Diffusion pseudotime robustly reconstructs lineage branching

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


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Animals
  • Cell Differentiation / genetics*
  • Cell Lineage / genetics*
  • Cluster Analysis
  • Computer Simulation
  • Diffusion
  • Embryonic Stem Cells / cytology
  • High-Throughput Nucleotide Sequencing / methods*
  • Mice
  • Models, Genetic*
  • Models, Statistical*
  • Numerical Analysis, Computer-Assisted
  • Single-Cell Analysis / methods*