Bioinformatics Long-term Support WABI

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SciLifeLab Infrastructure Unit 2013–2020.

Primary: Shown in the list of current labels, if end date is not specified.

Started: 2013

Ended: 2020

Year 2023

PubMed DOI Crossref
BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.
Höjer P, Frick T, Siga H, ..., Martin M, Ahmadian A
Nucleic Acids Res. - (-) - [2023-11-06; online 2023-11-06]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service]
PubMed DOI Crossref
Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA.
Fracasso I, Zaccone C, Oskolkov N, ..., Ventura M, Borruso L
Sci. Total Environ. 908 (-) 168159 [2023-11-01; online 2023-11-01]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow.
Pochon Z, Bergfeldt N, Kırdök E, ..., Unneberg P, Oskolkov N
Genome Biol. 24 (1) 242 [2023-10-23; online 2023-10-23]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients.
Sarén T, Ramachandran M, Gammelgård G, ..., Enblad G, Essand M
Clin. Cancer Res. 29 (20) 4139-4152 [2023-10-13; online 2023-08-04]
Affinity Proteomics Uppsala [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The dynamics of touch-responsive gene expression in cereals.
Darwish E, Ghosh R, Bentzer J, ..., Sirijovski N, Van Aken O
Plant J. 116 (1) 282-302 [2023-10-00; online 2023-06-08]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae).
Steffen K, Proux-Wéra E, Soler L, ..., Sundh J, Cárdenas P
G3 (Bethesda) 13 (10) - [2023-09-30; online 2023-08-25]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genetic atlas of hygro-and thermosensory cells in the vinegar fly Drosophila melanogaster.
Corthals K, Andersson V, Churcher A, Reimegård J, Enjin A
Sci Rep 13 (1) 15202 [2023-09-14; online 2023-09-14]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Stratified genetic analysis reveals sex differences in MPO-ANCA-associated vasculitis.
Ekman D, Sennblad B, Knight A, ..., Lindblad-Toh K, Dahlqvist J
Rheumatology (Oxford) 62 (9) 3213-3218 [2023-09-01; online 2023-04-03]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI SNP genotyping [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Multi-modal single cell sequencing of B cells in primary Sjögren's Syndrome.
Arvidsson G, Czarnewski P, Johansson A, ..., Nordmark G, Syvänen A
Arthritis & rheumatology (Hoboken, N.J.) - (-) - [2023-08-23; online 2023-08-23]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Molecular and spatial landmarks of early mouse skin development.
Jacob T, Annusver K, Czarnewski P, ..., Björklund ÅK, Kasper M
Dev. Cell - (-) - [2023-08-13; online 2023-08-13]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Facilitating accessible, rapid, and appropriate processing of ancient metagenomic data with AMDirT
Borry M, Forsythe A, Andrades Valtueña A, ..., Warinner C, Fellows Yates JA
F1000Res 12 (-) 926 [2023-08-02; online 2023-08-02]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Large-scale benchmarking of circRNA detection tools reveals large differences in sensitivity but not in precision.
Vromman M, Anckaert J, Bortoluzzi S, ..., Vandesompele J, Volders PJ
Nat. Methods 20 (8) 1159-1169 [2023-08-00; online 2023-07-13]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Historical RNA expression profiles from the extinct Tasmanian tiger.
Mármol-Sánchez E, Fromm B, Oskolkov N, ..., Dalén L, Friedländer MR
Genome Res. 33 (8) 1299-1316 [2023-08-00; online 2023-07-18]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
PVT1 interacts with polycomb repressive complex 2 to suppress genomic regions with pro-apoptotic and tumour suppressor functions in multiple myeloma.
Nylund P, Garrido-Zabala B, Párraga AA, ..., Kalushkova A, Wiklund HJ
Haematologica - (-) - [2023-07-27; online 2023-07-27]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Autologous hematopoietic stem cell transplantation significantly alters circulating ceramides in peripheral blood of relapsing-remitting multiple sclerosis patients.
Vaivade A, Wiberg A, Khoonsari PE, ..., Burman J, Kultima K
Lipids Health Dis 22 (1) 97 [2023-07-07; online 2023-07-07]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Expanding the stdpopsim species catalog, and lessons learned for realistic genome simulations.
Lauterbur ME, Cavassim MIA, Gladstein AL, ..., Schrider DR, Gronau I
Elife 12 (-) - [2023-06-21; online 2023-06-21]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Disease phenotype prediction in multiple sclerosis.
Herman S, Arvidsson McShane S, Zjukovskaja C, ..., Spjuth O, Kultima K
iScience 26 (6) 106906 [2023-06-16; online 2023-05-19]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
The evolutionary maintenance of ancient recombining sex chromosomes in the ostrich.
Yazdi HP, Olito C, Kawakami T, ..., Hansson B, Cornwallis CK
PLoS Genet. 19 (6) e1010801 [2023-06-00; online 2023-06-30]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Pathogenic antibody response to glucose-6-phosphate isomerase targets a modified epitope uniquely exposed on joint cartilage.
Li T, Ge C, Krämer A, ..., Gjertsson I, Holmdahl R
Ann. Rheum. Dis. 82 (6) 799-808 [2023-06-00; online 2023-03-01]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
The Swedish childhood tumor biobank: systematic collection and molecular characterization of all pediatric CNS and other solid tumors in Sweden.
Díaz de Ståhl T, Shamikh A, Mayrhofer M, ..., Sandgren J, Nistér M
J Transl Med 21 (1) 342 [2023-05-23; online 2023-05-23]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI SNP genotyping [Service] NGI Short read [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Delayed generation of functional virus-specific circulating T follicular helper cells correlates with severe COVID-19.
Yu M, Charles A, Cagigi A, ..., Loré K, Smed-Sörensen A
Nat Commun 14 (1) 2164 [2023-04-15; online 2023-04-15]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
A small noncoding RNA links ribosome recovery and translation control to dedifferentiation during salamander limb regeneration.
Subramanian E, Elewa A, Brito G, ..., Andersson O, Simon A
Dev. Cell 58 (6) 450-460.e6 [2023-03-27; online 2023-03-08]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
DOI Crossref
Micro-scale spatial preference and temporal cyclicity linked to foraging in harbour porpoises
Stedt J, Wahlberg M, Carlström J, ..., Oskolkov N, Carlsson P
Mar. Ecol. Prog. Ser. 708 (-) 143-161 [2023-03-23; online 2023-03-23]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland.
Sarhan MS, Wurst C, Tzankov A, ..., Zink A, Maixner F
BMC Biol. 21 (1) 9 [2023-02-07; online 2023-02-07]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Proteogenomics decodes the evolution of human ipsilateral breast cancer.
De Marchi T, Pyl PT, Sjöström M, ..., Malmstöm J, Niméus E
Commun Biol 6 (1) 139 [2023-02-02; online 2023-02-02]
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
High cardiomyocyte diversity in human early prenatal heart development.
Sylvén C, Wärdell E, Månsson-Broberg A, ..., Björklund Å, Giacomello S
iScience 26 (1) 105857 [2023-01-20; online 2022-12-21]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Bayesian mixed model analysis uncovered 21 risk loci for chronic kidney disease in boxer dogs.
Lingaas F, Tengvall K, Jansen JH, ..., Lindblad-Toh K, Wang C
PLoS Genet. 19 (1) e1010599 [2023-01-00; online 2023-01-24]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Year 2022

PubMed DOI Crossref
Loss of Y in leukocytes as a risk factor for critical COVID-19 in men
Bruhn-Olszewska B, Davies H, Sarkisyan D, ..., Frithiof R, Dumanski JP
Genome Med 14 (1) 139 [2022-12-14; online 2022-12-14]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Bayesian model and selection signature analyses reveal risk factors for canine atopic dermatitis.
Tengvall K, Sundström E, Wang C, ..., Andersson G, Lindblad-Toh K
Commun Biol 5 (1) 1348 [2022-12-08; online 2022-12-08]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Early fate bias in neuroepithelial progenitors of hippocampal neurogenesis.
von Berlin L, Westholm JO, Ratz M, Frisén J
Hippocampus - (-) - [2022-12-05; online 2022-12-05]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Integration of small RNAs from plasma and cerebrospinal fluid for classification of multiple sclerosis.
Needhamsen M, Khoonsari PE, Zheleznyakova GY, ..., Ekman D, Jagodic M
Front Genet 13 (-) 1042483 [2022-11-17; online 2022-11-17]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Read-Based Phasing and Analysis of Phased Variants with WhatsHap.
Martin M, Ebert P, Marschall T
Methods Mol. Biol. 2590 (-) 127-138 [2022-11-07; online 2022-11-07]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
ZEB2 haploinsufficient Mowat-Wilson syndrome induced pluripotent stem cells show disrupted GABAergic transcriptional regulation and function.
Schuster J, Klar J, Khalfallah A, ..., Birnir B, Dahl N
Front Mol Neurosci 15 (-) 988993 [2022-10-24; online 2022-10-24]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level.
Gutiérrez-Valencia J, Fracassetti M, Berdan EL, ..., Arroyo J, Slotte T
Curr. Biol. 32 (20) 4360-4371.e6 [2022-10-24; online 2022-09-09]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma.
Peña-Pérez L, Frengen N, Hauenstein J, ..., Lindstrand A, Månsson R
Blood Adv 6 (17) 5009-5023 [2022-09-13; online 2022-06-09]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
PRC2-mediated repression is essential to maintain identity and function of differentiated dopaminergic and serotonergic neurons.
Toskas K, Yaghmaeian-Salmani B, Skiteva O, ..., Perlmann T, Holmberg J
Sci Adv 8 (34) eabo1543 [2022-08-26; online 2022-08-26]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome.
van der Valk T, Dehasque M, Chacón-Duque JC, ..., Díez-Del-Molino D, Dalén L
iScience 25 (8) 104826 [2022-08-19; online 2022-08-01]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids.
Zhao C, Biondic S, Vandal K, ..., Reik W, Petropoulos S
Genome Res. 32 (9) 1627-1641 [2022-08-10; online 2022-08-10]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Single cell [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Nuclear-specific gene expression in heterokaryons of the filamentous ascomycete Neurospora tetrasperma.
Meunier C, Darolti I, Reimegård J, Mank JE, Johannesson H
Proc. Biol. Sci. 289 (1980) 20220971 [2022-08-10; online 2022-08-10]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Metatranscriptomics of Nasopharyngeal Microbiota and Host Distinguish between Pneumonia and Health.
Nannapaneni P, Sundh J, Prast-Nielsen S, ..., Naucler P, Henriques-Normark B
Am. J. Respir. Crit. Care Med. - (-) - [2022-08-10; online 2022-08-10]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Ageing desexualizes the Drosophila brain transcriptome.
Malacrinò A, Brengdahl MI, Kimber CM, ..., Mirabello C, Friberg U
Proc. Biol. Sci. 289 (1980) 20221115 [2022-08-10; online 2022-08-10]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Identification and functional characterization of a novel susceptibility locus for small vessel vasculitis with MPO-ANCA.
Dahlqvist J, Ekman D, Sennblad B, ..., Eriksson P, Lindblad-Toh K
Rheumatology (Oxford) 61 (8) 3461-3470 [2022-08-03; online 2021-12-11]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI SNP genotyping [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes.
Westerdahl H, Mellinger S, Sigeman H, ..., Wolf JBW, Strandh M
Mol Ecol Resour 22 (6) 2379-2395 [2022-08-00; online 2022-04-11]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
High-throughput muscle fiber typing from RNA sequencing data.
Oskolkov N, Santel M, Parikh HM, ..., Pääbo S, Hansson O
Skelet Muscle 12 (1) 16 [2022-07-02; online 2022-07-02]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Regulatory networks and 5' partner usage of miRNA host gene fusions in breast cancer.
Hafstað V, Søkilde R, Häkkinen J, ..., Rovira C, Persson H
Int. J. Cancer 151 (1) 95-106 [2022-07-01; online 2022-02-26]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Genomic dynamics of brown trout populations released to a novel environment.
Kurland S, Rafati N, Ryman N, Laikre L
Ecol Evol 12 (7) e9050 [2022-07-00; online 2022-07-03]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests.
Law SR, Serrano AR, Daguerre Y, ..., Street NR, Hurry V
Proc. Natl. Acad. Sci. U.S.A. 119 (26) e2118852119 [2022-06-28; online 2022-06-21]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The immune cell atlas of human neuroblastoma.
Verhoeven BM, Mei S, Olsen TK, ..., Johnsen JI, Baryawno N
Cell Reports Medicine 3 (6) 100657 [2022-06-21; online 2022-06-09]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] Spatial Proteomics [Service]
PubMed DOI Crossref
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species.
Kutschera VE, Kierczak M, van der Valk T, ..., Dalén L, Díez-Del-Molino D
BMC Bioinformatics 23 (1) 228 [2022-06-13; online 2022-06-13]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
PubMed DOI Crossref
FOXO1 and FOXO3 Cooperatively Regulate Innate Lymphoid Cell Development.
Luu TT, Søndergaard JN, Peña-Pérez L, ..., Månsson R, Kadri N
Front Immunol 13 (-) 854312 [2022-06-09; online 2022-06-09]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Bioarchaeological evidence of one of the earliest Islamic burials in the Levant.
Srigyan M, Bolívar H, Ureña I, ..., Günther T, Valdiosera C
Commun Biol 5 (1) 554 [2022-06-07; online 2022-06-07]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species.
Feiner N, Radersma R, Vasquez L, ..., Heijmans BT, Uller T
iScience 25 (5) 104303 [2022-05-20; online 2022-04-25]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability.
Kierczak M, Rafati N, Höglund J, ..., Karlsson T, Johansson Å
Nat Commun 13 (1) 2532 [2022-05-09; online 2022-05-09]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
FOXO Dictates Initiation of B Cell Development and Myeloid Restriction in Common Lymphoid Progenitors.
Peña-Pérez L, Kharazi S, Frengen N, ..., Luc S, Månsson R
Front Immunol 13 (-) 880668 [2022-05-04; online 2022-05-04]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Satellite DNA evolution in Corvoidea inferred from short and long reads.
Peona V, Kutschera VE, Blom MPK, Irestedt M, Suh A
Mol. Ecol. - (-) - [2022-04-30; online 2022-04-30]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Findzx: an automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data.
Sigeman H, Sinclair B, Hansson B
BMC Genomics 23 (1) 328 [2022-04-27; online 2022-04-27]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
App-based COVID-19 syndromic surveillance and prediction of hospital admissions in COVID Symptom Study Sweden.
Kennedy B, Fitipaldi H, Hammar U, ..., Franks PW, Fall T
Nat Commun 13 (1) 2110 [2022-04-21; online 2022-04-21]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Silencing of STE20-type kinase STK25 in human aortic endothelial and smooth muscle cells is atheroprotective.
Cansby E, Kumari S, Caputo M, ..., Goncalves I, Mahlapuu M
Commun Biol 5 (1) 379 [2022-04-19; online 2022-04-19]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Glycoproteomics [Service] Systems Biology [Collaborative]
PubMed DOI Crossref
Evaluation of polarity switching for untargeted lipidomics using liquid chromatography coupled to high resolution mass spectrometry.
Carlsson H, Vaivade A, Emami Khoonsari P, Burman J, Kultima K
Journal of Chromatography B 1195 (-) 123200 [2022-04-15; online 2022-02-28]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Clonotypic analysis of protective influenza M2e-specific lung resident Th17 memory cells reveals extensive functional diversity
Omokanye A, Ong LC, Lebrero-Fernandez C, ..., Czarnewski P, Lycke N
Mucosal Immunol 15 (4) 717-729 [2022-04-00; online 2022-04-00]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Acute sleep loss alters circulating fibroblast growth factor 21 levels in humans: A randomised crossover trial.
Mateus Brandão LE, Espes D, Westholm JO, ..., Benedict C, Cedernaes J
J Sleep Res 31 (2) e13472 [2022-04-00; online 2021-09-02]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.
Ratz M, von Berlin L, Larsson L, ..., Lundeberg J, Frisén J
Nat. Neurosci. 25 (3) 285-294 [2022-03-00; online 2022-02-24]
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DOI Crossref
Transposon- and Genome Dynamics in the Fungal Genus Neurospora: Insights from Nearly Gapless Genome Assemblies
Nguyen D, Peona V, Unneberg P, ..., Jern P, Johannesson H
Fungal Genetics Reports 66 (1) - [2022-02-18; online 2022-02-18]
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Plasma proteins elevated in severe asthma despite oral steroid use and unrelated to Type-2 inflammation
Sparreman Mikus M, Kolmert J, Andersson LI, ..., Dahlén SE, James A
Eur Respir J 59 (2) 2100142 [2022-02-00; online 2021-11-04]
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A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component.
Christmas MJ, Jones JC, Olsson A, ..., Miller-Struttmann NE, Webster MT
Mol. Ecol. 31 (4) 1111-1127 [2022-02-00; online 2021-12-07]
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PubMed DOI Crossref
Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression.
Stratmann S, Yones SA, Garbulowski M, ..., Komorowski J, Holmfeldt L
Blood Adv 6 (1) 152-164 [2022-01-11; online 2021-10-08]
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PubMed DOI Crossref
Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.
Gutiérrez-Valencia J, Fracassetti M, Horvath R, ..., Kolář F, Slotte T
Mol. Biol. Evol. 39 (1) - [2022-01-07; online 2021-12-09]
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Whole-genome resequencing confirms reproductive isolation between sympatric demes of brown trout (Salmo trutta) detected with allozymes.
Saha A, Andersson A, Kurland S, ..., Ryman N, Laikre L
Mol. Ecol. 31 (2) 498-511 [2022-01-00; online 2021-11-15]
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PubMed DOI Crossref
Novel loss-of-function variant in DENND5A impedes melanosomal cargo transport and predisposes to familial cutaneous melanoma.
Yang M, Johnsson P, Bräutigam L, ..., Cao Y, Höiom V
Genet Med 24 (1) 157-169 [2022-01-00; online 2021-11-30]
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Year 2021

PubMed DOI Crossref
Comparison of sequencing data processing pipelines and application to underrepresented African human populations.
Breton G, Johansson ACV, Sjödin P, Schlebusch CM, Jakobsson M
BMC Bioinformatics 22 (1) 488 [2021-10-09; online 2021-10-09]
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PubMed DOI Crossref
Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis.
Hallingbäck HR, Pucholt P, Ingvarsson PK, Rönnberg-Wästljung AC, Berlin S
BMC Genomics 22 (1) 710 [2021-10-02; online 2021-10-02]
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PubMed DOI Crossref
Population genomics of the critically endangered kākāpō
Dussex N, van der Valk T, Morales HE, ..., Robertson BC, Dalén L
Cell Genomics 1 (1) 100002 [2021-10-00; online 2021-10-00]
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DOI Crossref
In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies
Montoliu-Nerin M, Sánchez-García M, Bergin C, ..., Bever JD, Rosling A
Front. Fungal Biol. 2 (-) - [2021-09-29; online 2021-09-29]
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PubMed DOI Crossref
Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid.
Peters K, Herman S, Khoonsari PE, ..., Neumann S, Kultima K
Sci Rep 11 (1) 18822 [2021-09-22; online 2021-09-22]
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PubMed DOI Crossref
Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration.
Sigeman H, Strandh M, Proux-Wéra E, ..., Westerdahl H, Hansson B
Mol. Biol. Evol. 38 (12) 5275-5291 [2021-09-20; online 2021-09-20]
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PubMed DOI Crossref
Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response.
Glaros V, Rauschmeier R, Artemov AV, ..., Busslinger M, Kreslavsky T
Immunity 54 (9) 2005-2023.e10 [2021-09-14; online 2021-09-16]
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PubMed DOI Crossref
Mitochondrial dysfunction in adult midbrain dopamine neurons triggers an early immune response.
Filograna R, Lee S, Tiklová K, ..., Perlmann T, Larsson NG
PLoS Genet. 17 (9) e1009822 [2021-09-00; online 2021-09-27]
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PubMed DOI Crossref
Pulmonary and blood dendritic cells from sarcoidosis patients more potently induce IFNγ-producing Th1 cells compared with monocytes.
Lepzien R, Nie M, Czarnewski P, ..., Grunewald J, Smed-Sörensen A
J Leukoc Biol - (-) - [2021-08-25; online 2021-08-25]
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PubMed DOI Crossref
Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia.
Sayyab S, Lundmark A, Larsson M, ..., Nordlund J, Syvänen A
Sci Rep 11 (1) 15988 [2021-08-06; online 2021-08-06]
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PubMed DOI Crossref
Human MAIT cells endowed with HBV specificity are cytotoxic and migrate towards HBV-HCC while retaining antimicrobial functions.
Healy K, Pavesi A, Parrot T, ..., Bertoletti A, Sällberg Chen M
JHEP Rep 3 (4) 100318 [2021-08-00; online 2021-06-11]
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PubMed DOI Crossref
Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics.
Christmas MJ, Jones JC, Olsson A, ..., Geib JC, Webster MT
Mol. Biol. Evol. 38 (8) 3126-3143 [2021-07-29; online 2021-04-07]
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PubMed DOI Crossref
Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater.
Mehrshad M, Lopez-Fernandez M, Sundh J, ..., Bertilsson S, Dopson M
Nat Commun 12 (1) 4253 [2021-07-12; online 2021-07-12]
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PubMed DOI Crossref
Monocytes in sarcoidosis are potent tumour necrosis factor producers and predict disease outcome.
Lepzien R, Liu S, Czarnewski P, ..., Grunewald J, Smed-Sörensen A
Eur. Respir. J. 58 (1) 2003468 [2021-07-00; online 2021-07-22]
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PubMed DOI Crossref
Molecular evaluation of five different isolation methods for extracellular vesicles reveals different clinical applicability and subcellular origin.
Veerman RE, Teeuwen L, Czarnewski P, ..., Gabrielsson S, Eldh M
J Extracell Vesicles 10 (9) e12128 [2021-07-00; online 2021-07-22]
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PubMed DOI Crossref
Profiling of Extracellular Small RNAs Highlights a Strong Bias towards Non-Vesicular Secretion.
Sork H, Conceicao M, Corso G, ..., El Andaloussi S, Mäger I
Cells 10 (6) 1543 [2021-06-18; online 2021-06-18]
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PubMed DOI Crossref
Single-cell BCR and transcriptome analysis after influenza infection reveals spatiotemporal dynamics of antigen-specific B cells
Mathew NR, Jayanthan JK, Smirnov IV, ..., Bemark M, Angeletti D
Cell Rep 35 (12) 109286 [2021-06-00; online 2021-06-00]
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PubMed DOI Crossref
Genomic Characterization of the Barnacle Balanus improvisus Reveals Extreme Nucleotide Diversity in Coding Regions.
Alm Rosenblad M, Abramova A, Lind U, ..., Nystedt B, Blomberg A
Mar Biotechnol (NY) 23 (3) 402-416 [2021-06-00; online 2021-05-01]
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PubMed DOI Crossref
A combined approach for single-cell mRNA and intracellular protein expression analysis.
Reimegård J, Tarbier M, Danielsson M, ..., Friedländer MR, Gallant CJ
Commun Biol 4 (1) 624 [2021-05-25; online 2021-05-25]
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PubMed DOI Crossref
X-chromosome variants are associated with aldosterone producing adenomas.
Dutta RK, Larsson M, Arnesen T, ..., Gimm O, Söderkvist P
Sci Rep 11 (1) 10562 [2021-05-18; online 2021-05-18]
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PubMed DOI Crossref
A plasma lipid signature predicts incident coronary artery disease.
Ottosson F, Emami Khoonsari P, Gerl MJ, ..., Melander O, Fernandez C
Int. J. Cardiol. 331 (-) 249-254 [2021-05-15; online 2021-02-03]
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PubMed DOI Crossref
The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes.
Boman J, Mugal CF, Backström N
Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-25]
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PubMed DOI Crossref
Metabolic Characterization of Plasma and Cyst Fluid from Cystic Precursors to Pancreatic Cancer Patients Reveal Metabolic Signatures of Bacterial Infection.
Morgell A, Reisz JA, Ateeb Z, ..., Chen MS, D'Alessandro A
J. Proteome Res. 20 (5) 2725-2738 [2021-05-07; online 2021-03-15]
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PubMed DOI Crossref
Tissue-specific transcriptional imprinting and heterogeneity in human innate lymphoid cells revealed by full-length single-cell RNA-sequencing.
Mazzurana L, Czarnewski P, Jonsson V, ..., Almer S, Mjösberg J
Cell Res 31 (5) 554-568 [2021-05-00; online 2021-01-08]
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PubMed DOI Crossref
In vivo screen identifies a SIK inhibitor that induces β cell proliferation through a transient UPR.
Charbord J, Ren L, Sharma RB, ..., Alonso LC, Andersson O
Nat Metab 3 (5) 682-700 [2021-05-00; online 2021-05-20]
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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. 121 (5) 573-583 [2021-05-00; online 2020-11-17]
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PubMed DOI Crossref
Small noncoding RNA profiling across cellular and biofluid compartments and their implications for multiple sclerosis immunopathology.
Zheleznyakova GY, Piket E, Needhamsen M, ..., Piehl F, Jagodic M
Proc. Natl. Acad. Sci. U.S.A. 118 (17) e2011574118 [2021-04-27; online 2021-04-22]
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PubMed DOI Crossref
Genomic insights into the conservation status of the world's last remaining Sumatran rhinoceros populations.
von Seth J, Dussex N, Díez-Del-Molino D, ..., Götherström A, Dalén L
Nat Commun 12 (1) 2393 [2021-04-26; online 2021-04-26]
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PubMed DOI Crossref
A QTL for conformation of back and croup influences lateral gait quality in Icelandic horses.
Rosengren MK, Sigurðardóttir H, Eriksson S, ..., Solé M, Lindgren G
BMC Genomics 22 (1) 267 [2021-04-14; online 2021-04-14]
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Characterization of the nuclear and cytosolic transcriptomes in human brain tissue reveals new insights into the subcellular distribution of RNA transcripts.
Zaghlool A, Niazi A, Björklund ÅK, ..., Ameur A, Feuk L
Sci Rep 11 (1) 4076 [2021-02-18; online 2021-02-18]
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PubMed DOI Crossref
Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce.
Schneider AN, Sundh J, Sundström G, ..., Hurry V, Street NR
mSystems 6 (1) - [2021-02-16; online 2021-02-16]
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PubMed DOI Crossref
Genomic characterization of relapsed acute myeloid leukemia reveals novel putative therapeutic targets.
Stratmann S, Yones SA, Mayrhofer M, ..., Cavelier L, Holmfeldt L
Blood Adv 5 (3) 900-912 [2021-02-09; online 2021-02-10]
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PubMed DOI Crossref
Endophilin A2 deficiency protects rodents from autoimmune arthritis by modulating T cell activation.
Norin U, Rintisch C, Meng L, ..., Bäckdahl L, Holmdahl R
Nat Commun 12 (1) 610 [2021-01-27; online 2021-01-27]
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PubMed DOI Crossref
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 [2021-01-00; 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]

Year 2020

PubMed DOI Crossref
Moose genomes reveal past glacial demography and the origin of modern lineages.
Dussex N, Alberti F, Heino MT, ..., Dalén L, Díez-Del-Molino D
BMC Genomics 21 (1) 854 [2020-12-02; online 2020-12-02]
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PubMed DOI Crossref
The methylation landscape and its role in domestication and gene regulation in the chicken.
Höglund A, Henriksen R, Fogelholm J, ..., Jensen P, Wright D
Nat Ecol Evol 4 (12) 1713-1724 [2020-12-00; online 2020-09-21]
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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]
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PubMed 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) 45 [2020-10-12; online 2020-10-12]
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PubMed DOI Crossref
Pre-extinction Demographic Stability and Genomic Signatures of Adaptation in the Woolly Rhinoceros.
Lord E, Dussex N, Kierczak M, ..., Götherström A, Dalén L
Curr. Biol. 30 (19) 3871-3879.e7 [2020-10-05; online 2020-08-13]
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PubMed DOI Crossref
Sources of variation in cell-type RNA-Seq profiles.
Gustafsson J, Held F, Robinson JL, ..., Jörnsten R, Nielsen J
PLoS ONE 15 (9) e0239495 [2020-09-21; online 2020-09-21]
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PubMed DOI Crossref
Integration of molecular profiles in a longitudinal wellness profiling cohort.
Tebani A, Gummesson A, Zhong W, ..., Uhlen M, Fagerberg L
Nat Commun 11 (1) 4487 [2020-09-08; online 2020-09-08]
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PubMed DOI Crossref
Comparative analysis of genome-wide DNA methylation in Neurospora.
Hosseini S, Meunier C, Nguyen D, Reimegård J, Johannesson H
Epigenetics 15 (9) 972-987 [2020-09-00; online 2020-03-31]
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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
Proc. Natl. Acad. Sci. U.S.A. 117 (30) 17854-17863 [2020-07-28; online 2020-07-09]
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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) 338 [2020-07-03; online 2020-07-03]
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PubMed DOI Crossref
Genome assembly of the basket willow, Salix viminalis, reveals earliest stages of sex chromosome expansion.
Almeida P, Proux-Wera E, Churcher A, ..., Berlin S, Mank JE
BMC Biol. 18 (1) 78 [2020-06-30; online 2020-06-30]
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PubMed 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) 127 [2020-06-09; online 2020-06-09]
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PubMed DOI Crossref
Analysis of DNA methylation patterns in the tumor immune microenvironment of metastatic melanoma.
Mitra S, Lauss M, Cabrita R, ..., Brown KM, Jönsson G
Mol Oncol 14 (5) 933-950 [2020-05-00; online 2020-03-21]
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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) 1842 [2020-04-15; online 2020-04-15]
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PubMed DOI Crossref
Building blocks are synthesized on demand during the yeast cell cycle.
Campbell K, Westholm J, Kasvandik S, ..., Mormino M, Nielsen J
Proc. Natl. Acad. Sci. U.S.A. 117 (14) 7575-7583 [2020-04-07; online 2020-03-25]
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PubMed DOI Crossref
Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses.
Phad GE, Pushparaj P, Tran K, ..., Wyatt RT, Karlsson Hedestam GB
J. Exp. Med. 217 (2) - [2020-02-03; online 2019-11-11]
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PubMed 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
Diabetes Care 43 (2) 366-373 [2020-02-00; online 2019-12-08]
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Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants.
Garcia M, Juhos S, Larsson M, ..., Käller M, Nystedt B
F1000Res 9 (-) 63 [2020-01-29; online 2020-01-29]
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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) 1303 [2020-01-28; online 2020-01-28]
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PubMed DOI Crossref
DNA methylation changes in Down syndrome derived neural iPSCs uncover co-dysregulation of ZNF and HOX3 families of transcription factors.
Laan L, Klar J, Sobol M, ..., Schuster J, Dahl N
Clin Epigenetics 12 (1) 9 [2020-01-08; online 2020-01-08]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [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
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
Philos. Trans. R. Soc. Lond., B, Biol. Sci. 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
A Spatiotemporal Organ-Wide Gene Expression and Cell Atlas of the Developing Human Heart.
Asp M, Giacomello S, Larsson L, ..., Sylvén C, Lundeberg J
Cell 179 (7) 1647-1660.e19 [2019-12-12; online 2019-12-14]
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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]
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PubMed 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
Neurobiol. Dis. 132 (-) 104583 [2019-12-00; online 2019-08-21]
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PubMed DOI Crossref
The genomic footprint of sexual conflict.
Sayadi A, Martinez Barrio A, Immonen E, ..., Nystedt B, Arnqvist G
Nat Ecol Evol 3 (12) 1725-1730 [2019-12-00; online 2019-11-18]
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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]
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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]
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PubMed DOI Crossref
ATAC-seq reveals alterations in open chromatin in pancreatic islets from subjects with type 2 diabetes
Bysani M, Agren R, Davegårdh C, ..., Bacos K, Ling C
Sci Rep 9 (1) - [2019-12-00; online 2019-05-23]
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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 [2019-11-07; online 2019-11-07]
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PubMed 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 [2019-10-00; online 2019-04-13]
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PubMed DOI Crossref
Exploring a Pool-seq-only approach for gaining population genomic insights in nonmodel species.
Kurland S, Wheat CW, de la Paz Celorio Mancera M, ..., Ryman N, Laikre L
Ecol Evol 9 (19) 11448-11463 [2019-10-00; online 2019-09-26]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Lack of gene flow: Narrow and dispersed differentiation islands in a triplet of Leptidea butterfly species
Talla V, Johansson A, Dincă V, ..., Wiklund C, Backström N
Mol Ecol 28 (6) 3756-3770 [2019-08-08; online 2019-08-08]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed 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) 9810 [2019-07-08; online 2019-07-08]
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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]
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PubMed DOI Crossref
Hemostatic Genes Exhibit a High Degree of Allele-Specific Regulation in Liver.
Olsson Lindvall M, Hansson L, Klasson S, ..., Jern C, Stanne TM
Thromb. Haemost. 119 (7) 1072-1083 [2019-07-00; online 2019-04-29]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Systems Biology [Collaborative]
PubMed DOI Crossref
Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis.
Lundmark A, Hu YOO, Huss M, ..., Andersson AF, Yucel-Lindberg T
Front. Cell. Infect. Microbiol. 9 (-) 216 [2019-06-21; online 2019-06-21]
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DOI Crossref
Shotgun Environmental DNA, Pollen, and Macrofossil Analysis of Lateglacial Lake Sediments From Southern Sweden
Parducci L, Alsos IG, Unneberg P, ..., Slotte T, Wohlfarth B
Front. Ecol. Evol. 7 (-) 189 [2019-06-20; online 2019-06-20]
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PubMed DOI Crossref
Somatic mutation that affects transcription factor binding upstream of CD55 in the temporal cortex of a late-onset Alzheimer disease patient
Helgadottir HT, Lundin P, Wallén Arzt E, ..., Graff C, Eriksson M
Hum Mol Genet 28 (16) 2675-2685 [2019-04-24; online 2019-04-24]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Breast cancer quantitative proteome and proteogenomic landscape.
Johansson HJ, Socciarelli F, Vacanti NM, ..., Børresen-Dale AL, Lehtiö J
Nat Commun 10 (1) 1600 [2019-04-08; online 2019-04-08]
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PubMed 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 (-) 660 [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
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]
PubMed 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
Nat Commun 10 (1) 581 [2019-02-04; 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]

Year 2018

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) 5150 [2018-12-04; online 2018-12-04]
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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 major locus controls local adaptation and adaptive life history variation in a perennial plant
Wang J, Ding J, Tan B, ..., Street NR, Ingvarsson PK
Genome Biol. 19 (1) - [2018-12-00; online 2018-06-04]
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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
Nat Commun 9 (1) - [2018-12-00; online 2018-03-26]
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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
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
Nat Med - (-) - [2018-11-12; online 2018-11-12]
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PubMed DOI Crossref
Preparation of plant tissue to enable Spatial Transcriptomics profiling using barcoded microarrays.
Giacomello S, Lundeberg J
Nat Protoc 13 (11) 2425-2446 [2018-11-00; online 2018-10-26]
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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
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
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]
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PubMed DOI Crossref
Autosomal Recessive Osteogenesis Imperfecta Caused by a Novel Homozygous COL1A2 Mutation
Costantini A, Tournis S, Kämpe A, ..., Doulgeraki A, Mäkitie O
Calcif Tissue Int 103 (3) 353-358 [2018-09-00; online 2018-03-23]
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
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]
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PubMed DOI Crossref
Exploratory Profiling of Urine MicroRNAs in the dy Mouse Model of LAMA2-CMD: Relation to Disease Progression.2J/dy2J
Moreira Soares Oliveira B, Gawlik KI, Durbeej M, Holmberg J
PLoS Curr 10 (-) - [2018-08-27; online 2018-08-27]
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PubMed DOI Crossref
Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.
Marques S, van Bruggen D, Vanichkina DP, ..., Taft RJ, Castelo-Branco G
Dev. Cell 46 (4) 504-517.e7 [2018-08-20; online 2018-08-02]
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PubMed DOI Crossref
Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems.
Hu YOO, Ndegwa N, Alneberg J, ..., Fagerberg J, Andersson AF
Sci Rep 8 (1) 11907 [2018-08-09; online 2018-08-09]
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PubMed DOI Crossref
Comprehensive RNA sequencing analysis in serum and muscle reveals novel small RNA signatures with biomarker potential for Duchenne Muscular Dystrophy
Coenen-Stass AML, Sork H, Gatto S, ..., Wood MJA, Roberts TC
Mol Ther Nucleic Acids - (-) - [2018-08-00; online 2018-08-00]
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PubMed DOI Crossref
Acute sleep loss results in tissue-specific alterations in genome-wide DNA methylation state and metabolic fuel utilization in humans
Cedernaes J, Schönke M, Westholm JO, ..., Zierath JR, Benedict C
Sci Adv 4 (8) eaar8590 [2018-08-00; online 2018-08-22]
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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
Sci Rep 8 (1) 10813 [2018-07-17; online 2018-07-17]
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PubMed DOI Crossref
SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments
Andermann T, Cano Á, Zizka A, Bacon C, Antonelli A
PeerJ 6 (-) e5175 [2018-07-13; online 2018-07-13]
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PubMed DOI Crossref
Bioconda: sustainable and comprehensive software distribution for the life sciences
Grüning B, Dale R, Sjödin A, ..., Valieris R, Köster J
Nat Methods 15 (7) 475-476 [2018-07-00; online 2018-07-02]
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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
Nat Commun 9 (1) 903 [2018-03-02; 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] Global Proteomics and Proteogenomics [Technology development]
DOI Crossref
Archaeal community changes in Lateglacial lake sediments: Evidence from ancient DNA
Ahmed E, Parducci L, Unneberg P, ..., Slotte T, Wohlfarth B
Quaternary Science Reviews 181 (-) 19-29 [2018-02-00; online 2018-02-00]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]
PubMed DOI Crossref
Metabolome dynamics of diapause in the butterfly Pieris napi: distinguishing maintenance, termination and post-diapause phases.
Lehmann P, Pruisscher P, Koštál V, ..., Wheat CW, Gotthard K
J Exp Biol 221 (Pt 2) - [2018-01-25; online 2018-01-25]
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PubMed DOI Crossref
A protein interaction network centered on leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) regulates growth factor receptors
Faraz M, Herdenberg C, Holmlund C, Henriksson R, Hedman H
J. Biol. Chem. - (-) jbc.M117.807487 [2018-01-09; online 2018-01-09]
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Year 2017

PubMed DOI Crossref
Mutational and putative neoantigen load predict clinical benefit of adoptive T cell therapy in melanoma
Lauss M, Donia M, Harbst K, ..., Svane IM, Jönsson G
Nat Commun 8 (1) - [2017-12-00; online 2017-11-23]
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PubMed DOI Crossref
Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size.
Pečnerová P, Palkopoulou E, Wheat CW, ..., Díez-Del-Molino D, Dalén L
Evolution Letters 1 (6) 292-303 [2017-12-00; online 2017-11-28]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Genome-Based Sexing Provides Clues about Behavior and Social Structure in the Woolly Mammoth.
Pečnerová P, Díez-Del-Molino D, Dussex N, ..., Vartanyan S, Dalén L
Curr. Biol. 27 (22) 3505-3510.e3 [2017-11-20; online 2017-11-02]
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
SweGen: a whole-genome data resource of genetic variability in a cross-section of the Swedish population.
Ameur A, Dahlberg J, Olason P, ..., Magnusson PK, Gyllensten U
Eur. J. Hum. Genet. 25 (11) 1253-1260 [2017-11-00; online 2017-08-23]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The Evolution of Dark Matter in the Mitogenome of Seed Beetles
Sayadi A, Immonen E, Tellgren-Roth C, Arnqvist G
Genome Biol Evol 9 (10) 2697-2706 [2017-10-01; online 2017-09-27]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
PubMed DOI Crossref
TIDDIT, an efficient and comprehensive structural variant caller for massive parallel sequencing data.
Eisfeldt J, Vezzi F, Olason P, Nilsson D, Lindstrand A
F1000Res 6 (-) 664 [2017-05-10; online 2017-05-10]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatially resolved transcriptome profiling in model plant species.
Giacomello S, Salmén F, Terebieniec BK, ..., Street NR, Lundeberg J
NPLANTS 3 (-) 17061 [2017-05-08; online 2017-05-08]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana
Reimegård J, Kundu S, Pendle A, ..., Sundström JF, Emanuelsson O
Nucleic Acids Res 45 (6) 3253-3265 [2017-04-07; online 2017-02-08]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology
Viļuma A, Mikko S, Hahn D, ..., Andersson G, Bergström TF
Sci Rep 7 (-) 45518 [2017-03-31; online 2017-03-31]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Proteogenomics produces comprehensive and highly accurate protein-coding gene annotation in a complete genome assembly of Malassezia sympodialis.
Zhu Y, Engström PG, Tellgren-Roth C, ..., Scheynius A, Lehtiö J
Nucleic Acids Res. 45 (5) 2629-2643 [2017-03-17; online 2017-01-20]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Proteomics Mass spectrometry [Technology development] Global Proteomics and Proteogenomics [Technology development] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Massive parallel sequencing questions the pathogenic role of missense variants in dilated cardiomyopathy
Dalin MG, Engström PG, Ivarsson EG, ..., Andersson B, Bergo MO
International Journal of Cardiology 228 (-) 742-748 [2017-02-00; online 2017-02-00]
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]
PubMed DOI Crossref
Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora.
Steige KA, Laenen B, Reimegård J, Scofield DG, Slotte T
Proc. Natl. Acad. Sci. U.S.A. 114 (5) 1087-1092 [2017-01-31; online 2017-01-17]
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
Identification of endoribonuclease specific cleavage positions reveals novel targets of RNase III inStreptococcus pyogenes
Le Rhun A, Lécrivain AL, Reimegård J, ..., Della Beffa C, Charpentier E
Nucleic Acids Res - (-) gkw1316 [2017-01-12; online 2017-01-12]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Single-Cell Analysis Reveals a Close Relationship between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages.
Kee N, Volakakis N, Kirkeby A, ..., Parmar M, Perlmann T
Cell Stem Cell 20 (1) 29-40 [2017-01-05; online 2016-10-27]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Year 2016

PubMed DOI Crossref
Production of individualized V gene databases reveals high levels of immunoglobulin genetic diversity.
Corcoran MM, Phad GE, Néstor VB, ..., Martin M, Karlsson Hedestam GB
Nat Commun 7 (-) 13642 [2016-12-20; online 2016-12-20]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Identification of Shared and Unique Serum Lipid Profiles in Diabetes Mellitus and Myocardial Infarction.
Kjellqvist S, Klose C, Surma MA, ..., Melander O, Fernandez C
J Am Heart Assoc 5 (12) e004503 [2016-11-29; online 2016-11-29]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]
DOI Crossref
WhatsHap: fast and accurate read-based phasing
Martin M, Patterson M, Garg S, ..., Schöenhuth A, Marschall T
bioRxiv - (-) - [2016-11-02; online 2016-11-02]
Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
PubMed DOI Crossref
Computational pan-genomics: status, promises and challenges.
Computational Pan-Genomics Consortium
Brief. Bioinformatics - (-) - [2016-10-21; online 2016-10-21]
Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
PubMed DOI Crossref
Massive and parallel expression profiling using microarrayed single-cell sequencing.
Vickovic S, Ståhl PL, Salmén F, ..., Frisén J, Lundeberg J
Nat Commun 7 (-) 13182 [2016-10-14; online 2016-10-14]
Advanced FISH Technologies 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
Deep targeted sequencing in pediatric acute lymphoblastic leukemia unveils distinct mutational patterns between genetic subtypes and novel relapse-associated genes.
Lindqvist CM, Lundmark A, Nordlund J, ..., Berglund EC, Syvänen AC
Oncotarget 7 (39) 64071-64088 [2016-09-27; online 2016-09-04]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
The Impact of Endurance Training on Human Skeletal Muscle Memory, Global Isoform Expression and Novel Transcripts.
Lindholm ME, Giacomello S, Werne Solnestam B, ..., Kjellqvist S, Sundberg CJ
PLoS Genet. 12 (9) e1006294 [2016-09-00; online 2016-09-22]
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
Cloche is a bHLH-PAS transcription factor that drives haemato-vascular specification.
Reischauer S, Stone OA, Villasenor A, ..., Andersson O, Stainier DY
Nature 535 (7611) 294-298 [2016-07-14; online 2016-07-15]
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PubMed DOI Crossref
Visualization and analysis of gene expression in tissue sections by spatial transcriptomics.
Ståhl PL, Salmén F, Vickovic S, ..., Lundeberg J, Frisén J
Science 353 (6294) 78-82 [2016-07-01; online 2016-07-02]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Fluorescence Tissue Profiling [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Tissue Profiling [Collaborative]
PubMed DOI Crossref
The role of germline alterations in the DNA damage response genes BRIP1 and BRCA2 in melanoma susceptibility.
Tuominen R, Engström PG, Helgadottir H, ..., Hansson J, Höiom V
Genes Chromosomes Cancer 55 (7) 601-611 [2016-07-00; online 2016-04-14]
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
Distinct transcription factor complexes act on a permissive chromatin landscape to establish regionalized gene expression in CNS stem cells.
Hagey DW, Zaouter C, Combeau G, ..., Huss M, Muhr J
Genome Res. 26 (7) 908-917 [2016-07-00; online 2016-05-02]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them.
Humble E, Martinez-Barrio A, Forcada J, ..., Wolf JB, Hoffman JI
Mol Ecol Resour 16 (4) 909-921 [2016-07-00; online 2015-12-20]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Read-based phasing of related individuals.
Garg S, Martin M, Marschall T
Bioinformatics 32 (12) i234-i242 [2016-06-15; online 2016-06-17]
Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
PubMed DOI Crossref
Changes in variation at the MHC class II DQA locus during the final demise of the woolly mammoth.
Pečnerová P, Díez-Del-Molino D, Vartanyan S, Dalén L
Sci Rep 6 (-) 25274 [2016-05-04; online 2016-05-04]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
The genetic basis for ecological adaptation of the Atlantic herring revealed by genome sequencing.
Martinez Barrio A, Lamichhaney S, Fan G, ..., Xu X, Andersson L
Elife 5 (-) - [2016-05-03; online 2016-05-03]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
The role of transposable elements for gene expression in Capsella hybrids and allopolyploids
Steige K, Reimegård J, Rebernig CA, ..., Scofield DG, Slotte T
bioRxiv - (-) - [2016-03-16; online 2016-03-16]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Evolutionary history of host use, rather than plant phylogeny, determines gene expression in a generalist butterfly.
Celorio-Mancera Mde L, Wheat CW, Huss M, ..., Nylin S, Janz N
BMC Evol. Biol. 16 (-) 59 [2016-03-08; online 2016-03-08]
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) [Collaborative] National Genomics Infrastructure [Service]

Year 2015

PubMed DOI Crossref
RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes.
Le Rhun A, Beer YY, Reimegård J, Chylinski K, Charpentier E
RNA Biol 13 (2) 177-195 [2015-11-19; online 2015-11-19]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers.
Burri R, Nater A, Kawakami T, ..., Török J, Ellegren H
Genome Res. 25 (11) 1656-1665 [2015-11-00; online 2015-09-09]
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
Assessing the consistency of public human tissue RNA-seq data sets.
Danielsson F, James T, Gomez-Cabrero D, Huss M
Brief. Bioinformatics 16 (6) 941-949 [2015-11-00; online 2015-04-02]
Bioinformatics Long-term Support WABI [Technology development] Bioinformatics Support, Infrastructure and Training [Technology development]
PubMed DOI Crossref
The Human Gut Microbiome as a Transporter of Antibiotic Resistance Genes between Continents.
Bengtsson-Palme J, Angelin M, Huss M, ..., Larsson DGJ, Johansson A
Antimicrob. Agents Chemother. 59 (10) 6551-6560 [2015-10-00; online 2015-08-12]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Cis-Regulatory Changes Associated with a Recent Mating System Shift and Floral Adaptation in Capsella.
Steige KA, Reimegård J, Koenig D, Scofield DG, Slotte T
Mol. Biol. Evol. 32 (10) 2501-2514 [2015-10-00; online 2015-08-28]
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
The human cardiac and skeletal muscle proteomes defined by transcriptomics and antibody-based profiling.
Lindskog C, Linné J, Fagerberg L, ..., Pontén F, Uhlén M
BMC Genomics 16 (-) 475 [2015-06-25; online 2015-06-25]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Tissue Profiling [Collaborative]
PubMed DOI Crossref
The mutational landscape in pediatric acute lymphoblastic leukemia deciphered by whole genome sequencing.
Lindqvist CM, Nordlund J, Ekman D, ..., Syvänen AC, Berglund EC
Hum. Mutat. 36 (1) 118-128 [2015-01-00; online 2014-10-31]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Reprogramming of Yersinia from virulent to persistent mode revealed by complex in vivo RNA-seq analysis.
Avican K, Fahlgren A, Huss M, ..., Dersch P, Fällman M
PLoS Pathog. 11 (1) e1004600 [2015-01-00; online 2015-01-15]
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Year 2014

PubMed DOI Crossref
The human skeletal muscle transcriptome: sex differences, alternative splicing, and tissue homogeneity assessed with RNA sequencing.
Lindholm ME, Huss M, Solnestam BW, ..., Lundeberg J, Sundberg CJ
FASEB J. 28 (10) 4571-4581 [2014-10-00; online 2014-07-11]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
The genomic landscape underlying phenotypic integrity in the face of gene flow in crows
Poelstra JW, Vijay N, Bossu CM, ..., Grabherr MG, Wolf JBW
Science 344 (6190) 1410-1414 [2014-06-20; online 2014-06-19]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
SciLifeLab Data Centre
Publications 9.5.0