Bioinformatics Support for Computational Resources

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SciLifeLab Infrastructure Unit since 2013. From 2013 to 2023 called “Bioinformatics Compute and Storage”.

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

Started: 2013

Ended: Current

Year 2024

PubMed DOI Crossref
Sex-limited experimental evolution drives transcriptomic divergence in a hermaphrodite.
Cīrulis A, Nordén AK, Churcher AM, ..., Zadesenets KS, Abbott JK
Genome Biol Evol 16 (1) - [2024-01-05; online 2023-12-29]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Population genomics of the muskox' resilience in the near absence of genetic variation.
Pečnerová P, Lord E, Garcia-Erill G, ..., Moltke I, Siegismund HR
Mol. Ecol. 33 (2) e17205 [2024-01-00; online 2023-11-16]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data.
Kurland S, Saha A, Keehnen N, ..., Ryman N, Laikre L
Mol. Ecol. 33 (2) e17213 [2024-01-00; online 2023-11-28]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
DNA metabarcoding reveals spatial and temporal variation of fish eye fluke communities in lake ecosystems.
Diaz-Suarez A, Noreikiene K, Kahar S, ..., Kisand V, Vasemägi A
Int J Parasitol 54 (1) 33-46 [2024-01-00; online 2023-08-24]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2023

PubMed DOI Crossref
Gastrointestinal parasite community structure in horses after the introduction of selective anthelmintic treatment strategies.
Halvarsson P, Grandi G, Hägglund S, Höglund J
Vet Parasitol 326 (-) 110111 [2023-12-25; online 2023-12-25]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Effects of environmental translocation and host characteristics on skin microbiomes of sun-basking fish.
Berggren H, Nordahl O, Yıldırım Y, ..., Tibblin P, Forsman A
Proc. Biol. Sci. 290 (2013) 20231608 [2023-12-20; online 2023-12-20]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Dissecting the genetic landscape of GPCR signaling through phenotypic profiling in C. elegans.
Pu L, Wang J, Lu Q, ..., Henriksson J, Chen C
Nat Commun 14 (1) 8410 [2023-12-18; online 2023-12-18]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A chromosome-level assembly of the seed beetle Callosobruchus maculatus genome with annotation of its repetitive elements.
Arnqvist G, Westerberg I, Galbraith J, ..., Ewels P, Suh A
G3 (Bethesda) - (-) - [2023-12-13; online 2023-12-13]
Bioinformatics Support for Computational Resources [Service] NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatial transcriptomics of B cell and T cell receptors reveals lymphocyte clonal dynamics.
Engblom C, Thrane K, Lin Q, ..., Lundeberg J, Frisén J
Science 382 (6675) eadf8486 [2023-12-08; online 2023-12-08]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Short read NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Complex Evolutionary History With Extensive Ancestral Gene Flow in an African Primate Radiation.
Jensen A, Swift F, de Vries D, ..., Roos C, Guschanski K
Mol. Biol. Evol. 40 (12) - [2023-12-01; online 2023-11-21]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Patterns of phylogenetic diversification in the Dollarbird (Eurystomus orientalis) and Azure Roller (Eurystomus azureus) complex.
Johansson US, Irestedt M, Ericson PGP
Mol. Phylogenet. Evol. 189 (-) 107909 [2023-12-00; online 2023-08-22]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genome-scale phylogeny and comparative genomics of the fungal order Sordariales.
Hensen N, Bonometti L, Westerberg I, ..., Hiltunen Thorén M, Johannesson H
Mol. Phylogenet. Evol. 189 (-) 107938 [2023-12-00; online 2023-10-10]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
An enriched maternal environment and stereotypies of sows differentially affect the neuro-epigenome of brain regions related to emotionality in their piglets.
Tatemoto P, Pértille F, Bernardino T, ..., Guerrero-Bosagna C, Zanella AJ
Epigenetics 18 (1) 2196656 [2023-12-00; online 2023-05-16]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The genetic legacy of the expansion of Bantu-speaking peoples in Africa.
Fortes-Lima CA, Burgarella C, Hammarén R, ..., Bostoen K, Schlebusch CM
Nature - (-) - [2023-11-29; online 2023-11-29]
Bioinformatics Support for Computational Resources [Service] NGI SNP genotyping [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Ovarian ERβ cistrome and transcriptome reveal chromatin interaction with LRH-1.
Birgersson M, Indukuri R, Lindquist L, ..., Archer A, Williams C
BMC Biol. 21 (1) 277 [2023-11-29; online 2023-11-29]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Identification of constrained sequence elements across 239 primate genomes.
Kuderna LFK, Ulirsch JC, Rashid S, ..., Marques Bonet T, Farh KK
Nature - (-) - [2023-11-29; online 2023-11-29]
Bioinformatics Support for Computational Resources [Service]
DOI Crossref
Sociodemographic characteristics and COVID-19 testing rates: spatiotemporal patterns and impact of test accessibility in Sweden
Kennedy B, Varotsis G, Hammar U, ..., Björk J, Fall T
- - (-) - [2023-11-27; online 2023-11-27]
Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
RecView: an interactive R application for locating recombination positions using pedigree data.
Zhang H, Hansson B
BMC Genomics 24 (1) 712 [2023-11-25; online 2023-11-25]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Evaluation of circulating plasma proteins in breast cancer using Mendelian randomisation.
Mälarstig A, Grassmann F, Dahl L, ..., Czene K, Hedman ÅK
Nat Commun 14 (1) 7680 [2023-11-24; online 2023-11-24]
Affinity Proteomics Uppsala [Service] Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
Shotgun metagenomes from productive lakes in an urban region of Sweden.
Rodríguez-Gijón A, Hampel JJ, Dharamshi J, Bertilsson S, Garcia SL
Sci Data 10 (1) 810 [2023-11-17; online 2023-11-17]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Demonstration of reduced efficacy against cyathostomins without change in species composition after pyrantel embonate treatment in Swedish equine establishments.
Hedberg Alm Y, Halvarsson P, Martin F, ..., Törngren V, Tydén E
International Journal for Parasitology: Drugs and Drug Resistance 23 (-) 78-86 [2023-11-14; online 2023-11-14]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Whole-genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species.
Estravis Barcala M, van der Valk T, Chen Z, ..., Nilsson O, Wu HX
Plant J. - (-) - [2023-11-10; online 2023-11-10]
Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
The genomics and evolution of inter-sexual mimicry and female-limited polymorphisms in damselflies.
Willink B, Tunström K, Nilén S, ..., Svensson EI, Wheat CW
Nat Ecol Evol - (-) - [2023-11-06; online 2023-11-06]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
BLR: a flexible pipeline for haplotype analysis of multiple linked-read technologies.
Höjer P, Frick T, Siga H, ..., Martin M, Ahmadian A
Nucleic Acids Res. - (-) - [2023-11-06; online 2023-11-06]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Antigen-presenting autoreactive B cells activate regulatory T cells and suppress autoimmune arthritis in mice.
Aoun M, Coelho A, Krämer A, ..., Burkhardt H, Holmdahl R
J. Exp. Med. 220 (11) - [2023-11-06; online 2023-09-11]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Novel PNKP mutations associated with reduced DNA single-strand break repair and severe microcephaly, seizures, and developmental delay.
Thuresson A, Brazina J, Akram T, ..., Soussi Zander C, Caldecott KW
Mol Genet Genomic Med - (-) e2295 [2023-11-02; online 2023-11-02]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Evidence of Site-Specific and Male-Biased Germline Mutation Rate in a Wild Songbird.
Zhang H, Lundberg M, Tarka M, Hasselquist D, Hansson B
Genome Biol Evol 15 (11) - [2023-11-01; online 2023-10-04]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Targeting oxidation sites on boreal acid sulfate soil macropore surfaces mitigates acid and metal release to recipient water streams
Högfors-Rönnholm E, Stén P, Christel S, ..., Dopson M, Engblom S
Applied Geochemistry 158 (-) 105779 [2023-11-00; online 2023-11-00]
Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
Smoking affects epigenetic ageing of lung bronchoalveolar lavage cells in Multiple Sclerosis.
Klose D, Needhamsen M, Ringh MV, ..., Jagodic M, Kular L
Mult Scler Relat Disord 79 (-) 104991 [2023-11-00; online 2023-09-09]
Bioinformatics Support for Computational Resources [Service] NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Nutrient availability and grazing influence the strength of priority effects during freshwater bacterial community coalescence.
Lumpi T, Guo X, Lindström ES
Environ. Microbiol. 25 (11) 2289-2302 [2023-11-00; online 2023-06-28]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities.
Broman E, Abdelgadir M, Bonaglia S, ..., Nascimento FJA, Sjöling S
Microb. Ecol. 86 (4) 2357-2372 [2023-11-00; online 2023-05-24]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Host Phylogeny Structures the Gut Bacterial Community Within Galerucella Leaf Beetles.
An Y, Braga MP, Garcia SL, Grudzinska-Sterno M, Hambäck PA
Microb. Ecol. 86 (4) 2477-2487 [2023-11-00; online 2023-06-14]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comprehensive analyses of circulating cardiometabolic proteins and objective measures of fat mass.
Titova OE, Brunius C, Warensjö Lemming E, ..., Michaëlsson K, Larsson SC
Int J Obes (Lond) 47 (11) 1043-1049 [2023-11-00; online 2023-08-07]
Affinity Proteomics Uppsala [Service] Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
Body Mass Index and the Risk of Rheumatic Disease: Linear and Nonlinear Mendelian Randomization Analyses.
Karlsson T, Hadizadeh F, Rask-Andersen M, Johansson Å, Ek WE
Arthritis & rheumatology (Hoboken, N.J.) 75 (11) 2027-2035 [2023-11-00; online 2023-09-28]
Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
Screening for atypical porcine pestivirus in Swedish boar semen used for artificial insemination and a characterisation of the seminal RNA microbiome including the virome.
Stenberg H, Malmberg M, Hayer J
BMC Vet Res 19 (1) 219 [2023-10-20; online 2023-10-20]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Low mutation rate in epaulette sharks is consistent with a slow rate of evolution in sharks.
Sendell-Price AT, Tulenko FJ, Pettersson M, ..., Andersson L, Schartl M
Nat Commun 14 (1) 6628 [2023-10-19; online 2023-10-19]
Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
Range-wide and temporal genomic analyses reveal the consequences of near-extinction in Swedish moose.
Dussex N, Kurland S, Olsen RA, ..., Dalén L, Laikre L
Commun Biol 6 (1) 1035 [2023-10-17; online 2023-10-17]
Bioinformatics Support for Computational Resources [Service] NGI Other [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Deficiency of the Heterogeneous Nuclear Ribonucleoprotein U locus leads to delayed hindbrain neurogenesis.
Mastropasqua F, Oksanen M, Soldini C, ..., Bölte S, Tammimies K
Biol Open 12 (10) - [2023-10-15; online 2023-10-10]
Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Rewiring of the promoter-enhancer interactome and regulatory landscape in glioblastoma orchestrates gene expression underlying neurogliomal synaptic communication.
Chakraborty C, Nissen I, Vincent CA, ..., Hörnblad A, Remeseiro S
Nat Commun 14 (1) 6446 [2023-10-13; online 2023-10-13]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Integrated Genomic and Transcriptomic Analysis Improves Disease Classification and Risk Stratification of MDS with Ring Sideroblasts.
Todisco G, Creignou M, Bernard E, ..., Papaemmanuil E, Hellström-Lindberg E
Clin. Cancer Res. 29 (20) 4256-4267 [2023-10-13; online 2023-07-27]
Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Multivalent antigen display on nanoparticle immunogens increases B cell clonotype diversity and neutralization breadth to pneumoviruses.
Ols S, Lenart K, Arcoverde Cerveira R, ..., King NP, Loré K
Immunity 56 (10) 2425-2441.e14 [2023-10-10; online 2023-09-08]
Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Service]
PubMed DOI Crossref
Genomic, transcriptomic and epigenomic sequencing data of the B-cell leukemia cell line REH.
Lysenkova Wiklander M, Övernäs E, Lagensjö J, ..., Liljedahl U, Nordlund J
BMC Res Notes 16 (1) 265 [2023-10-10; online 2023-10-10]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Low mutation load in a supergene underpinning alternative male mating strategies in ruff (Calidris pugnax).
Hill J, Enbody ED, Bi H, ..., Widemo F, Andersson L
Mol. Biol. Evol. 40 (12) msad224 [2023-10-06; online 2023-10-06]
Bioinformatics Support for Computational Resources [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
Introgression underlies phylogenetic uncertainty but not parallel plumage evolution in a recent songbird radiation.
Rancilhac L, Enbody ED, Harris R, ..., Andersson L, Alström P
Syst. Biol. - (-) - [2023-10-06; online 2023-10-06]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Metabolomic and transcriptomic analyses identify external conditions and key genes underlying high levels of toxic glycoalkaloids in tubers of stress-sensitive potato cultivars.
Merino I, Guasca AO, Krmela A, ..., Schulzova V, Sitbon F
Front Plant Sci 14 (-) 1210850 [2023-10-04; online 2023-10-04]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Copy number variations and their effect on the plasma proteome.
Schmitz D, Li Z, Lo Faro V, ..., Rafati N, Johansson Å
Genetics - (-) - [2023-10-04; online 2023-10-04]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Similarity in milk microbiota in replicates.
Dahlberg J, Pelve E, Dicksved J
Microbiologyopen 12 (5) e1383 [2023-10-00; online 2023-10-25]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae).
Steffen K, Proux-Wéra E, Soler L, ..., Sundh J, Cárdenas P
G3 (Bethesda) 13 (10) - [2023-09-30; online 2023-08-25]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Long read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Community-wide genome sequencing reveals 30 years of Darwin's finch evolution.
Enbody ED, Sendell-Price AT, Sprehn CG, ..., Grant PR, Andersson L
Science 381 (6665) eadf6218 [2023-09-29; online 2023-09-29]
Bioinformatics Support for Computational Resources [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
The relative impact of parental and current environment on plant transcriptomes depends on type of stress and genotype.
Earley TS, Feiner N, Alvarez MF, Coolon JD, Sultan SE
Proc. Biol. Sci. 290 (2007) 20230824 [2023-09-27; online 2023-09-27]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single-cell transcriptomics delineates the immune cell landscape in equine lower airways and reveals upregulation of FKBP5 in horses with asthma.
Riihimäki M, Fegraeus K, Nordlund J, ..., Hellman L, Raine A
Sci Rep 13 (1) 16261 [2023-09-27; online 2023-09-27]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Collaborative] NGI Single cell [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
The draft genome of the microscopic Nemertoderma westbladi sheds light on the evolution of Acoelomorpha genomes.
Abalde S, Tellgren-Roth C, Heintz J, Vinnere Pettersson O, Jondelius U
Front Genet 14 (-) 1244493 [2023-09-26; online 2023-09-26]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Molecular anatomy of adult mouse leptomeninges.
Pietilä R, Del Gaudio F, He L, ..., Andrae J, Betsholtz C
Neuron - (-) - [2023-09-25; online 2023-09-25]
Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
Fast and sensitive validation of fusion transcripts in whole-genome sequencing data.
Hafstað V, Häkkinen J, Persson H
BMC Bioinformatics 24 (1) 359 [2023-09-23; online 2023-09-23]
Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
Detection of transcriptome-wide microRNA-target interactions in single cells with agoTRIBE.
Sekar V, Mármol-Sánchez E, Kalogeropoulos P, ..., Biryukova I, Friedländer MR
Nat. Biotechnol. - (-) - [2023-09-21; online 2023-09-21]
Bioinformatics Support for Computational Resources [Service] 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
Single-cell sequencing of tumor-associated macrophages in a Drosophila model.
Khalili D, Mohammed M, Kunc M, ..., Ankarklev J, Theopold U
Front Immunol 14 (-) 1243797 [2023-09-19; online 2023-09-19]
Bioinformatics Support for Computational Resources [Service] Microbial Single Cell Genomics [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick.
Rahlff J, Wietz M, Giebel HA, ..., Antson A, Holmfeldt K
ISME COMMUN. 3 (1) 97 [2023-09-18; online 2023-09-18]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
In vivo gene expression profile of Haemophilus influenzae during human pneumonia.
Polland L, Rydén H, Su Y, Paulsson M
Microbiol Spectr 11 (5) e0163923 [2023-09-14; online 2023-09-14]
Bioinformatics Support for Computational Resources [Service] Clinical Genomics Lund [Service]
PubMed DOI Crossref
Genetic atlas of hygro-and thermosensory cells in the vinegar fly Drosophila melanogaster.
Corthals K, Andersson V, Churcher A, Reimegård J, Enjin A
Sci Rep 13 (1) 15202 [2023-09-14; online 2023-09-14]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Dissecting the genetic basis of drought responses in common bean using natural variation.
Labastida D, Ingvarsson PK, Rendón-Anaya M
Front Plant Sci 14 (-) 1143873 [2023-09-14; online 2023-09-14]
Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
Ectomycorrhizal fungi integrate nitrogen mobilisation and mineral weathering in boreal forest soil.
Mahmood S, Fahad Z, Bolou-Bi EB, ..., Ekblad A, Finlay RD
New Phytol. - (-) - [2023-09-11; online 2023-09-11]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A novel kleptoplastidic symbiosis revealed in the marine centrohelid Meringosphaera with evidence of genetic integration.
Sørensen MES, Zlatogursky VV, Onuţ-Brännström I, ..., Foster RA, Burki F
Curr. Biol. 33 (17) 3571-3584.e6 [2023-09-11; online 2023-08-02]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The Genomic Basis of Adaptation to High Elevations in Africanized Honey Bees.
Everitt T, Wallberg A, Christmas MJ, ..., Neumann P, Webster MT
Genome Biol Evol 15 (9) - [2023-09-01; online 2023-08-26]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [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) 62 (9) 3213-3218 [2023-09-01; online 2023-04-03]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] 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
IBS randomized study: FODMAPs alter bile acids, phenolic- and tryptophan metabolites, while gluten modifies lipids.
Nordin E, Hellström PM, Vuong E, ..., Brunius C, Landberg R
Am. J. Physiol. Regul. Integr. Comp. Physiol. 325 (3) R248-R259 [2023-09-01; online 2023-07-03]
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Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity.
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Circular RNAs arising from synaptic host genes during human neuronal differentiation are modulated by SFPQ RNA-binding protein.
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BMC Ecol Evol 23 (1) 21 [2023-05-25; online 2023-05-25]
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Structural, vibrational, elastic, electronic, and piezoelectric properties of binary <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML">γ<mml:mtext>−</mml:mtext><mml:mrow>GeX</mml:mrow></mml:math> and ternary <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML">γ<mml:mtext>−</mml:mtext><mml:mrow><mml:msub>Ge2</mml:msub>X<mml:msup>X′</mml:msup></mml:mrow></mml:math> monolayers ( <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML">X</mml:math> , <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup>X′</mml:msup>=<mml:mi mathvariant="normal">S</mml:math> , Se, and Te)
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Three-dimensional genome rewiring in loci with human accelerated regions.
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Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.
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Integrating gene annotation with orthology inference at scale.
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Evolutionary constraint and innovation across hundreds of placental mammals.
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A genomic timescale for placental mammal evolution.
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Red clover root-associated microbiota is shaped by geographic location and choice of farming system.
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PIK3CA is recurrently mutated in canine mammary tumors, similarly to in human mammary neoplasia.
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Year 2022

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Upper gut heat shock proteins HSP70 and GRP78 promote insulin resistance, hyperglycemia, and non-alcoholic steatohepatitis.
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Gallionella and Sulfuricella populations are dominant during the transition of boreal potential to actual acid sulfate soils
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Lundtoft C, Sjöwall C, Rantapää-Dahlqvist S, ..., Leonard D, Rönnblom L
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ZEB2 haploinsufficient Mowat-Wilson syndrome induced pluripotent stem cells show disrupted GABAergic transcriptional regulation and function.
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Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level.
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Spatiotemporal variations in retrovirus-host interactions among Darwin's finches.
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Pax3 loss of function delays tumour progression in kRAS-induced zebrafish rhabdomyosarcoma models.
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The effects of pH on the production of volatile fatty acids and microbial dynamics in long-term reactor operation.
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Pontiller B, Martínez-García S, Joglar V, ..., Teira E, Pinhassi J
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Prostate cancer disease recurrence after radical prostatectomy is associated with HLA type and local cytomegalovirus immunity.
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Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.
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Saha A, Andersson A, Kurland S, ..., Ryman N, Laikre L
Mol. Ecol. 31 (2) 498-511 [2022-01-00; online 2021-11-15]
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Zool Scr 51 (1) 32-40 [2022-01-00; online 2021-11-04]
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New Phytol. 233 (1) 443-457 [2022-01-00; online 2021-10-27]
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Limnol Oceanogr 67 (1) 135-146 [2022-01-00; online 2021-11-18]
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Novel loss-of-function variant in DENND5A impedes melanosomal cargo transport and predisposes to familial cutaneous melanoma.
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Genet Med 24 (1) 157-169 [2022-01-00; online 2021-11-30]
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Improved breast cancer histological grading using deep learning.
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Dev. Comp. Immunol. 126 (-) 104181 [2022-01-00; online 2021-06-24]
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Genes from oxidative phosphorylation complexes II-V and two dual-function subunits of complex I are transcribed in Viscum album despite absence of the entire mitochondrial holo-complex I.
Petersen G, Shyama Prasad Rao R, Anderson B, ..., Rasmusson AG, Max Møller I
Mitochondrion 62 (-) 1-12 [2022-01-00; online 2021-11-02]
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Cell type-specific analysis by single-cell profiling identifies a stable mammalian tRNA-mRNA interface and increased translation efficiency in neurons.
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Genome Res. 32 (1) 97-110 [2022-01-00; online 2021-12-02]
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Vacancy assisted growth of copper tantalum sulfide nanocrystals
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Year 2021

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Exploring bycatch diversity of organisms in whole genome sequencing of Erebidae moths (Lepidoptera).
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Sci Rep 11 (1) 24499 [2021-12-30; online 2021-12-30]
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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]
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Phys. Rev. B 104 (24) - [2021-12-09; online 2021-12-09]
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The SEQC2 epigenomics quality control (EpiQC) study.
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Seidel L, Broman E, Turner S, Ståhle M, Dopson M
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Insights into the changes in the proteome of Alzheimer disease elucidated by a meta-analysis.
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Spatial Transcriptomics to define transcriptional patterns of zonation and structural components in the mouse liver.
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Sci Rep 11 (1) 23214 [2021-12-01; online 2021-12-01]
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Nat Commun 12 (1) 6651 [2021-11-17; online 2021-11-17]
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Cell Rep 37 (7) 110015 [2021-11-16; online 2021-11-18]
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Do different growth rates of trees cause distinct habitat qualities for saproxylic assemblages?
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The performance of common SNP arrays in assigning African mitochondrial haplogroups.
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Transcriptome Analysis of Potato Infected with the Necrotrophic Pathogen Alternaria solani.
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Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens.
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Philippine Ayta possess the highest level of Denisovan ancestry in the world.
Larena M, McKenna J, Sanchez-Quinto F, ..., Endicott P, Jakobsson M
Curr. Biol. 31 (19) 4219-4230.e10 [2021-10-11; online 2021-08-12]
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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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BMC Bioinformatics 22 (1) 488 [2021-10-09; online 2021-10-09]
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Hakim R, Zachariadis V, Sankavaram SR, ..., Enge M, Svensson M
J. Neurosci. 41 (40) 8441-8459 [2021-10-06; online 2021-08-20]
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Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis.
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BMC Genomics 22 (1) 710 [2021-10-02; online 2021-10-02]
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Spatiotemporally flexible subnetworks reveal the quasi-cyclic nature of integration and segregation in the human brain.
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Neuroimage 239 (-) 118287 [2021-10-01; online 2021-06-18]
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Bioaugmentation as a strategy for tailor-made volatile fatty acid production.
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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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Serum 25-hydroxyvitamin D is associated with fracture risk only during periods of seasonally high levels in women with a high body mass index.
Michaëlsson K, Byberg L, Svennblad B, ..., Baron JA, Melhus H
J. Bone Miner. Res. 36 (10) 1957-1966 [2021-10-00; online 2021-07-10]
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Rapid evolution of sexual size dimorphism facilitated by Y-linked genetic variance.
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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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Maternal genetic origin of the late and final Neolithic human populations from present-day Poland.
Juras A, Ehler E, Chyleński M, ..., Jakobsson M, Dabert M
Am. J. Phys. Anthropol. 176 (2) 223-236 [2021-10-00; online 2021-07-26]
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Hammarsjö A, Pettersson M, Chitayat D, ..., Lindstrand A, Grigelioniene G
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.
Sundbaum JK, Baecklund E, Eriksson N, ..., Wadelius M, Hallberg P
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.
Lagercrantz U, Billhardt A, Rousku SN, ..., Reza SH, Eklund DM
New Phytol. 232 (2) 595-609 [2021-10-00; online 2021-08-19]
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Montoliu-Nerin M, Sánchez-García M, Bergin C, ..., Bever JD, Rosling A
Front. Fungal Biol. 2 (-) - [2021-09-29; online 2021-09-29]
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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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Metabolic drift in the aging nervous system is reflected in human cerebrospinal fluid.
Peters K, Herman S, Khoonsari PE, ..., Neumann S, Kultima K
Sci Rep 11 (1) 18822 [2021-09-22; online 2021-09-22]
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Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration.
Sigeman H, Strandh M, Proux-Wéra E, ..., Westerdahl H, Hansson B
Mol. Biol. Evol. 38 (12) 5275-5291 [2021-09-20; online 2021-09-20]
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Single-Cell Analysis Reveals Major Histocompatibility Complex II‒Expressing Keratinocytes in Pressure Ulcers with Worse Healing Outcomes.
Li D, Cheng S, Pei Y, ..., Deng Q, Xu Landén N
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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Limited access to antigen drives generation of early B cell memory while restraining the plasmablast response.
Glaros V, Rauschmeier R, Artemov AV, ..., Busslinger M, Kreslavsky T
Immunity 54 (9) 2005-2023.e10 [2021-09-14; online 2021-09-16]
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Dual RNA-seq transcriptome analysis of caecal tissue during primary Eimeria tenella infection in chickens.
Sandholt AKS, Wattrang E, Lilja T, ..., Svärd SG, Söderlund R
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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Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues.
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Monocytes in sarcoidosis are potent tumour necrosis factor producers and predict disease outcome.
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Mammuthus sp. (Early and Middle Pleistocene Mammoths).
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