ArticleNature communications2024
Adapting nanopore sequencing basecalling models for modification detection via incremental learning and anomaly detection.
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 20 papers.
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Who cites it
20 citing papers in PubMed.
- Oxford Nanopore Sequencing, a Promising Technology for Precision Diagnostics in Intensive Care Units: A Narrative Review.Biomedicines · 2026Review
- ModiCal: A Targeted Calibration Workflow for Site-Specific mACS chemical biology · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Review
- Pseudouridylation landscape across 42bioRxiv : the preprint server for biology · 2026Article
- Nanopore direct RNA sequencing for RNA modification analysis: workflow assessment and computational tool benchmarking.Advanced biotechnology · 2026Article
- Review
- The new era of single-molecule RNA modification detection through nanopore base-calling models.Nature reviews. Molecular cell biology · 2026Review
- Advances in Detecting RNA Modifications Using Direct RNA Nanopore Sequencing.Advanced genetics (Hoboken, N.J.) · 2025Review
- A reference-guided iterative approach to polish the nanopore sequencing basecalling for therapeutic RNA quality control.Communications biology · 2025Article
- The Secret Life of NJournal of molecular biology · 2025Review
- NANOME: A Nextflow pipeline for haplotype-aware allele-specific consensus DNA methylation detection by nanopore long-read sequencing.bioRxiv : the preprint server for biology · 2025Article
- Past, Present and Future Perspectives of Forensic Genetics.Biomolecules · 2025Review
- De novo non-canonical nanopore basecalling enables private communication using heavily-modified DNA data at single-molecule level.Nature communications · 2025Article
- The RMaP challenge of predicting RNA modifications by nanopore sequencing.Communications chemistry · 2025Article
- Training data diversity enhances the basecalling of novel RNA modification-induced nanopore sequencing readouts.Nature communications · 2025Article
- Profiling the epigenome using long-read sequencing.Nature genetics · 2025Review
- Moving Beyond Oxford Nanopore Standard Procedures: New Insights from Water and Multiple Fish Microbiomes.International journal of molecular sciences · 2024Article
- The Precise Basecalling of Short-Read Nanopore Sequencing.bioRxiv : the preprint server for biology · 2024Article
- Training Data Diversity Enhances the Basecalling of Novel RNA Modification-Induced Nanopore Sequencing Readouts.bioRxiv : the preprint server for biology · 2024Article
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8 authors.
Funding
Abstract
We leverage machine learning approaches to adapt nanopore sequencing basecallers for nucleotide modification detection. We first apply the incremental learning (IL) technique to improve the basecalling of modification-rich sequences, which are usually of high biological interest. With sequence backbones resolved, we further run anomaly detection (AD) on individual nucleotides to determine their modification status. By this means, our pipeline promises the single-molecule, single-nucleotide, and sequence context-free detection of modifications. We benchmark the pipeline using control oligos, further apply it in the basecalling of densely-modified yeast tRNAs and E.coli genomic DNAs, the cross-species detection of N6-methyladenosine (m6A) in mammalian mRNAs, and the simultaneous detection of N1-methyladenosine (m1A) and m6A in human mRNAs. Our IL-AD workflow is available at: https://github.com/wangziyuan66/IL-AD .
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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.