Après une thèse d’informatique sur l’analyse de graphes de réseaux métaboliques et interactions des petits ARN avec les ARN messagers, j’ai effectué un premier post-doc dans l’équipe DSIMB (INTS) sur la modélisation structurale des laccases. J’ai ensuite rejoint l’INRA de Jouy-en-Josas à Metagenopolis où j’ai été initié à l’analyse de données de métagénomique quantitative de flore intestinale humaine. J’ai enfin été recruté au HUB en 2015 où je développe des méthodes d’analyses des données métagénomiques par l’utilisation d’approche de métagénomique quantitative, statistiques, de modélisation structurale et d’analyse de graphe.
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Courses
Bioinformatics program for PhD students 2023 2024
This training program in statistics, bioinformatics and image analysis, financed by INCEPTION program, begins with a mandatory common core during which we will present all the tracks, and follow short courses on computer science, […]
Bioinformatics and Biostatistics HUB
Image Analysis Hub
INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations
Research and Resource Centre for Scientific Informatics
Emeline Perthame
Emmanuelle Permal
Marvin Albert
Jean-Yves Tinevez
Victoire Baillet
Thomas Bigot
Pascal Campagne
Elodie Chapeaublanc
Claudia Chica
Anđela Davidović
Stephan Fischer
Amine Ghozlane
Julien Guglielmini
Vincent Guillemot
Elise Jacquemet
Bernd Jagla
Hanna Julienne
Julia Kende
Vincent Laville
Frédéric Lemoine
Gaëlle Letort
Blaise Li
Yann Loe-Mie
Hélène Lopez-Maestre
Nicolas Maillet
Sébastien MELLA
Juliette Meyer
Olivier Mirabeau
Damien Mornico
Thomas Obadia
Adrien Pain
Minh-Son Phan
Natalia Pietrosemoli
Stéphane Rigaud
Violaine Saint-André
Rachel Torchet
Hugo Varet
Amaury Vaysse
Laura Xénard
2023-10-23 09:30:00
2024-06-28 17:00:00
Europe/Paris
Bioinformatics program for PhD students 2023 2024
This training program in statistics, bioinformatics and image analysis, financed by INCEPTION program, begins with a mandatory common core during which we will present all the tracks, and follow short courses on computer science, […]
25-28 Rue du Docteur Roux, Paris, France
Cours Bioinformatique Assemblage / Métagénomique
2022-10-17 09:00:00
2022-10-21 17:00:00
Europe/Paris
Cours Bioinformatique Assemblage / Métagénomique
Université Paris-Diderot, rue Thomas-Mann, Paris, France
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 […]
Image Analysis Hub
Bioinformatics and Biostatistics HUB
INCEPTION – Institut Convergence for the study of Emergence of Pathology Through Individuals and Populations
Computational Biology
Center for Technological Resources and Research
Vincent Guillemot
Christophe Malabat
Jean-Yves Tinevez
Marie-Agnès Dillies
Frédéric Lemoine
Nicolas Maillet
Blaise Li
Stevenn Volant
Pascal Campagne
Hugo Varet
Hanna Julienne
Violaine Saint-André
Julien Guglielmini
Thomas Bigot
Quentin Giai Gianetto
Claudia Chica
Rachel Legendre
Adrien Pain
Natalia Pietrosemoli
Emeline Perthame
Stéphane Rigaud
Benoît Lelandais
Dmitry Ershov
Sébastien MELLA
Anđela Davidović
Thomas Obadia
Véronique Hourdel
Amine Ghozlane
Alexis Criscuolo
Amaury Vaysse
2020-10-15 09:30:00
2021-06-03 17:00:00
Europe/Paris
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 […]
25-28 Rue du Dr Roux, 75015 Paris, France
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 […]
2016-05-10 09:00:00
2016-06-28 12:00:00
Europe/Paris
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 […]
28 Rue du Dr Roux, Paris, France
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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2024Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases., Microbiome 2024 Mar; 12(1): 50.
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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 Mar; 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 Anopheles stephensi., Front Microbiol 2020 ; 11(): 306.
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