Bioinformatics tool development to analyze and integrate genomics data generated by high-throughput sequencing / Développement d'outils bio-info analysant les données de séquençage

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High-throughput DNA sequencing (HTS) is significantly changing modern biology and is already becoming a very important tool for most laboratories interested in genetics and molecular biology. While advances in HTS technologies continue to improve our ability to collect data, it is becoming increasingly clear that the bottleneck in translating these gains into scientific breakthroughs now resides in data mining and integrative analysis. There is currently no tool exploiting the publicly available epigenomics data sets in order to help understanding new data sets. To fulfill that need, we propose to develop the Genomic Correlator and Enrichment (GeCorE) tool that will be running on a supercomputer and accessible to end users through a web interface. This will allow non-bioinformatician users to benefit from this tool without having to install anything. GeCorE will be using thousands of published whole-genome data sets downloaded, uniformly processed and organized on our server. Through private account, users working on all organisms, thus including many model organisms, will be able to upload their own private epigenomics data and use the GeCorE application to characterize them.On another aspect, the recent publication of incorrectly analyzed epigenomics data leading to erroneous biological conclusion prompted us to develop a tool based on a method initiated during my post-doctoral training. The Aggregate Profiler (TAggPro) tool will allow biologists with any type of computational skills to efficiently capture trends in its whole data by easily generating aggregate profiles over genes or regions of interest. As illustrated by the popular adage, a picture is worth a thousand words. TAggPro will therefore be designed to be highly flexible by integrating many parameters, and will be accessible for the users through a user-friendly interface. It will also greatly benefit of being on the same server than GeCorE by having access to the wealth of collected and organized public epigenomics data.