WASABI: a dynamic iterative framework for gene regulatory network inference. - Arnaud Bonnaffoux; Ulysse Herbach; Angélique Richard; Anissa Guillemin; Sandrine Gonin-Giraud; Pierre-Alexis Gros; Olivier Gandrillon (BMC Bioinform., 2019)

Stochastic Gene Expression with a Multistate Promoter: Breaking Down Exact Distributions. - Ulysse Herbach (SIAM J. Appl. Math., 2019)

Harissa: Stochastic Simulation and Inference of Gene Regulatory Networks Based on Transcriptional Bursting. - Ulysse Herbach (CMSB, 2023)

One model fits all: Combining inference and simulation of gene regulatory networks. - Elias Ventre; Ulysse Herbach; Thibault Espinasse; Gérard Benoit; Olivier Gandrillon (PLoS Comput. Biol., 2023)