Section: Partnerships and Cooperations

International Initiatives

INRIA Associate Teams

INTEGRATIVEBIOCHILE

• Title: Bioinformatics and mathematical methods for heterogeneous omics data

• INRIA principal investigator: Anne Siegel

• International Partner:

  • Institution: University of Chile (Chile)

  • Laboratory: University of Chile, CMM

• Duration: 2011 - 2013

• See also: http://www.irisa.fr/symbiose/people/asiegel/EA/

IntegrativeBioChile is an Associate Team between INRIA project-team "Symbiose" and the "Laboratory of Bioinformatics and Mathematics of the Genome" hosted at CMM at University of Chile. The Associated team is funded from 2011 to 2013. The project aims at developping bioinformatics and mathematical methods for heterogeneous omics data. Within this program, we funded long-stay visitings in France to initiate long-term research lines, in complement to short visit funded by and inria-conycit program.

• Reconstruction of regulatory networks. This research line was developed within the visits of A. Aravena and A. Maass in March 2011 (funded by conycit-inria and by a mobility grant from UEB). It was pushed further during the visit of J. Bourdon in October 2011 and A. Siegel in November 2011 in Chile.

• Reconstruction and study of metabolic network with reduction methods. This research line was initiated during the one-month visit of Marko Budinich (engineer) in Rennes in April 2011. It was pushed further with visits from french researchers in Santiago funded by Inria-Conycit program (D. Eveillard and S. Prigent).

• Detection of structural variations in genomes This research line was studied during the one-month visit of Alex Di Genova (engineer) in Rennes in May 2011.

INRIA International Partners

• CWI, The Netherlands : In 2011 we have been collaborating very actively with the Algorithmic computational biology from CWI Life Sciences, The Netherlands in the domain of protein structure comparison. Inken Wohler, a PhD student from CWI visited Symbiose for 6 months partially supported by Inria internship grant. Two papers have been published in the framework of this cooperation [31] , [22] .

Visits of International Scientists

Internship

• Andres Aravena, from CMM (Chile) received a 3 months Mobility Grant from "University Européenne de Bretagne" to visit the Symbiose team between april and july.

• Inken Wohlers, from CWI (Amsterdam The Netherlands) received a 6 months Inria internship and visited Symbiose from December 2010 to May 2011.

Participation In International Programs

Chile. Inria-Conycit 2011-12

• Partner: University of Chile, Laboratory of Bioinformatics and Mathematics of the Genome, Chile.

• Title: IntegrativeBiomining

• Financial support: Conicyt-Inria program 2011-12

• INRIA principal investigator: Anne Siegel

The project wishes at developing methods combining combinatorial and constraint-based approaches with probabilistic/optimization approaches to integrate and explore heterogeneous, multi-scale and large-scale data produced in molecular biology.

Within the project, the following visits were funded (A) 2 monthes visit in Rennes (A. Aravena, phD student, February-March 2011) (B) 3 weeks visit in Rennes (A. Maass, professor, March 2011) (C) 15 days visit in Santiago de Chile (A. Siegel, assistant professor, july 2011). (D) 15 days visit in Santiago de Chile (F. Coste, junior researcher, october 2011) (E) 1 month visit in Santiago de Chile (S. Prigent, phD student, November 2011)

Argentina - MinCYT-Inria 2011-12

• Partner: Universidad Nacional de Córdoba, Grupo de Procesamiento de Lenguaje Natural (PLN), Argentina.

• Title: Modélisation linguistique de séquences génomiques par apprentissage de grammaires

• Financial support: MinCYT-Inria program 2011-12

The project aims at developing new grammatical inference methods to learn automatically linguistic models of genomic sequences.

Within the project, the following visits were funded (A) 15 days visit in Cordobà (F. Coste, junior researcher, June 2011) (B) 1 month visit in Rennes (R. Carrascosa, ph-D student, August 2011) (C) 15 days visit in Rennes (G. Infante-Lopez, professor, November 2011).

Germany. Egide Procope Program 2011-12

• Partner: Postdam university, Institut für Informatik Wissensverarbeitung und Informationssysteme, Germany

• Title: Querying Biological Systems with Answer Set Programming.

• Financial support: Egide Procope Program 2011-12

The project aims at developing new methods for constructing and querying biological networks with a new constraint-based programming (answer set programming) mastered in Postdam university.

Within the project, the following visits were funded (A) 1 week visit in Rennes (S. Thiele, phD student, May 2011) (B) 15 days visit in Postdam and Heidelberg (P. Blavy, phD student, June 2011) (C) 1 week visit in Rennes (T. Schaub, professor, October 2011) (D) 1 week visit in Rennes (M. Gebser, Post-doc, October 2011) (E) 1 week visit in Postdam (J. Nicolas, senior researcher, December 2011) (F) 1 week visit in Postdam (S. Videla, phD student, December 2011) (G) 1 week visit in Postdam (V. Wurcher, phD student, December 2011)