After a PhD in bioinformatics at Inria/IRISA, Université de Rennes 1, Rennes (France), under the supervision of Dominique Lavenier and Pierre Peterlongo, I did a postdoc in bioinformatics at Laboratory of Ecology and Evolution of Plankton in Stazione Zoologica Anton Dohrn of Naples, Italy. Both my thesis and my postdoc were about the Tara Oceans projet and the development of new software to analyze huge quantities of raw reads coming from metagenomics sample. I am currently occupying a research engineer position at the Hub and focus on different computing problems including metagenomics, protein assembly and several short term developments.
Bioinformatics program for PhD students 2020-2021
This mandatory training program, required for all Institut Pasteur PhD students, begins with a group of common core courses including a knowledge base in reproducible research, R Programming and Statistics. Each student then can […]
Introduction to Python Programming
Python is often used to learn programming as it is very readable and easy to write. Python is a very popular language in bioinformatics where many programs and libraries are written in python. This […]
Introduction to data analysis
This five weeks graduate level course will give participants basic skills and hands-on training in biostatistics. It will cover all the steps of an analysis workflow : design, collection, curation, hypothesis testing and data […]
Morning session – Introduction to NGS data analysis
The Hub of Bioinformatics and Biostatistics at the Institut Pasteur organizes thematic courses open to everybody. The second session, entitled “Introduction to NGS data analysis” will take place every Tuesday, from the May 10th […]
Rapid Peptides Generator (RPG)
Rapid Peptides Generator (RPG), is a standalone software dedicated to predict proteases-induced cleavage sites on sequences. RPG is a python tool taking a (multi-)fasta/fastq file of proteins as input and digest each of them. […]
Listeriomics: an Interactive Web Platform for Systems Biology of Listeria
Listeriomics integrates all complete genomes, transcriptomes and proteomes published for Listeria species to date. It allows navigating among all these datasets with enriched metadata in a user-friendly format. listeriomics.pasteur.fr The main purpose of the website is […]
Compareads is a tool designed to extract similar reads between potentially huge metagenomic datasets (i.e., hundreds of millions reads per dataset)
COMMET (“COmpare Multiple METagenomes”) provides a global similarity overview between all datasets of a large metagenomic project. Directly from non-assembled reads, all against all comparisons are performed through an efficient indexing strategy. Then, results […]
2013PhD in Bioinformatics
Genscale team, Inria/IRISA, Université de Rennes 1, Rennes, France
2010Research Master’s Degree of Science
Université de Rennes 1, Rennes, France
2008Bachelor’s Degree in Computer Science
Université de Bretagne Sud, Vannes, France
2006Higher National Diploma of Computer Science
IUT Informatique, Université de Bretagne Sud, Vannes, France
2004French Scientific Baccalaureate
Lycée Joubert, Ancenis, France
Pasteur (HUB, department C3BI)
2014Postdoctoral position in Bioinformatics
Stazione Zoologica Anton Dohrn of Naples, Italy (Laboratory of Ecology and Evolution of Plankton)
2019Rapid Peptides Generator: fast and efficient in silico protein digestion, NAR Genomics and Bioinformatics 2020 Mar;2(1):lqz004.
2019Community‐Level Responses to Iron Availability in Open Ocean Plankton Ecosystems, Global Biogeochemical Cycles 2019 Jan;33(3):391-419.
2017Marine diatoms change their gene expression profile when exposed to microscale turbulence under nutrient replete conditions, Sci. Rep. 7, 016303–11 (2017).
2017Listeriomics: an Interactive Web Platform for Systems Biology of Listeria, mSystems 2017 Mar-Apr;2(2).
2014COMMET: comparing and combining multiple metagenomic datasets, BIBM, IEEE 2014 Nov.
2013Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species, Gigascience 2013;2(1):10.
2012Compareads: comparing huge metagenomic experiments, BMC Bioinformatics 2012;13 Suppl 19:S10.
2012Genome-wide patterns of divergence during speciation: the lake whitefish case study, Philos. Trans. R. Soc. Lond., B, Biol. Sci. 2012 Feb;367(1587):354-63.
2011Assemblathon 1: a competitive assessment of de novo short read assembly methods, Genome Res. 2011 Dec;21(12):2224-41.