Master thesis of Vincent Marty

In Schiebinger et al. (2019), the authors introduce the Waddington-OT algorithm (WOTA). Based upon Optimal Transport theory, this approach studies developmental time courses to infer ancestor-descendant fates and model the regulatory programs that underlie them. This was initially applied to explain cellular reprogramming of murine fibroblasts into IPSCs based on the expression of a group of transcription factors.

We will assess the relevance of the WOTA in a different setting, the CD8 T cell differentiation after antigen presentation. Within the frame of the MEMOIRE (MultiscalE MOdeling of CD8 T cell Immune Responses) ANR project, we plan to identify, at the single cell level, signatures associated with functionally relevant memory CD8 T cell subsets in mice, to characterize dynamical molecular networks that are predictive of their generation, and to build a multiscale model of this process. One important part of the internship, co-mentored by Fabien Crauste and Olivier Gandrillon, will consist in assessing the impact of low-level single cell RNAseq treatment (filtering, doublet detection, normalization, feature selection, denoising, dimensionality reduction) on the final output. Furthermore, the resulting trajectories will be compared with mainstream algorithms like Monocle.

ANR project 2019 - 2022