ArticleNature protocols2020
Investigating RNA editing in deep transcriptome datasets with REDItools and REDIportal.
Article in Nature protocols, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 109 papers, 1 of them a synthesis that pooled it.
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Who cites it
109 citing papers in PubMed, 1 synthesis or guideline pooled it, 189 citations in OpenAlex.
- Meta-Analysis of Keratoconus Transcriptomic Data Revealed Altered RNA Editing Levels Impacting Keratin Genomic Clusters.Investigative ophthalmology & visual science · 2023Pooled it
- Spatial transcriptomics reveals laminar and cell-type-specific A-to-I RNA editing signatures in the macaque cortex.Nature communications · 2026Article
- Distinguishing self from non-self RNA by editing-specific inosine patterns.Nucleic acids research · 2026Article
- Article
- Epitranscriptomic Analysis of A-to-I RNA Editing and mInternational journal of molecular sciences · 2026Review
- AGAP1 and noncanonical GDP binding regulate triple-negative breast cancer development.Cellular and molecular life sciences : CMLS · 2026Article
- ADAR2 induces the differentiation of osteosarcoma cells by editing activity on IGFBP7: new implications for therapy.Bone research · 2026Article
- Identification of non-canonical peptides with moPepGen.Nature biotechnology · 2026Article
- A dual role of EZH2 in regulating A-to-I RNA editing and mRNA stability through ADAR.Nature communications · 2026Article
- Precise, minimally evolved adenine base editors generated through mutation reversion analysis.Nature biotechnology · 2026Article
- Multi-Tissue Genetic Regulation of RNA Editing in Pigs.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Identification of ADAR1i-124: The first effective A-to-I RNA editing inhibitor with promising cancer therapeutic potential.iScience · 2026Article
- Exogenous Epstein-Barr virus nuclear antigen 1 induces ADAR1-driven tumor resistance against immunotherapy.Signal transduction and targeted therapy · 2026Article
- RNA editing in cardiovascular health and disease.Communications biology · 2026Review
- Systematic evaluation of computational tools for multitype RNA modification detection using nanopore direct RNA sequencing.Nature methods · 2026Article
- Ab initio detection of multiple epitranscriptomic modifications from Oxford nanopore technology direct RNA sequencing data.Briefings in bioinformatics · 2026Article
- Biological and prognostic relevance of A-to-I RNA editing across consensus molecular subtypes of colon cancer.Scientific reports · 2026Article
- Rapid and Cost-Effective Digital Quantification of RNA Editing and Maturation in Organelle Transcripts by Oxford Nanopore Target-Indexed-PCR (TIP) Sequencing.Plant direct · 2025Article
- Plastid RNA Editing inGenes · 2025Article
- Analysis of the mRNA modification machinery alterations in breast cancer through the SCAN-B cohort.NAR cancer · 2025Article
49 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA editing is a widespread post-transcriptional mechanism able to modify transcripts through insertions/deletions or base substitutions. It is prominent in mammals, in which millions of adenosines are deaminated to inosines by members of the ADAR family of enzymes. A-to-I RNA editing has a plethora of biological functions, but its detection in large-scale transcriptome datasets is still an unsolved computational task. To this aim, we developed REDItools, the first software package devoted to the RNA editing profiling in RNA-sequencing (RNAseq) data. It has been successfully used in human transcriptomes, proving the tissue and cell type specificity of RNA editing as well as its pervasive nature. Outcomes from large-scale REDItools analyses on human RNAseq data have been collected in our specialized REDIportal database, containing more than 4.5 million events. Here we describe in detail two bioinformatic procedures based on our computational resources, REDItools and REDIportal. In the first procedure, we outline a workflow to detect RNA editing in the human cell line NA12878, for which transcriptome and whole genome data are available. In the second procedure, we show how to identify dysregulated editing at specific recoding sites in post-mortem brain samples of Huntington disease donors. On a 64-bit computer running Linux with ≥32 GB of random-access memory (RAM), both procedures should take ~76 h, using 4 to 24 cores. Our protocols have been designed to investigate RNA editing in different organisms with available transcriptomic and/or genomic reads. Scripts to complete both procedures and a docker image are available at https://github.com/BioinfoUNIBA/REDItools.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.