After a PhD in informatics on graph analysis (metabolic networks and sRNA-mRNA interaction graphs) at the LaBRI (Université de 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. I was recruited at the HUB in 2015, and since I pursue the development of methods dedicated to the treatment of metagenomic data by combining either the treatment of sequencing data, the statistics, the protein structural modeling and the graph analysis.
Host microbiota modification by epidemic Listeria monocytogenes
Listeriolysin S is a bacteriocin specifically produced in the intestine of orally infected mice and necessary for Listeria monocytogenes survival in this organ. In order to investigate whether this toxin might influence the composition […]
SHAMAN: SHiny Application for Metagenomic ANalysis
SHAMAN is a SHiny Application for Metagenomic ANalysis including the normalization, the differential analysis and mutiple visualization. SHAMAN is based on DESeq2 R package [Anders and Huber 2010] for the analysis of metagenomic data, […]
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.
|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).|
2018Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome, Parasit Vectors 2018 Mar;11(1):207.
2017Characteristics of Fecal Microbiota in Pediatric Crohn’s Disease and Their Dynamic Changes During Infliximab Therapy, J Crohns Colitis 2017 Nov;.
2017Protection of the human gut microbiome from antibiotics, J. Infect. Dis. 2017 Nov;.
2017Carryover effects of larval exposure to different environmental bacteria drive adult trait variation in a mosquito vector, Sci Adv 2017 Aug;3(8):e1700585.
2016Bacteriocin from epidemic Listeria strains alters the host intestinal microbiota to favor infection, Proc. Natl. Acad. Sci. U.S.A. 2016 May;.
2016Capturing the most wanted taxa through cross-sample correlations, ISME J 2016 Mar;.
2015Protein flexibility in the light of structural alphabets, Front Mol Biosci 2015;2:20.
2014Alterations of the human gut microbiome in liver cirrhosis, Nature 2014 Sep;513(7516):59-64.
2013Genome-wide detection of sRNA targets with rNAV, Biological Data Visualization,2013:81-88.
2012Flux Analysis of the Trypanosoma brucei Glycolysis Based on a Multiobjective-Criteria Bioinformatic Approach, Adv Bioinformatics 2012;2012:159423.
+View full list of publications