This list should hopefully be up-to-date.
U. Herbach. Gene regulatory network inference from single-cell data using a self-consistent proteomic field. [arXiv · HAL]
M.-A. Jean, L. Lenôtre, C.-A. Philip, E. Faller, U. Herbach, S. Warembourg, P. Branche, T. Milane, and G. Escriva-Boulley. Physical activity delivered by videoconference and symptoms management in endometriosis: a case series. [SportRxiv]
M. Gaillard and U. Herbach. Efficient stochastic simulation of gene regulatory networks using hybrid models of transcriptional bursting. In: Computational Methods in Systems Biology, Lecture Notes in Computer Science, 2025. [DOI · arXiv · HAL]
F. Prista von Bonhorst, O. Gandrillon, U. Herbach, C. Robert, C. Chazaud, Y. De Decker, D. Gonze, and G. Dupont. Uncovering candidate Nanog-Helper genes in early mouse embryo differentiation using differential entropy and network inference. Scientific Reports, 2025. [DOI · Res Sq · HAL]
A. Koshkin, U. Herbach, M. Rodríguez Martínez, O. Gandrillon, and F. Crauste. Stochastic modeling of a gene regulatory network driving B cell development in germinal centers. PLOS One, 2024. [DOI · bioRxiv · HAL]
G. Escriva-Boulley, CA. Philip, S. Warembourg, L. Lenôtre, P. Flore, P. Faure, T. Michy, V. Letouzey, C. Arnold, C. Piluso, L. Chalmel, R. Kacem, GF. Blum, R. Detayrac, C. Trocmé, I. Brigaud, U. Herbach, P. Branche, E. Faller, and A. Chalabaev. Effects of a physical activity and endometriosis-based education program delivered by videoconference on endometriosis symptoms: the CRESCENDO program (inCRease physical Exercise and Sport to Combat ENDOmetriosis) protocol study. Trials, 2023. [DOI · HAL]
U. Herbach. Harissa: stochastic simulation and inference of gene regulatory networks based on transcriptional bursting. In: Computational Methods in Systems Biology, Lecture Notes in Computer Science, 2023. [DOI · arXiv · HAL]
E. Ventre, U. Herbach, T. Espinasse, G. Benoit, and O. Gandrillon. One model fits all: combining inference and simulation of gene regulatory networks. PLOS Computational Biology, 2023. [DOI · bioRxiv · HAL]
N. Papili Gao, O. Gandrillon, A. Páldi, U. Herbach, and R. Gunawan. Single-cell transcriptional uncertainty landscape of cell differentiation. F1000Research, 2023. [DOI · bioRxiv · HAL]
U. Herbach. Stochastic gene expression with a multistate promoter: breaking down exact distributions. SIAM Journal on Applied Mathematics, 2019. [DOI · arXiv · HAL]
A. Bonnaffoux, U. Herbach, A. Richard, A. Guillemin, S. Giraud, P.-A. Gros, and O. Gandrillon. WASABI: a dynamic iterative framework for gene regulatory network inference. BMC Bioinformatics, 2019. [DOI · bioRxiv · HAL]
U. Herbach, A. Bonnaffoux, T. Espinasse, and O. Gandrillon. Inferring gene regulatory networks from single-cell data: a mechanistic approach. BMC Systems Biology, 2017. [DOI · arXiv · HAL]
A. Richard, L. Boullu, U. Herbach, A. Bonnaffoux, V. Morin, E. Vallin, A. Guillemin, N. Papili Gao, R. Gunawan, J. Cosette, O. Arnaud, J.-J. Kupiec, T. Espinasse, S. Gonin-Giraud, and O. Gandrillon. Single-cell-based analysis highlights a surge in cell-to-cell molecular variability preceding irreversible commitment in a differentiation process. PLOS Biology, 2016. [DOI · HAL]
D. Lamonica, U. Herbach, F. Orias, B. Clément, S. Charles, and C. Lopes. Mechanistic modelling of daphnid-algae dynamics within a laboratory microcosm. Ecological Modelling, 2016. [DOI · HAL]