Jacques Dainat

Jacques Dainat NBIS expert

genome annotation, transcriptome annotation, transcriptome assembly, phylogenetics, phylogenomics, comparative genomics, evolutionary sequence analysis


I studied Bioinformatics at the Science University of Montpellier (France), and obtained a Phd in Bioinformatics, Structural biochemistry and Genomics at the Marseille University (France). During my Phd I focused on the analysis and the detection of unitary pseudogenes in eukaryotes. For this purpose, I developed expert system modules that generate and analyze heterogeneous data (e.g phylogenetic trees, protein predictions, sequence ancestral reconstructions, sequence comparisons, parsimony reconstruction of events, etc.). This approach allowing detecting loss and pseudogenization events occurred during evolution and also detecting intact genes not yet annotated. Pseudogenization process at genomic level can be observed for recent pseudogenes. I was equally involved in the creation and analysis of phylome of the chordata proteome.

Then I was PostDoc during one year at the International Center for Higher Education In Agricultural Sciences. My work focused on the detection of positive selection at large scale among angiosperm genomes thanks to an original method. Instead to traditional method used (codeml) we used MapNH that provides a prior estimation of parameters, which allows to considerably improving the computational time. The aim is to study the impact of recurrent gene duplication on adaptation of plant genomes. I also worked on the highlight of the species tree of Triticeae. To address this issue I used super matrix and super tree methods. Since I started within NBIS early 2014 I focus mainly on whole genome annotations.

Selected publications

Gouret, P., Paganini, J., Dainat, J., Louati, D., Darbo, E., Levasseur, P. P., and Anthony (2011) Integration of evolutionary biology concepts for functional annotation and automation of complex research in evolution: The multi-agent software system DAGOBAH. In, Springer-Verlag (ed), Evolutionary Biology – Concepts, Biodiversity, Macroevolution and Genome Evolution., pp. 71–87.

Levasseur, A., Paganini, J., Dainat, J., Thompson, J. D., Poch, O., Pontarotti, P., and Gouret, P. (2012) The chordate proteome history database. Evolutionary bioinformatics online, 8, 437–47.

Dainat, J., Paganini, J., Pontarotti, P., and Gouret, P. (2012) GLADX: an automated approach to analyze the lineage-specific Loss and Pseudogenization of Genes. PLoS One, 7, e38792.