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Diffusion pseudotime robustly reconstructs lineage branching

Item Type:Article
Title:Diffusion pseudotime robustly reconstructs lineage branching
Creators Name:Haghverdi, L. and Büttner, M. and Wolf, F.A. and Buettner, F. and Theis, F.J.
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.
Keywords:Algorithms, Cell Differentiation, Cell Lineage, Cluster Analysis, Computer-Assisted Numerical Analysis, Computer Simulation, Diffusion, Embryonic Stem Cells, Genetic Models, High-Throughput Nucleotide Sequencing, Single-Cell Analysis, Statistical Models, Animals, Mice
Source:Nature Methods
ISSN:1548-7091
Publisher:Nature Publishing Group
Volume:13
Number:10
Page Range:845-848
Date:October 2016
Official Publication:https://doi.org/10.1038/nmeth.3971
PubMed:View item in PubMed
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https://edoc.mdc-berlin.de/19027/Preprint version

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