Bioinformatics Compute and Storage

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Publications

2021 (47)

2020 (592)

2019 (746)

2018 (664)

2017 (705)

2016 (673)

2015 (434)

2014 (376)

2013 (320)

2012 (243)

2011 (163)

2010 (139)

1989 (1)

All (5103)


Facilities

Journals

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

1121 publications

Year 2021

DOI Crossref
Sucrose synthase determines carbon allocation in developing wood and alters carbon flow at the whole tree level in aspen
Dominguez PG, Donev E, Derba‐Maceluch M, ..., Mellerowicz EJ, Niittylä T
New Phytol 229 (1) 186-198 [2021-01-00; online 2020-07-03]
Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) Swedish NMR Centre (SNC) [Collaborative]

Year 2020

DOI Crossref
Stem Girdling Affects The Onset of Autumn Senescence In Aspen In Interaction With Metabolic Signals
Lihavainen J, Edlund E, Björkén L, ..., Robinson KM, Jansson S
Physiol Plantarum - (-) - [2020-12-25; online 2020-12-25]
Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
The Bactericidal Fatty Acid Mimetic 2CCA-1 Selectively Targets Pneumococcal Extracellular Polyunsaturated Fatty Acid Metabolism
Reithuber E, Nannapaneni P, Rzhepishevska O, ..., Henriques-Normark B, Mellroth P
MBio 11 (6) e03027-20 [2020-12-22; online 2020-12-15]
Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
Variable degree of mosaicism for tetrasomy 18p in phenotypically discordant monozygotic twins-Diagnostic implications.
Rydzanicz M, Olszewski P, Kedra D, ..., Dumanski JP, Płoski R
Mol Genet Genomic Med - (-) e1526 [2020-12-14; online 2020-12-14]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Hybrid sequencing resolves two germline ultra-complex chromosomal rearrangements consisting of 137 breakpoint junctions in a single carrier.
Eisfeldt J, Pettersson M, Petri A, ..., Feuk L, Lindstrand A
pii: 10.1007/s00439-020-02242-3
Hum. Genet. - (-) - [2020-12-14; online 2020-12-14]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Hodgkin Lymphoma Monozygotic Triplets Reveal Divergences in DNA Methylation Signatures
Xia C, Olsen TK, Zirakzadeh AA, ..., Björkholm M, Strååt K
Front Oncol 10 (-) - [2020-12-09; online 2020-12-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Diversification of molecularly defined myenteric neuron classes revealed by single-cell RNA sequencing
Morarach K, Mikhailova A, Knoflach V, ..., Ernfors P, Marklund U
Nat Neurosci 24 (1) 34-46 [2020-12-07; online 2020-12-07]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Longitudinal plasma protein profiling of newly diagnosed type 2 diabetes.
Gummesson A, Björnson E, Fagerberg L, ..., Uhlén M, Bergström G
pii: S2352-3964(20)30523-5
EBioMedicine 63 (-) 103147 [2020-12-03; online 2020-12-03]
Bioinformatics Compute and Storage [Service] Translational Plasma Profiling [Collaborative]
PubMed DOI Crossref
Mitigation of the replication of SARS-CoV-2 by nitric oxide in vitro
Akaberi D, Krambrich J, Ling J, ..., Lennerstrand J, Lundkvist Å
Redox Biol 37 (-) 101734 [2020-12-02; online 2020-09-21]
Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Service]
DOI Crossref
A shotgun metagenomic investigation of the microbiota of udder cleft dermatitis in comparison to healthy skin in dairy cows
Ekman L, Bagge E, Nyman A, ..., Pringle M, Segerman B
PLoS ONE 15 (12) e0242880 [2020-12-02; online 2020-12-02]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia
Halvorsen M, Huh R, Oskolkov N, ..., Sullivan PF, Szatkiewicz JP
Nat Commun 11 (1) - [2020-12-00; online 2020-04-15]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service] Systems Biology [Collaborative]
DOI Crossref
Tissue-specific patterns of regulatory changes underlying gene expression differences among Ficedula flycatchers and their naturally occurring F1 hybrids
Mugal CF, Wang M, Backström N, ..., Qvarnström A, Ellegren H
Genome Res. 30 (12) 1727-1739 [2020-12-00; online 2020-11-03]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Features of increased malignancy in eosinophilic clear cell renal cell carcinoma.
Nilsson H, Lindgren D, Axelson H, ..., Lundgren J, Johansson ME
J. Pathol. 252 (4) 384-397 [2020-12-00; online 2020-09-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
The regulation and pharmacological modulation of immune complex induced type III IFN production by plasmacytoid dendritic cells
Hjorton K, Hagberg N, Pucholt P, Eloranta ML, Rönnblom L
Arthritis Res. Ther. 22 (1) - [2020-12-00; online 2020-06-05]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Identification of cell surface markers and establishment of monolayer differentiation to retinal pigment epithelial cells
Plaza Reyes A, Petrus-Reurer S, Padrell Sánchez S, ..., Kvanta A, Lanner F
Nat Commun 11 (1) - [2020-12-00; online 2020-03-30]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]
DOI Crossref
Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans
Cortázar-Chinarro M, Meyer-Lucht Y, Van der Valk T, ..., Laurila A, Höglund J
BMC Genet. 21 (1) - [2020-12-00; online 2020-03-30]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Whole genome sequencing of familial isolated oesophagus atresia uncover shared structural variants
Klar J, Engstrand-Lilja H, Maqbool K, ..., Feuk L, Dahl N
BMC Med Genomics 13 (1) - [2020-12-00; online 2020-06-26]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Evaluation of the efficiency of genomic versus pedigree predictions for growth and wood quality traits in Scots pine
Calleja-Rodriguez A, Pan J, Funda T, ..., Abrahamsson S, Wu HX
BMC Genomics 21 (1) 796 [2020-12-00; online 2020-11-16]
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
Amplification-free long-read sequencing reveals unforeseen CRISPR-Cas9 off-target activity
Höijer I, Johansson J, Gudmundsson S, ..., Gyllensten U, Ameur A
Genome Biol. 21 (1) 290 [2020-12-00; online 2020-12-01]
Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
DOI Crossref
Integrative genomics approach identifies molecular features associated with early-stage ovarian carcinoma histotypes
Engqvist H, Parris TZ, Biermann J, ..., Karlsson P, Helou K
Sci Rep 10 (1) - [2020-12-00; online 2020-05-14]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Spatio-molecular domains identified in the mouse subthalamic nucleus and neighboring glutamatergic and GABAergic brain structures
Wallén-Mackenzie Å, Dumas S, Papathanou M, ..., König N, Björklund ÅK
Commun Biol 3 (1) - [2020-12-00; online 2020-07-03]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG)
DOI Crossref
Defining eligible patients for allele-selective chemotherapies targeting NAT2 in colorectal cancer
Rendo V, Kundu S, Rameika N, ..., Stoimenov I, Sjöblom T
Sci Rep 10 (1) - [2020-12-00; online 2020-12-31]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Single cell RNA sequencing identifies early diversity of sensory neurons forming via bi-potential intermediates
Faure L, Wang Y, Kastriti ME, ..., Adameyko I, Hadjab S
Nat Commun 11 (1) - [2020-12-00; online 2020-08-21]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]
DOI Crossref
Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells
Tarbier M, Mackowiak SD, Frade J, ..., Gallant CJ, Friedländer MR
Nat Commun 11 (1) - [2020-12-00; online 2020-10-28]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG)
PubMed DOI Crossref
Building de novo reference genome assemblies of complex eukaryotic microorganisms from single nuclei
Montoliu-Nerin M, Sánchez-García M, Bergin C, ..., Johannesson H, Rosling A
Sci Rep 10 (1) - [2020-12-00; online 2020-01-28]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Microbial Single Cell Genomics [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells.
Appelberg S, Gupta S, Svensson Akusjärvi S, ..., Mirazimi A, Neogi U
pmc: PMC7473213
Emerg Microbes Infect 9 (1) 1748-1760 [2020-12-00; online 2020-07-22]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
DOI Crossref
Restoration of KMT2C/MLL3 in human colorectal cancer cells reinforces genome-wide H3K4me1 profiles and influences cell growth and gene expression
Larsson C, Cordeddu L, Siggens L, ..., Ekwall K, Sjöblom T
Clin Epigenetics 12 (1) - [2020-12-00; online 2020-05-29]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Combining transcriptomics and genetic linkage based information to identify candidate genes associated with Heterobasidion-resistance in Norway spruce
Chaudhary R, Lundén K, Dalman K, ..., Stenlid J, Elfstrand M
Sci Rep 10 (1) - [2020-12-00; online 2020-07-29]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Translating GWAS-identified loci for cardiac rhythm and rate using an in vivo image- and CRISPR/Cas9-based approach
von der Heyde B, Emmanouilidou A, Mazzaferro E, ..., Brooke HL, den Hoed M
Sci Rep 10 (1) 11831 [2020-12-00; online 2020-07-16]
BioImage Informatics Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Genome Engineering Zebrafish [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
DOI Crossref
Transcriptome analysis of fibroblasts from schizophrenia patients reveals differential expression of schizophrenia-related genes
Etemadikhah M, Niazi A, Wetterberg L, Feuk L
Sci Rep 10 (1) - [2020-12-00; online 2020-01-20]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Disturbance history can increase functional stability in the face of both repeated disturbances of the same type and novel disturbances
Renes SE, Sjöstedt J, Fetzer I, Langenheder S
Sci Rep 10 (1) - [2020-12-00; online 2020-07-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Single cell transcriptomics identifies stem cell-derived graft composition in a model of Parkinson’s disease
Tiklová K, Nolbrant S, Fiorenzano A, ..., Perlmann T, Parmar M
Nat Commun 11 (1) - [2020-12-00; online 2020-05-15]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
DOI Crossref
Single-cell analysis of human ovarian cortex identifies distinct cell populations but no oogonial stem cells
Wagner M, Yoshihara M, Douagi I, ..., Lanner F, Damdimopoulou P
Nat Commun 11 (1) - [2020-12-00; online 2020-03-02]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]
DOI Crossref
Naming the untouchable – environmental sequences and niche partitioning as taxonomical evidence in fungi
Kalsoom Khan F, Kluting K, Tångrot J, ..., Ryberg M, Rosling A
IMA Fungus 11 (1) - [2020-12-00; online 2020-11-03]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Epigenome-wide meta-analysis of blood DNA methylation in newborns and children identifies numerous loci related to gestational age
Merid SK, Novoloaca A, Sharp GC, ..., London SJ, Melén E
Genome Med 12 (1) - [2020-12-00; online 2020-03-02]
Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative]
DOI Crossref
Targeted sequencing reveals the somatic mutation landscape in a Swedish breast cancer cohort
Mathioudaki A, Ljungström V, Melin M, ..., Sjöblom T, Lindblad-Toh K
Sci Rep 10 (1) - [2020-12-00; online 2020-11-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Presynaptic dysfunction in CASK-related neurodevelopmental disorders
Becker M, Mastropasqua F, Reising JP, ..., Bölte S, Tammimies K
Transl Psychiatry 10 (1) - [2020-12-00; online 2020-09-14]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG)
DOI Crossref
The influence of common polygenic risk and gene sets on social skills group training response in autism spectrum disorder
Li D, Choque-Olsson N, Jiao H, ..., Bölte S, Tammimies K
npj Genom. Med. 5 (1) - [2020-12-00; online 2020-10-12]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
DOI Crossref
The conifer root rot pathogens Heterobasidion irregulare and Heterobasidion occidentale employ different strategies to infect Norway spruce
Hu Y, Elfstrand M, Stenlid J, Durling MB, Olson Å
Sci Rep 10 (1) - [2020-12-00; online 2020-04-03]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Integration of whole-body [18F]FDG PET/MRI with non-targeted metabolomics can provide new insights on tissue-specific insulin resistance in type 2 diabetes
Diamanti K, Visvanathar R, Pereira MJ, ..., Wadelius C, Ahlström H
Sci Rep 10 (1) - [2020-12-00; online 2020-05-20]
Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]
DOI Crossref
Temporal changes in the vaginal microbiota in self-samples and its association with persistent HPV16 infection and CIN2+
Berggrund M, Gustavsson I, Aarnio R, ..., Olovsson M, Gyllensten U
Virol J 17 (1) - [2020-12-00; online 2020-10-07]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Discovery and population genomics of structural variation in a songbird genus
Weissensteiner MH, Bunikis I, Catalán A, ..., Warmuth VM, Wolf JBW
Nat Commun 11 (1) - [2020-12-00; online 2020-07-07]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
DOI Crossref
Exploiting loss of heterozygosity for allele-selective colorectal cancer chemotherapy
Rendo V, Stoimenov I, Mateus A, ..., Cheong I, Sjöblom T
Nat Commun 11 (1) - [2020-12-00; online 2020-03-11]
Bioinformatics Compute and Storage [Service] Chemical Biology Consortium Sweden (CBCS) [Collaborative] Drug Discovery and Development (DDD) [Service]
DOI Crossref
Using null models to compare bacterial and microeukaryotic metacommunity assembly under shifting environmental conditions
Vass M, Székely AJ, Lindström ES, Langenheder S
Sci Rep 10 (1) - [2020-12-00; online 2020-02-12]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Whole-genome sequencing of glioblastoma reveals enrichment of non-coding constraint mutations in known and novel genes
Sakthikumar S, Roy A, Haseeb L, ..., Lindblad-Toh K, Forsberg-Nilsson K
Genome Biol. 21 (1) - [2020-12-00; online 2020-06-09]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Transcriptional responses in Parascaris univalens after in vitro exposure to ivermectin, pyrantel citrate and thiabendazole
Martin F, Dube F, Karlsson Lindsjö O, ..., Bergström TF, Tydén E
Parasit Vectors 13 (1) - [2020-12-00; online 2020-07-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
A metabolite roadmap of the wood‐forming tissue in Populus tremula
Abreu IN, Johansson AI, Sokołowska K, ..., Street NR, Moritz T
New Phytol 228 (5) 1559-1572 [2020-12-00; online 2020-08-27]
Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Collaborative]
PubMed DOI Crossref
Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets.
Feuerborn TR, Palkopoulou E, van der Valk T, ..., Dalén L, Díez-Del-Molino D
pii: 10.1186/s12864-020-07229-y
BMC Genomics 21 (1) 844 [2020-11-30; online 2020-11-30]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Evaluation of Single-Molecule Sequencing Technologies for Structural Variant Detection in Two Swedish Human Genomes
Fatima N, Petri A, Gyllensten U, Feuk L, Ameur A
Genes 11 (12) 1444 [2020-11-30; online 2020-11-30]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
DOI Crossref
Single nucleus transcriptomics data integration recapitulates the major cell types in human liver
Diamanti K, Inda Díaz JS, Raine A, ..., Wadelius C, Cavalli M
Hepatol Res 51 (2) 233-238 [2020-11-28; online 2020-11-28]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
DOI Crossref
New Insights into the Microbial Profiles of Infected Root Canals in Traumatized Teeth
Manoharan L, Brundin M, Rakhimova O, Chávez de Paz L, Romani Vestman N
J Clin Med 9 (12) 3877 [2020-11-28; online 2020-11-28]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
High CD45 expression of CD8+ and CD4+ T cells correlates with the size of HIV-1 reservoir in blood.
Petkov S, Bekele Y, Lakshmikanth T, ..., Brodin P, Chiodi F
pii: 10.1038/s41598-020-77433-z pmc: PMC7686502
Sci Rep 10 (1) 20425 [2020-11-24; online 2020-11-24]
Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative]
PubMed DOI Crossref
Capillary leakage provides nutrients and antioxidants for rapid pneumococcal proliferation in influenza-infected lower airways.
Sender V, Hentrich K, Pathak A, ..., Normark S, Henriques-Normark B
pii: 2012265117
Proc. Natl. Acad. Sci. U.S.A. 117 (49) 31386-31397 [2020-11-23; online 2020-11-23]
Bioinformatics Compute and Storage [Service] Chemical Proteomics [Collaborative]
PubMed DOI Crossref
Host plant diet affects growth and induces altered gene expression and microbiome composition in the wood white (Leptidea sinapis) butterfly.
Näsvall K, Wiklund C, Mrazek V, ..., Vila R, Backström N
Mol. Ecol. 30 (2) 499-516 [2020-11-20; online 2020-11-20]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
In Situ Assembly of Choline Acetyltransferase Ligands by a Hydrothiolation Reaction Reveals Key Determinants for Inhibitor Design
Wiktelius D, Allgardsson A, Bergström T, ..., Linusson A, Ekström F
Angew. Chem. Int. Ed. 60 (2) 813-819 [2020-11-20; online 2020-11-20]
Bioinformatics Compute and Storage [Service] Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
Comparison of DNA Methylation Profiles of Hemostatic Genes between Liver Tissue and Peripheral Blood within Individuals.
Olsson Lindvall M, Angerfors A, Andersson B, ..., Stanne TM, Jern C
Thromb. Haemost. - (-) - [2020-11-17; online 2020-11-17]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
Distinct oligodendrocyte populations have spatial preference and different responses to spinal cord injury.
Floriddia EM, Lourenço T, Zhang S, ..., Nilsson M, Castelo-Branco G
pii: 10.1038/s41467-020-19453-x pmc: PMC7673029
Nat Commun 11 (1) 5860 [2020-11-17; online 2020-11-17]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) In Situ Sequencing (ISS) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Differential DNA methylation of the genes for amyloid precursor protein, tau and neurofilaments in human traumatic brain injury.
Abu Hamdeh S, Ciuculete DM, Sarkisyan D, ..., Schiöth H, Marklund N
J. Neurotrauma - (-) - [2020-11-15; online 2020-11-15]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
DOI Crossref
Identification of Pre-Diagnostic Metabolic Patterns for Glioma Using Subset Analysis of Matched Repeated Time Points
Jonsson P, Antti H, Späth F, Melin B, Björkblom B
Cancers (Basel) 12 (11) 3349 [2020-11-12; online 2020-11-12]
Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
Development of a highly efficient 50K SNP genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome re-sequencing and its transferability to other spruce species.
Bernhardsson C, Zan Y, Chen Z, Ingvarsson PK, Wu HX
Mol Ecol Resour - (-) - [2020-11-11; online 2020-11-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-Scale Mapping Reveals Complex Regulatory Activities of RpoN in Yersinia pseudotuberculosis
Mahmud AKMF, Nilsson K, Fahlgren A, ..., Avican K, Fällman M
mSystems 5 (6) - [2020-11-10; online 2020-11-10]
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]
DOI Crossref
How to make a rodent giant: Genomic basis and tradeoffs of gigantism in the capybara, the world’s largest rodent
Herrera-Álvarez S, Karlsson E, Ryder OA, Lindblad-Toh K, Crawford AJ
Mol. Biol. Evol. - (-) - [2020-11-10; online 2020-11-10]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Identification of candidate genetic variants and altered protein expression in neural stem and mature neural cells support altered microtubule function to be an essential component in bipolar disorder.
Truvé K, Parris TZ, Vizlin-Hodzic D, ..., Ågren H, Funa K
pii: 10.1038/s41398-020-01056-1 pmc: PMC7652854
Transl Psychiatry 10 (1) 390 [2020-11-09; online 2020-11-09]
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]
DOI Crossref
Drought legacy affects microbial community trait distributions related to moisture along a savanna‐grassland precipitation gradient
Leizeaga A, Hicks LC, Manoharan L, Hawkes CV, Rousk J
J Ecol - (-) - [2020-11-05; online 2020-11-05]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Draft Genome Assembly of the Freshwater Apex Predator Wels Catfish ( Silurus glanis) Using Linked-Read Sequencing.
Ozerov MY, Flajšhans M, Noreikiene K, Vasemägi A, Gross R
pii: g3.120.401711 pmc: PMC7642921
G3 (Bethesda) 10 (11) 3897-3906 [2020-11-05; online 2020-11-05]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue
Gyllborg D, Langseth CM, Qian X, ..., Lein ES, Nilsson M
- 48 (19) e112-e112 [2020-11-04; online 2020-09-29]
Bioinformatics Compute and Storage [Service] In Situ Sequencing (ISS) [Technology development]
PubMed DOI Crossref
MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells.
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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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From Inquilines to Gall Inducers: Genomic Signature of a Life-Style Transition in Synergus Gall Wasps.
Gobbo E, Lartillot N, Hearn J, ..., Ide T, Ronquist F
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Genome Biol Evol 12 (11) 2060-2073 [2020-11-03; online 2020-09-29]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Leaf shape in Populus tremula is a complex, omnigenic trait.
Mähler N, Schiffthaler B, Robinson KM, ..., Hvidsten TR, Street NR
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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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Crown‐fire severity is more important than ground‐fire severity in determining soil fungal community development in the boreal forest
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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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Pericyte dysfunction due to Shb gene deficiency increases B16F10 melanoma lung metastasis
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Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Sahelian pastoralism from the perspective of variants associated with lactase persistence
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Activation of RAS Signalling is Associated with Altered Cell Adhesion in Phaeochromocytoma.
Rossitti HM, Dutta RK, Larsson C, ..., Söderkvist P, Gimm O
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Int J Mol Sci 21 (21) 8072 [2020-10-29; online 2020-10-29]
Bioinformatics Compute and Storage [Service] Clinical Genomics Linköping
DOI Crossref
Intra-Individual Behavioural Variability: A Trait under Genetic Control
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Int J Mol Sci 21 (21) 8069 [2020-10-29; online 2020-10-29]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Population genomics reveals lack of greater white-fronted introgression into the Swedish lesser white-fronted goose.
Díez-Del-Molino D, von Seth J, Gyllenstrand N, ..., Sjögren-Gulve P, Dalén L
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Sci Rep 10 (1) 18347 [2020-10-27; online 2020-10-27]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Function of multiple sclerosis-protective HLA class I alleles revealed by genome-wide protein-quantitative trait loci mapping of interferon signalling.
Lundtoft C, Pucholt P, Imgenberg-Kreuz J, ..., Rönnblom L, Hagberg N
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PLoS Genet. 16 (10) e1009199 [2020-10-26; online 2020-10-26]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Epigenetic alterations in skin homing CD4 +CLA+ T cells of atopic dermatitis patients.
Acevedo N, Benfeitas R, Katayama S, ..., Söderhäll C, Scheynius A
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Sci Rep 10 (1) 18020 [2020-10-22; online 2020-10-22]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure Bioinformatics Support, Infrastructure and Training
PubMed DOI Crossref
Automated identification of the mouse brain's spatial compartments from in situ sequencing data.
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BioImage Informatics Bioinformatics Compute and Storage [Service]
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Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise
Peona V, Blom MPK, Xu L, ..., Irestedt M, Suh A
Mol Ecol Resour 21 (1) 263-286 [2020-10-10; online 2020-10-10]
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 (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
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Molecular pathways in patients with systemic lupus erythematosus revealed by gene-centred DNA sequencing
Sandling JK, Pucholt P, Hultin Rosenberg L, ..., Rönnblom L, None
Ann Rheum Dis 80 (1) annrheumdis-2020-218636 [2020-10-09; online 2020-10-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
GeneSetCluster: a tool for summarizing and integrating gene-set analysis results.
Ewing E, Planell-Picola N, Jagodic M, Gomez-Cabrero D
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BMC Bioinformatics 21 (1) 443 [2020-10-07; online 2020-10-07]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Transcriptional responses in developing lesions of European common ash (Fraxinus excelsior) reveal genes responding to infection by Hymenoscyphus fraxineus.
Sahraei SE, Cleary M, Stenlid J, Brandström Durling M, Elfstrand M
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BMC Plant Biol. 20 (1) 455 [2020-10-06; online 2020-10-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Khoe-San Genomes Reveal Unique Variation and Confirm the Deepest Population Divergence in Homo sapiens
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Mol. Biol. Evol. 37 (10) 2944-2954 [2020-10-01; online 2020-07-22]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Taste perception and lifestyle: insights from phenotype and genome data among Africans and Asians
Sjöstrand AE, Sjödin P, Hegay T, ..., Heyer E, Jakobsson M
Eur J Hum Genet - (-) - [2020-10-01; online 2020-10-01]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Notch activation in the mouse mammary luminal lineage leads to ductal hyperplasia and altered partitioning of luminal cell subtypes.
Phoon YP, Chivukula IV, Tsoi YL, ..., Kuiper R, Lendahl U
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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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Whole genome sequencing of apparently mutation-negative MEN1 patients
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Eur. J. Endocrinol. 182 (1) 35-45 [2020-10-00; online 2019-10-00]
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]
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Metagenomic analysis of bacteria in stallion semen
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Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Profiles of histidine-rich glycoprotein associate with age and risk of all-cause mortality.
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Autoimmunity Profiling [Service] Bioinformatics Compute and Storage [Service] Translational Plasma Profiling [Collaborative]
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High-fat diet and estrogen impacts the colon and its transcriptome in a sex-dependent manner.
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Streamlined and Abundant Bacterioplankton Thrive in Functional Cohorts
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mSystems 5 (5) - [2020-09-29; online 2020-09-29]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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A recently isolated human commensal Escherichia coli ST10 clone member mediates enhanced thermotolerance and tetrathionate respiration on a P1 phage-derived IncY plasmid.
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Labile Dissolved Organic Matter Compound Characteristics Select for Divergence in Marine Bacterial Activity and Transcription.
Pontiller B, Martínez-García S, Lundin D, Pinhassi J
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DOI Crossref
Small-scale population divergence is driven by local larval environment in a temperate amphibian
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Heredity - (-) - [2020-09-21; online 2020-09-21]
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The methylation landscape and its role in domestication and gene regulation in the chicken
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Nat Ecol Evol 4 (12) 1713-1724 [2020-09-21; online 2020-09-21]
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PubMed DOI Crossref
Generation of Sequencing Libraries for Structural Analysis of Bacterial 5' UTRs.
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Reconstruction of the birth of a male sex chromosome present in Atlantic herring.
Rafati N, Chen J, Herpin A, ..., Schartl M, Andersson L
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Compositional and functional differences of the mucosal microbiota along the intestine of healthy individuals.
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Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne
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A whole-genome sequenced control population in northern Sweden reveals subregional genetic differences
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PLoS ONE 15 (9) e0237721 [2020-09-11; online 2020-09-11]
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PubMed DOI Crossref
Integration of molecular profiles in a longitudinal wellness profiling cohort.
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Nat Commun 11 (1) 4487 [2020-09-08; online 2020-09-08]
Autoimmunity Profiling [Collaborative] Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Mass Cytometry [Collaborative] Swedish Metabolomics Centre (SMC) [Collaborative] Translational Plasma Profiling [Collaborative]
PubMed DOI Crossref
An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction.
Hanke L, Vidakovics Perez L, Sheward DJ, ..., Murrell B, McInerney GM
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Nat Commun 11 (1) 4420 [2020-09-04; online 2020-09-04]
Bioinformatics Compute and Storage [Service] Protein Science Facility (PSF) [Service]
PubMed DOI Crossref
Genome sequence of segmented filamentous bacteria present in the human intestine.
Jonsson H, Hugerth LW, Sundh J, Lundin E, Andersson AF
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Commun Biol 3 (1) 485 [2020-09-04; online 2020-09-04]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
DOI Crossref
A ribonucleotide reductase from Clostridium botulinum reveals distinct evolutionary pathways to regulation via the overall activity site
Martínez-Carranza M, Jonna VR, Lundin D, ..., Stenmark P, Hofer A
PDB: 6ZJK
J. Biol. Chem. 295 (46) jbc.RA120.014895 [2020-09-03; online 2020-09-03]
Bioinformatics Compute and Storage [Service] Protein Science Facility (PSF) [Service]
DOI Crossref
Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum
Mahajan M, Seeger C, Yee B, Andersson SGE
Genome Biol Evol 12 (9) 1528-1548 [2020-09-01; online 2020-08-06]
Bioinformatics Compute and Storage [Service] Cryo-EM [Service]
DOI Crossref
River biofilms adapted to anthropogenic disturbances are more resistant to WWTP inputs
Freixa A, Perujo N, Langenheder S, Romaní AM
FEMS Microbiol. Ecol. 96 (9) - [2020-09-01; online 2020-08-07]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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Sci Adv 6 (38) - [2020-09-00; online 2020-09-16]
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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The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19
Consiglio CR, Cotugno N, Sardh F, ..., Palma P, Brodin P
Cell 183 (4) 968-981.e7 [2020-09-00; online 2020-09-00]
Autoimmunity Profiling [Service] Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative] Translational Plasma Profiling [Service]
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Reconstructing marine plankton food web interactions using DNA metabarcoding.
Zamora-Terol S, Novotny A, Winder M
Mol. Ecol. 29 (17) 3380-3395 [2020-09-00; online 2020-08-09]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure
Singh A, Nylander JAA, Schnürer A, Bongcam-Rudloff E, Müller B
Front Microbiol 11 (-) - [2020-08-27; online 2020-08-27]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Four SARS-CoV-2 Genome Sequences from Late April in Stockholm, Sweden, Reveal a Rare Mutation in the Spike Protein.
Soratto TAT, Darban H, Bjerkner A, ..., Allander T, Andersson B
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Microbiol Resour Announc 9 (35) - [2020-08-27; online 2020-08-27]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Brain transcriptomics of wild and domestic rabbits suggests that changes in dopamine signalling and ciliary function contributed to evolution of tameness
Sato DX, Rafati N, Ring H, ..., Carneiro M, Andersson L
Genome Biol Evol 12 (10) 1918-1928 [2020-08-24; online 2020-08-24]
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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Whole-genome sequencing and gene network modules predict gemcitabine/carboplatin-induced myelosuppression in non-small cell lung cancer patients.
Björn N, Badam TVS, Spalinskas R, ..., Gustafsson M, Gréen H
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npj Syst Biol Appl 6 (1) 25 [2020-08-24; online 2020-08-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Unraveling the Immune Response in Severe COVID-19
Rodriguez L, Brodin P
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Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative]
PubMed DOI Crossref
Natural killer cell immunotypes related to COVID-19 disease severity.
Maucourant C, Filipovic I, Ponzetta A, ..., Björkström NK, Karolinska COVID-19 Study Group
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Sci Immunol 5 (50) eabd6832 [2020-08-21; online 2020-08-23]
Bioinformatics Compute and Storage [Service] Translational Plasma Profiling [Service]
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Metagenome assembled-genomes reveal similar functional profiles of CPR/Patescibacteria phyla in soils.
Nascimento Lemos L, Manoharan L, William Mendes L, ..., Satler Pylro V, Tsai SM
Environ Microbiol Rep 12 (6) 651-655 [2020-08-19; online 2020-08-19]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Designing custom CRISPR libraries for hypothesis-driven drug target discovery.
Iyer VS, Jiang L, Shen Y, ..., Schmierer B, Wermeling F
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Computational and Structural Biotechnology Journal 18 (-) 2237-2246 [2020-08-18; online 2020-08-18]
Bioinformatics Compute and Storage [Service] High-throughput Genome Engineering (HTGE) [Collaborative]
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Gsta4 controls apoptosis of differentiating adult oligodendrocytes during homeostasis and remyelination via the mitochondria-associated Fas-Casp8-Bid-axis.
Carlström KE, Zhu K, Ewing E, ..., Castelo-Branco G, Piehl F
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Nat Commun 11 (1) 4071 [2020-08-13; online 2020-08-13]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Allergome-wide peptide microarrays enable epitope deconvolution in allergen-specific immunotherapy.
Mikus M, Zandian A, Sjöberg R, ..., van Hage M, Ohlin M
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Autoimmunity Profiling [Collaborative] Bioinformatics Compute and Storage [Service]
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Identification and rescue of a tRNA wobble inosine deficiency causing intellectual disability disorder
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Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging.
Zhang H, Waldmann L, Manuel R, ..., Haitina T, Allalou A
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Biomed. Opt. Express 11 (8) 4290-4305 [2020-08-01; online 2020-07-15]
BioImage Informatics Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]
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Association between proteomics and obstructive sleep apnea phenotypes in a community-based cohort of women.
Ljunggren M, Theorell-Haglöw J, Freyhult E, ..., Janson C, Lindberg E
J Sleep Res 29 (4) e13041 [2020-08-00; online 2020-04-08]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly
Juottonen H, Fontaine L, Wurzbacher C, ..., Peura S, Eiler A
Environ Microbiol 22 (8) 3158-3171 [2020-08-00; online 2020-06-03]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Management of an outbreak of postpartum Streptococcus pyogenes emm75 infections.
Trell K, Jörgensen J, Rasmussen M, Senneby E
pii: S0195-6701(20)30280-2
J. Hosp. Infect. 105 (4) 752-756 [2020-08-00; online 2020-06-01]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Determinants of genetic variation across eco-evolutionary scales in pinnipeds
Peart CR, Tusso S, Pophaly SD, ..., Shafer ABA, Wolf JBW
Nat Ecol Evol 4 (8) 1095-1104 [2020-08-00; online 2020-06-08]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Lysophosphatidic Acid-Mediated GPR35 Signaling in CX3CR1+ Macrophages Regulates Intestinal Homeostasis
Kaya B, Doñas C, Wuggenig P, ..., Villablanca EJ, Niess JH
Cell Rep 32 (5) 107979 [2020-08-00; online 2020-08-00]
Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]
DOI Crossref
Preclinical safety studies of human embryonic stem cell‐derived retinal pigment epithelial cells for the treatment of age‐related macular degeneration
Petrus‐Reurer S, Kumar P, Padrell Sánchez S, ..., Kvanta A, Lanner F
STEM CELLS Transl Med 9 (8) 936-953 [2020-08-00; online 2020-04-22]
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DOI Crossref
The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders
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Am J Phys Anthropol 172 (4) 638-649 [2020-08-00; online 2020-06-04]
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Higher host plant specialization of root‐associated endophytes than mycorrhizal fungi along an arctic elevational gradient
Abrego N, Huotari T, Tack AJM, ..., Ovaskainen O, Roslin T
Ecol Evol 10 (16) 8989-9002 [2020-08-00; online 2020-08-06]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Systems-level immunomonitoring from acute to recovery phase of severe COVID-19
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Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative] Translational Plasma Profiling [Service]
PubMed DOI Crossref
Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros
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Current Biology 30 (19) 3871-3879.e7 [2020-08-00; online 2020-08-00]
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]
DOI Crossref
The importance of the ZBED6‐IGF2 axis for metabolic regulation in mouse myoblast cells
Younis S, Naboulsi R, Wang X, ..., Welsh N, Andersson L
The FASEB Journal 34 (8) 10250-10266 [2020-08-00; online 2020-06-19]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation.
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Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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The genetic regulation of size variation in the transcriptome of the cerebrum in the chicken and its role in domestication and brain size evolution.
Höglund A, Strempfl K, Fogelholm J, Wright D, Henriksen R
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PubMed DOI Crossref
Prototypical pacemaker neurons interact with the resident microbiota.
Klimovich A, Giacomello S, Björklund Å, ..., Adameyko I, Bosch TCG
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Proc. Natl. Acad. Sci. U.S.A. 117 (30) 17854-17863 [2020-07-28; online 2020-07-09]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
A decade of epigenetic change in aging twins: Genetic and environmental contributions to longitudinal DNA methylation.
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Aging Cell 19 (8) e13197 [2020-07-24; online 2020-07-24]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient.
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Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Descriptive Proteome Analysis to Investigate Context-Dependent Treatment Responses to OXPHOS Inhibition in Colon Carcinoma Cells Grown as Monolayer and Multicellular Tumor Spheroids.
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ACS Omega 5 (28) 17242-17254 [2020-07-21; online 2020-07-06]
Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Service]
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Seamless integration of image and molecular analysis for spatial transcriptomics workflows.
Bergenstråhle J, Larsson L, Lundeberg J
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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 Patient-Derived Cell Atlas Informs Precision Targeting of Glioblastoma.
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Cell Rep 32 (2) 107897 [2020-07-14; online 2020-07-16]
Bioinformatics Compute and Storage [Service] Drug Discovery and Development (DDD) [Service]
DOI Crossref
Single-cell analysis of mosquito hemocytes identifies signatures of immune cell sub-types and cell differentiation
Kwon H, Franzén O, Mohammed M, Ankarklev J, Smith RC
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Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Collaborative]
PubMed DOI Crossref
Low Abundance of Methanotrophs in Sediments of Shallow Boreal Coastal Zones With High Water Methane Concentrations.
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Front Microbiol 11 (-) 1536 [2020-07-07; online 2020-07-07]
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Systems biology of acidophile biofilms for efficient metal extraction.
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Sci Data 7 (1) 215 [2020-07-07; online 2020-07-07]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
meQTL and ncRNA functional analyses of 102 GWAS-SNPs associated with depression implicate HACE1 and SHANK2 genes.
Ciuculete DM, Voisin S, Kular L, ..., Mwinyi J, Schiöth HB
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Clin Epigenetics 12 (1) 99 [2020-07-02; online 2020-07-02]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Y-Chromosome Variation in Southern African Khoe-San Populations Based on Whole-Genome Sequences
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Genome Biol Evol 12 (7) 1031-1039 [2020-07-01; online 2020-07-22]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Loqusdb: added value of an observations database of local genomic variation.
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Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Service]
DOI Crossref
Growth-Inhibitory Activity of Bone Morphogenetic Protein 4 in Human Glioblastoma Cell Lines Is Heterogeneous and Dependent on Reduced SOX2 Expression
Dalmo E, Johansson P, Niklasson M, ..., Nelander S, Westermark B
Mol Cancer Res 18 (7) 981-991 [2020-07-00; online 2020-03-31]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Odorant receptor phylogeny confirms conserved channels for sex pheromone and host plant signals in tortricid moths.
Gonzalez F, Borrero-Echeverry F, Jósvai JK, ..., Bengtsson M, Walker WB
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Ecol Evol 10 (14) 7334-7348 [2020-07-00; online 2020-06-30]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Gastric Microbiota in a Low-Helicobacter pylori Prevalence General Population and Their Associations With Gastric Lesions.
Ndegwa N, Ploner A, Andersson AF, ..., Agreus L, Ye W
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Clin Transl Gastroenterol 11 (7) e00191 [2020-07-00; online 2020-08-09]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comparison of spleen transcriptomes of two wild rodent species reveals differences in the immune response against Borrelia afzelii.
Zhong X, Lundberg M, Råberg L
pii: ECE36377 pmc: PMC7381583 Dryad: 10.5061/dryad.t1g1jwt02
Ecol Evol 10 (13) 6421-6434 [2020-07-00; online 2020-05-25]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Human Immune System Variation during 1 Year
Lakshmikanth T, Muhammad SA, Olin A, ..., Uhlen M, Brodin P
Cell Rep 32 (3) 107923 [2020-07-00; online 2020-07-00]
Bioinformatics Compute and Storage [Service] Mass Cytometry [Collaborative] Translational Plasma Profiling [Service]
DOI Crossref
Female-biased gene flow between two species of Darwin’s finches
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Nat Ecol Evol 4 (7) 979-986 [2020-07-00; online 2020-05-04]
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Transcriptomes from German shepherd dogs reveal differences in immune activity between atopic dermatitis affected and control skin
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Immunogenetics 72 (5) 315-323 [2020-07-00; online 2020-06-18]
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Support systems to guide clinical decision-making in precision oncology: The Cancer Core Europe Molecular Tumor Board Portal.
Tamborero D, Dienstmann R, Rachid MH, ..., Rodon J, Lehtiö J
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Bioinformatics Compute and Storage [Service] Clinical Genomics Stockholm [Collaborative] Proteogenomics [Technology development]
PubMed DOI Crossref
Meiofauna improve oxygenation and accelerate sulfide removal in the seasonally hypoxic seabed.
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DOI Crossref
Evolutionary History of the Marchantia polymorpha Complex
Linde AM, Sawangproh W, Cronberg N, Szövényi P, Lagercrantz U
Front Plant Sci 11 (-) - [2020-06-26; online 2020-06-26]
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Novel form of rhizomelic skeletal dysplasia associated with a homozygous variant in GNPNAT1.
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Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Lysine-specific demethylase 1A (LSD1) restricts ex vivo propagation of human HSCs and is a target of UM171
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Blood 136 (19) 2151-2161 [2020-06-24; online 2020-06-24]
Bioinformatics Compute and Storage [Service] Chemical Proteomics [Collaborative]
PubMed DOI Crossref
Whole-genome sequence association analysis of blood proteins in a longitudinal wellness cohort.
Zhong W, Gummesson A, Tebani A, ..., Fagerberg L, Uhlén M
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Genome Med 12 (1) 53 [2020-06-23; online 2020-06-23]
Bioinformatics Compute and Storage [Service] Translational Plasma Profiling [Collaborative]
PubMed DOI Crossref
Skeletal Muscle Transcriptomic Comparison between Long-Term Trained and Untrained Men and Women.
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Cell Rep 31 (12) 107808 [2020-06-23; online 2020-06-25]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Association of aberrant ASNS imprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL.
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Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Altered levels of CSF proteins in patients with FTD, presymptomatic mutation carriers and non-carriers.
Remnestål J, Öijerstedt L, Ullgren A, ..., Graff C, Nilsson P
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Transl Neurodegener 9 (1) 27 [2020-06-23; online 2020-06-23]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
A sample preparation protocol for high throughput immunofluorescence of suspension cells
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Bioinformatics Compute and Storage [Service] Cell Profiling [Technology development]
PubMed DOI Crossref
Xdrop: Targeted sequencing of long DNA molecules from low input samples using droplet sorting.
Madsen EB, Höijer I, Kvist T, Ameur A, Mikkelsen MJ
Hum. Mutat. - (-) - [2020-06-09; online 2020-06-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
PubMed DOI Crossref
CYCLIN-B1/2 and -D1 act in opposition to coordinate cortical progenitor self-renewal and lineage commitment.
Hagey DW, Topcic D, Kee N, ..., Perlmann T, Muhr J
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Nat Commun 11 (1) 2898 [2020-06-09; online 2020-06-09]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
LPS-treatment of bovine endometrial epithelial cells causes differential DNA methylation of genes associated with inflammation and endometrial function.
Jhamat N, Niazi A, Guo Y, ..., Andersson G, Humblot P
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BMC Genomics 21 (1) 385 [2020-06-03; online 2020-06-03]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Radiation Triggers a Dynamic Sequence of Transient Microglial Alterations in Juvenile Brain
Osman AM, Sun Y, Burns TC, ..., Kele J, Blomgren K
Cell Rep 31 (9) 107699 [2020-06-00; online 2020-06-00]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service]
DOI Crossref
Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations
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Am J Phys Anthropol 172 (2) 176-188 [2020-06-00; online 2020-04-15]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Illuminating Genetic Mysteries of the Dead Sea Scrolls
Anava S, Neuhof M, Gingold H, ..., Jakobsson M, Rechavi O
Cell 181 (6) 1218-1231.e27 [2020-06-00; online 2020-06-00]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-wide CRISPR screen identifies ZIC2 as an essential gene that controls the cell fate of early mesodermal precursors to human heart progenitors.
Xu J, Zhou C, Foo KS, ..., Sahara M, Chien KR
Stem Cells 38 (6) 741-755 [2020-06-00; online 2020-03-10]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Activated carbon stimulates microbial diversity and PAH biodegradation under anaerobic conditions in oil-polluted sediments.
Bonaglia S, Broman E, Brindefalk B, ..., Udekwu K, Gunnarsson JS
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Chemosphere 248 (-) 126023 [2020-06-00; online 2020-01-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
An immune gene expression signature distinguishes central nervous system metastases from primary tumours in non-small-cell lung cancer.
Tsakonas G, Lewensohn R, Botling J, ..., Hydbring P, Ekman S
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Eur. J. Cancer 132 (-) 24-34 [2020-06-00; online 2020-04-20]
Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative]
PubMed DOI Crossref
Linked-read sequencing enables haplotype-resolved resequencing at population scale.
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Mol Ecol Resour 20 (5) 1311-1322 [2020-05-18; online 2020-05-18]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Parallel Evolution of Bower-Building Behavior in Two Groups of Bowerbirds Suggested by Phylogenomics.
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PubMed DOI Crossref
Myocardial micro-biopsy procedure for molecular characterization with increased precision and reduced trauma.
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Sci Rep 10 (1) 8029 [2020-05-15; online 2020-05-15]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Balancing selection in Pattern Recognition Receptor signalling pathways is associated with gene function and pleiotropy in a wild rodent.
Lundberg M, Zhong X, Konrad A, Olsen R, Råberg L
Mol. Ecol. 29 (11) 1990-2003 [2020-05-06; online 2020-05-06]
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PubMed DOI Crossref
Srebf1 Controls Midbrain Dopaminergic Neurogenesis.
Toledo EM, Yang S, Gyllborg D, ..., Linnarsson S, Arenas E
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Cell Rep 31 (5) 107601 [2020-05-05; online 2020-05-07]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Joint impact of common risk factors on incident dementia: A cohort study of the Swedish Twin Registry.
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J. Intern. Med. 288 (2) 234-247 [2020-05-03; online 2020-05-03]
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Differential Expression of Immune Genes between Two Closely Related Beetle Species with Different Immunocompetence following Attack by Asecodes parviclava.
Yang X, Fors L, Slotte T, ..., Wheat CW, Hambäck PA
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Genome Biol Evol 12 (5) 522-534 [2020-05-01; online 2020-04-14]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Behavioural characterization of dmrt3a mutant zebrafish reveals crucial aspects of vertebrate locomotion through phenotypes related to acceleration
del Pozo Cano A, Manuel R, Iglesias Gonzalez AB, ..., Kullander K, Boije H
eNeuro 7 (3) ENEURO.0047-20.2020 [2020-05-01; online 2020-05-01]
BioImage Informatics Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [Service]
PubMed DOI Crossref
Transcriptome profiling of Ewing sarcomas - treatment resistance pathways and IGF-dependency.
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pmc: PMC7191197
Mol Oncol 14 (5) 1101-1117 [2020-05-00; online 2020-03-13]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Whole-genome sequencing reveals complex chromosome rearrangement disrupting NIPBL in infant with Cornelia de Lange syndrome.
Plesser Duvdevani M, Pettersson M, Eisfeldt J, ..., Lindstrand A, Harel T
Am. J. Med. Genet. A 182 (5) 1143-1151 [2020-05-00; online 2020-03-03]
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DOI Crossref
Analysis of DNA methylation patterns in the tumor immune microenvironment of metastatic melanoma
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Mol Oncol 14 (5) 933-950 [2020-05-00; online 2020-03-21]
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DOI Crossref
Recurrent Fusions Between YAP1 and KMT2A in Morphologically Distinct Neoplasms Within the Spectrum of Low-grade Fibromyxoid Sarcoma and Sclerosing Epithelioid Fibrosarcoma
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Whole-genome sequencing of human remains to enable genealogy DNA database searches – A case report
Tillmar A, Sjölund P, Lundqvist B, ..., Älgenäs C, Green H
Forensic Sci Int Genet 46 (-) 102233 [2020-05-00; online 2020-05-00]
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PubMed DOI Crossref
Genetic identification of cell types underlying brain complex traits yields insights into the etiology of Parkinson's disease.
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Nat. Genet. 52 (5) 482-493 [2020-04-27; online 2020-04-27]
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Biodiversity between sand grains: Meiofauna composition across southern and western Sweden assessed by metabarcoding.
Atherton S, Jondelius U
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Dramatic changes in blood protein levels during the first week of life in extremely preterm infants
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PubMed DOI Crossref
Trade-off between somatic and germline repair in a vertebrate supports the expensive germ line hypothesis.
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Proc. Natl. Acad. Sci. U.S.A. 117 (16) 8973-8979 [2020-04-21; online 2020-04-03]
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Genome-Scale Metabolic Modeling of Glioblastoma Reveals Promising Targets for Drug Development.
Larsson I, Uhlén M, Zhang C, Mardinoglu A
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PubMed DOI Crossref
Whole-genome genotyping and resequencing reveal the association of a deletion in the complex interferon alpha gene cluster with hypothyroidism in dogs.
Bianchi M, Rafati N, Karlsson Å, ..., Lindblad-Toh K, Rosengren Pielberg G
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Automation of Spatial Transcriptomics library preparation to enable rapid and robust insights into spatial organization of tissues.
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Generation of Retinal Pigment Epithelial Cells Derived from Human Embryonic Stem Cells Lacking Human Leukocyte Antigen Class I and II.
Petrus-Reurer S, Winblad N, Kumar P, ..., Kvanta A, Lanner F
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Stem Cell Reports 14 (4) 648-662 [2020-04-14; online 2020-03-19]
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Microorganisms 8 (4) 522 [2020-04-05; online 2020-04-05]
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Effects of whole-grain wheat, rye, and lignan supplementation on cardiometabolic risk factors in men with metabolic syndrome: a randomized crossover trial.
Eriksen AK, Brunius C, Mazidi M, ..., Dicksved J, Landberg R
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Am. J. Clin. Nutr. 111 (4) 864-876 [2020-04-01; online 2020-02-26]
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Paralogization and New Protein Architectures in Planctomycetes Bacteria with Complex Cell Structures.
Mahajan M, Yee B, Hägglund E, ..., Fuerst JA, Andersson SGE
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Mol. Biol. Evol. 37 (4) 1020-1040 [2020-04-01; online 2019-12-07]
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A Multi-Omics Approach to Liver Diseases: Integration of Single Nuclei Transcriptomics with Proteomics and HiCap Bulk Data in Human Liver.
Cavalli M, Diamanti K, Pan G, ..., Komorowski J, Wadelius C
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OMICS 24 (4) 180-194 [2020-04-00; online 2020-03-16]
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ABCB1 single-nucleotide variants and survival in patients with glioblastoma treated with radiotherapy concomitant with temozolomide.
Malmström A, Łysiak M, Åkesson L, ..., Green H, Söderkvist P
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The acute effect of metabolic cofactor supplementation: a potential therapeutic strategy against non-alcoholic fatty liver disease.
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An mRNA-mRNA Interaction Couples Expression of a Virulence Factor and Its Chaperone in Listeria monocytogenes.
Ignatov D, Vaitkevicius K, Durand S, ..., Condon C, Johansson J
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Cell Rep 30 (12) 4027-4040.e7 [2020-03-24; online 2020-03-27]
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Ivanov Öfverholm I, Zachariadis V, Taylan F, ..., Nordlund J, Barbany G
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Benedict C, Blennow K, Zetterberg H, Cedernaes J
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Inherited DNA Repair Gene Mutations in Men with Lethal Prostate Cancer.
Rantapero T, Wahlfors T, Kähler A, ..., Schleutker J, Wiklund F
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Genes 11 (3) 314 [2020-03-14; online 2020-03-14]
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Sunde J, Yıldırım Y, Tibblin P, Forsman A
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Alneberg J, Bennke C, Beier S, ..., Pinhassi J, Andersson AF
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Commun Biol 3 (1) 119 [2020-03-13; online 2020-03-13]
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Forsberg A, Huoman J, Söderholm S, ..., Gustafsson M, Jenmalm MC
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Broman E, Bonaglia S, Holovachov O, ..., Hall POJ, Nascimento FJA
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Commun Biol 3 (1) 106 [2020-03-06; online 2020-03-06]
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Sjöstedt E, Zhong W, Fagerberg L, ..., Uhlén M, Mulder J
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Science 367 (6482) eaay5947 [2020-03-06; online 2020-03-07]
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Reid S, Alexsson A, Frodlund M, ..., Rönnblom L, Leonard D
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Ann. Rheum. Dis. 79 (3) 363-369 [2020-03-01; online 2019-12-11]
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Danielsson M, Halvardson J, Davies H, ..., Dumanski JP, Forsberg LA
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Eur. J. Hum. Genet. 28 (3) 349-357 [2020-03-01; online 2019-10-25]
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Börjesson S, Greko C, Myrenås M, ..., Nilsson O, Pedersen K
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Functionally distinct subgroups of oligodendrocyte precursor cells integrate neural activity and execute myelin formation.
Marisca R, Hoche T, Agirre E, ..., Castelo-Branco G, Czopka T
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Nat. Neurosci. 23 (3) 363-374 [2020-03-00; online 2020-02-17]
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Marine Sediments Illuminate Chlamydiae Diversity and Evolution
Dharamshi JE, Tamarit D, Eme L, ..., Spang A, Ettema TJG
Current Biology 30 (6) 1032-1048.e7 [2020-03-00; online 2020-03-00]
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Evidence for widespread selection in shaping the genomic landscape during speciation of Populus.
Wang J, Street NR, Park EJ, Liu J, Ingvarsson PK
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Footprints of natural selection at the mannose-6-phosphate isomerase locus in barnacles
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Hollfelder N, Erasmus JC, Hammaren R, ..., Greeff JM, Schlebusch CM
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Rasmussen ER, Hallberg P, Baranova EV, ..., Palmer CNA, Wadelius M
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Dussex N, Stanton DWG, Sigeman H, ..., Hansson B, Dalén L
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Commun Biol 3 (1) 84 [2020-02-21; online 2020-02-21]
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Engqvist H, Parris TZ, Kovács A, ..., Karlsson P, Helou K
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Lind A, Eriksson D, Akel O, ..., Elding Larsson H, Landegren N
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Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing.
Nordlund J, Marincevic-Zuniga Y, Cavelier L, ..., Lönnerholm G, Syvänen AC
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Sci Rep 10 (1) 2512 [2020-02-13; online 2020-02-13]
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Li X, Ploner A, Wang Y, ..., Jylhävä J, Hägg S
pii: 51507 pmc: PMC7012595
Elife 9 (-) - [2020-02-11; online 2020-02-11]
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Whole genome sequencing unveils genetic heterogeneity in optic nerve hypoplasia.
Dahl S, Pettersson M, Eisfeldt J, ..., Anderlid BM, Lindstrand A
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PLoS ONE 15 (2) e0228622 [2020-02-10; online 2020-02-10]
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Demography and Natural Selection Have Shaped Genetic Variation in the Widely Distributed Conifer Norway Spruce (Picea abies).
Wang X, Bernhardsson C, Ingvarsson PK
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Genome Biol Evol 12 (2) 3803-3817 [2020-02-01; online 2020-01-21]
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rs953413 Regulates Polyunsaturated Fatty Acid Metabolism by Modulating ELOVL2 Expression
Pan G, Cavalli M, Carlsson B, ..., Kumar C, Wadelius C
iScience 23 (2) 100808 [2020-02-00; online 2020-02-00]
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Genomic and transcriptomic features of dermatofibrosarcoma protuberans: Unusual chromosomal origin of the COL1A1-PDGFB fusion gene and synergistic effects of amplified regions in tumor development
Köster J, Arbajian E, Viklund B, ..., Mandahl N, Mertens F
Cancer Genet 241 (-) 34-41 [2020-02-00; online 2020-02-00]
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Ström P, Kartasalo K, Olsson H, ..., Egevad L, Eklund M
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Lancet Oncol 21 (2) 222-232 [2020-02-00; online 2020-01-08]
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Joost S, Annusver K, Jacob T, ..., Sandberg R, Kasper M
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Diversity and Host Interactions Among Virulent and Temperate Baltic Sea Flavobacterium Phages.
Nilsson E, Bayfield OW, Lundin D, Antson AA, Holmfeldt K
pii: v12020158 pmc: PMC7077304
Viruses 12 (2) 158 [2020-01-30; online 2020-01-30]
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Painting of Fourth and the X-Linked 1.688 Satellite in D. melanogaster is Involved in Chromosome-Wide Gene Regulation.
Ekhteraei-Tousi S, Lewerentz J, Larsson J
pii: cells9020323 pmc: PMC7072490
Cells 9 (2) 323 [2020-01-30; online 2020-01-30]
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Garcia M, Juhos S, Larsson M, ..., Käller M, Nystedt B
F1000Res 9 (-) 63 [2020-01-29; online 2020-01-29]
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Extracellular Vesicles Released From the Skin Commensal Yeast Malassezia sympodialis Activate Human Primary Keratinocytes
Vallhov H, Johansson C, Veerman RE, Scheynius A
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CREBBP and WDR 24 Identified as Candidate Genes for Quantitative Variation in Red-Brown Plumage Colouration in the Chicken.
Fogelholm J, Henriksen R, Höglund A, ..., Jensen P, Wright D
pii: 10.1038/s41598-020-57710-7 pmc: PMC6981141
Sci Rep 10 (1) 1161 [2020-01-24; online 2020-01-24]
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Buetti-Dinh A, Herold M, Christel S, ..., Friedman R, Dopson M
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BMC Bioinformatics 21 (1) 23 [2020-01-21; online 2020-01-21]
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Hallberg P, Yue QY, Eliasson E, ..., Ås J, Wadelius M
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Gene regulatory response to hyposalinity in the brown seaweed Fucus vesiculosus.
Rugiu L, Panova M, Pereyra RT, Jormalainen V
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BMC Genomics 21 (1) 42 [2020-01-13; online 2020-01-13]
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Development and characterization of an EMS-mutagenized wheat population and identification of salt-tolerant wheat lines.
Lethin J, Shakil SSM, Hassan S, ..., Olsson O, Aronsson H
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A regulatory role for CHD2 in myelopoiesis.
Shahin Varnoosfaderani F, Palau A, Dong W, ..., Svensson JP, Lennartsson A
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Molecular characterization of a large unselected cohort of metastatic colorectal cancers in relation to primary tumor location, rare metastatic sites and prognosis.
Nunes L, Aasebø K, Mathot L, ..., Sjöblom T, Glimelius B
Acta Oncol 59 (4) 1-10 [2020-01-10; online 2020-01-10]
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DAF-16/FOXO requires Protein Phosphatase 4 to initiate transcription of stress resistance and longevity promoting genes.
Sen I, Zhou X, Chernobrovkin A, ..., Zubarev RA, Riedel CG
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Nat Commun 11 (1) 138 [2020-01-09; online 2020-01-09]
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Integrative discovery of treatments for high-risk neuroblastoma.
Almstedt E, Elgendy R, Hekmati N, ..., Krona C, Nelander S
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Genome Biol Evol 12 (1) 3586-3598 [2020-01-01; online 2019-11-27]
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The Genome of the Endangered Dryas Monkey Provides New Insights into the Evolutionary History of the Vervets
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Mol. Biol. Evol. 37 (1) 183-194 [2020-01-01; online 2019-09-16]
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Genome-wide signatures of environmental adaptation in European aspen ( Populus tremula) under current and future climate conditions.
Ingvarsson PK, Bernhardsson C
pii: EVA12792 pmc: PMC6935590
Evol Appl 13 (1) 132-142 [2020-01-00; online 2019-04-02]
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The Proteome of the Dentate Terminal Zone of the Perforant Path Indicates Presynaptic Impairment in Alzheimer Disease.
Haytural H, Mermelekas G, Emre C, ..., Tjernberg LO, Frykman S
pii: RA119.001737
Mol. Cell Proteomics 19 (1) 128-141 [2020-01-00; online 2019-11-07]
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Protein and DNA methylation-based scores as surrogate markers for interferon system activation in patients with primary Sjögren’s syndrome
Björk A, Richardsdotter Andersson E, Imgenberg-Kreuz J, ..., Nordmark G, Wahren-Herlenius M
RMD Open 6 (1) e000995 [2020-01-00; online 2020-01-07]
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Variable neurodevelopmental and morphological phenotypes of carriers with 12q12 duplications.
Myers L, Blyth M, Moradkhani K, ..., Anderlid BM, Tammimies K
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Mol Genet Genomic Med 8 (1) e1013 [2020-01-00; online 2019-11-15]
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Yuan S, Larsson SC
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Diabetologia 63 (1) 116-123 [2020-01-00; online 2019-11-05]
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Probabilistic cell typing enables fine mapping of closely related cell types in situ
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In Situ Sequencing: A High-Throughput, Multi-Targeted Gene Expression Profiling Technique for Cell Typing in Tissue Sections
Hilscher MM, Gyllborg D, Yokota C, Nilsson M
Methods Mol. Biol. - (-) 313-329 [2020-00-00; online 2020-05-12]
Bioinformatics Compute and Storage [Service] In Situ Sequencing (ISS) [Collaborative]
DOI Crossref
In-plate toxicometabolomics of single zebrafish embryos
Ribbenstedt A, Posselt M, Brunius C, Benskin JP
Mol Omics 16 (3) 185-194 [2020-00-00; online 2020-00-00]
Bioinformatics Compute and Storage [Service] Genome Engineering Zebrafish [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. 120 (02) 229-242 [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
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] Translational 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
J. Clin. Endocrinol. Metab. 104 (11) 5595-5600 [2019-11-01; online 2019-07-17]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Genetic differentiation between and within ecotypes of pike (Esox lucius) in the Baltic Sea
Nordahl O, Koch‐Schmidt P, Sunde J, ..., Forsman A, Larsson P
Aquatic Conserv: Mar Freshw Ecosyst 29 (11) 1923-1935 [2019-11-00; online 2019-08-16]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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 331 (-) 108522 [2019-11-00; online 2019-11-00]
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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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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]
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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]
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A chromosome-level assembly of the Atlantic herring genome-detection of a supergene and other signals of selection.
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Genome Res. - (-) - [2019-10-24; online 2019-10-24]
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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]
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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]
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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]
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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
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Mol. Biol. Evol. - (-) - [2019-10-08; online 2019-10-08]
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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]
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Skeletal Mineralization in Association with Type X Collagen Expression Is an Ancestral Feature for Jawed Vertebrates
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Interoperable and scalable data analysis with microservices: applications in metabolomics
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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]
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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]
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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]
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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]
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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]
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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]
Bioinformatics Compute and Storage [Service] Swedish Metabolomics Centre (SMC) [Service]
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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]
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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]
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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
Biol. Lett. 15 (9) 20190491 [2019-09-27; online 2019-09-04]
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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]
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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]
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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]
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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
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Appl. Environ. Microbiol. 85 (18) - [2019-09-15; online 2019-08-29]
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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]
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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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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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
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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]
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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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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]
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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]
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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]
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Seeking the ultimate challenge.
Brodin P
Nat Med - (-) - [2019-07-03; online 2019-07-03]
Bioinformatics Compute and Storage [Service] Mass Cytometry [Technology development]
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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]
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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]
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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]
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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]
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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]
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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]
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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] Proteogenomics [Technology development] Translational Plasma Profiling [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]
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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
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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]
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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]
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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
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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]
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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]
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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) 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]
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PAD2-Mediated Citrullination Contributes to Efficient Oligodendrocyte Differentiation and Myelination.
Falcão AM, Meijer M, Scaglione A, ..., Casaccia P, Castelo-Branco G
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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
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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
- - (-) - [2019-02-07; online 2019-02-07]
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]
PubMed DOI Crossref
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]
PubMed DOI Crossref
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] Translational 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
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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]
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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]
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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]
PubMed DOI Crossref
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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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
pii: 10.1038/s41598-018-31074-5 pmc: PMC6109123 BioProject: PRJNA392017
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] Translational 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 (1) 180160 [2018-08-21; online 2018-08-21]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) 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]
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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]
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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]
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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
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PLoS ONE 13 (8) e0201669 [2018-08-09; online 2018-08-09]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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Epigenetics in pediatric acute lymphoblastic leukemia.
Nordlund J, Syvänen AC
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Semin. Cancer Biol. 51 (-) 129-138 [2018-08-00; online 2017-09-05]
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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]
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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]
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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]
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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
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JACC Basic Transl Sci 3 (4) 464-480 [2018-08-00; online 2018-08-01]
Bioinformatics Compute and Storage [Service] Proteogenomics [Collaborative] Translational Plasma Profiling [Collaborative]
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Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans
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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]
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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]
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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
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Arch. Toxicol. 92 (8) 2487-2500 [2018-08-00; online 2018-06-08]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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