My researches in bioinformatics aim to understand and model the evolution of molecular sequences : proteins, genes, genomes and genome communities.
I have worked on the design of Bayesian phylogenetic models, first applied to the proteins' and genes' evolution (Blanquart and Lartillot 2006, 2008, see below : "Bayesian models for phylogenetic reconstruction"), now applied to the inference of ancestral genome arrangements.
I have work on several applications of phylogenetic models linked to the inference of ancestral sequences (Boussau et al 2008, Richter et al 2010, Groussin et al 2013, Reisinger et al 2014, and see below "Ancestral sequences reconstruction").
More recently, I worked on the architecture of the eukaryotic gene and to estimate how new exons, alternative transcripts, splices and translations appeared and evolved in eukaryote species (see below "Gene architecture in Eukaryotes").
Bayesian models for phylogenetic reconstruction
The phylogenetic models "BP" (Blanquart and Lartillot 2006) and "CAT+BP" (Blanquart and Lartillot 2008) implement non-stationary and non-homogeneous stochastic processes for both amino-acid and nucleotide substitutions. Both the models allow to fit global compositional variations along the phylogenetic tree branches, and CAT+BP moreover implements the CAT model component (Lartillot and Philippe 2004) estimating a mixture of site specific substitution processes.
Those models are implemented into the NH_PhyloBayes package for phylogenetic reconstruction.
Ancestral sequences reconstruction
Phylogenetic inferences basically produce prediction on the past.
One possible prediction is the inferred ancestral gene at any internal node of the phylogenetic tree.
The ancestral gene could be subsequently synthesised, expressed and translated in order to estimate the biological properties of its protein product.
I was involved in few collaborations pursuing such an objective.
In Boussau et al (2008) and Groussin et al (2013), we interpreted the ancestral compositions of large protein alignment concatenations as reflecting the temperatures of paleo-environments (collaborations with the "Laboratoire de Biométrie et Biologie Évolutive", CNRS Lyon 1 University, France).
In Richter et al (2010) and Reisinger et al (2014) we estimate the ancestors of Histidine H and Histidine F co-enzymes at le root of the cellular tree, LUCA. Those reconstructions yield functional enzymes as well as indications on the deep evolution of the TIM barrels folds (collaborations with the "Institut für Biophysik und physikalische Biochemie", Regensburg University, Germany).
Finally, an ongoing work focuses on the estimation of a "pathway" of several malate dehydrogenase ancestors adapting to high salt concentrations in Archaea (collaborations with the "Institut de Biologie Structurale", CNRS, Grenoble, France).
Gene architecture in Eukaryotes
Understanding and modelling the architecture of the eukaryote gene is the objective of the associated team CG-Alcode .
This three years long funding starts in 2014.
Some papers are in preparation.