Section: Partnerships and Cooperations

International Initiatives

Inria Associate Teams

ITSNAP

• Title: Intelligent Techniques for Structure of Nucleic Acids and Proteins

• Inria principal investigator: Julie Bernauer

• International Partner (Institution - Laboratory - Researcher):

  • Stanford University (United States) - Computational Structural Biology, School of Medicine, Structural Biology - Julie Bernauer

• Duration: 2012 - 2014

• See also: http://www.lix.polytechnique.fr/~bernauer/EA_ITSNAP/

• The ITSNAP Associated Team project is dedicated to the computational study of RNA 3D structure and interactions. By developing new molecular hierarchical models for knowledge-based and machine learning techniques, we can provide new insights on the biologically important structural features of RNA and its dynamics. This knowledge of RNA molecules is key in understanding and predicting the function of current and future therapeutic targets.

Inria International Partners

Declared Inria International Partners

CARNAGE

• 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 - Mireille Régnier

• Duration: 2012- 2014

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

• 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.

Informal International Partners

Polytechnique/UPSud and McGill/U. Montréal

• Program: CFQCU

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

• Inria principal investigator: Jean-Marc Steyaert

• International Partner (Institution - Laboratory - Researcher):

  • Mc Gill and Université de Montréal (Canada)

  • Computer Science Department

  • Jérôme Waldispühl

• Duration: 2012 - 2014

• Résumé : The partners have developped complementary expertise on RNA : bioinformatics, combinatorics 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.

Inria International Labs

R. Fonseca spent 5 months at SLAC in Stanford to work with Henry van den Bedem. J. Bernauer spent two weeks at SLAC. The associated team members also presented their work at the Inria BIS 2013 Workshop in Stanford https://project.inria.fr/inria-siliconvalley/workshops/bis2013/ .

Participation In other International Programs

NII International Internship Program

Adrien Rougny has been an intern at Nii from February to August 2013 with a support of "Nii International Internship Program. He worked on the topic "Inference and Learning for Systems Biology and Network Dynamics" in Pr. Katsumi Inoue's group, a long-term collaboration of Ch. Froidevaux.

PHC Procore

J. Bernauer is coordinator with Pr. X. Huang at the Hong-Kong University of Science and Technology of a Partenariat Hubert Curien (PHC) Procore project (2012-2013). The project is entitled Computational studies of conformational dynamics of the RNA-induced silencing complex and design of miRNAs to target oncogenes.