Section: Partnerships and Cooperations

International Initiatives

Inria International Labs

The Dyliss team is strongly involved in the Inria CIRIC center, and the research line "Omics integrative center". The associated team "IntegrativeBioChile", the post-doc of S. Thiele (2012) and the co-supervision of A. Aravena (2010-2013) contributed to reinforce the complementarity of both Chilean and French teams. In 2013, a workshop was organized in Chile to develop new French-Chilean collaborations within the framework of the CIRIC center. In 2014, Marie Chevallier joined the team as an engineer to improve softwares resulting from collaborations.

Inria Chile

Associate Team involved in the International Lab:

BIOINTEGRATIVECHILE

• Title: Integrative Biology in Extreme Environments

• International Partner (Institution - Laboratory - Researcher):

  • Universidad de Chile (Chile) - Center for Mathematical Modeling (CMM) - Alejandro Maass

• Start year: 2014

• See also: http://www.irisa.fr/dyliss/public/EA/index.html

• The project is in the area of bioinformatics, with a special focus on bacteria living in extreme environments, more precisely on microorganisms involved in bio-remediation or bio-production processes. We are particularly interested in bioprocesses such as copper extraction, salmon lethality, metal-resistance, all having an economical interest in Chile. Since the last decade, huge databases of microbial genomic sequences, together with multi-scale and large-scale cellular observations (genomics, transcriptomics, proteomics, metabolomics) have been produced. Each one can be considered as a different scale of a biological process, either in time or space. But ultimately they are related through networks of biological interactions that control the behavior of the system. The reconstruction, analysis and modeling of such networks using all levels of information are biologically, mathematically and computationally challenging. Applied on microorganisms living in extreme environments, this question is even more challenging since relatively few knowledge is publicly available on the species, requiring to develop methods which are robust to uncertainty. We are developing methods to integrate and manage heterogeneous omics and uncertain data, this in the purpose of extracting suitable biomarkers from this multi-scale information. This question will be addressed by coupling probabilistic and static dynamical systems methods with recent and efficient paradigms of constraint programming (Answer Set Programming).

Inria Associate Teams

INTEGRATIVEBIOCHILE

• Title: Bioinformatics and mathematical methods for heterogeneous omics data

• Inria principal investigator: Anne Siegel

• International Partner (Institution - Laboratory - Researcher):

  • University of Chile (Chile) - Center for Mathematical Modeling - Alejandro Maass

• Duration: 2011 - 2016

• See also: http://www.irisa.fr/dyliss/public/EA/index.html

• IntegrativeBioChile is an Associate Team between Inria project-team "Dyliss" 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 2016. The project aims at developing bioinformatics and mathematical methods for heterogeneous omics data. Within this program, we funded long and short stay visitings in France.