In construction …
The bioinformatic group involved specialists in text algorithm focusing on the design of new tools and structures for RNA-Seq analysis. We have created a new data structure capable of organizing reads for very quickly queries and developed a software (called CRAC) noticed by Nature as a competitor over existing softwares for the analysis of RNA-Seq data (TopHat, Star..).
We are currently developing additional modules using CRAC (CracTools). One of them is dedicated to the characterization and classification of fusion RNA or chimeric RNA (chRNA) in cancer (F Ruffle et al, in preparation, 2016). The classification of chRNA is refined with machine learning approaches in myeloid leukemia data sets (France Génomique sequencing project and IGR collaboration, LEUCEGENE project).
All our work led to the production
of 4 softwares in the field of bioinformatics and high-throughput
sequencing (Gk-Arrays, CRAC, CracTools, ChimCT), we file a “software deposit” for those software in 2015.
Another important development is the distribution of CRAC-V2 and the CracTools. CRAC-V2 includes not only bug corrections but also major improvements with an impact in memory using Jellyfish lib. We also developped best practices for gene expression analysis and a benchmark pipeline (J Audoux et al, submitted, FRM project). For “data mining” projects, the team has developed an integrated pipeline dedicated to the characterization of novel non-coding RNAs including long non-coding RNA in collaboration with J Devos Group (J Bouckenheimer et al, 2016).
We developed our interdisciplinary projects in collaboration of the team “Methods and Algorithms for Bioinformatics (MAB)” at LIRMM Montpellier and our projects have been included into the “Institut de Biologie Computationnelle” (IBC) (ANR, AAP-Investissement d’avenir, 2012-2017) and T Commes is the co-advisor of the research axis entitled “Methods for the analysis of high-throughput sequencing data” see IBC web site. For 2015-2016, we have welcomed R. Alvés, a post-doctoral researcher specialist in “data mining and machine learning” (S Beaumeunier et al, 2016).