evolutionary computational biology

• Protein motif detection and evolution

Short linear sequence motifs in proteins are essential for proteins to interact with each other and other (macro-)molecules. While we know millions of proteins, our knowledge of protein motifs is rather limited: the Eukaryotic Linear Motif (ELM) database lists to date only ~5000 known and experimentally verified protein motifs. 
Experimentally, it is labor- and time-intensive to identify novel protein motifs. Computationally, the task is equally difficult, due to the shortness and generally low conservation of motifs.
Protein motifs are also interesting in the light of evolution: by motif gain or loss, protein function can be easily modified: as protein motifs are very short - and are thought to reside primarily in disordered regions of proteins, ex nihilo motif evolution can lead to novel protein functions. 

We are interested in de novo motif prediction, as well as understanding motif evolution.

• Predator-prey co-evolution

In evolution, the Red Queen Hypothesis states that species must constantly adapt, evolve and proliferate  to survive in the constant battle against co-evolving species. Many examples exist in the animal kingdom that demonstrate this co-evolutionary process.

We look at predator-prey evolution in a much simpler world, the world of bacteria. In a very close collaboration with the team of Tam Mignot (from LCB, Marseille), we investigate how the predatory bacteria Myxococcus xanthus and its prey, E. coli, co-evolve and develop higher predatory or higher defense skills. We use a combination of metabolic modelling and phylogenetic analysis to integrate -omics data from our collaboration partners, and to understand better the metabolic warfare between predatory and prey. 

We recently received ANR funding for this project (ANR project FattyMix, led by Emmanuelle Bouveret (Institut Pasteur) and togethter with Tam MIgnot (LCB).

Sponges (Porifera) are at the base of animal evolution; they are some of the first, metazoan (multicellular) animals. Sponges are also popular model organisms to study early traits of multicellular animals. One such trait is the presence of an epithelium, which helps define an 'inner' and an 'outer' side of a body or an organ. 

Using the homoscleromorph sponge Oscarella lobularis and in close collaboration with the labs of Andre le Bivic (IBDM) and Carole Borchiellini (IMBE), we are looking at the evolution of epithelia in these animals.