Bioinformatics & Biomarkers
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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.. http://crac.gforge inria.fr), we file a “software deposit” for those software in 2015. Another important development is the distribution of CRAC-V2 and the CracTools (http://crac.gforge.inria.fr/; http://cractools.gforge.inria.fr/). 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, http://www.ibc-montpellier.fr/). For 2015-2016, we have welcomed R Alvés, a post-doctoral researcher specialist in "data mining and machine learning" (S Beaumeunier et al, 2016). Two major developpements: * CORTECT “maturation project” (T Commes, N Philippe, G Buwalda, SATT-AxLR, Fev 2015-Fev2017). The project is supported by LRI (Languedoc Roussillon incubator, 30k€), BIC (2ieme european business incubator). N Philippe is the fellowship of « concours I-LAB,jeune créateur d'entreprise innovante, supported also by BPI, Transfert-LR, Synersud, Eurobiomed. *Bio2M platform creation with CHU-Montpellier for bioinformatic services for RNA-seq analysis, (T Commes, A Boureux). Expertises in biology and bioinformatics: Invited conferences: Genotoul biostat bioinfo day, Auzeville, Dec 2016; NGS’2016 Barcelone (Avril, 2016). Symposium of computational medicine, Montpellier-Vancouver (sept 2015), Institute of computational Biology, IBC days, 2012; 2014; 2017; Journées scientifiques de France Génomique, july, 2014; 5ieme international conference on Biomarkers and clinical research,Oxford, april 2014; IBCG conference « Université Bordeaux Segalen, Bordeaux, Feb 2014; 5ieme Workshop « Genome, Structure and Functions »,Toulouse, Feb 2014; 10ieme journées GSO, Toulouse, Oct 2014; Grandes avancées du pole Rabelais, Montpellier, Nov 2014; HDR jury and rewiever in biology and bioinformatics Grants for cancer and Bioinformatics projects: FRM appel d’offres bioinformatique (2014-2017)-IBC-ANR (post-doctorant; 2012-2017), Cortect maturation project (2015-2017) with SATT-AxLR. Teaching responsibilities in UM programs: In Sept 2015, we have created a new NGS platform (“Technologie Biomoléculaire Haut-débit”) to develop student practices in “Licence Professionnelle: Biologie Analytique et experimentale” (initial and professional learning) in collaboration with the LABEX CeMEB, the faculté des Sciences and the CFA de Montpellier (PIAA@sud.alternance). The students of this pathway are trained in new “Omics techniques” (NGS, Proteomics ...) and bioinformatics analysis. New training in Master2BioMED : TC3 : UE Bioinformatique et Biologie des Systèmes - 2015-2019 Références bibliographiques
Publications 2014-2016:
Pour plus de références, cliquez sur PubMed:
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Details
email: therese.commes[a]inserm.fr Group:
COMMES Thérèse ( PU/UM) BOUREUX Anthony (MCF/UM) RUFFLE Florence ( TR/UM) RIQUIER Sébastien (Doctorant MENRT/ 2ème année) AUDOUX Jérome ( Doctorant INSERM/ 3ème année) PHILIPPE Nicolas (Post doc/CDD AxLR) BUWALDA Guillaume ( IR/ CDD AxLR) BEAUMEUNIER Sacha ( IE/CDD AxLR) 
Keywords
Bioinformatique Algorithmique Cellules souches cancéreuses Leucémies Transcriptomes RNA-seq lncRNA Anomalies transcriptonnelles Technical skills
Transcriptome RNAseq QPCR bioinformatique développement de logiciels Benchmark Valorisation |
