ArticleNature methods2021
Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing.
Article in Nature methods, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers.
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Who cites it
124 citing papers in PubMed, 199 citations in OpenAlex.
- Lineage-associated differences in adenine methylation patterns of mammalian-associatedMicrobiology spectrum · 2026Article
- Comprehensive benchmarking of tools for nanopore-based detection of DNA methylation.Nature communications · 2026Article
- Long-read metagenomics and methylation-based binning support the discovery of antibiotic resistance gene-host associations in complex communities.Genome biology · 2026Article
- Comparative genomics and methylome profiling ofMicrobial genomics · 2026Article
- CMA-Nano: A DNA Methylation Detection Method for Nanopore Sequencing Data Based on a Cross-Modal Attention Mechanism.ACS omega · 2026Article
- Epigenetic Phase Variation in Bacterial Adaptation to Environmental Stress: A Narrative Review.Current microbiology · 2026Review
- A review of computational approaches for metagenomics by long-read sequencing.Science China. Life sciences · 2026Review
- Nanopore Sequencing in Veterinary Pathogen Detection: A Review of Technologies and Applications.Veterinary sciences · 2026Review
- Recovery and microbial host assignment of mobile genetic elements in complex microbiomes: insights from a spiked gut sample.mSystems · 2026Article
- Article
- A pentose, as a cytosine nucleobase modification inApplied and environmental microbiology · 2026Article
- Review
- Comprehensive mapping of RNA modification dynamics and crosstalk via deep learning and nanopore direct RNA-sequencing.Nature communications · 2026Article
- Epigenetic regulation in prokaryotes: transcriptional and phenotypic outcomes of DNA methyltransferase activity.FEMS microbiology reviews · 2026Review
- Replication-coupled hemimethylation inFrontiers in microbiology · 2026Review
- Article
- Gene regulation inMicrobiology and molecular biology reviews : MMBR · 2025Review
- Long-read metagenomics for strain tracking after faecal microbiota transplant.Nature microbiology · 2025Article
- Adenine DNA methylation associated with transcriptionally permissive chromatin is widespread across eukaryotes.Nature genetics · 2025Article
- UsingACS synthetic biology · 2025Article
64 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Bacterial DNA methylation occurs at diverse sequence contexts and plays important functional roles in cellular defense and gene regulation. Existing methods for detecting DNA modification from nanopore sequencing data do not effectively support de novo study of unknown bacterial methylomes. In this work, we observed that a nanopore sequencing signal displays complex heterogeneity across methylation events of the same type. To enable nanopore sequencing for broadly applicable methylation discovery, we generated a training dataset from an assortment of bacterial species and developed a method, named nanodisco ( https://github.com/fanglab/nanodisco ), that couples the identification and fine mapping of the three forms of methylation into a multi-label classification framework. We applied it to individual bacteria and the mouse gut microbiome for reliable methylation discovery. In addition, we demonstrated the use of DNA methylation for binning metagenomic contigs, associating mobile genetic elements with their host genomes and identifying misassembled metagenomic contigs.
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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 OpenQuestion graph.