Publications 2015

Sequence and gene expression evolution of paralogous genes in willows.

Harikrishnan SL, Pucholt P, Berlin S

Sci Rep 5 (-) 18662 [2015-12-22; online 2015-12-22]

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

Transcriptome analysis reveals mucin 4 to be highly associated with periodontitis and identifies pleckstrin as a link to systemic diseases.

Lundmark A, Davanian H, Båge T, ..., Lundeberg J, Yucel-Lindberg T

Sci Rep 5 (-) 18475 [2015-12-21; online 2015-12-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genome-wide genetic homogeneity between sexes and populations for human height and body mass index.

Yang J, Bakshi A, Zhu Z, ..., Ingelsson E, Visscher PM

Hum. Mol. Genet. 24 (25) 7445-7449 [2015-12-20; online 2015-10-22]

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

Exploring water as building bricks in enzyme engineering.

Hendil-Forssell P, Martinelle M, Syrén PO

Chem. Commun. (Camb.) 51 (97) 17221-17224 [2015-12-18; online 2015-10-02]

A significant risk locus on 19q13 for bipolar disorder identified using a combined genome-wide linkage and copy number variation analysis.

Lekman M, Karlsson R, Graae L, Hössjer O, Kockum I

BioData Mining 8 (-) 42 [2015-12-18; online 2015-12-18]

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

Powerful Populations Respond to Viruses and Vaccines.

Brodin P

Immunity 43 (6) 1035-1037 [2015-12-15; online 2015-12-20]

Cellular Immunomonitoring [Technology development]

Metagenome-assembled genomes uncover a global brackish microbiome.

Hugerth LW, Larsson J, Alneberg J, ..., Pinhassi J, Andersson AF

Genome Biol. 16 (-) 279 [2015-12-14; online 2015-12-14]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Metagenome-Based Metabolic Reconstruction Reveals the Ecophysiological Function of Epsilonproteobacteria in a Hydrocarbon-Contaminated Sulfidic Aquifer.

Keller AH, Schleinitz KM, Starke R, ..., Vogt C, Kleinsteuber S

Front Microbiol 6 (-) 1396 [2015-12-10; online 2015-12-10]

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

High levels of WNT-5A in human glioma correlate with increased presence of tumor-associated microglia/monocytes.

Dijksterhuis JP, Arthofer E, Marinescu VD, ..., Mulder J, Schulte G

Exp. Cell Res. 339 (2) 280-288 [2015-12-10; online 2015-10-25]

Pleiotrophin promotes vascular abnormalization in gliomas and correlates with poor survival in patients with astrocytomas.

Zhang L, Kundu S, Feenstra T, ..., Dieterich LC, Dimberg A

Sci Signal 8 (406) ra125 [2015-12-08; online 2015-12-08]

Sixteen new lung function signals identified through 1000 Genomes Project reference panel imputation.

Soler Artigas M, Wain LV, Miller S, ..., Hall IP, Tobin MD

Nat Commun 6 (-) 8658 [2015-12-04; online 2015-12-04]

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

Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken.

Johnsson M, Jonsson KB, Andersson L, Jensen P, Wright D

G3 (Bethesda) 6 (2) 311-319 [2015-12-04; online 2015-12-04]

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

Structural insights into the DNA-binding specificity of E2F family transcription factors.

Morgunova E, Yin Y, Jolma A, ..., Nilsson L, Taipale J

Nat Commun 6 (1) 10050 [2015-12-03; online 2015-12-03]

Karolinska High Throughput Center (KHTC) Protein Science Facility (PSF)

Population structure and genetic diversity in the nannandrous moss Homalothecium lutescens: does the dwarf male system facilitate gene flow?

Rosengren F, Hansson B, Cronberg N

BMC Evol. Biol. 15 (-) 270 [2015-12-03; online 2015-12-03]

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

Within-species divergence in the seminal fluid proteome and its effect on male and female reproduction in a beetle.

Goenaga J, Yamane T, Rönn J, Arnqvist G

BMC Evol. Biol. 15 (-) 266 [2015-12-02; online 2015-12-02]

Mass Spectrometry-based Proteomics, Uppsala

A Combination of Culture Conditions and Gene Expression Analysis Can Be Used to Investigate and Predict hES Cell Differentiation Potential towards Male Gonadal Cells.

Kjartansdóttir KR, Reda A, Panula S, ..., Hovatta O, Stukenborg JB

PLoS ONE 10 (12) e0144029 [2015-12-02; online 2015-12-02]

Protein profiling reveals consequences of lifestyle choices on predicted biological aging.

Enroth S, Enroth SB, Johansson Å, Gyllensten U

Sci Rep 5 (1) 17282 [2015-12-01; online 2015-12-01]

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

Multi-level omics analysis in a murine model of dystrophin loss and therapeutic restoration.

Roberts TC, Johansson HJ, McClorey G, ..., El Andaloussi S, Wood MJ

Hum. Mol. Genet. 24 (23) 6756-6768 [2015-12-01; online 2015-09-20]

Metabolic Profiling of Chicken Embryos Exposed to Perfluorooctanoic Acid (PFOA) and Agonists to Peroxisome Proliferator-Activated Receptors.

Mattsson A, Kärrman A, Pinto R, Brunström B

PLoS ONE 10 (12) e0143780 [2015-12-01; online 2015-12-01]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Highly Sensitive FRET-FCS Detects Amyloid β-Peptide Oligomers in Solution at Physiological Concentrations.

Wennmalm S, Chmyrov V, Widengren J, Tjernberg L

Anal. Chem. 87 (23) 11700-11705 [2015-12-01; online 2015-10-23]

Fluorescence Correlation Spectroscopy [Collaborative] Integrated Microscopy Technologies Stockholm

Gene-based meta-analysis of genome-wide association studies implicates new loci involved in obesity.

Hägg S, Ganna A, Van Der Laan SW, ..., Pawitan Y, Ingelsson E

Hum. Mol. Genet. 24 (23) 6849-6860 [2015-12-01; online 2015-09-18]

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

Dietary Fiber-Induced Improvement in Glucose Metabolism Is Associated with Increased Abundance of Prevotella.

Kovatcheva-Datchary P, Nilsson A, Akrami R, ..., Björck I, Bäckhed F

Cell Metab. 22 (6) 971-982 [2015-12-01; online 2015-11-11]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The body mass index (BMI) is significantly correlated with levels of cytokines and chemokines in cerebrospinal fluid.

Larsson A, Carlsson L, Lind AL, ..., Kamali-Moghaddam M, Thulin M

Cytokine 76 (2) 514-518 [2015-12-00; online 2015-07-15]

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

The Plant Genome Integrative Explorer Resource: PlantGenIE.org.

Sundell D, Mannapperuma C, Netotea S, ..., Hvidsten TR, Street NR

New Phytol. 208 (4) 1149-1156 [2015-12-00; online 2015-07-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The Constrained Maximal Expression Level Owing to Haploidy Shapes Gene Content on the Mammalian X Chromosome.

Hurst LD, Ghanbarian AT, Forrest AR, FANTOM consortium , Huminiecki L

PLoS Biol. 13 (12) e1002315 [2015-12-00; online 2015-12-18]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Susceptibility to infections, without concomitant hyper-IgE, reported in 1976, is caused by hypomorphic mutation in the phosphoglucomutase 3 (PGM3) gene.

Lundin KE, Hamasy A, Backe PH, ..., Stenmark S, Smith CI

Clin. Immunol. 161 (2) 366-372 [2015-12-00; online 2015-10-19]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Selenium metabolism to the trimethylselenonium ion (TMSe) varies markedly because of polymorphisms in the indolethylamine N-methyltransferase gene.

Kuehnelt D, Engström K, Skröder H, ..., Broberg K, Vahter M

Am. J. Clin. Nutr. 102 (6) 1406-1415 [2015-12-00; online 2015-11-06]

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

Phenotypic expansion of visceral myopathy associated with ACTG2 tandem base substitution.

Klar J, Raykova D, Gustafson E, ..., Wanders A, Dahl N

Eur. J. Hum. Genet. 23 (12) 1679-1683 [2015-12-00; online 2015-03-18]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Oral microbiota in patients with atherosclerosis.

Fåk F, Tremaroli V, Bergström G, Bäckhed F

Atherosclerosis 243 (2) 573-578 [2015-12-00; online 2015-11-05]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Nanocellulose from green algae modulates the in vitro inflammatory response of monocytes/macrophages

Hua K, Strømme M, Mihranyan A, Ferraz N

Cellulose 22 (6) 3673-3688 [2015-12-00; online 2015-10-03]

Multi-ancestry genome-wide association study of 21,000 cases and 95,000 controls identifies new risk loci for atopic dermatitis.

Paternoster L, Standl M, Waage J, ..., Weidinger S, EArly Genetics and Lifecourse Epidemiology (EAGLE) Eczema Consortium

Nat. Genet. 47 (12) 1449-1456 [2015-12-00; online 2015-10-21]

Identification of proteins from human permanent erupted enamel.

Castiblanco GA, Rutishauser D, Ilag LL, ..., Castellanos JE, Mejía W

Eur. J. Oral Sci. 123 (6) 390-395 [2015-12-00; online 2015-10-04]

Hormone Replacement Therapy Associated White Blood Cell DNA Methylation and Gene Expression are Associated With Within-Pair Differences of Body Adiposity and Bone Mass.

Bahl A, Pöllänen E, Ismail K, ..., Kovanen V, Ollikainen M

Twin Res Hum Genet 18 (6) 647-661 [2015-12-00; online 2015-12-19]

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

Genetic fine mapping and genomic annotation defines causal mechanisms at type 2 diabetes susceptibility loci.

Gaulton KJ, Ferreira T, Lee Y, ..., Morris AP, DIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium

Nat. Genet. 47 (12) 1415-1425 [2015-12-00; online 2015-11-09]

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

Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus.

Bentham J, Morris DL, Cunninghame Graham DS, ..., Alarcón-Riquelme ME, Vyse TJ

Nat. Genet. 47 (12) 1457-1464 [2015-12-00; online 2015-10-27]

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

Freshwater protists do not go with the flow: population structure in Gonyostomum semen independent of connectivity among lakes.

Sassenhagen I, Sefbom J, Säll T, Godhe A, Rengefors K

Environ. Microbiol. 17 (12) 5063-5072 [2015-12-00; online 2015-07-18]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Experiences with workflows for automating data-intensive bioinformatics

Spjuth O, Bongcam-Rudloff E, Hernández GC, ..., Siretskiy A, Vassilev D

Biol. Direct 10 (1) - [2015-12-00; online 2015-08-19]

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

Emmprin Expression Predicts Response and Survival following Cisplatin Containing Chemotherapy for Bladder Cancer: A Validation Study.

Hemdan T, Malmström PU, Jahnson S, Segersten U

J. Urol. 194 (6) 1575-1581 [2015-12-00; online 2015-06-30]

Tissue Profiling

Discovery of New Risk Markers for Ischemic Stroke Using a Novel Targeted Proteomics Chip.

Lind L, Siegbahn A, Lindahl B, ..., Sundström J, Ärnlöv J

Stroke 46 (12) 3340-3347 [2015-12-00; online 2015-11-05]

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

Characterization of human organ donors testing positive for type 1 diabetes-associated autoantibodies.

Wiberg A, Granstam A, Ingvast S, ..., Korsgren O, Skog O

Clin. Exp. Immunol. 182 (3) 278-288 [2015-12-00; online 2015-08-28]

Tissue Profiling

Captured metagenomics: large-scale targeting of genes based on 'sequence capture' reveals functional diversity in soils.

Manoharan L, Kushwaha SK, Hedlund K, Ahrén D

DNA Res. 22 (6) 451-460 [2015-12-00; online 2015-10-23]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Bioenergetic cues shift FXR splicing towards FXRα2 to modulate hepatic lipolysis and fatty acid metabolism.

Correia JC, Massart J, de Boer JF, ..., Groen AK, Ruas JL

Mol Metab 4 (12) 891-902 [2015-12-00; online 2015-09-26]

Bacterial diversity along a 2600 km river continuum.

Savio D, Sinclair L, Ijaz UZ, ..., Farnleitner AH, Eiler A

Environ. Microbiol. 17 (12) 4994-5007 [2015-12-00; online 2015-04-30]

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

Associations between circulating proteins and corresponding genes expressed in coronary thrombi in patients with acute myocardial infarction.

Helseth R, Weiss TW, Opstad TB, ..., Arnesen H, Seljeflot S

Thromb. Res. 136 (6) 1240-1244 [2015-12-00; online 2015-10-08]

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

Amelioration of the Fitness Costs of Antibiotic Resistance Due To Reduced Outer Membrane Permeability by Upregulation of Alternative Porins.

Knopp M, Andersson DI

Mol. Biol. Evol. 32 (12) 3252-3263 [2015-12-00; online 2015-09-12]

Mass Spectrometry-based Proteomics, Uppsala

De novo assembly of Dekkera bruxellensis: a multi technology approach using short and long-read sequencing and optical mapping.

Olsen RA, Bunikis I, Tiukova I, ..., Käller M, Vezzi F

Gigascience 4 (-) 56 [2015-11-26; online 2015-11-26]

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

Genome-Wide Association Study Identifies That the ABO Blood Group System Influences Interleukin-10 Levels and the Risk of Clinical Events in Patients with Acute Coronary Syndrome.

Johansson Å, Alfredsson J, Eriksson N, Wallentin L, Siegbahn A

PLoS ONE 10 (11) e0142518 [2015-11-24; online 2015-11-24]

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

Complete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel.

Zubair S, Fischer A, Liljander A, ..., Bongcam-Rudloff E, Jores J

Stand Genomic Sci 10 (-) 109 [2015-11-20; online 2015-11-20]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Combinations of Genetic Data Present in Bipolar Patients, but Absent in Control Persons.

Mellerup E, Andreassen OA, Bennike B, ..., Werge T, Moeller GL

PLoS ONE 10 (11) e0143432 [2015-11-20; online 2015-11-20]

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

RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes.

Le Rhun A, Beer YY, Reimegård J, Chylinski K, Charpentier E

RNA Biol 13 (2) 177-195 [2015-11-19; online 2015-11-19]

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

DNA-dependent formation of transcription factor pairs alters their binding specificity.

Jolma A, Yin Y, Nitta KR, ..., Morgunova E, Taipale J

Nature 527 (7578) 384-388 [2015-11-19; online 2015-11-10]

Karolinska High Throughput Center (KHTC) Protein Science Facility (PSF)

A Conserved Odorant Receptor Detects the Same 1-Indanone Analogs in a Tortricid and a Noctuid Moth

Gonzalez F, Bengtsson JM, Walker WB, ..., Ignell R, Bengtsson M

Front. Ecol. Evol. 3 (-) - [2015-11-19; online 2015-11-19]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Single cell analysis of cancer cells using an improved RT-MLPA method has potential for cancer diagnosis and monitoring.

Kvastad L, Werne Solnestam B, Johansson E, ..., Latta D, Lundeberg J

Sci Rep 5 (-) 16519 [2015-11-12; online 2015-11-12]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Working draft genome sequence of the mesophilic acetate oxidizing bacterium Syntrophaceticus schinkii strain Sp3.

Manzoor S, Müller B, Niazi A, Schnürer A, Bongcam-Rudloff E

Stand Genomic Sci 10 (-) 99 [2015-11-11; online 2015-11-11]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Normalization of Host Intestinal Mucus Layers Requires Long-Term Microbial Colonization.

Johansson ME, Jakobsson HE, Holmén-Larsson J, ..., Bäckhed F, Hansson GC

Cell Host Microbe 18 (5) 582-592 [2015-11-11; online 2015-11-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Immunocapture strategies in translational proteomics.

Fredolini C, Byström S, Pin E, ..., Nilsson P, Schwenk JM

Expert Rev Proteomics 13 (1) 83-98 [2015-11-11; online 2015-11-11]

Affinity Proteomics Stockholm [Technology development]

Effect of genetic and environmental factors on protein biomarkers for common non-communicable disease and use of personally normalized plasma protein profiles (PNPPP).

Enroth S, Bosdotter Enroth S, Johansson Å, Gyllensten U

Biomarkers 20 (6-7) 355-364 [2015-11-09; online 2015-11-09]

Affinity Proteomics Uppsala [Service] Clinical Biomarkers [Service] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure PLA and Single Cell Proteomics [Service]

Meta-analysis identifies seven susceptibility loci involved in the atopic march.

Marenholz I, Esparza-Gordillo J, Rüschendorf F, ..., Henderson AJ, Lee YA

Nat Commun 6 (-) 8804 [2015-11-06; online 2015-11-06]

Intra-mitochondrial Methylation Deficiency Due to Mutations in SLC25A26.

Kishita Y, Pajak A, Bolar NA, ..., Okazaki Y, Wedell A

Am. J. Hum. Genet. 97 (5) 761-768 [2015-11-05; online 2015-11-03]

Clinical Genomics Clinical Genomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

In search for symmetries in the metabolism of cancer.

Gatto F, Nielsen J

Wiley Interdiscip Rev Syst Biol Med 8 (1) 23-35 [2015-11-05; online 2015-11-05]

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

Dominant Genetic Variation and Missing Heritability for Human Complex Traits: Insights from Twin versus Genome-wide Common SNP Models.

Chen X, Kuja-Halkola R, Rahman I, ..., Pedersen NL, Magnusson PK

Am. J. Hum. Genet. 97 (5) 708-714 [2015-11-05; online 2015-11-07]

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

Quantitative proteogenomics of human pathogens using DIA-MS.

Malmström L, Bakochi A, Svensson G, ..., Karlsson C, Malmström J

J Proteomics 129 (-) 98-107 [2015-11-03; online 2015-09-19]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Elevated expression of the C-type lectin CD93 in the glioblastoma vasculature regulates cytoskeletal rearrangements that enhance vessel function and reduce host survival.

Langenkamp E, Zhang L, Lugano R, ..., Smits A, Dimberg A

Cancer Res. 75 (21) 4504-4516 [2015-11-01; online 2015-09-11]

Variant Profiling of Candidate Genes in Pancreatic Ductal Adenocarcinoma.

Huang J, Löhr JM, Nilsson M, ..., Zheng Z, Ye W

Clin. Chem. 61 (11) 1408-1416 [2015-11-00; online 2015-09-16]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The Role of FTO and Vitamin D for the Weight Loss Effect of Roux-en-Y Gastric Bypass Surgery in Obese Patients.

Bandstein M, Schultes B, Ernst B, ..., Schiöth HB, Benedict C

Obes Surg 25 (11) 2071-2077 [2015-11-00; online 2015-03-01]

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

The Human Endometrium-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling.

Zieba A, Sjöstedt E, Olovsson M, ..., Uhlen M, Ponten F

OMICS 19 (11) 659-668 [2015-11-00; online 2015-10-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Technology development]

Single-cell genomics of a rare environmental alphaproteobacterium provides unique insights into Rickettsiaceae evolution.

Martijn J, Schulz F, Zaremba-Niedzwiedzka K, ..., Guy L, Ettema TJ

ISME J 9 (11) 2373-2385 [2015-11-00; online 2015-04-07]

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

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data.

Nater A, Burri R, Kawakami T, Smeds L, Ellegren H

Syst. Biol. 64 (6) 1000-1017 [2015-11-00; online 2015-07-19]

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

Rescue of primary ubiquinone deficiency due to a novel COQ7 defect using 2,4-dihydroxybensoic acid.

Freyer C, Stranneheim H, Naess K, ..., Wredenberg A, Wedell A

J. Med. Genet. 52 (11) 779-783 [2015-11-00; online 2015-06-19]

Clinical Genomics Clinical Genomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Population genetic differentiation of height and body mass index across Europe.

Robinson MR, Hemani G, Medina-Gomez C, ..., Yang J, Visscher PM

Nat. Genet. 47 (11) 1357-1362 [2015-11-00; online 2015-09-14]

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

Mutation in CEP63 co-segregating with developmental dyslexia in a Swedish family.

Einarsdottir E, Svensson I, Darki F, ..., Kere J, Matsson H

Hum. Genet. 134 (11-12) 1239-1248 [2015-11-00; online 2015-09-25]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers.

Burri R, Nater A, Kawakami T, ..., Török J, Ellegren H

Genome Res. 25 (11) 1656-1665 [2015-11-00; online 2015-09-09]

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

Inactivation of the Deg protease family in the cyanobacterium Synechocystis sp. PCC 6803 has impact on the outer cell layers.

Cheregi O, Miranda H, Gröbner G, Funk C

Journal of Photochemistry and Photobiology B: Biology 152 (Pt B) 383-394 [2015-11-00; online 2015-05-22]

Swedish NMR Centre (SNC) [Service]

Impact of asymmetric male and female gamete dispersal on allelic diversity and spatial genetic structure in valley oak (Quercus lobata Née)

Sork VL, Smouse PE, Grivet D, Scofield DG

Evol Ecol 29 (6) 927-945 [2015-11-00; online 2015-11-12]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

High-Throughput Sequencing Reveals Drastic Changes in Fungal Communities in the Phyllosphere of Norway Spruce (Picea abies) Following Invasion of the Spruce Bud Scale (Physokermes piceae).

Menkis A, Marčiulynas A, Gedminas A, Lynikienė J, Povilaitienė A

Microb. Ecol. 70 (4) 904-911 [2015-11-00; online 2015-06-10]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Herring and Beef Meals Lead to Differences in Plasma 2-Aminoadipic Acid, β-Alanine, 4-Hydroxyproline, Cetoleic Acid, and Docosahexaenoic Acid Concentrations in Overweight Men.

Ross AB, Svelander C, Undeland I, Pinto R, Sandberg AS

J. Nutr. 145 (11) 2456-2463 [2015-11-00; online 2015-09-25]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

HaloPlex Targeted Resequencing for Mutation Detection in Clinical Formalin-Fixed, Paraffin-Embedded Tumor Samples.

Moens LN, Falk-Sörqvist E, Ljungström V, ..., Nilsson M, Botling J

J Mol Diagn 17 (6) 729-739 [2015-11-00; online 2015-09-03]

Clinical Genomics Clinical Genomics Uppsala NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin.

Wu G, Zhao H, Li C, ..., Nagarajan N, Dawson TL

PLoS Genet. 11 (11) e1005614 [2015-11-00; online 2015-11-05]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Fibroblast Growth Factor 23 and Incidence of Subarachnoid Hemorrhage: Nested Case-Control Study.

Söderholm M, Engström G

Stroke 46 (11) 3260-3262 [2015-11-00; online 2015-09-22]

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

Exploring the genetics of irritable bowel syndrome: a GWA study in the general population and replication in multinational case-control cohorts.

Ek WE, Reznichenko A, Ripke S, ..., Wouters MM, D'Amato M

Gut 64 (11) 1774-1782 [2015-11-00; online 2014-09-23]

Mutation Analysis Facility (MAF) NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Early Exposure to Dogs and Farm Animals and the Risk of Childhood Asthma.

Fall T, Lundholm C, Örtqvist AK, ..., Ingelsson E, Almqvist C

JAMA Pediatr 169 (11) e153219 [2015-11-00; online 2015-11-02]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Assessing the consistency of public human tissue RNA-seq data sets.

Danielsson F, James T, Gomez-Cabrero D, Huss M

Brief. Bioinformatics 16 (6) 941-949 [2015-11-00; online 2015-04-02]

Bioinformatics (NBIS) [Technology development] Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Assessing the Barley Genome Zipper and Genomic Resources for Breeding Purposes.

Silvar C, Martis MM, Nussbaumer T, ..., Ordon F, Perovic D

Plant Genome 8 (3) eplantgenome2015.06.0045 [2015-11-00; online 2015-11-01]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities.

Sanli K, Bengtsson-Palme J, Nilsson RH, ..., Blanck H, Eriksson KM

Front Microbiol 6 (-) 1192 [2015-10-30; online 2015-10-30]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Quinolone resistance mutations in the faecal microbiota of Swedish travellers to India.

Johnning A, Kristiansson E, Angelin M, ..., Johansson A, Larsson DG

BMC Microbiol. 15 (-) 235 [2015-10-24; online 2015-10-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Nurr1 and Retinoid X Receptor Ligands Stimulate Ret Signaling in Dopamine Neurons and Can Alleviate α-Synuclein Disrupted Gene Expression.

Volakakis N, Tiklova K, Decressac M, ..., Björklund A, Perlmann T

J. Neurosci. 35 (42) 14370-14385 [2015-10-21; online 2015-10-23]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetic Polymorphisms in Vitamin D Metabolism and Signaling Genes and Risk of Breast Cancer: A Nested Case-Control Study.

Clendenen TV, Ge W, Koenig KL, ..., Sund M, Zeleniuch-Jacquotte A

PLoS ONE 10 (10) e0140478 [2015-10-21; online 2015-10-21]

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

Structure-activity relationships for lipoprotein lipase agonists that lower plasma triglycerides in vivo.

Caraballo R, Larsson M, Nilsson SK, ..., Enquist P, Elofsson M

Eur J Med Chem 103 (-) 191-209 [2015-10-20; online 2015-09-12]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Membrane vesicle-mediated release of bacterial RNA.

Sjöström AE, Sandblad L, Uhlin BE, Wai SN

Sci Rep 5 (-) 15329 [2015-10-20; online 2015-10-20]

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

Noncanoncial signal recognition particle RNAs in a major eukaryotic phylum revealed by purification of SRP from the human pathogen Cryptococcus neoformans.

Dumesic PA, Rosenblad MA, Samuelsson T, ..., Yates JR, Madhani HD

Nucleic Acids Res. 43 (18) 9017-9027 [2015-10-15; online 2015-08-16]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Mutation in NRAS in familial Noonan syndrome--case report and review of the literature.

Ekvall S, Wilbe M, Dahlgren J, ..., Annerén G, Bondeson ML

BMC Med. Genet. 16 (-) 95 [2015-10-14; online 2015-10-14]

Clinical Genomics Clinical Genomics Uppsala

The folate-coupled enzyme MTHFD2 is a nuclear protein and promotes cell proliferation.

Gustafsson Sheppard N, Jarl L, Mahadessian D, ..., Jain M, Nilsson R

Sci Rep 5 (-) 15029 [2015-10-13; online 2015-10-13]

Spatial Proteomics

Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes.

Pucholt P, Sjödin P, Weih M, Rönnberg-Wästljung AC, Berlin S

BMC Plant Biol. 15 (-) 244 [2015-10-12; online 2015-10-12]

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

Brachyspira suanatina sp. nov., an enteropathogenic intestinal spirochaete isolated from pigs and mallards: genomic and phenotypic characteristics.

Mushtaq M, Zubair S, Råsbäck T, Bongcam-Rudloff E, Jansson DS

BMC Microbiol. 15 (-) 208 [2015-10-12; online 2015-10-12]

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

Many obesity-associated SNPs strongly associate with DNA methylation changes at proximal promoters and enhancers.

Voisin S, Almén MS, Zheleznyakova GY, ..., Rask-Andersen M, Schiöth HB

Genome Med 7 (-) 103 [2015-10-08; online 2015-10-08]

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

Growth of Chitinophaga pinensis on Plant Cell Wall Glycans and Characterisation of a Glycoside Hydrolase Family 27 β-l-Arabinopyranosidase Implicated in Arabinogalactan Utilisation.

McKee LS, Brumer H

PLoS ONE 10 (10) e0139932 [2015-10-08; online 2015-10-08]

Protein Science Facility (PSF) [Service]

Evaluation of whole-genome sequencing of four Chinese crested dogs for variant detection using the ion proton system.

Viluma A, Sayyab S, Mikko S, Andersson G, Bergström TF

Canine Genet Epidemiol 2 (-) 16 [2015-10-08; online 2015-10-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Comparative Sigma Factor-mRNA Levels in Mycobacterium marinum under Stress Conditions and during Host Infection.

Pettersson BM, Das S, Behra PR, ..., Ennis DG, Kirsebom LA

PLoS ONE 10 (10) e0139823 [2015-10-07; online 2015-10-07]

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

Crosstalk between Gut Microbiota and Dietary Lipids Aggravates WAT Inflammation through TLR Signaling.

Caesar R, Tremaroli V, Kovatcheva-Datchary P, Cani PD, Bäckhed F

Cell Metab. 22 (4) 658-668 [2015-10-06; online 2015-09-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Standing genetic variation as a major contributor to adaptation in the Virginia chicken lines selection experiment.

Sheng Z, Pettersson ME, Honaker CF, Siegel PB, Carlborg Ö

Genome Biol. 16 (-) 219 [2015-10-01; online 2015-10-01]

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

Spatiotemporal Heterogeneity Characterizes the Genetic Landscape of Pheochromocytoma and Defines Early Events in Tumorigenesis.

Crona J, Backman S, Maharjan R, ..., Hellman P, Björklund P

Clin. Cancer Res. 21 (19) 4451-4460 [2015-10-01; online 2015-05-21]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Homozygous loss-of-function variants in European cosmopolitan and isolate populations.

Kaiser VB, Svinti V, Prendergast JG, ..., Semple CA, Wilson JF

Hum. Mol. Genet. 24 (19) 5464-5474 [2015-10-01; online 2015-07-14]

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

Candidate gene analysis and exome sequencing confirm LBX1 as a susceptibility gene for idiopathic scoliosis.

Grauers A, Wang J, Einarsdottir E, ..., Kere J, Gerdhem P

Spine J 15 (10) 2239-2246 [2015-10-01; online 2015-05-20]

Mutation Analysis Facility (MAF) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Trimeric microsomal glutathione transferase 2 displays one third of the sites reactivity.

Ahmad S, Thulasingam M, Palombo I, ..., Haeggström JZ, Rinaldo-Matthis A

Biochim. Biophys. Acta 1854 (10 Pt A) 1365-1371 [2015-10-00; online 2015-06-13]

Transcriptome Profiling Reveals Degree of Variability in Induced Pluripotent Stem Cell Lines: Impact for Human Disease Modeling.

Schuster J, Halvardson J, Pilar Lorenzo L, ..., Feuk L, Dahl N

Cell Reprogram 17 (5) 327-337 [2015-10-00; online 2015-09-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

The use of gene arrays and corresponding connectivity mapping (Cmap) to identify novel anti-ageing ingredients.

Gillbro JM, Merinville E, Olsson M, ..., Visdal-Johnsen L, Mavon A

Int J Cosmet Sci 37 Suppl 1 (-) 9-14 [2015-10-00; online 2015-06-27]

The effects of age and gender on plasma levels of 63 cytokines.

Larsson A, Carlsson L, Gordh T, ..., Thulin M, Kamali-Moghaddam M

J. Immunol. Methods 425 (-) 58-61 [2015-10-00; online 2015-06-14]

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

The Influence of Age and Sex on Genetic Associations with Adult Body Size and Shape: A Large-Scale Genome-Wide Interaction Study.

Winkler TW, Justice AE, Graff M, ..., Kutalik Z, Loos RJ

PLoS Genet. 11 (10) e1005378 [2015-10-00; online 2015-10-01]

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

The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents.

Bengtsson-Palme J, Angelin M, Huss M, ..., Larsson DGJ, Johansson A

Antimicrob. Agents Chemother. 59 (10) 6551-6560 [2015-10-00; online 2015-08-12]

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

The Human Glioblastoma Cell Culture Resource: Validated Cell Models Representing All Molecular Subtypes.

Xie Y, Bergström T, Jiang Y, ..., Forsberg-Nilsson K, Uhrbom L

EBioMedicine 2 (10) 1351-1363 [2015-10-00; online 2015-08-15]

Signatures of post-zygotic structural genetic aberrations in the cells of histologically normal breast tissue that can predispose to sporadic breast cancer.

Forsberg LA, Rasi C, Pekar G, ..., Tot T, Dumanski JP

Genome Res. 25 (10) 1521-1535 [2015-10-00; online 2015-10-03]

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

Quantitative Mass Spectrometry Reveals Partial Translational Regulation for Dosage Compensation in Chicken.

Uebbing S, Konzer A, Xu L, ..., Bergquist J, Ellegren H

Mol. Biol. Evol. 32 (10) 2716-2725 [2015-10-00; online 2015-06-26]

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

Profound parental bias associated with chromosome 14 acquired uniparental disomy indicates targeting of an imprinted locus.

Chase A, Leung W, Tapper W, ..., Dumanski JP, Cross NC

Leukemia 29 (10) 2069-2074 [2015-10-00; online 2015-06-27]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Positive Modulation of the Glycine Receptor by Means of Glycine Receptor-Binding Aptamers.

Shalaly ND, Aneiros E, Blank M, ..., Andersson CV, Sandberg K

J Biomol Screen 20 (9) 1112-1123 [2015-10-00; online 2015-06-12]

Drug Discovery and Development (DDD) [Collaborative]

Isolation of novel IncA/C and IncN fluoroquinolone resistance plasmids from an antibiotic-polluted lake.

Flach CF, Johnning A, Nilsson I, ..., Kristiansson E, Larsson DG

J. Antimicrob. Chemother. 70 (10) 2709-2717 [2015-10-00; online 2015-07-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetic variance estimation with imputed variants finds negligible missing heritability for human height and body mass index.

Yang J, Bakshi A, Zhu Z, ..., Goddard ME, Visscher PM

Nat. Genet. 47 (10) 1114-1120 [2015-10-00; online 2015-09-01]

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

Dibenzocyclooctadiene lignans from Schisandra spp. selectively inhibit the growth of the intracellular bacteria Chlamydia pneumoniae and Chlamydia trachomatis.

Hakala E, Hanski L, Uvell H, ..., Elofsson M, Vuorela PM

J. Antibiot. 68 (10) 609-614 [2015-10-00; online 2015-05-07]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Cytostatic Effect of Repeated Exposure to Simvastatin: A Mechanism for Chronic Myotoxicity Revealed by the Use of Mesodermal Progenitors Derived from Human Pluripotent Stem Cells.

Peric D, Barragan I, Giraud-Triboult K, ..., Laustriat D, Peschanski M

Stem Cells 33 (10) 2936-2948 [2015-10-00; online 2015-07-18]

Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella.

Steige KA, Reimegård J, Koenig D, Scofield DG, Slotte T

Mol. Biol. Evol. 32 (10) 2501-2514 [2015-10-00; online 2015-08-28]

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

BCG Skin Infection Triggers IL-1R-MyD88-Dependent Migration of EpCAMlow CD11bhigh Skin Dendritic cells to Draining Lymph Node During CD4+ T-Cell Priming.

Bollampalli VP, Harumi Yamashiro L, Feng X, ..., Nylén S, Rothfuchs AG

PLoS Pathog. 11 (10) e1005206 [2015-10-00; online 2015-10-06]

Integrated Microscopy Technologies Stockholm [Service]

Acid-Base Catalyst Discriminates between a Fructose 6-Phosphate Aldolase and a Transaldolase

Stellmacher L, Sandalova T, Leptihn S, ..., Sprenger GA, Samland AK

ChemCatChem 7 (19) 3140-3151 [2015-10-00; online 2015-08-06]

A comprehensive 1,000 Genomes-based genome-wide association meta-analysis of coronary artery disease.

Nikpay M, Goel A, Won HH, ..., Farrall M, CARDIoGRAMplusC4D Consortium

Nat. Genet. 47 (10) 1121-1130 [2015-10-00; online 2015-09-08]

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

A New Method for Detecting Associations with Rare Copy-Number Variants.

Tzeng JY, Magnusson PK, Sullivan PF, Swedish Schizophrenia Consortium , Szatkiewicz JP

PLoS Genet. 11 (10) e1005403 [2015-10-00; online 2015-10-02]

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

Cerebrospinal fluid monoamine metabolite concentrations as intermediate phenotypes between glutamate-related genes and psychosis.

Andreou D, Söderman E, Axelsson T, ..., Agartz I, Jönsson EG

Psychiatry Res 229 (1-2) 497-504 [2015-09-30; online 2015-07-06]

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

Virtual Screening for Transition State Analogue Inhibitors of IRAP Based on Quantum Mechanically Derived Reaction Coordinates

Svensson F, Engen K, Lundbäck T, Larhed M, Sköld C

J. Chem. Inf. Model. 55 (9) 1984-1993 [2015-09-28; online 2015-09-28]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies).

Delhomme N, Sundström G, Zamani N, ..., Grabherr MG, Street NR

PLoS ONE 10 (9) e0139080 [2015-09-28; online 2015-09-28]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Identification of Novel Epigenetic Markers of Prostate Cancer by NotI-Microarray Analysis.

Dmitriev AA, Rosenberg EE, Krasnov GS, ..., Senchenko VN, Kashuba VI

Dis. Markers 2015 (-) 241301 [2015-09-28; online 2015-09-28]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes.

Saw JH, Spang A, Zaremba-Niedzwiedzka K, ..., Guy L, Ettema TJG

Philos. Trans. R. Soc. Lond., B, Biol. Sci. 370 (1678) 20140328 [2015-09-26; online 2015-09-02]

Microbial Single Cell Genomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

The genomes of three stocks comprising the most widely utilized live sporozoite Theileria parva vaccine exhibit very different degrees and patterns of sequence divergence.

Norling M, Bishop RP, Pelle R, ..., Daubenberger CA, Silva JC

BMC Genomics 16 (-) 729 [2015-09-24; online 2015-09-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Ancient genomes link early farmers from Atapuerca in Spain to modern-day Basques.

Günther T, Valdiosera C, Malmström H, ..., Götherström A, Jakobsson M

Proc. Natl. Acad. Sci. U.S.A. 112 (38) 11917-11922 [2015-09-22; online 2015-09-08]

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

Gene expression profiling of pre-eclamptic placentae by RNA sequencing.

Kaartokallio T, Cervera A, Kyllönen A, ..., Laivuori H, FINNPEC Core Investigator Group

Sci Rep 5 (-) 14107 [2015-09-21; online 2015-09-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Draft genome sequence of 'Treponema phagedenis' strain V1, isolated from bovine digital dermatitis.

Mushtaq M, Manzoor S, Pringle M, Rosander A, Bongcam-Rudloff E

Stand Genomic Sci 10 (-) 67 [2015-09-21; online 2015-09-21]

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

Dormant phages of Helicobacter pylori reveal distinct populations in Europe.

Vale FF, Vadivelu J, Oleastro M, ..., Mégraud F, Lehours P

Sci Rep 5 (-) 14333 [2015-09-21; online 2015-09-21]

Clinical Genomics [Collaborative] Clinical Genomics Stockholm [Collaborative]

PARP1- and CTCF-Mediated Interactions between Active and Repressed Chromatin at the Lamina Promote Oscillating Transcription.

Zhao H, Sifakis EG, Sumida N, ..., Imreh MP, Göndör A

Mol. Cell 59 (6) 984-997 [2015-09-17; online 2015-08-27]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetic and morphological evidence for introgression between three species of willows.

Fogelqvist J, Verkhozina AV, Katyshev AI, ..., Lascoux M, Berlin S

BMC Evol. Biol. 15 (-) 193 [2015-09-16; online 2015-09-16]

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

WNT3 involvement in human bladder exstrophy and cloaca development in zebrafish.

Baranowska Körberg I, Hofmeister W, Markljung E, ..., Lindstrand A, Nordenskjöld A

Hum. Mol. Genet. 24 (18) 5069-5078 [2015-09-15; online 2015-06-25]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

HLA class I is most tightly linked to levels of tapasin compared with other antigen-processing proteins in glioblastoma.

Thuring C, Follin E, Geironson L, ..., Buus S, Paulsson KM

Br. J. Cancer 113 (6) 952-962 [2015-09-15; online 2015-08-28]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Glioma-derived plasminogen activator inhibitor-1 (PAI-1) regulates the recruitment of LRP1 positive mast cells.

Roy A, Coum A, Marinescu VD, ..., Pontén F, Tchougounova E

Oncotarget 6 (27) 23647-23661 [2015-09-15; online 2015-07-15]

Genetics and Prognostication in Splenic Marginal Zone Lymphoma: Revelations from Deep Sequencing.

Parry M, Rose-Zerilli MJ, Ljungström V, ..., Oscier D, Strefford JC

Clin. Cancer Res. 21 (18) 4174-4183 [2015-09-15; online 2015-03-18]

Clinical Genomics Clinical Genomics Uppsala

Comprehensive analysis of microRNA expression in regionalized human neural progenitor cells reveals microRNA-10 as a caudalizing factor.

Jönsson ME, Nelander Wahlestedt J, Åkerblom M, ..., Jakobsson J, Parmar M

Development 142 (18) 3166-3177 [2015-09-15; online 2015-09-24]

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

Surface Chemistry of Nanocellulose Fibers Directs Monocyte/Macrophage Response.

Hua K, Ålander E, Lindström T, ..., Strømme M, Ferraz N

Biomacromolecules 16 (9) 2787-2795 [2015-09-14; online 2015-08-08]

Determination of obesity associated gene variants related to TMEM18 through ultra-deep targeted re-sequencing in a case-control cohort for pediatric obesity.

Rask-Andersen M, Sällman Almén M, Jacobsson JA, ..., Fredriksson R, Schiöth HB

Genet Res (Camb) 97 (-) e16 [2015-09-14; online 2015-09-14]

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

Rare and low-frequency variants and their association with plasma levels of fibrinogen, FVII, FVIII, and vWF.

Huffman JE, de Vries PS, Morrison AC, ..., O'Donnell CJ, Smith NL

Blood 126 (11) e19-e29 [2015-09-10; online 2015-06-25]

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

The epigenetic signature of subcutaneous fat cells is linked to altered expression of genes implicated in lipid metabolism in obese women.

Arner P, Sinha I, Thorell A, ..., Dahlman-Wright K, Dahlman I

Clin Epigenetics 7 (-) 93 [2015-09-08; online 2015-09-08]

Tandem Benzophenone Amino Pyridines, Potent and Selective Inhibitors of Human Leukotriene C4 Synthase

Kleinschmidt TK, Haraldsson M, Basavarajappa D, ..., Lindbom L, Haeggstrom JZ

Journal of Pharmacology and Experimental Therapeutics 355 (1) 108-116 [2015-09-08; online 2015-08-17]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Paternally expressed imprinted genes establish postzygotic hybridization barriers in Arabidopsis thaliana.

Wolff P, Jiang H, Wang G, Santos-González J, Köhler C

Elife 4 (-) - [2015-09-07; online 2015-09-07]

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

Quest for Missing Proteins: Update 2015 on Chromosome-Centric Human Proteome Project.

Horvatovich P, Lundberg EK, Chen YJ, ..., Paik YK, Hancock WS

J. Proteome Res. 14 (9) 3415-3431 [2015-09-04; online 2015-07-23]

Spatial Proteomics

Metrics for the Human Proteome Project 2015: Progress on the Human Proteome and Guidelines for High-Confidence Protein Identification.

Omenn GS, Lane L, Lundberg EK, ..., Nesvizhskii AI, Deutsch EW

J. Proteome Res. 14 (9) 3452-3460 [2015-09-04; online 2015-07-15]

Spatial Proteomics

High cortisol in 5-year-old children causes loss of DNA methylation in SINE retrotransposons: a possible role for ZNF263 in stress-related diseases.

Nätt D, Johansson I, Faresjö T, Ludvigsson J, Thorsell A

Clin Epigenetics 7 (-) 91 [2015-09-04; online 2015-09-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Pseudomonas aeruginosa lasI/rhlI quorum sensing genes promote phagocytosis and aquaporin 9 redistribution to the leading and trailing regions in macrophages.

Holm A, Karlsson T, Vikström E

Front Microbiol 6 (-) 915 [2015-09-03; online 2015-09-03]

Integrated Microscopy Technologies Stockholm [Service]

Mutations in SLC12A5 in epilepsy of infancy with migrating focal seizures.

Stödberg T, McTague A, Ruiz AJ, ..., Wedell A, Kurian MA

Nat Commun 6 (-) 8038 [2015-09-03; online 2015-09-03]

Clinical Genomics Clinical Genomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Transplanted Bone Marrow-Derived Cells Contribute to Human Adipogenesis.

Rydén M, Uzunel M, Hård JL, ..., Mattsson J, Arner P

Cell Metab. 22 (3) 408-417 [2015-09-01; online 2015-07-21]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

An Exopolysaccharide-Deficient Mutant of Lactobacillus rhamnosus GG Efficiently Displays a Protective Llama Antibody Fragment against Rotavirus on Its Surface.

Álvarez B, Krogh-Andersen K, Tellgren-Roth C, ..., Hammarström L, Marcotte H

Appl. Environ. Microbiol. 81 (17) 5784-5793 [2015-09-01; online 2015-06-21]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Widespread non-additive and interaction effects within HLA loci modulate the risk of autoimmune diseases.

Lenz TL, Deutsch AJ, Han B, ..., de Bakker PI, Raychaudhuri S

Nat. Genet. 47 (9) 1085-1090 [2015-09-00; online 2015-08-10]

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

Whole exome sequencing identifies LRP1 as a pathogenic gene in autosomal recessive keratosis pilaris atrophicans.

Klar J, Schuster J, Khan TN, ..., Baig SM, Dahl N

J. Med. Genet. 52 (9) 599-606 [2015-09-00; online 2015-07-05]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Use of a proximity extension assay proteomics chip to discover new biomarkers for human atherosclerosis.

Lind L, Ärnlöv J, Lindahl B, ..., Sundström J, Ingelsson E

Atherosclerosis 242 (1) 205-210 [2015-09-00; online 2015-07-14]

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

Transcriptomics of colour patterning and coloration shifts in crows.

Poelstra JW, Vijay N, Hoeppner MP, Wolf JB

Mol. Ecol. 24 (18) 4617-4628 [2015-09-00; online 2015-08-25]

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

Towards a stereoselective synthesis of α,α-disubstituted proline analogues

Das SK, Bhatt N, Mujahid M, ..., Naicker T, Govender T

Tetrahedron Letters 56 (37) 5172-5174 [2015-09-00; online 2015-09-00]

Drug Discovery and Development (DDD) [Collaborative]

Synthesis of enantiopure angiotensin II type 2 receptor [AT2R] antagonist EMA401

Wakchaure PB, Bremberg U, Wannberg J, Larhed M

Tetrahedron 71 (38) 6881-6887 [2015-09-00; online 2015-09-00]

Drug Discovery and Development (DDD)

Shared immunological targets in the lungs and joints of patients with rheumatoid arthritis: identification and validation.

Ytterberg AJ, Joshua V, Reynisdottir G, ..., Klareskog L, Catrina AI

Ann. Rheum. Dis. 74 (9) 1772-1777 [2015-09-00; online 2014-05-13]

Polymorphisms in the FK506 binding protein 5 gene are associated with attention deficit hyperactivity disorder and diurnal cortisol levels.

Isaksson J, Allen M, Nilsson KW, Lindblad F

Acta Paediatr. 104 (9) 910-915 [2015-09-00; online 2015-06-03]

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

Half-of-the-Sites Reactivity of the Castor Δ9-18:0-Acyl Carrier Protein Desaturase.

Liu Q, Chai J, Moche M, ..., Lindqvist Y, Shanklin J

Plant Physiol. 169 (1) 432-441 [2015-09-00; online 2015-08-01]

Exome sequencing followed by genotyping suggests SYPL2 as a susceptibility gene for morbid obesity.

Jiao H, Arner P, Gerdhem P, ..., Kere J, Dahlman I

Eur. J. Hum. Genet. 23 (9) 1216-1222 [2015-09-00; online 2014-11-20]

Mutation Analysis Facility (MAF) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Design, Synthesis and Inhibitory Activity of Photoswitchable RET Kinase Inhibitors

Ferreira R, Nilsson JR, Solano C, Andréasson J, Grøtli M

Sci Rep 5 (1) - [2015-09-00; online 2015-05-06]

Chemical Biology Consortium Sweden (CBCS) [Service]

Auxotrophy and intrapopulation complementary in the 'interactome' of a cultivated freshwater model community.

Garcia SL, Buck M, McMahon KD, ..., Eiler A, Warnecke F

Mol. Ecol. 24 (17) 4449-4459 [2015-09-00; online 2015-07-17]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Analysis of the genetic architecture of susceptibility to cervical cancer indicates that common SNPs explain a large proportion of the heritability.

Chen D, Cui T, Ek WE, ..., Wang H, Gyllensten U

Carcinogenesis 36 (9) 992-998 [2015-09-00; online 2015-06-06]

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

Altered serotonin (5-HT) 1D and 2A receptor expression may contribute to defective insulin and glucagon secretion in human type 2 diabetes.

Bennet H, Balhuizen A, Medina A, ..., Wierup N, Fex M

Peptides 71 (-) 113-120 [2015-09-00; online 2015-07-25]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Acute Sleep Loss Induces Tissue-Specific Epigenetic and Transcriptional Alterations to Circadian Clock Genes in Men.

Cedernaes J, Osler ME, Voisin S, ..., Schiöth HB, Benedict C

J. Clin. Endocrinol. Metab. 100 (9) E1255-E1261 [2015-09-00; online 2015-07-15]

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

Molecular profiling of prostate cancer derived exosomes may reveal a predictive signature for response to docetaxel.

Kharaziha P, Chioureas D, Rutishauser D, ..., Nilsson S, Panaretakis T

Oncotarget 6 (25) 21740-21754 [2015-08-28; online 2015-04-07]

BEX1 acts as a tumor suppressor in acute myeloid leukemia.

Lindblad O, Li T, Su X, ..., Rönnstrand L, Kazi JU

Oncotarget 6 (25) 21395-21405 [2015-08-28; online 2015-06-06]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Microfluidic screening and whole-genome sequencing identifies mutations associated with improved protein secretion by yeast.

Huang M, Bai Y, Sjostrom SL, ..., Andersson-Svahn H, Nielsen J

Proc. Natl. Acad. Sci. U.S.A. 112 (34) E4689-E4696 [2015-08-25; online 2015-08-12]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Transcriptomic changes in the plant pathogenic fungus Rhizoctonia solani AG-3 in response to the antagonistic bacteria Serratia proteamaculans and Serratia plymuthica.

Gkarmiri K, Finlay RD, Alström S, ..., Cubeta MA, Högberg N

BMC Genomics 16 (-) 630 [2015-08-22; online 2015-08-22]

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

Structure of the Glycosyltransferase Ktr4p from Saccharomyces cerevisiae.

Possner DD, Claesson M, Guy JE

PLoS ONE 10 (8) e0136239 [2015-08-21; online 2015-08-21]

Personality and intelligence: persistence, not self-directedness, cooperativeness or self-transcendence, is related to twins' cognitive abilities.

Mousavi F, Rozsa S, Nilsson T, ..., Anckarsäter H, Garcia D

PeerJ 3 (-) e1195 [2015-08-20; online 2015-08-20]

In Vitro and In Vivo Response to Low-Modulus PMMA-Based Bone Cement.

Carlsson E, Mestres G, Treerattrakoon K, ..., Larsson S, Persson C

Biomed Res Int 2015 (-) 594284 [2015-08-20; online 2015-08-20]

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium.

Yu NY, Hallström BM, Fagerberg L, ..., Uhlén M, Daub CO

Nucleic Acids Res. 43 (14) 6787-6798 [2015-08-18; online 2015-06-27]

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

The Ty1-copia LTR retroelement family PARTC is highly conserved in conifers over 200 MY of evolution.

Zuccolo A, Scofield DG, De Paoli E, Morgante M

Gene 568 (1) 89-99 [2015-08-15; online 2015-05-20]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Genome-wide association study of toxic metals and trace elements reveals novel associations.

Ng E, Lind PM, Lindgren C, ..., Morris A, Lind L

Hum. Mol. Genet. 24 (16) 4739-4745 [2015-08-15; online 2015-05-31]

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

Gene × dietary pattern interactions in obesity: analysis of up to 68 317 adults of European ancestry.

Nettleton JA, Follis JL, Ngwa JS, ..., Loos RJ, Franks PW

Hum. Mol. Genet. 24 (16) 4728-4738 [2015-08-15; online 2015-05-23]

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

Sex-Specific Effects of Adiponectin on Carotid Intima-Media Thickness and Incident Cardiovascular Disease.

Persson J, Strawbridge RJ, McLeod O, ..., Hamsten A, IMPROVE Study Group

J Am Heart Assoc 4 (8) e001853 [2015-08-14; online 2015-08-14]

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

Whole Exome- and mRNA-Sequencing of an AT/RT Case Reveals Few Somatic Mutations and Several Deregulated Signalling Pathways in the Context of SMARCB1 Deficiency.

Sandgren J, Holm S, Marino AM, ..., Nistér M, Díaz de Ståhl T

Biomed Res Int 2015 (-) 862039 [2015-08-12; online 2015-08-12]

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

Adaptive mutations in sugar metabolism restore growth on glucose in a pyruvate decarboxylase negative yeast strain.

Zhang Y, Liu G, Engqvist MK, ..., Siewers V, Nielsen J

Microb. Cell Fact. 14 (-) 116 [2015-08-08; online 2015-08-08]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Microstructural White Matter Properties Mediate the Association between APOE and Perceptual Speed in Very Old Persons without Dementia.

Laukka EJ, Lövdén M, Kalpouzos G, ..., Fratiglioni L, Bäckman L

PLoS ONE 10 (8) e0134766 [2015-08-07; online 2015-08-07]

Effect of a Bromo Substituent on the Glutathione Peroxidase Activity of a Pyridoxine-like Diselenide.

Singh VP, Poon JF, Butcher RJ, ..., Ott MK, Engman L

J. Org. Chem. 80 (15) 7385-7395 [2015-08-07; online 2015-07-03]

Comprehensive genomic profiles of small cell lung cancer

George J, Lim JS, Jang SJ, ..., Sage J, Thomas RK

Nature 524 (7563) 47-53 [2015-08-06; online 2015-07-13]

Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]

Roux-en-Y Gastric Bypass and Vertical Banded Gastroplasty Induce Long-Term Changes on the Human Gut Microbiome Contributing to Fat Mass Regulation.

Tremaroli V, Karlsson F, Werling M, ..., Nielsen J, Bäckhed F

Cell Metab. 22 (2) 228-238 [2015-08-04; online 2015-08-06]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Crystal structure, biochemical and cellular activities demonstrate separate functions of MTH1 and MTH2.

Carter M, Jemth AS, Hagenkort A, ..., Helleday T, Stenmark P

Nat Commun 6 (-) 7871 [2015-08-04; online 2015-08-04]

MicroRNA-132 enhances transition from inflammation to proliferation during wound healing.

Li D, Wang A, Liu X, ..., Ståhle M, Landén NX

J. Clin. Invest. 125 (8) 3008-3026 [2015-08-03; online 2015-06-30]

Identifying and Assessing Interesting Subgroups in a Heterogeneous Population.

Lee W, Alexeyenko A, Pernemalm M, ..., Lehtiö J, Pawitan Y

Biomed Res Int 2015 (-) 462549 [2015-08-03; online 2015-08-03]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Heat differentiated complement factor profiling.

Hamsten C, Skattum L, Truedsson L, ..., Nilsson P, Neiman M

J Proteomics 126 (-) 155-162 [2015-08-03; online 2015-06-07]

Affinity Proteomics Stockholm [Technology development]

Genome-wide mapping of promoter-anchored interactions with close to single-enhancer resolution.

Sahlén P, Abdullayev I, Ramsköld D, ..., Lundeberg J, Sandberg R

Genome Biol. 16 (-) 156 [2015-08-03; online 2015-08-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Analysis of the Human Prostate-Specific Proteome Defined by Transcriptomics and Antibody-Based Profiling Identifies TMEM79 and ACOXL as Two Putative, Diagnostic Markers in Prostate Cancer.

O'Hurley G, Busch C, Fagerberg L, ..., Uhlén M, Pontén F

PLoS ONE 10 (8) e0133449 [2015-08-03; online 2015-08-03]

Affinity Proteomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling [Technology development]

Effect of genetic variations on ticagrelor plasma levels and clinical outcomes.

Varenhorst C, Eriksson N, Johansson Å, ..., Wallentin L, PLATO Investigators

Eur. Heart J. 36 (29) 1901-1912 [2015-08-01; online 2015-05-04]

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

Whole-exome sequencing of Ethiopian patients with ichthyosis vulgaris and atopic dermatitis.

Taylan F, Nilsson D, Asad S, ..., Nordenskjöld M, Bradley M

J. Allergy Clin. Immunol. 136 (2) 507-9.e19 [2015-08-00; online 2015-03-31]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Representation of selected-reaction monitoring data in the mzQuantML data standard.

Qi D, Lawless C, Teleman J, ..., Hubbard S, Jones AR

Proteomics 15 (15) 2592-2596 [2015-08-00; online 2015-04-18]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Prevalence of polymorphisms with significant resistance to NS5A inhibitors in treatment-naive patients with hepatitis C virus genotypes 1a and 3a in Sweden.

Lindström I, Kjellin M, Palanisamy N, ..., Lannergard A, Lennerstrand J

Infect Dis (Lond) 47 (8) 555-562 [2015-08-00; online 2015-04-09]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Manganese lipoxygenase of F. oxysporum and the structural basis for biosynthesis of distinct 11-hydroperoxy stereoisomers.

Wennman A, Magnuson A, Hamberg M, Oliw EH

J. Lipid Res. 56 (8) 1606-1615 [2015-08-00; online 2015-06-27]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Inbreeding Affects Gene Expression Differently in Two Self-Incompatible Arabidopsis lyrata Populations with Similar Levels of Inbreeding Depression.

Menzel M, Sletvold N, Ågren J, Hansson B

Mol. Biol. Evol. 32 (8) 2036-2047 [2015-08-00; online 2015-04-10]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Association of the LINGO2-related SNP rs10968576 with body mass in a cohort of elderly Swedes.

Rask-Andersen M, Almén MS, Lind L, Schiöth HB

Mol. Genet. Genomics 290 (4) 1485-1491 [2015-08-00; online 2015-02-26]

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

A prezygotic transmission distorter acting equally in female and male zebra finches Taeniopygia guttata.

Knief U, Schielzeth H, Ellegren H, Kempenaers B, Forstmeier W

Mol. Ecol. 24 (15) 3846-3859 [2015-08-00; online 2015-06-20]

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

Bioinformatic Challenges in Clinical Diagnostic Application of Targeted Next Generation Sequencing: Experience from Pheochromocytoma.

Crona J, Ljungström V, Welin S, ..., Hellman P, Björklund P

PLoS ONE 10 (7) e0133210 [2015-07-31; online 2015-07-31]

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

Identification of New Potential Interaction Partners for Human Cytoplasmic Copper Chaperone Atox1: Roles in Gene Regulation?

Öhrvik H, Wittung-Stafshede P

Int J Mol Sci 16 (8) 16728-16739 [2015-07-23; online 2015-07-23]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Directional dominance on stature and cognition in diverse human populations.

Joshi PK, Esko T, Mattsson H, ..., Polašek O, Wilson JF

Nature 523 (7561) 459-462 [2015-07-23; online 2015-07-02]

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

Compaction of rolling circle amplification products increases signal integrity and signal-to-noise ratio.

Clausson C, Arngården L, Ishaq O, ..., Wählby C, Söderberg O

Sci Rep 5 (-) 12317 [2015-07-23; online 2015-07-23]

BioImage Informatics [Technology development] Bioinformatics (NBIS) [Technology development] Integrated Microscopy Technologies Stockholm [Collaborative]

lobChIP: from cells to sequencing ready ChIP libraries in a single day.

Wallerman O, Nord H, Bysani M, Borghini L, Wadelius C

Epigenetics Chromatin 8 (-) 25 [2015-07-21; online 2015-07-21]

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

Two new loci and gene sets related to sex determination and cancer progression are associated with susceptibility to testicular germ cell tumor.

Kristiansen W, Karlsson R, Rounge TB, ..., Grotmol T, Wiklund F

Hum. Mol. Genet. 24 (14) 4138-4146 [2015-07-15; online 2015-04-17]

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

Predisposition to Childhood Otitis Media and Genetic Polymorphisms within the Toll-Like Receptor 4 (TLR4) Locus.

Hafrén L, Einarsdottir E, Kentala E, ..., Kere J, Mattila PS

PLoS ONE 10 (7) e0132551 [2015-07-15; online 2015-07-15]

Evaluation of the protein biomarkers and the analgesic response to systemic methylene blue in patients with refractory neuropathic pain: a double-blind, controlled study.

Miclescu AA, Svahn M, Gordh TE

J Pain Res 8 (-) 387-397 [2015-07-15; online 2015-07-15]

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

Distinguishing Mast Cell Progenitors from Mature Mast Cells in Mice.

Dahlin JS, Ding Z, Hallgren J

Stem Cells Dev. 24 (14) 1703-1711 [2015-07-15; online 2015-03-10]

Differential Expression Analysis by RNA-Seq Reveals Perturbations in the Platelet mRNA Transcriptome Triggered by Pathogen Reduction Systems.

Osman A, Hitzler WE, Ameur A, Provost P

PLoS ONE 10 (7) e0133070 [2015-07-14; online 2015-07-14]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Metagenomic insights into strategies of aerobic and anaerobic carbon and nitrogen transformation in boreal lakes.

Peura S, Sinclair L, Bertilsson S, Eiler A

Sci Rep 5 (-) 12102 [2015-07-10; online 2015-07-10]

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

SF3B1 mutation identifies a distinct subset of myelodysplastic syndrome with ring sideroblasts.

Malcovati L, Karimi M, Papaemmanuil E, ..., Cazzola M, Hellström Lindberg E

Blood 126 (2) 233-241 [2015-07-09; online 2015-05-10]

Clinical Genomics Clinical Genomics Uppsala NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Cell periphery-related proteins as major genomic targets behind the adaptive evolution of an industrial Saccharomyces cerevisiae strain to combined heat and hydrolysate stress.

Wallace-Salinas V, Brink DP, Ahrén D, Gorwa-Grauslund MF

BMC Genomics 16 (-) 514 [2015-07-09; online 2015-07-09]

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

Identification of large variation in pfcrt, pfmdr-1 and pfubp-1 markers in Plasmodium falciparum isolates from Ethiopia and Tanzania.

Golassa L, Kamugisha E, Ishengoma DS, ..., Choy A, Swedberg G

Malar. J. 14 (-) 264 [2015-07-08; online 2015-07-08]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation.

Tan TC, Kracher D, Gandini R, ..., Ludwig R, Divne C

Nat Commun 6 (-) 7542 [2015-07-07; online 2015-07-07]

Scaffolding of a bacterial genome using MinION nanopore sequencing.

Karlsson E, Lärkeryd A, Sjödin A, Forsman M, Stenberg P

Sci Rep 5 (-) 11996 [2015-07-07; online 2015-07-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genome Characterization, Prevalence and Distribution of a Macula-Like Virus from Apis mellifera and Varroa destructor.

de Miranda JR, Cornman RS, Evans JD, ..., Neumann P, Gauthier L

Viruses 7 (7) 3586-3602 [2015-07-06; online 2015-07-06]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Foxf2 Is Required for Brain Pericyte Differentiation and Development and Maintenance of the Blood-Brain Barrier.

Reyahi A, Nik AM, Ghiami M, ..., Johansson BR, Carlsson P

Dev. Cell 34 (1) 19-32 [2015-07-06; online 2015-06-25]

The TOPCONS web server for consensus prediction of membrane protein topology and signal peptides.

Tsirigos KD, Peters C, Shu N, Käll L, Elofsson A

Nucleic Acids Res. 43 (W1) W401-W407 [2015-07-01; online 2015-05-15]

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

Using Genetic Variants to Assess the Relationship Between Circulating Lipids and Type 2 Diabetes.

Fall T, Xie W, Poon W, ..., Frayling TM, Ingelsson E

Diabetes 64 (7) 2676-2684 [2015-07-00; online 2015-05-08]

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

UV irradiation responses in Giardia intestinalis.

Einarsson E, Svärd SG, Troell K

Exp. Parasitol. 154 (-) 25-32 [2015-07-00; online 2015-04-01]

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

Toward Rare Blood Cell Preservation for RNA Sequencing.

Vickovic S, Ahmadian A, Lewensohn R, Lundeberg J

J Mol Diagn 17 (4) 352-359 [2015-07-00; online 2015-05-16]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Proteomics for the detection of indirect markers of steroids treatment in bovine muscle.

Stella R, Biancotto G, Arrigoni G, ..., Angeletti R, James P

Proteomics 15 (13) 2332-2341 [2015-07-00; online 2015-03-12]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Potential role of milk fat globule membrane in modulating plasma lipoproteins, gene expression, and cholesterol metabolism in humans: a randomized study.

Rosqvist F, Smedman A, Lindmark-Månsson H, ..., Dahlman I, Risérus U

Am. J. Clin. Nutr. 102 (1) 20-30 [2015-07-00; online 2015-05-29]

Polymorphisms in DCDC2 and S100B associate with developmental dyslexia.

Matsson H, Huss M, Persson H, ..., Peyrard-Janvid M, Kere J

J. Hum. Genet. 60 (7) 399-401 [2015-07-00; online 2015-04-17]

Mutation Analysis Facility (MAF) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Meta-analysis of Genome-wide Association Studies for Neuroticism, and the Polygenic Association With Major Depressive Disorder.

Genetics of Personality Consortium , de Moor MH, van den Berg SM, ..., Martin NG, Boomsma DI

JAMA Psychiatry 72 (7) 642-650 [2015-07-00; online 2015-05-21]

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

Identifying glycoside hydrolase family 18 genes in the mycoparasitic fungal species Clonostachys rosea.

Tzelepis G, Dubey M, Jensen DF, Karlsson M

Microbiology (Reading, Engl.) 161 (7) 1407-1419 [2015-07-00; online 2015-04-18]

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

HHEX_23 AA Genotype Exacerbates Effect of Diabetes on Dementia and Alzheimer Disease: A Population-Based Longitudinal Study.

Xu WL, Pedersen NL, Keller L, ..., Bäckman L, Fratiglioni L

PLoS Med. 12 (7) e1001853 [2015-07-00; online 2015-07-14]

Global Multilocus Sequence Type Analysis of Chlamydia trachomatis Strains from 16 Countries.

Herrmann B, Isaksson J, Ryberg M, ..., Gravningen K, Bruisten S

J. Clin. Microbiol. 53 (7) 2172-2179 [2015-07-00; online 2015-05-01]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Genome-wide association study of plasma levels of polychlorinated biphenyls disclose an association with the CYP2B6 gene in a population-based sample.

Ng E, Salihovic S, Lind PM, ..., Morris AP, Lind L

Environ. Res. 140 (-) 95-101 [2015-07-00; online 2015-04-04]

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

Genome-wide association study identifies new susceptibility loci for cutaneous lupus erythematosus.

Kunz M, König IR, Schillert A, ..., Kuhn A, Ibrahim SM

Exp. Dermatol. 24 (7) 510-515 [2015-07-00; online 2015-04-02]

Function of Isolated Pancreatic Islets From Patients at Onset of Type 1 Diabetes: Insulin Secretion Can Be Restored After Some Days in a Nondiabetogenic Environment In Vitro: Results From the DiViD Study.

Krogvold L, Skog O, Sundström G, ..., Korsgren O, Dahl-Jørgensen K

Diabetes 64 (7) 2506-2512 [2015-07-00; online 2015-02-14]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Epigenetic activation of a cryptic TBC1D16 transcript enhances melanoma progression by targeting EGFR.

Vizoso M, Ferreira HJ, Lopez-Serra P, ..., Marais R, Esteller M

Nat. Med. 21 (7) 741-750 [2015-07-00; online 2015-06-01]

Elevated Plasma Levels of MMP-12 Are Associated With Atherosclerotic Burden and Symptomatic Cardiovascular Disease in Subjects With Type 2 Diabetes.

Goncalves I, Bengtsson E, Colhoun HM, ..., Nilsson J, SUMMIT Consortium

Arterioscler. Thromb. Vasc. Biol. 35 (7) 1723-1731 [2015-07-00; online 2015-05-07]

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

Discovery and Fine-Mapping of Glycaemic and Obesity-Related Trait Loci Using High-Density Imputation.

Horikoshi M, Mӓgi R, van de Bunt M, ..., Morris AP, ENGAGE Consortium

PLoS Genet. 11 (7) e1005230 [2015-07-00; online 2015-07-01]

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

Detection of leukemia-associated mutations in peripheral blood DNA of hematologically normal elderly individuals.

Score J, Chase A, Forsberg LA, ..., Gale RE, Cross NC

Leukemia 29 (7) 1600-1602 [2015-07-00; online 2015-01-30]

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

CTCF/cohesin-binding sites are frequently mutated in cancer.

Katainen R, Dave K, Pitkänen E, ..., Taipale J, Aaltonen LA

Nat. Genet. 47 (7) 818-821 [2015-07-00; online 2015-06-09]

Karolinska High Throughput Center (KHTC)

Structural Basis for the Specificity of Human NUDT16 and Its Regulation by Inosine Monophosphate

Trésaugues L, Lundbäck T, Welin M, ..., Gräslund S, Nordlund P

PLoS ONE 10 (6) e0131507 [2015-06-29; online 2015-06-29]

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

High BRAF Mutation Frequency and Marked Survival Differences in Subgroups According to KRAS/BRAF Mutation Status and Tumor Tissue Availability in a Prospective Population-Based Metastatic Colorectal Cancer Cohort.

Sorbye H, Dragomir A, Sundström M, ..., Qvortrup C, Glimelius B

PLoS ONE 10 (6) e0131046 [2015-06-29; online 2015-06-29]

The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling.

Lindskog C, Linné J, Fagerberg L, ..., Pontén F, Uhlén M

BMC Genomics 16 (-) 475 [2015-06-25; online 2015-06-25]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Tissue Profiling [Collaborative]

Ebf1 heterozygosity results in increased DNA damage in pro-B cells and their synergistic transformation by Pax5 haploinsufficiency.

Prasad MA, Ungerbäck J, Åhsberg J, ..., Hagman J, Sigvardsson M

Blood 125 (26) 4052-4059 [2015-06-25; online 2015-04-02]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Structure of the nuclease subunit of human mitochondrial RNase P.

Reinhard L, Sridhara S, Hällberg BM

Nucleic Acids Res. 43 (11) 5664-5672 [2015-06-23; online 2015-05-09]

The Plasmodiophora brassicae genome reveals insights in its life cycle and ancestry of chitin synthases.

Schwelm A, Fogelqvist J, Knaust A, ..., Ludwig-Müller J, Dixelius C

Sci Rep 5 (-) 11153 [2015-06-18; online 2015-06-18]

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

Dynamics of Cell Generation and Turnover in the Human Heart.

Bergmann O, Zdunek S, Felker A, ..., Druid H, Frisén J

Cell 161 (7) 1566-1575 [2015-06-18; online 2015-06-16]

Integrated Microscopy Technologies Stockholm [Service]

Confrontation of fibroblasts with cancer cells in vitro: gene network analysis of transcriptome changes and differential capacity to inhibit tumor growth.

Alexeyenko A, Alkasalias T, Pavlova T, ..., Guven H, Klein G

J. Exp. Clin. Cancer Res. 34 (-) 62 [2015-06-18; online 2015-06-18]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Transglutaminase 4 as a prostate autoantigen in male subfertility

Landegren N, Sharon D, Shum AK, ..., Snyder M, Kämpe O

Sci. Transl. Med. 7 (292) 292ra101 [2015-06-17; online 2015-06-17]

Affinity Proteomics Uppsala [Service] Autoimmunity and Serology Profiling [Service] Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training PLA and Single Cell Proteomics

Elevated Serum GAD65 and GAD65-GADA Immune Complexes in Stiff Person Syndrome.

Gu Urban GJ, Friedman M, Ren P, ..., Landegren U, Kamali-Moghaddam M

Sci Rep 5 (1) 11196 [2015-06-16; online 2015-06-16]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Characterization of Three Mycobacterium spp. with Potential Use in Bioremediation by Genome Sequencing and Comparative Genomics.

Das S, Pettersson BM, Behra PR, ..., Bhattacharya A, Kirsebom LA

Genome Biol Evol 7 (7) 1871-1886 [2015-06-16; online 2015-06-16]

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

Whiteboard: a framework for the programmatic visualization of complex biological analyses.

Sundström G, Zamani N, Grabherr MG, Mauceli E

Bioinformatics 31 (12) 2054-2055 [2015-06-15; online 2015-02-11]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

IFN-α production by plasmacytoid dendritic cell associations with polymorphisms in gene loci related to autoimmune and inflammatory diseases.

Berggren O, Alexsson A, Morris DL, ..., Rönnblom L, Eloranta ML

Hum. Mol. Genet. 24 (12) 3571-3581 [2015-06-15; online 2015-03-18]

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

Defining the Human Brain Proteome Using Transcriptomics and Antibody-Based Profiling with a Focus on the Cerebral Cortex.

Sjöstedt E, Fagerberg L, Hallström BM, ..., Uhlén M, Mulder J

PLoS ONE 10 (6) e0130028 [2015-06-15; online 2015-06-15]

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

Contribution of common non-synonymous variants in PCSK1 to body mass index variation and risk of obesity: a systematic review and meta-analysis with evidence from up to 331 175 individuals.

Nead KT, Li A, Wehner MR, ..., Anand SS, Meyre D

Hum. Mol. Genet. 24 (12) 3582-3594 [2015-06-15; online 2015-03-17]

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

Proximity-dependent initiation of hybridization chain reaction.

Koos B, Cane G, Grannas K, ..., Kamali-Moghaddam M, Söderberg O

Nat Commun 6 (-) 7294 [2015-06-12; online 2015-06-12]

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

Phasing of single DNA molecules by massively parallel barcoding.

Borgström E, Redin D, Lundin S, ..., Andersson AF, Ahmadian A

Nat Commun 6 (-) 7173 [2015-06-09; online 2015-06-09]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Functional Identification of Target by Expression Proteomics (FITExP) reveals protein targets and highlights mechanisms of action of small molecule drugs.

Chernobrovkin A, Marin-Vicente C, Visa N, Zubarev RA

Sci Rep 5 (-) 11176 [2015-06-08; online 2015-06-08]

Advanced Mass Spectrometry Proteomics Chemical Proteomics [Technology development]

Evolutionary analysis of the female-specific avian W chromosome.

Smeds L, Warmuth V, Bolivar P, ..., Török J, Ellegren H

Nat Commun 6 (-) 7330 [2015-06-04; online 2015-06-04]

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

A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data.

Siretskiy A, Sundqvist T, Voznesenskiy M, Spjuth O

Gigascience 4 (-) 26 [2015-06-04; online 2015-06-04]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Processing of protein ADP-ribosylation by Nudix hydrolases.

Palazzo L, Thomas B, Jemth AS, ..., Helleday T, Ahel I

Biochem. J. 468 (2) 293-301 [2015-06-01; online 2015-03-20]

Protein Science Facility (PSF) [Service]

Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia.

Mansouri L, Sutton LA, Ljungström V, ..., Nilsson M, Rosenquist R

J. Exp. Med. 212 (6) 833-843 [2015-06-01; online 2015-05-18]

Array and Analysis Facility NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure

Ancient wolf genome reveals an early divergence of domestic dog ancestors and admixture into high-latitude breeds.

Skoglund P, Ersmark E, Palkopoulou E, Dalén L

Curr. Biol. 25 (11) 1515-1519 [2015-06-01; online 2015-05-26]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Zebrafish: A possible tool to evaluate bioactive ions.

Montazerolghaem M, Nyström L, Engqvist H, Karlsson Ott M

Acta Biomater 19 (-) 10-14 [2015-06-00; online 2015-03-17]

Genome Engineering Zebrafish

PubMed

Whole-genome Linkage Analysis and Sequence Analysis of Candidate Loci in Familial Breast Cancer.

Marikkannu R, Aravidis C, Rantala J, ..., Nilsson D, Lindblom A

Anticancer Res. 35 (6) 3155-3165 [2015-06-00; online 2015-05-31]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Tumor vessel up-regulation of INSR revealed by single-cell expression analysis of the tyrosine kinome and phosphatome in human cancers.

Kiflemariam S, Ljungström V, Pontén F, Sjöblom T

Am. J. Pathol. 185 (6) 1600-1609 [2015-06-00; online 2015-04-10]

Three-Dimensional Cell Culture-Based Screening Identifies the Anthelmintic Drug Nitazoxanide as a Candidate for Treatment of Colorectal Cancer.

Senkowski W, Zhang X, Olofsson MH, ..., Larsson R, Fryknäs M

Mol Cancer Ther 14 (6) 1504-1516 [2015-06-00; online 2015-04-24]

Drug Discovery and Development (DDD) [Service]

The potential clinical impact of the tissue-based map of the human proteome.

Lindskog C

Expert Rev Proteomics 12 (3) 213-215 [2015-06-00; online 2015-04-30]

Tissue Profiling [Technology development]

The impact of low-frequency and rare variants on lipid levels.

Surakka I, Horikoshi M, Mägi R, ..., Ripatti S, ENGAGE Consortium

Nat. Genet. 47 (6) 589-597 [2015-06-00; online 2015-05-12]

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

Single locus sex determination and female heterogamety in the basket willow (Salix viminalis L.).

Pucholt P, Rönnberg-Wästljung AC, Berlin S

Heredity (Edinb) 114 (6) 575-583 [2015-06-00; online 2015-02-04]

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

Non-reciprocal Interspecies Hybridization Barriers in the Capsella Genus Are Established in the Endosperm.

Rebernig CA, Lafon-Placette C, Hatorangan MR, Slotte T, Köhler C

PLoS Genet. 11 (6) e1005295 [2015-06-00; online 2015-06-18]

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

NLRC4 Inflammasome Is an Important Regulator of Interleukin-18 Levels in Patients With Acute Coronary Syndromes: Genome-Wide Association Study in the PLATelet inhibition and patient Outcomes Trial (PLATO).

Johansson Å, Eriksson N, Becker RC, ..., Siegbahn A, PLATO Investigators

Circ Cardiovasc Genet 8 (3) 498-506 [2015-06-00; online 2015-03-10]

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

Multiple Changes of Gene Expression and Function Reveal Genomic and Phenotypic Complexity in SLE-like Disease.

Wilbe M, Kozyrev SV, Farias FH, ..., Hansson-Hamlin H, Lindblad-Toh K

PLoS Genet. 11 (6) e1005248 [2015-06-00; online 2015-06-09]

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

Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring.

Ininbergs K, Bergman B, Larsson J, Ekman M

Ambio 44 Suppl 3 (-) 439-450 [2015-06-00; online 2015-05-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Loss of ASRGL1 expression is an independent biomarker for disease-specific survival in endometrioid endometrial carcinoma.

Edqvist PH, Huvila J, Forsström B, ..., Pontén F, Auranen A

Gynecol. Oncol. 137 (3) 529-537 [2015-06-00; online 2015-04-07]

Human adaptation to arsenic-rich environments.

Schlebusch CM, Gattepaille LM, Engström K, ..., Jakobsson M, Broberg K

Mol. Biol. Evol. 32 (6) 1544-1555 [2015-06-00; online 2015-03-03]

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

High-throughput mutational screening adds clinically important information in myelodysplastic syndromes and secondary or therapy-related acute myeloid leukemia.

Karimi M, Nilsson C, Dimitriou M, ..., Kere J, Hellström-Lindberg E

Haematologica 100 (6) e223-e225 [2015-06-00; online 2015-03-15]

Mutation Analysis Facility (MAF) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Hemophagocytic lymphohistiocytosis in 2 patients with underlying IFN-γ receptor deficiency

Tesi B, Sieni E, Neves C, ..., Azzari C, Bryceson YT

Journal of Allergy and Clinical Immunology 135 (6) 1638-1641.e5 [2015-06-00; online 2015-06-00]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Exome sequencing of contralateral breast cancer identifies metastatic disease.

Klevebring D, Lindberg J, Rockberg J, ..., Sandberg M, Czene K

Breast Cancer Res. Treat. 151 (2) 319-324 [2015-06-00; online 2015-04-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Exome Sequencing and CNV Analysis on Chromosome 18 in Small Intestinal Neuroendocrine Tumors: Ruling Out a Suspect?

Delgado Verdugo A, Crona J, Maharjan R, ..., Westin G, Björklund P

Horm. Metab. Res. 47 (6) 452-455 [2015-06-00; online 2014-10-30]

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

Effect of host plant and immune challenge on the levels of chemosensory and odorant-binding proteins in caterpillar salivary glands.

Celorio-Mancera Mde L, Ytterberg AJ, Rutishauser D, Janz N, Zubarev RA

Insect Biochem. Mol. Biol. 61 (-) 34-45 [2015-06-00; online 2015-04-29]

Differential Gene Regulation in Fibroblasts in Co-culture with Keratinocytes and Head and Neck SCC Cells.

PubMed

Hakelius M, Saiepour D, Göransson H, ..., Gerdin B, Nowinski D

Anticancer Res. 35 (6) 3253-3265 [2015-06-00; online 2015-05-31]

Consequences of increased terrestrial dissolved organic matter and temperature on bacterioplankton community composition during a Baltic Sea mesocosm experiment.

Lindh MV, Lefébure R, Degerman R, ..., Andersson A, Pinhassi J

Ambio 44 Suppl 3 (-) 402-412 [2015-06-00; online 2015-05-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

CETSA: a target engagement assay with potential to transform drug discovery

Jensen AJ, Molina DM, Lundbäck T

Future Medicinal Chemistry 7 (8) 975-978 [2015-06-00; online 2015-06-00]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A nucleosome turnover map reveals that the stability of histone H4 Lys20 methylation depends on histone recycling in transcribed chromatin.

Svensson JP, Shukla M, Menendez-Benito V, ..., Allshire RC, Ekwall K

Genome Res. 25 (6) 872-883 [2015-06-00; online 2015-03-18]

Circulating microRNA expression pattern separates patients with anti-neutrophil cytoplasmic antibody associated vasculitis from healthy controls.

PubMed

Skoglund C, Carlsen AL, Weiner M, ..., Heegaard NH, Segelmark M

Clin. Exp. Rheumatol. 33 (2 Suppl 89) S-64-71 [2015-05-26; online 2015-05-26]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Phylogeny, evolution and classification of gall wasps: the plot thickens.

Ronquist F, Nieves-Aldrey JL, Buffington ML, ..., Liljeblad J, Nylander JA

PLoS ONE 10 (5) e0123301 [2015-05-20; online 2015-05-20]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth.

Palkopoulou E, Mallick S, Skoglund P, ..., Reich D, Dalén L

Curr. Biol. 25 (10) 1395-1400 [2015-05-18; online 2015-04-23]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

CGGBP1 mitigates cytosine methylation at repetitive DNA sequences.

Agarwal P, Collier P, Fritz MH, ..., Westermark B, Singh U

BMC Genomics 16 (-) 390 [2015-05-16; online 2015-05-16]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Phylogeographical pattern of Francisella tularensis in a nationwide outbreak of tularaemia in Norway, 2011.

Afset JE, Larssen KW, Bergh K, ..., Johansson A, Forsman M

Euro Surveill. 20 (19) 9-14 [2015-05-14; online 2015-05-14]

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

Complex archaea that bridge the gap between prokaryotes and eukaryotes.

Spang A, Saw JH, Jørgensen SL, ..., Guy L, Ettema TJ

Nature 521 (7551) 173-179 [2015-05-14; online 2015-05-07]

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

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.

Rivas MA, Pirinen M, Conrad DF, ..., Lappalainen T, MacArthur DG

Science 348 (6235) 666-669 [2015-05-08; online 2015-05-09]

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

Complement inhibitor CD55 governs the integrity of membrane rafts in pancreatic beta cells, but plays no role in insulin secretion.

Nagaraj V, King B, Storm P, ..., Blom AM, Renström E

Biochem. Biophys. Res. Commun. 460 (3) 518-524 [2015-05-08; online 2015-03-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait.

Husby A, Kawakami T, Rönnegård L, ..., Ellegren H, Qvarnström A

Proc. Biol. Sci. 282 (1806) 20150156 [2015-05-07; online 2015-04-04]

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

Intestinal dysbiosis in children with short bowel syndrome is associated with impaired outcome.

Engstrand Lilja H, Wefer H, Nyström N, Finkel Y, Engstrand L

Microbiome 3 (-) 18 [2015-05-04; online 2015-05-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Tracking the origin of metastatic prostate cancer.

Lindberg J, Kristiansen A, Wiklund P, Grönberg H, Egevad L

Eur. Urol. 67 (5) 819-822 [2015-05-00; online 2014-09-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The role of genetic factors for hearing deterioration across 20 years: a twin study.

Bogo R, Farah A, Johnson AC, ..., Svartengren M, Skjönsberg Å

J. Gerontol. A Biol. Sci. Med. Sci. 70 (5) 647-653 [2015-05-00; online 2015-02-11]

Plant-mediated gene silencing restricts growth of the potato late blight pathogen Phytophthora infestans.

Jahan SN, Åsman AK, Corcoran P, ..., Vetukuri RR, Dixelius C

J. Exp. Bot. 66 (9) 2785-2794 [2015-05-00; online 2015-03-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

NOTA: a potent metallo-β-lactamase inhibitor.

Somboro AM, Tiwari D, Bester LA, ..., Naicker T, Essack SY

J. Antimicrob. Chemother. 70 (5) 1594-1596 [2015-05-00; online 2015-01-06]

Drug Discovery and Development (DDD) [Collaborative]

Mixed ancestry and admixture in Kauai's feral chickens: invasion of domestic genes into ancient Red Junglefowl reservoirs.

Gering E, Johnsson M, Willis P, Getty T, Wright D

Mol. Ecol. 24 (9) 2112-2124 [2015-05-00; online 2015-02-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Genome-wide meta-analysis identifies six novel loci associated with habitual coffee consumption.

Coffee and Caffeine Genetics Consortium , Cornelis MC, Byrne EM, ..., van Dam RM, Chasman DI

Mol. Psychiatry 20 (5) 647-656 [2015-05-00; online 2014-10-08]

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

Genetic regulation of bone metabolism in the chicken: similarities and differences to Mammalian systems.

Johnsson M, Jonsson KB, Andersson L, Jensen P, Wright D

PLoS Genet. 11 (5) e1005250 [2015-05-00; online 2015-05-29]

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

Dietary fat quality impacts genome-wide DNA methylation patterns in a cross-sectional study of Greek preadolescents.

Voisin S, Almén MS, Moschonis G, ..., Manios Y, Schiöth HB

Eur. J. Hum. Genet. 23 (5) 654-662 [2015-05-00; online 2014-07-31]

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

PubMed

Diagnostic urinary proteome profile for immunoglobulin a nephropathy.

Samavat S, Kalantari S, Nafar M, ..., Parvin M, Zubarev RA

Iran J Kidney Dis 9 (3) 239-248 [2015-05-00; online 2015-05-10]

Cu(OAc)2-Catalysed Oxidative Dual C-H/N-H Activation of Terminal Alkynes andN-Deprotected Sulfonimidamides: An Easy Access toN-Alkynylated Sulfonimidamides

Nandi GC, Kota SR, Naicker T, ..., Kruger HG, Arvidsson PI

Eur. J. Org. Chem. 2015 (13) 2861-2867 [2015-05-00; online 2015-03-17]

Drug Discovery and Development (DDD) [Technology development]

Cooperative genetic changes in pediatric B-cell precursor acute lymphoblastic leukemia with deletions or mutations of IKZF1.

Olsson L, Albitar F, Castor A, ..., Paulsson K, Johansson B

Genes Chromosomes Cancer 54 (5) 315-325 [2015-05-00; online 2015-03-03]

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

Autosomal recessive mutations in the COL2A1 gene cause severe spondyloepiphyseal dysplasia.

Tham E, Nishimura G, Geiberger S, ..., Nordenskjöld M, Grigelioniene G

Clin. Genet. 87 (5) 496-498 [2015-05-00; online 2014-07-26]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Age- and sex-specific causal effects of adiposity on cardiovascular risk factors.

Fall T, Hägg S, Ploner A, ..., Ingelsson E, ENGAGE Consortium

Diabetes 64 (5) 1841-1852 [2015-05-00; online 2015-02-26]

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

Nanoparticle-stabilized microbubbles for multimodal imaging and drug delivery.

Mørch Ý, Hansen R, Berg S, ..., de Lange Davies C, Stenstad PM

Contrast Media Mol Imaging 10 (5) 356-366 [2015-04-30; online 2015-04-30]

Integrated Microscopy Technologies Stockholm [Collaborative]

Deep sequencing and SNP array analyses of pediatric T-cell acute lymphoblastic leukemia reveal NOTCH1 mutations in minor subclones and a high incidence of uniparental isodisomies affecting CDKN2A.

Karrman K, Castor A, Behrendtz M, ..., Paulsson K, Johansson B

J Hematol Oncol 8 (-) 42 [2015-04-24; online 2015-04-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Genetically determined height and coronary artery disease.

Nelson CP, Hamby SE, Saleheen D, ..., Samani NJ, CARDIoGRAM+C4D Consortium

N. Engl. J. Med. 372 (17) 1608-1618 [2015-04-23; online 2015-04-09]

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

Circulating carnosine dipeptidase 1 associates with weight loss and poor prognosis in gastrointestinal cancer.

Arner P, Henjes F, Schwenk JM, ..., Nilsson P, Rydén M

PLoS ONE 10 (4) e0123566 [2015-04-21; online 2015-04-21]

Affinity Proteomics Stockholm

Polymorphisms in chloroquine resistance-associated genes in Plasmodium vivax in Ethiopia.

Golassa L, Erko B, Baliraine FN, Aseffa A, Swedberg G

Malar. J. 14 (-) 164 [2015-04-16; online 2015-04-16]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Combination effects of AHR agonists and Wnt/β-catenin modulators in zebrafish embryos: Implications for physiological and toxicological AHR functions.

Wincent E, Stegeman JJ, Jönsson ME

Toxicol. Appl. Pharmacol. 284 (2) 163-179 [2015-04-15; online 2015-02-21]

Genome Engineering Zebrafish [Service]

AP-1-mediated chromatin looping regulates ZEB2 transcription: new insights into TNFα-induced epithelial-mesenchymal transition in triple-negative breast cancer.

Qiao Y, Shiue CN, Zhu J, ..., Zhao C, Dahlman-Wright K

Oncotarget 6 (10) 7804-7814 [2015-04-10; online 2015-03-13]

Common genetic variants influence human subcortical brain structures.

Hibar DP, Stein JL, Renteria ME, ..., Thompson PM, Medland SE

Nature 520 (7546) 224-229 [2015-04-09; online 2015-01-22]

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

Inter-relationships between the metrics of instrumental meat color and microbial growth during aerobic storage of beef at 4°C

Li S, Zamaratskaia G, Roos S, ..., Borch E, Johansson M

Acta Agriculturae Scandinavica, Section A - Animal Science 65 (2) 97-106 [2015-04-03; online 2015-09-00]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities.

Lindh MV, Figueroa D, Sjöstedt J, ..., Legrand C, Pinhassi J

Front Microbiol 6 (-) 223 [2015-04-01; online 2015-04-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A prognosis based classification of undifferentiated uterine sarcomas: identification of mitotic index, hormone receptors and YWHAE-FAM22 translocation status as predictors of survival.

Gremel G, Liew M, Hamzei F, ..., Pontén F, Carlson JW

Int. J. Cancer 136 (7) 1608-1618 [2015-04-01; online 2014-08-19]

Tissue Profiling

Using genetics to test the causal relationship of total adiposity and periodontitis: Mendelian randomization analyses in the Gene-Lifestyle Interactions and Dental Endpoints (GLIDE) Consortium.

Shungin D, Cornelis MC, Divaris K, ..., Johansson I, Franks PW

Int J Epidemiol 44 (2) 638-650 [2015-04-00; online 2015-06-06]

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

Oseltamivir-resistant influenza A (H1N1) virus strain with an H274Y mutation in neuraminidase persists without drug pressure in infected mallards.

Gillman A, Muradrasoli S, Söderström H, ..., Olsen B, Järhult JD

Appl. Environ. Microbiol. 81 (7) 2378-2383 [2015-04-00; online 2015-01-27]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Mixture effects of levonorgestrel and ethinylestradiol: estrogenic biomarkers and hormone receptor mRNA expression during sexual programming.

Säfholm M, Jansson E, Fick J, Berg C

Aquat. Toxicol. 161 (-) 146-153 [2015-04-00; online 2015-02-24]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Is the adiposity-associated FTO gene variant related to all-cause mortality independent of adiposity? Meta-analysis of data from 169,551 Caucasian adults.

Zimmermann E, Ängquist LH, Mirza SS, ..., Sonestedt E, Sørensen TIA

Obes Rev 16 (4) 327-340 [2015-04-00; online 2015-03-05]

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

Is label-free LC-MS/MS ready for biomarker discovery?

Sandin M, Chawade A, Levander F

Proteomics Clin Appl 9 (3-4) 289-294 [2015-04-00; online 2015-02-07]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Immunohistochemistry-based prognostic biomarkers in NSCLC: novel findings on the road to clinical use?

Lindskog C, Edlund K, Mattsson JS, Micke P

Expert Rev. Mol. Diagn. 15 (4) 471-490 [2015-04-00; online 2015-01-19]

Identification and validation of N-acetyltransferase 2 as an insulin sensitivity gene.

Knowles JW, Xie W, Zhang Z, ..., Walker M, Quertermous T

J. Clin. Invest. 125 (4) 1739-1751 [2015-04-00; online 2015-03-23]

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

GWAS-identified loci for coronary heart disease are associated with intima-media thickness and plaque presence at the carotid artery bulb.

den Hoed M, Strawbridge RJ, Almgren P, ..., Melander O, Lind L

Atherosclerosis 239 (2) 304-310 [2015-04-00; online 2015-02-16]

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

Functional anti-CD94/NKG2A and anti-CD94/NKG2C autoantibodies in patients with systemic lupus erythematosus.

Hagberg N, Theorell J, Hjorton K, ..., Bryceson YT, Rönnblom L

Arthritis & rheumatology (Hoboken, N.J.) 67 (4) 1000-1011 [2015-04-00; online 2014-12-17]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Fluctuating expression of microRNAs in adenovirus infected cells.

Zhao H, Chen M, Tellgren-Roth C, Pettersson U

Virology 478 (-) 99-111 [2015-04-00; online 2015-03-07]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Duffy antigen receptor genetic variant and the association with Interleukin 8 levels.

Moreno Velásquez I, Kumar J, Björkbacka H, ..., de Faire U, Gigante B

Cytokine 72 (2) 178-184 [2015-04-00; online 2015-01-31]

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

Birth weight as an independent predictor of ADHD symptoms: a within-twin pair analysis.

Pettersson E, Sjölander A, Almqvist C, ..., Lichtenstein P, Larsson H

J Child Psychol Psychiatry 56 (4) 453-459 [2015-04-00; online 2014-07-22]

Adiposity as a cause of cardiovascular disease: a Mendelian randomization study.

Hägg S, Fall T, Ploner A, ..., Ingelsson E, European Network for Genetic and Genomic Epidemiology Consortium

Int J Epidemiol 44 (2) 578-586 [2015-04-00; online 2015-05-27]

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

Methylation levels of SLC23A2 and NCOR2 genes correlate with spinal muscular atrophy severity.

Zheleznyakova GY, Nilsson EK, Kiselev AV, ..., Baranov VS, Schiöth HB

PLoS ONE 10 (3) e0121964 [2015-03-30; online 2015-03-30]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Site-specific programming of the host epithelial transcriptome by the gut microbiota.

Sommer F, Nookaew I, Sommer N, Fogelstrand P, Bäckhed F

Genome Biol. 16 (-) 62 [2015-03-28; online 2015-03-28]

Array and Analysis Facility Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Modulation of genetic associations with serum urate levels by body-mass-index in humans.

Huffman JE, Albrecht E, Teumer A, ..., Köttgen A, Vitart V

PLoS ONE 10 (3) e0119752 [2015-03-26; online 2015-03-26]

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

Age-associated DNA methylation changes in immune genes, histone modifiers and chromatin remodeling factors within 5 years after birth in human blood leukocytes.

Acevedo N, Reinius LE, Vitezic M, ..., Greco D, Kere J

Clin Epigenetics 7 (-) 34 [2015-03-26; online 2015-03-26]

Discovery of molecular markers to discriminate corneal endothelial cells in the human body.

Yoshihara M, Ohmiya H, Hara S, ..., Tsujikawa M, Nishida K

PLoS ONE 10 (3) e0117581 [2015-03-25; online 2015-03-25]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Crystal structures of the kinase domain of the sulfate-activating complex in Mycobacterium tuberculosis.

Poyraz Ö, Brunner K, Lohkamp B, ..., Schnell R, Schneider G

PLoS ONE 10 (3) e0121494 [2015-03-25; online 2015-03-25]

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

Low elastin content of carotid plaques is associated with increased risk of ipsilateral stroke.

Asciutto G, Dias NV, Edsfeldt A, ..., Nilsson J, Gonçalves I

PLoS ONE 10 (3) e0121086 [2015-03-24; online 2015-03-24]

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

Complete genome sequence of Borrelia afzelii K78 and comparative genome analysis.

Schüler W, Bunikis I, Weber-Lehman J, ..., Bergström S, Lundberg U

PLoS ONE 10 (3) e0120548 [2015-03-23; online 2015-03-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Structural basis for lack of ADP-ribosyltransferase activity in poly(ADP-ribose) polymerase-13/zinc finger antiviral protein.

Karlberg T, Klepsch M, Thorsell AG, ..., Linusson A, Schüler H

J. Biol. Chem. 290 (12) 7336-7344 [2015-03-20; online 2015-01-31]

Complete Genome Sequence of Francisella guangzhouensis Strain 08HL01032T, Isolated from Air-Conditioning Systems in China.

Svensson D, Öhrman C, Bäckman S, ..., Forsman M, Sjödin A

Genome Announc 3 (2) - [2015-03-19; online 2015-03-19]

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

Comparative proteomic analysis of hyphae and germinating cysts of Phytophthora pisi and Phytophthora sojae.

Hosseini S, Resjö S, Liu Y, ..., Andreasson E, Karlsson M

J Proteomics 117 (-) 24-40 [2015-03-18; online 2015-01-24]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis.

Vigil-Stenman T, Larsson J, Nylander JA, Bergman B

BMC Genomics 16 (-) 193 [2015-03-17; online 2015-03-17]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Conservation of transcription factor binding specificities across 600 million years of bilateria evolution.

Nitta KR, Jolma A, Yin Y, ..., Furlong EE, Taipale J

Elife 4 (-) - [2015-03-17; online 2015-03-17]

Karolinska High Throughput Center (KHTC)

Analysis of the role of interleukin 6 receptor haplotypes in the regulation of circulating levels of inflammatory biomarkers and risk of coronary heart disease.

Gigante B, Strawbridge RJ, Velasquez IM, ..., Humphries SE, de Faire U

PLoS ONE 10 (3) e0119980 [2015-03-17; online 2015-03-17]

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

SLC10A4 is a vesicular amine-associated transporter modulating dopamine homeostasis.

Larhammar M, Patra K, Blunder M, ..., Wallén-Mackenzie Å, Kullander K

Biol. Psychiatry 77 (6) 526-536 [2015-03-15; online 2014-09-02]

Integrated Microscopy Technologies Stockholm [Collaborative]

Microsatellite instability and mutations in BRAF and KRAS are significant predictors of disseminated disease in colon cancer.

Birgisson H, Edlund K, Wallin U, ..., Glimelius B, Sundström M

BMC Cancer 15 (-) 125 [2015-03-14; online 2015-03-14]

Variations of gastric corpus microbiota are associated with early esophageal squamous cell carcinoma and squamous dysplasia.

Nasrollahzadeh D, Malekzadeh R, Ploner A, ..., Dawsey SM, Ye W

Sci Rep 5 (-) 8820 [2015-03-06; online 2015-03-06]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris.

Douglas GM, Gos G, Steige KA, ..., Slotte T, Wright SI

Proc. Natl. Acad. Sci. U.S.A. 112 (9) 2806-2811 [2015-03-03; online 2015-02-19]

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

Proteomic profiling reveals autoimmune targets in sarcoidosis.

Häggmark A, Hamsten C, Wiklundh E, ..., Grunewald J, Nilsson P

Am. J. Respir. Crit. Care Med. 191 (5) 574-583 [2015-03-01; online 2015-01-22]

Autoimmunity and Serology Profiling [Collaborative] Tissue Profiling [Collaborative]

The H1-receptor antagonist cetirizine ameliorates high-fat diet-induced glucose intolerance in male C57BL/6 mice, but not diabetes outcome in female non-obese diabetic (NOD) mice.

Anvari E, Wang X, Sandler S, Welsh N

Ups. J. Med. Sci. 120 (1) 40-46 [2015-03-00; online 2014-10-08]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The Fun30 chromatin remodeler Fft3 controls nuclear organization and chromatin structure of insulators and subtelomeres in fission yeast.

Steglich B, Strålfors A, Khorosjutina O, ..., Javerzat JP, Ekwall K

PLoS Genet. 11 (3) e1005101 [2015-03-00; online 2015-03-23]

Bioinformatics and Expression Analysis (BEA) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Targeted next-generation sequencing in chronic lymphocytic leukemia: a high-throughput yet tailored approach will facilitate implementation in a clinical setting.

Sutton LA, Ljungström V, Mansouri L, ..., Stamatopoulos K, Rosenquist R

Haematologica 100 (3) 370-376 [2015-03-00; online 2014-12-07]

Clinical Genomics Clinical Genomics Uppsala

Structural characterization of substrate and inhibitor binding to farnesyl pyrophosphate synthase from Pseudomonas aeruginosa.

Schmidberger JW, Schnell R, Schneider G

Acta Crystallogr. D Biol. Crystallogr. 71 (Pt 3) 721-731 [2015-03-00; online 2015-02-26]

Preclinical characterization of acyl sulfonimidamides: potential carboxylic acid bioisosteres with tunable properties.

Borhade SR, Svensson R, Brandt P, ..., Arvidsson PI, Sandström A

ChemMedChem 10 (3) 455-460 [2015-03-00; online 2015-01-30]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

MuSK: a new target for lethal fetal akinesia deformation sequence (FADS).

Wilbe M, Ekvall S, Eurenius K, ..., Annerén G, Bondeson ML

J. Med. Genet. 52 (3) 195-202 [2015-03-00; online 2015-01-22]

Clinical Genomics Clinical Genomics Uppsala NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

High-resolution crystal structure of a polyextreme GH43 glycosidase from Halothermothrix orenii with α-L-arabinofuranosidase activity.

Hassan N, Kori LD, Gandini R, ..., Divne C, Tan TC

Acta Crystallogr F Struct Biol Commun 71 (Pt 3) 338-345 [2015-03-00; online 2015-02-19]

High-density genotyping of immune loci in Koreans and Europeans identifies eight new rheumatoid arthritis risk loci.

Kim K, Bang SY, Lee HS, ..., Plenge RM, Bae SC

Ann. Rheum. Dis. 74 (3) e13 [2015-03-00; online 2014-02-14]

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

Genomewide association study of body weight traits in Baluchi sheep.

Gholizadeh M, Rahimi-Mianji G, Nejati-Javaremi A

J. Genet. 94 (1) 143-146 [2015-03-00; online 2015-04-08]

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

FGF2 as a potential prognostic biomarker for proneural glioma patients.

Sooman L, Freyhult E, Jaiswal A, ..., Bergqvist M, Ekman S

Acta Oncol 54 (3) 385-394 [2015-03-00; online 2014-09-30]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training Tissue Profiling

Evaluation of human papillomavirus DNA detection in samples obtained for routine Chlamydia trachomatis screening.

Söderlund-Strand A, Wikström A, Dillner J

J. Clin. Virol. 64 (-) 88-91 [2015-03-00; online 2015-01-13]

Effects of ecological engineered oxygenation on the bacterial community structure in an anoxic fjord in western Sweden.

Forth M, Liljebladh B, Stigebrandt A, Hall PO, Treusch AH

ISME J 9 (3) 656-669 [2015-03-00; online 2014-09-23]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Detection of cell aggregation and altered cell viability by automated label-free video microscopy: a promising alternative to endpoint viability assays in high-throughput screening.

Aftab O, Fryknäs M, Hammerling U, Larsson R, Gustafsson MG

J Biomol Screen 20 (3) 372-381 [2015-03-00; online 2014-12-17]

Drug Discovery and Development (DDD)

Amplification-free sequencing of cell-free DNA for prenatal non-invasive diagnosis of chromosomal aberrations.

Karlsson K, Sahlin E, Iwarsson E, ..., Nordenskjöld M, Linnarsson S

Genomics 105 (3) 150-158 [2015-03-00; online 2014-12-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

A genomic duplication is associated with ectopic eomesodermin expression in the embryonic chicken comb and two duplex-comb phenotypes.

Dorshorst B, Harun-Or-Rashid M, Bagherpoor AJ, ..., Hallböök F, Andersson L

PLoS Genet. 11 (3) e1004947 [2015-03-00; online 2015-03-19]

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

MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics.

Kushwaha SK, Manoharan L, Meerupati T, Hedlund K, Ahrén D

BMC Bioinformatics 16 (-) 65 [2015-02-28; online 2015-02-28]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Roux-en Y gastric bypass surgery induces genome-wide promoter-specific changes in DNA methylation in whole blood of obese patients.

Nilsson EK, Ernst B, Voisin S, ..., Schultes B, Schiöth HB

PLoS ONE 10 (2) e0115186 [2015-02-24; online 2015-02-24]

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

The roles of SNF2/SWI2 nucleosome remodeling enzymes in blood cell differentiation and leukemia.

Prasad P, Lennartsson A, Ekwall K

Biomed Res Int 2015 (-) 347571 [2015-02-19; online 2015-02-19]

Evolution of Darwin's finches and their beaks revealed by genome sequencing.

Lamichhaney S, Berglund J, Almén MS, ..., Webster MT, Andersson L

Nature 518 (7539) 371-375 [2015-02-19; online 2015-02-18]

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

DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia.

Nordlund J, Bäcklin CL, Zachariadis V, ..., Forestier E, Syvänen AC

Clin Epigenetics 7 (-) 11 [2015-02-17; online 2015-02-17]

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

New genetic loci link adipose and insulin biology to body fat distribution.

Shungin D, Winkler TW, Croteau-Chonka DC, ..., Lindgren CM, Mohlke KL

Nature 518 (7538) 187-196 [2015-02-12; online 2015-02-13]

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

Genetic studies of body mass index yield new insights for obesity biology.

Locke AE, Kahali B, Berndt SI, ..., Loos RJF, Speliotes EK

Nature 518 (7538) 197-206 [2015-02-12; online 2015-02-13]

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

Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing.

Cavelier L, Ameur A, Häggqvist S, ..., Olsson-Strömberg U, Hermanson M

BMC Cancer 15 (-) 45 [2015-02-12; online 2015-02-12]

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

Data processing has major impact on the outcome of quantitative label-free LC-MS analysis.

Chawade A, Sandin M, Teleman J, Malmström J, Levander F

J. Proteome Res. 14 (2) 676-687 [2015-02-06; online 2014-11-20]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Microbial community composition and diversity via 16S rRNA gene amplicons: evaluating the illumina platform.

Sinclair L, Osman OA, Bertilsson S, Eiler A

PLoS ONE 10 (2) e0116955 [2015-02-03; online 2015-02-03]

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

Risk of childhood asthma is associated with CpG-site polymorphisms, regional DNA methylation and mRNA levels at the GSDMB/ORMDL3 locus.

Acevedo N, Reinius LE, Greco D, ..., Kere J, Söderhäll C

Hum. Mol. Genet. 24 (3) 875-890 [2015-02-01; online 2014-09-27]

Bioinformatics and Expression Analysis (BEA) Mutation Analysis Facility (MAF)

Transcriptional responses of the bacterial antagonist Serratia plymuthica to the fungal phytopathogen Rhizoctonia solani.

Neupane S, Finlay RD, Alström S, Elfstrand M, Högberg N

Environ Microbiol Rep 7 (1) 123-127 [2015-02-00; online 2014-08-21]

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

The composition of the gut microbiota shapes the colon mucus barrier.

Jakobsson HE, Rodríguez-Piñeiro AM, Schütte A, ..., Hansson GC, Johansson ME

EMBO Rep. 16 (2) 164-177 [2015-02-00; online 2014-12-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

The GH receptor exon 3 deleted/full-length polymorphism is associated with central adiposity in the general population.

Glad CA, Carlsson LM, Melander O, ..., Svensson PA, Johannsson G

Eur. J. Endocrinol. 172 (2) 123-128 [2015-02-00; online 2014-11-14]

Proposal of Thorsellia kenyensis sp. nov. and Thorsellia kandunguensis sp. nov., isolated from larvae of Anopheles arabiensis, as members of the family Thorselliaceae fam. nov.

Kämpfer P, Glaeser SP, Nilsson LKJ, ..., Busse H, Terenius O

Int. J. Syst. Evol. Microbiol. 65 (Pt 2) 444-451 [2015-02-00; online 2014-11-12]

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

Predicting venous thrombosis in women using a combination of genetic markers and clinical risk factors.

Bruzelius M, Bottai M, Sabater-Lleal M, ..., Hamsten A, Odeberg J

J. Thromb. Haemost. 13 (2) 219-227 [2015-02-00; online 2014-12-05]

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

Novel high-throughput screening method for identification of fungal dimorphism blockers.

Stylianou M, Uvell H, Lopes JP, ..., Elofsson M, Urban CF

J Biomol Screen 20 (2) 285-291 [2015-02-00; online 2014-10-05]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Multi-omic data analysis using Galaxy.

Boekel J, Chilton JM, Cooke IR, ..., Moerland PD, Griffin TJ

Nat. Biotechnol. 33 (2) 137-139 [2015-02-00; online 2015-02-07]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training Clinical Proteomics Mass spectrometry

Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date.

Leong SL, Lantz H, Pettersson OV, ..., Tellgren-Roth C, Schnürer J

Environ. Microbiol. 17 (2) 496-513 [2015-02-00; online 2014-08-22]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling.

Edqvist PH, Fagerberg L, Hallström BM, ..., Uhlén M, Pontén F

J. Histochem. Cytochem. 63 (2) 129-141 [2015-02-00; online 2014-11-19]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling [Technology development]

Environmental and genetic factors in the development of anticitrullinated protein antibodies (ACPAs) and ACPA-positive rheumatoid arthritis: an epidemiological investigation in twins.

Hensvold AH, Magnusson PK, Joshua V, ..., Klareskog L, Catrina AI

Ann. Rheum. Dis. 74 (2) 375-380 [2015-02-00; online 2013-11-28]

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

CTNND2-a candidate gene for reading problems and mild intellectual disability.

Hofmeister W, Nilsson D, Topa A, ..., Syk Lundberg E, Lindstrand A

J. Med. Genet. 52 (2) 111-122 [2015-02-00; online 2014-12-05]

Clinical Genomics Clinical Genomics Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Biochemical and structural characterization of a thermostable β-glucosidase from Halothermothrix orenii for galacto-oligosaccharide synthesis.

Hassan N, Nguyen TH, Intanon M, ..., Divne C, Tan TC

Appl. Microbiol. Biotechnol. 99 (4) 1731-1744 [2015-02-00; online 2014-09-01]

Associations between the 17q21 region and allergic rhinitis in 5 birth cohorts.

Fuertes E, Söderhäll C, Acevedo N, ..., Carlsten C, Melén E

J. Allergy Clin. Immunol. 135 (2) 573-576 [2015-02-00; online 2014-09-30]

Low-frequency and rare exome chip variants associate with fasting glucose and type 2 diabetes susceptibility.

Wessel J, Chu AY, Willems SM, ..., Scott RA, Goodarzi MO

Nat Commun 6 (-) 5897 [2015-01-29; online 2015-01-29]

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

Prognostic impact of COX-2 in non-small cell lung cancer: a comprehensive compartment-specific evaluation of tumor and stromal cell expression.

Mattsson JS, Bergman B, Grinberg M, ..., Micke P, Gulyas M

Cancer Lett. 356 (2 Pt B) 837-845 [2015-01-28; online 2014-10-31]

Endonuclease specificity and sequence dependence of type IIS restriction enzymes.

Lundin S, Jemt A, Terje-Hegge F, ..., Lexow P, Lundeberg J

PLoS ONE 10 (1) e0117059 [2015-01-28; online 2015-01-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Next-generation sequencing reveals low-dose effects of cationic dendrimers in primary human bronchial epithelial cells.

Feliu N, Kohonen P, Ji J, ..., Nyström A, Fadeel B

ACS Nano 9 (1) 146-163 [2015-01-27; online 2014-12-23]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Intratumoral genome diversity parallels progression and predicts outcome in pediatric cancer.

Mengelbier LH, Karlsson J, Lindgren D, ..., Mayrhofer M, Gisselsson D

Nat Commun 6 (-) 6125 [2015-01-27; online 2015-01-27]

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

TGF-β1-Induced Epithelial-Mesenchymal Transition Promotes Monocyte/Macrophage Properties in Breast Cancer Cells.

Johansson J, Tabor V, Wikell A, Jalkanen S, Fuxe J

Front Oncol 5 (-) 3 [2015-01-26; online 2015-01-26]

Proteomics. Tissue-based map of the human proteome.

Uhlén M, Fagerberg L, Hallström BM, ..., Nielsen J, Pontén F

Science 347 (6220) 1260419 [2015-01-23; online 2015-01-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics Tissue Profiling [Technology development]

Biological interpretation of genome-wide association studies using predicted gene functions.

Pers TH, Karjalainen JM, Chan Y, ..., Hirschhorn JN, Franke L

Nat Commun 6 (-) 5890 [2015-01-19; online 2015-01-19]

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

Drug-induced mRNA signatures are enriched for the minority of genes that are highly heritable.

Gao T, Brodin P, Davis MM, Jojic V

Pac Symp Biocomput - (-) 395-406 [2015-01-17; online 2015-01-17]

Cellular Immunomonitoring [Collaborative]

Variation in the human immune system is largely driven by non-heritable influences.

Brodin P, Jojic V, Gao T, ..., Maecker HT, Davis MM

Cell 160 (1-2) 37-47 [2015-01-15; online 2015-01-17]

Cellular Immunomonitoring [Collaborative]

Transcription-coupled recruitment of human CHD1 and CHD2 influences chromatin accessibility and histone H3 and H3.3 occupancy at active chromatin regions.

Siggens L, Cordeddu L, Rönnerblad M, Lennartsson A, Ekwall K

Epigenetics Chromatin 8 (1) 4 [2015-01-15; online 2015-01-15]

The statistical geometry of transcriptome divergence in cell-type evolution and cancer.

Liang C, FANTOM Consortium , Forrest AR, Wagner GP

Nat Commun 6 (-) 6066 [2015-01-14; online 2015-01-14]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

Comparison of heritability of Cystatin C- and creatinine-based estimates of kidney function and their relation to heritability of cardiovascular disease.

Arpegård J, Viktorin A, Chang Z, ..., Magnusson PK, Svensson P

J Am Heart Assoc 4 (1) e001467 [2015-01-14; online 2015-01-14]

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

The higher frequency of IgA deficiency among Swedish twins is not explained by HLA haplotypes.

Frankowiack M, Kovanen RM, Repasky GA, ..., Pedersen NL, Hammarström L

Genes Immun. 16 (3) 199-205 [2015-01-08; online 2015-01-08]

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

Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea.

Karlsson M, Durling MB, Choi J, ..., Lee YH, Jensen DF

Genome Biol Evol 7 (2) 465-480 [2015-01-08; online 2015-01-08]

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

Defects of CRB2 cause steroid-resistant nephrotic syndrome.

Ebarasi L, Ashraf S, Bierzynska A, ..., Hildebrandt F, Majumdar A

Am. J. Hum. Genet. 96 (1) 153-161 [2015-01-08; online 2015-01-06]

Genome Engineering Zebrafish

A genetic study on C5-TRAF1 and progression of joint damage in rheumatoid arthritis.

van Steenbergen HW, Rodríguez-Rodríguez L, Berglin E, ..., Rantapää-Dahlqvist S, van der Helm-van Mil AH

Arthritis Res. Ther. 17 (-) 1 [2015-01-08; online 2015-01-08]

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

Parallel protein detection by solid-phase proximity ligation assay with real-time PCR or sequencing.

Ebai T, Kamali-Moghaddam M, Landegren U

Curr Protoc Mol Biol 109 (-) 20.10.1-20.1025 [2015-01-05; online 2015-01-05]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics [Technology development]

Mutagenesis. Smoking is associated with mosaic loss of chromosome Y.

Dumanski JP, Rasi C, Lönn M, ..., Ingelsson E, Forsberg LA

Science 347 (6217) 81-83 [2015-01-02; online 2014-12-06]

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

A secretagogin locus of the mammalian hypothalamus controls stress hormone release.

Romanov RA, Alpár A, Zhang MD, ..., Hökfelt T, Harkany T

EMBO J. 34 (1) 36-54 [2015-01-02; online 2014-11-27]

Fluorescence Tissue Profiling

The mutational landscape in pediatric acute lymphoblastic leukemia deciphered by whole genome sequencing.

Lindqvist CM, Nordlund J, Ekman D, ..., Syvänen AC, Berglund EC

Hum. Mutat. 36 (1) 118-128 [2015-01-00; online 2014-10-31]

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

The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling.

Gremel G, Wanders A, Cedernaes J, ..., Uhlén M, Pontén F

J. Gastroenterol. 50 (1) 46-57 [2015-01-00; online 2014-05-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Tissue Profiling

The Biobanking Analysis Resource Catalogue (BARCdb): a new research tool for the analysis of biobank samples.

Galli J, Oelrich J, Taussig MJ, ..., Ortega-Paino E, Landegren U

Nucleic Acids Res. 43 (Database issue) D1158-D1162 [2015-01-00; online 2014-10-23]

Affinity Proteomics Uppsala [Technology development] PLA and Single Cell Proteomics

Synthesis of Vinyl- and Aryl-Acyl Sulfonimidamides Through Pd-Catalyzed Carbonylation Using Mo(CO)6as ex situ CO Source

Wakchaure PB, Borhade SR, Sandström A, Arvidsson PI

Eur. J. Org. Chem. 2015 (1) 213-219 [2015-01-00; online 2014-11-19]

Drug Discovery and Development (DDD) [Technology development]

Scavenging effect of Trolox released from brushite cements.

Mestres G, Santos CF, Engman L, Persson C, Ott MK

Acta Biomater 11 (-) 459-466 [2015-01-00; online 2014-09-16]

Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis.

Avican K, Fahlgren A, Huss M, ..., Dersch P, Fällman M

PLoS Pathog. 11 (1) e1004600 [2015-01-00; online 2015-01-15]

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

Phenotypic plasticity and differentiation in an invasive freshwater microalga

Sassenhagen I, Wilken S, Godhe A, Rengefors K

Harmful Algae 41 (-) 38-45 [2015-01-00; online 2015-01-00]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Methylated RASSF1A in malignant peripheral nerve sheath tumors identifies neurofibromatosis type 1 patients with inferior prognosis.

Danielsen SA, Lind GE, Kolberg M, ..., Picci P, Lothe RA

Neuro-oncology 17 (1) 63-69 [2015-01-00; online 2014-07-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure

Lessons and implications from association studies and post-GWAS analyses of cervical cancer.

Chen D, Gyllensten U

Trends Genet. 31 (1) 41-54 [2015-01-00; online 2014-12-04]

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

Identification and functional characterization of G6PC2 coding variants influencing glycemic traits define an effector transcript at the G6PC2-ABCB11 locus.

Mahajan A, Sim X, Ng HJ, ..., Gloyn AL, T2D-GENES consortium and GoT2D consortium

PLoS Genet. 11 (1) e1004876 [2015-01-00; online 2015-01-27]

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

High plasma levels of heparin-binding epidermal growth factor are associated with a more stable plaque phenotype and reduced incidence of coronary events.

Rattik S, Wigren M, Björkbacka H, ..., Gonçalves I, Nilsson J

Arterioscler. Thromb. Vasc. Biol. 35 (1) 222-228 [2015-01-00; online 2014-10-30]

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

Healthy Nordic diet downregulates the expression of genes involved in inflammation in subcutaneous adipose tissue in individuals with features of the metabolic syndrome.

Kolehmainen M, Ulven SM, Paananen J, ..., Arner P, Dahlman I

Am. J. Clin. Nutr. 101 (1) 228-239 [2015-01-00; online 2014-12-21]

Expression of human leukocyte antigen class I in endocrine and exocrine pancreatic tissue at onset of type 1 diabetes.

Skog O, Korsgren S, Wiberg A, ..., Korsgren O, Dahl-Jørgensen K

Am. J. Pathol. 185 (1) 129-138 [2015-01-00; online 2014-12-20]

NGI Uppsala (Uppsala Genome Center) National Genomics Infrastructure

Combining an amyloid-beta (Aβ) cleaving enzyme inhibitor with a γ-secretase modulator results in an additive reduction of Aβ production.

Strömberg K, Eketjäll S, Georgievska B, ..., Cowburn RF, Dabrowski M

FEBS J. 282 (1) 65-73 [2015-01-00; online 2014-11-07]

Drug Discovery and Development (DDD) [Collaborative]

Body composition and bone mineral density in women with Cushing's syndrome in remission and the association with common genetic variants influencing glucocorticoid sensitivity.

Ragnarsson O, Glad CA, Bergthorsdottir R, ..., Wängberg B, Johannsson G

Eur. J. Endocrinol. 172 (1) 1-10 [2015-01-00; online 2014-11-26]

Applied Enantioselective Aminocatalysis: α-Heteroatom Functionalization Reactions on the Carbapenem (β-Lactam Antibiotic) Core

Cele ZED, Arvidsson PI, Kruger HG, Govender T, Naicker T

Eur. J. Org. Chem. 2015 (3) 638-646 [2015-01-00; online 2014-12-11]

Drug Discovery and Development (DDD) [Collaborative]

A Machine Learning Approach to Explain Drug Selectivity to Soluble and Membrane Protein Targets.

Freyhult E, Gustafsson MG, Strömbergsson H

Mol Inform 34 (1) 44-52 [2015-01-00; online 2015-01-08]

Bioinformatics (NBIS) Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training

The effect of N-methylation of amino acids (Ac-X-OMe) on solubility and conformation: a DFT study

Md. Abdur Rauf S, Arvidsson PI, Albericio F, ..., Kruger HG, Honarparvar B

Org. Biomol. Chem. 13 (39) 9993-10006 [2015-00-00; online 2015-00-00]

Drug Discovery and Development (DDD) [Collaborative]

Pd-catalyzed C–N coupling of vinylbromides and sulfonimidamides: a facile synthesis of N′-vinylsulfonimidamides

Nandi GC, Kota SR, Wakchaure PB, ..., Naicker T, Arvidsson PI

RSC Adv. 5 (76) 62084-62090 [2015-00-00; online 2015-00-00]

Drug Discovery and Development (DDD) [Technology development]

Cytotoxicity, <i>in Vivo</i> Skin Irritation and Acute Systemic Toxicity of the Mesoporous Magnesium Carbonate Upsalite<sup>®</sup>

Frykstrand S, Forsgren J, Zhang P, Strømme M, Ferraz N

JBNB 06 (04) 257-266 [2015-00-00; online 2015-00-00]