evolutionary computational biology

Our Darwinian view on evolution states that evolution is the result of random changes of our genetic code combined with the process of natural selection. Many small changes over a long period of time have a major evolutionary impact. As a result, even true orthologs can share only low sequence similarity, which we refer to as conservation in the twilight or midnight zone.

We are interested in several aspects of evolutionary biology:

functional evolution

The process of evolution is universal and never-ending. It allows organisms to adapt to their environment, can create novel function, but can also lead to deleterious loss. Computationally, as well as experimentally, evolution is studied in many ways and from many different angles. We approach this questions from two different sides.

Crystal structure of the binding of a WD40 protein with one of its ligands (crystal structure 3EU7, binding motif LIG_PALB2_WD40_1 )

• 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 ... more

E. coli developing a defense strategy against M. xanthus

• 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 combine our experiments with -omics techniques to identify causative and so, adaptive mutations ... more

evolutionary developmental biology / evo-devo

Oscarella lobularis
Image credits: Dorian Guillemain from Service de Plongée OSU Pytheas, Marseille, France

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 ... more

genome biology: repeats in genomes

Transposable elements are DNA sequences that can jump within a genome. Sometimes, they are also referred to 'jumping genes'. They are very frequent in our genomes and make up large parts of the genomes of eukaryotes. Some of them have meanwhile evolved to fulfill crucial functions in our genomes, for instance for regulating gene expression.

In one of our projects, led by Sebastien Tempel, we are interested in the analysis of the evolution of transposable elements by detecting and comparing their internal patterns. We also study of the evolution of transposable elements and their relationship with their host genome ... more

genome biology: de novo sequencing and assembly of transcriptomes and genomes

We are involved in a number of de novo genome and transcriptome sequencing, assembly and annotation projects, including the genome and transcriptome from mexican Axolotl, which has one of the largest vertebrate genomes sequenced to date (30GB); from the homoscleromorph sponge Oscarella lobularis; and some bacterial species we or our collaborators are working with ... more