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.

ANR project GraphEn

Coordinators: (General) Dieter Kratsch, LITA, University of Lorraine, France, (in Clermont-Ferrand) Mamadou Moustapha Kanté, LIMOS, University of Clermont-Ferrand, France, (in Bordeaux) Paul Dorbec, LABRI, University of Bordeaux, France; Participant in BAOBAB-ERABLE Teams LBBE-UCBL-INRIA: Arnaud Mary.
Duration: 2016-2020

Brief description
The P vs. NP question is arguably the most important open question in Theoretical Computer Science these days. Under the widely believed assumption that the complexity classes P and NP are not equal, there are problems that cannot be solved efficiently with the help of computers. Thus it is important to identify such problems and to find other ways of dealing with them, different from the traditional means of polynomial-time algorithms. Unfortunately, many problems of great theoretical importance and also many problems that arise from real applications turn out to be intractable in the general case.

While optimisation is ubiquitous in Computer Science and a lot of research has been done on algorithms and complexity on optimisation problems, surprisingly little attention has been given to enumeration. A solution of the enumeration version of a problem typically provides an immediate solution for the optimisation version of the problem. This seems to suggest that enumeration is “much harder” than optimisation, which, among others, directed the search for tractability and efficient algorithms to optimisation problems. New insights from the recent research on the exact complexity of hard problems indicate that the relation between enumeration and optimisation is more subtle and worth a fundamental study from theoretical point of view.

Listing, generating or enumerating objects of specified type and properties has important applications in various domains of Computer Science as e.g. data mining, machine learning and artificial intelligence, as well as in other sciences, in particular in biology, and also many applications in real life. This is one of the motivations of our interest in enumeration. The scientific goals of the project are of theoretical nature and oriented towards better understanding of the complexity of enumeration and the study of algorithmic techniques to solve enumeration problems. This project will concentrate focus on problems for graphs and hypergraphs and study three different approaches to the algorithmics of enumeration.

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.

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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