Gavish, Avishai;
Chain, Benny;
Salame, Tomer M;
Antebi, Yaron E;
Nevo, Shir;
Reich-Zeliger, Shlomit;
Friedman, Nir;
(2023)
From pseudo to real-time dynamics of T cell thymic differentiation.
iScience
, 26
(1)
, Article 105826. 10.1016/j.isci.2022.105826.
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Abstract
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 to 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.
| Type: | Article |
|---|---|
| Title: | From pseudo to real-time dynamics of T cell thymic differentiation |
| Location: | United States |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1016/j.isci.2022.105826 |
| Publisher version: | https://doi.org/10.1016/j.isci.2022.105826 |
| Language: | English |
| Additional information: | © 2022 The Author(s). This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). |
| Keywords: | Bioinformatics, Developmental biology, Stem cells research |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Div of Infection and Immunity |
| URI: | https://discovery-pp.ucl.ac.uk/id/eprint/10163321 |
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