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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.

Version 2. F1000Res. 2017 Aug 2 [revised 2017 Jan 1];6. pii: ISCB Comm J-1302. doi: 10.12688/f1000research.11352.2. eCollection 2017.


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

Bougé AL, Rufflé F, Riquier S, Guibert B, Audoux J, Commes T.

Methods Mol Biol. 2018;1769:133-156. doi: 10.1007/978-1-4939-7780-2_9.


Differential long non-coding RNA expression profiles in human oocytes and cumulus cells.

Bouckenheimer J, Fauque P, Lecellier CH, Bruno C, Commes T, Lemaître JM, De Vos J, Assou S.

Sci Rep. 2018 Feb 2;8(1):2202. doi: 10.1038/s41598-018-20727-0.


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. doi: 10.1186/s13059-017-1372-2.


New insights into diagnosis and therapeutic options for proliferative hepatoblastoma.

Hooks KB, Audoux J, Fazli H, Lesjean S, Ernault T, Dugot-Senant N, Leste-Lasserre T, Hagedorn M, Rousseau B, Danet C, Branchereau S, Brugières L, Taque S, Guettier C, Fabre M, Rullier A, Buendia MA, Commes T, Grosset CF, Raymond AA.

Hepatology. 2018 Jul;68(1):89-102. doi: 10.1002/hep.29672. Epub 2018 May 14.


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

Audoux J, Salson M, Grosset CF, Beaumeunier S, Holder JM, Commes T, Philippe N.

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


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, Alves R.

BioData Min. 2016 Nov 2;9:34. eCollection 2016.


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

Bouckenheimer J, Assou S, Riquier S, Hou C, Philippe N, Sansac C, Lavabre-Bertrand T, Commes T, Lemaître JM, Boureux A, De Vos J.

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


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. doi: 10.1038/ncomms10767.


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, Moreaux J.

Biomed Res Int. 2014;2014:423174. doi: 10.1155/2014/423174. Epub 2014 May 5.


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, Commes T.

Nucleic Acids Res. 2014 Mar;42(5):2820-32. doi: 10.1093/nar/gkt1300. Epub 2013 Dec 18.


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

Assou S, Al-edani T, Haouzi D, Philippe N, Lecellier CH, Piquemal D, Commes T, Aït-Ahmed O, Dechaud H, Hamamah S.

Hum Reprod. 2013 Nov;28(11):3038-49. doi: 10.1093/humrep/det321. Epub 2013 Jul 30.


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

Philippe N, Salson M, Commes T, Rivals E.

Genome Biol. 2013 Mar 28;14(3):R30. doi: 10.1186/gb-2013-14-3-r30.


Identification of cetrimonium bromide and irinotecan as compounds with synthetic lethality against NDRG1 deficient prostate cancer cells.

Wissing MD, Mendonca J, Kim E, Kim E, Shim JS, Kaelber NS, Kant H, Hammers H, Commes T, Van Diest PJ, Liu JO, Kachhap SK.

Cancer Biol Ther. 2013 May;14(5):401-10. doi: 10.4161/cbt.23759. Epub 2013 Feb 1.


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, Commes T.

Br J Haematol. 2012 May;157(3):347-56. doi: 10.1111/j.1365-2141.2012.09069.x. Epub 2012 Mar 6.


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

Philippe N, Salson M, Lecroq T, Léonard M, Commes T, Rivals E.

BMC Bioinformatics. 2011 Jun 17;12:242. doi: 10.1186/1471-2105-12-242.


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. doi: 10.1093/nar/gkp492. Epub 2009 Jun 16.


Serial analysis of gene expression adapted for downsized extracts (SAGE/SADE) analysis in reticulocytes.

Bonafoux B, Commes T.

Methods Mol Biol. 2009;496:299-311. doi: 10.1007/978-1-59745-553-4_20. Review.


Simultaneous gene expression profiling in human macrophages infected with Leishmania major parasites using SAGE.

Guerfali FZ, Laouini D, Guizani-Tabbane L, Ottones F, Ben-Aissa K, Benkahla A, Manchon L, Piquemal D, Smandi S, Mghirbi O, Commes T, Marti J, Dellagi K.

BMC Genomics. 2008 May 21;9:238. doi: 10.1186/1471-2164-9-238.

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