Publications 2025

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40 publications

PubMed DOI Crossref
Identification of a SNAI1 enhancer RNA that drives cancer cell plasticity.
Fan C, Wang Q, Krijger PHL, ..., de Laat W, Ten Dijke P
Nat Commun 16 (1) 2890 [2025-03-25; online 2025-03-25]
CRISPR Functional Genomics [Service]
PubMed DOI Crossref
Historic manioc genomes illuminate maintenance of diversity under long-lived clonal cultivation.
Kistler L, de Oliveira Freitas F, Gutaker RM, ..., Capriles JM, Allaby RG
Science 387 (6738) eadq0018 [2025-03-07; online 2025-03-07]
Ancient DNA [Collaborative]
PubMed DOI Crossref
Associations of PFAS and OH-PCBs with risk of multiple sclerosis onset and disability worsening.
Vaivade A, Erngren I, Carlsson H, ..., Burman J, Kultima K
Nat Commun 16 (1) 2014 [2025-02-27; online 2025-02-27]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
PubMed DOI Crossref
Duplexed CeTEAM drug biosensors reveal determinants of PARP inhibitor selectivity in cells.
Pires MJ, Alam S, Lovric A, ..., Altun M, Valerie NCK
J. Biol. Chem. - (-) 108361 [2025-02-26; online 2025-02-26]
Chemical Biology Consortium Sweden (CBCS) [Service]
DOI Crossref
Dissecting the properties of circulating IgG against streptococcal pathogens through a combined systems antigenomics-serology workflow
Gomez Toledo A, Chowdhury S, Hjortswang E, ..., Rasmussen M, Malmström J
Nat Commun 16 (1) - [2025-02-24; online 2025-02-24]
Structural Proteomics [Collaborative]
DOI Crossref
Spatial mapping of DNA synthesis reveals dynamics and geometry of human replication nanostructures
Hawgood M, Urién González B, Agostinho A, ..., Blom H, Lemmens B
- - (-) - [2025-02-23; online 2025-02-23]
Integrated Microscopy Technologies Stockholm [Service]
PubMed DOI Crossref
Temporal dynamics of airborne fungi in Swedish forest nurseries.
Larsson R, Menkis A, Olson Å
Appl. Environ. Microbiol. 91 (2) e0130624 [2025-02-19; online 2025-01-16]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Measuring plasma membrane fluidity using confocal microscopy.
Carravilla P, Andronico L, Schlegel J, ..., Lorent J, Sezgin E
Nat Protoc - (-) - [2025-02-19; online 2025-02-19]
Integrated Microscopy Technologies Stockholm [Service]
PubMed DOI Crossref
A chromosome-level genome assembly of the European green toad (Bufotes viridis).
Rödin-Mörch P, Bunikis I, Choi E, ..., Proux-Wéra E, Höglund J
G3 (Bethesda) - (-) - [2025-02-19; online 2025-02-19]
NGI Long read [Collaborative] NGI Stockholm (Genomics Production) [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]
PubMed DOI Crossref
Circular RNA circASH1L(4,5) protects microRNA-129-5p from target-directed microRNA degradation in human skin wound healing.
Wang Q, Niu G, Liu Z, ..., Sommar P, Xu Landén N
Br J Dermatol 192 (3) 468-480 [2025-02-18; online 2024-10-18]
Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
Microbial communities in slow sand filters for drinking water treatment adapt to organic matter altered by ozonation.
Rosenqvist T, Hilding J, Suarez C, Paul CJ
Water Res. 270 (-) 122843 [2025-02-15; online 2024-11-23]
Bioinformatics Support for Computational Resources [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]
PubMed DOI Crossref
Imaging Single Particle Profiler to Study Nanoscale Bioparticles Using Conventional Confocal Microscopy.
Sych T, Görgens A, Steiner L, ..., El Andaloussi S, Sezgin E
Nano Lett. 25 (6) 2173-2180 [2025-02-12; online 2025-01-29]
Integrated Microscopy Technologies Stockholm [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
The expanded genome of Hexamita inflata, a free-living diplomonad.
Akdeniz Z, Havelka M, Stoklasa M, ..., Andersson JO, Tachezy J
Sci Data 12 (1) 192 [2025-02-01; online 2025-02-01]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
DOI Crossref
Single cell sequencing reveals shared clonal signatures in non-malignant B- and tumor cells in T-prolymphocytic leukemia
Hesselager C, Thörn I, Marincevic M, ..., Baliakas P, Amini RM
Blood Neoplasia - (-) 100076 [2025-02-00; online 2025-02-00]
Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]
DOI Crossref
Modelling age at death reveals Nordic Corded Ware paleodemography
Tornberg A, Vandkilde H
Archaeol Anthropol Sci 17 (2) - [2025-02-00; online 2025-01-20]
Ancient DNA [Service]
DOI Crossref
Impact of plant diversity in potato-ley strip-cropping systems on soil microbial communities
Riggi LGA, Ranheim Sveen T, Castaño C, ..., Clemmensen KE, Bahram M
Applied Soil Ecology 206 (-) 105777 [2025-02-00; online 2025-02-00]
Bioinformatics Support for Computational Resources [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
Earliest modern human genomes constrain timing of Neanderthal admixture.
Sümer AP, Rougier H, Villalba-Mouco V, ..., Prüfer K, Krause J
Nature 638 (8051) 711-717 [2025-02-00; online 2024-12-12]
Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
Modulation of biological activities in adipose derived stem cells by histone deacetylation.
Abdallah S, Tabebi M, Qanadilo S, ..., Elmasry M, El-Serafi A
Sci Rep 15 (1) 3629 [2025-01-29; online 2025-01-29]
Clinical Genomics [Collaborative] Clinical Genomics Linköping [Collaborative]
PubMed DOI Crossref
The di-leucine motif in the host defense peptide LL-37 is essential for initiation of autophagy in human macrophages.
Rekha RS, Padhi A, Frengen N, ..., Guðmundsson GH, Bergman P
Cell Rep 44 (1) 115031 [2025-01-28; online 2024-12-20]
Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
Association between alcohol consumption and peripheral artery disease: two de novo prospective cohorts and a systematic review with meta-analysis.
Yuan S, Wu J, Chen J, ..., Åkesson A, Larsson SC
Eur J Prev Cardiol 32 (2) 149-155 [2025-01-27; online 2024-04-16]
Bioinformatics Support for Computational Resources [Service]
PubMed DOI Crossref
Ultra-Sensitive Detection of Bacterial Spores via SERS.
Segervald J, Malyshev D, Öberg R, ..., Wågberg T, Andersson M
ACS Sens. - (-) - [2025-01-23; online 2025-01-23]
Integrated Microscopy Technologies Umeå [Service]
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
Visualization using NIPTviewer support the clinical interpretation of noninvasive prenatal testing results.
Smeds P, Baranowska Körberg I, Melin M, Ladenvall C
BMC Med Genomics 18 (1) 15 [2025-01-20; online 2025-01-20]
Clinical Genomics [Technology development] Clinical Genomics Uppsala [Technology development]
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
Somatic CAG repeat expansion in blood associates with biomarkers of neurodegeneration in Huntington's disease decades before clinical motor diagnosis.
Scahill RI, Farag M, Murphy MJ, ..., Langbehn DR, Tabrizi SJ
Nat. Med. - (-) - [2025-01-17; online 2025-01-17]
Glycoproteomics and MS Proteomics [Service]
PubMed DOI Crossref
Structure of the T=13 capsid of infectious pancreatic necrosis virus (IPNV)-a salmonid birnavirus.
Munke A, Ahmed Abdelrahim Gamil A, Mikalsen AB, ..., Evensen Ø, Okamoto K
J. Virol. - (-) e0145424 [2025-01-16; online 2025-01-16]
Cryo-EM [Service]
PubMed DOI Crossref
A thermoplastic chip for 2D and 3D correlative assays combining screening and high-resolution imaging of immune cell responses.
van Ooijen H, Verron Q, Zhang H, ..., Sandström N, Önfelt B
Cell Reports Methods - (-) 100965 [2025-01-16; online 2025-01-16]
Integrated Microscopy Technologies Stockholm [Service]
PubMed DOI Crossref
The Progression of Mycosis Fungoides During Treatment with Mogamulizumab: A BIO-MUSE Case Study of the Tumor and Immune Response in Peripheral Blood and Tissue.
Johansson A, Kalliara E, Belfrage E, ..., Drott K, Ek S
Biomedicines 13 (1) - [2025-01-14; online 2025-01-14]
Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]
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
Model-informed drug development for antimicrobials: translational pharmacokinetic-pharmacodynamic modelling of apramycin to facilitate prediction of efficacious dose in complicated urinary tract infections.
Hernández-Lozano I, Aranzana-Climent V, Cao S, ..., Vingsbo Lundberg C, Friberg LE
J. Antimicrob. Chemother. 80 (1) 301-310 [2025-01-03; online 2024-11-16]
Bioinformatics Support for Computational Resources [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]
PubMed DOI Crossref
Trees First Inhibit Then Promote Litter Decomposition in the Subarctic.
Jonsson M, Clemmensen KE, Castaño C, Parker TC
Ecol. Lett. 28 (1) e70063 [2025-01-00; online 2025-01-20]
NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]
PubMed DOI Crossref
Evaluation of nationwide analysis surveillance for methicillin-resistant Staphylococcus aureus within Genomic Medicine Sweden.
Tång Hallbäck E, Björkman JT, Dyrkell F, ..., Sikora P, Mölling P
Microb Genom 11 (1) - [2025-01-00; online 2025-01-27]
Clinical Genomics [Collaborative] Clinical Genomics Uppsala [Collaborative]
SciLifeLab Data Centre
Publications 9.5.1