Table of Contents

Professional experience

Since 2015 — CNRS Research Engineer, Senior Class (IRHC), IRCAN, Nice

Head of the Bioinformatics & IT Service. Development and coordination of bioinformatics support, scientific computing infrastructure, data analysis pipelines and IT services for cancer and aging research teams.

Main activities:

2012 to mid-2015 — CNRS Research Engineer, URMITE / IHU, Marseille

Bioinformatics platform of the IHU (Institut hospitalo-universitaire) located at the Faculty of Medicine, La Timone, Marseille (previously known as the Rickettsia unit, URMITE - UMR 7278). The institute was headed by Pr. Didier Raoult. [permanent position at CNRS since 2012]

Activities : bioinformatics in microbiology, genomics and comparative genomics, including genome analysis, sequence annotation, database management, software development and support for collaborative research projects

Post-doctoral experiences

Earlier experiences

See also: old trainings and other past experiences:

See also: old trainings and other past experiences:

  • 2001: Trainee in computer sciences (Master2), INRIA Sophia-Antipolis.
    Developing of prototype software to control an experimental marine simulator device (project «COMORE»).
  • from 2001 to 2003 : Miscellaneous Informatics

- Trainings: Linux administration, Perl programming, training centre PCS Avolys
- Individual project: creating a management software for legal information, Gubernatis lawyers institute
- Assistant network administrator : intrusion detection on the university network, University of Corte.

  • from 1999 to 2000 : Miscellaneous Biology - Ecology

- Technician in bacteriological analyses: Environmental Laboratory of Nice
- Training of Master 2: Environmental Impact of wild ungulate populations, Office National de la Chasse
- Training in ethology: ethology wolf in the wild, Mercantour National Park
- Training in ecology: analysis of the littoral fauna of Embiez island, Study Centre for Marine Animal Resources
- Training in entomology: study of the biodiversity of arthropods alpine meadows, Natural Park of Queyras


Education

PhD

PhD in Bioinformatics (obtained in 2005)- Nice Sophia Antipolis University
Thesis title: “DNA chip design for the identification of micro-organisms”.
Jury: M. Gouy, J.M. François, G. Perrière, R. Christen.

See also: PhD summary:

See also: PhD summary:

The identification of organisms are still often based on phenotypical characters. However, such as an identification is approximate and difficult for micro-organisms. DNA micro-arrays appear to be a solution for a fast and reliable identification of a large number of species. This technique is relatively recent and it is still necessary to improve it, in particular at the conceptual level. Within this framework, the objective of my thesis was to implement new means for chip design. This work was completed through two projects: The project “Aquachip” aimed in designing a DNA array for the identification of pathogenic bacteria present in bathing and drinking water. The project grouped several European laboratories that had to exchange a large amount of data. Such significant flow of information is often badly managed and slows down research. Consequently, we developed a dynamic numerical platform, the “E-dashboard” (MySQL, PHP), allowing all partners to manage data. This tool made it possible on the one hand to follow the progress of the various steps of the project and on the other hand to optimize exchanges between partners. In a second project, “Mycochip”, the objective was to develop a DNA array to identify ectomychorizian fungi. ITS sequences (Internal Transcribed Spacers) from a very divergent area located between ribosomal RNA genes are used for this study. The project initially required the development of a tool to retrieve sequences, « EmblEx » (Perl, MySQL), which is more specific and powerful than Entrez, SRS or ACNUC. Then, the ambiguous taxonomy of fungi led us to conceive a new method of classification through partitioning without alignment. Biological experiments showed that reliable probes could be determined by this approach.


University degrees