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Integration of CLIP experiments of RNA-binding proteins: a novel approach to predict context-dependent splicing factors from transcriptomic data.
BMC Genomics. 2019 Jun 25;20(1):521. doi: 10.1186/s12864-019-5900-1.
BMC Genomics. 2019.
PMID: 31238884
Free PMC article.
ISOGO: Functional annotation of protein-coding splice variants.
Ferrer-Bonsoms JA, Cassol I, Fernández-Acín P, Castilla C, Carazo F, Rubio A.
Ferrer-Bonsoms JA, et al.
Sci Rep. 2020 Jan 23;10(1):1069. doi: 10.1038/s41598-020-57974-z.
Sci Rep. 2020.
PMID: 31974522
Free PMC article.
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EventPointer 3.0: flexible and accurate splicing analysis that includes studying the differential usage of protein-domains.
Ferrer-Bonsoms JA, Gimeno M, Olaverri D, Sacristan P, Lobato C, Castilla C, Carazo F, Rubio A.
Ferrer-Bonsoms JA, et al.
NAR Genom Bioinform. 2022 Sep 15;4(3):lqac067. doi: 10.1093/nargab/lqac067. eCollection 2022 Sep.
NAR Genom Bioinform. 2022.
PMID: 36128425
Free PMC article.
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Rediscover: an R package to identify mutually exclusive mutations.
Ferrer-Bonsoms JA, Jareno L, Rubio A.
Ferrer-Bonsoms JA, et al.
Bioinformatics. 2022 Jan 12;38(3):844-845. doi: 10.1093/bioinformatics/btab709.
Bioinformatics. 2022.
PMID: 34664620
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On the identifiability of the isoform deconvolution problem: application to select the proper fragment length in an RNA-seq library.
Ferrer-Bonsoms JA, Morales X, Afshar PT, Wong WH, Rubio A.
Ferrer-Bonsoms JA, et al.
Bioinformatics. 2022 Mar 4;38(6):1491-1496. doi: 10.1093/bioinformatics/btab873.
Bioinformatics. 2022.
PMID: 34978563
Free PMC article.
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