ArticleNucleic acids research2025
Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications.
Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- The role of RNA modifications in cancer translational control.RNA biology · 2026Review
- The pseudouridine epitranscriptomic landscape of advanced prostate cancer therapeutic resistance identifies TIMM17A as a key player.Translational oncology · 2026Article
- Compendium of RNA modifications for bacterial stress adaptation.Microbiology and molecular biology reviews : MMBR · 2026Review
- Characterization of METTL3/14-mediated m6A modification in human transcriptome using Nanopore direct RNA sequencing.PLoS genetics · 2026Article
- Primer-Less Species Identification Throughout Fungal (International journal of molecular sciences · 2026Article
- Epitranscriptomic Analysis of A-to-I RNA Editing and mInternational journal of molecular sciences · 2026Review
- Systematic benchmarking of dorado basecalling models for RNA modification detection with highly multiplexed nanopore sequencing.Nucleic acids research · 2026Article
- Integrating mass spectrometry with Nanopore direct RNA sequencing forbioRxiv : the preprint server for biology · 2026Article
- NanoSimFormer: an end-to-end transformer-based nanopore signal simulator with basecaller guidance.Bioinformatics (Oxford, England) · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Assessment of nanopore RNA modification calling in human cell lines and synthetic systems.Genome biology · 2026Article
- Article
- The bladder cancer mEMBO reports · 2026Article
- Mapping human pre-rRNA processing and modification at single nucleotide resolution using long read nanopore sequencing.Nature communications · 2026Article
- Genomic language model mitigates chimera artifacts in nanopore direct RNA sequencing.Nature communications · 2026Article
- Current status and prospects of nanopore sequencing technology in the detection of pathogenic microorganisms.Frontiers in microbiology · 2026Review
- Advances in Massive Parallel Sequencing: From Genomics to Spatial Transcriptomics.Advances in experimental medicine and biology · 2026Review
- Pseudouridine increases ribosome stability in a thermophilic eukaryote.Nucleic acids research · 2025Article
- FTO depletion does not alter mbioRxiv : the preprint server for biology · 2025Article
- ModiDeC: a multi-RNA modification classifier for direct nanopore sequencing.Nucleic acids research · 2025Article
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Authors and funding
26 authors.
Funding
Abstract
Direct RNA sequencing (DRS) is a Nanopore-based technique for analyzing RNA in its native form. This technique promises breakthroughs in diagnostics and biomarker development. Coupled to RNA002 sequencing chemistry, its clinical implementation has been challenging due to low throughput, low accuracy, and lack of large-scale RNA-modification models. In this study, we evaluate the improvements achieved by pairing the latest RNA004 chemistry with novel modified-base-calling models for pseudouridine and N6-methyladenosine using diverse RNA samples from cell lines, synthetic oligos, and human blood. Finally, we present the first clinical application of DRS by confirming the loss of RNA methylation in a patient carrying truncating mutations in the methyltransferase METTL5. Conclusively, the combined use of RNA004 chemistry with the base-calling models significantly improved the throughput, accuracy, and site-specific detection of modifications. From this perspective, we offer an outlook on the potential suitability of DRS for use in routine diagnostics, as well as the first comprehensive benchmark of human peripheral blood. Furthermore, we demonstrate on the basis of a stop-codon readthrough enhancing agent potential roadblocks for routine quality assessments of RNA therapeutics.
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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.