Bioinformatics Compute and Storage

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]

Consequences of past climate change and recent human persecution on mitogenomic diversity in the arctic fox

Larsson P, von Seth J, Hagen IJ, ..., Stanton DWG, Dalén L

Phil. Trans. R. Soc. B 374 (1788) 20190212 [2019-12-23; online 2019-11-04]

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

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]

A genome-wide transcriptomic analysis of protein-coding genes in human blood cells.

Uhlen M, Karlsson MJ, Zhong W, ..., Fagerberg L, Brodin P

Science 366 (6472) - [2019-12-20; online 2019-12-21]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [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]

A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.

Asp M, Giacomello S, Larsson L, ..., Sylvén C, Lundeberg J

Cell 179 (7) 1647-1660.e19 [2019-12-12; online 2019-12-14]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing (ISS) [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [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]

Plasma Lipidome and Prediction of Type 2 Diabetes in the Population-Based Malmö Diet and Cancer Cohort

Fernandez C, Surma MA, Klose C, ..., Simons K, Melander O

Dia Care - (-) dc191199 [2019-12-08; online 2019-12-08]

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

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]

Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria.

Nicholls TJ, Spåhr H, Jiang S, ..., Larsson NG, Gustafsson CM

Mol. Cell 76 (5) 784-796.e6 [2019-12-05; online 2019-10-03]

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

GLUL Ablation Can Confer Drug Resistance to Cancer Cells via a Malate-Aspartate Shuttle-Mediated Mechanism

Muthu M, Kumar R, Syed Khaja AS, ..., Persson JL, Nordström A

Cancers (Basel) 11 (12) 1945 [2019-12-05; online 2019-12-05]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [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]

Molecular Characterization and Comparative Genomics of Clinical Hybrid Shiga Toxin-Producing and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains in Sweden

Bai X, Zhang J, Ambikan A, ..., Xiong Y, Matussek A

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

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

Genome expansion of an obligate parthenogenesis-associated Wolbachia poses an exception to the symbiont reduction model

Kampfraath AA, Klasson L, Anvar SY, ..., Kraaijeveld K, Ellers J

BMC Genomics 20 (1) - [2019-12-00; online 2019-02-06]

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

Proteogenomics and Hi-C reveal transcriptional dysregulation in high hyperdiploid childhood acute lymphoblastic leukemia

Yang M, Vesterlund M, Siavelis I, ..., Lehtiö J, Paulsson K

Nat Commun 10 (1) - [2019-12-00; online 2019-04-03]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Service] Proteogenomics [Technology development]

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]

A cell fitness selection model for neuronal survival during development

Wang Y, Wu H, Fontanet P, ..., Hadjab S, Lallemend F

Nat Commun 10 (1) - [2019-12-00; online 2019-09-12]

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

Inhibition of translation termination by small molecules targeting ribosomal release factors

Ge X, Oliveira A, Hjort K, ..., Sanyal S, Åqvist J

Sci Rep 9 (1) - [2019-12-00; online 2019-10-28]

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

Genome and plasmid diversity of Extended-Spectrum β-Lactamase-producing Escherichia coli ST131 – tracking phylogenetic trajectories with Bayesian inference

Ny S, Sandegren L, Salemi M, Giske CG

Sci Rep 9 (1) - [2019-12-00; online 2019-07-16]

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

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]

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]

Association between Copy Number Variation and Response to Social Skills Training in Autism Spectrum Disorder

Tammimies K, Li D, Rabkina I, ..., Choque-Olsson N, Bölte S

Sci Rep 9 (1) - [2019-12-00; online 2019-07-08]

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

Prediction of response to anti-cancer drugs becomes robust via network integration of molecular data

Franco M, Jeggari A, Peuget S, ..., Selivanova G, Alexeyenko A

Sci Rep 9 (1) - [2019-12-00; online 2019-02-20]

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

Undifferentiated pleomorphic sarcomas with PRDM10 fusions have a distinct gene expression profile

Hofvander J, Puls F, Pillay N, ..., Nilsson J, Mertens F

J. Pathol 249 (4) 425-434 [2019-12-00; online 2019-08-27]

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

Intra- and inter-individual metabolic profiling highlights carnitine and lysophosphatidylcholine pathways as key molecular defects in type 2 diabetes

Diamanti K, Cavalli M, Pan G, ..., Komorowski J, Wadelius C

Sci Rep 9 (1) - [2019-12-00; online 2019-07-04]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [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]

Whole genome DNA sequencing provides an atlas of somatic mutagenesis in healthy human cells and identifies a tumor-prone cell type

Franco I, Helgadottir HT, Moggio A, ..., Supek F, Eriksson M

Genome Biol. 20 (1) - [2019-12-00; online 2019-12-18]

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

Linkage and exome analysis implicate multiple genes in non-syndromic intellectual disability in a large Swedish family

Lindholm Carlström E, Halvardson J, Etemadikhah M, ..., Gustavson KH, Feuk L

BMC Med Genomics 12 (1) - [2019-12-00; online 2019-11-06]

Bioinformatics Compute and Storage [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]

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]

Meckel syndrome: Clinical and mutation profile in six fetuses.

Radhakrishnan P, Nayak SS, Shukla A, Lindstrand A, Girisha KM

Clin. Genet. 96 (6) 560-565 [2019-12-00; online 2019-08-21]

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

Breast cancer quantitative proteome and proteogenomic landscape

Johansson HJ, None , Socciarelli F, ..., Børresen-Dale AL, Lehtiö J

Nat Commun 10 (1) - [2019-12-00; online 2019-04-08]

Advanced Light Microscopy (ALM) [Service] Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Proteogenomics [Technology development]

Conbase: a software for unsupervised discovery of clonal somatic mutations in single cells through read phasing

Hård J, Al Hakim E, Kindblom M, ..., Mold JE, Frisén J

Genome Biol. 20 (1) - [2019-12-00; online 2019-04-01]

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

PECTIN ACETYLESTERASE9 Affects the Transcriptome and Metabolome and Delays Aphid Feeding

Kloth KJ, Abreu IN, Delhomme N, ..., Moritz T, Albrectsen BR

Plant Physiol. 181 (4) 1704-1720 [2019-12-00; online 2019-09-24]

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

Single-cell RNA sequencing reveals midbrain dopamine neuron diversity emerging during mouse brain development

Tiklová K, Björklund ÅK, Lahti L, ..., Parmar M, Perlmann T

GEO

Nat Commun 10 (1) - [2019-12-00; online 2019-02-04]

Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] In Situ Sequencing (ISS) [Collaborative]

From cytogenetics to cytogenomics: whole-genome sequencing as a first-line test comprehensively captures the diverse spectrum of disease-causing genetic variation underlying intellectual disability

Lindstrand A, Eisfeldt J, Pettersson M, ..., Lundin J, Nilsson D

Genome Med 11 (1) - [2019-12-00; online 2019-11-07]

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

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

The human secretome

Uhlén M, Karlsson MJ, Hober A, ..., Fagerberg L, Sivertsson Å

Sci. Signal. 12 (609) eaaz0274 [2019-11-26; online 2019-11-26]

MYCN-enhanced Oxidative and Glycolytic Metabolism Reveals Vulnerabilities for Targeting Neuroblastoma.

Oliynyk G, Ruiz-Pérez MV, Sainero-Alcolado L, ..., Lehtiö J, Arsenian-Henriksson M

pmc

iScience 21 (-) 188-204 [2019-11-22; online 2019-10-11]

Bioinformatics Compute and Storage [Service] Proteogenomics [Collaborative]

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]

BET and Aurora Kinase A inhibitors synergize against MYCN-positive human glioblastoma cells.

Čančer M, Drews LF, Bengtsson J, ..., Weishaupt H, Swartling FJ

Cell Death Dis 10 (12) 881 [2019-11-21; online 2019-11-21]

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

Fast and Efficient Fc-Specific Photoaffinity Labeling To Produce Antibody-DNA Conjugates.

Stiller C, Aghelpasand H, Frick T, ..., Ahmadian A, Karlström AE

Bioconjug. Chem. 30 (11) 2790-2798 [2019-11-20; online 2019-10-25]

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

Human induced pluripotent stem cells from two azoospermic patients with Klinefelter syndrome show similar X chromosome inactivation behavior to female pluripotent stem cells.

Panula S, Kurek M, Kumar P, ..., Lanner F, Stukenborg JB

Hum. Reprod. - (-) - [2019-11-19; online 2019-11-19]

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

Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen ( Populus tremula).

Apuli RP, Bernhardsson C, Schiffthaler B, ..., Street NR, Ingvarsson PK

G3 (Bethesda) - (-) - [2019-11-19; online 2019-11-19]

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

Lithium treatment reverses irradiation-induced changes in rodent neural progenitors and rescues cognition.

Zanni G, Goto S, Fragopoulou AF, ..., Hermanson O, Blomgren K

Mol. Psychiatry - (-) - [2019-11-14; online 2019-11-14]

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

On-demand virtual research environments using microservices

Capuccini M, Larsson A, Carone M, ..., Toor S, Spjuth O

- 5 (-) e232 [2019-11-11; online 2019-11-11]

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

Long‐read metabarcoding of the eukaryotic rDNA operon to phylogenetically and taxonomically resolve environmental diversity

Jamy M, Foster R, Barbera P, ..., Bass D, Burki F

Mol Ecol Resour - (-) - [2019-11-09; online 2019-11-09]

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

Cell‐of‐origin determined by both gene expression profiling and immunohistochemistry is the strongest predictor of survival in patients with diffuse large B‐cell lymphoma

Abdulla M, Hollander P, Pandzic T, ..., Rosenquist R, Amini R

Am J Hematol - (-) - [2019-11-07; online 2019-11-07]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative]

Viromics Reveal a Number of Novel RNA Viruses in Swedish Mosquitoes.

Öhlund P, Hayer J, Lundén H, Hesson JC, Blomström AL

Viruses 11 (11) - [2019-11-05; online 2019-11-05]

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

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]

Humanized Stem Cell Models of Pediatric Medulloblastoma Reveal an Oct4/mTOR Axis that Promotes Malignancy

Čančer M, Hutter S, Holmberg KO, ..., Weishaupt H, Swartling FJ

Cell Stem Cell - (-) - [2019-11-00; online 2019-11-00]

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

Genetic differentiation between and within ecotypes of pike ( Esox lucius ) in the Baltic Sea

Nordahl O, Koch‐Schmidt P, Sunde J, ..., Forsman A, Larsson P

Aquatic Conserv: Mar Freshw Ecosyst 29 (11) 1923-1935 [2019-11-00; online 2019-08-16]

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

A rapid and accurate method to quantify neurite outgrowth from cell and tissue cultures: Two image analytic approaches using adaptive thresholds or machine learning

Ossinger A, Bajic A, Pan S, ..., Hailer NP, Schizas N

Journal of Neuroscience Methods - (-) 108522 [2019-11-00; online 2019-11-00]

BioImage Informatics [Service] Bioinformatics Compute and Storage [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]

Influence of blue mussel (Mytilus edulis) intake on fatty acid composition in erythrocytes and plasma phospholipids and serum metabolites in women with rheumatoid arthritis

Lindqvist HM, Gjertsson I, Andersson S, Calder PC, Bärebring L

Prostaglandins, Leukotrienes and Essential Fatty Acids (PLEFA) 150 (-) 7-15 [2019-11-00; online 2019-11-00]

Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Service]

High-grade progression confers poor survival in pancreatic neuroendocrine tumors.

Botling J, Lamarca A, Bajic D, ..., Skogseid B, Crona J

Neuroendocrinology - (-) - [2019-10-29; online 2019-10-29]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative]

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]

A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.

Pettersson ME, Rochus CM, Han F, ..., Folkvord A, Andersson L

Genome Res. - (-) - [2019-10-24; online 2019-10-24]

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

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]

Considerations and Implications in the Purification of Extracellular Vesicles – A Cautionary Tale

Lee YXF, Johansson H, Wood MJA, El Andaloussi S

Front. Neurosci. 13 (-) - [2019-10-18; online 2019-10-18]

Bioinformatics Compute and Storage [Service] Proteogenomics [Service]

Whole‐genome sequencing of synchronous thyroid carcinomas identifies aberrant DNA repair in thyroid cancer dedifferentiation

Paulsson JO, Backman S, Wang N, ..., Zedenius J, Juhlin CC

J. Pathol - (-) - [2019-10-17; online 2019-10-17]

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

A Shh/Gli-driven three-node timer motif controls temporal identity and fate of neural stem cells

Dias JM, Alekseenko Z, Jeggari A, ..., Iber D, Ericson J

- - (-) - [2019-10-17; online 2019-10-17]

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

Microbe-host interplay in atopic dermatitis and psoriasis.

Fyhrquist N, Muirhead G, Prast-Nielsen S, ..., Andersson B, Alenius H

pmc

Nat Commun 10 (1) 4703 [2019-10-16; online 2019-10-16]

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

Above-below surface interactions mediate effects of seagrass disturbance on meiobenthic diversity, nematode and polychaete trophic structure.

Nascimento FJA, Dahl M, Deyanova D, ..., Creer S, Gullström M

pmc

Commun Biol 2 (-) 362 [2019-10-04; online 2019-10-04]

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

Skeletal Mineralization in Association with Type X Collagen Expression Is an Ancestral Feature for Jawed Vertebrates

Debiais-Thibaud M, Simion P, Ventéo S, ..., Mazan S, Haitina T

- 36 (10) 2265-2276 [2019-10-01; online 2019-07-04]

Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]

Interoperable and scalable data analysis with microservices: applications in metabolomics

Emami Khoonsari P, Moreno P, Bergmann S, ..., Kultima K, Spjuth O

- 35 (19) 3752-3760 [2019-10-01; online 2019-03-09]

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

Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species.

Talla V, Soler L, Kawakami T, ..., Wiklund C, Backström N

pmc

Genome Biol Evol 11 (10) 2875-2886 [2019-10-01; online 2019-10-04]

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

Genome-wide evidence supports mitochondrial relationships and pervasive parallel phenotypic evolution in open-habitat chats.

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

Mol. Phylogenet. Evol. 139 (-) 106568 [2019-10-00; online 2019-07-23]

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

High-definition spatial transcriptomics for in situ tissue profiling.

Vickovic S, Eraslan G, Salmén F, ..., Regev A, Ståhl PL

pmc mid

Nat. Methods 16 (10) 987-990 [2019-10-00; online 2019-09-09]

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

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]

Cell generation dynamics underlying naive T-cell homeostasis in adult humans.

Mold JE, Réu P, Olin A, ..., Brodin P, Frisén J

PLoS Biol. 17 (10) e3000383 [2019-10-00; online 2019-10-29]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative]

Leaf metabolic signatures induced by real and simulated herbivory in black mustard (Brassica nigra)

Papazian S, Girdwood T, Wessels BA, ..., Moritz T, Albrectsen BR

Metabolomics 15 (10) - [2019-10-00; online 2019-09-28]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [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]

Clinical candidate and genistein analogue AXP107-11 has chemoenhancing functions in pancreatic adenocarcinoma through G protein-coupled estrogen receptor signaling.

Mesmar F, Dai B, Ibrahim A, ..., Fleming J, Williams C

Cancer Med - (-) - [2019-09-30; online 2019-09-30]

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

Complete genomes of two extinct New Zealand passerines show responses to climate fluctuations but no evidence for genomic erosion prior to extinction.

Dussex N, von Seth J, Knapp M, ..., Robertson BC, Dalén L

pmc

Biol. Lett. 15 (9) 20190491 [2019-09-27; online 2019-09-04]

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

Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1.

Masser AE, Kang W, Roy J, ..., Friedländer MR, Andréasson C

pmc GEO

Elife 8 (-) - [2019-09-25; online 2019-09-25]

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

Novel Y-Chromosome Long Non-Coding RNAs Expressed in Human Male CNS During Early Development

Johansson MM, Pottmeier P, Suciu P, ..., Peuckert C, Jazin E

Front Genet 10 (-) - [2019-09-24; online 2019-09-24]

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

Ataxia in Patients With Bi-Allelic NFASC Mutations and Absence of Full-Length NF186.

Kvarnung M, Shahsavani M, Taylan F, ..., Lindstrand A, Falk A

pmc

Front Genet 10 (-) 896 [2019-09-24; online 2019-09-24]

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

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]

Genomic and Seasonal Variations among Aquatic Phages Infecting the Baltic Sea Gammaproteobacterium Rheinheimera sp. Strain BAL341.

Nilsson E, Li K, Fridlund J, ..., Pinhassi J, Holmfeldt K

pmc

Appl. Environ. Microbiol. 85 (18) - [2019-09-15; online 2019-08-29]

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

Metagenomes from Coastal Marine Sediments Give Insights into the Ecological Role and Cellular Features of Loki- and Thorarchaeota

Manoharan L, Kozlowski JA, Murdoch RW, ..., Sousa FL, Schleper C

MBio 10 (5) - [2019-09-10; online 2019-09-10]

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

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]

Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly.

Höök L, Leal L, Talla V, Backström N

pmc

Genome Biol Evol 11 (9) 2633-2652 [2019-09-01; online 2019-08-11]

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

Direct effects of organic pollutants on the growth and gene expression of the Baltic Sea model bacterium Rheinheimera sp. BAL341.

Karlsson CMG, Cerro-Gálvez E, Lundin D, ..., Vila-Costa M, Pinhassi J

pmc GENBANK

Microb Biotechnol 12 (5) 892-906 [2019-09-00; online 2019-07-04]

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

Combined mRNA and protein single cell analysis in a dynamic cellular system using SPARC

Reimegård J, Danielsson M, Tarbier M, ..., Friedländer MR, Gallant CJ

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

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

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]

Profiling surface proteins on individual exosomes using a proximity barcoding assay.

Wu D, Yan J, Shen X, ..., Landegren U, Kamali-Moghaddam M

pmc

Nat Commun 10 (1) 3854 [2019-08-26; online 2019-08-26]

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

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]

Boreal tree species affect soil organic matter composition and saprotrophic mineralization rates

Segura JH, Nilsson MB, Sparrman T, ..., Tolu J, Öquist MG

Plant Soil 441 (1-2) 173-190 [2019-08-00; online 2019-05-24]

Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Collaborative]

Goodbye reference, hello genome graphs.

Ameur A

Nat. Biotechnol. 37 (8) 866-868 [2019-08-00; online 2019-08-04]

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

Microbial utilization of simple carbon substrates in boreal peat soils at low temperatures

Segura JH, Nilsson MB, Schleucher J, ..., Bertilsson S, Öquist MG

Soil Biology and Biochemistry 135 (-) 438-448 [2019-08-00; online 2019-08-00]

Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Collaborative]

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]

Reply to "CRISPR screens are feasible in TP53 wild-type cells".

Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J

pmc

Mol. Syst. Biol. 15 (8) e9059 [2019-08-00; online 2019-08-30]

Bioinformatics Compute and Storage [Service] High-throughput Genome Engineering (HTGE) [Collaborative]

Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return.

Jønsson KA, Blom MPK, Marki PZ, ..., Ericson PGP, Irestedt M

Mol. Phylogenet. Evol. 137 (-) 200-209 [2019-08-00; online 2019-03-23]

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

Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem.

Broman E, Raymond C, Sommer C, ..., Creer S, Nascimento FJA

pmc GENBANK

Mol. Ecol. 28 (16) 3813-3829 [2019-08-00; online 2019-09-05]

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

Multiplex plasma protein profiling identifies novel markers to discriminate patients with adenocarcinoma of the lung.

Djureinovic D, Pontén V, Landelius P, ..., Micke P, Ståhle E

pmc

BMC Cancer 19 (1) 741 [2019-07-29; online 2019-07-29]

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

Impact of vitamin D and vitamin D receptor TaqI polymorphism in primary human myoblasts.

Saini A, Björkhem-Bergman L, Boström J, ..., Rullman E, Gustafsson T

pmc

Endocr Connect 8 (7) 1070-1081 [2019-07-29; online 2019-07-29]

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

Evolved for success in novel environments: The round goby genome

Adrian-Kalchhauser I, Blomberg A, Larsson T, ..., Schloissnig S, Winkler S

- - (-) - [2019-07-19; online 2019-07-19]

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

TGF-β family ligands exhibit distinct signalling dynamics that are driven by receptor localisation.

Miller DSJ, Schmierer B, Hill CS

pmc

J. Cell. Sci. 132 (14) - [2019-07-15; online 2019-07-15]

Bioinformatics Compute and Storage [Service] High-throughput Genome Engineering (HTGE) [Collaborative]

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]

GUESSmyLT: Software to guess the RNA-Seq library type of paired and single end read files

Wik E, Olin H, Haughey C, Klasson L, Dainat J

JOSS 4 (39) 1344 [2019-07-07; online 2019-07-07]

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

Global gene expression analysis in etiolated and de-etiolated seedlings in conifers.

Ranade SS, Delhomme N, García-Gil MR

pmc

PLoS ONE 14 (7) e0219272 [2019-07-05; online 2019-07-05]

Biochemical Imaging Centre Umeå [Service] Bioinformatics Compute and Storage [Service] Cryo-EM [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Comparison of boreal acid sulfate soil microbial communities in oxidative and reductive environments.

Christel S, Yu C, Wu X, ..., Åström ME, Dopson M

Res. Microbiol. 170 (6-7) 288-295 [2019-07-03; online 2019-07-03]

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

Seeking the ultimate challenge.

Brodin P

Nat Med - (-) - [2019-07-03; online 2019-07-03]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development]

Surface activated polyethylene separator promoting Li+ ion transport in gel polymer electrolytes and cycling stability of Li-metal anode

Qiu Z, Shi L, Wang Z, ..., Zhao Y, Yuan S

Chemical Engineering Journal 368 (-) 321-330 [2019-07-00; online 2019-07-00]

Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Service]

Transcriptome analysis of shade avoidance and shade tolerance in conifers.

Ranade SS, Delhomme N, García-Gil MR

Planta 250 (1) 299-318 [2019-07-00; online 2019-04-26]

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

Single cell analysis of autism patient with bi-allelic NRXN1-alpha deletion reveals skewed fate choice in neural progenitors and impaired neuronal functionality

Lam M, Moslem M, Bryois J, ..., Sullivan PF, Falk A

Experimental Cell Research 383 (1) 111469 [2019-07-00; online 2019-07-00]

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

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]

Hemostatic Genes Exhibit a High Degree of Allele-Specific Regulation in Liver.

Olsson Lindvall M, Hansson L, Klasson S, ..., Jern C, Stanne TM

Thromb. Haemost. 119 (7) 1072-1083 [2019-07-00; online 2019-04-29]

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

Expanding the phenotypic spectrum of osteogenesis imperfecta type V including heterotopic ossification of muscle origins and attachments.

Clewemar P, Hailer NP, Hailer Y, ..., Ljunggren Ö, Stattin EL

pmc

Mol Genet Genomic Med 7 (7) e00723 [2019-07-00; online 2019-05-16]

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

Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi.

Ferrante MI, Entrambasaguas L, Johansson M, ..., Montresor M, Godhe A

pmc

Genes 10 (7) - [2019-06-28; online 2019-06-28]

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

Model System for the Formation of Tick-Borne Encephalitis Virus Replication Compartments without Viral RNA Replication

Yau WL, Nguyen-Dinh V, Larsson E, ..., Överby AK, Lundmark R

J Virol 93 (18) - [2019-06-26; online 2019-08-28]

Biochemical Imaging Centre Umeå [Collaborative] Bioinformatics Compute and Storage [Service] Cryo-EM [Service]

Genomic Characterization of the Emerging Pathogen Streptococcus pseudopneumoniae.

Garriss G, Nannapaneni P, Simões AS, ..., de Lencastre H, Henriques-Normark B

pmc

MBio 10 (3) - [2019-06-25; online 2019-06-25]

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

Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis.

Lundmark A, Hu YOO, Huss M, ..., Andersson AF, Yucel-Lindberg T

pmc

Front. Cell. Infect. Microbiol. 9 (-) 216 [2019-06-21; online 2019-06-21]

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

Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden

Parducci L, Alsos IG, Unneberg P, ..., Slotte T, Wohlfarth B

Front. Ecol. Evol. 7 (-) 189 [2019-06-20; online 2019-06-20]

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

Single-nuclei transcriptomic analysis of the subthalamic nucleus reveals different Pitx2-positive subpopulations

Papathanou M, Björklund ÅK, Martis-Thiele MM, Wallén-Mackenzie Å

- - (-) - [2019-06-20; online 2019-06-20]

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

A Call for Blood-In Human Immunology.

Brodin P, Duffy D, Quintana-Murci L

Immunity 50 (6) 1335-1336 [2019-06-18; online 2019-06-20]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development]

Ouabain-regulated phosphoproteome reveals molecular mechanisms for Na+, K+–ATPase control of cell adhesion, proliferation, and survival

Panizza E, Zhang L, Fontana JM, ..., Lehtiö J, Aperia A

The FASEB Journal - (-) fj.201900445R [2019-06-14; online 2019-06-14]

Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Compute and Storage [Service] Proteogenomics [Technology development]

Systematic assessment of antibody selectivity in plasma based on a resource of enrichment profiles.

Fredolini C, Byström S, Sanchez-Rivera L, ..., Lehtiö J, Schwenk JM

pmc

Sci Rep 9 (1) 8324 [2019-06-06; online 2019-06-06]

Autoimmunity Profiling [Technology development] Bioinformatics Compute and Storage [Service] Plasma Profiling [Technology development] Proteogenomics [Technology development]

Serum Metabolite Markers of Dementia Through Quantitative NMR Analysis: The Importance of Threonine-Linked Metabolic Pathways

Figueira J, Adolfsson R, Nordin Adolfsson A, Nyberg L, Öhman A

JAD 69 (3) 763-774 [2019-06-04; online 2019-06-04]

Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Collaborative]

Gene fusion involving the insulin‐like growth factor 1 receptor in an ALK ‐negative inflammatory myofibroblastic tumour

Piarulli G, Puls F, Wängberg B, ..., Arbajian E, Mertens F

Histopathology 74 (7) 1098-1102 [2019-06-00; online 2019-04-24]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [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 targeted proteomics approach reveals a serum protein signature as diagnostic biomarker for resectable gastric cancer.

Shen Q, Polom K, Williams C, ..., Roviello F, Kamali-Moghaddam M

pmc

EBioMedicine 44 (-) 322-333 [2019-06-00; online 2019-05-28]

Bioinformatics Compute and Storage [Service] Clinical Biomarkers [Service] Glycoproteomics [Collaborative] PLA and Single Cell Proteomics [Technology development]

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]

Further support linking the 22q11.2 microduplication to an increased risk of bladder exstrophy and highlighting LZTR1 as a candidate gene.

Lundin J, Markljung E, Baranowska Körberg I, ..., Lindstrand A, Nordenskjöld A

pmc

Mol Genet Genomic Med 7 (6) e666 [2019-06-00; online 2019-05-01]

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

The viral protein corona directs viral pathogenesis and amyloid aggregation.

Ezzat K, Pernemalm M, Pålsson S, ..., Spetz AL, El Andaloussi S

pmc

Nat Commun 10 (1) 2331 [2019-05-27; online 2019-05-27]

Bioinformatics Compute and Storage [Service] Proteogenomics [Technology development]

Crystal structure of the catalytic domain of the Weissela oryzae botulinum-like toxin

Košenina S, Masuyer G, Zhang S, Dong M, Stenmark P

FEBS Lett - (-) - [2019-05-20; online 2019-05-20]

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

Ancient DNA from mastics solidifies connection between material culture and genetics of mesolithic hunter-gatherers in Scandinavia.

Kashuba N, Kırdök E, Damlien H, ..., Persson P, Götherström A

pmc Dryad

Commun Biol 2 (-) 185 [2019-05-15; online 2019-05-15]

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

Periodontal Health and Oral Microbiota in Patients with Rheumatoid Arthritis.

Eriksson K, Fei G, Lundmark A, ..., Jansson L, Yucel-Lindberg T

pmc

J Clin Med 8 (5) - [2019-05-08; online 2019-05-08]

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

Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus.

Abramova A, Alm Rosenblad M, Blomberg A, Larsson TA

pmc

PLoS ONE 14 (5) e0216294 [2019-05-02; online 2019-05-02]

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

SciPipe: A workflow library for agile development of complex and dynamic bioinformatics pipelines

Lampa S, Dahlö M, Alvarsson J, Spjuth O

Gigascience 8 (5) - [2019-05-01; online 2019-04-26]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]

Prompt apoptotic response to high glucose in SGLT-expressing renal cells

Nilsson LM, Zhang L, Bondar A, ..., Scott L, Aperia A

American Journal of Physiology-Renal Physiology 316 (5) F1078-F1089 [2019-05-01; online 2019-05-01]

Advanced Light Microscopy (ALM) [Service] Bioinformatics Compute and Storage [Service]

Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise.

Prost S, Armstrong EE, Nylander J, ..., Ericson PGP, Irestedt M

pmc

Gigascience 8 (5) - [2019-05-01; online 2019-01-29]

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

Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds.

Xu L, Auer G, Peona V, ..., Irestedt M, Zhou Q

Nat Ecol Evol 3 (5) 834-844 [2019-05-00; online 2019-04-01]

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

Spatial proteomics: a powerful discovery tool for cell biology

Lundberg E, Borner GHH

Nat Rev Mol Cell Biol 20 (5) 285-302 [2019-05-00; online 2019-01-18]

Bioinformatics Compute and Storage [Service] Cell Profiling [Collaborative]

An Atlas of Vagal Sensory Neurons and Their Molecular Specialization

Kupari J, Häring M, Agirre E, Castelo-Branco G, Ernfors P

Cell Rep 27 (8) 2508-2523.e4 [2019-05-00; online 2019-05-00]

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

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]

Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient

Helgadottir HT, Lundin P, Wallén Arzt E, ..., Graff C, Eriksson M

Hum Mol Genet 28 (16) 2675-2685 [2019-04-24; online 2019-04-24]

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

PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination.

Falcão AM, Meijer M, Scaglione A, ..., Casaccia P, Castelo-Branco G

pmc

Cell Rep 27 (4) 1090-1102.e10 [2019-04-23; online 2019-04-25]

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

The complex barnacle perfume: identification of waterborne pheromone homologues in Balanus improvisus and their differential expression during settlement

Abramova A, Lind U, Blomberg A, Rosenblad MA

Biofouling 35 (4) 416-428 [2019-04-21; online 2019-05-30]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [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]

The Genome of Blue-Capped Cordon-Bleu Uncovers Hidden Diversity of LTR Retrotransposons in Zebra Finch.

Boman J, Frankl-Vilches C, da Silva Dos Santos M, ..., Gahr M, Suh A

pmc

Genes 10 (4) - [2019-04-13; online 2019-04-13]

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

SQSTM1/p62-Directed Metabolic Reprogramming Is Essential for Normal Neurodifferentiation.

Calvo-Garrido J, Maffezzini C, Schober FA, ..., Freyer C, Wredenberg A

pmc

Stem Cell Reports 12 (4) 696-711 [2019-04-09; online 2019-02-28]

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

A hybrid de novo genome assembly of the honeybee, Apis mellifera, with chromosome-length scaffolds.

Wallberg A, Bunikis I, Pettersson OV, ..., Robinson GE, Webster MT

BMC Genomics 20 (1) 275 [2019-04-08; online 2019-04-08]

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

SAMURAI (Solid-phase Assisted Mutagenesis by Uracil Restriction for Accurate Integration) for antibody affinity maturation and paratope mapping.

Hu FJ, Lundqvist M, Uhlén M, Rockberg J

pmc

Nucleic Acids Res. 47 (6) e34 [2019-04-08; online 2019-02-05]

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

High-Quality Library Preparation for NGS-Based Immunoglobulin Germline Gene Inference and Repertoire Expression Analysis

Vázquez Bernat N, Corcoran M, Hardt U, ..., Martin M, Karlsson Hedestam GB

Front Immunol 10 (-) - [2019-04-05; online 2019-04-05]

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

Osteoporosis and skeletal dysplasia caused by pathogenic variants in SGMS2.

Pekkinen M, Terhal PA, Botto LD, ..., Holthuis JC, Mäkitie O

pmc

JCI Insight 4 (7) - [2019-04-04; online 2019-04-04]

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

Mesenchymal stem cells transplanted into spinal cord injury adopt immune cell-like characteristics.

Hakim R, Covacu R, Zachariadis V, ..., Brundin L, Svensson M

pmc

Stem Cell Res Ther 10 (1) 115 [2019-04-03; online 2019-04-03]

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

B cell profiling in malaria reveals expansion and remodelling of CD11c+ B cell subsets.

Sundling C, Rönnberg C, Yman V, ..., Persson KE, Färnert A

JCI Insight 5 (-) - [2019-04-02; online 2019-04-02]

Bioinformatics Compute and Storage [Service] Mass Cytometry [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]

Leukocytosis is associated with retinopathy of prematurity in extremely preterm infants.

Lundgren P, Klevebro S, Brodin P, ..., Hallberg B, Hellström A

Acta Paediatr. - (-) - [2019-03-28; online 2019-03-28]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative]

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]

Helicase/SUMO-targeted ubiquitin ligase Uls1 interacts with the Holliday junction resolvase Yen1

Bauer SL, Chen J, Åström SU

PLoS ONE 14 (3) e0214102 [2019-03-21; online 2019-03-21]

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

The repertoire of maternal anti-viral antibodies in human newborns.

Pou C, Nkulikiyimfura D, Henckel E, ..., Bohlin K, Brodin P

Nat. Med. - (-) - [2019-03-18; online 2019-03-18]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [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]

Index hopping on the Illumina HiseqX platform and its consequences for ancient DNA studies.

van der Valk T, Vezzi F, Ormestad M, Dalén L, Guschanski K

Mol Ecol Resour - (-) - [2019-03-08; online 2019-03-08]

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

Single-Cell RNA-Seq Reveals Cellular Heterogeneity of Pluripotency Transition and X Chromosome Dynamics during Early Mouse Development.

Cheng S, Pei Y, He L, ..., Jing N, Deng Q

Cell Rep 26 (10) 2593-2607.e3 [2019-03-05; online 2019-03-07]

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

In situ quantification of individual mRNA transcripts in melanocytes discloses gene regulation of relevance to speciation

Wu CC, Klaesson A, Buskas J, ..., Söderberg O, Wolf JBW

J Exp Biol 222 (5) jeb194431 [2019-03-01; online 2019-02-04]

BioImage Informatics [Service] Bioinformatics Compute and Storage [Service]

Chromosomal inversions associated with environmental adaptation in honeybees

Christmas MJ, Wallberg A, Bunikis I, ..., Wallerman O, Webster MT

Mol Ecol 28 (6) 1358-1374 [2019-03-00; online 2018-12-21]

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

Regulatory changes in pterin and carotenoid genes underlie balanced color polymorphisms in the wall lizard

Andrade P, Pinho C, Pérez i de Lanuza G, ..., Andersson L, Carneiro M

Proc Natl Acad Sci USA - (-) 201820320 [2019-02-28; online 2019-02-28]

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

Transcriptomics of cardiac biopsies reveals differences in patients with or without diagnostic parameters for heart failure with preserved ejection fraction.

Das S, Frisk C, Eriksson MJ, ..., Linde C, Persson B

pmc

Sci Rep 9 (1) 3179 [2019-02-28; online 2019-02-28]

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

Whole-Genome Analysis of Domestic Chicken Selection Lines Suggests Segregating Variation in ERV Makeups

Pettersson ME, Jern P

Genes 10 (2) 162 [2019-02-20; online 2019-02-20]

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

Mass cytometry identifies distinct CD4+ T cell clusters distinguishing HIV-1–infected patients according to antiretroviral therapy initiation

Bekele Y, Lakshmikanth T, Chen Y, ..., Brodin P, Chiodi F

JCI Insight 4 (3) - [2019-02-07; online 2019-02-07]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Service]

Spatiotemporal dissection of the cell cycle regulated human proteome

Mahdessian D, Sullivan D, Danielsson F, ..., Lindskog C, Lundberg E

- - (-) - [2019-02-07; online 2019-02-07]

Bioinformatics Compute and Storage [Service] Cell Profiling [Collaborative]

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]

Parental legacy, demography, and admixture influenced the evolution of the two subgenomes of the tetraploid Capsella bursa-pastoris (Brassicaceae).

Kryvokhyzha D, Salcedo A, Eriksson MC, ..., Wright SI, Lascoux M

pmc

PLoS Genet. 15 (2) e1007949 [2019-02-00; online 2019-02-15]

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

Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements.

Eisfeldt J, Pettersson M, Vezzi F, ..., Carvalho CMB, Lindstrand A

pmc

PLoS Genet. 15 (2) e1007858 [2019-02-00; online 2019-02-08]

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

The antimicrobial protein S100A12 identified as a potential autoantigen in a subgroup of atopic dermatitis patients.

Mikus M, Johansson C, Acevedo N, Nilsson P, Scheynius A

pmc

Clin Transl Allergy 9 (-) 6 [2019-01-31; online 2019-01-31]

Autoimmunity Profiling [Collaborative] Bioinformatics Compute and Storage [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]

Systems-Level Immune Monitoring by Mass Cytometry.

Lakshmikanth T, Brodin P

Methods Mol. Biol. 1913 (-) 33-48 [2019-01-23; online 2019-01-23]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development]

Altered human oligodendrocyte heterogeneity in multiple sclerosis

Jäkel S, Agirre E, Falcão AM, ..., Williams A, Castelo-Branco G

Nature - (-) - [2019-01-23; online 2019-01-23]

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

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]

The Versatility of SMRT Sequencing.

Hestand MS, Ameur A

Genes 10 (1) - [2019-01-04; online 2019-01-04]

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

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]

Systems-level patterns emerge

Brodin P

Nat Rev Immunol - (-) - [2019-01-03; online 2019-01-03]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development]

Single-Molecule Sequencing: Towards Clinical Applications.

Ameur A, Kloosterman WP, Hestand MS

Trends Biotechnol. 37 (1) 72-85 [2019-01-01; online 2018-08-13]

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

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]

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]

SubCellBarCode: Proteome-wide Mapping of Protein Localization and Relocalization

Orre LM, Vesterlund M, Pan Y, ..., Fredlund E, Lehtiö J

Molecular Cell 73 (1) 166-182.e7 [2019-01-00; online 2019-01-00]

Bioinformatics Compute and Storage [Service] Proteogenomics [Technology development]

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]

Automated Cell Processing for Mass Cytometry Experiments.

Mikes J, Olin A, Lakshmikanth T, Chen Y, Brodin P

Methods Mol. Biol. 1989 (-) 111-123 [2019-00-00]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development]

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

Gossing M, Smialowska A, Nielsen J

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

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

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]

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

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

GENBANK

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

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

Targeting PFKFB3 radiosensitizes cancer cells and suppresses homologous recombination

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

PDB

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

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

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]

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

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

SRA

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

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

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]

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

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

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

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

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

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

GENBANK

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

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

Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow

Zhu Y, Orre LM, Johansson HJ, ..., Branca RMM, Lehtiö J

Nat Commun 9 (1) - [2018-12-00; online 2018-03-02]

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

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

Baltrušis P, Halvarsson P, Höglund J

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

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

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]

Somatic mutagenesis in satellite cells associates with human skeletal muscle aging

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

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

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

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

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

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

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

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]

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

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

PDB GEO

Nat Commun 9 (1) - [2018-12-00; online 2018-03-16]

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

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]

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

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

pmc

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

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

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

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

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

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

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

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

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]

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

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

Nat Commun 9 (1) - [2018-12-00; online 2018-12-04]

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

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

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

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

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

Targeted NUDT5 inhibitors block hormone signaling in breast cancer cells

Page BDG, Valerie NCK, Wright RHG, ..., Beato M, Helleday T

PDB PDB

Nat Commun 9 (1) - [2018-12-00; online 2018-01-17]

Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Service] Protein Science Facility (PSF) [Service]

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

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

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

Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Compute and Storage [Service] Cryo-EM [Service] Proteogenomics [Collaborative]

Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome

Sork H, Corso G, Krjutskov K, ..., Mäger I, EL Andaloussi S

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

Sci Rep 8 (1) - [2018-12-00; online 2018-07-17]

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

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

GEO

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

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

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

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

PDB PDB PDB PDB PDB

Nat Commun 9 (1) - [2018-12-00; online 2018-09-17]

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

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]

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

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

pmc

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

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

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

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

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

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

Effect of CTLA4-Ig (abatacept) Treatment on T cells and B cells in Peripheral Blood of Patients with Polymyositis and Dermatomyositis.

Tang Q, Ramsköld D, Krystufkova O, ..., Lundberg IE, Malmström V

Scand. J. Immunol. - (-) e12732 [2018-11-19; online 2018-11-19]

Bioinformatics Compute and Storage [Service] Mass Cytometry [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]

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

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

Science 362 (6416) 834-839 [2018-11-16; online 2018-11-15]

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

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

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

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

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

Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis

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

GEO

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

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

The biology of the cell: insights from mass cytometry.

Brodin P

FEBS J. - (-) - [2018-11-03; online 2018-11-03]

Bioinformatics Compute and Storage [Service] Mass Cytometry [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]

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

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

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

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

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]

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

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

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

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

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

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

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

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

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

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

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

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

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

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

J. of Cardiovasc. Trans. Res. - (-) - [2018-10-26; online 2018-10-26]

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

Targeted Analysis of Serum Proteins Encoded at Known Inflammatory Bowel Disease Risk Loci

Drobin K, Assadi G, Hong MG, ..., D’Amato M, Halfvarson J

- - (-) - [2018-10-24; online 2018-10-24]

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

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

Giacomello S, Lundeberg J

Nat Protoc - (-) - [2018-10-23; online 2018-10-23]

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

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

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

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

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

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

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

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

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

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

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

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

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

Chorea, psychosis, acanthocytosis, and prolonged survival associated with

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

pmc

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

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

Enhanced validation of antibodies for research applications.

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

pmc BioProject BioProject

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

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

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

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

pmc

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

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

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

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

pmc

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

Bioinformatics Compute and Storage [Service] Cell Profiling [Service]

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

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

pmc

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

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

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

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

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]

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

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

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

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

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

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

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

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

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]

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

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

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

Bioinformatics Compute and Storage [Service]

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]

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

Maturi V, Enroth S, Heldin CH, Moustakas A

pmc

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

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

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

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

pmc BioProject

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

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

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

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

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

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

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

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

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

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

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

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

pmc

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

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

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

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

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

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

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

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

Eur. J. Hum. Genet. - (-) - [2018-09-24; online 2018-09-24]

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

Introducing ribosomal tandem repeat barcoding for fungi

Wurzbacher C, Larsson E, Bengtsson-Palme J, ..., Kagami M, Nilsson RH

GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK

Mol Ecol Resour. 19 (1) 118-127 [2018-09-21; online 2018-09-21]

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

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

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

pmc GEO

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

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

Comprehensive analysis of intra- and interpatient evolution of enterovirus D68 by whole-genome deep sequencing

Dyrdak R, Mastafa M, Hodcroft E, Neher R, Albert J

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

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

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

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

Clin. Genet. - (-) - [2018-09-16; online 2018-09-16]

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

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

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

pmc

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

Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development]

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

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

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

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

Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system.

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

pmc GEO

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

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

Contribution of allelic imbalance to colorectal cancer.

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

pmc

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

Bioinformatics Compute and Storage [Service] High-throughput Genome Engineering (HTGE) [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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

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

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

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

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

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

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

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

Inflammatory markers in women with postpartum depressive symptoms

Bränn E, Fransson E, White RA, ..., Sundström-Poromaa I, Skalkidou A

J Neuro Res - (-) - [2018-09-05; online 2018-09-05]

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

Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.

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

pmc

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

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

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]

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

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

Lung Cancer - (-) - [2018-09-00; online 2018-09-00]

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

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

Johansson US, Irestedt M, Qu Y, Ericson PGP

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

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

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]

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

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

pmc mid SRA

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

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

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

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

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

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

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

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

Human Mutation 39 (9) 1262-1272 [2018-09-00; online 2018-07-12]

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

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

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

pmc

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

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

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

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

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

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

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]

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

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

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

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

Human plasma cell derived monoclonal antibodies to post-translationally modified proteins recognize amino acid motifs rather than specific proteins.

Steen J, Forsström B, Sahlström P, ..., Klareskog L, Malmström V

Arthritis & rheumatology (Hoboken, N.J.) - (-) - [2018-08-27; online 2018-08-27]

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

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

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

pmc BioProject

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

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

Stereotypic Immune System Development in Newborn Children.

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

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

Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Plasma Profiling [Service]

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

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

pmc GEO GEO GEO

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

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

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

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

Br J Haematol - (-) - [2018-08-20; online 2018-08-20]

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

Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.

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

pmc GEO GEO

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

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

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]

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

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

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

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

Molecular Architecture of the Mouse Nervous System.

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

pmc SRA

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

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

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

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

pmc

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

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

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

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

pmc

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

Autoimmunity Profiling [Service] Bioinformatics Compute and Storage [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]

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

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

GEO

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

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

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

Papoli Yazdi H, Ellegren H

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

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

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

Nascimento FJA, Lallias D, Bik HM, Creer S

pmc

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

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

Image-Based Detection of Patient-Specific Drug-Induced Cell-Cycle Effects in Glioblastoma

Matuszewski DJ, Wählby C, Krona C, Nelander S, Sintorn IM

SLAS DISCOVERY: Advancing Life Sciences R&D - (-) 247255521879141 [2018-08-03; online 2018-08-03]

BioImage Informatics [Collaborative] Bioinformatics Compute and Storage [Service]

Contrasting distribution patterns between aquatic and terrestrial Phytophthora species along a climatic gradient are linked to functional traits

Redondo MA, Boberg J, Stenlid J, Oliva J

ISME J - (-) - [2018-08-02; online 2018-08-02]

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

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]

CD93 promotes β1 integrin activation and fibronectin fibrillogenesis during tumor angiogenesis.

Lugano R, Vemuri K, Yu D, ..., Dejana E, Dimberg A

pmc

J. Clin. Invest. 128 (8) 3280-3297 [2018-08-01; online 2018-06-25]

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

RNA velocity of single cells.

La Manno G, Soldatov R, Zeisel A, ..., Linnarsson S, Kharchenko PV

pmc mid

Nature 560 (7719) 494-498 [2018-08-00; online 2018-08-08]

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

Comprehensive RNA sequencing analysis in serum and muscle reveals novel small RNA signatures with biomarker potential for Duchenne Muscular Dystrophy

Coenen-Stass AML, Sork H, Gatto S, ..., Wood MJA, Roberts TC

SRA

Mol Ther Nucleic Acids - (-) - [2018-08-00; online 2018-08-00]

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

An imidazole based H-Phe-Phe-NH 2 peptidomimetic with anti-allodynic effect in spared nerve injury mice

Skogh A, Lesniak A, Sköld C, ..., Hallberg M, Sandström A

Bioorganic & Medicinal Chemistry Letters 28 (14) 2446-2450 [2018-08-00; online 2018-08-00]

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

Characterization of an activating R1353H insulin-like growth factor 1 receptor variant in a male with extreme tall height.

Lin Y, van Duyvenvoorde HA, Liu H, ..., Wit JM, Larsson O

Eur. J. Endocrinol. 179 (2) 85-95 [2018-08-00; online 2018-05-22]

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

Data on the nucleotide composition of the first codons encoding the complementary determining region 3 (CDR3) in immunoglobulin heavy chains.

Thörnqvist L, Ohlin M

pmc

Data Brief 19 (-) 337-352 [2018-08-00; online 2018-05-04]

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

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]

Plasma Protein Profiling Reveal Osteoprotegerin as a Marker of Prognostic Impact for Colorectal Cancer

Birgisson H, Tsimogiannis K, Freyhult E, Kamali-Moghaddam M

Transl Oncol 11 (4) 1034-1043 [2018-08-00; online 2018-08-00]

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

Characterization of Swedish Campylobacter coli clade 2 and clade 3 water isolates.

Nilsson A, Skarp A, Johansson C, ..., Engstrand L, Rautelin H

pmc

Microbiologyopen 7 (4) e00583 [2018-08-00; online 2018-02-09]

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

A novel RAD21 p.(Gln592del) variant expands the clinical description of Cornelia de Lange syndrome type 4 – Review of the literature

Gudmundsson S, Annerén G, Marcos-Alcalde Í, ..., Gómez-Puertas P, Bondeson ML

European Journal of Medical Genetics - (-) - [2018-08-00; online 2018-08-00]

Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative]

Novel Multiomics Profiling of Human Carotid Atherosclerotic Plaques and Plasma Reveals Biliverdin Reductase B as a Marker of Intraplaque Hemorrhage.

Matic LP, Jesus Iglesias M, Vesterlund M, ..., Odeberg J, Hedin U

pmc

JACC Basic Transl Sci 3 (4) 464-480 [2018-08-00; online 2018-08-01]

Bioinformatics Compute and Storage [Service] Plasma Profiling [Collaborative] Proteogenomics [Collaborative]

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]

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]

Coupling biogeochemical process rates and metagenomic blueprints of coastal bacterial assemblages in the context of environmental change.

Markussen T, Happel EM, Teikari JE, ..., Middelboe M, Kisand V

Environ. Microbiol. 20 (8) 3083-3099 [2018-08-00; online 2018-09-19]

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

BARM and BalticMicrobeDB, a reference metagenome and interface to meta-omic data for the Baltic Sea.

Alneberg J, Sundh J, Bennke C, ..., Labrenz M, Andersson AF

pmc SRA SRA

Sci Data 5 (-) 180146 [2018-07-31; online 2018-07-31]

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

Regulation of Neuronal Na,K-ATPase by Extracellular Scaffolding Proteins

Liebmann T, Fritz N, Kruusmägi M, ..., Aperia A, Brismar H

Int J Mol Sci 19 (8) 2214 [2018-07-29; online 2018-07-29]

Advanced Light Microscopy (ALM) [Service] Bioinformatics Compute and Storage [Service]

Response of Microbial Communities to Changing Climate Conditions During Summer Cyanobacterial Blooms in the Baltic Sea.

Berner C, Bertos-Fortis M, Pinhassi J, Legrand C

pmc SRA

Front Microbiol 9 (-) 1562 [2018-07-25; online 2018-07-25]

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

A patient-derived xenograft pre-clinical trial reveals treatment responses and a resistance mechanism to karonudib in metastatic melanoma.

Einarsdottir BO, Karlsson J, Söderberg EMV, ..., Helleday T, Nilsson JA

pmc

Cell Death Dis 9 (8) 810 [2018-07-24; online 2018-07-24]

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

The psoriasis risk allele HLA-Cw0602 shows evidence of association with chronic or recurrent streptococcal tonsillitis.

Haapasalo K, Koskinen LLE, Suvilehto J, ..., Jokiranta TS, Saavalainen P

Infect. Immun. - (-) - [2018-07-23; online 2018-07-23]

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

Characterisation of the Virome of Tonsils from Conventional Pigs and from Specific Pathogen-Free Pigs

Blomström AL, Ye X, Fossum C, Wallgren P, Berg M

Viruses 10 (7) 382 [2018-07-20; online 2018-07-20]

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

Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure.

Broman E, Li L, Fridlund J, ..., Legrand C, Dopson M

BioProject

Microb. Ecol. - (-) - [2018-07-17; online 2018-07-17]

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

SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments

Andermann T, Cano Á, Zizka A, Bacon C, Antonelli A

SRA

PeerJ 6 (-) e5175 [2018-07-13; online 2018-07-13]

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

Microdeletion of 7p12.1p13, including IKZF1, causes intellectual impairment, overgrowth, and susceptibility to leukaemia.

Järviaho T, Zachariadis V, Tesi B, ..., Harila-Saari A, Nordgren A

Br. J. Haematol. - (-) - [2018-07-13; online 2018-07-13]

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

Notch signaling promotes a HIF2α-driven hypoxic response in multiple tumor cell types.

Mutvei AP, Landor SK, Fox R, ..., Jin S, Lendahl U

Oncogene - (-) - [2018-07-11; online 2018-07-11]

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

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]

EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.

Jeggari A, Alekseenko Z, Petrov I, ..., Ericson J, Alexeyenko A

pmc GEO

Nucleic Acids Res. 46 (W1) W163-W170 [2018-07-02; online 2018-06-13]

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

OLMα2 Cells Bidirectionally Modulate Learning

Siwani S, França ASC, Mikulovic S, ..., Tort ABL, Kullander K

Neuron 99 (2) 404-412.e3 [2018-07-00; online 2018-07-00]

Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Compute and Storage [Service]

Genotype-Phenotype Correlation of PLOD2 Skeletal Dysplasias Using Structural Information.

Tham E, Grigelionis G, Hammarsjö A, Grigelioniene G

J. Bone Miner. Res. 33 (7) 1377-1378 [2018-07-00; online 2018-06-07]

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

A heterogeneous response of liver and skeletal muscle fat to the combination of a Paleolithic diet and exercise in obese individuals with type 2 diabetes: a randomised controlled trial

Otten J, Stomby A, Waling M, ..., Hauksson J, Olsson T

Diabetologia 61 (7) 1548-1559 [2018-07-00; online 2018-04-26]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [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]

Identification of inhibitors of Tartrate-resistant acid phosphatase (TRAP/ACP5) activity by small-molecule screening

Reithmeier A, Lundbäck T, Haraldsson M, ..., Gustavsson AL, Andersson G

Chem Biol Drug Des 92 (1) 1255-1271 [2018-07-00; online 2018-03-30]

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

In Vitro Evolution of Antibodies Inspired by In Vivo Evolution

Persson H, Kirik U, Thörnqvist L, ..., Levander F, Ohlin M

Front Immunol 9 (-) - [2018-06-21; online 2018-06-21]

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

Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity.

Berglund E, Maaskola J, Schultz N, ..., Helleday T, Lundeberg J

pmc

Nat Commun 9 (1) 2419 [2018-06-20; online 2018-06-20]

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

Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics.

Lundmark A, Gerasimcik N, Båge T, ..., Lundeberg J, Yucel-Lindberg T

pmc

Sci Rep 8 (1) 9370 [2018-06-19; online 2018-06-19]

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

Novel genetic associations for blood pressure identified via gene-alcohol interaction in up to 570K individuals across multiple ancestries.

Feitosa MF, Kraja AT, Chasman DI, ..., Province MA, Levy D

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]

Stabilized Cyclic Peptides as Scavengers of Autoantibodies: Neutralization of Anticitrullinated Protein/Peptide Antibodies in Rheumatoid Arthritis

Gunasekera S, Fernandes-Cerqueira C, Wennmalm S, ..., Jakobsson PJ, Göransson U

ACS Chem. Biol. 13 (6) 1525-1535 [2018-06-15; online 2018-04-09]

Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Service]

Investigating Holocene human population history in North Asia using ancient mitogenomes.

Kılınç GM, Kashuba N, Yaka R, ..., Storå J, Götherström A

pmc

Sci Rep 8 (1) 8969 [2018-06-12; online 2018-06-12]

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

CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response

Haapaniemi E, Botla S, Persson J, Schmierer B, Taipale J

Nat Med - (-) - [2018-06-11; online 2018-06-11]

Bioinformatics Compute and Storage [Service] High-throughput Genome Engineering (HTGE) [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Protein Science Facility (PSF) [Service]

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

Cárdenas CA, González-Aravena M, Font A, ..., Malmberg M, Bongcam-Rudloff E

pmc

PeerJ 6 (-) e4935 [2018-06-07; online 2018-06-07]

Four evolutionary trajectories underlie genetic intratumoral variation in childhood cancer

Karlsson J, Valind A, Holmquist Mengelbier L, ..., Bexell D, Gisselsson D

Nat Genet 50 (7) 944-950 [2018-06-04; online 2018-06-04]

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

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]

Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum

Schmidt R, Durling MB, de Jager V, ..., Karlsson M, Garbeva P

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

FEMS Microbiol. Ecol. 94 (6) - [2018-06-01; online 2018-04-30]

Genomewide binding of transcription factor Snail1 in triple-negative breast cancer cells

Maturi V, Morén A, Enroth S, Heldin CH, Moustakas A

Mol Oncol 12 (7) 1153-1174 [2018-06-00; online 2018-05-21]

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

Topology of membrane proteins — predictions, limitations and variations

Tsirigos KD, Govindarajan S, Bassot C, ..., Shu N, Elofsson A

Current Opinion in Structural Biology 50 (-) 9-17 [2018-06-00; online 2018-06-00]

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

Design, synthesis and evaluation of potent and selective inhibitors of mono-(ADP-ribosyl)transferases PARP10 and PARP14

Holechek J, Lease R, Thorsell AG, ..., Schüler H, Ferraris D

Bioorganic & Medicinal Chemistry Letters 28 (11) 2050-2054 [2018-06-00; online 2018-06-00]

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

Assessing Cu impacts on freshwater diatoms: biochemical and metabolomic responses of Tabellaria flocculosa (Roth) Kützing

Gonçalves S, Kahlert M, Almeida SFP, Figueira E

Science of The Total Environment 625 (-) 1234-1246 [2018-06-00; online 2018-06-00]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]

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]

A novel ECEL1 mutation expands the phenotype of distal arthrogryposis multiplex congenita type 5D to include pretibial vertical skin creases

Stattin EL, Johansson J, Gudmundsson S, ..., Bondeson ML, Wilbe M

Am J Med Genet 176 (6) 1405-1410 [2018-06-00; online 2018-04-16]

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

Neuronal atlas of the dorsal horn defines its architecture and links sensory input to transcriptional cell types.

Häring M, Zeisel A, Hochgerner H, ..., Linnarsson S, Ernfors P

Nat. Neurosci. 21 (6) 869-880 [2018-06-00; online 2018-04-23]

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

Mechanistic study of hydrothermally aged Cu/SSZ-13 catalysts for ammonia-SCR

Leistner K, Kumar A, Kamasamudram K, Olsson L

Catalysis Today 307 (-) 55-64 [2018-06-00; online 2018-06-00]

Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Service]

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]

Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces).

Blåhed IM, Königsson H, Ericsson G, Spong G

pmc

PLoS ONE 13 (5) e0197364 [2018-05-30; online 2018-05-30]

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

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]

SWI/SNF regulates half of its targets without the need of ATP-driven nucleosome remodeling by Brahma.

Jordán-Pla A, Yu S, Waldholm J, ..., Östlund Farrants AK, Visa N

pmc GEO

BMC Genomics 19 (1) 367 [2018-05-18; online 2018-05-18]

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

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]

Soil microclimate changes affect soil fungal communities in a Mediterranean pine forest

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

New Phytol - (-) - [2018-05-14; online 2018-05-14]

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

Transcriptomic analysis of the harvested endothelial cells in a swine model of mechanical thrombectomy.

Jaff N, Grankvist R, Muhl L, ..., Eriksson U, Holmin S

pmc

Neuroradiology - (-) - [2018-05-14; online 2018-05-14]

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

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]

Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants

Garcia M, Juhos S, Larsson M, ..., Nystedt B, Käller M

- - (-) - [2018-05-09; online 2018-05-09]

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

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 multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma.

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

pmc GEO

Oncotarget 9 (35) 24140-24154 [2018-05-08; online 2018-05-08]

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

High-Density Antigen Microarrays for the Assessment of Antibody Selectivity and Off-Target Binding.

Sjöberg R, Andersson E, Hellström C, ..., Nilsson P, Ayoglu B

Methods Mol. Biol. 1785 (-) 231-238 [2018-05-02; online 2018-05-02]

Autoimmunity Profiling [Technology development] Bioinformatics Compute and Storage [Service] Plasma Profiling [Technology development]

O6-methylguanine–induced transcriptional mutagenesis reduces p53 tumor-suppressor function

Ezerskyte M, Paredes JA, Malvezzi S, ..., Scicchitano DA, Dreij K

Proc. Natl. Acad. Sci. U.S.A. 115 (18) 4731-4736 [2018-05-01; online 2018-04-17]

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

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]

Combined BET bromodomain and CDK2 inhibition in MYC-driven medulloblastoma

Bolin S, Borgenvik A, Persson CU, ..., Weishaupt H, Swartling FJ

Oncogene 37 (21) 2850-2862 [2018-05-00; online 2018-03-07]

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

Mitochondrial Translation Efficiency Controls Cytoplasmic Protein Homeostasis

Suhm T, Kaimal JM, Dawitz H, ..., Andréasson C, Ott M

Cell Metabolism - (-) - [2018-05-00; online 2018-05-00]

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

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]

Fatal demyelinating disease is induced by monocyte-derived macrophages in the absence of TGF-β signaling.

Lund H, Pieber M, Parsa R, ..., Zhang XM, Harris RA

Nat. Immunol. 19 (5) 1-7 [2018-05-00; online 2018-04-16]

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

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]

Quantification of endogenous and exogenous protein expressions of Na,K-ATPase with super-resolution PALM/STORM imaging

Bernhem K, Blom H, Brismar H

Dryad

PLoS ONE 13 (4) e0195825 [2018-04-25; online 2018-04-25]

Advanced Light Microscopy (ALM) [Technology development] Bioinformatics Compute and Storage [Service]

Experimental validation of predicted cancer genes using FRET

Guala D, Bernhem K, Blal HA, ..., Brismar H, Sonnhammer ELL

Methods Appl. Fluoresc. 6 (3) 035007 [2018-04-25; online 2018-04-25]

Advanced Light Microscopy (ALM) [Collaborative] Bioinformatics Compute and Storage [Service]

Repeated evolution of self-compatibility for reproductive assurance.

Nieuwenhuis BPS, Tusso S, Bjerling P, ..., Wolf JBW, Immler S

pmc

Nat Commun 9 (1) 1639 [2018-04-24; online 2018-04-24]

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

Genome-Guided Analysis of Clostridium ultunense and Comparative Genomics Reveal Different Strategies for Acetate Oxidation and Energy Conservation in Syntrophic Acetate-Oxidising Bacteria

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

Genes 9 (4) 225 [2018-04-23; online 2018-04-23]

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

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]

Expression of scavenger receptor MARCO defines a targetable tumor-associated macrophage subset in non-small cell lung cancer.

La Fleur L, Boura VF, Alexeyenko A, ..., Karlsson MCI, Botling J

Int. J. Cancer - (-) - [2018-04-18; online 2018-04-18]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics Uppsala [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Complete Remission with Reduction of High-Risk Clones following Haploidentical NK-Cell Therapy against MDS and AML

Björklund AT, Carlsten M, Sohlberg E, ..., Ljunggren HG, Malmberg KJ

Clin. Cancer Res. 24 (8) 1834-1844 [2018-04-15; online 2018-02-14]

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

Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia.

Danielsson F, Fasterius E, Sullivan D, ..., Williams C, Lundberg E

pmc GEO

Oncotarget 9 (28) 19730-19744 [2018-04-13; online 2018-04-13]

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

Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima.

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

pmc

Elife 7 (-) - [2018-04-11; online 2018-04-11]

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

Expression levels of long non-coding RNAs are prognostic for AML outcome.

Mer AS, Lindberg J, Nilsson C, ..., Lehmann S, Rantalainen M

pmc

J Hematol Oncol 11 (1) 52 [2018-04-07; online 2018-04-07]

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

Long Non-Coding RNAs Associated with Metabolic Traits in Human White Adipose Tissue.

Gao H, Kerr A, Jiao H, ..., Dahlman I, Arner P

pmc

EBioMedicine 30 (-) 248-260 [2018-04-00; online 2018-03-15]

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

Differential removal of human pathogenic viruses from sewage by conventional and ozone treatments

Wang H, Sikora P, Rutgersson C, ..., Larsson DGJ, Norder H

International Journal of Hygiene and Environmental Health 221 (3) 479-488 [2018-04-00; online 2018-04-00]

Bioinformatics Compute and Storage [Service] Clinical Genomics Gothenburg [Collaborative]

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]

GABA Regulates Release of Inflammatory Cytokines From Peripheral Blood Mononuclear Cells and CD4 + T Cells and Is Immunosuppressive in Type 1 Diabetes

Bhandage AK, Jin Z, Korol SV, ..., Kamali-Moghaddam M, Birnir B

EBioMedicine 30 (-) 283-294 [2018-04-00; online 2018-04-00]

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

Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce.

Jokipii-Lukkari S, Delhomme N, Schiffthaler B, ..., Street NR, Tuominen H

pmc

Plant Physiol. 176 (4) 2851-2870 [2018-04-00; online 2018-02-27]

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

The functional 3'-end of immunoglobulin heavy chain variable (IGHV) genes.

Thörnqvist L, Ohlin M

Mol. Immunol. 96 (-) 61-68 [2018-04-00; online 2018-02-28]

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

Confocal super-resolution imaging of the glomerular filtration barrier enabled by tissue expansion

Unnersjö-Jess D, Scott L, Sevilla SZ, ..., Blom H, Brismar H

Kidney International 93 (4) 1008-1013 [2018-04-00; online 2018-04-00]

Advanced Light Microscopy (ALM) [Technology development] Bioinformatics Compute and Storage [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]

Multiancestry genome-wide association study of 520,000 subjects identifies 32 loci associated with stroke and stroke subtypes.

Malik R, Chauhan G, Traylor M, ..., MEGASTROKE Consortium , MEGASTROKE Consortium:

Nat. Genet. 50 (4) 524-537 [2018-04-00; online 2018-03-12]

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

Modulation of saturation and chain length of fatty acids in Saccharomyces cerevisiae for production of cocoa butter-like lipids

Bergenholm D, Gossing M, Wei Y, Siewers V, Nielsen J

Biotechnol. Bioeng. 115 (4) 932-942 [2018-04-00; online 2018-01-24]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]

Evaluation of the ISL1 gene in the pathogenesis of bladder exstrophy in a Swedish cohort.

Arkani S, Cao J, Lundin J, ..., Matsson H, Nordenskjöld A

pmc

Hum Genome Var 5 (-) 18009 [2018-03-29; online 2018-03-29]

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

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]

AMYCNE: Confident copy number assessment using whole genome sequencing data.

Eisfeldt J, Nilsson D, Andersson-Assarsson JC, Lindstrand A

pmc

PLoS ONE 13 (3) e0189710 [2018-03-26; online 2018-03-26]

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

Protein Expression in Tonsillar and Base of Tongue Cancer and in Relation to Human Papillomavirus (HPV) and Clinical Outcome

Ramqvist T, Näsman A, Franzén B, ..., Dalianis T, Munck-Wikland E

Int J Mol Sci 19 (4) 978 [2018-03-25; online 2018-03-25]

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

Multiscale patterns and drivers of arbuscular mycorrhizal fungal communities in the roots and root-associated soil of a wild perennial herb

Rasmussen PU, Hugerth LW, Blanchet FG, ..., Lindahl BD, Tack AJM

SRA SRA

New Phytol - (-) - [2018-03-24; online 2018-03-24]

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

A Meta-Analysis of Genome-Wide Association Studies of Growth Differentiation Factor-15 Concentration in Blood.

Jiang J, Thalamuthu A, Ho JE, ..., Sachdev PS, Mather KA

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]

Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury.

Dias DO, Kim H, Holl D, ..., Göritz C, Frisén J

pmc GEO

Cell 173 (1) 153-165.e22 [2018-03-22; online 2018-03-01]

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

ILF2 and ILF3 are autoantigens in canine systemic autoimmune disease.

Bremer HD, Landegren N, Sjöberg R, ..., Kämpe O, Hansson-Hamlin H

pmc

Sci Rep 8 (1) 4852 [2018-03-19; online 2018-03-19]

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

Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics

Ardui S, Ameur A, Vermeesch JR, Hestand MS

Nucleic Acids Res 46 (5) 2159-2168 [2018-03-16; online 2018-02-01]

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

Recurrent, low-frequency coding variants contributing to colorectal cancer in the Swedish population.

Jiao X, Liu W, Mahdessian H, ..., Dunlop M, Lindblom A

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]

Clinical Presentation of a Complex Neurodevelopmental Disorder Caused by Mutations in ADNP.

Van Dijck A, Vulto-van Silfhout AT, Cappuyns E, ..., Vandeweyer G, Kooy RF

pmc mid

Biol. Psychiatry - (-) - [2018-03-15; online 2018-03-15]

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

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

Seyfferth C, Wessels B, Jokipii-Lukkari S, ..., Felten J, Tuominen H

pmc

Front Plant Sci 9 (-) 272 [2018-03-14; online 2018-03-14]

High-resolution detection of chromosomal rearrangements in leukemias through mate pair whole genome sequencing.

Tran AN, Taylan F, Zachariadis V, ..., Nilsson D, Barbany G

pmc SRA

PLoS ONE 13 (3) e0193928 [2018-03-12; online 2018-03-12]

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

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]

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]

Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death.

Reza SH, Delhomme N, Street NR, ..., Minina EA, Bozhkov PV

pmc

PLoS ONE 13 (3) e0192945 [2018-03-02; online 2018-03-02]

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

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]

Impact of genetic risk loci for multiple sclerosis on expression of proximal genes in patients.

James T, Lindén M, Morikawa H, ..., Gomez-Cabrero D, Kockum I

Hum. Mol. Genet. 27 (5) 912-928 [2018-03-01; online 2018-01-13]

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

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

BioProject Dryad

ISME J 12 (3) 791-801 [2018-03-00; online 2018-01-05]

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

Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste

Marathe NP, Janzon A, Kotsakis SD, ..., Kristiansson E, Larsson DGJ

Environment International 112 (-) 279-286 [2018-03-00; online 2018-03-00]

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

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

BioProject Dryad

R. Soc. open sci. 5 (3) 171752 [2018-03-00; online 2018-03-21]

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

Fungal community shifts underpin declining mycelial production and turnover across a Pinus sylvestris chronosequence

Hagenbo A, Kyaschenko J, Clemmensen KE, Lindahl BD, Fransson P

J Ecol 106 (2) 490-501 [2018-03-00; online 2018-02-13]

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

Relicts of the lost arc: High-throughput sequencing of the Eutrichomyias rowleyi (Aves: Passeriformes) holotype uncovers an ancient biogeographic link between the Philippines and Fiji.

Jønsson KA, Blom MPK, Päckert M, Ericson PGP, Irestedt M

Mol. Phylogenet. Evol. 120 (-) 28-32 [2018-03-00; online 2017-12-02]

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

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]

A molecular atlas of cell types and zonation in the brain vasculature.

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

GEO GEO GEO

Nature 554 (7693) 475-480 [2018-02-22; online 2018-02-14]

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

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]

In Situ Target Engagement Studies in Adherent Cells

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

ACS Chem. Biol. - (-) - [2018-02-21; online 2018-02-21]

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

Antibodies in children with malaria to PfEMP1, RIFIN and SURFIN expressed at the Plasmodium falciparum parasitized red blood cell surface.

Quintana MDP, Ch'ng JH, Moll K, ..., Qundos U, Wahlgren M

pmc

Sci Rep 8 (1) 3262 [2018-02-19; online 2018-02-19]

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

Two novel colorectal cancer risk loci in the region on chromosome 9q22.32

Thutkawkorapin J, Mahdessian H, Barber T, ..., Jiao X, Lindblom A

Oncotarget 9 (13) - [2018-02-16; online 2018-01-30]

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

Affinity proteomic profiling of plasma for proteins associated to area-based mammographic breast density.

Byström S, Eklund M, Hong MG, ..., Schwenk JM, Gabrielson M

pmc

Breast Cancer Res. 20 (1) 14 [2018-02-14; online 2018-02-14]

Bioinformatics Compute and Storage [Service] Plasma Profiling [Collaborative]

Kynurenic Acid and Gpr35 Regulate Adipose Tissue Energy Homeostasis and Inflammation.

Agudelo LZ, Ferreira DMS, Cervenka I, ..., Berggren P, Ruas JL

Cell Metab. 27 (2) 378-392.e5 [2018-02-06; online 2018-02-08]

Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative]

Ten steps to get started in Genome Assembly and Annotation

Dominguez Del Angel V, Hjerde E, Sterck L, ..., Binzer-Panchal M, Lantz H

F1000Res 7 (-) 148 [2018-02-05; online 2018-02-05]

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

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]

Small molecule PGC-1α1 protein stabilizers induce adipocyte Ucp1 expression and uncoupled mitochondrial respiration

Pettersson-Klein AT, Izadi M, Ferreira DMS, ..., Griffin PR, Ruas JL

Mol Metab - (-) - [2018-02-00; online 2018-02-00]

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

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]

Life after tree death: Does restored dead wood host different fungal communities to natural woody substrates?

Pasanen H, Junninen K, Boberg J, ..., Stenlid J, Kouki J

Forest Ecology and Management 409 (-) 863-871 [2018-02-00; online 2018-02-00]

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

Red meat intake in chronic kidney disease patients: Two sides of the coin

Mafra D, Borges NA, Cardozo LFMdF, ..., Lindholm B, Stenvinkel P

Nutrition 46 (-) 26-32 [2018-02-00; online 2018-02-00]

Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]

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]

Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing.

Hochgerner H, Zeisel A, Lönnerberg P, Linnarsson S

Nat. Neurosci. 21 (2) 290-299 [2018-02-00; online 2018-01-15]

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

Complete genome sequence of the marine Rhodococcus sp. H-CA8f isolated from Comau fjord in Northern Patagonia, Chile

Undabarrena A, Salvà-Serra F, Jaén-Luchoro D, ..., Seeger M, Cámara B

GENBANK BioProject

Marine Genomics - (-) - [2018-02-00; online 2018-02-00]

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

Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA

Ahmed E, Parducci L, Unneberg P, ..., Slotte T, Wohlfarth B

Quaternary Science Reviews 181 (-) 19-29 [2018-02-00; online 2018-02-00]

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

In Situ Analyses Directly in Diarrheal Stool Reveal Large Variations in Bacterial Load and Active Toxin Expression of Enterotoxigenic Escherichia coli and Vibrio cholerae

Begum YA, Rydberg HA, Thorell K, ..., Qadri F, Sjöling Å

mSphere 3 (1) e00517-17 [2018-01-24; online 2018-01-24]

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

Genetical genomics of growth in a chicken model.

Johnsson M, Henriksen R, Höglund A, ..., Jensen P, Wright D

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]

Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D

Jenjaroenpun P, Wongsurawat T, Pereira R, ..., Nielsen J, Nookaew I

Nucleic Acids Res - (-) - [2018-01-13; online 2018-01-13]

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

Rapid hybrid speciation in Darwin’s finches

Lamichhaney S, Han F, Webster MT, ..., Grant BR, Grant PR

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]

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]

A protein interaction network centered on leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) regulates growth factor receptors

Faraz M, Herdenberg C, Holmlund C, Henriksson R, Hedman H

J. Biol. Chem. - (-) jbc.M117.807487 [2018-01-09; online 2018-01-09]

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

Discovering viral genomes in human metagenomic data by predicting unknown protein families.

Barrientos-Somarribas M, Messina DN, Pou C, ..., Andersson B, Sonnhammer ELL

pmc

Sci Rep 8 (1) 28 [2018-01-08; online 2018-01-08]

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

Analysis of the hybrid genomes of two field isolates of the soil-borne fungal species Verticillium longisporum.

Fogelqvist J, Tzelepis G, Bejai S, ..., Schwelm A, Dixelius C

pmc

BMC Genomics 19 (1) 14 [2018-01-03; online 2018-01-03]

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

Evaluating vacquinol-1 in rats carrying glioblastoma models RG2 and NS1

Ahlstedt J, Förnvik K, Zolfaghari S, ..., Salford LG, Redebrandt HN

Oncotarget - (-) - [2018-01-03; online 2018-01-03]

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

Angiopoietin-1 deficiency increases renal capillary rarefaction and tubulointerstitial fibrosis in mice

Loganathan K, Salem Said E, Winterrowd E, ..., Quaggin SE, Jeansson M

PLoS ONE 13 (1) e0189433 [2018-01-02; online 2018-01-02]

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

SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy

Bernhem K, Brismar H

Bioinformatics 34 (1) 137-138 [2018-01-01; online 2017-09-04]

Advanced Light Microscopy (ALM) [Technology development] Bioinformatics Compute and Storage [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]

Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive.

Low GW, Chattopadhyay B, Garg KM, ..., Wu S, Rheindt FE

pmc

Heredity (Edinb) 120 (2) 138-153 [2018-01-00; online 2017-12-11]

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

Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest-tundra ecotone

Vowles T, Lindwall F, Ekblad A, ..., Ryberg M, Björk RG

Ecol Evol 8 (2) 1019-1030 [2018-01-00; online 2017-12-14]

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

Minimizing inequality in access to precision medicine in breast cancer by real-time population-based molecular analysis in the SCAN-B initiative.

Rydén L, Loman N, Larsson C, ..., Saal LH, Borg Å

Br J Surg 105 (2) e158-e168 [2018-01-00; online 2018-01-18]

Bioinformatics Compute and Storage [Service] Clinical Genomics Lund [Collaborative]

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]

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]

The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.

Salvatore M, Shu N, Elofsson A

pmc

Protein Sci. 27 (1) 195-201 [2018-01-00; online 2017-10-24]

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

Single-molecule DNA sequencing of acute myeloid leukemia and myelodysplastic syndromes with multiple TP53 alterations

Lodé L, Ameur A, Coste T, ..., Lavabre-Bertrand T, Soussi T

Haematologica 103 (1) e13-e16 [2018-01-00; online 2017-10-27]

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

Natural product inspired library synthesis - Identification of 2,3-diarylbenzofuran and 2,3-dihydrobenzofuran based inhibitors of Chlamydia trachomatis

Saleeb M, Mojica S, Eriksson AU, ..., Gylfe Å, Elofsson M

European Journal of Medicinal Chemistry 143 (-) 1077-1089 [2018-01-00; online 2018-01-00]

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

Viral metagenomics reveals the presence of highly divergent quaranjavirus in Rhipicephalus ticks from Mozambique

Cholleti H, Hayer J, Mulandane FC, ..., Berg M, Blomström AL

Infect Ecol Epidemiol 8 (1) 1478585 [2018-01-00; online 2018-05-28]

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

Homozygosity for a missense variant in COMP gene associated with severe pseudoachondroplasia

Tariq M, Khan TN, Lundin L, ..., Dahl N, Klar J

Clin Genet 93 (1) 182-186 [2018-01-00; online 2017-11-21]

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

Effect of various structure directing agents (SDAs) on low-temperature deactivation of Cu/SAPO-34 during NH3-SCR reaction

Woo J, Leistner K, Bernin D, ..., Zammit M, Olsson L

Catal. Sci. Technol. 8 (12) 3090-3106 [2018-00-00; online 2018-00-00]

Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Service]

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]

Inflammatory infiltrates in parathyroid tumors.

Haglund F, Hallström BM, Nilsson IL, ..., Juhlin CC, Larsson C

pmc

Eur. J. Endocrinol. 177 (6) 445-453 [2017-12-00; online 2017-08-30]

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

Multiple genotypes within aecial clusters in Puccinia graminis and Puccinia coronata: improved understanding of the biology of cereal rust fungi

Berlin A, Samils B, Andersson B

Fungal Biol Biotechnol 4 (1) - [2017-12-00; online 2017-05-03]

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

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]

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]

SNX10 gene mutation leading to osteopetrosis with dysfunctional osteoclasts

Stattin EL, Henning P, Klar J, ..., Wikström J, Lerner UH

Sci Rep 7 (1) - [2017-12-00; online 2017-06-07]

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

Fluorescent CRISPR Adaptation Reporter for rapid quantification of spacer acquisition

Amlinger L, Hoekzema M, Wagner EGH, Koskiniemi S, Lundgren M

Sci Rep 7 (1) - [2017-12-00; online 2017-09-04]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [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]

Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics.

Marathe NP, Pal C, Gaikwad SS, ..., Kristiansson E, Larsson DGJ

Water Res. 124 (-) 388-397 [2017-11-01; online 2017-07-25]

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

High abundance and expression of transposases in bacteria from the Baltic Sea.

Vigil-Stenman T, Ininbergs K, Bergman B, Ekman M

pmc

ISME J 11 (11) 2611-2623 [2017-11-00; online 2017-07-21]

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

Ninety-nine de novo assembled genomes from the moose (Alces alces) rumen microbiome provide new insights into microbial plant biomass degradation.

Svartström O, Alneberg J, Terrapon N, ..., Aspeborg H, Andersson AF

pmc mid BioProject

ISME J 11 (11) 2538-2551 [2017-11-00; online 2017-07-21]

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

A nonsense mutation in CEP55 defines a new locus for a Meckel-like syndrome, an autosomal recessive lethal fetal ciliopathy.

Bondeson M, Ericson K, Gudmundsson S, ..., Frykholm C, Wilbe M

Clin. Genet. 92 (5) 510-516 [2017-11-00; online 2017-05-03]

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

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]

Efficient protein production by yeast requires global tuning of metabolism.

Huang M, Bao J, Hallström BM, Petranovic D, Nielsen J

pmc

Nat Commun 8 (1) 1131 [2017-10-25; online 2017-10-25]

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

Polysome-profiling in small tissue samples.

Liang S, Bellato HM, Lorent J, ..., Hajj GNM, Larsson O

BioProject

Nucleic Acids Res. - (-) - [2017-10-23; online 2017-10-23]

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

Below-ground organic matter accumulation along a boreal forest fertility gradient relates to guild interaction within fungal communities

Kyaschenko J, Clemmensen KE, Karltun E, Lindahl BD

Ecol Lett - (-) - [2017-10-22; online 2017-10-22]

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

De novo design and synthesis of a 30-cistron translation-factor module

Shepherd TR, Du L, Liljeruhm J, ..., Yomo T, Forster AC

Nucleic Acids Res 45 (18) 10895-10905 [2017-10-13; online 2017-09-04]

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

Spatial detection of fetal marker genes expressed at low level in adult human heart tissue.

Asp M, Salmén F, Ståhl PL, ..., Linde C, Lundeberg J

pmc

Sci Rep 7 (1) 12941 [2017-10-11; online 2017-10-11]

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

Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments.

Broman E, Sachpazidou V, Dopson M, Hylander S

pmc BioProject BioProject

Proc. Biol. Sci. 284 (1864) - [2017-10-11; online 2017-10-06]

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

Exome sequencing reveals NAA15 and PUF60 as candidate genes associated with intellectual disability.

Zhao JJ, Halvardson J, Zander CS, ..., Thuresson AC, Feuk L

Am. J. Med. Genet. B Neuropsychiatr. Genet. - (-) - [2017-10-09; online 2017-10-09]

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

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]

DNA methylation profiles in red blood cells of adult hens correlate with their rearing conditions

Pértille F, Brantsæter M, Nordgreen J, ..., Jensen P, Guerrero-Bosagna C

J Exp Biol 220 (19) 3579-3587 [2017-10-01; online 2017-08-07]

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

Shaping the Tumor Stroma and Sparking Immune Activation by CD40 and 4-1BB Signaling Induced by an Armed Oncolytic Virus

Eriksson E, Milenova I, Wenthe J, ..., Alemany R, Loskog A

Clin. Cancer Res. 23 (19) 5846-5857 [2017-10-01; online 2017-05-23]

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

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]

Quantitative interactions between the biocontrol fungus Phlebiopsis gigantea , the forest pathogen Heterobasidion annosum and the fungal community inhabiting Norway spruce stumps

Oliva J, Messal M, Wendt L, Elfstrand M

Forest Ecology and Management 402 (-) 253-264 [2017-10-00; online 2017-10-00]

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

NorWood: a gene expression resource for evo-devo studies of conifer wood development.

Jokipii-Lukkari S, Sundell D, Nilsson O, ..., Street NR, Tuominen H

New Phytol. 216 (2) 482-494 [2017-10-00; online 2017-02-10]

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

Conflicting results from mitochondrial genomic data challenge current views of Rubiaceae phylogeny

Rydin C, Wikström N, Bremer B

Am. J. Bot. 104 (10) 1522-1532 [2017-10-00; online 2017-10-18]

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

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]

The complete genome sequence of human adenovirus 84, a highly recombinant new Human mastadenovirus D type with a unique fiber gene.

Kaján GL, Kajon AE, Pinto AC, Bartha D, Arnberg N

Virus Res. 242 (-) 79-84 [2017-09-18; online 2017-09-18]

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

A novel approach using long-read sequencing and ddPCR to investigate gonadal mosaicism and estimate recurrence risk in two families with developmental disorders.

Wilbe M, Gudmundsson S, Johansson J, ..., Frykholm C, Bondeson M

Prenat. Diagn. - (-) - [2017-09-16; online 2017-09-16]

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

Acute doses of caffeine shift nervous system cell expression profiles toward promotion of neuronal projection growth.

Yu NY, Bieder A, Raman A, ..., Daub CO, Kere J

pmc BioProject

Sci Rep 7 (1) 11458 [2017-09-13; online 2017-09-13]

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

A female Viking warrior confirmed by genomics.

Hedenstierna-Jonson C, Kjellström A, Zachrisson T, ..., Götherström A, Storå J

Am. J. Phys. Anthropol. - (-) - [2017-09-08; online 2017-09-08]

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

Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing.

Hugerth LW, Andersson AF

pmc

Front Microbiol 8 (-) 1561 [2017-09-04; online 2017-09-04]

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

Retention of seed trees fails to lifeboat ectomycorrhizal fungal diversity in harvested Scots pine forests.

Varenius K, Lindahl BD, Dahlberg A

FEMS Microbiol. Ecol. 93 (9) - [2017-09-01; online 2017-09-29]

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

The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves.

Evkaikina AI, Berke L, Romanova MA, ..., Pawlowski K, Voitsekhovskaja OV

pmc BioProject

Genome Biol Evol 9 (9) 2444-2460 [2017-09-01; online 2017-09-29]

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

A CRISPR-Cas9 Generated MDCK Cell Line Expressing Human MDR1 Without Endogenous Canine MDR1 (cABCB1): An Improved Tool for Drug Efflux Studies.

Karlgren M, Simoff I, Backlund M, ..., Oswald S, Artursson P

J Pharm Sci 106 (9) 2909-2913 [2017-09-00; online 2017-04-24]

Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Technology development] Drug Discovery and Development (DDD) [Technology development] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

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]

Identification of NCAN as a candidate gene for developmental dyslexia.

Einarsdottir E, Peyrard-Janvid M, Darki F, ..., Leinonen E, Kere J

pmc BioProject

Sci Rep 7 (1) 9294 [2017-08-24; online 2017-08-24]

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

A pathology atlas of the human cancer transcriptome.

Uhlen M, Zhang C, Lee S, ..., Mardinoglu A, Ponten F

Science 357 (6352) - [2017-08-18; online 2017-08-19]

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

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]

Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.

Broman E, Sjöstedt J, Pinhassi J, Dopson M

pmc

Microbiome 5 (1) 96 [2017-08-09; online 2017-08-09]

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

Rho-associated kinase is a therapeutic target in neuroblastoma.

Dyberg C, Fransson S, Andonova T, ..., Johnsen JI, Wickström M

pmc

Proc. Natl. Acad. Sci. U.S.A. 114 (32) E6603-E6612 [2017-08-08; online 2017-07-24]

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

PLS3 Deletions Lead to Severe Spinal Osteoporosis and Disturbed Bone Matrix Mineralization.

Kämpe AJ, Costantini A, Levy-Shraga Y, ..., Grasemann C, Mäkitie O

J. Bone Miner. Res. - (-) - [2017-08-04; online 2017-08-04]

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

A MUTYH germline mutation is associated with small intestinal neuroendocrine tumors.

Dumanski JP, Rasi C, Björklund P, ..., Hellman P, Tiensuu Janson E

pmc

Endocr. Relat. Cancer 24 (8) 427-443 [2017-08-00; online 2017-06-20]

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

Regional genetic differentiation in the blue mussel from the Baltic Sea area

Larsson J, Lind EE, Corell H, ..., Smolarz K, Lönn M

Estuarine, Coastal and Shelf Science 195 (-) 98-109 [2017-08-00; online 2017-08-00]

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

Data on haplotype-supported immunoglobulin germline gene inference.

Kirik U, Greiff L, Levander F, Ohlin M

pmc

Data Brief 13 (-) 620-640 [2017-08-00; online 2017-06-27]

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

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]

Low temperature, autotrophic microbial denitrification using thiosulfate or thiocyanate as electron donor.

Broman E, Jawad A, Wu X, ..., Sundkvist JE, Dopson M

pmc

Biodegradation 28 (4) 287-301 [2017-08-00; online 2017-06-02]

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

Genetic differences between willow warbler migratory phenotypes are few and cluster in large haplotype blocks

Lundberg M, Liedvogel M, Larson K, ..., Åkesson S, Bensch S

Evolution Letters 1 (3) 155-168 [2017-08-00; online 2017-06-16]

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

Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules.

Redin D, Borgström E, He M, ..., Käller M, Ahmadian A

pmc

Nucleic Acids Res. 45 (13) e125 [2017-07-27; online 2017-05-20]

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

PLS3 sequencing in childhood-onset primary osteoporosis identifies two novel disease-causing variants.

Kämpe AJ, Costantini A, Mäkitie RE, ..., Jiao H, Mäkitie O

pmc

Osteoporos Int - (-) - [2017-07-26; online 2017-07-26]

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

Transcriptional profiling of the rat nucleus accumbens after modest or high alcohol exposure.

Morud J, Ashouri A, Larsson E, Ericson M, Söderpalm B

pmc GEO

PLoS ONE 12 (7) e0181084 [2017-07-17; online 2017-07-17]

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

Analysis of aquaporins from the euryhaline barnacle Balanus improvisus reveals differential expression in response to changes in salinity.

Lind U, Järvå M, Alm Rosenblad M, ..., Hedfalk K, Blomberg A

pmc GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK GENBANK

PLoS ONE 12 (7) e0181192 [2017-07-17; online 2017-07-17]

Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] 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]

Does antifouling paint select for antibiotic resistance?

Flach CF, Pal C, Svensson CJ, ..., Tysklind M, Larsson DG

Sci. Total Environ. 590-591 (-) 461-468 [2017-07-15; online 2017-03-08]

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

Whole mitochondrial genome capture from faecal samples and museum-preserved specimens.

van der Valk T, Lona Durazo F, Dalén L, Guschanski K

Mol Ecol Resour - (-) - [2017-07-04; online 2017-07-04]

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

Mineral Type Structures Soil Microbial Communities

Ahmed E, Hugerth LW, Logue JB, ..., Andersson AF, Holmström SJM

Geomicrobiology Journal - (-) 1-8 [2017-07-03; online 2016-08-25]

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

Interspecific Plastome Recombination Reflects Ancient Reticulate Evolution in Picea (Pinaceae).

Sullivan AR, Schiffthaler B, Thompson SL, Street NR, Wang XR

pmc

Mol. Biol. Evol. 34 (7) 1689-1701 [2017-07-01; online 2017-04-07]

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

Wholegrain oat diet changes the expression of genes associated with intestinal bile acid transport.

Andersson KE, Chawade A, Thuresson N, ..., Olsson O, Hellstrand P

Mol Nutr Food Res 61 (7) - [2017-07-00; online 2017-03-30]

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

2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.

Hernandez-Castro LE, Paterno M, Villacís AG, ..., Grijalva MJ, Llewellyn MS

pmc

PLoS Negl Trop Dis 11 (7) e0005710 [2017-07-00; online 2017-07-19]

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

Parallel antibody germline gene and haplotype analyses support the validity of immunoglobulin germline gene inference and discovery.

Kirik U, Greiff L, Levander F, Ohlin M

Mol. Immunol. 87 (-) 12-22 [2017-07-00; online 2017-04-04]

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

BioProject BioProject

Mol. Ecol. 26 (14) 3603-3617 [2017-07-00; online 2017-04-24]

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) [Service] National Genomics Infrastructure [Service]

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]

Leucine Biosynthesis Is Involved in Regulating High Lipid Accumulation in Yarrowia lipolytica.

Kerkhoven EJ, Kim YM, Wei S, ..., Metz TO, Nielsen J

pmc

MBio 8 (3) - [2017-06-20; online 2017-06-20]

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

Genome Sequence of Roseovarius mucosus Strain SMR3, Isolated from a Culture of the Diatom Skeletonema marinoi.

Töpel M, Pinder MIM, Johansson ON, ..., Godhe A, Clarke AK

pmc

Genome Announc 5 (22) - [2017-06-01; online 2017-06-01]

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

A 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]

A missense variant in ITPR1 provides evidence for autosomal recessive SCA29 with asymptomatic cerebellar hypoplasia in carriers

Klar J, Ali Z, Farooq M, ..., Baig SM, Dahl N

Eur J Hum Genet 25 (7) 848-853 [2017-06-00; online 2017-05-10]

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

Separating the effects of forage source and field microbiota on silage fermentation quality and aerobic stability

Mogodiniyai Kasmaei K, Dicksved J, Spörndly R, Udén P

Grass Forage Sci - (-) - [2017-06-00; online 2016-06-06]

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

A subcellular map of the human proteome.

Thul PJ, Åkesson L, Wiking M, ..., Uhlén M, Lundberg E

Science 356 (6340) - [2017-05-26; online 2017-05-11]

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

Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes.

Väremo L, Henriksen TI, Scheele C, ..., Pedersen BK, Nielsen J

pmc

Genome Med 9 (1) 47 [2017-05-25; online 2017-05-25]

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

Genome Sequence of a Bovine Rhinitis B Virus Identified in Cattle in Sweden

Blomström AL, Oma V, Khatri M, ..., Berg M, Myrmel M

Genome Announc 5 (19) e00172-17 [2017-05-11; online 2017-05-11]

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

TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data.

Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A

pmc

F1000Res 6 (-) 664 [2017-05-10; online 2017-05-10]

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

Spatially resolved transcriptome profiling in model plant species.

Giacomello S, Salmén F, Terebieniec BK, ..., Street NR, Lundeberg J

NPLANTS 3 (-) 17061 [2017-05-08; online 2017-05-08]

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

Regulation of PfEMP1-VAR2CSA translation by a Plasmodium translation-enhancing factor.

Chan S, Frasch A, Mandava CS, ..., Sanyal S, Wahlgren M

Nat Microbiol 2 (-) 17068 [2017-05-08; online 2017-05-08]

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

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]

Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.

Engström K, Wojdacz TK, Marabita F, ..., Vahter M, Broberg K

pmc

Arch. Toxicol. 91 (5) 2067-2078 [2017-05-00; online 2016-11-12]

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