Publications 2024

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138 publications

DOI Crossref
GenePioneer: A Comprehensive Python Package for Identification of Essential Genes and Modules in Cancer
Taheri G, Haerianardakani A
- - (-) - [2024-12-21; online 2024-12-21]
DDLS Fellow Golnaz Taheri
PubMed DOI Crossref
Author Correction: AutoTransOP: translating omics signatures without orthologue requirements using deep learning.
Meimetis N, Pullen KM, Zhu DY, ..., Magliacane S, Lauffenburger DA
NPJ Syst Biol Appl 10 (1) 148 [2024-12-13; online 2024-12-13]
Avlant Nilsson DDLS Fellow
DOI Crossref
Plasma proteomics for novel biomarker discovery in childhood tuberculosis
Fossati A, Wambi P, Jaganath D, ..., Zar HJ, Swaney DL
- - (-) - [2024-12-08; online 2024-12-08]
Andrea Fossati DDLS Fellow
PubMed DOI Crossref
A landscape of X-inactivation during human T cell development.
Gylemo B, Bensberg M, Hennings V, ..., Ekwall O, Nestor CE
Nat Commun 15 (1) 10527 [2024-12-04; online 2024-12-04]
Antonio Lentini DDLS Fellow
PubMed DOI Crossref
Characterising and preventing the gut microbiota's inactivation of trifluridine, a colorectal cancer drug.
McCoubrey LE, Shen C, Mwasambu S, ..., Globisch D, Basit AW
Eur J Pharm Sci 203 (-) 106922 [2024-12-01; online 2024-10-03]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
The last of their kind: Is the genus Scutiger (Anura: Megophryidae) a relict element of the paleo-Transhimalaya biota?
Hofmann S, Podsiadlowski L, Andermann T, ..., Jablonski D, Schmidt J
Mol. Phylogenet. Evol. 201 (-) 108166 [2024-12-00; online 2024-08-09]
DDLS Fellow Tobias Andermann
DOI Crossref
Microneedles loaded with lipid nanocarriers for local treatment of vulvovaginal candidiasis
Udayakumar P, Škalko-Basnet N, Salas Cotaquispe CF, ..., Du J, Teleki A
- - (-) - [2024-11-25; online 2024-11-25]
Alexandra Teleki SciLifeLab Fellow
PubMed DOI Crossref
The early transcriptional and post-transcriptional responses to fluconazole in sensitive and resistant Candida albicans.
Stevens I, Silao FG, Huch S, ..., Ljungdahl PO, Pelechano V
Sci Rep 14 (1) 29012 [2024-11-22; online 2024-11-22]
SciLifeLab Fellow Vicent Pelechano
PubMed DOI Crossref
Flipping a switch on BRD4: How to control the do-it-all.
van Hout FAH, Vihervaara A
Mol. Cell 84 (22) 4257-4259 [2024-11-21; online 2024-11-23]
Anniina Vihervaara SciLifeLab Fellow
PubMed DOI Crossref
Single-molecule states link transcription factor binding to gene expression.
Doughty BR, Hinks MM, Schaepe JM, ..., Bintu L, Greenleaf WJ
Nature - (-) - [2024-11-20; online 2024-11-20]
Emil Marklund SciLifeLab Fellow
PubMed DOI Crossref
Complete genome sequences of the prosthecate dimorphic bacteria Brevundimonas intermedia CB63T and Brevundimonas staleyi FWC43T.
Hallgren J, Daneby F, Jonas K
Microbiol Resour Announc - (-) e0105024 [2024-11-20; online 2024-11-20]
Kristina Jonas SciLifeLab Fellow
DOI Crossref
A Phylogenomic Analysis of Genipa (Rubiaceae) Using Target Sequence Capture Data
Ridley R, Persson C, Oxelman B, Andermann T, Bacon CD
Systematic Botany 49 (3) 617-625 [2024-11-19; online 2024-11-19]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
JAK2-mutant clonal hematopoiesis is associated with venous thromboembolism.
Zon RL, Sekar A, Clapham K, ..., Natarajan P, Ebert BL
Blood 144 (20) 2149-2154 [2024-11-14; online 2024-08-05]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Colchicine prevents accelerated atherosclerosis in TET2-mutant clonal haematopoiesis.
Zuriaga MA, Yu Z, Matesanz N, ..., Natarajan P, Fuster JJ
Eur. Heart J. 45 (43) 4601-4615 [2024-11-14; online 2024-09-01]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Annotated genome sequences of Salmonella Haifa, Salmonella Bangkok, and Salmonella Reading, isolated from chicken meat in South Africa.
Mathole M, Carroll L, Khabo-Mmekoa C, Mabogoane N, Matle I
Microbiol Resour Announc 13 (11) e0028424 [2024-11-12; online 2024-10-09]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Progestagens and progesterone receptor modulation: Effects on the brain, mood, stress, and cognition in females.
Bencker C, Gschwandtner L, Nayman S, ..., Bixo M, Comasco E
Front Neuroendocrinol - (-) 101160 [2024-11-06; online 2024-11-06]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Loss of heterozygosity of CYP2D6 enhances the sensitivity of hepatocellular carcinomas to talazoparib.
Zhang X, Rameika N, Zhong L, ..., Globisch D, Sjöblom T
EBioMedicine 109 (-) 105368 [2024-11-00; online 2024-10-04]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
Integration across biophysical scales identifies molecular and cellular correlates of person-to-person variability in human brain connectivity.
Ng B, Tasaki S, Greathouse KM, ..., Gaiteri C, Herskowitz JH
Nat. Neurosci. 27 (11) 2240-2252 [2024-11-00; online 2024-10-31]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Building pangenome graphs.
Garrison E, Guarracino A, Heumos S, ..., Williams RW, Prins P
Nat. Methods 21 (11) 2008-2012 [2024-11-00; online 2024-10-21]
DDLS Fellow Kaisa Thorell
PubMed DOI Crossref
An ancient ecospecies of Helicobacter pylori.
Tourrette E, Torres RC, Svensson SL, ..., Thorell K, Falush D
Nature 635 (8037) 178-185 [2024-11-00; online 2024-10-16]
DDLS Fellow Kaisa Thorell
PubMed DOI Crossref
The ABCF ATPase New1 resolves translation termination defects associated with specific tRNAArg and tRNALys isoacceptors in the P site.
Turnbull K, Paternoga H, von der Weth E, ..., Wilson DN, Hauryliuk V
Nucleic Acids Res. 52 (19) 12005-12020 [2024-10-28; online 2024-09-01]
SciLifeLab Fellow Vicent Pelechano
PubMed DOI Crossref
White matter integrity upon progesterone antagonism in individuals with premenstrual dysphoric disorder: A randomized placebo-controlled diffusion tensor imaging study.
Kaltsouni E, Gu X, Wikström J, ..., Sundström-Poromaa I, Comasco E
Prog Neuropsychopharmacol Biol Psychiatry 136 (-) 111179 [2024-10-23; online 2024-10-23]
Erika Comasco SciLifeLab Fellow
DOI Crossref
Fish are poor sentinels for surveillance of riverine AMR
Tskhay F, Köbsch C, Elena AX, ..., Berendonk TU, Klümper U
- - (-) - [2024-10-22; online 2024-10-22]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Resilience of genetic diversity in forest trees over the Quaternary.
Milesi P, Kastally C, Dauphin B, ..., Pyhäjärvi T, GenTree Consortium
Nat Commun 15 (1) 8538 [2024-10-14; online 2024-10-14]
Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
Metagenomic assemblies tend to break around antibiotic resistance genes.
Abramova A, Karkman A, Bengtsson-Palme J
BMC Genomics 25 (1) 959 [2024-10-14; online 2024-10-14]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Properties and limitations of eDNA substrates for terrestrial animal monitoring
Zhao B, Andermann T
- - (-) - [2024-10-10; online 2024-10-10]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Peripartum depression symptom trajectories, telomere length and genotype, and adverse childhood experiences.
Vrettou M, Lager S, Toffoletto S, ..., Skalkidou A, Comasco E
BMC Psychiatry 24 (1) 661 [2024-10-08; online 2024-10-08]
Erika Comasco SciLifeLab Fellow
DOI Crossref
Genetic Adaptation to Amoxicillin inEscherichia coli: The Limited Role ofdinBandkatE
Teichmann L, Wenne M, Luitwieler S, ..., Bengtsson-Palme J, Kuile Bt
- - (-) - [2024-10-06; online 2024-10-06]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Multiplexed chromatin immunoprecipitation sequencing for quantitative study of histone modifications and chromatin factors.
Kumar B, Navarro C, Yung PYK, ..., Martin M, Elsässer SJ
Nat Protoc - (-) - [2024-10-03; online 2024-10-03]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
The genetic architecture of repeated local adaptation to climate in distantly related plants.
Whiting JR, Booker TR, Rougeux C, ..., Zhou L, Yeaman S
Nat Ecol Evol 8 (10) 1933-1947 [2024-10-00; online 2024-08-26]
Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
The ACROBAT 2022 challenge: Automatic registration of breast cancer tissue.
Weitz P, Valkonen M, Solorzano L, ..., Ruusuvuori P, Rantalainen M
Med Image Anal 97 (-) 103257 [2024-10-00; online 2024-07-01]
DDLS Fellow Kimmo Kartasalo
PubMed DOI Crossref
The 'queen of the Andes' (Puya raimondii) is genetically fragile and fragmented: a consequence of long generation time and semelparity?
Liu L, James J, Zhang Y, ..., Lascoux M, Ge X
New Phytol. 244 (1) 277-291 [2024-10-00; online 2024-08-12]
DDLS Fellow Jennifer James
PubMed DOI Crossref
Proteomic changes in Alzheimer's disease associated with progressive Aβ plaque and tau tangle pathologies.
Pichet Binette A, Gaiteri C, Wennström M, ..., Vogel JW, Hansson O
Nat. Neurosci. 27 (10) 1880-1891 [2024-10-00; online 2024-08-26]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Lipidome changes due to improved dietary fat quality inform cardiometabolic risk reduction and precision nutrition.
Eichelmann F, Prada M, Sellem L, ..., Schulze MB, Wittenbecher C
Nat. Med. 30 (10) 2867-2877 [2024-10-00; online 2024-07-11]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Bayesian polynomial neural networks and polynomial neural ordinary differential equations.
Fronk C, Yun J, Singh P, Petzold L
PLoS Comput Biol 20 (10) e1012414 [2024-10-00; online 2024-10-10]
Prashant Singh SciLifeLab Fellow
PubMed DOI Crossref
Assessment of the exposure to cytotoxic Bacillus cereus group genotypes through high-temperature, short-time milk consumption.
Su J, Chandross-Cohen T, Qian C, ..., Wiedmann M, Kovac J
J Dairy Sci 107 (10) 7631-7647 [2024-10-00; online 2024-06-06]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
The regulatory landscape of interacting RNA and protein pools in cellular homeostasis and cancer.
Gallardo-Dodd CJ, Kutter C
Hum Genomics 18 (1) 109 [2024-09-27; online 2024-09-27]
Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
Introducing synthetic thermostable RNase inhibitors to single-cell RNA-seq.
Noble JC, Lentini A, Hagemann-Jensen M, Sandberg R, Reinius B
Nat Commun 15 (1) 8373 [2024-09-27; online 2024-09-27]
Antonio Lentini DDLS Fellow
DOI Crossref
The Organelle in the Ointment: improved detection of cryptic mitochondrial reads resolves many unknown sequences in cross-species microbiome analyses
Sonett D, Brown T, Bengtsson-Palme J, Padilla-Gamiño JL, Zaneveld JR
ISME Commun - (-) - [2024-09-24; online 2024-09-24]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Improved sub-genomic RNA prediction with the ARTIC protocol.
Baudeau T, Sahlin K
Nucleic Acids Res. 52 (17) e82 [2024-09-23; online 2024-08-16]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Integrating amyloid and tau imaging with proteomics and genomics in Alzheimer's disease.
Vilkaite G, Vogel J, Mattsson-Carlgren N
Cell Rep Med 5 (9) 101735 [2024-09-17; online 2024-09-19]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Sequence variants influencing the regulation of serum IgG subclass levels.
Olafsdottir TA, Thorleifsson G, Lopez de Lapuente Portilla A, ..., Nilsson B, Stefansson K
Nat Commun 15 (1) 8054 [2024-09-14; online 2024-09-14]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Epigenetic regulation of cell state by H2AFY governs immunogenicity in high-risk neuroblastoma.
Nagarajan D, Parracho RT, Corujo D, ..., Buschbeck M, Mao Y
J. Clin. Invest. - (-) - [2024-09-10; online 2024-09-10]
SciLifeLab Fellow Yumeng Mao
PubMed DOI Crossref
Long-term longitudinal analysis of 4,187 participants reveals insights into determinants of clonal hematopoiesis.
Uddin MM, Saadatagah S, Niroula A, ..., Ballantyne CM, Natarajan P
Nat Commun 15 (1) 7858 [2024-09-09; online 2024-09-09]
Abhishek Niroula DDLS Fellow
DOI Crossref
The protein domains of vertebrate species in which selection is more effective have greater intrinsic structural disorder
Weibel CA, Wheeler AL, James JE, ..., McShea H, Masel J
Elife 12 (-) - [2024-09-06; online 2024-09-06]
DDLS Fellow Jennifer James
DOI Crossref
Comprehensive analysis of the RBP regulome reveals functional modules and drug candidates in liver cancer
Garbulowski M, Mosca R, Gallardo-Dodd CJ, Kutter C, Sonnhammer ELL
- - (-) - [2024-09-06; online 2024-09-06]
Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
Development of a three-dimensional scoring model for the assessment of continuous glucose monitoring data in type 1 diabetes.
Dawnbringer J, Hill H, Lundgren M, ..., Carlsson PO, Espes D
BMJ Open Diabetes Res Care 12 (4) - [2024-09-05; online 2024-09-05]
Daniel Espes SciLifeLab Fellow
DOI Crossref
Deep learning segmentation model produces accurate biodiversity predictions at 10 m spatial resolution
Andermann T, Häggmark J, Olsson P, Högström A
- - (-) - [2024-09-05; online 2024-09-05]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
Caveolin assemblies displace one bilayer leaflet to organize and bend membranes.
Doktorova M, Daum S, Ebenhan J, ..., Kenworthy AK, Levental I
bioRxiv - (-) - [2024-09-04; online 2024-09-04]
DDLS Fellow Milka Doktorova
PubMed DOI Crossref
Cryo-EM images of phase-separated lipid bilayer vesicles analyzed with a machine-learning approach.
Sharma KD, Doktorova M, Waxham MN, Heberle FA
Biophys. J. 123 (17) 2877-2891 [2024-09-03; online 2024-04-30]
DDLS Fellow Milka Doktorova
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
Mol. Ecol. 33 (17) - [2024-09-00; online 2024-08-15]
Pascal Milesi SciLifeLab Fellow
DOI Crossref
MDverse, shedding light on the dark matter of molecular dynamics simulations
Tiemann JK, Szczuka M, Bouarroudj L, ..., Chavent M, Poulain P
Elife 12 (-) - [2024-08-30; online 2024-08-30]
Lucie Delemotte SciLifeLab Fellow
DOI Crossref
Structure prediction of alternative protein conformations
Bryant P, Noé F
Nat Commun 15 (1) - [2024-08-26; online 2024-08-26]
DDLS Fellow Patrick Bryant
PubMed DOI Crossref
Mechanistic modeling of cell viability assays with in silico lineage tracing.
Mutsuddy A, Huggins JR, Amrit A, ..., Calhoun JC, Birtwistle MR
bioRxiv - (-) - [2024-08-26; online 2024-08-26]
Cemal Erdem DDLS Fellow
DOI Crossref
Multi-layered dosage compensation of the avian Z chromosome
Papanicolaou N, Lentini A, Wettersten S, ..., Wright D, Reinius B
- - (-) - [2024-08-20; online 2024-08-20]
Antonio Lentini DDLS Fellow
PubMed DOI Crossref
Defining Vaginal Community Dynamics: daily microbiome transitions, the role of menstruation, bacteriophages, and bacterial genes.
Hugerth LW, Krog MC, Vomstein K, ..., Nielsen HS, Schuppe-Koistinen I
Microbiome 12 (1) 153 [2024-08-19; online 2024-08-19]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Escherichia coli in urban marine sediments: interpreting virulence, biofilm formation, halotolerance, and antibiotic resistance to infer contamination or naturalization.
Erb IK, Suarez C, Frank EM, ..., Lindberg E, Paul CJ
FEMS Microbes 5 (-) xtae024 [2024-08-14; online 2024-08-14]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Deciphering the genetics and mechanisms of predisposition to multiple myeloma.
Went M, Duran-Lozano L, Halldorsson GH, ..., Houlston R, Nilsson B
Nat Commun 15 (1) 6644 [2024-08-05; online 2024-08-05]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Exploring Paleogene Tibet's warm temperate environments through target enrichment and phylogenetic niche modelling of Himalayan spiny frogs (Paini, Dicroglossidae).
Hofmann S, Rödder D, Andermann T, ..., Schmidt J, Podsiadlowski L
Mol. Ecol. 33 (15) e17446 [2024-08-00; online 2024-07-01]
DDLS Fellow Tobias Andermann
PubMed DOI Crossref
OCT1 (SLC22A1) transporter kinetics and regulation in primary human hepatocyte 3D spheroids.
Mickols E, Meyer A, Handin N, ..., Karlgren M, Artursson P
Sci Rep 14 (1) 17334 [2024-07-27; online 2024-07-27]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles.
Leal JL, Milesi P, Hodková E, ..., Salojärvi J, Lascoux M
Syst. Biol. 73 (2) 392-418 [2024-07-27; online 2024-04-13]
DDLS Fellow Jennifer James Pascal Milesi SciLifeLab Fellow
DOI Crossref
Adaptive Robust Learning using Latent Bernoulli Variables
Karakulev A, Zachariah D, Singh P
Proceedings of the 41st International Conference on Machine Learning, PMLR 235 (-) 23105-23122 [2024-07-27; online 2023-12-04]
Prashant Singh SciLifeLab Fellow
DOI Crossref
Improved protein complex prediction with AlphaFold-multimer by denoising the MSA profile
Bryant P, Noé F
PLoS Comput Biol 20 (7) e1012253 [2024-07-25; online 2024-07-25]
DDLS Fellow Patrick Bryant
PubMed DOI Crossref
Multiscale photocatalytic proximity labeling reveals cell surface neighbors on and between cells.
Lin Z, Schaefer K, Lui I, ..., Sali A, Wells JA
Science (New York, N.Y.) 385 (6706) eadl5763 [2024-07-19; online 2024-07-19]
Andrea Fossati DDLS Fellow
PubMed DOI Crossref
An intracellular hydrophobic nexus critical for hERG1 channel slow deactivation.
Stevens-Sostre WA, Flores-Aldama L, Bustos D, ..., Delemotte L, Robertson GA
Biophys. J. 123 (14) 2024-2037 [2024-07-16; online 2024-01-12]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
Characterization of a lipid-based jumbo phage compartment as a hub for early phage infection.
Mozumdar D, Fossati A, Stevenson E, ..., Swaney DL, Bondy-Denomy J
Cell Host Microbe 32 (7) 1050-1058.e7 [2024-07-10; online 2024-06-12]
Andrea Fossati DDLS Fellow
PubMed DOI Crossref
Broadcasters, receivers, functional groups of metabolites, and the link to heart failure by revealing metabolomic network connectivity.
Yazdani A, Mendez-Giraldez R, Yazdani A, ..., Larson MG, Elsea SH
Metabolomics 20 (4) 71 [2024-07-07; online 2024-07-07]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
A generalizable data-driven model of atrophy heterogeneity and progression in memory clinic settings.
Baumeister H, Vogel JW, Insel PS, ..., Hansson O, Berron D
Brain 147 (7) 2400-2413 [2024-07-05; online 2024-04-24]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Investigations of microbiota composition and neuroactive pathways in association with symptoms of stress and depression in a cohort of healthy women.
Bashir Z, Hugerth LW, Krog MC, ..., Fransson E, Nielsen HS
Front. Cell. Infect. Microbiol. 14 (-) 1324794 [2024-07-02; online 2024-07-02]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
CCG-1423-derived compounds reduce global RNA synthesis and inhibit transcriptional responses.
Prajapati B, Sokolova M, Sidorenko E, ..., Vihervaara A, Vartiainen MK
J. Cell. Sci. 137 (13) - [2024-07-01; online 2024-07-15]
Anniina Vihervaara SciLifeLab Fellow
PubMed DOI Crossref
Detection and quantification of Na,K-ATPase dimers in the plasma membrane of living cells by FRET-FCS.
Nordahl L, Akkuratov EE, Heimgärtner J, ..., Wennmalm S, Brismar H
Biochim Biophys Acta Gen Subj 1868 (7) 130619 [2024-07-00; online 2024-04-20]
SciLifeLab Fellow Simon Elsässer
PubMed DOI Crossref
Comparison of Xrn1 and Rat1 5' → 3' exoribonucleases in budding yeast supports the specific role of Xrn1 in cotranslational mRNA decay.
Pérez-Ortín JE, Jordán-Pla A, Zhang Y, ..., Pelechano V, García-Martínez J
Yeast 41 (7) 458-472 [2024-07-00; online 2024-06-14]
SciLifeLab Fellow Vicent Pelechano
DOI Crossref
Design of linear and cyclic peptide binders of different lengths from protein sequence information
Li Q, Vlachos EN, Bryant P
- - (-) - [2024-06-22; online 2024-06-22]
DDLS Fellow Patrick Bryant
PubMed DOI Crossref
Deciphering the functional specialization of whole-brain spatiomolecular gradients in the adult brain.
Vogel JW, Alexander-Bloch AF, Wagstyl K, ..., Satterthwaite TD, Seidlitz J
Proc. Natl. Acad. Sci. U.S.A. 121 (25) e2219137121 [2024-06-18; online 2024-06-11]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Disease progression modelling reveals heterogeneity in trajectories of Lewy-type α-synuclein pathology.
Mastenbroek SE, Vogel JW, Collij LE, ..., Beach TG, Hansson O
Nat Commun 15 (1) 5133 [2024-06-15; online 2024-06-15]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Cortical morphology variations during the menstrual cycle in individuals with and without premenstrual dysphoric disorder.
Dubol M, Stiernman L, Sundström-Poromaa I, Bixo M, Comasco E
J Affect Disord 355 (-) 470-477 [2024-06-15; online 2024-03-27]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Pharmaceutical Quality by Design Approach to Develop High-Performance Nanoparticles for Magnetic Hyperthermia.
Ansari SR, Suárez-López YDC, Thersleff T, ..., Rinaldi-Ramos CM, Teleki A
ACS Nano 18 (23) 15284-15302 [2024-06-11; online 2024-05-30]
Alexandra Teleki SciLifeLab Fellow
DOI Crossref
Fluoroquinolone-Specific Resistance Trajectories inE. coliand their Dependence on the SOS-Response
Teichmann L, Luitwieler S, Bengtsson-Palme J, ter Kuile B
- - (-) - [2024-06-06; online 2024-06-06]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Chemical signatures delineate heterogeneous amyloid plaque populations across the Alzheimer's disease spectrum.
Koutarapu S, Ge J, Dulewicz M, ..., Schöll M, Hanrieder J
bioRxiv - (-) - [2024-06-03; online 2024-06-03]
SciLifeLab Fellow Wojciech Michno
PubMed DOI Crossref
Atrial Fibrillation and Clonal Hematopoiesis in TET2 and ASXL1.
Saadatagah S, Naderian M, Uddin M, ..., Kullo IJ, Ballantyne CM
JAMA Cardiol 9 (6) 497-506 [2024-06-01; online 2024-04-10]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Mid-pregnancy allopregnanolone levels and trajectories of perinatal depressive symptoms.
Björväng RD, Walldén Y, Fransson E, ..., Sundström-Poromaa I, Skalkidou A
Psychoneuroendocrinology 164 (-) 107009 [2024-06-00; online 2024-02-28]
Erika Comasco SciLifeLab Fellow
DOI Crossref
Structure prediction of protein-ligand complexes from sequence information with Umol
Bryant P, Kelkar A, Guljas A, Clementi C, Noé F
Nat Commun 15 (1) - [2024-05-28; online 2024-05-28]
DDLS Fellow Patrick Bryant
PubMed DOI Crossref
Bacillamide D produced by Bacillus cereus from the mouse intestinal bacterial collection (miBC) is a potent cytotoxin in vitro.
Hohmann M, Brunner V, Johannes W, ..., Janßen KP, Gulder TAM
Commun Biol 7 (1) 655 [2024-05-28; online 2024-05-28]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
The protective role of commensal gut microbes and their metabolites against bacterial pathogens.
Cheng L, Correia MSP, Higdon SM, ..., Globisch D, Du J
Gut Microbes 16 (1) 2356275 [2024-05-26; online 2024-05-26]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
Effectiveness and Cost-effectiveness of Artificial Intelligence-assisted Pathology for Prostate Cancer Diagnosis in Sweden: A Microsimulation Study.
Du X, Hao S, Olsson H, ..., Eklund M, Clements M
Eur Urol Oncol - (-) - [2024-05-23; online 2024-05-23]
DDLS Fellow Kimmo Kartasalo
DOI Crossref
An atlas of protein-protein associations of human tissues prioritizes candidate disease genes
Laman Trip DS, van Oostrum M, Memon D, ..., Wollscheid B, Beltrao P
- - (-) - [2024-05-17; online 2024-05-17]
Andrea Fossati DDLS Fellow
PubMed DOI Crossref
The full spectrum of SLC22 OCT1 mutations illuminates the bridge between drug transporter biophysics and pharmacogenomics.
Yee SW, Macdonald CB, Mitrovic D, ..., Giacomini KM, Coyote-Maestas W
Mol. Cell 84 (10) 1932-1947.e10 [2024-05-16; online 2024-05-03]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
Compositional and functional differences of the vaginal microbiota of women with and without cervical dysplasia.
Norenhag J, Edfeldt G, Stålberg K, ..., Schuppe-Koistinen I, Olovsson M
Sci Rep 14 (1) 11183 [2024-05-16; online 2024-05-16]
DDLS Fellow Luisa Hugerth
PubMed DOI Crossref
Modeling brain sex in the limbic system as phenotype for female-prevalent mental disorders.
Matte Bon G, Kraft D, Comasco E, Derntl B, Kaufmann T
Biol Sex Differ 15 (1) 42 [2024-05-15; online 2024-05-15]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Iron oxide nanoparticles for treatment and diagnosis of chronic inflammatory diseases: A systematic review.
Ansari SR, Mahajan J, Teleki A
Wiley Interdiscip Rev Nanomed Nanobiotechnol 16 (3) e1963 [2024-05-10; online 2024-05-10]
Alexandra Teleki SciLifeLab Fellow
PubMed DOI Crossref
Cerebrospinal fluid reference proteins increase accuracy and interpretability of biomarkers for brain diseases.
Karlsson L, Vogel J, Arvidsson I, ..., Mattsson-Carlgren N, Hansson O
Nat Commun 15 (1) 3676 [2024-05-01; online 2024-05-01]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
White matter volume and treatment with selective progesterone receptor modulator in patients with premenstrual dysphoric disorder.
Kaltsouni E, Wikström J, Lanzenberger R, Sundström-Poromaa I, Comasco E
Psychoneuroendocrinology 163 (-) 106977 [2024-05-00; online 2024-01-22]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Disease staging of Alzheimer's disease using a CSF-based biomarker model.
Salvadó G, Horie K, Barthélemy NR, ..., Bateman RJ, Hansson O
Nat Aging 4 (5) 694-708 [2024-05-00; online 2024-03-21]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Cellular energy regulates mRNA degradation in a codon-specific manner.
Tomaz da Silva P, Zhang Y, Theodorakis E, ..., Pelechano V, Gagneur J
Mol Syst Biol 20 (5) 506-520 [2024-05-00; online 2024-03-15]
SciLifeLab Fellow Vicent Pelechano
PubMed DOI Crossref
Clonal Hematopoiesis of Indeterminate Potential With Loss of Tet2 Enhances Risk for Atrial Fibrillation Through Nlrp3 Inflammasome Activation.
Lin AE, Bapat AC, Xiao L, ..., Ellinor PT, Ebert BL
Circulation 149 (18) 1419-1434 [2024-04-30; online 2024-02-15]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Loss of NEDD8 in cancer cells causes vulnerability to immune checkpoint blockade in triple-negative breast cancer.
Papakyriacou I, Kutkaite G, Rúbies Bedós M, ..., Menden MP, Mao Y
Nat Commun 15 (1) 3581 [2024-04-27; online 2024-04-27]
SciLifeLab Fellow Yumeng Mao
PubMed DOI Crossref
Inference of drug off-target effects on cellular signaling using interactome-based deep learning.
Meimetis N, Lauffenburger DA, Nilsson A
iScience 27 (4) 109509 [2024-04-19; online 2024-03-14]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Comparison of the performance of multiple whole-genome sequence-based tools for the identification of Bacillus cereus sensu stricto biovar Thuringiensis.
Chung T, Salazar A, Harm G, ..., Carroll LM, Kovac J
Applied and environmental microbiology 90 (4) e0177823 [2024-04-17; online 2024-03-12]
DDLS Fellow Laura Carroll
PubMed DOI Crossref
Efficient calculation of orientation-dependent lipid dynamics from membrane simulations.
Doktorova M, Khelashvili G, Brown MF
bioRxiv - (-) - [2024-04-15; online 2024-04-15]
DDLS Fellow Milka Doktorova
PubMed DOI Crossref
Identification of New Ketamine Metabolites and Their Detailed Distribution in the Mammalian Brain.
Vallianatou T, de Souza Anselmo C, Tsiara I, ..., Lundgaard I, Globisch D
ACS Chem Neurosci 15 (7) 1335-1341 [2024-04-03; online 2024-03-20]
Daniel Globisch SciLifeLab Fellow
PubMed DOI Crossref
Rapid and Bifunctional Chemoselective Metabolome Analysis of Liver Disease Plasma Using the Reagent 4-Nitrophenyl-2H-azirine.
Lin W, Gerullat L, Braadland PR, ..., Hov JR, Globisch D
Angew. Chem. Int. Ed. Engl. 63 (14) e202318579 [2024-04-02; online 2024-01-31]
Daniel Globisch
PubMed DOI Crossref
Lifetime Duration of Breastfeeding and Cardiovascular Risk in Women With Type 2 Diabetes or a History of Gestational Diabetes: Findings From Two Large Prospective Cohorts.
Birukov A, Guasch-Ferré M, Ley SH, ..., Hu FB, Zhang C
Diabetes Care 47 (4) 720-728 [2024-04-01; online 2024-02-20]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Hybridization mediated range expansion and climate change resilience in two keystone tree species of boreal forests.
Karunarathne P, Zhou Q, Lascoux M, Milesi P
Glob Chang Biol 30 (4) e17262 [2024-04-00; online 2024-03-28]
Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
Estrogen receptor activation remodels TEAD1 gene expression to alleviate hepatic steatosis.
Sommerauer C, Gallardo-Dodd CJ, Savva C, ..., Williams C, Kutter C
Mol Syst Biol 20 (4) 374-402 [2024-04-00; online 2024-03-08]
Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
Direct Salmonella injection into enteroid cells allows the study of host-pathogen interactions in the cytosol with high spatiotemporal resolution.
Ernst C, Andreassen PR, Giger GH, ..., Hardt WD, Vorholt JA
PLoS Biol. 22 (4) e3002597 [2024-04-00; online 2024-04-29]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
Despite structural identity, ace-1 heterogenous duplication resistance alleles are quite diverse in Anopheles mosquitoes.
Claret JL, Di-Liegro M, Namias A, ..., Milesi P, Labbé P
Heredity (Edinb) 132 (4) 179-191 [2024-04-00; online 2024-01-27]
Pascal Milesi SciLifeLab Fellow
PubMed DOI Crossref
DIP-MS: ultra-deep interaction proteomics for the deconvolution of protein complexes.
Frommelt F, Fossati A, Uliana F, ..., Ciuffa R, Gstaiger M
Nat. Methods 21 (4) 635-647 [2024-04-00; online 2024-03-26]
Andrea Fossati DDLS Fellow
PubMed DOI Crossref
Biomarker-based staging of Alzheimer disease: rationale and clinical applications.
Therriault J, Schindler SE, Salvadó G, ..., Jack CR, Rosa-Neto P
Nat Rev Neurol 20 (4) 232-244 [2024-04-00; online 2024-03-01]
DDLS Fellow Jacob W Vogel
PubMed DOI Crossref
Designing efficient randstrobes for sequence similarity analyses.
Karami M, Soltani Mohammadi A, Martin M, ..., Patro R, Sahlin K
Bioinformatics 40 (4) - [2024-03-29; online 2024-04-05]
Kristoffer Sahlin SciLifeLab Fellow
PubMed DOI Crossref
Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity.
Moraes Zenker M, Portella TP, Pessoa FAC, Bengtsson-Palme J, Galetti PM
Sci Rep 14 (1) 7432 [2024-03-28; online 2024-03-28]
DDLS Fellow Johan Bengtsson-Palme
PubMed DOI Crossref
Salmonella T3SS-2 virulence enhances gut-luminal colonization by enabling chemotaxis-dependent exploitation of intestinal inflammation.
Gül E, Huuskonen J, Abi Younes A, ..., Bakkeren E, Hardt WD
Cell Reports 43 (3) 113925 [2024-03-26; online 2024-03-07]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
ProQ-dependent activation of Salmonella virulence genes mediated by post-transcriptional control of PhoP synthesis.
Bergman S, Andresen L, Kjellin J, ..., Sellin ME, Holmqvist E
mSphere 9 (3) e0001824 [2024-03-26; online 2024-02-27]
Mikael Sellin SciLifeLab Fellow
DOI Crossref
Cluster-free annotation of single cells using Earth mover’s distance-based classification
Forlin R, Tajvar P, Wang N, Dimarogonas D, Brodin P
- - (-) - [2024-03-20; online 2024-03-20]
DDLS-WASP
PubMed DOI Crossref
Plasma metabolites of a healthy lifestyle in relation to mortality and longevity: Four prospective US cohort studies.
Tessier AJ, Wang F, Liang L, ..., Hu FB, Guasch-Ferré M
Med 5 (3) 224-238.e5 [2024-03-08; online 2024-02-15]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Clonal haematopoiesis of indeterminate potential predicts incident cardiac arrhythmias.
Schuermans A, Vlasschaert C, Nauffal V, ..., Natarajan P, Honigberg MC
Eur. Heart J. 45 (10) 791-805 [2024-03-07; online 2023-11-12]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Uncovering driver genes in breast cancer through an innovative machine learning mutational analysis method.
Taheri G, Habibi M
Comput Biol Med 171 (-) 108234 [2024-03-00; online 2024-02-29]
DDLS Fellow Golnaz Taheri
PubMed DOI Crossref
The association of the RSC remodeler complex with chromatin is influenced by the prefoldin-like Bud27 and determines nucleosome positioning and polyadenylation sites usage in Saccharomyces cerevisiae.
Cuevas-Bermúdez A, Martínez-Fernández V, Garrido-Godino AI, ..., Pelechano V, Navarro F
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1867 (1) 194995 [2024-03-00; online 2023-11-13]
SciLifeLab Fellow Vicent Pelechano
PubMed DOI Crossref
Association of Somatic TET2 Mutations With Giant Cell Arteritis.
Robinette ML, Weeks LD, Kramer RJ, ..., Rao DA, Ebert BL
Arthritis & rheumatology (Hoboken, N.J.) 76 (3) 438-443 [2024-03-00; online 2024-02-02]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Risk factors for clonal hematopoiesis of indeterminate potential in people with HIV: a report from the REPRIEVE trial.
Bhattacharya R, Uddin MM, Patel AP, ..., Grinspoon SK, Natarajan P
Blood Adv 8 (4) 959-967 [2024-02-27; online 2024-01-10]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Predictive biomarkers of rapidly developing insulin deficiency in children with type 1 diabetes.
Lundkvist P, Grönberg A, Carlsson PO, Ludvigsson J, Espes D
BMJ Open Diabetes Res Care 12 (1) - [2024-02-27; online 2024-02-27]
Daniel Espes SciLifeLab Fellow
PubMed DOI Crossref
Equine enteroid-derived monolayers recapitulate key features of parasitic intestinal nematode infection.
Hellman S, Martin F, Tydén E, ..., Svedberg P, Fossum C
Vet Res 55 (1) 25 [2024-02-27; online 2024-02-27]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods.
Critical Assessment of Genome Interpretation Consortium
Genome Biol. 25 (1) 53 [2024-02-22; online 2024-02-22]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Spatial Neurolipidomics at the Single Amyloid-β Plaque Level in Postmortem Human Alzheimer's Disease Brain.
Michno W, Bowman A, Jha D, ..., Heeren RMA, Hanrieder J
ACS Chem Neurosci 15 (4) 877-888 [2024-02-21; online 2024-02-01]
SciLifeLab Fellow Wojciech Michno
PubMed DOI Crossref
Targeting MYC induces lipid droplet accumulation by upregulation of HILPDA in clear cell renal cell carcinoma.
Sainero-Alcolado L, Garde-Lapido E, Snaebjörnsson MT, ..., Schulze A, Arsenian-Henriksson M
Proc. Natl. Acad. Sci. U.S.A. 121 (7) e2310479121 [2024-02-13; online 2024-02-09]
SciLifeLab Fellow Vicent Pelechano
PubMed DOI Crossref
Stress biology: Complexity and multifariousness in health and disease.
Mayer MP, Blair L, Blatch GL, ..., Wang SXY, Zininga T
Cell Stress Chaperones 29 (1) 143-157 [2024-02-00; online 2024-02-03]
Anniina Vihervaara SciLifeLab Fellow
PubMed DOI Crossref
Plasma metabolite predictors of metabolic syndrome incidence and reversion.
Semnani-Azad Z, Toledo E, Babio N, ..., Hu FB, Guasch-Ferré M
Metabolism 151 (-) 155742 [2024-02-00; online 2023-11-24]
Clemens Wittenbecher DDLS Fellow
PubMed DOI Crossref
Multivalent insulin receptor activation using insulin-DNA origami nanostructures.
Spratt J, Dias JM, Kolonelou C, ..., Ruas JL, Teixeira AI
Nat Nanotechnol 19 (2) 237-245 [2024-02-00; online 2023-10-09]
Antonio Lentini DDLS Fellow
PubMed DOI Crossref
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]
Claudia Kutter SciLifeLab Fellow
PubMed DOI Crossref
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]
Mikael Sellin SciLifeLab Fellow
PubMed DOI Crossref
AutoTransOP: translating omics signatures without orthologue requirements using deep learning.
Meimetis N, Pullen KM, Zhu DY, ..., Magliacane S, Lauffenburger DA
NPJ Syst Biol Appl 10 (1) 13 [2024-01-29; online 2024-01-29]
Avlant Nilsson DDLS Fellow
PubMed DOI Crossref
Soluble and multivalent Jag1 DNA origami nanopatterns activate Notch without pulling force.
Smyrlaki I, Fördős F, Rocamonde-Lago I, ..., Teixeira AI, Högberg B
Nat Commun 15 (1) 465 [2024-01-18; online 2024-01-18]
Antonio Lentini DDLS Fellow
PubMed DOI Crossref
A structurally precise mechanism links an epilepsy-associated KCNC2 potassium channel mutation to interneuron dysfunction.
Clatot J, Currin CB, Liang Q, ..., Covarrubias M, Goldberg EM
Proc. Natl. Acad. Sci. U.S.A. 121 (3) e2307776121 [2024-01-16; online 2024-01-09]
Lucie Delemotte SciLifeLab Fellow
PubMed DOI Crossref
Longevity interventions modulate mechanotransduction and extracellular matrix homeostasis in C. elegans.
Teuscher AC, Statzer C, Goyala A, ..., Aebersold R, Ewald CY
Nat Commun 15 (1) 276 [2024-01-04; online 2024-01-04]
Andrea Fossati DDLS Fellow
PubMed DOI Crossref
Clonal Hematopoiesis Risk Score and All-Cause and Cardiovascular Mortality in Older Adults.
Saadatagah S, Uddin MM, Weeks LD, ..., Natarajan P, Ballantyne CM
JAMA Netw Open 7 (1) e2351927 [2024-01-02; online 2024-01-02]
Abhishek Niroula DDLS Fellow
PubMed DOI Crossref
Non-invasive imaging of sympathetic innervation of the pancreas in individuals with type 2 diabetes.
Vyakaranam AR, Mahamed MM, Hellman P, ..., Christoffersson G, Sundin A
Diabetologia 67 (1) 199-208 [2024-01-00; online 2023-11-07]
Daniel Espes Gustaf Christoffersson SciLifeLab Fellow
PubMed DOI Crossref
Electroencephalography findings in menstrually-related mood disorders: A critical review.
Kaltsouni E, Schmidt F, Zsido RG, ..., Sumner RL, Comasco E
Front Neuroendocrinol 72 (-) 101120 [2024-01-00; online 2024-01-02]
Erika Comasco SciLifeLab Fellow
PubMed DOI Crossref
Aberrant microbiomes are associated with increased antibiotic resistance gene load in hybrid mice.
Jarquín-Díaz VH, Ferreira SCM, Balard A, ..., Forslund-Startceva SK, Heitlinger E
ISME Commun 4 (1) ycae053 [2024-01-00; online 2024-04-15]
DDLS Fellow Johan Bengtsson-Palme
DOI Crossref
Transfer Learning-Assisted Inverse Modeling in Nanophotonics Based on Mixture Density Networks
Cheng L, Singh P, Ferranti F
IEEE Access 12 (-) 55218-55224 [2024-00-00; online 2024-00-00]
Prashant Singh SciLifeLab Fellow
SciLifeLab Data Centre
Publications 9.5.1