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Nat Methods. 2016 Oct;13(10):845-8. doi: 10.1038/nmeth.3971. Epub 2016 Aug 29.

Diffusion pseudotime robustly reconstructs lineage branching.

Author information

1
Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.
2
Department of Mathematics, Technische Universität München, Munich, Germany.
3
European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

Abstract

The temporal order of differentiating cells is intrinsically encoded in their single-cell expression profiles. We describe an efficient way to robustly estimate this order according to diffusion pseudotime (DPT), which measures transitions between cells using diffusion-like random walks. Our DPT software implementations make it possible to reconstruct the developmental progression of cells and identify transient or metastable states, branching decisions and differentiation endpoints.

PMID:
27571553
DOI:
10.1038/nmeth.3971
[Indexed for MEDLINE]

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