Section: Partnerships and Cooperations

International Initiatives

• Title: AMAVI - Combinatorics and Algorithms for the Genomic sequences

• International Partner (Institution - Laboratory - Researcher):

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

• Duration: 2013 - 2017

• Start year: 2013

• 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.

• Simon Fraser University (Vancouver, Canada). The Mathematics department at SFU has ongoing projects on RNA design, comparative genomics and RNA structure comparison with our team. M. Mishna (SFU) will also visit Inria Saclay in January 2017 to push an oingoing collaboration on 2D walks;

• McGill University (Montréal, Canada). Following our productive collaboration with J. Waldispühl (Computer Science Dept, McGill), and the recent defense of V. Reinharz's PhD, whose thesis was co-supervised by AMIB members, we plan to increase our interactions on SHAPE data analysis by applying for an Inria associate team;

• King's college (London, UK). Our collaboration with L. Mouchard (AMIB associate) and S. Pissis on string processing and data structures is at the core of Alice Héliou's PhD. To finalize the implementation of her algorithms and apply them on real data, Alice has spent a two month period during the summer of 2016 at the EBI.

• France-Stanford exchange program

• Duration: 2014 - 2016

• Start year: 2014

• See also: http://francestanford.stanford.edu/collaborative_projects

• Amélie Héliou is co-supervised by H. Van Den Bedem in Stanford. Her tow-months visit to Stanford during the Fall of 2016 was funded by France-Stanford.