From pseudo to real time dynamics of T cell thymic differentiation

Avishai Gavish, Benny Chain, Tomer M. Salame, Yaron E. Antebi, Shir Katz, Shlomit Reich-Zeliger, Nir Friedman

Research output: Contribution to journalArticlepeer-review


Numerous methods have recently emerged for ordering single cells along developmental trajectories. However, accurate depiction of developmental dynamics can only be achieved after rescaling the trajectory according to the relative time spent at each developmental point. We formulate a model which estimates local cell densities and fluxes, and incorporates cell division and apoptosis rates, to infer the real time dimension of the developmental trajectory. We validate the model using mathematical simulations, and apply it on experimental high dimensional cytometry data obtained from the mouse thymus to construct the true time-profile of the thymocyte developmental process. Our method can easily be implemented in any of the existing tools for trajectory inference.
Original languageEnglish
Article number105826
Number of pages15
Issue number1
Early online date17 Dec 2022
StatePublished - 20 Jan 2023


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