Biological systems rely on complex interaction networks at various scales. Using published datasets or working in collaboration with experimentalists, we are building models to understand emergent phenomena in biology as well as predict their temporal evolution. We are particularly interested by decision making in early embryogenesis and in building predictive dynamical models for microbial communities. All our projects rely on the theory of non-linear dynamics, statistical learning and statistical physics techniques.
- Embryonic development: How do cells take decisions about their fates? What are the molecular mechanisms underlying these decisions? To answer those questions and understand reproducibility in the process, we focus on the early embryonic development of ascidians which are marine animals with a very simple embryogenesis. We are particularly interested in the link between the geometry of the embryo, via the surfaces of contact between cells, and cell fate assignment. More recently, we started working on information transmission and ask if the geometry of the embryo is optimally set for the establishment of cell fates. Eventually we aim at integrating signaling and mechanics to link the cell fate map to the fertilized egg. This work is done in collaboration with the lab of H. Yasuo, Geneviève Dupont and Aleksandra Walczak.
- Engineering genetic circuits for synthetic biology: In the long term, we aim to design bottom-up microbial cell factories for the production of bioplastics, in collaboration with Eveline Peeters and Wim Vranken. In the short term, we aim to 1) develop and optimise metabolite-responsive biosensor modules and 2) rationally design synthetic regulatory circuits to improve the performance of production pathways in E. coli - the most studied prokaryotic organism.
- Dynamical modeling of microbial communities: We aim at building dynamical models for human-associated microbial communities. We are interested in mechanisms leading to community structure and in predicting responses to perturbations, such as antibiotic treatments.
Papers
Rossana Bettoni, Genevieve Dupont, Aleksandra M. Walczak & Sophie de Buyl
Géraldine Williaume, Sophie de Buyl, Cathy Sirour, Nicolas Haupaix, Kaoru Imai, Yutaka Satou, Geneviève Dupont, Rossana Bettoni, Clare Hudson & Hitoyoshi Yasuo
