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

Autor: Chloé Bessière, Haoliang Xue, Benoit Guibert, Anthony Boureux, Florence Rufflé, Julien Viot, Rayan Chikhi, Mikaël Salson, Camille Marchet, Thérèse Commes, Daniel Gautheret

Publikováno v: Genome Biology, Vol 25, Iss 1, Pp 1-16 (2024)

Abstract Indexing techniques relying on k-mers have proven effective in searching for RNA sequences across thousands of RNA-seq libraries, but without enabling direct RNA quantification. We show here that arbitrary RNA sequences can be quantified in

Externí odkaz: https://doaj.org/article/a609a092c730485c832b8c973417638f

Long non-coding RNA exploration for mesenchymal stem cell characterisation

Autor: Anthony Boureux, Chloé Bessière, Marc Mathieu, Farida Djouad, Nicolas Gilbert, Sébastien Riquier, Jean-Marc Lemaitre, Thérèse Commes, Florence Ruffle

Publikováno v: BMC Genomics
BMC Genomics, BioMed Central, 2021, 22 (1), pp.412. ⟨10.1186/s12864-020-07289-0⟩
BMC Genomics, Vol 22, Iss 1, Pp 1-23 (2021)

Background The development of RNA sequencing (RNAseq) and the corresponding emergence of public datasets have created new avenues of transcriptional marker search. The long non-coding RNAs (lncRNAs) constitute an emerging class of transcripts with a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::ce21a09f7a02a1b81f67492d4d5ae05f
https://doi.org/10.1186/s12864-020-07289-0

Kmerator Suite: design of specific

Autor: Sébastien, Riquier, Chloé, Bessiere, Benoit, Guibert, Anne-Laure, Bouge, Anthony, Boureux, Florence, Ruffle, Jérôme, Audoux, Nicolas, Gilbert, Haoliang, Xue, Daniel, Gautheret, Thérèse, Commes

Publikováno v: NAR Genomics and Bioinformatics

The huge body of publicly available RNA-sequencing (RNA-seq) libraries is a treasure of functional information allowing to quantify the expression of known or novel transcripts in tissues. However, transcript quantification commonly relies on alignme

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=pmid________::308bd94b0536b2057b1a51dc83668244
https://pubmed.ncbi.nlm.nih.gov/34179780

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

Autor: Anne-Laure Bougé, Florence Ruffle, Benoit Guibert, Thérèse Commes, Sébastien Riquier, Jérôme Audoux

Publikováno v: Chromothripsis-Methods and Protocols
Franck Pellestor. Chromothripsis-Methods and Protocols, Humana Press, New York, NY-, pp.133-156, 2018, Hardcover ISBN 978-1-4939-7779-6 ; Softcover ISBN 978-1-4939-9283-6 ; eBook ISBN 978-1-4939-7780-2. ⟨10.1007/978-1-4939-7780-2_9⟩
Methods in Molecular Biology ISBN: 9781493977796

International audience; RNA-Seq approach enables the detection and characterization of fusion or chimeric transcript associated to complex genome rearrangement. Until now, these events are classically identified at DNA level.Here we describe a comple

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::77a116eaeed173ca38564e9e0a66a7b7
https://hal.umontpellier.fr/hal-02503709

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

Autor: Ronnie Alves, Anthony Boureux, Thérèse Commes, Sacha Beaumeunier, Jérôme Audoux, Florence Ruffle, Nicolas Philippe

Publikováno v: BioData Mining
BioData Mining, BioMed Central, 2016, 9 (1), pp.34. ⟨10.1186/s13040-016-0112-6⟩
BioData Mining, 2016, 9 (1), pp.34. ⟨10.1186/s13040-016-0112-6⟩

Background High-throughput sequencing technology and bioinformatics have identified chimeric RNAs (chRNAs), raising the possibility of chRNAs expressing particularly in diseases can be used as potential biomarkers in both diagnosis and prognosis. Res

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::62379a3440186c4c24e44e1899dee7a9
https://www.hal.inserm.fr/inserm-01390470/document