ArticleGenome biology2023
DeepEdit: single-molecule detection and phasing of A-to-I RNA editing events using nanopore direct RNA sequencing.
Article in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed.
- Review
- A-to-I mRNA editing: Why not simply incorporate inosine during mRNA synthesis?Molecular biology reports · 2026Review
- Structure-aware graph learning predicts RNA editability across tissues and species.Research square · 2026Article
- Nanopore direct RNA sequencing for RNA modification analysis: workflow assessment and computational tool benchmarking.Advanced biotechnology · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- Comprehensive mapping of RNA modification dynamics and crosstalk via deep learning and nanopore direct RNA-sequencing.Nature communications · 2026Article
- Epitranscriptomic control of cancer hallmarks: Functions, mechanisms, and therapeutics of RNA modifications.Cancer cell · 2026Review
- RMPore: a comprehensive database of single-molecule RNA modifications detected by Nanopore direct RNA sequencing.Nucleic acids research · 2026Article
- ADARs: pleiotropy in function, versatility in application.Nucleic acids research · 2025Review
- Long-read RNA sequencing: A transformative technology for exploring transcriptome complexity in human diseases.Molecular therapy : the journal of the American Society of Gene Therapy · 2025Review
- RNA editing in disease: mechanisms and therapeutic potential.RNA (New York, N.Y.) · 2025Review
- ncRNA Editing: Functional Characterization and Computational Resources.Methods in molecular biology (Clifton, N.J.) · 2025Article
- 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 · 2024Article
- Bioinformatics for Inosine: Tools and Approaches to Trace This Elusive RNA Modification.Genes · 2024Review
- Article
- Detecting haplotype-specific transcript variation in long reads with FLAIR2.Genome biology · 2024Article
- Exploring functional conservation in silico: a new machine learning approach to RNA-editing.Briefings in bioinformatics · 2024Article
- Navigating the landscape of epitranscriptomics and host immunity.Genome research · 2024Review
- Transfer learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing.Nature communications · 2024Article
- RNA editing enzymes: structure, biological functions and applications.Cell & bioscience · 2024Review
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Authors and funding
10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Single-molecule detection and phasing of A-to-I RNA editing events remain an unresolved problem. Long-read and PCR-free nanopore native RNA sequencing offers a great opportunity for direct RNA editing detection. Here, we develop a neural network model, DeepEdit, that not only recognizes A-to-I editing events in single reads of Oxford Nanopore direct RNA sequencing, but also resolves the phasing of RNA editing events on transcripts. We illustrate the robustness of DeepEdit by applying it to Schizosaccharomyces pombe and Homo sapiens transcriptome data. We anticipate DeepEdit to be a powerful tool for the study of RNA editing from a new perspective.
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Registered trials
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