Section: Partnerships and Cooperations

International Initiatives

• AMAVI

• Title: Combinatorics and Algorithms for the Genomic sequences

• International Partners (Institution - Laboratory - Researcher):

  • Vavilov Institute of General Genetics (Russia (Russian Federation)) - Department of Computational Biology - Vsevolod Makeev

• Start year: 2013

• See also: https://team.inria.fr/amib/carnage/

• VIGG and AMIB teams has a more than 12 years long collaboration on sequence analysis. The two groups aim at identifying DNA motifs for a functional annotation, with a special focus on conserved regulatory regions. In the current 3-years project CARNAGE, our collaboration, that includes Inria-team MAGNOME, is oriented towards new trends that arise from Next Generation Sequencing data. Combinatorial issues in genome assembly are addressed. RNA structure and interactions are also studied.

  The toolkit is pattern matching algorithms and analytic combinatorics, leading to common software.

• Conseil franco-québécois de coopération universitaire exchange program

  • Title: Réseau franco-québecois de recherche sur l’ARN

  • International Partners (Institution - Laboratory - Researcher):

    • Univ. McGill (Canada) - CS Dept - J. Waldispühl, M. Blanchette

    • Univ. Montréal (Canada) - Biology Dept & IRIC - E. Lecuyer, F. Major

  • Start year: 2012

  • The partners have developped complementary expertise on RNA : bioinformatics, combi- natorics and algorithms. machine learning, physics and genomics. Methodologies will be developed that combine theoretical simulations and new (high throughput) experimental data. A common high level training at Master and PhD level is organized.

• PHC Germaine de Stael exchange program

  • Title: Random constrained permutations

  • International Partners (Institution - Laboratory - Researcher):

    • Univ. Zürich (Swiss) - Institut für Mathematik - M. Bouvel, V. Féray

  • Start year: 2015

  • The partners wish to develop new technique for the enumeration, analysis and random generation of constrained permutations.

• CNRS UMI PIMS-Vancouver Exchange program

  • Title: Extended research stay of Y. Ponty at the Simon Fraser University

    • Simon Fraser University - Maths Dept - C. Chauve, M. Mishna, L. Stacho

    • Univ. British Columbia - CS Dept - J. Manuch

  • Start year: 2013

  • Extended research stay in Vancouver to foster new collaborations between EPI Amib and colleagues at SFU on comparative genomics, RNA structures, and enumerative combinatorics.