Bio2m Articles


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 - doi: 10.12688/f1000research.11352.1.

Software

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.

ChimCT: https://github.com/Bio2M/cractools-chimct

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., Coz, J.L., Commes, T., and Gautheret, D. (2017) BioRxiv 122937 & Genome Biol. 18, 243.

De-Kupl, https://transipedia.github.io/dekupl/.

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. (2017). BMC Bioinformatics. Sep 29;18(1):428. doi: 10.1186/s12859-017-1831-5.

SimBA, https://github.com/jaudoux/simba-publication-pipeline

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. (2014). Nucleic Acids Res. 42, 2820–2832.

DigiTAG, http://cractools.gforge.inria.fr/softwares/digitagct

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

Philippe, N., Salson, M., Commes, T., and Rivals, E. (2013).Genome Biology 14, R30.

CRAC, http://crac.gforge.inria.fr/documentation/crac/

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

Philippe, N., Salson, M., Lecroq, T., Léonard, M., Commes, T., and Rivals, E. (2011). BMC Bioinformatics 12, 242.

GkArrays, http://www.atgc-montpellier.fr/ngs/

Data Mining

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.

New chimeric RNAs in acute myeloid leukemia

Ruffle, F., Audoux, J., Boureux, A., Beaumeunier, S., Gaillard, JB., BouSamra, E., Megarbane, A., Cassinat, B., Chomienne, C., Alves, R., Riquier, S., Gilbert, N., Lemaitre, JM., Bacq-Daian, D., Bougé, A L., Philippe, N., and Commes T. F1000Research 02 Aug 2017, 6 (ISCB CommJ):1302 doi: 10.12688/f1000research.11352.

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. (2016). BioData Mining 9, 34.

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 Itzykson R, de Botton S, Quesnel B, et al. (2016). Nat Commun 7, 10767.

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., et al. (2016). Hum Reprod Update. Dec;23(1):19-40. Epub 2016 Sep 21.

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. (2014). Biomed Res Int 2014, 423174.

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.

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

Samra, E.B., Klein, B., Commes, T., and Moreaux, J. (2012). Oncotarget 3, 824–832. IF=6;4.

A Scalable Indexing Solution to Mine Huge Genomic Sequence Collections

E. Rivals, N. Philippe, M. Salson, M. Leonard, T. Commes, T. Lecroq (2012). ERCIM News, Vol. 89, p. 20-21.

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. (2012). Br. J. Haematol. 157, 347–356.