My PhD thesis adressed formal verification of embedded systems. It was defended at IRCCyN (Nantes, France) on December 13, 2007. It focused on a time extension of Petri nets incorporating the concept of clock that could be stopped and resumed: Petri nets with stopwatches. These suspension/resuming mechanisms are an integral part of preemptive scheduling policies for embedded systems, but are also at the roots of many biological regulatory networks.
After my PhD, I felt the need to study the living instead of machines. That’s how I got interested in this new area of application of formal methods that are biological systems.
Once I have been recruited as an Associate Professor in Computer Science at Ecole Centrale de Nantes (ECN) in 2008, I have joined the MeForBio (Formal Methods Applied to Bio-Informatics) team at IRCCyN. In Systems Biology, we study biological systems (such as regulatory networks of genes) that can be expressed as formal models. In order to verify (and control) properties of these systems, it is possible to implement model-checking methods instead of simulating all possible behaviors.
My main research interests involve the application of formal verification methods in bioinformatics, including:
Model-checking genetic regulatory networks
Inference of temporal parameters in biological regulatory networks
Methodological approaches based on the complementarity between models