University professor
Invited Research Professor (part-time) at the Cancer Sciences Institute, National University of Singapore
computational biology, dynamical modelling of cellular networks
Department of Biology
, updated on
21 December 2021
Denis Thieffry
2ème étage, bureau 240a
46, rue d'Ulm 75230 Paris cedex 05
01 44 322352

Professor of Systems Biology at ENS, I lead a computational biology research team at IBENS. Our team aims to decipher the regulatory networks that control proliferation, differentiation and cell death, as well as to model their dynamical behaviors

Field of research

Our team combines three interdisciplinary approaches to model the behaviour of molecular regulatory networks.

The first approach leans on the development of the software suite RSAT devoted to the analysis of functional genomic data (ChIP-seq, transcriptome) in order to delineate cis-regulatory regions (promoters, enhancers) and their role in the control of gene expression.

The second approach leans on the development of methodologies for the joint analysis of complementary large-scale functional genomic data (RNA-seq, miRNA-seq, ChIP-seq at bulk and single-cell resolution) in order to decipher the molecular mechanisms driving specific biological states.

The third approach leans on the development of the software GINsim devoted to the dynamical modelling and the analysis or large signalling/regulatory networks.

These methodological developments are motivated by and applied to the study of regulatory networks controlling cell specification, differentiation and reprogramming in animals, in particular of cells of the immune system, in close collaboration with several experimental teams.

Tools and models are systematically made available to the scientific community.


  •  Floc’hlay S, Molina MD, Hernandez C, Haillot E, Thomas-Chollier M, Lepage T, Thieffry D (2021). Deciphering and modelling the TGF-β signalling interplays specifying the dorsal-ventral axis of the sea urchin embryo. Development 148: dev189944.
  • Grandclaudon M, Perrot-Dockès M, Trichot C, Karpf L, Abouzid O, Chauvin C, Sirven P, Abou-Jaoudé W, Berger F, Hupé P, Thieffry D, Sansonnet L, Chiquet J, Levy-Leduc C, Soumelis V (2019). A quantitative multivariate model of human dendritic cell-T helper cell communication. Cell 179: 432-447.
  • Naldi A*, Hernandez C, Abou-Jaoudé W, Monteiro PT, Chaouiya C*, Thieffry D* (2018). Logical modelling and analysis of cellular regulatory networks with GINsim 3.0. Frontiers in Physiology 9: 646.
  • Collombet S, van Oevelen C, Sardina-Ortega JL , Abou-Jaoudé W , Thomas-Chollier M, Graf T*, Thieffry D* (2017). Logical modeling of hematopoietic cell specification and reprogramming. Proceedings of the National Academy of Sciences of the United States of America 114: 5792-9.
  • Di Stefano B, Collombet S, Jakobsen JS, Wierer M, Lackner A, Sardina JL, Segura-Morales C, Stadhouders R, Limone F, Mann M, Porse B, Thieffry D, Graf T (2016). How C/EBPα creates elite cells for pluripotency. Nature Cell Biology 18: 371-81.