NGI Uppsala (SNP&amp;SEQ Technology Platform)

Pre- and postnatal Lactobacillus reuteri treatment alters DNA methylation of infant T helper cells.

Forsberg A, Huoman J, Söderholm S, ..., Gustafsson M, Jenmalm MC

Pediatr Allergy Immunol - (-) - [2020-03-09; online 2020-03-09]

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

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

Marques JP, Sotelo G, Galindo J, ..., Hollander J, Faria R

Sci Data 7 (1) 73 [2020-03-03; online 2020-03-03]

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

Oral Microbiota Profile Associates with Sugar Intake and Taste Preference Genes.

Esberg A, Haworth S, Hasslöf P, Lif Holgerson P, Johansson I

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

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

Immune Profiling of Human Gut-Associated Lymphoid Tissue Identifies a Role for Isolated Lymphoid Follicles in Priming of Region-Specific Immunity

Fenton TM, Jørgensen PB, Niss K, ..., Johansson-Lindbom B, Agace WW

Immunity 52 (3) 557-570.e6 [2020-03-00; online 2020-03-00]

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

The Relationship Between Polygenic Risk Scores and Cognition in Schizophrenia.

Richards AL, Pardiñas AF, Frizzati A, ..., O'Donovan MC, Walters JTR

Schizophr Bull 46 (2) 336-344 [2020-02-26; online 2019-06-18]

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

Patterns of African and Asian admixture in the Afrikaner population of South Africa.

Hollfelder N, Erasmus JC, Hammaren R, ..., Greeff JM, Schlebusch CM

BMC Biol. 18 (1) 16 [2020-02-24; online 2020-02-24]

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

Genome-wide association study of angioedema induced by angiotensin-converting enzyme inhibitor and angiotensin receptor blocker treatment.

Rasmussen ER, Hallberg P, Baranova EV, ..., Palmer CNA, Wadelius M

Pharmacogenomics J. - (-) - [2020-02-21; online 2020-02-21]

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

Genome-Wide Association Analysis in Humans Links Nucleotide Metabolism to Leukocyte Telomere Length.

Li C, Stoma S, Lotta LA, ..., Langenberg C, Codd V

Am. J. Hum. Genet. - (-) - [2020-02-20; online 2020-02-20]

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

Shared genetic risk between eating disorder- and substance-use-related phenotypes: Evidence from genome-wide association studies.

Munn-Chernoff MA, Johnson EC, Chou YL, ..., Bulik CM, Agrawal A

Addict Biol - (-) e12880 [2020-02-16; online 2020-02-16]

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

Longitudinal trajectories, correlations and mortality associations of nine biological ages across 20-years follow-up.

Li X, Ploner A, Wang Y, ..., Jylhävä J, Hägg S

pmc

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

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

Clinicopathological features and prognostic value of SOX11 in childhood acute lymphoblastic leukemia.

Grönroos T, Mäkinen A, Laukkanen S, ..., Heinäniemi M, Lohi O

pmc

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

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

CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken.

Fogelholm J, Henriksen R, Höglund A, ..., Jensen P, Wright D

pmc

Sci Rep 10 (1) 1161 [2020-01-24; online 2020-01-24]

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

SWEDEGENE-a Swedish nation-wide DNA sample collection for pharmacogenomic studies of serious adverse drug reactions.

Hallberg P, Yue QY, Eliasson E, ..., Ås J, Wadelius M

Pharmacogenomics J. - (-) - [2020-01-17; online 2020-01-17]

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

Analysis of the genetic variants associated with circulating levels of sgp130. Results from the IMPROVE study.

Bonomi A, Veglia F, Baldassarre D, ..., Gigante B, on behalf of the IMPROVE study group

Genes Immun. - (-) - [2020-01-14; online 2020-01-14]

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

Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure.

Shah S, Henry A, Roselli C, ..., Swerdlow DI, Lumbers RT

Nat Commun 11 (1) 163 [2020-01-09; online 2020-01-09]

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

DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors.

Laan L, Klar J, Sobol M, ..., Schuster J, Dahl N

pmc

Clin Epigenetics 12 (1) 9 [2020-01-08; online 2020-01-08]

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

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

Rykaczewska U, Suur BE, Röhl S, ..., Hedin U, Matic L

Circ. Res. - (-) - [2020-01-02; online 2020-01-02]

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

The Genome of the Endangered Dryas Monkey Provides New Insights into the Evolutionary History of the Vervets

van der Valk T, Gonda CM, Silegowa H, ..., Detwiler KM, Guschanski K

- 37 (1) 183-194 [2020-01-01; online 2019-09-16]

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

Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sjögren’s syndrome

Björk A, Richardsdotter Andersson E, Imgenberg-Kreuz J, ..., Nordmark G, Wahren-Herlenius M

RMD Open 6 (1) e000995 [2020-01-00; online 2020-01-07]

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

Variable neurodevelopmental and morphological phenotypes of carriers with 12q12 duplications.

Myers L, Blyth M, Moradkhani K, ..., Anderlid BM, Tammimies K

pmc

Mol Genet Genomic Med 8 (1) e1013 [2020-01-00; online 2019-11-15]

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

Association of genetic variants related to plasma fatty acids with type 2 diabetes mellitus and glycaemic traits: a Mendelian randomisation study.

Yuan S, Larsson SC

pmc

Diabetologia 63 (1) 116-123 [2020-01-00; online 2019-11-05]

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

Gene transfer across species boundaries in bryophytes: evidence from major life cycle stages in Homalothecium lutescens and H. sericeum.

Sawangproh W, Hedenäs L, Lang AS, Hansson B, Cronberg N

Ann. Bot. - (-) - [2019-12-24; online 2019-12-24]

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

Inoculum Source Determines Acetate and Lactate Production during Anaerobic Digestion of Sewage Sludge and Food Waste

Moestedt J, Westerholm M, Isaksson S, Schnürer A

Bioengineering 7 (1) 3 [2019-12-23; online 2019-12-23]

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

Genetic Screening of Plasticity Regulating Nogo-Type Signaling Genes in Migraine.

Smedfors G, Liesecke F, Ran C, ..., Karlsson TE, Carmine Belin A

Brain Sci 10 (1) - [2019-12-20; online 2019-12-20]

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

Longitudinal DNA methylation changes at MET may alter HGF/c-MET signalling in adolescents at risk for depression.

Ciuculete DM, Voisin S, Kular L, ..., Mwinyi J, Schiöth HB

Epigenetics - (-) 1-18 [2019-12-19; online 2019-12-19]

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

High genetic risk score is associated with early disease onset, damage accrual and decreased survival in systemic lupus erythematosus.

Reid S, Alexsson A, Frodlund M, ..., Rönnblom L, Leonard D

Ann. Rheum. Dis. - (-) - [2019-12-11; online 2019-12-11]

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

Comprehensive longitudinal study of epigenetic mutations in aging.

Wang Y, Karlsson R, Jylhävä J, ..., Almgren M, Hägg S

Clin Epigenetics 11 (1) 187 [2019-12-09; online 2019-12-09]

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

A Gene-Environment Interaction Between Smoking and Gene polymorphisms Provides a High Risk of Two Subgroups of Sarcoidosis.

Rivera NV, Patasova K, Kullberg S, ..., Grunewald J, Padyukov L

Sci Rep 9 (1) 18633 [2019-12-09; online 2019-12-09]

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

Epigenome-wide meta-analysis of blood DNA methylation and its association with subcortical volumes: findings from the ENIGMA Epigenetics Working Group.

Jia T, Chu C, Liu Y, ..., Schumann G, Desrivières S

Mol. Psychiatry - (-) - [2019-12-06; online 2019-12-06]

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

Replicating associations between DNA methylation and body mass index in a longitudinal sample of older twins.

Karlsson IK, Ericsson M, Wang Y, ..., Reynolds CA, Dahl Aslan AK

Int J Obes (Lond) - (-) - [2019-12-04; online 2019-12-04]

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

Population history and genetic adaptation of the Fulani nomads: inferences from genome-wide data and the lactase persistence trait.

Vicente M, Priehodová E, Diallo I, ..., Černý V, Schlebusch CM

BMC Genomics 20 (1) 915 [2019-12-02; online 2019-12-02]

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

The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons

Batista RA, Moreno-Romero J, Qiu Y, ..., Figueiredo DD, Köhler C

Elife 8 (-) - [2019-12-02; online 2019-12-02]

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

DNA methylation profiles in chronic lymphocytic leukemia patients treated with chemoimmunotherapy.

Tsagiopoulou M, Papakonstantinou N, Moysiadis T, ..., Rosenquist R, Stamatopoulos K

Clin Epigenetics 11 (1) 177 [2019-12-02; online 2019-12-02]

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

Arteria: An automation system for a sequencing core facility

Dahlberg J, Hermansson J, Sturlaugsson S, ..., Hofmann O, Larsson P

Gigascience 8 (12) - [2019-12-01; online 2019-12-11]

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

Transmission dynamics study of tuberculosis isolates with whole genome sequencing in southern Sweden

Alaridah N, Hallbäck ET, Tångrot J, ..., Kaijser B, Godaly G

Sci Rep 9 (1) - [2019-12-00; online 2019-03-20]

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

Transcriptomes of Dravet syndrome iPSC derived GABAergic cells reveal dysregulated pathways for chromatin remodeling and neurodevelopment

Schuster J, Laan L, Klar J, ..., Birnir B, Dahl N

Neurobiology of Disease 132 (-) 104583 [2019-12-00; online 2019-12-00]

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

Genotyping by low-coverage whole-genome sequencing in intercross pedigrees from outbred founders: a cost-efficient approach

Zan Y, Payen T, Lillie M, ..., Siegel PB, Carlborg Ö

Genet. Sel. Evol. 51 (1) - [2019-12-00; online 2019-08-14]

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

Transcriptomic and proteomic analyses reveal new insights into the regulation of immune pathways during adenovirus type 2 infection

Zhao H, Chen M, Valdés A, Lind SB, Pettersson U

BMC Microbiol. 19 (1) - [2019-12-00; online 2019-01-14]

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

TAF1, associated with intellectual disability in humans, is essential for embryogenesis and regulates neurodevelopmental processes in zebrafish

Gudmundsson S, Wilbe M, Filipek-Górniok B, ..., Annerén G, Bondeson ML

Sci Rep 9 (1) - [2019-12-00; online 2019-07-24]

BioImage Informatics [Collaborative] Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics Uppsala [Collaborative] Genome Engineering Zebrafish [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

doepipeline: a systematic approach to optimizing multi-level and multi-step data processing workflows

Svensson D, Sjögren R, Sundell D, Sjödin A, Trygg J

BMC Bioinformatics 20 (1) - [2019-12-00; online 2019-10-15]

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

Exploring the genetics of trotting racing ability in horses using a unique Nordic horse model

Velie BD, Lillie M, Fegraeus KJ, ..., Strand E, Lindgren G

BMC Genomics 20 (1) - [2019-12-00; online 2019-02-04]

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

Tissue-specific transposon-associated small RNAs in the gymnosperm tree, Norway spruce

Nakamura M, Köhler C, Hennig L

BMC Genomics 20 (1) - [2019-12-00; online 2019-12-19]

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

Genetic variation in CADM2 as a link between psychological traits and obesity

Morris J, Bailey MES, Baldassarre D, ..., Smith DJ, Strawbridge RJ

Sci Rep 9 (1) - [2019-12-00; online 2019-05-14]

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

Genetic Prediction of Serum 25-Hydroxyvitamin D, Calcium, and Parathyroid Hormone Levels in Relation to Development of Type 2 Diabetes: A Mendelian Randomization Study.

Yuan S, Jiang X, Michaëlsson K, Larsson SC

Diabetes Care 42 (12) 2197-2203 [2019-12-00; online 2019-09-23]

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

Comparative genomics of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members emphasizing tRNA and non-coding RNA

Behra PRK, Pettersson BMF, Das S, Dasgupta S, Kirsebom LA

BMC Evol. Biol. 19 (1) - [2019-12-00; online 2019-06-18]

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

Genomic regions of speciation and adaptation among three species of grouse

Kozma R, Rödin-Mörch P, Höglund J

Sci Rep 9 (1) - [2019-12-00; online 2019-01-28]

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

RNA Sequencing Provides Novel Insights into the Transcriptome of Aldosterone Producing Adenomas

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

Sci Rep 9 (1) - [2019-12-00; online 2019-04-18]

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

Insight into the biology of Mycobacterium mucogenicum and Mycobacterium neoaurum clade members

Behra PRK, Pettersson BMF, Ramesh M, Dasgupta S, Kirsebom LA

Sci Rep 9 (1) - [2019-12-00; online 2019-12-17]

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

The effect of Wolbachia on gene expression in Drosophila paulistorum and its implications for symbiont-induced host speciation

Baião GC, Schneider DI, Miller WJ, Klasson L

BMC Genomics 20 (1) - [2019-12-00; online 2019-06-07]

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

Studies of liver tissue identify functional gene regulatory elements associated to gene expression, type 2 diabetes, and other metabolic diseases

Cavalli M, Baltzer N, Pan G, ..., Komorowski J, Wadelius C

Hum Genomics 13 (1) - [2019-12-00; online 2019-04-29]

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

Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers

Höglund J, Rafati N, Rask-Andersen M, ..., Ek WE, Johansson Å

Sci Rep 9 (1) - [2019-12-00; online 2019-11-14]

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

Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm

Moreno-Romero J, Del Toro-De León G, Yadav VK, Santos-González J, Köhler C

Genome Biol. 20 (1) - [2019-12-00; online 2019-02-21]

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

Mercury methylating microbial communities of boreal forest soils

Xu J, Buck M, Eklöf K, ..., Bertilsson S, Bravo AG

Sci Rep 9 (1) - [2019-12-00; online 2019-01-24]

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

Oxygen induces the expression of invasion and stress response genes in the anaerobic salmon parasite Spironucleus salmonicida

Stairs CW, Kokla A, Ástvaldsson Á, ..., Svärd S, Ettema TJG

BMC Biol. 17 (1) - [2019-12-00; online 2019-03-01]

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

The genomics of major psychiatric disorders in a large pedigree from Northern Sweden

Szatkiewicz J, Crowley JJ, Adolfsson AN, ..., Adolfsson R, Sullivan PF

Transl Psychiatry 9 (1) - [2019-12-00; online 2019-02-04]

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

The genomic footprint of sexual conflict.

Sayadi A, Martinez Barrio A, Immonen E, ..., Nystedt B, Arnqvist G

Nat Ecol Evol 3 (12) 1725-1730 [2019-12-00; online 2019-11-18]

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

Sulfide level in municipal sludge digesters affects microbial community response to long-chain fatty acid loads

Shakeri Yekta S, Liu T, Axelsson Bjerg M, ..., Björn A, Schnürer A

Biotechnol Biofuels 12 (1) - [2019-12-00; online 2019-11-02]

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

The Swedish Twin Registry: Content and Management as a Research Infrastructure.

Zagai U, Lichtenstein P, Pedersen NL, Magnusson PKE

Twin Res Hum Genet - (-) 1-9 [2019-11-21; online 2019-11-21]

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

Evidence that genes involved in hedgehog signaling are associated with both bipolar disorder and high BMI.

Pisanu C, Williams MJ, Ciuculete DM, ..., Squassina A, Schiöth HB

Transl Psychiatry 9 (1) 315 [2019-11-21; online 2019-11-21]

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

Genetic predisposition to mosaic Y chromosome loss in blood

Thompson DJ, None , Genovese G, ..., None , None

Nature 575 (7784) 652-657 [2019-11-20; online 2019-11-20]

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

Genotype-dependent epigenetic regulation of DLGAP2 in alcohol use and dependence.

Meng W, Sjöholm LK, Kononenko O, ..., Rüegg J, Liu Y

Mol. Psychiatry - (-) - [2019-11-19; online 2019-11-19]

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

Genetic regulation of gene expression and splicing during a 10-year period of human aging.

Balliu B, Durrant M, Goede O, ..., Ingelsson E, Montgomery SB

pmc

Genome Biol. 20 (1) 230 [2019-11-04; online 2019-11-04]

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

EZH2 upregulates the PI3K/AKT pathway through IGF1R and MYC in clinically aggressive chronic lymphocytic leukaemia

Kosalai ST, Morsy MHA, Papakonstantinou N, ..., Rosenquist R, Kanduri M

Epigenetics 14 (11) 1125-1140 [2019-11-02; online 2019-06-26]

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

A genomic inference of the White Plymouth Rock genealogy

Guo Y, Lillie M, Zan Y, ..., Siegel PB, Carlborg Ö

Poult. Sci. 98 (11) 5272-5280 [2019-11-01; online 2019-07-15]

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

Serum Parathyroid Hormone and Risk of Coronary Artery Disease: Exploring Causality Using Mendelian Randomization.

Melhus H, Michaëlsson K, Larsson SC

J. Clin. Endocrinol. Metab. 104 (11) 5595-5600 [2019-11-01; online 2019-07-17]

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

Characterization of Bacterial Communities in Breeding Waters of Anopheles darlingi in Manaus in the Amazon Basin Malaria-Endemic Area

Nilsson LKJ, de Oliveira MR, Marinotti O, ..., de Souza AQL, Terenius O

Microb Ecol 78 (4) 781-791 [2019-11-00; online 2019-04-15]

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

Associations of autozygosity with a broad range of human phenotypes.

Clark DW, Okada Y, Moore KHS, ..., Kubo M, Wilson JF

pmc

Nat Commun 10 (1) 4957 [2019-10-31; online 2019-10-31]

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

Longitudinal changes in the frequency of mosaic chromosome Y loss in peripheral blood cells of aging men varies profoundly between individuals.

Danielsson M, Halvardson J, Davies H, ..., Dumanski JP, Forsberg LA

Eur. J. Hum. Genet. - (-) - [2019-10-25; online 2019-10-25]

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

Overexpression of chromatin remodeling and tyrosine kinase genes in iAMP21-positive acute lymphoblastic leukemia

Ivanov Öfverholm I, Zachariadis V, Taylan F, ..., Nordlund J, Barbany G

Leukemia & Lymphoma - (-) 1-10 [2019-10-22; online 2019-10-22]

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

Genetic architecture of subcortical brain structures in 38,851 individuals

Satizabal CL, Adams HHH, Hibar DP, ..., Seshadri S, Ikram MA

Nat Genet - (-) - [2019-10-21; online 2019-10-21]

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

Associations Between Attention-Deficit/Hyperactivity Disorder and Various Eating Disorders: A Swedish Nationwide Population Study Using Multiple Genetically Informative Approaches.

Yao S, Kuja-Halkola R, Martin J, ..., Bulik CM, Larsson H

Biol. Psychiatry 86 (8) 577-586 [2019-10-15; online 2019-05-15]

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

The genomic ancestry of the Scandinavian Battle Axe Culture people and their relation to the broader Corded Ware horizon

Malmström H, Günther T, Svensson EM, ..., Storå J, Jakobsson M

Proc. R. Soc. B 286 (1912) 20191528 [2019-10-09; online 2019-10-09]

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

Along the Indian Ocean coast: genomic variation in Mozambique provides new insights into the Bantu expansion.

Semo A, Gayà-Vidal M, Fortes-Lima C, ..., Schlebusch C, Rocha J

Mol. Biol. Evol. - (-) - [2019-10-08; online 2019-10-08]

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

Target genes, variants, tissues and transcriptional pathways influencing human serum urate levels.

Tin A, Marten J, Halperin Kuhns VL, ..., Vitart V, Köttgen A

Nat. Genet. - (-) - [2019-10-02; online 2019-10-02]

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

Distribution of bacteria between different milk fractions, investigated using culture‐dependent methods and molecular‐based and fluorescent microscopy approaches

Sun L, Dicksved J, Priyashantha H, Lundh Å, Johansson M

J Appl Microbiol 127 (4) 1028-1037 [2019-10-00; online 2019-07-22]

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

Genetic variations in A20 DUB domain provide a genetic link to citrullination and neutrophil extracellular traps in systemic lupus erythematosus

Odqvist L, Jevnikar Z, Riise R, ..., Collins B, Vaarala O

Ann Rheum Dis 78 (10) 1363-1370 [2019-10-00; online 2019-07-12]

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

Exploring a Pool‐seq‐only approach for gaining population genomic insights in nonmodel species

Kurland S, Wheat CW, Paz Celorio Mancera M, ..., Ryman N, Laikre L

Ecol Evol 9 (19) 11448-11463 [2019-10-00; online 2019-09-26]

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

Genetic basis and timing of a major mating system shift in Capsella

Bachmann JA, Tedder A, Laenen B, ..., Castric V, Slotte T

New Phytol 224 (1) 505-517 [2019-10-00; online 2019-08-00]

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

Predisposition to childhood acute lymphoblastic leukemia caused by a constitutional translocation disrupting ETV6.

Järviaho T, Bang B, Zachariadis V, ..., Niinimäki R, Nordgren A

Blood Adv 3 (18) 2722-2731 [2019-09-24; online 2019-09-15]

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

Discovery of Novel Sequences in 1,000 Swedish Genomes.

Eisfeldt J, Mårtensson G, Ameur A, Nilsson D, Lindstrand A

Mol. Biol. Evol. - (-) - [2019-09-24; online 2019-09-24]

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

IGEMS: The Consortium on Interplay of Genes and Environment Across Multiple Studies - An Update.

Pedersen NL, Gatz M, Finch BK, ..., Sachdev P, Whitfield KE

Twin Res Hum Genet - (-) 1-8 [2019-09-23; online 2019-09-23]

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

Hypermethylation-associated downregulation of microRNA-4456 in hypersexual disorder with putative influence on oxytocin signalling: A DNA methylation analysis of miRNA genes.

Boström AE, Chatzittofis A, Ciuculete DM, ..., Schiöth HB, Jokinen J

Epigenetics - (-) 1-16 [2019-09-22; online 2019-09-22]

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

Phylogenetic microbiota profiling in fecal samples depends on combination of sequencing depth and choice of NGS analysis method

Rajan SK, Lindqvist M, Brummer RJ, Schoultz I, Repsilber D

PLoS ONE 14 (9) e0222171 [2019-09-17; online 2019-09-17]

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

Genome-wide association meta-analyses and fine-mapping elucidate pathways influencing albuminuria.

Teumer A, Li Y, Ghasemi S, ..., Pattaro C, Köttgen A

pmc

Nat Commun 10 (1) 4130 [2019-09-11; online 2019-09-11]

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

Evaluation of the Genetic Association Between Adult Obesity and Neuropsychiatric Disease.

Stahel P, Nahmias A, Sud SK, ..., Batterham RL, Dash S

Diabetes - (-) - [2019-09-10; online 2019-09-10]

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

Recurrent convergent evolution at amino acid residue 261 in fish rhodopsin

Hill J, Enbody ED, Pettersson ME, ..., Scheerer P, Andersson L

Proc Natl Acad Sci USA 116 (37) 18473-18478 [2019-09-10; online 2019-08-26]

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

Associations of Smoking and Alcohol and Coffee Intake with Fracture and Bone Mineral Density: A Mendelian Randomization Study.

Yuan S, Michaëlsson K, Wan Z, Larsson SC

Calcif. Tissue Int. - (-) - [2019-09-04; online 2019-09-04]

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

Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast.

Tusso S, Nieuwenhuis BPS, Sedlazeck FJ, ..., Jeffares DC, Wolf JBW

pmc

Mol. Biol. Evol. 36 (9) 1975-1989 [2019-09-01; online 2019-06-22]

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

Copy number variation and neuropsychiatric problems in females and males in the general population.

Martin J, Tammimies K, Karlsson R, ..., Lichtenstein P, Magnusson PKE

Am. J. Med. Genet. B Neuropsychiatr. Genet. 180 (6) 341-350 [2019-09-00; online 2018-10-11]

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

Impact of demography on linked selection in two outcrossing Brassicaceae species

Mattila TM, Laenen B, Horvath R, ..., Savolainen O, Slotte T

Ecol Evol 9 (17) 9532-9545 [2019-09-00; online 2019-08-13]

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

Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior.

Ganna A, Verweij KJH, Nivard MG, ..., Neale BM, Zietsch BP

Science 365 (6456) - [2019-08-30; online 2019-08-31]

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

Neuroticism as a predictor of frailty in old age: a genetically informative approach.

Danielsdottir HB, Jylhävä J, Hägg S, ..., Mosing MA, Lehto K

Psychosom Med - (-) - [2019-08-28; online 2019-08-28]

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

In search of causal pathways in diabetes: a study using proteomics and genotyping data from a cross-sectional study.

Beijer K, Nowak C, Sundström J, ..., Fall T, Lind L

Diabetologia - (-) - [2019-08-24; online 2019-08-24]

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

Lack of gene flow: Narrow and dispersed differentiation islands in a triplet of Leptidea butterfly species

Talla V, Johansson A, Dincă V, ..., Wiklund C, Backström N

Mol Ecol 28 (6) 3756-3770 [2019-08-08; online 2019-08-08]

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

Classical Human Leukocyte Antigen Alleles and C4 Haplotypes Are Not Significantly Associated With Depression.

Glanville KP, Coleman JRI, Hanscombe KB, ..., O'Reilly PF, Lewis CM

Biol. Psychiatry - (-) - [2019-08-05; online 2019-08-05]

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

Maintenance of High Genome Integrity over Vegetative Growth in the Fairy-Ring Mushroom Marasmius oreades

Hiltunen M, Grudzinska-Sterno M, Wallerman O, Ryberg M, Johannesson H

Current Biology 29 (16) 2758-2765.e6 [2019-08-00; online 2019-08-00]

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

Linkage analysis revealed risk loci on 6p21 and 18p11.2-q11.2 in familial colon and rectal cancer, respectively.

von Holst S, Jiao X, Liu W, ..., Bryant P, Lindblom A

Eur. J. Hum. Genet. 27 (8) 1286-1295 [2019-08-00; online 2019-04-05]

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

Tobacco smoking induces changes in true DNA methylation, hydroxymethylation and gene expression in bronchoalveolar lavage cells.

Ringh MV, Hagemann-Jensen M, Needhamsen M, ..., Öckinger J, Ekström TJ

pmc

EBioMedicine 46 (-) 290-304 [2019-08-00; online 2019-07-12]

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

Shared and Unique Patterns of DNA Methylation in Systemic Lupus Erythematosus and Primary Sjögren's Syndrome.

Imgenberg-Kreuz J, Almlöf JC, Leonard D, ..., Sandling JK, Nordmark G

pmc

Front Immunol 10 (-) 1686 [2019-07-30; online 2019-07-30]

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

Combinations of Spok genes create multiple meiotic drivers in Podospora.

Vogan AA, Ament-Velásquez SL, Granger-Farbos A, ..., Saupe SJ, Johannesson H

pmc Dryad

Elife 8 (-) - [2019-07-26; online 2019-07-26]

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

Genetic analyses supporting colorectal, gastric, and prostate cancer syndromes.

Wallander K, Liu W, von Holst S, ..., Lindblom A, Lagerstedt-Robinson K

Genes Chromosomes Cancer - (-) - [2019-07-23; online 2019-07-23]

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

Genetic affinities among southern Africa hunter-gatherers and the impact of admixing farmer and herder populations.

Vicente M, Jakobsson M, Ebbesen P, Schlebusch CM

Mol. Biol. Evol. - (-) - [2019-07-09; online 2019-07-09]

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

Mutation dynamics of CpG dinucleotides during a recent event of vertebrate diversification

Pértille F, Da Silva VH, Johansson AM, ..., Jensen P, Guerrero-Bosagna C

Epigenetics 14 (7) 685-707 [2019-07-03; online 2019-05-09]

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

Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods.

Torabi Moghadam B, Etemadikhah M, Rajkowska G, ..., Feuk L, Carlström EL

J Psychiatr Res 114 (-) 41-47 [2019-07-00; online 2019-04-02]

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

Epigenome-wide association study of lung function level and its change.

Imboden M, Wielscher M, Rezwan FI, ..., Jarvis D, Probst-Hensch NM

pmc

Eur. Respir. J. 54 (1) - [2019-07-00; online 2019-07-04]

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

Influence of ABO Locus on PFA-100 Collagen-ADP Closure Time Is Not Totally Dependent on the Von Willebrand Factor. Results of a GWAS on GAIT-2 Project Phenotypes.

Pujol-Moix N, Martinez-Perez A, Sabater-Lleal M, ..., Souto JC, Soria JM

Int J Mol Sci 20 (13) - [2019-06-30; online 2019-06-30]

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

Allelic Variation in Taste Genes Is Associated with Taste and Diet Preferences and Dental Caries.

Eriksson L, Esberg A, Haworth S, Holgerson PL, Johansson I

pmc

Nutrients 11 (7) - [2019-06-29; online 2019-06-29]

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

Pharmacogenomics of statin-related myopathy: Meta-analysis of rare variants from whole-exome sequencing.

Floyd JS, Bloch KM, Brody JA, ..., Alfirevic A, PREDICTION-ADR Consortium and EUDRAGENE

PLoS ONE 14 (6) e0218115 [2019-06-26; online 2019-06-26]

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

Genome-wide analysis of dental caries and periodontitis combining clinical and self-reported data.

Shungin D, Haworth S, Divaris K, ..., Timpson NJ, Johansson I

pmc

Nat Commun 10 (1) 2773 [2019-06-24; online 2019-06-24]

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

Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination

Dahlberg J, Sun L, Persson Waller K, ..., Agenäs S, Dicksved J

PLoS ONE 14 (6) e0218257 [2019-06-13; online 2019-06-13]

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

Genetic basis of amphibian larval development along a latitudinal gradient: Gene diversity, selection and links with phenotypic variation in transcription factor C/EBP‐1

Meyer‐Lucht Y, Luquet E, Jóhannesdóttir F, ..., Höglund J, Laurila A

Mol Ecol - (-) - [2019-06-07; online 2019-06-07]

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

Multiancestry Genome-Wide Association Study of Lipid Levels Incorporating Gene-Alcohol Interactions

de Vries PS, Brown MR, Bentley AR, ..., Rao DC, Morrison AC

Am. J. Epidemiol. 188 (6) 1033-1054 [2019-06-01; online 2019-01-29]

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

Identification of DNA methylation patterns predisposing for an efficient response to BCG vaccination in healthy BCG-naïve subjects.

Das J, Verma D, Gustafsson M, Lerm M

pmc

Epigenetics 14 (6) 589-601 [2019-06-00; online 2019-04-22]

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

A catalog of genetic loci associated with kidney function from analyses of a million individuals

Wuttke M, None , Li Y, ..., Pattaro C, None

Nat Genet 51 (6) 957-972 [2019-06-00; online 2019-05-31]

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

Can markers of biological age predict dependency in old age?

Jylhävä J, Jiang M, Foebel AD, Pedersen NL, Hägg S

pmc

Biogerontology 20 (3) 321-329 [2019-06-00; online 2019-01-21]

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

Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers

Nadachowska‐Brzyska K, Burri R, Ellegren H

Mol Ecol 28 (9) 2290-2304 [2019-05-29; online 2019-05-29]

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

Genetical Genomics of Tonic Immobility in the Chicken.

Fogelholm J, Inkabi S, Höglund A, ..., Henriksen R, Wright D

Genes 10 (5) - [2019-05-07; online 2019-05-07]

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

Shared Genetic Risk Factors Across Carbamazepine-Induced Hypersensitivity Reactions.

Nicoletti P, Barrett S, McEvoy L, ..., Alfirevic A, Pirmohamed M

Clin. Pharmacol. Ther. - (-) - [2019-05-07; online 2019-05-07]

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

Genotype‐free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data

Warmuth VM, Ellegren H

Mol Ecol Resour 19 (3) 586-596 [2019-05-00; online 2019-04-17]

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

How Linked Selection Shapes the Diversity Landscape in Ficedula Flycatchers

Rettelbach A, Nater A, Ellegren H

Genetics 212 (1) 277-285 [2019-05-00; online 2019-03-14]

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

Interferon signature in patients with STAT1 gain‐of‐function mutation is epigenetically determined

Kaleviste E, Saare M, Leahy TR, ..., Peterson P, Kisand K

Eur. J. Immunol. 49 (5) 790-800 [2019-05-00; online 2019-03-07]

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

EnsembleCNV: an ensemble machine learning algorithm to identify and genotype copy number variation using SNP array data.

Zhang Z, Cheng H, Hong X, ..., Wang X, Hao K

pmc

Nucleic Acids Res. 47 (7) e39 [2019-04-23; online 2019-02-06]

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

A Genome-Wide Association Study of Bisphosphonate-Associated Atypical Femoral Fracture.

Kharazmi M, Michaëlsson K, Schilcher J, ..., Wadelius M, Hallberg P

Calcif. Tissue Int. - (-) - [2019-04-20; online 2019-04-20]

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

Transcriptome and Proteome Profiling of Neural Induced Pluripotent Stem Cells from Individuals with Down Syndrome Disclose Dynamic Dysregulations of Key Pathways and Cellular Functions

Sobol M, Klar J, Laan L, ..., Falk A, Dahl N

Mol Neurobiol 56 (10) 7113-7127 [2019-04-13; online 2019-04-13]

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

A multi-ancestry genome-wide study incorporating gene-smoking interactions identifies multiple new loci for pulse pressure and mean arterial pressure.

Sung YJ, de Las Fuentes L, Winkler TW, ..., Rao DC, Morrison AC

pmc

Hum. Mol. Genet. - (-) - [2019-04-10; online 2019-04-10]

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

Asthma and affective traits in adults: a genetically informative study

Lehto K, Pedersen NL, Almqvist C, Lu Y, Brew BK

Eur Respir J - (-) 1802142 [2019-04-07; online 2019-04-07]

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

Parental Education and Genetics of BMI from Infancy to Old Age: A Pooled Analysis of 29 Twin Cohorts

Silventoinen K, Jelenkovic A, Latvala A, ..., Sørensen TIA, Kaprio J

Obesity - (-) - [2019-04-05; online 2019-04-05]

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

Genetic Architectures of Childhood- and Adult-Onset Asthma Are Partly Distinct

Ferreira MAR, Mathur R, Vonk JM, ..., Koppelman GH, Almqvist C

The American Journal of Human Genetics 104 (4) 665-684 [2019-04-00; online 2019-04-00]

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

Post‐glacial colonization routes coincide with a life‐history breakpoint along a latitudinal gradient

Luquet E, Rödin Mörch P, Cortázar‐Chinarro M, ..., Höglund J, Laurila A

J Evol Biol 32 (4) 356-368 [2019-04-00; online 2019-02-14]

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

Multi-ancestry genome-wide gene–smoking interaction study of 387,272 individuals identifies new loci associated with serum lipids

Bentley AR, None , Sung YJ, ..., None , None

Nat Genet 51 (4) 636-648 [2019-04-00; online 2019-03-29]

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

Mutation patterns in a population-based non-small cell lung cancer cohort and prognostic impact of concomitant mutations in KRAS and TP53 or STK11

La Fleur L, Falk-Sörqvist E, Smeds P, ..., Moens L, Botling J

Lung Cancer 130 (-) 50-58 [2019-04-00; online 2019-04-00]

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

A geographically matched control population efficiently limits the number of candidate disease-causing variants in an unbiased whole-genome analysis

Rentoft M, Svensson D, Sjödin A, ..., Melin BS, Johansson E

PLoS ONE 14 (3) e0213350 [2019-03-27; online 2019-03-27]

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

Subsequent Event Risk in Individuals with Established Coronary Heart Disease: Design and Rationale of the GENIUS-CHD Consortium.

Patel R, Tragante V, Schmidt AF, ..., Hingorani AD, Asselbergs FW

Circ Genom Precis Med - (-) - [2019-03-21; online 2019-03-21]

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

Association of Chromosome 9p21 with Subsequent Coronary Heart Disease Events: A GENIUS-CHD Study of Individual Participant Data.

Patel RS, Schmidt AF, Tragante V, ..., Hingorani AD, Asselbergs FW

Circ Genom Precis Med - (-) - [2019-03-21; online 2019-03-21]

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

Detecting selection signatures in three Iranian sheep breeds

Manzari Z, Mehrabani‐Yeganeh H, Nejati‐Javaremi A, Moradi MH, Gholizadeh M

Anim Genet - (-) - [2019-03-18; online 2019-03-18]

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

Extended insight into the Mycobacterium chelonae-abscessus complex through whole genome sequencing of Mycobacterium salmoniphilum outbreak and Mycobacterium salmoniphilum-like strains.

Behra PRK, Das S, Pettersson BMF, ..., Ennis DG, Kirsebom LA

pmc

Sci Rep 9 (1) 4603 [2019-03-14; online 2019-03-14]

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

A rare regulatory variant in the MEF2D gene affects gene regulation and splicing and is associated with a SLE sub-phenotype in Swedish cohorts

Farias FHG, Dahlqvist J, Kozyrev SV, ..., Rönnblom L, Lindblad-Toh K

Eur J Hum Genet 27 (3) 432-441 [2019-03-01; online 2018-11-20]

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

Genome-wide meta-analysis reveals shared new loci in systemic seropositive rheumatic diseases.

Acosta-Herrera M, Kerick M, González-Serna D, ..., Mayes MD, Martin J

Ann. Rheum. Dis. 78 (3) 311-319 [2019-03-00; online 2018-12-20]

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

Protein-coding variants implicate novel genes related to lipid homeostasis contributing to body-fat distribution.

Justice AE, Karaderi T, Highland HM, ..., North KE, Lindgren CM

Nat. Genet. 51 (3) 452-469 [2019-03-00; online 2019-02-18]

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

New genetic signals for lung function highlight pathways and chronic obstructive pulmonary disease associations across multiple ancestries.

Shrine N, Guyatt AL, Erzurumluoglu AM, ..., Tobin MD, Wain LV

pmc mid

Nat. Genet. 51 (3) 481-493 [2019-03-00; online 2019-02-25]

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

Genome-wide meta-analysis identifies new loci and functional pathways influencing Alzheimer's disease risk.

Jansen IE, Savage JE, Watanabe K, ..., Andreassen OA, Posthuma D

Nat. Genet. 51 (3) 404-413 [2019-03-00; online 2019-01-07]

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

Estimating the Fitness Effect of Deleterious Mutations During the Two Phases of the Life Cycle: A New Method Applied to the Root-Rot Fungus Heterobasidion parviporum

Clergeot PH, Rode NO, Glémin S, ..., Ihrmark K, Olson Å

Genetics 211 (3) 963-976 [2019-03-00; online 2018-12-31]

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

A genome-wide association study identifies new loci for factor VII and implicates factor VII in ischemic stroke etiology.

de Vries PS, Sabater-Lleal M, Huffman JE, ..., O'Donnell CJ, Smith NL

Blood 133 (9) 967-977 [2019-02-28; online 2019-01-14]

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

Exome sequencing in 51 early onset non-familial CRC cases

Thutkawkorapin J, Lindblom A, Tham E

Mol Genet Genomic Med - (-) e605 [2019-02-27; online 2019-02-27]

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

Fine-Tuning of Sox17 and Canonical Wnt Coordinates the Permeability Properties of the Blood-Brain Barrier

Corada M, Orsenigo F, Bhat GP, ..., Magnusson P, Dejana E

Circ Res 124 (4) 511-525 [2019-02-15; online 2019-02-15]

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

Genetics and epigenetics in primary Sjögren's syndrome.

Imgenberg-Kreuz J, Rasmussen A, Sivils K, Nordmark G

Rheumatology (Oxford) - (-) - [2019-02-15; online 2019-02-15]

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

Association of the coronary artery disease risk gene GUCY1A3 with ischaemic events after coronary intervention.

Kessler T, Wolf B, Eriksson N, ..., Kastrati A, Schunkert H

Cardiovasc. Res. - (-) - [2019-02-14; online 2019-02-14]

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

Bidirectional Selection for Body Weight on Standing Genetic Variation in a Chicken Model

Lillie M, Honaker CF, Siegel PB, Carlborg Ö

G3 (Bethesda) 9 (4) 1165-1173 [2019-02-08; online 2019-02-08]

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

Introgression of resistance to Rhopalosiphum padi L. from wild barley into cultivated barley facilitated by doubled haploid and molecular marker techniques.

Åhman I, Bengtsson T

Theor. Appl. Genet. - (-) - [2019-02-02; online 2019-02-02]

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

Disentangling the genetics of lean mass.

Karasik D, Zillikens MC, Hsu YH, ..., Kiel DP, Ohlsson C

Am. J. Clin. Nutr. 109 (2) 276-287 [2019-02-01; online 2019-02-06]

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

Genome-wide association analyses of risk tolerance and risky behaviors in over 1 million individuals identify hundreds of loci and shared genetic influences.

Karlsson Linnér R, Biroli P, Kong E, ..., Koellinger PD, Beauchamp JP

Nat. Genet. 51 (2) 245-257 [2019-02-00; online 2019-01-14]

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

Whole-genome sequencing identifies complex contributions to genetic risk by variants in genes causing monogenic systemic lupus erythematosus

Almlöf JC, Nystedt S, Leonard D, ..., Sandling JK, Syvänen AC

Hum Genet 138 (2) 141-150 [2019-02-00; online 2019-02-01]

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

Two Basidiomycete Fungi in the Cortex of Wolf Lichens

Tuovinen V, Ekman S, Thor G, ..., Spribille T, Johannesson H

Current Biology 29 (3) 476-483.e5 [2019-02-00; online 2019-02-00]

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

Longitudinal changes in the genetic and environmental influences on the epigenetic clocks across old age: Evidence from two twin cohorts.

Jylhävä J, Hjelmborg J, Soerensen M, ..., Pedersen NL, Reynolds CA

pmc

EBioMedicine 40 (-) 710-716 [2019-02-00; online 2019-01-28]

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

CD99 expression is strongly associated with clinical outcome in children with B-cell precursor acute lymphoblastic leukaemia

Chen D, Camponeschi A, Wu Q, ..., Fogelstrand L, Mårtensson IL

Br J Haematol 184 (3) 418-423 [2019-02-00; online 2018-11-28]

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

Pandemrix-induced narcolepsy is associated with genes related to immunity and neuronal survival.

Hallberg P, Smedje H, Eriksson N, ..., Wadelius M, Swedegene

EBioMedicine - (-) - [2019-01-30; online 2019-01-30]

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

Carbonic Anhydrase 6 Gene Variation influences Oral Microbiota Composition and Caries Risk in Swedish adolescents.

Esberg A, Haworth S, Brunius C, Lif Holgerson P, Johansson I

pmc

Sci Rep 9 (1) 452 [2019-01-24; online 2019-01-24]

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

Multi-ancestry study of blood lipid levels identifies four loci interacting with physical activity.

Kilpeläinen TO, Bentley AR, Noordam R, ..., Rao DC, Loos RJF

pmc

Nat Commun 10 (1) 376 [2019-01-22; online 2019-01-22]

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

Genetic and lifestyle risk factors for MRI-defined brain infarcts in a population-based setting.

Chauhan G, Adams HHH, Satizabal CL, ..., Debette S, Stroke Genetics Network (SiGN), the International Stroke Genetics Consortium (ISGC), METASTROKE, Alzheimer's Disease Genetics Consortium (ADGC), and the Neurology Working Group of the Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Consortium

pmc

Neurology - (-) - [2019-01-16; online 2019-01-16]

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

Decreased Snow Cover Stimulates Under-Ice Primary Producers but Impairs Methanotrophic Capacity

Garcia SL, Szekely AJ, Bergvall C, Schattenhofer M, Peura S

mSphere 4 (1) - [2019-01-09; online 2019-01-09]

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

Trans-ethnic kidney function association study reveals putative causal genes and effects on kidney-specific disease aetiologies.

Morris AP, Le TH, Wu H, ..., Humphreys BD, Franceschini N

pmc

Nat Commun 10 (1) 29 [2019-01-03; online 2019-01-03]

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

Tracking the Epigenetic Clock Across the Human Life Course: A Meta-analysis of Longitudinal Cohort Data.

Marioni RE, Suderman M, Chen BH, ..., Deary IJ, Hägg S

pmc

J. Gerontol. A Biol. Sci. Med. Sci. 74 (1) 57-61 [2019-01-01; online 2018-05-03]

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

Exploring rare and low-frequency variants in the Saguenay–Lac-Saint-Jean population identified genes associated with asthma and allergy traits

Morin A, Madore AM, Kwan T, ..., Pastinen T, Laprise C

Eur J Hum Genet 27 (1) 90-101 [2019-01-00; online 2018-09-11]

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

Genetic risk for neuroticism predicts emotional health depending on childhood adversity

Lehto K, Karlsson I, Lundholm C, Pedersen NL

Psychol. Med. 49 (02) 260-267 [2019-01-00; online 2018-03-26]

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

Mosaic loss of chromosome Y in leukocytes matters

Forsberg LA, Halvardson J, Rychlicka-Buniowska E, ..., Ingelsson M, Dumanski JP

Nat Genet 51 (1) 4-7 [2019-01-00; online 2018-10-29]

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

ZBED6 negatively regulates insulin production, neuronal differentiation, and cell aggregation in MIN6 cells

Wang X, Jiang L, Wallerman O, ..., Welsh N, Andersson L

The FASEB Journal 33 (1) 88-100 [2019-01-00; online 2019-01-00]

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

Endosperm-specific transcriptome analysis by applying the INTACT system

Del Toro-De León G, Köhler C

Plant Reprod 32 (1) 55-61 [2018-12-26; online 2018-12-26]

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

An integrated transcriptome analysis in T-cell acute lymphoblastic leukemia links DNA methylation subgroups to dysregulated TAL1 and ANTP homeobox gene expression

Haider Z, Larsson P, Landfors M, ..., Hultdin M, Degerman S

Cancer Med - (-) - [2018-12-21; online 2018-12-21]

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

Association of Genetic Risk Factors for Psychiatric Disorders and Traits of These Disorders in a Swedish Population Twin Sample

Taylor MJ, Martin J, Lu Y, ..., Larsson H, Lichtenstein P

JAMA Psychiatry - (-) - [2018-12-19; online 2018-12-19]

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

Allele-Specific Methylation of SPDEF: A Novel Moderator of Psychosocial Stress and Substance Abuse.

Tay N, Macare C, Liu Y, ..., Schumann G, IMAGEN Consortium

Am J Psychiatry - (-) appiajp201817121360 [2018-12-11; online 2018-12-11]

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

Whole genome sequencing of consanguineous families reveals novel pathogenic variants in intellectual disability

Thuresson AC, Soussi Zander C, Zhao JJ, ..., Öhrner Y, Feuk L

Clin Genet 95 (3) 436-439 [2018-12-07; online 2018-12-07]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

BioProject

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

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

Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas

van der Valk T, Sandoval-Castellanos E, Caillaud D, ..., Dalén L, Guschanski K

GENBANK

Sci Rep 8 (1) - [2018-12-00; online 2018-04-25]

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

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

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

Clin Epigenetics 10 (1) - [2018-12-00; online 2018-12-13]

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

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

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

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

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

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

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

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

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

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

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

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

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

Genome sequencing and conservation genomics in the Scandinavian wolverine population

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

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

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

Effects of predation stress and food ration on perch gut microbiota

Zha Y, Eiler A, Johansson F, Svanbäck R

SRA

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

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

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

Hines HN, Onsbring H, Ettema TJG, Esteban GF

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

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

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

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

Dryad SRA SRA SRA SRA SRA BioProject

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

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

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

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

BioProject

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Integrated epigenomic and transcriptomic analysis reveals TP63 as a novel player in clinically aggressive chronic lymphocytic leukemia

Papakonstantinou N, Ntoufa S, Tsagiopoulou M, ..., Rosenquist R, Stamatopoulos K

Int. J. Cancer - (-) - [2018-11-16; online 2018-11-16]

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

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

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

pmc

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

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

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

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

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

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

Asexual reproduction and growth rate: independent and plastic life history traits in Neurospora crassa

Anderson JL, Nieuwenhuis BPS, Johannesson H

ISME J 13 (3) 780-788 [2018-11-09; online 2018-11-09]

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

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

Nordlund J, Bäcklin C, Raine A

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

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

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

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

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

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

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

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

pmc mid

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

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

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

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

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

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

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

Sokolowski M, Wasserman J, Wasserman D

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

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

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

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

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

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

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

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

SRA

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

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

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

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

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

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

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

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

SRA

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

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

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

Liu X, Karrenberg S

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

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

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

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

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

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

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

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

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

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

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

Hagberg N, Rönnblom L

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

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

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

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

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

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

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

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

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

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

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

Graells T, Ishak H, Larsson M, Guy L

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

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

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

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

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

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

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

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

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

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

Multi-ethnic genome-wide association study for atrial fibrillation.

Roselli C, Chaffin MD, Weng LC, ..., Lunetta KL, Ellinor PT

pmc mid

Nat. Genet. 50 (9) 1225-1233 [2018-09-00; online 2018-06-11]

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

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

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

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

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

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

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

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

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

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

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

SRA

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

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

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

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

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

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

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

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

GEO GEO

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

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

Papoli Yazdi H, Ellegren H

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

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

Substrate-Induced Response in Biogas Process Performance and Microbial Community Relates Back to Inoculum Source

Liu T, Sun L, Nordberg Å, Schnürer A

Microorganisms 6 (3) 80 [2018-08-05; online 2018-08-05]

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

Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling

Lopez-Fernandez M, Broman E, Turner S, ..., Bertilsson S, Dopson M

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

FEMS Microbiol. Ecol. 94 (8) - [2018-08-01; online 2018-06-19]

Epigenetics in pediatric acute lymphoblastic leukemia.

Nordlund J, Syvänen AC

Semin. Cancer Biol. 51 (-) 129-138 [2018-08-00; online 2017-09-05]

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

Sex-specific manifestation of genetic risk for attention deficit hyperactivity disorder in the general population.

Martin J, Taylor MJ, Rydell M, ..., Thapar A, Lichtenstein P

pmc

J Child Psychol Psychiatry 59 (8) 908-916 [2018-08-00; online 2018-02-16]

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

Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans

Cedernaes J, Schönke M, Westholm JO, ..., Zierath JR, Benedict C

Sci Adv 4 (8) eaar8590 [2018-08-00; online 2018-08-22]

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

Proteome‐wide analysis of phospho‐regulated PDZ domain interactions

Sundell GN, Arnold R, Ali M, ..., Chi CN, Ivarsson Y

Mol. Syst. Biol. 14 (8) e8129 [2018-08-00; online 2018-08-20]

Drug Discovery and Development (DDD) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Gene discovery and polygenic prediction from a genome-wide association study of educational attainment in 1.1 million individuals.

Lee JJ, Wedow R, Okbay A, ..., Benjamin DJ, Cesarini D

Nat. Genet. 50 (8) 1112-1121 [2018-08-00; online 2018-07-23]

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

Prenatal arsenic exposure is associated with increased plasma IGFBP3 concentrations in 9-year-old children partly via changes in DNA methylation.

Gliga AR, Engström K, Kippler M, ..., Raqib R, Broberg K

pmc

Arch. Toxicol. 92 (8) 2487-2500 [2018-08-00; online 2018-06-08]

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

Insights into Avian Incomplete Dosage Compensation: Sex-Biased Gene Expression Coevolves with Sex Chromosome Degeneration in the Common Whitethroat

Sigeman H, Ponnikas S, Videvall E, ..., Naurin S, Hansson B

Genes 9 (8) 373 [2018-07-26; online 2018-07-26]

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

The psoriasis risk allele HLA-Cw0602 shows evidence of association with chronic or recurrent streptococcal tonsillitis.

Haapasalo K, Koskinen LLE, Suvilehto J, ..., Jokiranta TS, Saavalainen P

Infect. Immun. - (-) - [2018-07-23; online 2018-07-23]

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

Microdeletion of 7p12.1p13, including IKZF1, causes intellectual impairment, overgrowth, and susceptibility to leukaemia.

Järviaho T, Zachariadis V, Tesi B, ..., Harila-Saari A, Nordgren A

Br. J. Haematol. - (-) - [2018-07-13; online 2018-07-13]

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

Primary glioblastoma cells for precision medicine: a quantitative portrait of genomic (in)stability during the first 30 passages.

Baskaran S, Mayrhofer M, Kultima HG, ..., Isaksson A, Nelander S

Neuro-oncology 20 (8) 1080-1091 [2018-07-05; online 2018-02-21]

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

Genome-wide association meta-analysis in 269,867 individuals identifies new genetic and functional links to intelligence.

Savage JE, Jansen PR, Stringer S, ..., Wright MJ, Posthuma D

Nat. Genet. 50 (7) 912-919 [2018-07-00; online 2018-06-25]

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

The mycoparasitic fungus Clonostachys rosea responds with both common and specific gene expression during interspecific interactions with fungal prey

Nygren K, Dubey M, Zapparata A, ..., Jensen DF, Karlsson M

SRA SRA SRA SRA SRA SRA

Evol Appl 11 (6) 931-949 [2018-07-00; online 2018-03-14]

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

The contribution of common genetic risk variants for ADHD to a general factor of childhood psychopathology.

Brikell I, Larsson H, Lu Y, ..., Lichtenstein P, Martin J

Mol. Psychiatry - (-) - [2018-06-22; online 2018-06-22]

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

Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries.

Feitosa MF, Kraja AT, Chasman DI, ..., Province MA, Levy D

dbGaP

PLoS ONE 13 (6) e0198166 [2018-06-18; online 2018-06-18]

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

Presence of Aedes and Anopheles mosquito larvae is correlated to bacteria found in domestic water-storage containers

Nilsson LKJ, Sharma A, Bhatnagar RK, Bertilsson S, Terenius O

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

FEMS Microbiol. Ecol. 94 (6) - [2018-06-01; online 2018-03-29]

Paternally expressed imprinted genes associate with hybridization barriers in Capsella

Lafon-Placette C, Hatorangan MR, Steige KA, ..., Slotte T, Köhler C

GEO

NPLANTS 4 (6) 352-357 [2018-06-00; online 2018-05-28]

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

PubMed

A genome scan for quantitative trait loci affecting average daily gain and Kleiber ratio in Baluchi Sheep.

Pasandideh M, Rahimi-Mianji G, Gholizadeh M

J. Genet. 97 (2) 493-503 [2018-06-00; online 2018-06-23]

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

Equilibrative nucleoside transporter 1 gene polymorphisms and clinical outcomes following acute coronary syndromes: findings from the PLATelet inhibition and patient Outcomes (PLATO) study.

Parker WAE, Eriksson N, Becker RC, ..., Storey RF, PLATO Investigators

Platelets - (-) 1-10 [2018-05-31; online 2018-05-31]

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

Common genetic variation in the autoimmune regulator (AIRE) locus is associated with autoimmune Addison's disease in Sweden.

Eriksson D, Bianchi M, Landegren N, ..., Rosengren Pielberg G, Kämpe O

pmc

Sci Rep 8 (1) 8395 [2018-05-30; online 2018-05-30]

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

Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function.

Davies G, Lam M, Harris SE, ..., Lencz T, Deary IJ

pmc

Nat Commun 9 (1) 2098 [2018-05-29; online 2018-05-29]

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

A genome-wide association study of IgM antibody against phosphorylcholine: shared genetics and phenotypic relationship to chronic lymphocytic leukemia.

Chen X, Gustafsson S, Whitington T, ..., Frostegård J, Magnusson PKE

Hum. Mol. Genet. 27 (10) 1809-1818 [2018-05-15; online 2018-03-17]

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

Habitual coffee consumption and cognitive function: a Mendelian randomization meta-analysis in up to 415,530 participants.

Zhou A, Taylor AE, Karhunen V, ..., Llewellyn DJ, Hyppönen E

pmc

Sci Rep 8 (1) 7526 [2018-05-14; online 2018-05-14]

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

Genome-wide association meta-analysis of circulating odd-numbered chain saturated fatty acids: Results from the CHARGE Consortium.

de Oliveira Otto MC, Lemaitre RN, Sun Q, ..., Siscovick DS, Mozaffarian D

pmc

PLoS ONE 13 (5) e0196951 [2018-05-08; online 2018-05-08]

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

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.

Wray NR, Ripke S, Mattheisen M, ..., Sullivan PF, Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium

pmc mid

Nat. Genet. 50 (5) 668-681 [2018-05-00; online 2018-04-26]

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

Sulfasalazine-Induced Agranulocytosis Is Associated With the Human Leukocyte Antigen Locus

Wadelius M, Eriksson N, Kreutz R, ..., Hallberg P, None

Clin Pharmacol Ther 103 (5) 843-853 [2018-05-00; online 2017-09-28]

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

Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies

Pent M, Hiltunen M, Põldmaa K, ..., Ryberg M, Bahram M

Environ Microbiol 20 (5) 1641-1650 [2018-05-00; online 2018-03-25]

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

Transcription profiling of peripheral B cells in antibody-positive primary Sjögren's syndrome reveals upregulated expression of CX3CR1 and a type I and type II interferon signature

Imgenberg-Kreuz J, Sandling JK, Björk A, ..., Syvänen AC, Nordmark G

Scand J Immunol 87 (5) e12662 [2018-05-00; online 2018-04-18]

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

DNA methylation mapping identifies gene regulatory effects in patients with systemic lupus erythematosus.

Imgenberg-Kreuz J, Carlsson Almlöf J, Leonard D, ..., Syvänen AC, Sandling JK

pmc

Ann. Rheum. Dis. 77 (5) 736-743 [2018-05-00; online 2018-02-01]

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

Eleven loci with new reproducible genetic associations with allergic disease risk.

Ferreira MAR, Vonk JM, Baurecht H, ..., Koppelman GH, Paternoster L

J. Allergy Clin. Immunol. - (-) - [2018-04-19; online 2018-04-19]

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

A GWAS meta-analysis from 5 population-based cohorts implicates ion channel genes in the pathogenesis of irritable bowel syndrome.

Bonfiglio F, Henström M, Nag A, ..., Zhernakova A, D'Amato M

GENBANK

Neurogastroenterol. Motil. - (-) e13358 [2018-04-19; online 2018-04-19]

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

Data quality of whole genome bisulfite sequencing on Illumina platforms.

Raine A, Liljedahl U, Nordlund J

pmc BioProject GEO

PLoS ONE 13 (4) e0195972 [2018-04-18; online 2018-04-18]

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

Genetic and Environmental Contributions to the Covariation Between Cardiometabolic Traits.

Chen X, Kuja-Halkola R, Chang Z, ..., Pedersen NL, Magnusson PKE

J Am Heart Assoc 7 (9) - [2018-04-18; online 2018-04-18]

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

Female-specific Association Between Variants on Chromosome 9 and Self-reported Diagnosis of Irritable Bowel Syndrome.

Bonfiglio F, Zheng T, Garcia-Etxebarria K, ..., Zhernakova A, D'Amato M

Gastroenterology - (-) - [2018-04-04; online 2018-04-04]

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

RNA Sequencing of Stentor Cell Fragments Reveals Transcriptional Changes during Cellular Regeneration

Onsbring H, Jamy M, Ettema TJG

GENBANK SRA

Current Biology 28 (8) 1281-1288.e3 [2018-04-00; online 2018-04-00]

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

An in vitro evaluation of browser and grazer fermentation efficiency and microbiota using European moose spring and summer foods

Krizsan SJ, Mateos-Rivera A, Bertilsson S, ..., Gidlund H, Huhtanen P

Ecol Evol 8 (8) 4183-4196 [2018-04-00; online 2018-03-31]

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

Refining the accuracy of validated target identification through coding variant fine-mapping in type 2 diabetes.

Mahajan A, Wessel J, Willems SM, ..., Rotter JI, McCarthy MI

pmc mid

Nat. Genet. 50 (4) 559-571 [2018-04-00; online 2018-04-09]

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

Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes.

Malik R, Chauhan G, Traylor M, ..., MEGASTROKE Consortium , MEGASTROKE Consortium:

Nat. Genet. 50 (4) 524-537 [2018-04-00; online 2018-03-12]

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

Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia

Valdiosera C, Günther T, Vera-Rodríguez JC, ..., Smith CI, Jakobsson M

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

Proc Natl Acad Sci USA 115 (13) 3428-3433 [2018-03-27; online 2018-03-12]

Changes in methylation within the STK32B promoter are associated with an increased risk for generalized anxiety disorder in adolescents.

Ciuculete DM, Boström AE, Tuunainen AK, ..., Mwinyi J, Schiöth HB

J Psychiatr Res 102 (-) 44-51 [2018-03-26; online 2018-03-26]

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

A Meta-Analysis of Genome-Wide Association Studies of Growth Differentiation Factor-15 Concentration in Blood.

Jiang J, Thalamuthu A, Ho JE, ..., Sachdev PS, Mather KA

pmc

Front Genet 9 (-) 97 [2018-03-23; online 2018-03-23]

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

Recurrent, low-frequency coding variants contributing to colorectal cancer in the Swedish population.

Jiao X, Liu W, Mahdessian H, ..., Dunlop M, Lindblom A

pmc

PLoS ONE 13 (3) e0193547 [2018-03-16; online 2018-03-16]

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

Biological annotation of genetic loci associated with intelligence in a meta-analysis of 87,740 individuals.

Coleman JRI, Bryois J, Gaspar HA, ..., Posthuma D, Breen G

Mol. Psychiatry - (-) - [2018-03-08; online 2018-03-08]

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

Genome-wide analysis yields new loci associating with aortic valve stenosis.

Helgadottir A, Thorleifsson G, Gretarsdottir S, ..., Holm H, Stefansson K

pmc

Nat Commun 9 (1) 987 [2018-03-07; online 2018-03-07]

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

Novel gene variants associated with cardiovascular disease in systemic lupus erythematosus and rheumatoid arthritis.

Leonard D, Svenungsson E, Dahlqvist J, ..., Criswell LA, Rönnblom L

Ann. Rheum. Dis. - (-) - [2018-03-07; online 2018-03-07]

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

Global analysis of A-to-I RNA editing reveals association with common disease variants

Franzén O, Ermel R, Sukhavasi K, ..., Schadt EE, Björkegren JLM

PeerJ 6 (-) e4466 [2018-03-06; online 2018-03-06]

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

DNA methylation holds prognostic information in relapsed precursor B-cell acute lymphoblastic leukemia.

Borssén M, Nordlund J, Haider Z, ..., Lönnerholm G, Degerman S

pmc

Clin Epigenetics 10 (-) 31 [2018-03-05; online 2018-03-05]

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

A Large-Scale Multi-ancestry Genome-wide Study Accounting for Smoking Behavior Identifies Multiple Significant Loci for Blood Pressure.

Sung YJ, Winkler TW, de Las Fuentes L, ..., Rao DC, Chasman DI

Am. J. Hum. Genet. 102 (3) 375-400 [2018-03-01; online 2018-02-15]

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

Genetic variants influencing phenotypic variance heterogeneity.

Ek WE, Rask-Andersen M, Karlsson T, ..., Gyllensten U, Johansson Å

Hum. Mol. Genet. 27 (5) 799-810 [2018-03-01; online 2018-01-13]

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

Genomic signatures of 60 years of bidirectional selection for 8-week body weight in chickens

Lillie M, Sheng ZY, Honaker CF, ..., Siegel PB, Carlborg Ö

Poult. Sci. 97 (3) 781-790 [2018-03-01; online 2017-12-20]

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

The fungus that came in from the cold: dry rot’s pre-adapted ability to invade buildings

Balasundaram SV, Hess J, Durling MB, ..., Eastwood DC, Skrede I

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

ISME J 12 (3) 791-801 [2018-03-00; online 2018-01-05]

Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases

Bravo AG, Zopfi J, Buck M, ..., Poté J, Cosio C

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

ISME J 12 (3) 802-812 [2018-03-00; online 2018-01-10]

Cleaner fish escape salmon farms and hybridize with local wrasse populations

Faust E, Halvorsen KT, Andersen P, Knutsen H, André C

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

R. Soc. open sci. 5 (3) 171752 [2018-03-00; online 2018-03-21]

The ZBED6–IGF2 axis has a major effect on growth of skeletal muscle and internal organs in placental mammals

Younis S, Schönke M, Massart J, ..., Zierath JR, Andersson L

SRA

Proc Natl Acad Sci USA 115 (9) E2048-E2057 [2018-02-27; online 2018-02-12]

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

The STAT4 SLE risk allele rs7574865[T] is associated with increased IL-12-induced IFN-γ production in T cells from patients with SLE

Hagberg N, Joelsson M, Leonard D, ..., Bryceson YT, Rönnblom L

Ann. Rheum. Dis. - (-) - [2018-02-23; online 2018-02-23]

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

Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella

Bachmann JA, Tedder A, Laenen B, Steige KA, Slotte T

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

G3 (Bethesda) 8 (4) 1327-1333 [2018-02-23; online 2018-02-23]

Disruption of Accumbens and Thalamic White Matter Connectivity Revealed by Diffusion Tensor Tractography in Young Men with Genetic Risk for Obesity

Olivo G, Latini F, Wiemerslage L, Larsson EM, Schiöth HB

Front Hum Neurosci 12 (-) - [2018-02-22; online 2018-02-22]

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

Two novel colorectal cancer risk loci in the region on chromosome 9q22.32

Thutkawkorapin J, Mahdessian H, Barber T, ..., Jiao X, Lindblom A

Oncotarget 9 (13) - [2018-02-16; online 2018-01-30]

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

CheckQC: Quick quality control of Illumina sequencing runs

Åslin M, Brandt M, Dahlberg J

JOSS 3 (22) 556 [2018-02-05; online 2018-02-05]

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

De novo mutations implicate novel genes in systemic lupus erythematosus

Pullabhatla V, Roberts AL, Lewis MJ, ..., Syvänen AC, Vyse TJ

Hum Mol Genet 27 (3) 421-429 [2018-02-01; online 2017-11-21]

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

Slow evolution of sex-biased genes in the reproductive tissue of the dioecious plant Salix viminalis

Darolti I, Wright AE, Pucholt P, Berlin S, Mank JE

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

Mol Ecol 27 (3) 694-708 [2018-02-00; online 2018-01-22]

Formation of mercury methylation hotspots as a consequence of forestry operations

Eklöf K, Bishop K, Bertilsson S, ..., Kronberg RM, Bravo AG

Science of The Total Environment 613-614 (-) 1069-1078 [2018-02-00; online 2018-02-00]

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

Copy Number Variation Analysis of 100 Twin Pairs Enriched for Neurodevelopmental Disorders.

Stamouli S, Anderlid BM, Willfors C, ..., Tammimies K, Bölte S

Twin Res Hum Genet 21 (1) 1-11 [2018-02-00; online 2018-01-08]

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

Transposon-derived small RNAs triggered by miR845 mediate genome dosage response in Arabidopsis

Borges F, Parent JS, van Ex F, ..., Köhler C, Martienssen RA

GEO GEO GEO GEO GEO SRA BioProject

Nat Genet 50 (2) 186-192 [2018-02-00; online 2018-01-15]

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

A DNA methylation biomarker of alcohol consumption.

Liu C, Marioni RE, Hedman ÅK, ..., Ingelsson E, Levy D

pmc mid dbGaP

Mol. Psychiatry 23 (2) 422-433 [2018-02-00; online 2016-11-15]

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

Paternal easiRNAs regulate parental genome dosage in Arabidopsis

Martinez G, Wolff P, Wang Z, ..., Slotkin RK, Köhler C

GEO

Nat Genet 50 (2) 193-198 [2018-02-00; online 2018-01-15]

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

Gene expression profiling across ontogenetic stages in the wood white (Leptidea sinapis) reveals pathways linked to butterfly diapause regulation.

Leal L, Talla V, Källman T, ..., Vila R, Backström N

BioProject

Mol. Ecol. 27 (4) 935-948 [2018-02-00; online 2018-02-26]

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

Dispersal timing determines the importance of priority effects in bacterial communities

Svoboda P, Lindström ES, Ahmed Osman O, Langenheder S

ISME J 12 (2) 644-646 [2018-02-00; online 2017-10-20]

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

T cells are influenced by a long non-coding RNA in the autoimmune associated PTPN2 locus

Houtman M, Shchetynsky K, Chemin K, ..., Malmström V, Padyukov L

Journal of Autoimmunity 90 (-) 28-38 [2018-02-00; online 2018-02-00]

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

Demography and mating system shape the genome-wide impact of purifying selection inArabis alpina

Laenen B, Tedder A, Nowak MD, ..., Coupland G, Slotte T

Proc Natl Acad Sci USA 115 (4) 816-821 [2018-01-23; online 2018-01-04]

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

Genetical genomics of growth in a chicken model.

Johnsson M, Henriksen R, Höglund A, ..., Jensen P, Wright D

pmc

BMC Genomics 19 (1) 72 [2018-01-23; online 2018-01-23]

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

Genome-wide association study in 79,366 European-ancestry individuals informs the genetic architecture of 25-hydroxyvitamin D levels.

Jiang X, O'Reilly PF, Aschard H, ..., Kraft P, Kiel DP

pmc

Nat Commun 9 (1) 260 [2018-01-17; online 2018-01-17]

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

Meta-analysis of exome array data identifies six novel genetic loci for lung function.

Jackson VE, Latourelle JC, Wain LV, ..., Tobin MD, London SJ

pmc

Wellcome Open Res 3 (-) 4 [2018-01-12; online 2018-01-12]

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

Rapid hybrid speciation in Darwin’s finches

Lamichhaney S, Han F, Webster MT, ..., Grant BR, Grant PR

SRA

Science 359 (6372) 224-228 [2018-01-12; online 2017-11-23]

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

Identification of shared genetic variants between schizophrenia and lung cancer.

Zuber V, Jönsson EG, Frei O, ..., Mills IG, Andreassen OA

pmc

Sci Rep 8 (1) 674 [2018-01-12; online 2018-01-12]

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

Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation

Günther T, Malmström H, Svensson EM, ..., Götherström A, Jakobsson M

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

PLoS Biol. 16 (1) e2003703 [2018-01-09; online 2018-01-09]

Angiopoietin-1 deficiency increases renal capillary rarefaction and tubulointerstitial fibrosis in mice

Loganathan K, Salem Said E, Winterrowd E, ..., Quaggin SE, Jeansson M

PLoS ONE 13 (1) e0189433 [2018-01-02; online 2018-01-02]

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

Cytokine Autoantibody Screening in the Swedish Addison Registry Identifies Patients With Undiagnosed APS1

Eriksson D, Dalin F, Eriksson GN, ..., Munoz KD, None

J Clin Endocrinol Metab 103 (1) 179-186 [2018-01-01; online 2017-10-20]

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

Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity.

Turcot V, Lu Y, Highland HM, ..., MAGIC Investigators , Understanding Society Scientific Group

pmc mid

Nat. Genet. 50 (1) 26-41 [2018-01-00; online 2017-12-22]

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

Epigenetic Changes in the CRH Gene are Related to Severity of Suicide Attempt and a General Psychiatric Risk Score in Adolescents.

Jokinen J, Boström AE, Dadfar A, ..., Åsberg M, Schiöth HB

pmc

EBioMedicine 27 (-) 123-133 [2018-01-00; online 2017-12-18]

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

Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes

Suh A, Smeds L, Ellegren H

Mol Ecol 27 (1) 99-111 [2018-01-00; online 2017-12-12]

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

Genomic consequences of intensive inbreeding in an isolated wolf population

Kardos M, Åkesson M, Fountain T, ..., Wikenros C, Ellegren H

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

Nat Ecol Evol 2 (1) 124-131 [2018-01-00; online 2017-11-20]

Methylation-based estimated biological age and cardiovascular disease

Lind L, Ingelsson E, Sundström J, Siegbahn A, Lampa E

Eur J Clin Invest - (-) e12872 [2017-12-27; online 2017-12-27]

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

A family-based genome-wide association study of chronic rhinosinusitis with nasal polyps implicates several genes in the disease pathogenesis

Bohman A, Juodakis J, Oscarsson M, ..., Bende M, Torinsson Naluai Å

PLoS ONE 12 (12) e0185244 [2017-12-18; online 2017-12-18]

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

CELSR2 is a candidate susceptibility gene in idiopathic scoliosis

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

PLoS ONE 12 (12) e0189591 [2017-12-14; online 2017-12-14]

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

Overexpression of PaNAC03, a stress induced NAC gene family transcription factor in Norway spruce leads to reduced flavonol biosynthesis and aberrant embryo development

Dalman K, Wind JJ, Nemesio-Gorriz M, ..., Ezcurra I, Elfstrand M

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

BMC Plant Biol. 17 (1) - [2017-12-00; online 2017-01-06]

Transcriptome sequencing in pediatric acute lymphoblastic leukemia identifies fusion genes associated with distinct DNA methylation profiles

Marincevic-Zuniga Y, Dahlberg J, Nilsson S, ..., Nordlund J, Syvänen AC

J Hematol Oncol 10 (1) - [2017-12-00; online 2017-08-14]

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

Large meta-analysis of genome-wide association studies identifies five loci for lean body mass

Zillikens MC, Demissie S, Hsu YH, ..., Ohlsson C, Kiel DP

Nat Commun 8 (1) - [2017-12-00; online 2017-07-19]

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

Genetic- and Lifestyle-dependent Dental Caries Defined by the Acidic Proline-rich Protein Genes PRH1 and PRH2

Strömberg N, Esberg A, Sheng N, ..., Danielsson K, Källestål C

EBioMedicine 26 (-) 38-46 [2017-12-00; online 2017-12-00]

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

Genome-wide standing variation facilitates long-term response to bidirectional selection for antibody response in chickens

Lillie M, Sheng Z, Honaker CF, ..., Siegel PB, Carlborg Ö

SRA SRA SRA SRA SRA

BMC Genomics 18 (1) - [2017-12-00; online 2017-01-18]

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

Mapping of leptin and its syntenic genes to chicken chromosome 1p

Seroussi E, Pitel F, Leroux S, ..., Anderson L, Friedman-Einat M

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

BMC Genet. 18 (1) - [2017-12-00; online 2017-08-09]

RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study

Berghoff BA, Karlsson T, Källman T, Wagner EGH, Grabherr MG

BioData Mining 10 (1) - [2017-12-00; online 2017-09-05]

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

Draft genome of the brown-rot fungus Fomitopsis pinicola GR9-4

Kancherla RP, Durling MB, Stenlid J, Högberg N

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

Data Brief 15 (-) 496-500 [2017-12-00; online 2017-12-00]

Heterogeneous Patterns of Genetic Diversity and Differentiation in European and Siberian Chiffchaff (Phylloscopus collybita abietinus/P. tristis)

Talla V, Kalsoom F, Shipilina D, Marova I, Backström N

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

G3 (Bethesda) 7 (12) 3983-3998 [2017-12-00; online 2017-10-20]

Influence of pulsed and continuous substrate inputs on freshwater bacterial community composition and functioning in bioreactors

Ricão Canelhas M, Andersson M, Eiler A, Lindström ES, Bertilsson S

SRA

Environ Microbiol 19 (12) 5078-5087 [2017-12-00; online 2017-12-04]

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

Drift, selection, or migration? Processes affecting genetic differentiation and variation along a latitudinal gradient in an amphibian

Cortázar-Chinarro M, Lattenkamp EZ, Meyer-Lucht Y, ..., Laurila A, Höglund J

BMC Evol. Biol. 17 (1) - [2017-12-00; online 2017-08-14]

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

Novel risk genes for systemic lupus erythematosus predicted by random forest classification

Almlöf JC, Alexsson A, Imgenberg-Kreuz J, ..., Sandling JK, Syvänen AC

Sci Rep 7 (1) - [2017-12-00; online 2017-07-24]

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

Detection of QTL for greasy fleece weight in sheep using a 50 K single nucleotide polymorphism chip

Ebrahimi F, Gholizadeh M, Rahimi-Mianji G, Farhadi A

Trop Anim Health Prod 49 (8) 1657-1662 [2017-12-00; online 2017-08-11]

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

Correspondence on Lovell et al.: identification of chicken genes previously assumed to be evolutionarily lost

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

Genome Biol. 18 (1) - [2017-12-00; online 2017-06-14]

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

Identification and description of three families with familial Alzheimer disease that segregate variants in the SORL1 gene

Thonberg H, Chiang HH, Lilius L, ..., Rönnbäck A, Graff C

Acta Neuropathol Commun 5 (1) - [2017-12-00; online 2017-06-09]

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

Cancer risk susceptibility loci in a Swedish population

Liu W, Jiao X, Thutkawkorapin J, Mahdessian H, Lindblom A

Oncotarget - (-) - [2017-11-25; online 2017-11-25]

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

RNA-Seq de novo assembly and differential transcriptome analysis of the nematode Ascaridia galli in relation to in vivo exposure to flubendazole

Martis MM, Tarbiat B, Tydén E, Jansson DS, Höglund J

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

PLoS ONE 12 (11) e0185182 [2017-11-03; online 2017-11-03]

Brief Report: Rare X Chromosome Abnormalities in Systemic Lupus Erythematosus and Sjögren's Syndrome

Sharma R, Harris VM, Cavett J, ..., Sivils KL, Scofield RH

Arthritis Rheumatol 69 (11) 2187-2192 [2017-11-00; online 2017-10-12]

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

An Expanded Genome-Wide Association Study of Type 2 Diabetes in Europeans

Scott RA, Scott LJ, Mägi R, ..., McCarthy MI, Prokopenko I

Diabetes 66 (11) 2888-2902 [2017-11-00; online 2017-05-31]

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

Genotype-based recall to study metabolic effects of genetic variation: a pilot study of PPARG Pro12Ala carriers.

Kamble PG, Gustafsson S, Pereira MJ, ..., Eriksson JW, Ingelsson E

pmc

Ups. J. Med. Sci. 122 (4) 234-242 [2017-11-00; online 2018-01-05]

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

Integrative studies implicate matrix metalloproteinase-12 as a culprit gene for large-artery atherosclerotic stroke

Mahdessian H, Perisic Matic L, Lengquist M, ..., Mälarstig A, None

J Intern Med 282 (5) 429-444 [2017-11-00; online 2017-08-28]

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

SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.

Ameur A, Dahlberg J, Olason P, ..., Magnusson PK, Gyllensten U

Eur. J. Hum. Genet. 25 (11) 1253-1260 [2017-11-00; online 2017-08-23]

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

Vitamin and Amino Acid Auxotrophy in Anaerobic Consortia Operating under Methanogenic Conditions

Hubalek V, Buck M, Tan B, ..., Bertilsson S, Eiler A

mSystems 2 (5) e00038-17 [2017-10-31; online 2017-10-31]

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

Exome-wide association study of plasma lipids in >300,000 individuals.

Liu DJ, Peloso GM, Yu H, ..., Willer CJ, Kathiresan S

Nat. Genet. - (-) - [2017-10-30; online 2017-10-30]

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

Shared genetic origin of asthma, hay fever and eczema elucidates allergic disease biology.

Ferreira MA, Vonk JM, Baurecht H, ..., Koppelman GH, Paternoster L

Nat. Genet. - (-) - [2017-10-30; online 2017-10-30]

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

Rapid Increase in Genome Size as a Consequence of Transposable Element Hyperactivity in Wood-White (Leptidea) Butterflies.

Talla V, Suh A, Kalsoom F, ..., Wiklund C, Backström N

BioProject GENBANK

Genome Biol Evol 9 (10) 2491-2505 [2017-10-01; online 2017-10-06]

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

The Evolution of Dark Matter in the Mitogenome of Seed Beetles

Sayadi A, Immonen E, Tellgren-Roth C, Arnqvist G

GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK

Genome Biol Evol 9 (10) 2697-2706 [2017-10-01; online 2017-09-27]

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

A MIR4646 associated methylation locus is hypomethylated in adolescent depression.

Boström AE, Ciuculete DM, Attwood M, ..., Mwinyi J, Schiöth HB

J Affect Disord 220 (-) 117-128 [2017-10-01; online 2017-05-17]

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

The evolutionary history of the DMRT3 ‘Gait keeper’ haplotype

Staiger EA, Almén MS, Promerová M, ..., Rubin CJ, Andersson L

Anim Genet 48 (5) 551-559 [2017-10-00; online 2017-07-25]

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

Reduced cell surface levels of GPI-linked markers in a new case with PIGG loss of function

Zhao JJ, Halvardson J, Knaus A, ..., Thuresson AC, Feuk L

Human Mutation 38 (10) 1394-1401 [2017-10-00; online 2017-06-12]

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

Novel genetic loci associated HLA-B*08:01 positive myasthenia gravis

Varade J, Wang N, Lim CK, ..., Xu X, Hammarström L

Journal of Autoimmunity - (-) - [2017-10-00; online 2017-10-00]

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

Artificial Selection Response due to Polygenic Adaptation from a Multilocus, Multiallelic Genetic Architecture

Zan Y, Sheng Z, Lillie M, ..., Siegel PB, Carlborg Ö

- 34 (10) 2678-2689 [2017-10-00; online 2017-07-11]

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

Identification of a novel proinsulin-associated SNP and demonstration that proinsulin is unlikely to be a causal factor in subclinical vascular remodelling using Mendelian randomisation.

Strawbridge RJ, Silveira A, Hoed MD, ..., Hamsten A, IMPROVE study group

Atherosclerosis 266 (-) 196-204 [2017-09-28; online 2017-09-28]

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

Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago

Schlebusch CM, Malmström H, Günther T, ..., Lombard M, Jakobsson M

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

Science - (-) eaao6266 [2017-09-28; online 2017-09-28]

Epidemiological characterization of a nosocomial outbreak of extended spectrum β-lactamase Escherichia coli ST-131 confirms the clinical value of core genome multilocus sequence typing

Woksepp H, Ryberg A, Berglind L, Schön T, Söderman J

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

APMIS - (-) - [2017-09-28; online 2017-09-28]

Anti-mycobacterial activity correlates with altered DNA methylation pattern in immune cells from BCG-vaccinated subjects.

Verma D, Parasa VR, Raffetseder J, ..., Netea M, Lerm M

pmc

Sci Rep 7 (1) 12305 [2017-09-26; online 2017-09-26]

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

Genetic risk scores and family history as predictors of schizophrenia in Nordic registers.

Lu Y, Pouget JG, Andreassen OA, ..., Werge T, Sullivan PF

Psychol Med - (-) 1-9 [2017-09-25; online 2017-09-25]

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

Impact of common genetic determinants of Hemoglobin A1c on type 2 diabetes risk and diagnosis in ancestrally diverse populations: A transethnic genome-wide meta-analysis

Wheeler E, Leong A, Liu CT, ..., None , None

PLoS Med. 14 (9) e1002383 [2017-09-12; online 2017-09-12]

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

A practical guide to build de-novo assemblies for single tissues of non-model organisms: the example of a Neotropical frog

Montero-Mendieta S, Grabherr M, Lantz H, ..., Webster MT, Vilà C

SRA GENBANK BioProject

PeerJ 5 (-) e3702 [2017-09-01; online 2017-09-01]

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

Novel Blood Pressure Locus and Gene Discovery Using Genome-Wide Association Study and Expression Data Sets From Blood and the KidneyNovelty and Significance

Wain LV, Vaez A, Jansen R, ..., None , None

GEO

Hypertension 70 (3) e4-e19 [2017-09-00; online 2017-07-24]

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

Regulation of gene expression is associated with tolerance of the Arctic copepod Calanus glacialis to CO2-acidified sea water

Bailey A, De Wit P, Thor P, ..., Thompson C, Hop H

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

Ecol Evol 7 (18) 7145-7160 [2017-09-00; online 2017-08-02]

The relative contribution of DNA methylation and genetic variants on protein biomarkers for human diseases.

Ahsan M, Ek WE, Rask-Andersen M, ..., Gyllensten U, Johansson Å

pmc GEO

PLoS Genet. 13 (9) e1007005 [2017-09-00; online 2017-09-15]

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

A genomic exploration identifies mechanisms that may explain adverse cardiovascular effects of COX-2 inhibitors.

Brænne I, Willenborg C, Tragante V, ..., Erdmann J, Schunkert H

pmc

Sci Rep 7 (1) 10252 [2017-08-31; online 2017-08-31]

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

Genomic correlates of glatiramer acetate adverse cardiovascular effects lead to a novel locus mediating coronary risk

Brænne I, Zeng L, Willenborg C, ..., None , None

PLoS ONE 12 (8) e0182999 [2017-08-22; online 2017-08-22]

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

Tea and coffee consumption in relation to DNA methylation in four European cohorts.

Ek WE, Tobi EW, Ahsan M, ..., Johansson Å, Epigenome-Wide Association Study Consortium

Hum. Mol. Genet. 26 (16) 3221-3231 [2017-08-15; online 2017-05-24]

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

Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life

Spang A, Caceres EF, Ettema TJG

Science 357 (6351) eaaf3883 [2017-08-11; online 2017-08-10]

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

Comparison of four DNA extraction methods for comprehensive assessment of 16S rRNA bacterial diversity in marine biofilms using high-throughput sequencing

Corcoll N, Österlund T, Sinclair L, ..., Backhaus T, Eriksson KM

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

FEMS Microbiol. Lett. 364 (14) - [2017-08-01; online 2017-06-29]

Low-Frequency Synonymous Coding Variation in CYP2R1 Has Large Effects on Vitamin D Levels and Risk of Multiple Sclerosis

Manousaki D, Dudding T, Haworth S, ..., Timpson NJ, Richards JB

The American Journal of Human Genetics 101 (2) 227-238 [2017-08-00; online 2017-08-00]

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

CKM Glu83Gly Is Associated With Blunted Creatine Kinase Variation, but Not With Myalgia

Siddiqui MK, Veluchamy A, Maroteau C, ..., Chasman DI, Palmer CNA

Circ Cardiovasc Genet 10 (4) e001737 [2017-08-00; online 2017-08-08]

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

Genome-Wide Association Study of Angioedema Induced by Ace Inhibitors or Arbs in Sweden

Wadelius M, Eriksson N, Johansson C, ..., Magnusson PKE, Hallberg P

Clinical Therapeutics 39 (8) e76 [2017-08-00; online 2017-08-00]

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

Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations.

Hollfelder N, Schlebusch CM, Günther T, ..., Hassan HY, Jakobsson M

pmc Dryad

PLoS Genet. 13 (8) e1006976 [2017-08-00; online 2017-08-24]

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

Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa

Vijay N, Weissensteiner M, Burri R, ..., Ellegren H, Wolf JBW

Mol Ecol 26 (16) 4284-4295 [2017-08-00; online 2017-06-27]

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

Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference

Shafer ABA, Peart CR, Tusso S, ..., Wheat CW, Wolf JBW

BioProject Dryad Dryad

Methods Ecol Evol 8 (8) 907-917 [2017-08-00; online 2016-11-28]

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

Differences in genetic and environmental variation in adult BMI by sex, age, time period, and region: an individual-based pooled analysis of 40 twin cohorts

Silventoinen K, Jelenkovic A, Sund R, ..., Sørensen TI, Kaprio J

Am J Clin Nutr 106 (2) 457-466 [2017-08-00; online 2017-07-05]

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

Poorly known microbial taxa dominate the microbiome of permafrost thaw ponds

Wurzbacher C, Nilsson RH, Rautio M, Peura S

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

ISME J 11 (8) 1938-1941 [2017-08-00; online 2017-04-21]

Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds

Kawakami T, Mugal CF, Suh A, ..., Smeds L, Ellegren H

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

Mol Ecol 26 (16) 4158-4172 [2017-08-00; online 2017-07-05]

Haploid selection within a single ejaculate increases offspring fitness

Alavioon G, Hotzy C, Nakhro K, ..., Maklakov AA, Immler S

Proc Natl Acad Sci USA 114 (30) 8053-8058 [2017-07-25; online 2017-07-11]

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

Association analyses based on false discovery rate implicate new loci for coronary artery disease

Nelson CP, Goel A, Butterworth AS, ..., Watkins H, Deloukas P

Nat Genet 49 (9) 1385-1391 [2017-07-17; online 2017-07-17]

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

Loss of DIP2C in RKO cells stimulates changes in DNA methylation and epithelial-mesenchymal transition.

Larsson C, Ali MA, Pandzic T, ..., He L, Sjöblom T

pmc

BMC Cancer 17 (1) 487 [2017-07-17; online 2017-07-17]

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

Transancestral mapping and genetic load in systemic lupus erythematosus.

Langefeld CD, Ainsworth HC, Cunninghame Graham DS, ..., Gaffney PM, Vyse TJ

pmc

Nat Commun 8 (-) 16021 [2017-07-17; online 2017-07-17]

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

Genotype–covariate interaction effects and the heritability of adult body mass index

Robinson MR, English G, Moser G, ..., Cesarini D, Visscher PM

Nat Genet 49 (8) 1174-1181 [2017-07-10; online 2017-07-10]

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

Genetics of phenotypic plasticity and biomass traits in hybrid willows across contrasting environments and years

Berlin S, Hallingbäck HR, Beyer F, ..., Weih M, Rönnberg-Wästljung AC

- 120 (1) 87-100 [2017-07-01; online 2017-04-25]

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

A Low-Frequency Inactivating AKT2 Variant Enriched in the Finnish Population Is Associated With Fasting Insulin Levels and Type 2 Diabetes Risk.

Manning A, Highland HM, Gasser J, ..., Gloyn AL, Lindgren CM

pmc mid

Diabetes 66 (7) 2019-2032 [2017-07-00; online 2017-03-24]

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

EGR2 mutations define a new clinically aggressive subgroup of chronic lymphocytic leukemia

Young E, Noerenberg D, Mansouri L, ..., Rosenquist R, Damm F

Leukemia 31 (7) 1547-1554 [2017-07-00; online 2017-01-03]

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

Relations between lipoprotein(a) concentrations, LPA genetic variants, and the risk of mortality in patients with established coronary heart disease: a molecular and genetic association study

Zewinger S, Kleber ME, Tragante V, ..., März W, Speer T

The Lancet Diabetes & Endocrinology 5 (7) 534-543 [2017-07-00; online 2017-07-00]

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

Blood transcriptomes and de novo identification of candidate loci for mating success in lekking great snipe (Gallinago media)

Höglund J, Wang B, Saether SA, ..., Kålås JA, Ekblom R

Mol Ecol 26 (13) 3458-3471 [2017-07-00; online 2017-04-28]

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

Genomewide analysis of admixture and adaptation in the Africanized honeybee.

Nelson RM, Wallberg A, Simões ZLP, Lawson DJ, Webster MT

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

Mol. Ecol. 26 (14) 3603-3617 [2017-07-00; online 2017-04-24]

Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate

Feng C, Pettersson M, Lamichhaney S, ..., Folkvord A, Andersson L

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

Elife 6 (-) - [2017-06-30; online 2017-06-30]

Identification of a Sjögren's syndrome susceptibility locus at OAS1 that influences isoform switching, protein expression, and responsiveness to type I interferons

Li H, Reksten TR, Ice JA, ..., Sivils KL, None

PLoS Genet. 13 (6) e1006820 [2017-06-22; online 2017-06-22]

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

Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions

Shungin D, Deng WQ, Varga TV, ..., Franks PW, None

PLoS Genet. 13 (6) e1006812 [2017-06-14; online 2017-06-14]

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

Genetic loci associated with heart rate variability and their effects on cardiac disease risk.

Nolte IM, Munoz ML, Tragante V, ..., Snieder H, de Geus EJC

pmc

Nat Commun 8 (-) 15805 [2017-06-14; online 2017-06-14]

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

Functional and Compositional Stability of Bacterial Metacommunities in Response to Salinity Changes

Berga M, Zha Y, Székely AJ, Langenheder S

Front Microbiol 8 (-) - [2017-06-08; online 2017-06-08]

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

Fast and general tests of genetic interaction for genome-wide association studies

Frånberg M, Strawbridge RJ, Hamsten A, ..., Sennblad B, None

PLoS Comput. Biol. 13 (6) e1005556 [2017-06-06; online 2017-06-06]

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

Methylation of HPA axis related genes in men with hypersexual disorder

Jokinen J, Boström AE, Chatzittofis A, ..., Arver S, Schiöth HB

Psychoneuroendocrinology 80 (-) 67-73 [2017-06-00; online 2017-06-00]

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

Methylation of HPA axis related genes in men with hypersexual disorder.

Jokinen J, Boström AE, Chatzittofis A, ..., Arver S, Schiöth HB

Psychoneuroendocrinology 80 (-) 67-73 [2017-06-00; online 2017-03-10]

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

A DNA methylation site within the KLF13 gene is associated with orexigenic processes based on neural responses and ghrelin levels.

Wiemerslage L, Islam R, van der Kamp C, ..., Benedict C, Schiöth HB

Int J Obes (Lond) 41 (6) 990-994 [2017-06-00; online 2017-02-14]

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

No evidence for MHC class II-based non-random mating at the gametic haplotype in Atlantic salmon

Promerová M, Alavioon G, Tusso S, Burri R, Immler S

Heredity 118 (6) 563-567 [2017-06-00; online 2017-01-18]

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

Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches

Han F, Lamichhaney S, Grant BR, ..., Andersson L, Webster MT

Genome Res. 27 (6) 1004-1015 [2017-06-00; online 2017-04-25]

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

Large-Scale Identification of Common Trait and Disease Variants Affecting Gene Expression

Hauberg ME, Zhang W, Giambartolomei C, ..., Domenici E, Devlin B

The American Journal of Human Genetics 100 (6) 885-894 [2017-06-00; online 2017-06-00]

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

Contribution of different bacterial dispersal sources to lakes: Population and community effects in different seasons

Comte J, Berga M, Severin I, Logue JB, Lindström ES

Environ Microbiol 19 (6) 2391-2404 [2017-06-00; online 2017-05-05]

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

Genetic susceptibility to cardiovascular disease and risk of dementia

Karlsson IK, Ploner A, Song C, ..., Pedersen NL, Hägg S

Transl Psychiatry 7 (5) e1142 [2017-05-30; online 2017-05-30]

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

Genome-wide association meta-analysis of 78,308 individuals identifies new loci and genes influencing human intelligence

Sniekers S, Stringer S, Watanabe K, ..., van Duijn CM, Posthuma D

Nat Genet 49 (7) 1107-1112 [2017-05-22; online 2017-05-22]

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

Two extended haplotype blocks are associated with adaptation to high altitude habitats in East African honey bees.

Wallberg A, Schöning C, Webster MT, Hasselmann M

pmc BioProject Dryad

PLoS Genet. 13 (5) e1006792 [2017-05-00; online 2017-05-25]

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

Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations

Wang M, Uebbing S, Ellegren H

Genome Biol Evol 9 (5) 1266-1279 [2017-05-00; online 2017-05-01]

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

Combination of short-read, long-read, and optical mapping assemblies reveals large-scale tandem repeat arrays with population genetic implications.

Weissensteiner MH, Pang AWC, Bunikis I, ..., Suh A, Wolf JBW

pmc

Genome Res. 27 (5) 697-708 [2017-05-00; online 2017-03-30]

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

QTL mapping of stress related gene expression in a cross between domesticated chickens and ancestral red junglefowl

Fallahsharoudi A, de Kock N, Johnsson M, ..., Wright D, Jensen P

Molecular and Cellular Endocrinology 446 (-) 52-58 [2017-05-00; online 2017-05-00]

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

Loss of chromosome Y (LOY) in blood cells is associated with increased risk for disease and mortality in aging men

Forsberg LA

Hum Genet 136 (5) 657-663 [2017-05-00; online 2017-04-19]

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

Does the sex of one's co-twin affect height and BMI in adulthood? A study of dizygotic adult twins from 31 cohorts.

Bogl LH, Jelenkovic A, Vuoksimaa E, ..., Silventoinen K, Kaprio J

pmc

Biol Sex Differ 8 (-) 14 [2017-04-27; online 2017-04-27]

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

Genome-wide meta-analysis of 241,258 adults accounting for smoking behaviour identifies novel loci for obesity traits

Justice AE, Winkler TW, Feitosa MF, ..., North KE, Cupples LA

Nat Commun 8 (-) 14977 [2017-04-26; online 2017-04-26]

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

Parallel adaptive evolution of geographically distant herring populations on both sides of the North Atlantic Ocean

Lamichhaney S, Fuentes-Pardo AP, Rafati N, ..., Ruzzante DE, Andersson L

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

Proc Natl Acad Sci USA 114 (17) E3452-E3461 [2017-04-25; online 2017-04-07]

Genomic analyses identify hundreds of variants associated with age at menarche and support a role for puberty timing in cancer risk

Day FR, Thompson DJ, Helgason H, ..., Ong KK, Perry JRB

Nat Genet 49 (6) 834-841 [2017-04-24; online 2017-04-24]

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

Gain-of-function SAMD9L mutations cause a syndrome of cytopenia, immunodeficiency, MDS, and neurological symptoms

Tesi B, Davidsson J, Voss M, ..., Cammenga J, Bryceson YT

Blood 129 (16) 2266-2279 [2017-04-20; online 2017-02-15]

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

Large-scale analyses of common and rare variants identify 12 new loci associated with atrial fibrillation

Christophersen IE, Rienstra M, Roselli C, ..., Lubitz SA, Ellinor PT

Nat Genet 49 (6) 946-952 [2017-04-17; online 2017-04-17]

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

Adaptation to infectious disease exposure in indigenous Southern African populations

Owers KA, Sjödin P, Schlebusch CM, ..., Soodyall H, Jakobsson M

Proc. R. Soc. B 284 (1852) 20170226 [2017-04-12; online 2017-04-05]

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

Large-scale genome-wide analysis identifies genetic variants associated with cardiac structure and function

Wild PS, Felix JF, Schillert A, ..., Vasan RS, Dörr M

J Clin Invest. 127 (5) 1798-1812 [2017-04-10; online 2017-04-10]

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

SPlinted Ligation Adapter Tagging (SPLAT), a novel library preparation method for whole genome bisulphite sequencing

Raine A, Manlig E, Wahlberg P, Syvänen AC, Nordlund J

Nucleic Acids Res 45 (6) e36-e36 [2017-04-07; online 2016-11-29]

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

Interactions of Freshwater Cyanobacteria with Bacterial Antagonists

Osman OA, Beier S, Grabherr M, Bertilsson S

Appl. Environ. Microbiol. 83 (7) e02634-16 [2017-04-01; online 2017-01-23]

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

Epigenome-wide DNA methylation study of IgE concentration in relation to self-reported allergies.

Ek WE, Ahsan M, Rask-Andersen M, ..., Gyllensten U, Johansson Å

Epigenomics 9 (4) 407-418 [2017-04-00; online 2017-03-21]

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

Mapping of 79 loci for 83 plasma protein biomarkers in cardiovascular disease.

Folkersen L, Fauman E, Sabater-Lleal M, ..., Hamsten A, Mälarstig A

pmc

PLoS Genet. 13 (4) e1006706 [2017-04-00; online 2017-04-03]

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

Whole-Genome Bisulfite Sequencing of Human Pancreatic Islets Reveals Novel Differentially Methylated Regions in Type 2 Diabetes Pathogenesis

Volkov P, Bacos K, Ofori JK, ..., Rönn T, Ling C

Diabetes 66 (4) 1074-1085 [2017-04-00; online 2017-01-04]

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

PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c.

Pan G, Ameur A, Enroth S, ..., Gyllensten U, Wadelius C

pmc

Nucleic Acids Res. 45 (5) 2408-2422 [2017-03-17; online 2016-12-10]

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

Microbial community assembly and evolution in subseafloor sediment

Starnawski P, Bataillon T, Ettema TJG, ..., Schramm A, Kjeldsen KU

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

Proc Natl Acad Sci USA 114 (11) 2940-2945 [2017-03-14; online 2017-02-27]

Damaged reward areas in human alcoholics: neuronal proportion decline and astrocyte activation.

Sarkisyan D, Bazov I, Watanabe H, ..., Yakovleva T, Bakalkin G

Acta Neuropathol. 133 (3) 485-487 [2017-03-00; online 2017-01-17]

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

DNA methylation profiling of pediatric B-cell lymphoblastic leukemia with KMT2A rearrangement identifies hypomethylation at enhancer sites.

Bergmann AK, Castellano G, Alten J, ..., Schrappe M, Siebert R

Pediatr Blood Cancer 64 (3) - [2017-03-00; online 2016-10-28]

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

A genetic risk score is significantly associated with statin therapy response in the elderly population.

Ciuculete DM, Bandstein M, Benedict C, ..., Schiöth HB, Mwinyi J

Clin. Genet. 91 (3) 379-385 [2017-03-00; online 2016-12-13]

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

Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in Ficedula Flycatcher Genome Sequences

Kardos M, Qvarnström A, Ellegren H

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

Genetics 205 (3) 1319-1334 [2017-03-00; online 2017-01-18]

Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting

Dutoit L, Vijay N, Mugal CF, ..., Wolf J, Ellegren H

Proc. R. Soc. B 284 (1849) 20162756 [2017-02-22; online 2017-02-15]

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

Genome-wide Association for Major Depression Through Age at Onset Stratification: Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium.

Power RA, Tansey KE, Buttenschøn HN, ..., Breen G, Lewis CM

pmc

Biol. Psychiatry 81 (4) 325-335 [2017-02-15; online 2016-08-16]

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

Distinct Anaerobic Bacterial Consumers of Cellobiose-Derived Carbon in Boreal Fens with Different CO2/CH4 Production Ratios

Juottonen H, Eiler A, Biasi C, ..., Yrjälä K, Fritze H

SRA

Appl. Environ. Microbiol. 83 (4) e02533-16 [2017-02-15; online 2016-12-02]

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

Detection of Somatic Mutations in Gastroenteropancreatic Neuroendocrine Tumors Using Targeted Deep Sequencing

BACKMAN S, NORLÉN O, ERIKSSON B, ..., STÅLBERG P, CRONA J

AR 37 (2) 705-712 [2017-02-10; online 2017-02-10]

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

Rare and low-frequency coding variants alter human adult height.

Marouli E, Graff M, Medina-Gomez C, ..., Deloukas P, Lettre G

pmc mid

Nature 542 (7640) 186-190 [2017-02-09; online 2017-02-01]

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

Posttranscriptional Regulation in Adenovirus Infected Cells

Zhao H, Konzer A, Mi J, ..., Pettersson U, Lind SB

J. Proteome Res. 16 (2) 872-888 [2017-02-03; online 2016-12-13]

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

Causal Effect of Genetic Variants Associated With Body Mass Index on Multiple Sclerosis Susceptibility.

Gianfrancesco MA, Glymour MM, Walter S, ..., Alfredsson L, Barcellos LF

pmc

Am. J. Epidemiol. 185 (3) 162-171 [2017-02-01; online 2017-01-12]

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

Evidence for three genetic loci involved in both anorexia nervosa risk and variation of body mass index.

Hinney A, Kesselmeier M, Jall S, ..., Müller TD, Hebebrand J

pmc mid

Mol. Psychiatry 22 (2) 192-201 [2017-02-00; online 2016-05-18]

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

Distinct global binding patterns of the Wilms tumor gene 1 (WT1) -KTS and +KTS isoforms in leukemic cells.

Ullmark T, Järvstråt L, Sandén C, ..., Nilsson B, Gullberg U

pmc

Haematologica 102 (2) 336-345 [2017-02-00; online 2016-09-11]

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

A meta-analysis of reflux genome-wide association studies in 6750 Northern Europeans from the general population.

Bonfiglio F, Hysi PG, Ek W, ..., Schmidt PT, D'Amato M

Neurogastroenterol. Motil. 29 (2) - [2017-02-00; online 2016-08-04]

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

Novel seminal fluid proteins in the seed beetleCallosobruchus maculatusidentified by a proteomic and transcriptomic approach

Bayram H, Sayadi A, Goenaga J, Immonen E, Arnqvist G

Insect Mol Biol 26 (1) 58-73 [2017-02-00; online 2016-10-24]

Bioinformatics Compute and Storage [Service] Mass Spectrometry-based Proteomics, Uppsala [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Genetic and Targeted eQTL Mapping Reveals Strong Candidate Genes Modulating the Stress Response During Chicken Domestication

Fallahsharoudi A, de Kock N, Johnsson M, ..., Wright D, Jensen P

G3 (Bethesda) 7 (2) 497-504 [2017-02-00; online 2016-12-14]

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

PCSK9 genetic variants and risk of type 2 diabetes: a mendelian randomisation study.

Schmidt AF, Swerdlow DI, Holmes MV, ..., UCLEB consortium , Sattar N

pmc

Lancet Diabetes Endocrinol 5 (2) 97-105 [2017-02-00; online 2016-12-03]

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

Genomic analysis reveals major determinants ofcis-regulatory variation inCapsella grandiflora

Steige KA, Laenen B, Reimegård J, Scofield DG, Slotte T

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

Proc Natl Acad Sci USA 114 (5) 1087-1092 [2017-01-31; online 2017-01-17]

Meta-Analysis of Genome-Wide Association Studies for Abdominal Aortic Aneurysm Identifies Four New Disease-Specific Risk Loci.

Jones GT, Tromp G, Kuivaniemi H, ..., Samani NJ, Bown MJ

pmc mid

Circ. Res. 120 (2) 341-353 [2017-01-20; online 2016-12-03]

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

Novel genetic loci associated with hippocampal volume.

Hibar DP, Adams HH, Jahanshad N, ..., Thompson PM, Ikram MA

pmc

Nat Commun 8 (-) 13624 [2017-01-18; online 2017-01-18]

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

A methylome-wide mQTL analysis reveals associations of methylation sites with GAD1 and HDAC3 SNPs and a general psychiatric risk score.

Ciuculete DM, Boström AE, Voisin S, ..., Mwinyi J, Schiöth HB

pmc

Transl Psychiatry 7 (1) e1002 [2017-01-17; online 2017-01-17]

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

Asgard archaea illuminate the origin of eukaryotic cellular complexity

Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, ..., Spang A, Ettema TJG

BioProject GENBANK GENBANK BioProject GENBANK BioProject GENBANK GENBANK GENBANK GENBANK GENBANK

Nature 541 (7637) 353-358 [2017-01-11; online 2017-01-11]

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

Mapping eQTLs with RNA-seq reveals novel susceptibility genes, non-coding RNAs and alternative-splicing events in systemic lupus erythematosus

Odhams CA, Cortini A, Chen L, ..., Vyse TJ, Cunninghame Graham DS

Hum. Mol. Genet. - (-) ddw417 [2017-01-05; online 2017-01-05]

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

Imputation-Based Fine-Mapping Suggests That Most QTL in an Outbred Chicken Advanced Intercross Body Weight Line Are Due to Multiple, Linked Loci.

Brandt M, Ahsan M, Honaker CF, Siegel PB, Carlborg Ö

pmc

G3 (Bethesda) 7 (1) 119-128 [2017-01-05; online 2017-01-05]

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

Genome-wide association study with additional genetic and post-transcriptional analyses reveals novel regulators of plasma factor XI levels

Sennblad B, Basu S, Mazur J, ..., Trégouët DA, Sabater-Lleal M

Hum. Mol. Genet. - (-) ddw401 [2017-01-04; online 2017-01-04]

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

Epigenetic changes as prognostic predictors in endometrial carcinomas.

Farkas SA, Sorbe BG, Nilsson TK

pmc

Epigenetics 12 (1) 19-26 [2017-01-02; online 2016-11-23]

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

Emerging microbiota during cold storage and temperature abuse of ready-to-eat salad

Söderqvist K, Ahmed Osman O, Wolff C, ..., Vågsholm I, Boqvist S

Infect Ecol Epidemiol 7 (1) 1328963 [2017-01-00; online 2017-06-06]

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

A combined large-scale meta-analysis identifies COG6 as a novel shared risk locus for rheumatoid arthritis and systemic lupus erythematosus.

Márquez A, Vidal-Bralo L, Rodríguez-Rodríguez L, ..., Alarcón-Riquelme ME, Martín J

Ann. Rheum. Dis. 76 (1) 286-294 [2017-01-00; online 2016-05-20]

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

Association of Body Mass Index with DNA Methylation and Gene Expression in Blood Cells and Relations to Cardiometabolic Disease: A Mendelian Randomization Approach.

Mendelson MM, Marioni RE, Joehanes R, ..., Levy D, Deary IJ

pmc

PLoS Med. 14 (1) e1002215 [2017-01-00; online 2017-01-17]

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

Multiethnic genome-wide meta-analysis of ectopic fat depots identifies loci associated with adipocyte development and differentiation.

Chu AY, Deng X, Fisher VA, ..., Steinhauser ML, Fox CS

Nat. Genet. 49 (1) 125-130 [2017-01-00; online 2016-12-06]

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

Epigenetic Patterns in Blood Associated With Lipid Traits Predict Incident Coronary Heart Disease Events and Are Enriched for Results From Genome-Wide Association Studies.

Hedman ÅK, Mendelson MM, Marioni RE, ..., Levy D, Ingelsson E

pmc mid

Circ Cardiovasc Genet 10 (1) - [2017-01-00; online 2017-02-19]

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

Genetic and methylation variation in the CYP2B6 gene is related to circulating p,p'-dde levels in a population-based sample.

Lind L, Ng E, Ingelsson E, ..., Morris AP, Lind PM

pmc

Environ Int 98 (-) 212-218 [2017-01-00; online 2016-11-15]

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

Investigating kinship of Neolithic post-LBK human remains from Krusza Zamkowa, Poland using ancient DNA.

Juras A, Chyleński M, Krenz-Niedbała M, ..., Jakobsson M, Dabert M

GENBANK GENBANK GENBANK GENBANK

Forensic Sci Int Genet 26 (-) 30-39 [2017-01-00; online 2016-10-25]

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

Meta-GWAS Accuracy and Power (MetaGAP) Calculator Shows that Hiding Heritability Is Partially Due to Imperfect Genetic Correlations across Studies.

de Vlaming R, Okbay A, Rietveld CA, ..., Thurik AR, Koellinger PD

pmc

PLoS Genet. 13 (1) e1006495 [2017-01-00; online 2017-01-17]

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

Contribution of different dispersal sources to the metabolic response of lake bacterioplankton following a salinity change.

Comte J, Langenheder S, Berga M, Lindström ES

SRA

Environ. Microbiol. 19 (1) 251-260 [2017-01-00; online 2016-11-22]

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

VAV1 regulates experimental autoimmune arthritis and is associated with anti-CCP negative rheumatoid arthritis

Guerreiro-Cacais AO, None , Norin U, ..., Kockum I, Padyukov L

Genes Immun 18 (1) 48-56 [2017-01-00; online 2017-01-05]

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

124 CHANGES IN GENE EXPRESSION FOLLOWING EXPOSURE OF BOVINE ENDOMETRIAL EPITHELIAL CELLS (bEEC) TO ESCHERICHIA COLI LPS; THEIR POSSIBLE EFFECT ON IMPLANTATION

Guo Y, Jahmat N, Van Shaik T, ..., Andersson G, Humblot P

Reprod. Fertil. Dev. 29 (1) 170 [2017-00-00; online 2017-00-00]

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

Single-Nucleotide Polymorphisms and Cancer Risk, Tumor Recurrence, or Survival of Head and Neck Cancer Patients.

Laytragoon-Lewin N, Cederblad L, Andersson BÅ, ..., Löfgren S, Lewin F

Oncology 92 (3) 161-169 [2016-12-21; online 2016-12-21]

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

Identification of a Differentially Expressed TIR-NBS-LRR Gene in a Major QTL Associated to Leaf Rust Resistance in Salix

Martin T, Rönnberg-Wästljung AC, Stenlid J, Samils B

PLoS ONE 11 (12) e0168776 [2016-12-21; online 2016-12-21]

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

Genome-wide association study of caffeine metabolites provides new insights to caffeine metabolism and dietary caffeine-consumption behavior.

Cornelis MC, Kacprowski T, Menni C, ..., Grabe HJ, Ingelsson E

Hum. Mol. Genet. 25 (24) 5472-5482 [2016-12-15; online 2016-10-06]

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

Transposon Mutagenesis Reveals Fludarabine Resistance Mechanisms in Chronic Lymphocytic Leukemia.

Pandzic T, Larsson J, He L, ..., Sjöblom T, Hellström M

Clin. Cancer Res. 22 (24) 6217-6227 [2016-12-15; online 2016-03-10]

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

TRPM8 polymorphisms associated with increased risk of IBS-C and IBS-M.

Henström M, Hadizadeh F, Beyder A, ..., Farrugia G, D'Amato M

Gut - (-) - [2016-12-14; online 2016-12-14]

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

Clonal Variation in Drug and Radiation Response among Glioma-Initiating Cells Is Linked to Proneural-Mesenchymal Transition.

Segerman A, Niklasson M, Haglund C, ..., Segerman B, Westermark B

Cell Rep 17 (11) 2994-3009 [2016-12-13; online 2016-12-16]

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

A genetic risk score composed of rheumatoid arthritis risk alleles, HLA-DRB1 haplotypes, and response to TNFi therapy - results from a Swedish cohort study.

Jiang X, Askling J, Saevarsdottir S, ..., Viatte S, Frisell T

pmc

Arthritis Res. Ther. 18 (1) 288 [2016-12-03; online 2016-12-03]

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

Viral Metagenomic Analysis Displays the Co-Infection Situation in Healthy and PMWS Affected Pigs.

Blomström AL, Fossum C, Wallgren P, Berg M

pmc

PLoS ONE 11 (12) e0166863 [2016-12-01; online 2016-12-01]

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

Extended exome sequencing identifies BACH2 as a novel major risk locus for Addison's disease.

Eriksson D, Bianchi M, Landegren N, ..., Kämpe O, Pielberg GR

J. Intern. Med. 280 (6) 595-608 [2016-12-00; online 2016-11-04]

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

The domesticated brain: genetics of brain mass and brain structure in an avian species

Henriksen R, Johnsson M, Andersson L, Jensen P, Wright D

Sci Rep 6 (1) - [2016-12-00; online 2016-09-30]

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

Genome-wide analysis identifies 12 loci influencing human reproductive behavior.

Barban N, Jansen R, de Vlaming R, ..., Snieder H, Mills MC

Nat. Genet. 48 (12) 1462-1472 [2016-12-00; online 2016-11-01]

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

The disappearing San of southeastern Africa and their genetic affinities.

Schlebusch CM, Prins F, Lombard M, Jakobsson M, Soodyall H

pmc

Hum. Genet. 135 (12) 1365-1373 [2016-12-00; online 2016-09-22]

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

Novel genetic loci underlying human intracranial volume identified through genome-wide association.

Adams HH, Hibar DP, Chouraki V, ..., Ikram MA, Thompson PM

pmc mid

Nat. Neurosci. 19 (12) 1569-1582 [2016-12-00; online 2016-11-01]

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

Coetzeea brasiliensis gen. nov., sp. nov. isolated from larvae of Anopheles darlingi.

Kämpfer P, Glaeser SP, Marinotti O, ..., Busse HJ, Terenius O

Int. J. Syst. Evol. Microbiol. 66 (12) 5211-5217 [2016-12-00; online 2016-09-15]

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

DNA methylation patterns associated with oxidative stress in an ageing population.

Hedman ÅK, Zilmer M, Sundström J, Lind L, Ingelsson E

pmc

BMC Med Genomics 9 (1) 72 [2016-11-25; online 2016-11-25]

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

Functional variants in the sucrase-isomaltase gene associate with increased risk of irritable bowel syndrome.

Henström M, Diekmann L, Bonfiglio F, ..., Naim HY, D'Amato M

Gut - (-) - [2016-11-21; online 2016-11-21]

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

Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects

Marshall CR, Howrigan DP, Merico D, ..., Neale BM, Sebat J

Nat Genet 49 (1) 27-35 [2016-11-21; online 2016-11-21]

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

Novel genetic loci associated with long-term deterioration in blood lipid concentrations and coronary artery disease in European adults.

Varga TV, Kurbasic A, Aine M, ..., Renström F, Franks PW

Int J Epidemiol - (-) - [2016-11-17; online 2016-11-17]

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

Targeted high-throughput sequencing of candidate genes for chronic obstructive pulmonary disease.

Matsson H, Söderhäll C, Einarsdottir E, ..., Lundbäck B, Klar J

pmc

BMC Pulm Med 16 (1) 146 [2016-11-11; online 2016-11-11]

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

Discovery and refinement of genetic loci associated with cardiometabolic risk using dense imputation maps.

Iotchkova V, Huang J, Morris JA, ..., Auer PL, Soranzo N

pmc mid

Nat. Genet. 48 (11) 1303-1312 [2016-11-00; online 2016-10-28]

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

Common variants at PVT1, ATG13-AMBRA1, AHI1 and CLEC16A are associated with selective IgA deficiency.

Bronson PG, Chang D, Bhangale T, ..., Graham RR, Behrens TW

pmc mid

Nat. Genet. 48 (11) 1425-1429 [2016-11-00; online 2016-10-28]

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

Genome-wide DNA methylation analysis in multiple tissues in primary Sjögren's syndrome reveals regulatory effects at interferon-induced genes.

Imgenberg-Kreuz J, Sandling JK, Almlöf JC, ..., Syvänen AC, Nordmark G

pmc

Ann. Rheum. Dis. 75 (11) 2029-2036 [2016-11-00; online 2016-02-10]

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

Genome-wide repression of eRNA and target gene loci by the ETV6-RUNX1 fusion in acute leukemia.

Teppo S, Laukkanen S, Liuksiala T, ..., Heinäniemi M, Lohi O

pmc

Genome Res. 26 (11) 1468-1477 [2016-11-00; online 2016-09-12]

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

Evolution of heterogeneous genome differentiation across multiple contact zones in a crow species complex

Vijay N, Bossu CM, Poelstra JW, ..., Kryukov AP, Wolf JBW

Nat Commun 7 (-) 13195 [2016-10-31; online 2016-10-31]

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

Introduction and persistence of tularemia in Bulgaria.

Myrtennäs K, Marinov K, Johansson A, ..., Byström M, Forsman M

pmc

Infect Ecol Epidemiol 6 (-) 32838 [2016-10-26; online 2016-10-26]

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

Relation between Established Glioma Risk Variants and DNA Methylation in the Tumor.

Dahlin AM, Wibom C, Ghasimi S, ..., Andersson U, Melin B

pmc

PLoS ONE 11 (10) e0163067 [2016-10-25; online 2016-10-25]

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

No Association of Coronary Artery Disease with X-Chromosomal Variants in Comprehensive International Meta-Analysis.

Loley C, Alver M, Assimes TL, ..., Erdmann J, König IR

pmc

Sci Rep 6 (-) 35278 [2016-10-12; online 2016-10-12]

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

Analysis of the brain mural cell transcriptome.

He L, Vanlandewijck M, Raschperger E, ..., Keller A, Betsholtz C

pmc

Sci Rep 6 (-) 35108 [2016-10-11; online 2016-10-11]

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

The Demographic Development of the First Farmers in Anatolia.

Kılınç GM, Omrak A, Özer F, ..., Jakobsson M, Götherström A

pmc

Curr. Biol. 26 (19) 2659-2666 [2016-10-10; online 2016-08-09]

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

Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis.

Hammond M, Homa F, Andersson-Svahn H, Ettema TJ, Joensson HN

pmc

Microbiome 4 (1) 52 [2016-10-06; online 2016-10-06]

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

Whole-Exome Sequencing Suggests LAMB3 as a Susceptibility Gene for Morbid Obesity.

Jiao H, Kulyté A, Näslund E, ..., Arner P, Dahlman I

Diabetes 65 (10) 2980-2989 [2016-10-00; online 2016-07-20]

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

Trans-ancestry meta-analyses identify rare and common variants associated with blood pressure and hypertension.

Surendran P, Drenos F, Young R, ..., Howson JM, Munroe PB

pmc mid

Nat. Genet. 48 (10) 1151-1161 [2016-10-00; online 2016-09-13]

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

DNA methylome analysis of acute lymphoblastic leukemia cells reveals stochastic de novo DNA methylation in CpG islands.

Wahlberg P, Lundmark A, Nordlund J, ..., Lönnerholm G, Syvänen AC

Epigenomics 8 (10) 1367-1387 [2016-10-00; online 2016-08-24]

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

Connectivity to the surface determines diversity patterns in subsurface aquifers of the Fennoscandian shield.

Hubalek V, Wu X, Eiler A, ..., Bertilsson S, Ionescu D

pmc

ISME J 10 (10) 2447-2458 [2016-10-00; online 2016-03-30]

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

Effect of Insulin Resistance on Monounsaturated Fatty Acid Levels: A Multi-cohort Non-targeted Metabolomics and Mendelian Randomization Study.

Nowak C, Salihovic S, Ganna A, ..., Ingelsson E, Fall T

pmc

PLoS Genet. 12 (10) e1006379 [2016-10-00; online 2016-10-21]

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

Polygenic associations of neurodevelopmental genes in suicide attempt.

Sokolowski M, Wasserman J, Wasserman D

Mol. Psychiatry 21 (10) 1381-1390 [2016-10-00; online 2015-12-17]

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

The genetics of blood pressure regulation and its target organs from association studies in 342,415 individuals.

Ehret GB, Ferreira T, Chasman DI, ..., Newton-Cheh C, Munroe PB

pmc mid

Nat. Genet. 48 (10) 1171-1184 [2016-10-00; online 2016-09-13]

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

Clonality of erythromycin resistance in Francisella tularensis.

Karlsson E, Golovliov I, Lärkeryd A, ..., Forsman M, Johansson A

J. Antimicrob. Chemother. 71 (10) 2815-2823 [2016-10-00; online 2016-06-24]

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

Soluble CD93 Is Involved in Metabolic Dysregulation but Does Not Influence Carotid Intima-Media Thickness.

Strawbridge RJ, Hilding A, Silveira A, ..., Bäcklund A, IMPROVE Study Group

pmc

Diabetes 65 (10) 2888-2899 [2016-10-00; online 2016-09-24]

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

Personality Polygenes, Positive Affect, and Life Satisfaction.

Weiss A, Baselmans BM, Hofer E, ..., Bartels M, Luciano M

pmc mid

Twin Res Hum Genet 19 (5) 407-417 [2016-10-00; online 2016-08-23]

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

Mutations in HECW2 are associated with intellectual disability and epilepsy.

Halvardson J, Zhao JJ, Zaghlool A, ..., Thuresson AC, Feuk L

pmc

J. Med. Genet. 53 (10) 697-704 [2016-10-00; online 2016-06-24]

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

Non-targeted metabolomics combined with genetic analyses identifies bile acid synthesis and phospholipid metabolism as being associated with incident type 2 diabetes.

Fall T, Salihovic S, Brandmaier S, ..., Ingelsson E, Lind L

Diabetologia 59 (10) 2114-2124 [2016-10-00; online 2016-07-14]

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

Effects of multiple dimensions of bacterial diversity on functioning, stability and multifunctionality.

Roger F, Bertilsson S, Langenheder S, Osman OA, Gamfeldt L

Ecology 97 (10) 2716-2728 [2016-10-00; online 2016-09-15]

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

Genome-Wide Association Study of the Modified Stumvoll Insulin Sensitivity Index Identifies BCL2 and FAM19A2 as Novel Insulin Sensitivity Loci.

Walford GA, Gustafsson S, Rybin D, ..., Ingelsson E, Florez JC

pmc

Diabetes 65 (10) 3200-3211 [2016-10-00; online 2016-07-16]

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

Genomic Regions Associated With Interspecies Communication in Dogs Contain Genes Related to Human Social Disorders.

Persson ME, Wright D, Roth LS, Batakis P, Jensen P

pmc

Sci Rep 6 (-) 33439 [2016-09-29; online 2016-09-29]

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

Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes.

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

pmc

Oncotarget 7 (39) 64071-64088 [2016-09-27; online 2016-09-04]

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

Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome.

Dutoit L, Burri R, Nater A, Mugal CF, Ellegren H

GENBANK

Mol Ecol Resour 17 (4) 586-597 [2016-09-26; online 2016-09-26]

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

Genome-wide association analysis reveals variants on chromosome 19 that contribute to childhood risk of chronic otitis media with effusion.

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

pmc

Sci Rep 6 (-) 33240 [2016-09-16; online 2016-09-16]

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

Epigenome-wide association study reveals differential DNA methylation in individuals with a history of myocardial infarction

Rask-Andersen M, Martinsson D, Ahsan M, ..., Gyllensten U, Johansson Å

Hum. Mol. Genet. - (-) ddw302 [2016-09-15; online 2016-09-15]

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

Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells.

Morin A, Kwan T, Ge B, ..., Lathrop MG, Pastinen T

pmc

BMC Med Genomics 9 (1) 59 [2016-09-13; online 2016-09-13]

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

Sequence variation between 462 human individuals fine-tunes functional sites of RNA processing.

Ferreira PG, Oti M, Barann M, ..., Guigó R, Sammeth M

pmc

Sci Rep 6 (-) 32406 [2016-09-12; online 2016-09-12]

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

Trans-ethnic Fine Mapping Highlights Kidney-Function Genes Linked to Salt Sensitivity.

Mahajan A, Rodan AR, Le TH, ..., Morris AP, Franceschini N

pmc

Am. J. Hum. Genet. 99 (3) 636-646 [2016-09-01; online 2016-09-03]

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

Direct estimate of the rate of germline mutation in a bird.

Smeds L, Qvarnström A, Ellegren H

pmc

Genome Res. 26 (9) 1211-1218 [2016-09-00; online 2016-07-15]

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

A genetic variant in proximity to the gene LYPLAL1 is associated with lower hunger feelings and increased weight loss following Roux-en-Y gastric bypass surgery.

Bandstein M, Mwinyi J, Ernst B, ..., Schultes B, Schiöth HB

pmc

Scand. J. Gastroenterol. 51 (9) 1050-1055 [2016-09-00; online 2016-05-18]

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

Epigenome-wide analysis of DNA methylation reveals a rectal cancer-specific epigenomic signature.

Vymetalkova V, Vodicka P, Pardini B, ..., Nilsson TK, Farkas SA

Epigenomics 8 (9) 1193-1207 [2016-09-00; online 2016-08-17]

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

Data on the expression of cellular lncRNAs in human adenovirus infected cells.

Chen M, Zhao H, Lind SB, Pettersson U

pmc

Data Brief 8 (-) 1263-1279 [2016-09-00; online 2016-08-23]

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

A Genetic Risk Score Is Associated with Weight Loss Following Roux-en Y Gastric Bypass Surgery.

Bandstein M, Voisin S, Nilsson EK, ..., Mwinyi J, Schiöth HB

pmc

Obes Surg 26 (9) 2183-2189 [2016-09-00; online 2016-02-03]

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

A Rickettsiales symbiont of amoebae with ancient features.

Schulz F, Martijn J, Wascher F, ..., Ettema TJ, Horn M

Environ. Microbiol. 18 (8) 2326-2342 [2016-09-00; online 2015-04-25]

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

Cystatin C and Cardiovascular Disease: A Mendelian Randomization Study.

van der Laan SW, Fall T, Soumaré A, ..., Holmes MV, Asselbergs FW

J. Am. Coll. Cardiol. 68 (9) 934-945 [2016-08-30; online 2016-08-27]

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

One-night sleep deprivation induces changes in the DNA methylation and serum activity indices of stearoyl-CoA desaturase in young healthy men.

Skuladottir GV, Nilsson EK, Mwinyi J, Schiöth HB

pmc

Lipids Health Dis 15 (1) 137 [2016-08-26; online 2016-08-26]

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

Identification of Multiple QTLs Linked to Neuropathology in the Engrailed-1 Heterozygous Mouse Model of Parkinson's Disease.

Kurowska Z, Jewett M, Brattås PL, ..., Brundin P, Swanberg M

pmc

Sci Rep 6 (-) 31701 [2016-08-23; online 2016-08-23]

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

Cardiometabolic risk loci share downstream cis- and trans-gene regulation across tissues and diseases.

Franzén O, Ermel R, Cohain A, ..., Schadt EE, Björkegren JL

Science 353 (6301) 827-830 [2016-08-19; online 2016-08-20]

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

Single base resolution analysis of 5-hydroxymethylcytosine in 188 human genes: implications for hepatic gene expression.

Ivanov M, Kals M, Lauschke V, ..., Milani L, Ingelman-Sundberg M

pmc

Nucleic Acids Res. 44 (14) 6756-6769 [2016-08-19; online 2016-04-29]

Bioinformatics Compute and Storage [Service] Clinical Proteomics Mass spectrometry [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]

The genetic architecture of type 2 diabetes.

Fuchsberger C, Flannick J, Teslovich TM, ..., Altshuler D, McCarthy MI

pmc mid mid

Nature 536 (7614) 41-47 [2016-08-04; online 2016-07-12]

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

Rapid and specific hypomethylation of enhancers in endothelial cells during adaptation to cell culturing.

Magnusson M, Larsson P, Lu EX, ..., Carén H, Jern S

pmc

Epigenetics 11 (8) 614-624 [2016-08-02; online 2016-06-16]

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

ω-3 Polyunsaturated Fatty Acid Biomarkers and Coronary Heart Disease: Pooling Project of 19 Cohort Studies.

Del Gobbo LC, Imamura F, Aslibekyan S, ..., Mozaffarian D, Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE) Fatty Acids and Outcomes Research Consortium (FORCe)

pmc mid

JAMA Intern Med 176 (8) 1155-1166 [2016-08-01; online 2016-07-01]

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

On the reversibility of parasitism: adaptation to a free-living lifestyle via gene acquisitions in the diplomonad Trepomonas sp. PC1.

Xu F, Jerlström-Hultqvist J, Kolisko M, ..., Svärd SG, Andersson JO

pmc

BMC Biol. 14 (-) 62 [2016-08-01; online 2016-08-01]

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

Genome-wide association meta-analysis in Chinese and European individuals identifies ten new loci associated with systemic lupus erythematosus.

Morris DL, Sheng Y, Zhang Y, ..., Cui Y, Vyse TJ

pmc mid

Nat. Genet. 48 (8) 940-946 [2016-08-00; online 2016-07-12]

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

A novel splicing mutation in the IQSEC2 gene that modulates the phenotype severity in a family with intellectual disability.

Madrigal I, Alvarez-Mora MI, Rosell J, ..., Syvänen AC, Mila M

pmc

Eur. J. Hum. Genet. 24 (8) 1117-1123 [2016-08-00; online 2016-01-07]

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

Genetic determinants of warfarin maintenance dose and time in therapeutic treatment range: a RE-LY genomics substudy.

Eriksson N, Wallentin L, Berglund L, ..., Yusuf S, Wadelius M

Pharmacogenomics 17 (13) 1425-1439 [2016-08-00; online 2016-08-04]

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

Postprandial alterations in whole-blood DNA methylation are mediated by changes in white blood cell composition.

Rask-Andersen M, Bringeland N, Nilsson EK, ..., Benedict C, Schiöth HB

Am. J. Clin. Nutr. 104 (2) 518-525 [2016-08-00; online 2016-07-08]

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

Novel regulatory variant detected on the VKORC1 haplotype that is associated with warfarin dose.

Cavalli M, Pan G, Nord H, ..., Wadelius C, Wadelius M

Pharmacogenomics 17 (12) 1305-1314 [2016-08-00; online 2016-02-06]

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

Meta-analysis of 375,000 individuals identifies 38 susceptibility loci for migraine.

Gormley P, Anttila V, Winsvold BS, ..., Nyholt DR, Palotie A

pmc mid

Nat. Genet. 48 (8) 856-866 [2016-08-00; online 2016-06-21]

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

Genetic and environmental effects on body mass index from infancy to the onset of adulthood: an individual-based pooled analysis of 45 twin cohorts participating in the COllaborative project of Development of Anthropometrical measures in Twins (CODATwins) study.

Silventoinen K, Jelenkovic A, Sund R, ..., Boomsma DI, Kaprio J

pmc

Am. J. Clin. Nutr. 104 (2) 371-379 [2016-08-00; online 2016-07-15]

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

Remnants of marine bacterial communities can be retrieved from deep sediments in lakes of marine origin.

Langenheder S, Comte J, Zha Y, ..., Eiler A, Lindström ES

Environ Microbiol Rep 8 (4) 479-485 [2016-08-00; online 2016-03-02]

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

Rapid Evolution of Genomic Imprinting in Two Species of the Brassicaceae.

Hatorangan MR, Laenen B, Steige KA, Slotte T, Köhler C

pmc

Plant Cell 28 (8) 1815-1827 [2016-08-00; online 2016-07-29]

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

The De Novo Transcriptome and Its Functional Annotation in the Seed Beetle Callosobruchus maculatus.

Sayadi A, Immonen E, Bayram H, Arnqvist G

pmc

PLoS ONE 11 (7) e0158565 [2016-07-21; online 2016-07-21]

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

Integrative functional genomics identifies regulatory mechanisms at coronary artery disease loci.

Miller CL, Pjanic M, Wang T, ..., Björkegren JL, Quertermous T

pmc

Nat Commun 7 (-) 12092 [2016-07-08; online 2016-07-08]

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

Large Deletions at the SHOX Locus in the Pseudoautosomal Region Are Associated with Skeletal Atavism in Shetland Ponies.

Rafati N, Andersson LS, Mikko S, ..., Lindgren G, Rubin CJ

pmc

G3 (Bethesda) 6 (7) 2213-2223 [2016-07-07; online 2016-05-22]

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

Long-term genetic stability and a high-altitude East Asian origin for the peoples of the high valleys of the Himalayan arc.

Jeong C, Ozga AT, Witonsky DB, ..., Di Rienzo A, Warinner C

pmc

Proc. Natl. Acad. Sci. U.S.A. 113 (27) 7485-7490 [2016-07-05; online 2016-06-22]

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

Pooled analysis of genome-wide association studies of cervical intraepithelial neoplasia 3 (CIN3) identifies a new susceptibility locus.

Chen D, Enroth S, Liu H, ..., Xu S, Gyllensten U

pmc

Oncotarget 7 (27) 42216-42224 [2016-07-05; online 2016-06-11]

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

Genome-wide association study identifies multiple susceptibility loci for multiple myeloma.

Mitchell JS, Li N, Weinhold N, ..., Nilsson B, Houlston RS

pmc

Nat Commun 7 (-) 12050 [2016-07-01; online 2016-07-01]

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

Increasing the power of genome wide association studies in natural populations using repeated measures - evaluation and implementation.

Rönnegård L, McFarlane SE, Husby A, ..., Ellegren H, Qvarnström A

pmc

Methods Ecol Evol 7 (7) 792-799 [2016-07-00; online 2016-02-05]

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

A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them.

Humble E, Martinez-Barrio A, Forcada J, ..., Wolf JB, Hoffman JI

GENBANK

Mol Ecol Resour 16 (4) 909-921 [2016-07-00; online 2015-12-20]

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

An Integrative Genomic Analysis of Formalin Fixed Paraffin-Embedded Archived Serous Ovarian Carcinoma Comparing Long-term and Short-term Survivors.

Stålberg K, Crona J, Razmara M, ..., Skogseid B, Stålberg P

Int. J. Gynecol. Cancer 26 (6) 1027-1032 [2016-07-00; online 2016-05-14]

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

Genetic and environmental influences on height from infancy to early adulthood: An individual-based pooled analysis of 45 twin cohorts.

Jelenkovic A, Sund R, Hur YM, ..., Kaprio J, Silventoinen K

pmc

Sci Rep 6 (-) 28496 [2016-06-23; online 2016-06-23]

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

Cryptosporidium as a testbed for single cell genome characterization of unicellular eukaryotes.

Troell K, Hallström B, Divne AM, ..., Beser J, Bertilsson S

pmc

BMC Genomics 17 (-) 471 [2016-06-23; online 2016-06-23]

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

Parental epigenetic asymmetry of PRC2-mediated histone modifications in the Arabidopsis endosperm.

Moreno-Romero J, Jiang H, Santos-González J, Köhler C

pmc

EMBO J. 35 (12) 1298-1311 [2016-06-15; online 2016-04-27]

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

Recommendations on e-infrastructures for next-generation sequencing.

Spjuth O, Bongcam-Rudloff E, Dahlberg J, ..., Vezzi F, Korpelainen E

pmc

Gigascience 5 (-) 26 [2016-06-07; online 2016-06-07]

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

Mosaic Loss of Chromosome Y in Blood Is Associated with Alzheimer Disease.

Dumanski JP, Lambert JC, Rasi C, ..., Lind L, Forsberg LA

pmc

Am. J. Hum. Genet. 98 (6) 1208-1219 [2016-06-02; online 2016-05-28]

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

Allele-specific transcription factor binding in liver and cervix cells unveils many likely drivers of GWAS signals.

Cavalli M, Pan G, Nord H, ..., Wallerman O, Wadelius C

Genomics 107 (6) 248-254 [2016-06-00; online 2016-04-30]

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

Somatic, positive and negative domains of the Center for Epidemiological Studies Depression (CES-D) scale: a meta-analysis of genome-wide association studies.

Demirkan A, Lahti J, Direk N, ..., van Duijn CM, Räikkönen K

Psychol Med 46 (8) 1613-1623 [2016-06-00; online 2016-03-22]

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

Genetic variants associated with antithyroid drug-induced agranulocytosis: a genome-wide association study in a European population.

Hallberg P, Eriksson N, Ibañez L, ..., Wadelius M, EuDAC collaborators

Lancet Diabetes Endocrinol 4 (6) 507-516 [2016-06-00; online 2016-05-10]

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

Epigenomics of Total Acute Sleep Deprivation in Relation to Genome-Wide DNA Methylation Profiles and RNA Expression.

Nilsson EK, Boström AE, Mwinyi J, Schiöth HB

pmc

OMICS 20 (6) 334-342 [2016-06-00; online 2016-06-17]

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

Genetic variants associated with subjective well-being, depressive symptoms, and neuroticism identified through genome-wide analyses.

Okbay A, Baselmans BM, De Neve JE, ..., Bartels M, Cesarini D

pmc mid

Nat. Genet. 48 (6) 624-633 [2016-06-00; online 2016-04-19]

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

Epigenome-wide DNA methylation patterns associated with fatigue in primary Sjögren's syndrome.

Brække Norheim K, Imgenberg-Kreuz J, Jonsdottir K, ..., Nordmark G, Omdal R

Rheumatology (Oxford) 55 (6) 1074-1082 [2016-06-00; online 2016-03-12]

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

Disruptive selection without genome-wide evolution across a migratory divide.

von Rönn JA, Shafer AB, Wolf JB

GENBANK GENBANK

Mol. Ecol. 25 (11) 2529-2541 [2016-06-00; online 2016-01-11]

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

Common and Rare Genetic Variation in CCR2, CCR5, or CX3CR1 and Risk of Atherosclerotic Coronary Heart Disease and Glucometabolic Traits.

Golbus JR, Stitziel NO, Zhao W, ..., Reilly MP, CARDIoGRAMplusC4D, Myocardial Infarction Genetics (MIGen), Exome Sequencing Project and Early-Onset Myocardial Infarction (ESP EOMI), and the Pakistan Risk of Myocardial Infarction Study (PROMIS) Consortia*

pmc mid

Circ Cardiovasc Genet 9 (3) 250-258 [2016-06-00; online 2016-03-26]

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

Variants within the SP110 nuclear body protein modify risk of canine degenerative myelopathy.

Ivansson EL, Megquier K, Kozyrev SV, ..., Coates JR, Lindblad-Toh K

pmc GENBANK GENBANK

Proc. Natl. Acad. Sci. U.S.A. 113 (22) E3091-E3100 [2016-05-31; online 2016-05-18]

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

Genome-wide association study identifies 74 loci associated with educational attainment.

Okbay A, Beauchamp JP, Fontana MA, ..., Cesarini D, Benjamin DJ

pmc mid

Nature 533 (7604) 539-542 [2016-05-26; online 2016-05-11]

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

Effects of Dispersal and Initial Diversity on the Composition and Functional Performance of Bacterial Communities.

Zha Y, Berga M, Comte J, Langenheder S

pmc

PLoS ONE 11 (5) e0155239 [2016-05-16; online 2016-05-16]

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

Epigenetic silencing of miR-26A1 in chronic lymphocytic leukemia and mantle cell lymphoma: Impact on EZH2 expression.

Kopparapu PK, Bhoi S, Mansouri L, ..., Rosenquist R, Kanduri M

pmc

Epigenetics 11 (5) 335-343 [2016-05-03; online 2016-04-08]

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

The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.

Martinez Barrio A, Lamichhaney S, Fan G, ..., Xu X, Andersson L

pmc Dryad SRA SRA SRA

Elife 5 (-) - [2016-05-03; online 2016-05-03]

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

Schizophrenia and subsequent neighborhood deprivation: revisiting the social drift hypothesis using population, twin and molecular genetic data.

Sariaslan A, Fazel S, D'Onofrio BM, ..., Kuja-Halkola R, Lichtenstein P

pmc

Transl Psychiatry 6 (-) e796 [2016-05-03; online 2016-05-03]

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

Evidence for Genetic Overlap Between Schizophrenia and Age at First Birth in Women.

Mehta D, Tropf FC, Gratten J, ..., Weiser M, Wu JQ

JAMA Psychiatry 73 (5) 497-505 [2016-05-01; online 2016-03-24]

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

High-Density Genetic Mapping Identifies New Susceptibility Variants in Sarcoidosis Phenotypes and Shows Genomic-driven Phenotypic Differences.

Rivera NV, Ronninger M, Shchetynsky K, ..., Padyukov L, Grunewald J

pmc

Am. J. Respir. Crit. Care Med. 193 (9) 1008-1022 [2016-05-01; online 2015-12-15]

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

mRNA GPR162 changes are associated with decreased food intake in rat, and its human genetic variants with impairments in glucose homeostasis in two Swedish cohorts.

Caruso V, Sreedharan S, Carlini VP, ..., Fredriksson R, Schiöth HB

Gene 581 (2) 139-145 [2016-05-01; online 2016-02-02]

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

Distinct temporal changes in host cell lncRNA expression during the course of an adenovirus infection.

Zhao H, Chen M, Lind SB, Pettersson U

Virology 492 (-) 242-250 [2016-05-00; online 2016-03-24]

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

Genetic loci on chromosome 5 are associated with circulating levels of interleukin-5 and eosinophil count in a European population with high risk for cardiovascular disease.

McLeod O, Silveira A, Valdes-Marquez E, ..., Strawbridge RJ, IMPROVE Study Group

pmc

Cytokine 81 (-) 1-9 [2016-05-00; online 2016-01-29]

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

Genetic risk variants in the CDKN2A/B, RTEL1 and EGFR genes are associated with somatic biomarkers in glioma.

Ghasimi S, Wibom C, Dahlin AM, ..., Andersson U, Melin B

pmc

J. Neurooncol. 127 (3) 483-492 [2016-05-00; online 2016-02-04]

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

High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree.

Smeds L, Mugal CF, Qvarnström A, Ellegren H

pmc

PLoS Genet. 12 (5) e1006044 [2016-05-00; online 2016-05-24]

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

Utilizing the Dog Genome in the Search for Novel Candidate Genes Involved in Glioma Development-Genome Wide Association Mapping followed by Targeted Massive Parallel Sequencing Identifies a Strongly Associated Locus.

Truvé K, Dickinson P, Xiong A, ..., Bannasch D, Lindblad-Toh K

pmc

PLoS Genet. 12 (5) e1006000 [2016-05-00; online 2016-05-12]

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

Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression.

Cavalli M, Pan G, Nord H, ..., Lindblad Toh K, Wadelius C

pmc

Hum. Genet. 135 (5) 485-497 [2016-05-00; online 2016-03-20]

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

Divergence in gene expression within and between two closely related flycatcher species.

Uebbing S, Künstner A, Mäkinen H, ..., Searle SM, Ellegren H

pmc GENBANK GENBANK GENBANK

Mol. Ecol. 25 (9) 2015-2028 [2016-05-00; online 2016-03-02]

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

Whole-genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations.

Kardos M, Husby A, McFarlane SE, Qvarnström A, Ellegren H

Mol Ecol Resour 16 (3) 727-741 [2016-05-00; online 2015-12-10]

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

Microbial metagenomes from three aquifers in the Fennoscandian shield terrestrial deep biosphere reveal metabolic partitioning among populations.

Wu X, Holmfeldt K, Hubalek V, ..., Bertilsson S, Dopson M

pmc

ISME J 10 (5) 1192-1203 [2016-05-00; online 2015-10-21]

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

Association mapping in Salix viminalis L. (Salicaceae) - identification of candidate genes associated with growth and phenology.

Hallingbäck HR, Fogelqvist J, Powers SJ, ..., Berlin S, Rönnberg-Wästljung AC

pmc

Glob Change Biol Bioenergy 8 (3) 670-685 [2016-05-00; online 2015-07-29]

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

Longitudinal genome-wide methylation study of Roux-en-Y gastric bypass patients reveals novel CpG sites associated with essential hypertension.

Boström AE, Mwinyi J, Voisin S, ..., Zhang K, Schiöth HB

pmc

BMC Med Genomics 9 (-) 20 [2016-04-22; online 2016-04-22]

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

A beak size locus in Darwin's finches facilitated character displacement during a drought.

Lamichhaney S, Han F, Berglund J, ..., Grant PR, Andersson L

Science 352 (6284) 470-474 [2016-04-22; online 2016-04-23]

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

Associations between a locus downstream DRD1 gene and cerebrospinal fluid dopamine metabolite concentrations in psychosis.

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

Neurosci. Lett. 619 (-) 126-130 [2016-04-21; online 2016-03-10]

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

The Mycobacterium phlei Genome: Expectations and Surprises.

Das S, Pettersson BM, Behra PR, ..., Bhattacharya A, Kirsebom LA

pmc

Genome Biol Evol 8 (4) 975-985 [2016-04-08; online 2016-03-05]

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

CopyNumber450kCancer: baseline correction for accurate copy number calling from the 450k methylation array.

Marzouka NA, Nordlund J, Bäcklin CL, ..., Syvänen AC, Carlsson Almlöf J

pmc

Bioinformatics 32 (7) 1080-1082 [2016-04-01; online 2015-11-11]

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

Genome-wide association and Mendelian randomization study of NT-proBNP in patients with acute coronary syndrome.

Johansson Å, Eriksson N, Lindholm D, ..., Wallentin L, PLATO Investigators

ClinicalTrials.gov

Hum. Mol. Genet. 25 (7) 1447-1456 [2016-04-01; online 2016-02-26]

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

One CNV Discordance in NRXN1 Observed Upon Genome-wide Screening in 38 Pairs of Adult Healthy Monozygotic Twins.

Magnusson PK, Lee D, Chen X, ..., Feuk L, Pawitan Y

Twin Res Hum Genet 19 (2) 97-103 [2016-04-00; online 2016-02-24]

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

Gene regulatory mechanisms underpinning prostate cancer susceptibility.

Whitington T, Gao P, Song W, ..., Wei GH, Wiklund F

Nat. Genet. 48 (4) 387-397 [2016-04-00; online 2016-03-08]

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

Effect of PTPN22 Gene Variant R620W on Type I Interferon Production Stimulated by Different Toll-like Receptor 7 Agonists: Comment on the Article by Wang et al.

Berggren O, Rönnblom L, Eloranta ML

Arthritis & rheumatology (Hoboken, N.J.) 68 (4) 1045 [2016-04-00; online 2016-01-11]

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

Adaptive major histocompatibility complex (MHC) and neutral genetic variation in two native Baltic Sea fishes (perch Perca fluviatilis and zander Sander lucioperca) with comparisons to an introduced and disease susceptible population in Australia (P. fluviatilis): assessing the risk of disease epidemics.

Faulks LK, Östman Ö

J. Fish Biol. 88 (4) 1564-1583 [2016-04-00; online 2016-03-05]

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

Coordinated Changes in Gene Expression Throughout Encystation of Giardia intestinalis.

Einarsson E, Troell K, Hoeppner MP, ..., Ribacke U, Svärd SG

pmc

PLoS Negl Trop Dis 10 (3) e0004571 [2016-03-00; online 2016-03-25]

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

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers.

Nadachowska-Brzyska K, Burri R, Smeds L, Ellegren H

pmc

Mol. Ecol. 25 (5) 1058-1072 [2016-03-00; online 2016-01-23]

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

Genetic influences on schizophrenia and subcortical brain volumes: large-scale proof of concept.

Franke B, Stein JL, Ripke S, ..., Medland SE, Sullivan PF

pmc mid

Nat. Neurosci. 19 (3) 420-431 [2016-03-00; online 2016-02-09]

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

Meta-analysis of Genome-Wide Association Studies for Extraversion: Findings from the Genetics of Personality Consortium.

van den Berg SM, de Moor MH, Verweij KJ, ..., Martin NG, Boomsma DI

pmc mid

Behav. Genet. 46 (2) 170-182 [2016-03-00; online 2015-09-13]

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

Whole-exome sequencing in relapsing chronic lymphocytic leukemia: clinical impact of recurrent RPS15 mutations.

Ljungström V, Cortese D, Young E, ..., Sjöblom T, Rosenquist R

pmc

Blood 127 (8) 1007-1016 [2016-02-25; online 2015-12-18]

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

GeneiASE: Detection of condition-dependent and static allele-specific expression from RNA-seq data without haplotype information.

Edsgärd D, Iglesias MJ, Reilly SJ, ..., Odeberg J, Emanuelsson O

pmc

Sci Rep 6 (-) 21134 [2016-02-18; online 2016-02-18]

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

Resting-State Brain and the FTO Obesity Risk Allele: Default Mode, Sensorimotor, and Salience Network Connectivity Underlying Different Somatosensory Integration and Reward Processing between Genotypes.

Olivo G, Wiemerslage L, Nilsson EK, ..., Brooks SJ, Schiöth HB

pmc

Front Hum Neurosci 10 (-) 52 [2016-02-17; online 2016-02-17]

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

Genomic comparison of Escherichia coli serotype O103:H2 isolates with and without verotoxin genes: implications for risk assessment of strains commonly found in ruminant reservoirs.

Söderlund R, Hurel J, Jinnerot T, ..., Eriksson E, Bongcam-Rudloff E

pmc

Infect Ecol Epidemiol 6 (-) 30246 [2016-02-16; online 2016-02-16]

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

Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea.

Baker BJ, Saw JH, Lind AE, ..., Teske AP, Ettema TJG

Nat Microbiol 1 (-) 16002 [2016-02-15; online 2016-02-15]

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

Genome-wide DNA methylation study identifies genes associated with the cardiovascular biomarker GDF-15.

Ek WE, Hedman ÅK, Enroth S, ..., Lind L, Johansson Å

Hum. Mol. Genet. 25 (4) 817-827 [2016-02-15; online 2015-12-19]

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

Exome sequencing in one family with gastric- and rectal cancer.

Thutkawkorapin J, Picelli S, Kontham V, ..., Nilsson D, Lindblom A

pmc

BMC Genet. 17 (-) 41 [2016-02-13; online 2016-02-13]

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

New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk.

Lu Y, Day FR, Gustafsson S, ..., Kilpeläinen TO, Loos RJ

pmc

Nat Commun 7 (-) 10495 [2016-02-01; online 2016-02-01]

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

Genome-wide meta-analysis uncovers novel loci influencing circulating leptin levels.

Kilpeläinen TO, Carli JF, Skowronski AA, ..., Leibel RL, Loos RJ

pmc

Nat Commun 7 (-) 10494 [2016-02-01; online 2016-02-01]

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

Are freshwater bacterioplankton indifferent to variable types of amino acid substrates?

Ricão Canelhas M, Eiler A, Bertilsson S

FEMS Microbiol. Ecol. 92 (2) - [2016-02-00; online 2016-01-08]

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

Genome-Wide Association Analysis of Young-Onset Stroke Identifies a Locus on Chromosome 10q25 Near HABP2.

Cheng YC, Stanne TM, Giese AK, ..., Saleheen D, Mitchell BD

pmc mid ISRCTN

Stroke 47 (2) 307-316 [2016-02-00; online 2016-01-07]

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

Association analysis of copy numbers of FC-gamma receptor genes for rheumatoid arthritis and other immune-mediated phenotypes.

Franke L, el Bannoudi H, Jansen DT, ..., Toes RE, Zhernakova A

pmc

Eur. J. Hum. Genet. 24 (2) 263-270 [2016-02-00; online 2015-05-15]

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

Regulatory mutations in TBX3 disrupt asymmetric hair pigmentation that underlies Dun camouflage color in horses.

Imsland F, McGowan K, Rubin CJ, ..., Barsh GS, Andersson L

pmc mid

Nat. Genet. 48 (2) 152-158 [2016-02-00; online 2015-12-23]

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

Epigenetic profiling in CD4+ and CD8+ T cells from Graves' disease patients reveals changes in genes associated with T cell receptor signaling.

Limbach M, Saare M, Tserel L, ..., Milani L, Peterson P

J. Autoimmun. 67 (-) 46-56 [2016-02-00; online 2015-10-16]

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

Biobanking multifocal breast carcinomas: sample adequacy with regard to histology and DNA content.

Pekar G, Davies H, Lukacs AP, ..., Dumanski J, Tot T

Histopathology 68 (3) 411-421 [2016-02-00; online 2015-06-18]

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

Six Novel Loci Associated with Circulating VEGF Levels Identified by a Meta-analysis of Genome-Wide Association Studies.

Choi SH, Ruggiero D, Sorice R, ..., Seshadri S, Ciullo M

pmc

PLoS Genet. 12 (2) e1005874 [2016-02-00; online 2016-02-24]

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

Genomic Evidence Establishes Anatolia as the Source of the European Neolithic Gene Pool.

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

Curr. Biol. 26 (2) 270-275 [2016-01-25; online 2016-01-11]

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

Genetic associations at 53 loci highlight cell types and biological pathways relevant for kidney function.

Pattaro C, Teumer A, Gorski M, ..., Kao WH, Fox CS

pmc mid

Nat Commun 7 (-) 10023 [2016-01-21; online 2016-01-21]

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

Genetic Determinants of Thrombin Generation and Their Relation to Venous Thrombosis: Results from the GAIT-2 Project.

Martin-Fernandez L, Ziyatdinov A, Carrasco M, ..., Souto JC, Soria JM

pmc

PLoS ONE 11 (1) e0146922 [2016-01-19; online 2016-01-19]

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

Geographical distribution of genetic diversity in Secale landrace and wild accessions.

Hagenblad J, Oliveira HR, Forsberg NE, Leino MW

pmc

BMC Plant Biol. 16 (-) 23 [2016-01-19; online 2016-01-19]

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

A meta-analysis of 120 246 individuals identifies 18 new loci for fibrinogen concentration.

de Vries PS, Chasman DI, Sabater-Lleal M, ..., Strachan DP, Dehghan A

pmc

Hum. Mol. Genet. 25 (2) 358-370 [2016-01-15; online 2015-11-13]

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

Identifying Novel Gene Variants in Coronary Artery Disease and Shared Genes With Several Cardiovascular Risk Factors.

LeBlanc M, Zuber V, Andreassen BK, ..., Dale AM, Andreassen OA

Circ. Res. 118 (1) 83-94 [2016-01-08; online 2015-10-22]

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

F11 is associated with recurrent VTE in women. A prospective cohort study.

Bruzelius M, Ljungqvist M, Bottai M, ..., Lärfars G, Odeberg J

Thromb. Haemost. 115 (2) 406-414 [2016-01-00; online 2015-10-02]

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

An Immunochip-based interaction study of contrasting interaction effects with smoking in ACPA-positive versus ACPA-negative rheumatoid arthritis.

Jiang X, Källberg H, Chen Z, ..., Padyukov L, Alfredsson L

Rheumatology (Oxford) 55 (1) 149-155 [2016-01-00; online 2015-08-15]

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

Adaptive radiation of Darwin's finches revisited using whole genome sequencing.

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

Bioessays 38 (1) 14-20 [2016-01-00; online 2015-11-26]

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

Gene-Environment Interplay in Physical, Psychological, and Cognitive Domains in Mid to Late Adulthood: Is APOE a Variability Gene?

Reynolds CA, Gatz M, Christensen K, ..., Pedersen NL, Interplay of Genes and Environment across Multiple Studies (IGEMS) consortium

pmc mid

Behav. Genet. 46 (1) 4-19 [2016-01-00; online 2015-11-06]

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

PAX5-ESRRB is a recurrent fusion gene in B-cell precursor pediatric acute lymphoblastic leukemia.

Marincevic-Zuniga Y, Zachariadis V, Cavelier L, ..., Syvänen AC, Nordlund J

pmc

Haematologica 101 (1) e20-e23 [2016-01-00; online 2015-10-24]

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

Protein Biomarkers for Insulin Resistance and Type 2 Diabetes Risk in Two Large Community Cohorts.

Nowak C, Sundström J, Gustafsson S, ..., Ingelsson E, Fall T

Diabetes 65 (1) 276-284 [2016-01-00; online 2015-10-01]

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