Publications 2015

PubMed DOI Crossref

Sequence and gene expression evolution of paralogous genes in willows.

Harikrishnan SL, Pucholt P, Berlin S

pmc

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

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

PubMed DOI Crossref

The Urinary Bladder Transcriptome and Proteome Defined by Transcriptomics and Antibody-Based Profiling.

Habuka M, Fagerberg L, Hallström BM, ..., Yamamoto T, Uhlen M

pmc

PLoS ONE 10 (12) e0145301 [2015-12-22; online 2015-12-22]

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

PubMed DOI Crossref

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

pmc

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

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]

PubMed DOI Crossref

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

pmc

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

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

PubMed DOI Crossref

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]

Protein Science Facility (PSF)

PubMed DOI Crossref

Metagenome-assembled genomes uncover a global brackish microbiome.

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

pmc

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

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

pmc

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

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

PubMed DOI Crossref

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]

Tissue Profiling [Collaborative]

PubMed DOI Crossref

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]

Tissue Profiling [Collaborative]

PubMed DOI Crossref

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

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

pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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

pmc

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

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

PubMed DOI Crossref

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

pmc Dryad

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

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

PubMed DOI Crossref

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

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

pmc BioProject PDB

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

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

PubMed DOI Crossref

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

pmc

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

Mass Spectrometry-based Proteomics, Uppsala

PubMed DOI Crossref

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

pmc

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

Bioinformatics and Expression Analysis (BEA)

PubMed DOI Crossref

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

pmc

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

Bioinformatics and Expression Analysis (BEA)

PubMed DOI Crossref

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

Enroth S, Enroth SB, Johansson Å, Gyllensten U

pmc

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

Clinical Biomarkers

PubMed DOI Crossref

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)

PubMed DOI Crossref

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]

PubMed DOI Crossref

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

pmc

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

Bioinformatics Support and Infrastructure

PubMed DOI Crossref

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

pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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]

Clinical Biomarkers [Service]

PubMed DOI Crossref

Bacterial diversity along a 2600 km river continuum.

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

pmc mid

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

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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]

Advanced Mass Spectrometry Proteomics

PubMed DOI Crossref

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

Manoharan L, Kushwaha SK, Hedlund K, Ahrén D

pmc

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

Bioinformatics Support and Infrastructure

PubMed DOI Crossref

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

pmc mid

Nat. Genet. 47 (12) 1415-1425 [2015-12-00; online 2015-11-10]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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

PubMed DOI Crossref

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

pmc mid GEO

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

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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

pmc

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

Bioinformatics Support and Infrastructure

PubMed DOI Crossref

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)

PubMed DOI Crossref

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

PubMed DOI Crossref

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

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

pmc

Eur. J. Hum. Genet. 23 (12) 1679-1683 [2015-12-00; online 2015-03-19]

NGI Uppsala (Uppsala Genome Center)

PubMed DOI Crossref

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 2015-12-00]

Clinical Biomarkers [Service] PLA Proteomics [Collaborative]

PubMed DOI Crossref

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

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

pmc

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

Tissue Profiling

PubMed DOI Crossref

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

pmc

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

Bioinformatics and Expression Analysis (BEA)

PubMed DOI Crossref

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 2015-11-07]

Clinical Biomarkers

PubMed DOI Crossref

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)

DOI Crossref

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]

BioMaterial Interactions (BioMat)

PubMed DOI Crossref

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 Support and Infrastructure [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

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

pmc

Clin. Immunol. 161 (2) 366-372 [2015-12-00; online 2015-10-21]

Clinical Genomics Uppsala [Collaborative]

PubMed DOI Crossref

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

pmc mid

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

Mutation Analysis Facility (MAF)

PubMed DOI Crossref

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)

PubMed DOI Crossref

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

ISRCTN

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

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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]

PubMed DOI Crossref

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

pmc

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

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

PubMed DOI Crossref

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

pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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

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

pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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

pmc

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

Bioinformatics Support and Infrastructure

DOI Crossref

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)

PubMed DOI Crossref

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

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

pmc

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

Bioinformatics Long-term Support WABI [Collaborative]

PubMed DOI Crossref

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

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

BioProject PDB PDB PDB

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

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

PubMed DOI Crossref

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

pmc

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

Immunocapture strategies in translational proteomics.

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

pmc

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

Plasma Profiling [Technology development]

PubMed DOI Crossref

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

pmc

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

NGI Uppsala (Uppsala Genome Center)

PubMed DOI Crossref

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

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

pmc mid

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

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]

Clinical Biomarkers [Service] NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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

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

pmc

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

Mutation Analysis Facility (MAF)

PubMed DOI Crossref

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

pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

Intra-mitochondrial Methylation Deficiency Due to Mutations in SLC25A26.

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

pmc

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

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

PubMed DOI Crossref

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]

Systems Biology [Technology development]

PubMed DOI Crossref

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 Support and Infrastructure

PubMed DOI Crossref

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]

Tissue Profiling [Collaborative]

PubMed DOI Crossref

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

pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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

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

pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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)

PubMed DOI Crossref

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

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

pmc

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

NGI Uppsala (Uppsala Genome Center)

PubMed DOI Crossref

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

pmc

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

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

pmc mid

ISME J 9 (11) 2373-2385 [2015-11-00; online 2015-04-08]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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

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

pmc mid

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

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

PubMed DOI Crossref

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) Tissue Profiling [Technology development]

PubMed DOI Crossref

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 Support and Infrastructure

PubMed DOI Crossref

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 (-) 383-394 [2015-11-00; online 2015-11-00]

Swedish NMR Centre (SNC) [Service]

PubMed DOI Crossref

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

ClinicalTrials.gov

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

Bioinformatics Support and Infrastructure

PubMed DOI Crossref

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

pmc

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

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

PubMed DOI Crossref

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 2015-09-12]

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

PubMed DOI Crossref

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]

Clinical Biomarkers [Service]

PubMed DOI Crossref

Risks and benefits of sex-mismatched hematopoietic cell transplantation differ according to conditioning strategy.

Nakasone H, Remberger M, Tian L, ..., Miklos DB, Meyer E

pmc

Haematologica 100 (11) 1477-1485 [2015-11-00; online 2015-08-06]

Mass Cytometry [Collaborative]

PubMed DOI Crossref

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

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

pmc

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

Bioinformatics Long-term Support WABI [Technology development]

PubMed DOI Crossref

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

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

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Bioinformatics Support and Infrastructure

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

Tissue Profiling [Collaborative]

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BioMaterial Interactions (BioMat)

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

NGI Uppsala (SNP&SEQ Technology Platform)

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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

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

Bioinformatics and Expression Analysis (BEA)

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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]

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

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

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NGI Uppsala (SNP&SEQ Technology Platform)

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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

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

Cell Profiling

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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 2015-06-16]

Cell Profiling

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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

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NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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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

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

Advanced Light Microscopy (ALM) [Service]

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

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

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

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

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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

pmc GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK

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

NGI Uppsala (Uppsala Genome Center)

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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)

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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)

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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

pmc

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

Protein Science Facility (PSF)

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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

ClinicalTrials.gov

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

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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) - [2015-09-00; online 2015-06-16]

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Transcriptomics of colour patterning and coloration shifts in crows.

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NGI Uppsala (SNP&SEQ Technology Platform)

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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 2015-07-24]

Clinical Biomarkers

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

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

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Advanced Mass Spectrometry Proteomics

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

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

Drug Discovery and Development (DDD)

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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]

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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)

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

pmc mid

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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)

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pmc

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Advanced Mass Spectrometry Proteomics

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BEX1 acts as a tumor suppressor in acute myeloid leukemia.

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

pmc

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Bioinformatics Support and Infrastructure

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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

pmc

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NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

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Possner DD, Claesson M, Guy JE

pmc

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Protein Science Facility (PSF)

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

pmc

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

BioMaterial Interactions (BioMat)

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

pmc

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

Mutation Analysis Facility (MAF)

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

pmc

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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 Support and Infrastructure

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

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

pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

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

pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

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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

pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

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

pmc

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

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

pmc

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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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

pmc

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

Mutation Analysis Facility (MAF)

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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]

BioMaterial Interactions (BioMat)

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Comprehensive genomic profiles of small cell lung cancer.

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

pmc mid GEO

Nature 524 (7563) 47-53 [2015-08-06; online 2015-07-15]

Clinical Genomics Uppsala

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

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

pmc

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

Protein Science Facility (PSF)

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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

pmc

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

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

pmc

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

Bioinformatics and Expression Analysis (BEA)

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

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

pmc GEO SRA SRA

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

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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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]

Plasma Profiling [Technology development]

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Identifying and Assessing Interesting Subgroups in a Heterogeneous Population.

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

pmc

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

Bioinformatics Support and Infrastructure

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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

pmc

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

Cell Profiling NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) Plasma Profiling Tissue Profiling [Technology development]

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

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

ClinicalTrials.gov

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

NGI Uppsala (SNP&SEQ Technology Platform)

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

Wennman A, Magnuson A, Hamberg M, Oliw EH

pmc

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

NGI Uppsala (Uppsala Genome Center)

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

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

pmc

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

Bioinformatics Support and Infrastructure

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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)

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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)

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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)

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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

pmc

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

Bioinformatics Support and Infrastructure

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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)

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

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

pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

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

Öhrvik H, Wittung-Stafshede P

pmc

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

Bioinformatics Support and Infrastructure

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Directional dominance on stature and cognition in diverse human populations.

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

pmc mid

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

NGI Uppsala (SNP&SEQ Technology Platform)

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

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

pmc

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

Advanced Light Microscopy (ALM) [Collaborative] BioImage Informatics [Technology development] Bioinformatics Support and Infrastructure

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

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

pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

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Targeted sequencing of tonsillar and base of tongue cancer and human papillomavirus positive unknown primary of the head and neck reveals prognostic effects of mutated FGFR3

Bersani C, Sivars L, Haeggblom L, ..., Ramqvist T, Dalianis T

Oncotarget - (-) - [2015-07-18; online 2015-07-18]

Bioinformatics Support and Infrastructure [Collaborative]

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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)

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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

pmc

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

Mutation Analysis Facility (MAF)

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Distinguishing Mast Cell Progenitors from Mature Mast Cells in Mice.

Dahlin JS, Ding Z, Hallgren J

pmc

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

Array and Analysis Facility

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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

pmc

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

Clinical Biomarkers

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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

pmc

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

NGI Uppsala (Uppsala Genome Center)

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

Peura S, Sinclair L, Bertilsson S, Eiler A

pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

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

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

pmc

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

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

PubMed DOI Crossref

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

pmc

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

Bioinformatics Support and Infrastructure [Collaborative]

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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

pmc

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

NGI Uppsala (Uppsala Genome Center)

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Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation.

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

pmc PDB PDB PDB PDB PDB PDB

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

Protein Science Facility (PSF)

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Scaffolding of a bacterial genome using MinION nanopore sequencing.

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

pmc

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

NGI Uppsala (Uppsala Genome Center)

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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

pmc GENBANK GENBANK GENBANK

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

NGI Uppsala (Uppsala Genome Center)

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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]

Tissue Profiling [Collaborative]

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

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

pmc

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

Bioinformatics Support and Infrastructure [Collaborative]

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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

ClinicalTrials.gov

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

Bioinformatics and Expression Analysis (BEA)

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Polymorphisms in DCDC2 and S100B associate with developmental dyslexia.

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

pmc

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)

PubMed DOI Crossref

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

pmc

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

Mutation Analysis Facility (MAF)

PubMed DOI Crossref

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)

PubMed DOI Crossref

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)

PubMed DOI Crossref

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

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

pmc mid

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

Tissue Profiling [Collaborative]

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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

pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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)

DOI Crossref

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

Goncalves I, Bengtsson E, Colhoun HM, ..., Schnecke V, Nilsson J

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

Clinical Biomarkers [Service]

PubMed DOI Crossref

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]

Mutation Analysis Facility (MAF)

PubMed DOI Crossref

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

pmc

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

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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)

PubMed DOI Crossref

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

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

pmc

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

Bioinformatics Support and Infrastructure

PubMed DOI Crossref

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 Support and Infrastructure

PubMed DOI Crossref

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)

PubMed DOI Crossref

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

pmc mid

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

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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 2015-05-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

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

Tzelepis G, Dubey M, Jensen DF, Karlsson M

GENBANK

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

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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

Trésaugues L, Lundbäck T, Welin M, ..., Gräslund S, Nordlund P

PDB PDB

PLoS ONE 10 (6) e0131507 [2015-06-29; online 2015-06-29]

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

PubMed DOI Crossref

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

pmc

PLoS ONE 10 (6) e0131046 [2015-06-29; online 2015-06-29]

Tissue Profiling [Collaborative]

PubMed DOI Crossref

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

pmc

Blood 125 (26) 4052-4059 [2015-06-25; online 2015-04-04]

Bioinformatics Support and Infrastructure

PubMed DOI Crossref

The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling.

Lindskog C, Linné J, Fagerberg L, ..., Pontén F, Uhlén M

pmc GEO GEO

BMC Genomics 16 (-) 475 [2015-06-25; online 2015-06-25]

Bioinformatics Long-term Support WABI [Collaborative] Tissue Profiling [Collaborative]

PubMed DOI Crossref

Structure of the nuclease subunit of human mitochondrial RNase P.

Reinhard L, Sridhara S, Hällberg BM

pmc PDB PDB

Nucleic Acids Res. 43 (11) 5664-5672 [2015-06-23; online 2015-05-09]

Protein Science Facility (PSF)

PubMed DOI Crossref

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

pmc

Sci Rep 5 (-) 11153 [2015-06-18; online 2015-06-18]

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

PubMed DOI Crossref

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]

Advanced Light Microscopy (ALM) [Service]

PubMed DOI Crossref

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

pmc GEO

J. Exp. Clin. Cancer Res. 34 (-) 62 [2015-06-18; online 2015-06-18]

Bioinformatics Support and Infrastructure

PubMed DOI Crossref

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 2015-06-19]

Autoimmunity Profiling [Service] Bioinformatics Support and Infrastructure PLA Proteomics

PubMed DOI Crossref

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

pmc GENBANK GENBANK GENBANK

Genome Biol Evol 7 (7) 1871-1886 [2015-06-16; online 2015-06-16]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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)

PubMed DOI Crossref

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

pmc

PLoS ONE 10 (6) e0130028 [2015-06-15; online 2015-06-15]

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

PubMed DOI Crossref

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 Support and Infrastructure

PubMed DOI Crossref

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

pmc

Hum. Mol. Genet. 24 (12) 3582-3594 [2015-06-15; online 2015-03-17]

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

PubMed DOI Crossref

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]

PLA Proteomics [Technology development]

PubMed DOI Crossref

Phasing of single DNA molecules by massively parallel barcoding.

Borgström E, Redin D, Lundin S, ..., Andersson AF, Ahmadian A

pmc SRA

Nat Commun 6 (-) 7173 [2015-06-09; online 2015-06-09]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

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

pmc

Sci Rep 5 (-) 11176 [2015-06-08; online 2015-06-08]

Advanced Mass Spectrometry Proteomics

PubMed DOI Crossref

A quantitative assessment of the Hadoop framework for analyzing massively parallel DNA sequencing data.

Siretskiy A, Sundqvist T, Voznesenskiy M, Spjuth O

pmc

Gigascience 4 (-) 26 [2015-06-04; online 2015-06-04]

Bioinformatics Support and Infrastructure

PubMed DOI Crossref

Evolutionary analysis of the female-specific avian W chromosome.

Smeds L, Warmuth V, Bolivar P, ..., Török J, Ellegren H

pmc mid BioProject

Nat Commun 6 (-) 7330 [2015-06-04; online 2015-06-04]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

Functional loss of IκBε leads to NF-κB deregulation in aggressive chronic lymphocytic leukemia.

Mansouri L, Sutton LA, Ljungström V, ..., Nilsson M, Rosenquist R

pmc

J. Exp. Med. 212 (6) 833-843 [2015-06-01; online 2015-05-20]

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

PubMed DOI Crossref

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)

PubMed DOI Crossref

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 2015-03-06]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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 DOI Crossref

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)

PubMed DOI Crossref

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

pmc GEO

PLoS Genet. 11 (6) e1005295 [2015-06-00; online 2015-06-18]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed

Differential Gene Regulation in Fibroblasts in Co-culture with Keratinocytes and Head and Neck SCC Cells.

Hakelius M, Saiepour D, Göransson H, ..., Gerdin B, Nowinski D

Anticancer Res. 35 (6) 3253-3265 [2015-06-00; online 2015-05-31]

Array and Analysis Facility

PubMed DOI Crossref

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 2015-05-03]

Advanced Mass Spectrometry Proteomics

PubMed DOI Crossref

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

pmc

PLoS Genet. 11 (6) e1005248 [2015-06-00; online 2015-06-09]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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

pmc

Ambio 44 Suppl 3 (-) 402-412 [2015-06-00; online 2015-05-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

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

pmc GEO

Genome Res. 25 (6) 872-883 [2015-06-00; online 2015-03-18]

Bioinformatics and Expression Analysis (BEA)

PubMed DOI Crossref

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

pmc

Haematologica 100 (6) e223-e225 [2015-06-00; online 2015-03-15]

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

PubMed DOI Crossref

Single locus sex determination and female heterogamety in the basket willow (Salix viminalis L.).

Pucholt P, Rönnberg-Wästljung AC, Berlin S

pmc

Heredity (Edinb) 114 (6) 575-583 [2015-06-00; online 2015-02-04]

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

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)

PubMed DOI Crossref

Microbial metagenomics in the Baltic Sea: Recent advancements and prospects for environmental monitoring.

Ininbergs K, Bergman B, Larsson J, Ekman M

pmc

Ambio 44 Suppl 3 (-) 439-450 [2015-06-00; online 2015-05-30]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

The impact of low-frequency and rare variants on lipid levels.

Surakka I, Horikoshi M, Mägi R, ..., Ripatti S, ENGAGE Consortium

pmc mid

Nat. Genet. 47 (6) 589-597 [2015-06-00; online 2015-05-12]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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]

PubMed DOI Crossref

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)

PubMed DOI Crossref

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]

PubMed DOI Crossref

Hemophagocytic lymphohistiocytosis in 2 patients with underlying IFN-γ receptor deficiency.

Tesi B, Sieni E, Neves C, ..., Azzari C, Bryceson YT

J. Allergy Clin. Immunol. 135 (6) 1638-1641 [2015-06-00; online 2015-01-17]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

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)

PubMed DOI Crossref

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]

Tissue Profiling [Collaborative]

PubMed DOI Crossref

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]

Tissue Profiling [Collaborative]

PubMed

Circulating microRNA expression pattern separates patients with anti-neutrophil cytoplasmic antibody associated vasculitis from healthy controls.

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 Support and Infrastructure

PubMed DOI Crossref

Phylogeny, evolution and classification of gall wasps: the plot thickens.

Ronquist F, Nieves-Aldrey JL, Buffington ML, ..., Liljeblad J, Nylander JA

pmc

PLoS ONE 10 (5) e0123301 [2015-05-20; online 2015-05-20]

Bioinformatics Support and Infrastructure

PubMed DOI Crossref

Complete genomes reveal signatures of demographic and genetic declines in the woolly mammoth.

Palkopoulou E, Mallick S, Skoglund P, ..., Reich D, Dalén L

pmc mid

Curr. Biol. 25 (10) 1395-1400 [2015-05-18; online 2015-04-29]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

CGGBP1 mitigates cytosine methylation at repetitive DNA sequences.

Agarwal P, Collier P, Fritz MH, ..., Westermark B, Singh U

pmc

BMC Genomics 16 (-) 390 [2015-05-16; online 2015-05-16]

NGI Uppsala (Uppsala Genome Center)

PubMed DOI Crossref

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)

PubMed DOI Crossref

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)

PubMed DOI Crossref

Human genomics. Effect of predicted protein-truncating genetic variants on the human transcriptome.

Rivas MA, Pirinen M, Conrad DF, ..., Lappalainen T, MacArthur DG

pmc mid dbGaP dbGaP dbGaP

Science 348 (6235) 666-669 [2015-05-08; online 2015-05-09]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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)

PubMed DOI Crossref

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

pmc Dryad

Proc. Biol. Sci. 282 (1806) 20150156 [2015-05-07; online 2015-04-04]

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

PubMed DOI Crossref

Intestinal dysbiosis in children with short bowel syndrome is associated with impaired outcome.

Engstrand Lilja H, Wefer H, Nyström N, Finkel Y, Engstrand L

pmc

Microbiome 3 (-) 18 [2015-05-04; online 2015-05-04]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

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)

DOI Crossref

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]

PubMed DOI Crossref

Genetic regulation of bone metabolism in the chicken: similarities and differences to Mammalian systems.

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

pmc

PLoS Genet. 11 (5) e1005250 [2015-05-00; online 2015-05-29]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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

pmc mid

Mol. Psychiatry 20 (5) 647-656 [2015-05-00; online 2014-10-08]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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

BioProject Dryad SRA

Mol. Ecol. 24 (9) 2112-2124 [2015-05-00; online 2015-02-07]

NGI Uppsala (Uppsala Genome Center)

DOI Crossref

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]

PubMed DOI Crossref

Age- and sex-specific causal effects of adiposity on cardiovascular risk factors.

Fall T, Hägg S, Ploner A, ..., Ingelsson E, ENGAGE Consortium

pmc

Diabetes 64 (5) 1841-1852 [2015-05-00; online 2015-02-26]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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)

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]

Advanced Mass Spectrometry Proteomics

PubMed DOI Crossref

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)

PubMed DOI Crossref

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

pmc

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)

PubMed DOI Crossref

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]

Mutation Analysis Facility (MAF)

PubMed DOI Crossref

Plant-mediated gene silencing restricts growth of the potato late blight pathogen Phytophthora infestans.

Jahan SN, Åsman AK, Corcoran P, ..., Vetukuri RR, Dixelius C

pmc

J. Exp. Bot. 66 (9) 2785-2794 [2015-05-00; online 2015-03-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

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]

Advanced Light Microscopy (ALM) [Collaborative]

PubMed DOI Crossref

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

pmc

J Hematol Oncol 8 (-) 42 [2015-04-24; online 2015-04-24]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

Genetically determined height and coronary artery disease.

Nelson CP, Hamby SE, Saleheen D, ..., Samani NJ, CARDIoGRAM+C4D Consortium

pmc mid

N. Engl. J. Med. 372 (17) 1608-1618 [2015-04-23; online 2015-04-09]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

Circulating carnosine dipeptidase 1 associates with weight loss and poor prognosis in gastrointestinal cancer.

Arner P, Henjes F, Schwenk JM, ..., Nilsson P, Rydén M

pmc

PLoS ONE 10 (4) e0123566 [2015-04-21; online 2015-04-21]

Plasma Profiling

PubMed DOI Crossref

Polymorphisms in chloroquine resistance-associated genes in Plasmodium vivax in Ethiopia.

Golassa L, Erko B, Baliraine FN, Aseffa A, Swedberg G

pmc

Malar. J. 14 (-) 164 [2015-04-16; online 2015-04-16]

NGI Uppsala (Uppsala Genome Center)

PubMed DOI Crossref

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

pmc mid

Toxicol. Appl. Pharmacol. 284 (2) 163-179 [2015-04-15; online 2015-02-21]

Genome Engineering Zebrafish [Service]

PubMed DOI Crossref

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

pmc

Oncotarget 6 (10) 7804-7814 [2015-04-10; online 2015-03-13]

Bioinformatics and Expression Analysis (BEA)

PubMed DOI Crossref

Common genetic variants influence human subcortical brain structures.

Hibar DP, Stein JL, Renteria ME, ..., Thompson PM, Medland SE

pmc mid

Nature 520 (7546) 224-229 [2015-04-09; online 2015-01-22]

NGI Uppsala (SNP&SEQ Technology Platform)

DOI Crossref

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)

PubMed DOI Crossref

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

pmc

Front Microbiol 6 (-) 223 [2015-04-01; online 2015-04-01]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

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

PubMed DOI Crossref

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 Support and Infrastructure

PubMed DOI Crossref

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

pmc

Int J Epidemiol 44 (2) 578-586 [2015-04-00; online 2015-05-27]

NGI Uppsala (SNP&SEQ Technology Platform)

PubMed DOI Crossref

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

pmc

Int J Epidemiol 44 (2) 638-650 [2015-04-00; online 2015-06-06]

NGI Uppsala (SNP&SEQ Technology Platform)

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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]

Tissue Profiling [Collaborative]

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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]

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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

pmc mid

Obes Rev 16 (4) 327-340 [2015-04-00; online 2015-03-05]

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

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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)

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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)

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Birth weight as an independent predictor of ADHD symptoms: a within-twin pair analysis.

Pettersson E, Sjölander A, Almqvist C, ..., Lichtenstein P, Larsson H

pmc mid

J Child Psychol Psychiatry 56 (4) 453-459 [2015-04-00; online 2014-07-22]

Mutation Analysis Facility (MAF)

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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)

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Identification and validation of N-acetyltransferase 2 as an insulin sensitivity gene.

Knowles JW, Xie W, Zhang Z, ..., Walker M, Quertermous T

pmc

J. Clin. Invest. 125 (4) 1739-1751 [2015-04-00; online 2015-03-23]

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

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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)

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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

pmc

Appl. Environ. Microbiol. 81 (7) 2378-2383 [2015-04-00; online 2015-01-27]

NGI Uppsala (Uppsala Genome Center)

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Methylation levels of SLC23A2 and NCOR2 genes correlate with spinal muscular atrophy severity.

Zheleznyakova GY, Nilsson EK, Kiselev AV, ..., Baranov VS, Schiöth HB

pmc

PLoS ONE 10 (3) e0121964 [2015-03-30; online 2015-03-30]

NGI Uppsala (Uppsala Genome Center)

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Site-specific programming of the host epithelial transcriptome by the gut microbiota.

Sommer F, Nookaew I, Sommer N, Fogelstrand P, Bäckhed F

pmc

Genome Biol. 16 (-) 62 [2015-03-28; online 2015-03-28]

Array and Analysis Facility Bioinformatics Support and Infrastructure

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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

pmc

Clin Epigenetics 7 (-) 34 [2015-03-26; online 2015-03-26]

Bioinformatics and Expression Analysis (BEA)

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Modulation of genetic associations with serum urate levels by body-mass-index in humans.

Huffman JE, Albrecht E, Teumer A, ..., Köttgen A, Vitart V

pmc

PLoS ONE 10 (3) e0119752 [2015-03-26; online 2015-03-26]

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

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Crystal Structures of the Kinase Domain of the Sulfate-Activating Complex in Mycobacterium tuberculosis

Poyraz Ö, Brunner K, Lohkamp B, ..., Schnell R, Schneider G

PDB PDB PDB PDB

PLoS ONE 10 (3) e0121494 [2015-03-25; online 2015-03-25]

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

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Discovery of molecular markers to discriminate corneal endothelial cells in the human body.

Yoshihara M, Ohmiya H, Hara S, ..., Tsujikawa M, Nishida K

pmc

PLoS ONE 10 (3) e0117581 [2015-03-25; online 2015-03-25]

Bioinformatics Support and Infrastructure

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Complete genome sequence of Borrelia afzelii K78 and comparative genome analysis.

Schüler W, Bunikis I, Weber-Lehman J, ..., Bergström S, Lundberg U

pmc

PLoS ONE 10 (3) e0120548 [2015-03-23; online 2015-03-23]

NGI Uppsala (Uppsala Genome Center)

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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

pmc

J. Biol. Chem. 290 (12) 7336-7344 [2015-03-20; online 2015-01-31]

Protein Science Facility (PSF)

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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

pmc

Genome Announc 3 (2) - [2015-03-19; online 2015-03-19]

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

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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 Support and Infrastructure

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Conservation of transcription factor binding specificities across 600 million years of bilateria evolution.

Nitta KR, Jolma A, Yin Y, ..., Furlong EE, Taipale J

pmc

Elife 4 (-) - [2015-03-17; online 2015-03-17]

Karolinska High Throughput Center (KHTC)

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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

pmc

BMC Genomics 16 (-) 193 [2015-03-17; online 2015-03-17]

Bioinformatics Support and Infrastructure

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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]

Advanced Light Microscopy (ALM) [Collaborative]

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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

pmc GEO

BMC Cancer 15 (-) 125 [2015-03-14; online 2015-03-14]

Array and Analysis Facility

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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

pmc

Sci Rep 5 (-) 8820 [2015-03-06; online 2015-03-06]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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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

pmc

Proc. Natl. Acad. Sci. U.S.A. 112 (9) 2806-2811 [2015-03-03; online 2015-02-19]

NGI Uppsala (SNP&SEQ Technology Platform)

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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 Profiling [Collaborative] Tissue Profiling [Collaborative]

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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)

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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

pmc

Haematologica 100 (3) 370-376 [2015-03-00; online 2014-12-07]

Clinical Genomics Uppsala

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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 2015-01-24]

Clinical Genomics Uppsala NGI Uppsala (Uppsala Genome Center)

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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

pmc PDB

Acta Crystallogr F Struct Biol Commun 71 (Pt 3) 338-345 [2015-03-00; online 2015-02-19]

Protein Science Facility (PSF)

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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]

Mutation Analysis Facility (MAF)

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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)

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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

pmc

PLoS Genet. 11 (3) e1004947 [2015-03-00; online 2015-03-19]

NGI Uppsala (SNP&SEQ Technology Platform)

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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

pmc GEO

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)

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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

pmc

Ups. J. Med. Sci. 120 (1) 40-46 [2015-03-00; online 2014-10-08]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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Structural characterization of substrate and inhibitor binding to farnesyl pyrophosphate synthase from Pseudomonas aeruginosa.

Schmidberger JW, Schnell R, Schneider G

pmc PDB PDB PDB PDB PDB

Acta Crystallogr. D Biol. Crystallogr. 71 (Pt 3) 721-731 [2015-03-00; online 2015-02-26]

Protein Science Facility (PSF)

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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

pmc

ISME J 9 (3) 656-669 [2015-03-00; online 2014-09-23]

NGI Uppsala (Uppsala Genome Center)

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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

pmc mid

Ann. Rheum. Dis. 74 (3) e13 [2015-03-00; online 2014-02-14]

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

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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]

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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 Support and Infrastructure Tissue Profiling

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MetCap: a bioinformatics probe design pipeline for large-scale targeted metagenomics.

Kushwaha SK, Manoharan L, Meerupati T, Hedlund K, Ahrén D

pmc

BMC Bioinformatics 16 (-) 65 [2015-02-28; online 2015-02-28]

Bioinformatics Support and Infrastructure

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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

pmc ClinicalTrials.gov

PLoS ONE 10 (2) e0115186 [2015-02-24; online 2015-02-24]

NGI Uppsala (SNP&SEQ Technology Platform)

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The roles of SNF2/SWI2 nucleosome remodeling enzymes in blood cell differentiation and leukemia.

Prasad P, Lennartsson A, Ekwall K

pmc

Biomed Res Int 2015 (-) 347571 [2015-02-19; online 2015-02-19]

Bioinformatics and Expression Analysis (BEA)

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Evolution of Darwin's finches and their beaks revealed by genome sequencing.

Lamichhaney S, Berglund J, Almén MS, ..., Webster MT, Andersson L

BioProject GENBANK

Nature 518 (7539) 371-375 [2015-02-19; online 2015-02-18]

NGI Uppsala (SNP&SEQ Technology Platform)

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DNA methylation-based subtype prediction for pediatric acute lymphoblastic leukemia.

Nordlund J, Bäcklin CL, Zachariadis V, ..., Forestier E, Syvänen AC

pmc

Clin Epigenetics 7 (-) 11 [2015-02-17; online 2015-02-17]

NGI Uppsala (SNP&SEQ Technology Platform)

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Genetic studies of body mass index yield new insights for obesity biology.

Locke AE, Kahali B, Berndt SI, ..., Loos RJ, Speliotes EK

pmc mid

Nature 518 (7538) 197-206 [2015-02-12; online 2015-02-13]

NGI Uppsala (SNP&SEQ Technology Platform)

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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

pmc

BMC Cancer 15 (-) 45 [2015-02-12; online 2015-02-12]

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

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New genetic loci link adipose and insulin biology to body fat distribution.

Shungin D, Winkler TW, Croteau-Chonka DC, ..., Lindgren CM, Mohlke KL

pmc mid

Nature 518 (7538) 187-196 [2015-02-12; online 2015-02-13]

NGI Uppsala (SNP&SEQ Technology Platform)

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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 Support and Infrastructure

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Microbial community composition and diversity via 16S rRNA gene amplicons: evaluating the illumina platform.

Sinclair L, Osman OA, Bertilsson S, Eiler A

pmc SRA SRA

PLoS ONE 10 (2) e0116955 [2015-02-03; online 2015-02-03]

NGI Uppsala (SNP&SEQ Technology Platform)

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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

pmc

Hum. Mol. Genet. 24 (3) 875-890 [2015-02-01; online 2014-09-27]

Bioinformatics and Expression Analysis (BEA) Mutation Analysis Facility (MAF)

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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]

Mutation Analysis Facility (MAF)

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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]

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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)

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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)

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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

pmc PDB PDB PDB

Appl. Microbiol. Biotechnol. 99 (4) 1731-1744 [2015-02-00; online 2014-09-01]

Protein Science Facility (PSF)

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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

GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK

Int. J. Syst. Evol. Microbiol. 65 (Pt 2) 444-451 [2015-02-00; online 2014-11-12]

NGI Uppsala (SNP&SEQ Technology Platform)

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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 Support and Infrastructure NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)

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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 Stockholm NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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Expression of human skin-specific genes defined by transcriptomics and antibody-based profiling.

Edqvist PH, Fagerberg L, Hallström BM, ..., Uhlén M, Pontén F

pmc

J. Histochem. Cytochem. 63 (2) 129-141 [2015-02-00; online 2014-11-19]

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

PubMed DOI Crossref

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 Support and Infrastructure Clinical Proteomics Mass spectrometry

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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]

Mutation Analysis Facility (MAF)

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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)

PubMed DOI Crossref

The composition of the gut microbiota shapes the colon mucus barrier.

Jakobsson HE, Rodríguez-Piñeiro AM, Schütte A, ..., Hansson GC, Johansson ME

pmc

EMBO Rep. 16 (2) 164-177 [2015-02-00; online 2014-12-20]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

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

pmc mid

Nat Commun 6 (-) 5897 [2015-01-29; online 2015-01-29]

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

PubMed DOI Crossref

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]

Tissue Profiling [Collaborative]

PubMed DOI Crossref

Endonuclease specificity and sequence dependence of type IIS restriction enzymes.

Lundin S, Jemt A, Terje-Hegge F, ..., Lexow P, Lundeberg J

pmc SRA

PLoS ONE 10 (1) e0117059 [2015-01-28; online 2015-01-28]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

PubMed DOI Crossref

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)

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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)

PubMed DOI Crossref

TGF-β1-Induced Epithelial-Mesenchymal Transition Promotes Monocyte/Macrophage Properties in Breast Cancer Cells.

Johansson J, Tabor V, Wikell A, Jalkanen S, Fuxe J

pmc

Front Oncol 5 (-) 3 [2015-01-26; online 2015-01-26]

Bioinformatics and Expression Analysis (BEA)

PubMed DOI Crossref

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]

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

PubMed DOI Crossref

Biological interpretation of genome-wide association studies using predicted gene functions.

Pers TH, Karjalainen JM, Chan Y, ..., Hirschhorn JN, Franke L

pmc mid

Nat Commun 6 (-) 5890 [2015-01-19; online 2015-01-19]

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

PubMed DOI Crossref

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]

Mass Cytometry [Collaborative]

PubMed DOI Crossref

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

pmc

Epigenetics Chromatin 8 (1) 4 [2015-01-15; online 2015-01-15]

Bioinformatics and Expression Analysis (BEA)

PubMed DOI Crossref

Variation in the human immune system is largely driven by non-heritable influences.

Brodin P, Jojic V, Gao T, ..., Maecker HT, Davis MM

pmc mid

Cell 160 (1-2) 37-47 [2015-01-15; online 2015-01-17]

Mass Cytometry [Collaborative]

PubMed DOI Crossref

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 Support and Infrastructure

PubMed DOI Crossref

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

pmc

J Am Heart Assoc 4 (1) e001467 [2015-01-14; online 2015-01-14]

NGI Uppsala (SNP&SEQ Technology Platform)

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Defects of CRB2 cause steroid-resistant nephrotic syndrome.

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Publications 2015

424 publications