ArticleNature communications2024
LoDEI: a robust and sensitive tool to detect transcriptome-wide differential A-to-I editing in RNA-seq data.
Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed.
- A genome-scale CRISPRi perturbation atlas of human induced pluripotent stem cells.Nature biotechnology · 2026Article
- A cytoplasmic index for quantifying immune-related A-to-I RNA editing.Genome biology · 2026Article
- Knockdown of RNA editing proteins reshapes the HepaRG transcriptome and pharmacogene expression.Scientific reports · 2026Article
- RNA editing in cardiovascular health and disease.Communications biology · 2026Review
- TSniffer: unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data.Genome biology · 2026Article
- Regulatable In Vivo Gene Expression via Adaptamers.bioRxiv : the preprint server for biology · 2025Article
- ADARs: pleiotropy in function, versatility in application.Nucleic acids research · 2025Review
- LoDEI: a robust and sensitive tool to detect transcriptome-wide differential A-to-I editing in RNA-seq data.Nature communications · 2024Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
RNA editing is a highly conserved process. Adenosine deaminase acting on RNA (ADAR) mediated deamination of adenosine (A-to-I editing) is associated with human disease and immune checkpoint control. Functional implications of A-to-I editing are currently of broad interest to academic and industrial research as underscored by the fast-growing number of clinical studies applying base editors as therapeutic tools. Analyzing the dynamics of A-to-I editing, in a biological or therapeutic context, requires the sensitive detection of differential A-to-I editing, a currently unmet need. We introduce the local differential editing index (LoDEI) to detect differential A-to-I editing in RNA-seq datasets using a sliding-window approach coupled with an empirical q value calculation that detects more A-to-I editing sites at the same false-discovery rate compared to existing methods. LoDEI is validated on known and novel datasets revealing that the oncogene MYCN increases and that a specific small non-coding RNA reduces A-to-I editing.
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Registered trials
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