Section: Application Domains
The main stakes of bioinformatics are to assist biologists in the processes of discovering prognostic, diagnostic and therapeutic targets and the understanding of biological mechanisms. The local context of Biogenouest provides us with a lot of collaborations with biology laboratories. We emphasize here three types of applications with major achievements in the project.
Whole genome analysis is made practical through dedicated data structures and reconfigurable architectures. We have for instance implemented very fast Blast comparisons (Plast), built a software for bacterial genome fragmentation, GenoFrag, that helps to study genomes variations via Long Range PCR, and studied the occurrences of various structures like retro-transposons in the genome of Arabidopsis thaliana or micro-RNA in Drosophilia melanogaster .
Targeted gene discovery is studied with a syntactical approach. Models are built for proteins or promoters and then searched in whole genomes. We have for instance applied this strategy for the discovery of new beta-defensins, a family of anti-microbial peptides, in the human genome or the identification of all olfactive receptors genes in the dog genome.
Cancer is a privilegied domain for the application of systems biology. Each cancer has its specificities, resulting from different functioning modes of interacting pathways, within different environments and submitted to different genetic alterations. This implies experiments producing large and heterogeneous data sets. Developing modeling tools should have an impact on development of new drugs, on diagnosis and prognosis and on multiple therapy optimisations when a combination of drugs is used.
We have studied the pathways of TGF- and NF- B, that are central to the control of proliferation and apoptosis. We plan to consider also the Notch pathway. This project includes collaborations with INSERM Rennes, Curie Institute and NCBS Bangalore.