Team

History of the team

ERABLE is a follow-up of the team BAMBOO.

Goal

Cells are seen as the basic structural, functional and biological units of all living systems. They represent the smallest units of life that can replicate independently, and are often referred to as the building blocks of life. Living organisms are then classified into unicellular ones – this is the case of most bacteria and archea – or multicellular – this is the case of animals and plants. Actually, multicellular organisms, such as for instance human, may be seen as composed of native (human) cells, but also of extraneous cells represented by the diverse bacteria living inside the organism. The proportion in the number of the latter in relation to the number of native cells is believed to be high: this is for example of 90% in humans. Multicellular organisms have thus been described also as “superorganisms with an internal ecosystem of diverse symbiotic microbiota and parasites” (Nicholson et al, Nat Biotechnol, 22(10):1268-1274, 2004) where symbiotic means that the extraneous unicellular organisms (cells) live a close, and in this case, long-term relation both with the multicellular organisms they inhabit and among themselves. On the other hand, bacteria sometimes group into colonies of genetically identical individuals which may acquire both the ability to adhere together and to become specialised for different tasks. An example of this is the cyanobacterium Anabaena sphaerica who may group to form filaments of differentiated cells, some – the heterocysts – specialised for nitrogen fixation while the others are capable of photosynthesis. Such filaments have been seen as first examples of multicellular patterning.

At its extreme, one could then see life as one collection, or a collection of collections of genetically identical or distinct self-replicating cells who interact, sometimes closely and for long periods of evolutionary time, with same or distinct functional objectives. The interaction may be at equilibrium, meaning that it is beneficial or neutral to all, or it may be unstable meaning that the interaction may be or become at some time beneficial only to some and detrimental to other cells or collections of cells. The interaction may involve other living systems, or systems that have been described as being at the edge of life such as viruses, or else genetic or inorganic material such as, respectively, transposable elements and chemical compounds.

The application goal of ERABLE (European Research team in Algorithms and Biology, formaL and Experimental) is, through the use of mathematical models and algorithms, to better understand such close and often persistent interactions, with a longer term objective of becoming able in some cases to suggest the means of controlling for or of re-establishing equilibrium in an interacting community by acting on its environment or on its players, how they play and who plays.

This goal requires to identify who are the partners in a closely interacting community, who is interacting with whom, how and by which means. Any model is a simplification of reality, but once selected, the algorithms to explore such model should address questions that are precisely defined and, whenever possible, be exact in the answer as well as exhaustive when more than one exists in order to guarantee an accurate interpretation of the results within the given model.

This fits well the mathematical and computational expertise of the team, and drives the methodological goal of ERABLE which will be to substantially and systematically contribute to the field of exact enumeration algorithms for problems that most often will be hard in terms of their complexity, and as such to also contribute to the field of combinatorics in as much as this may help in enlarging the scope of application of exact methods.

The key objective will be, by constantly crossing ideas from different models and types of approaches, to look for and to infer “patterns”, as simple and general as possible, either at the level of the biological application or in terms of methodology. This objective will drive which biological systems are considered, and also which models and in which order, going from simple discrete ones first on to more complex continuous models later if necessary and possible.

Partners

A project such as proposed by ERABLE requires experts in disciplines which cover the spectrum from mathematics and algorithmics to theoretical and experimental biology. The difficulties in implementing such a team ask for original solutions, that may also benefit from the chances offered by an open European landscape.
As scientists, we are naturally attracted by and have a strong taste for such original solutions, and for experimenting new approaches in general. This is why we propose the creation of an Inria European Project-Team gathering members from France (Inria, CNRS, Insa-Lyon), Italy (Sapienza University of Rome, University of Florence, University of Pisa, University of Rome Tor Vergata) and the Netherlands (CWI and Free University of Amsterdam) who have already a long and solid history of collaborations among them, through projects and shared co-supervision of PhD students and postdocs.
The benefits of a European team are many. Extending the limits of the teams beyond the national frontiers is indeed an important way of acquiring and of multiplying the manpower and the strengths of all involved teams.

Main international relations

There are other groups from Brazil with whom ERABLE maintains a collaboration, including through shared students who have been representing the main pool of PhD students and postdocs of the previous Project-Team BAMBOO since 2001.

  • Fabien Jourdan from the “Metabolism of Xenobiotics” team in the Toxalim Laboratory at Inra-Toulouse who is an expert on (mainly but not only) metabolic network reconstruction, analysis, and visualisation.
  • Paulo Gustavo Soares da Fonseca from the Federal University of Pernambuco (UFPE), Recife, Brazil, who is an expert on (mainly but not only) sequence algorithms and on data-structures.
  • The GenScale Team at Inria that has an expertise on NGS and parallel algorithms, data structures, and genomics and evolution more in general.
  • The Swiss Institute of Bioinformatics, and notably Anne Morgat.
  • Biologists with whom members of ERABLE have been interacting in the past, notably the groups of Roderic Guigó and Toni Galbadón at Barcelona in Spain, and of Andrés Moya at Valencia in Spain.
  • Catherine Matias (University of Évry), Etienne Birmelé (University of Paris 5), and more generally the French Statistics for Systems Biology (SSB) group mainly attached to the MIA Department of Inra.
  • Steven Kelk (University of Maastricht) and Leo van Iersel (http://leovaniersel.wordpress.com/) who are experts on phylogenetic networks, a topic closely related to co-phylogeny.
  • AlgoLab Group, University of Milano Bicocca, Italy
  • Lodewyk Wessels who is an expert in cancer research, the Netherlands Cancer Institute
  • The Plateforme Bio-Informatique Gilles Thomas at the Centre Léon Bérard in Lyon, all experts in cancer research: Alain Viari is a member if the Scientific Committee of the Plateforme and collaborates extensively with its members as well as with other researchers at the Centre Léon Bérard.

More recent collaborations that may develop further in the future include both biology- and computation/math-oriented groups.

The main current industrial collaborators of ERABLE are:

  • TecSinapse, Brazil, on biotechnology.
  • Chr. Hansen A/S (Denmark, global supplier of bioscience based ingredients to the food industry) who was a partner in a European project, BachBerry, with Erable, and is member in another, MicroWine, to which the team also participates.
  • Maat Pharma with whom the team started interacting in July 2017.

Permanent link to this article: https://team.inria.fr/erable/en/