TY - JOUR
T1 - From pseudo to real time dynamics of T cell thymic differentiation
AU - Gavish, Avishai
AU - Chain, Benny
AU - Salame, Tomer M.
AU - Antebi, Yaron E.
AU - Katz, Shir
AU - Reich-Zeliger, Shlomit
AU - Friedman, Nir
PY - 2023/1/20
Y1 - 2023/1/20
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85145292410&partnerID=8YFLogxK
U2 - 10.1016/j.isci.2022.105826
DO - 10.1016/j.isci.2022.105826
M3 - مقالة
SN - 2589-0042
VL - 26
JO - iScience
JF - iScience
IS - 1
M1 - 105826
ER -