Email chris at lri . fr Home page http://www.lri.fr/~chris Position Professor Phone +33 1 69 15 65 07 FAX +33 1 69 15 65 86 Office 151 Address LRI, CNRS UMR 8623 Bat 490 - Université Paris-Sud 11 F-91405 Orsay Cedex France

General presentation

RESEARCH

• Genome Bioinformatics
  
  
  • Interoperability and knowledge extraction in genomic data sources
    
  • Semi-automatic genome annotation
  
  Computational methods
  • Integration of multiple and heterogeneous data sources; ontologies mapping ; Data warehouse design
  • Knowledge representation; knowledge-based reasoning

• DILS'2007, DILS'2008 (co-chair), DILS'2009 (Data Integration in the Life Sciences)
  
• IEEE CBMS (Computer-Based Medical Systems), special track on Computational Proteomics, 2006, 2007, 2008
  
• Workshop Bioinformatics' Challenges to Computer Science de la conférence, ICCS 2008, 2009
• JOBIM (Journées Ouvertes Biologie, Informatique et Mathématiques, 2006, 2007, 2009)
  
• EGC (Extraction et Gestion des Connaissances, 2002-2008, 2009 )
  

• Microbiogenomics project "Optimal extraction of relevant information from complex and heterogeneous data provided by exhaustive genomic comparisons ", (ANR project, part of the "Action de Recherche Amont" ARA Masse de Données), in collaboration with MIG (INRA Jouy) and IGM.
• RAFALE project about Semi-automatic Functional annotation rules for microbial genomes, ACI IMPBio, in collaboration with MIG (INRA Jouy) and IBBMC
• Pluridisciplinary Program in Bioinformatics and Genomics PPF at the University of Paris Sud
• Working group ISIBio "Intégration des Systèmes d'Information en Biologie" (ACI IMPBio)
• Action spécifique STIC-CNRS (2003-2004) AS 127 "Intégration et interopérabiité de sources de données génomiques"
• European project HKIS, R&D, FTP5 (2002-2004) "Integrated Software Platform For Biological and Biomedical Data processing in Cancerology", in collaboration with the Ulm University (Germany), the European Institute of Oncology (Milan), the Curie Institute and the French company ISoft

• PhD theses
  
  
  • New methodological and algorithmic approaches for semi-automatic annotation of high-level genoms (Frederic Lemoine) with Pr. Bernard Labedan as a co-supervisor
    
  • Data mining and integration in heterogeneous biological databases (Bastien Rance)
    
  • Design of a semi-automatic module for annotating genomes (Lucie Gentils)
    
  • Integrating biological data: Selecting sources following a user-centric approach (Sarah Cohen Boulakia, PhD defended in 2005; post-doctoral position at the University of Pennsylvania with Susan Davidson, 2005-2007)
    
  • Towards a computational model and an automatic detection of -1 eukaryotic frameshifting sites (Jean-Paul Forest, PhD defended June 2005, with Alain Denise as a co-supervisor)
    
  • Refining Queries in a Mediator Approach (Alain Bidault, PhD defended in 2002, with Brigitte Safar as a co-supervisor)
  
  
  
• M Sc dissertations
  
  
  • Representation of motifs in proteins (Bastien Rance, in collaboration with Frédérique Lisacek at Swiss Institute of Bioinformatics, SIB)
    
  • Automatic assignment of a function to proteins from genome sequencing (Nicolas Guet, in collaboration with MIG, INRA)
    
  • Search for relevant features to discover regularities in genomics: application to transcriptomic data (Jérémie Mary, in collaboration with the Curie Institute, Orsay)
  
  

• GenoQuery is a querying module for functional annotation in a genomic warehouse. This software has been developed by Frédéric Lemoine and has been designed in collaboration with Bernard Labedan from IGM.
• SNK is a data mining tool which detects Sequential Nuggets of Knowledge from a set of sequential data. The current application is dedicated to understanding protein domain architecture underlying protein family grouping. This software has been developed by Bastien Rance and designed in collaboration with Frédérique Lisacek from the Swiss Institute of Bioinformatics (SIB).
• BioGuide is a generic algorithm for automatic selection of relevant data sources, that can be adapted to various users, taking into account both preferences and querying strategies. This software has been developed by Sarah Cohen Boulakia and designed in collaboration with Susan Davidson from the University of Pennsylvania.
• BioRelief is an analysis tool for microarrays. It has been developed by Jérémie Mary and designed in collaboration with Antoine Cornuéjols.

TEACHING ACTIVITIES

• Bioinformatics and Biostatistics (BIBS)
  • Data Bases (B Sc, 3rd year level)
  • Data Mining (M Sc, 4th year level)
  • Algorithmics (M Sc, 4th year level)
  • Mining huge heterogeneous data sources (M Sc, 5th year level)
  
  
• B Sc in Computer Science (licence)
  • Combinatorics for computer science (L2) .
  
  
• M Sc Research in Computer Science
  • Foundations of Knowledge Representation (DEA I3-TC)