title: Diffusion pseudotime robustly reconstructs lineage branching.
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.
authors: Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.|Department of Mathematics, Technische Universität München, Munich, Germany.
authors: Laleh
authors: L
authors: Haghverdi
authors: Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.
authors: Maren
authors: 0000-0002-6189-3792
authors: M
authors: Büttner
authors: Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.
authors: F Alexander
authors: FA
authors: Wolf
authors: Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.|European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.
authors: Florian
authors: F
authors: Buettner
authors: Helmholtz Zentrum München, German Research Center for Environmental Health, Institute of Computational Biology, Neuherberg, Germany.|Department of Mathematics, Technische Universität München, Munich, Germany.
authors: Fabian J
authors: 0000-0002-2419-1943
authors: FJ
authors: Theis
mesh_terms: D000465:Algorithms; D000818:Animals; D002454:Cell Differentiation / Q000235:genetics*; D019070:Cell Lineage / Q000235:genetics*; D016000:Cluster Analysis; D003198:Computer Simulation; D004058:Diffusion; D053595:Embryonic Stem Cells / Q000166:cytology; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D051379:Mice; D008957:Models, Genetic; D015233:Models, Statistical; D009716:Numerical Analysis, Computer-Assisted; D059010:Single-Cell Analysis / Q000379:methods*