Bioinformatics Compute and Storage

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Publications

2021 (1)

2020 (314)

2019 (741)

2018 (663)

2017 (698)

2016 (671)

2015 (432)

2014 (376)

2013 (320)

2012 (243)

2011 (163)

2010 (139)

All (4761)


Facilities

Journals

SciLifeLab National facility since 2013. Previously associated with the UPPNEX project at UPPMAX.

870 publications

Year 2020

PubMed DOI Crossref
Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants
Garcia M, Juhos S, Larsson M, ..., Käller M, Nystedt B
F1000Res 9 (-) 63 [2020-01-29; online 2020-01-29]
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] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A regulatory role for CHD2 in myelopoiesis.
Shahin Varnoosfaderani F, Palau A, Dong W, ..., Svensson JP, Lennartsson A
Epigenetics - (-) 1-13 [2020-01-10; online 2020-01-10]
Bioinformatics Compute and Storage [Service] High-throughput Genome Engineering (HTGE) [Service] NGI Stockholm (Genomics Production) [Service]

Year 2019

PubMed DOI Crossref
A Comprehensive Sequencing-Based Analysis of Allelic Methylation Patterns in Hemostatic Genes in Human Liver
Olsson Lindvall M, Davila Lopez M, Klasson S, ..., Stanne TM, Jern C
Thromb. Haemost. - (-) - [2019-12-30; online 2019-12-30]
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]
PubMed DOI Crossref
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
pii: 5686322
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Genetic Screening of Plasticity Regulating Nogo-Type Signaling Genes in Migraine.
Smedfors G, Liesecke F, Ran C, ..., Karlsson TE, Carmine Belin A
pii: brainsci10010005
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]
PubMed DOI Crossref
A genome-wide transcriptomic analysis of protein-coding genes in human blood cells.
Uhlen M, Karlsson MJ, Zhong W, ..., Fagerberg L, Brodin P
pii: 366/6472/eaax9198
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.
Asp M, Giacomello S, Larsson L, ..., Sylvén C, Lundeberg J
pii: S0092-8674(19)31282-6
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]
PubMed DOI Crossref
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
pii: annrheumdis-2019-216227
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]
PubMed DOI Crossref
Comprehensive longitudinal study of epigenetic mutations in aging.
Wang Y, Karlsson R, Jylhävä J, ..., Almgren M, Hägg S
pii: 10.1186/s13148-019-0788-9
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]
PubMed DOI Crossref
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
pii: 10.1038/s41598-019-54612-1
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]
DOI Crossref
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]
PubMed DOI Crossref
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
pii: 10.1038/s41380-019-0605-z
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]
PubMed DOI Crossref
Dinucleotide Degradation by REXO2 Maintains Promoter Specificity in Mammalian Mitochondria.
Nicholls TJ, Spåhr H, Jiang S, ..., Larsson NG, Gustafsson CM
pii: S1097-2765(19)30695-1 PDB: 6RCI PDB: 6RCL PDB: 6RCN
Mol. Cell 76 (5) 784-796.e6 [2019-12-05; online 2019-10-03]
Bioinformatics Compute and Storage [Service] Protein Science Facility (PSF) [Service]
DOI Crossref
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]
PubMed DOI Crossref
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
pii: 10.1038/s41366-019-0498-6
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]
PubMed DOI Crossref
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
pii: 10.1186/s12864-019-6296-7
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]
DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
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]
DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
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]
DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
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
pii: dc19-1247
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]
DOI Crossref
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]
DOI Crossref
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]
DOI Crossref
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]
DOI Crossref
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]
DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
DOI Crossref
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]
DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
The genomic footprint of sexual conflict.
Sayadi A, Martinez Barrio A, Immonen E, ..., Nystedt B, Arnqvist G
pii: 10.1038/s41559-019-1041-9
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
DOI Crossref
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: GSE116138
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]
PubMed DOI Crossref
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) 68 [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]
PubMed DOI Crossref
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]
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]
PubMed DOI Crossref
MYCN-enhanced Oxidative and Glycolytic Metabolism Reveals Vulnerabilities for Targeting Neuroblastoma.
Oliynyk G, Ruiz-Pérez MV, Sainero-Alcolado L, ..., Lehtiö J, Arsenian-Henriksson M
pii: S2589-0042(19)30399-2 pmc: PMC6889365
iScience 21 (-) 188-204 [2019-11-22; online 2019-10-11]
Bioinformatics Compute and Storage [Service] Proteogenomics [Collaborative]
PubMed DOI Crossref
The Swedish Twin Registry: Content and Management as a Research Infrastructure.
Zagai U, Lichtenstein P, Pedersen NL, Magnusson PKE
pii: S1832427419000999
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]
PubMed DOI Crossref
BET and Aurora Kinase A inhibitors synergize against MYCN-positive human glioblastoma cells.
Čančer M, Drews LF, Bengtsson J, ..., Weishaupt H, Swartling FJ
pii: 10.1038/s41419-019-2120-1
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]
PubMed DOI Crossref
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
pii: 10.1038/s41398-019-0652-x
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Genotype-dependent epigenetic regulation of DLGAP2 in alcohol use and dependence.
Meng W, Sjöholm LK, Kononenko O, ..., Rüegg J, Liu Y
pii: 10.1038/s41380-019-0588-9
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]
PubMed DOI Crossref
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
pii: 5621184
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]
PubMed DOI Crossref
Inferring the Genomic Landscape of Recombination Rate Variation in European Aspen ( Populus tremula).
Apuli RP, Bernhardsson C, Schiffthaler B, ..., Street NR, Ingvarsson PK
pii: g3.119.400504
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]
PubMed DOI Crossref
Lithium treatment reverses irradiation-induced changes in rodent neural progenitors and rescues cognition.
Zanni G, Goto S, Fragopoulou AF, ..., Hermanson O, Blomgren K
pii: 10.1038/s41380-019-0584-0
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]
DOI Crossref
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]
PubMed DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
Viromics Reveal a Number of Novel RNA Viruses in Swedish Mosquitoes.
Öhlund P, Hayer J, Lundén H, Hesson JC, Blomström AL
pii: v11111027
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]
DOI Crossref
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]
PubMed DOI Crossref
Serum Parathyroid Hormone and Risk of Coronary Artery Disease: Exploring Causality Using Mendelian Randomization.
Melhus H, Michaëlsson K, Larsson SC
pii: 5532038
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Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
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]
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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]
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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]
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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]
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DOI Crossref
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]
PubMed DOI Crossref
High-grade progression confers poor survival in pancreatic neuroendocrine tumors.
Botling J, Lamarca A, Bajic D, ..., Skogseid B, Crona J
pii: 000504392
Neuroendocrinology - (-) - [2019-10-29; online 2019-10-29]
Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative]
PubMed DOI Crossref
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
pii: 10.1038/s41431-019-0533-z
Eur. J. Hum. Genet. - (-) - [2019-10-25; online 2019-10-25]
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PubMed DOI Crossref
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
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Genome Res. - (-) - [2019-10-24; online 2019-10-24]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
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 61 (3) 1-10 [2019-10-22; online 2019-10-22]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
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]
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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]
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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
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PubMed DOI Crossref
Microbe-host interplay in atopic dermatitis and psoriasis.
Fyhrquist N, Muirhead G, Prast-Nielsen S, ..., Andersson B, Alenius H
pii: 10.1038/s41467-019-12253-y pmc: PMC6795799
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]
PubMed DOI Crossref
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
pii: 5583770
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]
PubMed DOI Crossref
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
pii: 610 pmc: PMC6778119
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]
DOI Crossref
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
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Interoperable and scalable data analysis with microservices: applications in metabolomics
Emami Khoonsari P, Moreno P, Bergmann S, ..., Kultima K, Spjuth O
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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
pii: 5580498 pmc: PMC6795238
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]
PubMed DOI Crossref
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
pii: S1055-7903(19)30221-0
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) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
High-definition spatial transcriptomics for in situ tissue profiling.
Vickovic S, Eraslan G, Salmén F, ..., Regev A, Ståhl PL
pii: 10.1038/s41592-019-0548-y pmc: PMC6765407 mid: NIHMS1536533
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]
DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
Cell generation dynamics underlying naive T-cell homeostasis in adult humans.
Mold JE, Réu P, Olin A, ..., Brodin P, Frisén J
pii: PBIOLOGY-D-19-01355
PLoS Biol. 17 (10) e3000383 [2019-10-00; online 2019-10-29]
Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative]
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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]
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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]
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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]
PubMed DOI Crossref
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: PMC6769136
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Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Cytoplasmic protein misfolding titrates Hsp70 to activate nuclear Hsf1.
Masser AE, Kang W, Roy J, ..., Friedländer MR, Andréasson C
pii: 47791 pmc: PMC6779467 GEO: GSE78136
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]
DOI Crossref
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]
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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: PMC6769111
Front Genet 10 (-) 896 [2019-09-24; online 2019-09-24]
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Predisposition to childhood acute lymphoblastic leukemia caused by a constitutional translocation disrupting ETV6.
Järviaho T, Bang B, Zachariadis V, ..., Niinimäki R, Nordgren A
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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]
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Discovery of Novel Sequences in 1,000 Swedish Genomes.
Eisfeldt J, Mårtensson G, Ameur A, Nilsson D, Lindstrand A
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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 [Collaborative]
PubMed DOI Crossref
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]
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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
pii: AEM.01003-19 pmc: PMC6715854
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]
DOI Crossref
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]
DOI Crossref
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]
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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
pii: 10.1007/s00223-019-00606-0
Calcif. Tissue Int. - (-) - [2019-09-04; online 2019-09-04]
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PubMed DOI Crossref
Ancestral Admixture Is the Main Determinant of Global Biodiversity in Fission Yeast.
Tusso S, Nieuwenhuis BPS, Sedlazeck FJ, ..., Jeffares DC, Wolf JBW
pii: 5492083 pmc: PMC6736153
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]
PubMed DOI Crossref
Multilayered Tuning of Dosage Compensation and Z-Chromosome Masculinization in the Wood White (Leptidea sinapis) Butterfly.
Höök L, Leal L, Talla V, Backström N
pii: 5545957 pmc: PMC6761951
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]
PubMed DOI Crossref
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]
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DOI Crossref
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]
PubMed DOI Crossref
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: PMC6680617 GENBANK: KM586890
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]
PubMed DOI Crossref
Large-scale GWAS reveals insights into the genetic architecture of same-sex sexual behavior.
Ganna A, Verweij KJH, Nivard MG, ..., Neale BM, Zietsch BP
pii: 365/6456/eaat7693
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]
DOI Crossref
Combined mRNA and protein single cell analysis in a dynamic cellular system using SPARC
Reimegård J, Danielsson M, Tarbier M, ..., Friedländer MR, Gallant CJ
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Bioinformatics Compute and Storage [Service] PLA and Single Cell Proteomics [Technology development]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Profiling surface proteins on individual exosomes using a proximity barcoding assay.
Wu D, Yan J, Shen X, ..., Landegren U, Kamali-Moghaddam M
pii: 10.1038/s41467-019-11486-1 pmc: PMC6710248
Nat Commun 10 (1) 3854 [2019-08-26; online 2019-08-26]
Bioinformatics Compute and Storage [Service] PLA and Single Cell Proteomics [Technology development]
PubMed DOI Crossref
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
pii: 10.1007/s00125-019-4960-8
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]
PubMed DOI Crossref
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
ENA: PRJEB21838
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]
DOI Crossref
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]
PubMed DOI Crossref
Goodbye reference, hello genome graphs.
Ameur A
pii: 10.1038/s41587-019-0199-7
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]
DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Complete subspecies-level phylogeny of the Oriolidae (Aves: Passeriformes): Out of Australasia and return.
Jønsson KA, Blom MPK, Marki PZ, ..., Ericson PGP, Irestedt M
pii: S1055-7903(18)30644-4
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]
PubMed DOI Crossref
Salinity drives meiofaunal community structure dynamics across the Baltic ecosystem.
Broman E, Raymond C, Sommer C, ..., Creer S, Nascimento FJA
pmc: PMC6852176 GENBANK: PRJNA497177
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]
PubMed DOI Crossref
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
pii: 10.1038/s41431-019-0388-3
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]
PubMed DOI Crossref
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
pii: S2352-3964(19)30441-4 pmc: PMC6710853
EBioMedicine 46 (-) 290-304 [2019-08-00; online 2019-07-12]
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PubMed DOI Crossref
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: PMC6688520
Front Immunol 10 (-) 1686 [2019-07-30; online 2019-07-30]
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PubMed DOI Crossref
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
pii: 10.1186/s12885-019-5943-3 pmc: PMC6664554
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]
PubMed DOI Crossref
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
pii: EC-19-0194.R1 pmc: PMC6652245
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]
PubMed DOI Crossref
Combinations of Spok genes create multiple meiotic drivers in Podospora.
Vogan AA, Ament-Velásquez SL, Granger-Farbos A, ..., Saupe SJ, Johannesson H
pii: 46454 pmc: PMC6660238 Dryad: 10.5061/dryad.vm1192g
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]
PubMed DOI Crossref
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]
DOI Crossref
Evolved for success in novel environments: The round goby genome
Adrian-Kalchhauser I, Blomberg A, Larsson T, ..., Schloissnig S, Winkler S
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Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Genetic affinities among southern Africa hunter-gatherers and the impact of admixing farmer and herder populations.
Vicente M, Jakobsson M, Ebbesen P, Schlebusch CM
pii: 5475268
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]
DOI Crossref
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]
PubMed DOI Crossref
Global gene expression analysis in etiolated and de-etiolated seedlings in conifers.
Ranade SS, Delhomme N, García-Gil MR
pii: PONE-D-19-06007 pmc: PMC6611632
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]
PubMed DOI Crossref
Comparison of boreal acid sulfate soil microbial communities in oxidative and reductive environments.
Christel S, Yu C, Wu X, ..., Åström ME, Dopson M
pii: S0923-2508(19)30059-2
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]
PubMed DOI Crossref
Seeking the ultimate challenge.
Brodin P
Nat Med - (-) - [2019-07-03; online 2019-07-03]
Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development]
DOI Crossref
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]
PubMed DOI Crossref
Transcriptome analysis of shade avoidance and shade tolerance in conifers.
Ranade SS, Delhomme N, García-Gil MR
pii: 10.1007/s00425-019-03160-z
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Analyzing DNA methylation patterns in subjects diagnosed with schizophrenia using machine learning methods.
Torabi Moghadam B, Etemadikhah M, Rajkowska G, ..., Feuk L, Carlström EL
pii: S0022-3956(18)31394-3
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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: PMC6625150
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]
PubMed DOI Crossref
Exploring Molecular Signs of Sex in the Marine Diatom Skeletonema marinoi.
Ferrante MI, Entrambasaguas L, Johansson M, ..., Montresor M, Godhe A
pii: genes10070494 pmc: PMC6678668
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]
DOI Crossref
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]
PubMed DOI Crossref
Genomic Characterization of the Emerging Pathogen Streptococcus pseudopneumoniae.
Garriss G, Nannapaneni P, Simões AS, ..., de Lencastre H, Henriques-Normark B
pii: mBio.01286-19 pmc: PMC6593409
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]
PubMed DOI Crossref
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: PMC6598052
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]
DOI Crossref
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]
DOI Crossref
Single-nuclei transcriptomic analysis of the subthalamic nucleus reveals different Pitx2-positive subpopulations
Papathanou M, Björklund ÅK, Martis-Thiele MM, Wallén-Mackenzie Å
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Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
A Call for Blood-In Human Immunology.
Brodin P, Duffy D, Quintana-Murci L
pii: S1074-7613(19)30232-8
Immunity 50 (6) 1335-1336 [2019-06-18; online 2019-06-20]
Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
pii: 10.1038/s41598-019-43552-5 pmc: PMC6554399
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]
DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
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: PMC6557603
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]
PubMed DOI Crossref
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
pii: S2352-3964(19)30352-4 pmc: PMC6606959
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]
PubMed DOI Crossref
Can markers of biological age predict dependency in old age?
Jylhävä J, Jiang M, Foebel AD, Pedersen NL, Hägg S
pii: 10.1007/s10522-019-09795-5 pmc: PMC6535415
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]
PubMed DOI Crossref
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: PMC6565582
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]
DOI Crossref
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]
PubMed DOI Crossref
The viral protein corona directs viral pathogenesis and amyloid aggregation.
Ezzat K, Pernemalm M, Pålsson S, ..., Spetz AL, El Andaloussi S
pii: 10.1038/s41467-019-10192-2 pmc: PMC6536551
Nat Commun 10 (1) 2331 [2019-05-27; online 2019-05-27]
Bioinformatics Compute and Storage [Service] Proteogenomics [Technology development]
DOI Crossref
Crystal structure of the catalytic domain of the Weissela oryzae botulinum-like toxin
Košenina S, Masuyer G, Zhang S, Dong M, Stenmark P
PDB: 6RIM
FEBS Lett - (-) - [2019-05-20; online 2019-05-20]
Bioinformatics Compute and Storage [Service] Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
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
pii: 399 pmc: PMC6520363 Dryad: 10.5061/dryad.j3k19p9
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]
PubMed DOI Crossref
Periodontal Health and Oral Microbiota in Patients with Rheumatoid Arthritis.
Eriksson K, Fei G, Lundmark A, ..., Jansson L, Yucel-Lindberg T
pii: jcm8050630 pmc: PMC6572048
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]
PubMed DOI Crossref
Genetical Genomics of Tonic Immobility in the Chicken.
Fogelholm J, Inkabi S, Höglund A, ..., Henriksen R, Wright D
pii: genes10050341
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]
PubMed DOI Crossref
Sensory receptor repertoire in cyprid antennules of the barnacle Balanus improvisus.
Abramova A, Alm Rosenblad M, Blomberg A, Larsson TA
pii: PONE-D-18-32972 pmc: PMC6497305
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]
DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
Comparative analyses identify genomic features potentially involved in the evolution of birds-of-paradise.
Prost S, Armstrong EE, Nylander J, ..., Ericson PGP, Irestedt M
pii: 5300102 pmc: PMC6497032
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]
DOI Crossref
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]
PubMed DOI Crossref
Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds.
Xu L, Auer G, Peona V, ..., Irestedt M, Zhou Q
pii: 10.1038/s41559-019-0850-1
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]
DOI Crossref
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]
PubMed DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination.
Falcão AM, Meijer M, Scaglione A, ..., Casaccia P, Castelo-Branco G
pii: S2211-1247(19)30455-3 pmc: PMC6486480
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
A Genome-Wide Association Study of Bisphosphonate-Associated Atypical Femoral Fracture.
Kharazmi M, Michaëlsson K, Schilcher J, ..., Wadelius M, Hallberg P
pii: 10.1007/s00223-019-00546-9
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]
PubMed DOI Crossref
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
pii: genes10040301 pmc: PMC6523648
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]
DOI Crossref
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]
PubMed DOI Crossref
SQSTM1/p62-Directed Metabolic Reprogramming Is Essential for Normal Neurodifferentiation.
Calvo-Garrido J, Maffezzini C, Schober FA, ..., Freyer C, Wredenberg A
pii: S2213-6711(19)30025-6 pmc: PMC6449840
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]
PubMed DOI Crossref
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
pii: 10.1186/s12864-019-5642-0
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]
PubMed DOI Crossref
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
pii: 5304719 pmc: PMC6451119
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]
DOI Crossref
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]
PubMed DOI Crossref
Osteoporosis and skeletal dysplasia caused by pathogenic variants in SGMS2.
Pekkinen M, Terhal PA, Botto LD, ..., Holthuis JC, Mäkitie O
pii: 126180 pmc: PMC6483641
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]
PubMed DOI Crossref
Mesenchymal stem cells transplanted into spinal cord injury adopt immune cell-like characteristics.
Hakim R, Covacu R, Zachariadis V, ..., Brundin L, Svensson M
pii: 10.1186/s13287-019-1218-9 pmc: PMC6448247
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]
PubMed DOI Crossref
B cell profiling in malaria reveals expansion and remodelling of CD11c+ B cell subsets.
Sundling C, Rönnberg C, Yman V, ..., Persson KE, Färnert A
pii: 126492
JCI Insight 5 (-) - [2019-04-02; online 2019-04-02]
Bioinformatics Compute and Storage [Service] Mass Cytometry [Service]
DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
The repertoire of maternal anti-viral antibodies in human newborns.
Pou C, Nkulikiyimfura D, Henckel E, ..., Bohlin K, Brodin P
pii: 10.1038/s41591-019-0392-8
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]
PubMed DOI Crossref
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
pii: 10.1038/s41598-019-40922-x pmc: PMC6418233
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
pii: S2211-1247(19)30202-5
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]
PubMed DOI Crossref
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]
DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
pii: 10.1038/s41598-019-39445-2 pmc: PMC6395693
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]
DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
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]
DOI Crossref
Spatiotemporal dissection of the cell cycle regulated human proteome
Mahdessian D, Sullivan D, Danielsson F, ..., Lindskog C, Lundberg E
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Bioinformatics Compute and Storage [Service] Cell Profiling [Collaborative]
DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
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
pii: PGENETICS-D-18-01932 pmc: PMC6395008
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]
PubMed DOI Crossref
Comprehensive structural variation genome map of individuals carrying complex chromosomal rearrangements.
Eisfeldt J, Pettersson M, Vezzi F, ..., Carvalho CMB, Lindstrand A
pii: PGENETICS-D-18-00854 pmc: PMC6368290
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]
PubMed DOI Crossref
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
pii: 240 pmc: PMC6354350
Clin Transl Allergy 9 (-) 6 [2019-01-31; online 2019-01-31]
Autoimmunity Profiling [Collaborative] Bioinformatics Compute and Storage [Service]
PubMed DOI Crossref
Pandemrix-induced narcolepsy is associated with genes related to immunity and neuronal survival.
Hallberg P, Smedje H, Eriksson N, ..., Wadelius M, Swedegene
pii: S2352-3964(19)30048-9
EBioMedicine - (-) - [2019-01-30; online 2019-01-30]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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
pii: 10.1038/s41598-018-36832-z pmc: PMC6345836
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
DOI Crossref
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]
PubMed DOI Crossref
The Versatility of SMRT Sequencing.
Hestand MS, Ameur A
pii: genes10010024
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]
PubMed DOI Crossref
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
pii: 10.1038/s41467-018-07867-7 pmc: PMC6318312
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Single-Molecule Sequencing: Towards Clinical Applications.
Ameur A, Kloosterman WP, Hestand MS
pii: S0167-7799(18)30204-X
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]
PubMed DOI Crossref
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
pii: 4944478 pmc: PMC6298183
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]
DOI Crossref
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]
DOI Crossref
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]
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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]
DOI Crossref
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]
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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]

Year 2018

PubMed DOI Crossref
Impact of forced fatty acid synthesis on metabolism and physiology of Saccharomyces cerevisiae.
Gossing M, Smialowska A, Nielsen J
pii: 5086656
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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: MG833031
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]
PubMed DOI Crossref
Targeting PFKFB3 radiosensitizes cancer cells and suppresses homologous recombination
Gustafsson NMS, Färnegårdh K, Bonagas N, ..., Olin T, Helleday T
PDB: 6ETJ
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]
PubMed DOI Crossref
Convergent evolution of complex genomic rearrangements in two fungal meiotic drive elements
Svedberg J, Hosseini S, Chen J, ..., Lascoux M, Johannesson H
BioProject: PRJNA486257 figshare: https://doi.org/10.6084/m9.figshare.c.4202669.v1
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]
PubMed DOI Crossref
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: PRJNA297202
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]
PubMed DOI Crossref
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: NC_037853 ENA: PRJEB21370
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]
PubMed DOI Crossref
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
EBI: E-MTAB-6407
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]
PubMed DOI Crossref
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
ENA: ERR2307093 ENA: ERR2307094 ENA: ERR2307095 ENA: ERR2307096 ENA: ERR2307097 ENA: ERR2307098 GENBANK: MG372066
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]
PubMed DOI Crossref
Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow
Zhu Y, Orre LM, Johansson HJ, ..., Branca RMM, Lehtiö J
EBI: PXD006291 EBI: E-MTAB-5285 EBI: E-MTAB-2836
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
BioProject: PRJEB23373
BMC Genomics 19 (1) - [2018-12-00; online 2018-04-26]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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: 6ET4 GEO: GSE87577
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]
PubMed DOI Crossref
Effects of predation stress and food ration on perch gut microbiota
Zha Y, Eiler A, Johansson F, Svanbäck R
SRA: SRP090413
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]
PubMed DOI Crossref
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
pii: S1936-5233(18)30358-9 pmc: PMC6132178
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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: https://doi.org/10.5061/dryad.3jj7f SRA: ERP001813 SRA: SRA051254 SRA: SRR578029 SRA: SRR578191 SRA: SRR578192 BioProject: PRJEB27654
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Targeted NUDT5 inhibitors block hormone signaling in breast cancer cells
Page BDG, Valerie NCK, Wright RHG, ..., Beato M, Helleday T
PDB: 5NQR PDB: 5NWH
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]
PubMed DOI Crossref
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
jPOSTrepo: JPST000288
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]
PubMed DOI Crossref
Heterogeneity and interplay of the extracellular vesicle small RNA transcriptome and proteome
Sork H, Corso G, Krjutskov K, ..., Mäger I, EL Andaloussi S
BioProject: PRJNA408072 SRA: SRP118970
Sci Rep 8 (1) - [2018-12-00; online 2018-07-17]
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]
PubMed DOI Crossref
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: GSE107656
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]
PubMed DOI Crossref
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: 6GN0 PDB: 6GN8 PDB: 6GNJ PDB: 6GNK PDB: 6GNN
Nat Commun 9 (1) - [2018-12-00; online 2018-09-17]
Bioinformatics Compute and Storage [Service] Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
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: PRJNA419878 https://www.ebi.ac.uk/pride/archive/: PXD008382
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]
PubMed DOI Crossref
Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
Alneberg J, Karlsson CMG, Divne AM, ..., Andersson AF, Pinhassi J
BioProject: PRJNA273799 SRA: SRP058493
Microbiome 6 (1) - [2018-12-00; online 2018-09-28]
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]
PubMed DOI Crossref
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
pii: 10.1186/s13073-018-0595-5 pmc: PMC6247769
Genome Med 10 (1) 85 [2018-11-21; online 2018-05-11]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Expression profiling and in situ screening of circular RNAs in human tissues.
Zaghlool A, Ameur A, Wu C, ..., Nilsson M, Feuk L
pii: 10.1038/s41598-018-35001-6
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]
PubMed DOI Crossref
Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis
Falcão AM, van Bruggen D, Marques S, ..., Guerreiro-Cacais AO, Castelo-Branco G
GEO: GSE113973
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Genomes of two archaeal endosymbionts show convergent adaptations to an intracellular lifestyle
Lind AE, Lewis WH, Spang A, ..., Embley TM, Ettema TJG
BioProject: PRJNA380999
ISME J 12 (11) 2655-2667 [2018-11-00; online 2018-07-10]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
European Nucleotide Archive: PRJEB23585 PlantGenie.org: pnas201801437
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Targeted Analysis of Serum Proteins Encoded at Known Inflammatory Bowel Disease Risk Loci
Drobin K, Assadi G, Hong MG, ..., D’Amato M, Halfvarson J
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Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Collaborative] Plasma Profiling [Collaborative]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
pii: S2211-1247(18)31504-3 ArrayExpress: E-MTAB-6583 ArrayExpress: E-MTAB-6686
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]
PubMed DOI Crossref
Spatially Resolved Transcriptomics Enables Dissection of Genetic Heterogeneity in Stage III Cutaneous Malignant Melanoma.
Thrane K, Eriksson H, Maaskola J, Hansson J, Lundeberg J
pii: 0008-5472.CAN-18-0747
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Chorea, psychosis, acanthocytosis, and prolonged survival associated with
Paucar M, Pajak A, Freyer C, ..., Wredenberg A, Svenningsson P
pii: WNL.0000000000006320 pmc: PMC6177277
Neurology 91 (15) 710-712 [2018-10-09; online 2018-09-14]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
Enhanced validation of antibodies for research applications.
Edfors F, Hober A, Linderbäck K, ..., Forsström B, Uhlen M
pii: 10.1038/s41467-018-06642-y pmc: PMC6175901 ProteomeXchange: PXD005914 ProteomeXchange: PXD010178 Panorama Public Datasets: https://panoramaweb.org/western_blot.url BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA183192 BioProject: PRJNA183192
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]
PubMed DOI Crossref
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
pii: S0002-9297(18)30314-8 pmc: PMC6174323
Am. J. Hum. Genet. 103 (4) 553-567 [2018-10-04; online 2018-10-06]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
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
pii: 10.1038/s41598-018-32859-4 pmc: PMC6168570
Sci Rep 8 (1) 14668 [2018-10-02; online 2018-10-02]
Bioinformatics Compute and Storage [Service] Cell Profiling [Service]
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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
pii: 4916692 pmc: PMC6186516
J. Natl. Cancer Inst. 110 (10) 1094-1101 [2018-10-01; online 2018-03-06]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
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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: ERP001377
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Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
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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]
PubMed DOI Crossref
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
EGA: EGAS00001001795
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]
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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
pii: 10.1038/s41588-018-0205-x
Nat. Genet. 50 (10) 1412-1425 [2018-10-00; online 2018-09-17]
Bioinformatics Compute and Storage [Service]
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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]
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Genome-wide binding of transcription factor ZEB1 in triple-negative breast cancer cells.
Maturi V, Enroth S, Heldin CH, Moustakas A
pmc: PMC6055758
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]
PubMed DOI Crossref
Microbial Community and Metabolic Activity in Thiocyanate Degrading Low Temperature Microbial Fuel Cells.
Ni G, Canizales S, Broman E, ..., Sleutels T, Dopson M
pmc: PMC6172326 BioProject: PRJNA473625
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]
PubMed DOI Crossref
Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins
Wang Y, Karlsson R, Lampa E, ..., Pedersen NL, Hägg S
EBI: E-MTAB-7309
Epigenetics - (-) - [2018-09-28; online 2018-09-28]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
pii: 5661 pmc: PMC6161700
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]
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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]
PubMed DOI Crossref
Stereocilin gene variants associated with episodic vertigo: expansion of the DFNB16 phenotype.
Frykholm C, Klar J, Tomanovic T, Ameur A, Dahl N
pii: 10.1038/s41431-018-0256-6
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]
PubMed DOI Crossref
Introducing ribosomal tandem repeat barcoding for fungi
Wurzbacher C, Larsson E, Bengtsson-Palme J, ..., Kagami M, Nilsson RH
ENA: PRJEB26696 GENBANK: MH356537 GENBANK: MH356538 GENBANK: MH356539 GENBANK: MH356540 GENBANK: MH356541 GENBANK: MH356542 GENBANK: MH356543 GENBANK: MH356544 GENBANK: MH356545
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]
PubMed DOI Crossref
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
pii: 5025902 pmc: PMC6144808 GEO: GSE95236
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]
DOI Crossref
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
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Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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: PMC6143687
Front Mol Biosci 5 (-) 81 [2018-09-12; online 2018-09-12]
Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development]
PubMed DOI Crossref
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
pii: 1078-0432.CCR-18-1943
Clin. Cancer Res. - (-) - [2018-09-12; online 2018-09-12]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
Neuronal heterogeneity and stereotyped connectivity in the auditory afferent system.
Petitpré C, Wu H, Sharma A, ..., Hadjab S, Lallemend F
pii: 10.1038/s41467-018-06033-3 pmc: PMC6135759 GEO: GSE117055
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]
PubMed DOI Crossref
Contribution of allelic imbalance to colorectal cancer.
Palin K, Pitkänen E, Turunen M, ..., Taipale J, Aaltonen LA
pii: 10.1038/s41467-018-06132-1 pmc: PMC6131244 European Nucleotide Archive: PRJEB25645 European Genome-phenome Archive: EGAS00001002966 European Genome-phenome Archive: EGAS00001003010 Zenodo: https://doi.org/10.5281/zenodo.1222172
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]
PubMed DOI Crossref
Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town.
Krzewińska M, Kjellström A, Günther T, ..., Storå J, Götherström A
pii: S0960-9822(18)30844-3 European Nucleotide Archive: PRJEB27220
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Draft Genome Sequence for the Tree Pathogen Phytophthora plurivora.
Vetukuri RR, Tripathy S, Malar C M, ..., Grenville-Briggs LJ, Whisson SC
pii: 5061551 pmc: PMC6152947
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]
PubMed DOI Crossref
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
pii: 4049562
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Phylogenetic relationships of rollers (Coraciidae) based on complete mitochondrial genomes and fifteen nuclear genes.
Johansson US, Irestedt M, Qu Y, Ericson PGP
pii: S1055-7903(17)30880-1
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]
PubMed DOI Crossref
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
BioProject: PRJEB2984 SRA: ERP001377
Mol Ecol 27 (18) 3572-3581 [2018-09-00; online 2018-09-04]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The molecular genetic basis of herbivory between butterflies and their host plants.
Nallu S, Hill JA, Don K, ..., Wheat CW, Kronforst MR
pii: 10.1038/s41559-018-0629-9 pmc: PMC6149523 mid: NIHMS979338 SRA: SRP134094 Transcriptome Shotgun Assembly Sequence Database: GGJX00000000 Transcriptome Shotgun Assembly Sequence Database: GGKA00000000 Transcriptome Shotgun Assembly Sequence Database: GGJQ00000000 Transcriptome Shotgun Assembly Sequence Database: GGJO00000000 Transcriptome Shotgun Assembly Sequence Database: GGJY00000000 Transcriptome Shotgun Assembly Sequence Database: GGJZ00000000 Transcriptome Shotgun Assembly Sequence Database: GGKB00000000 Transcriptome Shotgun Assembly Sequence Database: GGKC00000000
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]
DOI Crossref
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]
PubMed DOI Crossref
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
GitHub: https://github.com/NationalGenomicsInfrastructure/HTT-repeat-analysis
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]
PubMed DOI Crossref
The Protozoan Parasite Toxoplasma gondii Selectively Reprograms the Host Cell Translatome.
Leroux LP, Lorent J, Graber TE, ..., Larsson O, Jaramillo M
pii: IAI.00244-18 pmc: PMC6105892
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
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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]
PubMed DOI Crossref
Stereotypic Immune System Development in Newborn Children.
Olin A, Henckel E, Chen Y, ..., Bohlin K, Brodin P
pii: S0092-8674(18)30848-1 FlowRepository: FR-FCM-ZYKQ Mendeley: 10.17632/ynhdrcxtcc.1
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]
PubMed DOI Crossref
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
pii: sdata2018160 pmc: PMC6103262 GEO: GSE98816 GEO: GSE99235 GEO: GSE99058 figshare: https://doi.org/10.6084/m9.figshare.c.4077260).
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.
Marques S, van Bruggen D, Vanichkina DP, ..., Taft RJ, Castelo-Branco G
pii: S1534-5807(18)30558-6 pmc: PMC6104814 GEO: GSE95194 GEO: GSE95093
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]
PubMed DOI Crossref
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: SRP076290
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Molecular Architecture of the Mouse Nervous System.
Zeisel A, Hochgerner H, Lönnerberg P, ..., Marklund U, Linnarsson S
pii: S0092-8674(18)30789-X pmc: PMC6086934 SRA: SRP135960
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]
PubMed DOI Crossref
Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.
Hu YOO, Ndegwa N, Alneberg J, ..., Fagerberg J, Andersson AF
pii: 10.1038/s41598-018-29920-7 pmc: PMC6085348 European Nucleotide Archive: PRJEB20562
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]
PubMed DOI Crossref
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
pii: PONE-D-18-10007 pmc: PMC6084945
PLoS ONE 13 (8) e0201669 [2018-08-09; online 2018-08-09]
Autoimmunity Profiling [Service] Bioinformatics Compute and Storage [Service]
PubMed DOI Crossref
Clonal relatedness in tumour pairs of breast cancer patients.
Biermann J, Parris TZ, Nemes S, ..., Karlsson P, Helou K
pii: 10.1186/s13058-018-1022-y GEO: GSE97293 GEO: GSE97177
Breast Cancer Res. 20 (1) 96 [2018-08-09; online 2018-08-09]
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]
PubMed DOI Crossref
Huntingtin Aggregation Impairs Autophagy, Leading to Argonaute-2 Accumulation and Global MicroRNA Dysregulation.
Pircs K, Petri R, Madsen S, ..., Barker RA, Jakobsson J
pii: S2211-1247(18)31107-0 GEO: GSE78928
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]
PubMed DOI Crossref
A genetic map of ostrich Z chromosome and the role of inversions in avian sex chromosome evolution.
Papoli Yazdi H, Ellegren H
pii: 5067707
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]
PubMed DOI Crossref
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
pii: 10.1038/s41598-018-30179-1 pmc: PMC6078945 figshare: doi:10.6084/m9.figshare.4993667
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]
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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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
BioProject: PRJNA431355 SRA: SRP131350
FEMS Microbiol. Ecol. 94 (8) - [2018-08-01; online 2018-06-19]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
CD93 promotes β1 integrin activation and fibronectin fibrillogenesis during tumor angiogenesis.
Lugano R, Vemuri K, Yu D, ..., Dejana E, Dimberg A
pii: 97459 pmc: PMC6063507
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]
PubMed DOI Crossref
RNA velocity of single cells.
La Manno G, Soldatov R, Zeisel A, ..., Linnarsson S, Kharchenko PV
pii: 10.1038/s41586-018-0414-6 pmc: PMC6130801 mid: EMS78511
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]
PubMed DOI Crossref
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: SRP102619
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]
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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]
PubMed DOI Crossref
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
pii: EJE-18-0176
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]
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Data on the nucleotide composition of the first codons encoding the complementary determining region 3 (CDR3) in immunoglobulin heavy chains.
Thörnqvist L, Ohlin M
pii: S2352-3409(18)30478-5 pmc: PMC5992955 European Nucleotide Archive: PRJEB18926
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]
PubMed DOI Crossref
Epigenetics in pediatric acute lymphoblastic leukemia.
Nordlund J, Syvänen AC
pii: S1044-579X(17)30091-3
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]
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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]
PubMed DOI Crossref
Characterization of Swedish Campylobacter coli clade 2 and clade 3 water isolates.
Nilsson A, Skarp A, Johansson C, ..., Engstrand L, Rautelin H
pmc: PMC6079167
Microbiologyopen 7 (4) e00583 [2018-08-00; online 2018-02-09]
Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
pii: S2452-302X(18)30096-2 pmc: PMC6115646
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
pii: 10.1038/s41588-018-0147-3
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]
PubMed DOI Crossref
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
pii: 10.1007/s00204-018-2239-3 pmc: PMC6063321
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
pii: sdata2018146 pmc: PMC6067050 European Nucleotide Archive: PRJEB22997 SRA: SRP058493 figshare: https://doi.org/10.6084/m9.figshare.c.3831631 SRA: SRP077551
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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: PMC6068395 SRA: SRP120581
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]
PubMed DOI Crossref
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
pii: 10.1038/s41419-018-0865-6 pmc: PMC6057880
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]
PubMed DOI Crossref
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
pii: IAI.00304-18
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Spring and Late Summer Phytoplankton Biomass Impact on the Coastal Sediment Microbial Community Structure.
Broman E, Li L, Fridlund J, ..., Legrand C, Dopson M
pii: 10.1007/s00248-018-1229-6 BioProject: PRJNA323408
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]
PubMed DOI Crossref
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: SRP131660 Zenodo: 10.5281/zenodo.1162653
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Notch signaling promotes a HIF2α-driven hypoxic response in multiple tumor cell types.
Mutvei AP, Landor SK, Fox R, ..., Jin S, Lendahl U
pii: 10.1038/s41388-018-0400-3
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]
PubMed DOI Crossref
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
pii: 4860173
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]
PubMed DOI Crossref
EviNet: a web platform for network enrichment analysis with flexible definition of gene sets.
Jeggari A, Alekseenko Z, Petrov I, ..., Ericson J, Alexeyenko A
pii: 5035166 pmc: PMC6030852 GEO: GSE112698
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]
PubMed DOI Crossref
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]
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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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
pii: 10.1038/s41588-018-0152-6
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]
PubMed DOI Crossref
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: SRX3389264 SRA: SRX3389265 SRA: SRX3389266 SRA: SRX3389267 SRA: SRX3389268 SRA: SRX3389269
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Spatial maps of prostate cancer transcriptomes reveal an unexplored landscape of heterogeneity.
Berglund E, Maaskola J, Schultz N, ..., Helleday T, Lundeberg J
pii: 10.1038/s41467-018-04724-5 pmc: PMC6010471 European Genome-phenome Archive: EGAS0000100300
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]
PubMed DOI Crossref
Gene expression profiling of periodontitis-affected gingival tissue by spatial transcriptomics.
Lundmark A, Gerasimcik N, Båge T, ..., Lundeberg J, Yucel-Lindberg T
pii: 10.1038/s41598-018-27627-3 pmc: PMC6008462
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]
PubMed DOI Crossref
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
pii: PONE-D-18-04838 dbGaP: phs000930
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Investigating Holocene human population history in North Asia using ancient mitogenomes.
Kılınç GM, Kashuba N, Yaka R, ..., Storå J, Götherström A
pii: 10.1038/s41598-018-27325-0 pmc: PMC5997703 Popset: 1405681532
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]
PubMed DOI Crossref
High similarity in the microbiota of cold-water sponges of the Genus
Cárdenas CA, González-Aravena M, Font A, ..., Malmberg M, Bongcam-Rudloff E
pii: 4935 pmc: PMC5994334
PeerJ 6 (-) e4935 [2018-06-07; online 2018-06-07]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
BioProject: PRJEB23603
FEMS Microbiol. Ecol. 94 (6) - [2018-06-01; online 2018-03-29]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum
Schmidt R, Durling MB, de Jager V, ..., Karlsson M, Garbeva P
BioProject: PRJNA375977
FEMS Microbiol. Ecol. 94 (6) - [2018-06-01; online 2018-04-30]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
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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]
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Paternally expressed imprinted genes associate with hybridization barriers in Capsella
Lafon-Placette C, Hatorangan MR, Steige KA, ..., Slotte T, Köhler C
GEO: GSE103209
NPLANTS 4 (6) 352-357 [2018-06-00; online 2018-05-28]
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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]
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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
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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]
DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
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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]
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Discovery of SNPs for individual identification by reduced representation sequencing of moose (Alces alces).
Blåhed IM, Königsson H, Ericsson G, Spong G
pii: PONE-D-17-39125 pmc: PMC5976195 Zenodo: https://doi.org/10.5281/zenodo.1237474
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]
PubMed DOI Crossref
Study of 300,486 individuals identifies 148 independent genetic loci influencing general cognitive function.
Davies G, Lam M, Harris SE, ..., Lencz T, Deary IJ
pii: 10.1038/s41467-018-04362-x pmc: PMC5974083
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]
PubMed DOI Crossref
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
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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]
PubMed DOI Crossref
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
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Hum. Mol. Genet. 27 (10) 1809-1818 [2018-05-15; online 2018-03-17]
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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]
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PubMed DOI Crossref
Transcriptomic analysis of the harvested endothelial cells in a swine model of mechanical thrombectomy.
Jaff N, Grankvist R, Muhl L, ..., Eriksson U, Holmin S
pii: 10.1007/s00234-018-2033-1 pmc: PMC5995995
Neuroradiology - (-) - [2018-05-14; online 2018-05-14]
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PubMed DOI Crossref
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
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Sci Rep 8 (1) 7526 [2018-05-14; online 2018-05-14]
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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
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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]
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Genome-wide multi-omics profiling of the 8p11-p12 amplicon in breast carcinoma.
Parris TZ, Rönnerman EW, Engqvist H, ..., Karlsson P, Helou K
pii: 25329 pmc: PMC5963621 GEO: GSE97293
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]
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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]
PubMed DOI Crossref
O6-methylguanine–induced transcriptional mutagenesis reduces p53 tumor-suppressor function
Ezerskyte M, Paredes JA, Malvezzi S, ..., Scicchitano DA, Dreij K
pii: 1721764115
Proc. Natl. Acad. Sci. U.S.A. 115 (18) 4731-4736 [2018-05-01; online 2018-04-17]
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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
pii: 10.1038/s41588-018-0090-3 pmc: PMC5934326 mid: NIHMS943355
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Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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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]
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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]
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PubMed DOI Crossref
Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies
Pent M, Hiltunen M, Põldmaa K, ..., Ryberg M, Bahram M
www.mg-rast.org: mgp20495
Environ Microbiol 20 (5) 1641-1650 [2018-05-00; online 2018-03-25]
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PubMed DOI Crossref
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
pii: 10.1038/s41590-018-0091-5
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
pii: annrheumdis-2017-212379 pmc: PMC5909746
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]
PubMed DOI Crossref
Quantification of endogenous and exogenous protein expressions of Na,K-ATPase with super-resolution PALM/STORM imaging
Bernhem K, Blom H, Brismar H
Dryad: https://doi.org/10.5061/dryad.kc42g
PLoS ONE 13 (4) e0195825 [2018-04-25; online 2018-04-25]
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PubMed DOI Crossref
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]
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Repeated evolution of self-compatibility for reproductive assurance.
Nieuwenhuis BPS, Tusso S, Bjerling P, ..., Wolf JBW, Immler S
pii: 10.1038/s41467-018-04054-6 pmc: PMC5915400
Nat Commun 9 (1) 1639 [2018-04-24; online 2018-04-24]
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PubMed DOI Crossref
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]
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PubMed DOI Crossref
Eleven loci with new reproducible genetic associations with allergic disease risk.
Ferreira MAR, Vonk JM, Baurecht H, ..., Koppelman GH, Paternoster L
pii: S0091-6749(18)30558-X
J. Allergy Clin. Immunol. - (-) - [2018-04-19; online 2018-04-19]
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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: rs17112758
Neurogastroenterol. Motil. - (-) e13358 [2018-04-19; online 2018-04-19]
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PubMed DOI Crossref
Data quality of whole genome bisulfite sequencing on Illumina platforms.
Raine A, Liljedahl U, Nordlund J
pii: PONE-D-17-37428 pmc: PMC5905984 BioProject: PRJNA407440 GEO: GSE89213
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Genetic and Environmental Contributions to the Covariation Between Cardiometabolic Traits.
Chen X, Kuja-Halkola R, Chang Z, ..., Pedersen NL, Magnusson PKE
pii: JAHA.117.007806
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]
PubMed DOI Crossref
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]
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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
pii: 24808 pmc: PMC5929421 GEO: GSE109367
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]
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Two distinct DNA sequences recognized by transcription factors represent enthalpy and entropy optima.
Morgunova E, Yin Y, Das PK, ..., Nilsson L, Taipale J
pii: 32963 pmc: PMC5896879
Elife 7 (-) - [2018-04-11; online 2018-04-11]
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Expression levels of long non-coding RNAs are prognostic for AML outcome.
Mer AS, Lindberg J, Nilsson C, ..., Lehmann S, Rantalainen M
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J Hematol Oncol 11 (1) 52 [2018-04-07; online 2018-04-07]
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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
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Gastroenterology - (-) - [2018-04-04; online 2018-04-04]
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Long Non-Coding RNAs Associated with Metabolic Traits in Human White Adipose Tissue.
Gao H, Kerr A, Jiao H, ..., Dahlman I, Arner P
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EBioMedicine 30 (-) 248-260 [2018-04-00; online 2018-03-15]
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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]
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RNA Sequencing of Stentor Cell Fragments Reveals Transcriptional Changes during Cellular Regeneration
Onsbring H, Jamy M, Ettema TJG
GENBANK: GGGV00000000 SRA: SRP132767 data.mendeley.com: https://doi.org/10.17632/nmgz3m3ptn.1
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]
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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]
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Transcriptional Roadmap to Seasonal Variation in Wood Formation of Norway Spruce.
Jokipii-Lukkari S, Delhomme N, Schiffthaler B, ..., Street NR, Tuominen H
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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]
PubMed DOI Crossref
The functional 3'-end of immunoglobulin heavy chain variable (IGHV) genes.
Thörnqvist L, Ohlin M
pii: S0161-5890(18)30043-9 European Nucleotide Archive: PRJEB18926
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]
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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]
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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]
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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:
pii: 10.1038/s41588-018-0058-3
Nat. Genet. 50 (4) 524-537 [2018-04-00; online 2018-03-12]
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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]
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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: PMC5874392 ArrayExpress: E-MTAB-5143
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]
PubMed DOI Crossref
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
BioProject: PRJEB23467
Proc Natl Acad Sci USA 115 (13) 3428-3433 [2018-03-27; online 2018-03-12]
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PubMed DOI Crossref
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
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J Psychiatr Res 102 (-) 44-51 [2018-03-26; online 2018-03-26]
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PubMed DOI Crossref
AMYCNE: Confident copy number assessment using whole genome sequencing data.
Eisfeldt J, Nilsson D, Andersson-Assarsson JC, Lindstrand A
pii: PONE-D-17-18300 pmc: PMC5868770
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]
PubMed DOI Crossref
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]
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PubMed DOI Crossref
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: SRP132598 SRA: SRP132591
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]
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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: PMC5876753
Front Genet 9 (-) 97 [2018-03-23; online 2018-03-23]
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Reducing Pericyte-Derived Scarring Promotes Recovery after Spinal Cord Injury.
Dias DO, Kim H, Holl D, ..., Göritz C, Frisén J
pii: S0092-8674(18)30148-X pmc: PMC5871719 GEO: GSE93976
Cell 173 (1) 153-165.e22 [2018-03-22; online 2018-03-01]
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ILF2 and ILF3 are autoantigens in canine systemic autoimmune disease.
Bremer HD, Landegren N, Sjöberg R, ..., Kämpe O, Hansson-Hamlin H
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Sci Rep 8 (1) 4852 [2018-03-19; online 2018-03-19]
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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]
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Recurrent, low-frequency coding variants contributing to colorectal cancer in the Swedish population.
Jiao X, Liu W, Mahdessian H, ..., Dunlop M, Lindblom A
pii: PONE-D-17-41609 pmc: PMC5856271
PLoS ONE 13 (3) e0193547 [2018-03-16; online 2018-03-16]
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Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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High-resolution detection of chromosomal rearrangements in leukemias through mate pair whole genome sequencing.
Tran AN, Taylan F, Zachariadis V, ..., Nilsson D, Barbany G
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Biological annotation of genetic loci associated with intelligence in a meta-analysis of 87,740 individuals.
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Mol. Psychiatry - (-) - [2018-03-08; online 2018-03-08]
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Novel gene variants associated with cardiovascular disease in systemic lupus erythematosus and rheumatoid arthritis.
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Transcriptome analysis of embryonic domains in Norway spruce reveals potential regulators of suspensor cell death.
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Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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
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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]
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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
pii: 4792999
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]
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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]
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The fungus that came in from the cold: dry rot’s pre-adapted ability to invade buildings
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Functional metagenomics reveals a novel carbapenem-hydrolyzing mobile beta-lactamase from Indian river sediments contaminated with antibiotic production waste
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Environment International 112 (-) 279-286 [2018-03-00; online 2018-03-00]
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Geobacteraceae are important members of mercury-methylating microbial communities of sediments impacted by waste water releases
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ISME J 12 (3) 802-812 [2018-03-00; online 2018-01-10]
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]
PubMed DOI Crossref
Cleaner fish escape salmon farms and hybridize with local wrasse populations
Faust E, Halvorsen KT, Andersen P, Knutsen H, André C
BioProject: PRJNA415388 Dryad: https://doi.org/10.5061/dryad.tv553
R. Soc. open sci. 5 (3) 171752 [2018-03-00; online 2018-03-21]
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DOI Crossref
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]
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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
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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]
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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
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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]
PubMed DOI Crossref
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
pii: annrheumdis-2017-212794
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]
PubMed DOI Crossref
Targeted Long-Read Sequencing of a Locus Under Long-Term Balancing Selection in Capsella
Bachmann JA, Tedder A, Laenen B, Steige KA, Slotte T
BioProject: PRJEB24927
G3 (Bethesda) 8 (4) 1327-1333 [2018-02-23; online 2018-02-23]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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A molecular atlas of cell types and zonation in the brain vasculature.
Vanlandewijck M, He L, Mäe MA, ..., Lendahl U, Betsholtz C
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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]
PubMed DOI Crossref
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]
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In Situ Target Engagement Studies in Adherent Cells
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ACS Chem. Biol. - (-) - [2018-02-21; online 2018-02-21]
Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Technology development]
PubMed DOI Crossref
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
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Sci Rep 8 (1) 3262 [2018-02-19; online 2018-02-19]
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Two novel colorectal cancer risk loci in the region on chromosome 9q22.32
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Affinity proteomic profiling of plasma for proteins associated to area-based mammographic breast density.
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Kynurenic Acid and Gpr35 Regulate Adipose Tissue Energy Homeostasis and Inflammation.
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Ten steps to get started in Genome Assembly and Annotation
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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]
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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
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Mol Ecol 27 (3) 694-708 [2018-02-00; online 2018-01-22]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Small molecule PGC-1α1 protein stabilizers induce adipocyte Ucp1 expression and uncoupled mitochondrial respiration
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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]
PubMed DOI Crossref
Copy Number Variation Analysis of 100 Twin Pairs Enriched for Neurodevelopmental Disorders.
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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]
DOI Crossref
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]
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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]
PubMed DOI Crossref
A DNA methylation biomarker of alcohol consumption.
Liu C, Marioni RE, Hedman ÅK, ..., Ingelsson E, Levy D
pii: mp2016192 pmc: PMC5575985 mid: NIHMS855941 dbGaP: phs000930
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]
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Conserved properties of dentate gyrus neurogenesis across postnatal development revealed by single-cell RNA sequencing.
Hochgerner H, Zeisel A, Lönnerberg P, Linnarsson S
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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]
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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: CP023720 BioProject: PRJNA411856
Marine Genomics - (-) - [2018-02-00; online 2018-02-00]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Dispersal timing determines the importance of priority effects in bacterial communities
Svoboda P, Lindström ES, Ahmed Osman O, Langenheder S
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Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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T cells are influenced by a long non-coding RNA in the autoimmune associated PTPN2 locus
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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]
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Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA
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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]
PubMed DOI Crossref
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]
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Genetical genomics of growth in a chicken model.
Johnsson M, Henriksen R, Höglund A, ..., Jensen P, Wright D
pii: 10.1186/s12864-018-4441-3 pmc: PMC5782384 ArrayExpress: E-MTAB-5572
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]
PubMed DOI Crossref
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
pii: 10.1038/s41467-017-02662-2 pmc: PMC5772647
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Rapid hybrid speciation in Darwin’s finches
Lamichhaney S, Han F, Webster MT, ..., Grant BR, Grant PR
SRA: PRJNA392917 TreeBASE: S21803
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]
PubMed DOI Crossref
Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation
Günther T, Malmström H, Svensson EM, ..., Götherström A, Jakobsson M
BioProject: PRJEB21940
PLoS Biol. 16 (1) e2003703 [2018-01-09; online 2018-01-09]
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Discovering viral genomes in human metagenomic data by predicting unknown protein families.
Barrientos-Somarribas M, Messina DN, Pou C, ..., Andersson B, Sonnhammer ELL
pii: 10.1038/s41598-017-18341-7 pmc: PMC5758519 European Nucleotide Archive: PRJEB17838
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]
PubMed DOI Crossref
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
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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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Urban landscape genomics identifies fine-scale gene flow patterns in an avian invasive.
Low GW, Chattopadhyay B, Garg KM, ..., Wu S, Rheindt FE
pii: 10.1038/s41437-017-0026-1 pmc: PMC5837122
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
pii: 10.1038/s41588-017-0011-x pmc: PMC5945951 mid: NIHMS920811
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Genomic consequences of intensive inbreeding in an isolated wolf population
Kardos M, Åkesson M, Fountain T, ..., Wikenros C, Ellegren H
BioProject: PRJEB20635
Nat Ecol Evol 2 (1) 124-131 [2018-01-00; online 2017-11-20]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The SubCons webserver: A user friendly web interface for state-of-the-art subcellular localization prediction.
Salvatore M, Shu N, Elofsson A
pmc: PMC5734273
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
DOI Crossref
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]

Year 2017

PubMed DOI Crossref
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]
PubMed DOI Crossref
Inflammatory infiltrates in parathyroid tumors.
Haglund F, Hallström BM, Nilsson IL, ..., Juhlin CC, Larsson C
pii: EJE-17-0277 pmc: PMC5642267
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Draft genome of the brown-rot fungus Fomitopsis pinicola GR9-4
Kancherla RP, Durling MB, Stenlid J, Högberg N
BioProject: PRJNA354689
Data Brief 15 (-) 496-500 [2017-12-00; online 2017-12-00]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Untreated urban waste contaminates Indian river sediments with resistance genes to last resort antibiotics.
Marathe NP, Pal C, Gaikwad SS, ..., Kristiansson E, Larsson DGJ
pii: S0043-1354(17)30633-4 MG-RAST: 19878
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]
PubMed DOI Crossref
High abundance and expression of transposases in bacteria from the Baltic Sea.
Vigil-Stenman T, Ininbergs K, Bergman B, Ekman M
pii: ismej2017114 pmc: PMC5649170
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]
PubMed DOI Crossref
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
pii: ismej2017108 pmc: PMC5648042 mid: EMS73237 BioProject: PRJEB12797
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
pii: ejhg2017130 swefreq: swegen
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]
PubMed DOI Crossref
Efficient protein production by yeast requires global tuning of metabolism.
Huang M, Bao J, Hallström BM, Petranovic D, Nielsen J
pii: 10.1038/s41467-017-00999-2 pmc: PMC5656615 ENA: ERP019558
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]
PubMed DOI Crossref
Polysome-profiling in small tissue samples.
Liang S, Bellato HM, Lorent J, ..., Hajj GNM, Larsson O
pii: 4561642 BioProject: PRJNA390060
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
pii: 10.1038/s41598-017-13462-5 pmc: PMC5636908
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]
PubMed DOI Crossref
Diatoms dominate the eukaryotic metatranscriptome during spring in coastal 'dead zone' sediments.
Broman E, Sachpazidou V, Dopson M, Hylander S
pii: rspb.2017.1617 pmc: PMC5647304 BioProject: PRJNA347538 BioProject: PRJNA322450
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
pii: 4091610 BioProject: PRJEB21838 GENBANK: FZQP00000000
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
The Evolution of Dark Matter in the Mitogenome of Seed Beetles
Sayadi A, Immonen E, Tellgren-Roth C, Arnqvist G
GENBANK: KY856743 GENBANK: KY856744 GENBANK: KY856745 GENBANK: KY942060 GENBANK: KY942061 GENBANK: KY942062 GENBANK: MF925724
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]
DOI Crossref
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]
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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]
PubMed DOI Crossref
NorWood: a gene expression resource for evo-devo studies of conifer wood development.
Jokipii-Lukkari S, Sundell D, Nilsson O, ..., Street NR, Tuominen H
ENA: ERP017340
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
pii: S0021-9150(17)31317-5
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]
PubMed DOI Crossref
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
BioProject: PRJEB22660
Science - (-) eaao6266 [2017-09-28; online 2017-09-28]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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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
pii: 10.1038/s41598-017-12110-2 pmc: PMC5615063
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]
PubMed DOI Crossref
Genetic risk scores and family history as predictors of schizophrenia in Nordic registers.
Lu Y, Pouget JG, Andreassen OA, ..., Werge T, Sullivan PF
pii: S0033291717002665
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]
PubMed DOI Crossref
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
pii: S0168-1702(17)30628-7
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]
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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]
PubMed DOI Crossref
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
pii: 10.1038/s41598-017-11574-6 pmc: PMC5597620 BioProject: PRJEB20092
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Analysing Microbial Community Composition through Amplicon Sequencing: From Sampling to Hypothesis Testing.
Hugerth LW, Andersson AF
pmc: PMC5591341
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]
PubMed DOI Crossref
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: SRP106442 GENBANK: GFNJ00000000 BioProject: PRJNA384528
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]
PubMed DOI Crossref
Retention of seed trees fails to lifeboat ectomycorrhizal fungal diversity in harvested Scots pine forests.
Varenius K, Lindahl BD, Dahlberg A
pii: 4094915
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]
PubMed DOI Crossref
The Huperzia selago Shoot Tip Transcriptome Sheds New Light on the Evolution of Leaves.
Evkaikina AI, Berke L, Romanova MA, ..., Pawlowski K, Voitsekhovskaja OV
pii: 4097580 pmc: PMC5622374 BioProject: PRJNA281995
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]
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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
pii: S0022-3549(17)30251-4
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]
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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
pii: PGENETICS-D-17-00622 pmc: PMC5617224 GEO: GSE87571
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]
PubMed DOI Crossref
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
pii: 10.1038/s41598-017-10928-4 pmc: PMC5579257
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]
PubMed DOI Crossref
Identification of NCAN as a candidate gene for developmental dyslexia.
Einarsdottir E, Peyrard-Janvid M, Darki F, ..., Leinonen E, Kere J
pii: 10.1038/s41598-017-10175-7 pmc: PMC5570950 BioProject: PRJEB12695
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]
PubMed DOI Crossref
A pathology atlas of the human cancer transcriptome.
Uhlen M, Zhang C, Lee S, ..., Mardinoglu A, Ponten F
pii: 357/6352/eaan2507
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]
PubMed DOI Crossref
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
pii: 3848993
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
Shifts in coastal sediment oxygenation cause pronounced changes in microbial community composition and associated metabolism.
Broman E, Sjöstedt J, Pinhassi J, Dopson M
pii: 10.1186/s40168-017-0311-5 pmc: PMC5549381
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]
PubMed DOI Crossref
Rho-associated kinase is a therapeutic target in neuroblastoma.
Dyberg C, Fransson S, Andonova T, ..., Johnsen JI, Wickström M
pii: 1706011114 pmc: PMC5559038
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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
BioProject: PRJNA378915
FEMS Microbiol. Lett. 364 (14) - [2017-08-01; online 2017-06-29]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A MUTYH germline mutation is associated with small intestinal neuroendocrine tumors.
Dumanski JP, Rasi C, Björklund P, ..., Hellman P, Tiensuu Janson E
pii: ERC-17-0196 pmc: PMC5527373
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]
DOI Crossref
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]
PubMed DOI Crossref
Data on haplotype-supported immunoglobulin germline gene inference.
Kirik U, Greiff L, Levander F, Ohlin M
pii: S2352-3409(17)30275-5 pmc: PMC5502703
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]
PubMed DOI Crossref
Northeast African genomic variation shaped by the continuity of indigenous groups and Eurasian migrations.
Hollfelder N, Schlebusch CM, Günther T, ..., Hassan HY, Jakobsson M
pii: PGENETICS-D-17-00483 pmc: PMC5587336 Dryad: doi:10.5061/dryad.bs06h
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]
DOI Crossref
Bioinformatic processing of RAD-seq data dramatically impacts downstream population genetic inference
Shafer ABA, Peart CR, Tusso S, ..., Wheat CW, Wolf JBW
BioProject: PRJNA349123 Dryad: https://doi.org/10.5061/dryad.q14c1 Dryad: https://doi.org/10.5061/dryad.8kn8c.2 Assembly: GCF_000349705.1 Assembly: GCF_000321225.1
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]
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Low temperature, autotrophic microbial denitrification using thiosulfate or thiocyanate as electron donor.
Broman E, Jawad A, Wu X, ..., Sundkvist JE, Dopson M
pii: 10.1007/s10532-017-9796-7 pmc: PMC5500686
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]
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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]
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Droplet Barcode Sequencing for targeted linked-read haplotyping of single DNA molecules.
Redin D, Borgström E, He M, ..., Käller M, Ahmadian A
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Nucleic Acids Res. 45 (13) e125 [2017-07-27; online 2017-05-20]
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PLS3 sequencing in childhood-onset primary osteoporosis identifies two novel disease-causing variants.
Kämpe AJ, Costantini A, Mäkitie RE, ..., Jiao H, Mäkitie O
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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
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BMC Cancer 17 (1) 487 [2017-07-17; online 2017-07-17]
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Transcriptional profiling of the rat nucleus accumbens after modest or high alcohol exposure.
Morud J, Ashouri A, Larsson E, Ericson M, Söderpalm B
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PLoS ONE 12 (7) e0181084 [2017-07-17; online 2017-07-17]
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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
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PLoS ONE 12 (7) e0181192 [2017-07-17; online 2017-07-17]
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Transancestral mapping and genetic load in systemic lupus erythematosus.
Langefeld CD, Ainsworth HC, Cunninghame Graham DS, ..., Gaffney PM, Vyse TJ
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Does antifouling paint select for antibiotic resistance?
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Mol Ecol Resour - (-) - [2017-07-04; online 2017-07-04]
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Sullivan AR, Schiffthaler B, Thompson SL, Street NR, Wang XR
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Mol. Biol. Evol. 34 (7) 1689-1701 [2017-07-01; online 2017-04-07]
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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
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EGR2 mutations define a new clinically aggressive subgroup of chronic lymphocytic leukemia
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Leukemia 31 (7) 1547-1554 [2017-07-00; online 2017-01-03]
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Mol Nutr Food Res 61 (7) - [2017-07-00; online 2017-03-30]
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2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.
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Genomewide analysis of admixture and adaptation in the Africanized honeybee.
Nelson RM, Wallberg A, Simões ZLP, Lawson DJ, Webster MT
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Mol. Ecol. 26 (14) 3603-3617 [2017-07-00; online 2017-04-24]
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Moderate nucleotide diversity in the Atlantic herring is associated with a low mutation rate
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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
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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
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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]
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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
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Int J Obes (Lond) 41 (6) 990-994 [2017-06-00; online 2017-02-14]
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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]
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Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches
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Genome Res. 27 (6) 1004-1015 [2017-06-00; online 2017-04-25]
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Mogodiniyai Kasmaei K, Dicksved J, Spörndly R, Udén P
Grass Forage Sci - (-) - [2017-06-00; online 2016-06-06]
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A subcellular map of the human proteome.
Thul PJ, Åkesson L, Wiking M, ..., Uhlén M, Lundberg E
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Science 356 (6340) - [2017-05-26; online 2017-05-11]
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Type 2 diabetes and obesity induce similar transcriptional reprogramming in human myocytes.
Väremo L, Henriksen TI, Scheele C, ..., Pedersen BK, Nielsen J
pii: 10.1186/s13073-017-0432-2 pmc: PMC5444103
Genome Med 9 (1) 47 [2017-05-25; online 2017-05-25]
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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]
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Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A
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F1000Res 6 (-) 664 [2017-05-10; online 2017-05-10]
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Spatially resolved transcriptome profiling in model plant species.
Giacomello S, Salmén F, Terebieniec BK, ..., Street NR, Lundeberg J
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NPLANTS 3 (-) 17061 [2017-05-08; online 2017-05-08]
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Regulation of PfEMP1-VAR2CSA translation by a Plasmodium translation-enhancing factor.
Chan S, Frasch A, Mandava CS, ..., Sanyal S, Wahlgren M
pii: nmicrobiol201768
Nat Microbiol 2 (-) 17068 [2017-05-08; online 2017-05-08]
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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
pii: PGENETICS-D-17-00165 pmc: PMC5444601 BioProject: PRJNA357367 Dryad: https://doi.org/10.5061/dryad.jn630
PLoS Genet. 13 (5) e1006792 [2017-05-00; online 2017-05-25]
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Transcriptomics and methylomics of CD4-positive T cells in arsenic-exposed women.
Engström K, Wojdacz TK, Marabita F, ..., Vahter M, Broberg K
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