PhD thesis, Van Hoa Nguyen
Parallel Intensive Genomic Sequence Comparison  The thesis was supervised by D. Lavenier.
The sequence comparison process is one of the main bioinformatics task. The new sequencing technologies lead to a fast increasing of genomic data and strengthen the need of fast and efficient tools to perform this task.
In this thesis, a new algorithm for intensive sequence comparison is proposed. It has been specifically designed to exploit all forms of parallelism of today microprocessors (SIMD instructions, multi-core architecture). This algorithm is also well suited for hardware accelerators such as FPGA or GPU boards.
The algorithm has been implemented into the PLAST software (Parallel Local Alignment Search Tool). Different versions are available according to the data to process (protein and/or DNA). A MPI version has also been developed. According to the nature of the data and the type of technologies, speedup from 3 to 20 has been measured compared with the reference software, BLAST, with the same level of quality.
PhD thesis, Jérémie Gruel
From biological data to molecular modelisation; application to TGF-beta signaling and hepatic fibrosis  The thesis was co-advised by Michel Le Borgne and Nathalie Théret.
Hepatic fibrosis is a complex pathology mainly due to chronic viral or toxic aggressions. In this context, hepatic stellate cells are the main producers of the excess of extra-cellular matrix modifying liver normal activity. The main pro-fibrotic cytokine is the TGF-beta and a perturbation of the TGF-beta signaling pathways is observed in hepatic stellate cells in the pathological context. The thesis aimed at a better understanding of these cellular regulation perturbations.
In the first part of this work, we studied the impact of the protein ADAM12 on TGF-beta receptors trafficking. Using a combination of differential models and qualitative experimental data, we have obtained predictions about the modifications induced by ADAM12 in this system.
In the second part of this work, we studied the transcriptional signatures present in the promoters of cytokine regulated genes, including TGF-beta. We have proposed an algorithm allowing to gather genes potentially sharing the same expression regulation mechanisms than a given gene of interest.