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SEQUOIA Research team

Algorithms for large-scale sequence analysis for molecular biology

  • Leader : Grigory Koutcherov
  • Research center(s) : CRI Lille - Nord Europe
  • Field : Computational Sciences for Biology, Medicine and the Environment
  • Theme : Computational Biology and Bioinformatics
  • Partner(s) : Université des sciences et technologies de Lille (Lille 1),CNRS,Université Charles de Gaulle (Lille 3)
  • Collaborator(s) : U. LILLE 1 (USTL), CNRS, U. LILLE 3 (UCDG)

Team presentation

For the last fifteen years bioinformatics has undergone a remarkable evolution and became a rich and very active research field. This advancement is associated with a breakthrough development of sequencing technologies that resulted in the availability of a large body of genomic data, as well as with the emergence of new high-throughput genomic and proteomic technologies (DNA chips for monitoring gene expression, mass spectrometry, ...). Moreover, recent discoveries in molecular biology, such as the new understanding of the role of non-coding DNA, gave rise to new challenging bioinformatics problems. While modern bioinformatics features various mathematical models and methods, sequence analysis still remains its central component.

The main goal of this project-team is to define appropriate combinatorial models and efficient algorithms for large-scale sequence analysis in molecular biology. An emphasis is made on the annotation of non-coding regions in genomes -- RNA genes and regulatory sequences -- via comparative genomics methods. Other research subjects include the analysis of protein sequence and the development of a database and associated tools for nonribosomal peptides. A special attention is given to the development of robust software, its validation on biological data and its availability from the software platform of the team and by other means. Most of the research projects are carried out in collaboration with biologists.

Research themes

  • Sequence similarity and repetitions
  • Non-coding RNA analysis
  • Cis-regulatory sequence analysis
  • Large-scale annotation of non-coding regions
  • Computational analysis of nonribosomal peptides
  • Protein sequence analysis

International and industrial relations

  • Local collaborations : UMR 8161 (Biological Institute of Lille, CNRS -- Lille Pasteur Institute - University of Lille 1 - University of Lille 2), ProBioGem laboratory, IRI
  • National projects : ANR "Brasero", ARC INRIA "Flash", inter-genopole project, GDR Molecular bioinformatics, GDR Informatique Mathématique
  • International collaborations : Warsaw University (Polonium project), Russian Institute of Mathematical Problems in Biology (ECO-NET project), Université Libre de Bruxelles, Université de Montréal, Haifa University, Moscow University, Boston University

Keywords: Bioinformatics Computational biology Sequence analysis Comparative genomics Noncoding RNAs Nonribosomal peptides High performance computing