Ulysse Herbach

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.

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.

The paper uses CALISTA to reconstruct transcriptional uncertainty landscapes from single-cell data, revealing universal patterns in cell differentiation trajectories.

This paper combines two methods to use a single gene regulatory network model for both inference and simulation of transcriptional profiles from time-course single-cell data.

WASABI infers causal gene regulatory networks from time-stamped single-cell data, revealing a distributed network structure without hub genes in avian erythroid differentiation.