Bioinformatics & Biomarkers

Thérèse COMMES

Team Leader

Team Contact :

For all member’s Email:  firstname.lastname@inserm.fr
Phone :                                        +33 4 67 33 57 11                           +33 4 67 33 94 88

Team members :

Anthony BOUREUX (MCF/UM)

Thérèse COMMES ( PU/UM)

Nicolas GILBERT (CRCN-Inserm)

Michel GOMES (M2 Bioinformatics)

Benoit GUIBERT (IE CDD UM)

Raissa LORENNA (Ph.D. UM)

Jérôme REBOUL (CRCN-inserm)

Cedric RIEDEL (M2 Bioinformatics)

Florence RUFFLE (AI/UM)

Keywords :

Bioinformatics

Machine Learning

RNAsequencing

Public dataset

Biomarkers

Chimeric RNA

Long non coding

RNA

Mobile Elements

Kmers

Cancer stem cell

Know how :

Transcriptome

RNAseq

QPCR

Bioinformatics

Software

Development

Benchmark

Mobile Elements

Valuation

photolabo2

Our main scientific objective is to establish novel analysis frameworks for large scale omics analysis in human health.

 

The bioinformatics group includes biologists and bioinformaticians specialists in text-based algorithms who focus on designing new tools and structures for RNA-Seq analysis. We develop software and data structures for RNA-Seq data analysis (such as Gk-Arrays, CRAC, CracTools, ChimCT).  We create new strategies based on kmers capable of organizing reads to quickly respond to specific queries, such as the following pipelines: De-Kupl, Kmerator Suite and KmerExploR. see also: https://bio2m.montp.inserm.fr/)

As example of application of our tools, we used CRAC and its dedicated modules to characterize and classify fusion RNA or chimeric RNA (chRNA) in cancer (F Ruffle et al, 2017). The chRNA classification was later refined with machine learning approaches using private and public myeloid leukemia data sets (France Génomique sequencing project and LEUCEGENE cohort).

Another example of application is the use of “Kmerator Suite”, a bioinformatics pipeline we developed, in the purpose of building a cell-specific catalogue of unannotated long non-coding RNAs (lncRNAs). The pipeline uses a specific k-mer approach methodologies for naive quantification of expression in numerous RNAseq data (Riquier et al, BMC Genomics, 2021).

New development now seeks to establish a novel analysis framework for large scale OMICS data analysis in human health. In a primary approach, as a proof of concept, we attempt to establish a complete Encyclopedia of kmers as signature of abnormal transcripts in the context of acute myeloid leukemia (AML). The establishment of such signature should allow to explore better diagnostic and prognosis models for new therapeutic strategies

In 2015, the team, in association with CHU-Montpellier, created a bioinformatic platform for RNA-seq analysis called “BIO2M”. Link to Bio2M web page (https://bio2m.montp.inserm.fr/)

 
  • 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 :

  • Master2 BioMED : TC3 : UE Bioinformatique et Biologie des Systèmes – since 2015
  • Master2 Bioinformatique : UE Bioanalyse transcriptomique – since 2021

Former group members

  • Bessière Chloé Post-Doc (2019-2021) Post-Doc CRCT-Toulouse
  • Bernadas Camille, Bsc info (alternance 2020-2021)
  • Riquier Sébastien Ph.D. (2016-2020)
  • Bouge Anne-Laure Post-doc (2017-2019) Chief Operating Officer at SeqOne
  • Beaumeunier Sacha IE CDD (2015-2016) Chief Operating Officer at SeqOne
  • Audoux Jerome Ph.D (2014-2018) Chief Operating Officer at SeqOne
  • Bou Samra Elias Ph.D (2008-2012) Research and Innovation L’Oréal
  • Philippe Nicolas PhD and Post-doc (2008-2013) CEO SeqOne

Recent Publications

Kmerator Suite: design of specific k-mer signatures and automatic metadata discovery in large RNA-seq datasets. Riquier S, Bessiere C, Guibert B, Bouge AL, Boureux A, Ruffle F, Audoux J, Gilbert N, Xue H, Gautheret D, Commes T. NAR Genom Bioinform. 2021 Jun 23;3(3):lqab058. doi: 10.1093/nargab/lqab058.

Long non-coding RNA exploration for mesenchymal stem cell characterisation. Riquier S, Mathieu M, Bessiere C, Boureux A, Ruffle F, Lemaitre JM, Djouad F, Gilbert N, Commes T. BMC Genomics. 2021 Jun 4;22(1):412. doi: 10.1186/s12864-020-07289-0.

New chimeric RNAs in acute myeloid leukemia. Rufflé F, Audoux J, Boureux A, Beaumeunier S, Gaillard JB, Bou Samra E, Megarbane A, Cassinat B, Chomienne C, Alves R, Riquier S, Gilbert N, Lemaitre JM, Bacq-Daian D, Bougé AL, Philippe N, Commes T. F1000Res. 2017 Aug 2;6:ISCB Comm J-1302. doi: 10.12688/f1000research.11352.2.

For more publications, clic on PubMed icon:

T. Commes