biostudies-literatureUnknown7Chen JSingle-cell RNA-sequencing offers unprecedented resolution of the continuum of state transition during cell differentiation and development. However, tools for constructing multi-branching cell lineages from single-cell data are limited. Here we present Mpath, an algorithm that derives multi-branching developmental trajectories using neighborhood-based cell state transitions. Applied to mouse conventional dendritic cell (cDC) progenitors, Mpath constructs multi-branching trajectories spanning from macrophage/DC progenitors through common DC progenitor to pre-dendritic cells (preDC). The Mpath-generated trajectories detect a branching event at the preDC stage revealing preDC subsets that are exclusively committed to cDC1 or cDC2 lineages. Reordering cells along cDC development reveals sequeNature communications11988https://www.ebi.ac.uk/biostudies/studies/S-EPMC4931327biostudies-literatureMpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development.PMC4931327Ginhoux FChen JSchlitzer APoidinger MChakarov SfalseMpath maps multi-branching single-cell trajectories revealing progenitor cell progression during development.Single-cell RNA-sequencing offers unprecedented resolution of the continuum of state transition during cell differentiation and development. However, tools for constructing multi-branching cell lineages from single-cell data are limited. Here we present Mpath, an algorithm that derives multi-branching developmental trajectories using neighborhood-based cell state transitions. Applied to mouse conventional dendritic cell (cDC) progenitors, Mpath constructs multi-branching trajectories spanning from macrophage/DC progenitors through common DC progenitor to pre-dendritic cells (preDC). The Mpath-generated trajectories detect a branching event at the preDC stage revealing preDC subsets that are exclusively committed to cDC1 or cDC2 lineages. Reordering cells along cDC development reveals seque2016-01-01T00:00:00Z2016 Jun2026-05-04T10:43:21.069Z2019-03-27T02:17:27ZS-EPMC49313272735650310.1038/ncomms11988