Publications 2023

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212 publications

PubMed DOI Crossref
RNA Pol II Assembly Affects ncRNA Expression.
Garrido-Godino AI, Gupta I, Pelechano V, Navarro F
Int J Mol Sci 25 (1) - [2023-12-29; online 2023-12-29]
SciLifeLab Fellow Vicent Pelechano
PubMed DOI Crossref
Mapping of the gene network that regulates glycan clock of ageing.
Frkatović-Hodžić A, Mijakovac A, Miškec K, ..., Zoldoš V, Lauc G
Aging (Albany NY) 15 (24) 14509-14552 [2023-12-26; online 2023-12-26]
Clemens Wittenbecher DDLS Fellow
DOI Crossref
A community-curated, global atlas ofBacillus cereus sensu latogenomes for epidemiological surveillance
Ramnath V, Larralde M, Menchik P, ..., Henriksson J, Carroll LM
- - (-) - [2023-12-21; online 2023-12-21]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Undiscovered bird extinctions obscure the true magnitude of human-driven extinction waves.
Cooke R, Sayol F, Andermann T, ..., Antonelli A, Faurby S
Nat Commun 14 (1) 8116 [2023-12-19; online 2023-12-19]
DDLS Fellow Tobias Andermann
DOI Crossref
Modelling Pathogen Response of the Human Immune System in a Reduced State Space
Tajvar P, Forlin R, Brodin P, Dimarogonas DV
- - (-) 715-720 [2023-12-13; online 2023-12-13]
DDLS-WASP
PubMed DOI Crossref
Seeing the Membrane from Both Sides Now: Lipid Asymmetry and Its Strange Consequences.
Doktorova M, Levental I, Heberle FA
Cold Spring Harbor Perspectives in Biology 15 (12) - [2023-12-01; online 2023-12-01]
DDLS Fellow Milka Doktorova
PubMed DOI Crossref
Subtype-specific modulation of human KV 7 channels by the anticonvulsant cannabidiol through a lipid-exposed pore-domain site.
Pökl M, Sridhar A, Frampton DJA, ..., Delemotte L, Liin SI
Br J Pharmacol 180 (23) 2956-2972 [2023-12-00; online 2023-07-27]
Lucie Delemotte SciLifeLab Fellow
DOI Crossref
Improved multimer prediction using massive sampling with AlphaFold in CASP15
Wallner B
Proteins 91 (12) 1734-1746 [2023-12-00; online 2023-08-07]
DDLS-WASP
PubMed DOI Crossref
Nutritional control of bacterial DNA replication.
Hallgren J, Jonas K
Curr Opin Microbiol 77 (-) 102403 [2023-11-29; online 2023-11-29]
Kristina Jonas SciLifeLab Fellow
PubMed DOI Crossref
Gasdermin D is the only Gasdermin that provides protection against acute Salmonella gut infection in mice.
Fattinger SA, Maurer L, Geiser P, ..., Sellin ME, Hardt WD
Proc. Natl. Acad. Sci. U.S.A. 120 (48) e2315503120 [2023-11-28; online 2023-11-21]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Phosphate starvation decouples cell differentiation from DNA replication control in the dimorphic bacterium Caulobacter crescentus.
Hallgren J, Koonce K, Felletti M, ..., Turco E, Jonas K
PLoS Genet 19 (11) e1010882 [2023-11-27; online 2023-11-27]
Kristina Jonas SciLifeLab Fellow
PubMed DOI Crossref
Coevolution-Driven Method for Efficiently Simulating Conformational Changes in Proteins Reveals Molecular Details of Ligand Effects in the β2AR Receptor.
Mitrovic D, Chen Y, Marciniak A, Delemotte L
J Phys Chem B 127 (46) 9891-9904 [2023-11-23; online 2023-11-10]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
The heat shock protein LarA activates the Lon protease in response to proteotoxic stress.
Omnus DJ, Fink MJ, Kallazhi A, ..., Landreh M, Jonas K
Nat Commun 14 (1) 7636 [2023-11-22; online 2023-11-22]
Kristina Jonas SciLifeLab Fellow
DOI Crossref
A conserved ribosomal protein has entirely dissimilar structures in different organisms
Schierholz L, Brown CR, Helena-Bueno K, ..., Barandun J, Melnikov SV
Molecular Biology and Evolution - (-) - [2023-11-21; online 2023-11-21]
Jonas Barandun SciLifeLab Fellow
PubMed DOI Crossref
Spatial host-microbiome sequencing reveals niches in the mouse gut.
Lötstedt B, Stražar M, Xavier R, Regev A, Vickovic S
Nat. Biotechnol. - (-) - [2023-11-20; online 2023-11-20]
Sanja Vickovic SciLifeLab Fellow
PubMed DOI Crossref
Dual stop codon suppression in mammalian cells with genomically integrated genetic code expansion machinery.
Meineke B, Heimgärtner J, Caridha R, ..., Landreh M, Elsässer SJ
Cell Rep Methods 3 (11) 100626 [2023-11-20; online 2023-11-06]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
CCR5 promoter region polymorphisms in systemic lupus erythematosus.
Schauren JDS, de Oliveira AH, Consiglio CR, ..., Ellwanger JH, Chies JAB
Int J Immunogenet - (-) - [2023-11-20; online 2023-11-20]
Camila Consiglio DDLS Fellow
PubMed DOI Crossref
Multi-omics network analysis on samples from sequential biopsies reveals vital role of proliferation arrest for Macrosteatosis related graft failure in rats after liver transplantation.
Liu Z, Wang W, Li X, ..., Mardinoglu A, Zheng S
Genomics 115 (6) 110748 [2023-11-19; online 2023-11-19]
Adil Mardinoglu SciLifeLab Fellow
DOI Crossref
Genomic analyses elucidate the causes and consequences of breakdown of distyly inLinum trigynum
Gutiérrez-Valencia J, Zervakis PI, Postel Z, ..., Arroyo J, Slotte T
- - (-) - [2023-11-17; online 2023-11-17]
SciLifeLab Fellow Tanja Slotte
PubMed DOI Crossref
Synergistic stabilization of emulsion gel by nanoparticles and surfactant enables 3D printing of lipid-rich solid oral dosage forms.
Johannesson J, Pathare MM, Johansson M, Bergström CAS, Teleki A
J Colloid Interface Sci 650 (Pt B) 1253-1264 [2023-11-15; online 2023-07-10]
Alexandra Teleki SciLifeLab Fellow
PubMed DOI Crossref
Novel styryl-thiazole hybrids as potential anti-Alzheimer's agents.
Gouleni N, Di Rienzo A, Yılmaz A, ..., Vassiliou S, Cacciatore I
RSC Med Chem 14 (11) 2315-2326 [2023-11-15; online 2023-09-21]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Inhibition of CDK12 elevates cancer cell dependence on P-TEFb by stimulation of RNA polymerase II pause release.
Wang Z, Himanen SV, Haikala HM, ..., Vihervaara A, Barborič M
Nucleic Acids Res. 51 (20) 10970-10991 [2023-11-10; online 2023-10-09]
Anniina Vihervaara SciLifeLab Fellow
DOI Crossref
Core genes driving climate adaptation in plants
Yeaman S, Whiting J, Booker T, ..., Wright S, Zhou L
- - (-) - [2023-11-10; online 2023-11-10]
Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
Anticancer Potential of Novel Cinnamoyl Derivatives against U87MG and SHSY-5Y Cell Lines.
Gouleni N, Di Rienzo A, Oner S, ..., Vassiliou S, Cacciatore I
Anticancer Agents Med Chem - (-) - [2023-11-10; online 2023-11-10]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
NIPMAP: niche-phenotype mapping of multiplex histology data by community ecology.
El Marrahi A, Lipreri F, Kang Z, ..., Alber D, Hausser J
Nat Commun 14 (1) 7182 [2023-11-07; online 2023-11-07]
Jean Hausser SciLifeLab Fellow
PubMed DOI Crossref
Regulation of the general stress response sigma factor σT by Lon-mediated proteolysis.
Akar R, Fink MJ, Omnus DJ, Jonas K
J. Bacteriol. 205 (11) e0022823 [2023-11-06; online 2023-11-06]
Kristina Jonas SciLifeLab Fellow
PubMed DOI Crossref
PRO-IP-seq tracks molecular modifications of engaged Pol II complexes at nucleotide resolution.
Vihervaara A, Versluis P, Himanen SV, Lis JT
Nat Commun 14 (1) 7039 [2023-11-03; online 2023-11-03]
Anniina Vihervaara SciLifeLab Fellow
PubMed DOI Crossref
Between but Not Within-Species Variation in the Distribution of Fitness Effects.
James J, Kastally C, Budde KB, ..., Consortium G, ,
Mol. Biol. Evol. 40 (11) - [2023-11-03; online 2023-10-14]
DDLS Fellow Jennifer James Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
SRCAP mutations drive clonal hematopoiesis through epigenetic and DNA repair dysregulation.
Chen CW, Zhang L, Dutta R, ..., Sperling AS, Goodell MA
Cell Stem Cell 30 (11) 1503-1519.e8 [2023-11-02; online 2023-10-19]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes.
Tomaszkiewicz M, Sahlin K, Medvedev P, Makova KD
Genome Biol Evol 15 (11) - [2023-11-01; online 2023-11-15]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Open MoA: revealing the mechanism of action (MoA) based on network topology and hierarchy.
Liao X, Ozcan M, Shi M, ..., Mardinoglu A, Zhang C
Bioinformatics 39 (11) - [2023-11-01; online 2023-11-06]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Identification of nutritional biomarkers through highly sensitive and chemoselective metabolomics.
Lin W, Mellinghaus K, Rodriguez-Mateos A, Globisch D
Food Chem 425 (-) 136481 [2023-11-01; online 2023-06-01]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
Functional and molecular profiling of hematopoietic stem cells during regeneration.
Rydström A, Grahn THM, Niroula A, ..., Larsson J, Karlsson S
Exp. Hematol. 127 (-) 40-51 [2023-11-00; online 2023-09-04]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Artificial intelligence for natural product drug discovery.
Mullowney MW, Duncan KR, Elsayed SS, ..., Robinson SL, Medema MH
Nat Rev Drug Discov 22 (11) 895-916 [2023-11-00; online 2023-09-11]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
A comprehensive framework for detecting copy number variants from single nucleotide polymorphism data: 'rCNV', a versatile r package for paralogue and CNV detection.
Karunarathne P, Zhou Q, Schliep K, Milesi P
Mol Ecol Resour 23 (8) 1772-1789 [2023-11-00; online 2023-07-29]
Pascal Milesi SciLifeLab Fellow
DOI Crossref
aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow
Pochon Z, Bergfeldt N, Kırdök E, ..., Unneberg P, Oskolkov N
Genome Biol. 24 (1) - [2023-10-23; online 2023-10-23]
DDLS Fellow Tom van der Valk
PubMed DOI Crossref
Three-dimensional Co-culture Model for Live Imaging of Pancreatic Islets, Immune Cells, and Neurons in Agarose Gel.
Muntjewerff EM, Josyula VS, Christoffersson G
Bio Protoc 13 (20) e4852 [2023-10-20; online 2023-10-20]
Gustaf Christoffersson SciLifeLab Fellow
PubMed DOI Crossref
PACMan: A software package for automated single-cell chlorophyll fluorometry.
Pontén O, Xiao L, Kutter J, ..., Wählby C, Behrendt L
Cytometry A - (-) - [2023-10-20; online 2023-10-20]
Lars Behrendt SciLifeLab Fellow
PubMed DOI Crossref
Characterization of an in vitro steatosis model simulating activated de novo lipogenesis in MAFLD patients.
Kim W, Li M, Jin H, ..., Zhang C, Mardinoglu A
iScience 26 (10) 107727 [2023-10-20; online 2023-08-25]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Coinhibition of topoisomerase 1 and BRD4-mediated pause release selectively kills pancreatic cancer via readthrough transcription.
Cameron DP, Grosser J, Ladigan S, ..., Hahn SA, Baranello L
Sci Adv 9 (41) eadg5109 [2023-10-13; online 2023-10-13]
Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
Discovery and characterisation of quinazolines and 8-Azaquinazolines as NLRP3 agonists with oral bioavailability in mice.
O' Donovan DH, Baker D, Ciotta G, ..., Tang H, Valge-Archer V
Bioorg. Med. Chem. Lett. 96 (-) 129518 [2023-10-12; online 2023-10-12]
SciLifeLab Fellow Yumeng Mao
DOI Crossref
Recurrent hybridization and gene flow shaped Norway and Siberian spruce evolutionary history over multiple glacial cycles
Zhou Q, Karunarathne P, Andersson-Li L, ..., Lascoux M, Milesi P
- - (-) - [2023-10-06; online 2023-10-06]
Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
Functional imaging studies of acute administration of classic psychedelics, ketamine, and MDMA: Methodological limitations and convergent results.
Linguiti S, Vogel JW, Sydnor VJ, ..., Dworkin RH, Satterthwaite TD
Neurosci Biobehav Rev 154 (-) 105421 [2023-10-05; online 2023-10-05]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Long-Term Effects of Perinatal Exposure to a Glyphosate-Based Herbicide on Melatonin Levels and Oxidative Brain Damage in Adult Male Rats.
Cattani D, Pierozan P, Zamoner A, Brittebo E, Karlsson O
Antioxidants (Basel) 12 (10) - [2023-10-03; online 2023-10-03]
Oskar Karlsson SciLifeLab Fellow
PubMed DOI Crossref
Crosstalk between small-cell lung cancer cells and astrocytes mimics brain development to promote brain metastasis.
Qu F, Brough SC, Michno W, ..., Pasca AM, Sage J
Nat. Cell Biol. 25 (10) 1506-1519 [2023-10-00; online 2023-10-02]
SciLifeLab Fellow Wojciech Michno
PubMed DOI Crossref
Connectome-based modelling of neurodegenerative diseases: towards precision medicine and mechanistic insight.
Vogel JW, Corriveau-Lecavalier N, Franzmeier N, ..., Jones DT, Ewers M
Nat Rev Neurosci 24 (10) 620-639 [2023-10-00; online 2023-08-24]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Short tandem repeats bind transcription factors to tune eukaryotic gene expression.
Horton CA, Alexandari AM, Hayes MGB, ..., Kundaje A, Fordyce PM
Science (New York, N.Y.) 381 (6664) eadd1250 [2023-09-22; online 2023-09-22]
Emil Marklund SciLifeLab Fellow
PubMed DOI Crossref
Detection of transcriptome-wide microRNA-target interactions in single cells with agoTRIBE.
Sekar V, Mármol-Sánchez E, Kalogeropoulos P, ..., Biryukova I, Friedländer MR
Nat. Biotechnol. - (-) - [2023-09-21; online 2023-09-21]
Marc Friedländer SciLifeLab Fellow
PubMed DOI Crossref
Plasma metabolomic profiles associated with mortality and longevity in a prospective analysis of 13,512 individuals.
Wang F, Tessier AJ, Liang L, ..., Hu FB, Guasch-Ferré M
Nat Commun 14 (1) 5744 [2023-09-16; online 2023-09-16]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Genetic modification of inflammation- and clonal hematopoiesis-associated cardiovascular risk.
Yu Z, Fidler TP, Ruan Y, ..., Tall AR, Natarajan P
J. Clin. Invest. 133 (18) - [2023-09-15; online 2023-09-15]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Identification of essential genes associated with SARS-CoV-2 infection as potential drug target candidates with machine learning algorithms.
Taheri G, Habibi M
Sci Rep 13 (1) 15141 [2023-09-13; online 2023-09-13]
DDLS Fellow Golnaz Taheri
PubMed DOI Crossref
Systems-level temporal immune-metabolic profile in Crimean-Congo hemorrhagic fever virus infection.
Ambikan AT, Elaldi N, Svensson-Akusjärvi S, ..., Mirazimi A, Neogi U
Proc. Natl. Acad. Sci. U.S.A. 120 (37) e2304722120 [2023-09-12; online 2023-09-05]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
A novel kleptoplastidic symbiosis revealed in the marine centrohelid Meringosphaera with evidence of genetic integration.
Sørensen MES, Zlatogursky VV, Onuţ-Brännström I, ..., Foster RA, Burki F
Curr. Biol. 33 (17) 3571-3584.e6 [2023-09-11; online 2023-08-02]
Fabien Burki SciLifeLab Fellow
DOI Crossref
Estrogen receptor activation remodelsTEAD1gene expression to alleviate nonalcoholic fatty liver disease
Sommerauer C, Gallardo-Dodd CJ, Savva C, ..., Williams C, Kutter C
- - (-) - [2023-09-08; online 2023-09-08]
Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
Digital assay for rapid electronic quantification of clinical pathogens using DNA nanoballs.
Tayyab M, Barrett D, van Riel G, ..., Javanmard M, Pelechano V
Sci Adv 9 (36) eadi4997 [2023-09-08; online 2023-09-06]
SciLifeLab Fellow Vicent Pelechano
PubMed DOI Crossref
EGb 761 reduces Ca2+ influx and apoptosis after pentylenetetrazole treatment in a neuroblastoma cell line.
Ovey IS, Ozsimsek A, Velioglu HA, ..., Mardinoglu A, Yulug B
Front. Cell. Neurosci. 17 (-) 1195303 [2023-09-07; online 2023-09-07]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation.
Jin H, Zhang C, Zwahlen M, ..., Uhlén M, Mardinoglu A
Nat Commun 14 (1) 5417 [2023-09-05; online 2023-09-05]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Structure-based virtual screening discovers potent and selective adenosine A1 receptor antagonists.
Matricon P, Nguyen AT, Vo DD, ..., May LT, Carlsson J
Eur J Med Chem 257 (-) 115419 [2023-09-05; online 2023-05-01]
Jens Carlsson SciLifeLab Fellow
PubMed DOI Crossref
AFsample: improving multimer prediction with AlphaFold using massive sampling.
Wallner B
Bioinformatics 39 (9) - [2023-09-02; online 2023-09-15]
DDLS-WASP
PubMed DOI Crossref
Sex differences in distribution and identity of aromatase gene expressing cells in the young adult rat brain.
Immenschuh J, Thalhammer SB, Sundström-Poromaa I, ..., Dumas S, Comasco E
Biol Sex Differ 14 (1) 54 [2023-09-01; online 2023-09-01]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Vesicular glutamate transporter 2 expression in the ventral tegmental area of outbred male rats following exposure to nicotine and alcohol.
Vrettou M, Thalhammer SB, Svensson AL, ..., Nylander I, Comasco E
Drug Alcohol Depend Rep 8 (-) 100180 [2023-09-00; online 2023-07-13]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Real-life data of hypoglycemic events in children and adolescents with type 1 diabetes.
Hill H, Klaar P, Espes D
BMJ Open Diabetes Res Care 11 (5) - [2023-09-00; online 2023-09-23]
Daniel Espes SciLifeLab Fellow
PubMed DOI Crossref
Pubertal sexual development and endpoints for disrupted spermatogenesis in the model Xenopus tropicalis.
Svanholm S, Roza M, Marini D, ..., Karlsson O, Berg C
Reprod. Toxicol. 120 (-) 108435 [2023-09-00; online 2023-07-01]
Oskar Karlsson SciLifeLab Fellow
PubMed DOI Crossref
Infection with COVID-19 is no longer a public emergency: But what about degenerative dementia?
Yulug B, Ayyıldız B, Ayyıldız S, ..., Velioglu HA, Mardinoglu A
J Med Virol 95 (9) e29072 [2023-09-00; online 2023-09-19]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Development of microsatellite markers for sister species Linum suffruticosum and Linum tenuifolium in their overlapping ranges.
Olmedo-Vicente E, Désamoré A, Simón-Porcar VI, Slotte T, Arroyo J
Mol. Biol. Rep. 50 (9) 7927-7933 [2023-09-00; online 2023-07-17]
SciLifeLab Fellow Tanja Slotte
PubMed DOI Crossref
Tissue pleiotropic effect of biotin and prebiotic supplementation in established obesity.
Voland L, Yuan M, Lecoutre S, ..., Soula H, Clément K
Am. J. Physiol. Endocrinol. Metab. - (-) - [2023-08-30; online 2023-08-30]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells.
Gallardo-Dodd CJ, Oertlin C, Record J, ..., Ponomarev SA, Westerberg LS
Sci Adv 9 (34) eadg1610 [2023-08-25; online 2023-08-25]
Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
A Multi-Stain Breast Cancer Histological Whole-Slide-Image Data Set from Routine Diagnostics.
Weitz P, Valkonen M, Solorzano L, ..., Ruusuvuori P, Rantalainen M
Sci Data 10 (1) 562 [2023-08-24; online 2023-08-24]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
Immobilized Enzymes on Magnetic Beads for Separate Mass Spectrometric Investigation of Human Phase II Metabolite Classes.
Tsiara I, Riemer A, Correia MSP, Rodriguez-Mateos A, Globisch D
Anal. Chem. 95 (33) 12565-12571 [2023-08-22; online 2023-08-08]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
The acute effect of different NAD+ precursors included in the combined metabolic activators.
Li X, Yang H, Jin H, ..., Borén J, Mardinoglu A
Free Radic. Biol. Med. 205 (-) 77-89 [2023-08-20; online 2023-06-02]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Broadcasters, receivers, functional groups of metabolites and the link to heart failure progression using polygenic factors.
Yazdani A, Mendez-Giraldez R, Yazdani A, ..., Larson M, Elsea S
Res Sq - (-) - [2023-08-18; online 2023-08-18]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Association of the human gut microbiota with vascular stiffness.
Cuadrat RRC, Goris T, Birukov A, ..., Wittenbecher C, Schulze MB
Sci Rep 13 (1) 13348 [2023-08-16; online 2023-08-16]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Epithelial inflammasomes, gasdermins, and mucosal inflammation - Lessons from Salmonella and Shigella infected mice.
Gül E, Fattinger SA, Sellin ME, Hardt WD
Semin Immunol 70 (-) 101812 [2023-08-08; online 2023-08-08]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Altered gut microbiota community structure and correlated immune system changes in dibutyl phthalate exposed mice.
Almamoun R, Pierozan P, Manoharan L, Karlsson O
Ecotoxicology and Environmental Safety 262 (-) 115321 [2023-08-05; online 2023-08-05]
Oskar Karlsson SciLifeLab Fellow
PubMed DOI Crossref
Longitudinal metabolomics analysis reveals the acute effect of cysteine and NAC included in the combined metabolic activators.
Yang H, Li X, Jin H, ..., Borén J, Mardinoglu A
Free Radic. Biol. Med. 204 (-) 347-358 [2023-08-01; online 2023-05-26]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Umbilical cord-derived mesenchymal stromal cells preserve endogenous insulin production in type 1 diabetes: a Phase I/II randomised double-blind placebo-controlled trial.
Carlsson PO, Espes D, Sisay S, ..., Smith CIE, Svahn MG
Diabetologia 66 (8) 1431-1441 [2023-08-00; online 2023-05-24]
Daniel Espes SciLifeLab Fellow
PubMed DOI Crossref
Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs?
Bengtsson-Palme J, Abramova A, Berendonk TU, ..., Wester AL, Zahra R
Environ Int 178 (-) 108089 [2023-08-00; online 2023-07-05]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Historical RNA expression profiles from the extinct Tasmanian tiger.
Mármol-Sánchez E, Fromm B, Oskolkov N, ..., Dalén L, Friedländer MR
Genome Res 33 (8) 1299-1316 [2023-08-00; online 2023-07-18]
Marc Friedländer SciLifeLab Fellow
PubMed DOI Crossref
A global baseline for qPCR-determined antimicrobial resistance gene prevalence across environments.
Abramova A, Berendonk TU, Bengtsson-Palme J
Environ Int 178 (-) 108084 [2023-08-00; online 2023-07-03]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Cell Membranes Sustain Phospholipid Imbalance Via Cholesterol Asymmetry
Doktorova M, Symons JL, Zhang X, ..., Levental KR, Levental I
- - (-) - [2023-07-31; online 2023-07-31]
DDLS Fellow Milka Doktorova
DOI Crossref
A new codon adaptation metric predicts vertebrate body size and tendency to protein disorder
Weibel CA, Wheeler AL, James JE, Willis SM, Masel J
- - (-) - [2023-07-26; online 2023-07-26]
DDLS Fellow Jennifer James
PubMed DOI Crossref
Naltrexone blocks alcohol-induced effects on kappa-opioid receptors in the plasma membrane.
Terenius L, Oasa S, Sezgin E, ..., Martin-Fardon R, Vukojevic V
Res Sq - (-) - [2023-07-21; online 2023-07-21]
Erdinc Sezgin SciLifeLab Fellow
PubMed DOI Crossref
Genus-wide genomic characterization of Macrococcus: insights into evolution, population structure, and functional potential.
Carroll LM, Pierneef R, Mafuna T, Magwedere K, Matle I
Front Microbiol 14 (-) 1181376 [2023-07-20; online 2023-07-20]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Development of an Effective Functional Lipid Anchor for Membranes (FLAME) for the Bioorthogonal Modification of the Lipid Bilayer of Mesenchymal Stromal Cells.
Sternstein C, Böhm TM, Fink J, ..., Ebert R, Seibel J
Bioconjug. Chem. 34 (7) 1221-1233 [2023-07-19; online 2023-06-16]
Erdinc Sezgin SciLifeLab Fellow
PubMed DOI Crossref
Next generation pan-cancer blood proteome profiling using proximity extension assay.
Álvez MB, Edfors F, von Feilitzen K, ..., Fagerberg L, Uhlén M
Nat Commun 14 (1) 4308 [2023-07-18; online 2023-07-18]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Nanopore sequencing of PCR products enables multicopy gene family reconstruction.
Namias A, Sahlin K, Makoundou P, ..., Belkhir K, Weill M
Comput Struct Biotechnol J 21 (-) 3656-3664 [2023-07-16; online 2023-07-16]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
A data-driven study of Alzheimer's disease related amyloid and tau pathology progression.
Aksman LM, Oxtoby NP, Scelsi MA, ..., Altmann A, ADNI
Brain - (-) - [2023-07-11; online 2023-07-11]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Establishing mammalian GLUT kinetics and lipid composition influences in a reconstituted-liposome system.
Suades A, Qureshi A, McComas SE, ..., Carlsson J, Drew D
Nat Commun 14 (1) 4070 [2023-07-10; online 2023-07-10]
Jens Carlsson SciLifeLab Fellow
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MOBILE pipeline enables identification of context-specific networks and regulatory mechanisms.
Erdem C, Gross SM, Heiser LM, Birtwistle MR
Nat Commun 14 (1) 3991 [2023-07-06; online 2023-07-06]
Cemal Erdem DDLS Fellow
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Reconstructing the transport cycle in the sugar porter superfamily using coevolution-powered machine learning.
Mitrovic D, McComas SE, Alleva C, ..., Drew D, Delemotte L
Elife 12 (-) - [2023-07-05; online 2023-07-05]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
Determinants of sugar-induced influx in the mammalian fructose transporter GLUT5.
McComas SE, Reichenbach T, Mitrovic D, ..., Delemotte L, Drew D
Elife 12 (-) - [2023-07-05; online 2023-07-05]
Lucie Delemotte SciLifeLab Fellow
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Cardiomyocyte-specific PCSK9 deficiency compromises mitochondrial bioenergetics and heart function.
Laudette M, Lindbom M, Arif M, ..., Levin MC, Borén J
Cardiovasc Res 119 (7) 1537-1552 [2023-07-04; online 2023-03-08]
Adil Mardinoglu SciLifeLab Fellow
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Birth Weight Is Associated With Clonal Hematopoiesis of Indeterminate Potential and Cardiovascular Outcomes in Adulthood.
Schuermans A, Nakao T, Ruan Y, ..., Natarajan P, Honigberg MC
J Am Heart Assoc 12 (13) e030220 [2023-07-04; online 2023-06-22]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Sex and gender in infection and immunity: addressing the bottlenecks from basic science to public health and clinical applications.
Pasin C, Consiglio CR, Huisman JS, ..., Kouyos RD, Bonhoeffer S
R Soc Open Sci 10 (7) 221628 [2023-07-00; online 2023-07-05]
Camila Consiglio DDLS Fellow
PubMed DOI Crossref
How Hi-C ignited the era of 3D genome biology.
Bienko M
Nat. Rev. Genet. 24 (7) 418 [2023-07-00; online 2023-02-03]
Magda Bienko SciLifeLab Fellow
PubMed DOI Crossref
HLA Class I Genotype Is Associated with Relapse Risk after Allogeneic Stem Cell Transplantation for NPM1-Mutated Acute Myeloid Leukemia.
Narayan R, Niroula A, Wang T, ..., Spellman S, Lee SJ
Transplant Cell Ther 29 (7) 452.e1-452.e11 [2023-07-00; online 2023-03-29]
Abhishek Niroula DDLS Fellow
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Esr1+ hypothalamic-habenula neurons shape aversive states.
Calvigioni D, Fuzik J, Le Merre P, ..., Carlén M, Meletis K
Nat. Neurosci. 26 (7) 1245-1255 [2023-07-00; online 2023-06-22]
Antonio Lentini DDLS Fellow
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Entropy predicts sensitivity of pseudorandom seeds.
Maier BD, Sahlin K
Genome Res 33 (7) 1162-1174 [2023-07-00; online 2023-05-22]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Efficient mapping of accurate long reads in minimizer space with mapquik.
Ekim B, Sahlin K, Medvedev P, Berger B, Chikhi R
Genome Res 33 (7) 1188-1197 [2023-07-00; online 2023-06-30]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
A multidrug-resistant Salmonella enterica Typhimurium DT104 complex lineage circulating among humans and cattle in the USA lost the ability to produce pertussis-like toxin ArtAB.
Carroll LM, Piacenza N, Cheng RA, Wiedmann M, Guldimann C
Microb Genom 9 (7) - [2023-07-00; online 2023-07-04]
DDLS Fellow Laura Carroll
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isONform: reference-free transcriptome reconstruction from Oxford Nanopore data.
Petri AJ, Sahlin K
Bioinformatics 39 (39 Suppl 1) i222-i231 [2023-06-30; online 2023-06-30]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Modulation of Pore Opening of Eukaryotic Sodium Channels by π-Helices in S6.
Choudhury K, Delemotte L
J Phys Chem Lett 14 (25) 5876-5881 [2023-06-29; online 2023-06-21]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
Building Asymmetric Lipid Bilayers for Molecular Dynamics Simulations: What Methods Exist and How to Choose One?
Chaisson EH, Heberle FA, Doktorova M
Membranes (Basel) 13 (7) - [2023-06-29; online 2023-06-29]
DDLS Fellow Milka Doktorova
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Interplay between VSD, pore, and membrane lipids in electromechanical coupling in HCN channels.
Elbahnsi A, Cowgill J, Burtscher V, ..., Chanda B, Delemotte L
Elife 12 (-) - [2023-06-21; online 2023-06-21]
Lucie Delemotte SciLifeLab Fellow
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Persistent immunosuppressive effects of dibutyl phthalate exposure in adult male mice.
Pierozan P, Källsten L, Theodoropoulou E, Almamoun R, Karlsson O
Sci. Total Environ. 878 (-) 162741 [2023-06-20; online 2023-03-11]
Oskar Karlsson SciLifeLab Fellow
PubMed DOI Crossref
Host Phylogeny Structures the Gut Bacterial Community Within Galerucella Leaf Beetles.
An Y, Braga MP, Garcia SL, Grudzinska-Sterno M, Hambäck PA
Microb. Ecol. - (-) - [2023-06-14; online 2023-06-14]
Sarahi Garcia SciLifeLab Fellow
PubMed DOI Crossref
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. - (-) - [2023-06-12; online 2023-06-12]
Erdinc Sezgin SciLifeLab Fellow
DOI Crossref
Autoencoder Model for Translating Omics Signatures
Meimetis N, Pullen KM, Zhu DY, ..., Magliacane S, Lauffenburger DA
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Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
More than mcr: canonical plasmid- and transposon-encoded mobilized colistin resistance genes represent a subset of phosphoethanolamine transferases.
Gaballa A, Wiedmann M, Carroll LM
Front. Cell. Infect. Microbiol. 13 (-) 1060519 [2023-06-08; online 2023-06-08]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Generation of Amber Suppression Cell Lines Using CRISPR-Cas9.
Meineke B, Elsässer SJ
Methods in molecular biology (Clifton, N.J.) 2676 (-) 169-180 [2023-06-06; online 2023-06-06]
SciLifeLab Fellow Simon Elsässer
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Contrasting outcomes of genome reduction in mikrocytids and microsporidians.
Žárský V, Karnkowska A, Boscaro V, ..., Burki F, Keeling PJ
BMC Biol. 21 (1) 137 [2023-06-06; online 2023-06-06]
Fabien Burki SciLifeLab Fellow
PubMed DOI Crossref
RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy.
Øvrebø Ø, Ojansivu M, Kartasalo K, ..., Holme MN, Stevens MM
BMC Bioinformatics 24 (1) 237 [2023-06-05; online 2023-06-05]
DDLS Fellow Kimmo Kartasalo
DOI Crossref
Ribosome clustering and surface layer reorganization in the microsporidian host-invasion apparatus
Sharma H, Jespersen N, Ehrenbolger K, Carlson LA, Barandun J
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Jonas Barandun SciLifeLab Fellow
PubMed DOI Crossref
Obesity-induced inflammation exacerbates clonal hematopoiesis.
Pasupuleti SK, Ramdas B, Burns SS, ..., Natarajan P, Kapur R
J. Clin. Invest. 133 (11) - [2023-06-01; online 2023-06-01]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Barcoded Consortium Infections: A Scalable, Internally Controlled Method to Study Host Cell Binding and Invasion by Pathogenic Bacteria.
Di Martino ML, Sellin ME
Methods in molecular biology (Clifton, N.J.) 2674 (-) 295-311 [2023-06-01; online 2023-06-01]
Mikael Sellin SciLifeLab Fellow
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A survey of mapping algorithms in the long-reads era.
Sahlin K, Baudeau T, Cazaux B, Marchet C
Genome Biol. 24 (1) 133 [2023-06-01; online 2023-06-01]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Replacement of dietary saturated with unsaturated fatty acids is associated with beneficial effects on lipidome metabolites: a secondary analysis of a randomized trial.
Sellem L, Eichelmann F, Jackson KG, ..., Schulze MB, Lovegrove JA
Am. J. Clin. Nutr. 117 (6) 1248-1261 [2023-06-00; online 2023-04-11]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Intraluminal neutrophils limit epithelium damage by reducing pathogen assault on intestinal epithelial cells during Salmonella gut infection.
Gül E, Enz U, Maurer L, ..., Sellin ME, Hardt WD
PLoS Pathog 19 (6) e1011235 [2023-06-00; online 2023-06-29]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
High-throughput biochemistry in RNA sequence space: predicting structure and function.
Marklund E, Ke Y, Greenleaf WJ
Nat. Rev. Genet. 24 (6) 401-414 [2023-06-00; online 2023-01-12]
Emil Marklund SciLifeLab Fellow
PubMed DOI Crossref
Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments.
Bargheet A, Klingenberg C, Esaiassen E, ..., Bengtsson-Palme J, Pettersen VK
EBioMedicine 92 (-) 104613 [2023-06-00; online 2023-05-13]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Classification of Hypoglycemic Events in Type 1 Diabetes Using Machine Learning Algorithms.
Cederblad L, Eklund G, Vedal A, ..., Carlsson PO, Espes D
Diabetes Ther 14 (6) 953-965 [2023-06-00; online 2023-04-13]
Daniel Espes SciLifeLab Fellow
DOI Crossref
Chemical safety and the exposome
Karlsson O
Emerging Contaminants 9 (2) 100225 [2023-06-00; online 2023-06-00]
Oskar Karlsson SciLifeLab Fellow
Efficient Resource Scheduling for Distributed Infrastructures using Negotiation Capabilities
Chu J, Singh PS, Toor S
IEEE CLOUD 2023 - (-) - [2023-05-29]
Prashant Singh SciLifeLab Fellow
PubMed DOI Crossref
Chemoselective bicyclobutane-based mass spectrometric detection of biological thiols uncovers human and bacterial metabolites.
Kaur A, Lin W, Dovhalyuk V, ..., Sellin ME, Globisch D
Chem Sci 14 (20) 5291-5301 [2023-05-24; online 2023-04-06]
Daniel Globisch Mikael Sellin SciLifeLab Fellow
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Clonal Hematopoiesis of Indeterminate Potential Predicts Adverse Outcomes in Patients With Atherosclerotic Cardiovascular Disease.
Gumuser ED, Schuermans A, Cho SMJ, ..., Natarajan P, Honigberg MC
J. Am. Coll. Cardiol. 81 (20) 1996-2009 [2023-05-23; online 2023-05-18]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Design of Drug Efficacy Guided by Free Energy Simulations of the β2 -Adrenoceptor.
Panel N, Vo DD, Kahlous NA, ..., Gmeiner P, Carlsson J
Angew. Chem. Int. Ed. Engl. 62 (22) e202218959 [2023-05-22; online 2023-04-20]
Jens Carlsson Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
Atlas of mRNA translation and decay for bacteria.
Huch S, Nersisyan L, Ropat M, ..., Engstrand L, Pelechano V
Nat. Microbiol - (-) - [2023-05-22; online 2023-05-22]
SciLifeLab Fellow Vicent Pelechano
PubMed DOI Crossref
Drug repositioning targeting glutaminase reveals drug candidates for the treatment of Alzheimer's disease patients.
Bayraktar A, Li X, Kim W, ..., Shoaie S, Mardinoglu A
J Transl Med 21 (1) 332 [2023-05-20; online 2023-05-20]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Development and Characterization of Novel Selective, Non-Basic Dopamine D2 Receptor Antagonists for the Treatment of Schizophrenia.
Stępnicki P, Wośko S, Bartyzel A, ..., Castro M, Kaczor AA
Molecules 28 (10) - [2023-05-20; online 2023-05-20]
Jens Carlsson SciLifeLab Fellow
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Membranes in focus.
Sezgin E, Levental I
Biophys. J. - (-) - [2023-05-19; online 2023-05-19]
Erdinc Sezgin SciLifeLab Fellow
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Striking allelic diversity despite structural homogeneity of ace-1 duplications in Anopheles mosquitoes
Claret JL, Di-Liegro M, Namias A, ..., Milesi P, Labbé P
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Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami.
Doye JPK, Fowler H, Prešern D, ..., Poppleton E, Snodin BEK
Methods in molecular biology (Clifton, N.J.) 2639 (-) 93-112 [2023-05-11; online 2023-05-11]
Erik Benson SciLifeLab Fellow
PubMed DOI Crossref
Sensitive quantification of short-chain fatty acids combined with global metabolomics in microbiome cultures.
Lin W, García FR, Norin EL, ..., Du J, Globisch D
Chem. Commun. (Camb.) 59 (39) 5843-5846 [2023-05-11; online 2023-05-11]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
A Multiparametric and High-Throughput Platform for Host-Virus Binding Screens.
Schlegel J, Porebski B, Andronico L, ..., Fernandez-Capetillo O, Sezgin E
Nano Lett. 23 (9) 3701-3707 [2023-05-10; online 2023-03-09]
Erdinc Sezgin SciLifeLab Fellow
PubMed DOI Crossref
Data-driven neuropathological staging and subtyping of TDP-43 proteinopathies.
Young AL, Vogel JW, Robinson JL, ..., Lee EB, Hansson O
Brain - (-) - [2023-05-08; online 2023-05-08]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Comparison of Group-Level and Individualized Brain Regions for Measuring Change in Longitudinal Tau Positron Emission Tomography in Alzheimer Disease.
Leuzy A, Binette AP, Vogel JW, ..., Hansson O, Alzheimer’s Disease Neuroimaging Initiative
JAMA Neurol - (-) - [2023-05-08; online 2023-05-08]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
A practical approach to curate clonal hematopoiesis of indeterminate potential in human genetic data sets.
Vlasschaert C, Mack T, Heimlich JB, ..., Jaiswal S, Bick AG
Blood 141 (18) 2214-2223 [2023-05-04; online 2023-01-19]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Nontarget Analysis of Polluted Surface Waters in Bangladesh Using Open Science Workflows.
Bonnefille B, Karlsson O, Rian MB, ..., Islam MS, Martin JW
Environ. Sci. Technol. 57 (17) 6808-6824 [2023-05-02; online 2023-04-21]
Oskar Karlsson SciLifeLab Fellow
DOI Crossref
Adrenomedullin promotes interneuron migration in a dual human model for hypoxic interneuronopathy of prematurity
Michno WP, Puno A, Li L, ..., Willsey AJ, Pasca AM
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SciLifeLab Fellow Wojciech Michno
PubMed DOI Crossref
Trophozoite fitness dictates the intestinal epithelial cell response to Giardia intestinalis infection.
Grüttner J, van Rijn JM, Geiser P, ..., Sellin ME, Svärd SG
PLoS Pathog 19 (5) e1011372 [2023-05-00; online 2023-05-04]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Revisiting the role of serine metabolism in hepatic lipogenesis.
Yang H, Zhang C, Turkez H, ..., Boren J, Mardinoglu A
Nat Metab 5 (5) 760-761 [2023-05-00; online 2023-05-11]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Prediction of risk for myeloid malignancy in clonal hematopoiesis.
Weeks LD, Niroula A, Neuberg D, ..., Natarajan P, Ebert BL
NEJM Evid 2 (5) - [2023-05-00; online 2023-04-25]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Plasma lipidome and risk of atrial fibrillation: results from the PREDIMED trial.
Toledo E, Wittenbecher C, Razquin C, ..., Hu FB, Martínez-González MA
J Physiol Biochem 79 (2) 355-364 [2023-05-00; online 2023-04-01]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
New Pharmacological Approaches to the Management of Premenstrual Dysphoric Disorder.
Sundström-Poromaa I, Comasco E
CNS Drugs 37 (5) 371-379 [2023-05-00; online 2023-05-12]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Intrinsic lipolysis rate for systematic design of lipid-based formulations
Jacobsen AC, Kabedev A, Sinko PD, ..., Bergström CAS, Teleki A
Drug Deliv. and Transl. Res. 13 (5) 1288-1304 [2023-05-00; online 2022-10-08]
Alexandra Teleki SciLifeLab Fellow
PubMed DOI Crossref
Interobserver reproducibility of cribriform cancer in prostate needle biopsies and validation of International Society of Urological Pathology criteria.
Egevad L, Delahunt B, Iczkowski KA, ..., Eklund M, Kartasalo K
Histopathology 82 (6) 837-845 [2023-05-00; online 2023-01-25]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
Discovery of drug targets and therapeutic agents based on drug repositioning to treat lung adenocarcinoma.
Graves OK, Kim W, Özcan M, ..., Mardinoglu A, Li X
Biomed. Pharmacother. 161 (-) 114486 [2023-05-00; online 2023-03-10]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Acute nicotine exposure blocks aromatase in the limbic brain of healthy women: A [11C]cetrozole PET study.
Dubol M, Immenschuh J, Jonasson M, ..., Sundström-Poromaa I, Comasco E
Compr Psychiatry 123 (-) 152381 [2023-05-00; online 2023-03-05]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Exploration of Novel Urolithin C Derivatives as Non-Competitive Inhibitors of Liver Pyruvate Kinase.
Battisti UM, Monjas L, Akladios F, ..., Mardinoğlu A, Grøtli M
Pharmaceuticals (Basel, Switzerland) 16 (5) - [2023-04-28; online 2023-04-28]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Reconfigurable self-assembled DNA devices.
Benson E, Bath J
Sci Robot 8 (77) eadh8148 [2023-04-26; online 2023-04-26]
Erik Benson SciLifeLab Fellow
PubMed DOI Crossref
Antibodies against the Ebola virus soluble glycoprotein are associated with long-term vaccine-mediated protection of non-human primates.
Gunn BM, McNamara RP, Wood L, ..., Simon JK, Alter G
Cell Reports 42 (4) 112402 [2023-04-25; online 2023-04-15]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Normalization of hepatic ChREBP activity does not protect against liver disease progression in a mouse model for Glycogen Storage Disease type Ia.
Rutten MGS, Lei Y, Hoogerland JH, ..., van de Sluis B, Oosterveer MH
Cancer Metab 11 (1) 5 [2023-04-21; online 2023-04-21]
Adil Mardinoglu SciLifeLab Fellow
PubMed DOI Crossref
Time-Lapse Imaging of Inflammasome-Dependent Cell Death and Extrusion in Enteroid-Derived Intestinal Epithelial Monolayers.
Geiser P, van Rijn JM, Sellin ME
Methods in molecular biology (Clifton, N.J.) 2641 (-) 203-221 [2023-04-19; online 2023-04-19]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Development of top-down cortical propagations in youth.
Pines A, Keller AS, Larsen B, ..., Fair DA, Satterthwaite TD
Neuron 111 (8) 1316-1330.e5 [2023-04-19; online 2023-02-17]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Monitoring beta cell survival after intrahepatic islet transplantation using dynamic exendin PET imaging: a proof-of-concept study in individuals with type 1 diabetes.
Jansen TJP, Buitinga M, Boss M, ..., de Koning EJP, Gotthardt M
Diabetes - (-) - [2023-04-17; online 2023-04-17]
Olof Eriksson SciLifeLab Fellow
PubMed DOI Crossref
Microscopy-based phenotypic monitoring of MDA-MB-231 spheroids allows the evaluation of phenotype-directed therapy.
Mahmoud L, Cougnoux A, Bekiari C, ..., Gsell L, Hausser J
Exp. Cell Res. 425 (2) 113527 [2023-04-15; online 2023-03-06]
Jean Hausser SciLifeLab Fellow
PubMed DOI Crossref
Emotion-induced brain activation across the menstrual cycle in individuals with premenstrual dysphoric disorder and associations to serum levels of progesterone-derived neurosteroids.
Stiernman L, Dubol M, Comasco E, ..., Johansson M, Bixo M
Transl Psychiatry 13 (1) 124 [2023-04-14; online 2023-04-14]
Erika Comasco SciLifeLab Fellow
DOI Crossref
CRISPR-Cas9-mediated genome engineering exaggerates genomic deletion at 10q23.31 including the<i>PTEN</i>gene locus mimicking cancer profiles
Geng K, Merino LG, Veiga RG, ..., Brinkman EK, Kutter C
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Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
Differential Retention of Pfam Domains Contributes to Long-term Evolutionary Trends.
James JE, Nelson PG, Masel J
Mol. Biol. Evol. 40 (4) - [2023-04-04; online 2023-03-23]
DDLS Fellow Jennifer James
PubMed DOI Crossref
Mucosal and Plasma Metabolomes in New-onset Paediatric Inflammatory Bowel Disease: Correlations with Disease Characteristics and Plasma Inflammation Protein Markers.
Nyström N, Prast-Nielsen S, Correia M, ..., Schuppe-Koistinen I, Halfvarson J
J Crohns Colitis 17 (3) 418-432 [2023-04-03; online 2022-10-12]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
IL-1 receptor-associated kinase-3 acts as an immune checkpoint in myeloid cells to limit cancer immunotherapy.
Tunalı G, Rúbies Bedós M, Nagarajan D, ..., Papakyriacou I, Mao Y
J. Clin. Invest. 133 (7) - [2023-04-03; online 2023-04-03]
SciLifeLab Fellow Yumeng Mao
PubMed DOI Crossref
Plasma Lipidomic n-6 Polyunsaturated Fatty Acids and Type 2 Diabetes Risk in the EPIC-Potsdam Prospective Cohort Study.
Prada M, Eichelmann F, Wittenbecher C, Kuxhaus O, Schulze MB
Diabetes Care 46 (4) 836-844 [2023-04-01; online 2023-02-15]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Low-Carbohydrate Diet Scores and Mortality Among Adults With Incident Type 2 Diabetes.
Hu Y, Liu G, Yu E, ..., Hu FB, Sun Q
Diabetes Care 46 (4) 874-884 [2023-04-01; online 2023-02-15]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Epithelial and microbial determinants of colonic drug distribution.
Hammar R, Sellin ME, Artursson P
Eur J Pharm Sci 183 (-) 106389 [2023-04-01; online 2023-01-20]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Voices of the new generation: normalizing career choices outside academia.
Sezgin E
Nat. Rev. Mol. Cell Biol. 24 (4) 237 [2023-04-00; online 2023-01-20]
Erdinc Sezgin SciLifeLab Fellow
PubMed DOI Crossref
The liver kinase B1 supports mammary epithelial morphogenesis by inhibiting critical factors that mediate epithelial-mesenchymal transition.
Tzavlaki K, Ohata Y, Morén A, ..., Heldin CH, Moustakas A
J. Cell. Physiol. 238 (4) 790-812 [2023-04-00; online 2023-02-15]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Gray matter hypoperfusion is a late pathological event in the course of Alzheimer's disease.
Ahmadi K, Pereira JB, Berron D, ..., Mutsaerts HJ, Hansson O
J. Cereb. Blood Flow Metab. 43 (4) 565-580 [2023-04-00; online 2022-11-22]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Dynamic antagonism between key repressive pathways maintains the placental epigenome.
Weigert R, Hetzel S, Bailly N, ..., Smith ZD, Meissner A
Nat. Cell Biol. 25 (4) 579-591 [2023-04-00; online 2023-04-06]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Dietary intake of total, heme and non-heme iron and the risk of colorectal cancer in a European prospective cohort study.
Aglago EK, Cross AJ, Riboli E, ..., Tsilidis KK, Jenab M
Br. J. Cancer 128 (8) 1529-1540 [2023-04-00; online 2023-02-09]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Deep mutational scan of a drug efflux pump reveals its structure-function landscape.
Meier G, Thavarasah S, Ehrenbolger K, ..., Barandun J, Seeger MA
Nat. Chem. Biol. 19 (4) 440-450 [2023-04-00; online 2022-11-28]
Jonas Barandun SciLifeLab Fellow
PubMed DOI Crossref
Clonal haematopoiesis and risk of chronic liver disease.
Wong WJ, Emdin C, Bick AG, ..., Ebert BL, Natarajan P
Nature 616 (7958) 747-754 [2023-04-00; online 2023-04-12]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
A frame-shift mutation in COMTD1 is associated with impaired pheomelanin pigmentation in chicken.
Bi H, Tranell J, Harper DC, ..., Globisch D, Andersson L
PLoS Genet 19 (4) e1010724 [2023-04-00; online 2023-04-17]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
Do lipids tune B cell signaling?
Urbančič I, Eggeling C, Sezgin E
Nat. Chem. Biol. - (-) - [2023-03-30; online 2023-03-30]
Erdinc Sezgin SciLifeLab Fellow
PubMed DOI Crossref
Diverticulosis is not associated with altered gut microbiota nor is it predictive of future diverticulitis: a population-based colonoscopy study.
Alexandersson BT, Hugerth LW, Hedin C, ..., Andreasson A, Schmidt PT
Scand. J. Gastroenterol. 58 (10) 1131-1138 [2023-03-29; online 2023-03-29]
DDLS Fellow Luisa Hugerth
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Linking prokaryotic genome size variation to metabolic potential and environment.
Rodríguez-Gijón A, Buck M, Andersson AF, ..., Nascimento FJA, Garcia SL
ISME Commun 3 (1) 25 [2023-03-27; online 2023-03-27]
Sarahi Garcia SciLifeLab Fellow
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Correlative Chemical Imaging and Spatial Chemometrics Delineate Alzheimer Plaque Heterogeneity at High Spatial Resolution.
Wehrli PM, Ge J, Michno W, ..., Blennow K, Hanrieder J
JACS Au 3 (3) 762-774 [2023-03-27; online 2023-03-07]
SciLifeLab Fellow Wojciech Michno
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Costunolide and Parthenolide Ameliorate MPP+ Induced Apoptosis in the Cellular Parkinson's Disease Model.
Arslan ME, Türkez H, Sevim Y, ..., Öner S, Mardinoğlu A
Cells 12 (7) - [2023-03-24; online 2023-03-24]
Adil Mardinoglu SciLifeLab Fellow
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Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format.
Mutsuddy A, Erdem C, Huggins JR, ..., Feltus FA, Birtwistle MR
Bioinform Adv 3 (1) vbad039 [2023-03-23; online 2023-03-23]
Cemal Erdem DDLS Fellow
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Molecular simulations and NMR reveal how lipid fluctuations affect membrane mechanics.
Doktorova M, Khelashvili G, Ashkar R, Brown MF
Biophys. J. 122 (6) 984-1002 [2023-03-21; online 2022-12-05]
DDLS Fellow Milka Doktorova
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Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences.
Leal JL, Milesi P, Salojärvi J, Lascoux M
Syst. Biol. - (-) - [2023-03-18; online 2023-03-18]
Pascal Milesi SciLifeLab Fellow
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TASL Practice Guidance on the Clinical Assessment and Management of Patients with Nonalcoholic Fatty Liver Disease.
Yilmaz Y, Zeybel M, Adali G, ..., Kaymakoglu S, Gunsar F
Hepatol Forum 4 (Suppl 1) 1-32 [2023-03-15; online 2023-03-15]
Adil Mardinoglu SciLifeLab Fellow
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MEMMAL: A tool for expanding large-scale mechanistic models with machine learned associations and big datasets
Erdem C, Birtwistle MR
Front. Syst. Biol. 3 (-) - [2023-03-09; online 2023-03-09]
Cemal Erdem DDLS Fellow
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Pre-pregnancy complications - associated factors and wellbeing in early pregnancy: a Swedish cohort study.
Gudnadottir U, Du J, Hugerth LW, ..., Fransson E, Brusselaers N
BMC Pregnancy Childbirth 23 (1) 153 [2023-03-08; online 2023-03-08]
DDLS Fellow Luisa Hugerth
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Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes.
Inda-Díaz JS, Lund D, Parras-Moltó M, ..., Bengtsson-Palme J, Kristiansson E
Microbiome 11 (1) 44 [2023-03-08; online 2023-03-08]
DDLS Fellow Johan Bengtsson-Palme
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A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea).
Onuț-Brännström I, Stairs CW, Campos KIA, ..., Bass D, Burki F
Genome Biol Evol 15 (3) - [2023-03-03; online 2023-02-16]
Fabien Burki SciLifeLab Fellow
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Clonal Hematopoiesis and Risk of Incident Lung Cancer.
Tian R, Wiley B, Liu J, ..., Bolton KL, Cao Y
J Clin Oncol 41 (7) 1423-1433 [2023-03-01; online 2022-12-08]
Abhishek Niroula DDLS Fellow
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Structural basis of mitochondrial membrane bending by the I-II-III2-IV2 supercomplex.
Mühleip A, Flygaard RK, Baradaran R, ..., Sharma V, Amunts A
Nature 615 (7954) 934-938 [2023-03-00; online 2023-03-22]
Alexey Amunts SciLifeLab Fellow
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PET Imaging of Neutrophil Elastase with 11C-GW457427 in Acute Respiratory Distress Syndrome in Pigs.
Puuvuori E, Chiodaroli E, Estrada S, ..., Eriksson O, Antoni G
Journal of nuclear medicine : official publication, Society of Nuclear Medicine 64 (3) 423-429 [2023-03-00; online 2022-09-15]
Olof Eriksson SciLifeLab Fellow
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PCYT2-regulated lipid biosynthesis is critical to muscle health and ageing.
Cikes D, Elsayad K, Sezgin E, ..., Banka S, Penninger JM
Nat Metab 5 (3) 495-515 [2023-03-00; online 2023-03-20]
Erdinc Sezgin SciLifeLab Fellow
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In silico tissue generation and power analysis for spatial omics.
Baker EAG, Schapiro D, Dumitrascu B, Vickovic S, Regev A
Nat. Methods 20 (3) 424-431 [2023-03-00; online 2023-03-02]
Sanja Vickovic SciLifeLab Fellow
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A palmitate-rich metastatic niche enables metastasis growth via p65 acetylation resulting in pro-metastatic NF-κB signaling.
Altea-Manzano P, Doglioni G, Liu Y, ..., Malanchi I, Fendt SM
Nat Cancer 4 (3) 344-364 [2023-03-00; online 2023-02-02]
SciLifeLab Fellow Vicent Pelechano
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Magnetoresponsive fluorescent core-shell nanoclusters for biomedical applications.
Saladino GM, Kakadiya R, Ansari SR, Teleki A, Toprak MS
Nanoscale Adv 5 (5) 1323-1330 [2023-02-28; online 2023-01-31]
Alexandra Teleki SciLifeLab Fellow
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Single-Cell Transcriptomics To Define Plasmodium falciparum Stage Transition in the Mosquito Midgut.
Mohammed M, Dziedziech A, Sekar V, ..., Vega-Rodriguez J, Ankarklev J
Microbiol Spectr 11 (2) e0367122 [2023-02-27; online 2023-02-27]
Marc Friedländer SciLifeLab Fellow
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Reconstructing clonal tree for phylo-phenotypic characterization of cancer using single-cell transcriptomics.
Jun SH, Toosi H, Mold J, ..., Roth A, Lagergren J
Nat Commun 14 (1) 982 [2023-02-22; online 2023-02-22]
Camilla Engblom SciLifeLab Fellow
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Not1 and Not4 inversely determine mRNA solubility that sets the dynamics of co-translational events.
Allen G, Weiss B, Panasenko OO, ..., Pelechano V, Collart MA
Genome Biol. 24 (1) 30 [2023-02-20; online 2023-02-20]
SciLifeLab Fellow Vicent Pelechano
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Differential regulation of mRNA stability modulates transcriptional memory and facilitates environmental adaptation.
Li B, Zeis P, Zhang Y, ..., Steinmetz LM, Pelechano V
Nat Commun 14 (1) 910 [2023-02-17; online 2023-02-17]
SciLifeLab Fellow Vicent Pelechano
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Network-based multi-omics integration reveals metabolic at-risk profile within treated HIV-infection.
Mikaeloff F, Gelpi M, Benfeitas R, ..., Nielsen SD, Neogi U
Elife 12 (-) - [2023-02-16; online 2023-02-16]
Adil Mardinoglu SciLifeLab Fellow
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An α-π transition in S6 shapes the conformational cycle of the bacterial sodium channel NavAb.
Choudhury K, Howard RJ, Delemotte L
J. Gen. Physiol. 155 (2) - [2023-02-06; online 2022-12-14]
Lucie Delemotte SciLifeLab Fellow
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[18F]MK-7246 for Positron Emission Tomography Imaging of the Beta-Cell Surface Marker GPR44.
Cheung P, Amin MA, Zhang B, ..., Odell LR, Eriksson O
Pharmaceutics 15 (2) - [2023-02-02; online 2023-02-02]
Olof Eriksson SciLifeLab Fellow
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Combined metabolic activators improve metabolic functions in the animal models of neurodegenerative diseases.
Turkez H, Altay O, Yildirim S, ..., Uhlén M, Mardinoglu A
Life Sci 314 (-) 121325 [2023-02-01; online 2022-12-26]
Adil Mardinoglu SciLifeLab Fellow
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High-content analysis shows synergistic effects of low perfluorooctanoic acid (PFOS) and perfluorooctane sulfonic acid (PFOA) mixture concentrations on human breast epithelial cell carcinogenesis.
Pierozan P, Kosnik M, Karlsson O
Environ Int 172 (-) 107746 [2023-02-00; online 2023-01-12]
Oskar Karlsson SciLifeLab Fellow
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Diversity and enrichment of breeding material for resilience in European forests
Olsson S, Dauphin B, Jorge V, ..., Bastien C, Alia R
Forest Ecology and Management 530 (-) 120748 [2023-02-00; online 2023-02-00]
Pascal Milesi SciLifeLab Fellow
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Carnitine octanoyltransferase is important for the assimilation of exogenous acetyl-L-carnitine into acetyl-CoA in mammalian cells.
Hsu J, Fatuzzo N, Weng N, ..., Nasca C, Khosla C
J Biol Chem 299 (2) 102848 [2023-02-00; online 2022-12-30]
SciLifeLab Fellow Wojciech Michno
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A GC-centered view of 3D genome organization.
Bouwman BA, Crosetto N, Bienko M
Curr. Opin. Genet. Dev. 78 (-) 102020 [2023-02-00; online 2023-01-05]
Magda Bienko SciLifeLab Fellow
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Editorial: Effects of hormonal contraceptives on the brain.
Pletzer B, Comasco E, Hidalgo-Lopez E, Lacreuse A, Derntl B
Front Endocrinol (Lausanne) 14 (-) 1129203 [2023-01-31; online 2023-01-31]
Erika Comasco SciLifeLab Fellow
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Combined metabolic activators improve cognitive functions in Alzheimer's disease patients: a randomised, double-blinded, placebo-controlled phase-II trial.
Yulug B, Altay O, Li X, ..., Uhlén M, Mardinoglu A
Transl Neurodegener 12 (1) 4 [2023-01-26; online 2023-01-26]
Adil Mardinoglu SciLifeLab Fellow
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Ellagic Acid and Its Metabolites as Potent and Selective Allosteric Inhibitors of Liver Pyruvate Kinase.
Battisti UM, Gao C, Akladios F, ..., Mardinoglu A, Grøtli M
Nutrients 15 (3) - [2023-01-22; online 2023-01-22]
Adil Mardinoglu SciLifeLab Fellow
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TP53-mediated clonal hematopoiesis confers increased risk for incident atherosclerotic disease.
Zekavat SM, Viana-Huete V, Matesanz N, ..., Fuster JJ, Klarin D
Nat Cardiovasc Res 2 (-) 144-158 [2023-01-16; online 2023-03-24]
Abhishek Niroula DDLS Fellow
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Synchronous effective population size changes and genetic stability of forest trees through glacial cycles
Milesi P, Kastally C, Dauphin B, ..., Pyhäjärvi T, None
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Pascal Milesi SciLifeLab Fellow
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Serendipitous Identification of a Covalent Activator of Liver Pyruvate Kinase.
Battisti UM, Gao C, Nilsson O, ..., Mardinoglu A, Grøtli M
Chembiochem 24 (1) e202200339 [2023-01-03; online 2022-11-09]
Adil Mardinoglu SciLifeLab Fellow
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In Vivo Visualization and Quantification of Neutrophil Elastase in Lungs of COVID-19 Patients: A First-in-Humans PET Study with 11C-NES.
Antoni G, Lubberink M, Sörensen J, ..., Skorup P, Lipcsey M
Journal of nuclear medicine : official publication, Society of Nuclear Medicine 64 (1) 145-148 [2023-01-00; online 2022-06-09]
Olof Eriksson SciLifeLab Fellow
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A Risk Management Framework for Emergence of Novel Antibiotic Resistance Determinants
Heß S, Bengtsson-Palme J
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DDLS Fellow Johan Bengtsson-Palme
SciLifeLab Data Centre
Publications 9.5.1