ArticleNature communications2024
Transfer learning enables identification of multiple types of RNA modifications using nanopore direct RNA sequencing.
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 54 papers.
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Who cites it
54 citing papers in PubMed.
- The role of RNA modifications in cancer translational control.RNA biology · 2026Review
- Advanced deep learning strategies in nanopore RNA sequencing.RNA biology · 2026Review
- The RNA structural code: orchestrating gene expression and enabling precision therapies.Acta pharmacologica Sinica · 2026Review
- The mRNA covalent modification dihydrouridine regulates transcript turnover and photosynthetic capacity during plant abiotic stress.The Plant cell · 2026Article
- ModiCal: A Targeted Calibration Workflow for Site-Specific mACS chemical biology · 2026Article
- Integrating mass spectrometry with Nanopore direct RNA sequencing forbioRxiv : the preprint server for biology · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Emerging roles of non-mNature plants · 2026Review
- RNA Aptamers and Epitranscriptomics: Charting Unexplored Territories in RNA Biology.Molecular diagnosis & therapy · 2026Review
- The 5-Methylcytosine RNA Modification in Hepatitis B Virus-Negative Hepatocellular Carcinoma: Insights From Long-Read Nanopore Sequencing.Molecular carcinogenesis · 2026Article
- Nanopore direct RNA sequencing for RNA modification analysis: workflow assessment and computational tool benchmarking.Advanced biotechnology · 2026Article
- Emerging roles of mRNA acetylation in plants.Plant communications · 2026Article
- Stoichiometry-preserving and stochasticity-aware identification of m6A from direct RNA sequencing.Briefings in bioinformatics · 2026Article
- Multi-omics and network pharmacology identify IGFBP1 as an m6A-Epigenetic target of pueraria in NSCLC therapy.PLoS computational biology · 2026Article
- Review
- Hidden in plain sight: illuminating the tRNA landscape by sequencing.Genome biology · 2026Review
- Systematic evaluation of computational tools for multitype RNA modification detection using nanopore direct RNA sequencing.Nature methods · 2026Article
- A dual context-aware basecaller for nanopore direct RNA sequencing.Nature communications · 2026Article
- A Comprehensive Review of Epigenetic Regulation of Vascular Smooth Muscle Cells During Development and Disease.Biomolecules · 2026Review
- Comprehensive mapping of RNA modification dynamics and crosstalk via deep learning and nanopore direct RNA-sequencing.Nature communications · 2026Article
Corrections and comments
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Authors and funding
11 authors.
Funding
Abstract
Nanopore direct RNA sequencing (DRS) has emerged as a powerful tool for RNA modification identification. However, concurrently detecting multiple types of modifications in a single DRS sample remains a challenge. Here, we develop TandemMod, a transferable deep learning framework capable of detecting multiple types of RNA modifications in single DRS data. To train high-performance TandemMod models, we generate in vitro epitranscriptome datasets from cDNA libraries, containing thousands of transcripts labeled with various types of RNA modifications. We validate the performance of TandemMod on both in vitro transcripts and in vivo human cell lines, confirming its high accuracy for profiling m
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