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Started: -

Ended: Current

Year 2025

PubMed DOI Crossref
Diel Bacterioplankton Community Dynamics Under Contrasting Light Regimes.
Papadopoulou S, Linkhorst A, Balmonte JP, ..., Bertilsson S, Székely AJ
Environ Microbiol Rep 17 (3) e70099 [2025-06-00; online 2025-05-09]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
CpG island methylator phenotype classification improves risk assessment in pediatric T-cell acute lymphoblastic leukemia.
Schäfer Hackenhaar F, Refhagen N, Hagleitner M, ..., Hultdin M, Degerman S
Blood 145 (19) 2161-2178 [2025-05-08; online 2025-01-22]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Sex pheromone biosynthesis in the Oriental fruit moth Grapholita molesta involves Δ8 desaturation.
Dam MI, Ding BJ, Brauburger K, ..., Heckel DG, Löfstedt C
Insect Biochem. Mol. Biol. - (-) 104307 [2025-03-30; online 2025-03-30]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Phylogeny of Palicoureeae (Rubiaceae) based on 353 low-copy nuclear genes - With particular focus on Hymenocoleus Robbr.
Thilén L, Lachenaud O, Thureborn O, Razafimandimbison SG, Rydin C
Mol. Phylogenet. Evol. - (-) 108338 [2025-03-28; online 2025-03-28]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Neural ensembles that encode nocifensive mechanical and heat pain in mouse spinal cord.
Zhang MD, Kupari J, Su J, ..., Lagerström MC, Ernfors P
Nat. Neurosci. - (-) - [2025-03-24; online 2025-03-24]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Intestinal estrogen receptor beta modulates the murine colon tumor immune microenvironment.
Birgersson M, Holm M, Gallardo-Dodd CJ, ..., Archer A, Williams C
Cancer Lett. - (-) 217661 [2025-03-20; online 2025-03-20]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Sox9 and nuclear factor I transcription factors regulate the timing of neurogenesis and ependymal maturation in dopamine progenitors.
Lahti L, Volakakis N, Gillberg L, ..., Gronostajski R, Perlmann T
Development 152 (6) - [2025-03-15; online 2025-03-26]
Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Continuous map of early hematopoietic stem cell differentiation across human lifetime.
Komic H, Schmachtel T, Simoes C, ..., Thorén FB, Rieger MA
Nat Commun 16 (1) 2287 [2025-03-07; online 2025-03-07]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Comprehensive Gene Expression Analysis in Papillary Thyroid Carcinoma Reveals a Transcriptional Profile Associated with Reduced Radioiodine Avidity.
Condello V, Marchettini C, Ihre-Lundgren C, Nilsson JN, Juhlin CC
Endocr. Pathol. 36 (1) 4 [2025-02-21; online 2025-02-21]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Methodological aspects of investigating the resistome in pig farm environments.
Ladyhina V, Rajala E, Sternberg-Lewerin S, ..., Bongcam-Rudloff E, Dicksved J
J Microbiol Methods 230-231 (-) 107103 [2025-02-13; online 2025-02-13]
Clinical Genomics [Collaborative] Clinical Genomics Linköping [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Rare and common single nucleotide variants in childhood-onset systemic lupus erythematosus.
Sayadi A, Sandling JK, Eloranta ML, ..., Rönnblom L, DISSECT Consortium
Lupus Sci Med 12 (1) - [2025-02-11; online 2025-02-11]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Whole genome sequencing in early onset advanced heart failure.
Linnér E, Czuba T, Gidlöf O, ..., Ehrencrona H, Smith JG
Sci Rep 15 (1) 4306 [2025-02-05; online 2025-02-05]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Impact of excess sugar on the whole genome DNA methylation pattern in human sperm.
Jönsson J, Perfilyev A, Kugelberg U, ..., Öst A, Ling C
Epigenomics 17 (2) 89-104 [2025-02-00; online 2024-12-20]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Evolved and Plastic Gene Expression in Adaptation of a Specialist Fly to a Novel Niche.
Steward RA, Ortega Giménez J, Choudhary S, ..., Van Aken O, Runemark A
Mol. Ecol. 34 (4) e17653 [2025-02-00; online 2025-01-09]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Diffusion Smart-seq3 of breast cancer spheroids to explore spatial tumor biology and test evolutionary principles of tumor heterogeneity.
Cougnoux A, Mahmoud L, Johnsson PA, ..., Sandberg R, Hausser J
Sci Rep 15 (1) 3811 [2025-01-30; online 2025-01-30]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Exploring a pico-well based scRNA-seq method (HIVE) for simplified processing of equine bronchoalveolar lavage cells.
Fegraeus K, Riihimäki M, Nordlund J, ..., Wernersson S, Raine A
PLoS ONE 20 (1) e0317343 [2025-01-24; online 2025-01-24]
NGI Short read [Technology development] NGI Uppsala (SNP&SEQ Technology Platform) [Technology development] National Genomics Infrastructure [Technology development]
PubMed DOI Crossref
A de novo, mosaic and complex chromosome 21 rearrangement causes APP triplication and familial autosomal dominant early onset Alzheimer disease.
Ehn E, Eisfeldt J, Laffita-Mesa JM, ..., Nennesemo I, Graff C
Sci Rep 15 (1) 2912 [2025-01-23; online 2025-01-23]
Clinical Genomics [Service] Clinical Genomics Stockholm [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Chromosome-scale genome assembly reveals how repeat elements shape non-coding RNA landscapes active during newt limb regeneration.
Brown T, Mishra K, Elewa A, ..., Yun MH, Simon A
Cell Genomics - (-) 100761 [2025-01-22; online 2025-01-22]
NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Systems-level immunomonitoring in children with solid tumors to enable precision medicine.
Chen Q, Zhao B, Tan Z, ..., Ljungblad L, Brodin P
Cell - (-) - [2025-01-17; online 2025-01-17]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatial transcriptomics unveils estrogen-modulated immune responses and structural alterations in the ectocervical mucosa of depot medroxyprogesterone acetate users.
Kaldhusdal V, Boger MF, Tjernlund A, ..., Czarnewski P, Broliden K
Sci Rep 15 (1) 1014 [2025-01-06; online 2025-01-06]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Spatial omics [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Single-cell proteo-transcriptomic profiling reveals altered characteristics of stem and progenitor cells in patients receiving cytoreductive hydroxyurea in early-phase chronic myeloid leukemia.
Komic H, Nilsson MS, Wennström L, ..., Thorén FB, Martner A
Haematologica 110 (1) 117-128 [2025-01-01; online 2025-01-01]
NGI Short read [Service] NGI Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Dark carbon fixation is a common process in the water column of stratified boreal lakes.
Martin G, Rissanen AJ, Garcia SL, Peura S
Sci. Total Environ. 958 (-) 177433 [2025-01-01; online 2024-12-10]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2024

PubMed DOI Crossref
Phthalate esters in baltic lagoons: Spatial distribution, ecological risks, and novel insights into their fate using transcriptomics.
Lorre E, Bianchi F, Broman E, ..., Woźniczka A, Zilius M
Sci. Total Environ. 957 (-) 177526 [2024-12-20; online 2024-11-18]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatiotemporal single-cell roadmap of human skin wound healing.
Liu Z, Bian X, Luo L, ..., Li D, Landén NX
Cell Stem Cell - (-) - [2024-12-18; online 2024-12-18]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Multi-omics analysis detail a submicroscopic inv(15)(q14q15) generating fusion transcripts and MEIS2 and NUSAP1 haploinsufficiency.
Ek M, Kvarnung M, Pettersson M, ..., Eisfeldt J, Lindstrand A
Sci Rep 14 (1) 30343 [2024-12-05; online 2024-12-05]
NGI Long read [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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 [Collaborative] 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
A transcriptome atlas of zygotic and somatic embryogenesis in Norway spruce.
Stojkovič K, Canovi C, Le KC, ..., Egertsdotter U, Street NR
Plant J. 120 (5) 2238-2252 [2024-12-00; online 2024-10-27]
Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
A dataset of 40 assembled and annotated transcriptomes from 34 species in Silene and related genera.
Cangren P, Bertrand YJK, Braverman JM, ..., Hamilton MB, Oxelman B
Data Brief 57 (-) 111094 [2024-12-00; online 2024-11-01]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Systematic screens for fertility genes essential for malaria parasite transmission reveal conserved aspects of sex in a divergent eukaryote.
Sayers C, Pandey V, Balakrishnan A, ..., Berntsson R, Billker O
Cell Syst 15 (11) 1075-1091.e6 [2024-11-20; online 2024-11-13]
NGI Short read [Service] NGI Stockholm (Genomics Production) [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]
Bioinformatics Support for Computational Resources [Service] 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]
Bioinformatics Support for Computational Resources [Service] 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 (NBIS) [Collaborative] 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 (NBIS) [Collaborative] 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]
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Species-genetic diversity correlation in a metacommunity of urban pond invertebrates
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Basic and Applied Ecology 79 (-) 114-122 [2024-09-00; online 2024-09-00]
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Mol. Phylogenet. Evol. 198 (-) 108117 [2024-09-00; online 2024-06-07]
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Plastome evolution in Santalales involves relaxed selection prior to loss of ndh genes and major boundary shifts of the inverted repeat.
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Ann. Bot. - (-) - [2024-08-30; online 2024-08-30]
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Five centuries of consanguinity, isolation, health, and conflict in Las Gobas: A Northern Medieval Iberian necropolis.
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Sci Adv 10 (35) eadp8625 [2024-08-30; online 2024-08-28]
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Rubin CJ, Hodge M, Naboulsi R, ..., Lindgren G, Andersson L
Nat Commun 15 (1) 7510 [2024-08-29; online 2024-08-29]
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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]
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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]
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Sonavane S, Hassan S, Chatterjee U, ..., Reimegård J, Rising A
Sci Adv 10 (33) eadn0597 [2024-08-16; online 2024-08-14]
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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]
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Few chemoreceptor genes in the ambrosia beetle Trypodendron lineatum may reflect its specialized ecology.
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BMC Genomics 25 (1) 764 [2024-08-06; online 2024-08-06]
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Unneberg P, Larsson M, Olsson A, ..., Meyer B, Wallberg A
Nat Commun 15 (1) 6297 [2024-08-01; online 2024-08-01]
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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]
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Selection against domestication alleles in introduced rabbit populations.
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Nat Ecol Evol 8 (8) 1543-1555 [2024-08-00; online 2024-06-21]
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Plasticity for the win: Flexible transcriptional response to host plant switches in the comma butterfly (Polygonia c-album).
Schneider K, Steward RA, Celorio-Mancera MdlP, ..., Wheat CW, Nylin S
Mol. Ecol. 33 (16) e17479 [2024-08-00; online 2024-07-22]
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Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids.
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Evolution Letters 8 (4) 550-560 [2024-08-00; online 2024-03-17]
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A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing.
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Life Sci. Alliance 7 (8) - [2024-08-00; online 2024-05-22]
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A pipeline for identification of causal mutations in barley identifies Xantha-j as the chlorophyll synthase gene.
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Plant Physiol. 195 (4) 2877-2890 [2024-07-31; online 2024-04-17]
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A genetic-epigenetic interplay at 1q21.1 locus underlies CHD1L-mediated vulnerability to primary progressive multiple sclerosis.
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Nat Commun 15 (1) 6419 [2024-07-30; online 2024-07-30]
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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]
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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]
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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]
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Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci.
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Cell Genomics 4 (7) 100590 [2024-07-10; online 2024-06-21]
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DNA methylation of exercise-responsive genes differs between trained and untrained men.
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BMC Biol. 22 (1) 147 [2024-07-04; online 2024-07-04]
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Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring.
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Genome Biol Evol 16 (7) - [2024-07-03; online 2024-06-26]
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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]
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Unravelling reference bias in ancient DNA datasets.
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Bioinformatics 40 (7) - [2024-07-01; online 2024-07-04]
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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]
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Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215.
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BMC Microbiol. 24 (1) 215 [2024-06-19; online 2024-06-19]
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Integrative transcriptomic and proteomic profiling of the effects of cell confluency on gene expression.
Lobo V, Shcherbinina E, Westholm JO, ..., Anastasakis DG, Sarshad AA
Sci Data 11 (1) 617 [2024-06-12; online 2024-06-12]
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Climate change induces shifts in coastal Baltic Sea surface water microorganism stress and photosynthesis gene expression.
Seidel L, Broman E, Ståhle M, ..., Ketzer M, Dopson M
Front Microbiol 15 (-) 1393538 [2024-06-07; online 2024-06-07]
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ASXLs binding to the PHD2/3 fingers of MLL4 provides a mechanism for the recruitment of BAP1 to active enhancers.
Zhang Y, Xie G, Lee JE, ..., Ge K, Kutateladze TG
Nat Commun 15 (1) 4883 [2024-06-07; online 2024-06-07]
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MLL4 binds TET3.
Becht DC, Mohid SA, Lee JE, ..., Zhang Y, Kutateladze TG
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Detection of rare variants among nuclei populating the arbuscular mycorrhizal fungal model species Rhizophagus irregularis DAOM197198.
Manyara D, Sánchez-García M, Montoliu-Nerin M, Rosling A
G3 (Bethesda) 14 (6) - [2024-06-05; online 2024-04-24]
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Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region.
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Genome Biol Evol 16 (6) - [2024-06-04; online 2024-05-25]
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Spatial Transcriptomics in a Case of Follicular Thyroid Carcinoma Reveals Clone-Specific Dysregulation of Genes Regulating Extracellular Matrix in the Invading Front.
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Endocr. Pathol. 35 (2) 122-133 [2024-06-00; online 2024-01-27]
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Phylogenomic analysis of Stylops reveals the evolutionary history of a Holarctic Strepsiptera radiation parasitizing wild bees.
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Mol. Phylogenet. Evol. 195 (-) 108068 [2024-06-00; online 2024-03-28]
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Expedient Bayesian prediction of subfossil bone protein content using portable ATR-FTIR data
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Quaternary International 694 (-) 1-12 [2024-06-00; online 2024-06-00]
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An endothelial regulatory module links blood pressure regulation with elite athletic performance.
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PLoS Genet. 20 (6) e1011285 [2024-06-00; online 2024-06-17]
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Regulatory and evolutionary impact of DNA methylation in two songbird species and their naturally occurring F1 hybrids.
Boman J, Qvarnström A, Mugal CF
BMC Biol. 22 (1) 124 [2024-05-29; online 2024-05-29]
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Species-specific dynamics may cause deviations from general biogeographical predictions - evidence from a population genomics study of a New Guinean endemic passerine bird family (Melampittidae).
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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Plastid phylogenomics and cytonuclear discordance in Rubioideae, Rubiaceae.
Thureborn O, Wikström N, Razafimandimbison SG, Rydin C
PLoS ONE 19 (5) e0302365 [2024-05-20; online 2024-05-20]
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Defining the contribution of Troy-positive progenitor cells to the mouse esophageal epithelium.
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Dev. Cell 59 (10) 1269-1283.e6 [2024-05-20; online 2024-04-01]
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Prediction models of persistent taxane-induced peripheral neuropathy among breast cancer survivors using whole-exome sequencing.
Engvall K, Uvdal H, Björn N, Åvall-Lundqvist E, Gréen H
NPJ Precis Oncol 8 (1) 102 [2024-05-16; online 2024-05-16]
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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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The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees.
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Mol Plant 17 (5) 725-746 [2024-05-06; online 2024-03-13]
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Colonial-driven extinction of the blue antelope despite genomic adaptation to low population size.
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Curr. Biol. 34 (9) 2020-2029.e6 [2024-05-06; online 2024-04-12]
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Meiotic drive against chromosome fusions in butterfly hybrids.
Boman J, Wiklund C, Vila R, Backström N
Chromosome Res. 32 (2) 7 [2024-05-04; online 2024-05-04]
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Mar. Ecol. Prog. Ser. 735 (-) 63-76 [2024-05-02; online 2024-05-02]
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Sex-biased gene expression during neural differentiation of human embryonic stem cells
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Male-transmitted transgenerational effects of the herbicide linuron on DNA methylation profiles in Xenopus tropicalis brain and testis.
Roza M, Eriksson ANM, Svanholm S, Berg C, Karlsson O
Sci. Total Environ. 923 (-) 170949 [2024-05-01; online 2024-02-15]
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Chromatin accessibility during human first-trimester neurodevelopment.
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Nature - (-) - [2024-05-01; online 2024-05-01]
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Whole-genome sequencing in prenatally detected congenital malformations: prospective cohort study in clinical setting.
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Ultrasound Obstet Gynecol 63 (5) 658-663 [2024-05-00; online 2024-04-14]
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Unlocking the secret life of blue mussels: Exploring connectivity in the Skagerrak through biophysical modeling and population genomics.
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Evol Appl 17 (5) e13704 [2024-05-00; online 2024-05-20]
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Head-to-head comparison of relevant cell sources of small extracellular vesicles for cardiac repair: Superiority of embryonic stem cells.
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J Extracell Vesicles 13 (5) e12445 [2024-05-00; online 2024-05-07]
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Fluorescently labeled prey surrogates in combination with fluorescence‐activated cell sorting successfully discriminate actively feeding mixotrophs in a lake water sample
Florenza J, Divne A, Bertilsson S
Limnol Oceanogr 69 (5) 1030-1044 [2024-05-00; online 2024-03-13]
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Comparison and optimization of protocols and whole-genome capture conditions for ancient DNA samples.
Yaka R, Lagerholm VK, Linderholm A, ..., Somel M, Götherström A
BioTechniques 76 (5) 216-223 [2024-05-00; online 2024-03-26]
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Population genomic history of the endangered Anatolian and Cyprian mouflons in relation to worldwide wild, feral and domestic sheep lineages.
Atağ G, Kaptan D, Yüncü E, ..., Hadjisterkotis E, Somel M
Genome Biol Evol - (-) - [2024-04-27; online 2024-04-27]
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Phenotypic characterization and candidate gene analysis of a short kernel and brassinosteroid insensitive mutant from hexaploid oat (Avena sativa).
Tsardakas Renhuldt N, Bentzer J, Ahrén D, Marmon S, Sirijovski N
Front Plant Sci 15 (-) 1358490 [2024-04-26; online 2024-04-26]
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High clonal diversity and spatial genetic admixture in early prostate cancer and surrounding normal tissue.
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Nat Commun 15 (1) 3475 [2024-04-24; online 2024-04-24]
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Effects of bottom trawling and environmental factors on benthic bacteria, meiofauna and macrofauna communities and benthic ecosystem processes.
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Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes.
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Nucleic Acids Res. - (-) - [2024-04-13; online 2024-04-13]
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Elife 12 (-) - [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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Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network.
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A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea.
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Global Transcriptome Analysis Reveals Distinct Phases of the Endothelial Response to TNF.
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Whole-genome selective sweep analyses identifies the region and candidate gene associated with white earlobe color in Mediterranean chickens.
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The genetic legacy of the expansion of Bantu-speaking peoples in Africa.
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Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae).
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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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DOI Crossref
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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DOI Crossref
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]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
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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.
Zhang H, Hansson B
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]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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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PubMed DOI Crossref
Single-Cell RNA Analysis Reveals Cell-Intrinsic Functions of CAR T Cells Correlating with Response in a Phase II Study of Lymphoma Patients.
Sarén T, Ramachandran M, Gammelgård G, ..., Enblad G, Essand M
Clin. Cancer Res. 29 (20) 4139-4152 [2023-10-13; online 2023-08-04]
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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
Nat Cancer - (-) - [2023-10-02; online 2023-10-02]
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PubMed DOI Crossref
The dynamics of touch-responsive gene expression in cereals.
Darwish E, Ghosh R, Bentzer J, ..., Sirijovski N, Van Aken O
Plant J. 116 (1) 282-302 [2023-10-00; online 2023-06-08]
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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.
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Northwest African Neolithic initiated by migrants from Iberia and Levant.
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Diagnostic Yield From a Nationwide Implementation of Precision Medicine for all Children With Cancer.
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Climate change-related warming reduces thermal sensitivity and modifies metabolic activity of coastal benthic bacterial communities.
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Triazole fungicides induce adipogenesis and repress osteoblastogenesis in zebrafish.
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Circular RNAs arising from synaptic host genes during human neuronal differentiation are modulated by SFPQ RNA-binding protein.
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The Swedish childhood tumor biobank: systematic collection and molecular characterization of all pediatric CNS and other solid tumors in Sweden.
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Base-resolution UV footprinting by sequencing reveals distinctive damage signatures for DNA-binding proteins.
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Warmer temperatures favor slower-growing bacteria in natural marine communities.
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SAG-RAD: A Method for Single-Cell Population Genomics of Unicellular Eukaryotes.
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Mol. Biol. Evol. 40 (5) - [2023-05-02; online 2023-04-20]
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Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon.
Mosquera KD, Nilsson LKJ, de Oliveira MR, ..., de Souza AQL, Terenius O
Parasit Vectors 16 (1) 156 [2023-05-01; online 2023-05-01]
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Trophozoite fitness dictates the intestinal epithelial cell response to Giardia intestinalis infection.
Grüttner J, van Rijn JM, Geiser P, ..., Sellin ME, Svärd SG
PLoS Pathog. 19 (5) e1011372 [2023-05-00; online 2023-05-04]
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Profiling spatiotemporal gene expression of the developing human spinal cord and implications for ependymoma origin.
Li X, Andrusivova Z, Czarnewski P, ..., Lundeberg J, Sundström E
Nat. Neurosci. 26 (5) 891-901 [2023-05-00; online 2023-04-24]
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Functional genome annotation and transcriptome analysis of Pseudozyma hubeiensis BOT-O, an oleaginous yeast that utilizes glucose and xylose at equal rates.
Mierke F, Brink DP, Norbeck J, Siewers V, Andlid T
Fungal Genet. Biol. 166 (-) 103783 [2023-05-00; online 2023-03-03]
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Different spatial structure of plant-associated fungal communities above- and belowground.
Faticov M, Abdelfattah A, Hambäck P, Roslin T, Tack AJM
Ecol Evol 13 (5) e10065 [2023-05-00; online 2023-05-21]
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An extracellular matrix stiffness-induced breast cancer cell transcriptome resembles the transition from ductal carcinoma in situ (DCIS) to invasive ductal carcinoma (IDC).
Göransson S, Chen S, Olofsson H, Larsson O, Strömblad S
Biochem. Biophys. Res. Commun. 654 (-) 73-79 [2023-04-30; online 2023-03-02]
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​Comparative genomics of Balto, a famous historic dog, captures lost diversity of 1920s sled dogs.
Moon KL, Huson HJ, Morrill K, ..., Karlsson EK, Shapiro B
Science 380 (6643) eabn5887 [2023-04-28; online 2023-04-28]
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Three-dimensional genome rewiring in loci with human accelerated regions.
Keough KC, Whalen S, Inoue F, ..., Pollen A, Pollard KS
Science 380 (6643) eabm1696 [2023-04-28; online 2023-04-28]
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The functional and evolutionary impacts of human-specific deletions in conserved elements.
Xue JR, Mackay-Smith A, Mouri K, ..., Sabeti PC, Reilly SK
Science 380 (6643) eabn2253 [2023-04-28; online 2023-04-28]
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The contribution of historical processes to contemporary extinction risk in placental mammals.
Wilder AP, Supple MA, Subramanian A, ..., Ryder OA, Shapiro B
Science 380 (6643) eabn5856 [2023-04-28; online 2023-04-28]
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Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.
Kaplow IM, Lawler AJ, Schäffer DE, ..., Meyer WK, Pfenning AR
Science 380 (6643) eabm7993 [2023-04-28; online 2023-04-28]
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Mammalian evolution of human cis-regulatory elements and transcription factor binding sites.
Andrews G, Fan K, Pratt HE, ..., Moore JE, Weng Z
Science 380 (6643) eabn7930 [2023-04-28; online 2023-04-28]
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Leveraging base-pair mammalian constraint to understand genetic variation and human disease.
Sullivan PF, Meadows JRS, Gazal S, ..., Karlsson EK, Lindblad-Toh K
Science 380 (6643) eabn2937 [2023-04-28; online 2023-04-28]
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PubMed DOI Crossref
Integrating gene annotation with orthology inference at scale.
Kirilenko BM, Munegowda C, Osipova E, ..., Zoonomia Consortium‡ , Hiller M
Science 380 (6643) eabn3107 [2023-04-28; online 2023-04-28]
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Insights into mammalian TE diversity through the curation of 248 genome assemblies.
Osmanski AB, Paulat NS, Korstian J, ..., Lindblad-Toh K, Ray DA
Science 380 (6643) eabn1430 [2023-04-28; online 2023-04-28]
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PubMed DOI Crossref
Evolutionary constraint and innovation across hundreds of placental mammals.
Christmas MJ, Kaplow IM, Genereux DP, ..., Lindblad-Toh K, Karlsson EK
Science 380 (6643) eabn3943 [2023-04-28; online 2023-04-28]
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A genomic timescale for placental mammal evolution.
Foley NM, Mason VC, Harris AJ, ..., Springer MS, Murphy WJ
Science 380 (6643) eabl8189 [2023-04-28; online 2023-04-28]
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Low-grade glioma risk SNP rs11706832 is associated with type I interferon response pathway genes in cell lines.
Rosenbaum A, Dahlin AM, Andersson U, ..., Wibom C, Melin B
Sci Rep 13 (1) 6777 [2023-04-25; online 2023-04-25]
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Age Rather Than Supplementation with Oat β-Glucan Influences Development of the Intestinal Microbiota and SCFA Concentrations in Suckling Piglets.
Arapovic L, Huang Y, Manell E, ..., Lindberg JE, Dicksved J
Animals (Basel) 13 (8) - [2023-04-14; online 2023-04-14]
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The genetic basis of wing spots in Pieris canidia butterflies.
Wee JLQ, Murugesan SN, Wheat CW, Monteiro A
BMC Genomics 24 (1) 169 [2023-04-04; online 2023-04-04]
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PubMed DOI Crossref
Red clover root-associated microbiota is shaped by geographic location and choice of farming system.
Jambagi S, Hodén KP, Öhlund L, Dixelius C
J Appl Microbiol 134 (4) - [2023-04-03; online 2023-04-04]
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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.
Pappas F, Kurta K, Vanhala T, ..., Beirão J, Palaiokostas C
Evol Appl 16 (4) 797-813 [2023-04-00; online 2023-02-27]
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The human bone marrow plasma cell compartment in rheumatoid arthritis - Clonal relationships and anti-citrulline autoantibody producing cells.
Hensvold A, Horuluoglu B, Sahlström P, ..., Malmström V, Grönwall C
J. Autoimmun. 136 (-) 103022 [2023-04-00; online 2023-03-29]
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Imputed genomes and haplotype-based analyses of the Picts of early medieval Scotland reveal fine-scale relatedness between Iron Age, early medieval and the modern people of the UK.
Morez A, Britton K, Noble G, ..., Donald C, Girdland-Flink L
PLoS Genet. 19 (4) e1010360 [2023-04-00; online 2023-04-27]
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From high masked to high realized genetic load in inbred Scandinavian wolves.
Smeds L, Ellegren H
Mol. Ecol. 32 (7) 1567-1580 [2023-04-00; online 2022-12-13]
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SLC38A10 Deficiency in Mice Affects Plasma Levels of Threonine and Histidine in Males but Not in Females: A Preliminary Characterization Study of SLC38A10-/- Mice.
Lindberg FA, Nordenankar K, Forsberg EC, Fredriksson R
Genes 14 (4) - [2023-03-30; online 2023-03-30]
NGI Short read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service] Swedish Metabolomics Centre (SMC) [Service]
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Long-term warming modulates diversity, vertical structuring of microbial communities, and sulfate reduction in coastal Baltic Sea sediments.
Seidel L, Sachpazidou V, Ketzer M, ..., Forsman A, Dopson M
Front Microbiol 14 (-) 1099445 [2023-03-29; online 2023-03-29]
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Linking prokaryotic genome size variation to metabolic potential and environment.
Rodríguez-Gijón A, Buck M, Andersson AF, ..., Nascimento FJA, Garcia SL
ISME COMMUN. 3 (1) 25 [2023-03-27; online 2023-03-27]
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RNA silencing proteins and small RNAs in oomycete plant pathogens and biocontrol agents.
Piombo E, Kelbessa BG, Sundararajan P, ..., Vetukuri RR, Dubey M
Front Microbiol 14 (-) 1076522 [2023-03-24; online 2023-03-24]
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Evidence for a single, ancient origin of a genus-wide alternative life history strategy.
Tunström K, Woronik A, Hanly JJ, ..., Martin A, Wheat CW
Sci Adv 9 (12) eabq3713 [2023-03-22; online 2023-03-22]
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An integrated single cell and spatial transcriptomic map of human white adipose tissue.
Massier L, Jalkanen J, Elmastas M, ..., Rydén M, Mejhert N
Nat Commun 14 (1) 1438 [2023-03-15; online 2023-03-15]
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Enhanced glycerol assimilation and lipid production in Rhodotorula toruloides CBS14 upon addition of hemicellulose primarily correlates with early transcription of energy-metabolism-related genes.
Martín-Hernández GC, Chmielarz M, Müller B, ..., Hölzer M, Passoth V
Biotechnol Biofuels Bioprod 16 (1) 42 [2023-03-10; online 2023-03-10]
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Comprehensive transcriptome analysis of different potato cultivars provides insight into early blight disease caused by Alternaria solani.
Sajeevan RS, Abdelmeguid I, Saripella GV, Lenman M, Alexandersson E
BMC Plant Biol. 23 (1) 130 [2023-03-08; online 2023-03-08]
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Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.
Rifkin RF, Vikram S, Alcorta J, ..., Schlebusch CM, Lombard M
Commun Biol 6 (1) 240 [2023-03-03; online 2023-03-03]
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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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PubMed DOI Crossref
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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PubMed DOI Crossref
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]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service] Swedish Metabolomics Centre (SMC) [Service]
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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]
PubMed DOI Crossref
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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PubMed DOI Crossref
A topographic atlas defines developmental origins of cell heterogeneity in the human embryonic lung.
Sountoulidis A, Marco Salas S, Braun E, ..., Nilsson M, Samakovlis C
Nat Cell Biol 25 (2) 351-365 [2023-02-00; online 2023-01-16]
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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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PubMed DOI Crossref
Microbial communities mediating net methylmercury formation along a trophic gradient in a peatland chronosequence.
Wang B, Hu H, Bishop K, ..., Bertilsson S, Bravo AG
J Hazard Mater 442 (-) 130057 [2023-01-15; online 2022-09-23]
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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]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean.
Koptekin D, Yüncü E, Rodríguez-Varela R, ..., Götherström A, Somel M
Curr. Biol. 33 (1) 41-57.e15 [2023-01-09; online 2022-12-08]
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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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PubMed DOI Crossref
Novel cancer gene discovery using a forward genetic screen in RCAS-PDGFB-driven gliomas.
Weishaupt H, Čančer M, Rosén G, ..., Ameur A, Swartling FJ
Neuro-oncology 25 (1) 97-107 [2023-01-05; online 2022-06-24]
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PubMed DOI Crossref
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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PubMed DOI Crossref
A Phylogenomic Assessment of Processes Underpinning Convergent Evolution in Open-Habitat Chats.
Alaei Kakhki N, Schweizer M, Lutgen D, ..., Schielzeth H, Burri R
Mol. Biol. Evol. 40 (1) - [2023-01-04; online 2022-12-30]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
The path to immortalization of cells starts by managing stress through gene duplications.
Lewerentz J, Johansson AM, Stenberg P
Exp. Cell Res. 422 (1) 113431 [2023-01-01; online 2022-11-21]
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PubMed DOI Crossref
Rare tandem repeat expansions associate with genes involved in synaptic and neuronal signaling functions in schizophrenia.
Wen J, Trost B, Engchuan W, ..., Yuen RKC, Szatkiewicz JP
Mol. Psychiatry 28 (1) 475-482 [2023-01-00; online 2022-11-16]
NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Graphene oxide elicits microbiome-dependent type 2 immune responses via the aryl hydrocarbon receptor.
Peng G, Sinkko HM, Alenius H, ..., Bräutigam L, Fadeel B
Nat Nanotechnol 18 (1) 42-48 [2023-01-00; online 2022-12-12]
Bioinformatics Support for Computational Resources [Service] Eukaryotic Single Cell Genomics (ESCG) [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Year 2022

PubMed DOI Crossref
Investigation of the Virome and Characterization of Issyk-Kul Virus from Swedish Myotis brandtii Bats.
Cholleti H, de Jong J, Blomström AL, Berg M
Pathogens 12 (1) - [2022-12-21; online 2022-12-21]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Gene Networks and Pathways Involved in LPS-Induced Proliferative Response of Bovine Endometrial Epithelial Cells.
Najafi M, Guo Y, Andersson G, Humblot P, Bongcam-Rudloff E
Genes 13 (12) - [2022-12-12; online 2022-12-12]
NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
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]
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Functional responses of key marine bacteria to environmental change - toward genetic counselling for coastal waters.
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Ecol Evol 12 (12) e9701 [2022-12-00; online 2022-12-28]
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New Phytol. 236 (5) 1951-1963 [2022-12-00; online 2022-09-16]
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Sci Data 9 (1) 667 [2022-11-03; online 2022-11-03]
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Mycorrhiza 32 (5-6) 361-371 [2022-11-00; online 2022-09-26]
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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
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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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Colitis Induces Sex-Specific Intestinal Transcriptomic Responses in Mice.
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Genomic evidence that a sexually selected trait captures genome-wide variation and facilitates the purging of genetic load.
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Nat Ecol Evol 6 (9) 1330-1342 [2022-09-00; online 2022-07-18]
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Ericson PGP, Irestedt M, Zuccon D, ..., Werdelin L, Qu Y
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Zufia JA, Legrand C, Farnelid H
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Evolutionary consequences of genomic deletions and insertions in the woolly mammoth genome.
van der Valk T, Dehasque M, Chacón-Duque JC, ..., Díez-Del-Molino D, Dalén L
iScience 25 (8) 104826 [2022-08-19; online 2022-08-01]
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Ecosystem size-induced environmental fluctuations affect the temporal dynamics of community assembly mechanisms.
Bier RL, Vass M, Székely AJ, Langenheder S
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Osterholz H, Turner S, Alakangas LJ, ..., Kalinowski BE, Dopson M
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Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity.
Ambikan AT, Yang H, Krishnan S, ..., Benfeitas R, Neogi U
Cell Syst 13 (8) 665-681.e4 [2022-08-17; online 2022-07-08]
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Isolated Grauer's gorilla populations differ in diet and gut microbiome.
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Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem.
Broman E, Izabel-Shen D, Rodríguez-Gijón A, ..., Garcia SL, Nascimento FJA
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
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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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Metatranscriptomics of Nasopharyngeal Microbiota and Host Distinguish between Pneumonia and Health.
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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Identification and functional characterization of a novel susceptibility locus for small vessel vasculitis with MPO-ANCA.
Dahlqvist J, Ekman D, Sennblad B, ..., Eriksson P, Lindblad-Toh K
Rheumatology (Oxford) 61 (8) 3461-3470 [2022-08-03; online 2021-12-11]
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A Genome for Edith's Checkerspot Butterfly: An Insect with Complex Host-Adaptive Suites and Rapid Evolutionary Responses to Environmental Changes.
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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A relationship between phages and organic carbon in wastewater treatment plant effluents.
Modin O, Fuad N, Abadikhah M, ..., Persson F, Wilén BM
Water Res X 16 (-) 100146 [2022-08-01; online 2022-06-16]
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Spatially resolved clonal copy number alterations in benign and malignant tissue.
Erickson A, He M, Berglund E, ..., Lamb AD, Lundeberg J
Nature 608 (7922) 360-367 [2022-08-00; online 2022-08-10]
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Short- and long-read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing.
Latz MAC, Grujcic V, Brugel S, ..., Andersson A, Andersson AF
Mol Ecol Resour 22 (6) 2304-2318 [2022-08-00; online 2022-05-06]
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Mosaic Deletions of Known Genes Explain Skeletal Dysplasias With High and Low Bone Mass.
Muurinen M, Taylan F, Tournis S, ..., Mäkitie O, Costantini A
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Complement C4 Copy Number Variation is Linked to SSA/Ro and SSB/La Autoantibodies in Systemic Inflammatory Autoimmune Diseases.
Lundtoft C, Pucholt P, Martin M, ..., Svenungsson E, Rönnblom L
Arthritis & rheumatology (Hoboken, N.J.) 74 (8) 1440-1450 [2022-08-00; online 2022-06-27]
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A polygenic architecture with habitat-dependent effects underlies ecological differentiation in Silene.
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Characterization of Pipistrellus pygmaeus Bat Virome from Sweden.
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Restricted X chromosome introgression and support for Haldane's rule in hybridizing damselflies.
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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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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.
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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.
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Nat Commun 13 (1) 4092 [2022-07-14; online 2022-07-14]
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Single-cell transcriptional pharmacodynamics of trifluridine in a tumor-immune model.
Selvin T, Fasterius E, Jarvius M, ..., Larsson R, Andersson CR
Sci Rep 12 (1) 11960 [2022-07-13; online 2022-07-13]
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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.
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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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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.
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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
Nat Commun 13 (1) 3878 [2022-07-05; online 2022-07-05]
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Seasonal Dynamics in Carbon Cycling of Marine Bacterioplankton Are Lifestyle Dependent.
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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.
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Skelet Muscle 12 (1) 16 [2022-07-02; online 2022-07-02]
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Practical application of a Bayesian network approach to poultry epigenetics and stress.
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BMC Bioinformatics 23 (1) 261 [2022-07-01; online 2022-07-01]
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Weak population genetic structure in Eurasian spruce bark beetle over large regional scales in Sweden.
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Ecol Evol 12 (7) e9078 [2022-07-00; online 2022-07-06]
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Grey wolf genomic history reveals a dual ancestry of dogs.
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Nature 607 (7918) 313-320 [2022-07-00; online 2022-06-29]
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Genomic dynamics of brown trout populations released to a novel environment.
Kurland S, Rafati N, Ryman N, Laikre L
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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Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy.
Novotny A, Jan KMG, Dierking J, Winder M
Sci Rep 12 (1) 10952 [2022-06-29; online 2022-06-29]
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Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests.
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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.
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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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Stem Cell Reports 17 (6) 1458-1475 [2022-06-14; online 2022-06-16]
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CRISPR-Cas9 treatment partially restores amyloid-β 42/40 in human fibroblasts with the Alzheimer's disease PSEN 1 M146L mutation.
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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.
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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.
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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.
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Nature 606 (7912) 113-119 [2022-06-00; online 2022-05-18]
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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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Single base substitution and insertion/deletion mutational signatures in adult core binding factor acute myeloid leukemia.
Gunnarsson R, Yang M, Biloglav A, ..., Paulsson K, Johansson B
Leukemia 36 (6) 1681-1684 [2022-06-00; online 2022-04-01]
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Higher levels of Bifidobacteria and tumor necrosis factor in children with drug-resistant epilepsy are associated with anti-seizure response to the ketogenic diet.
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EBioMedicine 80 (-) 104061 [2022-06-00; online 2022-05-19]
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Ancient DNA from a 2700-year-old goitered gazelle (Gazella subgutturosa) supports gazelle hunting in Iron Age Central Asia.
Rodrigues Soares AE, Boroffka N, Schröder O, ..., Benecke N, Günther T
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Development of gut microbiota during the first 2 years of life.
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Sci Rep 12 (1) 9080 [2022-05-31; online 2022-05-31]
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An empirical evaluation of genotype imputation of ancient DNA.
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G3 (Bethesda) 12 (6) - [2022-05-30; online 2022-04-29]
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Inflammation and Interferon Signatures in Peripheral B-Lymphocytes and Sera of Individuals With Fibromyalgia.
Fineschi S, Klar J, Gustafsson KA, ..., Karlsson B, Dahl N
Front Immunol 13 (-) 874490 [2022-05-26; online 2022-05-26]
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Nitrogen Removal Capacity of Microbial Communities Developing in Compost- and Woodchip-Based Multipurpose Reactive Barriers for Aquifer Recharge With Wastewater.
Hellman M, Valhondo C, Martínez-Landa L, ..., Juhanson J, Hallin S
Front Microbiol 13 (-) 877990 [2022-05-24; online 2022-05-24]
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Quantitative Analysis of the Transcriptome of Two Commonly Used Human Monocytic Cell Lines-THP-1 and Mono Mac 6-Reveals Their Arrest during Early Monocyte/Neutrophil Differentiation.
Akula S, Lara S, Olsson AK, Hellman L
Int J Mol Sci 23 (10) - [2022-05-22; online 2022-05-22]
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Touch signaling and thigmomorphogenesis are regulated by complementary CAMTA3- and JA-dependent pathways.
Darwish E, Ghosh R, Ontiveros-Cisneros A, ..., Khan K, Van Aken O
Sci Adv 8 (20) eabm2091 [2022-05-20; online 2022-05-20]
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Environmentally induced DNA methylation is inherited across generations in an aquatic keystone species.
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iScience 25 (5) 104303 [2022-05-20; online 2022-04-25]
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Seasonal and Spatial Variations in Synechococcus Abundance and Diversity Throughout the Gullmar Fjord, Swedish Skagerrak.
Laber CP, Pontiller B, Bunse C, ..., Pinhassi J, Farnelid H
Front Microbiol 13 (-) 828459 [2022-05-09; online 2022-05-09]
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Contribution of rare whole-genome sequencing variants to plasma protein levels and the missing heritability.
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Nat Commun 13 (1) 2532 [2022-05-09; online 2022-05-09]
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Modulation of RNA stability regulates gene expression in two opposite ways: through buffering of RNA levels upon global perturbations and by supporting adapted differential expression.
Faucillion ML, Johansson AM, Larsson J
Nucleic Acids Res. 50 (8) 4372-4388 [2022-05-06; online 2022-04-08]
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Evaluating metagenomic assembly approaches for biome-specific gene catalogues.
Delgado LF, Andersson AF
Microbiome 10 (1) 72 [2022-05-06; online 2022-05-06]
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Ivermectin-induced gene expression changes in adult Parascaris univalens and Caenorhabditis elegans: a comparative approach to study anthelminthic metabolism and resistance in vitro.
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Parasit Vectors 15 (1) 158 [2022-05-05; online 2022-05-05]
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FOXO Dictates Initiation of B Cell Development and Myeloid Restriction in Common Lymphoid Progenitors.
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Front Immunol 13 (-) 880668 [2022-05-04; online 2022-05-04]
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Comparison of methodological approaches to the study of young sex chromosomes: A case study in Poecilia.
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Genomic Impact of Whaling in North Atlantic Fin Whales.
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Mol. Biol. Evol. 39 (5) - [2022-05-03; online 2022-05-06]
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The outcome of targeted NGS screening in patients with syndromic forms of sagittal and pansynostosis - IL11RA is an emerging core-gene for pansynostosis.
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Eur J Med Genet 65 (5) 104476 [2022-05-00; online 2022-03-21]
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Epicardium-derived cells organize through tight junctions to replenish cardiac muscle in salamanders.
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Nat Cell Biol 24 (5) 645-658 [2022-05-00; online 2022-05-12]
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Dual RNA Sequencing Reveals Key Events When Different Giardia Life Cycle Stages Interact With Human Intestinal Epithelial Cells In Vitro.
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Cell-lineage controlled epigenetic regulation in glioblastoma stem cells determines functionally distinct subgroups and predicts patient survival.
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Nat Commun 13 (1) 2236 [2022-04-25; online 2022-04-25]
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Multi-omics protein-coding units as massively parallel Bayesian networks: Empirical validation of causality structure.
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Influence of cysteine, serine, sulfate, and sulfide on anaerobic conversion of unsaturated long-chain fatty acid, oleate, to methane.
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Sci. Total Environ. 817 (-) 152967 [2022-04-15; online 2022-01-10]
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Development and Optimization of a Silica Column-Based Extraction Protocol for Ancient DNA.
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Transposon activity, local duplications and propagation of structural variants across haplotypes drive the evolution of the Drosophila S2 cell line.
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BMC Genomics 23 (1) 276 [2022-04-07; online 2022-04-07]
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Uterine fluid microRNAs are dysregulated in women with recurrent implantation failure.
von Grothusen C, Frisendahl C, Modhukur V, ..., Boggavarapu NR, Gemzell-Danielsson K
Hum. Reprod. 37 (4) 734-746 [2022-04-01; online 2022-02-12]
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Target sequence capture of Barnadesioideae (Compositae) demonstrates the utility of low coverage loci in phylogenomic analyses.
Ferreira PdL, Batista R, Andermann T, ..., Bacon CD, Antonelli A
Mol. Phylogenet. Evol. 169 (-) 107432 [2022-04-00; online 2022-02-04]
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Integrative multi-omics and drug response profiling of childhood acute lymphoblastic leukemia cell lines.
Leo IR, Aswad L, Stahl M, ..., Vesterlund M, Jafari R
Nat Commun 13 (1) 1691 [2022-03-30; online 2022-03-30]
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Inflammation and neutrophil extracellular traps in cerebral cavernous malformation.
Yau ACY, Globisch MA, Onyeogaziri FC, ..., Dejana E, Magnusson PU
Cell. Mol. Life Sci. 79 (4) 206 [2022-03-25; online 2022-03-25]
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Near Chromosome-Level Genome Assembly and Annotation of Rhodotorula babjevae Strains Reveals High Intraspecific Divergence.
Martín-Hernández GC, Müller B, Brandt C, ..., Viehweger A, Passoth V
JoF 8 (4) - [2022-03-22; online 2022-03-22]
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GBS-MeDIP: A protocol for parallel identification of genetic and epigenetic variation in the same reduced fraction of genomes across individuals.
Rezaei S, Uffenorde J, Gimm O, ..., Guerrero-Bosagna C, Pértille F
STAR Protoc 3 (1) 101202 [2022-03-18; online 2022-03-03]
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Salivary Microbiota and Host-Inflammatory Responses in Periodontitis Affected Individuals With and Without Rheumatoid Arthritis.
Eriksson K, Lundmark A, Delgado LF, ..., Andersson AF, Yucel-Lindberg T
Front. Cell. Infect. Microbiol. 12 (-) 841139 [2022-03-14; online 2022-03-14]
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DOI Crossref
Weakened resilience of benthic microbial communities in the face of climate change
Seidel L, Ketzer M, Broman E, ..., Hylander S, Dopson M
ISME COMMUN. 2 (1) - [2022-03-08; online 2022-03-08]
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Downregulation and Hypermethylation of GABPB1 Is Associated with Aggressive Thyroid Cancer Features.
Xing X, Mu N, Yuan X, ..., Neo SY, Xu D
Cancers (Basel) 14 (6) - [2022-03-08; online 2022-03-08]
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Identification of a discrete subpopulation of spinal cord ependymal cells with neural stem cell properties.
Stenudd M, Sabelström H, Llorens-Bobadilla E, ..., Barnabé-Heider F, Frisén J
Cell Rep 38 (9) 110440 [2022-03-01; online 2022-03-03]
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Whole-genome resequencing of temporally stratified samples reveals substantial loss of haplotype diversity in the highly inbred Scandinavian wolf population.
Viluma A, Flagstad Ø, Åkesson M, ..., Wabakken P, Ellegren H
Genome Res. 32 (3) 449-458 [2022-03-00; online 2022-02-08]
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Utilizing museomics to trace the complex history and species boundaries in an avian-study system of conservation concern.
Ernst M, Jønsson KA, Ericson PGP, Blom MPK, Irestedt M
Heredity (Edinb) 128 (3) 159-168 [2022-03-00; online 2022-01-26]
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Local selection signals in the genome of blue tits emphasize regulatory and neuronal evolution.
Mueller JC, Botero-Delgadillo E, Espíndola-Hernández P, ..., Gruselius J, Kempenaers B
Mol. Ecol. 31 (5) 1504-1514 [2022-03-00; online 2022-01-22]
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Genomic divergence and a lack of recent introgression between commercial and wild bumblebees (Bombus terrestris).
Kardum Hjort C, Paris JR, Olsson P, ..., Dudaniec RY, Smith HG
Evol Appl 15 (3) 365-382 [2022-03-00; online 2022-03-14]
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Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics.
Ratz M, von Berlin L, Larsson L, ..., Lundeberg J, Frisén J
Nat. Neurosci. 25 (3) 285-294 [2022-03-00; online 2022-02-24]
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ADAR1- and ADAR2-mediated regulation of maturation and targeting of miR-376b to modulate GABA neurotransmitter catabolism.
Widmark A, Sagredo EA, Karlström V, ..., Daniel C, Öhman M
J. Biol. Chem. 298 (3) 101682 [2022-03-00; online 2022-02-03]
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The Value of Whole-Genome Sequencing for Mitochondrial DNA Population Studies: Strategies and Criteria for Extracting High-Quality Mitogenome Haplotypes.
Sturk-Andreaggi K, Ring JD, Ameur A, ..., Marshall C, Allen M
Int J Mol Sci 23 (4) - [2022-02-17; online 2022-02-17]
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PubMed DOI Crossref
Populus SVL Acts in Leaves to Modulate the Timing of Growth Cessation and Bud Set.
André D, Zambrano JA, Zhang B, ..., Marcon A, Nilsson O
Front Plant Sci 13 (-) 823019 [2022-02-17; online 2022-02-17]
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Three-dimensional spatial transcriptomics uncovers cell type localizations in the human rheumatoid arthritis synovium.
Vickovic S, Schapiro D, Carlberg K, ..., Regev A, Ståhl PL
Commun Biol 5 (1) 129 [2022-02-11; online 2022-02-11]
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The spatial transcriptomic landscape of the healing mouse intestine following damage.
Parigi SM, Larsson L, Das S, ..., Lundeberg J, Villablanca EJ
Nat Commun 13 (1) 828 [2022-02-11; online 2022-02-11]
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PubMed DOI Crossref
Ionotropic receptors in the turnip moth Agrotis segetum respond to repellent medium-chain fatty acids.
Hou XQ, Zhang DD, Powell D, ..., Andersson MN, Löfstedt C
BMC Biol. 20 (1) 34 [2022-02-07; online 2022-02-07]
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Partial Monosomy 21 Mirrors Gene Expression of Trisomy 21 in a Patient-Derived Neuroepithelial Stem Cell Model.
Schuy J, Eisfeldt J, Pettersson M, ..., Falk A, Lindstrand A
Front Genet 12 (-) 803683 [2022-02-04; online 2022-02-04]
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Genomic basis for skin phenotype and cold adaptation in the extinct Steller's sea cow.
Le Duc D, Velluva A, Cassatt-Johnstone M, ..., Shapiro B, Schöneberg T
Sci Adv 8 (5) eabl6496 [2022-02-04; online 2022-02-04]
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The miRNome function transitions from regulating developmental genes to transposable elements during pollen maturation.
Oliver C, Annacondia ML, Wang Z, ..., Köhler C, Martinez G
Plant Cell 34 (2) 784-801 [2022-02-03; online 2021-11-11]
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PubMed DOI Crossref
Population genomics and geographic dispersal in Chagas disease vectors: Landscape drivers and evidence of possible adaptation to the domestic setting.
Hernandez-Castro LE, Villacís AG, Jacobs A, ..., Llewellyn MS, Grijalva MJ
PLoS Genet. 18 (2) e1010019 [2022-02-00; online 2022-02-04]
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PubMed DOI Crossref
Heterochiasmy and the establishment of gsdf as a novel sex determining gene in Atlantic halibut.
Edvardsen RB, Wallerman O, Furmanek T, ..., Norberg B, Rubin CJ
PLoS Genet. 18 (2) e1010011 [2022-02-00; online 2022-02-08]
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PubMed DOI Crossref
A genomic and morphometric analysis of alpine bumblebees: Ongoing reductions in tongue length but no clear genetic component.
Christmas MJ, Jones JC, Olsson A, ..., Miller-Struttmann NE, Webster MT
Mol. Ecol. 31 (4) 1111-1127 [2022-02-00; online 2021-12-07]
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PubMed DOI Crossref
A Verticillium longisporum pleiotropic drug transporter determines tolerance to the plant host β-pinene monoterpene.
Rafiei V, Ruffino A, Persson Hodén K, ..., Dubey M, Tzelepis G
Mol. Plant Pathol. 23 (2) 291-303 [2022-02-00; online 2021-11-26]
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PubMed DOI Crossref
Occasional paternal inheritance of the germline-restricted chromosome in songbirds.
Pei Y, Forstmeier W, Ruiz-Ruano FJ, ..., Suh A, Kempenaers B
Proc. Natl. Acad. Sci. U.S.A. 119 (4) - [2022-01-25; online 2022-01-22]
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PubMed DOI Crossref
Massive genome inversion drives coexistence of divergent morphs in common quails.
Sanchez-Donoso I, Ravagni S, Rodríguez-Teijeiro JD, ..., Leonard JA, Vilà C
Curr. Biol. 32 (2) 462-469.e6 [2022-01-24; online 2021-11-29]
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PubMed DOI Crossref
Fish Skin Microbiomes Are Highly Variable Among Individuals and Populations but Not Within Individuals.
Berggren H, Tibblin P, Yıldırım Y, ..., Lundin D, Forsman A
Front Microbiol 12 (-) 767770 [2022-01-21; online 2022-01-21]
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Transcriptome Analysis of an Aedes albopictus Cell Line Single- and Dual-Infected with Lammi Virus and WNV.
Öhlund P, Delhomme N, Hayer J, Hesson JC, Blomström AL
Int J Mol Sci 23 (2) - [2022-01-14; online 2022-01-14]
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Plant Growth-Promoting Activity of Pseudomonas aeruginosa FG106 and Its Ability to Act as a Biocontrol Agent against Potato, Tomato and Taro Pathogens.
Ghadamgahi F, Tarighi S, Taheri P, ..., Ortiz R, Vetukuri RR
Biology (Basel) 11 (1) - [2022-01-14; online 2022-01-14]
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PubMed DOI Crossref
The formation of avian montane diversity across barriers and along elevational gradients.
Pujolar JM, Blom MPK, Reeve AH, ..., Irestedt M, Jønsson KA
Nat Commun 13 (1) 268 [2022-01-12; online 2022-01-12]
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PubMed DOI Crossref
Transcriptomic analysis reveals proinflammatory signatures associated with acute myeloid leukemia progression.
Stratmann S, Yones SA, Garbulowski M, ..., Komorowski J, Holmfeldt L
Blood Adv 6 (1) 152-164 [2022-01-11; online 2021-10-08]
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PubMed DOI Crossref
Connectivity of Fennoscandian Shield terrestrial deep biosphere microbiomes with surface communities.
Westmeijer G, Mehrshad M, Turner S, ..., Bertilsson S, Dopson M
Commun Biol 5 (1) 37 [2022-01-11; online 2022-01-11]
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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]
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PubMed DOI Crossref
Genomic Signatures of Sexual Selection on Pollen-Expressed Genes in Arabis alpina.
Gutiérrez-Valencia J, Fracassetti M, Horvath R, ..., Kolář F, Slotte T
Mol. Biol. Evol. 39 (1) - [2022-01-07; online 2021-12-09]
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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]
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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]
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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]
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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]
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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]
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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]
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PubMed DOI Crossref
Avian neo-sex chromosomes reveal dynamics of recombination suppression and W degeneration.
Sigeman H, Strandh M, Proux-Wéra E, ..., Westerdahl H, Hansson B
Mol. Biol. Evol. 38 (12) 5275-5291 [2021-09-20; online 2021-09-20]
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PubMed DOI Crossref
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]
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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]
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Year 2010

PubMed DOI Crossref
Coexisting NRAS and BRAF mutations in primary familial melanomas with specific CDKN2A germline alterations.
Jovanovic B, Egyhazi S, Eskandarpour M, ..., Hayward NK, Hansson J
J. Invest. Dermatol. 130 (2) 618-620 [2010-02-00; online 2009-09-18]
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SciLifeLab Data Centre
Publications 9.5.1