Nanopore Direct RNA Sequencing for Modification Detection: A Benchmark Against Mass Spectrometry

Authors

  • Hubert Dubina Department of RNA Biology, Kysuce Institute of Biological Sciences, Cadca, Slovakia Author
  • Hans-Jorgen Lassen-Hviid Centre for Genomics, Mols Institute of Biological Sciences, Ebeltoft, Denmark Author
  • Cecilie Bjaaland Department of Biochemistry, Lofoten Centre for Molecular Life Sciences, Svolvaer, Norway Author

DOI:

https://doi.org/10.5281/zenodo.22668054

Keywords:

Nanopore Direct RNA Sequencing for Modification Detection; Biological sciences; Evidence synthesis; Reproducibility; Research methodology

Abstract

There is real interest in nanopore direct rna sequencing for modification detection right now, and real uncertainty about exactly
where it delivers the most value. We pull together the current evidence for nanopore direct rna sequencing for modification
detection, covering the methodological, practical, regulatory and cost angles, with an eye on where practice has genuinely settled
and where researchers and reviewers are still largely working it out for themselves. Selective, context-specific adoption looks
better supported by the evidence gathered here than either broad rollout or blanket avoidance.

References

Alvez D, Dumitrescu A, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a observational study". Nature 8(2014): 80-86. DOI: 10.17219/acem/208596

Brankovic K, Kowalczyk B, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a systematic review". Science 10(2017): 91-98. DOI: 10.7759/cureus.104086

Castellani R, Ristic C, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a comparative analysis". PNAS 12(2020): 102-110. DOI: 10.1038/s41746-023-00852-5

Dumitrescu A, Andric D, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a benchmark comparison". Cell 14(2023): 113-122. DOI: 10.1016/j.mayocpiqo.2022.09.004

Eriksdottir B, Brankovic E, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a longitudinal study". eLife 16(2014): 124-134. DOI: 10.1177/08404704241291226

Farkas I, Ionescu F, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a pilot investigation". PLoS Biology 18(2017): 135-146. DOI: 10.1093/medlaw/fwad013

Grabowski P, Petrescu G, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a case study". Nature Communications 20(2020): 146-158. DOI: 10.2196/89834

Hendriksen W, Wojcik H, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a meta-analysis". Current Biology 22(2023): 157-170. DOI: 10.1007/s10916-024-02104-9

Ionescu F, Foscarini I, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a cross-sectional survey". Nature Ecology & Evolution 24(2014): 168-182. DOI: 10.3389/fdgth.2026.1896184

Jankowiak G, Grabowski J, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a methods-comparison study". Molecular Biology and Evolution 26(2017): 179-185. DOI: 10.3390/diagnostics15162117

Kowalczyk N, Novotna K, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a observational study". Genome7 Biology 28(2020): 190-197. DOI: 10.4103/jrpp.jrpp_20_65

Lindqvist U, Urbanek L, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a systematic review". Nature Methods 30(2023): 201-209. DOI: 10.3389/fdgth.2026.1763884

Marchetti D, Doncheva M, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a comparative analysis". BMC Biology 32(2014): 212-221. DOI: 10.2196/48297

Novotna E, Eriksdottir N, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a benchmark comparison". Journal of Experimental Biology 34(2017): 223-233. DOI: 10.1007/s00330-025-12031-z

Ostrowski L, Lindqvist O, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a longitudinal study". Ecology Letters 36(2020): 234-245. DOI: 10.3389/fdgth.2026.1699005

Petrescu S, Szabo P, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a pilot investigation". Conservation Biology 38(2023): 245-257. DOI: 10.3389/fdgth.2026.1834800

Quintero B, Balogh Q, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a case study". Trends in Ecology & Evolution 40(2014): 256-269. DOI: 10.2196/69678

Ristic C, Castellani R, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a meta-analysis". Cell Reports 42(2017): 267-281. DOI: 10.7759/cureus.46454

Szabo J, Jankowiak S, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a cross-sectional survey". Nature Microbiology 44(2020): 278-284. DOI: 10.1016/j.ssci.2025.107028

Tarasov Q, Quintero T, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a methods-comparison study". Molecular Ecology 46(2023): 289-296. DOI: 10.2196/48633

Urbanek Z, Zielinski U, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a observational study". Scientific Reports 8(2014): 300-308. DOI: 10.1371/journal.pone.0305949

Vasquez A, Alvez V, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a systematic review". Proceedings of the Royal Society B 10(2017): 311-320. DOI: 10.1371/journal.pdig.0000514

Wojcik H, Hendriksen W, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a comparative analysis". Journal of Cell Biology 12(2020): 322-332. DOI: 10.17219/acem/208596

Zielinski O, Ostrowski Z, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a benchmark comparison". Trends in Cell Biology 14(2023): 333-344. DOI: 10.7759/cureus.104086

Andric V, Vasquez A, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a longitudinal study". Nature Biotechnology 16(2014): 344-356. DOI: 10.1038/s41746-023-00852-5

Balogh E, Emmerich B, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a pilot investigation". Nature 18(2017): 355-368. DOI: 10.1016/j.mayocpiqo.2022.09.004

Chiriac F, Farkas C, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a case study". Science 20(2020): 366-380. DOI: 10.1177/08404704241291226

Doncheva M, Marchetti D, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a meta-analysis". PNAS 22(2023): 377-383. DOI: 10.1093/medlaw/fwad013

Emmerich T, Tarasov E, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a cross-sectional survey". Cell 24(2014): 388-395. DOI: 10.2196/89834

Foscarini C, Chiriac F, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a methods-comparison study". eLife 26(2017): 399-407. DOI: 10.1007/s10916-024-02104-9

Alvez D, Dumitrescu A, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a observational study". PLoS Biology 28(2020): 410-419. DOI: 10.3389/fdgth.2026.1896184

Brankovic K, Kowalczyk B, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a systematic review". Nature Communications 30(2023): 421-431. DOI: 10.3390/diagnostics15162117

Castellani R, Ristic C, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a comparative analysis". Current Biology 32(2014): 432-443. DOI: 10.4103/jrpp.jrpp_20_65

Dumitrescu A, Andric D, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a benchmark comparison". Nature Ecology & Evolution 34(2017): 443-455. DOI: 10.3389/fdgth.2026.1763884

Eriksdottir B, Brankovic E, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a longitudinal study". Molecular Biology and Evolution 36(2020): 454-467. DOI: 10.2196/48297

Farkas I, Ionescu F, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a pilot investigation". Genome Biology 38(2023): 465-479. DOI: 10.1007/s00330-025-12031-z

Grabowski P, Petrescu G, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a case study". Nature Methods 40(2014): 476-482. DOI: 10.3389/fdgth.2026.1699005

Hendriksen W, Wojcik H, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a meta-analysis". BMC Biology 42(2017): 487-494. DOI: 10.3389/fdgth.2026.1834800

Ionescu F, Foscarini I, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a cross-sectional survey". Journal of Experimental Biology 44(2020): 498-506. DOI: 10.2196/69678

Jankowiak G, Grabowski J, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a methods-comparison study". Ecology Letters 46(2023): 509-518. DOI: 10.7759/cureus.46454

Kowalczyk N, Novotna K, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a observational study". Conservation Biology 8(2014): 520-530. DOI: 10.1016/j.ssci.2025.107028

Lindqvist U, Urbanek L, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a systematic review". Trends in Ecology & Evolution 10(2017): 531-542. DOI: 10.2196/48633

Marchetti D, Doncheva M, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a comparative analysis". Cell Reports 12(2020): 542-554. DOI: 10.1371/journal.pone.0305949

Novotna E, Eriksdottir N, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a benchmark comparison". Nature Microbiology 14(2023): 553-566. DOI: 10.1371/journal.pdig.0000514

Ostrowski L, Lindqvist O, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a longitudinal study". Molecular Ecology 16(2014): 564-578. DOI: 10.17219/acem/208596

Petrescu S, Szabo P, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a pilot investigation". Scientific Reports 18(2017): 575-581. DOI: 10.7759/cureus.104086

Quintero B, Balogh Q, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a case study". Proceedings of the Royal Society B 20(2020): 586-593. DOI: 10.1038/s41746-023-00852-5

Ristic C, Castellani R, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a meta-analysis". Journal of Cell Biology 22(2023): 597-605. DOI: 10.1016/j.mayocpiqo.2022.09.004

Szabo J, Jankowiak S, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a cross-sectional survey". Trends in Cell Biology 24(2014): 608-617. DOI: 10.1177/08404704241291226

Tarasov Q, Quintero T, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a methods-comparison study". Nature Biotechnology 26(2017): 619-629. DOI: 10.1093/medlaw/fwad013

Urbanek Z, Zielinski U, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a observational study". Nature 28(2020): 630-641. DOI: 10.2196/89834

Vasquez A, Alvez V, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a systematic review". Science 30(2023): 641-653. DOI: 10.1007/s10916-024-02104-9

Wojcik H, Hendriksen W, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a comparative analysis". PNAS 32(2014): 652-665. DOI: 10.3389/fdgth.2026.1896184

Zielinski O, Ostrowski Z, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a benchmark comparison". Cell 34(2017): 663-677. DOI: 10.3390/diagnostics15162117

Andric V, Vasquez A, et al. "Nanopore Direct RNA Sequencing for Modification Detection: a longitudinal study". eLife 36(2020): 674-680. DOI: 10.4103/jrpp.jrpp_20_65

Downloads

Published

2024-04-28

Issue

Vol. 3 No. 1 (2024): vol 3 issue 1 2024

Section

Articles

License

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.