Section: Application Domains

Application fields in biology

In terms of transfer and societal impact, we consider that our role is to develop fruitful collaborations with laboratories of biology in order to consolidate their studies by a smart use of our tools and prototypes and generate new biological hypotheses to be tested experimentally.

Marine Biology: seaweed enzymes and metabolism Our main field of field marine biology, in close collaborations with the Roscoff Biological Station, in the framework of the Idealg project. Our goal is to apply our methods based on combinatorial optimization to the reconstruction of genome-scale metabolic networks, the understanding of microbial consortia, and classification of enzyme families. A main application model is E. Siliculosus, for which we reconstructed a metabolic network, predicted HAD proteins, and suggested new annotations of 56 genes based on metabolic network considerations. These approaches also shed light on evolution of metabolic processes. As a further study, we reconstructed the metabolic network of a symbiot bacterium Ca. P. ectocarpi and used this reconstructed network to decipher interactions within the algal-bacteria holobiont, revealing several candidates metabolic pathways for algal-bacterial interactions. For instance, our analyses suggest that the bacterium Ca. P. ectocarpi is able to provide both $\beta$-alanine and vitamin B5 to the seaweed via the phosphopantothenate biosynthesis pathway. These studies are now extended to the understanding of full host-microbial interactions.

Micro-biology: elucidating the functioning of extremophile consortiums of bacteria In this application field, our main issue is the understanding of bacteria living in extreme environments, mainly in collaboration with the group of bioinformatics at Universidad de Chile. In order to elucidate the main characteristics of these bacteria. In particular, genome-scale metabolic network have been reconstructed for bacteria involved in biomining processes and in Salmon pathogenicity, already leading to a better understanding of bacterial interactions and growth.

Agriculture and environmental sciences: upstream controllers of pork and pea-aphid metabolism and regulation In this application field, our goal is to propose methods to identify regulators of very complex phenotypes related to environmental issues, in collaboration with the INRA centers of Rennes (Pegase, Igepp, Scribe). This is a relevant application field for our researches work on the identification of upstream regulators within large-scale knowledge databases and on semantic-based analysis of metabolic networks, in order to interpreting differences of gene expression in pork meat and figure out the main gene-regulators of the response of porks to several diets, or to decipher regulators of reproduction for the pea aphid, an insect that is a pest on plants.

Health: deciphering pathways involved in the TGF-$\beta$ signalling network This topic is studied with the IRSET laboratory of Rennes. TGF-$\beta$ is a multifunctional cytokine that regulates mammalian development, differentiation, and homeostasis with both benefical anti-tumor effect and pro-tumor effect. Deciphering protumor versus antitumor signaling requires to take into account a system-wide view and develop predictive models for therapeutic benefit. We are developping Cadbiom in order to identify gene networks associated with innate immune response to viral infection that combine TGF-$\beta$ and interleukine signaling pathways.