Network Modelling

Claudine Chaouiya

Thanks to great technological advances, regulatory networks are being uncovered that control cellular processes.

Complementary to experimental approaches, mathematical models allow to get further insights into the functioning of these complex networks and to formulate hypotheses, e.g. identify proper strategies to enforce or prevent certain properties.

In this context, considering the dimensions and complexity of the networks at stake, the research group mainly relies on the logical framework, which can uncover the key characteristics of the dynamics of such large networks, as demonstrated by a growing number of published models.

Their activity is mainly organized along three lines:

Methodological developments to enhance the analysis of large interaction networks (properties in terms of attractors, reachability, etc.);
Implementation of new methods in the form of software tools;
Development of models to tackle specific biological questions, in close collaboration with experimentalists.

Publications

Abou-Jaoudé, W., Traynard, P., Monteiro, P.T., Saez Rodriguez, J., Helikar, T., Thieffry, D., Chaouiya, C. (2016) Logical modeling and dynamical analysis of cellular networks. Front Genet. 7 : 00094
Sánchez, L., Chaouiya, C. (2016) Primary sex determination of placental mammals: a modelling study uncovers dynamical developmental constraints in the formation of Sertoli and granulosa cells. BMC Syst Biol. 10 : 37

Abou-Jaoudé, W., Monteiro, P.T. Naldi, A., Grandclaudon, M., Soumelis, V., Chaouiya, C.,, Thieffry, D. (2015) Model checking to assess T-helper cell plasticity.Front Bioeng Biotechnol. 2 : 00086
Naldi, A., Monteiro, P.T., Müssel, C., the Consortium for Logical Models and Tools, Kestler, H.A., Thieffry, D., Xenarios, I., Saez-Rodriguez, J., Helikar, T., Chaouiya, C.(2015) Cooperative development of logical modelling standards and tools with CoLoMoTo. Bioinformatics. 31 (7) : 1154-9
Remy, E., Rebouissou, S., Chaouiya, C., Zinovyev, A., Radvanyi, F., Calzone, L. (2015) A modelling approach to explain mutually exclusive and co-occurring genetic alterations in bladder tumorigenesis. Cancer Res. 75(19) : 4042-52
Fauré, A., Vreede, B.M.I., Sucena, É., Chaouiya, C. (2014) A discrete model of Drosophila eggshell patterning reveals cell-autonomous and juxtacrine effects PLoS Comput Biol. 10 : e1003527
Mombach, J.C.M., Bugs, C.A., Chaouiya, C. (2014) Modelling the onset of senescence at the G1/S cell cycle checkpoint. BMC Genom. 15 : S7