NGI Short read

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Secondary: Not shown in the list of current labels.

Started: -

Ended: Current

Year 2024

PubMed DOI Crossref
The evolutionary history of metastatic pancreatic neuroendocrine tumours reveals a therapy driven route to high-grade transformation.
Backman S, Botling J, Nord H, ..., Åkerström T, Crona J
J. Pathol. 264 (4) 357-370 [2024-12-00; online 2024-10-03]
Bioinformatics Support for Computational Resources [Service] Clinical Genomics Uppsala [Collaborative] NGI SNP genotyping [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomics of severe and treatment-resistant obsessive-compulsive disorder treated with deep brain stimulation: A preliminary investigation.
Chen LL, Naesström M, Halvorsen M, ..., Crowley JJ, Pascal D
Am. J. Med. Genet. B Neuropsychiatr. Genet. 195 (8) e32983 [2024-12-00; online 2024-04-22]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Genomic signals of adaptation to a natural CO2 gradient over a striking microgeographic scale
González-Delgado S, Pérez-Portela R, Ortega-Martínez O, ..., Pereyra RT, Hernández JC
Marine Pollution Bulletin 209 (-) 117225 [2024-12-00; online 2024-12-00]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Genetic diversity insights from population genomics and machine learning tools for Nordic Arctic charr (Salvelinus alpinus) populations
Palaiokostas C, Kurta K, Pappas F, ..., Janhunen M, Kause A
Aquaculture Reports 39 (-) 102495 [2024-12-00; online 2024-12-00]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Perfluorooctanesulfonic acid (PFOS) induced cancer related DNA methylation alterations in human breast cells: A whole genome methylome study.
Pierozan P, Höglund A, Theodoropoulou E, Karlsson O
Sci. Total Environ. 949 (-) 174864 [2024-11-01; online 2024-07-20]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The non-canonical BAF chromatin remodeling complex is a novel target of spliceosome dysregulation in SF3B1-mutated chronic lymphocytic leukemia.
Hägerstrand D, Oder B, Cortese D, ..., Sutton LA, Rosenquist R
Leukemia 38 (11) 2429-2442 [2024-11-00; online 2024-09-11]
Bioinformatics Support for Computational Resources [Service] Global Proteomics and Proteogenomics [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Local climate, air quality and leaf litter cover shape foliar fungal communities on an urban tree.
Faticov M, Amorim JH, Abdelfattah A, ..., Laforest-Lapointe I, Tack AJM
Ambio 53 (11) 1673-1685 [2024-11-00; online 2024-06-13]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Genomic and functional characterization of the Atlantic salmon gut microbiome in relation to nutrition and health.
Vera-Ponce de León A, Hensen T, Hoetzinger M, ..., Pope PB, La Rosa SL
Nat Microbiol 9 (11) 3059-3074 [2024-11-00; online 2024-10-14]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Examining the liver-pancreas crosstalk reveals a role for the molybdenum cofactor in β-cell regeneration.
Karampelias C, Băloiu B, Rathkolb B, ..., Hrabě de Angelis M, Andersson O
Life Sci. Alliance 7 (11) e202402771 [2024-11-00; online 2024-08-19]
Bioinformatics Support for Computational Resources [Service] NGI Short read NGI Stockholm (Genomics Production) National Genomics Infrastructure
PubMed DOI Crossref
Depth-specific distribution of bacterial MAGs in permafrost active layer in Ny Ålesund, Svalbard (79°N).
Sipes K, Buongiorno J, Steen AD, ..., Vishnivetskaya TA, Lloyd KG
Syst. Appl. Microbiol. 47 (6) 126544 [2024-11-00; online 2024-08-28]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Characterization of Pediatric Acute Myeloid Leukemia With t(7;12)(q36;p13)
Östlund A, Waraky A, Staffas A, ..., Abrahamsson J, Palmqvist L
Genes Chromosomes Cancer 63 (11) - [2024-11-00; online 2024-11-07]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope.
Shafighi S, Geras A, Jurzysta B, ..., Lagergren J, Szczurek E
Nat Commun 15 (1) 9343 [2024-10-29; online 2024-10-29]
NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivors.
Bian X, Piipponen M, Liu Z, ..., Halle M, Xu Landén N
Nat Commun 15 (1) 9286 [2024-10-28; online 2024-10-28]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
ADAR3 modulates neuronal differentiation and regulates mRNA stability and translation.
Karlström V, Sagredo EA, Planells J, ..., Visa N, Öhman M
Nucleic Acids Res. 52 (19) 12021-12038 [2024-10-28; online 2024-09-01]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A Phylogenomic Backbone for Acoelomorpha Inferred from Transcriptomic Data.
Abalde S, Jondelius U
Syst. Biol. - (-) - [2024-10-25; online 2024-10-25]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Oral-gut microbiome interactions in advanced cirrhosis: characterisation of pathogenic enterotypes and salivatypes, virulence factors and antimicrobial.
Lee S, Arefaine B, Begum N, ..., Shoaie S, Patel VC
J Hepatol - (-) - [2024-10-22; online 2024-10-22]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Persistent effects of di-n-butyl phthalate on liver transcriptome: impaired energy and lipid metabolic pathways.
Theodoropoulou E, Pierozan P, Marabita F, Höglund A, Karlsson O
Chemosphere - (-) 143605 [2024-10-21; online 2024-10-21]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Characteristics of gene expression in epicardial adipose tissue and subcutaneous adipose tissue in patients at risk for heart failure undergoing coronary artery bypass grafting.
Frisk C, Ekström M, Eriksson MJ, ..., Linde C, Persson B
BMC Genomics 25 (1) 938 [2024-10-07; online 2024-10-07]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Metagenomic characterization of viruses in the serum of children with newly diagnosed cancer.
Leijonhufvud G, Soratto TAT, Matos GM, ..., Ljungman G, Andersson B
J. Clin. Virol. 175 (-) 105736 [2024-10-06; online 2024-10-06]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The lncRNA SNHG26 drives the inflammatory-to-proliferative state transition of keratinocyte progenitor cells during wound healing.
Li D, Liu Z, Zhang L, ..., Sommar P, Xu Landén N
Nat Commun 15 (1) 8637 [2024-10-05; online 2024-10-05]
Bioinformatics Support for Computational Resources [Service] 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]
PubMed DOI Crossref
The Population History of Domestic Sheep Revealed by Paleogenomes.
Kaptan D, Atağ G, Vural KB, ..., Somel M, Özer F
Mol. Biol. Evol. 41 (10) - [2024-10-04; online 2024-10-23]
Ancient DNA [Service] NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Multi-omics analysis reveals the key factors involved in the severity of the Alzheimer's disease.
Meng L, Jin H, Yulug B, ..., Uhlén M, Mardinoglu A
Alzheimers Res Ther 16 (1) 213 [2024-10-02; online 2024-10-02]
Affinity Proteomics Uppsala [Service] Bioinformatics Support for Computational Resources [Service] NGI Short read NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Ebullition dominates methane emissions in stratified coastal waters.
Hermans M, Stranne C, Broman E, ..., Jilbert T, Humborg C
Sci. Total Environ. 945 (-) 174183 [2024-10-01; online 2024-06-21]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
High rate of gene family evolution in proximity to the origin of ectomycorrhizal symbiosis in Inocybaceae.
Khan FK, Sánchez-García M, Johannesson H, Ryberg M
New Phytol. 244 (1) 219-234 [2024-10-00; online 2024-08-07]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comparative proteomic analyses of potato leaves from field-grown plants grown under extremely long days.
Resjö S, Willforss J, Large A, ..., Levander F, Andreasson E
Plant Physiol Biochem 215 (-) 109032 [2024-10-00; online 2024-08-10]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] Swedish Metabolomics Centre (SMC) [Service]
PubMed DOI Crossref
"Metagenomics reveal the potential for geosmin and 2-methylisoborneol production across multiple bacterial phyla in recirculating aquaculture systems".
Zheng D, Wilén BM, Öberg O, Wik T, Modin O
Environ. Microbiol. 26 (10) e16696 [2024-10-00; online 2024-10-09]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Claustrum and dorsal endopiriform cortex complex cell-identity is determined by Nurr1 and regulates hallucinogenic-like states in mice.
Mantas I, Flais I, Masarapu Y, ..., Perlmann T, Svenningsson P
Nat Commun 15 (1) 8176 [2024-09-18; online 2024-09-18]
NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.
Mc Cartney AM, Formenti G, Mouton A, ..., Waterhouse RM, Mazzoni CJ
NPJ Biodivers 3 (1) 28 [2024-09-17; online 2024-09-17]
Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] 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
Unraveling the Genetics of Shared Clinical and Serological Manifestations in Patients With Systemic Inflammatory Autoimmune Diseases.
Bianchi M, Kozyrev SV, Notarnicola A, ..., Lindblad-Toh K, with the DISSECT consortium and the ImmunoArray consortium
Arthritis & rheumatology (Hoboken, N.J.) - (-) - [2024-09-16; online 2024-09-16]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Chromosome-level genome assembly of the morabine grasshopper Vandiemenella viatica19.
Li X, Jayaprasad S, Einarsdottir E, ..., Kawakami T, Palacios-Gimenez OM
Sci Data 11 (1) 997 [2024-09-12; online 2024-09-12]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Service] NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Enrichment of Cis-Acting Regulatory Elements in Differentially Methylated Regions Following Lipopolysaccharide Treatment of Bovine Endometrial Epithelial Cells.
Jhamat N, Guo Y, Han J, ..., Andersson G, Niazi A
Int J Mol Sci 25 (18) - [2024-09-11; online 2024-09-11]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Loss of Lamin A leads to the nuclear translocation of AGO2 and compromised RNA interference.
Lobo V, Nowak I, Fernandez C, ..., Angeletti D, Sarshad AA
Nucleic Acids Res. 52 (16) 9917-9935 [2024-09-09; online 2024-07-12]
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
Male-biased recombination at chromosome ends in a songbird revealed by precisely mapping crossover positions.
Zhang H, Lundberg M, Ponnikas S, Hasselquist D, Hansson B
G3 (Bethesda) 14 (9) - [2024-09-04; online 2024-07-10]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Immune system adaptation during gender-affirming testosterone treatment
Tadepally L, Consiglio C, Sardh F, ..., Landegren N, Brodin P
Nature 633 (-) 155-164 [2024-09-04]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Temporal dynamics of faster neo-Z evolution in butterflies.
Höök L, Vila R, Wiklund C, Backström N
Evolution 78 (9) 1554-1567 [2024-09-03; online 2024-05-30]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Gene-based association analysis of a large patient cohort provides insights into genetics of atypical femur fractures.
Zhou W, Ås J, Shore-Lorenti C, ..., Ebeling PR, Zillikens MC
J. Bone Miner. Res. 39 (9) 1315-1326 [2024-09-02; online 2024-08-10]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Transcriptomic and functional analyses on a Botrytis cinerea multidrug-resistant (MDR) strain provides new insights into the potential molecular mechanisms of MDR and fitness.
Sofianos G, Piombo E, Dubey M, ..., Karaoglanidis G, Tzelepis G
Mol. Plant Pathol. 25 (9) e70004 [2024-09-00; online 2024-09-08]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Species-genetic diversity correlation in a metacommunity of urban pond invertebrates
Johansson F, Yildirim Y, Hyseni C, ..., Höglund J, Bini LM
Basic and Applied Ecology 79 (-) 114-122 [2024-09-00; online 2024-09-00]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Speciation in savanna birds in South America: The case of the Least Nighthawk Chordeiles pusillus (Aves: Caprimulgidae) in and out of the Amazon.
Fernandes AM, Cohn-Haft M, Fábio Silveira L, ..., Nascimento N, Olsson U
Mol. Phylogenet. Evol. 198 (-) 108117 [2024-09-00; online 2024-06-07]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Plastome evolution in Santalales involves relaxed selection prior to loss of ndh genes and major boundary shifts of the inverted repeat.
Edlund M, Anderson BM, Su H, ..., Nickrent DL, Petersen G
Ann. Bot. - (-) - [2024-08-30; online 2024-08-30]
NGI Short read NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Five centuries of consanguinity, isolation, health, and conflict in Las Gobas: A Northern Medieval Iberian necropolis.
Rodríguez-Varela R, Yaka R, Pochon Z, ..., Azkarate A, Götherström A
Sci Adv 10 (35) eadp8625 [2024-08-30; online 2024-08-28]
Ancient DNA [Collaborative] Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
An intronic copy number variation in Syntaxin 17 determines speed of greying and melanoma incidence in Grey horses.
Rubin CJ, Hodge M, Naboulsi R, ..., Lindgren G, Andersson L
Nat Commun 15 (1) 7510 [2024-08-29; online 2024-08-29]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Massively parallel analysis of single-molecule dynamics on next-generation sequencing chips.
Aguirre Rivera J, Mao G, Sabantsev A, ..., Jinek M, Deindl S
Science 385 (6711) 892-898 [2024-08-23; online 2024-08-22]
NGI Short read [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]
PubMed DOI Crossref
CDK8 of the mediator kinase module connects leaf development to the establishment of correct stomata patterning by regulating the levels of the transcription factor SPEECHLESS (SPCH).
Hermida-Carrera C, Vergara A, Cervela-Cardona L, ..., Björklund S, Strand Å
Plant Cell Environ. - (-) - [2024-08-23; online 2024-08-23]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Origin, structure, and composition of the spider major ampullate silk fiber revealed by genomics, proteomics, and single-cell and spatial transcriptomics.
Sonavane S, Hassan S, Chatterjee U, ..., Reimegård J, Rising A
Sci Adv 10 (33) eadn0597 [2024-08-16; online 2024-08-14]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Spatial omics [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Decrease due to pollution in the rhizosphere microbial diversity can be amended by supplementation from adapted plants of another species.
Fetsiukh A, Pall T, Timmusk S
Sci Rep 14 (1) 18806 [2024-08-13; online 2024-08-13]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Few chemoreceptor genes in the ambrosia beetle Trypodendron lineatum may reflect its specialized ecology.
Biswas T, Vogel H, Biedermann PHW, ..., Yuvaraj JK, Andersson MN
BMC Genomics 25 (1) 764 [2024-08-06; online 2024-08-06]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins.
Unneberg P, Larsson M, Olsson A, ..., Meyer B, Wallberg A
Nat Commun 15 (1) 6297 [2024-08-01; online 2024-08-01]
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] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Why we thrive beneath a northern sky - genomic signals of selection in apple for adaptation to northern Sweden.
Skytte Af Sätra J, Garkava-Gustavsson L, Ingvarsson PK
Heredity (Edinb) 133 (2) 67-77 [2024-08-00; online 2024-06-04]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Selection against domestication alleles in introduced rabbit populations.
Andrade P, Alves JM, Pereira P, ..., Andersson L, Carneiro M
Nat Ecol Evol 8 (8) 1543-1555 [2024-08-00; online 2024-06-21]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids.
Duan T, Zhang Z, Genete M, ..., Castric V, Vekemans X
Evolution Letters 8 (4) 550-560 [2024-08-00; online 2024-03-17]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing.
Lysenkova Wiklander M, Arvidsson G, Bunikis I, ..., Ameur A, Nordlund J
Life Sci. Alliance 7 (8) - [2024-08-00; online 2024-05-22]
Bioinformatics Support for Computational Resources [Service] NGI Long read [Collaborative] NGI Short read [Collaborative] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
A pipeline for identification of causal mutations in barley identifies Xantha-j as the chlorophyll synthase gene.
Stuart D, Zakhrabekova S, Jørgensen ME, Dockter C, Hansson M
Plant Physiol. 195 (4) 2877-2890 [2024-07-31; online 2024-04-17]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A genetic-epigenetic interplay at 1q21.1 locus underlies CHD1L-mediated vulnerability to primary progressive multiple sclerosis.
Pahlevan Kakhki M, Giordano A, Starvaggi Cucuzza C, ..., Kular L, Jagodic M
Nat Commun 15 (1) 6419 [2024-07-30; online 2024-07-30]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Hybridization in birds-of-paradise: Widespread ancestral gene flow despite strong sexual selection in a lek-mating system.
Blom MPK, Peona V, Prost S, ..., Suh A, Irestedt M
iScience 27 (7) 110300 [2024-07-19; online 2024-06-19]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The rate of W chromosome degeneration across multiple avian neo-sex chromosomes.
Sigeman H, Downing PA, Zhang H, Hansson B
Sci Rep 14 (1) 16548 [2024-07-17; online 2024-07-17]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Temporal dynamics of woolly mammoth genome erosion prior to extinction.
Dehasque M, Morales HE, Díez-Del-Molino D, ..., Vartanyan S, Dalén L
Cell 187 (14) 3531-3540.e13 [2024-07-11; online 2024-06-27]
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
Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci.
Grochowski CM, Bengtsson JD, Du H, ..., Lupski JR, Carvalho CMB
Cell Genomics 4 (7) 100590 [2024-07-10; online 2024-06-21]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
DNA methylation of exercise-responsive genes differs between trained and untrained men.
Geiger C, Needhamsen M, Emanuelsson EB, ..., Reitzner SM, Lindholm ME
BMC Biol. 22 (1) 147 [2024-07-04; online 2024-07-04]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring.
Pettersson ME, Quintela M, Besnier F, ..., Glover KA, Andersson L
Genome Biol Evol 16 (7) - [2024-07-03; online 2024-06-26]
Bioinformatics Support for Computational Resources [Service] 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 Genomic Analysis of the Pattern of Evolution of Male and Female Reproductive Proteins in Seed Beetles.
Papachristos K, Sayadi A, Arnqvist G
Genome Biol Evol 16 (7) - [2024-07-03; online 2024-06-28]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support for Computational Resources [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
Chromosome-level genome assembly and annotation of the social amoeba Dictyostelium firmibasis.
Edelbroek B, Kjellin J, Jerlström-Hultqvist J, Koskiniemi S, Söderbom F
Sci Data 11 (1) 678 [2024-06-22; online 2024-06-22]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215.
Kellgren T, Dwibedi C, Widerström M, ..., Rydén P, Johansson A
BMC Microbiol. 24 (1) 215 [2024-06-19; online 2024-06-19]
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Sci Data 11 (1) 617 [2024-06-12; online 2024-06-12]
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Front Microbiol 15 (-) 1393538 [2024-06-07; online 2024-06-07]
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Nat Commun 15 (1) 4883 [2024-06-07; online 2024-06-07]
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G3 (Bethesda) 14 (6) - [2024-06-05; online 2024-04-24]
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Larsson MNA, Morell Miranda P, Pan L, ..., Storå J, Günther T
Genome Biol Evol 16 (6) - [2024-06-04; online 2024-05-25]
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Endocr. Pathol. 35 (2) 122-133 [2024-06-00; online 2024-01-27]
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Quaternary International 694 (-) 1-12 [2024-06-00; online 2024-06-00]
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Boman J, Qvarnström A, Mugal CF
BMC Biol. 22 (1) 124 [2024-05-29; online 2024-05-29]
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Müller IA, Thörn F, Rajan S, ..., Jønsson KA, Irestedt M
PLoS ONE 19 (5) e0293715 [2024-05-23; online 2024-05-23]
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Saccharomyces cerevisiae strains performing similarly during fermentation of lignocellulosic hydrolysates show pronounced differences in transcriptional stress responses.
Cámara E, Mormino M, Siewers V, Nygård Y
Appl. Environ. Microbiol. 90 (5) e0233023 [2024-05-21; online 2024-04-08]
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Thureborn O, Wikström N, Razafimandimbison SG, Rydin C
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Dev. Cell 59 (10) 1269-1283.e6 [2024-05-20; online 2024-04-01]
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Complex genetic architecture of the chicken Growth1 QTL region.
Ou JH, Rönneburg T, Carlborg Ö, ..., Siegel PB, Rubin CJ
PLoS ONE 19 (5) e0295109 [2024-05-13; online 2024-05-13]
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Mol Plant 17 (5) 725-746 [2024-05-06; online 2024-03-13]
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Meiotic drive against chromosome fusions in butterfly hybrids.
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Mar. Ecol. Prog. Ser. 735 (-) 63-76 [2024-05-02; online 2024-05-02]
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BioTechniques 76 (5) 216-223 [2024-05-00; online 2024-03-26]
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Front Plant Sci 15 (-) 1358490 [2024-04-26; online 2024-04-26]
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Nat Commun 15 (1) 3475 [2024-04-24; online 2024-04-24]
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Nucleic Acids Res. - (-) - [2024-04-13; online 2024-04-13]
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Cell 187 (8) 1990-2009.e19 [2024-04-11; online 2024-03-20]
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A time course analysis through diapause reveals dynamic temporal patterns of microRNAs associated with endocrine regulation in the butterfly Pieris napi.
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Biochem. Biophys. Res. Commun. 703 (-) 149658 [2024-04-09; online 2024-02-07]
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The HLA region in ANCA-associated vasculitis: characterisation of genetic associations in a Scandinavian patient population.
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Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures.
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Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis.
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Bergfeldt N, Kırdök E, Oskolkov N, ..., Storå J, Götherström A
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Genome Biol Evol 16 (3) - [2024-03-02; online 2024-02-22]
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Heredity (Edinb) 132 (3) 142-155 [2024-03-00; online 2024-01-30]
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The effect of nitrogen source and levels on hybrid aspen tree physiology and wood formation.
Renström A, Choudhary S, Gandla ML, ..., Jämtgård S, Tuominen H
Physiol Plantarum 176 (1) e14219 [2024-02-21; online 2024-02-21]
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Clonally heritable gene expression imparts a layer of diversity within cell types.
Mold JE, Weissman MH, Ratz M, ..., Michaëlsson J, Frisén J
Cell Syst 15 (2) 149-165.e10 [2024-02-21; online 2024-02-09]
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Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos.
Hold K, Lord E, Brealey JC, ..., Martin MD, Dussex N
Sci Rep 14 (1) 4143 [2024-02-20; online 2024-02-20]
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Lymphocytic colitis can be transcriptionally divided into channelopathic and inflammatory lymphocytic colitis.
Bhardwaj A, Münch A, Montague J, ..., Rosenstiel P, Escudero-Hernández C
United European Gastroenterol J - (-) - [2024-02-17; online 2024-02-17]
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Long noncoding RNA plasmacytoma variant translocation 1 is overexpressed in cutaneous squamous cell carcinoma and exon 2 is critical for its oncogenicity.
Li C, Sun C, Mahapatra KD, ..., Sonkoly E, Pivarcsi A
Br J Dermatol 190 (3) 415-426 [2024-02-16; online 2023-11-06]
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Gene co-expression network analysis reveal core responsive genes in Parascaris univalens tissues following ivermectin exposure.
Dube F, Delhomme N, Martin F, ..., Svärd S, Tydén E
PLoS ONE 19 (2) e0298039 [2024-02-15; online 2024-02-15]
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Phylogeography and phenotypic wing shape variation in a damselfly across populations in Europe.
Yildirim Y, Kristensson D, Outomuro D, ..., Sniegula S, Johansson F
BMC Ecol Evol 24 (1) 19 [2024-02-03; online 2024-02-03]
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Recent increase in species-wide diversity after interspecies introgression in the highly endangered Iberian lynx.
Lucena-Perez M, Paijmans JLA, Nocete F, ..., Barlow A, Godoy JA
Nat Ecol Evol 8 (2) 282-292 [2024-02-00; online 2024-01-15]
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Multimodal Single-Cell Sequencing of B Cells in Primary Sjögren's Syndrome.
Arvidsson G, Czarnewski P, Johansson A, ..., Nordmark G, Syvänen A
Arthritis & rheumatology (Hoboken, N.J.) 76 (2) 255-267 [2024-02-00; online 2023-12-18]
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Genetic diversity patterns in farmed rainbow trout (Oncorhynchus mykiss) populations using genome-wide SNP and haplotype data.
Longo A, Kurta K, Vanhala T, ..., de Koning DJ, Palaiokostas C
Anim Genet 55 (1) 87-98 [2024-02-00; online 2023-11-23]
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A survey of ficolin-3 activity in Systemic Lupus Erythematosus reveals a link to hematological disease manifestations and autoantibody profile.
Lindelöf L, Rantapää-Dahlqvist S, Lundtoft C, ..., Svenungsson E, Eriksson O
J. Autoimmun. 143 (-) 103166 [2024-02-00; online 2024-01-13]
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Batrachochytrium dendrobatidis strain affects transcriptomic response in liver but not skin in latitudinal populations of the common toad (Bufo bufo).
Chondrelli N, Kuehn E, Meurling S, ..., Laurila A, Höglund J
Sci Rep 14 (1) 2495 [2024-01-30; online 2024-01-30]
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A two-step activation mechanism enables mast cells to differentiate their response between extracellular and invasive enterobacterial infection.
von Beek C, Fahlgren A, Geiser P, ..., Pejler G, Sellin ME
Nat Commun 15 (1) 904 [2024-01-30; online 2024-01-30]
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Genetic diversity and recent ancestry based on whole-genome sequencing of endangered Swedish cattle breeds.
Harish A, Lopes Pinto FA, Eriksson S, Johansson AM
BMC Genomics 25 (1) 89 [2024-01-22; online 2024-01-22]
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Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton.
Grujčić V, Saarenpää S, Sundh J, ..., Foster RA, Andersson AF
PLoS ONE 19 (1) e0296672 [2024-01-19; online 2024-01-19]
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Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals.
Kırdök E, Kashuba N, Damlien H, ..., Aravena A, Götherström A
Sci Rep 13 (1) 22125 [2024-01-18; online 2024-01-18]
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Ciliate Grazing on the Bloom-Forming Microalga Gonyostomum semen.
Bergman I, Lindström ES, Sassenhagen I
Microb. Ecol. 87 (1) 33 [2024-01-18; online 2024-01-18]
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Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1-Mutant Myelodysplastic Syndromes with Ring Sideroblasts.
Moura PL, Mortera-Blanco T, Hofman IJ, ..., Jacobsen SEW, Hellström-Lindberg E
Cancer Res. 84 (2) 211-225 [2024-01-16; online 2023-11-03]
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Differential expression and alternative splicing analyses of multiple tissues reveal albinism-associated genes in the Wels catfish (Silurus glanis).
Ozerov MY, Noreikiene K, Kahar S, ..., Gross R, Vasemägi A
Comp Biochem Physiol B Biochem Mol Biol 271 (-) 110941 [2024-01-11; online 2024-01-11]
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Single-cell genomics of a bloom-forming phytoplankton species reveals population genetic structure across continents.
Gollnisch R, Ahrén D, Rengefors K
ISME J 18 (1) - [2024-01-08; online 2024-03-15]
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Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris.
Duan T, Sicard A, Glémin S, Lascoux M
Elife 12 (-) - [2024-01-08; online 2024-01-08]
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A pan-genomic approach reveals novel Sulfurimonas clade in the ferruginous meromictic Lake Pavin.
Biderre-Petit C, Courtine D, Hennequin C, ..., Divne A, Hochart C
Mol Ecol Resour - (-) e13923 [2024-01-08; online 2024-01-08]
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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]
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Identification of a Notch transcriptomic signature for breast cancer.
Braune EB, Geist F, Tang X, ..., Wienke D, Lendahl U
Breast Cancer Res. 26 (1) 4 [2024-01-03; online 2024-01-03]
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Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network.
Hunt G, Vaid R, Pirogov S, ..., Reimegård J, Mannervik M
Genome Biol. 25 (1) 2 [2024-01-02; online 2024-01-02]
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A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea.
Latz MAC, Andersson A, Brugel S, ..., Torstensson A, Andersson AF
Sci Data 11 (1) 18 [2024-01-02; online 2024-01-02]
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Global Transcriptome Analysis Reveals Distinct Phases of the Endothelial Response to TNF.
Struck EC, Belova T, Hsieh PH, ..., Dusart PJ, Butler LM
J. Immunol. 212 (1) 117-129 [2024-01-01; online 2023-11-29]
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Whole-genome selective sweep analyses identifies the region and candidate gene associated with white earlobe color in Mediterranean chickens.
Guo Y, Rubin CJ, Rönneburg T, ..., Hu X, Carlborg Ö
Poult. Sci. 103 (1) 103232 [2024-01-00; online 2023-10-24]
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The genetic legacy of the expansion of Bantu-speaking peoples in Africa.
Fortes-Lima CA, Burgarella C, Hammarén R, ..., Bostoen K, Schlebusch CM
Nature 625 (7995) 540-547 [2024-01-00; online 2023-11-29]
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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]
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Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae).
Thureborn O, Wikström N, Razafimandimbison SG, Rydin C
Ecol Evol 14 (1) e10868 [2024-01-00; online 2024-01-25]
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Novel candidate taxa contribute to key metabolic processes in Fennoscandian Shield deep groundwaters.
Dopson M, Rezaei Somee M, González-Rosales C, ..., Mehrshad M, Bertilsson S
ISME COMMUN. 4 (1) ycae113 [2024-01-00; online 2024-09-23]
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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]
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New chemical and microbial perspectives on vitamin B1 and vitamer dynamics of a coastal system.
Bittner MJ, Bannon CC, Rowland E, ..., Paerl RW, Riemann L
ISME COMMUN. 4 (1) ycad016 [2024-01-00; online 2024-01-10]
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Molecular profiling of high-level athlete skeletal muscle after acute endurance or resistance exercise – A systems biology approach
Reitzner SM, Emanuelsson EB, Arif M, ..., Chapman MA, Sundberg CJ
Mol Metab 79 (-) 101857 [2024-01-00; online 2024-01-00]
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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]
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Population genomic data reveal low genetic diversity, divergence and local adaptation among threatened Reeves's Pheasant (Syrmaticus reevesii)
Lu Q, Wang P, Chang J, ..., Höglund J, Zhang Z
Avian Research 15 (-) 100156 [2024-00-00; online 2024-00-00]
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A combination of long- and short-read genomics reveals frequent p-arm breakpoints within chromosome 21 complex genomic rearrangements
Schuy J, Sæther KB, Lisfeld J, ..., Eisfeldt J, Lindstrand A
Genetics in Medicine Open 2 (-) 101863 [2024-00-00; online 2024-00-00]
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Year 2023

PubMed DOI Crossref
Impact of the gut microbiome on immunological responses to COVID-19 vaccination in healthy controls and people living with HIV.
Ray S, Narayanan A, Vesterbacka J, ..., Sönnerborg A, Nowak P
NPJ Biofilms Microbiomes 9 (1) 104 [2023-12-20; online 2023-12-20]
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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]
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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]
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Short- and long-term effects of radiation exposure at low dose and low dose rate in normal human VH10 fibroblasts.
Akuwudike P, López-Riego M, Marczyk M, ..., Wojcik A, Lundholm L
Front Public Health 11 (-) 1297942 [2023-12-15; online 2023-12-15]
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Effect of anode material and dispersal limitation on the performance and biofilm community in microbial electrolysis cells.
Abadikhah M, Liu M, Persson F, ..., Sun J, Modin O
Biofilm 6 (-) 100161 [2023-12-15; online 2023-10-10]
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Balanced chromosomal rearrangements implicate YIPF5 and SPATC1L in non-obstructive oligoasthenozoospermia and oligozoospermia and of a derivative chromosome 22 in recurrent miscarriage.
David D, Fino J, Oliveira R, Dória S, Morton CC
Gene 887 (-) 147737 [2023-12-15; online 2023-08-23]
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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]
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The formation of the Indo-Pacific montane avifauna.
Reeve AH, Kennedy JD, Pujolar JM, ..., Nylander JAA, Jønsson KA
Nat Commun 14 (1) 8215 [2023-12-11; online 2023-12-11]
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The functional and molecular impact of triamcinolone acetonide on primary human bone marrow mesenchymal stem cells.
Kumlin M, Ungerstedt J, Cai H, ..., Felländer-Tsai L, Qian H
Sci Rep 13 (1) 21787 [2023-12-08; online 2023-12-08]
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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]
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Shared and distinct pathways and networks genetically linked to coronary artery disease between human and mouse.
Kurt Z, Cheng J, Barrere-Cain R, ..., Blencowe M, Yang X
Elife 12 (-) - [2023-12-07; online 2023-12-07]
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Lokatt: a hybrid DNA nanopore basecaller with an explicit duration hidden Markov model and a residual LSTM network.
Xu X, Bhalla N, Ståhl P, Jaldén J
BMC Bioinformatics 24 (1) 461 [2023-12-07; online 2023-12-07]
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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]
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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]
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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]
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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]
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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]
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DNA elements tether canonical Polycomb Repressive Complex 1 to human genes.
Barrasa JI, Kahn TG, Lundkvist MJ, Schwartz YB
Nucleic Acids Res. 51 (21) 11613-11633 [2023-11-27; online 2023-10-19]
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RecView: an interactive R application for locating recombination positions using pedigree data.
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BMC Genomics 24 (1) 712 [2023-11-25; online 2023-11-25]
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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]
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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]
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Improving diagnostic precision in primary ovarian insufficiency using comprehensive genetic and autoantibody testing.
Vogt EC, Bratland E, Berland S, ..., Husebye E, Øksnes M
Hum. Reprod. - (-) - [2023-11-09; online 2023-11-09]
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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]
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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]
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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]
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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]
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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]
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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]
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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]
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Translatome analysis of tuberous sclerosis complex 1 patient-derived neural progenitor cells reveals rapamycin-dependent and independent alterations.
Aksoylu IS, Martin P, Robert F, ..., Larsson O, Ramesh V
Mol Autism 14 (1) 39 [2023-10-25; online 2023-10-25]
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Complete Mitochondrial DNA Genome Variation in the Swedish Population.
Sturk-Andreaggi K, Bodner M, Ring JD, ..., Marshall C, Allen M
Genes 14 (11) - [2023-10-25; online 2023-10-25]
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Polymorphic parasitic larvae cooperate to build swimming colonies luring hosts.
Krupenko D, Miroliubov A, Kryukov E, ..., Kastriti ME, Adameyko I
Curr. Biol. 33 (20) 4524-4531.e4 [2023-10-23; online 2023-09-22]
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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]
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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]
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Associations between the Bacterial Composition of Farm Bulk Milk and the Microbiota in the Resulting Swedish Long-Ripened Cheese.
Sun L, Höjer A, Johansson M, ..., Dicksved J, Lundh Å
Foods 12 (20) - [2023-10-16; online 2023-10-16]
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Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients.
Sarén T, Ramachandran M, Gammelgård G, ..., Enblad G, Essand M
Clin. Cancer Res. 29 (20) 4139-4152 [2023-10-13; online 2023-08-04]
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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]
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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]
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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]
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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]
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Spatial transcriptomic analysis of virtual prostate biopsy reveals confounding effect of tissue heterogeneity on genomic signatures.
Figiel S, Yin W, Doultsinos D, ..., Cussenot O, Lamb AD
Mol. Cancer 22 (1) 162 [2023-10-03; online 2023-10-03]
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A T cell receptor targeting a recurrent driver mutation in FLT3 mediates elimination of primary human acute myeloid leukemia in vivo.
Giannakopoulou E, Lehander M, Virding Culleton S, ..., Woll PS, Olweus J
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The dynamics of touch-responsive gene expression in cereals.
Darwish E, Ghosh R, Bentzer J, ..., Sirijovski N, Van Aken O
Plant J. 116 (1) 282-302 [2023-10-00; online 2023-06-08]
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Similarity in milk microbiota in replicates.
Dahlberg J, Pelve E, Dicksved J
Microbiologyopen 12 (5) e1383 [2023-10-00; online 2023-10-25]
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B cell polygenic risk scores associate with anti-dsDNA antibodies and nephritis in systemic lupus erythematosus.
Hedenstedt A, Reid S, Sayadi A, ..., Sandling JK, Leonard D
Lupus Sci Med 10 (2) - [2023-10-00; online 2023-10-17]
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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]
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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]
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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]
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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]
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Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets.
Mihalič F, Benz C, Kassa E, ..., Jemth P, Ivarsson Y
Nat Commun 14 (1) 5636 [2023-09-13; online 2023-09-13]
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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]
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Placental growth factor exerts a dual function for cardiomyogenesis and vasculogenesis during heart development.
Witman N, Zhou C, Häneke T, ..., Chien KR, Sahara M
Nat Commun 14 (1) 5435 [2023-09-05; online 2023-09-05]
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Seasonal and age-related changes in sperm quality of farmed arctic charr (Salvelinus alpinus).
Kurta K, Jeuthe H, Naboulsi R, de Koning DJ, Palaiokostas C
BMC Genomics 24 (1) 519 [2023-09-04; online 2023-09-04]
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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]
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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]
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Milder Autumns May Increase Risk for Infection of Crops with Turnip Yellows Virus.
Puthanveed V, Singh K, Poimenopoulou E, ..., Siddique AB, Kvarnheden A
Phytopathology 113 (9) 1788-1798 [2023-09-00; online 2023-11-01]
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Contrasting genomic consequences of anthropogenic reintroduction and natural recolonization in high-arctic wild reindeer.
Burnett HA, Bieker VC, Le Moullec M, ..., Hansen BB, Martin MD
Evol Appl 16 (9) 1531-1548 [2023-09-00; online 2023-08-22]
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Chromatin accessibility, not 5mC methylation covaries with partial dosage compensation in crows.
Catalán A, Merondun J, Knief U, Wolf JBW
PLoS Genet. 19 (9) e1010901 [2023-09-00; online 2023-09-25]
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Inhibition of high level E2F in a RB1 proficient MYCN overexpressing chicken retinoblastoma model normalizes neoplastic behaviour.
Zhang H, Konjusha D, Rafati N, Tararuk T, Hallböök F
Cell Oncol (Dordr) - (-) - [2023-08-22; online 2023-08-22]
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Contrasting response of microeukaryotic and bacterial communities to the interplay of seasonality and local stressors in shallow soda lakes.
Márton Z, Csitári B, Felföldi T, ..., Szabó A, Székely AJ
FEMS Microbiol. Ecol. 99 (9) - [2023-08-22; online 2023-08-17]
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Expanding the genetic toolbox of Rhodotorula toruloides by identification and validation of six novel promoters induced or repressed under nitrogen starvation.
Brink DP, Mierke F, Norbeck J, Siewers V, Andlid T
Microb. Cell Fact. 22 (1) 160 [2023-08-19; online 2023-08-19]
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Multiplexed Guide RNA Expression Leads to Increased Mutation Frequency in Targeted Window Using a CRISPR-Guided Error-Prone DNA Polymerase in Saccharomyces cerevisiae.
Gossing M, Limeta A, Skrekas C, ..., Siewers V, David F
ACS Synth Biol 12 (8) 2271-2277 [2023-08-18; online 2023-07-24]
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Bacterial bioindicators enable biological status classification along the continental Danube river.
Fontaine L, Pin L, Savio D, ..., Farnleitner AH, Eiler A
Commun Biol 6 (1) 862 [2023-08-18; online 2023-08-18]
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An idiosyncratic zonated stroma encapsulates desmoplastic liver metastases and originates from injured liver.
Fernández Moro C, Geyer N, Harrizi S, ..., Bozóky B, Gerling M
Nat Commun 14 (1) 5024 [2023-08-18; online 2023-08-18]
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Environmental effects rather than relatedness determine gut microbiome similarity in a social mammal.
Bensch HM, Lundin D, Tolf C, Waldenström J, Zöttl M
J. Evol. Biol. - (-) - [2023-08-16; online 2023-08-16]
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Transcriptional maintenance of cortical somatostatin interneuron subtype identity during migration.
Munguba H, Nikouei K, Hochgerner H, ..., Linnarsson S, Hjerling-Leffler J
Neuron - (-) - [2023-08-15; online 2023-08-15]
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Feasibility to use whole-genome sequencing as a sole diagnostic method to detect genomic aberrations in pediatric B-cell acute lymphoblastic leukemia.
Rezayee F, Eisfeldt J, Skaftason A, ..., Rosenquist R, Barbany G
Front Oncol 13 (-) 1217712 [2023-08-14; online 2023-08-14]
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Molecular and spatial landmarks of early mouse skin development.
Jacob T, Annusver K, Czarnewski P, ..., Björklund ÅK, Kasper M
Dev. Cell - (-) - [2023-08-13; online 2023-08-13]
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Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe.
Mattila TM, Svensson EM, Juras A, ..., Malmström H, Jakobsson M
Commun Biol 6 (1) 793 [2023-08-09; online 2023-08-09]
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Megafaunal extinctions, not climate change, may explain Holocene genetic diversity declines in Numenius shorebirds.
Tan HZ, Jansen JJFJ, Allport GA, ..., Gwee CY, Rheindt FE
Elife 12 (-) - [2023-08-07; online 2023-08-07]
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Altered gut microbiota community structure and correlated immune system changes in dibutyl phthalate exposed mice.
Almamoun R, Pierozan P, Manoharan L, Karlsson O
Ecotoxicol Environ Saf 262 (-) 115321 [2023-08-05; online 2023-08-05]
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Relation between HLA and copy number variation of steroid 21-hydroxylase in a Swedish cohort of patients with autoimmune Addison's disease.
Lundtoft C, Eriksson D, Bianchi M, ..., Rönnblom L, Kämpe O
Eur. J. Endocrinol. 189 (2) 235-241 [2023-08-02; online 2023-08-09]
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Somatic Exonic Deletions in RUNX1 Constitutes a Novel Recurrent Genomic Abnormality in Acute Myeloid Leukemia.
Eriksson A, Engvall M, Mathot L, ..., Ladenvall C, Baliakas P
Clin. Cancer Res. 29 (15) 2826-2834 [2023-08-01; online 2023-04-07]
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Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age.
Chyleński M, Makarowicz P, Juras A, ..., Jakobsson M, Malmström H
Nat Commun 14 (1) 4395 [2023-08-01; online 2023-08-01]
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Base Composition, Codon Usage, and Patterns of Gene Sequence Evolution in Butterflies.
Näsvall K, Boman J, Talla V, Backström N
Genome Biol Evol 15 (8) - [2023-08-01; online 2023-08-11]
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Solid-phase capture and profiling of open chromatin by spatial ATAC.
Llorens-Bobadilla E, Zamboni M, Marklund M, ..., Frisén J, Ståhl PL
Nat. Biotechnol. 41 (8) 1085-1088 [2023-08-00; online 2023-01-05]
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Nascent evolution of recombination rate differences as a consequence of chromosomal rearrangements.
Näsvall K, Boman J, Höök L, ..., Wiklund C, Backström N
PLoS Genet. 19 (8) e1010717 [2023-08-00; online 2023-08-07]
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Methylation of lysine 36 on histone H3 is required to control transposon activities in somatic cells.
Lindehell H, Schwartz YB, Larsson J
Life Sci. Alliance 6 (8) - [2023-08-00; online 2023-05-11]
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Historical RNA expression profiles from the extinct Tasmanian tiger.
Mármol-Sánchez E, Fromm B, Oskolkov N, ..., Dalén L, Friedländer MR
Genome Res. 33 (8) 1299-1316 [2023-08-00; online 2023-07-18]
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Clones on the run: The genomics of a recently expanded partially clonal species.
Pereyra RT, Rafajlović M, De Wit P, ..., Töpel M, Johannesson K
Mol. Ecol. 32 (15) 4209-4223 [2023-08-00; online 2023-05-18]
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Characterisation of a low methane emission rice cultivar suitable for cultivation in high latitude light and temperature conditions.
Hu J, Bettembourg M, Moreno S, ..., Sundström J, Jin Y
Environ Sci Pollut Res 30 (40) 92950-92962 [2023-08-00; online 2023-07-27]
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scDual-Seq of Toxoplasma gondii-infected mouse BMDCs reveals heterogeneity and differential infection dynamics.
Hildebrandt F, Mohammed M, Dziedziech A, ..., Henriksson J, Ankarklev J
Front Immunol 14 (-) 1224591 [2023-07-27; online 2023-07-27]
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Cutaneous squamous cell carcinoma-derived extracellular vesicles exert an oncogenic role by activating cancer-associated fibroblasts.
Li C, Sun C, Lohcharoenkal W, ..., Sonkoly E, Pivarcsi A
Cell Death Discov 9 (1) 260 [2023-07-26; online 2023-07-26]
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Multiyear analysis uncovers coordinated seasonality in stocks and composition of the planktonic food web in the Baltic Sea proper.
Fridolfsson E, Bunse C, Lindehoff E, ..., Legrand C, Hylander S
Sci Rep 13 (1) 11865 [2023-07-22; online 2023-07-22]
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Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle.
Ginja C, Guimarães S, da Fonseca RR, ..., Pires AE, Valenzuela-Lamas S
iScience 26 (7) 107196 [2023-07-21; online 2023-06-24]
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FAVIS: Fast and versatile protocol for non-destructive metabarcoding of bulk insect samples.
Iwaszkiewicz-Eggebrecht E, Łukasik P, Buczek M, ..., Ronquist F, Miraldo A
PLoS ONE 18 (7) e0286272 [2023-07-19; online 2023-07-19]
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Salicylic acid metabolism and signalling coordinate senescence initiation in aspen in nature.
Lihavainen J, Šimura J, Bag P, ..., Ljung K, Jansson S
Nat Commun 14 (1) 4288 [2023-07-18; online 2023-07-18]
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Comparative transcriptome profiling provides insights into the growth promotion activity of Pseudomonas fluorescens strain SLU99 in tomato and potato plants.
Hanifah NASB, Ghadamgahi F, Ghosh S, ..., Vetukuri RR, Kalyandurg PB
Front Plant Sci 14 (-) 1141692 [2023-07-18; online 2023-07-18]
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Irradiation and lithium treatment alter the global DNA methylation pattern and gene expression underlying a shift from gliogenesis towards neurogenesis in human neural progenitors.
Neofytou C, Backlund A, Blomgren K, Hermanson O
Transl Psychiatry 13 (1) 258 [2023-07-13; online 2023-07-13]
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MBio 14 (3) e0044923 [2023-06-27; online 2023-04-25]
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A genomic timescale for placental mammal evolution.
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Sci Rep 13 (1) 6777 [2023-04-25; online 2023-04-25]
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BMC Genomics 24 (1) 169 [2023-04-04; online 2023-04-04]
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Red clover root-associated microbiota is shaped by geographic location and choice of farming system.
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Whole-genome re-sequencing provides key genomic insights in farmed Arctic charr (Salvelinus alpinus) populations of anadromous and landlocked origin from Scandinavia.
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Morez A, Britton K, Noble G, ..., Donald C, Girdland-Flink L
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RNA silencing proteins and small RNAs in oomycete plant pathogens and biocontrol agents.
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An integrated single cell and spatial transcriptomic map of human white adipose tissue.
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Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.
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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]
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Rapid adaptations of Legionella pneumophila to the human host.
Leenheer D, Moreno AB, Paranjape K, ..., Ginevra C, Guy L
Microb Genom 9 (3) - [2023-03-00; online 2023-03-23]
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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]
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Targeting the gut-lung axis by synbiotic feeding to infants in a randomized controlled trial.
Sjödin KS, Sjödin A, Ruszczyński M, ..., Szajewska H, West CE
BMC Biol. 21 (1) 38 [2023-02-20; online 2023-02-20]
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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 35 (2) 874-888 [2023-02-20; online 2022-11-26]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] Swedish Metabolomics Centre (SMC) [Service]
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Bacteroidetes to Firmicutes: captivity changes the gut microbiota composition and diversity in a social subterranean rodent.
Bensch HM, Tolf C, Waldenström J, Lundin D, Zöttl M
Anim Microbiome 5 (1) 9 [2023-02-10; online 2023-02-10]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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Larval transcriptomes reflect the evolutionary history of plant-insect associations.
de la Paz Celorio-Mancera M, Steward RA, Pruisscher P, ..., Wheat CW, Nylin S
Evolution 77 (2) 519-533 [2023-02-04; online 2023-01-11]
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Population genomics of the island thrush elucidates one of earth's great archipelagic radiations.
Reeve AH, Gower G, Pujolar JM, ..., Racimo F, Jønsson KA
Evolution Letters 7 (1) 24-36 [2023-02-01; online 2023-01-31]
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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]
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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]
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An allozyme polymorphism is associated with a large chromosomal inversion in the marine snail Littorina fabalis.
Le Moan A, Panova M, De Jode A, ..., Butlin R, Johannesson K
Evol Appl 16 (2) 279-292 [2023-02-00; online 2022-06-26]
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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]
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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]
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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]
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Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex.
Ottenburghs J, Honka J, Heikkinen ME, ..., Müskens GJDM, Ellegren H
BMC Ecol Evol 23 (1) 2 [2023-01-19; online 2023-01-19]
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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]
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PIK3CA is recurrently mutated in canine mammary tumors, similarly to in human mammary neoplasia.
Arendt ML, Sakthikumar S, Melin M, ..., Rönnberg H, Lindblad-Toh K
Sci Rep 13 (1) 632 [2023-01-12; online 2023-01-12]
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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]
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Longitudinal single-cell analysis of SARS-CoV-2-reactive B cells uncovers persistence of early-formed, antigen-specific clones.
Scharf L, Axelsson H, Emmanouilidi A, ..., Bemark M, Angeletti D
JCI Insight 8 (1) - [2023-01-10; online 2023-01-10]
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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]
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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]
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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]
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Experimental Life History Evolution Results in Sex-specific Evolution of Gene Expression in Seed Beetles.
Immonen E, Sayadi A, Stojković B, ..., Wiberg RAW, Arnqvist G
Genome Biol Evol 15 (1) - [2023-01-04; online 2022-12-22]
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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]
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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]
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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]
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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]
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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]
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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
Functional responses of key marine bacteria to environmental change - toward genetic counselling for coastal waters.
Pinhassi J, Farnelid H, García SM, ..., Labrenz M, Riemann L
Front Microbiol 13 (-) 869093 [2022-12-01; online 2022-12-01]
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PubMed DOI Crossref
Species composition of shoreline wolf spider communities vary with salinity, but their diets vary with wrack inflow.
Hambäck PA, Cirtwill AR, Grudzinska-Sterno M, ..., Langbak M, Åhlén D
Ecol Evol 12 (12) e9701 [2022-12-00; online 2022-12-28]
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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]
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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]
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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]
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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
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
A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition.
Altınışık NE, Kazancı DD, Aydoğan A, ..., Erim Özdoğan A, Somel M
Sci Adv 8 (44) eabo3609 [2022-11-04; online 2022-11-04]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The Dynamics of Adaptation to Stress from Standing Genetic Variation and de novo Mutations.
Ament-Velásquez SL, Gilchrist C, Rêgo A, ..., Rafati N, Stelkens R
Mol. Biol. Evol. 39 (11) - [2022-11-03; online 2022-11-06]
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Population dynamics and demographic history of Eurasian collared lemmings.
Lord E, Marangoni A, Baca M, ..., Fedorov VB, Dalén L
BMC Ecol Evol 22 (1) 126 [2022-11-03; online 2022-11-03]
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Mountain- and brown hare genetic polymorphisms to survey local adaptations and conservation status of the heath hare (Lepus timidus sylvaticus, Nilsson 1831).
Michell CT, Pohjoismäki JLO, Spong G, Thulin CG
Sci Data 9 (1) 667 [2022-11-03; online 2022-11-03]
NGI Short read [Service] NGI Stockholm (Genomics Production) [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]
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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]
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Multi-transcriptome analysis following an acute skeletal muscle growth stimulus yields tools for discerning global and MYC regulatory networks.
Murach KA, Liu Z, Jude B, ..., Vechetti IJ, von Walden F
J. Biol. Chem. 298 (11) 102515 [2022-11-00; online 2022-09-21]
NGI Short read [Service] NGI Stockholm (Genomics Production) [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]
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Linkage mapping and genome annotation give novel insights into gene family expansions and regional recombination rate variation in the painted lady (Vanessa cardui) butterfly.
Shipilina D, Näsvall K, Höök L, ..., Talavera G, Backström N
Genomics 114 (6) 110481 [2022-11-00; online 2022-09-14]
NGI Short read [Service] NGI Stockholm (Genomics Production) [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]
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PubMed DOI Crossref
Characterizing single extracellular vesicles by droplet barcode sequencing for protein analysis.
Banijamali M, Höjer P, Nagy A, ..., Viktorsson K, Ahmadian A
J Extracell Vesicles 11 (11) e12277 [2022-11-00; online 2022-11-05]
NGI Short read [Service] NGI Stockholm (Genomics Production) [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]
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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]
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PubMed DOI Crossref
Single-cell sequencing deconvolutes cellular responses to exercise in human skeletal muscle.
Lovrić A, Rassolie A, Alam S, ..., Gustafsson T, Rullman E
Commun Biol 5 (1) 1121 [2022-10-22; online 2022-10-22]
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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]
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PubMed DOI Crossref
Soil Microbiome Influences on Seedling Establishment and Growth of Prosopis chilensis and Prosopis tamarugo from Northern Chile.
Castro D, Concha C, Jamett F, Ibáñez C, Hurry V
Plants (Basel) 11 (20) - [2022-10-14; online 2022-10-14]
NGI Short read [Service] NGI Stockholm (Genomics Production) [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]
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PubMed DOI Crossref
Pax3 loss of function delays tumour progression in kRAS-induced zebrafish rhabdomyosarcoma models.
Kahsay A, Rodriguez-Marquez E, López-Pérez A, Hörnblad A, von Hofsten J
Sci Rep 12 (1) 17149 [2022-10-13; online 2022-10-13]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [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
Rapid bacterioplankton transcription cascades regulate organic matter utilization during phytoplankton bloom progression in a coastal upwelling system.
Pontiller B, Martínez-García S, Joglar V, ..., Teira E, Pinhassi J
ISME J 16 (10) 2360-2372 [2022-10-00; online 2022-07-08]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [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]
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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]
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PubMed DOI Crossref
Expression Levels of hgcAB Genes and Mercury Availability Jointly Explain Methylmercury Formation in Stratified Brackish Waters.
Capo E, Feng C, Bravo AG, ..., Hawkes J, Björn E
Environ. Sci. Technol. 56 (18) 13119-13130 [2022-09-20; online 2022-09-07]
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PubMed DOI Crossref
Spatio-temporal analysis of prostate tumors in situ suggests pre-existence of treatment-resistant clones.
Marklund M, Schultz N, Friedrich S, ..., Sonnhammer E, Lundeberg J
Nat Commun 13 (1) 5475 [2022-09-17; online 2022-09-17]
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BMC Vet Res 18 (1) 348 [2022-09-16; online 2022-09-16]
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Linked-read whole-genome sequencing resolves common and private structural variants in multiple myeloma.
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Blood Adv 6 (17) 5009-5023 [2022-09-13; online 2022-06-09]
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Immunodeficiency syndromes differentially impact the functional profile of SARS-CoV-2-specific T cells elicited by mRNA vaccination.
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Immunity 55 (9) 1732-1746.e5 [2022-09-13; online 2022-07-19]
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Thureborn O, Razafimandimbison SG, Wikström N, Rydin C
Front Plant Sci 13 (-) 967456 [2022-09-08; online 2022-09-08]
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Int J Mol Sci 23 (18) - [2022-09-08; online 2022-09-08]
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Sci Rep 12 (1) 14330 [2022-08-22; online 2022-08-22]
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van der Valk T, Dehasque M, Chacón-Duque JC, ..., Díez-Del-Molino D, Dalén L
iScience 25 (8) 104826 [2022-08-19; online 2022-08-01]
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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.
Osterholz H, Turner S, Alakangas LJ, ..., Kalinowski BE, Dopson M
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Cell Syst 13 (8) 665-681.e4 [2022-08-17; online 2022-07-08]
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Michel A, Minocher R, Niehoff PP, ..., Caillaud D, Guschanski K
Mol. Ecol. - (-) - [2022-08-17; online 2022-08-17]
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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.
Liu R, Pisco AO, Braun E, Linnarsson S, Zou J
J. Mol. Biol. 434 (15) 167606 [2022-08-15; online 2022-04-27]
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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]
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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]
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Nannapaneni P, Sundh J, Prast-Nielsen S, ..., Naucler P, Henriques-Normark B
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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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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
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Mol Ecol Resour 22 (6) 2304-2318 [2022-08-00; online 2022-05-06]
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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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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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New Phytol. 235 (4) 1641-1652 [2022-08-00; online 2022-06-23]
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Viruses 14 (8) - [2022-07-28; online 2022-07-28]
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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
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Targeted Chromosome Conformation Capture (HiCap).
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Methods Mol. Biol. 2532 (-) 75-94 [2022-07-23; online 2022-07-23]
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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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Claudin5 protects the peripheral endothelial barrier in an organ and vessel-type-specific manner.
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Elife 11 (-) - [2022-07-21; online 2022-07-21]
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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
iScience 25 (7) 104602 [2022-07-15; online 2022-06-11]
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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.
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Sci Rep 12 (1) 11960 [2022-07-13; online 2022-07-13]
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Integrated single cell and spatial transcriptomics reveal autoreactive differentiated B cells in joints of early rheumatoid arthritis.
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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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.
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Curr. Biol. 32 (13) 2988-2996.e4 [2022-07-11; online 2022-06-03]
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Co-Occurrence of Francisella, Spotted Fever Group Rickettsia, and Midichloria in Avian-Associated Hyalomma rufipes
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Microorganisms 10 (7) 1393 [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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Petitpré C, Faure L, Uhl P, ..., Hadjab S, Lallemend F
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Seasonal Dynamics in Carbon Cycling of Marine Bacterioplankton Are Lifestyle Dependent.
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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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BMC Bioinformatics 23 (1) 261 [2022-07-01; online 2022-07-01]
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Bergström A, Stanton DWG, Taron UH, ..., Dalén L, Skoglund P
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Kurland S, Rafati N, Ryman N, Laikre L
Ecol Evol 12 (7) e9050 [2022-07-00; online 2022-07-03]
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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
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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]
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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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Molecular profiling of stem cell-derived retinal pigment epithelial cell differentiation established for clinical translation.
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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.
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Mol Ther Nucleic Acids 28 (-) 450-461 [2022-06-14; online 2022-03-28]
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Long-Term Warming of Baltic Sea Coastal Waters Affects Bacterial Communities in Bottom Water and Sediments Differently.
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Front Microbiol 13 (-) 873281 [2022-06-10; online 2022-06-10]
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Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms.
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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.
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Commun Biol 5 (1) 554 [2022-06-07; online 2022-06-07]
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Developmental landscape of human forebrain at a single-cell level identifies early waves of oligodendrogenesis.
van Bruggen D, Pohl F, Langseth CM, ..., Sundström E, Castelo-Branco G
Dev. Cell 57 (11) 1421-1436.e5 [2022-06-06; online 2022-05-05]
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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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The mosaic oat genome gives insights into a uniquely healthy cereal crop.
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.
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PLoS Genet. 18 (6) e1010261 [2022-06-00; online 2022-06-17]
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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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R. Soc. open sci. 9 (6) 220104 [2022-06-00; online 2022-06-15]
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iScience 25 (5) 104303 [2022-05-20; online 2022-04-25]
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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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Hum. Reprod. 37 (4) 734-746 [2022-04-01; online 2022-02-12]
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Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population.
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Le Duc D, Velluva A, Cassatt-Johnstone M, ..., Shapiro B, Schöneberg T
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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
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Hernandez-Castro LE, Villacís AG, Jacobs A, ..., Llewellyn MS, Grijalva MJ
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Mol. Ecol. 31 (4) 1111-1127 [2022-02-00; online 2021-12-07]
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Fish Skin Microbiomes Are Highly Variable Among Individuals and Populations but Not Within Individuals.
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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]
Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Uppsala [Service] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
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]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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 Support for Computational Resources [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]
Bioinformatics Long-term Support WABI [Service] Bioinformatics Support for Computational Resources [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
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]

Year 2021

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
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
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 Long-term Support WABI [Collaborative] 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] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Chenodeoxycholic Acid Modulates Bile Acid Synthesis Independent of Fibroblast Growth Factor 19 in Primary Human Hepatocytes.
Johansson H, Søndergaard JN, Jorns C, Kutter C, Ellis ECS
Front Endocrinol (Lausanne) 11 (-) 554922 [2021-02-22; online 2021-02-22]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2019

PubMed DOI Crossref
Differential gene expression in bovine endometrial epithelial cells after challenge with LPS; specific implications for genes involved in embryo maternal interactions.
Guo Y, van Schaik T, Jhamat N, ..., Andersson G, Humblot P
PLoS ONE 14 (9) e0222081 [2019-09-05; online 2019-09-05]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]
NGI Short read [Service] NGI Stockholm (Genomics Applications) NGI Stockholm (Genomics Production) National Genomics Infrastructure [Service]
SciLifeLab Data Centre
Publications 9.5.1