Section: Partnerships and Cooperations

International Initiatives

Inria International Labs

ERABLE participates in a project within the Inria-Chile CIRIC (Communication and Information Research and Innovation Center) titled “Omics Integrative Sciences”. The main objectives of the project are the development and implementation of mathematical and computational methods and the associated computational platforms for the exploration and integration of large sets of heterogeneous omics data and their application to the production of biomarkers and bioidentification systems for important Chilean productive sectors. The project started in 2011 and is coordinated in Chile by Alejandro Maass, Mathomics, University of Chile, Santiago. It is in the context of this project that we are currently hosting Alex di Genova in ERABLE as a PhD sandwich student (for 18 to 24 months). Alex is co-supervised by Alejandro Maass and by Eric Goles from the University Adolfo Ibañez, Santiago, Chile.

Inria Associate Teams Not Involved in an Inria International Labs

ALEGRIA

• Title: ALgorithms for ExplorinG the inteRactions Involving Apicomplexa and kinetoplastida

• Duration: 2015 - 2017

• Coordinator: On the Brazilian side, Andréa Rodrigues Ávila; on the French side, Marie-France Sagot

• ERABLE participant(s): M. Ferrarini, L. Ishi Soares de Lima, A. Mary, H. T. Pusa, M.-F. Sagot, M. Wannagat

• Web page: http://team.inria.fr/erable/en/alegria/

Participation in other International Programs

ERABLE is coordinator of a CNRS-UCBL-Inria Laboratoire International Associé (LIA) with the Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Brazil. The LIA has for acronym LIRIO (“Laboratoire International de Recherche en bIOinformatique”) and is coordinated by Ana Tereza Vasconcelos from the LNCC and Marie-France Sagot from BAOBAB-ERABLE. The LIA was created in January 2012 for 4 years, renewable once. A web page for the LIA LIRIO is available at this address: http://team.inria.fr/erable/en/cnrs-lia-laboratoire-international-associe-lirio/.

ERABLE coordinates another project with Brazil. This is a CAPES-COFECUB project titled: “Multidisciplinary Approach to the Study of the Biodiversity, Interactions and Metabolism of the Microbial Ecosystem of Swines”, and its acronym MICO. The coordinators are M.-F. Sagot (France) and A. T. Vasconcelos (LNCC, Brazil) with also the participation of Arnaldo Zaha (Federal University of Rio Grande do Sul, Brazil). The project started in 2013 for 2 years, and was renewed for 2 more years starting from 2015. The main objective of this project is to experimentally and mathematically explore the biodiversity of the bacterial organisms living in the respiratory tract of swines, many of which are pathogenic. This project is strongly linked to the LIA LIRIO. More information on it may be found at this address: http://team.inria.fr/erable/en/cnrs-lia-laboratoire-international-associe-lirio/associated-projects/#CAPES-COFECUB_Microbial_Ecosystem_of_Swines.

ERABLE has a Stic AmSud project that started in 2016 for 2 years. The title of the project is “Methodological Approaches Investigated as Accurately as possible for applications to biology”, and its acronym MAIA. This project involves the following partners: (France) Marie-France Sagot, ERABLE Team, Inria; (Brazil) Roberto Marcondes César Jr, Instituto de Matemática e Estatística, Universidade de São Paulo; and Paulo Vieira Milreu, TecSinapse; (Chile) Vicente Acuña, Centro de Modelamiento Matemático, Santiago; and Gonzalo Ruz, University Adolfo Ibañez, Santiago. One of them, TecSinapse, is an industrial partner. MAIA has two main goals: one methodological that aims to explore how accurately hard problems can be solved theoretically by different approaches – exact, approximate, randomised, heuristic – and combinations thereof, and a second that aims to better understand the extent and the role of interspecific interactions in all main life processes by using the methodological insights gained in the first goal and the algorithms developed as a consequence. A preliminary web page for MAIA is available at this address: http://team.inria.fr/erable/en/projects/maia/.

Finally, we would like to mention the participation of one member of ERABLE (Alain Viari) in the Breast Cancer French Working Group of the International Cancer Genome Consortium (ICGC, https://icgc.org) led by the Institut National du Cancer (INCa, http://www.e-cancer.fr/Professionnels-de-la-recherche/Innovations/Les-progres-de-la-genomique/ICGC-France). This project was initiated by Pr. Gilles Thomas who passed away in 2014. Alain took the head of the bioinformatics platform located at the Centre Léon Bérard. The project aims at the genomic characterisation of 75 HER2-amplified breast cancers by using high-throughput sequencing (whole genome of paired tumour/normal samples and RNAseq of tumour samples). One of the scientific goals is to decipher whether the HER2/ERBB2 amplification is a driver or a passenger event in the course of tumour development.