This list of my contributions should hopefully be up-to-date.


[1] N. Papili Gao, O. Gandrillon, A. Paldi, U. Herbach, and R. Gunawan. Universality of cell differentiation trajectories revealed by a reconstruction of transcriptional uncertainty landscapes from single-cell transcriptomic data. [bioRxiv · HAL]

Published papers

[5] U. Herbach. Stochastic gene expression with a multistate promoter: breaking down exact distributions. SIAM Journal on Applied Mathematics, 2019. [DOI · arXiv · HAL]

[4] 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]

[3] 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]

[2] 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]

[1] 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]

PhD Thesis

U. Herbach. From stochastic modelling of gene expression to inference of regulatory networks (in French). PhD thesis, University of Lyon, 2018. [HAL]