Metagenomics methods provide public health sciences with the ability to detect a plethora of known and unknown viromes in clinical samples. In this context, Next-generation sequencing (NGS) technologies have a tremendous impact, taking into account currently available and possible future platforms and bioinformatics. The massive data produced by NGS presents a significant challenge for data analysis and management. As such, advanced bioinformatic tools have become essential for the successful application of NGS technology.
Metagenomics for Pathogen Detection
Pathogen detection and characterization methods in public health infectious disease surveillance rely on the identification of agents that are already known to be associated with a particular clinical syndrome. Metagenomics, as an emerging field […]
Summary of the project More than 60% of infectious diseases in humans are caused by pathogens likewise circulating in domestic animals and wildlife. Most of these pathogens are viruses whose genome is an RNA […]
Pôle de Génotypage des Pathogènes (PGP)
The Genotyping of Pathogens Pole, the centre for microbial genomics of the Environment and Infectious Risks Research and Expertise Unit, provides skills with genotyping and genomics technologies for the characterization of sensitive pathogens and/or […]
June 2006 – June 2012 : Mass-Spectrometry Proteomics and Genomics Bio-informatics – Systems Biology Lab, Institut Pasteur, Paris.
May 2005 – May 2006 : Post-doc Bio-informatics — Ecole Normale Supérieure, Paris.
May 2004 – May 2005 : Post-doc Systems Biology — University Basel, Switzerland.
Ph.D. (March 2004), computer science, Laboratoire bordelais de Recherche en Informatique (LABRI, Université de Bordeaux I, France), and Institut National de Recherche en Informatique et Automatique (I.N.R.I.A. Rocquencourt, France).
“Algorithms and statistical metrics or assessing the significance of functional motifs in biological regulatory sequences.” – Promotors: Dr. M. Régnier, Prof. Dr. S. Dulucq).
M.Sc. (June 2000), Laboratory of Protein Biochemistry and Protein Engineering, University of Ghent, Belgium.
“Cloning and expression of the Chlorobium limicola forma thiosulfatophylum cytochrome c-551 gene and its influence in the thio- sulfate consuming gene-cluster” – Promoteurs: Prof. Dr. J. Van Beeumen, Dr. ir. F. Verté; Laboratory for Biochemistry, microbiology et physiology.
2016MetaGenSense: A web-application for analysis and exploration of high throughput sequencing metagenomic data, Correia D, Doppelt-Azeroual O, Denis JB et al. MetaGenSense: A web-application for analysis and exploration of high throughput sequencing metagenomic data. F1000Research 2016, 4:86 (doi: 10.12688/f1000research.6139.3) .
2016Genomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis, Sci Rep 2016;6:30379.
2016Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications, BMC Genomics 2016 Feb;17:118.
2016Mycobacterial pan-genome analysis suggests important role of plasmids in the radiation of type VII secretion systems, Genome Biology and Evolution.
2015Distinct lineages of Ebola virus in Guinea during the 2014 West African epidemic, Nature 2015 Aug;524(7563):102-4.
2014Multicenter outbreak of infections by Saprochaete clavata, an unrecognized opportunistic fungal pathogen, MBio 2014 Dec;5(6).
2014Pantoea coffeiphila sp. nov., cause of the ‘potato taste’ of Arabica coffee from the African Great Lakes region, Int. J. Syst. Evol. Microbiol. 2015 Jan;65(Pt 1):23-9.
2014A preliminary study of viral metagenomics of French bat species in contact with humans: identification of new mammalian viruses, PLoS ONE 2014;9(1):e87194.
2012Automated phosphopeptide identification using multiple MS/MS fragmentation modes, J. Proteome Res. 2012 Dec;11(12):5695-703.
2008Alignment of LC-MS images, with applications to biomarker discovery and protein identification, Proteomics 2008 Feb;8(4):650-72.
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