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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 France 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, Maxime Folschette, Jacques Nicolas.
Methodologies are developed in close collaboration with the LS2N (fusion of LINA and IRCCyN) located at University of Nantes and École centrale de Nantes. 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 ongoing Ph-D student J. Laniau is co-supervised with a member of the LS2N laboratory. Finally, M. Folschette is a PostDoc working on on a project aiming at analyzing TGF-beta-related pathways evolutions after epithelial-mesenchymal transition in liver cancer, which is a recognized biological process leading to metastasis. This project is based on a topic shared with the LS2N: the use of graph coloring and reconstruction to witness expression changes, and is funded by the Université Bretagne Loire.
Regional partnership in Marine Biology
Participants : Meziane Aite, Arnaud Belcour, 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. Our approach based on parcimonious modelling allowed an in silico characterization of processes required within sea urchin translation [83], [95]. We are also strongly involved in the the IDEALG consortium, 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. Our methods based on combinatorial optimization for the reconstruction of genome-scale metabolic networks and on classification of enzyme families based on local and partial alignments allowed the E. Siliculosus seaweed metabolism to be deciphered [97], [67]. As a further study, we reconstructed the metabolic network of a symbiot bacterium Ca. P. ectocarpi [69] and used this reconstructed network to decipher interactions within the algal-bacteria holobiont [21].
Regional partnership in agriculture and environmental sciences
Participants : Catherine Belleannée, François Coste, Olivier Dameron, Xavier Garnier, François Moreews, Jacques Nicolas, Anne Siegel, Denis Tagu.
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/IGEPP who spends 20% of his time in the team to develop collaborative projects. This partnership has been supported by the co-supervision of phDs, post-docs and engineers. This collaboration was also reinforced by collaboration within ANR contracts (MirNadapt, FatInteger).
In collaboration with researchers from the PEGASE center (INRA) focused on breeding animals, we have contributed to several studies aiming at better integrating and investigating data in order to facilitate animal selection and alimentation. The NutritionAnalyzer prototype was developed to understand better the impact of several diaries or treatments for lactary cows over the composition of milk [37]. Our work on the identification of upstream regulators within large-scale knowledge databases (prototype KeyRegulatorFinder) [59] and on semantic-based analysis of metabolic networks [54] was also very valuable for interpreting differences of gene expression in pork meat [79] and figure out the main gene-regulators of the response of porks to several diets (see [74], [76] and [18]).
In addition, constraints-based programming also allows us to decipher regulators of reproduction for the pea aphid, an insect that is a pest on plants in the framework of the MirnAdapt project. In terms of biological output of the network studies on the pea aphid microRNAs, we have identified one new microRNA (apmir-3019, not present in any known species other than the pea aphid) who has more than 900 putative mRNA targets. All these targets, as well as apmir3019, are differentially expressed between sexual and asexual embryos [85], [119].
Regional partnership in health
Participants : Jean Coquet, Olivier Dameron, Victorien Delannée, Marine Louarn, Anne Siegel, Nathalie Théret, Pierre Vignet.
We also have a strong and long term collaboration in health, namely with the IRSET laboratory at Univ. Rennes 1. 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 [14], M. Conan (Metagenotox project, funded by Anses) and J. Coquet [12]. This partnership was reinforced 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).
A new application was initiated in 2017 through a collaboration with Rennes hospital, supported by a Inria-INSERM Ph-D thesis (M. Louarn).