Fabien Crauste A

Cell Trajectory Inference based on Optimal Transport and a mechanistic stochastic gene expression model

This paper introduces a method for cell trajectory inference using optimal transport with a mechanistic stochastic gene expression model, showing the Bursty model better captures gene dynamics than the Diffusive model.

Multiscale modeling of the spatial structure of stem cells in neuroblastoma patient-derived tumoroids reveals a critical role for a short-range diffusive process

This study uses a multiscale agent-based model to show that short-range diffusive signaling among stem cells is critical for reproducing the spatial structure of neuroblastoma tumoroids.

Stochastic modeling of a gene regulatory network driving B cell development in germinal centers

The paper uses a stochastic model to fit single-cell transcriptomic data and shows it can recapitulate mRNA distributions during B cell differentiation in germinal centers.

In silico modelling of CD8 T cell immune response links genetic regulation to population dynamics

This study models CD8 T cell immune response using a multiscale agent-based approach to link genetic regulation to population dynamics.

Practical Identifiability in the Frame of Nonlinear Mixed Effects Models: the Example of the in vitro Erythropoiesis

The paper assesses practical identifiability in nonlinear mixed effects models using a multistart approach to simplify a model of chicken erythropoiesis and improve parameter estimation.

Drugs modulating stochastic gene expression affect the erythroid differentiation process

The paper identifies drugs that modulate stochastic gene expression and shows their impact on erythroid differentiation.

Calibration, Selection and Identifiability Analysis of a Mathematical Model of the in vitro Erythropoiesis in Normal and Perturbed Contexts

The paper develops a mathematical model of in vitro erythropoiesis, identifies its parameters, and evaluates the impact of Rapamycin on cellular differentiation.