Novoa EM - Search Results

1

Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models.

Diensthuber G, Pryszcz LP, Llovera L, Lucas MC, Delgado-Tejedor A, Cruciani S, Roignant JY, Begik O, Novoa EM. Diensthuber G, et al. Among authors: novoa em. Genome Res. 2024 Nov 20;34(11):1865-1877. doi: 10.1101/gr.278849.123. Genome Res. 2024. PMID: 39271295

2

Molecular barcoding of native RNAs using nanopore sequencing and deep learning.

Smith MA, Ersavas T, Ferguson JM, Liu H, Lucas MC, Begik O, Bojarski L, Barton K, Novoa EM. Smith MA, et al. Among authors: novoa em. Genome Res. 2020 Sep;30(9):1345-1353. doi: 10.1101/gr.260836.120. Epub 2020 Sep 9. Genome Res. 2020. PMID: 32907883 Free PMC article.

3

Accurate detection of m⁶A RNA modifications in native RNA sequences.

Liu H, Begik O, Lucas MC, Ramirez JM, Mason CE, Wiener D, Schwartz S, Mattick JS, Smith MA, Novoa EM. Liu H, et al. Among authors: novoa em. Nat Commun. 2019 Sep 9;10(1):4079. doi: 10.1038/s41467-019-11713-9. Nat Commun. 2019. PMID: 31501426 Free PMC article.

4

MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets.

Cozzuto L, Liu H, Pryszcz LP, Pulido TH, Delgado-Tejedor A, Ponomarenko J, Novoa EM. Cozzuto L, et al. Among authors: novoa em. Front Genet. 2020 Mar 17;11:211. doi: 10.3389/fgene.2020.00211. eCollection 2020. Front Genet. 2020. PMID: 32256520 Free PMC article.

5

Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures.

Begik O, Lucas MC, Liu H, Ramirez JM, Mattick JS, Novoa EM. Begik O, et al. Among authors: novoa em. Genome Biol. 2020 May 7;21(1):97. doi: 10.1186/s13059-020-02009-z. Genome Biol. 2020. PMID: 32375858 Free PMC article.

6

Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing.

Begik O, Lucas MC, Pryszcz LP, Ramirez JM, Medina R, Milenkovic I, Cruciani S, Liu H, Vieira HGS, Sas-Chen A, Mattick JS, Schwartz S, Novoa EM. Begik O, et al. Among authors: novoa em. Nat Biotechnol. 2021 Oct;39(10):1278-1291. doi: 10.1038/s41587-021-00915-6. Epub 2021 May 13. Nat Biotechnol. 2021. PMID: 33986546

7

EpiNano: Detection of m⁶A RNA Modifications Using Oxford Nanopore Direct RNA Sequencing.

Liu H, Begik O, Novoa EM. Liu H, et al. Among authors: novoa em. Methods Mol Biol. 2021;2298:31-52. doi: 10.1007/978-1-0716-1374-0_3. Methods Mol Biol. 2021. PMID: 34085237

8

ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data.

Pryszcz LP, Novoa EM. Pryszcz LP, et al. Among authors: novoa em. Bioinformatics. 2021 Dec 22;38(1):257-260. doi: 10.1093/bioinformatics/btab539. Bioinformatics. 2021. PMID: 34293115

9

Computational methods for RNA modification detection from nanopore direct RNA sequencing data.

Furlan M, Delgado-Tejedor A, Mulroney L, Pelizzola M, Novoa EM, Leonardi T. Furlan M, et al. Among authors: novoa em. RNA Biol. 2021 Oct 15;18(sup1):31-40. doi: 10.1080/15476286.2021.1978215. Epub 2021 Sep 24. RNA Biol. 2021. PMID: 34559589 Free PMC article. Review.

10

Exploring the epitranscriptome by native RNA sequencing.

Begik O, Mattick JS, Novoa EM. Begik O, et al. Among authors: novoa em. RNA. 2022 Nov;28(11):1430-1439. doi: 10.1261/rna.079404.122. Epub 2022 Sep 14. RNA. 2022. PMID: 36104106 Free PMC article.

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