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.
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Timeline
Courses
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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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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2019Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea, Nat Microbiol 2019 Mar;.
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2018Prediction of the intestinal resistome by a three-dimensional structure-based method, Nat Microbiol 2019 Jan;4(1):112-123.
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2018Combined bacterial and fungal intestinal microbiota analyses: Impact of storage conditions and DNA extraction protocols, PLoS ONE 2018;13(8):e0201174.
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2018Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome, Parasit Vectors 2018 03;11(1):207.
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2017Characteristics of Fecal Microbiota in Pediatric Crohn’s Disease and Their Dynamic Changes During Infliximab Therapy, J Crohns Colitis 2017 Nov;.
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2017Protection of the human gut microbiome from antibiotics, J. Infect. Dis. 2017 Nov;.
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2017Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector, Sci Adv 2017 Aug;3(8):e1700585.
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2016Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection, Proc. Natl. Acad. Sci. U.S.A. 2016 May;.
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2016Capturing the most wanted taxa through cross-sample correlations, ISME J 2016 Mar;.
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