National Genomics Infrastructure

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SciLifeLab Infrastructure Unit from 2020, combining the four previous NGI Sweden units.

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

Started: 2020

Ended: Current

Year 2023

PubMed DOI Crossref
An epigenome-wide analysis of sex hormone levels and DNA methylation in male blood samples.
Harbs J, Rinaldi S, Keski-Rahkonen P, ..., Van Guelpen B, Harlid S
Epigenetics 18 (1) 2196759 [2023-12-00; online 2023-03-31]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Exchange of Carbapenem-Resistant Escherichia coli Sequence Type 38 Intercontinentally and among Wild Bird, Human, and Environmental Niches.
Ahlstrom CA, Woksepp H, Sandegren L, Ramey AM, Bonnedahl J
Appl. Environ. Microbiol. - (-) e0031923 [2023-05-17; online 2023-05-17]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
The Broad Spectrum of TP53 Mutations in CLL: Evidence of Multiclonality and Novel Mutation Hotspots
Lazarian G, Leroy B, Theves F, ..., Soussi T, None
Hum. Mutat. 2023 (-) 1-17 [2023-05-09; online 2023-05-09]
NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Examining neurodevelopmental problems in 15q11.2 (BP1-BP2) copy number variation carriers at ages 9/12 and 18 in a Swedish twin sample.
Jonsson L, Martin J, Lichtenstein P, ..., Westberg L, Tammimies K
Mol Genet Genomic Med - (-) e2191 [2023-05-08; online 2023-05-08]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
SAG-RAD: A Method for Single-Cell Population Genomics of Unicellular Eukaryotes.
Gollnisch R, Wallenius J, Gribble KE, Ahrén D, Rengefors K
Mol. Biol. Evol. 40 (5) - [2023-05-02; online 2023-04-20]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Micro Germline-Restricted Chromosome in Blue Tits: Evidence for Meiotic Functions.
Mueller JC, Schlebusch SA, Pei Y, ..., Suh A, Kempenaers B
Mol. Biol. Evol. 40 (5) - [2023-05-02; online 2023-04-28]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon.
Mosquera KD, Nilsson LKJ, de Oliveira MR, ..., de Souza AQL, Terenius O
Parasit Vectors 16 (1) 156 [2023-05-01; online 2023-05-01]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Trophozoite fitness dictates the intestinal epithelial cell response to Giardia intestinalis infection.
Grüttner J, van Rijn JM, Geiser P, ..., Sellin ME, Svärd SG
PLoS Pathog. 19 (5) e1011372 [2023-05-00; online 2023-05-04]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Prominent epigenetic and transcriptomic changes in CD4+ and CD8+ T cells during and after pregnancy in women with multiple sclerosis and controls.
Zenere A, Hellberg S, Papapavlou Lingehed G, ..., Gustafsson M, Ernerudh J
J Neuroinflammation 20 (1) 98 [2023-04-27; online 2023-04-27]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Longitudinal associations between use of antihypertensive, antidiabetic, and lipid-lowering medications and biological aging.
Tang B, Li X, Wang Y, ..., Pedersen NL, Hägg S
Geroscience - (-) - [2023-04-10; online 2023-04-10]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Seasonal and Site-Specific Patterns of Airborne Fungal Diversity Revealed Using Passive Spore Traps and High-Throughput DNA Sequencing
Marčiulynas A, Lynikienė J, Marčiulynienė D, Gedminas A, Menkis A
Diversity 15 (4) 539 [2023-04-09; online 2023-04-09]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Forensic prediction of sex, age, height, body mass index, hip-to-waist ratio, smoking status and lipid lowering drugs using epigenetic markers and plasma proteins.
Llobet MO, Johansson Å, Gyllensten U, Allen M, Enroth S
Forensic Sci Int Genet 65 (-) 102871 [2023-04-07; online 2023-04-07]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Cross-Sectional Gene-Smoking Interaction Analysis in Relation to Subclinical Atherosclerosis-Results From the IMPROVE Study.
Maitusong B, Laguzzi F, Strawbridge RJ, ..., Leander K, IMPROVE Study group†
Circ Genom Precis Med - (-) e003710 [2023-04-06; online 2023-04-06]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Red clover root-associated microbiota is shaped by geographic location and choice of farming system.
Jambagi S, Hodén KP, Öhlund L, Dixelius C
J Appl Microbiol 134 (4) - [2023-04-03; online 2023-04-04]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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) - (-) - [2023-04-02; online 2023-04-02]
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
Genetically and environmentally predicted obesity in relation to cardiovascular disease: a nationwide cohort study.
Ojalehto E, Zhan Y, Jylhävä J, ..., Dahl Aslan AK, Karlsson IK
EClinicalMedicine 58 (-) 101943 [2023-04-00; online 2023-04-06]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Epigenetic changes in the CYP2D6 gene are related to severity of suicide attempt: A cross-sectional study of suicide attempters.
Boström AED, Jamshidi E, Manu DM, ..., Åsberg M, Jokinen J
J Psychiatr Res 160 (-) 217-224 [2023-04-00; online 2023-02-24]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
SLC38A10 Deficiency in Mice Affects Plasma Levels of Threonine and Histidine in Males but Not in Females: A Preliminary Characterization Study of SLC38A10-/- Mice.
Lindberg FA, Nordenankar K, Forsberg EC, Fredriksson R
Genes 14 (4) - [2023-03-30; online 2023-03-30]
NGI Short read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
VEGF-D plasma levels and VEGFD genetic variants are independently associated with outcomes in patients with cardiovascular disease.
Davidsson P, Eketjäll S, Eriksson N, ..., White H, Wallentin L
Cardiovasc. Res. - (-) - [2023-03-03; online 2023-03-03]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
ARF suppression by MYC but not MYCN confers increased malignancy of aggressive pediatric brain tumors.
Mainwaring OJ, Weishaupt H, Zhao M, ..., Hutter S, Swartling FJ
Nat Commun 14 (1) 1221 [2023-03-03; online 2023-03-03]
NGI Short read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-wide analysis identifies genetic effects on reproductive success and ongoing natural selection at the FADS locus.
Mathieson I, Day FR, Barban N, ..., Mills MC, Perry JRB
Nat Hum Behav - (-) - [2023-03-02; online 2023-03-02]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Occupational inhalable agents constitute major risk factors for rheumatoid arthritis, particularly in the context of genetic predisposition and smoking.
Tang B, Liu Q, Ilar A, ..., Alfredsson L, Jiang X
Ann. Rheum. Dis. 82 (3) 316-323 [2023-03-00; online 2022-12-06]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Multiple introgressions shape mitochondrial evolutionary history in Drosophila paulistorum and the Drosophila willistoni group.
Baião GC, Schneider DI, Miller WJ, Klasson L
Mol. Phylogenet. Evol. 180 (-) 107683 [2023-03-00; online 2022-12-24]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Multi-ancestry genome-wide association analyses improve resolution of genes and pathways influencing lung function and chronic obstructive pulmonary disease risk.
Shrine N, Izquierdo AG, Chen J, ..., Hall IP, Tobin MD
Nat. Genet. 55 (3) 410-422 [2023-03-00; online 2023-03-13]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Ectomycorrhizal fungi with hydrophobic mycelia and rhizomorphs dominate in young pine trees surviving experimental drought stress
Castaño C, Suarez-Vidal E, Zas R, ..., Oliva J, Sampedro L
Soil Biology and Biochemistry 178 (-) 108932 [2023-03-00; online 2023-03-00]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.
Jun S, Toosi H, Mold J, ..., Roth A, Lagergren J
Nat Commun 14 (1) 982 [2023-02-22; online 2023-02-22]
NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Accelerated epigenetic aging in women with emotionally unstable personality disorder and a history of suicide attempts.
Boström ADE, Andersson P, Jamshidi E, ..., Åsberg M, Jokinen J
Transl Psychiatry 13 (1) 66 [2023-02-22; online 2023-02-22]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Associations of DNA Methylation With Behavioral Problems, Gray Matter Volumes, and Negative Life Events Across Adolescence: Evidence From the Longitudinal IMAGEN Study.
Sun Y, Jia T, Barker ED, ..., Schumann G, Desrivières S
Biol. Psychiatry 93 (4) 342-351 [2023-02-15; online 2022-06-22]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic architecture of migration timing in a long-distance migratory songbird.
de Greef E, Suh A, Thorstensen MJ, Delmore KE, Fraser KC
Sci Rep 13 (1) 2437 [2023-02-10; online 2023-02-10]
NGI Long read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Ten years of marine evolutionary biology-Challenges and achievements of a multidisciplinary research initiative.
Johannesson K, Leder EH, André C, ..., Thorndyke M, Blomberg A
Evol Appl 16 (2) 530-541 [2023-02-00; online 2023-01-07]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Migratory behaviour is positively associated with genetic diversity in butterflies.
García-Berro A, Talla V, Vila R, ..., Backström N, Talavera G
Mol. Ecol. 32 (3) 560-574 [2023-02-00; online 2022-11-23]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Carbon substrate selects for different lineages of N2O reducing communities in soils under anoxic conditions
Maheshwari A, Jones CM, Tiemann M, Hallin S
Soil Biology and Biochemistry 177 (-) 108909 [2023-02-00; online 2023-02-00]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.
Sountoulidis A, Marco Salas S, Braun E, ..., Nilsson M, Samakovlis C
Nat Cell Biol 25 (2) 351-365 [2023-02-00; online 2023-01-16]
BioImage Informatics [Collaborative] In Situ Sequencing (ISS) [Service] NGI Short read [Service] NGI Single cell [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Inversions maintain differences between migratory phenotypes of a songbird.
Lundberg M, Mackintosh A, Petri A, Bensch S
Nat Commun 14 (1) 452 [2023-01-27; online 2023-01-27]
NGI Long read [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
High-density linkage maps and chromosome level genome assemblies unveil direction and frequency of extensive structural rearrangements in wood white butterflies (Leptidea spp.).
Höök L, Näsvall K, Vila R, Wiklund C, Backström N
Chromosome Res. 31 (1) 2 [2023-01-20; online 2023-01-20]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Microbial communities mediating net methylmercury formation along a trophic gradient in a peatland chronosequence.
Wang B, Hu H, Bishop K, ..., Bertilsson S, Bravo AG
J Hazard Mater 442 (-) 130057 [2023-01-15; online 2022-09-23]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single-cell transcriptomics reveals correct developmental dynamics and high-quality midbrain cell types by improved hESC differentiation.
Nishimura K, Yang S, Lee KW, ..., Linnarsson S, Arenas E
Stem Cell Reports 18 (1) 337-353 [2023-01-10; online 2022-11-17]
NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.
Koptekin D, Yüncü E, Rodríguez-Varela R, ..., Götherström A, Somel M
Curr. Biol. 33 (1) 41-57.e15 [2023-01-09; online 2022-12-08]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The genetic history of Scandinavia from the Roman Iron Age to the present.
Rodríguez-Varela R, Moore KHS, Ebenesersdóttir SS, ..., Helgason A, Götherström A
Cell 186 (1) 32-46.e19 [2023-01-05; online 2023-01-08]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Solid-phase capture and profiling of open chromatin by spatial ATAC.
Llorens-Bobadilla E, Zamboni M, Marklund M, ..., Frisén J, Ståhl PL
Nat. Biotechnol. - (-) - [2023-01-05; online 2023-01-05]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Novel cancer gene discovery using a forward genetic screen in RCAS-PDGFB-driven gliomas.
Weishaupt H, Čančer M, Rosén G, ..., Ameur A, Swartling FJ
Neuro-oncology 25 (1) 97-107 [2023-01-05; online 2022-06-24]
Bioinformatics Compute and Storage [Service] NGI Short read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Methylation in MAD1L1 is associated with the severity of suicide attempt and phenotypes of depression.
Sokolov AV, Manu DM, Nordberg DOT, ..., Jokinen J, Schiöth HB
Clin Epigenetics 15 (1) 1 [2023-01-04; online 2023-01-04]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats.
Alaei Kakhki N, Schweizer M, Lutgen D, ..., Schielzeth H, Burri R
Mol. Biol. Evol. 40 (1) - [2023-01-04; online 2022-12-30]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The path to immortalization of cells starts by managing stress through gene duplications.
Lewerentz J, Johansson AM, Stenberg P
Exp. Cell Res. 422 (1) 113431 [2023-01-01; online 2022-11-21]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Rare tandem repeat expansions associate with genes involved in synaptic and neuronal signaling functions in schizophrenia.
Wen J, Trost B, Engchuan W, ..., Yuen RKC, Szatkiewicz JP
Mol. Psychiatry 28 (1) 475-482 [2023-01-00; online 2022-11-16]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Graphene oxide elicits microbiome-dependent type 2 immune responses via the aryl hydrocarbon receptor.
Peng G, Sinkko HM, Alenius H, ..., Bräutigam L, Fadeel B
Nat Nanotechnol 18 (1) 42-48 [2023-01-00; online 2022-12-12]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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 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
Implicating genes, pleiotropy, and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis.
Kanoni S, Graham SE, Wang Y, ..., Assimes TL, Peloso GM
Genome Biol. 23 (1) 268 [2022-12-27; online 2022-12-27]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Leukocyte DNA methylation in Alzheimer´s disease associated genes: replication of findings from neuronal cells.
Karlsson IK, Ploner A, Wang Y, ..., Pedersen NL, Hägg S
Epigenetics - (-) 1-5 [2022-12-26; online 2022-12-26]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Investigation of the Virome and Characterization of Issyk-Kul Virus from Swedish Myotis brandtii Bats.
Cholleti H, de Jong J, Blomström AL, Berg M
Pathogens 12 (1) - [2022-12-21; online 2022-12-21]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Gene Networks and Pathways Involved in LPS-Induced Proliferative Response of Bovine Endometrial Epithelial Cells.
Najafi M, Guo Y, Andersson G, Humblot P, Bongcam-Rudloff E
Genes 13 (12) - [2022-12-12; online 2022-12-12]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Blue Turns to Gray: Paleogenomic Insights into the Evolutionary History and Extinction of the Blue Antelope (Hippotragus leucophaeus).
Hempel E, Bibi F, Faith JT, ..., Hofreiter M, Westbury MV
Mol. Biol. Evol. 39 (12) - [2022-12-05; online 2022-11-03]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genetics of tibia bone properties of crossbred commercial laying hens in different housing systems.
Johnsson M, Wall H, Lopes Pinto FA, ..., Kindmark A, de Koning DJ
G3 (Bethesda) - (-) - [2022-12-01; online 2022-12-01]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Screening patients with autoimmune endocrine disorders for cytokine autoantibodies reveals monogenic immune deficiencies.
Sjøgren T, Bratland E, Røyrvik EC, ..., Husebye ES, Wolff ASB
J. Autoimmun. 133 (-) 102917 [2022-12-00; online 2022-09-30]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-wide association and Mendelian randomization study of fibroblast growth factor 21 reveals causal associations with hyperlipidemia and possibly NASH.
Larsson SC, Michaëlsson K, Mola-Caminal M, Höijer J, Mantzoros CS
Metabolism 137 (-) 155329 [2022-12-00; online 2022-10-05]
Affinity Proteomics Uppsala [Service] Bioinformatics Compute and Storage [Service] NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Cone-setting in spruce is regulated by conserved elements of the age-dependent flowering pathway.
Akhter S, Westrin KJ, Zivi N, ..., Emanuelsson O, Sundström JF
New Phytol. 236 (5) 1951-1963 [2022-12-00; online 2022-09-16]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Dynamic patterns of blood lipids and DNA methylation in response to statin therapy.
Qin X, Wang Y, Pedersen NL, Tang B, Hägg S
Clin Epigenetics 14 (1) 153 [2022-11-28; online 2022-11-28]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Anti-citrullinated protein antibody specificities and pulmonary fibrosis in relation to genetic loci in early rheumatoid arthritis.
Brink M, Ljung L, Hansson M, ..., Klareskog L, Rantapää-Dahlqvist S
Rheumatology (Oxford) 61 (12) 4985-4990 [2022-11-28; online 2022-05-10]
Bioinformatics Compute and Storage [Service] NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Endosperm cellularization failure induces a dehydration stress response leading to embryo arrest.
Xu W, Sato H, Bente H, Santos-González J, Köhler C
Plant Cell - (-) - [2022-11-25; online 2022-11-25]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Divergent gene expression responses in two Baltic Sea heterotrophic model bacteria to dinoflagellate dissolved organic matter.
Osbeck CMG, Lundin D, Karlsson C, ..., Moran MA, Pinhassi J
PLoS ONE 17 (11) e0243406 [2022-11-17; online 2022-11-17]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Stage-specific transposon activity in the life cycle of the fairy-ring mushroom <i>Marasmius oreades</i>.
Hiltunen M, Ament-Velásquez SL, Ryberg M, Johannesson H
Proc. Natl. Acad. Sci. U.S.A. 119 (46) e2208575119 [2022-11-16; online 2022-11-07]
Bioinformatics Compute and Storage [Service] NGI Long read [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Meta-analysis of genome-wide association studies of hoarding symptoms in 27,537 individuals.
Strom NI, Smit DJA, Silzer T, ..., Mataix-Cols D, Cath D
Transl Psychiatry 12 (1) 479 [2022-11-15; online 2022-11-15]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic Consequences of Fragmentation in the Endangered Fennoscandian Arctic Fox (Vulpes lagopus).
Cockerill CA, Hasselgren M, Dussex N, ..., Sokolova N, Norén K
Genes 13 (11) - [2022-11-15; online 2022-11-15]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Early changes in gene expression profiles in AML patients during induction chemotherapy.
Jakobsen I, Sundkvist M, Björn N, Gréen H, Lotfi K
BMC Genomics 23 (1) 752 [2022-11-14; online 2022-11-14]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genetic regulation of serum IgA levels and susceptibility to common immune, infectious, kidney, and cardio-metabolic traits.
Liu L, Khan A, Sanchez-Rodriguez E, ..., Gharavi AG, Kiryluk K
Nat Commun 13 (1) 6859 [2022-11-11; online 2022-11-11]
NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic trajectories of a near-extinction event in the Chatham Island black robin.
von Seth J, van der Valk T, Lord E, ..., Robertson BC, Dussex N
BMC Genomics 23 (1) 747 [2022-11-10; online 2022-11-10]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Fungal Communities in Leaves and Roots of Healthy-Looking and Diseased Ulmusglabra.
Marčiulynas A, Marčiulynienė D, Lynikienė J, Bakys R, Menkis A
Microorganisms 10 (11) - [2022-11-10; online 2022-11-10]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome Evolution of a Symbiont Population for Pathogen Defense in Honeybees.
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Mishra A, Malik R, Hachiya T, ..., Dichgans M, Debette S
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Mer-tyrosine kinase: a novel susceptibility gene for SLE related end-stage renal disease.
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Shipilina D, Näsvall K, Höök L, ..., Talavera G, Backström N
Genomics 114 (6) 110481 [2022-11-00; online 2022-09-14]
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Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative.
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Characterizing single extracellular vesicles by droplet barcode sequencing for protein analysis.
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J Extracell Vesicles 11 (11) e12277 [2022-11-00; online 2022-11-05]
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Forests 13 (11) 1780 [2022-10-27; online 2022-10-27]
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Front Mol Neurosci 15 (-) 988993 [2022-10-24; online 2022-10-24]
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Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level.
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Single-cell sequencing deconvolutes cellular responses to exercise in human skeletal muscle.
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Global patterns and rates of habitat transitions across the eukaryotic tree of life.
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Cavalli M, Eriksson N, Sundbaum JK, ..., Hallberg P, Wadelius M
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Parasitic strongyle nemabiome communities in wild ruminants in Sweden.
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Plant Cell 34 (10) 3860-3872 [2022-09-27; online 2022-07-07]
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Genomic evidence that a sexually selected trait captures genome-wide variation and facilitates the purging of genetic load.
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Genome-wide association analyses of physical activity and sedentary behavior provide insights into underlying mechanisms and roles in disease prevention.
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Uncovering the genomic basis of an extraordinary plant invasion.
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Genomic and gene expression associations to morphology of a sexual ornament in the chicken.
Bakovic V, Höglund A, Martin Cerezo ML, Henriksen R, Wright D
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A 14,000-year-old genome sheds light on the evolution and extinction of a Pleistocene vulture.
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Commun Biol 5 (1) 857 [2022-08-23; online 2022-08-23]
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Seasonal dynamics in picocyanobacterial abundance and clade composition at coastal and offshore stations in the Baltic Sea.
Zufia JA, Legrand C, Farnelid H
Sci Rep 12 (1) 14330 [2022-08-22; online 2022-08-22]
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Multi-Omic Investigations of a 17-19 Translocation Links MINK1 Disruption to Autism, Epilepsy and Osteoporosis.
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Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome.
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Characterization of hemocytes and hematopoietic cells of a freshwater crayfish based on single-cell transcriptome analysis.
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Ecosystem size-induced environmental fluctuations affect the temporal dynamics of community assembly mechanisms.
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Terrigenous dissolved organic matter persists in the energy-limited deep groundwaters of the Fennoscandian Shield.
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Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity.
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Cell Syst 13 (8) 665-681.e4 [2022-08-17; online 2022-07-08]
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Isolated Grauer's gorilla populations differ in diet and gut microbiome.
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Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem.
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Microbiome 10 (1) 126 [2022-08-15; online 2022-08-15]
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Dynamical Systems Model of RNA Velocity Improves Inference of Single-cell Trajectory, Pseudo-time and Gene Regulation.
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Estimation of the impact of three different bioinformatic pipelines on sheep nemabiome analysis.
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Parasit Vectors 15 (1) 290 [2022-08-11; online 2022-08-11]
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Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids.
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Genome Res. 32 (9) 1627-1641 [2022-08-10; online 2022-08-10]
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Nannapaneni P, Sundh J, Prast-Nielsen S, ..., Naucler P, Henriques-Normark B
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Dahn HA, Mountcastle J, Balacco J, ..., Jarvis ED, Fedrigo O
Gigascience 11 (-) - [2022-08-10; online 2022-08-11]
NGI Long read [Technology development] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
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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]
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Tellgren-Roth C, Couturier M
Methods Mol. Biol. 2516 (-) 39-50 [2022-08-04; online 2022-08-04]
NGI Long read [Technology development] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
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Ramdas S, Judd J, Graham SE, ..., Zhu X, Brown CD
Am. J. Hum. Genet. 109 (8) 1366-1387 [2022-08-04; online 2022-08-06]
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Dahlqvist J, Ekman D, Sennblad B, ..., Eriksson P, Lindblad-Toh K
Rheumatology (Oxford) 61 (8) 3461-3470 [2022-08-03; online 2021-12-11]
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Tunstrom K, Wheat CW, Parmesan C, Singer MC, Mikheyev AS
Genome Biol Evol 14 (8) - [2022-08-03; online 2022-07-26]
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Modin O, Fuad N, Abadikhah M, ..., Persson F, Wilén BM
Water Res X 16 (-) 100146 [2022-08-01; online 2022-06-16]
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Spatially resolved clonal copy number alterations in benign and malignant tissue.
Erickson A, He M, Berglund E, ..., Lamb AD, Lundeberg J
Nature 608 (7922) 360-367 [2022-08-00; online 2022-08-10]
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Latz MAC, Grujcic V, Brugel S, ..., Andersson A, Andersson AF
Mol Ecol Resour 22 (6) 2304-2318 [2022-08-00; online 2022-05-06]
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Mosaic Deletions of Known Genes Explain Skeletal Dysplasias With High and Low Bone Mass.
Muurinen M, Taylan F, Tournis S, ..., Mäkitie O, Costantini A
JBMR Plus 6 (8) e10660 [2022-08-00; online 2022-07-05]
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Human adaptation to arsenic in Bolivians living in the Andes.
De Loma J, Vicente M, Tirado N, ..., Schlebusch CM, Broberg K
Chemosphere 301 (-) 134764 [2022-08-00; online 2022-04-28]
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Host genotype interacts with aerial spore communities and influences the needle mycobiome of Norway spruce.
Redondo MA, Oliva J, Elfstrand M, ..., Karlsson B, Berlin A
Environ. Microbiol. 24 (8) 3640-3654 [2022-08-00; online 2022-03-22]
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J Ecol 110 (8) 1928-1941 [2022-08-00; online 2022-06-15]
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Lundtoft C, Pucholt P, Martin M, ..., Svenungsson E, Rönnblom L
Arthritis & rheumatology (Hoboken, N.J.) 74 (8) 1440-1450 [2022-08-00; online 2022-06-27]
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A polygenic architecture with habitat-dependent effects underlies ecological differentiation in Silene.
Gramlich S, Liu X, Favre A, Buerkle CA, Karrenberg S
New Phytol. 235 (4) 1641-1652 [2022-08-00; online 2022-06-23]
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Cholleti H, de Jong J, Blomström AL, Berg M
Viruses 14 (8) - [2022-07-28; online 2022-07-28]
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Restricted X chromosome introgression and support for Haldane's rule in hybridizing damselflies.
Swaegers J, Sánchez-Guillén RA, Chauhan P, Wellenreuther M, Hansson B
Proc. Biol. Sci. 289 (1979) 20220968 [2022-07-27; online 2022-07-20]
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Inputs of Terrestrial Dissolved Organic Matter Enhance Bacterial Production and Methylmercury Formation in Oxic Coastal Water.
Rodríguez J, Andersson A, Björn E, ..., Skrobonja A, Rowe O
Front Microbiol 13 (-) 809166 [2022-07-27; online 2022-07-27]
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Khatri B, Tessneer KL, Rasmussen A, ..., Nordmark G, Lessard CJ
Nat Commun 13 (1) 4287 [2022-07-27; online 2022-07-27]
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Proliferation and Immune Response Gene Signatures Associated with Clinical Outcome to Immunotherapy and Targeted Therapy in Metastatic Cutaneous Malignant Melanoma.
Costa Svedman F, Das I, Tuominen R, ..., Höiom V, Egyhazi Brage S
Cancers (Basel) 14 (15) - [2022-07-22; online 2022-07-22]
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Richards M, Nwadozi E, Pal S, ..., Nordling S, Claesson-Welsh L
Elife 11 (-) - [2022-07-21; online 2022-07-21]
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Schaal W, Ameur A, Olsson-Strömberg U, ..., Cavelier L, Spjuth O
Cancer Inform 21 (-) 11769351221110872 [2022-07-15; online 2022-07-15]
NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
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Lipoxins reduce obesity-induced adipose tissue inflammation in 3D-cultured human adipocytes and explant cultures.
Soták M, Rajan MR, Clark M, ..., Lange S, Börgeson E
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Equilibrated evolution of the mixed auto-/allopolyploid haplotype-resolved genome of the invasive hexaploid Prussian carp.
Kuhl H, Du K, Schartl M, ..., Stöck M, Lamatsch DK
Nat Commun 13 (1) 4092 [2022-07-14; online 2022-07-14]
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Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model.
Selvin T, Fasterius E, Jarvius M, ..., Larsson R, Andersson CR
Sci Rep 12 (1) 11960 [2022-07-13; online 2022-07-13]
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Hardt U, Carlberg K, Af Klint E, ..., Ståhl PL, Malmström V
Sci Rep 12 (1) 11876 [2022-07-13; online 2022-07-13]
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High Variability of Fungal Communities Associated with the Functional Tissues and Rhizosphere Soil of Picea abies in the Southern Baltics
Marčiulynas A, Marčiulynienė D, Mishcherikova V, ..., Gedminas A, Menkis A
Forests 13 (7) 1103 [2022-07-13; online 2022-07-13]
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An atlas of endogenous DNA double-strand breaks arising during human neural cell fate determination.
Ballarino R, Bouwman BAM, Agostini F, ..., Bienko M, Crosetto N
Sci Data 9 (1) 400 [2022-07-12; online 2022-07-12]
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FLOWERING LOCUS T paralogs control the annual growth cycle in Populus trees.
André D, Marcon A, Lee KC, ..., Schmid M, Nilsson O
Curr. Biol. 32 (13) 2988-2996.e4 [2022-07-11; online 2022-06-03]
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Hoffman T, Sjödin A, Öhrman C, ..., Lundkvist Å, Olsen B
Microorganisms 10 (7) - [2022-07-11; online 2022-07-11]
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Microplastic exposure across trophic levels: effects on the host-microbiota of freshwater organisms.
Varg JE, Outomuro D, Kunce W, ..., Svanbäck R, Johansson F
Environ Microbiome 17 (1) 36 [2022-07-06; online 2022-07-06]
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Single-cell RNA-sequencing analysis of the developing mouse inner ear identifies molecular logic of auditory neuron diversification.
Petitpré C, Faure L, Uhl P, ..., Hadjab S, Lallemend F
Nat Commun 13 (1) 3878 [2022-07-05; online 2022-07-05]
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Seasonal Dynamics in Carbon Cycling of Marine Bacterioplankton Are Lifestyle Dependent.
Martínez-García S, Bunse C, Pontiller B, ..., Legrand C, Pinhassi J
Front Microbiol 13 (-) 834675 [2022-07-05; online 2022-07-05]
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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]
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Videla Rodriguez EA, Pértille F, Guerrero-Bosagna C, ..., Jensen P, Smith VA
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Weak population genetic structure in Eurasian spruce bark beetle over large regional scales in Sweden.
Ellerstrand SJ, Choudhury S, Svensson K, ..., Hansson B, Runemark A
Ecol Evol 12 (7) e9078 [2022-07-00; online 2022-07-06]
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Grey wolf genomic history reveals a dual ancestry of dogs.
Bergström A, Stanton DWG, Taron UH, ..., Dalén L, Skoglund P
Nature 607 (7918) 313-320 [2022-07-00; online 2022-06-29]
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Genomic dynamics of brown trout populations released to a novel environment.
Kurland S, Rafati N, Ryman N, Laikre L
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Allorecognition genes drive reproductive isolation in Podospora anserina.
Ament-Velásquez SL, Vogan AA, Granger-Farbos A, ..., Clavé C, Johannesson H
Nat Ecol Evol 6 (7) 910-923 [2022-07-00; online 2022-05-12]
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Novotny A, Jan KMG, Dierking J, Winder M
Sci Rep 12 (1) 10952 [2022-06-29; online 2022-06-29]
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Kostecka A, Nowikiewicz T, Olszewski P, ..., Dumanski JP, Piotrowski A
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Law SR, Serrano AR, Daguerre Y, ..., Street NR, Hurry V
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MYCN induces cell-specific tumorigenic growth in RB1-proficient human retinal organoid and chicken retina models of retinoblastoma.
Blixt MKE, Hellsand M, Konjusha D, ..., Ring H, Hallböök F
Oncogenesis 11 (1) 34 [2022-06-21; online 2022-06-21]
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Genetic loci and prioritization of genes for kidney function decline derived from a meta-analysis of 62 longitudinal genome-wide association studies.
Gorski M, Rasheed H, Teumer A, ..., Kronenberg F, Heid IM
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Molecular profiling of stem cell-derived retinal pigment epithelial cell differentiation established for clinical translation.
Petrus-Reurer S, Lederer AR, Baqué-Vidal L, ..., La Manno G, Lanner F
Stem Cell Reports 17 (6) 1458-1475 [2022-06-14; online 2022-06-16]
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CRISPR-Cas9 treatment partially restores amyloid-β 42/40 in human fibroblasts with the Alzheimer's disease PSEN 1 M146L mutation.
Konstantinidis E, Molisak A, Perrin F, ..., Berezovska O, Ingelsson M
Mol Ther Nucleic Acids 28 (-) 450-461 [2022-06-14; online 2022-03-28]
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Differential and shared genetic effects on kidney function between diabetic and non-diabetic individuals.
Winkler TW, Rasheed H, Teumer A, ..., Pattaro C, Heid IM
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Seidel L, Broman E, Ståhle M, ..., Hylander S, Dopson M
Front Microbiol 13 (-) 873281 [2022-06-10; online 2022-06-10]
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Suarez C, Sedlacek CJ, Gustavsson DJI, ..., Hermansson M, Persson F
NPJ Biofilms Microbiomes 8 (1) 47 [2022-06-08; online 2022-06-08]
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Bioarchaeological evidence of one of the earliest Islamic burials in the Levant.
Srigyan M, Bolívar H, Ureña I, ..., Günther T, Valdiosera C
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van Bruggen D, Pohl F, Langseth CM, ..., Sundström E, Castelo-Branco G
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Jokinen J, Andersson P, Chatzittofis A, ..., Åsberg M, Boström ADE
Transl Psychiatry 12 (1) 224 [2022-06-02; online 2022-06-02]
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Robust derivation of transplantable dopamine neurons from human pluripotent stem cells by timed retinoic acid delivery.
Alekseenko Z, Dias JM, Adler AF, ..., Parmar M, Ericson J
Nat Commun 13 (1) 3046 [2022-06-01; online 2022-06-01]
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Kamal N, Tsardakas Renhuldt N, Bentzer J, ..., Spannagl M, Sirijovski N
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The HDAC9-associated risk locus promotes coronary artery disease by governing TWIST1.
Ma L, Bryce NS, Turner AW, ..., Björkegren JLM, Kovacic JC
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NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Single base substitution and insertion/deletion mutational signatures in adult core binding factor acute myeloid leukemia.
Gunnarsson R, Yang M, Biloglav A, ..., Paulsson K, Johansson B
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Johansson J, Frykholm C, Ericson K, ..., Bondeson ML, Wilbe M
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Bioinformatics Compute and Storage [Service] Clinical Genomics Uppsala [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
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Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet.
Dahlin M, Singleton SS, David JA, ..., Mazumder R, Prast-Nielsen S
EBioMedicine 80 (-) 104061 [2022-06-00; online 2022-05-19]
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Genetic determinants of mannose-binding lectin activity predispose to thromboembolic complications in critical COVID-19.
Hultström M, Frithiof R, Grip J, ..., Zeberg H, Eriksson O
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Chronic Obstructive Pulmonary Disease Is Associated with Epigenome-Wide Differential Methylation in BAL Lung Cells.
Eriksson Ström J, Kebede Merid S, Pourazar J, ..., Behndig AF, Melén E
Am J Respir Cell Mol Biol 66 (6) 638-647 [2022-06-00; online 2022-03-15]
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Ancient DNA from a 2700-year-old goitered gazelle (Gazella subgutturosa) supports gazelle hunting in Iron Age Central Asia.
Rodrigues Soares AE, Boroffka N, Schröder O, ..., Benecke N, Günther T
R. Soc. open sci. 9 (6) 220104 [2022-06-00; online 2022-06-15]
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Development of gut microbiota during the first 2 years of life.
Wernroth ML, Peura S, Hedman AM, ..., Dicksved J, Fall T
Sci Rep 12 (1) 9080 [2022-05-31; online 2022-05-31]
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An empirical evaluation of genotype imputation of ancient DNA.
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The long noncoding RNA ADIPINT regulates human adipocyte metabolism via pyruvate carboxylase.
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Nat Commun 13 (1) 2958 [2022-05-26; online 2022-05-26]
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Inflammation and Interferon Signatures in Peripheral B-Lymphocytes and Sera of Individuals With Fibromyalgia.
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Front Immunol 13 (-) 874490 [2022-05-26; online 2022-05-26]
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Nitrogen Removal Capacity of Microbial Communities Developing in Compost- and Woodchip-Based Multipurpose Reactive Barriers for Aquifer Recharge With Wastewater.
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Front Microbiol 13 (-) 877990 [2022-05-24; online 2022-05-24]
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Challenges in Analyzing Functional Epigenetic Data in Perspective of Adolescent Psychiatric Health.
Manu DM, Mwinyi J, Schiöth HB
Int J Mol Sci 23 (10) - [2022-05-23; online 2022-05-23]
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Quantitative Analysis of the Transcriptome of Two Commonly Used Human Monocytic Cell Lines-THP-1 and Mono Mac 6-Reveals Their Arrest during Early Monocyte/Neutrophil Differentiation.
Akula S, Lara S, Olsson AK, Hellman L
Int J Mol Sci 23 (10) - [2022-05-22; online 2022-05-22]
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Sci Adv 8 (20) eabm2091 [2022-05-20; online 2022-05-20]
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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]
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Genome-wide association meta-analysis identifies 48 risk variants and highlights the role of the stria vascularis in hearing loss.
Trpchevska N, Freidin MB, Broer L, ..., Williams FMK, Nagtegaal AP
Am. J. Hum. Genet. 109 (6) 1077-1091 [2022-05-12; online 2022-05-12]
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Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak.
Laber CP, Pontiller B, Bunse C, ..., Pinhassi J, Farnelid H
Front Microbiol 13 (-) 828459 [2022-05-09; online 2022-05-09]
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Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability.
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Nat Commun 13 (1) 2532 [2022-05-09; online 2022-05-09]
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Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression.
Faucillion M, Johansson A, Larsson J
Nucleic Acids Res. 50 (8) 4372-4388 [2022-05-06; online 2022-04-08]
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Microbiome 10 (1) 72 [2022-05-06; online 2022-05-06]
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Ivermectin-induced gene expression changes in adult Parascaris univalens and Caenorhabditis elegans: a comparative approach to study anthelminthic metabolism and resistance in vitro.
Dube F, Hinas A, Roy S, ..., Svärd S, Tydén E
Parasit Vectors 15 (1) 158 [2022-05-05; online 2022-05-05]
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Comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia.
Darolti I, Almeida P, Wright AE, Mank JE
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Genomic Impact of Whaling in North Atlantic Fin Whales.
Wolf M, de Jong M, Halldórsson SD, Árnason Ú, Janke A
Mol. Biol. Evol. 39 (5) - [2022-05-03; online 2022-05-06]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Genetic Landscape of the ACE2 Coronavirus Receptor.
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Circulation 145 (18) 1398-1411 [2022-05-03; online 2022-04-07]
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Eur J Med Genet 65 (5) 104476 [2022-05-00; online 2022-03-21]
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Nutrient driven transcriptional changes during phage infection in an aquatic Gammaproteobacterium.
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Environ. Microbiol. 24 (5) 2270-2281 [2022-05-00; online 2022-01-26]
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HLA variants associated with azathioprine-induced pancreatitis in patients with Crohn's disease.
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Clin Transl Sci 15 (5) 1249-1256 [2022-05-00; online 2022-02-20]
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Epicardium-derived cells organize through tight junctions to replenish cardiac muscle in salamanders.
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Nat Cell Biol 24 (5) 645-658 [2022-05-00; online 2022-05-12]
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Rojas L, Grüttner J, Ma'ayeh S, Xu F, Svärd SG
Front. Cell. Infect. Microbiol. 12 (-) 862211 [2022-04-27; online 2022-04-27]
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Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival.
Lu X, Maturi NP, Jarvius M, ..., Uhrbom L, Chen X
Nat Commun 13 (1) 2236 [2022-04-25; online 2022-04-25]
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Ann. Rheum. Dis. 81 (8) 1151-1161 [2022-04-25; online 2022-04-25]
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Moškrič A, Marinč A, Ferk P, ..., Soler L, Prešern J
Insects 13 (5) 403 [2022-04-22; online 2022-04-22]
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Multi-omics protein-coding units as massively parallel Bayesian networks: Empirical validation of causality structure.
Zenere A, Rundquist O, Gustafsson M, Altafini C
iScience 25 (4) 104048 [2022-04-15; online 2022-03-11]
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Influence of cysteine, serine, sulfate, and sulfide on anaerobic conversion of unsaturated long-chain fatty acid, oleate, to methane.
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Sci. Total Environ. 817 (-) 152967 [2022-04-15; online 2022-01-10]
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HPA-axis dysregulation is not associated with accelerated epigenetic aging in patients with hypersexual disorder.
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Psychoneuroendocrinology 141 (-) 105765 [2022-04-14; online 2022-04-14]
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Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA.
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Genes 13 (4) - [2022-04-13; online 2022-04-13]
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Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line.
Lewerentz J, Johansson A, Larsson J, Stenberg P
BMC Genomics 23 (1) 276 [2022-04-07; online 2022-04-07]
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scSPLAT, a scalable plate-based protocol for single cell WGBS library preparation.
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Sci Rep 12 (1) 5772 [2022-04-06; online 2022-04-06]
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Uterine fluid microRNAs are dysregulated in women with recurrent implantation failure.
von Grothusen C, Frisendahl C, Modhukur V, ..., Boggavarapu NR, Gemzell-Danielsson K
Hum. Reprod. 37 (4) 734-746 [2022-04-01; online 2022-02-12]
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Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses.
Ferreira PdL, Batista R, Andermann T, ..., Bacon CD, Antonelli A
Mol. Phylogenet. Evol. 169 (-) 107432 [2022-04-00; online 2022-02-04]
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Next Generation Plasma Proteomics Identifies High-Precision Biomarker Candidates for Ovarian Cancer.
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Cancers (Basel) 14 (7) - [2022-03-30; online 2022-03-30]
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Integrative multi-omics and drug response profiling of childhood acute lymphoblastic leukemia cell lines.
Leo IR, Aswad L, Stahl M, ..., Vesterlund M, Jafari R
Nat Commun 13 (1) 1691 [2022-03-30; online 2022-03-30]
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The genomic architecture of the passerine MHC region: High repeat content and contrasting evolutionary histories of single copy and tandemly duplicated MHC genes.
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Mol Ecol Resour - (-) - [2022-03-29; online 2022-03-29]
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Inflammation and neutrophil extracellular traps in cerebral cavernous malformation.
Yau ACY, Globisch MA, Onyeogaziri FC, ..., Dejana E, Magnusson PU
Cell. Mol. Life Sci. 79 (4) 206 [2022-03-25; online 2022-03-25]
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Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence.
Martín-Hernández GC, Müller B, Brandt C, ..., Viehweger A, Passoth V
JoF 8 (4) - [2022-03-22; online 2022-03-22]
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Comparative Genomics of Cyclic di-GMP Metabolism and Chemosensory Pathways in Shewanella algae Strains: Novel Bacterial Sensory Domains and Functional Insights into Lifestyle Regulation.
Martín-Rodríguez AJ, Higdon SM, Thorell K, ..., Krell T, Römling U
mSystems - (-) e0151821 [2022-03-21; online 2022-03-21]
NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
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STAR Protoc 3 (1) 101202 [2022-03-18; online 2022-03-03]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Salivary Microbiota and Host-Inflammatory Responses in Periodontitis Affected Individuals With and Without Rheumatoid Arthritis.
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Front. Cell. Infect. Microbiol. 12 (-) 841139 [2022-03-14; online 2022-03-14]
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Weakened resilience of benthic microbial communities in the face of climate change
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ISME COMMUN. 2 (1) - [2022-03-08; online 2022-03-08]
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Downregulation and Hypermethylation of GABPB1 Is Associated with Aggressive Thyroid Cancer Features.
Xing X, Mu N, Yuan X, ..., Neo SY, Xu D
Cancers (Basel) 14 (6) - [2022-03-08; online 2022-03-08]
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Identification of a discrete subpopulation of spinal cord ependymal cells with neural stem cell properties.
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Cell Rep 38 (9) 110440 [2022-03-01; online 2022-03-03]
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GWAS in people of Middle Eastern descent reveals a locus protective of kidney function-a cross-sectional study.
Mohamed SA, Fernadez-Tajes J, Franks PW, Bennet L
BMC Med 20 (1) 76 [2022-03-01; online 2022-03-01]
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Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population.
Viluma A, Flagstad Ø, Åkesson M, ..., Wabakken P, Ellegren H
Genome Res. 32 (3) 449-458 [2022-03-00; online 2022-02-08]
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Utilizing museomics to trace the complex history and species boundaries in an avian-study system of conservation concern.
Ernst M, Jønsson KA, Ericson PGP, Blom MPK, Irestedt M
Heredity (Edinb) 128 (3) 159-168 [2022-03-00; online 2022-01-26]
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The era of reference genomes in conservation genomics.
Formenti G, Theissinger K, Fernandes C, ..., Bálint M, European Reference Genome Atlas (ERGA) Consortium
Trends Ecol Evol 37 (3) 197-202 [2022-03-00; online 2022-01-24]
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The Genetic Architecture of Obsessive-Compulsive Disorder: Contribution of Liability to OCD From Alleles Across the Frequency Spectrum.
Mahjani B, Klei L, Mattheisen M, ..., Devlin B, Grice DE
Am J Psychiatry 179 (3) 216-225 [2022-03-00; online 2021-11-18]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Loss of Y and clonal hematopoiesis in blood-two sides of the same coin?
Ljungström V, Mattisson J, Halvardson J, ..., Baliakas P, Forsberg LA
Leukemia 36 (3) 889-891 [2022-03-00; online 2021-11-01]
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Local selection signals in the genome of blue tits emphasize regulatory and neuronal evolution.
Mueller JC, Botero-Delgadillo E, Espíndola-Hernández P, ..., Gruselius J, Kempenaers B
Mol. Ecol. 31 (5) 1504-1514 [2022-03-00; online 2022-01-22]
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Genomic divergence and a lack of recent introgression between commercial and wild bumblebees (Bombus terrestris).
Kardum Hjort C, Paris JR, Olsson P, ..., Dudaniec RY, Smith HG
Evol Appl 15 (3) 365-382 [2022-03-00; online 2022-03-14]
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Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long-read metabarcoding.
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Ecol Evol 12 (3) e8676 [2022-03-00; online 2022-03-08]
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Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.
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Nat. Neurosci. 25 (3) 285-294 [2022-03-00; online 2022-02-24]
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ADAR1- and ADAR2-mediated regulation of maturation and targeting of miR-376b to modulate GABA neurotransmitter catabolism.
Widmark A, Sagredo EA, Karlström V, ..., Daniel C, Öhman M
J. Biol. Chem. 298 (3) 101682 [2022-03-00; online 2022-02-03]
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The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes.
Sturk-Andreaggi K, Ring JD, Ameur A, ..., Marshall C, Allen M
Int J Mol Sci 23 (4) - [2022-02-17; online 2022-02-17]
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Populus SVL Acts in Leaves to Modulate the Timing of Growth Cessation and Bud Set.
André D, Zambrano JA, Zhang B, ..., Marcon A, Nilsson O
Front Plant Sci 13 (-) 823019 [2022-02-17; online 2022-02-17]
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Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium.
Vickovic S, Schapiro D, Carlberg K, ..., Regev A, Ståhl PL
Commun Biol 5 (1) 129 [2022-02-11; online 2022-02-11]
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The spatial transcriptomic landscape of the healing mouse intestine following damage.
Parigi SM, Larsson L, Das S, ..., Lundeberg J, Villablanca EJ
Nat Commun 13 (1) 828 [2022-02-11; online 2022-02-11]
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Ionotropic receptors in the turnip moth Agrotis segetum respond to repellent medium-chain fatty acids.
Hou XQ, Zhang DD, Powell D, ..., Andersson MN, Löfstedt C
BMC Biol. 20 (1) 34 [2022-02-07; online 2022-02-07]
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Partial Monosomy 21 Mirrors Gene Expression of Trisomy 21 in a Patient-Derived Neuroepithelial Stem Cell Model.
Schuy J, Eisfeldt J, Pettersson M, ..., Falk A, Lindstrand A
Front Genet 12 (-) 803683 [2022-02-04; online 2022-02-04]
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Mutation analysis of disease causing genes in patients with early onset or familial forms of Alzheimer's disease and frontotemporal dementia.
Pagnon de la Vega M, Näslund C, Brundin R, ..., Ingelsson M, Giedraitis V
BMC Genomics 23 (1) 99 [2022-02-04; online 2022-02-04]
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Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow.
Le Duc D, Velluva A, Cassatt-Johnstone M, ..., Shapiro B, Schöneberg T
Sci Adv 8 (5) eabl6496 [2022-02-04; online 2022-02-04]
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PubMed DOI Crossref
The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation.
Oliver C, Annacondia ML, Wang Z, ..., Köhler C, Martinez G
Plant Cell 34 (2) 784-801 [2022-02-03; online 2021-11-11]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
CRISPR-Cas9 induces large structural variants at on-target and off-target sites in vivo that segregate across generations.
Höijer I, Emmanouilidou A, Östlund R, ..., den Hoed M, Ameur A
Nat Commun 13 (1) 627 [2022-02-02; online 2022-02-02]
Bioinformatics Compute and Storage [Service] NGI Long read [Technology development] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
PubMed DOI Crossref
Population genomics and geographic dispersal in Chagas disease vectors: Landscape drivers and evidence of possible adaptation to the domestic setting.
Hernandez-Castro LE, Villacís AG, Jacobs A, ..., Llewellyn MS, Grijalva MJ
PLoS Genet. 18 (2) e1010019 [2022-02-00; online 2022-02-04]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Links between boreal forest management, soil fungal communities and below‐ground carbon sequestration
Jörgensen K, Granath G, Strengbom J, Lindahl BD
Functional Ecology 36 (2) 392-405 [2022-02-00; online 2021-12-22]
Bioinformatics Compute and Storage [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut.
Edvardsen RB, Wallerman O, Furmanek T, ..., Norberg B, Rubin CJ
PLoS Genet. 18 (2) e1010011 [2022-02-00; online 2022-02-08]
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PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
A Verticillium longisporum pleiotropic drug transporter determines tolerance to the plant host β-pinene monoterpene.
Rafiei V, Ruffino A, Persson Hodén K, ..., Dubey M, Tzelepis G
Mol. Plant Pathol. 23 (2) 291-303 [2022-02-00; online 2021-11-26]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Standards recommendations for the Earth BioGenome Project.
Lawniczak MKN, Durbin R, Flicek P, ..., Lewin HA, Richards S
Proc. Natl. Acad. Sci. U.S.A. 119 (4) - [2022-01-25; online 2022-01-20]
NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Occasional paternal inheritance of the germline-restricted chromosome in songbirds.
Pei Y, Forstmeier W, Ruiz-Ruano FJ, ..., Suh A, Kempenaers B
Proc. Natl. Acad. Sci. U.S.A. 119 (4) - [2022-01-25; online 2022-01-22]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Massive genome inversion drives coexistence of divergent morphs in common quails.
Sanchez-Donoso I, Ravagni S, Rodríguez-Teijeiro JD, ..., Leonard JA, Vilà C
Curr. Biol. 32 (2) 462-469.e6 [2022-01-24; online 2021-11-29]
NGI Short read [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
Fish Skin Microbiomes Are Highly Variable Among Individuals and Populations but Not Within Individuals.
Berggren H, Tibblin P, Yıldırım Y, ..., Lundin D, Forsman A
Front Microbiol 12 (-) 767770 [2022-01-21; online 2022-01-21]
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PubMed DOI Crossref
Cold case: The disappearance of Egypt bee virus, a fourth distinct master strain of deformed wing virus linked to honeybee mortality in 1970's Egypt.
de Miranda JR, Brettell LE, Chejanovsky N, ..., Martin SJ, Ball BV
Virol J 19 (1) 12 [2022-01-15; online 2022-01-15]
Bioinformatics Compute and Storage [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptome Analysis of an Aedes albopictus Cell Line Single- and Dual-Infected with Lammi Virus and WNV.
Öhlund P, Delhomme N, Hayer J, Hesson JC, Blomström AL
Int J Mol Sci 23 (2) - [2022-01-14; online 2022-01-14]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Plant Growth-Promoting Activity of Pseudomonas aeruginosa FG106 and Its Ability to Act as a Biocontrol Agent against Potato, Tomato and Taro Pathogens.
Ghadamgahi F, Tarighi S, Taheri P, ..., Ortiz R, Vetukuri RR
Biology (Basel) 11 (1) - [2022-01-14; online 2022-01-14]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The formation of avian montane diversity across barriers and along elevational gradients.
Pujolar JM, Blom MPK, Reeve AH, ..., Irestedt M, Jønsson KA
Nat Commun 13 (1) 268 [2022-01-12; online 2022-01-12]
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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
Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities.
Westmeijer G, Mehrshad M, Turner S, ..., Bertilsson S, Dopson M
Commun Biol 5 (1) 37 [2022-01-11; online 2022-01-11]
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PubMed DOI Crossref
Canonical WNT signaling-dependent gating of MYC requires a noncanonical CTCF function at a distal binding site.
Chachoua I, Tzelepis I, Dai H, ..., Mehmood R, Göndör A
Nat Commun 13 (1) 204 [2022-01-11; online 2022-01-11]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Fungal Perspective of Pine and Oak Colonization in Mediterranean Degraded Ecosystems
Adamo I, Dashevskaya S, Alday JG
Forests 13 (1) 88 [2022-01-08; online 2022-01-08]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Land-use intensification differentially affects bacterial, fungal and protist communities and decreases microbiome network complexity.
Romdhane S, Spor A, Banerjee S, ..., Saghai A, Philippot L
Environ Microbiome 17 (1) 1 [2022-01-06; online 2022-01-06]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Metabolic resistance to the inhibition of mitochondrial transcription revealed by CRISPR-Cas9 screen.
Mennuni M, Filograna R, Felser A, ..., Lytovchenko O, Larsson N
EMBO Rep. 23 (1) e53054 [2022-01-05; online 2021-11-15]
CRISPR Functional Genomics [Service] NGI Short read [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Risk of Revision After Arthroplasty Associated with Specific Gene Loci: A Genomewide Association Study of Single-Nucleotide Polymorphisms in 1,130 Twins Treated with Arthroplasty.
Brüggemann A, Eriksson N, Michaëlsson K, Hailer NP
J Bone Joint Surg Am 104 (7) 610-620 [2022-01-04; online 2022-01-04]
Bioinformatics Compute and Storage [Service] NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptome sequencing of archived lymphoma specimens is feasible and clinically relevant using exome capture technology.
Skaftason A, Qu Y, Abdulla M, ..., Rosenquist R, Mansouri L
Genes Chromosomes Cancer 61 (1) 27-36 [2022-01-00; online 2021-10-23]
Clinical Genomics Uppsala [Service] NGI Short read [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]
PubMed DOI Crossref
Proteome-scale mapping of binding sites in the unstructured regions of the human proteome.
Benz C, Ali M, Krystkowiak I, ..., Davey NE, Ivarsson Y
Mol. Syst. Biol. 18 (1) e10584 [2022-01-00; online 2022-01-20]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Phytophthora infestans Ago1-associated miRNA promotes potato late blight disease.
Hu X, Persson Hodén K, Liao Z, Åsman A, Dixelius C
New Phytol. 233 (1) 443-457 [2022-01-00; online 2021-10-27]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Common, low-frequency, rare, and ultra-rare coding variants contribute to COVID-19 severity.
Fallerini C, Picchiotti N, Baldassarri M, ..., Renieri A, Furini S
Hum. Genet. 141 (1) 147-173 [2022-01-00; online 2021-12-10]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Year 2021

PubMed DOI Crossref
Biased TCR gene usage in citrullinated Tenascin C specific T-cells in rheumatoid arthritis.
Sharma RK, Boddul SV, Yoosuf N, ..., Klareskog L, Malmström V
Sci Rep 11 (1) 24512 [2021-12-31; online 2021-12-31]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Pan-AMPK activator O304 prevents gene expression changes and remobilisation of histone marks in islets of diet-induced obese mice.
López-Pérez A, Norlin S, Steneberg P, ..., Edlund H, Hörnblad A
Sci Rep 11 (1) 24410 [2021-12-23; online 2021-12-23]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Taxon-Specific Shifts in Bacterial and Archaeal Transcription of Dissolved Organic Matter Cycling Genes in a Stratified Fjord.
Pontiller B, Pérez-Martínez C, Bunse C, ..., Lundin D, Pinhassi J
mSystems 6 (6) e0057521 [2021-12-21; online 2021-12-14]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Phytoplankton settling quality has a subtle but significant effect on sediment microeukaryotic and bacterial communities.
Albert S, Hedberg P, Motwani NH, ..., Winder M, Nascimento FJA
Sci Rep 11 (1) 24033 [2021-12-15; online 2021-12-15]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A polygenic risk score predicts mosaic loss of chromosome Y in circulating blood cells.
Riaz M, Mattisson J, Polekhina G, ..., Forsberg LA, Lacaze P
Cell Biosci 11 (1) 205 [2021-12-12; online 2021-12-12]
NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
The power of genetic diversity in genome-wide association studies of lipids.
Graham SE, Clarke SL, Wu KH, ..., Sun YV, Willer CJ
Nature - (-) - [2021-12-09; online 2021-12-09]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Meta-analyses identify DNA methylation associated with kidney function and damage.
Schlosser P, Tin A, Matias-Garcia PR, ..., Köttgen A, Teumer A
Nat Commun 12 (1) 7174 [2021-12-09; online 2021-12-09]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Epigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus.
Tin A, Schlosser P, Matias-Garcia PR, ..., Teumer A, Köttgen A
Nat Commun 12 (1) 7173 [2021-12-09; online 2021-12-09]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-wide spatial expression profiling in formalin-fixed tissues.
Gracia Villacampa E, Larsson L, Mirzazadeh R, ..., Carlson J, Lundeberg J
Cell Genomics 1 (3) 100065 [2021-12-08; online 2021-12-08]
NGI Short read [Service] NGI Spatial omics [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Male-biased migration from East Africa introduced pastoralism into southern Africa.
Vicente M, Lankheet I, Russell T, ..., Jongh M, Schlebusch CM
BMC Biol. 19 (1) 259 [2021-12-07; online 2021-12-07]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The SEQC2 epigenomics quality control (EpiQC) study.
Foox J, Nordlund J, Lalancette C, ..., Deng Y, Mason CE
Genome Biol. 22 (1) 332 [2021-12-06; online 2021-12-06]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Interplay between eutrophication and climate warming on bacterial communities in coastal sediments differs depending on water depth and oxygen history.
Seidel L, Broman E, Turner S, Ståhle M, Dopson M
Sci Rep 11 (1) 23384 [2021-12-03; online 2021-12-03]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Global similarity, and some key differences, in the metagenomes of Swedish varroa-surviving and varroa-susceptible honeybees.
Thaduri S, Marupakula S, Terenius O, ..., Locke B, de Miranda JR
Sci Rep 11 (1) 23214 [2021-12-01; online 2021-12-01]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Pyramiding of scald resistance genes in four spring barley MAGIC populations.
Hautsalo J, Novakazi F, Jalli M, ..., Bengtsson T, PPP Barley Consortium
Theor. Appl. Genet. 134 (12) 3829-3843 [2021-12-00; online 2021-08-04]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Long-term agricultural management impacts arbuscular mycorrhizal fungi more than short-term experimental drought
Kozjek K, Kundel D, Kushwaha SK, ..., Birkhofer K, Hedlund K
Applied Soil Ecology 168 (-) 104140 [2021-12-00; online 2021-12-00]
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]
PubMed DOI Crossref
Historical population declines prompted significant genomic erosion in the northern and southern white rhinoceros (Ceratotherium simum).
Sánchez-Barreiro F, Gopalakrishnan S, Ramos-Madrigal J, ..., Moodley Y, Gilbert MTP
Mol. Ecol. 30 (23) 6355-6369 [2021-12-00; online 2021-07-07]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genetic variants at the RTP4/MASP1 locus are associated with fatigue in Scandinavian patients with primary Sjögren's syndrome.
Norheim KB, Imgenberg-Kreuz J, Alexsson A, ..., Ronnblom L, Omdal R
RMD Open 7 (3) - [2021-12-00; online 2021-12-16]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Expression of BCL6 in paediatric B-cell acute lymphoblastic leukaemia and association with prognosis.
Mäkinen A, Nikkilä A, Mehtonen J, ..., Paavonen T, Lohi O
Pathology 53 (7) 875-882 [2021-12-00; online 2021-05-26]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
An atlas of the Norway spruce needle seasonal transcriptome.
Bag P, Lihavainen J, Delhomme N, ..., Robinson KM, Jansson S
Plant J. 108 (6) 1815-1829 [2021-12-00; online 2021-10-21]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Dredging and deposition of metal sulfide rich river sediments results in rapid conversion to acid sulfate soil materials.
Johnson A, Högfors-Rönnholm E, Engblom S, ..., Åström M, Dopson M
Sci. Total Environ. - (-) 151864 [2021-11-23; online 2021-11-23]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Interplay between copy number alterations and immune profiles in the early breast cancer Scandinavian Breast Group 2004-1 randomized phase II trial: results from a feasibility study.
Zerdes I, Simonetti M, Matikas A, ..., Crosetto N, Foukakis T
NPJ Breast Cancer 7 (1) 144 [2021-11-19; online 2021-11-19]
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
Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae.
Schön ME, Zlatogursky VV, Singh RP, ..., Wideman JG, Burki F
Nat Commun 12 (1) 6651 [2021-11-17; online 2021-11-17]
Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Root traits and soil microorganisms as drivers of plant‐soil feedbacks within the sub‐arctic tundra meadow
Spitzer CM, Wardle DA, Lindahl BD, ..., Fanin N, Kardol P
J Ecol - (-) - [2021-11-17; online 2021-11-17]
NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comparison of EM-seq and PBAT methylome library methods for low-input DNA.
Han Y, Zheleznyakova GY, Marincevic-Zuniga Y, ..., Needhamsen M, Jagodic M
Epigenetics 17 (10) 1195-1204 [2021-11-17; online 2021-11-17]
NGI Short read [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Rare variant analysis in eczema identifies exonic variants in DUSP1, NOTCH4 and SLC9A4.
Grosche S, Marenholz I, Esparza-Gordillo J, ..., Xu C, Lee Y
Nat Commun 12 (1) 6618 [2021-11-16; online 2021-11-16]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Palmdelphin Regulates Nuclear Resilience to Mechanical Stress in the Endothelium.
Sáinz-Jaspeado M, Smith RO, Plunde O, ..., Bäck M, Claesson-Welsh L
Circulation 144 (20) 1629-1645 [2021-11-16; online 2021-10-12]
Global Proteomics and Proteogenomics [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
MapToCleave: High-throughput profiling of microRNA biogenesis in living cells.
Kang W, Fromm B, Houben AJ, ..., Biryukova I, Friedländer MR
Cell Rep 37 (7) 110015 [2021-11-16; online 2021-11-18]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Whole genome and exome sequencing reference datasets from a multi-center and cross-platform benchmark study.
Zhao Y, Fang LT, Shen T, ..., Hong H, Xiao W
Sci Data 8 (1) 296 [2021-11-09; online 2021-11-09]
NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Tracing the evolution of aneuploid cancers by multiregional sequencing with CRUST.
Chattopadhyay S, Karlsson J, Valind A, Andersson N, Gisselsson D
Brief. Bioinformatics 22 (6) - [2021-11-05; online 2021-08-04]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A common polymorphism in the dopamine transporter gene predicts working memory performance and in vivo dopamine integrity in aging.
Karalija N, Köhncke Y, Düzel S, ..., Lindenberger U, Brandmaier AM
Neuroimage 245 (-) 118707 [2021-11-03; online 2021-11-03]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
BMP2-induction of FN14 promotes protumorigenic signaling in gynecologic cancer cells.
Fukuda T, Fukuda R, Koinuma D, ..., Miyazono K, Heldin CH
Cell. Signal. 87 (-) 110146 [2021-11-00; online 2021-09-10]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Small RNA Response to Infection of the Insect-Specific Lammi Virus and Hanko Virus in an Aedes albopictus Cell Line.
Öhlund P, Hayer J, Hesson JC, Blomström AL
Viruses 13 (11) - [2021-10-29; online 2021-10-29]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Microbial Plankton Community Structure and Function Responses to Vitamin B12 and B1 Amendments in an Upwelling System.
Joglar V, Pontiller B, Martínez-García S, ..., Fernández E, Teira E
Appl. Environ. Microbiol. 87 (22) e0152521 [2021-10-28; online 2021-09-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Massive parallel sequencing in individuals with multiple primary tumours reveals the benefit of re-analysis.
Wallander K, Thonberg H, Nilsson D, Tham E
Hered Cancer Clin Pract 19 (1) 46 [2021-10-28; online 2021-10-28]
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
Human AdV-20-42-42, a Promising Novel Adenoviral Vector for Gene Therapy and Vaccine Product Development.
Ballmann MZ, Raus S, Engelhart R, ..., Havenga M, Baker AH
J. Virol. 95 (22) e0038721 [2021-10-27; online 2021-09-01]
NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Adaptive Introgression Facilitates Adaptation to High Latitudes in European Aspen (Populus tremula L.).
Rendón-Anaya M, Wilson J, Sveinsson S, ..., Street NR, Ingvarsson PK
Mol. Biol. Evol. 38 (11) 5034-5050 [2021-10-27; online 2021-07-31]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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. - (-) - [2021-10-26; online 2021-10-26]
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]
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The oral microbiota of wild bears in Sweden reflects the history of antibiotic use by humans.
Brealey JC, Leitão HG, Hofstede T, Kalthoff DC, Guschanski K
Curr. Biol. 31 (20) 4650-4658.e6 [2021-10-25; online 2021-08-25]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Milking system and premilking routines have strong effect on the microbial community in bulk tank milk.
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RNA sequencing reveals metabolic and regulatory changes leading to more robust fermentation performance during short-term adaptation of Saccharomyces cerevisiae to lignocellulosic inhibitors.
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Biotechnol Biofuels 14 (1) 201 [2021-10-15; online 2021-10-15]
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Nat Commun 12 (1) 6012 [2021-10-14; online 2021-10-14]
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Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens.
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Proc. Natl. Acad. Sci. U.S.A. 118 (41) - [2021-10-12; online 2021-10-06]
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Philippine Ayta possess the highest level of Denisovan ancestry in the world.
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HPA axis dysregulation is associated with differential methylation of CpG-sites in related genes.
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Sci Rep 11 (1) 20134 [2021-10-11; online 2021-10-11]
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Chromosome-level genome assembly and transcriptome-based annotation of the oleaginous yeast Rhodotorula toruloides CBS 14.
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Genomics 113 (6) 4022-4027 [2021-10-11; online 2021-10-11]
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Cell Death Dis 12 (10) 914 [2021-10-06; online 2021-10-06]
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Distinct B cell subsets in Peyer's patches convey probiotic effects by Limosilactobacillus reuteri.
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Microbiome 9 (1) 198 [2021-10-03; online 2021-10-03]
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The role of H3K36 methylation and associated methyltransferases in chromosome-specific gene regulation.
Lindehell H, Glotov A, Dorafshan E, Schwartz YB, Larsson J
Sci Adv 7 (40) eabh4390 [2021-10-00; online 2021-10-01]
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Pregnancy-related hormones and COMT genotype: Associations with maternal working memory.
Amiel Castro R, Kunovac Kallak T, Sundström Poromaa I, ..., Ehlert U, Skalkidou A
Psychoneuroendocrinology 132 (-) 105361 [2021-10-00; online 2021-07-17]
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Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes.
Ilumäe AM, Post H, Flores R, ..., Rootsi S, Villems R
Eur. J. Hum. Genet. 29 (10) 1510-1519 [2021-10-00; online 2021-05-07]
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Maternal genetic origin of the late and final Neolithic human populations from present-day Poland.
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Am. J. Phys. Anthropol. 176 (2) 223-236 [2021-10-00; online 2021-07-26]
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High diagnostic yield in skeletal ciliopathies using massively parallel genome sequencing, structural variant screening and RNA analyses.
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J. Hum. Genet. 66 (10) 995-1008 [2021-10-00; online 2021-04-20]
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Genome-wide association study of liver enzyme elevation in rheumatoid arthritis patients starting methotrexate.
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Pharmacogenomics 22 (15) 973-982 [2021-10-00; online 2021-09-15]
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Ecologically coherent population structure of uncultivated bacterioplankton.
Sjöqvist C, Delgado LF, Alneberg J, Andersson AF
ISME J 15 (10) 3034-3049 [2021-10-00; online 2021-05-05]
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DE-ETIOLATED1 has a role in the circadian clock of the liverwort Marchantia polymorpha.
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New Phytol. 232 (2) 595-609 [2021-10-00; online 2021-08-19]
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ZBED6 regulates Igf2 expression partially through its regulation of miR483 expression.
Naboulsi R, Larsson M, Andersson L, Younis S
Sci Rep 11 (1) 19484 [2021-09-30; online 2021-09-30]
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In-depth Phylogenomic Analysis of Arbuscular Mycorrhizal Fungi Based on a Comprehensive Set of de novo Genome Assemblies
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Composition and Seasonality of Membrane Transporters in Marine Picoplankton.
Hagström Å, Zweifel UL, Sundh J, ..., Müller-Karulis B, Pinhassi J
Front Microbiol 12 (-) 714732 [2021-09-28; online 2021-09-28]
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Saturation mutagenesis charts the functional landscape of Salmonella ProQ and reveals a gene regulatory function of its C-terminal domain.
Rizvanovic A, Kjellin J, Söderbom F, Holmqvist E
Nucleic Acids Res. 49 (17) 9992-10006 [2021-09-27; online 2021-08-28]
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Comparison of DNA and RNA sequencing of total nucleic acids from human cervix for metagenomics.
Arroyo Mühr LS, Dillner J, Ure AE, Sundström K, Hultin E
Sci Rep 11 (1) 18852 [2021-09-22; online 2021-09-22]
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Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration.
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Mol. Biol. Evol. 38 (12) 5275-5291 [2021-09-20; online 2021-09-20]
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Single-Cell Analysis Reveals Major Histocompatibility Complex II‒Expressing Keratinocytes in Pressure Ulcers with Worse Healing Outcomes.
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J. Invest. Dermatol. - (-) - [2021-09-16; online 2021-09-16]
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Ancient and modern genomes unravel the evolutionary history of the rhinoceros family.
Liu S, Westbury MV, Dussex N, ..., Dalén L, Gilbert MTP
Cell 184 (19) 4874-4885.e16 [2021-09-16; online 2021-08-24]
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Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens.
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BMC Genomics 22 (1) 660 [2021-09-14; online 2021-09-14]
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The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities.
Peona V, Palacios-Gimenez OM, Blommaert J, ..., Jern P, Suh A
Philos. Trans. R. Soc. Lond., B, Biol. Sci. 376 (1833) 20200186 [2021-09-13; online 2021-07-26]
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A highly-contiguous genome assembly of the Eurasian spruce bark beetle, Ips typographus, provides insight into a major forest pest.
Powell D, Groβe-Wilde E, Krokene P, ..., Andersson MN, Schlyter F
Commun Biol 4 (1) 1059 [2021-09-09; online 2021-09-09]
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Temporally balanced selection during development of larval Pacific oysters (Crassostrea gigas) inherently preserves genetic diversity within offspring.
Durland E, De Wit P, Langdon C
Proc. Biol. Sci. 288 (1958) 20203223 [2021-09-08; online 2021-09-01]
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Selection on accessible chromatin regions in Capsella grandiflora.
Horvath R, Josephs EB, Pesquet E, ..., Scofield D, Slotte T
Mol. Biol. Evol. - (-) - [2021-09-08; online 2021-09-08]
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Spatial mapping reveals human adipocyte subpopulations with distinct sensitivities to insulin.
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Cell Metab. 33 (9) 1869-1882.e6 [2021-09-07; online 2021-08-10]
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Single-nuclei transcriptomes from human adrenal gland reveal distinct cellular identities of low and high-risk neuroblastoma tumors.
Bedoya-Reina OC, Li W, Arceo M, ..., Kogner P, Schlisio S
Nat Commun 12 (1) 5309 [2021-09-07; online 2021-09-07]
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The genomics of heart failure: design and rationale of the HERMES consortium.
Lumbers RT, Shah S, Lin H, ..., Vasan RS, Smith JG
ESC Heart Failure - (-) - [2021-09-03; online 2021-09-03]
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Stop codon readthrough alters the activity of a POU/Oct transcription factor during Drosophila development.
Zhao Y, Lindberg BG, Esfahani SS, ..., Piazza S, Engström Y
BMC Biol. 19 (1) 185 [2021-09-03; online 2021-09-03]
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Toward best practice in cancer mutation detection with whole-genome and whole-exome sequencing.
Xiao W, Ren L, Chen Z, ..., Wang C, Shi L
Nat. Biotechnol. 39 (9) 1141-1150 [2021-09-00; online 2021-09-09]
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The microRNA response associated with methyl jasmonate-induced resistance in Norway spruce bark
Wilkinson SW, Vivian-Smith A, Krokene P, Mageroy MH
Plant Gene 27 (-) 100301 [2021-09-00; online 2021-09-00]
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The genetic consequences of dog breed formation-Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels.
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PLoS Genet. 17 (9) e1009726 [2021-09-00; online 2021-09-02]
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Soil physico-chemical properties have a greater effect on soil fungi than host species in Mediterranean pure and mixed pine forests
Adamo I, Castaño C, Bonet JA, ..., Martínez de Aragón J, Alday JG
Soil Biology and Biochemistry 160 (-) 108320 [2021-09-00; online 2021-09-00]
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Reindeer control over subarctic treeline alters soil fungal communities with potential consequences for soil carbon storage.
Ylänne H, Madsen RL, Castaño C, Metcalfe DB, Clemmensen KE
Glob Chang Biol 27 (18) 4254-4268 [2021-09-00; online 2021-06-14]
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Regulatory T cells reduce endothelial neutral sphingomyelinase 2 to prevent T-cell migration into tumors.
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Eur. J. Immunol. 51 (9) 2317-2329 [2021-09-00; online 2021-07-29]
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Positive selection plays a major role in shaping signatures of differentiation across the genomic landscape of two independent Ficedula flycatcher species pairs.
Chase MA, Ellegren H, Mugal CF
Evolution 75 (9) 2179-2196 [2021-09-00; online 2021-05-03]
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Novel genome reveals susceptibility of popular gamebird, the red-legged partridge (Alectoris rufa, Phasianidae), to climate change.
Chattopadhyay B, Forcina G, Garg KM, ..., Barbanera F, Rheindt FE
Genomics 113 (5) 3430-3438 [2021-09-00; online 2021-08-13]
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Interaction between the STAT4 rs11889341(T) risk allele and smoking confers increased risk of myocardial infarction and nephritis in patients with systemic lupus erythematosus.
Reid S, Hagberg N, Sandling JK, ..., Rönnblom L, Leonard D
Ann. Rheum. Dis. 80 (9) 1183-1189 [2021-09-00; online 2021-03-25]
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Establishing community reference samples, data and call sets for benchmarking cancer mutation detection using whole-genome sequencing.
Fang LT, Zhu B, Zhao Y, ..., Xiao W, Somatic Mutation Working Group of Sequencing Quality Control Phase II Consortium
Nat. Biotechnol. 39 (9) 1151-1160 [2021-09-00; online 2021-09-09]
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Climate warming dominates over plant genotype in shaping the seasonal trajectory of foliar fungal communities on oak.
Faticov M, Abdelfattah A, Roslin T, ..., Lindahl BD, Tack AJM
New Phytol. 231 (5) 1770-1783 [2021-09-00; online 2021-06-18]
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A genome-wide association study with 1,126,563 individuals identifies new risk loci for Alzheimer's disease.
Wightman DP, Jansen IE, Savage JE, ..., Andreassen OA, Posthuma D
Nat. Genet. 53 (9) 1276-1282 [2021-09-00; online 2021-09-07]
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A genome-wide association study of the frailty index highlights brain pathways in ageing.
Atkins JL, Jylhävä J, Pedersen NL, ..., Williams DM, Pilling LC
Aging Cell 20 (9) e13459 [2021-09-00; online 2021-08-25]
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Exploring the β-tubulin gene family in a benzimidazole-resistant Parascaris univalens population.
Martin F, Halvarsson P, Delhomme N, Höglund J, Tydén E
International Journal for Parasitology: Drugs and Drug Resistance 17 (-) 84-91 [2021-08-26; online 2021-08-26]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Consistent B Cell Receptor Immunoglobulin Features Between Siblings in Familial Chronic Lymphocytic Leukemia.
Kolijn PM, Muggen AF, Ljungström V, ..., Rosenquist R, Langerak AW
Front Oncol 11 (-) 740083 [2021-08-26; online 2021-08-26]
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Chromoanagenesis Event Underlies a de novo Pericentric and Multiple Paracentric Inversions in a Single Chromosome Causing Coffin-Siris Syndrome.
Grochowski CM, Krepischi ACV, Eisfeldt J, ..., Lindstrand A, Carvalho CMB
Front Genet 12 (-) 708348 [2021-08-26; online 2021-08-26]
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Amnion signals are essential for mesoderm formation in primates.
Yang R, Goedel A, Kang Y, ..., Niu Y, Chien KR
Nat Commun 12 (1) 5126 [2021-08-26; online 2021-08-26]
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Small-scale sequencing enables quality assessment of Ribo-Seq data: an example from Arabidopsis cell culture.
Mahboubi A, Delhomme N, Häggström S, Hanson J
Plant Methods 17 (1) 92 [2021-08-24; online 2021-08-24]
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Ecological Specialization and Evolutionary Reticulation in Extant Hyaenidae.
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Mol. Biol. Evol. 38 (9) 3884-3897 [2021-08-23; online 2021-08-25]
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Community composition of aquatic fungi across the thawing Arctic.
Kluge M, Wurzbacher C, Wauthy M, ..., Stenlid J, Peura S
Sci Data 8 (1) 221 [2021-08-19; online 2021-08-19]
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Haplotype-Specific Expression Analysis of MHC Class II Genes in Healthy Individuals and Rheumatoid Arthritis Patients.
Houtman M, Hesselberg E, Rönnblom L, ..., Malmström V, Padyukov L
Front Immunol 12 (-) 707217 [2021-08-17; online 2021-08-17]
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Association of Variants Near the Bradykinin Receptor B2 Gene With Angioedema in Patients Taking ACE Inhibitors.
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J. Am. Coll. Cardiol. 78 (7) 696-709 [2021-08-17; online 2021-08-14]
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Microbiological Surveillance of Biogas Plants: Targeting Acetogenic Community.
Singh A, Moestedt J, Berg A, Schnürer A
Front Microbiol 12 (-) 700256 [2021-08-16; online 2021-08-16]
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Characterization of Dynamic Regulatory Gene and Protein Networks in Wheat Roots Upon Perceiving Water Deficit Through Comparative Transcriptomics Survey.
Rahimi Y, Ingvarsson PK, Bihamta MR, ..., Taleei A, Khoshnoodi Jabar Abadi S
Front Plant Sci 12 (-) 710867 [2021-08-16; online 2021-08-16]
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Transcriptome Analysis of Post-Mortem Brain Tissue Reveals Up-Regulation of the Complement Cascade in a Subgroup of Schizophrenia Patients.
Lindholm Carlström E, Niazi A, Etemadikhah M, ..., Nilsson B, Feuk L
Genes 12 (8) - [2021-08-13; online 2021-08-13]
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Site-Dependent Relationships Between Fungal Community Composition, Plant Genotypic Diversity and Environmental Drivers in a Salix Biomass System
Hoeber S, Baum C, Weih M, Manzoni S, Fransson P
Front. Fungal Biol. 2 (-) - [2021-08-13; online 2021-08-13]
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Single-cell analysis pinpoints distinct populations of cytotoxic CD4+ T cells and an IL-10+CD109+ TH2 cell population in nasal polyps.
Ma J, Tibbitt CA, Georén SK, ..., Bachert C, Coquet JM
Sci Immunol 6 (62) - [2021-08-13; online 2021-08-15]
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Candidatus Methylumidiphilus Drives Peaks in Methanotrophic Relative Abundance in Stratified Lakes and Ponds Across Northern Landscapes.
Martin G, Rissanen AJ, Garcia SL, ..., Buck M, Peura S
Front Microbiol 12 (-) 669937 [2021-08-12; online 2021-08-12]
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Diffusible signal factor signaling controls bioleaching activity and niche protection in the acidophilic, mineral-oxidizing leptospirilli.
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Sci Rep 11 (1) 16275 [2021-08-11; online 2021-08-11]
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Mutational patterns and clonal evolution from diagnosis to relapse in pediatric acute lymphoblastic leukemia.
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Complete Genome Sequence and Methylome of the Type Strain of Shewanella algae.
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Single-cell multimodal analysis in a case with reduced penetrance of Progranulin-Frontotemporal Dementia.
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PopulusPtERF85 Balances Xylem Cell Expansion and Secondary Cell Wall Formation in Hybrid Aspen.
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Genome-wide estrogen receptor β chromatin binding in human colon cancer cells reveals its tumor suppressor activity.
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Int. J. Cancer 149 (3) 692-706 [2021-08-01; online 2021-04-05]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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The exon-junction complex helicase eIF4A3 controls cell fate via coordinated regulation of ribosome biogenesis and translational output.
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Terrestrial dissolved organic matter inflow drives temporal dynamics of the bacterial community of a subarctic estuary (northern Baltic Sea).
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Environ. Microbiol. 23 (8) 4200-4213 [2021-08-00; online 2021-06-01]
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SFRP2 induces a mesenchymal subtype transition by suppression of SOX2 in glioblastoma.
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Oncogene 40 (32) 5066-5080 [2021-08-00; online 2021-05-21]
Global Proteomics and Proteogenomics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Molecular architecture of the developing mouse brain.
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Nature 596 (7870) 92-96 [2021-08-00; online 2021-07-28]
In Situ Sequencing (ISS) [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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Long- and short-read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities.
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Mol Ecol Resour 21 (6) 1833-1849 [2021-08-00; online 2021-05-06]
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Genomic inference of contemporary effective population size in a large island population of collared flycatchers (Ficedula albicollis).
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Mol. Ecol. 30 (16) 3965-3973 [2021-08-00; online 2021-07-01]
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Genetic insights into biological mechanisms governing human ovarian ageing.
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Nature 596 (7872) 393-397 [2021-08-00; online 2021-08-04]
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Dynamics of Baltic Sea phages driven by environmental changes.
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Genetic association study of childhood aggression across raters, instruments, and age.
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Genetic Barriers to Historical Gene Flow between Cryptic Species of Alpine Bumblebees Revealed by Comparative Population Genomics.
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Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure
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Complex population structure of the Atlantic puffin revealed by whole genome analyses.
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Commun Biol 4 (1) 922 [2021-07-29; online 2021-07-29]
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Unraveling negative biotic interactions determining soil microbial community assembly and functioning.
Romdhane S, Spor A, Aubert J, ..., Tsiknia M, Philippot L
ISME J - (-) - [2021-07-28; online 2021-07-28]
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Single-cell analysis of mosquito hemocytes identifies signatures of immune cell subtypes and cell differentiation.
Kwon H, Mohammed M, Franzén O, Ankarklev J, Smith RC
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Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99.
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Sci Rep 11 (1) 15160 [2021-07-26; online 2021-07-26]
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Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe.
Svensson E, Günther T, Hoischen A, ..., Netea MG, Jakobsson M
Curr. Biol. 31 (14) 2973-2983.e9 [2021-07-26; online 2021-05-18]
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Bifidobacteria-mediated immune system imprinting early in life.
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Cell 184 (15) 3884-3898.e11 [2021-07-22; online 2021-06-17]
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DNA Methylation-Based Interferon Scores Associate With Sub-Phenotypes in Primary Sjögren's Syndrome.
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Energy efficiency and biological interactions define the core microbiome of deep oligotrophic groundwater.
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Single-cell RNAseq and longitudinal proteomic analysis of a novel semi-spontaneous urothelial cancer model reveals tumor cell heterogeneity and pretumoral urine protein alterations.
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Genomic Predictions With Nonadditive Effects Improved Estimates of Additive Effects and Predictions of Total Genetic Values in Pinus sylvestris.
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Common and mutation specific phenotypes of KRAS and BRAF mutations in colorectal cancer cells revealed by integrative -omics analysis.
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High-Quality Genome Assembly and Comprehensive Transcriptome of the Painted Lady Butterfly Vanessa cardui.
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Candidate regulators and target genes of drought stress in needles and roots of Norway spruce.
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BMC Genomics 22 (1) 503 [2021-07-04; online 2021-07-04]
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Gene Regulatory Network of Human GM-CSF-Secreting T Helper Cells.
Éliás S, Schmidt A, Gomez-Cabrero D, Tegnér J
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Whole genome sequencing reveals high differentiation, low levels of genetic diversity and short runs of homozygosity among Swedish wels catfish.
Jensen A, Lillie M, Bergström K, Larsson P, Höglund J
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Variants in BANK1 are associated with lupus nephritis of European ancestry.
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Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues.
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Quality of phytoplankton deposition structures bacterial communities at the water-sediment interface.
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On the origin of the widespread self-compatible allotetraploid Capsella bursa-pastoris (Brassicaceae).
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Heredity (Edinb) 127 (1) 124-134 [2021-07-00; online 2021-04-19]
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Mammuthus sp. (Early and Middle Pleistocene Mammoths).
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Trends Genet. 37 (7) 682-683 [2021-07-00; online 2021-05-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Insights into the multitrophic interactions between the biocontrol agent Bacillus subtilis MBI 600, the pathogen Botrytis cinerea and their plant host.
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Microbiol Res 248 (-) 126752 [2021-07-00; online 2021-04-02]
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High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient.
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Genomic signatures of rapid adaptive divergence in a tropical montane species.
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FGFR1 overexpression in non-small cell lung cancer is mediated by genetic and epigenetic mechanisms and is a determinant of FGFR1 inhibitor response.
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Eur. J. Cancer 151 (-) 136-149 [2021-07-00; online 2021-05-10]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Extreme Y chromosome polymorphism corresponds to five male reproductive morphs of a freshwater fish.
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A group of ectomycorrhizal fungi restricts organic matter accumulation in boreal forest.
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Towards Bioleaching of a Vanadium Containing Magnetite for Metal Recovery.
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Front Microbiol 12 (-) 693615 [2021-06-30; online 2021-06-30]
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DNA metabarcoding reveals trophic niche diversity of micro and mesozooplankton species.
Novotny A, Zamora-Terol S, Winder M
Proc. Biol. Sci. 288 (1953) 20210908 [2021-06-30; online 2021-06-16]
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Combined prenatal Lactobacillus reuteri and ω-3 supplementation synergistically modulates DNA methylation in neonatal T helper cells.
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Clin Epigenetics 13 (1) 135 [2021-06-30; online 2021-06-30]
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Genome-wide association studies identify 137 genetic loci for DNA methylation biomarkers of aging.
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A multi-ethnic epigenome-wide association study of leukocyte DNA methylation and blood lipids.
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Nat Commun 12 (1) 3987 [2021-06-28; online 2021-06-28]
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Functional differences between TSHR alleles associate with variation in spawning season in Atlantic herring.
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Commun Biol 4 (1) 795 [2021-06-25; online 2021-06-25]
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Toll-like receptor 4 methylation grade is linked to depressive symptom severity.
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Transl Psychiatry 11 (1) 371 [2021-06-24; online 2021-06-24]
Affinity Proteomics Uppsala [Service] 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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Profiling temporal dynamics of acetogenic communities in anaerobic digesters using next-generation sequencing and T-RFLP.
Singh A, Müller B, Schnürer A
Sci Rep 11 (1) 13298 [2021-06-24; online 2021-06-24]
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COVseq is a cost-effective workflow for mass-scale SARS-CoV-2 genomic surveillance.
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Nat Commun 12 (1) 3903 [2021-06-23; online 2021-06-23]
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The γ-tubulin meshwork assists in the recruitment of PCNA to chromatin in mammalian cells.
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Commun Biol 4 (1) 767 [2021-06-22; online 2021-06-22]
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Development of a PacBio Long-Read Sequencing Assay for High Throughput Detection of Fungicide Resistance in Zymoseptoria tritici.
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Front Microbiol 12 (-) 692845 [2021-06-18; online 2021-06-18]
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Differential DNA Methylation of the Genes for Amyloid Precursor Protein, Tau, and Neurofilaments in Human Traumatic Brain Injury.
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Differences in the genome, methylome, and transcriptome do not differentiate isolates of Streptococcus equi subsp. equi from horses with acute clinical signs from isolates of inapparent carriers.
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PLoS ONE 16 (6) e0252804 [2021-06-14; online 2021-06-14]
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Leveraging breeding programs and genomic data in Norway spruce (Picea abies L. Karst) for GWAS analysis.
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Genome Biol. 22 (1) 179 [2021-06-13; online 2021-06-13]
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DNA Methylation Signatures Predict Cytogenetic Subtype and Outcome in Pediatric Acute Myeloid Leukemia (AML).
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Genes 12 (6) 895 [2021-06-10; online 2021-06-10]
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Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes.
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Reinforcing one-carbon metabolism via folic acid/Folr1 promotes β-cell differentiation.
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Nat Commun 12 (1) 3362 [2021-06-07; online 2021-06-07]
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Common variants in Alzheimer's disease and risk stratification by polygenic risk scores.
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Nat Commun 12 (1) 3417 [2021-06-07; online 2021-06-07]
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Low Energy Electron Irradiation Is a Potent Alternative to Gamma Irradiation for the Inactivation of (CAR-)NK-92 Cells in ATMP Manufacturing.
Walcher L, Kistenmacher AK, Sommer C, ..., Dünkel A, Fricke S
Front Immunol 12 (-) 684052 [2021-06-04; online 2021-06-04]
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Atg7 deficiency in microglia drives an altered transcriptomic profile associated with an impaired neuroinflammatory response.
Friess L, Cheray M, Keane L, Grabert K, Joseph B
Mol Brain 14 (1) 87 [2021-06-03; online 2021-06-03]
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RNA atlas of human bacterial pathogens uncovers stress dynamics linked to infection.
Avican K, Aldahdooh J, Togninalli M, ..., Rhen M, Fällman M
Nat Commun 12 (1) 3282 [2021-06-02; online 2021-06-02]
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Gene count from target sequence capture places three whole genome duplication events in Hibiscus L. (Malvaceae).
Eriksson JS, Bacon CD, Bennett DJ, ..., Oxelman B, Antonelli A
BMC Ecol Evol 21 (1) 107 [2021-06-02; online 2021-06-02]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Variation in the SERPINA6/SERPINA1 locus alters morning plasma cortisol, hepatic corticosteroid binding globulin expression, gene expression in peripheral tissues, and risk of cardiovascular disease.
Crawford AA, Bankier S, Altmaier E, ..., Walker BR, CORtisol NETwork (CORNET) consortium
J. Hum. Genet. 66 (6) 625-636 [2021-06-00; online 2021-01-20]
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The trans-ancestral genomic architecture of glycemic traits.
Chen J, Spracklen CN, Marenne G, ..., Barroso I, Meta-Analysis of Glucose and Insulin-related Traits Consortium (MAGIC)
Nat. Genet. 53 (6) 840-860 [2021-06-00; online 2021-05-31]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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RAG1 co-expression signature identifies ETV6-RUNX1-like B-cell precursor acute lymphoblastic leukemia in children.
Chen D, Camponeschi A, Nordlund J, ..., Fogelstrand L, Mårtensson IL
Cancer Med 10 (12) 3997-4003 [2021-06-00; online 2021-05-13]
NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
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Methylome and transcriptome signature of bronchoalveolar cells from multiple sclerosis patients in relation to smoking.
Ringh MV, Hagemann-Jensen M, Needhamsen M, ..., Öckinger J, Kular L
Mult. Scler. 27 (7) 1014-1026 [2021-06-00; online 2020-07-30]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Genomic and fitness consequences of inbreeding in an endangered carnivore.
Hasselgren M, Dussex N, von Seth J, ..., Dalén L, Norén K
Mol. Ecol. 30 (12) 2790-2799 [2021-06-00; online 2021-05-20]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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
Gene-educational attainment interactions in a multi-ancestry genome-wide meta-analysis identify novel blood pressure loci.
de Las Fuentes L, Sung YJ, Noordam R, ..., Rao DC, Fornage M
Mol. Psychiatry 26 (6) 2111-2125 [2021-06-00; online 2020-05-05]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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DNA methylation signatures of aggression and closely related constructs: A meta-analysis of epigenome-wide studies across the lifespan.
van Dongen J, Hagenbeek FA, Suderman M, ..., Bartels M, Boomsma DI
Mol. Psychiatry 26 (6) 2148-2162 [2021-06-00; online 2021-01-08]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives.
Bohutínská M, Vlček J, Yair S, ..., Slotte T, Kolář F
Proc. Natl. Acad. Sci. U.S.A. 118 (21) - [2021-05-25; online 2021-05-19]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Divergent clonal differentiation trajectories establish CD8+ memory T cell heterogeneity during acute viral infections in humans.
Mold JE, Modolo L, Hård J, ..., Michaëlsson J, Frisén J
Cell Rep 35 (8) 109174 [2021-05-25; online 2021-05-27]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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]
Affinity Proteomics Uppsala [Technology development] 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
Size Variation of the Nonrecombining Region on the Mating-Type Chromosomes in the Fungal Podospora anserina Species Complex.
Hartmann FE, Ament-Velásquez SL, Vogan AA, ..., Silar P, Giraud T
Mol. Biol. Evol. 38 (6) 2475-2492 [2021-05-19; online 2021-02-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Phage Biocontrol of Pseudomonas aeruginosa in Water.
Kauppinen A, Siponen S, Pitkänen T, ..., Torvinen E, Miettinen IT
Viruses 13 (5) 928 [2021-05-17; online 2021-05-17]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds.
Buck M, Garcia SL, Fernandez L, ..., Bertilsson S, Peura S
Sci Data 8 (1) 131 [2021-05-14; online 2021-05-14]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Ultralow amounts of DNA from long-term archived serum samples produce high-quality methylomes.
Wojewodzic MW, Leithaug M, Lauritzen M, ..., Grotmol T, Rounge TB
Clin Epigenetics 13 (1) 107 [2021-05-12; online 2021-05-12]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Progesterone Dampens Immune Responses in In Vitro Activated CD4+ T Cells and Affects Genes Associated With Autoimmune Diseases That Improve During Pregnancy.
Hellberg S, Raffetseder J, Rundquist O, ..., Ernerudh J, Gustafsson M
Front Immunol 12 (-) 672168 [2021-05-12; online 2021-05-12]
Affinity Proteomics Uppsala [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations.
Garcia SL, Mehrshad M, Buck M, ..., Greening C, Peura S
mSystems 6 (3) - [2021-05-11; online 2021-05-11]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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African and Asian leopards are highly differentiated at the genomic level.
Paijmans JLA, Barlow A, Becker MS, ..., Manica A, Hofreiter M
Curr. Biol. 31 (9) 1872-1882.e5 [2021-05-10; online 2021-04-12]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The Genetic Variation of Lactase Persistence Alleles in Sudan and South Sudan.
Hollfelder N, Babiker H, Granehäll L, Schlebusch CM, Jakobsson M
Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-25]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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
INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues of Arabidopsis.
Yadav VK, Santos-González J, Köhler C
Nucleic Acids Res. 49 (8) 4371-4385 [2021-05-07; online 2021-03-22]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genetically determined NLRP3 inflammasome activation associates with systemic inflammation and cardiovascular mortality.
Schunk SJ, Kleber ME, März W, ..., eQTLGen consortium , BIOS consortium
Eur. Heart J. 42 (18) 1742-1756 [2021-05-07; online 2021-03-23]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Chromosome Level Assembly of the Comma Butterfly (Polygonia c-album).
Celorio-Mancera MP, Rastas P, Steward RA, Nylin S, Wheat CW
Genome Biol Evol 13 (5) - [2021-05-07; online 2021-03-23]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed 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. 38 (5) 1715-1730 [2021-05-04; online 2020-11-11]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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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]
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) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
The association between genetically determined ABO blood types and major depressive disorder.
Garvert L, Baune BT, Berger K, ..., Grabe HJ, Van der Auwera S
Psychiatry Res 299 (-) 113837 [2021-05-00; online 2021-02-24]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The Enterprise, a massive transposon carrying Spok meiotic drive genes.
Vogan AA, Ament-Velásquez SL, Bastiaans E, ..., Suh A, Johannesson H
Genome Res. 31 (5) 789-798 [2021-05-00; online 2021-04-19]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Novel form of rhizomelic skeletal dysplasia associated with a homozygous variant in GNPNAT1.
Ain NU, Baroncelli M, Costantini A, ..., Mäkitie O, Naz S
J. Med. Genet. 58 (5) 351-356 [2021-05-00; online 2020-06-26]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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
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
Hum. Genet. 140 (5) 775-790 [2021-05-00; online 2020-12-14]
Bioinformatics Compute and Storage [Service] NGI Long read [Collaborative] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genetic basis of lacunar stroke: a pooled analysis of individual patient data and genome-wide association studies.
Traylor M, Persyn E, Tomppo L, ..., UK DNA Lacunar Stroke Study Investigators , International Stroke Genetics Consortium
Lancet Neurol 20 (5) 351-361 [2021-05-00; online 2021-03-25]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Dual RNA-Seq transcriptome analysis of chicken macrophage-like cells (HD11) infected in vitro with Eimeria tenella.
Sandholt AKS, Xu F, Söderlund R, ..., Svärd SG, Wattrang E
Parasitology 148 (6) 712-725 [2021-05-00; online 2021-02-04]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Cyanophage Diversity and Community Structure in Dead Zone Sediments.
Broman E, Holmfeldt K, Bonaglia S, Hall POJ, Nascimento FJA
mSphere 6 (2) - [2021-04-28; online 2021-04-28]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
An introgressed gene causes meiotic drive in Neurospora sitophila.
Svedberg J, Vogan AA, Rhoades NA, ..., Hammond TM, Johannesson H
Proc. Natl. Acad. Sci. U.S.A. 118 (17) e2026605118 [2021-04-27; online 2021-04-21]
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
Middle Pleistocene genome calibrates a revised evolutionary history of extinct cave bears.
Barlow A, Paijmans JLA, Alberti F, ..., Baryshnikov G, Hofreiter M
Curr. Biol. 31 (8) 1771-1779.e7 [2021-04-26; online 2021-02-15]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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
Functional Diversity Facilitates Stability Under Environmental Changes in an Outdoor Microalgal Cultivation System.
Mattsson L, Sörenson E, Capo E, ..., Lindehoff E, Legrand C
Front Bioeng Biotechnol 9 (-) 651895 [2021-04-22; online 2021-04-22]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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Epigenome-wide association study of level and change in cognitive abilities from midlife through late life.
Karlsson IK, Ericsson M, Wang Y, ..., Reynolds CA, Pedersen NL
Clin Epigenetics 13 (1) 85 [2021-04-21; online 2021-04-21]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
smartPARE: An R Package for Efficient Identification of True mRNA Cleavage Sites.
Persson Hodén K, Hu X, Martinez G, Dixelius C
Int J Mol Sci 22 (8) 4267 [2021-04-20; online 2021-04-20]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Active DNRA and denitrification in oxic hypereutrophic waters.
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Water Res. 194 (-) 116954 [2021-04-15; online 2021-02-21]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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A spinal organ of proprioception for integrated motor action feedback.
Picton LD, Bertuzzi M, Pallucchi I, ..., Shearing PR, El Manira A
Neuron 109 (7) 1188-1201.e7 [2021-04-07; online 2021-02-11]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Monoallelic and bi-allelic variants in NCDN cause neurodevelopmental delay, intellectual disability, and epilepsy.
Fatima A, Hoeber J, Schuster J, ..., Klar J, Dahl N
Am. J. Hum. Genet. 108 (4) 739-748 [2021-04-01; online 2021-03-11]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The heart microbiome of insectivorous bats from Central and South Eastern Europe.
Corduneanu A, Mihalca AD, Sándor AD, ..., Viso NP, Bongcam-Rudloff E
Comp Immunol Microbiol Infect Dis 75 (-) 101605 [2021-04-00; online 2021-01-07]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The effects of drift and selection on latitudinal genetic variation in Scandinavian common toads (Bufo bufo) following postglacial recolonisation.
Thörn F, Rödin-Mörch P, Cortazar-Chinarro M, ..., Laurila A, Höglund J
Heredity (Edinb) 126 (4) 656-667 [2021-04-00; online 2021-02-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Severe congenital lactic acidosis and hypertrophic cardiomyopathy caused by an intronic variant in NDUFB7.
Correia SP, Moedas MF, Naess K, ..., Wedell A, Wredenberg A
Hum. Mutat. 42 (4) 378-384 [2021-04-00; online 2021-02-04]
Clinical Genomics Stockholm [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
PD-L1 and IDO1 are potential targets for treatment in patients with primary diffuse large B-cell lymphoma of the CNS.
Abdulla M, Alexsson A, Sundström C, ..., Hollander P, Amini R
Acta Oncol 60 (4) 531-538 [2021-04-00; online 2021-02-12]
Clinical Genomics Uppsala [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Novel Mutation m.10372A>G in MT-ND3 Causing Sensorimotor Axonal Polyneuropathy.
Bruhn H, Samuelsson K, Schober FA, ..., Wedell A, Wredenberg A
Neurol Genet 7 (2) e566 [2021-04-00; online 2021-03-15]
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
Meta-analysis uncovers genome-wide significant variants for rapid kidney function decline.
Gorski M, Jung B, Li Y, ..., Pattaro C, Heid IM
Kidney Int. 99 (4) 926-939 [2021-04-00; online 2020-10-31]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Life-Time Covariation of Major Cardiovascular Diseases: A 40-Year Longitudinal Study and Genetic Studies.
Lind L, Sundström J, Ärnlöv J, ..., Lumbers RT, Lampa E
Circ Genom Precis Med 14 (2) e002963 [2021-04-00; online 2021-02-26]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Later Stone Age human hair from Vaalkrans Shelter, Cape Floristic Region of South Africa, reveals genetic affinity to Khoe groups.
Coutinho A, Malmström H, Edlund H, ..., Schlebusch CM, Jakobsson M
Am. J. Phys. Anthropol. 174 (4) 701-713 [2021-04-00; online 2021-02-04]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Immune cells lacking Y chromosome show dysregulation of autosomal gene expression.
Dumanski JP, Halvardson J, Davies H, ..., Ryś J, Forsberg LA
Cell. Mol. Life Sci. 78 (8) 4019-4033 [2021-04-00; online 2021-04-10]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root.
Abdelfattah A, Wisniewski M, Schena L, Tack AJM
Environ. Microbiol. 23 (4) 2199-2214 [2021-04-00; online 2021-01-21]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species.
Bernhardsson C, Zan Y, Chen Z, Ingvarsson PK, Wu HX
Mol Ecol Resour 21 (3) 880-896 [2021-04-00; online 2020-12-02]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The evolution of ancestral and species-specific adaptations in snowfinches at the Qinghai-Tibet Plateau.
Qu Y, Chen C, Chen X, ..., Zhang YE, Lei F
Proc. Natl. Acad. Sci. U.S.A. 118 (13) e2012398118 [2021-03-30; online 2021-03-24]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Multiple migrations to the Philippines during the last 50,000 years.
Larena M, Sanchez-Quinto F, Sjödin P, ..., Endicott P, Jakobsson M
Proc. Natl. Acad. Sci. U.S.A. 118 (13) - [2021-03-30; online 2021-03-24]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Estrogen Receptor Beta Influences the Inflammatory p65 Cistrome in Colon Cancer Cells.
Indukuri R, Hases L, Archer A, Williams C
Front Endocrinol (Lausanne) 12 (-) 650625 [2021-03-30; online 2021-03-30]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr (Salvelinus alpinus).
Pappas F, Palaiokostas C
Animals (Basel) 11 (3) - [2021-03-21; online 2021-03-21]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
PRDM16 regulates a temporal transcriptional program to promote progression of cortical neural progenitors.
He L, Jones J, He W, ..., Wen J, Dai Q
Development 148 (6) - [2021-03-17; online 2021-03-17]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager.
Fellows Yates JA, Lamnidis TC, Borry M, ..., Neukamm J, Peltzer A
PeerJ 9 (-) e10947 [2021-03-16; online 2021-03-16]
NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Expansions of adaptive-like NK cells with a tissue-resident phenotype in human lung and blood.
Brownlie D, Scharenberg M, Mold JE, ..., Marquardt N, Michaëlsson J
Proc. Natl. Acad. Sci. U.S.A. 118 (11) e2016580118 [2021-03-16; online 2021-04-11]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Transcriptional analysis of islets of Langerhans from organ donors of different ages.
Seiron P, Stenwall A, Hedin A, ..., Lundberg M, Skog O
PLoS ONE 16 (3) e0247888 [2021-03-12; online 2021-03-12]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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The Fennoscandian Shield deep terrestrial virosphere suggests slow motion 'boom and burst' cycles.
Holmfeldt K, Nilsson E, Simone D, ..., Bertilsson S, Dopson M
Commun Biol 4 (1) 307 [2021-03-08; online 2021-03-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Single cell transcriptomics of primate sensory neurons identifies cell types associated with chronic pain.
Kupari J, Usoskin D, Parisien M, ..., Diatchenko L, Ernfors P
Nat Commun 12 (1) 1510 [2021-03-08; online 2021-03-08]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France.
Seguin-Orlando A, Donat R, Der Sarkissian C, ..., Guilaine J, Orlando L
Curr. Biol. 31 (5) 1072-1083.e10 [2021-03-08; online 2021-01-13]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Sperm Methylome Profiling Can Discern Fertility Levels in the Porcine Biomedical Model.
Pértille F, Alvarez-Rodriguez M, da Silva AN, ..., Guerrero-Bosagna C, Rodriguez-Martinez H
Int J Mol Sci 22 (5) 2679 [2021-03-06; online 2021-03-06]
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PubMed DOI Crossref
Effluent solids recirculation to municipal sludge digesters enhances long-chain fatty acids degradation capacity.
Shakeri Yekta S, Liu T, Mendes Anacleto T, ..., Björn A, Schnürer A
Biotechnol Biofuels 14 (1) 56 [2021-03-04; online 2021-03-04]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Divergence in Coding Sequence and Expression of Different Functional Categories of Immune Genes between Two Wild Rodent Species.
Zhong X, Lundberg M, Råberg L
Genome Biol Evol 13 (3) - [2021-03-01; online 2021-02-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Comparative analysis of targeted next-generation sequencing panels for the detection of gene mutations in chronic lymphocytic leukemia: an ERIC multi-center study.
Sutton L, Ljungström V, Enjuanes A, ..., Stamatopoulos K, Rosenquist R
Haematologica 106 (3) 682-691 [2021-03-01; online 2021-03-01]
Clinical Genomics Uppsala [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Whole-genome analyses provide no evidence for dog introgression in Fennoscandian wolf populations.
Smeds L, Aspi J, Berglund J, ..., Tirronen K, Ellegren H
Evol Appl 14 (3) 721-734 [2021-03-00; online 2020-11-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics.
Muus C, Luecken MD, Eraslan G, ..., NHLBI LungMap Consortium , Human Cell Atlas Lung Biological Network
Nat. Med. 27 (3) 546-559 [2021-03-00; online 2021-03-02]
NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
RNA transcript response by an Acidithiobacillus spp. mixed culture reveals adaptations to growth on arsenopyrite.
Barragán CE, Márquez MA, Dopson M, Montoya D
Extremophiles 25 (2) 143-158 [2021-03-00; online 2021-02-22]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Million-year-old DNA sheds light on the genomic history of mammoths.
van der Valk T, Pečnerová P, Díez-Del-Molino D, ..., Götherström A, Dalén L
Nature 591 (7849) 265-269 [2021-03-00; online 2021-02-17]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Escherichia coli EC93 deploys two plasmid-encoded class I contact-dependent growth inhibition systems for antagonistic bacterial interactions.
Wäneskog M, Halvorsen T, Filek K, ..., Poole SJ, Koskiniemi S
Microb Genom 7 (3) - [2021-03-00; online 2021-03-01]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Cyclin A2 localises in the cytoplasm at the S/G2 transition to activate PLK1.
Silva Cascales H, Burdova K, Middleton A, ..., Macurek L, Lindqvist A
Life Sci. Alliance 4 (3) e202000980 [2021-03-00; online 2021-01-05]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Abundantly expressed class of noncoding RNAs conserved through the multicellular evolution of dictyostelid social amoebas.
Kjellin J, Avesson L, Reimegård J, ..., Schaap P, Söderbom F
Genome Res. 31 (3) 436-447 [2021-03-00; online 2021-01-21]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Sheep nemabiome diversity and its response to anthelmintic treatment in Swedish sheep herds.
Halvarsson P, Höglund J
Parasit Vectors 14 (1) 114 [2021-02-18; online 2021-02-18]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Distinct subtypes of proprioceptive dorsal root ganglion neurons regulate adaptive proprioception in mice.
Wu H, Petitpré C, Fontanet P, ..., Hadjab S, Lallemend F
Nat Commun 12 (1) 1026 [2021-02-15; online 2021-02-15]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Combined removal of organic micropollutants and ammonium in reactive barriers developed for managed aquifer recharge.
Modrzyński JJ, Aamand J, Wittorf L, ..., Hallin S, Albers CN
Water Res. 190 (-) 116669 [2021-02-15; online 2020-11-25]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Asymmetric introgression reveals the genetic architecture of a plumage trait.
Semenov GA, Linck E, Enbody ED, ..., Andersson L, Taylor SA
Nat Commun 12 (1) 1019 [2021-02-15; online 2021-02-15]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Temperature Stress Induces Shift From Co-Existence to Competition for Organic Carbon in Microalgae-Bacterial Photobioreactor Community - Enabling Continuous Production of Microalgal Biomass.
Sörenson E, Capo E, Farnelid H, Lindehoff E, Legrand C
Front Microbiol 12 (-) 607601 [2021-02-11; online 2021-02-11]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
A novel canine reference genome resolves genomic architecture and uncovers transcript complexity.
Wang C, Wallerman O, Arendt ML, ..., Meadows JRS, Lindblad-Toh K
Commun Biol 4 (1) 185 [2021-02-10; online 2021-02-10]
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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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]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Uppsala [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Halophytophthora fluviatilis Pathogenicity and Distribution along a Mediterranean-Subalpine Gradient.
Caballol M, Štraus D, Macia H, ..., Redondo MÁ, Oliva J
JoF 7 (2) 112 [2021-02-03; online 2021-02-03]
NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
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Genomic Evidence of an Ancient East Asian Divergence Event in Wild Saccharomyces cerevisiae.
Bendixsen DP, Gettle N, Gilchrist C, Zhang Z, Stelkens R
Genome Biol Evol 13 (2) - [2021-02-03; online 2021-01-13]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The one-carbon pool controls mitochondrial energy metabolism via complex I and iron-sulfur clusters.
Schober FA, Moore D, Atanassov I, ..., Freyer C, Wredenberg A
Sci Adv 7 (8) - [2021-02-00; online 2021-02-19]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed 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. 29 (2) 325-337 [2021-02-00; online 2020-10-01]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatiotemporal dissection of the cell cycle with single-cell proteogenomics.
Mahdessian D, Cesnik AJ, Gnann C, ..., Sullivan DP, Lundberg E
Nature 590 (7847) 649-654 [2021-02-00; online 2021-02-24]
Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure Spatial Proteomics [Collaborative]
PubMed DOI Crossref
Small-scale population divergence is driven by local larval environment in a temperate amphibian.
Rödin-Mörch P, Palejowski H, Cortazar-Chinarro M, ..., Höglund J, Laurila A
Heredity (Edinb) 126 (2) 279-292 [2021-02-00; online 2020-09-21]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed 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 [2021-02-00; online 2020-11-28]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Root trait-microbial relationships across tundra plant species.
Spitzer CM, Lindahl B, Wardle DA, ..., Fanin N, Kardol P
New Phytol. 229 (3) 1508-1520 [2021-02-00; online 2020-10-30]
NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Role of H1 and DNA methylation in selective regulation of transposable elements during heat stress.
Liu S, de Jonge J, Trejo-Arellano MS, ..., Köhler C, Hennig L
New Phytol. 229 (4) 2238-2250 [2021-02-00; online 2020-11-22]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Hybrid seed incompatibility in Capsella is connected to chromatin condensation defects in the endosperm.
Dziasek K, Simon L, Lafon-Placette C, ..., Slotte T, Köhler C
PLoS Genet. 17 (2) e1009370 [2021-02-00; online 2021-02-11]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-wide single nucleotide polymorphism markers reveal population structure and dispersal direction of an expanding nuisance algal bloom species.
Rengefors K, Gollnisch R, Sassenhagen I, ..., Bassham S, Ahrén D
Mol. Ecol. 30 (4) 912-925 [2021-02-00; online 2021-01-20]
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
Comparative genomics highlights the importance of drug efflux transporters during evolution of mycoparasitism in Clonostachys subgenus Bionectria (Fungi, Ascomycota, Hypocreales).
Broberg M, Dubey M, Iqbal M, ..., Brandström Durling M, Karlsson M
Evol Appl 14 (2) 476-497 [2021-02-00; online 2020-09-28]
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 recently isolated human commensal Escherichia coli ST10 clone member mediates enhanced thermotolerance and tetrathionate respiration on a P1 phage-derived IncY plasmid.
Kamal SM, Cimdins-Ahne A, Lee C, ..., Mogk A, Römling U
Mol. Microbiol. 115 (2) 255-271 [2021-02-00; online 2020-10-12]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The Importance of Sex in the Discovery of Colorectal Cancer Prognostic Biomarkers.
Hases L, Ibrahim A, Chen X, ..., Hartman J, Williams C
Int J Mol Sci 22 (3) 1354 [2021-01-29; online 2021-01-29]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Chemical Biology Consortium Sweden (CBCS) [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Ecological adaptation in European eels is based on phenotypic plasticity.
Enbody ED, Pettersson ME, Sprehn CG, ..., Wickström H, Andersson L
Proc. Natl. Acad. Sci. U.S.A. 118 (4) e2022620118 [2021-01-26; online 2021-01-23]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Divergence and Remarkable Diversity of the Y Chromosome in Guppies.
Almeida P, Sandkam BA, Morris J, ..., Breden F, Mank JE
Mol. Biol. Evol. 38 (2) 619-633 [2021-01-23; online 2020-10-07]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-wide association study and pathway analysis identify NTRK2 as a novel candidate gene for litter size in sheep.
Esmaeili-Fard SM, Gholizadeh M, Hafezian SH, Abdollahi-Arpanahi R
PLoS ONE 16 (1) e0244408 [2021-01-22; online 2021-01-22]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The overlap of genetic susceptibility to schizophrenia and cardiometabolic disease can be used to identify metabolically different groups of individuals.
Strawbridge RJ, Johnston KJA, Bailey MES, ..., Sennblad B, Smith DJ
Sci Rep 11 (1) 632 [2021-01-12; online 2021-01-12]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
DNA-Metabarcoding of Belowground Fungal Communities in Bare-Root Forest Nurseries: Focus on Different Tree Species.
Marčiulynienė D, Marčiulynas A, Lynikienė J, ..., Gedminas A, Menkis A
Microorganisms 9 (1) - [2021-01-11; online 2021-01-11]
NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Temporal changes in DNA methylation and RNA expression in a small song bird: within- and between-tissue comparisons.
Lindner M, Verhagen I, Viitaniemi HM, ..., Husby A, van Oers K
BMC Genomics 22 (1) 36 [2021-01-07; online 2021-01-07]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Sex-dimorphic genetic effects and novel loci for fasting glucose and insulin variability.
Lagou V, Mägi R, Hottenga JJ, ..., Prokopenko I, Meta-Analyses of Glucose and Insulin-related traits Consortium (MAGIC)
Nat Commun 12 (1) 24 [2021-01-05; online 2021-01-05]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Post-treatment of dewatered digested sewage sludge by thermophilic high-solid digestion for pasteurization with positive energy output.
Nordell E, Moestedt J, Österman J, ..., Sun L, Schnürer A
Waste Management 119 (-) 11-21 [2021-01-01; online 2020-10-05]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [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 9 (1) e1526 [2021-01-00; online 2020-12-14]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) National Genomics Infrastructure
PubMed DOI Crossref
Urbanization is associated with modifications in DNA methylation in a small passerine bird.
Watson H, Powell D, Salmón P, Jacobs A, Isaksson C
Evol Appl 14 (1) 85-98 [2021-01-00; online 2020-11-13]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Shared genetic risk between eating disorder- and substance-use-related phenotypes: Evidence from genome-wide association studies.
Munn-Chernoff MA, Johnson EC, Chou YL, ..., Bulik CM, Agrawal A
Addict Biol 26 (1) e12880 [2021-01-00; online 2020-02-16]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Severe congenital neutropenia-associated JAGN1 mutations unleash a calpain-dependent cell death programme in myeloid cells.
Khandagale A, Holmlund T, Entesarian M, ..., Nordenskjöld M, Fadeel B
Br. J. Haematol. 192 (1) 200-211 [2021-01-00; online 2020-11-18]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Molecular pathways in patients with systemic lupus erythematosus revealed by gene-centred DNA sequencing.
Sandling JK, Pucholt P, Hultin Rosenberg L, ..., Lindblad-Toh K, Rönnblom L
Ann. Rheum. Dis. 80 (1) 109-117 [2021-01-00; online 2020-10-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
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]
PubMed DOI Crossref
Human population dynamics and Yersinia pestis in ancient northeast Asia.
Kılınç GM, Kashuba N, Koptekin D, ..., Storå J, Götherström A
Sci Adv 7 (2) - [2021-01-00; online 2021-01-06]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
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 [2021-01-00; online 2020-12-14]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Evaluating totipotency using criteria of increasing stringency.
Posfai E, Schell JP, Janiszewski A, ..., Lanner F, Rossant J
Nat Cell Biol 23 (1) 49-60 [2021-01-00; online 2021-01-08]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Epigenome-wide cross-tissue correlation of human bone and blood DNA methylation - can blood be used as a surrogate for bone?
Ebrahimi P, Luthman H, McGuigan FE, Akesson KE
Epigenetics 16 (1) 92-105 [2021-01-00; online 2020-07-21]
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
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 [2021-01-00; online 2020-12-07]
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
Crown‐fire severity is more important than ground‐fire severity in determining soil fungal community development in the boreal forest
Pérez‐Izquierdo L, Clemmensen KE, Strengbom J, ..., Nilsson M, Lindahl BD
J Ecol 109 (1) 504-518 [2021-01-00; online 2020-11-00]
Bioinformatics Compute and Storage [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Year 2020

PubMed 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) 22436 [2020-12-31; online 2020-12-31]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic Adaptations and Evolutionary History of the Extinct Scimitar-Toothed Cat, Homotherium latidens.
Barnett R, Westbury MV, Sandoval-Velasco M, ..., Yamaguchi N, Gilbert MTP
Curr. Biol. 30 (24) 5018-5025.e5 [2020-12-21; online 2020-10-15]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
You Had Me at "MAGIC"!: Four Barley MAGIC Populations Reveal Novel Resistance QTL for Powdery Mildew.
Novakazi F, Krusell L, Jensen JD, ..., Jahoor A, Bengtsson T
Genes 11 (12) 1512 [2020-12-18; online 2020-12-18]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed 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 (-) 598872 [2020-12-09; online 2020-12-09]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
BMP signaling is a therapeutic target in ovarian cancer.
Fukuda T, Fukuda R, Tanabe R, ..., Miyazono K, Heldin CH
Cell Death Discov 6 (1) 139 [2020-12-05; online 2020-12-05]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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]
NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed 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
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 [2020-12-01; 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]
PubMed 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]
DOI Crossref
Morphological characters and SNP markers suggest hybridization and introgression in sympatric populations of the pleurocarpous mosses Homalothecium lutescens and H. sericeum
Sawangproh W, Lang AS, Hedenäs L, Cronberg N
Org Divers Evol 20 (4) 619-637 [2020-12-00; online 2020-09-07]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-wide association study of angioedema induced by angiotensin-converting enzyme inhibitor and angiotensin receptor blocker treatment.
Rasmussen ER, Hallberg P, Baranova EV, ..., Palmer CNA, Wadelius M
Pharmacogenomics J. 20 (6) 770-783 [2020-12-00; online 2020-02-21]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genetic Studies of Leptin Concentrations Implicate Leptin in the Regulation of Early Adiposity.
Yaghootkar H, Zhang Y, Spracklen CN, ..., Loos RJF, Kilpeläinen TO
Diabetes 69 (12) 2806-2818 [2020-12-00; online 2020-09-11]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genetic Predisposition to Coronary Artery Disease in Type 2 Diabetes Mellitus.
van Zuydam NR, Ladenvall C, Voight BF, ..., Palmer CNA, SUMMIT Steering Committee; CARDIOGRAMplusC4D Steering Committee*
Circ Genom Precis Med 13 (6) e002769 [2020-12-00; online 2020-08-13]
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]
PubMed DOI Crossref
Exome Sequencing Reveals Common and Rare Variants in F5 Associated With ACE Inhibitor and Angiotensin Receptor Blocker-Induced Angioedema.
Maroteau C, Siddiqui MK, Veluchamy A, ..., Palmer CNA, PREDICTION-ADR
Clin. Pharmacol. Ther. 108 (6) 1195-1202 [2020-12-00; online 2020-07-18]
NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Effect of RNA silencing suppression activity of chrysanthemum virus B p12 protein on small RNA species.
Vetukuri RR, Kalyandurg PB, Saripella GV, ..., Grenville-Briggs LJ, Savenkov EI
Arch Virol 165 (12) 2953-2959 [2020-12-00; online 2020-10-10]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Discovery of rare variants associated with blood pressure regulation through meta-analysis of 1.3 million individuals.
Surendran P, Feofanova EV, Lahrouchi N, ..., Munroe PB, Howson JMM
Nat. Genet. 52 (12) 1314-1332 [2020-12-00; online 2020-11-23]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Deep sequencing detects human papillomavirus (HPV) in cervical cancers negative for HPV by PCR.
Arroyo Mühr LS, Lagheden C, Lei J, ..., Sundström K, Dillner J
Br. J. Cancer 123 (12) 1790-1795 [2020-12-00; online 2020-10-06]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
CRISPR and Long-Read Sequencing: A Perfect Match.
Ameur A
CRISPR J 3 (6) 425-427 [2020-12-00; online 2020-11-30]
NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]
PubMed DOI Crossref
A genome-wide association study revealed five SNPs affecting 8-month weight in sheep.
Pasandideh M, Gholizadeh M, Rahimi-Mianji G
Anim Genet 51 (6) 973-976 [2020-12-00; online 2020-09-10]
NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed 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]
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
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]
PubMed DOI Crossref
Immobilization of sulfate and thiosulfate-reducing biomass on sand under haloalkaline conditions.
Sousa JAB, Bolgár A, Christel S, ..., Stams AJM, Plugge CM
Sci. Total Environ. 745 (-) 141017 [2020-11-25; online 2020-07-22]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-wide identification of Argonautes in Solanaceae with emphasis on potato.
Liao Z, Hodén KP, Singh RK, Dixelius C
Sci Rep 10 (1) 20577 [2020-11-25; online 2020-11-25]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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
Nat Commun 11 (1) 5860 [2020-11-17; online 2020-11-17]
Bioinformatics Compute and Storage [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] In Situ Sequencing (ISS) [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Association between Aquatic Micropollutant Dissipation and River Sediment Bacterial Communities.
Coll C, Bier R, Li Z, ..., Gorokhova E, Sobek A
Environ. Sci. Technol. 54 (22) 14380-14392 [2020-11-17; online 2020-10-26]
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 [2020-11-16; 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
Association of aberrant ASNS imprinting with asparaginase sensitivity and chromosomal abnormality in childhood BCP-ALL.
Watanabe A, Miyake K, Nordlund J, ..., Sugita K, Inukai T
Blood 136 (20) 2319-2333 [2020-11-12; online 2020-06-24]
Bioinformatics Compute and Storage [Service] NGI Uppsala (SNP&SEQ Technology Platform) [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]
PubMed 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) 19304 [2020-11-09; online 2020-11-09]
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
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]
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
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]
PubMed DOI Crossref
Point-of-Care Approaches for Meningitis Diagnosis in a Low-Resource Setting (Southwestern Uganda): Observational Cohort Study Protocol of the "PI-POC" Trial.
Gaudenzi G, Kumbakumba E, Rasti R, ..., Mwanga-Amumpaire J, Alfvén T
JMIR Res Protoc 9 (11) e21430 [2020-11-04; online 2020-11-04]
NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
MYC as a driver of stochastic chromatin networks: implications for the fitness of cancer cells.
Sumida N, Sifakis EG, Kiani NA, ..., Göndör A, Ohlsson R
Nucleic Acids Res. 48 (19) 10867-10876 [2020-11-04; online 2020-10-15]
Bioinformatics Compute and Storage [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Evolution from adherent to suspension: systems biology of HEK293 cell line development.
Malm M, Saghaleyni R, Lundqvist M, ..., Nielsen J, Rockberg J
Sci Rep 10 (1) 18996 [2020-11-04; online 2020-11-04]
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