NGI Short read

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Started: -

Ended: Current

Year 2023

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
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]

Year 2022

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
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
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
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
Whole genome analyses based on single, field collected spores of the arbuscular mycorrhizal fungus Funneliformis geosporum.
Sahraei SE, Sánchez-García M, Montoliu-Nerin M, ..., Rosendahl S, Rosling A
Mycorrhiza 32 (5-6) 361-371 [2022-11-00; online 2022-09-26]
Bioinformatics Compute and Storage [Service] Microbial Single Cell Genomics [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Strong Association of Combined Genetic Deficiencies in the Classical Complement Pathway With Risk of Systemic Lupus Erythematosus and Primary Sjögren's Syndrome.
Lundtoft C, Sjöwall C, Rantapää-Dahlqvist S, ..., Leonard D, Rönnblom L
Arthritis & rheumatology (Hoboken, N.J.) 74 (11) 1842-1850 [2022-11-00; online 2022-10-07]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Mer-tyrosine kinase: a novel susceptibility gene for SLE related end-stage renal disease.
Yavuz S, Pucholt P, Sandling JK, ..., Lindblad-Toh K, Rönnblom L
Lupus Sci Med 9 (1) - [2022-11-00; online 2022-11-05]
Bioinformatics Compute and Storage [Service] NGI SNP genotyping [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative.
Butler-Laporte G, Povysil G, Kosmicki JA, ..., Ferreira MAR, Richards JB
PLoS Genet. 18 (11) e1010367 [2022-11-00; online 2022-11-03]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
ZEB2 haploinsufficient Mowat-Wilson syndrome induced pluripotent stem cells show disrupted GABAergic transcriptional regulation and function.
Schuster J, Klar J, Khalfallah A, ..., Birnir B, Dahl N
Front Mol Neurosci 15 (-) 988993 [2022-10-24; online 2022-10-24]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level.
Gutiérrez-Valencia J, Fracassetti M, Berdan EL, ..., Arroyo J, Slotte T
Curr. Biol. 32 (20) 4360-4371.e6 [2022-10-24; online 2022-09-09]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Comparative genome analysis of mycobacteria focusing on tRNA and non-coding RNA.
Behra PRK, Pettersson BMF, Ramesh M, ..., Dasgupta S, Kirsebom LA
BMC Genomics 23 (1) 704 [2022-10-15; online 2022-10-15]
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
Spatiotemporal variations in retrovirus-host interactions among Darwin's finches.
Hill J, Lillie M, Pettersson ME, ..., Andersson L, Jern P
Nat Commun 13 (1) 6033 [2022-10-13; online 2022-10-13]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Absence of oxygen effect on microbial structure and methane production during drying and rewetting events.
Liu T, Li X, Yekta SS, ..., Schnürer A, Enrich-Prast A
Sci Rep 12 (1) 16570 [2022-10-04; online 2022-10-04]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A possible genomic footprint of polygenic adaptation on population divergence in seed beetles?
Arnqvist G, Sayadi A
Ecol Evol 12 (10) e9440 [2022-10-00; online 2022-10-27]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Loss of SNAI1 induces cellular plasticity in invasive triple-negative breast cancer cells.
Tsirigoti C, Ali MM, Maturi V, Heldin CH, Moustakas A
Cell Death Dis 13 (9) 832 [2022-09-28; online 2022-09-28]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A novel neo-sex chromosome in Sylvietta brachyura (Macrosphenidae) adds to the extraordinary avian sex chromosome diversity among Sylvioidea songbirds.
Sigeman H, Zhang H, Ali Abed S, Hansson B
J. Evol. Biol. - (-) - [2022-09-26; online 2022-09-26]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Congenital tremor and splay leg in piglets - insights into the virome, local cytokine response, and histology.
Stenberg H, Hellman S, Lindström L, ..., Hayer J, Malmberg M
BMC Vet Res 18 (1) 348 [2022-09-16; 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
Genomic evidence that a sexually selected trait captures genome-wide variation and facilitates the purging of genetic load.
Parrett JM, Chmielewski S, Aydogdu E, ..., Konczal M, Radwan J
Nat Ecol Evol 6 (9) 1330-1342 [2022-09-00; online 2022-07-18]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Ecosystem size-induced environmental fluctuations affect the temporal dynamics of community assembly mechanisms.
Bier RL, Vass M, Székely AJ, Langenheder S
ISME J 16 (12) 2635-2643 [2022-08-18; online 2022-08-18]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Isolated Grauer's gorilla populations differ in diet and gut microbiome.
Michel A, Minocher R, Niehoff PP, ..., Caillaud D, Guschanski K
Mol. Ecol. - (-) - [2022-08-17; online 2022-08-17]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single-cell multi-omics of human preimplantation embryos shows susceptibility to glucocorticoids.
Zhao C, Biondic S, Vandal K, ..., Reik W, Petropoulos S
Genome Res. 32 (9) 1627-1641 [2022-08-10; online 2022-08-10]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Single cell [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Nuclear-specific gene expression in heterokaryons of the filamentous ascomycete Neurospora tetrasperma.
Meunier C, Darolti I, Reimegård J, Mank JE, Johannesson H
Proc. Biol. Sci. 289 (1980) 20220971 [2022-08-10; online 2022-08-10]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service]
PubMed DOI Crossref
Metatranscriptomics of Nasopharyngeal Microbiota and Host Distinguish between Pneumonia and Health.
Nannapaneni P, Sundh J, Prast-Nielsen S, ..., Naucler P, Henriques-Normark B
Am. J. Respir. Crit. Care Med. - (-) - [2022-08-10; online 2022-08-10]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Identification and functional characterization of a novel susceptibility locus for small vessel vasculitis with MPO-ANCA.
Dahlqvist J, Ekman D, Sennblad B, ..., Eriksson P, Lindblad-Toh K
Rheumatology (Oxford) 61 (8) 3461-3470 [2022-08-03; online 2021-12-11]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI SNP genotyping [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A relationship between phages and organic carbon in wastewater treatment plant effluents.
Modin O, Fuad N, Abadikhah M, ..., Persson F, Wilén BM
Water Res X 16 (-) 100146 [2022-08-01; online 2022-06-16]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Complement C4 Copy Number Variation is Linked to SSA/Ro and SSB/La Autoantibodies in Systemic Inflammatory Autoimmune Diseases.
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]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Characterization of Pipistrellus pygmaeus Bat Virome from Sweden.
Cholleti H, de Jong J, Blomström AL, Berg M
Viruses 14 (8) - [2022-07-28; online 2022-07-28]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Short read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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
iScience 25 (7) 104602 [2022-07-15; online 2022-06-11]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Single cell [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Co-Occurrence of Francisella, Spotted Fever Group Rickettsia, and Midichloria in Avian-Associated Hyalomma rufipes.
Hoffman T, Sjödin A, Öhrman C, ..., Lundkvist Å, Olsen B
Microorganisms 10 (7) - [2022-07-11; online 2022-07-11]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Practical application of a Bayesian network approach to poultry epigenetics and stress.
Videla Rodriguez EA, Pértille F, Guerrero-Bosagna C, ..., Jensen P, Smith VA
BMC Bioinformatics 23 (1) 261 [2022-07-01; online 2022-07-01]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests.
Law SR, Serrano AR, Daguerre Y, ..., Street NR, Hurry V
Proc. Natl. Acad. Sci. U.S.A. 119 (26) e2118852119 [2022-06-28; online 2022-06-21]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Short read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The HDAC9-associated risk locus promotes coronary artery disease by governing TWIST1.
Ma L, Bryce NS, Turner AW, ..., Björkegren JLM, Kovacic JC
PLoS Genet. 18 (6) e1010261 [2022-06-00; online 2022-06-17]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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
Leukemia 36 (6) 1681-1684 [2022-06-00; online 2022-04-01]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
An empirical evaluation of genotype imputation of ancient DNA.
Ausmees K, Sanchez-Quinto F, Jakobsson M, Nettelblad C
G3 (Bethesda) 12 (6) - [2022-05-30; online 2022-04-29]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Inflammation and Interferon Signatures in Peripheral B-Lymphocytes and Sera of Individuals With Fibromyalgia.
Fineschi S, Klar J, Gustafsson KA, ..., Karlsson B, Dahl N
Front Immunol 13 (-) 874490 [2022-05-26; online 2022-05-26]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [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
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]
NGI Short read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species.
Feiner N, Radersma R, Vasquez L, ..., Heijmans BT, Uller T
iScience 25 (5) 104303 [2022-05-20; online 2022-04-25]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
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]
Bioinformatics Compute and Storage [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia.
Darolti I, Almeida P, Wright AE, Mank JE
J. Evol. Biol. 35 (12) 1646-1658 [2022-05-04; online 2022-05-04]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Nutrient driven transcriptional changes during phage infection in an aquatic Gammaproteobacterium.
Nilsson E, Li K, Hoetzinger M, Holmfeldt K
Environ. Microbiol. 24 (5) 2270-2281 [2022-05-00; online 2022-01-26]
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
Dual RNA Sequencing Reveals Key Events When Different Giardia Life Cycle Stages Interact With Human Intestinal Epithelial Cells In Vitro.
Rojas L, Grüttner J, Ma'ayeh S, Xu F, Svärd SG
Front. Cell. Infect. Microbiol. 12 (-) 862211 [2022-04-27; online 2022-04-27]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Influence of cysteine, serine, sulfate, and sulfide on anaerobic conversion of unsaturated long-chain fatty acid, oleate, to methane.
Shakeri Yekta S, Elreedy A, Liu T, ..., Fujii M, Schnürer A
Sci. Total Environ. 817 (-) 152967 [2022-04-15; online 2022-01-10]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] Swedish NMR Centre (SNC) [Collaborative]
PubMed DOI Crossref
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]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
GBS-MeDIP: A protocol for parallel identification of genetic and epigenetic variation in the same reduced fraction of genomes across individuals.
Rezaei S, Uffenorde J, Gimm O, ..., Guerrero-Bosagna C, Pértille F
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]
DOI Crossref
Weakened resilience of benthic microbial communities in the face of climate change
Seidel L, Ketzer M, Broman E, ..., Hylander S, Dopson M
ISME COMMUN. 2 (1) - [2022-03-08; online 2022-03-08]
Bioinformatics Compute and Storage [Service] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Identification of a discrete subpopulation of spinal cord ependymal cells with neural stem cell properties.
Stenudd M, Sabelström H, Llorens-Bobadilla E, ..., Barnabé-Heider F, Frisén J
Cell Rep 38 (9) 110440 [2022-03-01; online 2022-03-03]
Bioinformatics Compute and Storage [Service] Integrated Microscopy Technologies Stockholm [Collaborative] NGI Short read [Service] NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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PubMed DOI Crossref
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]
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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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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Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.
Ratz M, von Berlin L, Larsson L, ..., Lundeberg J, Frisén J
Nat. Neurosci. 25 (3) 285-294 [2022-03-00; online 2022-02-24]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Single cell [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
Bioinformatics Compute and Storage [Service] 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]
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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]
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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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]
NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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]
NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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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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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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]
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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]
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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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A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component.
Christmas MJ, Jones JC, Olsson A, ..., Miller-Struttmann NE, Webster MT
Mol. Ecol. 31 (4) 1111-1127 [2022-02-00; online 2021-12-07]
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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]
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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]
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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]
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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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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]
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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]
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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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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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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]
PubMed DOI Crossref
Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.
Gutiérrez-Valencia J, Fracassetti M, Horvath R, ..., Kolář F, Slotte T
Mol. Biol. Evol. 39 (1) - [2022-01-07; online 2021-12-09]
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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]
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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]
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Year 2021

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 [2021-12-00; online 2021-12-00]
NGI Short read [Service] NGI Spatial omics [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
Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration.
Sigeman H, Strandh M, Proux-Wéra E, ..., Westerdahl H, Hansson B
Mol. Biol. Evol. 38 (12) 5275-5291 [2021-09-20; online 2021-09-20]
Bioinformatics Compute and Storage [Service] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Year 2010

PubMed DOI Crossref
Coexisting NRAS and BRAF mutations in primary familial melanomas with specific CDKN2A germline alterations.
Jovanovic B, Egyhazi S, Eskandarpour M, ..., Hayward NK, Hansson J
J. Invest. Dermatol. 130 (2) 618-620 [2010-02-00; online 2009-09-18]
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