Research overview
My research focuses on the
modelling and analysis of discrete events systems, relying on adequate mathematical frameworks. After working on a variety of industrial applications, I made a major change in the 2000s, when I started working on the modelling of biological networks. Since then, my activity has been organised along 3 main lines: methodological work, computational tools and standardisation and concrete biological applications.
- Methodological advances:
With diverse collaborators and members of my groups, we have defined original methods to analyse logical models of regulatory and signalling networks. Because they permit to study much larger models, these methods constitute altogether a significant breakthrough in the field. These advances include:
- Stable states identification and feedback circuit analysis (e.g. DOI)
- Model reduction preserving essential dynamical properties (e.g. DOI)
- Model-checking techniques to verify properties of biological relevance (e.g. DOI)
- Identification and reachability quantification of attractors in asynchronhous logical models (DOI)
- Definition of reverse models to efficiently assess basins of attraction in asynchronous dynamics (manuscript in preparation).
I have also considered the use of Petri nets (PN) in computational biology (e.g. DOI)
- Computational tools and standardisation:
This activity makes the links between methodological developments and concrete modelling studies. Indeed, to make the developed methods available to the community, but also to support our modelling work, we strive to develop appropriate software tools, the most well-known being GINsim, reference tool for the logical modelling of regulatory networks (e.g. DOI).
More recently, with P. Monteiro, we have developed EpiLog, a new software tool implementing a cellular
automaton framework for the logical modelling of pattern formation on epithelia (DOI).
To ensure reproducibility as well as supporting model exchange,
I was deeply involved in a collective work to set up SBML L3 Qualitative Models package (SBML qual), an SBML package defining a standard format for qualitative
models of biological networks.
I also contributed to the foundation of the Consortium for Logical Modeling and Tools (CoLoMoTo), which brings together modellers, developers of methods and tools, as well as curators.
- Biological case studies: These were performed in collaboration with biologists to develop models of networks controlling a variety of cellular processes, notably:
- Regulatory control of cell adhesion in EMT (DOI)
- Sex determination in different organisms (e.g. DOI)
- Patterns of genetic alterations (co-occurrences and exclusivities) in bladder cancer (DOI)
- Formation of dorsal appendages formation in the fly oocyte (DOI)
- T helper cell differentiation (e.g. DOI)
- Segmentation of the early embryo (DOI)
- Mammalian cell cycle (e.g. DOI)
