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About

I joined the C3BI Hub in 2016 after a curriculum widely dedicated to Bioinformatics studies, and more precisely to Phylogeny and Evolution, topics of my PhD thesis.

At Institut Pasteur, I am involved in projects dealing with sequences homology : alignments, hmm profiles, making homologous family databases, kmers signatures. I am also a developer (Python / C++) with a solid interest in optimization as well as in developing usable tools for final user such as automated pipeline for metagenomics sequence analysis.

I’m currently embedded in Marc Eloit’s team (80% of my work time). My main task in this team is to develop strategies to identify, in their metagenomics samples, new pathogens, or new combination pathogen / symptoms. The rest of my time, I manage small projects and participate to the Hub life. I am currently experimenting with functional programming (for now, using Python) and its applicability to bioinformatics issues.

CV

Education

PhD (2013)

Bioinformatics (Evolutionary Biology), supervised by Guy Perrière, LBBE, Université de Lyon (France). Automatic Pattern Matching in Phylogenetic Trees.
During this PhD, I studied how phylogenetical information can be efficiently extracted from a collection of numerous gene tree family, using topological information, mimicking a human scientist visually deciphering gene trees one by one. I designed a formalism to query a set of gene trees with some peculiar topological patterns. I also wrote a software to perform these queries among thousands of trees in seconds. This software suite has been published in BMC Bioinformatics: Bigot et al. 2013 (10.1186/1471-2105-14-109).
This concept of tree pattern has been used to select trees among large collections with peculiar explicit constrained pattern, but also with more generic criteria, eg. those containing only unicopy genes, or automatically find the best root according to a reference species tree, or using duplications in the gene tree.

PhD thesis [french]: https://tmgo.net/~thomas/these_doctorat

Masters Degree (2009)

Health and Populations (speciality Bioinformatics, Biostatistics, Genome), Université Claude Bernard Lyon 1.

Publications

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