Section: Partnerships and Cooperations

International Initiatives

Inria Associate Teams

  • Program: Inria-Russia

  • Title: CARNAGE: Combinatorics of Assembly and RNA in GEnomes

  • Inria principal investigator: Mireille Régnier

  • International Partner (Institution - Laboratory - Researcher):

    • State Research Institute of Genetics and Selection of Industrial Microorganisms (Russia (Russian Federation)) - Bioinformatics laboratory - Vsevolod Makeev

  • Duration: 2012–13

  • See also: http://en.inria.fr/domaines-epi/computational-sciences-for-biology-medicine-and-the-environment

  • CARNAGE addresses two main issues on genomic sequences, by combinatorial methods.

    Fast development of high throughput technologies has generated a new challenge for computational biology. The recently appeared competing technologies each promise dramatic breakthroughs in both biology and medicine. At the same time the main bottlenecks in applications are the computational analysis of experimental data. The sheer amount of this data as well as the throughput of the experimental dataflow represent a serious challenge to hardware and especially software. We aim at bridging some gaps between the new "next generation" sequencing technologies, and the current state of the art in computational techniques for whole genome comparison. Our focus is on combinatorial analysis for NGS data assembly, interspecies chromosomal comparison, and definition of standard pipelines for routine large scale comparison.

    This project also addresses combinatorics of RNA and the prediction of RNA structures, with their possible interactions.

Participation In International Programs

Génolevures and Dikaryome Consortia

Participants : David James Sherman [correspondant] , Pascal Durrens, Florian Lajus, Tiphaine Martin, Anna Zhukova.

Since 2000 our team is a member of the Génolevures Consortium (GDR CNRS), a large-scale comparative genomics project that aims to address fundamental questions of molecular evolution through the sequencing and the comparison of 14 species of hemiascomycetous yeasts. The Consortium is comprised of 16 partners, in France, Belgium, Spain, the Netherlands (see http://genolevures.org/ ). Within the Consortium, our team is responsible for bioinformatics, for research in new methods of analysis. Pascal Durrens and Tiphaine Martin of the CNRS are responsible for the development of resources for exploiting comparative genomic data. Pascal Durrens is the editorial manager of the Génolevures on-line resource.

The Dikaryome Consortium is a scientific collaboration between several international partners and the National Center for Sequencing (CEA–Génoscope, Évry) on the sequencing, annotation, and comparative analysis of fungal genomes.

These perennial collaborations continue in two ways. First, a number of new projects are underway, concerning several new genomes currently being sequenced, and new questions about the mechanisms of gene formation. Second, through the development and improvement of the Génolevures On Line database, in whose maintenance our team has a longstanding committment and the improvement of tools like the YAGA software.