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About

I joined the Bioinformatics 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 the Laboratory of Pathogen Discovery lead by Marc Eloit (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.

Courses

CV

Academic Degrees

PhD (2013)

Bioinformatics (Evolutionary Biology), under the supervision of Guy Perrière, LBBE, University of Lyon, France. Automated search for patterns in phylogenetic trees.
This PhD was an opportunity to investigate how to efficiently extract phylogenetic information from collections of trees of homologous gene families, using the topological information that these trees contain, in the same way as one does when analyzing a tree visually. I have created a formalism to describe these tree patterns and a software suite to execute these queries on thousands of trees in a few seconds. This software suite was published in BMC Bioinformatics: Bigot et al. 2013 (10.1186/1471-2105-14-109).
This concept of topological pattern searching can be used to describe specific patterns corresponding to a list of constraints, but also in a more generic way, to automatically extract trees containing only one gene version per species (unicopy trees) or to find the best root with respect to a reference species tree, or by using duplications contained in the gene tree.

PhD Thesis (in French) : https://tmgo.net/~thomas/these_doctorat

Master (2009)

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

Publications

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