Publications 2015

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]

Metagenome-assembled genomes uncover a global brackish microbiome.

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

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

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

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

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

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

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

Johnsson M, Jonsson KB, ..., Jensen P, Wright D

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

Bioinformatics Compute and Storage (UPPNEX) NGI Uppsala (SNP&SEQ Technology Platform)

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

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

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

Karolinska High Throughput Center (KHTC) Protein Science Facility

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

Goenaga J, Yamane T, Rönn J, Arnqvist G

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

Mass Spectrometry-based Proteomics, Uppsala

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

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

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

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

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

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

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

Enroth S, Enroth SB, Johansson Å, Gyllensten U

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

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

Kovatcheva-Datchary P, Nilsson A, ..., 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)

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

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

Mattsson A, Kärrman A, Pinto R, Brunström B

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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

Hägg S, Ganna A, ..., Pawitan Y, Ingelsson E

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

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

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

Thromb. Res. 136 (6) 1240-1244 [2015-12-00; online 2015-10-18]

Bacterial diversity along a 2600 km river continuum.

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

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

Identification of proteins from human permanent erupted enamel.

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

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

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

Manoharan L, Kushwaha SK, Hedlund K, Ahrén D

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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

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

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

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]

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

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

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

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

Hurst LD, Ghanbarian AT, ..., FANTOM consortium , Huminiecki L

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

Bioinformatics Short-term Support and Infrastructure (BILS)

The Plant Genome Integrative Explorer Resource: PlantGenIE.org.

Sundell D, Mannapperuma C, ..., 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)

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

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

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

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

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

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

Cytokine 76 (2) 514-518 [2015-12-00; online 2015-07-21]

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

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

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

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

Correia JC, Massart J, ..., Groen AK, Ruas JL

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

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

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

Stroke 46 (12) 3340-3347 [2015-12-00; online 2015-11-07]

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)

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]

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, ..., Stenmark S, Smith CI

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

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, ..., Weidinger S, EArly Genetics and Lifecourse Epidemiology (EAGLE) Eczema Consortium

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

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

Sassenhagen I, Sefbom J, ..., Godhe A, Rengefors K

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

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

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

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

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

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

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

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

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, ..., Wallentin L, Siegbahn A

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

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

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

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

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

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

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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

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

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

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

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

Le Rhun A, Beer YY, ..., Chylinski K, Charpentier E

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

Bioinformatics Long-term Support WABI

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

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

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

Karolinska High Throughput Center (KHTC) Protein Science Facility

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

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

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

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

Immunocapture strategies in translational proteomics.

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

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

Plasma Profiling

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

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

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

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

Johansson ME, Jakobsson HE, ..., Bäckhed F, Hansson GC

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

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

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 NGI Uppsala (SNP&SEQ Technology Platform)

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

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

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

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

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

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

Intra-mitochondrial Methylation Deficiency Due to Mutations in SLC25A26.

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

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

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

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

Quantitative proteogenomics of human pathogens using DIA-MS.

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

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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, ..., Schiöth HB, Benedict C

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

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

Nater A, Burri R, ..., Smeds L, Ellegren H

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

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, ..., Lynikienė J, Povilaitienė A

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

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

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

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

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

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

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

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

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

Martijn J, Schulz F, ..., Guy L, Ettema TJ

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

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

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

OMICS 19 (11) 659-668 [2015-11-00; online 2015-10-22]

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

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

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

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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, ..., Pinto R, Sandberg AS

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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

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

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

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

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

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

J Mol Diagn 17 (6) 729-739 [2015-11-00; online 2015-09-12]

Clinical Sequencing NGI Uppsala (SNP&SEQ Technology Platform)

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

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

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

Bioinformatics Long-term Support WABI NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

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

Gut 64 (11) 1774-1782 [2015-11-00; online 2014-09-25]

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

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

Genome Res. 25 (11) 1656-1665 [2015-11-00; online 2015-09-12]

Bioinformatics Long-term Support WABI NGI Uppsala (SNP&SEQ Technology Platform)

Variant Profiling of Candidate Genes in Pancreatic Ductal Adenocarcinoma.

Huang J, Löhr JM, ..., Zheng Z, Ye W

Clin. Chem. 61 (11) 1408-1416 [2015-11-00; online 2015-09-18]

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

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

Sork VL, Smouse PE, Grivet D, Scofield DG

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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

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

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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

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

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

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

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

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

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

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

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

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

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

Membrane vesicle-mediated release of bacterial RNA.

Sjöström AE, Sandblad L, Uhlin BE, Wai SN

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

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

Caraballo R, Larsson M, ..., Enquist PA, Elofsson M

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

Laboratories for Chemical Biology Umeå (LCBU) Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)

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

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

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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

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

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

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

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

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

Cell Profiling

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

Mushtaq M, Zubair S, ..., Bongcam-Rudloff E, Jansson DS

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

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)

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

Pucholt P, Sjödin P, ..., Rönnberg-Wästljung AC, Berlin S

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

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

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

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

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

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

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

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

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

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

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

Caesar R, Tremaroli V, ..., Cani PD, Bäckhed F

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

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

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

Sheng Z, Pettersson ME, ..., Siegel PB, Carlborg Ö

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Peric D, Barragan I, ..., Laustriat D, Peschanski M

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

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

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

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

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

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

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

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

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

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

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

Tzeng JY, Magnusson PK, ..., Swedish Schizophrenia Consortium , Szatkiewicz JP

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

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

Steige KA, Reimegård J, ..., Scofield DG, Slotte T

Mol. Biol. Evol. 32 (10) 2501-2514 [2015-10-00; online 2015-09-01]

Bioinformatics Long-term Support WABI Bioinformatics Short-term Support and Infrastructure (BILS) NGI Uppsala (SNP&SEQ Technology Platform)

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

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

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

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

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

J. Immunol. Methods 425 (-) 58-61 [2015-10-00; online 2015-06-17]

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

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

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

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

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

Bengtsson-Palme J, Angelin M, ..., Larsson DG, Johansson A

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

Bioinformatics Long-term Support WABI NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

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

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

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

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

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

Laboratories for Chemical Biology Umeå (LCBU)

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

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

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

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

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

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

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

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

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

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

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

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

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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

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

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

Bioinformatics Short-term Support and Infrastructure (BILS) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

Saw JH, Spang A, ..., Guy L, Ettema TJ

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

Microbial Single Cell Genomics NGI Uppsala (SNP&SEQ Technology Platform)

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

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

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

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

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

Proc. Natl. Acad. Sci. U.S.A. 112 (38) 11917-11922 [2015-09-22; online 2015-09-10]

Dormant phages of Helicobacter pylori reveal distinct populations in Europe.

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

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

Clinical Genomics

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

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

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

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

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

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

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

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

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

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

Mol. Cell 59 (6) 984-997 [2015-09-17; online 2015-09-01]

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

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

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

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

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)

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

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

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

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

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

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

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

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

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

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

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

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

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

Bioinformatics Short-term Support and Infrastructure (BILS)

Surface Chemistry of Nanocellulose Fibers Directs Monocyte/Macrophage Response.

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

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

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

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

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

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)

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

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

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

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, ..., Dahlman-Wright K, Dahlman I

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

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

Wolff P, Jiang H, ..., Santos-González J, Köhler C

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

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

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

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

Cell Profiling

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

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

J. Proteome Res. 14 (9) 3415-3431 [2015-09-04; online 2015-06-16]

Cell Profiling

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, ..., Ludvigsson J, Thorsell A

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

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

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

Holm A, Karlsson T, Vikström E

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

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

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

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

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

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, ..., Hammarström L, Marcotte H

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

Transplanted Bone Marrow-Derived Cells Contribute to Human Adipogenesis.

Rydén M, Uzunel M, ..., 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)

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

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

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

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

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

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

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

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

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

Transcriptomics of colour patterning and coloration shifts in crows.

Poelstra JW, Vijay N, Hoeppner MP, Wolf JB

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

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

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

Atherosclerosis 242 (1) 205-210 [2015-09-00; online 2015-07-24]

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

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

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

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

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

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

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

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

Wakchaure PB, Bremberg U, Wannberg J, Larhed M

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

Medicinal Chemistry – Lead Identification

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

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

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

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

Isaksson J, Allen M, Nilsson KW, Lindblad F

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

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

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

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

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

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

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

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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

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

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

BEX1 acts as a tumor suppressor in acute myeloid leukemia.

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

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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

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

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

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

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

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

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

Structure of the Glycosyltransferase Ktr4p from Saccharomyces cerevisiae.

Possner DD, Claesson M, Guy JE

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

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

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

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

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

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

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

Experiences with workflows for automating data-intensive bioinformatics.

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

Biol. Direct 10 (-) 43 [2015-08-19; online 2015-08-19]

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

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

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

Nucleic Acids Res. 43 (14) 6787-6798 [2015-08-18; online 2015-06-29]

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

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 Short-term Support and Infrastructure (BILS)

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Comparative Proteomic Analysis of Human Liver Tissue and Isolated Hepatocytes with a Focus on Proteins Determining Drug Exposure.

Vildhede A, Wiśniewski JR, ..., Karlgren M, Artursson P

J. Proteome Res. 14 (8) 3305-3314 [2015-08-07; online 2015-07-15]

Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)

Comprehensive genomic profiles of small cell lung cancer.

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

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

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

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

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

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, ..., Nielsen J, Bäckhed F

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

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

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

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

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

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

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

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

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

Heat differentiated complement factor profiling.

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

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

Plasma Profiling

Identifying and Assessing Interesting Subgroups in a Heterogeneous Population.

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

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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, ..., Uhlén M, Pontén F

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

Cell Profiling NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) Plasma Profiling

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

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

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

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

Wennman A, Magnuson A, Hamberg M, Oliw EH

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

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

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

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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

Taylan F, Nilsson D, ..., 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)

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

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

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

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]

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

Menzel M, Sletvold N, Ågren J, Hansson B

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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, ..., Lannergard A, Lennerstrand J

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

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

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

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

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

Öhrvik H, Wittung-Stafshede P

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

Bioinformatics Short-term Support and Infrastructure (BILS)

Directional dominance on stature and cognition in diverse human populations.

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

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

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

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

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

Advanced Light Microscopy Bioinformatics Short-term Support and Infrastructure (BILS)

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

Wallerman O, Nord H, ..., Borghini L, Wadelius C

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

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, ..., Grotmol T, Wiklund F

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

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

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

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

Distinguishing Mast Cell Progenitors from Mature Mast Cells in Mice.

Dahlin JS, Ding Z, Hallgren J

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

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

Miclescu AA, Svahn M, Gordh TE

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

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

Osman A, Hitzler WE, Ameur A, Provost P

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

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

Peura S, Sinclair L, Bertilsson S, Eiler A

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

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

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

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

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

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

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

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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

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

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

Structural basis for cellobiose dehydrogenase action during oxidative cellulose degradation.

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

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

Scaffolding of a bacterial genome using MinION nanopore sequencing.

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

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

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

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

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

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

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

Dev. Cell 34 (1) 19-32 [2015-07-06; online 2015-06-30]

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

Tsirigos KD, Peters C, ..., Käll L, Elofsson A

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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

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

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

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Bioinformatics Long-term Support WABI NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

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

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

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

Functional Identification of Target by Expression Proteomics (FITExP) reveals protein targets and highlights mechanisms of action of small molecule drugs.

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

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

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

PubMed

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

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

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

PubMed

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

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

Design, Synthesis and Inhibitory Activity of Photoswitchable RET Kinase Inhibitors.

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

Quantifying the impact of transporters on cellular drug permeability.

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Tracking the origin of metastatic prostate cancer.

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

PubMed

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

Dietary fat quality impacts genome-wide DNA methylation patterns in a cross-sectional study of Greek preadolescents.

Voisin S, Almén MS, ..., Manios Y, Schiöth HB

Eur. J. Hum. Genet. 23 (5) 654-662 [2015-05-00; online 2014-07-31]

NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)

The role of genetic factors for hearing deterioration across 20 years: a twin study.

Bogo R, Farah A, ..., Svartengren M, Skjönsberg Å

J. Gerontol. A Biol. Sci. Med. Sci. 70 (5) 647-653 [2015-05-00; online 2015-02-11]

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

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

Nanoparticle-stabilized microbubbles for multimodal imaging and drug delivery.

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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.

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

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

Genetically determined height and coronary artery disease.

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

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

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

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

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AP-1-mediated chromatin looping regulates ZEB2 transcription: new insights into TNFα-induced epithelial-mesenchymal transition in triple-negative breast cancer.

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Lindh MV, Figueroa D, ..., Legrand C, Pinhassi J

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

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

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, ..., Pontén F, Carlson JW

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Adiposity as a cause of cardiovascular disease: a Mendelian randomization study.

Hägg S, Fall T, ..., Ingelsson E, European Network for Genetic and Genomic Epidemiology Consortium

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

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.

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

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Functional anti-CD94/NKG2A and anti-CD94/NKG2C autoantibodies in patients with systemic lupus erythematosus.

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Oseltamivir-resistant influenza A (H1N1) virus strain with an H274Y mutation in neuraminidase persists without drug pressure in infected mallards.

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

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Array and Analysis Facility Bioinformatics Short-term Support and Infrastructure (BILS)

Age-associated DNA methylation changes in immune genes, histone modifiers and chromatin remodeling factors within 5 years after birth in human blood leukocytes.

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Crystal structures of the kinase domain of the sulfate-activating complex in Mycobacterium tuberculosis.

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

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

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

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

Structural basis for lack of ADP-ribosyltransferase activity in poly(ADP-ribose) polymerase-13/zinc finger antiviral protein.

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Complete Genome Sequence of Francisella guangzhouensis Strain 08HL01032T, Isolated from Air-Conditioning Systems in China.

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

Bioinformatics Compute and Storage (UPPNEX) NGI Uppsala (Uppsala Genome Center)

Comparative proteomic analysis of hyphae and germinating cysts of Phytophthora pisi and Phytophthora sojae.

Hosseini S, Resjö S, ..., Andreasson E, Karlsson M

J Proteomics 117 (-) 24-40 [2015-03-18; online 2015-01-24]

Bioinformatics Short-term Support and Infrastructure (BILS)

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

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

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

Karolinska High Throughput Center (KHTC)

Local hopping mobile DNA implicated in pseudogene formation and reductive evolution in an obligate cyanobacteria-plant symbiosis.

Vigil-Stenman T, Larsson J, Nylander JA, Bergman B

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

Bioinformatics Short-term Support and Infrastructure (BILS)

SLC10A4 is a vesicular amine-associated transporter modulating dopamine homeostasis.

Larhammar M, Patra K, ..., Wallén-Mackenzie Å, Kullander K

Biol. Psychiatry 77 (6) 526-536 [2015-03-15; online 2014-09-02]

Microsatellite instability and mutations in BRAF and KRAS are significant predictors of disseminated disease in colon cancer.

Birgisson H, Edlund K, ..., Glimelius B, Sundström M

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

Variations of gastric corpus microbiota are associated with early esophageal squamous cell carcinoma and squamous dysplasia.

Nasrollahzadeh D, Malekzadeh R, ..., Dawsey SM, Ye W

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

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

Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris.

Douglas GM, Gos G, ..., Slotte T, Wright SI

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

Genomewide association study of body weight traits in Baluchi sheep.

PubMed

Gholizadeh M, Rahimi-Mianji G, Nejati-Javaremi A

J. Genet. 94 (1) 143-146 [2015-03-00; online 2015-04-08]

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, ..., Stamatopoulos K, Rosenquist R

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

MuSK: a new target for lethal fetal akinesia deformation sequence (FADS).

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

J. Med. Genet. 52 (3) 195-202 [2015-03-00; online 2015-01-24]

Clinical Sequencing NGI Uppsala (Uppsala Genome Center)

High-resolution crystal structure of a polyextreme GH43 glycosidase from Halothermothrix orenii with α-L-arabinofuranosidase activity.

Hassan N, Kori LD, ..., Divne C, Tan TC

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

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]

Amplification-free sequencing of cell-free DNA for prenatal non-invasive diagnosis of chromosomal aberrations.

Karlsson K, Sahlin 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)

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, ..., Hallböök F, Andersson L

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

The Fun30 chromatin remodeler Fft3 controls nuclear organization and chromatin structure of insulators and subtelomeres in fission yeast.

Steglich B, Strålfors A, ..., Javerzat JP, Ekwall K

PLoS Genet. 11 (3) e1005101 [2015-03-00; online 2015-03-23]

Bioinformatics and Expression Analysis (BEA) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production)

The H1-receptor antagonist cetirizine ameliorates high-fat diet-induced glucose intolerance in male C57BL/6 mice, but not diabetes outcome in female non-obese diabetic (NOD) mice.

Anvari E, Wang X, Sandler S, Welsh N

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

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

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

Schmidberger JW, Schnell R, Schneider G

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

Effects of ecological engineered oxygenation on the bacterial community structure in an anoxic fjord in western Sweden.

Forth M, Liljebladh B, ..., Hall PO, Treusch AH

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

Preclinical characterization of acyl sulfonimidamides: potential carboxylic acid bioisosteres with tunable properties.

Borhade SR, Svensson R, ..., Arvidsson PI, Sandström A

ChemMedChem 10 (3) 455-460 [2015-03-00; online 2015-01-30]

Uppsala Drug Optimization and Pharmaceutical Profiling (UDOPP)

FGF2 as a potential prognostic biomarker for proneural glioma patients.

Sooman L, Freyhult E, ..., Bergqvist M, Ekman S

Acta Oncol 54 (3) 385-394 [2015-03-00; online 2014-09-30]

Bioinformatics Short-term Support and Infrastructure (BILS) Tissue Profiling

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

Kushwaha SK, Manoharan L, ..., Hedlund K, Ahrén D

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

Bioinformatics Short-term Support and Infrastructure (BILS)

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, ..., Schultes B, Schiöth HB

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

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

Prasad P, Lennartsson A, Ekwall K

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

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

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

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

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

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

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

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

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

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

Clonal distribution of BCR-ABL1 mutations and splice isoforms by single-molecule long-read RNA sequencing.

Cavelier L, Ameur A, ..., Olsson-Strömberg U, Hermanson M

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

Bioinformatics Compute and Storage (UPPNEX) Clinical Sequencing NGI Uppsala (Uppsala Genome Center)

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

Shungin D, Winkler TW, ..., Lindgren CM, Mohlke KL

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

Data processing has major impact on the outcome of quantitative label-free LC-MS analysis.

Chawade A, Sandin M, ..., Malmström J, Levander F

J. Proteome Res. 14 (2) 676-687 [2015-02-06; online 2014-11-20]

Bioinformatics Short-term Support and Infrastructure (BILS)

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

Sinclair L, Osman OA, Bertilsson S, Eiler A

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

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, ..., Kere J, Söderhäll C

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

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

The GH receptor exon 3 deleted/full-length polymorphism is associated with central adiposity in the general population.

Glad CA, Carlsson LM, ..., Svensson PA, Johannsson G

Eur. J. Endocrinol. 172 (2) 123-128 [2015-02-00; online 2014-11-14]

Novel high-throughput screening method for identification of fungal dimorphism blockers.

Stylianou M, Uvell H, ..., Elofsson M, Urban CF

J Biomol Screen 20 (2) 285-291 [2015-02-00; online 2014-10-05]

Laboratories for Chemical Biology Umeå (LCBU)

Transcriptional responses of the bacterial antagonist Serratia plymuthica to the fungal phytopathogen Rhizoctonia solani.

Neupane S, Finlay RD, ..., Elfstrand M, Högberg N

Environ Microbiol Rep 7 (1) 123-127 [2015-02-00; online 2014-08-21]

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

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, ..., Klareskog L, Catrina AI

Ann. Rheum. Dis. 74 (2) 375-380 [2015-02-00; online 2013-11-28]

Biochemical and structural characterization of a thermostable β-glucosidase from Halothermothrix orenii for galacto-oligosaccharide synthesis.

Hassan N, Nguyen TH, ..., Divne C, Tan TC

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

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, ..., Busse HJ, Terenius O

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

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

Genome and physiology of the ascomycete filamentous fungus Xeromyces bisporus, the most xerophilic organism isolated to date.

Leong SL, Lantz H, ..., Tellgren-Roth C, Schnürer J

Environ. Microbiol. 17 (2) 496-513 [2015-02-00; online 2014-08-22]

Bioinformatics Short-term Support and Infrastructure (BILS) NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) NGI Uppsala (Uppsala Genome Center)

CTNND2-a candidate gene for reading problems and mild intellectual disability.

Hofmeister W, Nilsson D, ..., Syk Lundberg E, Lindstrand A

J. Med. Genet. 52 (2) 111-122 [2015-02-00; online 2014-12-05]

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

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

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

J. Histochem. Cytochem. 63 (2) 129-141 [2015-02-00; online 2014-11-21]

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

Multi-omic data analysis using Galaxy.

Boekel J, Chilton JM, ..., Moerland PD, Griffin TJ

Nat. Biotechnol. 33 (2) 137-139 [2015-02-00; online 2015-02-07]

Bioinformatics Short-term Support and Infrastructure (BILS) Clinical Proteomics Mass spectrometry

Associations between the 17q21 region and allergic rhinitis in 5 birth cohorts.

Fuertes E, Söderhäll C, ..., Carlsten C, Melén E

J. Allergy Clin. Immunol. 135 (2) 573-576 [2015-02-00; online 2014-09-30]

Predicting venous thrombosis in women using a combination of genetic markers and clinical risk factors.

Bruzelius M, Bottai M, ..., Hamsten A, Odeberg J

J. Thromb. Haemost. 13 (2) 219-227 [2015-02-00; online 2014-12-05]

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

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

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

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

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, ..., Micke P, Gulyas M

Cancer Lett. 356 (2 Pt B) 837-845 [2015-01-28; online 2014-12-03]

Endonuclease specificity and sequence dependence of type IIS restriction enzymes.

Lundin S, Jemt A, ..., Lexow P, Lundeberg J

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

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

Next-generation sequencing reveals low-dose effects of cationic dendrimers in primary human bronchial epithelial cells.

Feliu N, Kohonen P, ..., 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)

Intratumoral genome diversity parallels progression and predicts outcome in pediatric cancer.

Mengelbier LH, Karlsson J, ..., Mayrhofer M, Gisselsson D

Nat Commun 6 (-) 6125 [2015-01-27; online 2015-01-27]

Array and Analysis Facility NGI Uppsala (Uppsala Genome Center)

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

Johansson J, Tabor V, ..., Jalkanen S, Fuxe J

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

Proteomics. Tissue-based map of the human proteome.

Uhlén M, Fagerberg L, ..., 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)

PubMed

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

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

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

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

Mass Cytometry

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, ..., Lennartsson A, Ekwall K

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

The statistical geometry of transcriptome divergence in cell-type evolution and cancer.

Liang C, FANTOM Consortium , Forrest AR, Wagner GP

Nat Commun 6 (-) 6066 [2015-01-14; online 2015-01-14]

Bioinformatics Short-term Support and Infrastructure (BILS)

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, ..., Magnusson PK, Svensson P

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

Defects of CRB2 cause steroid-resistant nephrotic syndrome.

Ebarasi L, Ashraf S, ..., Hildebrandt F, Majumdar A

Am. J. Hum. Genet. 96 (1) 153-161 [2015-01-08; online 2015-01-06]

Zebrafish

Insights on the evolution of mycoparasitism from the genome of Clonostachys rosea.

Karlsson M, Durling MB, ..., Lee YH, Jensen DF

Genome Biol Evol 7 (2) 465-480 [2015-01-08; online 2015-01-08]

The higher frequency of IgA deficiency among Swedish twins is not explained by HLA haplotypes.

Frankowiack M, Kovanen RM, ..., Pedersen NL, Hammarström L

Genes Immun. 16 (3) 199-205 [2015-01-08; online 2015-01-08]

A secretagogin locus of the mammalian hypothalamus controls stress hormone release.

Romanov RA, Alpár A, ..., Hökfelt T, Harkany T

EMBO J. 34 (1) 36-54 [2015-01-02; online 2014-11-29]

Fluorescence Tissue Profiling

Mutagenesis. Smoking is associated with mosaic loss of chromosome Y.

Dumanski JP, Rasi C, ..., Ingelsson E, Forsberg LA

Science 347 (6217) 81-83 [2015-01-02; online 2014-12-06]

Scavenging effect of Trolox released from brushite cements.

Mestres G, Santos CF, ..., Persson C, Ott MK

Acta Biomater 11 (-) 459-466 [2015-01-00; online 2014-09-18]

Body composition and bone mineral density in women with Cushing's syndrome in remission and the association with common genetic variants influencing glucocorticoid sensitivity.

Ragnarsson O, Glad CA, ..., Wängberg B, Johannsson G

Eur. J. Endocrinol. 172 (1) 1-10 [2015-01-00; online 2014-11-26]

Expression of human leukocyte antigen class I in endocrine and exocrine pancreatic tissue at onset of type 1 diabetes.

Skog O, Korsgren S, ..., Korsgren O, Dahl-Jørgensen K

Am. J. Pathol. 185 (1) 129-138 [2015-01-00; online 2014-12-20]

Identification and functional characterization of G6PC2 coding variants influencing glycemic traits define an effector transcript at the G6PC2-ABCB11 locus.

Mahajan A, Sim X, ..., Gloyn AL, T2D-GENES consortium and GoT2D consortium

PLoS Genet. 11 (1) e1004876 [2015-01-00; online 2015-01-27]

Phenotypic plasticity and differentiation in an invasive freshwater microalga

Sassenhagen I, Wilken S, Godhe A, Rengefors K

Harmful Algae 41 (-) 38-45 [2015-01-00; online 2015-01-00]

Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis.

Avican K, Fahlgren A, ..., Dersch P, Fällman M

PLoS Pathog. 11 (1) e1004600 [2015-01-00; online 2015-01-15]

Bioinformatics Long-term Support WABI

Lessons and implications from association studies and post-GWAS analyses of cervical cancer.

Chen D, Gyllensten U

Trends Genet. 31 (1) 41-54 [2015-01-00; online 2014-12-04]

The Biobanking Analysis Resource Catalogue (BARCdb): a new research tool for the analysis of biobank samples.

Galli J, Oelrich J, ..., Ortega-Paino E, Landegren U

Nucleic Acids Res. 43 (Database issue) D1158-D1162 [2015-01-00; online 2014-10-23]

PLA Proteomics

The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling.

Gremel G, Wanders A, ..., Uhlén M, Pontén F

J. Gastroenterol. 50 (1) 46-57 [2015-01-00; online 2014-05-03]

NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) Tissue Profiling

High plasma levels of heparin-binding epidermal growth factor are associated with a more stable plaque phenotype and reduced incidence of coronary events.

Rattik S, Wigren M, ..., Gonçalves I, Nilsson J

Arterioscler. Thromb. Vasc. Biol. 35 (1) 222-228 [2015-01-00; online 2014-11-02]

Methylated RASSF1A in malignant peripheral nerve sheath tumors identifies neurofibromatosis type 1 patients with inferior prognosis.

Danielsen SA, Lind GE, ..., Picci P, Lothe RA

Neuro-oncology 17 (1) 63-69 [2015-01-00; online 2014-07-20]

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

A Machine Learning Approach to Explain Drug Selectivity to Soluble and Membrane Protein Targets.

Freyhult E, Gustafsson MG, Strömbergsson H

Mol Inform 34 (1) 44-52 [2015-01-00; online 2015-01-08]

Bioinformatics Short-term Support and Infrastructure (BILS)

Healthy Nordic diet downregulates the expression of genes involved in inflammation in subcutaneous adipose tissue in individuals with features of the metabolic syndrome.

Kolehmainen M, Ulven SM, ..., Arner P, Dahlman I

Am. J. Clin. Nutr. 101 (1) 228-239 [2015-01-00; online 2014-12-21]

The mutational landscape in pediatric acute lymphoblastic leukemia deciphered by whole genome sequencing.

Lindqvist CM, Nordlund J, ..., Syvänen AC, Berglund EC

Hum. Mutat. 36 (1) 118-128 [2015-01-00; online 2014-10-31]

Anti-Obesity Effects and Metabolism in DIO Mice of a Novel Hybrid Lipid with Lauric and Lipoic Acid

Madawala SR, Manubolu M, ..., Malmlöf K, Dutta PC

J Obes Weight Loss Ther 05 (02) - [2015-00-00; online 2015-00-00]

Cytotoxicity, in Vivo Skin Irritation and Acute Systemic Toxicity of the Mesoporous Magnesium Carbonate Upsalite

Frykstrand S, Forsgren J, ..., Strømme M, Ferraz N

JBNB 06 (04) 257-266 [2015-00-00; online 2015-00-00]