Professor, Univ. Rennes 1
Dyliss team, Irisa / Inria Rennes-Bretagne Atlantique,
I develop methods based on ontologies for analyzing biomedical data. The main applications typically involve knowledge representation and bioinformatics.
My approach consists in exploiting symbolic domain knowledge for improving the integration and analysis of large, complex, highly interdependent and often incomplete datasets. I use Semantic Web tehnologies (such as RDF, SPARQL and OWL) for integrating distributed data and for combining different kinds of reasoning such as deduction, classification or comparison.
Keywords: data integration, symbolic knowledge, ontologies, Semantic Web, life science data, biomedical.
I am a professor at ISTIC, the computer science department of Rennes1 university. On the research side, I am (proud to be) the leader of the Dyliss team at IRISA and involved in b<>com. On the teaching side, I am (also proud to be) the co-head of the Bioinformatics MSc degree with Emmanuelle Becker.
Projects and collaborations
- AskOmics facilitates data integration in RDF, and intuitive automatic generation of SPARQL queries
- NeuroMarkers aims to develop new statistical and computational approaches to integrate multimodal imaging and “omics” data
- Sanofi R&D Chilly-Mazarin
- Calipho at the Swiss Institute for Bioinformatics
- IGDR : Gwenaël Rabut
- IGDR : CeDRE
- Empenn and Institut du thorax
- postdoc: 1
- PhD students: 9 (3 in progress)
- Engineers: 1
- MSc 2nd year: 12
- MSc 1st year: 11
- BSc 3rd year: 2
- ENS: 1
- I defended my Habilitation à diriger des recherches on 11th January 2016 about Ontology-based methods for analyzing life science data: manuscript, slides and video. The committee was composed of:
- Anita Burgun (Univ. rené Descartes, Paris)
- Marie-Dominique Devignes (LORIA Nancy)
- Michel Dumontier (Stanford Univ.)
- Christine Froidevaux (LRI Orsay)
- Fabien Gandon (Inria Sophia-Antipolis)
- Anne Siegel (IRISA Rennes)
- Alexandre Termier (IRISA Rennes)
- I defended my PhD on 21st December 2003 about Modeling, representing and sharing symbolic knowledge on brain cortex anatomy (supervisor: Bernard Gibaud). The abstract is available in English. The full dissertation in French is available as postscript (9.7Mb) and as pdf (6.5Mb)
- The list of my publications can be found at: FIXME