ArticleGenome biology2023
L-GIREMI uncovers RNA editing sites in long-read RNA-seq.
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 24 papers.
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Who cites it
24 citing papers in PubMed.
- A poly(A)-independent PacBio strategy for organellar transcriptome profiling.Plant physiology · 2026Article
- Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods.Nature reviews. Molecular cell biology · 2026Review
- RMPore: a comprehensive database of single-molecule RNA modifications detected by Nanopore direct RNA sequencing.Nucleic acids research · 2026Article
- Systematic revelation and meditation on the significance of long exons using representative eukaryotic genomes.BMC genomics · 2025Article
- 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
- Article
- Taking control with RNA.Nature methods · 2025Article
- ncRNA Editing: Functional Characterization and Computational Resources.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Long-read Ribo-STAMP simultaneously measures transcription and translation with isoform resolution.Genome research · 2024Article
- Alternative splicing of transposable elements in human breast cancer.bioRxiv : the preprint server for biology · 2024Article
- Bioinformatics for Inosine: Tools and Approaches to Trace This Elusive RNA Modification.Genes · 2024Review
- ADAR-Mediated A>I(G) RNA Editing in the Genotoxic Drug Response of Breast Cancer.International journal of molecular sciences · 2024Review
- Detecting haplotype-specific transcript variation in long reads with FLAIR2.Genome biology · 2024Article
- Navigating the landscape of epitranscriptomics and host immunity.Genome research · 2024Review
- RNA editing enzymes: structure, biological functions and applications.Cell & bioscience · 2024Review
- Recommendations for detection, validation, and evaluation of RNA editing events in cardiovascular and neurological/neurodegenerative diseases.Molecular therapy. Nucleic acids · 2024Review
- Article
- Harnessing ADAR-Mediated Site-Specific RNA Editing in Immune-Related Disease: Prediction and Therapeutic Implications.International journal of molecular sciences · 2023Review
- dsRID: in silico identification of dsRNA regions using long-read RNA-seq data.Bioinformatics (Oxford, England) · 2023Article
- Article
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Authors and funding
8 authors.
Funding
Abstract
Although long-read RNA-seq is increasingly applied to characterize full-length transcripts it can also enable detection of nucleotide variants, such as genetic mutations or RNA editing sites, which is significantly under-explored. Here, we present an in-depth study to detect and analyze RNA editing sites in long-read RNA-seq. Our new method, L-GIREMI, effectively handles sequencing errors and read biases. Applied to PacBio RNA-seq data, L-GIREMI affords a high accuracy in RNA editing identification. Additionally, our analysis uncovered novel insights about RNA editing occurrences in single molecules and double-stranded RNA structures. L-GIREMI provides a valuable means to study nucleotide variants in long-read RNA-seq.
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Registered trials
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