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 hosted Alex di Genova in ERABLE as a PhD sandwich student (for 18 months in 2015-2017). Alex has now defended his PhD. He was co-supervised by Gonzalo Ruz from the University Adolfo Ibañez, Santiago, Chile. He now, since Dec 2017, joined again ERABLE as postdoc.

Inria Associate Teams Not Involved in an Inria International Lab

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 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 succint web page for MAIA is available at this address: http://team.inria.fr/erable/en/projects/maia/.

ERABLE also participated to the BASIS project. This was funded by the European Community Seventh Framework Programme (Grant 242006 - 2010-2015). It was led by Dr. Mike Stratton and involved six European countries. It was primarily focused on ER+/HER2- breast cancers, but during the course of the project, was merged with the HER2+ French-ICGC and triple negative UK-ICGC projects, resulting in the analysis of the whole spectrum of breast cancers. The French group was initiated by Dr. Gilles Thomas and was pursued by Alain Viari after the loss of Dr. Thomas in 2014. The project resulted in the sequencing and thorough analysis of 560 breast cancer whole genomes (Nik-Zainai et al., Nature, 534:47-54, 2016), including 75 HER2+ performed by the French working group (Ferrari et al., Nature Communications, 7, 2016) and funded by the Institut National du Cancer and by Inserm.

Finally, Marie-France Sagot participates in a Portuguese FCT project, Perseids for “Personalizing cancer therapy through integrated modeling and decision” (2016-2019), with Susana Vinga and a number of other Portuguese researchers. The budget of Perseids is managed exclusively by the other Portuguese partner.