ReviewComputational and structural biotechnology journal2022
Detecting RNA modification using direct RNA sequencing: A systematic review.
Review in Computational and structural biotechnology journal, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it, 30 citations in OpenAlex.
- Systematic review and meta-analysis of bulk RNAseq studies in human Alzheimer's disease brain tissue.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Pooled it
- Compendium of RNA modifications for bacterial stress adaptation.Microbiology and molecular biology reviews : MMBR · 2026Review
- Epitranscriptomic Analysis of A-to-I RNA Editing and mInternational journal of molecular sciences · 2026Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Nanopore direct RNA sequencing for RNA modification analysis: workflow assessment and computational tool benchmarking.Advanced biotechnology · 2026Article
- The new era of single-molecule RNA modification detection through nanopore base-calling models.Nature reviews. Molecular cell biology · 2026Review
- RNA Modifications in T cell Immunity: Mechanisms, Disease Relevance, and Therapeutic Potential.Theranostics · 2026Review
- Advances in Detecting RNA Modifications Using Direct RNA Nanopore Sequencing.Advanced genetics (Hoboken, N.J.) · 2025Review
- Investigating RNA dynamics from single molecule transcriptomes.Trends in genetics : TIG · 2025Review
- WarpDemuX-tRNA: barcode multiplexing for nanopore tRNA sequencing.Nucleic acids research · 2025Article
- Epitranscriptomic alterations induced by environmental toxins: implications for RNA modifications and disease.Genes and environment : the official journal of the Japanese Environmental Mutagen Society · 2025Review
- RNA Through Time: From the Origin of Life to Therapeutic Frontiers in Transcriptomics and Epitranscriptional Medicine.International journal of molecular sciences · 2025Review
- Comprehensive nucleoside analysis of archaeal RNA modification profiles reveals an mCell reports · 2025Article
- The detection, function, and therapeutic potential of RNA 2'-O-methylation.The innovation life · 2025Article
- RNA modifications and their role in gene expression.Frontiers in molecular biosciences · 2025Review
- Systematic review and meta-analysis of bulk RNAseq studies in human Alzheimer's disease brain tissue.bioRxiv : the preprint server for biology · 2024Article
- Detection and Quantification of 5moU RNA Modification from Direct RNA Sequencing Data.Current genomics · 2024Article
- The rise of epitranscriptomics: recent developments and future directions.Trends in pharmacological sciences · 2024Review
- Combined Analysis of the Whole Transcriptome of Piglets Infected with SADS-CoV Virulent and Avirulent Strains.Microorganisms · 2023Article
- Current Insights into mPlants (Basel, Switzerland) · 2023Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Post-transcriptional RNA modifications are involved in a range of important cellular processes, including the regulation of gene expression and fine-tuning of the functions of RNA molecules. To decipher the context-specific functions of these post-transcriptional modifications, it is crucial to accurately determine their transcriptomic locations and modification levels under a given cellular condition. With the newly emerged sequencing technology, especially nanopore direct RNA sequencing, different RNA modifications can be detected simultaneously with a single molecular level resolution. Here we provide a systematic review of 15 published RNA modification prediction tools based on direct RNA sequencing data, including their computational models, input-output formats, supported modification types, and reported performances. Finally, we also discussed the potential challenges and future improvements of nanopore sequencing-based methods for RNA modification detection.
Identifiers
What Socratic holds
Registered trials
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 Socratic graph.