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Denis Thieffry

Computational systems biology

This team is part of the Computional Biology Center.

Main lines of research


Our team combines two interdisciplinary approaches to model the behaviour of molecular regulatory networks.
The first approach leans on the development of the software suite RSAT (http://www.rsat.eu) 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 the software GINsim (http://www.ginsim.org) 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.

Book

Van Helden J, Toussaint A, Thieffry D (eds.). Bacterial Molecular Networks. Methods in Molecular Biology Series. Humana Press, (2012) 546 pages.

Articles

Sardina JL*, Collombet S*, Tian TV, Gómez A, Di Stefano B, Berenguer C, Brumbaugh J, Stadhouders R, Segura-Morales C, Gut M, Gut IG,Heath S, Aranda S, Di Croce L, Hochedlinger K, Thieffry D and Graf T. Transcription factors drive Tet2-mediated enhancer demethylation to reprogram cell fate. Cell Stem Cell (2018) 23: 727-41.

Nga Thi Thuy Nguyen NT, Contreras-Moreira B, Castro-Mondragon JA, Santana-Garcia W, Ossio R, Robles-Espinoza CD, Bahin M, Collombet S, Vincens P, Thieffry D, van Helden J*, Medina-Rivera A*, Thomas-Chollier M*. RSAT 2018: Regulatory Sequence Analysis Tools 20th Anniversary. Nucleic Acids Research (2018) 46: W209-14.

Collombet S, van Oevelen C, Sardina Ortega JL, Abou-Jaoudé W, Di Stefano B, Thomas-Chollier M, Graf T, Thieffry D. Logical modeling of lymphoid and myeloid cell specification and transdifferentiation. PNAS (2017) 14:23 5792–5799.

Di Stefano B*, Collombet S*, Jakobsen JS, Wierer M, Sardina JL, Lackner A, Stadhouders R, Segura-Morales C, Francesconi M, Limone F, Mann M, Porse B, Thieffry D, Graf T. C/EBPα creates elite cells for iPSC reprogramming by upregulating Klf4 and increasing the levels of Lsd1 and Brd4. Nature Cell Biology (2016) 18: 371-81.

Medina-Rivera A, Defrance M, Sand O, Herrmann C, Castro-Mondragon JA, Delerce J, Jaeger S, Blanchet C, Vincens P, Caron C, Staines DM, Contreras-Moreira B, Artufel M, Charbonnier-Khamvongsa L, Hernandez C, Thieffry D, Thomas-Chollier M#, van Helden J#. RSAT 2015: Regulatory Sequence Analysis Tools. Nucleic Acids Research (2015) 43: W50-6.




ChIP-exo signal covering ChIP-seq peaks allows to infer genomic binding (...)
ChIP-exo signal covering ChIP-seq peaks allows to infer genomic binding modes of cooperating transcription factors
Molecular map for the main MAPK pathways (built with CellDesigner (...)
Molecular map for the main MAPK pathways (built with CellDesigner Software)
Logical model for the lymphoid and myeloid cell specification and (...)
Logical model for the lymphoid and myeloid cell specification and transdifferentiation (built with GINsim software)