Career overview
I have received my doctoral degree in Computer Science in 2000 from the University Bordeaux 1 under the direction of Antoine Rauzy, on the subject of binary decision diagrams and their application to the reliability analysis of complex industrial systems. I have subsequently worked for two years in the United States as a research engineer for Synopsys, before returning to France in 2002 to a position of Research Scientist (Chargee de Recherches) with the CNRS. As a founding member of the MaBioVis team in the LaBRI, I work with biologists in comparative genomics and systems biology. For the academic year 2009-2010 I was at the Poncelet CNRS Laboratory in Moscow, Russia where I also held the responsibility of a group leader at the NII Genetika Institute. After having returned to Bordeaux in september 2010, I have accepted the joint responsibility to direct the research group Modeling and Comparison of sequences and biological structures within the MaBioVis team at the LaBRI as well as the technological plateform CBiB (Centre de Bioinformatique de Bordeaux).
Research overview
My research focuses on algorithms and formal models for the study of complex systems, designed to help biologists understand the relations between genomes, their genetic elements, and the behavior of the resulting cellular systems. For the past ten years I have developed these subjects, as a natural continuation of my earlier work in formal methods, and in close collaboration with colleagues in the life sciences.
In particular I have worked in two distinct but related subjects: algorithms for pattern recognition, inference, and search for optimal solutions in large search spaces; and model- ing, for building rigorous descriptions of complex dynamic systems and establishing formal properties about their behaviors. At a practical level, the software developed by myself and those I have supervised addresses several challenges in knowledge engineering: integration of heterogenous data, interactive exploration of large data sets, and interoperability of data and programs. For the latter, the international standards we have helped define are adopted by national data centers and industry, attesting both to the scale of the problem and the pertinence of our approach.