Publications 2025

Antimicrobial resistance and serotype distribution of Salmonella spp. isolated from fresh foods in Cambodia.

Huoy L, Nasirzadeh L, Phan K, ..., Rudloff EB, Boqvist S

J Appl Microbiol - (-) - [2025-06-03; online 2025-06-03]

Clinical Genomics [Collaborative] Clinical Genomics Linköping [Collaborative]

Fin Whale as a Sink of Legacy and Emerging Contaminants: First Integrated Chemical Exposomics and Gene Expression Analysis in Cetaceans.

Fossi MC, Limonta G, Baini M, ..., Rosso M, Panti C

Environ. Sci. Technol. - (-) - [2025-06-02; online 2025-06-02]

Exposomics [Collaborative]

Shared requirement for MYC upstream super-enhancer region in tissue regeneration and cancer.

Sur I, Zhao W, Zhang J, ..., de la Roche M, Taipale J

Life Sci. Alliance 8 (6) - [2025-06-00; online 2025-04-03]

NGI Single cell [Service] NGI Stockholm (Genomics Applications) [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Frequent Hybridisation Between Parapatric Lekking Bird-of-Paradise Species.

Thörn F, Müller IA, Soares AER, ..., Blom MPK, Irestedt M

Mol. Ecol. 34 (11) e17780 [2025-06-00; online 2025-04-29]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Diffuse large B cell lymphoma in rheumatoid arthritis patients is associated with elevated B-cell driving factors including CXCL13.

Euler N, Hellbacher E, Klint EA, ..., Grönwall C, AUTO-LYMPHOMA study group

Clin. Immunol. 275 (-) 110476 [2025-06-00; online 2025-03-19]

Affinity Proteomics Stockholm [Service]

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 Stockholm (Genomics Production) NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Comprehensive transcriptome assessment in PBMCs of post-COVID patients at a median follow-up of 28 months after a mild COVID infection reveals upregulation of JAK/STAT signaling and a prolonged immune response.

Fineschi S, Klar J, Lopez Egido JR, ..., Kaden R, Dahl N

Front Immunol 16 (-) 1589589 [2025-05-30; online 2025-05-30]

NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Plasma membrane labelling efficiency, internalization and partitioning of functionalized fluorescent lipids as a function of lipid structure

Sezgin E

- - (-) - [2025-05-13; online 2025-05-13]

Integrated Microscopy Technologies Stockholm [Service]

Microbial transfer through fecal strings on eggs affects leaf beetle microbiome dynamics.

An Y, Garcia SL, Hambäck PA

mSystems - (-) e0172324 [2025-05-13; online 2025-05-13]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

Gut microbiota mediates SREBP-1c-driven hepatic lipogenesis and steatosis in response to zero-fat high-sucrose diet.

Bergentall M, Tremaroli V, Sun C, ..., Nieuwdorp M, Bäckhed F

Mol Metab 97 (-) 102162 [2025-05-07; online 2025-05-07]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Green Listed v2.0: A Web Application for Streamlined Design of Custom CRISPR Screens.

Henkel E, Li Z, Uvehag D, ..., Henkel M, Wermeling F

CRISPR J - (-) - [2025-05-07; online 2025-05-07]

CRISPR Functional Genomics [Technology development] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Single-cell MultiOmics and spatial transcriptomics demonstrate neuroblastoma developmental plasticity.

Xu Y, Lou D, Chen P, ..., Hu Y, Wang J

Dev. Cell - (-) - [2025-05-06; online 2025-05-06]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

External validation of plasma CSF1 as a preoperative prognostic marker in patients with resectable intrahepatic cholangiocarcinoma.

Akiki A, Jacobsson H, Nouairia G, ..., Taflin H, Jansson H

Eur J Surg Oncol 51 (8) 110123 [2025-05-04; online 2025-05-04]

Affinity Proteomics Stockholm [Service]

Ancient DNA [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Museum Ecologies

Fredengren C, Ewing A, Owman C, Holmstedt J

Mus. Soc. 23 (1) - [2025-05-01; online 2025-05-01]

High Content Imaging in Drug Discovery

- - (-) - [2025-04-30; online 2025-04-30]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

Conformal prediction enables disease course prediction and allows individualized diagnostic uncertainty in multiple sclerosis.

Sreenivasan AP, Vaivade A, Noui Y, ..., Spjuth O, Kultima K

NPJ Digit Med 8 (1) 224 [2025-04-24; online 2025-04-24]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Constraints to gene flow increase the risk of genome erosion in the Ngorongoro Crater lion population.

Dussex N, Jansson I, van der Valk T, ..., E Mjingo E, Spong G

Commun Biol 8 (1) 640 [2025-04-21; online 2025-04-21]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Structural mechanism of FusB-mediated rescue from fusidic acid inhibition of protein synthesis.

González-López A, Ge X, Larsson DSD, ..., Sanyal S, Selmer M

Nat Commun 16 (1) 3693 [2025-04-18; online 2025-04-18]

Cryo-EM [Service]

Challenging the "Undruggable"─Targeting STAT3 but Identifying Potent TrkA-Targeted Inhibitors.

Iliev P, McCutcheon C, Admas TH, ..., Frank DA, Page BDG

J. Med. Chem. - (-) - [2025-04-17; online 2025-04-17]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

In vivo composition of the mitochondrial nucleoid in mice.

García-Villegas R, Odenthal F, Giannoula Y, ..., Levander F, Larsson NG

Biochimica et Biophysica Acta (BBA) - Molecular Cell Research - (-) 119955 [2025-04-15; online 2025-04-15]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Choline levels in the pregenual anterior cingulate cortex associated with unpleasant pain experience and anxiety.

Hudhud L, Hauksson J, Haney M, ..., Eriksson J, Lindgren L

Neuroimage 310 (-) 121153 [2025-04-15; online 2025-03-16]

Cytoskeletal alterations in neuronal cells implicate Toxoplasma gondii secretory machinery and host microRNA-containing extracellular vesicles.

Mazza T, Aslanzadeh M, Berentsen L, ..., Friedländer MR, Barragan A

Sci Rep 15 (1) 12606 [2025-04-12; online 2025-04-12]

NGI Other [Collaborative] NGI Short read [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Collaborative]

Antibacterial compounds against non-growing and intracellular bacteria

Kaldalu N, Bērziņš N, Berglund Fick S, ..., Hauryliuk V, Tenson T

npj Antimicrob Resist 3 (1) - [2025-04-11; online 2025-04-11]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A red fluorescent lifeact marker to study actin morphology in podocytes.

Wiesner E, Binz-Lotter J, Tröder SE, ..., Wedlich-Söldner R, Hackl MJ

Sci Rep 15 (1) 12386 [2025-04-11; online 2025-04-11]

Integrated Microscopy Technologies Stockholm [Service]

Nuclear AGO2 supports influenza A virus replication through type-I interferon regulation.

Huang H, Fong M, Nowak I, ..., Angeletti D, Sarshad AA

Nucleic Acids Res. 53 (7) - [2025-04-10; online 2025-04-12]

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]

Dual GSK-3β/HDAC Inhibitors Enhance the Efficacy of Macrophages to Control Mycobacterium tuberculosis Infection.

Kalsum S, Xu R, Akber M, ..., Zhou Y, Brighenti S

Biomolecules 15 (4) 550 [2025-04-09; online 2025-04-09]

Chemical Biology Consortium Sweden (CBCS) [Service]

Design, Synthesis, and Biophysical Characterization of Pyridine Bis‐Quinazoline Derivatives as Selective G‐Quadruplex DNA Stabilizers

Nath Das R, Chorell E

Chem. Eur. J. 31 (21) - [2025-04-09; online 2025-03-05]

Chemical Biology Consortium Sweden (CBCS) [Service]

Metabolic readouts of tumor instructed normal tissues (TINT) identify aggressive prostate cancer subgroups for tailored therapy.

Dudka I, Figueira J, Wikström P, Bergh A, Gröbner G

Front Mol Biosci 12 (-) 1426949 [2025-04-07; online 2025-04-07]

Ectoderm barcoding reveals neural and cochlear compartmentalization.

de Haan S, He J, Corbat AA, ..., Kelley MW, Andersson ER

Science 388 (6742) 60-68 [2025-04-04; online 2025-04-03]

Bioinformatics (NBIS) [Service] Bioinformatics Long-term Support WABI [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Short read NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

A Million Years of Mammoth Mitogenome Evolution.

Chacón-Duque JC, Thomas Thorpe JA, Li W, ..., Heintzman PD, Dalén L

Mol. Biol. Evol. 42 (4) - [2025-04-01; online 2025-04-09]

Bioinformatics (NBIS) [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

The Development of Selective Chemical Probes for Serine Arginine Protein Kinase 3

Hanke D, McCutcheon C, Page BDG

Chem Biol Drug Des 105 (4) - [2025-04-00; online 2025-04-03]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Non‐Native Earthworms Alter Carbon Sequestration in Arctic Tundra Ecosystems

Jonsson H, Blume‐Werry G, Wackett AA, ..., Sparrman T, Klaminder J

JGR Biogeosciences 130 (4) - [2025-04-00; online 2025-04-14]

Centennial-scale atmospheric CO2 rise increased photosynthetic efficiency in a tropical tree species.

Zwartsenberg SA, Sterck FJ, Haddad L, ..., Heinrich I, Zuidema PA

New Phytol. 246 (1) 131-143 [2025-04-00; online 2025-02-12]

A genome-wide association study of imaging-defined atherosclerosis.

Gummesson A, Lundmark P, Chen QS, ..., Fall T, Gigante B

Nat Commun 16 (1) 2266 [2025-03-31; online 2025-03-31]

NGI SNP genotyping [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

The DNA methylation landscape of primary triple-negative breast cancer.

Aine M, Nacer DF, Arbajian E, ..., Borg Å, Staaf J

Nat Commun 16 (1) 3041 [2025-03-28; online 2025-03-28]

Clinical Genomics Lund [Service]

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]

Cell membranes sustain phospholipid imbalance via cholesterol asymmetry.

Doktorova M, Symons JL, Zhang X, ..., Levental KR, Levental I

Cell - (-) - [2025-03-26; online 2025-03-26]

Integrated Microscopy Technologies Stockholm [Service]

Blood-based biomarkers of Alzheimer's disease and incident dementia in the community.

Grande G, Valletta M, Rizzuto D, ..., Fratiglioni L, Vetrano DL

Nat. Med. - (-) - [2025-03-26; online 2025-03-26]

Affinity Proteomics Stockholm [Collaborative]

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] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

A large-scale sORF screen identifies putative microproteins involved in cancer cell fitness.

Schlesinger D, Dirks C, Navarro C, ..., Martinez TF, Elsässer SJ

iScience 28 (3) 111884 [2025-03-21; online 2025-01-23]

CRISPR Functional Genomics [Service]

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]

Computational drug repurposing: approaches, evaluation of in silico resources and case studies.

Tanoli Z, Fernández-Torras A, Özcan UO, ..., Carreras-Puigvert J, Aittokallio T

Nat Rev Drug Discov - (-) - [2025-03-18; online 2025-03-18]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Targeting TUBG1 in RB1‐negative tumors

Lindström L, Zhou J, Villoutreix BO, ..., Olsson R, Alvarado‐Kristensson M

The FASEB Journal 39 (5) - [2025-03-15; online 2025-02-28]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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]

Dietary patterns and blood-based biomarkers of Alzheimer's disease in cognitively intact older adults: Findings from a population-based study.

Mrhar A, Carballo-Casla A, Grande G, ..., Calderón-Larrañaga A, Vetrano DL

J Prev Alzheimers Dis - (-) 100124 [2025-03-14; online 2025-03-14]

Affinity Proteomics Stockholm [Collaborative]

Genetic liability for anxiety and treatment response to the monoamine stabilizer OSU6162 in alcohol dependence: a retrospective secondary analysis.

Hong MG, Khemiri L, Guterstam J, ..., Jayaram-Lindström N, Melas PA

Pharmacol Rep - (-) - [2025-03-12; online 2025-03-12]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

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]

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]

Antisense-mediated regulation of exon usage in the elastic spring region of Titin modulates sarcomere function.

Celik S, Hyrefelt L, Czuba T, ..., Smith JG, Gidlöf O

Cardiovasc. Res. - (-) - [2025-03-05; online 2025-03-05]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Decreased levels and function of dendritic cells in blood and airways predict COVID-19 severity.

Österberg B, Falck-Jones S, Vangeti S, ..., Färnert A, Smed-Sörensen A

Clin Transl Immunology 14 (3) e70026 [2025-03-03; online 2025-03-03]

Bioinformatics (NBIS) [Collaborative] Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Time-Resolved Hierarchical Modeling Highlights Metabolites Influencing Productivity and Cell Death in Chinese Hamster Ovary Cells.

Eriksson A, Richelle A, Trygg J, ..., Surowiec I, Jonsson P

Biotechnol J 20 (3) e202400624 [2025-03-00; online 2025-03-11]

Swedish NMR Centre (SNC) [Service]

Ultra-Sensitive Detection of Bacterial Spores via SERS.

Segervald J, Malyshev D, Öberg R, ..., Wågberg T, Andersson M

ACS Sens. 10 (2) 1237-1248 [2025-02-28; online 2025-01-23]

Integrated Microscopy Technologies Umeå [Service]

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]

Lithography-Free Water Stable Conductive Polymer Nanowires

Hughes D, Mousa AH, Musumeci C, ..., Olsson R, Hjort M

Nano Lett. 25 (8) 3059-3065 [2025-02-26; online 2025-02-13]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

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]

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]

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 [Collaborative]

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]

Toward target 2035: EUbOPEN - a public-private partnership to enable & unlock biology in the open.

Tredup C, Ackloo S, Beck H, ..., Arrowsmith CH, Knapp S

RSC Med Chem 16 (2) 457-464 [2025-02-19; online 2024-11-29]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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]

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]

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]

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]

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] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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]

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]

High-content morphological profiling by Cell Painting in 3D spheroids

Ringers C, Holmberg D, Flobak Å, ..., Carreras Puigvert J, Spjuth O

- - (-) - [2025-02-08; online 2025-02-08]

Chemical Biology Consortium Sweden (CBCS) [Technology development]

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]

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]

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]

Robust approach for production of the human oncology target Aurora kinase B in complex with its binding partner INCENP.

Mattsson J, Rogne P, Landström M, Wolf-Watz M

Biochimie 229 (-) 129-140 [2025-02-00; online 2024-10-18]

Swedish NMR Centre (SNC) [Service]

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] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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]

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]

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] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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]

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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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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]

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Nucleobase catalysts for the enzymatic activation of 8-oxoguanine DNA glycosylase 1

Hank EC, D'Arcy-Evans N, Scaletti ER, ..., Helleday T, Michel M

- - (-) - [2025-01-02; online 2025-01-02]

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A Rationally Designed Azobenzene Photoswitch for DNA G-Quadruplex Regulation in Live Cells.

Dudek M, López-Pacios L, Sabouri N, ..., Martinez-Fernandez L, Deiana M

Angew. Chem. Int. Ed. Engl. 64 (1) e202413000 [2025-01-02; online 2024-11-06]

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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]

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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]

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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]

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Influence of gas composition on carbonation of quicklime granules derived from different limestone types

Olovsson K, Ma C, Niinipuu M, Eriksson M, Broström M

Chemical Engineering Journal 506 (-) 159543 [2025-01-00; online 2025-01-00]

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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]

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Chemogenomic Screening in a Patient‐Derived 3D Fatty Liver Disease Model Reveals the CHRM1‐TRPM8 Axis as a Novel Module for Targeted Intervention

Youhanna S, Kemas AM, Wright SC, ..., Sundström M, Lauschke VM

Adv Sci (Weinh) 12 (3) - [2025-01-00; online 2024-11-28]

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