Diffusion pseudotime robustly reconstructs lineage branching

Laleh Haghverdi, Maren Büttner, F. Alexander Wolf, Florian Buettner, Fabian J. Theis

Research output: Contribution to journalArticlepeer-review

664 Scopus citations


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.

Original languageEnglish
Pages (from-to)845-848
Number of pages4
JournalNature Methods
Issue number10
StatePublished - 1 Oct 2016


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