Publications 2024

Male-transmitted transgenerational effects of the herbicide linuron on DNA methylation profiles in Xenopus tropicalis brain and testis.

Roza M, Eriksson ANM, Svanholm S, Berg C, Karlsson O

Sci. Total Environ. 923 (-) 170949 [2024-05-01; online 2024-02-15]

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

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]

Long-read sequencing and optical mapping generates near T2T assemblies that resolves a centromeric translocation.

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]

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

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]

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

Growth-regulated co-occupancy of Mediator and Lsm3 at intronic ribosomal protein genes.

Abdel-Fattah WR, Carlsson M, Hu GZ, ..., Ronne H, Björklund S

Nucleic Acids Res. - (-) - [2024-04-13; online 2024-04-13]

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

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]

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

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]

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

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]

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

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]

CRISPR Functional Genomics [Service]

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. - (-) - [2024-04-09; online 2024-04-09]

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

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]

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]

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

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]

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

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. - (-) - [2024-04-04; online 2024-04-04]

Clinical Genomics Stockholm [Collaborative]

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]

Affinity Proteomics Stockholm [Technology development]

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) - [2024-04-02; online 2024-04-02]

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]

Integrated Microscopy Technologies Stockholm [Technology development]

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]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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

MLL4 binds TET3.

Becht DC, Mohid SA, Lee JE, ..., Zhang Y, Kutateladze TG

Structure - (-) - [2024-03-27; online 2024-03-27]

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]

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

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) - [2024-03-20; online 2024-03-20]

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

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]

Swedish NMR Centre (SNC) [Collaborative]

Biochemical analysis of the endoribonuclease activity of the human mitochondrial topoisomerase 1

Bader CPJ, Kasho E, Forslund JME, Wessels M, Wanrooij PH

- - (-) - [2024-03-15; online 2024-03-15]

Chemical Biology Consortium Sweden (CBCS) [Service]

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]

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

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]

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

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. - (-) - [2024-03-08; online 2024-03-08]

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

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]

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

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]

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

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]

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

fhl2b mediates extraocular muscle protection in zebrafish models of muscular dystrophies and its ectopic expression ameliorates affected body muscles.

Dennhag N, Kahsay A, Nissen I, ..., von Hofsten J, Pedrosa Domellöf F

Nat Commun 15 (1) 1950 [2024-03-02; online 2024-03-02]

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

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]

Affinity Proteomics Stockholm [Collaborative]

Sorption of pharmaceuticals to foam and aerobic granular sludge with different morphologies

Burzio C, Mohammadi AS, Smith S, ..., Persson F, Wilén BM

Resources, Environment and Sustainability 15 (-) 100149 [2024-03-00; online 2024-03-00]

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

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]

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

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]

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

Genetic constraints in genes exhibiting splicing plasticity in facultative diapause.

Steward RA, Pruisscher P, Roberts KT, Wheat CW

Heredity (Edinb) 132 (3) 142-155 [2024-03-00; online 2024-01-30]

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

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]

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

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]

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

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]

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

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]

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

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]

Structural Proteomics [Service]

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]

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

Quantifying Fluorescence Lifetime Responsiveness of Environment-Sensitive Probes for Membrane Fluidity Measurements

Ragaller et al

J. Phys. Chem. B - (-) - [2024-02-28; online 2024-02-28] Open Access

Integrated Microscopy Technologies Stockholm [Technology development]

scCircle-seq unveils the diversity and complexity of extrachromosomal circular DNAs in single cells.

Chen JP, Diekmann C, Wu H, ..., Bienko M, Crosetto N

Nat Commun 15 (1) 1768 [2024-02-27; online 2024-02-27]

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

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]

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

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]

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

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]

NGI SNP genotyping [Service] NGI Short read [Service] National Genomics Infrastructure [Service]

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]

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

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]

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

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]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service] Swedish NMR Centre (SNC) [Collaborative]

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]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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]

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

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]

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

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]

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

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]

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

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]

Chemical Biology Consortium Sweden (CBCS) [Collaborative]

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]

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

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]

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

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]

Swedish NMR Centre (SNC) [Collaborative]

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]

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

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]

Cryo-EM [Service]

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]

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 [2024-02-01; online 2024-02-01]

Cryo-EM [Service]

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]

Bioinformatics Support and Infrastructure [Collaborative] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Other [Service] NGI Short read [Service] NGI Stockholm (Genomics Applications) [Collaborative] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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

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]

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]

Affinity Proteomics Stockholm [Service]

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]

Clinical Genomics Stockholm [Service]

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. - (-) - [2024-01-22; online 2024-01-22]

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

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]

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]

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]

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. - (-) - [2024-01-17; online 2024-01-17]

Chemical Biology Consortium Sweden (CBCS) [Service] Swedish NMR Centre (SNC) [Collaborative]

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]

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]

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 [2024-01-13; 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]

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]

Swedish NMR Centre (SNC) [Service]

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]

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 - (-) e0295623 [2024-01-11; online 2024-01-11]

Integrated Microscopy Technologies Umeå [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]

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]

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]

Bioinformatics Long-term Support WABI [Collaborative] Bioinformatics Support for Computational Resources [Service] Bioinformatics Support, Infrastructure and Training [Collaborative] NGI Short read [Service] NGI Uppsala (SNP&SEQ Technology Platform) [Service] National Genomics Infrastructure [Service]

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]

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]

Cryo-EM [Service]

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]

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

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]

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]

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

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]

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]

Swedish NMR Centre (SNC) [Collaborative]

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]

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]

Bioinformatics Support for Computational Resources [Service] NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] National Genomics Infrastructure [Service]

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]

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]

New chemical and microbial perspectives on vitamin B1 and vitamer dynamics of a coastal system.

Bittner MJ, Bannon CC, Rowland E, ..., Paerl RW, Riemann L

ISME COMMUN. 4 (1) ycad016 [2024-01-00; online 2024-01-10]

NGI Short read [Service] NGI Stockholm (Genomics Production) [Service] NGI Uppsala (SNP&SEQ Technology Platform) [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]

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]