Section: Partnerships and Cooperations

Regional Initiatives

Regional initiative: the Ecosyst project

Participants : Damien Eveillard, Marie Chevallier, Clémence Frioux, Anne Siegel, Camille Trottier.

EcoSyst is a Biogenouest inter-regional federating project (Brittany – Pays de la Loire) aiming at the emergence of Systems Ecology at the level of western regions. Drawing on the strengths and skills involved, EcoSyst targets the incubation of new ideas and new projects at disciplinary interfaces. Thanks to this community project, we want to develop the skills of Ecology, Environment, Modeling, Bioinformatics and Systems Biology and their application to organisms and ecosystems of interest in agronomy, sea and health. EcoSyst includes also the identification of the major issues and concerns, the fundamental and essential methods and the very real needs of the community (training, tools, ...); this in order to consider the construction of a community platform (or an offer of service within an existing platform) on complex systems modeling, meeting expectations of the community as fully as possible.

Regional partnership with computer science laboratories in Nantes

Participants : Anne Siegel, Jérémie Bourdon, Damien Eveillard, François Coste, Jacques Nicolas.

Methodologies are developed in close collaboration with university of Nantes (LINA) and Ecole centrale Nantes (IRCCyN). This is acted through the Biotempo and Idealg ANR projects and co-development of common software toolboxes within the Renabi-GO platform support. C. Trottier is a co-supervised bioianalysis and software development engineer within the Idealg project. M. Chevallier is a co-supervised development and animation engineer within the regional initiative "Ecosyst". In addition, the former Ph-D student V. Picard and the ongoing Ph-D student J. Laniau are also co-supervised with members of the LINA laboratory.

Regional partnership in Marine Biology

Participants : Catherine Belleannée, Jérémie Bourdon, Jean Coquet, François Coste, Damien Eveillard, Olivier Dameron, Clémence Frioux, Jeanne Got, Julie Laniau, Jacques Nicolas, Camille Trottier, Anne Siegel.

A strong application domain of the Dyliss project is marine Biology. This application domain is co-developed with the station biologique de Roscoff and their three UMR and involves several contracts. The IDEALG consortium is a long term project (10 years, ANR Investissement avenir) aiming at the development of macro-algae biotechnology. Among the research activities, we are particularly interested in the analysis and reconstruction of metabolism and the characterization of key enzymes. Other research contracts concern the modeling of the initiation of sea-urchin translation (former PEPS program Quantoursin, Ligue contre le cancer and ANR Biotempo), the analysis of extremophile archebacteria genomes and their PPI networks (former ANR MODULOME and PhD thesis of P.-F. Pluchon) and the identification of key actors implied in competition for light in the ocean (PELICAN ANR project). In addition, the team participates to a collaboration program (Inria Project Lab) with the Biocore and Ange teams, together with Ifremer-Nantes, focused on the understanding on micro-algae (Ph-D thesis of J. Laniau).

Regional partnership in agriculture and bio-medical domains

Participants : Aymeric Antoine-Lorquin, Catherine Belleannée, François Coste, Jean Coquet, Olivier Dameron, Victorien Delannée, Aurélie Evrard, François Moreews, Jacques Nicolas, Anne Siegel, Nathalie Théret, Denis Tagu, Pierre Vignet.

We have a strong and long term collaboration with biologists of INRA in Rennes : PEGASE and IGEPP units. F. Morrews is a permanent engineer from PEGASE center hosted in the team to develop methods for integrative biology applied to species of interest in agriculture. D. Tagu is a research director at INRA who spends 20% of his time in the team to develop collaborative projects. This partnership is supported by the co-supervision of one post-doctoral student and the co-supervision of several PhD students. The Ph-D thesis of V. Wucher was supported by collaborations with the IGEPP laboratory. The former post-doc of Ch. Bettembourg strengthened these collaborations. This collaboration was also reinforced by collaboration within ANR contracts (MirNadapt, FatInteger). Lately, A. Evrard joined the team at mid-part of her time in collaboration with Agrocampus Ouest and INRA to apply the semantic web to technologies developed within the mirnAdapt framework to new agriculture applications (Brassicae).

We also have a strong and long term collaboration in the bio-medical domain, namely with the IRSET laboratory at Univ. Rennes 1/Irset. N. Théret, research director at INSERM, is hosted in the team to strenghen our collaborative projects. Our collaborations are acted by the co-supervised Ph-D theses of V. Delannée (Metagenotox project, funded by Anses) and J. Coquet. This partnership was reinforced in the former years by the ANR contract Biotempo ended at the end of 2014. In 2015, the project of combining semantic web technologies and bi-clustering classification based on formal concept analysis was applied to systems biology within the PEPS CONFOCAL project. This scientific project has been recently pushed forward in the recent TGFSYSBio project funded by Plan Cancer on the modelling of the microenvironment of TGFbeta signaling network (P. Vignet has been recruited on this contract at the end of 2016).