e-mail cohen @ lri . fr web page http://www.lri.fr/~cohen position Assistant professor, Ph.D. in Computer Science phone +(33) 1 69 15 32 16 fax +(33) 1 69 15 65 86 office 145a adress LRI, Bâtiment 490 Université Paris-Sud 91405 Orsay cedex

News

• PhD Opportunity (for student with disabilities only)
  Towards an evaluation of the quality of predicted functional annotations
  • Type of contract: CNRS, please see this page for more information
  • Graduate school: 427 - Ecole Doctorale INFORMATIQUE DE PARIS SUD
  • Place : Laboratoire de Recherche en Informatique (LRI), Orsay
  • Abstract: The aim of this work is to develop automatic methods to find protein functions in microbial genomes. Functional annotation scenarios will have to be collected, formalized into workflows and the results obtained in different workflow executions should be compared. Supervised learning methods for predicting annotations will be proposed while an estimation of the quality of annotations obtained will be produced. This work will be done in close collaboration with biologists from IGM (Orsay).
  • PhD advisors: Ch. Froidevaux and S. Cohen-Boulakia (LRI, CNRS UMR 8623, University Paris Sud)
  
  
• I won the ICDE Outstanding Reviewer Award!

Interests

• Integrating and querying biological & biomedical databases
• Provenance in scientific workflows
• Semantic Web, metadata
• Workflow/dataflow design, software engineering, user requirements

Research Experience

• Provenance in scientific workflow systems
  This work is done in collaboration with members from the Database group at the University of Pennsylvania: S. Davidson, Z. Bao, S. Khanna and S. Roy.
  I am interested in the problem of storing and querying provenance in scientific workflows. In particular, I have worked on techniques to reduce the huge amount of data provenance to help users focus on relevant information (ZOOM*UserView project). We have demonstrated the benefit of using our techniques by participating in the "Provenance Challenge". More information can be found here. Another direction of research is on differencing workflow runs (PDiffview Project). Very recently, I have been involved in a project on secure views for scientific workflows.
  
  
• GeneValorization
  Collaborative work between LRI and the Institut Curie. GeneValorization is a tool which gives a clear and concise overview of the publications existing on a list of genes. We have used GeneValorization to study several lists of genes involved in Cancer. Please have a look at the GeneValorization Web site!
  
  
• BioGuide
  Collaborative work between the LRI bioinformatics group at Paris-Sud University and the database group at UPenn. Have a look at bioguide-project.net!
  BioGuide extends DSS (see below) to be adapted to many user profiles. I have elaborated a questionnaire and performed interviews of 20 scientists from various domains (cancer study, annotation project, ...) to evaluate their needs in the process of querying. In collaboration with C. Froidevaux and S. Davidson, I have designed BioGuide, a generic framework to guide the users to select the relevant sources to be queried and the tools to be used according to their preferences (e.g., the reliability level of the sources) and following their querying strategies. The biological significance of the results obtained with BioGuide has been shown in the context of Comparative Genomic Hybridization (CGH) analysis performed at the Curie Institute. I have developed the BioGuide system in JAVA (applet) with the help of Olivier Biton. BioGuide is available for use. The system is very flexible and can be adapted to any biological domain. I have recently developped a module to use BioGuide on top of the SRS system. BioGuideSRS provides acess to instances of data!
  Have a look at BioGuide-project.net!
  
  
• SHARQ (Sharing Heterogenous and Autonomous Resources and Queries) aims to develop generic tools and technologies for creating and maintaining confederations whose purpose is distributed data sharing that is, data cooperatives. SHARQ is a collaborative work with two biological partners: the Computational Biology and Informatics Laboratory, leaded by Chris Stoeckert, and the Pew project group leaded by Pete White from the Children Hospital of Philadelphia. We propose to develop a specific data cooperative as a biological testbed for evaluating the proposed technologies.
  In this project, I am working on the SHARQ Guide which is therefore being designed to enable biologists to find relevant information within a peer data management system. It provides assistance not only for users who ask queries, but also for owners of peers who wish to be registered within the Guide. This work is closely related to my work on BioGuide (see below). More information is available here.

Selected Publications

Service

• PC member
  
  
  • ICDE 2010, 25th International Conference on Data Engineering.
    I won the ICDE Outstanding Reviewer Award!
  • JOBIM 2010, the French conference in Bioinformatics.
  • SSDBM 2009, International Conference on Scientific and Statistical Database Management.
  • SWPM 2009, SWPM 2010, International Workshop on the role of Semantic Web in Provenance Management (ISWC workshop)
  • DILS 2007 to DILS 2010, International workshop on Data Integration in the Life Sciences (I was co-chair of DILS 2008),
  • BDA 2009, the French conference in Databases
  • IIMAS'08, Workshop on Information Integration Methods, Architectures, and Systems (ICDE workshop).
  • ISMB 2006, International conference on Intelligent Systems for Molecular Biology.
  
  
  
  
• Reviewer
  
  
• Briefings in Bioinformatics Journal, Oxford University Press.
• Bioinformatics Journal, Oxford University Press.
• BMC Bioinformatics Journal, BioMed Central.
• Proteomics Journal, Wiley InterScience.
• Journal of Bioinformatics and Computational Biology.
  
  
  
• Workshop co-organizer
  
  
  • DILS'08, the 5th Annual International workshop on Data Integration in the Life Sciences, University of Evry, France 2008.
    • Program co-Chair (with Amos Bairoch, SwissProt and Christine Froidevaux, LRI)
      
      
      
  • DILS'07, the 4th Annual International workshop on Data Integration in the Life Sciences, University of Pennsylvania, USA, 2007.
    • Proceedings co-editor (with Val Tannen), LNBI, Springer
    • Publicity Chair
    • Web Master
      
      
      
  • II 2007 (Workshop in Information Integration), University of Pennsylvania, USA.
    • Local organizer
    • Editor of the Proceedings (printed locally)
      
      
      

Participation in working groups

• Provenance Challenges, an international workshop which bring together researchers and indistrials interested in provenance for workflow systems.
• DB/IR day, an american workshop which bring together database and information retrieval researchers and students from academic and research institutions across the tristate area and beyond.
• ISIBio, a french interdisciplinary working group interested in various aspects of "Information Systems Integration in Biology". This group brings together researchers from seven computer science laboratories and from ten biological laboratories (2004-2006).
• AS127, the national CNRS Working group on integration and interoperability of genomic data sources. (2003-2004).
• PPF, multidisciplinary program "Programme PluriFormation" on Bioinformatics and Genomics. This PPF brings together the bioinformatics groups from three biological laboratories, two computer science laboratories and from the laboratory of mathematics at Orsay campus.

Teaching

• Faculty since Sept. 2007
  
  • Software Engineering: UML, JAVA (graduate)
    
  • Database Management Systems (junior, senior)
    
    
• Temporary Faculty (Attaché Temporaire d'Enseignement et de Recherche), Sept. 2005 - Dec. 2005
  
  • Software Engineering: UML, JAVA (graduate)
    
  • Database Management Systems (graduate)
    
    
• Teaching assistant, 2002-2005
  
  • Software Engineering: UML/OCL specifications (graduate)
    
  • Database Management Systems (graduate)
    
  • Algorithms (undergraduate)
    
  • ADA Programming (undergraduate)

Others