%0 Journal Article %A Laleh Haghverdi %A Maren Büttner %A F. Alexander Wolf %A Florian Buettner %A Fabian J. Theis %T Diffusion pseudonyme robustly reconstructs lineage branching %D 2016 %R 10.1101/041384 %J bioRxiv %P 041384 %X 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. %U https://www.biorxiv.org/content/biorxiv/early/2016/02/29/041384.full.pdf