Diffusion pseudotime robustly reconstructs lineage branching

Single-cell gene expression profiles of differentiating cells encode their intrinsic latent temporal order. We describe an efficient way to robustly estimate this order according to a diffusion pseudotime , which measures transitions on all length scales between cells using diffusion-like random walks. This allows us to identify cells that undergo branching decisions or are in metastable states, and thereby genes differentially regulated at these states.