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R2Dtool: integration and visualization of isoform-resolved RNA features.
Bioinformatics. 2024 Aug 2;40(8):btae495. doi: 10.1093/bioinformatics/btae495.
Bioinformatics. 2024.
PMID: 39110520
Free PMC article.
Prediction of m6A and m5C at single-molecule resolution reveals a transcriptome-wide co-occurrence of RNA modifications.
Acera Mateos P, J Sethi A, Ravindran A, Srivastava A, Woodward K, Mahmud S, Kanchi M, Guarnacci M, Xu J, W S Yuen Z, Zhou Y, Sneddon A, Hamilton W, Gao J, M Starrs L, Hayashi R, Wickramasinghe V, Zarnack K, Preiss T, Burgio G, Dehorter N, E Shirokikh N, Eyras E.
Acera Mateos P, et al.
Nat Commun. 2024 May 9;15(1):3899. doi: 10.1038/s41467-024-47953-7.
Nat Commun. 2024.
PMID: 38724548
Free PMC article.
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Concepts and methods for transcriptome-wide prediction of chemical messenger RNA modifications with machine learning.
Acera Mateos P, Zhou Y, Zarnack K, Eyras E.
Acera Mateos P, et al.
Brief Bioinform. 2023 May 19;24(3):bbad163. doi: 10.1093/bib/bbad163.
Brief Bioinform. 2023.
PMID: 37139545
Free PMC article.
Review.
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PACIFIC: a lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses.
Acera Mateos P, Balboa RF, Easteal S, Eyras E, Patel HR.
Acera Mateos P, et al.
Sci Rep. 2021 Feb 5;11(1):3209. doi: 10.1038/s41598-021-82043-4.
Sci Rep. 2021.
PMID: 33547380
Free PMC article.
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