Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes

Abstract

Nanopore direct RNA sequencing (DRS) has transformed transcriptomics by enabling single-molecule, long-read sequencing of native RNA without the need for reverse transcription or amplification. In contrast to short-read RNA-seq and cDNA-based long-read approaches, DRS can simultaneously capture multiple RNA modifications, full-length transcript architecture, alternative splicing patterns, and poly(A) tail features within individual molecules, thereby providing an integrated view of transcriptomic and epitranscriptomic regulation. In this comprehensive review, we outline the biophysical principles underlying nanopore DRS and trace its technological evolution. We compare its performance with short-read RNA sequencing, long-read cDNA sequencing, and conventional RNA-modification mapping strategies, highlighting its advantages in isoform-resolved quantification and multilayer RNA feature integration, while also clarifying contexts in which alternative or combined approaches may be more appropriate for robust biological interpretation. We further summarize optimized experimental workflows, including library construction strategies tailored to diverse RNA biotypes (mRNA, rRNA, tRNA, circRNA, miRNA, and nonpoly(A) transcripts), as well as recommended quality-control procedures and sequencing optimization practices. Emphasizing recent computational advances and translational applications of DRS, we cover state-of-the-art algorithms for RNA modification detection, transcript reconstruction, and isoform quantification. We also propose analytical pipelines for poly(A) tail length inference and integrative frameworks that jointly analyze these regulatory layers. We distinguish direct nanopore signals from computational inferences to define confidence levels and emphasize benchmarking and orthogonal validation of readouts. Practical implementation examples are included to facilitate reproducible analysis. Finally, we highlight emerging applications of integrated DRS, including the resolution of complex transcriptomes, the characterization of coordinated epitranscriptomic regulation, and the identification of disease-associated RNA signatures. We also discuss current technical challenges and future perspectives, particularly in relation to multi-omics integration and the broader deployment of DRS in precision medicine as well as in plant and animal research.

Keywords

direct RNA sequencing / long-read transcriptome / nanopore sequencing / poly(A) tail / RNA modification / SQK-RNA004 / human medicine

References

[1] Dai, Xiaofeng, Shuo Zhang, and Kathia Zaleta-Rivera. 2020. “RNA: Interactions Drive Functionalities.” Molecular Biology Reports 47: 1413–1434. https://doi.org/10.1007/s11033-019-05230-7

[2] Spitale, Robert C., and Danny Incarnato. 2023. “Probing the Dynamic RNA Structurome and Its Functions.” Nature Reviews Genetics 24: 178–196. https://doi.org/10.1038/s41576-022-00546-w

[3] Hao, Jin-Dong, Qian-Lan Liu, Meng-Xia Liu, Xing Yang, Liu-Ming Wang, Si-Yi Su, Wen Xiao, et al. 2024. “DDX21 Mediates Co-Transcriptional RNA m⁶A Modification to Promote Transcription Termination and Genome Stability.” Molecular Cell 84: 1711–1726. https://doi.org/10.1016/j.molcel.2024.03.006

[4] Xia, Zhen, Min Tang, Jiayan Ma, Hongyan Zhang, Ryan C. Gimple, Briana C. Prager, Hongzhen Tang, et al. 2021. “Epitranscriptomic Editing of the RNA N6-Methyladenosine Modification by dCasRx Conjugated Methyltransferase and Demethylase.” Nucleic Acids Research 49: 7361–7374. https://doi.org/10.1093/nar/gkab517

[5] Huang, Huilin, Hengyou Weng, Keren Zhou, Tong Wu, Boxuan Simen Zhao, Mingli Sun, Zhenhua Chen, et al. 2019. “Histone H3 Trimethylation at Lysine 36 Guides m⁶A RNA Modification Co-Transcriptionally.” Nature 567: 414–419. https://doi.org/10.1038/s41586-019-1016-7

[6] Gu, Xiang, Ai Zhuang, Jie Yu, Ludi Yang, Shengfang Ge, Jing Ruan, Renbing Jia, Xianqun Fan, and Peiwei Chai. 2024. “Histone Lactylation-Boosted ALKBH3 Potentiates Tumor Progression and Diminished Promyelocytic Leukemia Protein Nuclear Condensates by m¹A Demethylation of SP100A.” Nucleic Acids Research 52: 2273–2289. https://doi.org/10.1093/nar/gkad1193

[7] Birzele, Fabian, Jochen Schaub, Werner Rust, Christoph Clemens, Patrick Baum, Hitto Kaufmann, Andreas Weith, Torsten W. Schulz, and Tobias Hildebrandt. 2010. “Into the Unknown: Expression Profiling Without Genome Sequence Information in CHO by Next Generation Sequencing.” Nucleic Acids Research 38: 3999–4010. https://doi.org/10.1093/nar/gkq116

[8] Shi, Zhuo-Xing, Zhi-Chao Chen, Jia-Yong Zhong, Kun-Hua Hu, Ying-Feng Zheng, Ying Chen, Shang-Qian Xie, et al. 2023. “High-Throughput and High-Accuracy Single-Cell RNA Isoform Analysis Using PacBio Circular Consensus Sequencing.” Nature Communications 14: 2631. https://doi.org/10.1038/s41467-023-38324-9

[9] Garalde, Daniel R., Elizabeth A. Snell, Daniel Jachimowicz, Botond Sipos, Joseph H. Lloyd, Mark Bruce, Nadia Pantic, et al. 2018. “Highly Parallel Direct RNA Sequencing on an Array of Nanopores.” Nature Methods 15: 201–206. https://doi.org/10.1038/nmeth.4577

[10] Adams, Mark D., Jenny M. Kelley, Jeannine D. Gocayne, Mark Dubnick, Mihael H. Polymeropoulos, Hong Xiao, Carl R. Merril, et al. 1991. “Complementary DNA Sequencing: Expressed Sequence Tags and Human Genome Project.” Science 252: 1651–1656. https://doi.org/10.1126/science.2047873

[11] Velculescu, Victor E., Lin Zhang, Wei Zhou, Jacob Vogelstein, Munira A. Basrai, Douglas E. Bassett, Phil Hieter, Bert Vogelstein, and Kenneth W. Kinzler. 1997. “Characterization of the Yeast Transcriptome.” Cell 88: 243–251. https://doi.org/10.1016/S0092-8674(00)81845-0

[12] Wang, Zhong, Mark Gerstein, and Michael Snyder. 2009. “RNA-Seq: A Revolutionary Tool for Transcriptomics.” Nature Reviews Genetics 10: 57–63. https://doi.org/10.1038/nrg2484

[13] Steijger, Tamara, Josep F. Abril, Pär G. Engström, Felix Kokocinski, Tim J. Hubbard, Roderic Guigó, Jennifer Harrow, and Paul Bertone. 2013. “Assessment of Transcript Reconstruction Methods for RNA-seq.” Nature Methods 10: 1177–1184. https://doi.org/10.1038/nmeth.2714

[14] Stark, Rory, Marta Grzelak, and James Hadfield. 2019. “RNA Sequencing: The Teenage Years.” Nature Reviews Genetics 20: 631–656. https://doi.org/10.1038/s41576-019-0150-2

[15] Stanley, John, and Stanislav Vassilenko. 1978. “A Different Approach to RNA Sequencing.” Nature 274: 87–89. https://doi.org/10.1038/274087a0

[16] Grosjean, Henri, Gérard Keith, and Louis Droogmans. 2004. “Detection and Quantification of Modified Nucleotides in RNA Using Thin-Layer Chromatography.” In RNA Interference, Editing, and Modification: Methods and Protocols, edited by Jonatha M. Gott (pp. 357–391. Humana Press), https://doi.org/10.1385/1-59259-775-0:357

[17] Dominissini, Dan, Sharon Moshitch-Moshkovitz, Schraga Schwartz, Mali Salmon-Divon, Lior Ungar, Sivan Osenberg, Karen Cesarkas, et al. 2012. “Topology of the Human and Mouse m⁶A RNA Methylomes Revealed By m⁶A-seq.” Nature 485: 201–206. https://doi.org/10.1038/nature11112

[18] Meyer, Kate D., Yogesh Saletore, Paul Zumbo, Olivier Elemento, Christopher E. Mason, and Samie R. Jaffrey. 2012. “Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and Near Stop Codons.” Cell 149: 1635–1646. https://doi.org/10.1016/j.cell.2012.05.003

[19] Zhou, Wanding, Tenghui Chen, Zechen Chong, Mary A. Rohrdanz, James M. Melott, Chris Wakefield, Jia Zeng, et al. 2015. “TransVar: A Multilevel Variant Annotator for Precision Genomics.” Nature Methods 12: 1002–1003. https://doi.org/10.1038/nmeth.3622

[20] Linder, Bastian, Anya V. Grozhik, Anthony O. Olarerin-George, Cem Meydan, Christopher E. Mason, and Samie R. Jaffrey. 2015. “Single-Nucleotide-Resolution Mapping of m⁶A and m⁶Am Throughout the Transcriptome.” Nature Methods 12: 767–772. https://doi.org/10.1038/nmeth.3453

[21] Liu, Cong, Hanxiao Sun, Yunpeng Yi, Weiguo Shen, Kai Li, Ye Xiao, Fei Li, et al. 2023. “Absolute Quantification of Single-Base m⁶A Methylation in the Mammalian Transcriptome Using GLORI.” Nature Biotechnology 41: 355–366. https://doi.org/10.1038/s41587-022-01487-9

[22] Wang, Ye, Yu Xiao, Shunqing Dong, Qiong Yu, and Guifang Jia. 2020. “Antibody-Free Enzyme-Assisted Chemical Approach for Detection of N6-Methyladenosine.” Nature Chemical Biology 16: 896–903. https://doi.org/10.1038/s41589-020-0525-x

[23] Meyer, Kate D. 2019. “DART-seq: An Antibody-Free Method for Global m⁶A Detection.” Nature Methods 16: 1275–1280. https://doi.org/10.1038/s41592-019-0570-0

[24] Garcia-Campos, Miguel Angel, Sarit Edelheit, Ursula Toth, Modi Safra, Ran Shachar, Sergey Viukov, Roni Winkler, et al. 2019. “Deciphering the ‘m⁶A Code’ via Antibody-Independent Quantitative Profiling.” Cell 178: 731–747.e16. https://doi.org/10.1016/j.cell.2019.06.013

[25] Verwilt, Jasper, Pieter Mestdagh, and Jo Vandesompele. 2023. “Artifacts and Biases of the Reverse Transcription Reaction in RNA Sequencing.” RNA 29: 889–897. https://doi.org/10.1261/rna.079623.123

[26] Diensthuber, Gregor, and Eva Maria Novoa. 2025. “Charting the Epitranscriptomic Landscape Across RNA Biotypes Using Native RNA Nanopore Sequencing.” Molecular Cell 85: 276–289. https://doi.org/10.1016/j.molcel.2024.12.014

[27] Helm, Mark, and Yuri Motorin. 2017. “Detecting RNA Modifications in the Epitranscriptome: Predict and Validate.” Nature Reviews Genetics 18: 275–291. https://doi.org/10.1038/nrg.2016.169

[28] Sessegolo, Camille, Corinne Cruaud, Corinne Da Silva, Audric Cologne, Marion Dubarry, Thomas Derrien, Vincent Lacroix, and Jean-Marc Aury. 2019. “Transcriptome Profiling of Mouse Samples Using Nanopore Sequencing of cDNA and RNA Molecules.” Scientific Reports 9: 14908. https://doi.org/10.1038/s41598-019-51470-9

[29] Rachinger, Nicole, Stefan Fischer, Ines Böhme, Lisa Linck-Paulus, Silke Kuphal, Melanie Kappelmann-Fenzl, and Anja K. Bosserhoff. 2021. “Loss of Gene Information: Discrepancies Between RNA Sequencing, cDNA Microarray, and qRT-PCR.” International Journal of Molecular Sciences 22: 9349. https://doi.org/10.3390/ijms22179349

[30] Guo, Li-Tao, Rebecca L. Adams, Han Wan, Nicholas C. Huston, Olga Potapova, Sara Olson, Christian M. Gallardo, Brenton R. Graveley, Bruce E. Torbett, and Anna Marie Pyle. 2020. “Sequencing and Structure Probing of Long RNAs Using MarathonRT: A Next-Generation Reverse Transcriptase.” Journal of Molecular Biology 432: 3338–3352. https://doi.org/10.1016/j.jmb.2020.03.022

[31] Werner, Stephan, Lukas Schmidt, Virginie Marchand, Thomas Kemmer, Christoph Falschlunger, Maksim V. Sednev, Guillaume Bec, et al. 2020. “Machine Learning of Reverse Transcription Signatures of Variegated Polymerases Allows Mapping and Discrimination of Methylated Purines in Limited Transcriptomes.” Nucleic Acids Research 48: 3734–3746. https://doi.org/10.1093/nar/gkaa113

[32] Zheng, Ya Ying, Kaalak Reddy, Sweta Vangaveti, and Jia Sheng. 2024. “Inosine-Induced Base Pairing Diversity During Reverse Transcription.” ACS Chemical Biology 19: 348–356. https://doi.org/10.1021/acschembio.3c00555

[33] Yu, Feng, Huanhuan Qi, Li Gao, Sen Luo, Rebecca Njeri Damaris, Yinggen Ke, Wenhua Wu, and Pingfang Yang. 2023. “Identifying RNA Modifications by Direct RNA Sequencing Reveals Complexity of Epitranscriptomic Dynamics in Rice.” Genomics, Proteomics & Bioinformatics 21: 788–804. https://doi.org/10.1016/j.gpb.2023.02.002

[34] Leger, Adrien, Paulo P. Amaral, Luca Pandolfini, Charlotte Capitanchik, Federica Capraro, Valentina Miano, Valentina Migliori, et al. 2021. “RNA Modifications Detection by Comparative Nanopore Direct RNA Sequencing.” Nature Communications 12: 7198. https://doi.org/10.1038/s41467-021-27393-3

[35] Workman, Rachael E., Alison D. Tang, Paul S. Tang, Miten Jain, John R. Tyson, Roham Razaghi, Philip C. Zuzarte, et al. 2019. “Nanopore Native RNA Sequencing of a Human Poly(A) Transcriptome.” Nature Methods 16: 1297–1305. https://doi.org/10.1038/s41592-019-0617-2

[36] Thomas, Niki K., Vinay C. Poodari, Miten Jain, Hugh E. Olsen, Mark Akeson, and Robin L. Abu-Shumays. 2021. “Direct Nanopore Sequencing of Individual Full Length tRNA Strands.” ACS Nano 15: 16642–16653. https://doi.org/10.1021/acsnano.1c06488

[37] Smith, Martin A., Tansel Ersavas, James M. Ferguson, Huanle Liu, Morghan C. Lucas, Oguzhan Begik, Lilly Bojarski, Kirston Barton, and Eva Maria Novoa. 2020. “Molecular Barcoding of Native RNAs Using Nanopore Sequencing and Deep Learning.” Genome Research 30: 1345–1353. https://doi.org/10.1101/gr.260836.120

[38] Wan, Yuk Kei, Christopher Hendra, Ploy N. Pratanwanich, and Jonathan Göke. 2022. “Beyond Sequencing: Machine Learning Algorithms Extract Biology Hidden in Nanopore Signal Data.” Trends in Genetics 38: 246–257. https://doi.org/10.1016/j.tig.2021.09.001

[39] Wang, Yunhao, Yue Zhao, Audrey Bollas, Yuru Wang, and Kin Fai Au. 2021. “Nanopore Sequencing Technology, Bioinformatics and Applications.” Nature Biotechnology 39: 1348–1365. https://doi.org/10.1038/s41587-021-01108-x

[40] Wick, Ryan R., Louise M. Judd, and Kathryn E. Holt. 2019. “Performance of Neural Network Basecalling Tools for Oxford Nanopore Sequencing.” Genome Biology 20: 129. https://doi.org/10.1186/s13059-019-1727-y

[41] Pagès-Gallego, Marc, and Jeroen de Ridder. 2023. “Comprehensive Benchmark and Architectural Analysis of Deep Learning Models for Nanopore Sequencing Basecalling.” Genome Biology 24: 71. https://doi.org/10.1186/s13059-023-02903-2

[42] Jain, Miten, Hugh E. Olsen, Benedict Paten, and Mark Akeson. 2016. “The Oxford Nanopore MinION: Delivery of Nanopore Sequencing to the Genomics Community.” Genome Biology 17: 239. https://doi.org/10.1186/s13059-016-1103-0

[43] Deamer, David, Mark Akeson, and Daniel Branton. 2016. “Three Decades of Nanopore Sequencing.” Nature Biotechnology 34: 518–524. https://doi.org/10.1038/nbt.3423

[44] Gu, Li-Qun, Orit Braha, Sean Conlan, Stephen Cheley, and Hagan Bayley. 1999. “Stochastic Sensing of Organic Analytes by a Pore-Forming Protein Containing a Molecular Adapter.” Nature 398: 686–690. https://doi.org/10.1038/19491

[45] Bayley, Hagan, and Paul S. Cremer. 2001. “Stochastic Sensors Inspired by Biology.” Nature 413: 226–230. https://doi.org/10.1038/35093038

[46] Lechevalier, B., J. C. Andersson, and P. Morin. 1977. “Hemispheric Disconnection Syndrome With a ‘Crossed Avoiding’ Reaction in a Case of Marchiafava-Bignami Disease.” Journal of Neurology, Neurosurgery & Psychiatry 40: 483–497. https://doi.org/10.1136/jnnp.40.5.483

[47] Meller, Amit, Lucas Nivon, Eric Brandin, Jene Golovchenko, and Daniel Branton. 2000. “Rapid Nanopore Discrimination Between Single Polynucleotide Molecules.” Proceedings of the National Academy of Sciences 97: 1079–1084. https://doi.org/10.1073/pnas.97.3.1079

[48] Akeson, Mark, Daniel Branton, John J. Kasianowicz, Eric Brandin, and David W. Deamer. 1999. “Microsecond Time-Scale Discrimination Among Polycytidylic Acid, Polyadenylic Acid, and Polyuridylic Acid as Homopolymers or as Segments Within Single RNA Molecules.” Biophysical Journal 77: 3227–3233. https://doi.org/10.1016/S0006-3495(99)77153-5

[49] Magi, Alberto, Alessandra Roberto Semeraro, Betti Mingrino, Romina Giusti, and D'Aurizio . 2018. “Nanopore Sequencing Data Analysis: State of the Art, Applications and Challenges.” Briefings in Bioinformatics 19: 1256–1272. https://doi.org/10.1093/bib/bbx062

[50] Istace, Benjamin, Anne Friedrich, Léo d'Agata, Sébastien Faye, Emilie Payen, Odette Beluche, Claudia Caradec, et al. 2017. “De Novo Assembly and Population Genomic Survey of Natural Yeast Isolates With the Oxford Nanopore MinION Sequencer.” Gigascience 6: giw018. https://doi.org/10.1093/gigascience/giw018

[51] Sun, Kai, Jiaxin Li, Chaohao Chen, Xin Zhou, Guofang Ma, Lingfeng Mao, Qiao Tang, et al. 2025. “Advances in Nanopore Direct RNA Sequencing and Its Impact on Biological Research.” Biotechnology Advances 85: 108710. https://doi.org/10.1016/j.biotechadv.2025.108710

[52] Parker, Matthew T., Katarzyna Knop, Anna V. Sherwood, Nicholas J. Schurch, Katarzyna Mackinnon, Peter D. Gould, Anthony Jw Hall, Geoffrey J. Barton, and Gordon G. Simpson. 2020. “Nanopore Direct RNA Sequencing Maps the Complexity of Arabidopsis mRNA Processing and m⁶A Modification.” eLife 9: e49658. https://doi.org/10.7554/eLife.49658

[53] Esfahani, Neda Ghohabi, Andrew J. Stein, Stuart Akeson, Talia Tzadikario, and Miten Jain. 2025. “Evaluation of Nanopore Direct RNA Sequencing Updates for Modification Detection.” Preprint at bioRxiv 2025.05.01.651717. https://doi.org/10.1101/2025.05.01.651717

[54] Liu-Wei, Wang, Wiep van der Toorn, Patrick Bohn, Martin Hölzer, Redmond P. Smyth, and Max Von Kleist. 2024. “Sequencing Accuracy and Systematic Errors of Nanopore Direct RNA Sequencing.” BMC Genomics 25: 528. https://doi.org/10.1186/s12864-024-10440-w

[55] Mears, Megan C., Quentin D. Read, and Abhijeet Bakre. 2025. “Comparison of Direct RNA Sequencing of Orthoavulavirus javaense Using Two Different Chemistries on the MinION Platform.” Journal of Virological Methods 333: 115103. https://doi.org/10.1016/j.jviromet.2024.115103

[56] Liu, Huanle, Oguzhan Begik, Morghan C. Lucas, Jose Miguel Ramirez, Christopher E. Mason, David Wiener, Schraga Schwartz, John S. Mattick, Martin A. Smith, and Eva Maria Novoa. 2019. “Accurate Detection of m⁶A RNA Modifications in Native RNA Sequences.” Nature Communications 10: 4079. https://doi.org/10.1038/s41467-019-11713-9

[57] Huang, Sihao, Wen Zhang, Christopher D. Katanski, Devin Dersh, Qing Dai, Karen Lolans, Jonathan Yewdell, A. Murat Eren, and Tao Pan. 2021. “Interferon Inducible Pseudouridine Modification in Human mRNA by Quantitative Nanopore Profiling.” Genome Biology 22: 330. https://doi.org/10.1186/s13059-021-02557-y

[58] Tavakoli, Sepideh, Mohammad Nabizadeh, Amr Makhamreh, Howard Gamper, Caroline A. McCormick, Neda K. Rezapour, Ya-Ming Hou, Meni Wanunu, and Sara H. Rouhanifard. 2023. “Semi-Quantitative Detection of Pseudouridine Modifications and Type I/II Hypermodifications in Human mRNAs Using Direct Long-Read Sequencing.” Nature Communications 14: 334. https://doi.org/10.1038/s41467-023-35858-w

[59] Wang, Yu, Kiran M. Patil, Shuanghong Yan, Panke Zhang, Weiming Guo, Yuqin Wang, Hong-Yuan Chen, Dennis Gillingham, and Shuo Huang. 2019. “Nanopore Sequencing Accurately Identifies the Mutagenic DNA Lesion o6-Carboxymethyl Guanine and Reveals Its Behavior in Replication.” Angewandte Chemie International Edition 58: 8432–8436. https://doi.org/10.1002/anie.201902521

[60] Kim, Yerin, Luke Saville, Kieran O'Neill, Jean-Michel Garant, Yilin Liu, Simon Haile-Merhu, Maryam Ghashghaei, et al. 2025. “Nanopore Direct RNA Sequencing of Human Transcriptomes Reveals the Complexity of mRNA Modifications and Crosstalk Between Regulatory Features.” Cell Genomics 5: 100872. https://doi.org/10.1016/j.xgen.2025.100872

[61] Rübsam, Franziskus N. M., Wang Liu-Wei, Yu Sun, Bhargesh Indravadan Patel, Wiep van der Toorn, Michael Piechotta, Christoph Dieterich, Max von Kleist, and Ann E. Ehrenhofer-Murray. 2025. “MoDorado: Enhanced Detection of tRNA Modifications in Nanopore Sequencing by Off-Label Use of Modification Callers.” Nucleic Acids Research 53: gkaf795. https://doi.org/10.1093/nar/gkaf795

[62] Zou, Yongji, Mian Umair Ahsan, Joe Chan, Wen Meng, Shou-Jiang Gao, Yufei Huang, and Kai Wang. 2025. “A Comparative Evaluation of Computational Models for RNA Modification Detection Using Nanopore Sequencing With RNA004 Chemistry.” Briefings in Bioinformatics 26: bbaf404. https://doi.org/10.1093/bib/bbaf404

[63] Katopodi, Xanthi-Lida, Oguzhan Begik, and Eva Maria Novoa. 2025. “Toward the Use of Nanopore RNA Sequencing Technologies in the Clinic: Challenges and Opportunities.” Nucleic Acids Research 53: gkaf128. https://doi.org/10.1093/nar/gkaf128

[64] Draper, Ben J., Mark J. Dunning, and David C. James. 2025. “Selecting Differential Splicing Methods: Practical Considerations for Short-Read RNA Sequencing.” F1000Research 14: 47. https://doi.org/10.12688/f1000research.155223.2

[65] Aird, Daniel, Michael G. Ross, Wei-Sheng Chen, Maxwell Danielsson, Timothy Fennell, Carsten Russ, David B. Jaffe, Chad Nusbaum, and Andreas Gnirke. 2011. “Analyzing and Minimizing PCR Amplification Bias in Illumina Sequencing Libraries.” Genome Biology 12: R18. https://doi.org/10.1186/gb-2011-12-2-r18

[66] Jiang, Hui, and Wing Hung Wong. 2009. “Statistical Inferences for Isoform Expression in RNA-Seq.” Bioinformatics 25: 1026–1032. https://doi.org/10.1093/bioinformatics/btp113

[67] Liu, Tianyuan, and Ana Conesa. 2025. “Profiling the Epigenome Using Long-Read Sequencing.” Nature Genetics 57: 27–41. https://doi.org/10.1038/s41588-024-02038-5

[68] Alfonso-Gonzalez, Carlos, and Valérie Hilgers. 2026. “Elucidating the Coordination of RNA Processing Using Short-Read and Long-Read RNA-Sequencing Methods.” Nature Reviews Molecular Cell Biology 27: 194–212. https://doi.org/10.1038/s41580-025-00895-4

[69] Monzó, Carolina, Tianyuan Liu, and Ana Conesa. 2025. “Transcriptomics in the Era of Long-Read Sequencing.” Nature Reviews Genetics 26: 681–701. https://doi.org/10.1038/s41576-025-00828-z

[70] Gong, Binsheng, Dan Li, Paweł P. Łabaj, Bohu Pan, Natalia Novoradovskaya, Danielle Thierry-Mieg, Jean Thierry-Mieg, et al. 2024. “Targeted DNA-seq and RNA-seq of Reference Samples With Short-Read and Long-Read Sequencing.” Scientific Data 11: 892. https://doi.org/10.1038/s41597-024-03741-y

[71] Dobin, Alexander, Carrie A. Davis, Felix Schlesinger, Jorg Drenkow, Chris Zaleski, Sonali Jha, Philippe Batut, Mark Chaisson, and Thomas R. Gingeras. 2013. “STAR: Ultrafast Universal RNA-seq Aligner.” Bioinformatics 29: 15–21. https://doi.org/10.1093/bioinformatics/bts635

[72] Kim, Daehwan, Joseph M. Paggi, Chanhee Park, Christopher Bennett, and Steven L. Salzberg. 2019. “Graph-Based Genome Alignment and Genotyping With HISAT2 and HISAT-Genotype.” Nature Biotechnology 37: 907–915. https://doi.org/10.1038/s41587-019-0201-4

[73] Liao, Yang, Gordon K. Smyth, and Wei Shi. 2014. “Featurecounts: An Efficient General Purpose Program for Assigning Sequence Reads to Genomic Features.” Bioinformatics 30: 923–930. https://doi.org/10.1093/bioinformatics/btt656

[74] Anders, Simon, Paul Theodor Pyl, and Wolfgang Huber. 2015. “HTSeq—A Python Framework to Work With High-Throughput Sequencing Data.” Bioinformatics 31: 166–169. https://doi.org/10.1093/bioinformatics/btu638

[75] Lovejoy, Alexander F., Daniel P. Riordan, and Patrick O. Brown. 2014. “Transcriptome-Wide Mapping of Pseudouridines: Pseudouridine Synthases Modify Specific mRNAs in S. cerevisiae.” Plos One 9: e110799. https://doi.org/10.1371/journal.pone.0110799

[76] Robinson, Mark D., Davis J. McCarthy, and Gordon K. Smyth. 2010. “edgeR: A Bioconductor Package for Differential Expression Analysis of Digital Gene Expression Data.” Bioinformatics 26: 139–140. https://doi.org/10.1093/bioinformatics/btp616

[77] Law, Charity W., Yunshun Chen, Wei Shi, and Gordon K. Smyth. 2014. “Voom: Precision Weights Unlock Linear Model Analysis Tools for RNA-seq Read Counts.” Genome Biology 15: R29. https://doi.org/10.1186/gb-2014-15-2-r29

[78] Patro, Rob, Geet Duggal, Michael I. Love, Rafael A. Irizarry, and Carl Kingsford. 2017. “Salmon Provides Fast and Bias-Aware Quantification of Transcript Expression.” Nature Methods 14: 417–419. https://doi.org/10.1038/nmeth.4197

[79] Bray, Nicolas L., Harold Pimentel, Páll Melsted, and Lior Pachter. 2016. “Near-Optimal Probabilistic RNA-seq Quantification.” Nature Biotechnology 34: 525–527. https://doi.org/10.1038/nbt.3519

[80] Li, Bo, and Colin N. Dewey. 2011. “RSEM: Accurate Transcript Quantification From RNA-seq Data With or Without a Reference Genome.” BMC Bioinformatics 12: 323. https://doi.org/10.1186/1471-2105-12-323

[81] Chen, Ying, Nadia M. Davidson, Yuk Kei Wan, Fei Yao, Yan Su, Hasindu Gamaarachchi, Andre Sim, et al. 2025. “A Systematic Benchmark of Nanopore Long-Read RNA Sequencing for Transcript-Level Analysis in Human Cell Lines.” Nature Methods 22: 801–812. https://doi.org/10.1038/s41592-025-02623-4

[82] De Paoli-Iseppi, Ricardo, Josie Gleeson, and Michael B. Clark. 2021. “Isoform Age - Splice Isoform Profiling Using Long-Read Technologies.” Frontiers in Molecular Biosciences 8: 711733. https://doi.org/10.3389/fmolb.2021.711733

[83] Dong, Xueyi, Mei R. M. Du, Quentin Gouil, Luyi Tian, Jafar S. Jabbari, Rory Bowden, Pedro L. Baldoni, et al. 2023. “Benchmarking Long-Read RNA-Sequencing Analysis Tools Using In Silico Mixtures.” Nature Methods 20: 1810–1821. https://doi.org/10.1038/s41592-023-02026-3

[84] Pardo-Palacios, Francisco J., Dingjie Wang, Fairlie Reese, Mark Diekhans, Sílvia Carbonell-Sala, Brian Williams, Jane E. Loveland, et al. 2024. “Systematic Assessment of Long-Read RNA-seq Methods for Transcript Identification and Quantification.” Nature Methods 21: 1349–1363. https://doi.org/10.1038/s41592-024-02298-3

[85] Wyman, Dana, and Ali Mortazavi. 2019. “TranscriptClean: Variant-Aware Correction of Indels, Mismatches and Splice Junctions in Long-Read Transcripts.” Bioinformatics 35: 340–342. https://doi.org/10.1093/bioinformatics/bty483

[86] Gleeson, Josie, Adrien Leger, Yair D. J. Prawer, Tracy A. Lane, Paul J. Harrison, Wilfried Haerty, and Michael B. Clark. 2022. “Accurate Expression Quantification from Nanopore Direct RNA Sequencing With NanoCount.” Nucleic Acids Research 50: e19. https://doi.org/10.1093/nar/gkab1129

[87] Li, Heng. 2018. “Minimap2: Pairwise Alignment for Nucleotide Sequences.” Bioinformatics 34: 3094–3100. https://doi.org/10.1093/bioinformatics/bty191

[88] Tang, Alison D., Cameron M. Soulette, Marijke J. van Baren, Kevyn Hart, Eva Hrabeta-Robinson, Catherine J. Wu, and Angela N. Brooks. 2020. “Full-Length Transcript Characterization of SF3B1 Mutation in Chronic Lymphocytic Leukemia Reveals Downregulation of Retained Introns.” Nature Communications 11: 1438. https://doi.org/10.1038/s41467-020-15171-6

[89] Kovaka, Sam, Aleksey V. Zimin, Geo M. Pertea, Roham Razaghi, Steven L. Salzberg, and Mihaela Pertea. 2019. “Transcriptome Assembly from Long-Read RNA-seq Alignments With StringTie2.” Genome Biology 20: 278. https://doi.org/10.1186/s13059-019-1910-1

[90] Prjibelski, Andrey D., Alla Mikheenko, Anoushka Joglekar, Alexander Smetanin, Julien Jarroux, Alla L. Lapidus, and Hagen U. Tilgner. 2023. “Accurate Isoform Discovery With IsoQuant Using Long Reads.” Nature Biotechnology 41: 915–918. https://doi.org/10.1038/s41587-022-01565-y

[91] Chen, Ying, Andre Sim, Yuk Kei Wan, Keith Yeo, Joseph Jing Xian Lee, Min Hao Ling, Michael I. Love, and Jonathan Göke. 2023. “Context-Aware Transcript Quantification From Long-Read RNA-seq Data With Bambu.” Nature Methods 20: 1187–1195. https://doi.org/10.1038/s41592-023-01908-w

[92] Li, Haoran, Dingjie Wang, Qi Gao, Puwen Tan, Yunhao Wang, Xiaoyu Cai, Aifu Li, et al. 2025. “Improving Gene Isoform Quantification With MiniQuant.” Nature Biotechnology 44: 477–489. https://doi.org/10.1038/s41587-025-02633-9

[93] Shen, Shihao, Juw Won Park, Zhi-xiang Lu, Lan Lin, Michael D. Henry, Ying Nian Wu, Qing Zhou, and Yi Xing. 2014. “rMATS: Robust and Flexible Detection of Differential Alternative Splicing From Replicate RNA-Seq Data.” Proceedings of the National Academy of Sciences 111: 5593–5601. https://doi.org/10.1073/pnas.1419161111

[94] Trincado, Juan L., Juan C. Entizne, Gerald Hysenaj, Babita Singh, Miha Skalic, David J. Elliott, and Eduardo Eyras. 2018. “SUPPA2: Fast, Accurate, and Uncertainty-Aware Differential Splicing Analysis Across Multiple Conditions.” Genome Biology 19: 40. https://doi.org/10.1186/s13059-018-1417-1

[95] Vaquero-Garcia, Jorge, Alejandro Barrera, Matthew R. Gazzara, Juan González-Vallinas, Nicholas F. Lahens, John B. Hogenesch, Kristen W. Lynch, and Yoseph Barash. 2016. “A New View of Transcriptome Complexity and Regulation Through the Lens of Local Splicing Variations.” eLife 5: e11752. https://doi.org/10.7554/eLife.11752

[96] Anders, Simon, Alejandro Reyes, and Wolfgang Huber. 2012. “Detecting Differential Usage of Exons From RNA-seq Data.” Genome Research 22: 2008–2017. https://doi.org/10.1101/gr.133744.111

[97] Montañés, José Carlos, Marta Huertas, Simone G. Moro, William R. Blevins, Mercè Carmona, José Ayté, Elena Hidalgo, and M. Mar Albà. 2022. “Native RNA Sequencing in Fission Yeast Reveals Frequent Alternative Splicing Isoforms.” Genome Research 32: 1215–1227. https://doi.org/10.1101/gr.276516.121

[98] Nukaga, Shigenari, Kouya Shiraishi, Kenta Hamabe, Akifumi Mochizuki, Yu Hamaguchi, Emi Ogawa, Nguyen Thai Le, et al. 2025. “Mutation of CMTR2 in Lung Adenocarcinoma Alters RNA Alternative Splicing and Reveals Therapeutic Vulnerabilities.” Nature Communications 16: 9754. https://doi.org/10.1038/s41467-025-64821-0

[99] Nowicka, Malgorzata, and Mark D. Robinson. 2016. “DRIMSeq: A Dirichlet-Multinomial Framework for Multivariate Count Outcomes in Genomics.” F1000Research 5: 1356. https://doi.org/10.12688/f1000research.8900.2

[100] Van den Berge, Koen, Charlotte Soneson, Mark D. Robinson, and Lieven Clement. 2017. “Stager: A General Stage-Wise Method for Controlling the Gene-Level False Discovery Rate in Differential Expression and Differential Transcript Usage.” Genome Biology 18: 151. https://doi.org/10.1186/s13059-017-1277-0

[101] Vitting-Seerup, Kristoffer, and Albin Sandelin. 2019. “IsoformSwitchAnalyzeR: Analysis of Changes in Genome-Wide Patterns of Alternative Splicing and Its Functional Consequences.” Bioinformatics 35: 4469–4471. https://doi.org/10.1093/bioinformatics/btz247

[102] Wissel, David, Madison M. Mehlferber, Khue M. Nguyen, Vasilii Pavelko, Elizabeth Tseng, Mark D. Robinson, and Gloria M. Sheynkman. 2026. “A Systematic Benchmark of High-Accuracy PacBio Long-Read RNA Sequencing for Transcript-Level Quantification.” Genome Biology 27: 110. https://doi.org/10.1186/s13059-026-03988-1

[103] Udaondo, Zulema, Kanchana Sittikankaew, Tanaporn Uengwetwanit, Thidathip Wongsurawat, Chutima Sonthirod, Piroon Jenjaroenpun, Wirulda Pootakham, Nitsara Karoonuthaisiri, and Intawat Nookaew. 2021. “Comparative Analysis of PacBio and Oxford Nanopore Sequencing Technologies for Transcriptomic Landscape Identification of Penaeus monodon.” Life 11: 862. https://doi.org/10.3390/life11080862

[104] Wang, Bo, Elizabeth Tseng, Michael Regulski, Tyson A. Clark, Ting Hon, Yinping Jiao, Zhenyuan Lu, Andrew Olson, Joshua C. Stein, and Doreen Ware. 2016. “Unveiling the Complexity of the Maize Transcriptome by Single-Molecule Long-Read Sequencing.” Nature Communications 7: 11708. https://doi.org/10.1038/ncomms11708

[105] Zhong, Yuanyuan, Yuhong Luo, Jinliang Sun, Xuemei Qin, Ping Gan, Zuwen Zhou, Yongqing Qian, et al. 2024. “Pan-Transcriptomic Analysis Reveals Alternative Splicing Control of Cold Tolerance in Rice.” Plant Cell 36: 2117–2139. https://doi.org/10.1093/plcell/koae039

[106] Jaramillo Oquendo, Carolina, Federico Ferraro, Htoo A. Wai, Heather Ferrao, Herma van der Linde, Evita Karelioti, Liz Tseng, et al. 2026. “HiFi Long-Read RNA Sequencing Enhances Clinical Diagnostics in Rare Disorders.” European Journal of Human Genetics 34: 840–851. https://doi.org/10.1038/s41431-026-02042-9

[107] Mikheenko, Alla, Andrey D. Prjibelski, Anoushka Joglekar, and Hagen U. Tilgner. 2022. “Sequencing of Individual Barcoded cDNAs Using Pacific Biosciences and Oxford Nanopore Technologies Reveals Platform-Specific Error Patterns.” Genome Research 32: 726–737. https://doi.org/10.1101/gr.276405.121

[108] Al'Khafaji, Aziz M., Jonathan T. Smith, Kiran V. Garimella, Mehrtash Babadi, Victoria Popic, Moshe Sade-Feldman, Michael Gatzen, et al. 2024. “High-Throughput RNA Isoform Sequencing Using Programmed cDNA Concatenation.” Nature Biotechnology 42: 582–586. https://doi.org/10.1038/s41587-023-01815-7

[109] Soneson, Charlotte, Yao Yao, Anna Bratus-Neuenschwander, Andrea Patrignani, Mark D. Robinson, and Shobbir Hussain. 2019. “A Comprehensive Examination of Nanopore Native RNA Sequencing for Characterization of Complex Transcriptomes.” Nature Communications 10: 3359. https://doi.org/10.1038/s41467-019-11272-z

[110] Lahens, Nicholas F., Ibrahim Halil Kavakli, Ray Zhang, Katharina Hayer, Michael B. Black, Hannah Dueck, Angel Pizarro, et al. 2014. “IVT-seq Reveals Extreme Bias in RNA Sequencing.” Genome Biology 15: R86. https://doi.org/10.1186/gb-2014-15-6-r86

[111] Cocquet, Julie, Allen Chong, Guanglan Zhang, and Reiner A. Veitia. 2006. “Reverse Transcriptase Template Switching and False Alternative Transcripts.” Genomics 88: 127–131. https://doi.org/10.1016/j.ygeno.2005.12.013

[112] Coon, Steven L., Tianwei Li, James R. Iben, Sandy Mattijssen, Richard J. Maraia. 2021. “Chapter Six - Single-Molecule Polyadenylated Tail Sequencing (SM-PAT-Seq) to Measure PolyA Tail Lengths Transcriptome-Wide.” In Methods in Enzymology (pp. 119–137, Academic Press). https://doi.org/10.1016/bs.mie.2021.04.006

[113] Schulz, Laura, Manuel Torres-Diz, Mariela Cortés-López, Katharina E. Hayer, Mukta Asnani, Sarah K. Tasian, Yoseph Barash, et al. 2021. “Direct Long-Read RNA Sequencing Identifies a Subset of Questionable Exitrons Likely Arising From Reverse Transcription Artifacts.” Genome Biology 22: 190. https://doi.org/10.1186/s13059-021-02411-1

[114] Diensthuber, Gregor, Leszek P. Pryszcz, Laia Llovera, Morghan C. Lucas, Anna Delgado-Tejedor, Sonia Cruciani, Jean-Yves Roignant, Oguzhan Begik, and Eva Maria Novoa. 2024. “Enhanced Detection of RNA Modifications and Read Mapping With High-Accuracy Nanopore RNA Basecalling Models.” Genome Research 34: gr.278849.278123. https://doi.org/10.1101/gr.278849.123

[115] Thüring, Kathrin, Katharina Schmid, Patrick Keller, and Mark Helm. 2016. “Analysis of RNA Modifications by Liquid Chromatography–Tandem Mass Spectrometry.” Methods 107: 48–56. https://doi.org/10.1016/j.ymeth.2016.03.019

[116] Zhang, Yan, Liang Lu, and Xiaoyu Li. 2022. “Detection Technologies for RNA Modifications.” Experimental & Molecular Medicine 54: 1601–1616. https://doi.org/10.1038/s12276-022-00821-0

[117] Huang, Gefei, Feng Zhang, Dongying Xie, Yiming Ma, Pengxi Wang, Guodong Cao, Leijian Chen, Siyi Lin, Zhongying Zhao, and Zongwei Cai. 2023. “High-Throughput Profiling of RNA Modifications by Ultra-Performance Liquid Chromatography Coupled to Complementary Mass Spectrometry: Methods, Quality Control, and Applications.” Talanta 263: 124697. https://doi.org/10.1016/j.talanta.2023.124697

[118] Stephenson, William, Roham Razaghi, Steven Busan, Kevin M. Weeks, Winston Timp, and Peter Smibert. 2022. “Direct Detection of RNA Modifications and Structure Using Single-Molecule Nanopore Sequencing.” Cell Genomics 2: 100097. https://doi.org/10.1016/j.xgen.2022.100097

[119] Furlan, Mattia, Anna Delgado-Tejedor, Logan Mulroney, Mattia Pelizzola, Eva Maria Novoa, and Tommaso Leonardi. 2021. “Computational Methods for RNA Modification Detection from Nanopore Direct RNA Sequencing Data.” RNA Biology 18: 31–40. https://doi.org/10.1080/15476286.2021.1978215

[120] Jain, Miten, Robin Abu-Shumays, Hugh E. Olsen, and Mark Akeson. 2022. “Advances in Nanopore Direct RNA Sequencing.” Nature Methods 19: 1160–1164. https://doi.org/10.1038/s41592-022-01633-w

[121] Liu, Nian, Marc Parisien, Qing Dai, Guanqun Zheng, Chuan He, and Tao Pan. 2013. “Probing N6-Methyladenosine RNA Modification Status at Single Nucleotide Resolution in mRNA and Long Noncoding RNA.” RNA 19: 1848–1856. https://doi.org/10.1261/rna.041178.113

[122] Su, Dan, Clement T. Y. Chan, Chen Gu, Kok Seong Lim, Yok Hian Chionh, Megan E. McBee, Brandon S. Russell, I. Ramesh Babu, Thomas J. Begley, and Peter C. Dedon. 2014. “Quantitative Analysis of Ribonucleoside Modifications in tRNA by HPLC-Coupled Mass Spectrometry.” Nature Protocols 9: 828–841. https://doi.org/10.1038/nprot.2014.047

[123] Ross, Robert, Xiaoyu Cao, Ningxi Yu, and Patrick A. Limbach. 2016. “Sequence Mapping of Transfer RNA Chemical Modifications by Liquid Chromatography Tandem Mass Spectrometry.” Methods 107: 73–78. https://doi.org/10.1016/j.ymeth.2016.03.016

[124] Jora, Manasses, Peter A. Lobue, Robert L. Ross, Brittney Williams, and Balasubrahmanyam Addepalli. 2019. “Detection of Ribonucleoside Modifications by Liquid Chromatography Coupled With Mass Spectrometry.” Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 1862: 280–290. https://doi.org/10.1016/j.bbagrm.2018.10.012

[125] Zhang, Rui, Hailong Liu, Biao Bai, and Hailin Wang. 2025. “Quantification of Epigenetic DNA and RNA Modifications by UHPLC-MS/MS Technologies: New Concepts and New Improvements for the Special Collections.” Journal of Separation Science 48: e70159. https://doi.org/10.1002/jssc.70159

[126] Ammann, Gregor, Maximilian Berg, Jan Felix Dalwigk, and Stefanie M. Kaiser. 2023. “Pitfalls in RNA Modification Quantification Using Nucleoside Mass Spectrometry.” Accounts of Chemical Research 56: 3121–3131. https://doi.org/10.1021/acs.accounts.3c00402

[127] Yuan, Xiaohong, Yue Su, Benjamin Johnson, Michele Kirchner, Xudong Zhang, Sihang Xu, Sophia Jiang, et al. 2024. “Mass Spectrometry-Based Direct Sequencing of tRNAs De Novo and Quantitative Mapping of Multiple RNA Modifications.” Journal of the American Chemical Society 146: 25600–25613. https://doi.org/10.1021/jacs.4c07280

[128] Chen, Kai, Zhike Lu, Xiao Wang, Ye Fu, Guan-Zheng Luo, Nian Liu, Dali Han, et al. 2015. “High-Resolution N(6)-Methyladenosine (m⁶A) Map Using Photo-Crosslinking-Assisted m⁶A Sequencing.” Angewandte Chemie International Edition 54: 1587–1590. https://doi.org/10.1002/anie.201410647

[129] Ke, Shengdong, Endalkachew A. Alemu, Claudia Mertens, Emily Conn Gantman, John J. Fak, Aldo Mele, Bhagwattie Haripal, et al. 2015. “A Majority of m⁶A Residues Are in the Last Exons, Allowing the Potential for 3′ UTR Regulation.” Genes & Development 29: 2037–2053https://genesdev.cshlp.org/content/29/19/2037.abstract.

[130] Molinie, Benoit, Jinkai Wang, Kok Seong Lim, Roman Hillebrand, Zhi-xiang Lu, Nicholas Van Wittenberghe, Benjamin D. Howard, et al. 2016. “m⁶A-LAIC-Seq Reveals the Census and Complexity of the m⁶A Epitranscriptome.” Nature Methods 13: 692–698. https://doi.org/10.1038/nmeth.3898

[131] Edelheit, Sarit, Schraga Schwartz, Maxwell R. Mumbach, Omri Wurtzel, and Rotem Sorek. 2013. “Transcriptome-Wide Mapping of 5-Methylcytidine RNA Modifications in Bacteria, Archaea, and Yeast Reveals m5C Within Archaeal mRNAs.” PLoS Genetics 9: e1003602. https://doi.org/10.1371/journal.pgen.1003602

[132] Hussain, Shobbir, Abdulrahim A. Sajini, Sandra Blanco, Sabine Dietmann, Patrick Lombard, Yoichiro Sugimoto, Maike Paramor, et al. 2013. “NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing Into Regulatory Small RNAs.” Cell Reports 4: 255–261. https://doi.org/10.1016/j.celrep.2013.06.029

[133] Delatte, Benjamin, Fei Wang, Long Vo Ngoc, Evelyne Collignon, Elise Bonvin, Rachel Deplus, Emilie Calonne, et al. 2016. “Transcriptome-Wide Distribution and Function of RNA Hydroxymethylcytosine.” Science 351: 282–285. https://doi.org/10.1126/science.aac5253

[134] Munns, T. W., R. J. Oberst, H. F. Sims, and M. K. Liszewski. 1979. “Antibody-Nucleic Acid Complexes. Immunospecific Recognition of 7-Methylguanine- and N6-Methyladenine-Containing 5′-Terminal Oligonucleotides of mRNA.” Journal of Biological Chemistry 254: 4327–4330. https://doi.org/10.1016/S0021-9258(17)30008-X

[135] Schwartz, Schraga, Maxwell R. Mumbach, Marko Jovanovic, Tim Wang, Karolina Maciag, G. Guy Bushkin, Philipp Mertins, et al. 2014. “Perturbation of m⁶A Writers Reveals Two Distinct Classes of mRNA Methylation at Internal and 5' Sites.” Cell Reports 8: 284–296. https://doi.org/10.1016/j.celrep.2014.05.048

[136] Arango, Daniel, David Sturgill, Najwa Alhusaini, Allissa A. Dillman, Thomas J. Sweet, Gavin Hanson, Masaki Hosogane, et al. 2018. “Acetylation of Cytidine in mRNA Promotes Translation Efficiency.” Cell 175: 1872–1886.e24. https://doi.org/10.1016/j.cell.2018.10.030

[137] Dominissini, Dan, Sigrid Nachtergaele, Sharon Moshitch-Moshkovitz, Eyal Peer, Nitzan Kol, Moshe Shay Ben-Haim, Qing Dai, et al. 2016. “The Dynamic N1-Methyladenosine Methylome in Eukaryotic Messenger RNA.” Nature 530: 441–446. https://doi.org/10.1038/nature16998

[138] Li, Xiaoyu, Xushen Xiong, Kun Wang, Lixia Wang, Xiaoting Shu, Shiqing Ma, and Chengqi Yi. 2016. “Transcriptome-Wide Mapping Reveals Reversible and Dynamic N1-Methyladenosine Methylome.” Nature Chemical Biology 12: 311–316. https://doi.org/10.1038/nchembio.2040

[139] Zhang, Yiqian, and Michiaki Hamada. 2020. “MoAIMS: Efficient Software for Detection of Enriched Regions of MeRIP-Seq.” BMC Bioinformatics 21: 103. https://doi.org/10.1186/s12859-020-3430-0

[140] Xia, Wenjuan, Ling Guo, Huapeng Su, Jincheng Li, Jiafeng Lu, Hong Li, and Boxian Huang. 2024. “A Low-Cost, Low-Input Method Establishment for m⁶A MeRIP-Seq.” Bioscience Reports 44: BSR20231430. https://doi.org/10.1042/BSR20231430

[141] Shi, Yue, Zeming Wu, Weiqi Zhang, Jing Qu, Weimin Ci, and Guang-Hui Liu. 2023. “An Experimental Workflow for Identifying RNA m⁶A Alterations in Cellular Senescence by Methylated RNA Immunoprecipitation Sequencing.” Journal of Biological Methods 10: e99010004. https://doi.org/10.14440/jbm.2023.403

[142] McIntyre, Alexa B. R., Nandan S. Gokhale, Leandro Cerchietti, Samie R. Jaffrey, Stacy M. Horner, and Christopher E. Mason. 2020. “Limits in the Detection of m⁶A Changes Using MeRIP/m⁶A-seq.” Scientific Reports 10: 6590. https://doi.org/10.1038/s41598-020-63355-3

[143] Li, Yanjiao, Yunhao Wang, Maria Vera-Rodriguez, Leif Christopher Lindeman, Linda Ellevog Skuggen, Erik M. K. Rasmussen, Ingunn Jermstad, et al. 2024. “Single-Cell m⁶A Mapping In Vivo Using picoMeRIP–seq.” Nature Biotechnology 42: 591–596. https://doi.org/10.1038/s41587-023-01831-7

[144] Zhang, Meiling, Ye Xiao, Zhe Jiang, and Chengqi Yi. 2023. “Quantifying m⁶A and Ψ Modifications in the Transcriptome Via Chemical-Assisted Approaches.” Accounts of Chemical Research 56: 2980–2991. https://doi.org/10.1021/acs.accounts.3c00436

[145] Kong, Yimeng, Edward A. Mead, and Gang Fang. 2023. “Navigating the Pitfalls of Mapping DNA and RNA Modifications.” Nature Reviews Genetics 24: 363–381. https://doi.org/10.1038/s41576-022-00559-5

[146] Hartstock, Katja, Nadine A. Kueck, Petr Spacek, Anna Ovcharenko, Sabine Hüwel, Nicolas V. Cornelissen, Amarnath Bollu, Christoph Dieterich, and Andrea Rentmeister. 2023. “MePMe-seq: Antibody-Free Simultaneous m⁶A and m⁵C Mapping in mRNA by Metabolic Propargyl Labeling and Sequencing.” Nature Communications 14: 7154. https://doi.org/10.1038/s41467-023-42832-z

[147] Khoddami, Vahid, Archana Yerra, Timothy L. Mosbruger, Aaron M. Fleming, Cynthia J. Burrows, and Bradley R. Cairns. 2019. “Transcriptome-Wide Profiling of Multiple RNA Modifications Simultaneously at Single-Base Resolution.” Proceedings of the National Academy of Sciences 116: 6784–6789. https://doi.org/10.1073/pnas.1817334116

[148] Lin, Shuibin, Qi Liu, Yi-Zhou Jiang, and Richard I. Gregory. 2019. “Nucleotide Resolution Profiling of m⁷G tRNA Modification by TRAC-Seq.” Nature Protocols 14: 3220–3242. https://doi.org/10.1038/s41596-019-0226-7

[149] Amort, Thomas, Marie F. Soulière, Alexandra Wille, Xi-Yu Jia, Heidi Fiegl, Hildegard Wörle, Ronald Micura, and Alexandra Lusser. 2013. “Long Non-Coding RNAs as Targets for Cytosine Methylation.” RNA Biology 10: 1002–1008. https://doi.org/10.4161/rna.24454

[150] Schaefer, M., T. Pollex, K. Hanna, and F. Lyko. 2008. “RNA Cytosine Methylation Analysis by Bisulfite Sequencing.” Nucleic Acids Research 37: e12. https://doi.org/10.1093/nar/gkn954

[151] Squires, Jeffrey E., Hardip R. Patel, Marco Nousch, Tennille Sibbritt, David T. Humphreys, Brian J. Parker, Catherine M. Suter, and Thomas Preiss. 2012. “Widespread Occurrence of 5-Methylcytosine in Human Coding and Non-Coding RNA.” Nucleic Acids Research 40: 5023–5033. https://doi.org/10.1093/nar/gks144

[152] Burgess, Alice Louise, Rakesh David, and Iain Robert Searle. 2015. “Conservation of tRNA and rRNA 5-Methylcytosine in the Kingdom Plantae.” BMC Plant Biology 15: 199. https://doi.org/10.1186/s12870-015-0580-8

[153] Militello, Kevin T., Leanne M. Chen, Sarah E. Ackerman, Alexandra H. Mandarano, and Erika L. Valentine. 2014. “A Map of 5-Methylcytosine Residues in Trypanosoma brucei tRNA Revealed by Sodium Bisulfite Sequencing.” Molecular and Biochemical Parasitology 193: 122–126. https://doi.org/10.1016/j.molbiopara.2013.12.003

[154] Schaefer, Matthias. 2015. “Chapter Fourteen - RNA 5-Methylcytosine Analysis by Bisulfite Sequencing.” In Methods in Enzymology (pp. 297–329, Academic Press). https://doi.org/10.1016/bs.mie.2015.03.007

[155] Shen, Weiguo, Hanxiao Sun, Cong Liu, Yunpeng Yi, Yongkang Hou, Ye Xiao, Yufei Hu, et al. 2024. “GLORI for Absolute Quantification of Transcriptome-Wide m⁶a at Single-Base Resolution.” Nature Protocols 19: 1252–1287. https://doi.org/10.1038/s41596-023-00937-1

[156] Schwartz, Schraga, Douglas A. Bernstein, Maxwell R. Mumbach, Marko Jovanovic, Rebecca H. Herbst, Brian X. León-Ricardo, Jesse M. Engreitz, et al. 2014. “Transcriptome-Wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA.” Cell 159: 148–162. https://doi.org/10.1016/j.cell.2014.08.028

[157] Carlile, Thomas M., Maria F. Rojas-Duran, Boris Zinshteyn, Hakyung Shin, Kristen M. Bartoli, and Wendy V. Gilbert. 2014. “Pseudouridine Profiling Reveals Regulated mRNA Pseudouridylation in Yeast and Human Cells.” Nature 515: 143–146. https://doi.org/10.1038/nature13802

[158] Li, Xiaoyu, Ping Zhu, Shiqing Ma, Jinghui Song, Jinyi Bai, Fangfang Sun, and Chengqi Yi. 2015. “Chemical Pulldown Reveals Dynamic Pseudouridylation of the Mammalian Transcriptome.” Nature Chemical Biology 11: 592–597. https://doi.org/10.1038/nchembio.1836

[159] Arango, Daniel, David Sturgill, Renbin Yang, Tapan Kanai, Paulina Bauer, Jyoti Roy, Ziqiu Wang, Masaki Hosogane, Sarah Schiffers, and Shalini Oberdoerffer. 2022. “Direct Epitranscriptomic Regulation of Mammalian Translation Initiation Through N4-Acetylcytidine.” Molecular Cell 82: 2797–2814.e11. https://doi.org/10.1016/j.molcel.2022.05.016

[160] Sas-Chen, Aldema, Justin M. Thomas, Donna Matzov, Masato Taoka, Kellie D. Nance, Ronit Nir, Keri M. Bryson, et al. 2020. “Dynamic RNA Acetylation Revealed by Quantitative Cross-Evolutionary Mapping.” Nature 583: 638–643. https://doi.org/10.1038/s41586-020-2418-2

[161] Hu, Lulu, Shun Liu, Yong Peng, Ruiqi Ge, Rui Su, Chamara Senevirathne, Bryan T. Harada, et al. 2022. “m⁶A RNA Modifications Are Measured at Single-Base Resolution Across the Mammalian Transcriptome.” Nature Biotechnology 40: 1210–1219. https://doi.org/10.1038/s41587-022-01243-z

[162] Zhong, Zhen-Dong, Ying-Yuan Xie, Hong-Xuan Chen, Ye-Lin Lan, Xue-Hong Liu, Jing-Yun Ji, Fu Wu, et al. 2023. “Systematic Comparison of Tools Used for m⁶A Mapping From Nanopore Direct RNA Sequencing.” Nature Communications 14: 1906. https://doi.org/10.1038/s41467-023-37596-5

[163] Anreiter, Ina, Quoseena Mir, Jared T. Simpson, Sarath C. Janga, and Matthias Soller. 2021. “New Twists in Detecting mRNA Modification Dynamics.” Trends in Biotechnology 39: 72–89. https://doi.org/10.1016/j.tibtech.2020.06.002

[164] Lu, Liang, Xiaoting Zhang, Yuenan Zhou, Zuokun Shi, Xiwen Xie, Xinyue Zhang, Liaoliao Gao, et al. 2024. “Base-Resolution m5C Profiling Across the Mammalian Transcriptome By Bisulfite-Free Enzyme-Assisted Chemical Labeling Approach.” Molecular Cell 84: 2984–3000.e8. https://doi.org/10.1016/j.molcel.2024.06.021

[165] Ju, Cheng-Wei, Ruitu Lyu, Han Li, Jiangbo Wei, Alberto J. Parra Vitela, Urszula Dougherty, Akushika Kwesi, et al. 2026. “Modifications of Microbiome-Derived Cell-Free RNA in Plasma Discriminates Colorectal Cancer Samples.” Nature Biotechnology 44: 752–758. https://doi.org/10.1038/s41587-025-02731-8

[166] Zhang, Zhang, Li-Qian Chen, Yu-Li Zhao, Cai-Guang Yang, Ian A. Roundtree, Zijie Zhang, Jian Ren, Wei Xie, Chuan He, and Guan-Zheng Luo. 2019. “Single-Base Mapping of m⁶A by an Antibody-Independent Method.” Science Advances 5: eaax0250. https://doi.org/10.1126/sciadv.aax0250

[167] Khoddami, Vahid, and Bradley R. Cairns. 2013. “Identification of Direct Targets and Modified Bases of RNA Cytosine Methyltransferases.” Nature Biotechnology 31: 458–464. https://doi.org/10.1038/nbt.2566

[168] Zheng, Guanqun, Yidan Qin, Wesley C. Clark, Qing Dai, Chengqi Yi, Chuan He, Alan M. Lambowitz, and Tao Pan. 2015. “Efficient and Quantitative High-Throughput tRNA Sequencing.” Nature Methods 12: 835–837. https://doi.org/10.1038/nmeth.3478

[169] Cozen, Aaron E., Erin Quartley, Andrew D. Holmes, Eva Hrabeta-Robinson, Eric M. Phizicky, and Todd M. Lowe. 2015. “ARM-Seq: AlkB-Facilitated RNA Methylation Sequencing Reveals a Complex Landscape of Modified tRNA Fragments.” Nature Methods 12: 879–884. https://doi.org/10.1038/nmeth.3508

[170] Shi, Junchao, Yunfang Zhang, Dongmei Tan, Xudong Zhang, Menghong Yan, Ying Zhang, Reuben Franklin, et al. 2021. “PANDORA-seq Expands the Repertoire of Regulatory Small RNAs by Overcoming RNA Modifications.” Nature Cell Biology 23: 424–436. https://doi.org/10.1038/s41556-021-00652-7

[171] Birkedal, Ulf, Mikkel Christensen-Dalsgaard, Nicolai Krogh, Radhakrishnan Sabarinathan, Jan Gorodkin, and Henrik Nielsen. 2015. “Profiling of Ribose Methylations in RNA by High-Throughput Sequencing.” Angewandte Chemie International Edition 54: 451–455. https://doi.org/10.1002/anie.201408362

[172] Gao, Yubang, Xuqing Liu, Bizhi Wu, Huihui Wang, Feihu Xi, Markus V. Kohnen, Anireddy S. N. Reddy, and Lianfeng Gu. 2021. “Quantitative Profiling of N6-Methyladenosine at Single-Base Resolution in Stem-Differentiating Xylem of Populus trichocarpa Using Nanopore Direct RNA Sequencing.” Genome Biology 22: 22. https://doi.org/10.1186/s13059-020-02241-7

[173] Jenjaroenpun, Piroon, Thidathip Wongsurawat, Thidathip Wongsurawat, Taylor D. Wadley, Trudy M. Wassenaar, Jun Liu, Qing Dai, Visanu Wanchai, et al. 2021. “Decoding the Epitranscriptional Landscape From Native RNA Sequences.” Nucleic Acids Research 49: e7. https://doi.org/10.1093/nar/gkaa620

[174] Qin, Hang, Liang Ou, Jian Gao, Longxian Chen, Jia-Wei Wang, Pei Hao, and Xuan Li. 2022. “DENA: Training an Authentic Neural Network Model Using Nanopore Sequencing Data of Arabidopsis Transcripts for Detection and Quantification of N6-Methyladenosine on RNA.” Genome Biology 23: 25. https://doi.org/10.1186/s13059-021-02598-3

[175] Hendra, Christopher, Ploy N. Pratanwanich, Yuk Kei Wan, W. S. Sho Goh, Alexandre Thiery, and Jonathan Göke. 2022. “Detection of m⁶A From Direct RNA Sequencing Using a Multiple Instance Learning Framework.” Nature Methods 19: 1590–1598. https://doi.org/10.1038/s41592-022-01666-1

[176] Lorenz, Daniel A., Shashank Sathe, Jaclyn M. Einstein, and Gene W. Yeo. 2020. “Direct RNA Sequencing Enables m⁶A Detection in Endogenous Transcript Isoforms at Base-Specific Resolution.” RNA 26: 19–28. https://doi.org/10.1261/rna.072785.119

[177] Wu, You, Wenna Shao, Mengxiao Yan, Yuqin Wang, Pengfei Xu, Guoqiang Huang, Xiaofei Li, et al. 2024. “Transfer Learning Enables Identification of Multiple Types of RNA Modifications Using Nanopore Direct RNA Sequencing.” Nature Communications 15: 4049. https://doi.org/10.1038/s41467-024-48437-4

[178] Li, Yanqiang, Yang Yi, Xinlei Gao, Xin Wang, Dongyu Zhao, Rui Wang, Li-Sheng Zhang, et al. 2024. “2′-O-Methylation at Internal Sites on mRNA Promotes mRNA Stability.” Molecular Cell 84: 2320–2336.e6. https://doi.org/10.1016/j.molcel.2024.04.011

[179] Xie, Ying-Yuan, Zhen-Dong Zhong, Hong-Xuan Chen, Ze-Hui Ren, Yuan-Tao Qiu, Ye-Lin Lan, Fu Wu, et al. 2025. “Single-Molecule Direct RNA Sequencing Reveals the Shaping of Epitranscriptome Across Multiple Species.” Nature Communications 16: 5119. https://doi.org/10.1038/s41467-025-60447-4

[180] Zhang, Yuxin, Yuecheng Wu, Jiongming Ma, Yiyu Wu, Liying Li, Haozhe Wang, Guifang Jia, et al. 2025. “DirectRM: Integrated Detection of Landscape and Crosstalk Between Multiple RNA Modifications Using Direct RNA Sequencing.” Nature Communications 16: 9450. https://doi.org/10.1038/s41467-025-64495-8

[181] Chan, Adrian, Isabel S. Naarmann-de Vries, Carolin P. M. Scheitl, Claudia Höbartner, and Christoph Dieterich. 2024. “Detecting m⁶A at Single-Molecular Resolution via Direct RNA Sequencing and Realistic Training Data.” Nature Communications 15: 3323. https://doi.org/10.1038/s41467-024-47661-2

[182] Acera Mateos, P., A. J Sethi, A. Ravindran, A. Srivastava, K. Woodward, S. Mahmud, M. Kanchi, et al. 2024. “Prediction of m⁶A and m⁵C at Single-Molecule Resolution Reveals a Transcriptome-Wide Co-Occurrence of RNA Modifications.” Nature Communications 15: 3899. https://doi.org/10.1038/s41467-024-47953-7

[183] Huang, Sihao, Adam C. Wylder, and Tao Pan. 2024. “Simultaneous Nanopore Profiling of mRNA m⁶A and Pseudouridine Reveals Translation Coordination.” Nature Biotechnology 42: 1831–1835. https://doi.org/10.1038/s41587-024-02135-0

[184] Price, Alexander M., Katharina E. Hayer, Alexa B. R. McIntyre, Nandan S. Gokhale, Jonathan S. Abebe, Ashley N. Della Fera, Christopher E. Mason, et al. 2020. “Direct RNA Sequencing Reveals m⁶A Modifications on Adenovirus RNA Are Necessary for Efficient Splicing.” Nature Communications 11: 6016. https://doi.org/10.1038/s41467-020-19787-6

[185] Pratanwanich, Ploy N., Fei Yao, Ying Chen, Casslynn W. Q. Koh, Yuk Kei Wan, Christopher Hendra, Polly Poon, et al. 2021. “Identification of Differential RNA Modifications from Nanopore Direct RNA Sequencing With Xpore.” Nature Biotechnology 39: 1394–1402. https://doi.org/10.1038/s41587-021-00949-w

[186] Begik, Oguzhan, Morghan C. Lucas, Leszek P. Pryszcz, Jose Miguel Ramirez, Rebeca Medina, Ivan Milenkovic, Sonia Cruciani, et al. 2021. “Quantitative Profiling of Pseudouridylation Dynamics in Native RNAs With Nanopore Sequencing.” Nature Biotechnology 39: 1278–1291. https://doi.org/10.1038/s41587-021-00915-6

[187] Hassan, Doaa, Daniel Acevedo, Swapna Vidhur Daulatabad, Quoseena Mir, and Sarath Chandra Janga. 2022. “Penguin: A Tool for Predicting Pseudouridine Sites in Direct RNA Nanopore Sequencing Data.” Methods 203: 478–487. https://doi.org/10.1016/j.ymeth.2022.02.005

[188] Wu, You, Wenna Shao, Shuai Liu, Liyuan Wang, Pengfei Xu, Xingpeng Zhang, Haihan Song, Xiaofei Li, Jian Wang, and Xiang Yu. 2025. “Simultaneous Profiling of ac⁴C and m⁵C Modifications From Nanopore Direct RNA Sequencing.” International Journal of Biological Macromolecules 305: 140863. https://doi.org/10.1016/j.ijbiomac.2025.140863

[189] Hewel, Charlotte, Anna Wierczeiko, Johannes Miedema, Johannes Friedrich, Felix Hofmann, Stephan Weißbach, Vincent Dietrich, et al. 2025. “Direct RNA Sequencing Enables Improved Transcriptome Assessment and Tracking of RNA Modifications for Medical Applications.” Nucleic Acids Research 53: gkaf1314. https://doi.org/10.1093/nar/gkaf1314

[190] Cozzuto, Luca, Huanle Liu, Leszek P. Pryszcz, Toni Hermoso Pulido, Anna Delgado-Tejedor, Julia Ponomarenko, and Eva Maria Novoa. 2020. “MasterOfPores: A Workflow for the Analysis of Oxford Nanopore Direct RNA Sequencing Datasets.” Frontiers in Genetics 11: 221. https://doi.org/10.3389/fgene.2020.00211

[191] Grünberger, Felix, Sébastien Ferreira-Cerca, and Dina Grohmann. 2022. “Nanopore Sequencing of RNA and cDNA Molecules in Escherichia coli.” RNA 28: 400–417. https://doi.org/10.1261/rna.078937.121

[192] Lucas, Morghan C., Leszek P. Pryszcz, Rebeca Medina, Ivan Milenkovic, Noelia Camacho, Virginie Marchand, Yuri Motorin, Lluís Ribas de Pouplana, and Eva Maria Novoa. 2024. “Quantitative Analysis of tRNA Abundance and Modifications by Nanopore RNA Sequencing.” Nature Biotechnology 42: 72–86. https://doi.org/10.1038/s41587-023-01743-6

[193] Vo, Jenny Mai, Logan Mulroney, Jen Quick-Cleveland, Miten Jain, Mark Akeson, and Manuel Ares. 2021. “Synthesis of Modified Nucleotide Polymers by the Poly(U) Polymerase Cid1: Application to Direct RNA Sequencing on Nanopores.” RNA 27: 1497–1511. https://doi.org/10.1261/rna.078898.121

[194] Saville, Luke, Li Wu, Jemaneh Habtewold, Yubo Cheng, Babita Gollen, Liam Mitchell, Matthew Stuart-Edwards, Travis Haight, Majid Mohajerani, and Athanasios Zovoilis. 2024. “NERD-seq: A Novel Approach of Nanopore Direct RNA Sequencing That Expands Representation of Non-Coding RNAs.” Genome Biology 25: 233. https://doi.org/10.1186/s13059-024-03375-8

[195] Mulroney, Logan, Madalee G. Wulf, Ira Schildkraut, George Tzertzinis, John Buswell, Miten Jain, Hugh Olsen, et al. 2022. “Identification of High-Confidence Human Poly(A) RNA Isoform Scaffolds Using Nanopore Sequencing.” RNA 28: 162–176. https://doi.org/10.1261/rna.078703.121

[196] Putzeys, Leena, Maarten Boon, Eveline-Marie Lammens, Konstantin Kuznedelov, Konstantin Severinov, and Rob Lavigne. 2022. “Development of ONT-Cappable-Seq to Unravel the Transcriptional Landscape of Pseudomonas Phages.” Computational and Structural Biotechnology Journal 20: 2624–2638. https://doi.org/10.1016/j.csbj.2022.05.034

[197] Drexler, Heather L., Karine Choquet, and L. Stirling Churchman. 2020. “Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores.” Molecular Cell 77: 985–998. https://doi.org/10.1016/j.molcel.2019.11.017

[198] Long, Yanping, Jinbu Jia, Weipeng Mo, Xianhao Jin, and Jixian Zhai. 2021. “FLEP-Seq: Simultaneous Detection of RNA Polymerase II Position, Splicing Status, Polyadenylation Site and Poly(A) Tail Length at Genome-Wide Scale by Single-Molecule Nascent RNA Sequencing.” Nature Protocols 16: 4355–4381. https://doi.org/10.1038/s41596-021-00581-7

[199] Dioken, Didem Naz, Ibrahim Ozgul, Irem Yilmazbilek, Elanur Almeric, Irem Cemile Eroglu, Mustafa Cicek, Utku Cem Yilmaz, et al. 2025. “E2-Regulated Transcriptome Complexity Revealed by Long-Read Direct RNA Sequencing: From Isoform Discovery to Truncated Proteins.” RNA Biology 22: 1–21. https://doi.org/10.1080/15476286.2025.2563860

[200] Fahmi, Naima Ahmed, Sourav Saha, Qianqian Song, Qian Lou, Jeongsik Yong, and Wei Zhang. 2025. “Computational Methods for Alternative Polyadenylation and Splicing in Post-Transcriptional Gene Regulation.” Experimental & Molecular Medicine 57: 1631–1640. https://doi.org/10.1038/s12276-025-01496-z

[201] Li, Runsheng, Xiaoliang Ren, Qiutao Ding, Yu Bi, Dongying Xie, and Zhongying Zhao. 2020. “Direct Full-Length RNA Sequencing Reveals Unexpected Transcriptome Complexity During Caenorhabditis Elegans Development.” Genome Research 30: 287–298. https://doi.org/10.1101/gr.251512.119

[202] Zhu, Xi-Tong, Pablo Sanz-Jimenez, Xiao-Tong Ning, Muhammad Tahir ul Qamar, and Ling-Ling Chen. 2024. “Direct RNA Sequencing in Plants: Practical Applications and Future Perspectives.” Plant Communications 5: 101064. https://doi.org/10.1016/j.xplc.2024.101064

[203] Dioken, Didem Naz, Ibrahim Ozgul, and Ayse Elif Erson-Bensan. 2025. “The 3′ End of the Tale-Neglected Isoforms in Cancer.” FEBS Letters 599: 3029–3046. https://doi.org/10.1002/1873-3468.70122

[204] Reyes, Alejandro, and Wolfgang Huber. 2018. “Alternative Start and Termination Sites of Transcription Drive Most Transcript Isoform Differences Across Human Tissues.” Nucleic Acids Research 46: 582–592. https://doi.org/10.1093/nar/gkx1165

[205] Pelechano, Vicent, Wu Wei, and Lars M. Steinmetz. 2013. “Extensive Transcriptional Heterogeneity Revealed by Isoform Profiling.” Nature 497: 127–131. https://doi.org/10.1038/nature12121

[206] Yang, Ludong, Xinxin Zhang, Fan Wang, Li Zhang, Jing Li, and Jia-Xing Yue. 2024. “NanoTrans: An Integrated Computational Framework for Comprehensive Transcriptome Analysis With Nanopore Direct RNA Sequencing.” Journal of Genetics and Genomics 51: 1300–1309. https://doi.org/10.1016/j.jgg.2024.07.007

[207] Zhang, Shoudong, Runsheng Li, Li Zhang, Shengjie Chen, Min Xie, Liu Yang, Yiji Xia, Christine H. Foyer, Zhongying Zhao, and Hon-Ming Lam. 2020. “New Insights Into Arabidopsis Transcriptome Complexity Revealed by Direct Sequencing of Native RNAs.” Nucleic Acids Research 48: 7700–7711. https://doi.org/10.1093/nar/gkaa588

[208] Tan, Lu, Zhihao Guo, Yanwen Shao, Lianwei Ye, Miaomiao Wang, Xin Deng, Sheng Chen, and Runsheng Li. 2024. “Analysis of Bacterial Transcriptome and Epitranscriptome Using Nanopore Direct RNA Sequencing.” Nucleic Acids Research 52: 8746–8762. https://doi.org/10.1093/nar/gkae601

[209] Abebe, Jonathan S., Yasmine Alwie, Erik Fuhrmann, Jonas Leins, Julia Mai, Ruth Verstraten, Sabrina Schreiner, Angus C. Wilson, and Daniel P. Depledge. 2024. “Nanopore Guided Annotation of Transcriptome Architectures.” mSystems 9: e00505–e00524. https://doi.org/10.1128/msystems.00505-24

[210] Liang, Qiaoxia, Jizhou Zhang, Hon-Ming Lam, and Ting-Fung Chan. 2024. “Nanopore Direct RNA Sequencing Reveals N6-Methyladenosine and Polyadenylation Landscapes on Long Non-Coding RNAs in Arabidopsis thaliana.” BMC Plant Biology 24: 1126. https://doi.org/10.1186/s12870-024-05845-4

[211] Chua, Bernadette A., Inge Van Der Werf, Catriona Jamieson, and Robert A. J. Signer. 2020. “Post-Transcriptional Regulation of Homeostatic, Stressed, and Malignant Stem Cells.” Cell Stem Cell 26: 138–159. https://doi.org/10.1016/j.stem.2020.01.005

[212] Pal, Sharmistha, Ravi Gupta, Hyunsoo Kim, Priyankara Wickramasinghe, Valérie Baubet, Louise C. Showe, Nadia Dahmane, and Ramana V. Davuluri. 2011. “Alternative Transcription Exceeds Alternative Splicing in Generating the Transcriptome Diversity of Cerebellar Development.” Genome Research 21: 1260–1272. https://doi.org/10.1101/gr.120535.111

[213] Sharma, Yashica, Kevin Vo, Sharmin Shila, Anohita Paul, Vinesh Dahiya, Patrick E. Fields, and M. A. Karim Rumi. 2025. “mRNA Transcript Variants Expressed in Mammalian Cells.” International Journal of Molecular Sciences 26: 1052. https://doi.org/10.3390/ijms26031052

[214] Wang, Eric T., Rickard Sandberg, Shujun Luo, Irina Khrebtukova, Lu Zhang, Christine Mayr, Stephen F. Kingsmore, Gary P. Schroth, and Christopher B. Burge. 2008. “Alternative Isoform Regulation in Human Tissue Transcriptomes.” Nature 456: 470–476. https://doi.org/10.1038/nature07509

[215] Su, Yaqi, Zhejian Yu, Siqian Jin, Zhipeng Ai, Ruihong Yuan, Xinyi Chen, Ziwei Xue, et al. 2024. “Comprehensive Assessment of mRNA Isoform Detection Methods for Long-Read Sequencing Data.” Nature Communications 15: 3972. https://doi.org/10.1038/s41467-024-48117-3

[216] Tao, Yining, Qi Zhang, Haoyu Wang, Xiyu Yang, and Haoran Mu. 2024. “Alternative Splicing and Related RNA Binding Proteins in Human Health and Disease.” Signal Transduction and Targeted Therapy 9: 26. https://doi.org/10.1038/s41392-024-01734-2

[217] Alhabsi, Abdulrahman, Yu Ling, Martin Crespi, Anireddy S. N. Reddy, and Magdy Mahfouz. 2025. “Alternative Splicing Dynamics in Plant Adaptive Responses to Stress.” Annual Review of Plant Biology 76: 687–717. https://doi.org/10.1146/annurev-arplant-083123-090055

[218] Zhao, Liangzhen, Hangxiao Zhang, Markus V. Kohnen, Kasavajhala V. S. K. Prasad, Lianfeng Gu, and Anireddy S. N. Reddy. 2019. “Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing.” Frontiers in Genetics 10: 153. https://doi.org/10.3389/fgene.2019.00253

[219] Zhu, Chenchen, Jingyan Wu, Han Sun, Francesca Briganti, Benjamin Meder, Wu Wei, and Lars M. Steinmetz. 2021. “Single-Molecule, Full-Length Transcript Isoform Sequencing Reveals Disease-Associated RNA Isoforms in Cardiomyocytes.” Nature Communications 12: 4203. https://doi.org/10.1038/s41467-021-24484-z

[220] Cui, Jiawen, Nan shen, Zhaogeng Lu, Guolu Xu, Yuyao Wang, and Biao Jin. 2020. “Analysis and Comprehensive Comparison of PacBio and Nanopore-Based RNA Sequencing of the Arabidopsis Transcriptome.” Plant Methods 16: 85. https://doi.org/10.1186/s13007-020-00629-x

[221] Hu, Yu, Li Fang, Xuelian Chen, Jiang F. Zhong, Mingyao Li, and Kai Wang. 2021. “LIQA: Long-Read Isoform Quantification and Analysis.” Genome Biology 22: 182. https://doi.org/10.1186/s13059-021-02399-8

[222] Chothani, Sonia, Eleonora Adami, John F. Ouyang, Sivakumar Viswanathan, Norbert Hubner, Stuart A. Cook, Sebastian Schafer, and Owen J. L. Rackham. 2019. “deltaTE: Detection of Translationally Regulated Genes By Integrative Analysis of Ribo-Seq and RNA-Seq Data.” Current Protocols in Molecular Biology 129: e108. https://doi.org/10.1002/cpmb.108

[223] Wang, Bo, Elizabeth Tseng, Primo Baybayan, Kevin Eng, Michael Regulski, Yinping Jiao, Liya Wang, et al. 2020. “Variant Phasing and Haplotypic Expression From Long-Read Sequencing in Maize.” Communications Biology 3: 78. https://doi.org/10.1038/s42003-020-0805-8

[224] Deonovic, Benjamin, Yunhao Wang, Jason Weirather, Xiu-Jie Wang, and Kin Fai Au. 2017. “IDP-ASE: Haplotyping and Quantifying Allele-Specific Expression at the Gene and Gene Isoform Level by Hybrid Sequencing.” Nucleic Acids Research 45: e32. https://doi.org/10.1093/nar/gkw1076

[225] Mangul, Serghei, Taegyun Harry Yang, Farhad Hormozdiari, Alexandra Marie Dainis, Elizabeth Tseng, Euan A. Ashley, Eleazar Eskin, and Zelikovsky . 2017. “HapIso: An Accurate Method for the Haplotype-Specific Isoforms Reconstruction From Long Single-Molecule Reads.” IEEE Transactions on NanoBioscience 16: 108–115. https://doi.org/10.1109/TNB.2017.2675981

[226] Brouze, Aleksandra, Paweł Szczepan Krawczyk, Andrzej Dziembowski, and Seweryn Mroczek. 2023. “Measuring the Tail: Methods for Poly(A) Tail Profiling.” WIREs RNA 14: e1737. https://doi.org/10.1002/wrna.1737

[227] Fernandez, Mercedes, and Raul Mendez. 2025. “Cytoplasmic Regulation of the Poly(A) Tail Length as a Potential Therapeutic Target.” RNA 31: 402–415. https://doi.org/10.1261/rna.080333.124

[228] Krause, Maximilian, Adnan M. Niazi, Kornel Labun, Yamila N. Torres Cleuren, Florian S. Müller, and Eivind Valen. 2019. “Tailfindr: Alignment-Free Poly(A) Length Measurement for Oxford Nanopore RNA and DNA Sequencing.” RNA 25: 1229–1241. https://doi.org/10.1261/rna.071332.119

[229] Gumińska, Natalia, Katarzyna Matylla-Kulińska, Paweł S. Krawczyk, Michał, Maj, Wiktoria Orzeł, Zuzanna Mackiewicz, Aleksandra Brouze, Seweryn Mroczek, and Andrzej Dziembowski. 2025. “Direct Profiling of Non-Adenosines in Poly(A) Tails of Endogenous and Therapeutic mRNAs With Ninetails.” Nature Communications 16: 2664. https://doi.org/10.1038/s41467-025-57787-6

[230] Liu, Mengfei, Sien Linlin Hao, Xiaohui Yang, and Wu . 2022. “PolyAtailor: Measuring Poly(A) Tail Length From Short-Read and Long-Read Sequencing Data.” Briefings in Bioinformatics 23: bbac271. https://doi.org/10.1093/bib/bbac271

[231] Jia, Jinbu, Wenqin Lu, Bo Liu, Huihui Fang, Yiming Yu, Weipeng Mo, Hong Zhang, et al. 2022. “An Atlas of Plant Full-Length RNA Reveals Tissue-Specific and Monocots–Dicots Conserved Regulation of Poly(A) Tail Length.” Nature Plants 8: 1118–1126. https://doi.org/10.1038/s41477-022-01224-9

[232] Chang, Hyeshik, Jaechul Lim, Minju Ha, and V. Narry Kim. 2014. “TAIL-seq: Genome-Wide Determination of Poly(A) Tail Length and 3′ End Modifications.” Molecular Cell 53: 1044–1052. https://doi.org/10.1016/j.molcel.2014.02.007

[233] Yu, Fengyun, Yu Zhang, Chao Cheng, Wenqing Wang, Zisong Zhou, Wenliang Rang, Han Yu, Yaxun Wei, Qijia Wu, and Yi Zhang. 2020. “Poly(A)-Seq: A Method for Direct Sequencing and Analysis of the Transcriptomic Poly(A)-Tails.” Plos One 15: e0234696. https://doi.org/10.1371/journal.pone.0234696

[234] Nicholson, Angela L., and Amy E. Pasquinelli. 2019. “Tales of Detailed Poly(A) Tails.” Trends in Cell Biology 29: 191–200. https://doi.org/10.1016/j.tcb.2018.11.002

[235] Lima, Sarah Azoubel, Laura B. Chipman, Angela L. Nicholson, Ying-Hsin, Chen, Brian A. Yee, Gene W. Yeo, Jeff Coller, and Amy E. Pasquinelli. 2017. “Short Poly(A) Tails Are a Conserved Feature of Highly Expressed Genes.” Nature Structural & Molecular Biology 24: 1057–1063. https://doi.org/10.1038/nsmb.3499

[236] Subtelny, Alexander O., Stephen W. Eichhorn, Grace R. Chen, Hazel Sive, and David P. Bartel. 2014. “Poly(A)-Tail Profiling Reveals an Embryonic Switch in Translational Control.” Nature 508: 66–71. https://doi.org/10.1038/nature13007

[237] Zhang, Xueying, Feiyan Liu, and Yu Zhou. 2025. “Coupling of Alternative Splicing and Alternative Polyadenylation.” Acta Biochimica et Biophysica Sinica 57: 22–32. https://doi.org/10.3724/abbs.2024211

[238] Liu, Yusheng, Yiwei Zhang, Jiaqiang Wang, and Falong Lu. 2022. “Transcriptome-Wide Measurement of Poly(A) Tail Length and Composition at Subnanogram Total RNA Sensitivity by PAIso-Seq.” Nature Protocols 17: 1980–2007. https://doi.org/10.1038/s41596-022-00704-8

[239] Liu, Yaran, Yang Li, and Qiang Sun. 2025. “Advances in Detecting RNA Modifications Using Direct RNA Nanopore Sequencing.” Advanced Genetics 6: e00041. https://doi.org/10.1002/ggn2.202500041

[240] Zhang, Yuxin, Jie Jiang, Jiongming Ma, Zhen Wei, Yue Wang, Bowen Song, Jia Meng, et al. 2023. “DirectRMDB: A Database of Post-Transcriptional RNA Modifications Unveiled from Direct RNA Sequencing Technology.” Nucleic Acids Research 51: D106–D116. https://doi.org/10.1093/nar/gkac1061

[241] Diensthuber, Gregor, Ivan Milenkovic, Laia Llovera, Ana Milovanovic, Francesco Pelizzari, and Eva Maria Novoa. 2025. “Systematic Benchmarking of Basecalling Models for RNA Modification Detection With Highly-Multiplexed Nanopore Sequencing.” Preprint at bioRxiv https://doi.org/10.1101/2025.07.11.663424

[242] Sethi, Aditya J., Pablo Acera Mateos, Rippei Hayashi, Nikolay E. Shirokikh, Eduardo Eyras. 2024. “R2Dtool: Integration and Visualization of Isoform-Resolved RNA Features.” Bioinformatics 40: btae495. https://doi.org/10.1093/bioinformatics/btae495

[243] Shi, Hanhan, Peiwei Chai, Renbing Jia, and Xianqun Fan. 2020. “Novel Insight Into the Regulatory Roles of Diverse RNA Modifications: Re-Defining the Bridge Between Transcription and Translation.” Molecular Cancer 19: 78. https://doi.org/10.1186/s12943-020-01194-6

[244] Gilbert, Wendy V., Tristan A. Bell, and Cassandra Schaening. 2016. “Messenger RNA Modifications: Form, Distribution, and Function.” Science 352: 1408–1412. https://doi.org/10.1126/science.aad8711

[245] Akhtar, Junaid, Margot Lugoboni, and Guillaume Junion. 2021. “m⁶A RNA Modification in Transcription Regulation.” Transcription 12: 266–276. https://doi.org/10.1080/21541264.2022.2057177

[246] Fanari, Oleksandra, Michele Meseonznik, Dylan Bloch, and Sara H. Rouhanifard. 2025. “Protocol for Differential Analysis of Pseudouridine Modifications Using Nanopore DRS and Unmodified Transcriptome Control.” STAR Protocols 6: 103948. https://doi.org/10.1016/j.xpro.2025.103948

[247] Zhu, Yan, Longxian Chen, Xiangna Hong, Han Shi, and Xuan Li. 2022. “Revealing the Novel Complexity of Plant Long Non-Coding RNA by Strand-Specific and Whole Transcriptome Sequencing for Evolutionarily Representative Plant Species.” BMC Genomics 23: 381. https://doi.org/10.1186/s12864-022-08602-9

[248] Mattick, John S., Paulo P. Amaral, Piero Carninci, Susan Carpenter, Howard Y. Chang, Ling-Ling Chen, Runsheng Chen, et al. 2023. “Long Non-Coding RNAs: Definitions, Functions, Challenges and Recommendations.” Nature Reviews Molecular Cell Biology 24: 430–447. https://doi.org/10.1038/s41580-022-00566-8

[249] Kopp, Florian, and Joshua T. Mendell. 2018. “Functional Classification and Experimental Dissection of Long Noncoding RNAs.” Cell 172: 393–407. https://doi.org/10.1016/j.cell.2018.01.011

[250] Choudhari, Ramesh, Melina J. Sedano, Alana L. Harrison, Ramadevi Subramani, Ken Y. Lin, Enrique I. Ramos, Rajkumar Lakshmanaswamy, and Shrikanth S. Gadad. 2020. “Chapter Three - Long Noncoding RNAs in Cancer: From Discovery to Therapeutic Targets.” In Advances in Clinical Chemistry (pp. 105–147, Elsevier). https://doi.org/10.1016/bs.acc.2019.08.003

[251] Zhang, Jinyang, and Fangqing Zhao. 2025. “Circular RNA Discovery With Emerging Sequencing and Deep Learning Technologies.” Nature Genetics 57: 1089–1102. https://doi.org/10.1038/s41588-025-02157-7

[252] Zhang, Jinyang, Lingling Hou, Zhenqiang Zuo, Peifeng Ji, Xiaorong Zhang, Yuanchao Xue, and Fangqing Zhao. 2021. “Comprehensive Profiling of Circular RNAs With Nanopore Sequencing and CIRI-long.” Nature Biotechnology 39: 836–845. https://doi.org/10.1038/s41587-021-00842-6

[253] Kristensen, Lasse S., Maria S. Andersen, Lotte V. W. Stagsted, Karoline K. Ebbesen, Thomas B. Hansen, and Jørgen Kjems. 2019. “The Biogenesis, Biology and Characterization of Circular RNAs.” Nature Reviews Genetics 20: 675–691. https://doi.org/10.1038/s41576-019-0158-7

[254] Lin, He, Vanessa M. Conn, and Simon J. Conn. 2025. “Past, Present, and Future Strategies for Detecting and Quantifying Circular RNA Variants.” The FEBS Journal 292: 4073–4085. https://doi.org/10.1111/febs.70012

[255] Vo, Josh N. Marcin Cieslik, Yajia Zhang, Sudhanshu Shukla, Lanbo Xiao, Yuping Zhang, Yi-Mi Wu, et al. 2019. “The Landscape of Circular RNA in Cancer.” Cell 176: 869–881. https://doi.org/10.1016/j.cell.2018.12.021

[256] Shaw, Ethan A., Niki K. Thomas, Joshua D. Jones, Robin L. Abu-Shumays, Abigail L. Vaaler, Mark Akeson, Kristin S. Koutmou, Miten Jain, and David M. Garcia. 2024. “Combining Nanopore Direct RNA Sequencing With Genetics and Mass Spectrometry for Analysis of T-Loop Base Modifications Across 42 Yeast tRNA Isoacceptors.” Nucleic Acids Research 52: 12074–12092. https://doi.org/10.1093/nar/gkae796

[257] Jones, Joshua D., Kaley M. Simcox, Robert T. Kennedy, and Kristin S. Koutmou. 2023. “Direct Sequencing of Total Saccharomyces Cerevisiae tRNAs by LC–MS/MS.” RNA 29: 1201–1214. https://doi.org/10.1261/rna.079656.123

[258] White, Laura K., Kezia Dobson, Samantha del Pozo, Jill M. Bilodeaux, Shelby E. Andersen, Amber Baldwin, Chloe Barrington, et al. 2024. “Comparative Analysis of 43 Distinct RNA Modifications by Nanopore tRNA Sequencing.” Preprint at bioRxiv. https://doi.org/10.1101/2024.07.23.604651

[259] Shaw, Alan, Jonathan M. Craig, Hossein Amiri, Jeonghoon Kim, Heather E. Upton, Sydney C. Pimentel, Jesse R. Huang, et al. 2023. “Nanopore Molecular Trajectories of a Eukaryotic Reverse Transcriptase Reveal a Long-Range RNA Structure Sensing Mechanism.” Preprint at bioRxiv. https://doi.org/10.1101/2023.04.05.535757

[260] Aw, Jong Ghut Ashley, Shaun W. Lim, Jia Xu Wang, Finnlay R. P. Lambert, Wen Ting Tan, Yang Shen, Yu Zhang, et al. 2021. “Determination of Isoform-Specific RNA Structure With Nanopore Long Reads.” Nature Biotechnology 39: 336–346. https://doi.org/10.1038/s41587-020-0712-z

[261] Fleming, Aaron M., Nicole J. Mathewson, Shereen A. Howpay Manage, and Cynthia J. Burrows. 2021. “Nanopore Dwell Time Analysis Permits Sequencing and Conformational Assignment of Pseudouridine in SARS-CoV-2.” ACS Central Science 7: 1707–1717. https://doi.org/10.1021/acscentsci.1c00788

[262] Fleming, Aaron M., Praneeth Bommisetti, Songjun Xiao, Vahe Bandarian, and Cynthia J. Burrows. 2023. “Direct Nanopore Sequencing for the 17 RNA Modification Types in 36 Locations in the E. coli Ribosome Enables Monitoring of Stress-Dependent Changes.” ACS Chemical Biology 18: 2211–2223. https://doi.org/10.1021/acschembio.3c00166

[263] Saldi, Tassa, Kent Riemondy, Benjamin Erickson, and David L. Bentley. 2021. “Alternative RNA Structures Formed During Transcription Depend on Elongation Rate and Modify RNA Processing.” Molecular Cell 81: 1789–1801. https://doi.org/10.1016/j.molcel.2021.01.040

[264] Lewis, Cole J. T., Tao Pan, and Auinash Kalsotra. 2017. “RNA Modifications and Structures Cooperate to Guide RNA-Protein Interactions.” Nature Reviews Molecular Cell Biology 18: 202–210. https://doi.org/10.1038/nrm.2016.163

[265] Waldern, Justin M., Jayashree Kumar, and Alain Laederach. 2022. “Disease-Associated Human Genetic Variation Through the Lens of Precursor and Mature RNA Structure.” Human Genetics 141: 1659–1672. https://doi.org/10.1007/s00439-021-02395-9

[266] Taylor, Katarzyna, and Krzysztof Sobczak. 2020. “Intrinsic Regulatory Role of RNA Structural Arrangement in Alternative Splicing Control.” International Journal of Molecular Sciences 21: 5161. https://doi.org/10.3390/ijms21145161

[267] Ciesiolka, Adam, Magdalena Jazurek, Karolina Drazkowska, Wlodzimierz, J., and Krzyzosiak . 2017. “Structural Characteristics of Simple RNA Repeats Associated With Disease and Their Deleterious Protein Interactions.” Frontiers in Cellular Neuroscience 11: 97. https://doi.org/10.3389/fncel.2017.00097

[268] Zhang, Huakun, and Yiliang Ding. 2021. “Novel Insights Into the Pervasive Role of RNA Structure in Post-Transcriptional Regulation of Gene Expression in Plants.” Biochemical Society Transactions 49: 1829–1839. https://doi.org/10.1042/BST20210318

[269] Kramer, Marianne C., Kevin A. Janssen, Kyle Palos, Andrew D. L. Nelson, Lee E. Vandivier, Benjamin A. Garcia, Eric Lyons, Mark A. Beilstein, and Brian D. Gregory. 2020. “N6-Methyladenosine and RNA Secondary Structure Affect Transcript Stability and Protein Abundance During Systemic Salt Stress in Arabidopsis.” Plant Direct 4: e00239. https://doi.org/10.1002/pld3.239

[270] Bao, Nengcheng, Zhechao Wang, Jiayan Fu, Haiyang Dong, and Yongfeng Jin. 2025. “RNA Structure in Alternative Splicing Regulation: From Mechanism to Therapy.” Acta Biochimica et Biophysica Sinica 57: 3–21. https://doi.org/10.3724/abbs.2024119

[271] Delaunay, Sylvain, Mark Helm, and Michaela Frye. 2024. “RNA Modifications in Physiology and Disease: Towards Clinical Applications.” Nature Reviews Genetics 25: 104–122. https://doi.org/10.1038/s41576-023-00645-2

[272] Wang, Jiaxu, Jian Han, Wen Ting Tan, Anthony Youzhi Cheng, Jong Ghut Ashley Aw, Yue Wang, Guisheng Zeng, Niranjan Nagarajan, and Yue Wan. 2026. “Direct RNA Sequencing and Signal Alignment Reveal RNA Structure Ensembles in a Eukaryotic Cell.” Nature Methods 23: 914–923. https://doi.org/10.1038/s41592-026-03069-y

[273] Singh, Ajeet, Durdam Shafaque Zahra, Shailesh Das, and Kumar . 2019. “AtFusionDB: A Database of Fusion Transcripts in Arabidopsis thaliana.” Database 2019: bay135. https://doi.org/10.1093/database/bay135

[274] Cong, Jia, Sinan Zhang, Qi Zhang, Xiting Yu, Jiazhi Huang, Xin Wei, et al. 2024. “Conserved Features and Diversity Attributes of Chimeric RNAs Across Accessions in Four Plants.” Plant Biotechnology Journal 22: 3151–3163. https://doi.org/10.1111/pbi.14437

[275] Davidson, Nadia M., Ying Chen, Teresa Sadras, Georgina L. Ryland, Piers Blombery, Paul G. Ekert, Jonathan Göke, and Alicia Oshlack. 2022. “JAFFAL: Detecting Fusion Genes With Long-Read Transcriptome Sequencing.” Genome Biology 23: 10. https://doi.org/10.1186/s13059-021-02588-5

[276] Berthelier, Jérémy, Leonardo Furci, Shuta Asai, Munissa Sadykova, Tomoe, Shimazaki, Ken Shirasu, and Hidetoshi Saze. 2023. “Long-Read Direct RNA Sequencing Reveals Epigenetic Regulation of Chimeric Gene-Transposon Transcripts in Arabidopsis thaliana.” Nature Communications 14: 3248. https://doi.org/10.1038/s41467-023-38954-z

[277] Hong, Ari, Dongwan Kim, V. Narry Kim, and Hyeshik Chang. 2022. “Analyzing Viral Epitranscriptomes Using Nanopore Direct RNA Sequencing.” Journal of Microbiology 60: 867–876. https://doi.org/10.1007/s12275-022-2324-4

[278] Viehweger, Adrian, Sebastian Krautwurst, Kevin Lamkiewicz, Ramakanth, Madhugiri, John Ziebuhr, Martin Hölzer, and Manja Marz. 2019. “Direct RNA Nanopore Sequencing of Full-Length Coronavirus Genomes Provides Novel Insights Into Structural Variants and Enables Modification Analysis.” Genome Research 29: 1545–1554. https://doi.org/10.1101/gr.247064.118

[279] Kim, Dongwan, Joo-Yeon Lee, Jeong-Sun Yang, Jun Won Kim, V. Narry Kim, and Hyeshik Chang. 2020. “The Architecture of SARS-CoV-2 Transcriptome.” Cell 181: 914–921. https://doi.org/10.1016/j.cell.2020.04.011

[280] Thompson, Matthew G., Matthew T. Sacco, and Stacy M. Horner. 2021. “How RNA Modifications Regulate the Antiviral Response.” Immunological Reviews 304: 169–180. https://doi.org/10.1111/imr.13020

[281] Tan, Lu, Zhihao Guo, Xiaoming Wang, Young Kim, and Runsheng Li. 2024. “Utilization of Nanopore Direct RNA Sequencing to Analyze Viral RNA Modifications.” mSystems 9: e01163–01123. https://doi.org/10.1128/msystems.01163-23

[282] Li, Xiangrong, Lin Wu, Huihui Wang, Jun Zhang, Xiaoxia Jing, Zeyu Zhang, Yuhua Wang, et al. 2025. “N6-Methyladenosine and Poly(A) Tail-Mediated Posttranscriptional Regulation in Bamboo Mosaic Virus-Dendrocalamus Latiflorus Interactions.” The Plant Journal 124: e70604. https://doi.org/10.1111/tpj.70604

[283] Liu, Jia-Hui, Yujing Lin, Ying-Xin Li, Zhaobo Lang, Zhonghui Zhang, Cheng-Guo Duan. 2025. “A Mutually Antagonistic Mechanism Mediated by RNA m⁶A Modification in Plant-Virus Interactions.” Nature Communications 16: 10378. https://doi.org/10.1038/s41467-025-65355-1

[284] Li, Na, Hui Hui, Bill Bray, Gwendolyn Michelle Gonzalez, Mark Zeller, Kristian G. Anderson, Rob Knight, et al. 2021. “METTL3 Regulates Viral m⁶A RNA Modification and Host Cell Innate Immune Responses During SARS-CoV-2 Infection.” Cell Reports 35: 109091. https://doi.org/10.1016/j.celrep.2021.109091

[285] Duru, Ilhan Cem, Zlatka Plavec, Anne Ylinen, Pia Laine, Martyn James, Lotta, Riihimäki, Sarah J. Butcher, Maria Anastasina, and Petri Auvinen. 2025. “Direct RNA Sequencing Reveals m⁶A Modifications and Isoform Changes in SARS-CoV-2-Infected HEK Cells.” Access Microbiology 7: 001019. https://doi.org/10.1099/acmi.0.001019.v3

[286] Baek, Alice, Ga-Eun Lee, Sarah Golconda, Asif Rayhan, Anastasios A. Manganaris, Shuliang Chen, Nagaraja Tirumuru, et al. 2024. “Single-Molecule Epitranscriptomic Analysis of Full-Length HIV-1 RNAs Reveals Functional Roles of Site-Specific m⁶As.” Nature Microbiology 9: 1340–1355. https://doi.org/10.1038/s41564-024-01638-5

[287] Naquin, Delphine, Sandra Blanchet, Erwin van Dijk, Lisa Bertrand, Sylvie Grégoire, Bertha Cecilia Ramirez, Rania Ouazahrou, et al. 2025. “High-Resolution HIV-1 m⁶A Epitranscriptome Reveals Isoform-Dependent Methylation Clusters and Unique 2-LTR Transcript Modifications.” NAR Genomics and Bioinformatics 7: lqaf200. https://doi.org/10.1093/nargab/lqaf200

[288] Ding, Shuang, Haibin Liu, Lijuan Liu, Li Ma, Zhen Chen, Miao Zhu, Lishi Liu, et al. 2024. “Epigenetic Addition of m⁵C to HBV Transcripts Promotes Viral Replication and Evasion of Innate Antiviral Responses.” Cell Death & Disease 15: 39. https://doi.org/10.1038/s41419-023-06412-9

[289] Giambruno, Roberto, Elsa Zacco, Camilla Ugolini, Andrea Vandelli, Logan Mulroney, Manfredi D'Onghia, Bianca Giuliani, et al. 2023. “Unveiling the Role of PUS7-Mediated Pseudouridylation in Host Protein Interactions Specific for the SARS-CoV-2 RNA Genome.” Molecular Therapy Nucleic Acids 34: 102052. https://doi.org/10.1016/j.omtn.2023.102052

[290] Perlas, Albert, Tim Reska, Guillaume Croville, Ferran Tarrés-Freixas, Jean-Luc, Guérin, Natàlia Majó, and Lara Urban. 2025. “Improvements in RNA and DNA Nanopore Sequencing Allow for Rapid Genetic Characterization of Avian Influenza.” Virus Evolution 11: veaf010. https://doi.org/10.1093/ve/veaf010

[291] Wu, Kaiyuan, Yanqiang Li, Yang Yi, Yang Yu, Yunxia Wang, Lili Zhang, Qi, Cao, and Kaifu Chen. 2025. “The Detection, Function, and Therapeutic Potential of RNA 2′-O-Methylation.” The Innovation Life 3: 100112. https://doi.org/10.59717/j.xinn-life.2024.100112

[292] Baquero-Pérez, Belinda, Ivaylo D. Yonchev, Anna Delgado-Tejedor, Rebeca Medina, Mireia Puig-Torrents, Ian Sudbery, Oguzhan Begik, Stuart A. Wilson, Eva Maria Novoa, and Juana Díez. 2024. “N6-Methyladenosine Modification Is Not a General Trait of Viral RNA Genomes.” Nature Communications 15: 1964. https://doi.org/10.1038/s41467-024-46278-9

[293] Pan, Fuan, Jiaxian Jing, Yanhong Qiu, Maoying Li, Xueping Zhou, Shaofang Li. 2025. “Epi-Transcriptome Analysis Reveals the Lack of N6-Methyladenosine Modifications in Two RNA Viruses Infecting Watermelon.” Science Bulletin 70: 3960–3963. https://doi.org/10.1016/j.scib.2025.07.019

[294] Abebe, Jonathan S., Ruth Verstraten, and Daniel P. Depledge. 2022. “Nanopore-Based Detection of Viral RNA Modifications.” mBio 13: e0370221. https://doi.org/10.1128/mbio.03702-21

[295] Sztuba-Solińska, Joanna, Victor Stollar, and Jozef J. Bujarski. 2011. “Subgenomic Messenger RNAs: Mastering Regulation of (+)-Strand RNA Virus Life Cycle.” Virology 412: 245–255. https://doi.org/10.1016/j.virol.2011.02.007

[296] Depledge, Daniel P., Kalanghad Puthankalam Srinivas, Tomohiko Sadaoka, Devin Bready, Yasuko Mori, Dimitris G. Placantonakis, Ian Mohr, and Angus C. Wilson. 2019. “Direct RNA Sequencing on Nanopore Arrays Redefines the Transcriptional Complexity of a Viral Pathogen.” Nature Communications 10: 754. https://doi.org/10.1038/s41467-019-08734-9

[297] Ugolini, Camilla, Logan Mulroney, Adrien Leger, Matteo Castelli, Elena Criscuolo, Maia Kavanagh Williamson, Andrew D. Davidson, et al. 2022. “Nanopore ReCappable Sequencing Maps SARS-CoV-2 5′ Capping Sites and Provides New Insights Into the Structure of sgRNAs.” Nucleic Acids Research 50: 3475–3489. https://doi.org/10.1093/nar/gkac144

[298] Zhang, Riteng, Peixin Wang, Xin Ma, Yifan Wu, Chen Luo, Li Qiu, Basit Zeshan, Zengqi Yang, Yefei Zhou, and Xinglong Wang. 2021. “Nanopore-Based Direct RNA-Sequencing Reveals a High-Resolution Transcriptional Landscape of Porcine Reproductive and Respiratory Syndrome Virus.” Viruses 13: 2531. https://doi.org/10.3390/v13122531

[299] Hawes, Kailin, Benjamin Greene, Zachary A. Weishampel, Paul A. Beare, Sarah van Tol, Paul Schaughency, Skyler Kuhn, Alison J. Peel, Vincent J. Munster, and Claude K. Yinda. 2025. “Evaluation of a Probe-Based Enrichment Protocol for Nanopore Sequencing of Zoonotic Viruses.” Viruses 17: 1465. https://doi.org/10.3390/v17111465

[300] Bravo, Jonathan E., Kimberly J. Newsom, Noelle Noyes, and Christina Boucher. 2025. “Methods, Applications, and Computational Challenges in Bait Capture Enrichment.” Cell Reports Methods 5: 101174. https://doi.org/10.1016/j.crmeth.2025.101174

[301] Guo, Zhihao, Yanwen Shao, Lu Tan, and Runsheng Li. 2026. “Protocol for Generating Native and Unmodified Bacterial RNA for Nanopore Direct RNA Sequencing and Downstream Analysis.” STAR Protocols 7: 104279. https://doi.org/10.1016/j.xpro.2025.104279

[302] Naarmann-de Vries, Isabel S., Enio Gjerga, Catharina L. A. Gandor, Christoph Dieterich. 2023. “Adaptive Sampling for Nanopore Direct RNA-sequencing.” RNA 29: 1939–1949. https://doi.org/10.1261/rna.079727.123

[303] Martin, Samuel, Darren Heavens, Yuxuan Lan, Samuel Horsfield, Matthew D. Clark, and Richard M. Leggett. 2022. “Nanopore Adaptive Sampling: A Tool for Enrichment of Low Abundance Species in Metagenomic Samples.” Genome Biology 23: 11. https://doi.org/10.1186/s13059-021-02582-x

[304] DeBruyne, Nicole, Feng Wang, Yang Xu, and Lan Lin. 2025. “Evaluating the Potential and Limitations of Nanopore Adaptive Sampling for Targeted Transcriptome Sequencing.” Genome Biology 26: 349. https://doi.org/10.1186/s13059-025-03813-1

[305] Yang, Lang, Yanfeng Lin, Peihan Li, Kaiying Wang, Jinhui Li, Yuqi Liu, Xiaochen Bo, Ming Ni, Peng Li, and Hongbin Song. 2025. “A Comprehensive Benchmarking of Adaptive Sampling Tools for Nanopore Sequencing.” Genome Biology 26: 281. https://doi.org/10.1186/s13059-025-03729-w

[306] Kovaka, Sam, Yunfan Fan, Bohan Ni, Winston Timp, and Michael C. Schatz. 2021. “Targeted Nanopore Sequencing by Real-Time Mapping of Raw Electrical Signal With UNCALLED.” Nature Biotechnology 39: 431–441. https://doi.org/10.1038/s41587-020-0731-9

[307] Zhang, Haowen, Haoran Li, Chirag Jain, Haoyu Cheng, Kin Fai Au, Heng Li, and Srinivas Aluru. 2021. “Real-Time Mapping of Nanopore Raw Signals.” Bioinformatics 37: i477–i483. https://doi.org/10.1093/bioinformatics/btab264

[308] Payne, Alexander, Nadine Holmes, Thomas Clarke, Rory Munro, Bisrat J. Debebe, and Matthew Loose. 2021. “Readfish Enables Targeted Nanopore Sequencing of Gigabase-Sized Genomes.” Nature Biotechnology 39: 442–450. https://doi.org/10.1038/s41587-020-00746-x

[309] Ulrich, Jens-Uwe, Ahmad Lutfi, Kilian Rutzen, and Bernhard Y. Renard. 2022. “ReadBouncer: Precise and Scalable Adaptive Sampling for Nanopore Sequencing.” Bioinformatics 38: i153–i160. https://doi.org/10.1093/bioinformatics/btac223

[310] Edwards, Harrison S., Raga Krishnakumar, Anupama Sinha, Sara W. Bird, Kamlesh D. Patel, and Michael S. Bartsch. 2019. “Real-Time Selective Sequencing With RUBRIC: Read Until With Basecall and Reference-Informed Criteria.” Scientific Reports 9: 11475. https://doi.org/10.1038/s41598-019-47857-3

[311] Bao, Yuwei, Jack Wadden, John R. Erb-Downward, Piyush Ranjan, Weichen Zhou, Torrin L. McDonald, Ryan E. Mills, et al. 2021. “SquiggleNet: Real-Time, Direct Classification of Nanopore Signals.” Genome Biology 22: 298. https://doi.org/10.1186/s13059-021-02511-y

[312] Wang, Jiaxu, Lin Yang, Anthony Cheng, Cheng-Yong Tham, Wenting Tan, Jefferson Darmawan, Paola Florez de Sessions, and Yue Wan. 2024. “Direct RNA Sequencing Coupled With Adaptive Sampling Enriches RNAs of Interest in the Transcriptome.” Nature Communications 15: 481. https://doi.org/10.1038/s41467-023-44656-3

[313] Loose, Matthew, Sunir Malla, and Michael Stout. 2016. “Real-Time Selective Sequencing Using Nanopore Technology.” Nature Methods 13: 751–754. https://doi.org/10.1038/nmeth.3930

[314] Tan, Shaoyuan, Cheryl M. T. Dvorak, and Michael P. Murtaugh. 2019. “Rapid, Unbiased PRRSV Strain Detection Using MinION Direct RNA Sequencing and Bioinformatics Tools.” Viruses 11: 1132. https://doi.org/10.3390/v11121132

[315] Ji, Chun-Miao, Xiao-Yin Feng, Yao-Wei Huang, and Rui-Ai Chen. 2024. “The Applications of Nanopore Sequencing Technology in Animal and Human Virus Research.” Viruses 16: 798. https://doi.org/10.3390/v16050798

[316] Maździarz, Mateusz A., Katarzyna Krawczyk, Ewa Lepiarczyk, Łukasz Paukszto, Jakub Sawicki, and Marta Majewska. 2026. “Epitranscriptomic Signatures of m⁵C, m⁶A, and Pseudouridine in COVID-19 Reveal Host RNA Modifications Involved in Viral Pathogenesis.” Microbiology Spectrum 14: e02561–02525. https://doi.org/10.1128/spectrum.02561-25

[317] Chen, Pin, Zepeng Sun, Jiawei Wang, Xinlong Liu, Yun Bai, Jiang Chen, Anna Liu, et al. 2023. “Portable Nanopore-Sequencing Technology: Trends in Development and Applications.” Frontiers in Microbiology 14: 1043967. https://doi.org/10.3389/fmicb.2023.1043967

[318] Zheng, Peijie, Chuntao Zhou, Yuemin Ding, Bin Liu, Liuyi Lu, Feng Zhu, and Shiwei Duan. 2023. “Nanopore Sequencing Technology and Its Applications.” MedComm 4: e316. https://doi.org/10.1002/mco2.316

[319] Marcolungo, Luca, Alessandro Passera, Simone Maestri, Elena Segala, Massimiliano Alfano, Francesca Gaffuri, Giovanni Marturano, Paola Casati, Piero A. Bianco, and Massimo Delledonne. 2022. “Real-Time On-Site Diagnosis of Quarantine Pathogens in Plant Tissues by Nanopore-Based Sequencing.” Pathogens 11: 199. https://doi.org/10.3390/pathogens11020199

[320] Al kadi, Mohamad, Eiji Ishii, Tat Truong Dang, Daisuke Motooka, Shigeaki Matsuda, Tetsuya Iida, Toshio Kodama, Daisuke Okuzak. 2021. “Direct RNA Sequencing Unfolds the Complex Transcriptome of Vibrio Parahaemolyticus.” mSystems 6: e00996–00921. https://doi.org/10.1128/mSystems.00996-21

[321] Pitt, Miranda E., Son H. Nguyen, Tânia P. S. Duarte, Haotian Teng, Mark A. T. Blaskovich, Matthew A. Cooper, and Lachlan J. M. Coin. 2020. “Evaluating the Genome and Resistome of Extensively Drug-Resistant Klebsiella Pneumoniae Using Native DNA and RNA Nanopore Sequencing.” Gigascience 9: giaa002. https://doi.org/10.1093/gigascience/giaa002

[322] Forquet, Raphaël, Xuejiao Jiang, William Nasser, Florence Hommais, Sylvie, Reverchon, and Sam Meyer. 2022. “Mapping the Complex Transcriptional Landscape of the Phytopathogenic Bacterium Dickeya dadantii.” mBio 13: e00524–00522. https://doi.org/10.1128/mbio.00524-22

[323] Iturbe, Pablo, Alvaro San Martín, Hiroshi Hamamoto, Marina Marcet-Houben, Toni Galbaldón, Cristina Solano, and Iñigo Lasa. 2024. “Noncontiguous Operon Atlas for the Staphylococcus aureus Genome.” Microlife 5: uqae007. https://doi.org/10.1093/femsml/uqae007

[324] Mattick, John S. A., Robin E. Bromley, Kaylee J. Watson, Ricky S. Adkins, Christopher I. Holt, Jarrett F. Lebov, Benjamin C. Sparklin, Tyonna S. Tyson, David A. Rasko, and Julie C. Dunning Hotopp. 2024. “Deciphering Transcript Architectural Complexity in Bacteria and Archaea.” mBio 15: e02359–02324. https://doi.org/10.1128/mbio.02359-24

[325] Smith, Andrew M., Miten Jain, Logan Mulroney, Daniel R. Garalde, Mark Akeson. 2019. “Reading Canonical and Modified Nucleobases in 16S Ribosomal RNA Using Nanopore Native RNA Sequencing.” Plos One 14: e0216709. https://doi.org/10.1371/journal.pone.0216709

[326] Delgado-Tejedor, Anna, Oguzhan Rebeca Medina, Luca Begik, Judith Cozzuto, Sandra López, Julia Blanco, Eva Maria Ponomarenko, and Novoa . 2024. “Native RNA Nanopore Sequencing Reveals Antibiotic-Induced Loss of rRNA Modifications in the A- and P-Sites.” Nature Communications 15: 10054. https://doi.org/10.1038/s41467-024-54368-x

[327] Riquelme-Barrios, Sebastián, Siobhan A. Leonardo Vásquez-Camus, Korinna Cusack, Dimitar Plamenov Burdack, G. Nur Petrov, Stefanie Yeşiltaç-Tosun, Pascal Kaiser, Kirsten Giehr, and Jung . 2025. “Direct RNA Sequencing of the Escherichia coli Epitranscriptome Uncovers Alterations Under Heat Stress.” Nucleic Acids Research 53: gkaf175. https://doi.org/10.1093/nar/gkaf175

[328] Guo, Zhihao, Yanwen Shao, Lu Tan, Beifang Lu, Xin Deng, Sheng Chen, and Runsheng Li. 2025. “Enhanced Detection of RNA Modifications in Escherichia coli Utilizing Direct RNA Sequencing.” Cell Reports Methods 5: 101168. https://doi.org/10.1016/j.crmeth.2025.101168

[329] Grünberger, Felix, Michael Jüttner, Robert Knüppel, Sébastien Ferreira-Cerca, and Dina Grohmann. 2023. “Nanopore-Based RNA Sequencing Deciphers the Formation, Processing, and Modification Steps of rRNA Intermediates in Archaea.” RNA 29: 1255–1273. https://doi.org/10.1261/rna.079636.123

[330] Pust, Marie-Madlen, Colin Francis Davenport, Burkhard Lutz Wiehlmann, and Tümmler . 2022. “Direct RNA Nanopore Sequencing of Pseudomonas aeruginosa Clone C Transcriptomes.” Journal of Bacteriology 204: e00418–e00421. https://doi.org/10.1128/JB.00418-21

[331] Frommeyer, Yannick N., Nicolas O. Gomez, Matthias Preusse, Alejandro Arce-Rodriguez, Kerstin Neubauer, Benedikt Kennepohl, Julius Witte, et al. 2025. “tRNA Hydroxylation Is an Epitranscriptomic Modulator of Metabolic States Affecting Pseudomonas aeruginosa Pathogenicity.” Nucleic Acids Research 53: gkaf719. https://doi.org/10.1093/nar/gkaf719

[332] Zhang, Hailei, Huan Zhong, Xufeng Wang, Shoudong Zhang, Xiaojian Shao, Hao Hu, Zhiling Yu, Zongwei Cai, Xuemei Chen, and Yiji Xia. 2021. “Use of NAD Tagseq II to Identify Growth Phase-Dependent Alterations in E. coli RNA NAD+ Capping.” Proceedings of the National Academy of Sciences 118: e2026183118. https://doi.org/10.1073/pnas.2026183118

[333] Dmytrenko, Oleg, Biao Yuan, Kadin T. Crosby, Max Krebel, Xiye Chen, Jakub S. Nowak, Andrzej Chramiec-Głąbik, et al. 2026. “RNA-Triggered Cas12a3 Cleaves tRNA Tails to Execute Bacterial Immunity.” Nature 649: 1312–1321. https://doi.org/10.1038/s41586-025-09852-9

[334] Song, Junwei, Li-an Lin, Chao Tang, Chuan Chen, Qingxin Yang, Dan Zhang, Yuancun Zhao, et al. 2025. “DEMINERS Enables Clinical Metagenomics and Comparative Transcriptomic Analysis by Increasing Throughput and Accuracy of Nanopore Direct RNA Sequencing.” Genome Biology 26: 76. https://doi.org/10.1186/s13059-025-03536-3

[335] Yang, Manyun, Alyssa Cousineau, Xiaobo Liu, Yaguang Luo, Daniel Sun, Shaohua Li, Tingting Gu, et al. 2020. “Direct Metatranscriptome RNA-Seq and Multiplex RT-PCR Amplicon Sequencing on Nanopore MinION—Promising Strategies for Multiplex Identification of Viable Pathogens in Food.” Frontiers in Microbiology 11: 514. https://doi.org/10.3389/fmicb.2020.00514

[336] Poursalavati, Abdonaser, Vahid J. Javaran, Isabelle Laforest-Lapointe, and Mamadou L. Fall. 2023. “Soil Metatranscriptomics: An Improved RNA Extraction Method Toward Functional Analysis Using Nanopore Direct RNA Sequencing.” Phytobiomes Journal 7: 42–54. https://doi.org/10.1094/PBIOMES-12-22-0108-TA

[337] Semmouri, Ilias, Karel A. C. De Schamphelaere, Jan Colin R. Mees, Jana Janssen, and Asselman . 2020. “Evaluating the Potential of Direct RNA Nanopore Sequencing: Metatranscriptomics Highlights Possible Seasonal Differences in a Marine Pelagic Crustacean Zooplankton Community.” Marine Environmental Research 153: 104836. https://doi.org/10.1016/j.marenvres.2019.104836

[338] Zhang, Huakun, and Yiliang Ding. 2025. “RNA Structure: Function and Application in Plant Biology.” Annual Review of Plant Biology 76: 115–141. https://doi.org/10.1146/annurev-arplant-083123-055521

[339] Reddy, Anireddy S. N., Yamile Marquez, Maria Kalyna, Andrea Barta. 2013. “Complexity of the Alternative Splicing Landscape in Plants.” The Plant Cell 25: 3657–3683. https://doi.org/10.1105/tpc.113.117523

[340] Reddy, Anireddy S. N., Jie Huang, Naeem H. Syed, Asa Ben-Hur, Lianfeng Dong, and Gu . 2020. “Decoding Co-/Post-Transcriptional Complexities of Plant Transcriptomes and Epitranscriptome Using Next-Generation Sequencing Technologies.” Biochemical Society Transactions 48: 2399–2414. https://doi.org/10.1042/BST20190492

[341] Wang, Wei, Haosong Guo, Jianxin Bian, Fa Cui, and Xiaoqin Liu. 2025. “Identification of Post-Transcriptional Regulation Reveals Complexity in Peanut Pod Development by Direct RNA.” Abiotech 6: 554–568. https://doi.org/10.1007/s42994-025-00224-5

[342] Kollist, Hannes, Sara I. Zandalinas, Soham Sengupta, Maris Nuhkat, Jaakko Kangasjärvi, and Ron Mittler. 2019. “Rapid Responses to Abiotic Stress: Priming the Landscape for the Signal Transduction Network.” Trends in Plant Science 24: 25–37. https://doi.org/10.1016/j.tplants.2018.10.003

[343] Hu, Jianzhong, Jing Cai, Su Jung Park, Kwanuk Lee, Yuxia Li, Yao Chen, Jae-Young Yun, Tao Xu, and Hunseung Kang. 2021. “N6-Methyladenosine mRNA Methylation Is Important for Salt Stress Tolerance in Arabidopsis.” The Plant Journal 106: 1759–1775. https://doi.org/10.1111/tpj.15270

[344] Zhang, Shoudong, Zhixia Xiao, Ailin Liu, Dongpeng Ren, Shengjie Chen, Hanxue Zhang, Li Zhang, Zhili Wang, Jun Yang, and Hon-Ming Lam. 2025. “Salt Stress Adaptations in Soybean Involve Alterations in pre-mRNA Processing.” Plant, Cell & Environment 49: 4000–4014. https://doi.org/10.1111/pce.15515

[345] Qian, Qian, Yiming Zhou, Yuli Gan, Yongqing Ling, Jiantao Tan, Mengyuan Sheng, Xin Peng, Degui Zhou, Zhonghui Zhang, and Qi Liu. 2025. “Comprehensive Profiling of the Epitranscriptome and Translatome in Rice Seedlings Under Salt Stress.” Plant Physiology 199: kiaf481. https://doi.org/10.1093/plphys/kiaf481

[346] He, Shidong, Hui Wang, Minghao Lv, Shun Li, Junhui Li, Rongxin Song, Shaolong Wang, Lijun Jiang, Shuxin Zhang, and Xiang Li. 2024. “Nanopore Direct RNA Sequencing Reveals the Short-Term Salt Stress Response in Maize Roots.” Plants 13: 405. https://doi.org/10.3390/plants13030405

[347] Song, Zhihua, Qing Yang, Biying Dong, Shengjie Wang, Jingyi Xue, Ni Liu, Xiaomiao Zhou, Na Li, Abhaya M. Dandekar, and Lailiang Cheng. 2025. “Nanopore RNA Direct Sequencing Identifies That m⁶A Modification Is Essential for Sorbitol-Controlled Resistance to Alternaria alternata in Apple.” Developmental Cell 60: 1439–1453.e1435. https://doi.org/10.1016/j.devcel.2024.12.033

[348] Furci, Leonardo, Jérémy Berthelier, and Hidetoshi Saze. 2024. “RNA N6-Adenine Methylation Dynamics Impact Hyaloperonospora arabidopsidis Resistance in Arabidopsis.” Plant Physiology 196: 745–753. https://doi.org/10.1093/plphys/kiae373

[349] Lee, Sung-Il, and Nam-Soo Kim. 2014. “Transposable Elements and Genome Size Variations in Plants.” Genomics & Informatics 12: 87. https://doi.org/10.5808/GI.2014.12.3.87

[350] Negi, Pooja, Archana N. Rai, and Penna Suprasanna. 2016. “Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response.” Frontiers in Plant Science 7: 1448. https://doi.org/10.3389/fpls.2016.01448

[351] Tao, Xiao-Yuan, Shou-Li Feng, Lu Yuan, Yan-Jun Li, Xin-Jia Li, Xue-Ying Guan, Zhong-Hua Chen, and Sheng-Chun Xu. 2025. “Harnessing Transposable Elements for Plant Functional Genomics and Genome Engineering.” Trends in Plant Science 30: 1130–1146. https://doi.org/10.1016/j.tplants.2025.03.007

[352] Tian, Xuehan, Ruipeng Wang, Zhenping Liu, Sifan Lu, Xinyuan Chen, Zeyu, Zhang, Fang Liu, Hongbin Li, Xianlong Zhang, and Maojun Wang. 2025. “Widespread Impact of Transposable Elements on the Evolution of Post-Transcriptional Regulation in the Cotton Genus Gossypium.” Genome Biology 26: 60. https://doi.org/10.1186/s13059-025-03534-5

[353] Hassan, Asmaa H., Morad M. Mokhtar, and Achraf El Allali. 2024. “Transposable Elements: Multifunctional Players in the Plant Genome.” Frontiers in Plant Science 14: 1330127. https://doi.org/10.3389/fpls.2023.1330127

[354] Botet, Ramon, and Joost J. B. Keurentjes. 2020. “The Role of Transcriptional Regulation in Hybrid Vigor.” Frontiers in Plant Science 11: 410. https://doi.org/10.3389/fpls.2020.00410

[355] Aufiero, Gaetano, Carmine Fruggiero, Davide D'Angelo, and Nunzio D'Agostino. 2024. “Homoeologs in Allopolyploids: Navigating Redundancy as Both an Evolutionary Opportunity and a Technical Challenge—A Transcriptomics Perspective.” Genes 15: 977. https://doi.org/10.3390/genes15080977

[356] Li, Mengdi, Meimei Hu, Yafang Xiao, Xiaoming Wu, and Jianbo Wang. 2022. “The Activation of Gene Expression and Alternative Splicing in the Formation and Evolution of Allopolyploid Brassica napus.” Horticulture Research 9: uhab075. https://doi.org/10.1093/hr/uhab075

[357] Yan, Xu, Xiyan Chen, Yangyang Li, Yuhan Li, Fei Wang, Jiaqi Zhang, Guogui, Ning, and Manzhu Bao. 2023. “The Abundant and Unique Transcripts and Alternative Splicing of the Artificially Autododecaploid London Plane (Platanus × Acerifolia).” International Journal of Molecular Sciences 24: 14486. https://doi.org/10.3390/ijms241914486

[358] Wu, Guangliang, Shangwei Yu, Junru Fu, Linjuan Ouyang, Lifang Hu, Jianmin Bian, Xiaorong Chen, Jie Xu, Dahu Zhou, and Haohua He. 2025. “Alternative Polyadenylation and Metabolic Profiling in YoUnveils Complexities Acrossung Panicle Development of Hybrid Rice and Its Parents.” Rice 18: 80. https://doi.org/10.1186/s12284-025-00834-z

[359] Park, Dayea, and Can Cenik. 2025. “Long-Read RNA Sequencing Reveals Allele-Specific N6-Methyladenosine Modifications.” Genome Research 35: 999–1011. https://doi.org/10.1101/2024.07.08.602538

[360] Wu, Zhe, Xiaofeng Fang, Danling Zhu, and Caroline Dean. 2020. “Autonomous Pathway: FLOWERING LOCUS C Repression Through an Antisense-Mediated Chromatin-Silencing Mechanism.” Plant Physiology 182: 27–37. https://doi.org/10.1104/pp.19.01009

[361] Nielsen, Mathias, Govind Menon, Yusheng Zhao, Eduardo Mateo-Bonmati, Philip Wolff, Shaoli Zhou, et al. 2024. “COOLAIR and PRC2 Function in Parallel to Silence FLC During Vernalization.” Proceedings of the National Academy of Sciences 121: e2311474121. https://doi.org/10.1073/pnas.2311474121

[362] Parker, Matthew T., Katarzyna Knop, Vasiliki Zacharaki, Anna V. Sherwood, Daniel Tomé, Xuhong Yu, Pascal G. P. Martin, et al. 2021. “Widespread Premature Transcription Termination of Arabidopsis thaliana NLR Genes by the Spen Protein FPA.” eLife 10: e65537. https://doi.org/10.7554/eLife.65537

[363] Xu, Tao, Xiaowei Wu, Chui Eng Wong, Sheng Fan, Yu Zhang, Songyao Zhang, Zhe Liang, Hao Yu, Lisha Shen. 2022. “FIONA1-mediated m⁶A Modification Regulates the Floral Transition in Arabidopsis.” Advanced Science 9: 2103628. https://doi.org/10.1002/advs.202103628

[364] Sun, Bin, Kaushal Kumar Bhati, Peizhe Song, Ashleigh Edwards, Louise Petri, Valdeko Kruusvee, Anko Blaakmeer, et al. 2022. “FIONA1-Mediated Methylation of the 3′UTR of FLC Affects FLC Transcript Levels and Flowering in Arabidopsis.” PLoS Genetics 18: e1010386. https://doi.org/10.1371/journal.pgen.1010386

[365] Schiksnis, Erin C., Ian A. Nicastro, and Amy E. Pasquinelli. 2024. “Full-Length Direct RNA Sequencing Reveals Extensive Remodeling of RNA Expression, Processing and Modification in Aging Caenorhabditis elegans.” Nucleic Acids Research 52: 13896–13913. https://doi.org/10.1093/nar/gkae1064

[366] Bo, Jing, Wenyu Fang, Jing Wang, Shunping He, and Liandong Yang. 2025. “High Resolution of Full-Length RNA Sequencing Deciphers Massive Transcriptome Complexity During Zebrafish Embryogenesis.” BMC Biology 23: 155. https://doi.org/10.1186/s12915-025-02271-2

[367] Jiang, Chengfei, Ping Li, and Haiming Cao. 2025. “Unveiling Tissue-Specific RNA Landscapes in Mouse Organs During FastPamela, Michael Ante, Alexandering and Feeding Using Nanopore Direct RNA Sequencing.” Advanced Science 12: 2408054. https://doi.org/10.1002/advs.202408054

[368] Guo, Wenbing, Zhijun Ren, Xiang Huang, Jiayin Liu, Jingwen Shao, Xiaojun Ma, Chuanchuan Wei, et al. 2025. “Single-Molecule ^m6A Detection Empowered by Endogenous Labeling Unveils Complexities Across RNA Isoforms.” Molecular Cell 85: 1233–1246.e1237. https://doi.org/10.1016/j.molcel.2025.01.014

[369] Liao, Yaya, Zifeng Ding, Xiaoyun Chen, Chao Yin, Bin Yang, Qiang Yang, and Yuyun Xing. 2025. “Transcriptome-Wide m⁶A Landscape Across Diverse Porcine Tissues Revealed by Nanopore Direct RNA Sequencing.” Frontiers in Genetics 16: 1725608. https://doi.org/10.3389/fgene.2025.1725608

[370] Choquet, Karine, Louis-Philippe Chaumont, Simon Bache, Autum R. Baxter-Koenigs, and L. Stirling Churchman. 2025. “Genetic Regulation of Nascent RNA Maturation Revealed by Direct RNA Nanopore Sequencing.” Genome Research 35: 712–724. https://doi.org/10.1101/gr.279203.124

[371] Santos-Rodriguez, Gabriela, Akanksha Srivastava, Agin Ravindran, Favour O. Oyelami, Chi Kin, Pallavi Gupta, Jeanette Villanueva, et al. 2026. “Isoform-Specific m⁶A Deposition and Coordinated Splicing Shape Mammalian Transcriptome Evolution.” Nature Communications 17: 5075. https://doi.org/10.1038/s41467-026-72124-1

[372] Cruciani, Sonia, Anna Delgado-Tejedor, Leszek P. Pryszcz, Rebeca Medina, Laia Llovera, and Eva Maria Novoa. 2025. “De Novo Basecalling of RNA Modifications at Single Molecule and Nucleotide Resolution.” Genome Biology 26: 38. https://doi.org/10.1186/s13059-025-03498-6

[373] Teng, Haotian, Marcus Stoiber, Ziv Bar-Joseph, and Carl Kingsford. 2024. “Detecting m⁶A RNA Modification From Nanopore Sequencing Using a Semisupervised Learning Framework.” Genome Research 34: 1987–1999. https://doi.org/10.1101/gr.278960.124

[374] Naarmann-de Vries, Isabel S., Jessica Eschenbach, and Christoph Dieterich. 2022. “Improved Nanopore Direct RNA Sequencing of Cardiac Myocyte Samples by Selective mt-RNA Depletion.” Journal of Molecular and Cellular Cardiology 163: 175–186. https://doi.org/10.1016/j.yjmcc.2021.10.010

[375] Müller, Torsten, Etienne Boileau, Sweta Talyan, Dorothea Kehr, Karl Varadi, Martin Busch, Patrick Most, Jeroen Krijgsveld, and Christoph Dieterich. 2021. “Updated and Enhanced Pig Cardiac Transcriptome Based on Long-Read RNA Sequencing and Proteomics.” Journal of Molecular and Cellular Cardiology 150: 23–31. https://doi.org/10.1016/j.yjmcc.2020.10.005

[376] Roach, Nathan P., Norah Sadowski, Amelia F. Alessi, Winston Timp, James Taylor, John K. Kim. 2020. “The Full-Length Transcriptome of C. elegans Using Direct RNA Sequencing.” Genome Research 30: 299–312. https://doi.org/10.1101/gr.251314.119

[377] Bohn, Patrick, Anne-Sophie Gribling-Burrer, Uddhav B. Ambi, and Redmond P. Smyth. 2023. “Nano-DMS-MaP Allows Isoform-Specific RNA Structure Determination.” Nature Methods 20: 849–859. https://doi.org/10.1038/s41592-023-01862-7

[378] de Jong, Lucy C., Simone Cree, Vanessa Lattimore, George A. R. Wiggins, Amanda B. Spurdle, Allison Miller, Martin A. Kennedy, Logan C. Walker, and Investigators kConFab. 2017. “Nanopore Sequencing of Full-Length BRCA1 mRNA Transcripts Reveals Co-Occurrence of Known Exon Skipping Events.” Breast Cancer Research 19: 127. https://doi.org/10.1186/s13058-017-0919-1

[379] Maggi, Jordi, Jiradet Silke Feil, Kevin Gloggnitzer, Ruxandra Maggi, Christina Bachmann-Gagescu, Samuel Gerth-Kahlert, Wolfgang Koller, and Berger . 2024. “Nanopore Deep Sequencing as a Tool to Characterize and Quantify Aberrant Splicing Caused by Variants in Inherited Retinal Dystrophy Genes.” International Journal of Molecular Sciences 25: 9569. https://doi.org/10.3390/ijms25179569

[380] Ozaki, Kokoro, Takashi Irioka, Shohei Noma, Akira Machida, Moe Fukunaga, Tatsuro Murano, Chitose Takahashi, et al. 2025. “Isoform Analysis of Heterozygous Putative Splicing Variants at the Allele Level Using Nanopore Long-Read Sequencing.” Scientific Reports 15: 29001. https://doi.org/10.1038/s41598-025-14566-z

[381] He, Jingni, Devika Ganesamoorthy, Jessie J. Y. Chang, Jianshu Zhang, Sharon L. Trevor, Kristen S. Gibbons, Stephen J. McPherson, et al. 2025. “Utilizing Nanopore Direct RNA Sequencing of Blood From Patients with Sepsis for Discovery of Co- and Post-Transcriptional Disease Biomarkers.” BMC Infectious Diseases 25: 692. https://doi.org/10.1186/s12879-025-11078-z

[382] Leshkowitz, Dena, Yael Merav Kedmi, David Fried, Hadas Pilzer, Elena Keren-Shaul, Bareket Ainbinder, and Dassa . 2022. “Exploring Differential Exon Usage via Short- and Long-Read RNA Sequencing Strategies.” Open Biology 12: 220206. https://doi.org/10.1098/rsob.220206

[383] Tian, Luyi, Jafar S. Jabbari, Rachel Thijssen, Quentin Gouil, Shanika L. Amarasinghe, Oliver Voogd, Hasaru Kariyawasam, et al. 2021. “Comprehensive Characterization of Single-Cell Full-Length Isoforms in Human and Mouse with Long-Read Sequencing.” Genome Biology 22: 310. https://doi.org/10.1186/s13059-021-02525-6

[384] Begik, Oguzhan, Gregor Diensthuber, Huanle Liu, Anna Delgado-Tejedor, Cassandra Kontur, Adnan Muhammad Niazi, Eivind Valen, et al. 2023. “Nano3P-seq: Transcriptome-Wide Analysis of Gene Expression and Tail Dynamics Using End-Capture Nanopore cDNA Sequencing.” Nature Methods 20: 75–85. https://doi.org/10.1038/s41592-022-01714-w

[385] Passmore, Lori A., and Jeff Coller. 2022. “Roles of mRNA Poly(A) Tails in Regulation of Eukaryotic Gene Expression.” Nature Reviews Molecular Cell Biology 23: 93–106. https://doi.org/10.1038/s41580-021-00417-y

[386] Begik, Oguzhan, Leszek P. Pryszcz, Adnan Muhammad Niazi, Eivind Valen, and Eva Maria Novoa. 2025. “Nano3P-Seq: Charting the Coding and Noncoding Transcriptome at Single-Molecule Resolution.” Nature Protocols 20: 3607–3628. https://doi.org/10.1038/s41596-025-01205-0

[387] Abebe, Jonathan S., Alexander M. Price, Katharina E. Hayer, Ian Mohr, Matthew D. Weitzman, Angus C. Wilson, and Daniel P. Depledge. 2022. “DRUMMER-Rapid Detection of RNA Modifications Through Comparative Nanopore Sequencing.” Bioinformatics 38: 3113–3115. https://doi.org/10.1093/bioinformatics/btac274

[388] Begik, Oguzhan, John S. Mattick, and Eva Maria Novoa. 2022. “Exploring the Epitranscriptome by Native RNA Sequencing.” RNA 28: 1430–1439. https://doi.org/10.1261/rna.079404.122

[389] Mulroney, Logan, Ewan Birney, Tommaso Leonardi, and Francesco Nicassio. 2023. “Using Nanocompore to Identify RNA Modifications from Direct RNA Nanopore Sequencing Data.” Current Protocols 3: e683. https://doi.org/10.1002/cpz1.683

[390] Makhamreh, Amr, Sepideh Tavakoli, Ali Fallahi, Xinqi Kang, Howard Gamper, Mohammad Nabizadehmashhadtoroghi, Miten Jain, Ya-Ming Hou, Sara H. Rouhanifard, and Meni Wanunu. 2024. “Nanopore Signal Deviations From Pseudouridine Modifications in RNA Are Sequence-Specific: Quantification Requires Dedicated Synthetic Controls.” Scientific Reports 14: 22457. https://doi.org/10.1038/s41598-024-72994-9

[391] Mitschka, Sibylle, and Christine Mayr. 2022. “Context-Specific Regulation and Function of mRNA Alternative Polyadenylation.” Nature Reviews Molecular Cell Biology 23: 779–796. https://doi.org/10.1038/s41580-022-00507-5

[392] Ren, Fanggang, Na Zhang, Lan Zhang, Eric Miller, and Jeffrey J. Pu. 2020. “Alternative Polyadenylation: A New Frontier in Post Transcriptional Regulation.” Biomarker Research 8: 67. https://doi.org/10.1186/s40364-020-00249-6

[393] Gruber, Andreas J., and Mihaela Zavolan. 2019. “Alternative Cleavage and Polyadenylation in Health and Disease.” Nature Reviews Genetics 20: 599–614. https://doi.org/10.1038/s41576-019-0145-z

[394] Zhang, Ying, Zikun Huang, Weiqing Lu, and Zhaoyong Liu. 2025. “Alternative Cleavage and Polyadenylation: Key Regulatory Mechanisms in Health and Disease.” RNA Biology 22: 1–33. https://doi.org/10.1080/15476286.2025.2529033

[395] Blake, Davia, and Kristen W. Lynch. 2021. “The Three As: Alternative Splicing, Alternative Polyadenylation and Their Impact on Apoptosis in Immune Function.” Immunological Reviews 304: 30–50. https://doi.org/10.1111/imr.13018

[396] Vlasenok, Maria, Sergey Margasyuk, and Dmitri D. Pervouchine. 2023. “Transcriptome Sequencing Suggests That Pre-mRNA Splicing Counteracts Widespread Intronic Cleavage and Polyadenylation.” NAR Genomics and Bioinformatics 5: lqad051. https://doi.org/10.1093/nargab/lqad051

[397] Obeng, Esther A., Connor Stewart, and Omar Abdel-Wahab. 2019. “Altered RNA Processing in Cancer Pathogenesis and Therapy.” Cancer Discovery 9: 1493–1510. https://doi.org/10.1158/2159-8290.CD-19-0399

[398] Masamha, Chioniso P., and Eric J. Wagner. 2018. “The Contribution of Alternative Polyadenylation to the Cancer Phenotype.” Carcinogenesis 39: 2–10. https://doi.org/10.1093/carcin/bgx096

[399] Stopa, Victoria, Dimitra Dafou, Korina Karagianni, A. Yaël Nossent, Rosienne, Farrugia, Yvan Devaux, and Miron Sopic. 2025. “Epitranscriptomics in Atherosclerosis: Unraveling RNA Modifications, Editing and Splicing and Their Implications in Vascular Disease.” Vascular Pharmacology 159: 107496. https://doi.org/10.1016/j.vph.2025.107496

[400] Huang, Shanhe, Zonglin Li, Weilong Lin, Ruihui Xie, and Hai Huang. 2025. “RNA Epigenetics in Cancer: Current Knowledge and Therapeutic Implications.” MedComm 6: e70322. https://doi.org/10.1002/mco2.70322

[401] Barbieri, Isaia, and Tony Kouzarides. 2020. “Role of RNA Modifications in Cancer.” Nature Reviews Cancer 20: 303–322. https://doi.org/10.1038/s41568-020-0253-2

[402] Qiu, Lei, Qian Jing, Yanbo Li, and Junhong Han. 2023. “RNA Modification: Mechanisms and Therapeutic Targets.” Molecular Biomedicine 4: 25. https://doi.org/10.1186/s43556-023-00139-x

[403] Pilala, Katerina-Marina, Konstantina Panoutsopoulou, Maria-Alexandra Papadimitriou, Konstantinos Soureas, Andreas Scorilas, and Margaritis Avgeris. 2025. “Exploring the Methyl-Verse: Dynamic Interplay of Epigenome and m⁶A Epitranscriptome.” Molecular Therapy 33: 447–464. https://doi.org/10.1016/j.ymthe.2024.12.003

[404] Teng, Pai-Chi, Yanwen Liang, Aliaksandr A. Yarmishyn, Yu-Jer Hsiao, Ting-Yi Lin, Tzu-Wei Lin, Yuan-Chi Teng, et al. 2021. “RNA Modifications and Epigenetics in Modulation of Lung Cancer and Pulmonary Diseases.” International Journal of Molecular Sciences 22: 10592. https://doi.org/10.3390/ijms221910592

[405] Liu, Chuwei, Heng Liang, Arabella H. Wan, Min Xiao, Lei Sun, Yiling Yu, Shijia Yan, et al. 2025. “Decoding the m⁶A Epitranscriptomic Landscape for Biotechnological Applications Using a Direct RNA Sequencing Approach.” Nature Communications 16: 798. https://doi.org/10.1038/s41467-025-56173-6

[406] Yi, Yang, Yanqiang Li, Qingshu Meng, Qiaqia Li, Fuxi Li, Bing Lu, Jiangchuan Shen, et al. 2021. “A PRC2-Independent Function for EZH2 in Regulating rRNA 2′-O Methylation and IRES-Dependent Translation.” Nature Cell Biology 23: 341–354. https://doi.org/10.1038/s41556-021-00653-6

[407] Frietze, Luke R., and Tao Pan. 2024. “Internal mRNA 2′-O-methyl Mapping by Nanopore Sequencing and Consequence on mRNA Stability and Role in Cancer.” Molecular Cell 84: 2215–2217. https://doi.org/10.1016/j.molcel.2024.05.020

[408] Wang, Lin, Ling Shi, Yonghao Liang, Judy Kin-Wing Ng, Chan Hoi Yin, Lingyi Wang, Jinpao Hou, et al. 2023. “Dissecting the Effects of METTL3 on Alternative Splicing in Prostate Cancer.” Frontiers in Oncology 13: 1227016. https://doi.org/10.3389/fonc.2023.1227016

[409] Yi, Yang, Joshua Fry, Chaehyun Yum, Rui Wang, Siqi Wu, Sharath Narayan, Qi Liu, et al. 2025. “EZH2 Crosstalk With RNA Methylation Promotes Prostate Cancer Progression through Modulation of m⁶A Autoregulation Pathway.” The Journal of Clinical Investigation 136: e195840. https://doi.org/10.1172/JCI195840

[410] Petri, Belinda J., Kellianne M. Piell, Bailey L. Avila-Valdes, Christian G. Stanley, Laura J. Winkler, Johnny Tyler Brown, Rye Ulett, et al. 2025. “Integrated Nanopore and Short-Read RNA Sequencing Identifies Dysregulation of METTL3-m⁶A Modifications in Endocrine Therapy-Sensitive and Resistant Breast Cancer Cells.” Functional & integrative genomics 25: 149. https://doi.org/10.1007/s10142-025-01658-2

[411] Athanasopoulou, Konstantina, Panagiotis G. Adamopoulos, Panagiotis Tsiakanikas, Glykeria N. Daneva, Ioannis Prassas, George M. Yousef, Eleftherios P. Diamandis, and Andreas Scorilas. 2025. “Deciphering the m⁶A Epitranscriptomic Landscape of mRNAs in Breast Cancer Cells.” Molecular and Cellular Biology 45: 660–679. https://doi.org/10.1080/10985549.2025.2560956

[412] Athanasopoulou, Konstantina, Panagiotis G. Adamopoulos, Panagiotis Tsiakanikas, and Andreas Scorilas. 2025. “Exploring the m5C Epitranscriptome of mRNAs in Breast Cancer Cells Through Genome Engineering and Long-Read Sequencing Approaches.” Functional & Integrative Genomics 25: 136. https://doi.org/10.1007/s10142-025-01648-4

[413] Chen, Ziwei, Yingyu Guo, Zaifeng Zhang, Chang Li, Lili Zhang, Ye Liu, Gaoyuan Sun, Fei Xiao, Ru Feng, and Chunli Zhang. 2025. “mRNA m5C Alteration in Azacitidine Demethylation Treatment of Acute Myeloid Leukemia.” Molecular Carcinogenesis 64: 502–512. https://doi.org/10.1002/mc.23864

[414] Zhang, Zaifeng, Lili Zhang, Jiangtao Li, Ru Feng, Chang Li, Ye Liu, Gaoyuan Sun, Fei Xiao, and Chunli Zhang. 2024. “Comprehensive Analysis of m⁶A Methylome Alterations after Azacytidine Plus Venetoclax Treatment for Acute Myeloid Leukemia by Nanopore Sequencing.” Computational and Structural Biotechnology Journal 23: 1144–1153. https://doi.org/10.1016/j.csbj.2024.02.029

[415] Asnani, Mukta, Katharina E. Hayer, Ammar S. Naqvi, Sisi Zheng, Scarlett Y. Yang, Derek Oldridge, Fadia Ibrahim, et al. 2020. “Retention of CD19 Intron 2 Contributes to CART-19 Resistance in Leukemias With Subclonal Frameshift Mutations in CD19.” Leukemia 34: 1202–1207. https://doi.org/10.1038/s41375-019-0580-z

[416] Ang, Zhiwei Luca Paruzzo, Katharina E. Hayer, Carolin Schmidt, Manuel Torres Diz, Feng Xu, Urvi Zankharia, et al. 2023. “Alternative Splicing of Its 5′-UTR Limits CD20 mRNA Translation and Enables Resistance to CD20-Directed Immunotherapies.” Blood 142: 1724–1739. https://doi.org/10.1182/blood.2023020400

[417] Li, Yifei, Peng Jiao, Donghang Li, Yi Tian, Hexin Li, Gaoyuan Sun, Xiaonan Wu, et al. 2025. “Comprehensive Analysis of Aberrant m⁶A RNA Modifications Identifies Prognostic Biomarkers in Non-Small Cell Lung Cancer.” International Journal of Medical Sciences 22: 4396–4405. https://doi.org/10.7150/ijms.119651

[418] Sanchez-Delgado, Marta, Maurice Frank, Tomáš Šišmiš, Mustafa Kahraman, Alberto Daniel-Moreno, Emmika Mummery, Jessika Ceiler, et al. 2025. “Nanopore Based RNA Methylation Profiling of a Circulating Lung Cancer Biomarker.” Communications Medicine 5: 521. https://doi.org/10.1038/s43856-025-01235-5

[419] Zhang, Lili, Jian Cui, Jinxin Shi, Jiahui Cai, Tianhan Sun, Gaoyuan Sun, Yifei Li, et al. 2026. “Exon Skipping as a Potential Diagnostic Biomarker in Colorectal Cancer: An Integrated Epigenomic-Transcriptomic Analysis.” Human Genomics 20: 53. https://doi.org/10.1186/s40246-026-00931-0

[420] Krusnauskas, Raulas, Rytis Stakaitis, Giedrius Steponaitis, Kristian Almstrup, and Paulina Vaitkiene. 2023. “Identification and Comparison of m⁶A Modifications in Glioblastoma Non-Coding RNAs With MeRIP-seq and Nanopore dRNA-seq.” Epigenetics 18: 2163365. https://doi.org/10.1080/15592294.2022.2163365

[421] Steponaitis, Giedrius, Rugile Dragunaite, Rytis Stakaitis, Amit Sharma, Arimantas Tamasauskas, and Daina Skiriute. 2025. “m⁶A-lncRNA Landscape Highlights Reduced Levels of m⁶A Modification in Glioblastoma as Compared to Low-Grade Glioma.” Molecular Medicine 31: 195. https://doi.org/10.1186/s10020-025-01254-x

[422] Širvinskas, Dovydas, Giedrius Steponaitis, Rytis Stakaitis, Arimantas Tamašauskas, Paulina Vaitkienė, and Daina Skiriutė. 2023. “Antisense lncRNA CHROMR Is Linked to Glioma Patient Survival.” Frontiers in Molecular Biosciences 10: 1101953. https://doi.org/10.3389/fmolb.2023.1101953

[423] Liu, S. John, Martina Malatesta, Brian V. Lien, Parna Saha, Shivani S. Thombare, Sung Jun Hong, Leslie Pedraza, et al. 2020. “CRISPRi-based Radiation Modifier Screen Identifies Long Non-Coding RNA Therapeutic Targets in Glioma.” Genome Biology 21: 83. https://doi.org/10.1186/s13059-020-01995-4

[424] Lin, Gongbiao, Haoxi Cai, Yihong Hong, Min Yao, Weiwei Ye, Wenzhi Li, Wentao Liang, et al. 2024. “Implications of m5C Modifications in Ribosomal Proteins on Oxidative Stress, Metabolic Reprogramming, and Immune Responses in Patients with Mid-to-Late-Stage Head and Neck Squamous Cell Carcinoma: Insights From Nanopore Sequencing.” Heliyon 10: e34529. https://doi.org/10.1016/j.heliyon.2024.e34529

[425] Li, Hexin, Chang Li, Yuxiang Zhang, Weixing Jiang, Fubo Zhang, Xiaokun Tang, Gaoyuan Sun, et al. 2024. “Comprehensive Analysis of m⁶A Methylome and Transcriptome By Nanopore Sequencing in Clear Cell Renal Carcinoma.” Molecular Carcinogenesis 63: 677–687. https://doi.org/10.1002/mc.23680

[426] Lee, Joshua, Elizabeth A. Snell, Joanne Brown, Charlotte E. Booth, Rosamonde E. Banks, Daniel J. Turner, Naveen S. Vasudev, and Dimitris Lagos. 2024. “Long-Read RNA Sequencing of Archival Tissues Reveals Novel Genes and Transcripts Associated With Clear Cell Renal Cell Carcinoma Recurrence and Immune Evasion.” Genome Research 34: 1849–1864. https://doi.org/10.1101/gr.278801.123

[427] Crooks, Daniel R., Geetha Mariah Cawthon, Christina M. Fitzsimmons, Minervo Perez, Christopher J. Ricketts, Cathy D. Vocke, Ye Yang, et al. 2023. “Cryptic Splice Mutation in the Fumarate Hydratase Gene in Patients With Clinical Manifestations of Hereditary Leiomyomatosis and Renal Cell Cancer.” Human Molecular Genetics 32: 3135–3145. https://doi.org/10.1093/hmg/ddad131

[428] Zhang, Lili, Liying Zhou, Wenrui Xu, Pengjie Wu, Wen Chen, Hexin Li, Gaoyuan Sun, et al. 2025. “RNA m5C Modifications in the Development and Prognosis of Muscle-Invasive Bladder Cancer.” Molecular Carcinogenesis 64: 2017–2025. https://doi.org/10.1002/mc.70042

[429] Zhang, Lili, Ziwei Chen, Gaoyuan Sun, Chang Li, Pengjie Wu, Wenrui Xu, Hui Zhu, et al. 2024. “Dynamic Landscape of m⁶A Modifications and Related Post-Transcriptional Events in Muscle-Invasive Bladder Cancer.” Journal of Translational Medicine 22: 912. https://doi.org/10.1186/s12967-024-05701-x

[430] Fang, Yuanchang, Geng Chen, Feng Chen, En Hu, Xiuqing Dong, Zhenli Li, Lei He, et al. 2021. “Accurate Transcriptome Assembly by Nanopore RNA Sequencing Reveals Novel Functional Transcripts in Hepatocellular Carcinoma.” Cancer Science 112: 3555–3568. https://doi.org/10.1111/cas.15058

[431] Yoo, Yongjin, Sang-Yoon Park, Eun B. Jo, Minji Choi, Kyo W. Lee, Doopyo Hong, Sangmoon Lee, et al. 2021. “Overexpression of Replication-Dependent Histone Signifies a Subset of Dedifferentiated Liposarcoma With Increased Aggressiveness.” Cancers 13: 3122. https://doi.org/10.3390/cancers13133122

[432] Zhou, Bingqian, Ningdai Chen, Zheyi Chen, Shiyu Chen, Junyao Yang, Yingxia Zheng, and Lisong Shen. 2023. “Prmt5 Deficient Mouse B Cells Display RNA Processing Complexity and Slower Colorectal Tumor Progression.” European Journal of Immunology 53: 2250226. https://doi.org/10.1002/eji.202250226

[433] Adamopoulos, Panagiotis G., Konstantina Athanasopoulou, Panagiotis Tsiakanikas, and Andreas Scorilas. 2022. “A Comprehensive Nanopore Sequencing Methodology Deciphers the Complete Transcriptional Landscape of Cyclin-Dependent Kinase 4 (CDK4) in Human Malignancies.” The FEBS Journal 289: 712–729. https://doi.org/10.1111/febs.16201

[434] Chen, Yu, Yiqing Wang, Weisheng Chen, Zhengzhi Tan, Yuwei Song, Consortium Human Genome Structural Variation, Herbert Chen, and Zechen Chong. 2023. “Gene Fusion Detection and Characterization in Long-Read Cancer Transcriptome Sequencing Data With Fusionseeker.” Cancer Research 83: 28–33. https://doi.org/10.1158/0008-5472.CAN-22-1628

[435] Yi, Hyerim, Shu Zhang, Jason Swinderman, Yanbo Wang, Vishnupriya Kanakaveti, King L. Hung, Ivy Tsz-Lo Wong, et al. 2026. “EcDNA-borne Structural Variants Drive Oncogenic Fusion Transcript Amplification.” Cell 189: 906–921. https://doi.org/10.1016/j.cell.2025.12.009

[436] Li, Qin, Ziteng Li, Bing Chen, Jingjing Zhao, Hongwu Yu, Jia Hu, Hongyan Lai, et al. 2024. “RNA Splicing Junction Landscape Reveals Abundant Tumor-Specific Transcripts in Human Cancer.” Cell Reports 43: 114893. https://doi.org/10.1016/j.celrep.2024.114893

[437] Milenkovic, Ivan, Sonia Cruciani, Laia Llovera, Morghan C. Lucas, Rebeca Medina, Cornelius Pauli, Daniel Heid, et al. 2025. “Epitranscriptomic rRNA Fingerprinting Reveals Tissue-of-Origin and Tumor-Specific Signatures.” Molecular Cell 85: 177–190.e177. https://doi.org/10.1016/j.molcel.2024.11.014

[438] Li, Jiexin, Xiansong Wang, and Hongsheng Wang. 2024. “RNA Modifications in Long Non-Coding RNAs and Their Implications in Cancer Biology.” Bioorganic & Medicinal Chemistry 113: 117922. https://doi.org/10.1016/j.bmc.2024.117922

[439] Yang, Liqiong, Lu Tang, Qi Min, Hua Tian, Linwei Li, Yueshui Zhao, Xu Wu, et al. 2024. “Emerging Role of RNA Modification and Long Noncoding RNA Interaction in Cancer.” Cancer Gene Therapy 31: 816–830. https://doi.org/10.1038/s41417-024-00734-2

[440] Wei, Yongqi, Yin Li, and Chunlai Lu. 2023. “Exploring the Role of m⁶A Modification in Cancer.” Proteomics 23: 2200208. https://doi.org/10.1002/pmic.202200208

[441] Fanari, Oleksandra, Dylan Bloch, Yuchen Qiu, Michele Meseonznik, Dinara, Boyko, Amr Makhamreh, Meni Wanunu, and Sara H. Rouhanifard. 2025. “Pseudouridine Reprogramming in the Human T-Cell Epitranscriptome: From Primary to Immortalized States.” RNA 31: 1320–1334. https://doi.org/10.1261/rna.080633.125

[442] Jonkhout, Nicky, Julia Tran, Martin A. Smith, Nicole Schonrock, John S. Mattick, and Eva Maria Novoa. 2017. “The RNA Modification Landscape in Human Disease.” RNA 23: 1754–1769. https://doi.org/10.1261/rna.063503.117

[443] Zhang, Junjie, Shuilian Xie, Jingxiang Xu, Hui Liu, and Shaogui Wan. 2021. “Cancer Biomarkers Discovery of Methylation Modification With Direct High-Throughput Nanopore Sequencing.” Frontiers in Genetics 12: 672804. https://doi.org/10.3389/fgene.2021.672804

[444] Guo, Siyao, and Shuibin Lin. 2023. “mRNA Alternative Polyadenylation (APA) in Regulation of Gene Expression and Diseases.” Genes & Diseases 10: 165–174. https://doi.org/10.1016/j.gendis.2021.09.005

[445] Ogami, Koichi, Yuka Oishi, and Shin-ichi Hoshino. 2023. “Protocol for Analyzing Intact mRNA Poly(A) Tail Length Using Nanopore Direct RNA Sequencing.” STAR Protocols 4: 102340. https://doi.org/10.1016/j.xpro.2023.102340

[446] Mitsuhashi, Satomi, So Nakagawa, Mitsuru Sasaki-Honda, Hidetoshi Sakurai, Martin C. Frith, and Hiroaki Mitsuhashi. 2021. “Nanopore Direct RNA Sequencing Detects DUX4-Activated Repeats and Isoforms in Human Muscle Cells.” Human Molecular Genetics 30: 552–563. https://doi.org/10.1093/hmg/ddab063

[447] Jacob, Maureen, Heike Kölbel, Philip Harrer, Robert Kopajtich, Pinki Munot, Melanie T. Achleitner, Susann Badmann, et al. 2026. “Deciphering DST-Associated Disorders: Biallelic Variants Affecting DST-b Cause a Congenital Myopathy.” Brain 149: 653–667. https://doi.org/10.1093/brain/awaf227

[448] Schwartz, Mathias, Mathilde Filser, Kevin Merchadou, Elisa Lemaitre, Khadija Abidallah, Henrique Tenreiro, Catherine Dubois D'enghien, et al. 2025. “A Founder BRCA1 Exonic Duplication Involving Breakpoint in T2T Reference Genome-Specific Region Results in Constitutional Fusion Transcript.” npj Genomic Medicine 10: 58. https://doi.org/10.1038/s41525-025-00517-0

[449] Bryce-Smith, Sam, Anna-Leigh Brown, Max Z. Y. J. Chien, Dario Dattilo, Puja R. Mehta, Francesca Mattedi, Simone Barattucci, et al. 2025. “TDP-43 Loss Induces Cryptic Polyadenylation in ALS/FTD.” Nature Neuroscience 28: 2190–2200. https://doi.org/10.1038/s41593-025-02050-w

[450] Dermentzaki, Georgia, Mattia Furlan, Iris Tanaka, Tommaso Leonardi, Paola Rinchetti, Patricia M. S. Passos, Alliny Bastos, et al. 2024. “Depletion of METTL3 in Cholinergic Neurons Causes Adult-Onset Neuromuscular Degeneration.” Cell Reports 43: 113999. https://doi.org/10.1016/j.celrep.2024.113999

[451] Yen, Ya-Ping, Ting-Hsiang Lung, Ee Shan Liau, Chuan-Che Wu, Guan-Lin Huang, Fang-Yu Hsu, Mien Chang, et al. 2025. “The Motor Neuron m⁶A Repertoire Governs Neuronal Homeostasis and FTO Inhibition Mitigates ALS Symptom Manifestation.” Nature Communications 16: 4063. https://doi.org/10.1038/s41467-025-59117-2

[452] Bilinovich, Stephanie M., Katie L. Uhl, Kristy Lewis, Xavier Soehnlen, Michael Williams, Daniel Vogt, Jeremy W. Prokop, and Daniel B. Campbell. 2021. “Integrated RNA Sequencing Reveals Epigenetic Impacts of Diesel Particulate Matter Exposure in Human Cerebral Organoids.” Developmental Neuroscience 42: 195–207. https://doi.org/10.1159/000513536

[453] Xu, Zhongmou, Haiying Li, Xiang Li, Jinxin Lu, Chang Cao, Lu Peng, et al. 2025. “Fto-Dependent Vdac3 m⁶A Modification Regulates Neuronal Ferroptosis Induced by the post-ICH Mass Effect and Transferrin.” Neuroscience Bulletin 41: 970–986. https://doi.org/10.1007/s12264-025-01355-x

[454] Xin, Hai, Xingqiang He, Jun Li, Xiaomei Guan, Xukui Liu, Yuewei Wang, Liyuan Niu, et al. 2022. “Profiling of the Full-Length Transcriptome in Abdominal Aortic Aneurysm Using Nanopore-Based Direct RNA Sequencing.” Open Biology 12: 210172. https://doi.org/10.1098/rsob.210172

[455] Chen, Ye-shi, Xin-ping Ouyang, Xiao-hua Yu, Petr Novák, Le Zhou, Ping-ping He, Kai Yin. 2021. “N6-Adenosine Methylation (m⁶A) RNA Modification: An Emerging Role in Cardiovascular Diseases.” Journal of Cardiovascular Translational Research 14: 857–872. https://doi.org/10.1007/s12265-021-10108-w

[456] Draper, Isabelle, Wanting Huang, Suchita Pande, Aaron Zou, Timothy D. Calamaras, Richard H. Choe, Ana Correia-Branco, et al. 2024. “The Splicing Factor hnRNPL Demonstrates Conserved Myocardial Regulation Across Species and Is Altered in Heart Failure.” FEBS Letters 598: 2670–2682. https://doi.org/10.1002/1873-3468.15020

[457] Reis, Andre L. M., Jillian M. Hammond, Igor Stevanovski, Jonathon C. Arnold, Iain S. McGregor, Ira W. Deveson, and Anand Gururajan. 2022. “Sex-Specific Transcriptomic and Epitranscriptomic Signatures of PTSD-Like Fear Acquisition.” iScience 25: 104861. https://doi.org/10.1016/j.isci.2022.104861

[458] Saju, Adeela Fathima, Aditi Mukundan, M. S. Divyashree, Raghu Chandrashekar Hariharapura, and Archana Mahadev Rao. 2025. “RNA Diagnostics and Therapeutics: A Comprehensive Review.” RNA Biology 22: 1–11. https://doi.org/10.1080/15476286.2024.2449277

[459] Huang, Huilin, Hengyou Weng, Jianjun Chen. 2020. “m⁶A Modification in Coding and Non-Coding RNAs: Roles and Therapeutic Implications in Cancer.” Cancer Cell 37: 270–288. https://doi.org/10.1016/j.ccell.2020.02.004

[460] He, Bo, Yu Fan, Jizhou Liu, Yuting Chen, Jinmin Yang, Huifen Xiang, Jinying Peng, Chengqi Yi. 2025. “Advancing DNA and RNA Modification Detection via Nanopore Sequencing.” ACS Nano 19: 37468–37483. https://doi.org/10.1021/acsnano.5c11784

[461] Paval, Naomi-Eunicia, Olga Adriana Căliman-Sturdza, Andrei Lobiuc, Mihai Dimian, Ioan-Ovidiu Sirbu, and Mihai Covasa. 2025. “MicroRNAs in Long COVID: Roles, Diagnostic Biomarker Potential and Detection.” Human Genomics 19: 90. https://doi.org/10.1186/s40246-025-00810-0

[462] Zhang, Jinyue, Shuanghong Yan, Le Weiming Chang, Yuqin Guo, Yu Wang, Panke Wang, Hong-Yuan Zhang, Shuo Chen, and Huang . 2020. “Direct microRNA Sequencing Using Nanopore-Induced Phase-Shift Sequencing.” iScience 23: 100916. https://doi.org/10.1016/j.isci.2020.100916

[463] Pelletier, Dylan, Barbara Rivera, Marc R. Fabian, and William D. Foulkes. 2023. “miRNA Biogenesis and Inherited Disorders: Clinico-Molecular Insights.” Trends in Genetics 39: 401–414. https://doi.org/10.1016/j.tig.2023.01.009

[464] Sahin, Ugur Petra Oehm, Evelyna Derhovanessian, Robert A. Jabulowsky, Mathias Vormehr, Maike Gold, Daniel Maurus, et al. 2020. “An RNA Vaccine Drives Immunity in Checkpoint-Inhibitor-Treated Melanoma.” Nature 585: 107–112. https://doi.org/10.1038/s41586-020-2537-9

[465] Carvalho, Thiago. 2023. “Personalized Anti-Cancer Vaccine Combining mRNA and Immunotherapy Tested in Melanoma Trial.” Nature Medicine 29: 2379–2380. https://doi.org/10.1038/d41591-023-00072-0

[466] Vormehr, Mathias, Özlem Türeci, and Ugur Sahin. 2019. “Harnessing Tumor Mutations for Truly Individualized Cancer Vaccines.” Annual Review of Medicine 70: 395–407. https://doi.org/10.1146/annurev-med-042617-101816

[467] Żak, Magdalena M., and Lior Zangi. 2025. “Clinical Development of Therapeutic mRNA Applications.” Molecular Therapy 33: 2583–2609. https://doi.org/10.1016/j.ymthe.2025.03.034

[468] Gunter, Helen, M., Senel Idrisoglu, Swati Singh, Dae Jong Han, Emily Ariens, Jonathan R. Peters, Ted Wong, et al. 2023. “mRNA Vaccine Quality Analysis Using RNA Sequencing.” Nature Communications 14: 5663. https://doi.org/10.1038/s41467-023-41354-y

[469] Xiao, Yu-Lan, Shun Liu, Ruiqi Ge, Yuan Wu, Chuan He, Mengjie Chen, and Weixin Tang. 2023. “Transcriptome-Wide Profiling and Quantification of N6-Methyladenosine by Enzyme-Assisted Adenosine Deamination.” Nature Biotechnology 41: 993–1003. https://doi.org/10.1038/s41587-022-01587-6

[470] Winkler, Roni, Ella Gillis, Lior Lasman, Modi Safra, Shay Geula, Clara Soyris, Aharon Nachshon, et al. 2019. “m⁶A Modification Controls the Innate Immune Response to Infection by Targeting Type I Interferons.” Nature Immunology 20: 173–182. https://doi.org/10.1038/s41590-018-0275-z

[471] Shi, H., X. Zhang, Y. L. Weng, Z. Lu, Y. Liu, Z. Lu, J. Li, et al. 2018. “m(6)A Facilitates Hippocampus-Dependent Learning and Memory Through YTHDF1.” Nature 563: 249–253. https://doi.org/10.1038/s41586-018-0666-1

[472] Zhang, Chunxia, Yusheng Chen, Baofa Sun, Lu Wang, Ying Yang, Dongyuan Ma, Junhua Lv, et al. 2017. “m⁶A Modulates Haematopoietic Stem and Progenitor Cell Specification.” Nature 549: 273–276. https://doi.org/10.1038/nature23883

[473] Zhang, Li-Sheng, Chang Liu, Honghui Ma, Qing Dai, Hui-Lung Sun, Guanzheng Luo, Zijie Zhang, et al. 2019. “Transcriptome-Wide Mapping of Internal N7-Methylguanosine Methylome in Mammalian mRNA.” Molecular Cell 74: 1304–1316.e1308. https://doi.org/10.1016/j.molcel.2019.03.036

[474] Zhang, Linda, Jiangbo Wei, Zhongyu Zou, and Chuan He. 2026. “RNA Modification Systems as Therapeutic Targets.” Nature Reviews Drug Discovery 25: 59–78. https://doi.org/10.1038/s41573-025-01280-8

[475] August, Allison, Husain Z. Attarwala, Sunny Himansu, Shiva Kalidindi, Sophia Lu, Rolando Pajon, Shu Han, et al. 2021. “A Phase 1 Trial of Lipid-Encapsulated mRNA Encoding a Monoclonal Antibody With Neutralizing Activity Against Chikungunya Virus.” Nature Medicine 27: 2224–2233. https://doi.org/10.1038/s41591-021-01573-6

[476] Stadler, Christiane R., Ursula Ellinghaus, Leyla Fischer, Hayat Bähr-Mahmud, Martin Rao, Claudia Lindemann, Anuhar Chaturvedi, et al. 2024. “Preclinical Efficacy and Pharmacokinetics of an RNA-Encoded T Cell–Engaging Bispecific Antibody Targeting Human Claudin 6.” Science Translational Medicine 16: eadl2720. https://doi.org/10.1126/scitranslmed.adl2720

[477] Stadler, Christiane R., Hayat Bähr-Mahmud, Leyla Celik, Bernhard Hebich, Alexandra S. Roth, René P. Roth, Katalin Karikó, Özlem Türeci, and Ugur Sahin. 2017. “Elimination of Large Tumors in Mice by mRNA-Encoded Bispecific Antibodies.” Nature Medicine 23: 815–817. https://doi.org/10.1038/nm.4356

[478] Wierczeiko, Anna, Stefan Pastore, Stefan Mündnich, Anne M. Busch, Vincent, Dietrich, Mark Helm, Tamer Butto, and Susanne Gerber. 2023. “NanopoReaTA: A User-Friendly Tool for Nanopore-Seq Real-Time Transcriptional Analysis.” Bioinformatics 39: btad492. https://doi.org/10.1093/bioinformatics/btad492

[479] Nesselbush, Monica C., Bogdan A. Luca, Young-Jun Jeon, Isabel Jabara, Catherine B. Meador, Andrea Garofalo, Michael S. Binkley, et al. 2025. “An Ultrasensitive Method for Detection of Cell-Free RNA.” Nature 641: 759–768. https://doi.org/10.1038/s41586-025-08834-1

[480] Ibrahim, Fadia, Jan Oppelt, Manolis Maragkakis, and Zissimos Mourelatos. 2021. “TERA-Seq: True End-to-End Sequencing of Native RNA Molecules for Transcriptome Characterization.” Nucleic Acids Research 49: e115. https://doi.org/10.1093/nar/gkab713

[481] Prawer, Yair D. J., Josie Gleeson, Ricardo De Paoli-Iseppi, and Michael B. Clark. 2023. “Pervasive Effects of RNA Degradation on Nanopore Direct RNA Sequencing.” NAR Genomics and Bioinformatics 5: lqad060. https://doi.org/10.1093/nargab/lqad060

[482] Kusmirek, Wiktor, Natalia Strozynska, P. Martin-Arroyo Cerpa, Agnieszka Dziergowska, Grazyna Leszczynska, Robert Nowak, and Malgorzata Adamczyk. 2025. “Direct RNA Oxford Nanopore Sequencing Distinguishes Between Modifications in tRNA at the U(34) Position.” International Journal of Biological Macromolecules 320: 145877. https://doi.org/10.1016/j.ijbiomac.2025.145877

[483] Kochavi, Adva, Arno Velds, Maya Suzuki, Shinichiro Akichika, Tsutomu, Suzuki, Roderick L. Beijersbergen, and Reuven Agami. 2025. “Exploiting Nanopore Sequencing Advances for tRNA Sequencing of Human Cancer Models.” NAR Cancer 7: zcaf044. https://doi.org/10.1093/narcan/zcaf044

[484] Sun, Yu, Michael Piechotta, Isabel Naarmann-de Vries, Christoph Dieterich, and Ann E. Ehrenhofer-Murray. 2023. “Detection of Queuosine and Queuosine Precursors in tRNAs by Direct RNA Sequencing.” Nucleic Acids Research 51: 11197–11212. https://doi.org/10.1093/nar/gkad826

[485] Wang, Yongsheng, Huihui Wang, Feihu Xi, Huiyuan Wang, Ximei Han, Wentao Wei, Hangxiao Zhang, et al. 2020. “Profiling of Circular RNA N6-Methyladenosine in Moso Bamboo (Phyllostachys Edulis) Using Nanopore-Based Direct RNA Sequencing.” Journal of Integrative Plant Biology 62: 1823–1838. https://doi.org/10.1111/jipb.13002

[486] Xiao, Mei-Sheng, and Jeremy E. Wilusz. 2024. “Purification of Circular RNAs Using Poly(A) Tailing Followed by RNase R Digestion.” In Circular RNAs, edited by Christoph Dieterich and Marie-Laure Baudet (pp. 3–19, Springer US), https://doi.org/10.1007/978-1-0716-3678-7_1

[487] Xiao, Mei-Sheng, and Jeremy E. Wilusz. 2019. “An Improved Method for Circular RNA Purification Using RNase R That Efficiently Removes Linear RNAs Containing G-Quadruplexes or Structured 3′ Ends.” Nucleic Acids Research 47: 8755–8769. https://doi.org/10.1093/nar/gkz576

[488] Rafiq, Aleena, and Anastassia Kanavarioti. 2025. “The Potential and Limitations of the MinION/Yenos Platform for miRNA-Enabled Early Cancer Detection.” International Journal of Molecular Sciences 26: 3822. https://doi.org/10.3390/ijms26083822

[489] Zhang, Tianyuan, Hanzhou Li, Mian Jiang, Huiyu Hou, Yunyun Gao, Yali Li, Fuhao Wang, Jun Wang, Kai Peng, and Yong-Xin Liu. 2024. “Nanopore Sequencing: Flourishing in Its Teenage Years.” Journal of Genetics and Genomics 51: 1361–1374. https://doi.org/10.1016/j.jgg.2024.09.007

[490] Timp, Winston, Jeffrey Comer, and Aleksei Aksimentiev. 2013. “Nanopore Sequencing Using a Hidden Markov Model for Base-Calling.” Biophysical Journal 104: 211A. https://doi.org/10.1016/j.bpj.2012.11.1195

[491] Simpson, Jared T., Rachael E. Workman, P. C. Zuzarte, Matei David, L. J. Dursi, and Winston Timp. 2017. “Detecting DNA Cytosine Methylation Using Nanopore Sequencing.” Nature Methods 14: 407–410. https://doi.org/10.1038/nmeth.4184

[492] Teng, Haotian, Minh Duc Cao, Michael B. Hall, Tania Duarte, Sheng Wang, and Lachlan J. M. Coin. 2018. “Chiron: Translating Nanopore Raw Signal Directly Into Nucleotide Sequence Using Deep Learning.” Gigascience 7: giy037. https://doi.org/10.1093/gigascience/giy037

[493] Boža, Vladimír, Broňa Brejová, and Tomáš Vinař. 2017. “DeepNano: Deep Recurrent Neural Networks for Base Calling in MinION Nanopore Reads.” Plos One 12: e0178751. https://doi.org/10.1371/journal.pone.0178751

[494] Huang, Neng, Fan Nie, Peng Ni, Feng Luo, and Jianxin Wang. 2022. “SACall: A Neural Network Basecaller for Oxford Nanopore Sequencing Data Based on Self-Attention Mechanism.” IEEE/ACM Transactions on Computational Biology and Bioinformatics 19: 614–623. https://doi.org/10.1109/tcbb.2020.3039244

[495] Li, Qingwen, Chen Sun, Daqian Wang, and Jizhong Lou. 2024. “BaseNet: A Transformer-Based Toolkit for Nanopore Sequencing Signal Decoding.” Computational and Structural Biotechnology Journal 23: 3430–3444. https://doi.org/10.1016/j.csbj.2024.09.016

[496] Sahlin, Kristoffer, and Paul Medvedev. 2021. “Error Correction Enables Use of Oxford Nanopore Technology for Reference-Free Transcriptome Analysis.” Nature Communications 12: 2. https://doi.org/10.1038/s41467-020-20340-8

[497] Wang, Luotong, Li Qu, Longshu Yang, Yiying Wang, and Huaiqiu Zhu. 2020. “NanoReviser: An Error-Correction Tool for Nanopore Sequencing Based on a Deep Learning Algorithm.” Frontiers in Genetics 11: 900. https://doi.org/10.3389/fgene.2020.00900

[498] Xie, Shangqian, Amy Wing-Sze Leung, Zhenxian Zheng, Dake Zhang, Chuanle Xiao, Ruibang Luo, Ming Luo, and Shoudong Zhang. 2021. “Applications and Potentials of Nanopore Sequencing in the (Epi)Genome and (Epi)Transcriptome Era.” The Innovation 2: 100153. https://doi.org/10.1016/j.xinn.2021.100153

[499] Zhang, Yuxin, Huayuan Yan, Zhen Wei, Haifeng Hong, Daiyun Huang, Guopeng Liu, Qianshan Qin, et al. 2024. “NanoMUD: Profiling of Pseudouridine and N1-methylpseudouridine Using Oxford Nanopore Direct RNA Sequencing.” International Journal of Biological Macromolecules 270: 132433. https://doi.org/10.1016/j.ijbiomac.2024.132433

[500] Oxford Nanopore Technologies. 2024. “Dorado.”

[501] De Coster, Wouter, Svenn D'Hert, Darrin T. Schultz, Marc Cruts, and Christine Van Broeckhoven. 2018. “NanoPack: Visualizing and Processing Long-Read Sequencing Data.” Bioinformatics 34: 2666–2669. https://doi.org/10.1093/bioinformatics/bty149

[502] Chen, Shifu. 2023. “Ultrafast One-Pass FASTQ Data Preprocessing, Quality Control, and Deduplication Using Fastp.” iMeta 2: e107. https://doi.org/10.1002/imt2.107

[503] Dong, Han, Yongsheng Gao, Zhengyi Cai, Yi Li, Xing Li, Fangqing Zhao, Jinyang Zhang. 2026. “Comprehensive Mapping of RNA Modification Dynamics and Crosstalk Via Deep Learning and Nanopore Direct RNA-Sequencing.” Nature Communications 17: 1722. https://doi.org/10.1038/s41467-026-68419-y

[504] Neumann, Don, Anireddy S. N. Reddy, and Asa Ben-Hur. 2022. “RODAN: A Fully Convolutional Architecture for Basecalling Nanopore RNA Sequencing Data.” BMC Bioinformatics 23: 142. https://doi.org/10.1186/s12859-022-04686-y

[505] Li, Qingwen, Chen Sun, Daqian Wang, and Jizhong Lou. 2024. “GCRTcall: A Transformer Based Basecaller for Nanopore RNA Sequencing Enhanced by Gated Convolution and Relative Position Embedding via Joint Loss Training.” Frontiers in Genetics 15: 1443532. https://doi.org/10.3389/fgene.2024.1443532

[506] Xie, Shaohui, Lulu Ding, Yang Yu, Ling Liu, Yiwen Sun, Jianqiang Li, Jue Ruan, and Zexuan Zhu. 2026. “A Dual Context-Aware Basecaller for Nanopore Direct RNA Sequencing.” Nature Communications 17: 1851. https://doi.org/10.1038/s41467-026-68566-2

[507] Stoiber, Marcus, Joshua Quick, Rob Egan, Ji Eun Lee, Susan Celniker, Robert K. Neely, Nicholas Loman, Len A. Pennacchio, and James Brown. 2017. “De Novo Identification of DNA Modifications Enabled by Genome-Guided Nanopore Signal Processing.” Preprint at bioRxiv. https://doi.org/10.1101/094672

[508] Bansal, Mohit, Anamika Gupta, Jane Ding, Anirban Kundu, Katherine Marlow, Zhangli Gibson, Zhangli Su, Sunil Sudarshan, and Han-Fei Ding. 2026. “Integrative Analysis of Nanopore Direct RNA Sequencing Data Reveals a Global Impact of Pseudouridylation on m⁶A and m⁵C Modifications.” npj Precision Oncology 10: 52. https://doi.org/10.1038/s41698-026-01278-4

[509] Ni, Peng, Jinrui Xu, Zeyu Zhong, Feng Luo, Jianxin Wang. 2024. “RNA m⁶A Detection Using Raw Current Signals and Basecalling Errors From Nanopore Direct RNA Sequencing Reads.” Bioinformatics 40: btae375. https://doi.org/10.1093/bioinformatics/btae375

[510] Ramasamy, Soundhar, Shubham Mishra, Surbhi Sharma, Sangamithirai Subramanian Parimalam, Thangavel Vaijayanthi, Yoto Fujita, Basavaraj Kovi, Hiroshi Sugiyama, and Ganesh N. Pandian. 2022. “An Informatics Approach to Distinguish RNA Modifications in Nanopore Direct RNA Sequencing.” Genomics 114: 110372. https://doi.org/10.1016/j.ygeno.2022.110372

[511] Heng, Jia Wei Joel, and Meng How Tan. 2025. “Chapter Eight—Nanopore Sequencing to Detect A-to-I Editing Sites.” In Methods in Enzymology, edited by Peter Beal (pp. 187–205, Academic Press). https://doi.org/10.1016/bs.mie.2024.11.028

[512] Fonzino, Adriano, Caterina Manzari, Paola Spadavecchia, Uday Munagala, Serena Torrini, Silvestro Conticello, Graziano Pesole, and Ernesto Picardi. 2024. “Unraveling C-to-U RNA Editing Events From Direct RNA Sequencing.” RNA Biology 21: 113–126. https://doi.org/10.1080/15476286.2023.2290843

[513] Hassan, Doaa, Aditya Ariyur, Swapna Vidhur Daulatabad, Quoseena Mir, and Sarath Chandra Janga. 2024. “Nm-Nano: a Machine Learning Framework for Transcriptome-Wide Single-Molecule Mapping of 2′-O-Methylation (Nm) Sites in Nanopore Direct RNA Sequencing Datasets.” RNA Biology 21: 560–574. https://doi.org/10.1080/15476286.2024.2352192

[514] Li, Yanqiang, Jiayi Chen, Yunxia Wang, Dean Li, Jiahan Li, Yang Yi, Lili Zhang, Qi Cao, and Kaifu Chen. 2025. “Protocol for Mapping 2′-O-Methylation Using Nanopore Direct RNA-seq Data With NanoNm.” STAR Protocols 6: 104003. https://doi.org/10.1016/j.xpro.2025.104003

[515] Roundtree, Ian A., Molly E. Evans, Tao Pan, and Chuan He. 2017. “Dynamic RNA Modifications in Gene Expression Regulation.” Cell 169: 1187–1200. https://doi.org/10.1016/j.cell.2017.05.045

[516] Wang, Ziyuan, Ziyang Liu, Yinshan Fang, Hao Helen Zhang, Xiaoxiao Sun, Ning Hao, Jianwen Que, and Hongxu Ding. 2025. “Training Data Diversity Enhances the Basecalling of Novel RNA Modification-Induced Nanopore Sequencing Readouts.” Nature Communications 16: 679. https://doi.org/10.1038/s41467-025-55974-z

[517] Li, Jiayi, Shenglun Chen, Zhixing Wu, Haozhe Wang, Rong Xia, Jia Meng, and Yuxin Zhang. 2026. “CircRM: Profiling Circular RNA Modifications From Nanopore Direct RNA Sequencing.” Briefings in Bioinformatics 27: bbaf726. https://doi.org/10.1093/bib/bbaf726

[518] Luo, Tingting, Moping Xu, Miao Wang, Faying Chen, and Jiejun Shi. 2026. “Systematic Evaluation of Computational Tools for Multitype RNA Modification Detection Using Nanopore Direct RNA Sequencing.” Nature Methods 23: 438–450. https://doi.org/10.1038/s41592-025-02974-y

[519] Oxford Nanopore Technologies. 2021. “Remora.”

[520] Wang, Ziyuan, Yinshan Fang, Ziyang Liu, Ning Hao, Hao Helen Zhang, Xiaoxiao Sun, Jianwen Que, and Hongxu Ding. 2024. “Adapting Nanopore Sequencing Basecalling Models for Modification Detection via Incremental Learning and Anomaly Detection.” Nature Communications 15: 7148. https://doi.org/10.1038/s41467-024-51639-5

[521] Xuan, Jiajia, Lifan Chen, Zhirong Chen, Junjie Pang, Junhong Huang, Jinran Lin, Lingling Zheng, Bin Li, Lianghu Qu, and Jianhua Yang. 2024. “RMBase v3.0: Decode the Landscape, Mechanisms and Functions of RNA Modifications.” Nucleic Acids Research 52: D273–D284. https://doi.org/10.1093/nar/gkad1070

[522] Bao, Xiaoqiong, Qi Jiang, Weixuan Chen, Huiqin Li, Xuanye Li, Xiangyu Zuo, Zhuobin Lin, et al. 2026. “RM2Target v2.0: An Updated Database for the Target Genes of Writers, Erasers, and Readers of RNA Modifications.” Nucleic Acids Research 54: D279–D290. https://doi.org/10.1093/nar/gkaf1206

[523] Liu, Hui, Huaizhi Wang, Zhen Wei, Songyao Zhang, Gang Hua, Shao-Wu Zhang, Lin Zhang, et al. 2018. “MeT-DB V2.0: Elucidating Context-Specific Functions of N6-Methyl-Adenosine Methyltranscriptome.” Nucleic Acids Research 46: D281–D287. https://doi.org/10.1093/nar/gkx1080

[524] Liu, Shun, Allen Zhu, Chuan He, and Mengjie Chen. 2020. “REPIC: A Database for Exploring the N6-Methyladenosine Methylome.” Genome Biology 21: 100. https://doi.org/10.1186/s13059-020-02012-4

[525] Lang, Xiaoqiang, Chunyan Yu, Mengyuan Shen, Lei Gu, Qian Qian, Degui Zhou, Jiantao Tan, et al. 2024. “PRMD: An Integrated Database for Plant RNA Modifications.” Nucleic Acids Research 52: D1597–D1613. https://doi.org/10.1093/nar/gkad851

[526] Dai, Qing, Chang Ye, Iryna Irkliyenko, Yiding Wang, Hui-Lung Sun, Yun Gao, Yushuai Liu, et al. 2024. “Ultrafast Bisulfite Sequencing Detection of 5-Methylcytosine in DNA and RNA.” Nature Biotechnology 42: 1559–1570. https://doi.org/10.1038/s41587-023-02034-w

[527] Lichinchi, Gianluigi, Shang Gao, Yogesh Saletore, Gwendolyn Michelle Gonzalez, Vikas Bansal, Yinsheng Wang, Christopher E. Mason, and Tariq M. Rana. 2016. “Dynamics of the Human and Viral m⁶A RNA Methylomes During HIV-1 Infection of T Cells.” Nature Microbiology 1: 16011. https://doi.org/10.1038/nmicrobiol.2016.11

[528] Ozsolak, Fatih, and Patrice M. Milos. 2011. “Transcriptome Profiling Using Single-Molecule Direct RNA Sequencing.” In High-Throughput Next Generation Sequencing: Methods and Applications, edited by Young Min Kwon and Steven C. Ricke (pp. 51–61, Humana Press), https://doi.org/10.1007/978-1-61779-089-8_4

[529] Orabi, Baraa, Ning Xie, Brian McConeghy, Xuesen Dong, Cedric Chauve, and Faraz Hach. 2023. “Freddie: Annotation-Independent Detection and Discovery of Transcriptomic Alternative Splicing Isoforms Using Long-Read Sequencing.” Nucleic Acids Research 51: e11. https://doi.org/10.1093/nar/gkac1112

[530] Gao, Yuan, Feng Wang, Robert Wang, Eric Kutschera, Yang Xu, Stephan Xie, Yuanyuan Wang, Kathryn E. Kadash-Edmondson, Lan Lin, and Yi Xing. 2023. “ESPRESSO: Robust Discovery and Quantification of Transcript Isoforms From Error-Prone Long-Read RNA-Seq Data.” Science Advances 9: eabq5072. https://doi.org/10.1126/sciadv.abq5072

[531] Wyman, Dana, Gabriela Balderrama-Gutierrez, Fairlie Reese, Shan Jiang, Sorena Rahmanian, Stefania Forner, Dina Matheos, et al. 2020. “A Technology-Agnostic Long-Read Analysis Pipeline for Transcriptome Discovery and Quantification.” Preprint at bioRxiv. https://doi.org/10.1101/672931

[532] Holmqvist, Isak, Alan Bäckerholm, Yarong Tian, Guojiang Xie, Kaisa Thorell, and Ka-Wei Tang. 2021. “FLAME: Long-Read Bioinformatics Tool for Comprehensive Spliceome Characterization.” RNA 27: 1127–1139. https://doi.org/10.1261/rna.078800.121

[533] Pardo-Palacios, Francisco J., Angeles Arzalluz-Luque, Liudmyla Kondratova, Pedro Salguero, Jorge Mestre-Tomás, Rocío Amorín, Eva Estevan-Morió, et al. 2024. “SQANTI3: Curation of Long-Read Transcriptomes for Accurate Identification of Known and Novel Isoforms.” Nature Methods 21: 793–797. https://doi.org/10.1038/s41592-024-02229-2

[534] Fu, Yuntian, Heonseok Kim, Sharmili Roy, Sijia Huang, Jenea I. Adams, Susan M. Grimes, Billy T. Lau, Anuja Sathe, Hanlee P. Ji, and Nancy R. Zhang. 2025. “Single Cell and Spatial Alternative Splicing Analysis With Nanopore Long Read Sequencing.” Nature Communications 16: 6654. https://doi.org/10.1038/s41467-025-60902-2

[535] Sagniez, Mélanie, Anshul Budhraja, Bastien Paré, Shawn M. Simpson, Clément Vinet-Ouellette, Marieke Rozendaal, and Martin A. Smith. 2024. “Assembly Arena: Benchmarking RNA Isoform Reconstruction Algorithms for Nanopore Sequencing.” Preprint at bioRxiv. https://doi.org/10.1101/2024.03.21.586080

[536] Gallie, Daniel. R. 1991. “The Cap and Poly(A) Tail Function Synergistically to Regulate mRNA Translational Efficiency.” Genes & Development 5: 2108–2116. https://doi.org/10.1101/gad.5.11.2108

[537] Chang, Jessie J. Y., Xuan Yang, Haotian Teng, Jianshu Zhang, Benjamin Reames, Shuxin Zhang, Vincent Corbin, and Lachlan J. M. Coin. 2025. “Using Synthetic RNA to Benchmark Poly(A) Length Inference From Direct RNA Sequencing.” Gigascience 14: giaf098. https://doi.org/10.1093/gigascience/giaf098

[538] Maździarz, Mateusz, Łukasz Paukszto, and Jakub Sawicki. 2025. “TAILcaller: An R Package for Analyzing Differences in Poly(A) Tail Length for Oxford Nanopore RNA Sequencing.” Bioinformatics Advances 5: vbaf235. https://doi.org/10.1093/bioadv/vbaf235

[539] Zhang, Zhiping, Heather Glatt-Deeley, Lehan Zou, Dongyuan Song, Pedro Miura. 2025. “APALORD: An R-Based Tool for Differential Alternative Polyadenylation Analysis of Long-Read RNA-Seq Data.” Preprint at bioRxiv. https://doi.org/10.1101/2025.06.11.658931

[540] Çelik, Muhammed Hasan, and Ali Mortazavi. 2022. “Analysis of Alternative Polyadenylation From Long-Read or Short-Read RNA-Seq With LAPA.” Preprint at bioRxiv. https://doi.org/10.1101/2022.11.08.515683

[541] Balázs, Zsolt, Dóra Tombácz, Zsolt Csabai, Norbert Moldován, Michael Snyder, and Zsolt Boldogkői. 2019. “Template-Switching Artifacts Resemble Alternative Polyadenylation.” BMC Genomics 20: 824. https://doi.org/10.1186/s12864-019-6199-7

[542] Lienhard, Matthias, Twan van den Beucken, Bernd Timmermann, Myriam, Hochradel, Stefan Börno, Florian Caiment, Martin Vingron, and Ralf Herwig. 2023. “IsoTools: A Flexible Workflow for Long-Read Transcriptome Sequencing Analysis.” Bioinformatics 39: btad364. https://doi.org/10.1093/bioinformatics/btad364

[543] Bi, Yalan, Tom Lukas Lankenau, Matthias Lienhard, and Ralf Herwig. 2025. “IsoTools 2.0: Software for Comprehensive Analysis of Long-Read Transcriptome Sequencing Data.” Journal of Molecular Biology 437: 169049. https://doi.org/10.1016/j.jmb.2025.169049

[544] Kakuk, Balázs, Dóra Tombácz, Zsolt Balázs, Norbert Moldován, Zsolt Csabai, Gábor Torma, Klára Megyeri, Michael Snyder, and Zsolt Boldogkői. 2021. “Combined Nanopore and Single-Molecule Real-Time Sequencing Survey of Human Betaherpesvirus 5 Transcriptome.” Scientific Reports 11: 14487. https://doi.org/10.1038/s41598-021-93593-y

[545] Ivanov, Maxim, Albin Sandelin, and Sebastian Marquardt. 2021. “TrancriptomeReconstructoR: Data-Driven Annotation of Complex Transcriptomes.” BMC Bioinformatics 22: 290. https://doi.org/10.1186/s12859-021-04208-2

[546] Khan, Irtesam Mahmud, Xiaofei Carl Zang, Ange Teng, Tasfia Zahin, Mingfu Shao. 2025. “Boosting Transcript Assembly via Delineating Transcript Start and End Sites.” Preprint at bioRxiv. https://doi.org/10.1101/2025.10.13.682211

[547] Gimenez, Gregory, Peter A. Stockwell, Euan J. Rodger, and Aniruddha Chatterjee. 2023. “Strategy for RNA-Seq Experimental Design and Data Analysis.” In Oral Biology: Molecular Techniques and Applications (pp. 249–278, Springer US). https://doi.org/10.1007/978-1-0716-2780-8_16

[548] Williams, Alexander G., Sean Thomas, Stacia K. Wyman, and Alisha K. Holloway. 2014. “RNA-Seq Data: Challenges in and Recommendations for Experimental Design and Analysis.” Current Protocols in Human Genetics 83: 1.4.1–17.16.8. https://doi.org/10.1002/0471142905.hg1113s83

[549] Lafzi, Atefeh, Catia Moutinho, Simone Picelli, and Holger Heyn. 2018. “Tutorial: Guidelines for the Experimental Design of Single-Cell RNA Sequencing Studies.” Nature Protocols 13: 2742–2757. https://doi.org/10.1038/s41596-018-0073-y

[550] Conesa, Ana, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michal Wojciech Szcześniak, et al. 2016. “A Survey of Best Practices for RNA-Seq Data Analysis.” Genome Biology 17(1): 13. https://doi.org/10.1186/s13059-016-0881-8

[551] Deng, Enze, Qingmei Shen, Jingna Zhang, Yaowei Fang, Lei Chang, Guanzheng Luo, and Xiaoying Fan. 2025. “Systematic Evaluation of Single-Cell RNA-Seq Analyses Performance Based on Long-Read Sequencing Platforms.” Journal of Advanced Research 71: 141–153. https://doi.org/10.1016/j.jare.2024.05.020

[552] Qin, Rui, Wei Fan, Feng Ding, Sen Wang, Bing He, Mingming Hou, Qiang Lin, Peng Cui, and Wanfei Liu. 2025. “Synthesizing Human-Specific Spike-In Standards for RNA-Seq Experiments and Assessing Their Technical Performance.” Preprint at bioRxiv. https://doi.org/10.1101/2025.04.01.646725

[553] Paul, L., P. Kubala, G. Horner, M. Ante, Igor Hollaender, S. Alexander, and Torsten Reda. 2016. “SIRVs: Spike-In RNA Variants as External Isoform Controls in RNA-Sequencing.” Preprint at bioRxiv. https://doi.org/10.1101/080747

[554] Zhang, Zhang, Tao Chen, Hong-Xuan Chen, Ying-Yuan Xie, Li-Qian Chen, Yu-Li Zhao, Biao-Di Liu, et al. 2021. “Systematic Calibration of Epitranscriptomic Maps Using a Synthetic Modification-Free RNA Library.” Nature Methods 18: 1213–1222. https://doi.org/10.1038/s41592-021-01280-7

[555] Das, Saumya, Asim B. Abdel-Mageed, Catherine Adamidi, P. David Adelson, Kemal M. Akat, Eric Alsop, K. Mark Ansel, et al. 2019. “The Extracellular RNA Communication Consortium: Establishing Foundational Knowledge and Technologies for Extracellular RNA Research.” Cell 177: 231–242. https://doi.org/10.1016/j.cell.2019.03.023

[556] Qu, Luming, Andrew Lemire, Kristi Lea, Diana Batten, Sheila Heater, Jian Gu, Peen Whitley, Joel Brockman, Jeff Schageman, and Kelli Bramlett. 2011. “Development of ERCC RNA Spike-In Control Mixes.” Journal of biomolecular techniques 22: S46.

[557] Lee, Hangnoh, P. Scott Pine, Jennifer McDaniel, Marc Salit, and Brian Oliver. 2016. “External RNA Controls Consortium Beta Version Update.” Journal of Genomics 4: 19–22. https://doi.org/10.7150/jgen.16082

[558] Pine, P. Scott, Sarah A. Munro, Jerod R. Parsons, Jennifer McDaniel, Anne Bergstrom Lucas, Jean Lozach, Timothy G. Myers, Qin Su, Sarah M. Jacobs-Helber, and Marc Salit. 2016. “Evaluation of the External RNA Controls Consortium (ERCC) Reference Material Using a Modified Latin Square Design.” BMC Biotechnology 16: 54. https://doi.org/10.1186/s12896-016-0281-x

[559] External, R. N. A. Controls Consortium. 2005. “Proposed Methods for Testing and Selecting the ERCC External RNA Controls.” BMC Genomics 6: 150. https://doi.org/10.1186/1471-2164-6-150

[560] Ding, Bo, Lina Zheng, and Wei Wang. 2017. “Assessment of Single Cell RNA-Seq Normalization Methods.” G3 Genes|Genomes|Genetics 7: 2039–2045. https://doi.org/10.1534/g3.117.040683

[561] Jiang, Lichun, Felix Schlesinger, Carrie A. Davis, Yu Zhang, Renhua Li, Marc, Salit, Thomas R. Gingeras, and Brian Oliver. 2011. “Synthetic Spike-In Standards for RNA-seq Experiments.” Genome Research 21: 1543–1551. https://doi.org/10.1101/gr.121095.111

[562] Lun, T. L. Aaron, Fernando J. Calero-Nieto, Liora Haim-Vilmovsky, Berthold Göttgens, and John C. Marioni. 2017. “Assessing the Reliability of Spike-In Normalization for Analyses of Single-Cell RNA Sequencing Data.” Preprint at bioRxiv. https://doi.org/10.1101/119784

[563] Hardwick, Simon A., Wendy Y. Chen, Ted Wong, Ira W. Deveson, James Blackburn, Stacey B. Andersen, Lars K. Nielsen, John S. Mattick, and Tim R. Mercer. 2016. “Spliced Synthetic Genes as Internal Controls in RNA Sequencing Experiments.” Nature Methods 13: 792–798. https://doi.org/10.1038/nmeth.3958

[564] Tong, Li, Cheng Yang, Po-Yen Wu, and May D. Wang. 2016. “Evaluating the Impact of Sequencing Error Correction for RNA-Seq Data With ERCC RNA Spike-In Controls.” In 2016 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI), IEEE (pp. 74–77).

[565] Oikonomopoulos, Spyros, Yu Chang Wang, Haig Djambazian, Dunarel Badescu, and Jiannis Ragoussis. 2016. “Benchmarking of the Oxford Nanopore MinION Sequencing for Quantitative and Qualitative Assessment of cDNA Populations.” Scientific Reports 6: 31602. https://doi.org/10.1038/srep31602

[566] Grandi, Carmen, Martin Emmaneel, Frank H. T. Nelissen, and Maike M. K. Hansen. 2024. “Protocol for In Vitro Transcribing mRNAs With Defined Poly(A)-Tail Lengths and Visualizing Sequential PABP Binding.” STAR Protocols 5: 103284. https://doi.org/10.1016/j.xpro.2024.103284

[567] Kwon, Hyokyoung, Minjeong Kim, Yunmi Seo, Yae Seul Moon, Hwa Jeong Lee, Kyuri Lee, and Hyukjin Lee. 2018. “Emergence of Synthetic mRNA: In Vitro Synthesis of mRNA and Its Applications in Regenerative Medicine.” Biomaterials 156: 172–193. https://doi.org/10.1016/j.biomaterials.2017.11.034

[568] Leshkowitz, Dena, Ester Feldmesser, Gilgi Friedlander, Ghil Jona, Elena Ainbinder, Yisrael Parmet, and Shirley Horn-Saban. 2016. “Using Synthetic Mouse Spike-In Transcripts to Evaluate RNA-Seq Analysis Tools.” Plos One 11: e0153782. https://doi.org/10.1371/journal.pone.0153782

[569] Seo, Jina, Hyo-Jung Park, Ayoung Oh, Chang , Beom Jeong, Sohee Kim, Sojeong Lee, Chuna Kim, Hyeshik Chang, Jae-Hwan Nam, and Daechan Park. 2025. “3AIM-Seq: Quality Assessment of mRNA Therapeutics Using Sequencing for 3′ Poly(A) Tails of In Vitro-Transcribed mRNA.” Molecular Therapy 33: 4923–4936. https://doi.org/10.1016/j.ymthe.2025.06.033

[570] Medjmedj, Ayoub, Hugo Genon, Dounia Hezili, Albert Ngalle Loth, Rudy Clemençon, Cyril Guimpied, Lucile Mollet, et al. 2025. “Evaluation of Synthetic mRNA With Selected UTR Sequences and Alternative Poly(A) Tail, In Vitro and In Vivo.” Molecular Therapy Nucleic Acids 36: 102648. https://doi.org/10.1016/j.omtn.2025.102648

[571] Tarnowski, Matthew J., and Thomas E. Gorochowski. 2022. “Massively Parallel Characterization of Engineered Transcript Isoforms Using Direct RNA Sequencing.” Nature Communications 13: 434. https://doi.org/10.1038/s41467-022-28074-5

[572] Beverly, Michael, Caitlin Hagen, and Olga Slack. 2018. “Poly A Tail Length Analysis of in Vitro Transcribed mRNA by LC-MS.” Analytical and Bioanalytical Chemistry 410: 1667–1677. https://doi.org/10.1007/s00216-017-0840-6

[573] Kabza, Michal, Alexander Ritter, Ashley Byrne, Kostianna Sereti, Daniel Le, William Stephenson, and Tim Sterne-Weiler. 2024. “Accurate Long-Read Transcript Discovery and Quantification at Single-Cell, Pseudo-Bulk and Bulk Resolution With Isosceles.” Nature Communications 15: 7316. https://doi.org/10.1038/s41467-024-51584-3

[574] Kralj, Jason G., and Marc L. Salit. 2013. “Characterization of In Vitro Transcription Amplification Linearity and Variability in the Low Copy Number Regime Using External RNA Control Consortium (ERCC) Spike-Ins.” Analytical and Bioanalytical Chemistry 405: 315–320. https://doi.org/10.1007/s00216-012-6445-1

[575] Tan, Jazlynn, Xiu Min, Lurong Wang, W. Seow, Jeeranan Boonruangkan, Mike, Huang, Jiamin Toh, Kok Hao Chen, and Nigel Chou. 2025. “Guidestar: A Spike-In Approach to Improve RNA Detection Accuracy in Imaging-Based Spatial Transcriptomics.” Preprint at bioRxiv. https://doi.org/10.1101/2025.01.09.632272

[576] McCormick, Caroline A., Stuart Akeson, Sepideh Tavakoli, Dylan Bloch, Isabel N. Klink, Miten Jain, Sara H. Rouhanifard, et al. 2024. “Multicellular, IVT-derived, Unmodified Human Transcriptome for Nanopore-Direct RNA Analysis.” GigaByte 2024: 1–13. https://doi.org/10.46471/gigabyte.129

[577] Tzadikario, Talia, Stuart Akeson, Neda Ghohabi Esfahani, Andrew J. Stein, Urja Choudhary, Kshitij Amar, and Miten Jain. 2025. “Genomic In Vitro Transcription and Nanopore Direct RNA Sequencing of a Human B-Lymphocyte Cell Line.” Preprint at bioRxiv. https://doi.org/10.1101/2025.04.25.650674

[578] Zheng, Hong-xiang, Xian-sheng Zhang, and Na Sui. 2020. “Advances in the Profiling of N6-Methyladenosine (m⁶A) Modifications.” Biotechnology Advances 45: 107656. https://doi.org/10.1016/j.biotechadv.2020.107656

[579] Spangenberg, Jannes Stefan Mündnich, Anne Busch, Stefan Pastore, Anna Wierczeiko, Winfried Goettsch, Vincent Dietrich, et al. 2025. “The RMaP Challenge of Predicting RNA Modifications by Nanopore Sequencing.” Communications Chemistry 8: 115. https://doi.org/10.1038/s42004-025-01507-0

[580] Maestri, Simone, Mattia Furlan, Logan Mulroney, Lucia Coscujuela Tarrero, Camilla Ugolini, Fabio Dalla Pozza, Tommaso Leonardi, Ewan Birney, Francesco Nicassio, and Mattia Pelizzola. 2024. “Benchmarking of Computational Methods for m⁶A Profiling With Nanopore Direct RNA Sequencing.” Briefings in Bioinformatics 25: bbae001. https://doi.org/10.1093/bib/bbae001

[581] Moradian, Hanieh, Toralf Roch, Larissa Anthofer, Andreas Lendlein, and Manfred Gossen. 2022. “Chemical Modification of Uridine Modulates mRNA-Mediated Proinflammatory and Antiviral Response in Primary Human Macrophages.” Molecular Therapy Nucleic Acids 27: 854–869. https://doi.org/10.1016/j.omtn.2022.01.004

[582] Chen, Tien-Hao, Vladimir Potapov, Nan Dai, Jennifer L. Ong, and Bijoyita Roy. 2022. “N1-Methyl-Pseudouridine Is Incorporated With Higher Fidelity Than Pseudouridine in Synthetic RNAs.” Scientific Reports 12: 13017. https://doi.org/10.1038/s41598-022-17249-1

[583] Mulroney, Thomas E., Tuija Pöyry, Juan Carlos Yam-Puc, Maria Rust, Robert F. Harvey, Lajos Kalmar, Emily Horner, et al. 2024. “N1-Methylpseudouridylation of mRNA Causes +1 Ribosomal Frameshifting.” Nature 625: 189–194. https://doi.org/10.1038/s41586-023-06800-3

[584] Shen, Yuan, Dong-Qi Yang, Yuan Liu, Jia-En Lao, Chun-Qing Liu, Xing-Hong Gao, Yun-Ru He, and Heng Xia. 2025. “A Review of Advances in In Vitro RNA Preparation by ssRNAP.” International Journal of Biological Macromolecules 304: 141002. https://doi.org/10.1016/j.ijbiomac.2025.141002

[585] Bornewasser, Lisa, Christof Domnick, and Stephanie Kath-Schorr. 2022. “Stronger Together for In-Cell Translation: Natural and Unnatural Base Modified mRNA.” Chemical Science 13: 4753–4761. https://doi.org/10.1039/D2SC00670G

[586] Henderson, Jordana M., Andrew Ujita, Elizabeth Hill, Sally Yousif-Rosales, Cory Smith, Nicholas Ko, Taylor McReynolds, Charles R. Cabral, Julienne R. Escamilla-Powers, and Michael E. Houston. 2021. “Cap 1 Messenger RNA Synthesis With Co-Transcriptional Cleancap^® Analog by In Vitro Transcription.” Current Protocols 1: e39. https://doi.org/10.1002/cpz1.39

[587] Mandell, Zachary F., Andrew Ujita, Jordana Henderson, Anthony Truong, Coleen Vo, Farinaz Rezvani, Nona Abolhassani, et al. 2025. “CleanCap M6 Inhibits Decapping of Exogenously Delivered IVT mRNA.” Molecular Therapy Nucleic Acids 36: 102456. https://doi.org/10.1016/j.omtn.2025.102456

[588] Brunderová, Mária, Vojtěch Havlíček, Ján Matyašovský, Radek Pohl, Lenka Poštová Slavětínská, Matouš Krömer, and Michal Hocek. 2024. “Expedient Production of Site Specifically Nucleobase-Labelled or Hypermodified RNA With Engineered Thermophilic DNA Polymerases.” Nature Communications 15: 3054. https://doi.org/10.1038/s41467-024-47444-9

[589] Wilson, Christopher, Peter J. Chen, Zhuang Miao, and David R. Liu. 2020. “Programmable m⁶A Modification of Cellular RNAs With a Cas13-Directed Methyltransferase.” Nature Biotechnology 38: 1431–1440. https://doi.org/10.1038/s41587-020-0572-6

[590] Vlatkovic, Irena, János Ludwig, Gábor Boros, Gábor T. Szabó, Julia Reichert, Maximilian Buff, Markus Baiersdörfer, et al. 2022. “Ribozyme Assays to Quantify the Capping Efficiency of In Vitro-Transcribed mRNA.” Pharmaceutics 14: 328. https://doi.org/10.3390/pharmaceutics14020328

[591] Lyon, Seth E., Tien-Hao Chen, Andrew J. Wallace, Katie Adib, and Venkat Gopalan. 2018. “An RNase P-Based Assay for Accurate Determination of the 5′-Deoxy-5′-Azidoguanosine-Modified Fraction of In Vitro-Transcribed RNAs.” ChemBioChem 19: 2353–2359. https://doi.org/10.1002/cbic.201800447

[592] Scheitl, Carolin P. M., Mohammad Ghaem Maghami, Ann-Kathrin Lenz, and Claudia Höbartner. 2020. “Site-Specific RNA Methylation by a Methyltransferase Ribozyme.” Nature 587: 663–667. https://doi.org/10.1038/s41586-020-2854-z

[593] Cong, Deyuan, Kfir B. Steinbuch, Ryosuke Koyama, Tyler V. Lam, Jamie Y. Lam, and Yitzhak Tor. 2024. “Site-Specific RNA Modification via Initiation of In Vitro Transcription Reactions With m(6)a and Isomorphic Emissive Adenosine Analogs.” RSC Chemical Biology 5: 454–458. https://doi.org/10.1039/d4cb00045e

[594] Li, Jiayi, Feiyang Sun, Kunyang He, Lin Zhang, Jia Meng, Daiyun Huang, and Yu-Xin Zhang. 2024. “Detection and Quantification of 5moU RNA Modification From Direct RNA Sequencing Data.” Current Genomics 25: 212–225. https://doi.org/10.2174/0113892029288843240402042529

[595] Zhang, Meiling, Xiaoting Zhang, and C. Yi. 2024. “New Directions for Ψ and m1A Decoding in mRNA: Deciphering the Stoichiometry and Function.” RNA 30: 537–547. https://doi.org/10.1261/rna.079950.124

[596] Li, Yu, Renmin Han, Chongwei Bi, Mo Li, Sheng Wang, and Xin Gao. 2018. “DeepSimulator: A Deep Simulator for Nanopore Sequencing.” Bioinformatics 34: 2899–2908. https://doi.org/10.1093/bioinformatics/bty223

[597] Beslic, Denis, Martin Kucklick, Susanne Engelmann, Stephan Fuchs, Bernhard Y. Renard, and Nils Körber. 2024. “End-to-End Simulation of Nanopore Sequencing Signals With Feed-Forward Transformers.” Bioinformatics 41: btae744. https://doi.org/10.1093/bioinformatics/btae744

[598] Rohrandt, Christian, Nadine Kraft, Pay Gießelmann, Björn Brändl, Bernhard M. Schuldt, Ulrich Jetzek, and Franz-Josef Müller. 2018. “Nanopore SimulatION—A Raw Data Simulator for Nanopore Sequencing.” In 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), IEEE (pp. 1–8).

[599] Gamaarachchi, Hasindu, James M. Ferguson, Hiruna Samarakoon, Kisaru Liyanage, and Ira W. Deveson. 2024. “Simulation of Nanopore Sequencing Signal Data With Tunable Parameters.” Genome Research 34: 778–783. https://doi.org/10.1101/gr.278730.123

[600] Hafezqorani, Saber, Chen Yang, Theodora Lo, Ka Ming Nip, René L. Warren, Inanc Birol. 2020. “Trans-NanoSim Characterizes and Simulates Nanopore RNA-Sequencing Data.” Gigascience 9: giaa061. https://doi.org/10.1093/gigascience/giaa061

[601] Yang, Chen, Justin Chu, René L. Warren, and Inanç Birol. 2017. “NanoSim: Nanopore Sequence Read Simulator Based on Statistical Characterization.” Gigascience 6: 1–6. https://doi.org/10.1093/gigascience/gix010

[602] Ono, Yukiteru, Michiaki Hamada, and Kiyoshi Asai. 2022. “PBSIM3: A Simulator for All Types of PacBio and ONT Long Reads.” NAR Genomics and Bioinformatics 4: lqac092. https://doi.org/10.1093/nargab/lqac092

[603] Wick, Ryan R. 2019. “Badread: Simulation of Error-Prone Long Reads.” Journal of Open Source Software 4: 1316. https://doi.org/10.21105/joss.01316

[604] Goldfarb, Tamara, Vamsi K. Kodali, Shashikant Pujar, Vyacheslav Brover, Barbara Robbertse, Catherine M. Farrell, Dong-Ha Oh, et al. 2025. “NCBI RefSeq: Reference Sequence Standards Through 25 Years of Curation and Annotation.” Nucleic Acids Research 53: D243–D257. https://doi.org/10.1093/nar/gkae1038

[605] Dyer, Sarah C., Olanrewaju Austine-Orimoloye, Andrey G. Azov, Matthieu Barba, If Barnes, Vianey Paola Barrera-Enriquez, Arne Becker, et al. 2025. “Ensembl 2025.” Nucleic Acids Research 53: D948–D957. https://doi.org/10.1093/nar/gkae1071

[606] Mudge, Jonathan M., Sílvia Carbonell-Sala, Mark Diekhans, Jose Gonzalez Martinez, Toby Hunt, Irwin Jungreis, Jane E. Loveland, et al. 2025. “GENCODE 2025: Reference Gene Annotation for Human and Mouse.” Nucleic Acids Research 53: D966–D975. https://doi.org/10.1093/nar/gkae1078

[607] Abugessaisa, Imad, Shuhei Noguchi, Akira Hasegawa, Atsushi Kondo, Hideya Kawaji, Piero Carninci, and Takeya Kasukawa. 2019. “refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites.” Journal of Molecular Biology 431: 2407–2422. https://doi.org/10.1016/j.jmb.2019.04.045

[608] Yu, Shan, Wei Chun Chen, Luyang Wang, San Jewell, Ayna Mammedova, Seong Woo Han, Jayamanna Wickramasinghe, Yoseph Barash, Bin Tian. 2026. “PolyA_DB v4: Systematic PolyA Site Identification and Isoform Annotation in Human and Mouse Genomes Using 3′ End and Long-Read Sequencing Data.” Nucleic Acids Research 54: D247–D254. https://doi.org/10.1093/nar/gkaf1212

[609] Boccaletto, Pietro, Filip Stefaniak, Angana Ray, Andrea Cappannini, Sunandan Mukherjee, Elżbieta Purta, Małgorzata Kurkowska, et al. 2022. “MODOMICS: A Database of RNA Modification Pathways. 2021 Update.” Nucleic Acids Research 50: D231–D235. https://doi.org/10.1093/nar/gkab1083

[610] Picardi, Ernesto, Anna Maria D'Erchia, Claudio Lo Giudice, and Graziano Pesole. 2017. “REDIportal: A Comprehensive Database of a-to-i RNA Editing Events in Humans.” Nucleic Acids Research 45: D750–D757. https://doi.org/10.1093/nar/gkw767

[611] Hwang, Hyeonseo, Hee Ryung Chang, and Daehyun Baek. 2023. “Determinants of Functional microRNA Targeting.” Molecules and Cells 46: 21–32. https://doi.org/10.14348/molcells.2023.2157

[612] Shumate, Alaina, Brandon Wong, Geo Pertea, and Mihaela Pertea. 2022. “Improved Transcriptome Assembly Using a Hybrid of Long and Short Reads With StringTie.” PLoS Computational Biology 18: e1009730. https://doi.org/10.1371/journal.pcbi.1009730

[613] Kainth, Amoldeep S., Gabriela A. Haddad, Johnathon M. Hall, and Alexander J. Ruthenburg. 2023. “Merging Short and Stranded Long Reads Improves Transcript Assembly.” PLoS Computational Biology 19: e1011576. https://doi.org/10.1371/journal.pcbi.1011576

[614] Han, Seong Woo, San Jewell, Andrei Thomas-Tikhonenko, Yoseph Barash. 2024. “Contrasting and Combining Transcriptome Complexity Captured by Short and Long RNA Sequencing Reads.” Genome Research 34: 1624–1635. https://doi.org/10.1101/gr.278659.123

[615] Dong, Xueyi, Luyi Tian, Quentin Gouil, Hasaru Kariyawasam, Shian Su, Ricardo De Paoli-Iseppi, Yair David Joseph Prawer, et al. 2021. “The Long and the Short of It: Unlocking Nanopore Long-Read RNA Sequencing Data With Short-Read Differential Expression Analysis Tools.” NAR Genomics and Bioinformatics 3: lqab028. https://doi.org/10.1093/nargab/lqab028

[616] David, Julianne K., Sean K. Maden, Mary A. Wood, Reid F. Thompson, and Abhinav Nellore. 2022. “Retained Introns in Long RNA-Seq Reads Are Not Reliably Detected in Sample-Matched Short Reads.” Genome Biology 23: 240. https://doi.org/10.1186/s13059-022-02789-6

[617] Shiraki, Toshiyuki, Shinji Kondo, Shintaro Katayama, Kazunori Waki, Takeya Kasukawa, Hideya Kawaji, Rimantas Kodzius, et al. 2003. “Cap Analysis Gene Expression for High-Throughput Analysis of Transcriptional Starting Point and Identification of Promoter Usage.” Proceedings of the National Academy of Sciences 100: 15776–15781. https://doi.org/10.1073/pnas.2136655100

[618] Cvetesic, Nevena, Harry G. Leitch, Malgorzata Borkowska, Ferenc Müller, Piero Carninci, Petra Hajkova, and Boris Lenhard. 2018. “SLIC-CAGE: High-Resolution Transcription Start Site Mapping Using Nanogram-Levels of Total RNA.” Genome Research 28: 1943–1956. https://doi.org/10.1101/gr.235937.118

[619] Yan, Bo, George Tzertzinis, Ira Schildkraut, and Laurence Ettwiller. 2022. “Comprehensive Determination of Transcription Start Sites Derived from All RNA Polymerases Using ReCappable-Seq.” Genome Research 32: 162–174. https://doi.org/10.1101/gr.275784.121

[620] Duttke, Sascha H., Max W. Chang, Sven Heinz, and Christopher Benner. 2019. “Identification and Dynamic Quantification of Regulatory Elements Using Total RNA.” Genome Research 29: 1836–1846. https://doi.org/10.1101/gr.253492.119

[621] Elgood Hunt, Eleanor, Claudia Vivori, Richard Mitter, Vedis Agnadottir, and Folkert J. van Werven. 2026. “Mapping and Quantifying Nascent Transcript Start Sites Using TT-TSS-Seq.” Genome Research 36: 600–610. https://doi.org/10.1101/gr.280726.125

[622] Shepard, Peter J., Eun, A. Choi, Jente Lu, Lisa A. Flanagan, Klemens J. Hertel, and Yongsheng Shi. 2011. “Complex and Dynamic Landscape of RNA Polyadenylation Revealed by PAS-Seq.” RNA 17: 761–772. https://doi.org/10.1261/rna.2581711

[623] Dar, Daniel, Maya Shamir, J. R. Mellin, Mikael Koutero, Noam Stern-Ginossar, Pascale Cossart, and Rotem Sorek. 2016. “Term-Seq Reveals Abundant Ribo-Regulation of Antibiotics Resistance in Bacteria.” Science 352: aad9822. https://doi.org/10.1126/science.aad9822

[624] Mai, Liyao, Yinbin Qiu, Zhiwei Lian, Caiming Chen, Linlin Wang, Yao Yin, Siqi Wang, et al. 2021. “MustSeq, an Alternative Approach for Multiplexible Strand-Specific 3′ End Sequencing of mRNA Transcriptome Confers High Efficiency and Practicality.” RNA Biology 18: 232–243. https://doi.org/10.1080/15476286.2021.1974208

[625] Moll, Pamela, Michael Ante, Alexander, Seitz, Torsten Reda. 2014. “QuantSeq3′ mRNA Sequencing for RNA Quantification.” Nature Methods 11: i–iii. https://doi.org/10.1038/nmeth.f.376

[626] Tang, Yujiao, Kunqi Chen, Bowen Song, Jiongming Ma, Xiangyu Wu, Qingru Xu, Zhen Wei, et al. 2021. “m⁶A-Atlas: A Comprehensive Knowledgebase for Unraveling the N6-methyladenosine (m⁶A) Epitranscriptome.” Nucleic Acids Research 49: D134–D143. https://doi.org/10.1093/nar/gkaa692

[627] Zheng, Guanqun, John Arne Dahl, Yamei Niu, Peter Fedorcsak, Chun-Min Huang, Charles J. Li, Cathrine B. Vågbø, et al. 2013. “ALKBH5 Is a Mammalian RNA Demethylase That Impacts RNA Metabolism and Mouse Fertility.” Molecular Cell 49: 18–29. https://doi.org/10.1016/j.molcel.2012.10.015

[628] Liu, Jun, Xiaoyang Dou, Chuanyuan Chen, Chuan Chen, Chang Liu, Meng Michelle Xu, Siqi Zhao, et al. 2020. “N(6)-Methyladenosine of Chromosome-Associated Regulatory RNA Regulates Chromatin State and Transcription.” Science 367: 580–586. https://doi.org/10.1126/science.aay6018

[629] Zhang, Yuxin, Yuxuan Wu, Di Zhen, Kunqi Chen, and Jia Meng. 2021. “A Meta-Analysis: Evaluating the Effect of METTL3/METTL14 on m⁶A Level Based on Knockdown Samples.” In The Fifth International Conference on Biological Information and Biomedical Engineering (p. 37, Hangzhou, China: Association for Computing Machinery).

[630] Poh, Hui Xian, Aashiq H. Mirza, Brian, F., Samie, R., and Jaffrey . 2022. “Alternative Splicing of METTL3 Explains Apparently METTL3-Independent m⁶A Modifications in mRNA.” PLoS Biology 20: e3001683. https://doi.org/10.1371/journal.pbio.3001683

[631] Naarmann-de Vries, Isabel S., Christiane Zorbas, Amina Lemsara, Michael Piechotta, Felix G. M. Ernst, Ludivine Wacheul, Denis L. J. Lafontaine, Christoph Dieterich. 2023. “Comprehensive Identification of Diverse Ribosomal RNA Modifications By Targeted Nanopore Direct RNA Sequencing and JACUSA2.” RNA Biology 20: 652–665. https://doi.org/10.1080/15476286.2023.2248752

[632] Motorin, Yuri, and Virginie Marchand. 2021. “Analysis of RNA Modifications by Second- and Third-Generation Deep Sequencing: 2020 Update.” Genes 12: 278. https://doi.org/10.3390/genes12020278

[633] Lebret-Kogey, Valentyne, Lilia Ayadi, Sylvain Maenner, Yuri Motorin, Isabelle Behm-Ansmant, and Christelle Aigueperse. 2025. “Quantitative Detection of 2′-O-Methylated Residues in Non-Coding RNAs Using DNAzymes and Quantitative RT-PCR.” Biochimie 237: 26–39. https://doi.org/10.1016/j.biochi.2025.07.006

[634] Rang, Franka J., Wigard P. Kloosterman, and Jeroen de Ridder. 2018. “From Squiggle to Basepair: Computational Approaches for Improving Nanopore Sequencing Read Accuracy.” Genome Biology 19: 90. https://doi.org/10.1186/s13059-018-1462-9

[635] Viscardi, Marcus J., and Joshua A. Arribere. 2022. “Poly(a) Selection Introduces Bias and Undue Noise in Direct RNA-Sequencing.” BMC Genomics 23: 530. https://doi.org/10.1186/s12864-022-08762-8

[636] LaneRebecca, E., Eleanor Calcutt, Anandagopal Srinivasan, Vicki Gamble, Udo Oppermann, Jianfeng Sun, and Adam P. Cribbs. 2025. “Distinct 5′ and 3′ Coverage Biases Shape Transcriptome Interpretation in Nanopore Direct RNA Versus PCR-cDNA Sequencing.” Preprint at bioRxiv 2025.10.13.681987. https://doi.org/10.1101/2025.10.13.681987

[637] Naumenko, Fedor M., Irina I. Abnizova, Nathan Beka, Mikhail A. Genaev, and Yuriy L. Orlov. 2018. “Novel Read Density Distribution Score Shows Possible Aligner Artefacts, When Mapping a Single Chromosome.” BMC Genomics 19: 92. https://doi.org/10.1186/s12864-018-4475-6

[638] Musich, Ryan, Lance Cadle-Davidson, and Michael V. Osier. 2021. “Comparison of Short-Read Sequence Aligners Indicates Strengths and Weaknesses for Biologists to Consider.” Frontiers in Plant Science 12: 657240. https://doi.org/10.3389/fpls.2021.657240

[639] Carter, John Lawrence, Harlan Stevens, Perry G. Ridge, and Steven Michael Johnson. 2023. “Short Sequence Aligner Benchmarking for Chromatin Research.” International Journal of Molecular Sciences 24: 14074. https://doi.org/10.3390/ijms241814074

[640] Amarasinghe, S. L., S. Su, X. Dong, L. Zappia, M. E. Ritchie, and Q. Gouil. 2020. “Opportunities and Challenges in Long-Read Sequencing Data Analysis.” Genome Biology 21: 30. https://doi.org/10.1186/s13059-020-1935-5

[641] Weirather, Jason L., Mariateresa de Cesare, Yunhao Wang, Paolo Piazza, Vittorio Sebastiano, Xiu-Jie Wang, David Buck, and Kin Fai Au. 2017. “Comprehensive Comparison of Pacific Biosciences and Oxford Nanopore Technologies and Their Applications to Transcriptome Analysis.” F1000Research 6: 100. https://doi.org/10.12688/f1000research.10571.2

[642] Zook, Justin M., Daniel Samarov, Jennifer McDaniel, Shurjo K. Sen, Marc Salit. 2012. “Synthetic Spike-In Standards Improve Run-Specific Systematic Error Analysis for DNA and RNA Sequencing.” Plos One 7: e41356. https://doi.org/10.1371/journal.pone.0041356

[643] Sims, David J., Robin D. Harrington, Eric C. Polley, Thomas D. Forbes, Michele G. Mehaffey, Paul M. McGregor, 3rd, Corinne E. Camalier, et al. 2016. “Plasmid-Based Materials as Multiplex Quality Controls and Calibrators for Clinical Next-Generation Sequencing Assays.” The Journal of Molecular Diagnostics 18: 336–349. https://doi.org/10.1016/j.jmoldx.2015.11.008

[644] Hardwick, Simon A., Ira W. Deveson, and Tim R. Mercer. 2017. “Reference Standards for Next-Generation Sequencing.” Nature Reviews Genetics 18: 473–484. https://doi.org/10.1038/nrg.2017.44

[645] Engström, Pär G., Tamara Steijger, Botond Sipos, Gregory R. Grant, André Kahles, Gunnar Rätsch, Nick Goldman, et al. 2013. “Systematic Evaluation of Spliced Alignment Programs for RNA-Seq Data.” Nature Methods 10: 1185–1191. https://doi.org/10.1038/nmeth.2722

[646] Calvo-Roitberg, Ezequiel, Rachel F. Daniels, and Athma A. Pai. 2024. “Challenges in Identifying mRNA Transcript Starts and Ends From Long-Read Sequencing Data.” Genome Research 34: 1719–1734. https://doi.org/10.1101/gr.279559.124

[647] Baruzzo, Giacomo, Katharina E. Hayer, Eun Ji Kim, Barbara Di Camillo, Garret A. FitzGerald, and Gregory R. Grant. 2017. “Simulation-Based Comprehensive Benchmarking of RNA-Seq Aligners.” Nature Methods 14: 135–139. https://doi.org/10.1038/nmeth.4106

[648] Grant, Gregory R., Michael H. Farkas, Angel D. Pizarro, Nicholas F. Lahens, Jonathan Schug, Brian P. Brunk, Christian J. Stoeckert, John B. Hogenesch, and Eric A. Pierce. 2011. “Comparative Analysis of RNA-Seq Alignment Algorithms and the RNA-Seq Unified Mapper (RUM).” Bioinformatics 27: 2518–2528. https://doi.org/10.1093/bioinformatics/btr427

[649] Seki, Masahide, Yuta Kuze, Xiang Zhang, Ken-Ichi Kurotani, Michitaka Notaguchi, Haruki Nishio, Hiroshi Kudoh, et al. 2024. “An Improved Method for the Highly Specific Detection of Transcription Start Sites.” Nucleic Acids Research 52: e7. https://doi.org/10.1093/nar/gkad1116

[650] Policastro, Robert A., Daniel J. McDonald, Volker P. Brendel, and Gabriel E. Zentner. 2021. “Flexible Analysis of TSS Mapping Data and Detection of TSS Shifts With TSRexploreR.” NAR Genomics and Bioinformatics 3: lqab051. https://doi.org/10.1093/nargab/lqab051

[651] Adiconis, Xian, Adam L. Haber, Sean K. Simmons, Ami Levy Moonshine, Zhe Ji, Michele A. Busby, Xi Shi, et al. 2018. “Comprehensive Comparative Analysis of 5′-end RNA-Sequencing Methods.” Nature Methods 15: 505–511. https://doi.org/10.1038/s41592-018-0014-2

[652] Grigoriadis, Dimitris, Nikos Perdikopanis, Georgios K. Georgakilas, Artemis G. Hatzigeorgiou. 2022. “DeepTSS: Multi-Branch Convolutional Neural Network for Transcription Start Site Identification From CAGE Data.” BMC Bioinformatics 23: 395. https://doi.org/10.1186/s12859-022-04945-y

[653] Petri, Alexander J., and Kristoffer Sahlin. 2023. “isONform: Reference-Free Transcriptome Reconstruction From Oxford Nanopore Data.” Bioinformatics 39: i222–i231. https://doi.org/10.1093/bioinformatics/btad264

[654] Kasianova, Alexandra M., Anna V. Klepikova, Oleg A. Gusev, Guzel R. Gazizova, Maria D. Logacheva, and Aleksey A. Penin. 2025. “Full-Length Isoform Constructor (FLIC)—A Tool for Isoform Discovery Based on Long Reads.” Bioinformatics 41: btaf551. https://doi.org/10.1093/bioinformatics/btaf551

[655] Zhao, Xichen, Yuxin Zhang, Daiyun Hang, Jia Meng, and Zhen Wei. 2022. “Detecting RNA Modification Using Direct RNA Sequencing: A Systematic Review.” Computational and Structural Biotechnology Journal 20: 5740–5749. https://doi.org/10.1016/j.csbj.2022.10.023

[656] Wyss, Luis, Vincent Mallet, Wissam Karroucha, and C. Oliver Karsten Borgwardt. 2025. “A Comprehensive Benchmark for RNA 3D Structure-Function Modeling.” Preprint at ArXiv. https://doi.org/10.48550/arxiv.2503.21681

[657] Vromman, Marieke, Jasper Anckaert, Stefania Bortoluzzi, Alessia Buratin, Chia-Ying Chen, Qinjie Chu, Trees-Juen Chuang, et al. 2023. “Large-Scale Benchmarking of circRNA Detection Tools Reveals Large Differences in Sensitivity but Not in Precision.” Nature Methods 20: 1159–1169. https://doi.org/10.1038/s41592-023-01944-6

[658] Szabo, Linda, and Julia Salzman. 2016. “Detecting Circular RNAs: Bioinformatic and Experimental Challenges.” Nature Reviews Genetics 17: 679–692. https://doi.org/10.1038/nrg.2016.114

[659] Arora, Rohit, Murphy Angelo, Christian Choe, Courtney Shearer, Aaron Kollasch, Fiona Qu, Ruben Weitzman, et al. 2025. “RNAGym: Large-Scale Benchmarks for RNA Fitness and Structure Prediction.” Preprint at bioRxiv 2025.06.16.660049. https://doi.org/10.1101/2025.06.16.660049

[660] Jenjaroenpun, Piroon, Thidathip Wongsurawat, Rui Pereira, Preecha Patumcharoenpol, David W. Ussery, Jens Nielsen, and Intawat Nookaew. 2018. “Complete Genomic and Transcriptional Landscape Analysis Using Third-Generation Sequencing: A Case Study of Saccharomyces cerevisiae CEN.PK113-7D.” Nucleic Acids Research 46: e38. https://doi.org/10.1093/nar/gky014

[661] Maier, Kerstin C., Saskia Gressel, Patrick Cramer, and Björn Schwalb. 2020. “Native Molecule Sequencing by Nano-ID Reveals Synthesis and Stability of RNA Isoforms.” Genome Research 30: 1332–1344. https://doi.org/10.1101/gr.257857.119

[662] Drexler, Heather L., Karine Choquet, Hope E. Merens, Paul S. Tang, Jared T. Simpson, and L. Stirling Churchman. 2021. “Revealing Nascent RNA Processing Dynamics With nano-COP.” Nature Protocols 16: 1343–1375. https://doi.org/10.1038/s41596-020-00469-y

[663] Martinek, Vlastimil, Jessica Martin, Cedric Belair, Matthew J. Payea, Sulochan Malla, Panagiotis Alexiou, and Manolis Maragkakis. 2024. “Deep Learning and Direct Sequencing of Labeled RNA Captures Transcriptome Dynamics.” NAR Genomics and Bioinformatics 6: lqae116. https://doi.org/10.1093/nargab/lqae116

[664] Ietswaart, Robert, Brendan M. Smalec, Albert Xu, Karine Choquet, Erik McShane, Ziad Mohamoud Jowhar, Chantal K. Guegler, et al. 2024. “Genome-Wide Quantification of RNA Flow Across Subcellular Compartments Reveals Determinants of the Mammalian Transcript Life Cycle.” Molecular Cell 84: 2765–2784. https://doi.org/10.1016/j.molcel.2024.06.008

[665] García-Campa, Lara, Luis Valledor, and Jesús Pascual. 2023. “The Integration of Data From Different Long-Read Sequencing Platforms Enhances Proteoform Characterization in Arabidopsis.” Plants 12: 511. https://doi.org/10.3390/plants12030511

[666] Anvar, Seyed Yahya, Guy Allard, Elizabeth Tseng, Gloria M. Sheynkman, Eleonora de Klerk, Martijn Vermaat, Raymund H. Yin, et al. 2018. “Full-Length mRNA Sequencing Uncovers a Widespread Coupling Between Transcription Initiation and mRNA Processing.” Genome Biology 19: 46. https://doi.org/10.1186/s13059-018-1418-0

[667] Bagherian, Mojtaba, Georgina Harris, Pratosh Sathishkumar, and James P. B. Lloyd. 2025. “Start Right to End Right: Authentic Open Reading Frame Selection Matters for Nonsense-Mediated Decay Target Identification.” Genes 16: 1297. https://doi.org/10.3390/genes16111297

[668] Filichkin, Sergei A., Henry D. Priest, Scott A. Givan, Rongkun Shen, Douglas W. Bryant, Samuel E. Fox, Weng-Keen Wong, and Todd C. Mockler. 2010. “Genome-Wide Mapping of Alternative Splicing in Arabidopsis thaliana.” Genome Research 20: 45–58. https://doi.org/10.1101/gr.093302.109

[669] Orr, Mona Wu, Yuanhui Mao, Gisela Storz, and Shu-Bing Qian. 2020. “Alternative ORFs and Small ORFs: Shedding Light on the Dark Proteome.” Nucleic Acids Research 48: 1029–1042. https://doi.org/10.1093/nar/gkz734

[670] Kuo, Richard I., Yuanyuan Cheng, Runxuan Zhang, John W. S. Brown, Jacqueline Smith, Alan L. Archibald, and David W. Burt. 2020. “Illuminating the Dark Side of the Human Transcriptome With Long Read Transcript Sequencing.” BMC Genomics 21: 751. https://doi.org/10.1186/s12864-020-07123-7

[671] Tay, Aidan P., Joshua J. Hamey, Gabriella E. Martyn, Laurence O. W. Wilson, and Marc R. Wilkins. 2022. “Identification of Protein Isoforms Using Reference Databases Built From Long and Short Read RNA-Sequencing.” Journal of Proteome Research 21: 1628–1639. https://doi.org/10.1021/acs.jproteome.1c00968

[672] Monzó, Carolina, Adam Frankish, and Ana Conesa. 2025. “Notable Challenges Posed by Long-Read Sequencing for the Study of Transcriptional Diversity and Genome Annotation.” Genome Research 35: 583–592. https://doi.org/10.1101/gr.279865.124

[673] Potter, S. Steven. 2018. “Single-Cell RNA Sequencing for the Study of Development, Physiology and Disease.” Nature Reviews Nephrology 14: 479–492. https://doi.org/10.1038/s41581-018-0021-7

[674] Nesari, Ali Mohammad, Habib MotieGhader, and Saeid Ghorbian. 2026. “Advances and Challenges in Single-Cell RNA Sequencing Data Analysis: A Comprehensive Review.” Briefings in Bioinformatics 27: bbaf723. https://doi.org/10.1093/bib/bbaf723

[675] Zheng, Zhenxian, Xian Yu, Lei Chen, Yan-Lam Lee, Cheng Xin, Angel On Ki Wong, Miten Jain, Rupesh K. Kesharwani, Fritz J. Sedlazeck, and Ruibang Luo. 2025. “Clair3-RNA: A Deep Learning-Based Small Variant Caller for Long-Read RNA Sequencing Data.” Nature Communications 16: 11553. https://doi.org/10.1101/2024.11.17.624050

[676] Negi, Shloka, Sarah L. Stenton, Seth I. Berger, Paolo Canigiula, Brandy McNulty, Ivo Violich, Joshua Gardner, et al. 2025. “Advancing Long-Read Nanopore Genome Assembly and Accurate Variant Calling for Rare Disease Detection.” American Journal of Human Genetics 112: 428–449. https://doi.org/10.1016/j.ajhg.2025.01.002

[677] Antoszewski, Kamil, Klaudia Chmielewska, Karolina Jagiello, Tomasz Puzyn. 2026. “Designing RNA Sequencing Experiments: A Practical Guide to Reproducible Gene Expression Analysis.” Computational and Structural Biotechnology Journal 31: 101–119. https://doi.org/10.1016/j.csbj.2025.12.015

[678] Ibrahim, Fadia, and Zissimos Mourelatos. 2025. “Defining the True Native Ends of RNAs at Single-Molecule Level With TERA-Seq.” In mRNA Decay: Methods and Protocols, edited by Maxime Wery (pp. 359–372, Springer US). https://doi.org/10.1007/978-1-0716-4176-7_21

[679] Yang, Yuening, Yanming Lu, Yan Wang, Xianghui Wen, Changhai Qi, Weilan Piao, Hua Jin. 2024. “Current Progress in Strategies to Profile Transcriptomic m⁶a Modifications.” Frontiers in Cell and Developmental Biology 12: 1392159. https://doi.org/10.3389/fcell.2024.1392159

[680] Bosmeny, Michael S., Adrian A. Pater, Li Zhang, Lydia L. Larkai, Beverly E. Sha, Zidi Lyu, Masad J. Damha, João I. Mamede, and Keith T. Gagnon. 2026. “A Nanopore-Based HIV-1 Reference Epitranscriptome.” Nucleic Acids Research 54: gkag220. https://doi.org/10.1093/nar/gkag220

[681] Liang, Zhanmin, Haokai Ye, Jiongming Ma, Zhen Wei, Yue Wang, Yuxin Zhang, Daiyun Huang, et al. 2024. “m⁶A-Atlas v2.0: Updated Resources for Unraveling the N6-Methyladenosine (m⁶A) Epitranscriptome Among Multiple Species.” Nucleic Acids Research 52: D194–D202. https://doi.org/10.1093/nar/gkad691

[682] Nguyen, Tram, Jia Wei Joel Heng, Pornchai Kaewsapsak, Eng Piew Louis Kok, Dominik Stanojević, Hao Liu, Angelysia Cardilla, et al. 2022. “Direct Identification of a-to-I Editing Sites With Nanopore Native RNA Sequencing.” Nature Methods 19: 833–844. https://doi.org/10.1038/s41592-022-01513-3

[683] Watson, Kaylee J., Robin E. Bromley, Benjamin C. Sparklin, Mark T. Gasser, Tamanash Bhattacharya, Jarrett F. Lebov, Tyonna Tyson, et al. 2024. “Common Analysis of Direct RNA Sequencing Currently Leads to Misidentification of m5C at GCU Motifs.” Life Science Alliance 7: e202302201. https://doi.org/10.26508/lsa.202302201

[684] Sun, Hanxiao, Kai Li, Xiaoting Zhang, Jun'e Liu, Meiling Zhang, Haowei Meng, and Chengqi Yi. 2021. “m(⁶)Am-Seq Reveals the Dynamic m(⁶)Am Methylation in the Human Transcriptome.” Nature Communications 12: 4778. https://doi.org/10.1038/s41467-021-25105-5

[685] Wu, Zhixing, Jiayi Li, Rong Xia, Jiayin Dai, Jionglong Su, Jia Meng, and Yuxin Zhang. 2026. “Nanopore Direct RNA Sequencing for RNA Modification Analysis: Workflow Assessment and Computational Tool Benchmarking.” Advanced Biotechnology 4: 9. https://doi.org/10.1007/s44307-025-00093-5

[686] Kovaka, Sam, Paul W. Hook, Katharine M. Jenike, Vikram Shivakumar, Luke B. Morina, Roham Razaghi, Winston Timp, and Michael C. Schatz. 2025. “Uncalled4 Improves Nanopore DNA and RNA Modification Detection via Fast and Accurate Signal Alignment.” Nature Methods 22: 681–691. https://doi.org/10.1038/s41592-025-02631-4

[687] Yang, Fan, Huanjun Kong, Jie Ying, Zihong Chen, Tao Luo, Wanli Jiang, Zhonghang Yuan, et al. 2025. “SeedLLM·rice: A Large Language Model Integrated With Rice Biological Knowledge Graph.” Molecular Plant 18: 1118–1129. https://doi.org/10.1016/j.molp.2025.05.013

[688] Long, Yanping, Zhijian Liu, Jinbu Jia, Weipeng Mo, Liang Fang, Dongdong, Lu, Bo Liu, Hong Zhang, Wei Chen, and Jixian Zhai. 2021. “FlsnRNA-Seq: Protoplasting-Free Full-Length Single-Nucleus RNA Profiling in Plants.” Genome Biology 22: 66. https://doi.org/10.1186/s13059-021-02288-0

[689] Moskal, Kinga, Marta Puchta-Jasińska, Paulina Bolc, Adrian Motor, Aleksandra Frankowski, Anna Pietrusińska-Radzio, Anna Rucińska, Karolina Tomiczak, and Maja Boczkowska. 2025. “Why ‘Where’ Matters as Much as ‘How Much’: Single-Cell and Spatial Transcriptomics in Plants.” International Journal of Molecular Sciences 26: 11819. https://doi.org/10.3390/ijms262411819

[690] Zhu, Tao, Tianxiang Li, Peitao Lü, and Chenlong Li. 2025. “Single-Cell Omics in Plant Biology: Mechanistic Insights and Applications for Crop Improvement.” Advanced Biotechnology 3: 20. https://doi.org/10.1007/s44307-025-00074-8

[691] Demesa-Arevalo, Edgar, Hannah Dӧrpholz, Isaia Vardanega, Jan Eric Maika, Itzel Pineda-Valentino, Stella Eggels, Tobias Lautwein, et al. 2026. “Imputation Integrates Single-Cell and Spatial Gene Expression Data to Resolve Transcriptional Networks in Barley Shoot Meristem Development.” Nature Plants 12: 107–124. https://doi.org/10.1038/s41477-025-02176-6

[692] Yao, Jie, Alexandre P. Marand, Yinqi Bai, Robert J. Schmitz, and Longjiang Fan. 2026. “Advances in Plant Spatial Multi-Omics Data Analysis.” Trends in Plant Science 31: 337–352. https://doi.org/10.1016/j.tplants.2025.10.005

[693] Tang, Jun, Shuyan Chen, and Guifang Jia. 2023. “Detection, Regulation, and Functions of RNA N6-methyladenosine Modification in Plants.” Plant Communications 4: 100546. https://doi.org/10.1016/j.xplc.2023.100546

[694] Yao, Jiayu, Guiyu Xiao, Xuan Ma, Shugang Hui, Heyang Shang, Jisen, Zhang, and Qiutao Xu. 2025. “The Emerging Epitranscriptomic Modification ac4C Regulates Plant Development and Stress Adaptation.” Nature Plants 11: 2200–2203. https://doi.org/10.1038/s41477-025-02140-4

[695] Wang, Silu, Judith E. Mank, Daniel Ortiz-Barrientos, and Loren H. Rieseberg. 2025. “Genome Architecture and Speciation in Plants and Animals.” Molecular Ecology 34: e70004. https://doi.org/10.1111/mec.70004

[696] Yépez, Vicente A., Mirjana Gusic, Robert Kopajtich, Christian Mertes, Nicholas H. Smith, Charlotte L. Alston, Rui Ban, et al. 2022. “Clinical Implementation of RNA Sequencing for Mendelian Disease Diagnostics.” Genome Medicine 14: 38. https://doi.org/10.1186/s13073-022-01019-9

[697] Shuja, Arslan. 2025. “Advances in RNA-seq Data Analysis: Towards More Reliable Clinical Translation: Advances in RNA-Seq Data Analysis: Towards Reliable Clinical Translation.” Developmental Medico-Life Sciences 2: 1–2. https://doi.org/10.69750/dmls.02.08.0143

[698] Deveson, Ira W., Binsheng Gong, Kevin Lai, Jennifer S. LoCoco, Todd A. Richmond, Jeoffrey Schageman, Zhihong Zhang, et al. 2021. “Evaluating the Analytical Validity of Circulating Tumor DNA Sequencing Assays for Precision Oncology.” Nature Biotechnology 39: 1115–1128. https://doi.org/10.1038/s41587-021-00857-z

[699] Uhrig, Sebastian, Julia Ellermann, Tatjana Walther, Pauline Burkhardt, Martina Fröhlich, Barbara Hutter, Umut H. Toprak, et al. 2021. “Accurate and Efficient Detection of Gene Fusions From RNA Sequencing Data.” Genome Research 31: 448–460. https://doi.org/10.1101/gr.257246.119

[700] Sikosek, Tobias, Marco Heuvelman, Jagoda Mika, Mustafa Kahraman, Julia Jehn, Maurice Frank, Alberto Daniel-Moreno, et al. 2025. “Early Detection of Alzheimer's Disease Using Small RNAs. Results From the EPAD Cohort.” The Journal of Prevention of Alzheimer's Disease 12: 100257. https://doi.org/10.1016/j.tjpad.2025.100257

[701] Paz, Sean, Janet D. Robishaw, and Massimo Caputi. 2026. “An RNA Biomarker Panel for the Diagnosis of Alzheimer's Disease From Whole Blood.” Alzheimer's Research & Therapy 18: 51. https://doi.org/10.1186/s13195-026-01977-x

[702] Gao, Yubang, Xuqing Liu, Yandong Jin, Ji Wu, Shuang Li, Yaxing Li, Binqing Chen, et al. 2022. “Drought Induces Epitranscriptome and Proteome Changes in Stem-Differentiating Xylem of Populus Trichocarpa.” Plant Physiology 190: 459–479. https://doi.org/10.1093/plphys/kiac272

[703] Zou, Ren-Chao, Kun Su, Dong Wei, Qiuhong Wang, Bo Tang, Tao Wang, Lianming Wang, Peng Chen, Tao Wu, and Xiawei Yang. 2025. “Direct RNA Sequencing Reveals Multilayered Epitranscriptomic Remodeling in Macrophages Upon Mtb Infection.” Frontiers in Cellular and Infection Microbiology 15: 1689553. https://doi.org/10.3389/fcimb.2025.1689553

[704] Chatla, Kamalakar, Brian Roper, Luladey Ayalew, Peggy Ko, Steffen Lippold, Meenakshi Doma, and Julien Camperi. 2026. “Assessing mRNA and sgRNA Quality for Cell and Gene Therapy Applications Using Nanopore Direct RNA Sequencing.” Analytical Chemistry 98: 7452–7461. https://doi.org/10.1021/acs.analchem.5c06819

Rights & permissions

2026 The Author(s). iMeta published by John Wiley & Sons Australia, Ltd on behalf of iMeta Science.