Bio2M team & Plateform

Bio2m Articles

2025 - 2024 - 2023 - 2021 - Collaborations

2025

A strong internal promoter drives massive expression of YEATS-domain devoid MLLT3 transcripts in HSC and most lethal AML.

Bessière C, Zamani A, Pfeifer R, Dailhau S, Marchet C, Guibert B, Boureux A, Silva Da Silva R, Gilbert N, Commes T, Meggetto F, Touriol C, Récher C, Bousquet M, Pyronnet S.

2024

Effective requesting method to detect fusion transcripts in chronic myelomonocytic leukemia RNA-seq

Rufflé F, Reboul J, Boureux A, Guibert B, Bessière C, Lorena R, Jourdan E, Gaillard JB, Boland A, Deleuze JF, Sénamaud-Beaufort C, Selimoglu-Buet D, Solary E, Gilbert N,†, Commes T,† (†co-corresponding)

Transipedia.org: k-mer-based exploration of large RNA sequencing datasets and application to cancer data

Bessière C, Xue H, Guibert B, Boureux A, Rufflé F, Viot J, Chikhi R, Salson M, Marchet M, Commes T†, Gautheret D† (†co-corresponding).

2023

A k-mer based transcriptomics analysis for NPM1-mutated AML

Silva, R., Riedel, C., Guibert, B., Ruffle, F., Boureux, A., and Commes, T.

2021

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.

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.

2020

KmerExplR, a new tool to quickly explore large RNA-Seq datasets

Sébastien Riquier, Benoit Guibert, Chloé Bessiere, Anne-Laure Bougé, Anthony Boureux, Florence Rufflé, Nicolas Gilbert, Daniel Gautheret and Thérèse Commes.

Bio2M platform: find everything in your RNA-Seq data

Benoit Guibert, Florence Rufflé, Chloé Bessiere, Anthony Boureux and Thérèse Commes.

2018

RNA-Seq Analysis to Detect Abnormal Fusion Transcripts Linked to Chromothripsis

Anne-Laure Bougé, Florence Rufflé, Sébastien Riquier, Benoit Guibert, Jérôme Audoux, Thérèse Commes.

New insights into diagnosis and therapeutic options for proliferative hepatoblastoma

Hooks KH, Audoux J, Fazli H, Lesjean S, Ernault T, Dugot Senant N, Leste-Lasserre T, Hagedorn M, Rousseau B, Danet C, Branchereau S, Brugières L, Guettier C, Fabre M, Rullier A, Buendia MA, Commes T, Grosset CF, Raymond AA. (2018). Hepatology. 10.1002/hep.29672.

2017

New chimeric RNAs in acute myeloid leukemia

Florence Rufflé, Jérôme Audoux, Anthony Boureux, Sacha Beaumeunier, Jean-Baptiste Gaillard, Elias Bou Samra, Andre Megarbane, Bruno Cassinat, Christine Chomienne, Ronnie Alves, Sébastien Riquier, Nicolas Gilbert, Jean-Marc Lemaitre, Delphine Bacq-Daian, Anne Laure Bougé, Nicolas Philippe and Thérèse Commes. F1000Research 2017, 6(ISCB Comm J):1302

DE-kupl: exhaustive capture of biological variation in RNA-seq data through k-mer decomposition

Audoux J, Philippe N, Chikhi R, Salson M, Gallopin M, Gabriel M, Le Coz J, Drouineau E, Commes T, Gautheret D. Genome Biol. 2017 Dec 28;18(1):243

SimBA: A methodology and tools for evaluating the performance of RNA-Seq bioinformatic pipelines

Audoux J, Salson M, Grosset C, Beaumeunier S, Holder JM, Commes T, Philippe N. BMC Bioinformatics. 2017 Sep 29;18(1):428.

2016

On the evaluation of the fidelity of supervised classifiers in the prediction of chimeric RNAs

Beaumeunier, S., Audoux, J., Boureux, A., Ruffle, F., Commes, T., Philippe, N., and Alves, R BioData Min. 2016 Nov 2;9:34. eCollection 2016.

Mutation allele burden remains unchanged in chronic myelomonocytic leukaemia responding to hypomethylating agents

Merlevede J, Droin N, Qin T, Meldi K, Yoshida K, Morabito M, Chautard E, Auboeuf D, Fenaux P, Braun T, Itzykson R, de Botton S, Quesnel B, Commes T, Jourdan E, Vainchenker W, Bernard O, Pata-Merci N, Solier S, Gayevskiy V, Dinger ME, Cowley MJ, Selimoglu-Buet D, Meyer V, Artiguenave F, Deleuze JF, Preudhomme C, Stratton MR, Alexandrov LB, Padron E, Ogawa S, Koscielny S, Figueroa M, Solary E. Nat Commun. 2016 Feb 24;7:10767

2014

Identification of a 20-gene expression-based risk score as a predictor of clinical outcome in chronic lymphocytic leukemia patients

Bou Samra, E., Klein, B., Commes, T., and Moreaux, J. Biomed Res Int 2014, 423174.

Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome

Philippe, N., Bou Samra, E., Boureux, A., Mancheron, A., Rufflé, F., Bai, Q., De Vos, J., Rivals, E., and Commes, T. Nucleic Acids Res. 42, 2820–2832.

2013

CRAC: an integrated approach to the analysis of RNA-seq reads

Philippe, N., Salson, M., Commes, T., and Rivals, E. Genome Biology 14, R30.

2012

A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections

E. Rivals, N. Philippe, M. Salson, M. Leonard, T. Commes, T. Lecroq ERCIM News, Vol. 89, p. 20-21.

  • Tags: Software

New prognostic markers, determined using gene expression analyses, reveal two distinct subtypes of chronic myelomonocytic leukaemia patients

Bou Samra, E., Moreaux, J., Vacheret, F., Mills, K., Rufflé, F., Chiesa, J., Piquemal, D., Boureux, A., Lavabre-Bertrand, T., Jourdan, E., and Commes T. Br. J. Haematol. 157, 347–356.

Development of gene expression-based risk score in cytogenetically normal acute myeloid leukemia patients

Samra, E.B., Klein, B., Commes, T., and Moreaux, J. Oncotarget 3, 824–832. IF=6;4.

2011

Querying large read collections in main memory: a versatile data structure

Philippe, N., Salson, M., Lecroq, T., Léonard, M., Commes, T., and Rivals, E. BMC Bioinformatics 12, 242.

2009

Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity.

Philippe N, Boureux A, Bréhélin L, Tarhio J, Commes T, Rivals E. Nucleic Acids Res. 2009 Aug;37(15):e104

Collaborations

Gene Expression Signature Associated with Clinical Outcome in ALK-Positive Anaplastic Large Cell Lymphoma

Daugrois C, Bessiere C, Dejean S,Anton Leberre V, Commes T, Pyronnet S,Brousset P, spinos E, Brugiere L, Meggetto F, Lamant L. (2021)

Transformation Foci in IDH1-mutated Gliomas Show STAT3 Phosphorylation and Downregulate the Metabolic Enzyme ETNPPL, a Negative Regulator of Glioma Growth.

Leventoux N, Augustus M, Azar S, Riquier S, Villemin JP, Guelfi S, Falha L, Bauchet L, Gozé C, Ritchie W, Commes T, Duffau H, Rigau V, Hugnot JP.

  • Sci Rep. 2020 Mar 26;10(1):5504
  • doi: 10.1038/s41598-020-62145-1
  • PMID: 32218467
  • PMCID: PMC7099072
  • Post-doc S Riquier

Recurrent Genetic Abnormalities in Human Pluripotent Stem Cells: Definition and Routine Detection in Culture Supernatant by Targeted Droplet Digital PCR

Assou S, Girault N, Plinet M, Bouckenheimer J, Sansac C, Combe M, Mianné J, Bourguignon C, Fieldes M, Ahmed E, Commes T, Boureux A, Lemaître JM, De Vos J (2020) Stem Cell Reports. 2020 Jan 14;14(1):1-8.

Long non-coding RNAs in human early embryonic development and and their potential in ART

Bouckenheimer, J., Assou, S., Riquier, S., Hou, C., Philippe, N., Sansac, C., Lavabre-Bertrand, T., Commes, T., Lemaître, J.-M., Boureux, A., De Vos J. (2016) Hum Reprod Update. Dec;23(1):19-40. Epub 2016 Sep 21.

MicroRNAs: new candidates for the regulation of the human cumulus–oocyte complex

Assou, S., Al-edani T., Haouzi, D., Philippe, N., Lecellier, C.-H., Piquemal, D., Commes, T., Aït-Ahmed, O., Dechaud, H., and Hamamah, S. (2013) Hum. Reprod. Nov;28(11):3038-49.