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Lange, M. ; Piran, Z.* ; Klein, M.* ; Spanjaard, B.* ; Klein, D. ; Junker, J.P.* ; Theis, F.J. ; Nitzan, M.*

Mapping lineage-traced cells across time points with moslin.

Genome Biol. 25:277 (2024)
Verlagsversion DOI PMC
Open Access Gold
Creative Commons Lizenzvertrag
Simultaneous profiling of single-cell gene expression and lineage history holds enormous potential for studying cellular decision-making. Recent computational approaches combine both modalities into cellular trajectories; however, they cannot make use of all available lineage information in destructive time-series experiments. Here, we present moslin, a Gromov-Wasserstein-based model to couple cellular profiles across time points based on lineage and gene expression information. We validate our approach in simulations and demonstrate on Caenorhabditis elegans embryonic development how moslin predicts fate probabilities and putative decision driver genes. Finally, we use moslin to delineate lineage relationships among transiently activated fibroblast states during zebrafish heart regeneration.
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Publikationstyp Artikel: Journalartikel
Dokumenttyp Wissenschaftlicher Artikel
Korrespondenzautor
Schlagwörter Cellular Dynamics ; Fate Decisions ; Lineage Tracing ; Optimal Transport ; Regeneration; Heart Regeneration; Gene-expression; Sensory-neuron; Multi-omics; Fate; Identity; Protein; Differentiation; Reconstruction; Trajectories
ISSN (print) / ISBN 1474-760X
e-ISSN 1465-6906
Zeitschrift Genome Biology
Quellenangaben Band: 25, Heft: 1, Seiten: , Artikelnummer: 277 Supplement: ,
Verlag BioMed Central
Verlagsort Campus, 4 Crinan St, London N1 9xw, England
Nichtpatentliteratur Publikationen
Begutachtungsstatus Peer reviewed
Institut(e) Institute of Computational Biology (ICB)
Förderungen EU
BMBF
Israel Science Foundation
DZHK (German Centre for Cardiovascular Research)
Wellcome Leap, Delta Tissue
Wellcome Trust
ERC
European Union
Helmholtz Association
Azrieli Foundation
Joachim Herz Foundation
DFG