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Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.
RNA. 2023 Dec;29(12):1839-1855. doi: 10.1261/rna.079849.123. Epub 2023 Oct 10.
RNA. 2023.
PMID: 37816550
Free PMC article.
Review.
Extensible benchmarking of methods that identify and quantify polyadenylation sites from RNA-seq data.
Bryce-Smith S, Burri D, Gazzara MR, Herrmann CJ, Danecka W, Fitzsimmons CM, Wan YK, Zhuang F, Fansler MM, Fernández JM, Ferret M, Gonzalez-Uriarte A, Haynes S, Herdman C, Kanitz A, Katsantoni M, Marini F, McDonnel E, Nicolet B, Poon CL, Rot G, Schärfen L, Wu PJ, Yoon Y, Barash Y, Zavolan M.
Bryce-Smith S, et al. Among authors: katsantoni m.
bioRxiv [Preprint]. 2023 Jun 26:2023.06.23.546284. doi: 10.1101/2023.06.23.546284.
bioRxiv. 2023.
PMID: 37425672
Free PMC article.
Updated.
Preprint.
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Improved analysis of (e)CLIP data with RCRUNCH yields a compendium of RNA-binding protein binding sites and motifs.
Katsantoni M, van Nimwegen E, Zavolan M.
Katsantoni M, et al.
Genome Biol. 2023 Apr 17;24(1):77. doi: 10.1186/s13059-023-02913-0.
Genome Biol. 2023.
PMID: 37069586
Free PMC article.
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Structure of SRSF1 RRM1 bound to RNA reveals an unexpected bimodal mode of interaction and explains its involvement in SMN1 exon7 splicing.
Cléry A, Krepl M, Nguyen CKX, Moursy A, Jorjani H, Katsantoni M, Okoniewski M, Mittal N, Zavolan M, Sponer J, Allain FH.
Cléry A, et al. Among authors: katsantoni m.
Nat Commun. 2021 Jan 18;12(1):428. doi: 10.1038/s41467-020-20481-w.
Nat Commun. 2021.
PMID: 33462199
Free PMC article.
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The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.
SIB Swiss Institute of Bioinformatics Members.
SIB Swiss Institute of Bioinformatics Members.
Nucleic Acids Res. 2016 Jan 4;44(D1):D27-37. doi: 10.1093/nar/gkv1310. Epub 2015 Nov 28.
Nucleic Acids Res. 2016.
PMID: 26615188
Free PMC article.
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