ArticleNature methods2025
Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment.
Article in Nature methods, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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40 citing papers in PubMed.
- Advanced deep learning strategies in nanopore RNA sequencing.RNA biology · 2026Review
- Article
- Direct detection of alternative DNA conformations with long-read sequencing and machine learning approaches.bioRxiv : the preprint server for biology · 2026Article
- Evaluation of Dorado v5.2.0 de novo basecalling models for the detection of tRNA modifications using RNA004 chemistry.BMC genomics · 2026Article
- Systematic benchmarking of dorado basecalling models for RNA modification detection with highly multiplexed nanopore sequencing.Nucleic acids research · 2026Article
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- DamageFormer: a damage-aware multimodal deep learning framework for DNA lesion identification from nanopore sequencing.bioRxiv : the preprint server for biology · 2026Article
- From Spatial Epigenomes to Clinical Diagnostics: Integrative Methylomics Across Scales and Modalities.International journal of molecular sciences · 2026Review
- Systematic assessment of diverse RNA modifications using nanopore direct RNA sequencing.Nucleic acids research · 2026Article
- Nanopore direct RNA sequencing for RNA modification analysis: workflow assessment and computational tool benchmarking.Advanced biotechnology · 2026Article
- Raw signal segmentation for estimating RNA modification from Nanopore direct RNA sequencing data.eLife · 2026Article
- SquiDBase: a community resource of raw nanopore data from microbes.NAR genomics and bioinformatics · 2026Article
- Rawsamble: overlapping raw nanopore signals using a hash-based seeding mechanism.Bioinformatics (Oxford, England) · 2026Article
- Advances and challenges in non-canonical nucleic acids data storage.Nature communications · 2026Review
- Article
- Epitranscriptomic control of cancer hallmarks: Functions, mechanisms, and therapeutics of RNA modifications.Cancer cell · 2026Review
- Ab initio detection of multiple epitranscriptomic modifications from Oxford nanopore technology direct RNA sequencing data.Briefings in bioinformatics · 2026Article
- m6AHD: a new framework for identifying abnormal N6-methyladenosine (m6A) in heart diseases based on sequencing features.Frontiers in genetics · 2026Article
- Efficient lossless compression of nanopore sequencing signals.Bioinformatics advances · 2026Article
- A metabolism-chromatin axis promotes differential ribosomal RNA transcription in the human malaria parasite.Nature communications · 2025Article
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8 authors.
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Abstract
Nanopore signal analysis enables detection of nucleotide modifications from native DNA and RNA sequencing, providing both accurate genetic or transcriptomic and epigenetic information without additional library preparation. At present, only a limited set of modifications can be directly basecalled (for example, 5-methylcytosine), while most others require exploratory methods that often begin with alignment of nanopore signal to a nucleotide reference. We present Uncalled4, a toolkit for nanopore signal alignment, analysis and visualization. Uncalled4 features an efficient banded signal alignment algorithm, BAM signal alignment file format, statistics for comparing signal alignment methods and a reproducible de novo training method for k-mer-based pore models, revealing potential errors in Oxford Nanopore Technologies' state-of-the-art DNA model. We apply Uncalled4 to RNA 6-methyladenine (m6A) detection in seven human cell lines, identifying 26% more modifications than Nanopolish using m6Anet, including in several genes where m6A has known implications in cancer. Uncalled4 is available open source at github.com/skovaka/uncalled4 .
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