Natl. Acad. Sci. U.S.A. 115 (6) E1229-E1238 [2018-02-06; online 2018-01-26]

Global Proteomics and Proteogenomics [Collaborative]

Kynurenic Acid and Gpr35 Regulate Adipose Tissue Energy Homeostasis and Inflammation.

Agudelo LZ, Ferreira DMS, Cervenka I, ..., Berggren PO, Ruas JL

Cell Metab. 27 (2) 378-392.e5 [2018-02-06; online 2018-02-08]

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

Human NUDT22 Is a UDP-Glucose/Galactose Hydrolase Exhibiting a Unique Structural Fold.

Carter M, Jemth AS, Carreras-Puigvert J, ..., Helleday T, Stenmark P

Structure 26 (2) 295-303.e6 [2018-02-06; online 2018-02-08]

Crystal Structures and Inhibitor Interactions of Mouse and Dog MTH1 Reveal Species-Specific Differences in Affinity.

Narwal M, Jemth AS, Gustafsson R, ..., Helleday T, Stenmark P

Biochemistry 57 (5) 593-603 [2018-02-06; online 2018-01-16]

Ten steps to get started in Genome Assembly and Annotation

Dominguez Del Angel V, Hjerde E, Sterck L, ..., Binzer-Panchal M, Lantz H

F1000Res 7 (-) 148 [2018-02-05; online 2018-02-05]

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

Interferon γ treatment increases endocannabinoid and related N-acylethanolamine levels in T84 human colon carcinoma cells

Alhouayek M, Rankin L, Gouveia-Figueira S, Fowler CJ

British Journal of Pharmacology - (-) - [2018-02-05; online 2018-02-05]

CheckQC: Quick quality control of Illumina sequencing runs

Åslin M, Brandt M, Dahlberg J

JOSS 3 (22) 556 [2018-02-05; online 2018-02-05]

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

A Common Peptidolytic Mechanism for Targeting Peptide Degradation in Mitochondria and Chloroplasts.

Kmiec B, Branca RMM, Murcha MW, ..., Glaser E, Teixeira PF

Mol Plant 11 (2) 342-345 [2018-02-05; online 2017-11-26]

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service] Swedish Metabolomics Centre (SMC) [Service]

Mechanism of Peptide Binding and Cleavage by the Human Mitochondrial Peptidase Neurolysin.

Teixeira PF, Masuyer G, Pinho CM, ..., Stenmark P, Glaser E

J. Mol. Biol. 430 (3) 348-362 [2018-02-02; online 2017-11-26]

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service]

Novel ATP-cone-driven allosteric regulation of ribonucleotide reductase via the radical-generating subunit.

Rozman Grinberg I, Lundin D, Hasan M, ..., Logan DT, Sjöberg BM

Elife 7 (-) - [2018-02-01; online 2018-02-01]

Multi-omics Reveals the Lifestyle of the Acidophilic, Mineral-Oxidizing Model Species Leptospirillum ferriphilum T.

Christel S, Herold M, Bellenberg S, ..., Poetsch A, Dopson M

Appl. Environ. Microbiol. 84 (3) e02091-17 [2018-02-01; online 2018-01-17]

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

Isolated myelosarcoma is characterized by recurrent NFE2 mutations and concurrent preleukemic clones in the bone marrow.

Lazarevic V, Orsmark-Pietras C, Lilljebjörn H, ..., Juliusson G, Fioretos T

Blood 131 (5) 577-581 [2018-02-01; online 2017-11-30]

Clinical Genomics Lund [Collaborative]

Human Adenovirus Infection Causes Cellular E3 Ubiquitin Ligase MKRN1 Degradation Involving the Viral Core Protein pVII.

Inturi R, Mun K, Singethan K, Schreiner S, Punga T

J. Virol. 92 (3) - [2018-02-01; online 2018-01-17]

PLA and Single Cell Proteomics [Service]

De novo mutations implicate novel genes in systemic lupus erythematosus.

Pullabhatla V, Roberts AL, Lewis MJ, ..., Syvänen AC, Vyse TJ

Hum. Mol. Genet. 27 (3) 421-429 [2018-02-01; online 2017-11-28]

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

U-CAN: a prospective longitudinal collection of biomaterials and clinical information from adult cancer patients in Sweden.

Glimelius B, Melin B, Enblad G, ..., Palmqvist R, Sjöblom T

Acta Oncol 57 (2) 187-194 [2018-02-00; online 2017-06-20]

Tissue Profiling [Collaborative]

Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis

Borges F, Parent JS, van Ex F, ..., Köhler C, Martienssen RA

Nat Genet 50 (2) 186-192 [2018-02-00; online 2018-01-15]

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

The discovery of the virulence gene ToxA in the wheat and barley pathogen Bipolaris sorokiniana.

McDonald MC, Ahren D, Simpfendorfer S, Milgate A, Solomon PS

Mol. Plant Pathol. 19 (2) 432-439 [2018-02-00; online 2017-03-12]

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

The Influence of Heat Treatments on the Porosity of Suspension Plasma-Sprayed Yttria-Stabilized Zirconia Coatings

Ekberg J, Ganvir A, Klement U, Creci S, Nordstierna L

J Therm Spray Tech 27 (3) 391-401 [2018-02-00; online 2018-01-04]

Targeted proteomic analysis of habitual coffee consumption.

Cornelis MC, Gustafsson S, Ärnlöv J, ..., Lind L, Ingelsson E

J. Intern. Med. 283 (2) 200-211 [2018-02-00; online 2017-11-16]

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

T cells are influenced by a long non-coding RNA in the autoimmune associated PTPN2 locus

Houtman M, Shchetynsky K, Chemin K, ..., Malmström V, Padyukov L

Journal of Autoimmunity 90 (-) 28-38 [2018-02-00; online 2018-02-00]

Bioinformatics 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]

Small molecule PGC-1α1 protein stabilizers induce adipocyte Ucp1 expression and uncoupled mitochondrial respiration

Pettersson-Klein AT, Izadi M, Ferreira DMS, ..., Griffin PR, Ruas JL

Mol Metab - (-) - [2018-02-00; online 2018-02-00]

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

Slow evolution of sex-biased genes in the reproductive tissue of the dioecious plant Salix viminalis

Darolti I, Wright AE, Pucholt P, Berlin S, Mank JE

Mol Ecol 27 (3) 694-708 [2018-02-00; online 2018-01-22]

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

Red meat intake in chronic kidney disease patients: Two sides of the coin

Mafra D, Borges NA, Cardozo LFMdF, ..., Lindholm B, Stenvinkel P

Nutrition 46 (-) 26-32 [2018-02-00; online 2018-02-00]

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

Quantitative image analysis of protein expression and colocalisation in skin sections

Zhang H, Ericsson M, Virtanen M, ..., Vahlquist A, Törmä H

Exp Dermatol 27 (2) 196-199 [2018-02-00; online 2018-01-09]

BioImage Informatics [Service]

Paternal easiRNAs regulate parental genome dosage in Arabidopsis

Martinez G, Wolff P, Wang Z, ..., Slotkin RK, Köhler C

Nat Genet 50 (2) 193-198 [2018-02-00; online 2018-01-15]

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

Megakaryocytes harbour the del(5q) abnormality despite complete clinical and cytogenetic remission induced by lenalidomide treatment

Scharenberg C, Jansson M, Saft L, Hellström-Lindberg E

Br J Haematol 180 (4) 526-533 [2018-02-00; online 2018-01-29]

Life after tree death: Does restored dead wood host different fungal communities to natural woody substrates?

Pasanen H, Junninen K, Boberg J, ..., Stenlid J, Kouki J

Forest Ecology and Management 409 (-) 863-871 [2018-02-00; online 2018-02-00]

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

In situ protein detection with enhanced specificity using DNA-conjugated antibodies and proximity ligation.

Zieba A, Ponten F, Uhlén M, Landegren U

Mod. Pathol. 31 (2) 253-263 [2018-02-00; online 2017-09-22]

NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] PLA and Single Cell Proteomics [Technology development] Tissue Profiling [Collaborative]

Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation.

Leal L, Talla V, Källman T, ..., Vila R, Backström N

Mol. Ecol. 27 (4) 935-948 [2018-02-00; online 2018-02-26]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Formation of mercury methylation hotspots as a consequence of forestry operations

Eklöf K, Bishop K, Bertilsson S, ..., Kronberg RM, Bravo AG

Science of The Total Environment 613-614 (-) 1069-1078 [2018-02-00; online 2018-02-00]

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

Establishment of Photosynthesis through Chloroplast Development Is Controlled by Two Distinct Regulatory Phases.

Dubreuil C, Jin X, Barajas-López JD, ..., Small I, Strand Å

Plant Physiol. 176 (2) 1199-1214 [2018-02-00; online 2017-06-16]

Dispersal timing determines the importance of priority effects in bacterial communities

Svoboda P, Lindström ES, Ahmed Osman O, Langenheder S

ISME J 12 (2) 644-646 [2018-02-00; online 2017-10-20]

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

Copy Number Variation Analysis of 100 Twin Pairs Enriched for Neurodevelopmental Disorders.

Stamouli S, Anderlid BM, Willfors C, ..., Tammimies K, Bölte S

Twin Res Hum Genet 21 (1) 1-11 [2018-02-00; online 2018-01-08]

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

Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing.

Hochgerner H, Zeisel A, Lönnerberg P, Linnarsson S

Nat. Neurosci. 21 (2) 290-299 [2018-02-00; online 2018-01-15]

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

Bacterial secretion of D-arginine controls environmental microbial biodiversity.

Alvarez L, Aliashkevich A, de Pedro MA, Cava F

ISME J 12 (2) 438-450 [2018-02-00; online 2017-10-13]

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

Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA

Ahmed E, Parducci L, Unneberg P, ..., Slotte T, Wohlfarth B

Quaternary Science Reviews 181 (-) 19-29 [2018-02-00; online 2018-02-00]

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

Activating FGFR1 Mutations in Sporadic Pheochromocytomas.

Welander J, Łysiak M, Brauckhoff M, ..., Söderkvist P, Gimm O

World J Surg 42 (2) 482-489 [2018-02-00; online 2017-11-22]

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

A convenient transesterification method for synthesis of AT2 receptor ligands with improved stability in human liver microsomes

Wannberg J, Isaksson R, Bremberg U, ..., Hallberg M, Larhed M

Bioorganic & Medicinal Chemistry Letters 28 (3) 519-522 [2018-02-00; online 2018-02-00]

Drug Discovery and Development (DDD) [Collaborative]

A DNA methylation biomarker of alcohol consumption.

Liu C, Marioni RE, Hedman ÅK, ..., Ingelsson E, Levy D

Mol. Psychiatry 23 (2) 422-433 [2018-02-00; online 2016-11-15]

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

Pulmonary fibrosis in vivo displays increased p21 expression reduced by 5-HT2B receptor antagonists in vitro - a potential pathway affecting proliferation.

Löfdahl A, Rydell-Törmänen K, Larsson-Callerfelt A, Wenglén C, Westergren-Thorsson G

Sci Rep 8 (1) 1927 [2018-01-31; online 2018-01-31]

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

A Single Bout of Electroacupuncture Remodels Epigenetic and Transcriptional Changes in Adipose Tissue in Polycystic Ovary Syndrome.

Kokosar M, Benrick A, Perfilyev A, ..., Ling C, Stener-Victorin E

Sci Rep 8 (1) 1878 [2018-01-30; online 2018-01-30]

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

Innate immune alterations are elicited in microglial cells before plaque deposition in the Alzheimer's disease mouse model 5xFAD.

Boza-Serrano A, Yang Y, Paulus A, Deierborg T

Sci Rep 8 (1) 1550 [2018-01-24; online 2018-01-24]

In Situ Analyses Directly in Diarrheal Stool Reveal Large Variations in Bacterial Load and Active Toxin Expression of Enterotoxigenic Escherichia coli and Vibrio cholerae

Begum YA, Rydberg HA, Thorell K, ..., Qadri F, Sjöling Å

mSphere 3 (1) e00517-17 [2018-01-24; online 2018-01-24]

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

Genetical genomics of growth in a chicken model.

Johnsson M, Henriksen R, Höglund A, ..., Jensen P, Wright D

BMC Genomics 19 (1) 72 [2018-01-23; online 2018-01-23]

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

Demography and mating system shape the genome-wide impact of purifying selection in Arabis alpina.

Laenen B, Tedder A, Nowak MD, ..., Coupland G, Slotte T

Proc. Natl. Acad. Sci. U.S.A. 115 (4) 816-821 [2018-01-23; online 2018-01-04]

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

Targeted NUDT5 inhibitors block hormone signaling in breast cancer cells.

Page BDG, Valerie NCK, Wright RHG, ..., Beato M, Helleday T

Nat Commun 9 (1) 250 [2018-01-17; online 2018-01-17]

Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Service] Protein Science Facility (PSF) [Service]

Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels.

Jiang X, O'Reilly PF, Aschard H, ..., Kraft P, Kiel DP

Nat Commun 9 (1) 260 [2018-01-17; online 2018-01-17]

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

Alpha-actinin of the chlorarchiniophyte Bigelowiella natans.

Backman L

PeerJ 6 (-) e4288 [2018-01-17; online 2018-01-17]

Spotty Carotid Plaques Are Associated with Inflammation and the Occurrence of Cerebrovascular Symptoms.

Halak S, Östling G, Edsfeldt A, ..., Gonçalves I, Asciutto G

Cerebrovasc Dis Extra 8 (1) 16-25 [2018-01-15; online 2018-01-15]

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

Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D

Jenjaroenpun P, Wongsurawat T, Pereira R, ..., Nielsen J, Nookaew I

Nucleic Acids Res - (-) - [2018-01-13; online 2018-01-13]

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

Rapid hybrid speciation in Darwin’s finches

Lamichhaney S, Han F, Webster MT, ..., Grant BR, Grant PR

Science 359 (6372) 224-228 [2018-01-12; online 2017-11-23]

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

Meta-analysis of exome array data identifies six novel genetic loci for lung function.

Jackson VE, Latourelle JC, Wain LV, ..., Tobin MD, London SJ

Wellcome Open Res 3 (-) 4 [2018-01-12; online 2018-01-12]

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

Identification of shared genetic variants between schizophrenia and lung cancer.

Zuber V, Jönsson EG, Frei O, ..., Mills IG, Andreassen OA

Sci Rep 8 (1) 674 [2018-01-12; online 2018-01-12]

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

The Global Acetylome of the Human Pathogen Vibrio cholerae V52 Reveals Lysine Acetylation of Major Transcriptional Regulators.

Jers C, Ravikumar V, Lezyk M, ..., Wai SN, Mijakovic I

Front. Cell. Infect. Microbiol. 7 (-) 537 [2018-01-11; online 2018-01-11]

Splicing of platelet resident pre-mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications.

Nassa G, Giurato G, Cimmino G, ..., Weisz A, Tarallo R

Sci Rep 8 (1) 498 [2018-01-11; online 2018-01-11]

Global Proteomics and Proteogenomics [Collaborative]

Sample handling of gastric tissue and O-glycan alterations in paired gastric cancer and non-tumorigenic tissues.

Adamczyk B, Jin C, Polom K, ..., Roviello F, Karlsson NG

Sci Rep 8 (1) 242 [2018-01-10; online 2018-01-10]

Glycoproteomics [Technology development]

Bifidobacteria or Fiber Protects against Diet-Induced Microbiota-Mediated Colonic Mucus Deterioration.

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

Cell Host Microbe 23 (1) 27-40.e7 [2018-01-10; online 2017-12-21]

Integrated Microscopy Technologies Gothenburg [Service]

A protein interaction network centered on leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) regulates growth factor receptors

Faraz M, Herdenberg C, Holmlund C, Henriksson R, Hedman H

J. Biol. Chem. - (-) jbc.M117.807487 [2018-01-09; online 2018-01-09]

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

Discovering viral genomes in human metagenomic data by predicting unknown protein families.

Barrientos-Somarribas M, Messina DN, Pou C, ..., Andersson B, Sonnhammer ELL

Sci Rep 8 (1) 28 [2018-01-08; online 2018-01-08]

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

Comprehensive Mass Spectrometric Survey of Streptococcus pyogenes Subcellular Proteomes.

Wilk L, Happonen L, Malmström J, Herwald H

J. Proteome Res. 17 (1) 600-617 [2018-01-05; online 2017-12-04]

The ATPase activity of Asna1/TRC40 is required for pancreatic progenitor cell survival.

Norlin S, Parekh V, Edlund H

Development 145 (1) dev154468 [2018-01-03; online 2018-01-03]

Evaluating vacquinol-1 in rats carrying glioblastoma models RG2 and NS1

Ahlstedt J, Förnvik K, Zolfaghari S, ..., Salford LG, Redebrandt HN

Oncotarget - (-) - [2018-01-03; online 2018-01-03]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum.

Fogelqvist J, Tzelepis G, Bejai S, ..., Schwelm A, Dixelius C

BMC Genomics 19 (1) 14 [2018-01-03; online 2018-01-03]

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

A multi-omics approach reveals function of Secretory Carrier-Associated Membrane Proteins in wood formation of Populus trees.

Obudulu O, Mähler N, Skotare T, ..., Trygg J, Tuominen H

BMC Genomics 19 (1) 11 [2018-01-03; online 2018-01-03]

Differential impact of RB status on E2F1 reprogramming in human cancer.

McNair C, Xu K, Mandigo AC, ..., Brown M, Knudsen KE

J. Clin. Invest. 128 (1) 341-358 [2018-01-02; online 2017-12-04]

Clinical Genomics Stockholm [Service]

Angiopoietin-1 deficiency increases renal capillary rarefaction and tubulointerstitial fibrosis in mice

Loganathan K, Salem Said E, Winterrowd E, ..., Quaggin SE, Jeansson M

PLoS ONE 13 (1) e0189433 [2018-01-02; online 2018-01-02]

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

SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy

Bernhem K, Brismar H

Bioinformatics 34 (1) 137-138 [2018-01-01; online 2017-09-04]

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

Metabolism and Whole-Body Fat Oxidation Following Postexercise Carbohydrate or Protein Intake.

Andersson-Hall U, Pettersson S, Edin F, ..., Malmodin D, Madsen K

International Journal of Sport Nutrition and Exercise Metabolism 28 (1) 37-45 [2018-01-01; online 2018-01-17]

Cytokine Autoantibody Screening in the Swedish Addison Registry Identifies Patients With Undiagnosed APS1

Eriksson D, Dalin F, Eriksson GN, ..., Munoz KD, None

J. Clin. Endocrinol. Metab. 103 (1) 179-186 [2018-01-01; online 2017-10-20]

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

Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique

Cholleti H, Hayer J, Mulandane FC, ..., Berg M, Blomström AL

Infect Ecol Epidemiol 8 (1) 1478585 [2018-01-00; online 2018-05-28]

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

Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive.

Low GW, Chattopadhyay B, Garg KM, ..., Wu S, Rheindt FE

Heredity (Edinb) 120 (2) 138-153 [2018-01-00; online 2017-12-11]

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

The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.

Salvatore M, Shu N, Elofsson A

Protein Sci. 27 (1) 195-201 [2018-01-00; online 2017-10-24]

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

Surface treatment of cellulose nanocrystals (CNC): effects on dispersion rheology

Sahlin K, Forsgren L, Moberg T, ..., Rigdahl M, Westman G

Cellulose 25 (1) 331-345 [2018-01-00; online 2017-11-28]

Solid and fluid segments within the same molecule of stratum corneum ceramide lipid.

Pham QD, Mojumdar EH, Gooris GS, ..., Sparr E, Topgaard D

Quart. Rev. Biophys. 51 (-) e7 [2018-01-00; online 2018-01-01]

Single-molecule DNA sequencing of acute myeloid leukemia and myelodysplastic syndromes with multiple TP53 alterations.

Lodé L, Ameur A, Coste T, ..., Lavabre-Bertrand T, Soussi T

Haematologica 103 (1) e13-e16 [2018-01-00; online 2017-10-27]

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

Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity.

Turcot V, Lu Y, Highland HM, ..., MAGIC Investigators , Understanding Society Scientific Group

Nat. Genet. 50 (1) 26-41 [2018-01-00; online 2017-12-22]

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

Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation.

Günther T, Malmström H, Svensson EM, ..., Götherström A, Jakobsson M

PLoS Biol. 16 (1) e2003703 [2018-01-00; online 2018-01-09]

Bioinformatics 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]

Perspectives on NMR studies of CO2 adsorption

Bernin D, Hedin N

Current Opinion in Colloid & Interface Science 33 (-) 53-62 [2018-01-00; online 2018-01-00]

Normalization of mass spectrometry data (NOMAD).

Murie C, Sandri B, Sandberg AS, ..., Wendt C, Larsson O

Adv Biol Regul 67 (-) 128-133 [2018-01-00; online 2017-11-20]

Clinical Proteomics Mass spectrometry [Service] Global Proteomics and Proteogenomics [Service]

Natural product inspired library synthesis - Identification of 2,3-diarylbenzofuran and 2,3-dihydrobenzofuran based inhibitors of Chlamydia trachomatis

Saleeb M, Mojica S, Eriksson AU, ..., Gylfe Å, Elofsson M

European Journal of Medicinal Chemistry 143 (-) 1077-1089 [2018-01-00; online 2018-01-00]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Minimizing inequality in access to precision medicine in breast cancer by real-time population-based molecular analysis in the SCAN-B initiative.

Rydén L, Loman N, Larsson C, ..., Saal LH, Borg Å

Br J Surg 105 (2) e158-e168 [2018-01-00; online 2018-01-18]

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

MicroRNA expression profiles in non‑epithelial ovarian tumors.

Chang RK, Li X, Mu N, ..., Larsson C, Lui WO

Int. J. Oncol. 52 (1) 55-66 [2018-01-00; online 2017-11-10]

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

Leucocyte recruitment and molecular fortification of keratinocytes triggered by streptococcal M1 protein.

Persson ST, Hauri S, Malmström J, Herwald H

Cell. Microbiol. 20 (1) - [2018-01-00; online 2017-10-19]

Homozygosity for a missense variant in COMP gene associated with severe pseudoachondroplasia

Tariq M, Khan TN, Lundin L, ..., Dahl N, Klar J

Clin Genet 93 (1) 182-186 [2018-01-00; online 2017-11-21]

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

Herpesvirus deconjugases inhibit the IFN response by promoting TRIM25 autoubiquitination and functional inactivation of the RIG-I signalosome.

Gupta S, Ylä-Anttila P, Callegari S, ..., Delecluse HJ, Masucci MG

PLoS Pathog. 14 (1) e1006852 [2018-01-00; online 2018-01-22]

Global Proteomics and Proteogenomics [Service]

Genomic consequences of intensive inbreeding in an isolated wolf population

Kardos M, Åkesson M, Fountain T, ..., Wikenros C, Ellegren H

Nat Ecol Evol 2 (1) 124-131 [2018-01-00; online 2017-11-20]

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

Exome sequencing reveals NAA15 and PUF60 as candidate genes associated with intellectual disability.

Zhao JJ, Halvardson J, Zander CS, ..., Thuresson AC, Feuk L

Am. J. Med. Genet. B Neuropsychiatr. Genet. 177 (1) 10-20 [2018-01-00; online 2017-10-09]

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

Epigenetic Changes in the CRH Gene are Related to Severity of Suicide Attempt and a General Psychiatric Risk Score in Adolescents.

Jokinen J, Boström AE, Dadfar A, ..., Åsberg M, Schiöth HB

EBioMedicine 27 (-) 123-133 [2018-01-00; online 2017-12-18]

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

Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest-tundra ecotone

Vowles T, Lindwall F, Ekblad A, ..., Ryberg M, Björk RG

Ecol Evol 8 (2) 1019-1030 [2018-01-00; online 2017-12-14]

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

Clofazimine protects against Mycobacterium tuberculosis dissemination in the central nervous system following aerosol challenge in a murine model.

Baijnath S, Moodley C, Ngcobo B, ..., Pym A, Govender T

International Journal of Antimicrobial Agents 51 (1) 77-81 [2018-01-00; online 2017-08-24]

Drug Discovery and Development (DDD) [Collaborative]

Circulating proteins as predictors of incident heart failure in the elderly.

Stenemo M, Nowak C, Byberg L, ..., Fall T, Ärnlöv J

Eur. J. Heart Fail. 20 (1) 55-62 [2018-01-00; online 2017-10-02]

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

Characterization of gamma-tubulin filaments in mammalian cells.

Lindström L, Alvarado-Kristensson M

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 1865 (1) 158-171 [2018-01-00; online 2017-10-16]

Integrated Microscopy Technologies Gothenburg [Service]

Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes

Suh A, Smeds L, Ellegren H

Mol Ecol 27 (1) 99-111 [2018-01-00; online 2017-12-12]

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

Whole Slide Image Registration for the Study of Tumor Heterogeneity

Solorzano L, Almeida GM, Mesquita B, ..., Oliveira C, Wählby C

- - (-) 95-102 [2018-00-00; online 2018-09-14]

BioImage Informatics [Technology development]

The CO2 capturing ability of cellulose dissolved in NaOH(aq) at low temperature

Gunnarsson M, Bernin D, Östlund Å, Hasani M

Green Chem. 20 (14) 3279-3286 [2018-00-00; online 2018-00-00]

Synthesis of novel 1,2,4-thiadiazinane 1,1-dioxides via three component SuFEx type reaction

Khumalo MF, Akpan ED, Chinthakindi PK, ..., Naicker T, Arvidsson PI

RSC Adv. 8 (65) 37503-37507 [2018-00-00; online 2018-00-00]

Drug Discovery and Development (DDD) [Technology development]

Phylogeny, species delimitation and revision of Pleioluma (Sapotaceae) in New Caledonia, a frequently gynodioecious genus

Swenson U, Nylander JAA, Munzinger J

Aust. Systematic Bot. 31 (2) 120 [2018-00-00; online 2018-00-00]

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

Orange is the new white: rapid curing of an ethylene-glycidyl methacrylate copolymer with a Ti-bisphenolate type catalyst

Mauri M, Svenningsson L, Hjertberg T, ..., Prieto O, Müller C

Polym. Chem. 9 (13) 1710-1718 [2018-00-00; online 2018-00-00]

Optimising methods for the recovery and quantification of di- and tripeptides in soil

Jämtgård S, Robinson N, Moritz T, Colgrave ML, Schmidt S

Soil Res. 56 (4) 404 [2018-00-00; online 2018-00-00]

Improved Reconstruction of Low Intensity Magnetic Resonance Spectroscopy With Weighted Low Rank Hankel Matrix Completion

Guo D, Qu X

IEEE Access 6 (-) 4933-4940 [2018-00-00; online 2018-00-00]

High-fidelity spectroscopy reconstruction in accelerated NMR

Qu X, Qiu T, Guo D, ..., Orekhov V, Chen Z

Chem. Commun. 54 (78) 10958-10961 [2018-00-00; online 2018-00-00]

Swedish NMR Centre (SNC) [Technology development]

High purity and viability cell separation of a bacterivorous jakobid flagellate based on a steep velocity gradient induced soft inertial force

Deng P, Fu CJ, Wu Z

RSC Adv. 8 (62) 35512-35520 [2018-00-00; online 2018-00-00]

Microbial Single Cell Genomics [Service]

Efficient C–C coupling of bio-based furanics and carbonyl compounds to liquid hydrocarbon precursors over lignosulfonate derived acidic carbocatalysts

Konwar LJ, Samikannu A, Mäki-Arvela P, Mikkola JP

Catal. Sci. Technol. 8 (9) 2449-2459 [2018-00-00; online 2018-00-00]

Effect of various structure directing agents (SDAs) on low-temperature deactivation of Cu/SAPO-34 during NH3-SCR reaction

Woo J, Leistner K, Bernin D, ..., Zammit M, Olsson L

Catal. Sci. Technol. 8 (12) 3090-3106 [2018-00-00; online 2018-00-00]

Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Service]