Projects

ANR project ASTER

Coordinators: (General) Hélène Touzet, Bonsai team, CRIStAL-INRIA, (in Lille) David Hot, Institut Pasteur de Lille,(in Lyon) Vincent Lacroix BAOBAB-ERABLE Teams LBBE-UCBL-INRIA, (in Paris) Jean-Marc Aury, CEA.
Duration: 2016-2020

Brief description
The ANR project ASTER proposes to develop algorithms and software for analysing third generation sequencing data. Third generation is an emerging technology for RNA and DNA sequencing that promises to give a better picture for studying transcriptomes, metagenomes and metatranscriptomes of all living organisms. It will be key for discovering new fundamental mechanisms in cell biology, with broad implications in environmental research, health and agriculture. However, analysing the data is computationally challenging due to a very high rate of sequencing errors. There is a pressing need for models and algorithms that can accommodate this new kind of data and that are also scalable.

Stic AmSud project MAIA

Coordinators: (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.
Duration: 2016-2017

Brief description
This project 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.

Inria Associated Team ALEGRIA

Coordinator: (France) ERABLE Team, Inria and (Brazil) Instituto de Biologia Molecular do Paraná – Fiocruz-PR, Paraná.
Duration: 2015-2017

Brief description
Parasitic protists include agents of human and animal diseases that have a huge impact on world populations and economy. The major public health problems of protozoan organisms come mainly from the phylum Apicomplexa or the Class Kinetoplastida (from the phylum Euglenozoa).

An important subject yet largely under-explored is the fact that most members from these groups are pathogenic while a small fraction is not, which raises the question of what gives origin to the pathogenicity of these parasites. This is the main question we wish to address by means of computational methods and wet-lab experiments.

H2020-­MSCA-­ETN-­2014 project MicroWine

Coordinator: Lars Hestbjerg Hansen, Department of Environmental Science – Enviromental microbiology & biotechnology, Aarhus University, Aarhus, Danemark.
Duration: 2015-2018

Brief description
A diverse, complex, and poorly characterised community of microorganisms lies at the heart of the wine. These microorganisms play key roles at all stages of the viniculture and vinification processes, from helping the plants access nutrients from the soil, driving the plants’ health through protection against pathogens, to the fermentation process that transforms the must into wine with its complex array of aromas and flavours.

The main aim of MicroWine is to gain an improved understanding of such microbial community and of its interplay with the wine.

MIUR PRIN project AMANDA

Coordinator: Giuseppe di Battista, University of Roma 3
Duration: 2014-2017

Brief description
AMANDA will investigate algorithmics for massive data sets. On one hand the project will study emerging and realistic computational models and general algorithm design techniques; on the other hand it will focus on algorithmic issues specific for networked data sets. Pursuing these objectives raises hard research challenges, since the size of the data as well as their networked and evolving nature require a quantum leap in algorithmic design and engineering.

Investissement d’Avenir ANR ABS4NGS

Coordinator: Emmanuel Barillot, Curie Institute, Paris.
Duration: 2012-2017

Brief description
The ABS4NGS project is a French initiative, supported by the “Investment for the Future” program, to develop new methods and algorithms for the analysis of data produced by high-throughput sequencing.

CNRS-UCBL-INRIA International Associated Laboratory LIRIO

Coordinators: (France) ERABLE-BAOBAB LBBE and (Brazil) Labinfo LNCC
Duration: 2012-2015

Brief description
The CNRS-UCBL-INRIA International Associated Laboratory (Laboratoire International Associé – LIA) LIRIO builds upon a strong collaboration between the team of a French-Brazilian researcher with a background in discrete mathematics and algorithmics for the life sciences who has made her scientific career in France, since 2001 in the Laboratoire de Biométrie et Biologie Évolutive UMR 5558, and the team of a Brazilian researcher with a background in genetics and bioinformatics, and extensive national and international links in the area of bioinformatics. The research that will be conducted in the LIA will concern putting together all the activities currently conducted by each team separately or that each team has already planned to do, but also new research that the synergy between the two teams will enable to address in future. This synergy represented by the LIA should also allow us to apply for other sources of funding to support the research we wish to develop. Initially, this research will be concentrated on two main axes, one strongly concerned with the host-parasite relationship and the second with micro-environmental genomics and systems biology. Both address complex systems by a broad variety of experimental, bioinformatic and algorithmic approaches that reflect the complementarity of the two teams involved (biology including experimental part for the Brazilian team, algorithmics for the French one) while bioinformatics is a common language between the two. Besides fundamental issues, the two axes may have also important health-related implications. The topics in these two axes belong to one of the five “thématiques au cœur de l’INEE”, namely “Biodiversité et écologie fonctionnelle”, and cover three “thèmes d‘interface”, namely “Biodiversité, structure, dynamique et fonctionnalité”, “Mécanismes d’adaptation et d’évolution” and “Environment et santé”. Training will represent another key aspect of the LIA, and will aim at extending the already intensive exchanges of researchers, Master and PhD students between the two French and Brazilian partners of the LIA. The bioinformatic aspect of the two axes of research, both sequencing and data analysis, will also greatly benefit from an interaction between the platforms with which each partner is involved in her own country.

Associated with LIRIO, there are also a number of projects whose description may be found here.

Older projects

Information on older projects of the team may be found here. Notice that this page remains uncomplete.

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