My main research interest is in the field of evolution and phylogeny. My focus is on the mathematical and computational tools and concepts, which form an essential basis of evolutionary studies (2005 book, 2007 book).
I am working on algorithms for phylogenetic inference. I (co)authored several software programs, some widely diffused and well cited: BioNJ (Mol Biol Evol 1997), FastME (J Comp Biol 2002, Mol Biol Evol 2004, Mol Biol Evol 2015) , SDM (Syst Biol 2006), PhyD* (BMC Bioinformatics 2008), Phylogeny.fr (NAR 2008), SeaView (Mol Biol EVol 2010), and PhyML (Syst Biol 2003, Syst Biol 2010, Highly Cited!).
Beyond tree building, testing is essential. I coauthored fast tests for branch support (Syst Biol 2006, Syst Biol 2011). Currently, I have several projects along this line, to design fast, reliable tests for large phyogenies.
To build trees, estimate evolutionary distances and study sequence evolution, we need models. I coauthored probabilistic models to describe protein evolution (Phil Trans Roy Soc B 2008, Mol Biol Evol 2008, Syst Biol 2010, Mol Biol Evol 2012), and a new estimation method for amino acid replacement matrices, which was used to infer the the LG matrix (Mol Biol Evol 2008, Bioinformatics 2011).
We recently published a very fast dating method, implemented in the LSD software (Syst Biol 2015), with application to large (virus) phylogenies.
With Mike Steel and Fabio Pardi, we addressed several theoretical questions related to tree building from evolutionary distances (Mol Biol Evol 2006, Bull Math Biol 2010, PNAS 2012, Algorithmica 2015), and to reconstruct ancestral characters (Math Biosciences 2010, Syst Biol 2014).
During the last years, I turned part of my activities toward pathogens, most notably Plasmodium falciparum and HIV.
Regarding P. falciparum our main goal was to decipher the function of its genes, most of them being fully unknown. We used postgenomic data and machine learning approaches to propose functional predictions for a number of its genes (BMC Bioinformatics 2008, BMC Genomics 2010). We refined the annotation of its proteins in structural domains (Bioinformatics 2009, BMC Bioinformatics 2012) and designed the RED2 method and program to search for regulation motifs (Genome Biology 2012). We also studied the origin of P. falciparum (BMC Evol Biol 2011)
Regarding HIV and other viruses, notably Influenza, we implemented the PhyloType web server to extract relevant clusters or “phylotypes” from a phylogeny combined with extrinsic characters. PhyloType was applied to the phylogeography of HIV epidemics (Bioinformatics 2013) and to the trasmission of resistance mutations (AIDS 2015).
Current and recent services
- Center for Bioinformatics, Biostatistics and Integrative Biology , Institut Pasteur – Paris (director since launching, March 2015)
- Computational Biology Institute, Montpellier (director, until December 2015).
- Systematic Biology (associate editor)
- BMC Evolutionary Biology, BMC Bioinformatics, Algorithms for Molecular Biology, Evolutionary Bioinformatics (editorial board)
- Mathematical and Computational Evolutionary Biology, Montpellier, 2012, 2013, 2014, 2015 (co-chair)
- Computational Molecular Evolution, EMBO Courses, Heraklion 2016 (instructor)
- Wellcome Trust-EMBL-EBI advanced course on Computational Molecular Evolution, Hinxton 2015 (instructor)
- Fast Breaking Paper in 2005 and Current Classic in Environment & Ecology 2007 – 2011 (Science Watch, Thomson Reuters)
- Médaille d’Argent 2009 du Centre National de la Recherche Scientifique (CNRS)