Publications 2024

Occurrence of cancer in Marfan syndrome: Report of two patients with neuroblastoma and review of the literature

Maya‐González C, Delgado‐Vega AM, Taylan F, ..., Martinsson T, Nordgren A

Am J Med Genet 194 (12) - [2024-12-00; online 2024-07-11]

Lifestyle, biological, and genetic factors related to brain iron accumulation across adulthood.

Gustavsson J, Ištvánfyová Z, Papenberg G, ..., Mangialasche F, Kalpouzos G

Neurobiol. Aging 144 (-) 56-67 [2024-12-00; online 2024-09-10]

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

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]

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]

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]

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

Achieving optically selective coatings of silica fixated carbon nanotubes for solar energy applications

Zäll E, Segervald J, Mahmoodi H, ..., Edman L, Wågberg T

Solar Energy Materials and Solar Cells 278 (-) 113202 [2024-12-00; online 2024-12-00]

Unraveling the dynamics of lignin chemistry on decomposition to understand its contribution to soil organic matter accumulation

Thirunavukkarasu A, Hedenström M, Sparrman T, ..., Schleucher J, Öquist M

Plant Soil - (-) - [2024-11-19; online 2024-11-19]

Inhibition mechanism of potential antituberculosis compound lansoprazole sulfide.

Kovalova T, Król S, Gamiz-Hernandez AP, ..., Brzezinski P, Högbom M

Proc. Natl. Acad. Sci. U.S.A. 121 (47) e2412780121 [2024-11-19; online 2024-11-12]

Järn och gravar i Våmb

Gustafsson J, Nordman A, Hjärthner-Holdar E, Stilborg O

Jönköping läns museum arkeologisk rapport 2024:07 - (-) - [2024-11-15]

Design, synthesis, and in vitro biological evaluation of meta-sulfonamidobenzamide-based antibacterial LpxH inhibitors.

Benediktsdottir A, Sooriyaarachchi S, Cao S, ..., Sandström A, Karlén A

Eur J Med Chem 278 (-) 116790 [2024-11-15; online 2024-08-22]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

A genome-wide association study in Swedish colorectal cancer patients with gastric- and prostate cancer in relatives.

Samola Winnberg J, Vermani L, Liu W, ..., Lindblad M, Lindblom A

Hered Cancer Clin Pract 22 (1) 25 [2024-11-14; online 2024-11-14]

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

A comprehensive human embryo reference tool using single-cell RNA-sequencing data

Zhao C, Plaza Reyes A, Schell JP, ..., Petropoulos S, Lanner F

Nat Methods - (-) - [2024-11-14; online 2024-11-14]

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

Prospective Screening of Cancer Syndromes in Patients with Mesenchymal Tumors

Öfverholm I, Lin Y, Mondini J, ..., Haglund de Flon F, Wallander K

Cancers (Basel) 16 (22) 3816 [2024-11-13; online 2024-11-13]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

ATP1A3 dysfunction causes motor hyperexcitability and afterhyperpolarization loss in a dystonia model.

Akkuratov EE, Sorrell F, Picton L, ..., Miles GB, Aperia A

Brain - (-) - [2024-11-13; online 2024-11-13]

Integrated Microscopy Technologies Stockholm [Service]

Simultaneous detection of membrane contact dynamics and associated Ca2+ signals by reversible chemogenetic reporters.

García Casas P, Rossini M, Påvénius L, ..., Pizzo P, Filadi R

Nat Commun 15 (1) 9775 [2024-11-12; online 2024-11-12]

Integrated Microscopy Technologies Stockholm [Collaborative]

MassiveFold: unveiling AlphaFold's hidden potential with optimized and parallelized massive sampling.

Raouraoua N, Mirabello C, Véry T, ..., Lensink MF, Brysbaert G

Nat Comput Sci - (-) - [2024-11-11; online 2024-11-11]

Bioinformatics Support, Infrastructure and Training [Technology development]

Equid-human interactions in Medieval Rome: exploring the role and management of equids through an interdisciplinary approach

Claudia Minniti CCAMaDC

30th conference of the European Association of Archaeologists, session 3893 - (-) - [2024-11-11; online 2024-08-27]

A unique symbiosome in an anaerobic single-celled eukaryote.

Jerlström-Hultqvist J, Gallot-Lavallée L, Salas-Leiva DE, ..., Archibald JM, Roger AJ

Nat Commun 15 (1) 9726 [2024-11-09; online 2024-11-09]

SARS-CoV-2 and HSV-1 Induce Amyloid Aggregation in Human CSF Resulting in Drastic Soluble Protein Depletion.

Christ W, Kapell S, Sobkowiak MJ, ..., El Andaloussi S, Ezzat K

ACS Chem Neurosci - (-) - [2024-11-07; online 2024-11-07]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Cryo-EM structures of a bathy phytochrome histidine kinase reveal a unique light-dependent activation mechanism.

Bódizs S, Mészáros P, Grunewald L, Takala H, Westenhoff S

Structure 32 (11) 1952-1962.e3 [2024-11-07; online 2024-08-30]

Transmembrane peptide-loaded ionic liquid nanocarriers for targeting ErbB2-positive cancer

Abujubara H, Bharmoria P, Alvarez S, ..., Sayin V, Tietze A

- - (-) - [2024-11-06; online 2024-11-06]

Integrated Microscopy Technologies Gothenburg [Service]

The structure and function of P5A-ATPases.

Li P, Bågenholm V, Hägglund P, ..., Wang K, Gourdon P

Nat Commun 15 (1) 9605 [2024-11-06; online 2024-11-06]

DMI fungicide resistance in Zymoseptoria tritici is unlinked to geographical origin and genetic background: a case study in Europe.

Oreiro EG, Samils B, Kildea S, ..., Zhan J, Andersson B

Pest Manag Sci - (-) - [2024-11-06; online 2024-11-06]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Pasteurella multocida from deep nasal swabs and tracheobronchial lavage in bovine calves from Sweden.

Myrenås M, Pringle M, Harbom B, Bengtsson B

Acta Vet. Scand. 66 (1) 58 [2024-11-05; online 2024-11-05]

Urban Pigeons as Reservoirs of Critical Pathogens: Improved protocol for sequencing pigeon faeces in disease monitoring

Hermann E, Van Damme R, Bongcam-Rudloff E, Nasirzadeh L

EMBnet j. 30 (-) e1059 [2024-11-04; online 2024-11-04]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Population pharmacokinetic modelling of cetirizine concentrations in human breast milk-A contribution from the ConcePTION project.

Melander E, Nielsen EI, Lindqvist A, ..., Spigset O, Nordeng H

Basic Clin Pharmacol Toxicol - (-) - [2024-11-04; online 2024-11-04]

Drug Discovery and Development (DDD) [Collaborative]

Incontinentia pigmenti underlies thymic dysplasia, autoantibodies to type I IFNs, and viral diseases.

Rosain J, Le Voyer T, Liu X, ..., Anderson MS, Casanova JL

J. Exp. Med. 221 (11) - [2024-11-04; online 2024-10-01]

Spatial Multiomics Reveals Intratumoral Immune Heterogeneity with Distinct Cytokine Networks in Lung Cancer Brain Metastases.

Christensson G, Bocci M, Kazi JU, ..., Gonzalez Velozo H, Hagerling C

Cancer Res Commun 4 (11) 2888-2902 [2024-11-01; online 2024-10-14]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] Clinical Genomics Lund [Service]

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]

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

Leveraging the T2T assembly to resolve rare and pathogenic inversions in reference genome gaps.

Bilgrav Saether K, Eisfeldt J, Bengtsson JD, ..., Carvalho CMB, Lindstrand A

Genome Res. - (-) - [2024-11-01; online 2024-11-01]

NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Transcriptomic profiles of myxofibrosarcoma and undifferentiated pleomorphic sarcoma correlate with clinical and genomic features.

Mitra S, Farswan A, Piccinelli P, ..., Pillay N, Mertens F

J. Pathol. 264 (3) 293-304 [2024-11-00; online 2024-09-11]

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]

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

The TβRI promotes migration and metastasis through thrombospondin 1 and ITGAV in prostate cancer cells.

Mu Y, Wallenius A, Zang G, ..., Mateus A, Landström M

Oncogene 43 (45) 3321-3334 [2024-11-00; online 2024-09-20]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Sensitive and Specific Droplet Digital PCR Assays for Circulating Tumor HPV DNA: Development, Validation, and Clinical Application in HPV-Associated Cancers.

Qvick A, Andersson E, Oldaeus Almerén A, ..., Karlsson MG, Helenius G

Mol Diagn Ther 28 (6) 835-845 [2024-11-00; online 2024-09-26]

Clinical Genomics Örebro [Technology development]

Pushing the boundaries of rare disease diagnostics with the help of the first Undiagnosed Hackathon.

Delgado-Vega AM, Cederroth H, Taylan F, ..., Cederroth M, Nordgren A

Nat. Genet. 56 (11) 2287-2294 [2024-11-00; online 2024-10-22]

Clinical Genomics Gothenburg [Service] Clinical Genomics Stockholm [Collaborative] NGI Long read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Collaborative] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Local climate, air quality and leaf litter cover shape foliar fungal communities on an urban tree.

Faticov M, Amorim JH, Abdelfattah A, ..., Laforest-Lapointe I, Tack AJM

Ambio 53 (11) 1673-1685 [2024-11-00; online 2024-06-13]

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

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]

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

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]

Androgen receptor pathway inhibitors and taxanes in metastatic prostate cancer: an outcome-adaptive randomized platform trial.

De Laere B, Crippa A, Discacciati A, ..., Grönberg H, Lindberg J

Nat. Med. 30 (11) 3291-3302 [2024-11-00; online 2024-08-20]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Clinical Genomics Stockholm [Service]

A new species of Erinaceusyllis (Annelida: Syllidae) discovered at a wood-fall in the eastern Clarion-Clipperton Zone, central Pacific Ocean.

Nilsson CL, Wiklund H, Glover AG, Bribiesca-Contreras G, Dahlgren TG

Deep Sea Research Part I: Oceanographic Research Papers - (-) 104415 [2024-11-00; online 2024-11-00]

Integrated Microscopy Technologies Gothenburg [Service]

Orthopteran Neo-Sex Chromosomes Reveal Dynamics of Recombination Suppression and Evolution of Supergenes.

Jayaprasad S, Peona V, Ellerstrand SJ, ..., Schielzeth H, Palacios-Gimenez OM

Mol. Ecol. - (-) e17567 [2024-10-30; online 2024-10-30]

NGI Long read [Collaborative] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

High-parametric protein maps reveal the spatial organization in early-developing human lung.

Sariyar S, Sountoulidis A, Hansen JN, ..., Lundberg E, Ayoglu B

Nat Commun 15 (1) 9381 [2024-10-30; online 2024-10-30]

Resolving complex duplication variants in autism spectrum disorder using long-read genome sequencing.

Eisfeldt J, Higginbotham EJ, Lenner F, ..., Scherer SW, Feuk L

Genome Res. - (-) - [2024-10-29; online 2024-10-29]

NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Integrative spatial and genomic analysis of tumor heterogeneity with Tumoroscope.

Shafighi S, Geras A, Jurzysta B, ..., Lagergren J, Szczurek E

Nat Commun 15 (1) 9343 [2024-10-29; online 2024-10-29]

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

A national long-read sequencing study on chromosomal rearrangements uncovers hidden complexities.

Eisfeldt J, Ameur A, Lenner F, ..., Feuk L, Lindstrand A

Genome Res. - (-) - [2024-10-29; online 2024-10-29]

NGI Long read [Technology development] NGI Uppsala (Uppsala Genome Center) [Technology development] National Genomics Infrastructure [Technology development]

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]

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

Highly Active and Durable Nanostructured Nickel-Molybdenum Coatings as Hydrogen Electrocatalysts via Solution Precursor Plasma Spraying.

Wu X, Piñeiro-García A, Rafei M, ..., Canto-Aguilar EJ, Gracia-Espino E

ChemistryOpen - (-) e202400069 [2024-10-25; online 2024-10-25]

A Phylogenomic Backbone for Acoelomorpha Inferred from Transcriptomic Data.

Abalde S, Jondelius U

Syst. Biol. - (-) - [2024-10-25; online 2024-10-25]

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

Comparative Analysis of Plasma Protein Dynamics in Women with ST-Elevation Myocardial Infarction and Takotsubo Syndrome

Hussain S, Jha S, Berger E, ..., Omerovic E, Redfors B

Cells 13 (21) 1764 [2024-10-24; online 2024-10-24]

Epigenome-wide analysis across the development span of pediatric acute lymphoblastic leukemia: backtracking to birth.

Ghantous A, Nusslé SG, Nassar FJ, ..., Munthe-Kaas MC, Herceg Z

Mol. Cancer 23 (1) 238 [2024-10-23; online 2024-10-23]

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

Three Novel Spider Genomes Unveil Spidroin Diversification and Hox Cluster Architecture: Ryuthela nishihirai (Liphistiidae), Uloborus plumipes (Uloboridae) and Cheiracanthium punctorium (Cheiracanthiidae).

Schöneberg Y, Audisio TL, Ben Hamadou A, ..., Prost S, Kennedy S

Mol Ecol Resour - (-) e14038 [2024-10-22; online 2024-10-22]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Quantitative proteomics of patient fibroblasts reveal biomarkers and diagnostic signatures of mitochondrial disease.

Correia SP, Moedas MF, Taylor LS, ..., Wedell A, Wredenberg A

JCI Insight 9 (20) - [2024-10-22; online 2024-10-22]

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]

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

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]

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

Building pangenome graphs.

Garrison E, Guarracino A, Heumos S, ..., Williams RW, Prins P

Nat. Methods - (-) - [2024-10-21; online 2024-10-21]

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 - (-) - [2024-10-18; online 2024-10-18]

Phase-separated polymer blends for controlled drug delivery by tuning morphology

Olsson M, Storm R, Björn L, ..., Liebi M, Matic A

Commun Mater 5 (1) - [2024-10-18; online 2024-10-18]

In vivo dendritic cell reprogramming for cancer immunotherapy

Ascic E, Åkerström F, Sreekumar Nair M, ..., Rosa FF, Pereira CF

Science 386 (6719) - [2024-10-18; online 2024-10-18]

Early evolutionary branching across spatial domains predisposes to clonal replacement under chemotherapy in neuroblastoma.

Karlsson J, Yasui H, Mañas A, ..., Bexell D, Gisselsson D

Nat Commun 15 (1) 8992 [2024-10-18; online 2024-10-18]

Changes in circulating extracellular vesicle cargo are associated with cognitive decline after major surgery: an observational case-control study.

Mkrtchian S, Eldh M, Ebberyd A, ..., Eriksson LI, Gómez-Galán M

Br J Anaesth - (-) - [2024-10-18; online 2024-10-18]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Autoantibodies to protein S may explain rare cases of coagulopathy following COVID-19 vaccination.

Yalcinkaya A, Cavalli M, Aranda-Guillén M, ..., Hallberg P, Landegren N

Sci Rep 14 (1) 24512 [2024-10-18; online 2024-10-18]

Prevalent and persistent new-onset autoantibodies in mild to severe COVID-19.

Jernbom AF, Skoglund L, Pin E, ..., Månberg A, Nilsson P

Nat Commun 15 (1) 8941 [2024-10-17; online 2024-10-17]

Autoimmunity and Serology Profiling [Collaborative]

An ancient ecospecies of Helicobacter pylori.

Tourrette E, Torres RC, Svensson SL, ..., Thorell K, Falush D

Nature - (-) - [2024-10-16; online 2024-10-16]

The crucial role of bioimage analysts in scientific research and publication.

Cimini BA, Bankhead P, D'Antuono R, ..., Wiggins L, Eliceiri KW

J. Cell. Sci. 137 (20) - [2024-10-15; online 2024-10-30]

BioImage Informatics [Collaborative] Integrated Microscopy Technologies Gothenburg [Service]

Defective ribosome assembly impairs leukemia progression in a murine model of acute myeloid leukemia.

Sjövall D, Ghosh S, Fernandez-Fuentes N, ..., Guibentif C, Jaako P

Cell Rep 43 (11) 114864 [2024-10-15; online 2024-10-15]

Author Correction: 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) 31 [2024-10-15; online 2024-10-15]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

LRPPRC and SLIRP synergize to maintain sufficient and orderly mammalian mitochondrial translation.

Rubalcava-Gracia D, Bubb K, Levander F, ..., Koolmeister C, Larsson NG

Nucleic Acids Res. 52 (18) 11266-11282 [2024-10-14; online 2024-08-01]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] CRISPR Functional Genomics [Service]

Quaternary Mixed Oxides of Non-Noble Metals with Enhanced Stability during the Oxygen Evolution Reaction.

Piñeiro-García A, Wu X, Canto-Aguilar EJ, ..., Rafei M, Gracia-Espino E

ACS Appl Mater Interfaces - (-) - [2024-10-13; online 2024-10-13]

Smart variant filtering - A blueprint solution for massively parallel sequencing-based variant analysis.

Brahimllari O, Eloranta S, Georgii-Hemming P, ..., Wästerlid T, Boman M

Health Informatics J 30 (4) 14604582241290725 [2024-10-12; online 2024-10-12]

Clinical Genomics Stockholm [Collaborative]

Genomic Analyses of Methicillin-Resistant Staphylococcus pseudintermedius from Companion Animals Reveal Changing Clonal Populations, Multidrug Resistance, and Virulence

Myrenås M, Pedersen K, Windahl U

Antibiotics (Basel) 13 (10) 962 [2024-10-12; online 2024-10-12]

The power of hybridization capture - Illustrated using an expanded gene panel on 100 post mortem samples, focusing on sudden unexplained death.

Kling D, Adolfsson E, Gréen H, Gréen A

Forensic Sci Int Genet 74 (-) 103160 [2024-10-11; online 2024-10-11]

GCKIII Kinases Control Hepatocellular Lipid Homeostasis via Shared Mode of Action.

Cansby E, Caputo M, Andersson E, ..., Hoy AJ, Mahlapuu M

J. Lipid Res. - (-) 100669 [2024-10-10; online 2024-10-10]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] Systems Biology [Collaborative]

Unmasking AlphaFold to integrate experiments and predictions in multimeric complexes.

Mirabello C, Wallner B, Nystedt B, Azinas S, Carroni M

Nat Commun 15 (1) 8724 [2024-10-09; online 2024-10-09]

Bioinformatics Support, Infrastructure and Training [Technology development] Cryo-EM [Service]

The genome sequence of the white-tailed eagle, Haliaeetus albicilla (Linnaeus, 1758)

Pálsson S, Skarphéðinsson KH, Heintz J, ..., Bunikis I, Pettersson OV

Wellcome Open Res 9 (-) 575 [2024-10-09; online 2024-10-09]

NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

De novo production of protoberberine and benzophenanthridine alkaloids through metabolic engineering of yeast.

Jiao X, Fu X, Li Q, ..., Nielsen J, Chen Y

Nat Commun 15 (1) 8759 [2024-10-09; online 2024-10-09]

Integrated Microscopy Technologies Gothenburg [Service]

Estradiol-mediated enhancement of the human ectocervical epithelial barrier correlates with desmoglein-1 expression in the follicular menstrual phase.

Bradley F, Stern A, Franzén Boger M, ..., Fowke KR, Broliden K

Front Endocrinol (Lausanne) 15 (-) 1454006 [2024-10-08; online 2024-10-08]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

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]

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

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]

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]

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]

The single-cell transcriptomic atlas iPain identifies senescence of nociceptors as a therapeutical target for chronic pain treatment.

Techameena P, Feng X, Zhang K, Hadjab S

Nat Commun 15 (1) 8585 [2024-10-04; online 2024-10-04]

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

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]

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. - (-) - [2024-10-03; online 2024-10-03]

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

Early-Life Hygiene-Related Factors and Risk of Inflammatory Bowel Disease: A Scandinavian Birth Cohort Study.

Guo A, Östensson M, Størdal K, Ludvigsson J, Mårild K

Inflamm Bowel Dis 30 (10) 1820-1830 [2024-10-03; online 2023-11-03]

Childhood Socioeconomic Characteristics and Risk of Inflammatory Bowel Disease: A Scandinavian Birth Cohort Study.

Sigvardsson I, Størdal K, Östensson M, ..., Ludvigsson J, Mårild K

Inflamm Bowel Dis 30 (10) 1801-1811 [2024-10-03; online 2023-09-23]

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]

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

Spatial multiomic insights into acute cocaine exposure

Nezhyva M, Shahen-Zoabi S, Kabirova M, ..., Margulis K, Jansson ET

- 3 (10) - [2024-10-01; online 2024-10-10]

Spatial Transcriptome Mapping of the Desmoplastic Growth Pattern of Colorectal Liver Metastases by In Situ Sequencing Reveals a Biologically Relevant Zonation of the Desmoplastic Rim.

Andersson A, Escriva Conde M, Surova O, ..., Nilsson M, Nyström H

Clin. Cancer Res. 30 (19) 4517-4529 [2024-10-01; online 2024-07-26]

IL-7-dependent and -independent lineages of IL-7R-dependent human T cells.

Arango-Franco CA, Ogishi M, Unger S, ..., Casanova JL, Puel A

J. Clin. Invest. 134 (19) - [2024-10-01; online 2024-10-01]

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]

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

DockQ v2: improved automatic quality measure for protein multimers, nucleic acids, and small molecules.

Mirabello C, Wallner B

Bioinformatics 40 (10) - [2024-10-01; online 2024-09-30]

Bioinformatics Support, Infrastructure and Training [Technology development]

Sex estimation using long bones in the largest burial site of the Copper Age: Linear discriminant analysis and random forest

Díaz-Navarro S, Díez-Hermano S, Rojo-Guerra MA, ..., Gunther T, Uriarte MH

Journal of Archaeological Science: Reports 58 (-) 104730 [2024-10-00; online 2024-10-00]

Personalized mixture toxicity testing: A proof-of-principle in vitro study evaluating the steroidogenic effects of reconstructed contaminant mixtures measured in blood of individual adults.

Strand D, Lundgren B, Bergdahl IA, Martin JW, Karlsson O

Environ Int 192 (-) 108991 [2024-10-00; online 2024-08-30]

Drug Discovery and Development (DDD) [Collaborative]

Molecular Subtypes Are Associated With Clinical Benefit in Cisplatin-Treated Metastatic Urothelial Cancer Patients.

Holmsten K, Sjödahl G, Abrahamsson J, ..., Liedberg F, Ullén A

JCO Precision Oncology 8 (-) e2400209 [2024-10-00; online 2024-10-02]

Mini-heterochromatin domains constrain the cis-regulatory impact of SVA transposons in human brain development and disease.

Horváth V, Garza R, Jönsson ME, ..., Douse CH, Jakobsson J

Nat. Struct. Mol. Biol. 31 (10) 1543-1556 [2024-10-00; online 2024-06-04]

Clinical Genomics Lund [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Liquefaction of lignocellulosic biomass into phenolic monomers and dimers over multifunctional Pd/NbOPO4 catalyst

Jogi R, Samikannu A, Mäki-Arvela P, ..., Xu C, Mikkola JP

Renewable Energy 233 (-) 121148 [2024-10-00; online 2024-10-00]

Increased CSF DOPA Decarboxylase Correlates with Lower DaT-SPECT Binding: Analyses in Biopark and PPMI Cohorts.

Khosousi S, Sturchio A, Appleton E, ..., Iwaki H, Svenningsson P

Mov Disord 39 (10) 1881-1885 [2024-10-00; online 2024-05-26]

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]

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

Elucidation of cellulose phosphorylation with phytic acid

Orzan E, Barrio A, Spirk S, Nypelö T

Industrial Crops and Products 218 (-) 118858 [2024-10-00; online 2024-10-00]

Early unrecognised SARS-CoV-2 introductions shaped the first pandemic wave, Sweden, 2020.

Dyrdak R, Hodcroft EB, Broddesson S, ..., Neher RA, Albert J

Euro Surveill. 29 (41) - [2024-10-00; online 2024-10-11]

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]

Benchmarking long-read sequencing strategies for obtaining ASV-resolved rRNA operons from environmental microeukaryotes.

Overgaard CK, Jamy M, Radutoiu S, Burki F, Dueholm MKD

Mol Ecol Resour 24 (7) e13991 [2024-10-00; online 2024-07-09]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Associations between epigenetic aging and diabetes mellitus in a Swedish longitudinal study.

Wikström Shemer D, Mostafaei S, Tang B, ..., Fall T, Hägg S

Geroscience 46 (5) 5003-5014 [2024-10-00; online 2024-06-27]

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

"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]

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

A research data management (RDM) community for ELIXIR.

D'Anna F, Jareborg N, Jetten M, ..., Vondrasek J, Andrabi M

F1000Res 13 (-) - [2024-09-30; online 2024-09-30]

Bioinformatics Support, Infrastructure and Training [Collaborative]

NiO thin films fabricated using spray-pyrolysis technique: structural and optical characterization and ultrafast charge dynamics studies

Das L, Canto-Aguilar EJ, Tapani T, ..., Gracia-Espino E, Maccaferri N

J. Phys. D: Appl. Phys. 57 (38) 385303 [2024-09-27; online 2024-07-02]

Multiomic biomarkers after cardiac arrest.

Stopa V, Lileikyte G, Bakochi A, ..., Nielsen N, Devaux Y

Intensive Care Med Exp 12 (1) 83 [2024-09-27; online 2024-09-27]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Merging multi-omics with proteome integral solubility alteration unveils antibiotic mode of action.

Maity R, Zhang X, Liberati FR, ..., Aínsa JA, Sancho J

Elife 13 (-) - [2024-09-27; online 2024-09-27]

Single-cell genomics details the maturation block in BCP-ALL and identifies therapeutic vulnerabilities in DUX4-r cases.

Thorsson H, Henningsson R, Puente-Moncada N, ..., Lilljebjörn H, Fioretos T

Blood 144 (13) 1399-1411 [2024-09-26; online 2024-07-05]

CDK4 is co-amplified with either TP53 promoter gene fusions or MDM2 through distinct mechanisms in osteosarcoma.

Saba KH, Difilippo V, Styring E, ..., Baumhoer D, Nord KH

npj Genom. Med. 9 (1) 42 [2024-09-25; online 2024-09-25]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Analyzing Fusion Pore Dynamics and Counting the Number of Acetylcholine Molecules Released by Exocytosis.

Wang Y, Pradhan A, Gupta P, ..., Zetterberg H, Cans AS

J. Am. Chem. Soc. 146 (38) 25902-25906 [2024-09-25; online 2024-09-11]

Integrated Microscopy Technologies Gothenburg [Service]

Hematopoietic cells emerging from hemogenic endothelium exhibit lineage-specific oxidative stress responses.

Biezeman H, Nubiè M, Oburoglu L

J. Biol. Chem. 300 (11) 107815 [2024-09-24; online 2024-09-24]

Chemical Exposomics in Human Plasma by Lipid Removal and Large-Volume Injection Gas Chromatography–High-Resolution Mass Spectrometry

Xie H, Sdougkou K, Bonnefille B, ..., Rantakokko P, Martin JW

Environ. Sci. Technol. - (-) - [2024-09-24; online 2024-09-24]

Exposomics [Technology development]

A Versatile and Upgraded Version of the LundTax Classification Algorithm Applied to Independent Cohorts.

Cotillas EA, Bernardo C, Veerla S, ..., Sjödahl G, Eriksson P

J Mol Diagn - (-) - [2024-09-24; online 2024-09-24]

Enrichment Reveals Extensive Integration of Hepatitis B Virus DNA in Hepatitis Delta Virus-Infected Patients.

Ringlander J, Strömberg LG, Stenbäck JB, ..., Rydell GE, Lindh M

J. Infect. Dis. 230 (3) e684-e693 [2024-09-23; online 2024-01-25]

PITAR, a DNA damage-inducible cancer/testis long noncoding RNA, inactivates p53 by binding and stabilizing TRIM28 mRNA.

Jana S, Mondal M, Mahale S, ..., Kanduri C, Somasundaram K

Elife 12 (-) - [2024-09-20; online 2024-09-20]

Integrated Microscopy Technologies Gothenburg [Service]

Multi-omics analysis of aggregative multicellularity.

Edelbroek B, Westholm JO, Bergquist J, Söderbom F

iScience 27 (9) 110659 [2024-09-20; online 2024-08-03]

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

Cooperative folding as a molecular switch in an evolved antibody binder.

Jönsson M, Mushtaq AU, Nagy TM, ..., Wolf-Watz M, Hober S

J. Biol. Chem. 300 (11) 107795 [2024-09-19; online 2024-09-19]

Determining Marine Biodegradation Kinetics of Chemicals Discharged from Offshore Oil Platforms─Whole Mixture Testing at High Dilutions Increases Environmental Relevance.

Møller MT, Birch H, Sjøholm KK, ..., Papazian S, Mayer P

Environ. Sci. Technol. - (-) - [2024-09-18; online 2024-09-18]

Exposomics [Collaborative]

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]

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]

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Longitudinal Exposomics in a Multiomic Wellness Cohort Reveals Distinctive and Dynamic Environmental Chemical Mixtures in Blood.

Sdougkou K, Papazian S, Bonnefille B, ..., Martin LJ, Martin JW

Environ. Sci. Technol. 58 (37) 16302-16315 [2024-09-17; online 2024-09-05]

Exposomics [Collaborative]

Genetic differentiation and diversity do not explain variation in heterosis or inbreeding depression: empirical evidence from a long-lived iteroparous plant

Söderquist L, Karrenberg S, Sletvold N

Conserv Genet - (-) - [2024-09-17; online 2024-09-17]

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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]

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

Mosaic loss of Y chromosome and the association to mortality in Danish men aged 56-100 years.

Hozakowska-Roszkowska DM, Mengel-From J, Hristozova TK, ..., Röttger R, Nygaard M

Mech Ageing Dev 222 (-) 111979 [2024-09-16; online 2024-09-16]

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

An Improved Chromosome-scale Genome Assembly and Population Genetics resource for Populus tremula.

Robinson KM, Schiffthaler B, Liu H, ..., Ingvarsson PK, Street NR

Physiol Plantarum 176 (5) e14511 [2024-09-16; online 2024-09-16]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

The CHCHD2-CHCHD10 protein complex is modulated by mitochondrial dysfunction and alters lipid homeostasis in the mouse brain

Gerlach J, Pireddu P, Zhang X, ..., Svenningsson P, Filograna R

- - (-) - [2024-09-14; online 2024-09-14]

Solution-Processable Bismuthene Nanosheets for Ultrasensitive Sensing of Heavy Metal Ions via Anodic Stripping Voltammetry

Adeniyi KO, Manavalan G, Zainelabdin A, Mikkola JP, Tesfalidet S

ACS Appl. Nano Mater. 7 (17) 20217-20228 [2024-09-13; online 2024-08-30]

Exposure of Colon-Derived Epithelial Monolayers to Fecal Luminal Factors from Patients with Colon Cancer and Ulcerative Colitis Results in Distinct Gene Expression Patterns.

Magnusson MK, Bas Forsberg A, Verveda A, ..., Simrén M, Öhman L

Int J Mol Sci 25 (18) - [2024-09-13; online 2024-09-13]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Early-Life Diet Diversity and the Subsequent Risk of Inflammatory Bowel Disease: Findings From Two Scandinavian Birth Cohorts.

Guo A, Ludvigsson J, Hård Af Segerstad EM, ..., Størdal K, Mårild K

Inflamm Bowel Dis - (-) - [2024-09-13; online 2024-09-13]

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]

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]

Aberrant growth and expansion in Penium margaritaceum triggered by disruption of microtubules and the cell wall.

LoRicco JG, Malone S, Becker A, ..., Epstein R, Domozych DS

J. Exp. Bot. - (-) - [2024-09-12; online 2024-09-12]

Integrated Microscopy Technologies Gothenburg [Service]

Prokaryotic morphological features and maintenance activities governed by seasonal productivity conditions.

Verma A, Amnebrink D, Lee CC, ..., Pinhassi J, Wikner J

FEMS Microbiol. Ecol. - (-) - [2024-09-11; online 2024-09-11]

Integrated Microscopy Technologies Umeå [Collaborative]

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]

Inherited human RelB deficiency impairs innate and adaptive immunity to infection.

Le Voyer T, Maglorius Renkilaraj MRL, Moriya K, ..., Tangye SG, Puel A

Proc. Natl. Acad. Sci. U.S.A. 121 (37) e2321794121 [2024-09-10; online 2024-09-04]

Epigenetic regulation of cell state by H2AFY governs immunogenicity in high-risk neuroblastoma.

Nagarajan D, Parracho RT, Corujo D, ..., Buschbeck M, Mao Y

J. Clin. Invest. 134 (21) - [2024-09-10; online 2024-09-10]

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]

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MAIT cell heterogeneity across paired human tissues reveals specialization of distinct regulatory and enhanced effector profiles.

Kammann T, Cai C, Sekine T, ..., Buggert M, Sandberg JK

Sci Immunol 9 (99) eadn2362 [2024-09-06; online 2024-09-06]

Structure of the iminium reaction intermediate in an engineered aldolase explains the carboligation activity toward arylated ketones and aldehydes.

Hebert H, Sönmez E, Purhonen P, Widersten M

Structure 32 (9) 1322-1326.e4 [2024-09-05; online 2024-07-15]

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]

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

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]

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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]

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

In silico gepotidacin target mining among 33 213 global Neisseria gonorrhoeae genomes from 1928 to 2023 combined with gepotidacin MIC testing of 22 gonococcal isolates with different GyrA and ParC substitutions.

David A, Golparian D, Jacobsson S, ..., Davies C, Unemo M

J. Antimicrob. Chemother. 79 (9) 2221-2226 [2024-09-03; online 2024-07-15]

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]

Protective Non-neutralizing anti-N-terminal Domain mAb Maintains Fc-mediated Function against SARS-COV-2 Variants up to BA.2.86-JN.1 with Superfluous In Vivo Protection against JN.1 Due to Attenuated Virulence.

Izadi A, Godzwon M, Söderlund Strand A, ..., Ohlin M, Nordenfelt P

J. Immunol. 213 (5) 678-689 [2024-09-01; online 2024-07-17]

On the structure refinement of metal complexes against 3D electron diffraction data using multipolar scattering factors.

Pacoste L, Ignat'ev VM, Dominiak PM, Zou X

Int Union Crystallogr J IUCr J Int Union Cryst J IUCrJ 11 (Pt 5) 878-890 [2024-09-01; online 2024-09-01]

Microcrystal electron diffraction structure of Toll-like receptor 2 TIR-domain-nucleated MyD88 TIR-domain higher-order assembly.

Li Y, Pacoste LC, Gu W, ..., Xu H, Nanson JD

Acta Crystallogr D Struct Biol 80 (Pt 9) 699-712 [2024-09-01; online 2024-09-04]

ADAR3 modulates neuronal differentiation and regulates mRNA stability and translation.

Karlström V, Sagredo EA, Planells J, ..., Visa N, Öhman M

Nucleic Acids Res. - (-) - [2024-09-01; online 2024-09-01]

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

Transcriptomic and functional analyses on a Botrytis cinerea multidrug-resistant (MDR) strain provides new insights into the potential molecular mechanisms of MDR and fitness.

Sofianos G, Piombo E, Dubey M, ..., Karaoglanidis G, Tzelepis G

Mol. Plant Pathol. 25 (9) e70004 [2024-09-00; online 2024-09-08]

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

The CCTδ subunit of the molecular chaperone CCT is required for correct localisation of p150Glued to spindle poles during mitosis.

Córdoba-Beldad CM, Grantham J

Eur J Cell Biol 103 (3) 151430 [2024-09-00; online 2024-06-15]

Integrated Microscopy Technologies Gothenburg [Service]

Species-genetic diversity correlation in a metacommunity of urban pond invertebrates

Johansson F, Yildirim Y, Hyseni C, ..., Höglund J, Bini LM

Basic and Applied Ecology 79 (-) 114-122 [2024-09-00; online 2024-09-00]

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

Speciation in savanna birds in South America: The case of the Least Nighthawk Chordeiles pusillus (Aves: Caprimulgidae) in and out of the Amazon.

Fernandes AM, Cohn-Haft M, Fábio Silveira L, ..., Nascimento N, Olsson U

Mol. Phylogenet. Evol. 198 (-) 108117 [2024-09-00; online 2024-06-07]

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

Points2Regions: Fast, interactive clustering of imaging-based spatial transcriptomics data.

Andersson A, Behanova A, Avenel C, ..., Malmberg F, Wählby C

Cytometry A 105 (9) 677-687 [2024-09-00; online 2024-07-03]

BioImage Informatics [Collaborative]

New finds of European bison identified through the systematic DNA-based species identification of archaeological remains of large bovines from Scandinavia

Rosengren E, Rossi C, Heino MT, Sinding MHS

Journal of Archaeological Science: Reports 57 (-) 104668 [2024-09-00; online 2024-09-00]

Immune system adaptation during gender-affirming testosterone treatment.

Lakshmikanth T, Consiglio C, Sardh F, ..., Landegren N, Brodin P

Nature 633 (8028) 155-164 [2024-09-00; online 2024-09-04]

Affinity Proteomics Stockholm [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Dantrolene corrects cellular disease features of Darier disease and may be a novel treatment.

Hunt M, Wang N, Pupinyo N, ..., Bachar-Wikstrom E, Wikstrom JD

EMBO Mol Med 16 (9) 1986-2001 [2024-09-00; online 2024-07-26]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Contemporary intergeneric hybridization and backcrossing among birds-of-paradise.

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

Evolution Letters 8 (5) 680-694 [2024-09-00; online 2024-06-08]

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Activating mutations remodel the chromatin accessibility landscape to drive distinct regulatory networks in KMT2A-rearranged acute leukemia.

Zhang Q, Falqués-Costa T, Pilheden M, ..., Hyrenius-Wittsten A, Hagström-Andersson AK

Hemasphere 8 (9) e70006 [2024-09-00; online 2024-09-26]

Making Multiplexed Imaging Flexible: Combining Essential Markers With Established Antibody Panels.

Deen AJ, Thorsson J, O'Roberts EM, ..., Oses C, Stadler C

J. Histochem. Cytochem. 72 (8-9) 517-544 [2024-08-31; online 2024-08-31]

Joint single-cell genetic and transcriptomic analysis reveal pre-malignant SCP-like subclones in human neuroblastoma.

Olsen TK, Otte J, Mei S, ..., Kharchenko PV, Baryawno N

Mol. Cancer 23 (1) 180 [2024-08-31; online 2024-08-31]

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

Rapid and robust isolation of microglia and vascular cells from brain subregions for integrative single-cell analyses.

Preka E, Lastra Romero A, Sun Y, ..., Osman AM, Blomgren K

Heliyon 10 (16) e35838 [2024-08-30; online 2024-08-05]

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Posterior specification of multi-lineage axial assembloids from human pluripotent stem cells

Kee N, Leboeuf M, Gómez S, ..., Ericson J, Hedlund E

- - (-) - [2024-08-30; online 2024-08-30]

Integrated Microscopy Technologies Stockholm [Service]

Plastome evolution in Santalales involves relaxed selection prior to loss of ndh genes and major boundary shifts of the inverted repeat.

Edlund M, Anderson BM, Su H, ..., Nickrent DL, Petersen G

Ann. Bot. - (-) - [2024-08-30; online 2024-08-30]

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Five centuries of consanguinity, isolation, health, and conflict in Las Gobas: A Northern Medieval Iberian necropolis.

Rodríguez-Varela R, Yaka R, Pochon Z, ..., Azkarate A, Götherström A

Sci Adv 10 (35) eadp8625 [2024-08-30; online 2024-08-28]

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

DNA methylation governs the sensitivity of repeats to restriction by the HUSH-MORC2 corepressor.

Pandiloski N, Horváth V, Karlsson O, ..., Jakobsson J, Douse CH

Nat Commun 15 (1) 7534 [2024-08-30; online 2024-08-30]

Clinical Genomics Lund [Service] NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

Conference report: the first bacterial genome sequencing pan-European network conference.

Germuskova Z, Sosa E, Lagos AC, ..., Mölling P, Egli A

Microbes Infect - (-) 105410 [2024-08-30; online 2024-08-30]

Expression of inducible nitric oxide synthase, nitrotyrosine, eosinophilic peroxidase, eotaxin-3, and galectin-3 in patients with gastroesophageal reflux disease, eosinophilic esophagitis, and in healthy controls: a semiquantitative image analysis of 3,3'-diaminobenzidine-stained esophageal biopsies.

Plate J, Bove M, Larsson HM, ..., Johansson LE, Bergquist H

Dis Esophagus 37 (9) - [2024-08-29; online 2024-04-29]

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An intronic copy number variation in Syntaxin 17 determines speed of greying and melanoma incidence in Grey horses.

Rubin CJ, Hodge M, Naboulsi R, ..., Lindgren G, Andersson L

Nat Commun 15 (1) 7510 [2024-08-29; online 2024-08-29]

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Petersen I, Godec A, Ranjbarian F, ..., Mirabello C, Hultqvist G

PLoS ONE 19 (8) e0308521 [2024-08-29; online 2024-08-29]

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Bous J, Kinsolving J, Grätz L, ..., Adebali O, Schulte G

Nat Commun 15 (1) 7422 [2024-08-28; online 2024-08-28]

Polygenic Risk Scores and Twin Concordance for Schizophrenia and Bipolar Disorder.

Song J, Pasman JA, Johansson V, ..., Hultman CM, Sullivan PF

JAMA Psychiatry - (-) - [2024-08-28; online 2024-08-28]

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Akaberi D, Pourghasemi Lati M, Krambrich J, ..., Verho O, Lennerstrand J

Antimicrob Agents Chemother - (-) - [2024-08-28; online 2024-08-28]

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Sipes K, Buongiorno J, Steen AD, ..., Vishnivetskaya TA, Lloyd KG

Syst. Appl. Microbiol. 47 (6) 126544 [2024-08-28; online 2024-08-28]

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Intensified, Kilogram-Scaled, and Environment-Friendly: Chemoenzymatic Synthesis of Bio-Based Acylated Hydroxystyrenes.

Petermeier P, Domínguez de María P, Byström E, Kara S

ACS Sustainable Chem. Eng. 12 (34) 12869-12878 [2024-08-26; online 2024-08-15]

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Breton G, Barham L, Mudenda G, ..., Schlebusch CM, Jakobsson M

Nat Commun 15 (1) 7307 [2024-08-24; online 2024-08-24]

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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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Synthesis of Highly Porous Lignin-Sulfonate Sulfur-Doped Carbon for Efficient Adsorption of Sodium Diclofenac and Synthetic Effluents.

Dos Reis GS, Conrad S, Lima EC, ..., Dotto GL, Grimm A

Nanomaterials (Basel) 14 (16) - [2024-08-22; online 2024-08-22]

Hydrazide-based reactive matrices for the sensitive detection of aldehydes and ketones by MALDI mass spectrometry imaging.

Lodén H, Schembri LS, Nilsson A, ..., Odell LR, Andrén PE

Chem. Commun. (Camb.) 60 (69) 9238-9241 [2024-08-22; online 2024-08-22]

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Surface-Shaving of Staphylococcus aureus Strains and Quantitative Proteomic Analysis Reveal Differences in Protein Abundance of the Surfaceome.

Karlsson A, Alarcón LA, Piñeiro-Iglesias B, ..., Jin T, Karlsson R

Microorganisms 12 (8) - [2024-08-21; online 2024-08-21]

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FOXO-regulated OSER1 reduces oxidative stress and extends lifespan in multiple species.

Song J, Li Z, Zhou L, ..., Rasmussen LJ, Dai F

Nat Commun 15 (1) 7144 [2024-08-21; online 2024-08-21]

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The involvement of cyclotides in the heavy metal tolerance of Viola spp.

Sychta K, Słomka A, Shariatgorji R, ..., Göransson U, Slazak B

Sci Rep 14 (1) 19306 [2024-08-20; online 2024-08-20]

Gel-Assisted Proteome Position Integral Shift Assay Returns Molecular Weight to Shotgun Proteomics and Identifies Caspase 3 Substrates.

Meng Z, Saei AA, Gharibi H, ..., Gaetani M, Zubarev RA

Anal. Chem. 96 (33) 13533-13541 [2024-08-20; online 2024-08-07]

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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 Science Alliance 7 (11) e202402771 [2024-08-19]

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Type I Interferon Autoantibodies Correlate With Cellular Immune Alterations in Severe COVID-19.

Strunz B, Maucourant C, Mehta A, ..., Björkström NK, Karolinska KI/K COVID-19 Study Group

J. Infect. Dis. 230 (2) e318-e326 [2024-08-16; online 2024-02-29]

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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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Motor innervation directs the correct development of the mouse sympathetic nervous system.

Erickson AG, Motta A, Kastriti ME, ..., Bonanomi D, Adameyko I

Nat Commun 15 (1) 7065 [2024-08-16; online 2024-08-16]

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Genome Res. - (-) - [2024-08-15; online 2024-08-15]

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Escherichia coli in urban marine sediments: interpreting virulence, biofilm formation, halotolerance, and antibiotic resistance to infer contamination or naturalization.

Erb IK, Suarez C, Frank EM, ..., Lindberg E, Paul CJ

FEMS Microbes 5 (-) xtae024 [2024-08-14; online 2024-08-14]

Breaking barriers: pCF10 type 4 secretion system relies on a self-regulating muramidase to modulate the cell wall.

Sun W-S, Torrens G, Ter Beek J, Cava F, Berntsson RP-A

MBio 15 (8) e0048824 [2024-08-14; online 2024-06-28]

Screening persistent organic pollutants for effects on testosterone and estrogen synthesis at human-relevant concentrations using H295R cells in 96-well plates.

Strand D, Nylander E, Höglund A, ..., Martin JW, Karlsson O

Cell Biol. Toxicol. 40 (1) 69 [2024-08-13; online 2024-08-13]

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Fetsiukh A, Pall T, Timmusk S

Sci Rep 14 (1) 18806 [2024-08-13; online 2024-08-13]

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Martínez-Carranza M, Škerlová J, Lee PG, ..., Dong M, Stenmark P

Commun Chem 7 (1) 179 [2024-08-13; online 2024-08-13]

READv2: advanced and user-friendly detection of biological relatedness in archaeogenomics.

Alaçamlı E, Naidoo T, Güler MN, ..., Malmström H, Günther T

Genome Biol. 25 (1) 216 [2024-08-12; online 2024-08-12]

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Multifaceted Proteome Analysis at Solubility, Redox, and Expression Dimensions for Target Identification.

Saei AA, Lundin A, Lyu H, ..., Gygi SP, Zubarev RA

Adv Sci (Weinh) - (-) e2401502 [2024-08-09; online 2024-08-09]

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Nam K, Thodika ARA, Tischlik S, ..., Sauer-Eriksson AE, Wolf-Watz M

Sci Adv 10 (32) eado5504 [2024-08-09; online 2024-08-09]

AlphaFold accelerated discovery of psychotropic agonists targeting the trace amine-associated receptor 1.

Díaz-Holguín A, Saarinen M, Vo DD, ..., Carlsson J, Svenningsson P

Sci Adv 10 (32) eadn1524 [2024-08-09; online 2024-08-07]

Micro-costing of genetic diagnostics in acute leukemia in Sweden: from standard-of-care to whole-genome sequencing.

Thangavelu T, Wirta V, Orsmark-Pietras C, ..., Rosenquist R, Levin LÅ

J Med Econ 27 (1) 1053-1060 [2024-08-08; online 2024-08-08]

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JAK inhibition decreases the autoimmune burden in Down syndrome

Rachubinski AL, Wallace E, Gurnee E, ..., Norris DA, Espinosa JM

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Genetic diversity and signatures of selection in Icelandic horses and Exmoor ponies.

Sigurðardóttir H, Ablondi M, Kristjansson T, Lindgren G, Eriksson S

BMC Genomics 25 (1) 772 [2024-08-08; online 2024-08-08]

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The genetic architecture of dog ownership: large-scale genome-wide association study in 97,552 European-ancestry individuals.

Gong T, Karlsson R, Yao S, ..., Fall T, Almqvist C

G3 (Bethesda) 14 (8) - [2024-08-07; online 2024-05-31]

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Hypoxic-Ischemic Insult Alters Polyamine and Neurotransmitter Abundance in the Specific Neonatal Rat Brain Subregions.

Mácha H, Luptáková D, Juránek I, Andrén PE, Havlíček V

ACS Chem Neurosci 15 (15) 2811-2821 [2024-08-07; online 2024-07-26]

Applying Spatial Metabolomics To Investigate Age- and Drug-Induced Neurochemical Changes.

Vallianatou T, Angerer TB, Kaya I, ..., Svenningsson P, Andrén PE

ACS Chem Neurosci 15 (15) 2822-2829 [2024-08-07; online 2024-07-29]

Systematic review and feasibility study on pre-analytical factors and genomic analyses on archival formalin-fixed paraffin-embedded breast cancer tissue.

Salgkamis D, Sifakis EG, Agartz S, ..., Matikas A, Zerdes I

Sci Rep 14 (1) 18275 [2024-08-06; online 2024-08-06]

Hydrogen production by a fully de novo enzyme.

Berglund S, Bassy C, Kaya I, ..., Magnuson A, Glover SD

Dalton Trans 53 (31) 12905-12916 [2024-08-06; online 2024-08-06]

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Few chemoreceptor genes in the ambrosia beetle Trypodendron lineatum may reflect its specialized ecology.

Biswas T, Vogel H, Biedermann PHW, ..., Yuvaraj JK, Andersson MN

BMC Genomics 25 (1) 764 [2024-08-06; online 2024-08-06]

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AssemblyQC: a Nextflow pipeline for reproducible reporting of assembly quality.

Rashid U, Wu C, Shiller J, ..., Thomson S, Deng CH

Bioinformatics 40 (8) - [2024-08-02; online 2024-07-30]

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A genome-wide genetic screen identified targets for destabilizing the parasitophorous vacuole ofChlamydia trachomatis

Babu Sait MR, Jachmann LH, Milivojevic M, ..., Schmierer B, Sixt BS

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The novel 2024 WHO Neisseria gonorrhoeae reference strains for global quality assurance of laboratory investigations and superseded WHO N. gonorrhoeae reference strains-phenotypic, genetic and reference genome characterization.

Unemo M, Sánchez-Busó L, Golparian D, ..., Wi T, Lahra MM

J. Antimicrob. Chemother. 79 (8) 1885-1899 [2024-08-01; online 2024-06-18]

Exploring the interplay between antiretroviral therapy and the gut-oral microbiome axis in people living with HIV.

Narayanan A, Kieri O, Vesterbacka J, ..., Ray S, Nowak P

Sci Rep 14 (1) 17820 [2024-08-01; online 2024-08-01]

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Ecological genomics in the Northern krill uncovers loci for local adaptation across ocean basins.

Unneberg P, Larsson M, Olsson A, ..., Meyer B, Wallberg A

Nat Commun 15 (1) 6297 [2024-08-01; online 2024-08-01]

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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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Species-specific erosion of genetic diversity in grassland butterflies depends on landscape land cover

Nolen ZJ, Rundlöf M, Runemark A

Biological Conservation 296 (-) 110694 [2024-08-00; online 2024-08-00]

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Selection against domestication alleles in introduced rabbit populations.

Andrade P, Alves JM, Pereira P, ..., Andersson L, Carneiro M

Nat Ecol Evol 8 (8) 1543-1555 [2024-08-00; online 2024-06-21]

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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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One-year longitudinal changes of peripheral CD4+ T-lymphocyte counts, gut microbiome, and plaque vulnerability after an acute coronary syndrome.

I Fernández-Avila A, Gutiérrez-Ibanes E, Martín de Miguel I, ..., Correa R, Bermejo J

Int J Cardiol Heart Vasc 53 (-) 101438 [2024-08-00; online 2024-06-04]

Migratory CD103+CD11b+ cDC2s in Peyer's patches are critical for gut IgA responses following oral immunization.

Gribonika I, Strömberg A, Chandode RK, ..., Bemark M, Lycke N

Mucosal Immunol 17 (4) 509-523 [2024-08-00; online 2024-03-15]

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Fungal communities associated with Picea abiesPinus sylvestris and Larix sp. seeds of different geographic origin: Implications for disease management

Larsson R, Menkis A, Olson Å

For. Path. 54 (4) - [2024-08-00; online 2024-08-05]

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Sekar V, Mármol-Sánchez E, Kalogeropoulos P, ..., Biryukova I, Friedländer MR

Nat. Biotechnol. 42 (8) 1296-1302 [2024-08-00; online 2023-09-21]

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A multiomic characterization of the leukemia cell line REH using short- and long-read sequencing.

Lysenkova Wiklander M, Arvidsson G, Bunikis I, ..., Ameur A, Nordlund J

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Aging AdipoR2-deficient mice are hyperactive with enlarged brains excessively rich in saturated fatty acids.

Ruiz M, Devkota R, Bergh PO, ..., Borén J, Pilon M

FASEB J. 38 (14) e23815 [2024-07-31; online 2024-07-11]

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A pipeline for identification of causal mutations in barley identifies Xantha-j as the chlorophyll synthase gene.

Stuart D, Zakhrabekova S, Jørgensen ME, Dockter C, Hansson M

Plant Physiol. 195 (4) 2877-2890 [2024-07-31; online 2024-04-17]

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Front. Biomater. Sci. 3 (-) - [2024-07-30; online 2024-07-30]

A genetic-epigenetic interplay at 1q21.1 locus underlies CHD1L-mediated vulnerability to primary progressive multiple sclerosis.

Pahlevan Kakhki M, Giordano A, Starvaggi Cucuzza C, ..., Kular L, Jagodic M

Nat Commun 15 (1) 6419 [2024-07-30; online 2024-07-30]

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Mandolesi M, Das H, de Vries L, ..., Murrell B, Karlsson Hedestam GB

Nat Commun 15 (1) 6338 [2024-07-27; online 2024-07-27]

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Bifidobacterium longum subsp. longum BG-L47 boosts growth and activity of Limosilactobacillus reuteri DSM 17938 and its extracellular membrane vesicles.

Ermann Lundberg L, Pallabi Mishra P, Liu P, ..., Linninge C, Roos S

Appl. Environ. Microbiol. 90 (7) e0024724 [2024-07-24; online 2024-06-18]

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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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Separate hydrolysis and fermentation of softwood bark pretreated with 2-naphthol by steam explosion.

Averheim A, Stagge S, Jönsson LJ, Larsson SH, Thyrel M

Biotechnol Biofuels Bioprod 17 (1) 102 [2024-07-17; online 2024-07-17]

Insights into mechanisms of MALT1 allostery from NMR and AlphaFold dynamic analyses.

Wallerstein J, Han X, Levkovets M, ..., Agback T, Orekhov V

Commun Biol 7 (1) 868 [2024-07-16; online 2024-07-16]

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Enhancing Molecular Characterization of Dissolved Organic Matter by Integrative Direct Infusion and Liquid Chromatography Nontargeted Workflows.

Patrone J, Vila-Costa M, Dachs J, ..., Gago-Ferrero P, Gil-Solsona R

Environ. Sci. Technol. 58 (28) 12454-12466 [2024-07-16; online 2024-07-03]

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Maturation of Human Intestinal Epithelial Cell Layers Fortifies the Apical Surface againstSalmonellaAttack

van Rijn JM, Lopes ACC, Ceylan M, ..., Di Martino ML, Sellin ME

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Temporal dynamics of woolly mammoth genome erosion prior to extinction.

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Cell 187 (14) 3531-3540.e13 [2024-07-11; online 2024-06-27]

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Seroepidemiological assessment of the spread of SARS-CoV-2 among 25 and 28 year-old adult women in Finland between March 2020-June 2022.

Gray P, Eriksson T, Skoglund L, ..., Dillner J, Lehtinen M

PLoS ONE 19 (7) e0305285 [2024-07-11; online 2024-07-11]

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A cancer immunotherapy modality based on dendritic cell reprogrammingin vivo

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Regional Changes in Brain Biomolecular Markers in a Collagen-Induced Arthritis Rat Model.

Millen AME, Maluleke TT, Pienaar L, ..., Andrén PE, Baijnath S

Biology (Basel) 13 (7) - [2024-07-10; online 2024-07-10]

Inverted triplications formed by iterative template switches generate structural variant diversity at genomic disorder loci.

Grochowski CM, Bengtsson JD, Du H, ..., Lupski JR, Carvalho CMB

Cell Genomics 4 (7) 100590 [2024-07-10; online 2024-06-21]

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Spinocerebellar ataxia type 4 is caused by a GGC expansion in the ZFHX3 gene and is associated with prominent dysautonomia and motor neuron signs.

Paucar M, Nilsson D, Engvall M, ..., Wedell A, Svenningsson P

J. Intern. Med. - (-) - [2024-07-07; online 2024-07-07]

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eLife assessment: Nucleotide binding to the ATP-cone in anaerobic ribonucleotide reductases allosterically regulates activity by modulating substrate binding

Boal AK

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Nucleotide binding to the ATP-cone in anaerobic ribonucleotide reductases allosterically regulates activity by modulating substrate binding

Bimai O, Banerjee I, Rozman Grinberg I, ..., Sjöberg BM, Logan DT

Elife 12 (-) - [2024-07-05; online 2024-07-05]

Neonatal microbiota colonization drives maturation of primary and secondary goblet cell mediated protection in the pre-weaning colon.

Johansson Å, Subramani MV, Yilmaz B, ..., Johansson MEV, Birchenough GMH

bioRxiv - (-) - [2024-07-05; online 2024-07-05]

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Evaluating Bacterial Spore Preparation Methods for Scanning Electron Microscopy

Malyshev D, Lee CC, Andersson M

Microsc Microanal 30 (3) 564-573 [2024-07-04; online 2024-05-03]

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DNA methylation of exercise-responsive genes differs between trained and untrained men.

Geiger C, Needhamsen M, Emanuelsson EB, ..., Reitzner SM, Lindholm ME

BMC Biol. 22 (1) 147 [2024-07-04; online 2024-07-04]

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Thalén NB, Karlander M, Lundqvist M, ..., Ohlin M, Rockberg J

Commun Biol 7 (1) 805 [2024-07-03; online 2024-07-03]

Limited Parallelism in Genetic Adaptation to Brackish Water Bodies in European Sprat and Atlantic Herring.

Pettersson ME, Quintela M, Besnier F, ..., Glover KA, Andersson L

Genome Biol Evol 16 (7) - [2024-07-03; online 2024-06-26]

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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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Discovery of a novel inhibitor of macropinocytosis with antiviral activity.

Porebski B, Christ W, Corman A, ..., Hühn D, Fernandez-Capetillo O

Mol Ther - (-) - [2024-07-02; online 2024-07-02]

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CRISPR-Cas9 Knockout Screens Identify DNA Damage Response Pathways and BTK as Essential for Cisplatin Response in Diffuse Large B-Cell Lymphoma

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Cancers (Basel) 16 (13) 2437 [2024-07-02; online 2024-07-02]

Clinical and genetic factors associated with tumor response to neoadjuvant (chemo)radiotherapy, survival and recurrence risk in rectal cancer.

Hammarström K, Nunes L, Mathot L, ..., Sjöblom T, Glimelius B

Int. J. Cancer 155 (1) 40-53 [2024-07-01; online 2024-02-20]

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Carboxyl-group compounds activate voltage-gated potassium channels via a distinct mechanism.

Rönnelid O, Elinder F

J. Gen. Physiol. 156 (7) - [2024-07-01; online 2024-06-04]

Chemical Biology Consortium Sweden (CBCS) [Service]

Cancer Core Europe: Leveraging Institutional Synergies to Advance Oncology Research and Care Globally.

Carmona J, Chavarria E, Donoghue K, ..., Zwart W, Tabernero J

Cancer Discov 14 (7) 1147-1153 [2024-07-01; online 2024-06-13]

Clinical Genomics Stockholm [Collaborative]

Utilising ancient DNA to understand crop population dynamics across a millennium: A case study of archaeological barley (Hordeum vulgare L.) from Gran Canaria, Spain

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Journal of Archaeological Science 167 (-) 106001 [2024-07-00; online 2024-07-00]

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The WHO Enhanced Gonococcal Antimicrobial Surveillance Programme (EGASP) identifies high levels of ceftriaxone resistance across Vietnam, 2023.

Lan PT, Nguyen HT, Golparian D, ..., Unemo M, EGASP-Vietnam WGS study group

Lancet Reg Health West Pac 48 (-) 101125 [2024-07-00; online 2024-06-27]

Precision Diagnostics in Myeloid Malignancies: Development and Validation of a National Capture-Based Gene Panel.

Orsmark-Pietras C, Lyander A, Ladenvall C, ..., Fioretos T, SciLifeLab Clinical Genomics Platform and Genomic Medicine Sweden

Genes Chromosomes Cancer 63 (7) e23257 [2024-07-00; online 2024-07-20]

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Molecular basis for different substrate-binding sites and chaperone functions of the BRICHOS domain.

Chen G, Wang Y, Zheng Z, ..., Knight SD, Johansson J

Protein Sci. 33 (7) e5063 [2024-07-00; online 2024-06-12]

GABA-mediated inhibition of human CD4+ T cell functions is enhanced by insulin but impaired by high glucose levels.

Jin Z, Hammoud H, Bhandage AK, ..., Kamali-Moghaddam M, Birnir B

EBioMedicine 105 (-) 105217 [2024-07-00; online 2024-06-28]

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Distinct origin and region-dependent contribution of stromal fibroblasts to fibrosis following traumatic injury in mice.

Holl D, Hau WF, Julien A, ..., Dias DO, Göritz C

Nat. Neurosci. 27 (7) 1285-1298 [2024-07-00; online 2024-06-07]

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Diagnosis of external ventricular drainage related infections with real-time 16S PCR and third-generation 16S sequencing.

Widén J, Morén J, Mölling P, ..., Sundqvist M, Westman G

Infect Dis (Lond) 56 (7) 521-530 [2024-07-00; online 2024-03-26]

Detection and quantification of Na,K-ATPase dimers in the plasma membrane of living cells by FRET-FCS.

Nordahl L, Akkuratov EE, Heimgärtner J, ..., Wennmalm S, Brismar H

Biochimica et Biophysica Acta (BBA) - General Subjects 1868 (7) 130619 [2024-07-00; online 2024-04-20]

Integrated Microscopy Technologies Stockholm [Collaborative]

Box-Behnken design for the synthesis optimization of mesoporous sulfur-doped carbon-based materials from birch waste: Promising candidates for environmental and energy storage application

Laisné E, Thivet J, Manavalan G, ..., Lassi U, dos Reis GS

Colloids and Surfaces A: Physicochemical and Engineering Aspects 692 (-) 133899 [2024-07-00; online 2024-07-00]

Membrane topography and the overestimation of protein clustering in single molecule localisation microscopy – identification and correction

Adler J, Bernhem K, Parmryd I

Commun Biol 7 (1) - [2024-06-29; online 2024-06-29]

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The annotation of GBA1 has been concealed by its protein-coding pseudogene GBAP1.

Gustavsson EK, Sethi S, Gao Y, ..., Hardy J, Ryten M

Sci Adv 10 (26) eadk1296 [2024-06-28; online 2024-06-26]

Small molecules dominate organic phosphorus in NaOH-EDTA extracts of soils as determined by 31P NMR.

Haddad L, Vincent AG, Giesler R, Schleucher J

Sci. Total Environ. 931 (-) 172496 [2024-06-25; online 2024-04-16]

Predicting type 2 diabetes via machine learning integration of multiple omics from human pancreatic islets.

Rönn T, Perfilyev A, Oskolkov N, Ling C

Sci Rep 14 (1) 14637 [2024-06-25; online 2024-06-25]

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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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Quantification and Profiling of Early and Late Differentiation Stage T Cells in Mantle Cell Lymphoma Reveals Immunotherapeutic Targets in Subsets of Patients.

Lokhande L, Nilsson D, de Matos Rodrigues J, ..., Jerkeman M, Ek S

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MOXD1 is a lineage-specific gene and a tumor suppressor in neuroblastoma

Fredlund E, Andersson S, Hilgert E, ..., van Nes J, Mohlin S

Sci Adv 10 (25) - [2024-06-21; online 2024-06-21]

Cryo-electron microscopy reveals hydrogen positions and water networks in photosystem II.

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Science 384 (6702) 1349-1355 [2024-06-21; online 2024-06-20]

Cryo-EM [Collaborative]

Structures of the Staphylococcus aureus ribosome inhibited by fusidic acid and fusidic acid cyclopentane.

González-López A, Larsson DSD, Koripella RK, ..., Sanyal S, Selmer M

Sci Rep 14 (1) 14253 [2024-06-20; online 2024-06-20]

Long-range charge transfer mechanism of the III2IV2 mycobacterial supercomplex.

Riepl D, Gamiz-Hernandez AP, Kovalova T, ..., Brzezinski P, Kaila VRI

Nat Commun 15 (1) 5276 [2024-06-20; online 2024-06-20]

Hearing loss and its association with the proteome of perilymph, cerebrospinal fluid, and tumor tissue in patients with vestibular schwannoma.

Edvardsson Rasmussen J, Li P, Laurell G, Bergquist J, Eriksson PO

Sci Rep 14 (1) 14118 [2024-06-19; online 2024-06-19]

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Completed genome and emergence scenario of the multidrug-resistant nosocomial pathogen Staphylococcus epidermidis ST215.

Kellgren T, Dwibedi C, Widerström M, ..., Rydén P, Johansson A

BMC Microbiol. 24 (1) 215 [2024-06-19; online 2024-06-19]

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Pyrene Functionalized Norbornadiene-Quadricyclane Fluorescent Photoswitches: Characterization of their Spectral Properties and Application in Imaging of Amyloid Beta Plaques.

Ghasemi S, Shamsabadi M, Olesund A, ..., Dreos A, Moth-Poulsen K

Chemistry 30 (34) e202400322 [2024-06-17; online 2024-05-22]

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Exposing kinetic disparities between inflammasome readouts using time-resolved analysis.

Herring M, Persson A, Potter R, ..., Särndahl E, Ejdebäck M

Heliyon 10 (11) e32023 [2024-06-15; online 2024-05-29]

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Intestinal Ketogenesis and Permeability.

Casselbrant A, Elias E, Hallersund P, ..., Fändriks L, Wallenius V

Int J Mol Sci 25 (12) - [2024-06-14; online 2024-06-14]

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Comprehensive Genomic Profiling Alters Clinical Diagnoses in a Significant Fraction of Tumors Suspicious of Sarcoma.

Öfverholm I, Wallander K, Haglund C, ..., Lin Y, Haglund de Flon F

Clin. Cancer Res. 30 (12) 2647-2658 [2024-06-14; online 2024-04-04]

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Characterization of Limestone Surface Impurities and Resulting Quicklime Quality

Sandström K, Carlborg M, Eriksson M, Broström M

Minerals 14 (6) 608 [2024-06-13; online 2024-06-13]

descSPIM: an affordable and easy-to-build light-sheet microscope optimized for tissue clearing techniques.

Otomo K, Omura T, Nozawa Y, ..., Brismar H, Susaki EA

Nat Commun 15 (1) 4941 [2024-06-12; online 2024-06-12]

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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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Spatially resolved multiomics on the neuronal effects induced by spaceflight in mice.

Masarapu Y, Cekanaviciute E, Andrusivova Z, ..., Costes SV, Giacomello S

Nat Commun 15 (1) 4778 [2024-06-11; online 2024-06-11]

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DOPA-decarboxylase is elevated in CSF, but not plasma, in prodromal and de novo Parkinson's disease.

Appleton E, Khosousi S, Ta M, ..., Iwaki H, Svenningsson P

Transl Neurodegener 13 (1) 31 [2024-06-11; online 2024-06-11]

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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Structural diversity of Arc oligomers within the excitatory synapse

Damenti M, Coceano G, Mendes Silva M, ..., Jungmann R, Testa I

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Long-term impact of digital media on brain development in children.

Nivins S, Sauce B, Liebherr M, Judd N, Klingberg T

Sci Rep 14 (1) 13030 [2024-06-06; online 2024-06-06]

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Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images.

Wernersson E, Gelali E, Girelli G, ..., Crosetto N, Bienko M

Nat. Methods - (-) - [2024-06-06; online 2024-06-06]

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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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Structure and mechanism of the K+/H+ exchanger KefC.

Gulati A, Kokane S, Perez-Boerema A, ..., Matsuoka R, Drew D

Nat Commun 15 (1) 4751 [2024-06-04; online 2024-06-04]

Multimodal Mass Spectrometry Identifies a Conserved Protective Epitope in S. pyogenes Streptolysin O

Tang D, Gueto-Tettay C, Hjortswang E, ..., Malmström L, Malmström J

Anal. Chem. 96 (22) 9060-9068 [2024-06-04; online 2024-05-03]

Structural Proteomics [Technology development]

Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region.

Larsson MNA, Morell Miranda P, Pan L, ..., Storå J, Günther T

Genome Biol Evol 16 (6) - [2024-06-04; online 2024-05-25]

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A laboratory-based predictive pathway for the development of Neisseria gonorrhoeae high-level resistance to corallopyronin A, an inhibitor of bacterial RNA polymerase.

Balthazar JT, Golparian D, Unemo M, ..., Vassylyev DG, Shafer WM

Microbiol Spectr 12 (6) e0056024 [2024-06-04; online 2024-04-22]

Chemical signatures delineate heterogeneous amyloid plaque populations across the Alzheimer's disease spectrum.

Koutarapu S, Ge J, Dulewicz M, ..., Schöll M, Hanrieder J

bioRxiv - (-) - [2024-06-03; online 2024-06-03]

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Structure and interactions of the endogenous human Commander complex.

Laulumaa S, Kumpula EP, Huiskonen JT, Varjosalo M

Nat. Struct. Mol. Biol. 31 (6) 925-938 [2024-06-00; online 2024-03-08]

Recognising the importance and impact of Imaging Scientists: Global guidelines for establishing career paths within core facilities.

Wright GD, Thompson KA, Reis Y, ..., Vasconcelos ADS, Keppler A

J Microsc 294 (3) 397-410 [2024-06-00; online 2024-05-01]

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Proteomic profiling of polyglucosan bodies associated with glycogenin-1 deficiency in skeletal muscle.

Visuttijai K, Hedberg-Oldfors C, Costello DJ, Bermingham N, Oldfors A

Neuropathol Appl Neurobiol 50 (3) e12995 [2024-06-00; online 2024-06-26]

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Phylogenomic analysis of Stylops reveals the evolutionary history of a Holarctic Strepsiptera radiation parasitizing wild bees.

Lähteenaro M, Benda D, Straka J, Nylander JAA, Bergsten J

Mol. Phylogenet. Evol. 195 (-) 108068 [2024-06-00; online 2024-03-28]

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Pericyte-Specific Secretome Profiling in Hypoxia Using TurboID in a Multicellular in Vitro Spheroid Model.

Enström A, Carlsson R, Buizza C, Lewi M, Paul G

Mol. Cell Proteomics 23 (6) 100782 [2024-06-00; online 2024-05-04]

Macrophages upregulate mural cell-like markers and support healing of ischemic injury by adopting functions important for vascular support.

Amoedo-Leite C, Parv K, Testini C, ..., Christoffersson G, Phillipson M

Nat Cardiovasc Res 3 (6) 685-700 [2024-06-00; online 2024-06-06]

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Fine-Tuning Amyloid Precursor Protein Expression through Nonsense-Mediated mRNA Decay.

Rahmati M, Chebli J, Kumar Banote R, ..., Zetterberg H, Abramsson A

eNeuro 11 (6) - [2024-06-00; online 2024-06-10]

Expedient Bayesian prediction of subfossil bone protein content using portable ATR-FTIR data

Hixon S, Roberts P, Rodríguez-Varela R, ..., Lagia A, Fernandes R

Quaternary International 694 (-) 1-12 [2024-06-00; online 2024-06-00]

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Epigenetic dissection of human blood group genes reveals regulatory elements and detailed characteristics of KEL and four other loci.

Wu PC, McGowan EC, Lee YQ, ..., Hansson J, Olsson ML

Transfusion 64 (6) 1083-1096 [2024-06-00; online 2024-04-21]

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Childhood screening for type 1 diabetes comparing automated multiplex Antibody Detection by Agglutination-PCR (ADAP) with single plex islet autoantibody radiobinding assays.

Lind A, Freyhult E, de Jesus Cortez F, ..., Lernmark Å, Better Diabetes Diagnosis (BDD) study group

EBioMedicine 104 (-) 105144 [2024-06-00; online 2024-05-08]

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Cellulose gelation in aqueous hydroxide solutions by CO2(g): Fact and theory

Naserifar S, Karna NK, Kozlowski AM, Bernin D, Hasani M

Carbohydrate Polymer Technologies and Applications 7 (-) 100514 [2024-06-00; online 2024-06-00]

Blood biomarkers of Alzheimer's disease in the community: Variation by chronic diseases and inflammatory status.

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

Alzheimers Dement 20 (6) 4115-4125 [2024-06-00; online 2024-05-08]

Affinity Proteomics Stockholm [Collaborative]

Bacterial diversity in semen from stallions in three European countries evaluated by 16S sequencing.

Malaluang P, Niazi A, Guo Y, ..., Aurich C, Morrell JM

Vet Res Commun 48 (3) 1409-1421 [2024-06-00; online 2024-02-02]

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An endothelial regulatory module links blood pressure regulation with elite athletic performance.

Fegraeus K, Rosengren MK, Naboulsi R, ..., Meadows JRS, Lindgren G

PLoS Genet. 20 (6) e1011285 [2024-06-00; online 2024-06-17]

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A combination of long and short read genomics reveals frequent p-arm breakpoints within chromosome 21 complex genomic rearrangements

Schuy J, Sæther KB, Lisfeld J, ..., Eisfeldt J, Lindstrand A

Genetics in Medicine Open - (-) 101863 [2024-06-00; online 2024-06-00]

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Tobacco Smoke Exposure in Early Childhood and Later Risk of Inflammatory Bowel Disease: A Scandinavian Birth Cohort Study.

Sigvardsson I, Ludvigsson J, Andersson B, Størdal K, Mårild K

J Crohns Colitis 18 (5) 661-670 [2024-05-31; online 2024-02-08]

Structural conversion of the spidroin C-terminal domain during assembly of spider silk fibers.

De Oliveira DH, Gowda V, Sparrman T, ..., Lendel C, Hedhammar M

Nat Commun 15 (1) 4670 [2024-05-31; online 2024-05-31]

Sequential drug treatment targeting cell cycle and cell fate regulatory programs blocks non-genetic cancer evolution in acute lymphoblastic leukemia.

Malyukova A, Lahnalampi M, Falqués-Costa T, ..., Heinäniemi M, Sangfelt O

Genome Biol. 25 (1) 143 [2024-05-31; online 2024-05-31]

PIK3CA mutations in endocrine-resistant breast cancer.

Schagerholm C, Robertson S, Toosi H, Sifakis EG, Hartman J

Sci Rep 14 (1) 12542 [2024-05-31; online 2024-05-31]

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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NGS method for parallel processing of high quality, damaged or fragmented input material using target enrichment.

Lyander A, Gellerbring A, Hägglund M, Elhami K, Wirta V

PLoS ONE 19 (5) e0304411 [2024-05-29; online 2024-05-29]

Clinical Genomics Stockholm [Technology development]

Distinct Infiltration of T Cell Populations in Bladder Cancer Molecular Subtypes.

Sincic V, Arlenhold KF, Richtmann S, ..., Liedberg F, Lundberg K

Cells 13 (11) - [2024-05-28; online 2024-05-28]

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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MDM2 amplification in rod-shaped chromosomes provides clues to early stages of circularized gene amplification in liposarcoma.

Sydow S, Piccinelli P, Mitra S, ..., Spierings D, Mertens F

Commun Biol 7 (1) 606 [2024-05-20; online 2024-05-20]

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Retron-Eco1 assembles NAD+-hydrolyzing filaments that provide immunity against bacteriophages.

Carabias A, Camara-Wilpert S, Mestre MR, ..., Pinilla-Redondo R, Montoya G

Mol. Cell - (-) - [2024-05-18; online 2024-05-18]

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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Exploring carbon source related localization and phosphorylation in the Snf1/Mig1 network using population and single cell-based approaches.

Braam S, Tripodi F, Österberg L, ..., Coccetti P, Cvijovic M

Microb Cell 11 (-) 143-154 [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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Copy number variation and elevated genetic diversity at immune trait loci in Atlantic and Pacific herring.

Mohamadnejad Sangdehi F, Jamsandekar MS, Enbody ED, Pettersson ME, Andersson L

BMC Genomics 25 (1) 459 [2024-05-10; online 2024-05-10]

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Modulation of innate immune response to mRNA vaccination after SARS-CoV-2 infection or sequential vaccination in humans.

Hellgren F, Rosdahl A, Arcoverde Cerveira R, ..., Cajander S, Loré K

JCI Insight 9 (9) - [2024-05-08; online 2024-05-08]

All-photonic kinase inhibitors: light-controlled release-and-report inhibition.

Fleming CL, Benitez-Martin C, Bernson E, ..., Grøtli M, Andréasson J

Chem. Sci. 15 (18) 6897-6905 [2024-05-08; online 2024-04-12]

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Colonial-driven extinction of the blue antelope despite genomic adaptation to low population size.

Hempel E, Faith JT, Preick M, ..., Westbury MV, Hofreiter M

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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Genetic Causes and Genomic Consequences of Breakdown of Distyly in Linum trigynum.

Gutiérrez-Valencia J, Zervakis P, Postel Z, ..., Arroyo J, Slotte T

Mol. Biol. Evol. 41 (5) - [2024-05-03; online 2024-05-06]

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Recent dynamics in Neisseria gonorrhoeae genomic epidemiology in Brazil: antimicrobial resistance and genomic lineages in 2017-20 compared to 2015-16.

Golparian D, Bazzo ML, Ahlstrand J, ..., Unemo M, Brazilian-GASP Network

J. Antimicrob. Chemother. 79 (5) 1081-1092 [2024-05-02; online 2024-03-22]

Pharmacodynamic evaluation of ceftriaxone single-dose therapy (0.125-1 g) to eradicate ceftriaxone-susceptible and ceftriaxone-resistant Neisseria gonorrhoeae strains in a hollow fibre infection model for gonorrhoea.

Unemo M, Golparian D, Oxelbark J, ..., Drusano G, Jacobsson S

J. Antimicrob. Chemother. 79 (5) 1006-1013 [2024-05-02; online 2024-03-18]

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Clin Transl Immunology 13 (5) e1508 [2024-05-02; online 2024-05-02]

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Mar. Ecol. Prog. Ser. 735 (-) 63-76 [2024-05-02; online 2024-05-02]

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Hum. Reprod. 39 (5) 1141-1154 [2024-05-02; online 2024-03-09]

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Genome Biol Evol 16 (5) - [2024-05-02; online 2024-05-14]

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Front Cell Dev Biol 12 (-) - [2024-05-01; online 2024-05-01]

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Sci. Total Environ. 923 (-) 170949 [2024-05-01; online 2024-02-15]

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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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Acta Physiol (Oxf) 240 (5) e14128 [2024-05-00; online 2024-03-29]

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Diabetologia 67 (5) 874-884 [2024-05-00; online 2024-02-22]

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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

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Limnol Oceanogr 69 (5) 1030-1044 [2024-05-00; online 2024-03-13]

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New Phytol. 242 (4) 1725-1738 [2024-05-00; online 2024-01-11]

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NPJ Parkinsons Dis 10 (1) 93 [2024-04-29; online 2024-04-29]

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The hinge-engineered IgG1-IgG3 hybrid subclass IgGh47 potently enhances Fc-mediated function of anti-streptococcal and SARS-CoV-2 antibodies.

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Nat Commun 15 (1) 3600 [2024-04-27; online 2024-04-27]

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Papakyriacou I, Kutkaite G, Rúbies Bedós M, ..., Menden MP, Mao Y

Nat Commun 15 (1) 3581 [2024-04-27; online 2024-04-27]

Cyanotoxin Occurrence and Diversity in 98 Cyanobacterial Blooms from Swedish Lakes and the Baltic Sea.

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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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Deciphering the role of FUS::DDIT3 expression and tumor microenvironment in myxoid liposarcoma development.

Ranji P, Jonasson E, Andersson L, ..., Åman P, Ståhlberg A

J Transl Med 22 (1) 389 [2024-04-26; online 2024-04-26]

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Glycobiology 34 (6) - [2024-04-24; online 2024-04-09]

Glycoproteomics and MS Proteomics [Collaborative]

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Zhang N, Harbers L, Simonetti M, ..., Bienko M, Crosetto N

Nat Commun 15 (1) 3475 [2024-04-24; online 2024-04-24]

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A chemical inhibitor of IST1-CHMP1B interaction impairs endosomal recycling and induces noncanonical LC3 lipidation.

Knyazeva A, Li S, Corkery DP, ..., Waldmann H, Wu Y

Proc. Natl. Acad. Sci. U.S.A. 121 (17) e2317680121 [2024-04-23; online 2024-04-18]

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iScience 27 (4) 109344 [2024-04-19; online 2024-02-28]

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Radiolabeled 15-mer peptide internalization is mediated by megalin (LRP2 receptor) in a CRISPR/Cas9-based LRP2 knockout human kidney cell model.

Durinova A, Smutna L, Barta P, ..., Pavek P, Trejtnar F

EJNMMI Radiopharm Chem 9 (1) 32 [2024-04-18; online 2024-04-18]

CRISPR Functional Genomics [Collaborative]

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Ten Berk de Boer E, Ameur A, Bunikis I, ..., Eisfeldt J, Lindstrand A

Sci Rep 14 (1) 9000 [2024-04-18; online 2024-04-18]

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Effects of bottom trawling and environmental factors on benthic bacteria, meiofauna and macrofauna communities and benthic ecosystem processes.

Bradshaw C, Iburg S, Morys C, ..., Jonsson P, Nascimento FJA

Sci. Total Environ. 921 (-) 171076 [2024-04-15; online 2024-02-19]

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Amperometry and Electron Microscopy show Stress Granules Induce Homotypic Fusion of Catecholamine Vesicles.

Gu H, Gu C, Locker N, Ewing AG

Angew. Chem. Int. Ed. Engl. 63 (16) e202400422 [2024-04-15; online 2024-03-07]

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Abdel-Fattah WR, Carlsson M, Hu G, ..., Ronne H, Björklund S

Nucleic Acids Res. - (-) - [2024-04-13; online 2024-04-13]

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Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity.

Edelbroek B, Kjellin J, Biryukova I, ..., Friedländer MR, Söderbom F

Nucleic Acids Res. 52 (6) 3121-3136 [2024-04-12; online 2024-02-20]

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Dual molecule targeting HDAC6 leads to intratumoral CD4+ cytotoxic lymphocytes recruitment through MHC-II upregulation on lung cancer cells.

Ducellier S, Demeules M, Letribot B, ..., Nascimento M, Apcher S

J Immunother Cancer 12 (4) - [2024-04-11; online 2024-04-11]

Cellular architecture of evolving neuroinflammatory lesions and multiple sclerosis pathology.

Kukanja P, Langseth CM, Rubio Rodríguez-Kirby LA, ..., Nilsson M, Castelo-Branco G

Cell 187 (8) 1990-2009.e19 [2024-04-11; online 2024-03-20]

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A time course analysis through diapause reveals dynamic temporal patterns of microRNAs associated with endocrine regulation in the butterfly Pieris napi.

Roberts KT, Steward RA, Süess P, Lehmann P, Wheat CW

Mol. Ecol. - (-) e17348 [2024-04-10; online 2024-04-10]

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Exploring the short linear motif-mediated protein-protein interactions of CrkL through ProP-PD.

Pagano L, Simonetti L, Pennacchietti V, ..., Ivarsson Y, Gianni S

Biochem. Biophys. Res. Commun. 703 (-) 149658 [2024-04-09; online 2024-02-07]

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Deletion of the TMEM30A gene enables leukemic cell evasion of NK cell cytotoxicity.

Kristenson L, Badami C, Ljungberg A, ..., Tang KW, Thorén FB

Proc. Natl. Acad. Sci. U.S.A. 121 (15) e2316447121 [2024-04-09; online 2024-04-01]

Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria.

Huseby DL, Cao S, Zamaratski E, ..., Hughes D, Karlén A

Proc. Natl. Acad. Sci. U.S.A. 121 (15) e2317274121 [2024-04-09; online 2024-04-05]

Drug Discovery and Development (DDD) [Collaborative]

A phenotypic screening approach to target p60AmotL2-expressing invasive cancer cells.

Fonseca P, Cui W, Struyf N, ..., Östling P, Holmgren L

J. Exp. Clin. Cancer Res. 43 (1) 107 [2024-04-09; online 2024-04-09]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

Transcriptomic atlas of midbrain dopamine neurons uncovers differential vulnerability in a Parkinsonism lesion model.

Yaghmaeian Salmani B, Lahti L, Gillberg L, ..., Svenningsson P, Perlmann T

Elife 12 (-) - [2024-04-08; online 2024-04-08]

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Functional redundancy revealed by the deletion of the mimivirus GMC-oxidoreductase genes.

Alempic JM, Bisio H, Villalta A, ..., Couté Y, Abergel C

Microlife 5 (-) uqae006 [2024-04-05; online 2024-04-05]

Adaptive introgression reveals the genetic basis of a sexually selected syndrome in wall lizards.

Feiner N, Yang W, Bunikis I, While GM, Uller T

Sci Adv 10 (14) eadk9315 [2024-04-05; online 2024-04-03]

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Treatment Monitoring of a Patient with Synchronous Metastatic Angiosarcoma and Breast Cancer Using ctDNA.

Vannas C, Escobar M, Österlund T, ..., Fagman H, Ståhlberg A

Int J Mol Sci 25 (7) - [2024-04-04; online 2024-04-04]

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The HLA region in ANCA-associated vasculitis: characterisation of genetic associations in a Scandinavian patient population.

Lundtoft C, Knight A, Meadows JRS, ..., Lindblad-Toh K, Dahlqvist J

RMD Open 10 (2) - [2024-04-04; online 2024-04-04]

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Extracellular vesicles isolated from frozen and fresh human melanoma tissue are similar in purity and protein composition

D’Arrigo D, Lässer C, Urzì O, ..., Lötvall J, Crescitelli R

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Proteome profiling of home-sampled dried blood spots reveals proteins of SARS-CoV-2 infections.

Fredolini C, Dodig-Crnković T, Bendes A, ..., Roxhed N, Schwenk JM

Commun Med (Lond) 4 (1) 55 [2024-04-02; online 2024-04-02]

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Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.

David G, Bertolotti A, Layer R, ..., Jensen H, Husby A

Genome Biol Evol 16 (4) - [2024-04-02; online 2024-03-15]

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Morphology and phosphate distribution in bottom ash particles from fixed-bed co-combustion of sewage sludge and two agricultural residues.

Strandberg A, Thyrel M, Falk J, Öhman M, Skoglund N

Waste Management 177 (-) 56-65 [2024-04-01; online 2024-01-29]

Increased matrix stiffness enhances pro-tumorigenic traits in a physiologically relevant breast tissue- monocyte 3D model.

Abrahamsson A, Boroojeni FR, Naeimipour S, ..., Aili D, Dabrosin C

Acta Biomater 178 (-) 160-169 [2024-04-01; online 2024-02-20]

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Fast volumetric multifocus structured illumination microscopy of subcellular dynamics in living cells

Senftleben ML, Bajor A, Hirata E, Abrahamsson S, Brismar H

Biomed. Opt. Express 15 (4) 2281 [2024-04-01; online 2024-03-11]

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Expression of influenza A virus glycan receptor candidates in mallard, chicken, and tufted duck.

Nilsson J, Eriksson P, Naguib MM, ..., Larson G, Ellström P

Glycobiology 34 (3) - [2024-04-01; online 2023-12-21]

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Viridibacillus culture derived silver nanoparticles exert potent anticancer action in 2D and 3D models of lung cancer via mitochondrial depolarization-mediated apoptosis.

Joshi AS, Bapat MV, Singh P, Mijakovic I

Mater Today Bio 25 (-) 100997 [2024-04-00; online 2024-02-11]

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Novel ultrasensitive immunoassay for the selective quantification of tau oligomers and related soluble aggregates.

Islam T, Kvartsberg H, Sehrawat A, ..., Blennow K, Karikari TK

Alzheimers Dement 20 (4) 2894-2905 [2024-04-00; online 2024-03-23]

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Monitoring genome-wide diversity over contemporary time with new indicators applied to Arctic charr populations

Saha A, Kurland S, Kutschera VE, ..., Ryman N, Laikre L

Conserv Genet 25 (2) 513-531 [2024-04-00; online 2024-01-20]

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Microbial succession and denitrifying woodchip bioreactor performance at low water temperatures.

Hellman M, Juhanson J, Wallnäs F, Herbert RB, Hallin S

J Environ Manage 356 (-) 120607 [2024-04-00; online 2024-03-26]

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Meta-analysis of ACE inhibitor-induced angioedema identifies novel risk locus.

Mathey CM, Maj C, Eriksson N, ..., Nöthen MM, Forstner AJ

J. Allergy Clin. Immunol. 153 (4) 1073-1082 [2024-04-00; online 2024-01-31]

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Liprin-α proteins are master regulators of human presynapse assembly.

Marcó de la Cruz B, Campos J, Molinaro A, ..., Acuna C, Sterky FH

Nat. Neurosci. 27 (4) 629-642 [2024-04-00; online 2024-03-12]

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Hydrogen evolution mediated by sulfur vacancies and substitutional Mn in few-layered molybdenum disulfide

Rafei M, Piñeiro-García A, Wu X, ..., Wågberg T, Gracia-Espino E

Materials Today Energy 41 (-) 101524 [2024-04-00; online 2024-04-00]

High-throughput measurement of the content and properties of nano-sized bioparticles with single-particle profiler.

Sych T, Schlegel J, Barriga HMG, ..., Stevens MM, Sezgin E

Nat. Biotechnol. 42 (4) 587-590 [2024-04-00; online 2023-06-12]

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Habitat is more important than climate for structuring soil fungal communities associated in truffle sites.

Piñuela Y, Alday JG, Oliach D, ..., Peter M, Bonet JA

Fungal Biol 128 (2) 1724-1734 [2024-04-00; online 2024-02-24]

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Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis.

Sommerauer C, Gallardo-Dodd CJ, Savva C, ..., Williams C, Kutter C

Mol. Syst. Biol. 20 (4) 374-402 [2024-04-00; online 2024-03-08]

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Diagnostic yield and clinical impact of germline sequencing in children with CNS and extracranial solid tumors-a nationwide, prospective Swedish study.

Tesi B, Robinson KL, Abel F, ..., Taylan F, Nordgren A

Lancet Reg Health Eur 39 (-) 100881 [2024-04-00; online 2024-03-19]

Current and emerging sequencing-based tools for precision cancer medicine.

Edsjö A, Gisselsson D, Staaf J, ..., Cavelier L, Rosenquist R

Mol Aspects Med 96 (-) 101250 [2024-04-00; online 2024-02-07]

Cancer-associated fibroblasts rewire the estrogen receptor response in luminal breast cancer, enabling estrogen independence.

Reid SE, Pantaleo J, Bolivar P, ..., Seashore-Ludlow B, Pietras K

Oncogene 43 (15) 1113-1126 [2024-04-00; online 2024-02-22]

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A step towards more eco-friendly and efficient microalgal harvesting: Inducing flocculation in the non-naturally flocculating strain Chlorella vulgaris (13-1) without chemical additives

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VISION — an open-source software for automated multi-dimensional image analysis of cellular biophysics

Weber F, Iskrak S, Ragaller F, ..., Sezgin E, Andronico LA

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Designing efficient randstrobes for sequence similarity analyses.

Karami M, Soltani Mohammadi A, Martin M, ..., Patro R, Sahlin K

Bioinformatics 40 (4) - [2024-03-29; online 2024-04-05]

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Refining risk prediction in pediatric acute lymphoblastic leukemia through DNA methylation profiling.

Mosquera Orgueira A, Krali O, Pérez Míguez C, ..., Schmiegelow K, Nordlund J

Clin Epigenetics 16 (1) 49 [2024-03-28; online 2024-03-28]

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High Oestrogen receptor alpha expression correlates with adverse prognosis and promotes metastasis in colorectal cancer.

Topi G, Satapathy SR, Ghatak S, ..., Lydrup M, Sjölander A

Cell Commun Signal 22 (1) 198 [2024-03-28; online 2024-03-28]

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Defining the contribution of Troy-positive progenitor cells to the mouse esophageal epithelium.

Grommisch D, Wang M, Eenjes E, ..., Giselsson P, Genander M

Dev. Cell - (-) - [2024-03-28; online 2024-03-28]

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MLL4 binds TET3.

Becht DC, Mohid SA, Lee JE, ..., Zhang Y, Kutateladze TG

Structure - (-) - [2024-03-27; online 2024-03-27]

Effects of microgravity on neural crest stem cells.

Han Y, Barasa P, Zeger L, ..., Fredriksson R, Kozlova EN

Front. Neurosci. 18 (-) 1379076 [2024-03-27; online 2024-03-27]

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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 - (-) - [2024-03-26; online 2024-03-26]

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Novel Synonymous and Deep Intronic Variants Causing Primary and Secondary Pyruvate Dehydrogenase Complex Deficiency

Bruhn H, Naess K, Ygberg S, ..., Wedell A, Wredenberg A

Hum. Mutat. 2024 (-) 1-16 [2024-03-25; online 2024-03-25]

Abstract 2025: Zeb1 downregulation sensitizes pancreatic cancer-associated fibroblasts to killing by oncolytic reovirus through upregulation of the reovirus receptor junction adhesion molecule A

Dam N, Harryvan TJ, Schmierer B, Hawinkels LJAC, Kemp V

Cancer Res. 84 (6_Supplement) 2025-2025 [2024-03-22; online 2024-03-22]

Modelling age at death reveals Nordic Corded Ware paleodemography

Tornberg A, Vandkilde H

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Epigenetic modulators link mitochondrial redox homeostasis to cardiac function in a sex-dependent manner.

ElBeck Z, Hossain MB, Siga H, ..., Végvári Á, Betsholtz C

Nat Commun 15 (1) 2358 [2024-03-20; online 2024-03-20]

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Dominance between self-incompatibility alleles determines the mating system of Capsella allopolyploids

Duan T, Zhang Z, Genete M, ..., Castric V, Vekemans X

Evolution Letters - (-) - [2024-03-17; online 2024-03-17]

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Influence of divalent cations on the extraction of organic acids in coffee determined by GC-MS and NMR.

Bratthäll T, Figueira J, Nording ML

Heliyon 10 (5) e26625 [2024-03-15; online 2024-02-17]

Biochemical analysis of the endoribonuclease activity of the human mitochondrial topoisomerase 1

Bader CPJ, Kasho E, Forslund JME, Wessels M, Wanrooij PH

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A distinctive tumor compartment in pancreatic lobules defined by nascent stroma and classical tumor cell phenotype

Söderqvist S, Viljamaa A, Geyer N, ..., Moro CF, Gerling M

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Integrated preservation of water activity as key to intensified chemoenzymatic synthesis of bio-based styrene derivatives.

Petermeier P, Bittner JP, Jonsson T, ..., Byström E, Kara S

Commun Chem 7 (1) 57 [2024-03-14; online 2024-03-14]

Identification and surveillance of rare relapse-initiating stem cells during complete remission after transplantation.

Dimitriou M, Mortera-Blanco T, Tobiasson M, ..., Woll PS, Jacobsen SEW

Blood 143 (11) 953-966 [2024-03-14; online 2023-12-14]

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The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees.

Shi T, Zhang X, Hou Y, ..., Yin T, Wang J

Mol Plant - (-) - [2024-03-13; online 2024-03-13]

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Neutralizing IFN-γ autoantibodies are rare and pathogenic in HLA-DRB1*15:02 or 16:02 individuals.

Peel JN, Yang R, Le Voyer T, ..., Ku CL, Casanova JL

J. Clin. Invest. 134 (8) - [2024-03-12; online 2024-03-12]

Complete reference genomes of two ceftriaxone-resistant Neisseria gonorrhoeae strains identified in routine surveillance in Bangkok, Thailand, using Nanopore Q20+ chemistry, VolTRAX V2b, and Illumina sequencing.

Sangprasert P, Golparian D, Paopang P, ..., Kittiyaowanarn R, Unemo M

Microbiol Resour Announc 13 (3) e0123123 [2024-03-12; online 2024-02-01]

Biofilm colonization and succession in a full-scale partial nitritation-anammox moving bed biofilm reactor.

Suarez C, Rosenqvist T, Dimitrova I, ..., Hermansson M, Persson F

Microbiome 12 (1) 51 [2024-03-12; online 2024-03-12]

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Cardiac biopsies reveal differences in transcriptomics between left and right ventricle in patients with or without diagnostic signs of heart failure.

Frisk C, Das S, Eriksson MJ, ..., Linde C, Persson B

Sci Rep 14 (1) 5811 [2024-03-09; online 2024-03-09]

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Identification of microbial pathogens in Neolithic Scandinavian humans.

Bergfeldt N, Kırdök E, Oskolkov N, ..., Storå J, Götherström A

Sci Rep 14 (1) 5630 [2024-03-07; online 2024-03-07]

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Early-life diet and risk of inflammatory bowel disease: a pooled study in two Scandinavian birth cohorts.

Guo A, Ludvigsson J, Brantsæter AL, ..., Størdal K, Mårild K

Gut 73 (4) 590-600 [2024-03-07; online 2024-03-07]

The serological immunogenicity of the third and fourth doses of COVID-19 vaccine in patients with inflammatory rheumatic diseases on different biologic or targeted DMARDs: a Swedish nationwide study (COVID-19-REUMA).

Frodlund M, Nived P, Chatzidionysiou K, ..., Klareskog L, Kapetanovic M

Microbiol Spectr - (-) e0298123 [2024-03-05; online 2024-03-05]

Loss of chromosome Y in regulatory T cells.

Mattisson J, Halvardson J, Davies H, ..., Dumanski JP, Forsberg LA

BMC Genomics 25 (1) 243 [2024-03-05; online 2024-03-05]

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Genomic ancestry and social dynamics of the last hunter-gatherers of Atlantic France.

Simões LG, Peyroteo-Stjerna R, Marchand G, ..., Günther T, Jakobsson M

Proc. Natl. Acad. Sci. U.S.A. 121 (10) e2310545121 [2024-03-05; online 2024-02-26]

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Biohybrid Energy Storage Circuits Based on Electronically Functionalized Plant Roots.

Parker D, Dar AM, Armada-Moreira A, ..., Mantione D, Stavrinidou E

ACS Appl Mater Interfaces - (-) - [2024-03-05; online 2024-03-05]

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fhl2b mediates extraocular muscle protection in zebrafish models of muscular dystrophies and its ectopic expression ameliorates affected body muscles.

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Nat Commun 15 (1) 1950 [2024-03-02; online 2024-03-02]

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High-Quality Genome Assemblies of 4 Members of the Podospora anserina Species Complex.

Ament-Velásquez SL, Vogan AA, Wallerman O, ..., Giraud T, Johannesson H

Genome Biol Evol 16 (3) - [2024-03-02; online 2024-02-22]

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Multimodal bioimaging across disciplines and scales: challenges, opportunities and breaking down barriers

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npj Imaging 2 (1) - [2024-03-01; online 2024-03-01]

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Eur J Pharm Sci 194 (-) 106702 [2024-03-01; online 2024-01-12]

The regulation of methylation on the Z chromosome and the identification of multiple novel Male Hyper-Methylated regions in the chicken.

Höglund A, Henriksen R, Churcher AM, ..., Jensen P, Wright D

PLoS Genet. 20 (3) e1010719 [2024-03-00; online 2024-03-08]

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The impact of circulating protein levels identified by affinity proteomics on short-term, overall breast cancer risk.

Grassmann F, Mälarstig A, Dahl L, ..., Schwenk JM, Czene K

Br. J. Cancer 130 (4) 620-627 [2024-03-00; online 2023-12-22]

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Sorption of pharmaceuticals to foam and aerobic granular sludge with different morphologies

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Resources, Environment and Sustainability 15 (-) 100149 [2024-03-00; online 2024-03-00]

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Rare coding variants in NOX4 link high ROS levels to psoriatic arthritis mutilans.

Wang S, Nikamo P, Laasonen L, ..., Ståhle M, Tapia-Paez I

EMBO Mol Med 16 (3) 596-615 [2024-03-00; online 2024-02-20]

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Nat Cardiovasc Res 3 (3) 356-371 [2024-03-00; online 2024-03-11]

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Human PRH1, PRH2 susceptibility and resistance and Streptococcus mutans virulence phenotypes specify different microbial profiles in caries.

Sheng N, Mårell L, Sitaram RT, ..., Westerlund A, Strömberg N

EBioMedicine 101 (-) 105001 [2024-03-00; online 2024-02-15]

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Eur. J. Hum. Genet. 32 (3) 333-341 [2024-03-00; online 2023-06-05]

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Genetic constraints in genes exhibiting splicing plasticity in facultative diapause.

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Heredity (Edinb) 132 (3) 142-155 [2024-03-00; online 2024-01-30]

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Enhancer mutations modulate the severity of chemotherapy-induced myelosuppression.

Zhigulev A, Norberg Z, Cordier J, ..., Gréen H, Sahlén P

Life Sci. Alliance 7 (3) - [2024-03-00; online 2024-01-16]

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Comparison of high-throughput single-cell RNA-seq methods for ex vivo drug screening.

Gezelius H, Enblad AP, Lundmark A, ..., Andersson C, Nordlund J

NAR Genom Bioinform 6 (1) lqae001 [2024-03-00; online 2024-01-29]

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Whole genome case-control study of central nervous system toxicity due to antimicrobial drugs.

Ås J, Bertulyte I, Norgren N, ..., Wadelius M, Hallberg P

PLoS ONE 19 (2) e0299075 [2024-02-29; online 2024-02-29]

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Population genomic analyses reveal that salinity and geographic isolation drive diversification in a free-living protist.

Rengefors K, Annenkova N, Wallenius J, ..., Kremp A, Ahrén D

Sci Rep 14 (1) 4986 [2024-02-29; online 2024-02-29]

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New insights into complex formation by SARS-CoV-2 nsp10 and nsp14.

Sele C, Krupinska E, Andersson Rasmussen A, ..., Fisher SZ, Knecht W

Nucleosides Nucleotides Nucleic Acids - (-) 1-15 [2024-02-29; online 2024-02-29]

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Visualizing DNA single- and double-strand breaks in the Flash comet assay by DNA polymerase-assisted end-labelling.

Bivehed E, Hellman B, Wenson L, ..., Söderberg O, Heldin J

Nucleic Acids Res. 52 (4) e22 [2024-02-28; online 2024-01-23]

Transcriptomic analysis identifies candidate genes for Aphanomyces root rot disease resistance in pea.

Kälin C, Piombo E, Bourras S, ..., Elfstrand M, Karlsson M

BMC Plant Biol. 24 (1) 144 [2024-02-28; online 2024-02-28]

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Subcellular protein turnover in human neural progenitor cells revealed by correlative electron microscopy and nanoscale secondary ion mass spectrometry imaging.

Lork AA, Rabasco S, Ernst C, ..., Rizzoli SO, Phan NTN

Chem. Sci. 15 (9) 3311-3322 [2024-02-28; online 2024-01-29]

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Quantifying Fluorescence Lifetime Responsiveness of Environment-Sensitive Probes for Membrane Fluidity Measurements

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J. Phys. Chem. B - (-) - [2024-02-28; online 2024-02-28] Open Access

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Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer.

Fonseca NM, Maurice-Dror C, Herberts C, ..., Chi KN, Wyatt AW

Nat Commun 15 (1) 1828 [2024-02-28; online 2024-02-28]

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Chen JP, Diekmann C, Wu H, ..., Bienko M, Crosetto N

Nat Commun 15 (1) 1768 [2024-02-27; online 2024-02-27]

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Tumor Predisposing Post-Zygotic Chromosomal Alterations in Bladder Cancer-Insights from Histologically Normal Urothelium.

Stańkowska W, Sarkisyan D, Bruhn-Olszewska B, ..., Filipowicz N, Dumanski JP

Cancers (Basel) 16 (5) - [2024-02-27; online 2024-02-27]

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Structural and functional insight into the interaction of Clostridioides difficile toxin B and FZD7.

Kinsolving J, Bous J, Kozielewicz P, ..., Dong M, Schulte G

Cell Rep 43 (2) 113727 [2024-02-27; online 2024-02-02]

Gene flow and an anomaly zone complicate phylogenomic inference in a rapidly radiated avian family (Prunellidae).

Jiang Z, Zang W, Ericson PGP, ..., Lei F, Qu Y

BMC Biol. 22 (1) 49 [2024-02-27; online 2024-02-27]

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Equine enteroid-derived monolayers recapitulate key features of parasitic intestinal nematode infection.

Hellman S, Martin F, Tydén E, ..., Svedberg P, Fossum C

Vet Res 55 (1) 25 [2024-02-27; online 2024-02-27]

Epigenome-wide analysis of frailty: Results from two European twin cohorts.

Mak JKL, Skovgaard AC, Nygaard M, ..., Soerensen M, Jylhävä J

Aging Cell - (-) e14135 [2024-02-27; online 2024-02-27]

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Intestinal stroma guides monocyte differentiation to macrophages through GM-CSF.

Kvedaraite E, Lourda M, Mouratidou N, ..., Henter JI, Svensson M

Nat Commun 15 (1) 1752 [2024-02-26; online 2024-02-26]

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Dynamics of Gut Bacteria Across Different Zooplankton Genera in the Baltic Sea.

Xu T, Novotny A, Zamora-Terol S, Hambäck PA, Winder M

Microb. Ecol. 87 (1) 48 [2024-02-26; online 2024-02-26]

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UV-Induced Spectral and Morphological Changes in Bacterial Spores for Inactivation Assessment.

Öberg R, Sil TB, Johansson AC, ..., Andersson M, Andersson PO

J. Phys. Chem. B 128 (7) 1638-1646 [2024-02-22; online 2024-02-07]

No link between type I interferon autoantibody positivity and adverse reactions to COVID-19 vaccines.

Yalcinkaya A, Cavalli M, Cederholm A, ..., Wadelius M, Landegren N

NPJ Vaccines 9 (1) 42 [2024-02-22; online 2024-02-22]

The effect of nitrogen source and levels on hybrid aspen tree physiology and wood formation.

Renström A, Choudhary S, Gandla ML, ..., Jämtgård S, Tuominen H

Physiol Plantarum 176 (1) e14219 [2024-02-21; online 2024-02-21]

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Spatial Neurolipidomics at the Single Amyloid-β Plaque Level in Postmortem Human Alzheimer's Disease Brain.

Michno W, Bowman A, Jha D, ..., Heeren RMA, Hanrieder J

ACS Chem Neurosci 15 (4) 877-888 [2024-02-21; online 2024-02-01]

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Omega-3 and -6 Fatty Acids Alter the Membrane Lipid Composition and Vesicle Size to Regulate Exocytosis and Storage of Catecholamines.

Gu C, Philipsen MH, Ewing AG

ACS Chem Neurosci 15 (4) 816-826 [2024-02-21; online 2024-02-12]

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Inhibition of Insulin-Regulated Aminopeptidase by Imidazo [1,5-α]pyridines-Synthesis and Evaluation.

Engen K, Lundbäck T, Yadav A, ..., Hallberg M, Larhed M

Int J Mol Sci 25 (5) - [2024-02-21; online 2024-02-21]

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Diversity in genetic risk of recurrent stroke: a genome-wide association study meta-analysis

Aldridge CM, Armstrong ND, Sunmonu NA, ..., Irvin MR, Worrall BB

Front. Stroke 3 (-) - [2024-02-21; online 2024-02-21]

Clonally heritable gene expression imparts a layer of diversity within cell types.

Mold JE, Weissman MH, Ratz M, ..., Michaëlsson J, Frisén J

Cell Syst 15 (2) 149-165.e10 [2024-02-21; online 2024-02-09]

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Differential gene expression in two consecutive pregnancies between same sex siblings and implications on maternal constraint.

Kallak TK, Serapio S, Visser N, ..., Skalkidou A, Ahlsson F

Sci Rep 14 (1) 4210 [2024-02-20; online 2024-02-20]

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Ancient reindeer mitogenomes reveal island-hopping colonisation of the Arctic archipelagos.

Hold K, Lord E, Brealey JC, ..., Martin MD, Dussex N

Sci Rep 14 (1) 4143 [2024-02-20; online 2024-02-20]

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Lymphocytic colitis can be transcriptionally divided into channelopathic and inflammatory lymphocytic colitis.

Bhardwaj A, Münch A, Montague J, ..., Rosenstiel P, Escudero-Hernández C

United European Gastroenterol J - (-) - [2024-02-17; online 2024-02-17]

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Targeting the Main Protease (Mpro, nsp5) by Growth of Fragment Scaffolds Exploiting Structure-Based Methodologies.

Altincekic N, Jores N, Löhr F, ..., Sreeramulu S, Schwalbe H

ACS Chem. Biol. 19 (2) 563-574 [2024-02-16; online 2024-01-17]

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Long noncoding RNA plasmacytoma variant translocation 1 is overexpressed in cutaneous squamous cell carcinoma and exon 2 is critical for its oncogenicity.

Li C, Sun C, Mahapatra KD, ..., Sonkoly E, Pivarcsi A

Br J Dermatol 190 (3) 415-426 [2024-02-16; online 2023-11-06]

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Identification and evaluation of small-molecule inhibitors against the dNTPase SAMHD1 via a comprehensive screening funnel.

Zhang SM, Paulin CBJ, Shu H, ..., Helleday T, Rudd SG

iScience 27 (2) 108907 [2024-02-16; online 2024-01-13]

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Sustained looking at faces at 5 months of age is associated with socio-communicative skills in the second year of life.

Viktorsson C, Portugal AM, Taylor MJ, Ronald A, Falck-Ytter T

Infancy 29 (3) 459-478 [2024-02-15; online 2024-02-15]

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Gene co-expression network analysis reveal core responsive genes in Parascaris univalens tissues following ivermectin exposure.

Dube F, Delhomme N, Martin F, ..., Svärd S, Tydén E

PLoS ONE 19 (2) e0298039 [2024-02-15; online 2024-02-15]

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Genetic and environmental contributions to gaze lateralization across social and non-social stimuli in human infants.

Viktorsson C, Portugal AM, Falck-Ytter T

Sci Rep 14 (1) 3668 [2024-02-14; online 2024-02-14]

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Molecular basis for human aquaporin inhibition.

Huang P, Åbacka H, Wilson CJ, ..., Venskutonytė R, Lindkvist-Petersson K

Proc. Natl. Acad. Sci. U.S.A. 121 (7) e2319682121 [2024-02-13; online 2024-02-06]

Disability and emotional symptoms in women with lipedema: A comparison with overweight/obese women.

Chachaj A, Jeziorek M, Dudka I, ..., Kujawa K, Szuba A

Adv Clin Exp Med - (-) - [2024-02-13; online 2024-02-13]

AIRR-C IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes.

Collins AM, Ohlin M, Corcoran M, ..., Watson CT, Lees WD

Front Immunol 14 (-) 1330153 [2024-02-09; online 2024-02-09]

Exploring the Dispersion and Electrostatic Components in Arene-Arene Interactions between Ligands and G4 DNA to Develop G4-Ligands.

Andreasson M, Donzel M, Abrahamsson A, ..., Wanrooij S, Chorell E

J. Med. Chem. 67 (3) 2202-2219 [2024-02-08; online 2024-01-19]

Colony phase variation switch modulates antimicrobial tolerance and biofilm formation in Acinetobacter baumannii.

Mushtaq F, Nadeem A, Yabrag A, ..., Uhlin BE, Ahmad I

Microbiol Spectr 12 (2) e0295623 [2024-02-06; online 2024-01-11]

A macrophage-collagen fragment axis mediates subcutaneous adipose tissue remodeling in mice.

Vujičić M, Broderick I, Salmantabar P, ..., Sihlbom Wallem C, Wernstedt Asterholm I

Proc. Natl. Acad. Sci. U.S.A. 121 (6) e2313185121 [2024-02-06; online 2024-02-01]

Glycoproteomics and MS Proteomics [Collaborative]

Nigral transcriptomic profiles in Engrailed-1 hemizygous mouse models of Parkinson's disease reveal upregulation of oxidative phosphorylation-related genes associated with delayed dopaminergic neurodegeneration.

Belfiori LF, Dueñas Rey A, Ralbovszki DM, ..., Brolin KA, Swanberg M

Front Aging Neurosci 16 (-) 1337365 [2024-02-05; online 2024-02-05]

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N-(Heteroaryl)thiophene sulfonamides as angiotensin AT2 receptor ligands.

Wannberg J, Gising J, Henriksson M, ..., Hallberg M, Larhed M

Eur J Med Chem 265 (-) 116122 [2024-02-05; online 2024-01-03]

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Phylogeography and phenotypic wing shape variation in a damselfly across populations in Europe.

Yildirim Y, Kristensson D, Outomuro D, ..., Sniegula S, Johansson F

BMC Ecol Evol 24 (1) 19 [2024-02-03; online 2024-02-03]

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Asymmetric nucleosome PARylation at DNA breaks mediates directional nucleosome sliding by ALC1.

Bacic L, Gaullier G, Mohapatra J, ..., Sabantsev A, Deindl S

Nat Commun 15 (1) 1000 [2024-02-02; online 2024-02-02]

Xist ribonucleoproteins promote female sex-biased autoimmunity.

Dou DR, Zhao Y, Belk JA, ..., Utz PJ, Chang HY

Cell 187 (3) 733-749.e16 [2024-02-01; online 2024-02-03]

Reagentless impedimetric immunosensor for monitoring of methotrexate in human blood serum using multiwalled carbon nanotube@polypyrrole/polytyramine film electrode.

Adeniyi KO, Osmanaj B, Manavalan G, ..., Berisha A, Tesfalidet S

Talanta 268 (Pt 1) 125316 [2024-02-01; online 2023-10-16]

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Kahsay A, Dennhag N, Liu JX, ..., von Hofsten J, Pedrosa Domellöf F

Invest Ophthalmol Vis Sci 65 (2) 19 [2024-02-01; online 2024-02-09]

A Chromosome-Level Genome Assembly and Annotation for the Clouded Apollo Butterfly (Parnassius mnemosyne): A Species of Global Conservation Concern.

Höglund J, Dias G, Olsen RA, ..., Talla V, Backström N

Genome Biol Evol 16 (2) - [2024-02-01; online 2024-02-18]

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Vaginal candida infection is associated with host molecular signatures of neutrophil activation in the adjacent ectocervical mucosa in Kenyan sex workers

Hasselrot T, Boger MF, Kaldhusdal V, ..., Czarnewski P, Broliden K

American J Rep Immunol 91 (2) - [2024-02-00; online 2024-01-31]

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The cryo-EM structure of the BoNT/Wo-NTNH complex reveals two immunoglobulin-like domains.

Košenina S, Škerlová J, Zhang S, Dong M, Stenmark P

FEBS J. 291 (4) 676-689 [2024-02-00; online 2023-09-29]

Recent increase in species-wide diversity after interspecies introgression in the highly endangered Iberian lynx.

Lucena-Perez M, Paijmans JLA, Nocete F, ..., Barlow A, Godoy JA

Nat Ecol Evol 8 (2) 282-292 [2024-02-00; online 2024-01-15]

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Proteomic profiling of tumour tissue-derived extracellular vesicles in colon cancer.

Cvjetkovic A, Karimi N, Crescitelli R, ..., Lässer C, Lötvall J

J Extracell Biol 3 (2) e127 [2024-02-00; online 2024-02-06]

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Playing with Protic Additives to Improve the Outcome of Rhodium‐Catalyzed Hydroarylation of Fullerene C60 with Arylboronic Acids

Ergun Dönmez M, Eriksson M, Hulu G, Nordström M, Grennberg H

Helvetica Chimica Acta 107 (2) - [2024-02-00; online 2024-01-16]

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Multimodal Single-Cell Sequencing of B Cells in Primary Sjögren's Syndrome.

Arvidsson G, Czarnewski P, Johansson A, ..., Nordmark G, Syvänen A

Arthritis & rheumatology (Hoboken, N.J.) 76 (2) 255-267 [2024-02-00; online 2023-12-18]

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MiCId GUI: The Graphical User Interface for MiCId, a Fast Microorganism Classification and Identification Workflow with Accurate Statistics and High Recall.

Ogurtsov A, Alves G, Rubio A, ..., Moore ERB, Yu YK

J Comput Biol 31 (2) 175-178 [2024-02-00; online 2024-02-02]

Intrinsic deletion at 10q23.31, including the PTEN gene locus, is aggravated upon CRISPR-Cas9-mediated genome engineering in HAP1 cells mimicking cancer profiles.

Geng K, Merino LG, Veiga RG, ..., Brinkman EK, Kutter C

Life Sci. Alliance 7 (2) - [2024-02-00; online 2023-11-20]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Genetic diversity patterns in farmed rainbow trout (Oncorhynchus mykiss) populations using genome-wide SNP and haplotype data.

Longo A, Kurta K, Vanhala T, ..., de Koning DJ, Palaiokostas C

Anim Genet 55 (1) 87-98 [2024-02-00; online 2023-11-23]

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

Fine-scale genetic structure in the orchid Gymnadenia conopsea is not associated with local density of flowering plants.

Sletvold N, Joffard N, Söderquist L

Am. J. Bot. 111 (2) e16273 [2024-02-00; online 2024-01-30]

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

Complex In Vitro Model Characterization for Context of Use in Toxicologic Pathology: Use Cases by Collaborative Teams of Biologists, Bioengineers, and Pathologists.

Stokar-Regenscheit N, Bell L, Berridge B, ..., Sura R, Tomlinson L

Toxicol Pathol 52 (2-3) 123-137 [2024-02-00; online 2024-06-18]

Spatial Proteomics [Service]

Community-developed checklists for publishing images and image analyses.

Schmied C, Nelson MS, Avilov S, ..., Tischer C, Jambor HK

Nat. Methods 21 (2) 170-181 [2024-02-00; online 2023-09-14]

Integrated Microscopy Technologies Gothenburg [Service]

CPAP may promote an endothelial inflammatory milieu in sleep apnoea after coronary revascularization

Peker Y, Celik Y, Behboudi A, ..., Gottlieb DJ, Jelic S

EBioMedicine - (-) 105015 [2024-02-00; online 2024-02-00]

A survey of ficolin-3 activity in Systemic Lupus Erythematosus reveals a link to hematological disease manifestations and autoantibody profile.

Lindelöf L, Rantapää-Dahlqvist S, Lundtoft C, ..., Svenungsson E, Eriksson O

J. Autoimmun. 143 (-) 103166 [2024-02-00; online 2024-01-13]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

A cholesterol switch controls phospholipid scrambling by G protein-coupled receptors.

Menon I, Sych T, Son Y, ..., Levitz J, Menon AK

J. Biol. Chem. 300 (2) 105649 [2024-02-00; online 2024-01-16]

Integrated Microscopy Technologies Stockholm [Service]

Discovery of lipid binding sites in a ligand-gated ion channel by integrating simulations and cryo-EM

Bergh C, Rovšnik U, Howard R, Lindahl E

Elife 12 (-) - [2024-01-30; online 2024-01-30]

Batrachochytrium dendrobatidis strain affects transcriptomic response in liver but not skin in latitudinal populations of the common toad (Bufo bufo).

Chondrelli N, Kuehn E, Meurling S, ..., Laurila A, Höglund J

Sci Rep 14 (1) 2495 [2024-01-30; online 2024-01-30]

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

A two-step activation mechanism enables mast cells to differentiate their response between extracellular and invasive enterobacterial infection.

von Beek C, Fahlgren A, Geiser P, ..., Pejler G, Sellin ME

Nat Commun 15 (1) 904 [2024-01-30; online 2024-01-30]

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

Single-cell RNA-seq mapping of chicken peripheral blood leukocytes.

Maxwell M, Söderlund R, Härtle S, Wattrang E

BMC Genomics 25 (1) 124 [2024-01-29; online 2024-01-29]

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

Spatial Transcriptomics in a Case of Follicular Thyroid Carcinoma Reveals Clone-Specific Dysregulation of Genes Regulating Extracellular Matrix in the Invading Front.

Condello V, Paulsson JO, Zedenius J, Näsman A, Juhlin CC

Endocr. Pathol. - (-) - [2024-01-27; online 2024-01-27]

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

High-parametric protein maps reveal the spatial organization in early-developing human lung

Sariyar S, Sountoulidis A, Hansen JN, ..., Lundberg E, Ayoglu B

- - (-) - [2024-01-25; online 2024-01-25]

Spatial Proteomics [Service]

Whole-genome sequencing in prenatally detected congenital malformations: prospective cohort study in clinical setting.

Westenius E, Conner P, Pettersson M, ..., Lindstrand A, Iwarsson E

Ultrasound Obstet Gynecol - (-) - [2024-01-24; online 2024-01-24]

Genetic diversity and recent ancestry based on whole-genome sequencing of endangered Swedish cattle breeds.

Harish A, Lopes Pinto FA, Eriksson S, Johansson AM

BMC Genomics 25 (1) 89 [2024-01-22; online 2024-01-22]

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

Three immunizations with Novavax's protein vaccines increase antibody breadth and provide durable protection from SARS-CoV-2.

Lenart K, Arcoverde Cerveira R, Hellgren F, ..., Smith G, Loré K

NPJ Vaccines 9 (1) 17 [2024-01-20; online 2024-01-20]

Towards high-throughput parallel imaging and single-cell transcriptomics of microbial eukaryotic plankton.

Grujčić V, Saarenpää S, Sundh J, ..., Foster RA, Andersson AF

PLoS ONE 19 (1) e0296672 [2024-01-19; online 2024-01-19]

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]

Remodeling of the human skeletal muscle proteome found after long-term endurance training but not after strength training.

Emanuelsson EB, Arif M, Reitzner SM, ..., Sundberg CJ, Chapman MA

iScience 27 (1) 108638 [2024-01-19; online 2023-12-05]

Global Proteomics and Proteogenomics [Service]

Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals.

Kırdök E, Kashuba N, Damlien H, ..., Aravena A, Götherström A

Sci Rep 13 (1) 22125 [2024-01-18; online 2024-01-18]

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

Ciliate Grazing on the Bloom-Forming Microalga Gonyostomum semen.

Bergman I, Lindström ES, Sassenhagen I

Microb. Ecol. 87 (1) 33 [2024-01-18; online 2024-01-18]

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

High-throughput analysis of membrane fluidity unveils a hidden dimension in immune cell states

Andronico LA, Jiang Y, Carannante V, ..., Brodin P, Sezgin E

- - (-) - [2024-01-16; online 2024-01-16]

Integrated Microscopy Technologies Stockholm [Service]

Erythroid Differentiation Enhances RNA Mis-Splicing in SF3B1-Mutant Myelodysplastic Syndromes with Ring Sideroblasts.

Moura PL, Mortera-Blanco T, Hofman IJ, ..., Jacobsen SEW, Hellström-Lindberg E

Cancer Res. 84 (2) 211-225 [2024-01-16; online 2023-11-03]

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

Ultralight Ultrafast Enzymes.

Zhang X, Meng Z, Beusch CM, ..., Gaetani M, Zubarev RA

Angew. Chem. Int. Ed. Engl. 63 (3) e202316488 [2024-01-15; online 2023-12-07]

Apoptosis-mediated ADAM10 activation removes a mucin barrier promoting T cell efferocytosis.

Drexhage LZ, Zhang S, Dupont M, ..., Karaji N, Sattentau QJ

Nat Commun 15 (1) 541 [2024-01-15; online 2024-01-15]

Integrated Microscopy Technologies Stockholm [Service]

Profiling of Surface Protein Epitopes on Viral Particles by Multiplex Dual-Reporter Strategy

Sahi M, Andersson S, Mattson C, ..., Chiodi F, Fredolini C

J Vis Exp - (203) - [2024-01-12; online 2024-01-12]

Affinity Proteomics Stockholm [Technology development]

Furan Distribution as a Severity Indicator upon Organosolv Fractionation of Hardwood Sawdust through a Novel Ternary Solvent System

Thoresen PP, Delgado Vellosillo I, Lange H, ..., Christakopoulos P, Matsakas L

ACS Sustainable Chem. Eng. - (-) - [2024-01-12; online 2024-01-12]

Differential expression and alternative splicing analyses of multiple tissues reveal albinism-associated genes in the Wels catfish (Silurus glanis).

Ozerov MY, Noreikiene K, Kahar S, ..., Gross R, Vasemägi A

Comp Biochem Physiol B Biochem Mol Biol 271 (-) 110941 [2024-01-11; online 2024-01-11]

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

Identification of circulating autoantibodies to non-modified proteins associated with ACPA status in early rheumatoid arthritis.

Lourido L, Joshua V, Hansson M, ..., Klareskog L, Blanco FJ

Rheumatology (Oxford) - (-) - [2024-01-09; online 2024-01-09]

Autoimmunity and Serology Profiling [Collaborative]

Single-cell genomics of a bloom-forming phytoplankton species reveals population genetic structure across continents.

Gollnisch R, Ahrén D, Rengefors K

ISME J 18 (1) - [2024-01-08; online 2024-03-15]

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

Separating phases of allopolyploid evolution with resynthesized and natural Capsella bursa-pastoris.

Duan T, Sicard A, Glémin S, Lascoux M

Elife 12 (-) - [2024-01-08; online 2024-01-08]

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

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 [2024-01-08; online 2024-01-10]

Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

Climate acts as an environmental filter to plant pathogens.

Caballol M, Redondo MÁ, Catalán N, ..., Stenlid J, Oliva J

ISME J 18 (1) - [2024-01-08; online 2024-02-17]

NGI Long read [Service] NGI Uppsala (Uppsala Genome Center) [Service] National Genomics Infrastructure [Service]

A pan-genomic approach reveals novel Sulfurimonas clade in the ferruginous meromictic Lake Pavin.

Biderre-Petit C, Courtine D, Hennequin C, ..., Divne A, Hochart C

Mol Ecol Resour - (-) e13923 [2024-01-08; online 2024-01-08]

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

Antimicrobial Activity of Two Different Types of Silver Nanoparticles against Wide Range of Pathogenic Bacteria.

Holubnycha V, Husak Y, Korniienko V, ..., Ramanavicius A, Pogorielov M

Nanomaterials (Basel) 14 (2) - [2024-01-07; online 2024-01-07]

WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows.

Bouyssié D, Altıner P, Capella-Gutierrez S, ..., Winkelhardt D, Schwämmle V

J. Proteome Res. 23 (1) 418-429 [2024-01-05; online 2023-12-01]

Bioinformatics Support, Infrastructure and Training [Technology development]

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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Nuclear Hsp104 safeguards the dormant translation machinery during quiescence.

Kohler V, Kohler A, Berglund LL, ..., Andréasson C, Büttner S

Nat Commun 15 (1) 315 [2024-01-05; online 2024-01-05]

Global Proteomics and Proteogenomics [Service]

METTL3 drives telomere targeting of TERRA lncRNA through m6A-dependent R-loop formation: a therapeutic target for ALT-positive neuroblastoma.

Vaid R, Thombare K, Mendez A, ..., Fischer M, Mondal T

Nucleic Acids Res. - (-) - [2024-01-05; online 2024-01-05]

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

Humoral immune responses to the monovalent XBB.1.5-adapted BNT162b2 mRNA booster in Sweden.

Marking U, Bladh O, Aguilera K, ..., Sheward DJ, Thålin C

Lancet Infect Dis - (-) - [2024-01-05; online 2024-01-05]

Affinity Proteomics Uppsala [Collaborative]

Secretome Analyses Identify FKBP4 as a GBA1-Associated Protein in CSF and iPS Cells from Parkinson's Disease Patients with GBA1 Mutations.

Kojima R, Paslawski W, Lyu G, ..., Zhang X, Svenningsson P

Int J Mol Sci 25 (1) - [2024-01-04; online 2024-01-04]

METTL17 is an Fe-S cluster checkpoint for mitochondrial translation.

Ast T, Itoh Y, Sadre S, ..., Amunts A, Mootha VK

Mol. Cell - (-) - [2024-01-04; online 2024-01-04]

Exonic trinucleotide repeat expansions in ZFHX3 cause spinocerebellar ataxia type 4: A poly-glycine disease.

Wallenius J, Kafantari E, Jhaveri E, ..., Ehrencrona H, Puschmann A

Am. J. Hum. Genet. 111 (1) 82-95 [2024-01-04; online 2023-11-29]

NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

Elevated circulating adiponectin levels do not prevent anxiety-like behavior in a PCOS-like mouse model.

Samad M, Ek J, Börchers S, ..., Asterholm IW, Benrick A

Sci Rep 14 (1) 563 [2024-01-04; online 2024-01-04]

Glycoproteomics and MS Proteomics [Service]

Mutation of the cyclooxygenase 2 gene promoter and anastomotic leakage in colorectal cancer patients: retrospective cohort study.

Grahn O, Holmgren K, Hong MG, Sund M, Rutegård M

BJS Open 8 (1) - [2024-01-03; online 2024-01-30]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative]

Identification of a Notch transcriptomic signature for breast cancer.

Braune EB, Geist F, Tang X, ..., Wienke D, Lendahl U

Breast Cancer Res. 26 (1) 4 [2024-01-03; online 2024-01-03]

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

Tissue-specific RNA Polymerase II promoter-proximal pause release and burst kinetics in a Drosophila embryonic patterning network.

Hunt G, Vaid R, Pirogov S, ..., Reimegård J, Mannervik M

Genome Biol. 25 (1) 2 [2024-01-02; online 2024-01-02]

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Functional annotation of a divergent genome using sequence and structure-based similarity.

Svedberg D, Winiger RR, Berg A, ..., Vossbrinck CR, Barandun J

BMC Genomics 25 (1) 6 [2024-01-02; online 2024-01-02]

Bioinformatics Support, Infrastructure and Training [Service] NGI Long read [Collaborative] NGI Uppsala (Uppsala Genome Center) [Collaborative] National Genomics Infrastructure [Collaborative]

A comprehensive dataset on spatiotemporal variation of microbial plankton communities in the Baltic Sea.

Latz MAC, Andersson A, Brugel S, ..., Torstensson A, Andersson AF

Sci Data 11 (1) 18 [2024-01-02; online 2024-01-02]

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Metastasis and recurrence patterns in the molecular subtypes of urothelial bladder cancer.

Sjödahl G, Eriksson P, Holmsten K, ..., Ullén A, Liedberg F

Int. J. Cancer 154 (1) 180-190 [2024-01-01; online 2023-09-06]

Global Transcriptome Analysis Reveals Distinct Phases of the Endothelial Response to TNF.

Struck EC, Belova T, Hsieh PH, ..., Dusart PJ, Butler LM

J. Immunol. 212 (1) 117-129 [2024-01-01; online 2023-11-29]

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

Astrocytic Regulation of Endocannabinoid-Dependent Synaptic Plasticity in the Dorsolateral Striatum.

Adermark L, Stomberg R, Söderpalm B, Ericson M

Int J Mol Sci 25 (1) - [2024-01-01; online 2024-01-01]

Integrated Microscopy Technologies Gothenburg [Service]

A biobased binder of carboxymethyl cellulose, citric acid, chitosan and wheat gluten for nonwoven and paper.

Wennman M, Pinon AC, Svagan AJ, Hellberg M, Hedenqvist MS

Carbohydr Polym 323 (-) 121430 [2024-01-01; online 2023-09-23]

pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections.

Sánchez-Busó L, Sánchez-Serrano A, Golparian D, Unemo M

Microb Genom 10 (1) - [2024-01-00; online 2024-01-30]

Whole-genome selective sweep analyses identifies the region and candidate gene associated with white earlobe color in Mediterranean chickens.

Guo Y, Rubin CJ, Rönneburg T, ..., Hu X, Carlborg Ö

Poult. Sci. 103 (1) 103232 [2024-01-00; online 2023-10-24]

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

The functional role of CST1 and CCL26 in asthma development.

Hoyer A, Chakraborty S, Lilienthal I, ..., Katayama S, Söderhäll C

Immun Inflamm Dis 12 (1) e1162 [2024-01-00; online 2024-01-25]

Affinity Proteomics Stockholm [Service] Bioinformatics Support and Infrastructure [Service] Bioinformatics Support, Infrastructure and Training [Service]

Substance P, NPY, CCK and their receptors in five brain regions in major depressive disorder with transcriptomic analysis of locus coeruleus neurons.

Barde S, Aguila J, Zhong W, ..., Hedlund E, Hökfelt T

Eur Neuropsychopharmacol 78 (-) 54-63 [2024-01-00; online 2023-11-04]

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

Population genomics of the muskox' resilience in the near absence of genetic variation.

Pečnerová P, Lord E, Garcia-Erill G, ..., Moltke I, Siegismund HR

Mol. Ecol. 33 (2) e17205 [2024-01-00; online 2023-11-16]

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Phylogenomics and topological conflicts in the tribe Anthospermeae (Rubiaceae).

Thureborn O, Wikström N, Razafimandimbison SG, Rydin C

Ecol Evol 14 (1) e10868 [2024-01-00; online 2024-01-25]

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

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]

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

New indicators for monitoring genetic diversity applied to alpine brown trout populations using whole genome sequence data.

Kurland S, Saha A, Keehnen N, ..., Ryman N, Laikre L

Mol. Ecol. 33 (2) e17213 [2024-01-00; online 2023-11-28]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Multiplexed experimental strategies for fragment library screening against challenging drug targets using SPR biosensors.

FitzGerald EA, Vagrys D, Opassi G, ..., de Esch IJP, Danielson UH

SLAS DISCOVERY: Advancing Life Sciences R&D 29 (1) 40-51 [2024-01-00; online 2023-09-14]

Chemical Biology Consortium Sweden (CBCS) [Service] Drug Discovery and Development (DDD) [Service]

Molecular blueprints for spinal circuit modules controlling locomotor speed in zebrafish.

Pallucchi I, Bertuzzi M, Madrid D, ..., Higashijima SI, El Manira A

Nat. Neurosci. 27 (1) 78-89 [2024-01-00; online 2023-11-02]

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

Heat inactivation of foetal bovine serum performed after EV-depletion influences the proteome of cell-derived extracellular vesicles.

Urzì O, Bergqvist M, Lässer C, ..., Olofsson Bagge R, Crescitelli R

J Extracell Vesicles 13 (1) e12408 [2024-01-00; online 2024-01-24]

Integrated Microscopy Technologies Gothenburg [Service]

Effects of Wholegrain Compared to Refined Grain Intake on Cardiometabolic Risk Markers, Gut Microbiota, and Gastrointestinal Symptoms in Children: A Randomized Crossover Trial.

Madsen MTB, Landberg R, Nielsen DS, ..., Lauritzen L, Damsgaard CT

Am. J. Clin. Nutr. 119 (1) 18-28 [2024-01-00; online 2023-10-28]

Chalmers Mass Spectrometry Infrastructure [Collaborative]

Distinct molecular targets of ProEGCG from EGCG and superior inhibition of angiogenesis signaling pathways for treatment of endometriosis.

Hung SW, Gaetani M, Li Y, ..., Zubarev RA, Wang CC

J Pharm Anal 14 (1) 100-114 [2024-01-00; online 2023-09-11]

DNA metabarcoding reveals spatial and temporal variation of fish eye fluke communities in lake ecosystems.

Diaz-Suarez A, Noreikiene K, Kahar S, ..., Kisand V, Vasemägi A

Int J Parasitol 54 (1) 33-46 [2024-01-00; online 2023-08-24]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

Birth Weight, Childhood and Young Adult Overweight, and the Risk of Coronary Heart Disease in Men.

Bramsved R, Bygdell M, Martikainen J, ..., Ohlsson C, Kindblom JM

Arterioscler. Thromb. Vasc. Biol. 44 (1) 314-321 [2024-01-00; online 2023-11-16]

Visualizing the Microbial N Uptake During Arctic Extreme Winter Warming Events Using Nanosims

Rasmussen LH, Danielsen BK, Elberling B, ..., Micaroni M, Andresen LC

- - (-) - [2024-00-00; online 2024-00-00]

Integrated Microscopy Technologies Gothenburg [Service]

Strategies for Multimodal Image Data Transformation to a Common Format for Cloud Integration and Visualization

Camacho R, Berndtsson J, Micaroni M, Zhang K, Fernandez-Rodriguez J

BIO Web Conf. 129 (-) 13019 [2024-00-00; online 2024-10-17]

Integrated Microscopy Technologies Gothenburg [Service]

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]

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

Landscape of Epstein-Barr virus gene expression and perturbations in cancer

K. W. Tang YTGXABIHDVea

Res Sq - (-) - [2024-00-00]

Ionic liquid strategy for chitosan production from chitin and molecular insights

Dinh VM, Khokarale SG, May PO, ..., Irgum K, Mikkola JP

RSC Sustain. 2 (4) 1154-1164 [2024-00-00; online 2024-00-00]