Bio2m Articles


Detailed analysis of public RNAseq data and long non-coding RNA: a proposed enhancement to mesenchymal stem cell characterisation

Riquier Sebastien; Mathieu Marc, Boureux Anthony, Ruffle Florence, Lemaitre Jean-Marc, Djouad Farida, Gilbert Nicolas, Commes Therese

  • Submitted


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

Bougé AL, Rufflé F, Riquier S, Guibert B, Audoux J, Commes T. (2018) Methods in Molecular Biology (Clifton, N.J.) 1769 : 133.


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.

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. (2017). Hepatology. 10.1002/hep.29672.


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


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.


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

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


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.


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.


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


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.