After a PhD in Bioinformatics on the metabolic networks of Trypanosoma brucei and sRNA-mRNA interaction graphs at the LaBRI (Bordeaux), I joined the DSIMB team (INTS) for a post-doc on structural modeling. Then, I performed a second post-doc at Metagenopolis – INRA Jouy-en-Josas, where I was initiated to the analysis of metagenomic data by Dusko Ehrlich (Leader of the Metahit project). This second post-doc was crucial in my career. I was dedicated to project studying microbiome – immunity with Danone Nutricia and microbiome – antibiotic resistance with Davolterra and the European project EvoTAR. I discovered during these projects that metagenomics was a field where I could apply all my previous experience in graph analysis and structural modeling to study the microbiome.
I was recruited at Institut Pasteur Paris in 2015 as research engineer to pursue my work on metagenomics and microbiome. I develop software dedicated to the treatment of metagenomic data by combining either the treatment of sequencing data, statistics, protein structural modeling and graph analysis. SHAMAN is great example of the help that we provide to community with software that provide an easy access to the microbiome secrets.
Courses
Cours Bioinformatique Assemblage / Métagénomique
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 […]
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 […]
Projects
Software
Former Teams
CV
Professional experience :
September 2015 to present | Research engineer in the HUB of bioinformatics and biostatistics, Institut Pasteur |
2013-2015 | Postdoctoral researcher at Metagenopolis, INRA Jouy-en-Josas. Supervisors : Nicolas Pons, S. Dusko Ehrlich Developpement of pipeline dedicated to the assembly, annotation and differential analysis of metagenomic data. Involved in EVOTAR project (http://www.evotar.eu/), DAV132-CL1002 clinical study of DaVolterra company (http://www.davolterra.com/) and Danone research program. |
2012-2013 | Postdoctoral researcher INSERM UMR 665, INTS Paris, University of Paris Diderot. Supervisors : Alexandre G. de Brevern, Nathalie Caulet Subject:Structural modeling of laccase proteins |
March – April 2010 | Scientific consultant at the Institut Dermatologique d’Aquitaine (IDEA) Supervisor : Frédéric Nunzi (Directeur du département In Vitro chez IDEA ) Subject : Statistical analysis of phototoxicity of cosmetic compounds. |
Formation :
2012 | Ph.D of Bioinformatics – Laboratoire Bordelais de Recherche en Informatique (LaBRI) – University of Bordeaux 1 and Centre de Bioinformatique de Bordeaux (CBiB) (France). Subject : Methodological development for the analysis of metabolic networks and non coding RNA Supervisors : Maylis Delest, Patricia Thébault, Isabelle Dutour |
2009 | Master of Bioinformatics – University of Paris Diderot (France). |
2007 | Licence of Bioinformatics University of Paris Diderot (France). |
2006 | DUT (two-year university degree in technology) in biology University of Paris XII (France). |
Publications
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2023Antagonism of ALAS1 by the Measles Virus V protein contributes to degradation of the mitochondrial network and promotes interferon response., PLoS Pathog 2023 Feb; 19(2): e1011170.
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2023Genes mcr improve the intestinal fitness of pathogenic E. coli and balance their lifestyle to commensalism., Microbiome 2023 Jan; 11(1): 12.
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2022A Clinical Study Provides the First Direct Evidence That Interindividual Variations in Fecal β-Lactamase Activity Affect the Gut Mycobiota Dynamics in Response to β-Lactam Antibiotics., mBio 2022 Nov; 13(6): e0288022.
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2021Distinct systemic and mucosal immune responses during acute SARS-CoV-2 infection., Nat Immunol 2021 Sep; 22(11):1428-1439.
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2021Mining zebrafish microbiota reveals key community-level resistance against fish pathogen infection., ISME J 2021 03; 15(3): 702-719.
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2020SHAMAN: a user-friendly website for metataxonomic analysis from raw reads to statistical analysis., BMC Bioinformatics 2020 Aug; 21(1): 345.
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2020Exome-wide association study reveals largely distinct gene sets underlying specific resistance to dengue virus types 1 and 3 in Aedes aegypti., PLoS Genet 2020 05; 16(5): e1008794.
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2020Impact of the gut microbiota on the m6A epitranscriptome of mouse cecum and liver., Nat Commun 2020 03; 11(1): 1344.
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2020Leucine-Rich Immune Factor APL1 Is Associated With Specific Modulation of Enteric Microbiome Taxa in the Asian Malaria Mosquito, Front Microbiol 2020;11:306.
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2019A simple, reproducible and cost-effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach, Sci Rep 2019 Aug;9(1):11331.
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