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  • program_project
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  • tool
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  • Assistant Professor
  • Associate Professor
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  • Clinician Researcher
  • Department Manager
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  • Honorary Professor
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  • Permanent Researcher
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  • PhD Student
  • Physician
  • Post-doc
  • Prize
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  • Research Associate
  • Research Engineer
  • Retired scientist
  • Technician
  • Undergraduate Student
  • Veterinary
  • Visiting Scientist
  • Deputy Director of Center
  • Deputy Director of Department
  • Deputy Director of National Reference Center
  • Deputy Head of Facility
  • Director of Center
  • Director of Department
  • Director of Institute
  • Director of National Reference Center
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  • Labex Coordinator
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About

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

09:30
15
Oct 2020
Course

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
09:00
10
May 2016
Course

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 […]
Claudia Chica
Frédéric Lemoine
Jack Christophe Cossec
Hugo Varet
Anne Biton
Natalia Pietrosemoli
Guilhem Janbon
Varun Khanna
Rachel Torchet
Pierre Lechat
Amine Ghozlane
Nicolas Maillet
Axel Cournac
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

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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