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About

Phylogenetics

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).

Pathogens

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).

Publications & Citations (Google Scholar)

 

Current and recent services

Distinctions

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Events

MCEB 2016

Address: Hameau de l'Etoile, Saint-Martin-de-Londres, France
2016-06-12 17:00:00 2016-06-16 17:00:00 Europe/London MCEB 2016 Mathematical and Computational Evolutionary Biology Conference The huge amount of molecular data available nowadays can help addressing new and essential questions in evolution. Answering these questions require efficient and sound mathematical and computational models […] Hameau de l'Etoile, Saint-Martin-de-Londres, France

MCEB 2017

Address: Porquerolles, Hyères, France
2017-06-12 14:00:00 2017-06-16 14:00:00 Europe/London MCEB 2017 The huge amount of molecular data available nowadays can help addressing new and essential questions in evolution. Answering these questions require efficient and sound mathematical and computational models and tools. The Mathematical and Computation […] Porquerolles, Hyères, France

Projects

Publications