ArticleNature communications2025
Direct detection of 8-oxo-dG using nanopore sequencing.
Article in Nature communications, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
17 citing papers in PubMed.
- Click-code-seq protocol for genome-wide single-nucleotide-resolution mapping of major types of DNA modifications.STAR protocols · 2026Article
- Antioxidant Proline Carbon Dot-Composited Poly(L-methionine) Hydrogel Restores Mitophagy to Alleviate Cellular Senescence in Intervertebral Disc Degeneration.Advanced materials (Deerfield Beach, Fla.) · 2026Article
- MethyNano: supervised contrastive pretraining enables robust and generalizable methylation detection from nanopore sequencing.Bioinformatics (Oxford, England) · 2026Article
- DamageFormer: a damage-aware multimodal deep learning framework for DNA lesion identification from nanopore sequencing.bioRxiv : the preprint server for biology · 2026Article
- Oxidative DNA lesions destabilize centromeres and drive chromosome instability.bioRxiv : the preprint server for biology · 2026Article
- Advances and challenges in non-canonical nucleic acids data storage.Nature communications · 2026Review
- Review
- Dynamic genome-wide mapping reveals how chromatin context shapes OGG1-mediated repair and related mutagenesis in human cells.Nucleic acids research · 2025Article
- Single-Molecule Biodosimetry.Analytical chemistry · 2025Article
- Strand-specific quantification of 8-oxo-dG and apurinic sites via Ligation-Dependent Probe Amplification (LPA).Redox biology · 2025Article
- Nitro-oxidative nucleotide modifications in plants and associated microorganisms: signalling sensors or stress symptoms?Journal of experimental botany · 2025Review
- De novo non-canonical nanopore basecalling enables private communication using heavily-modified DNA data at single-molecule level.Nature communications · 2025Article
- Review
- Somatic mutation as an explanation for epigenetic aging.Nature aging · 2025Article
- Whole Genome Sequencing Analysis of Model Organisms Elucidates the Association Between Environmental Factors and Human Cancer Development.International journal of molecular sciences · 2024Article
- The Precise Basecalling of Short-Read Nanopore Sequencing.bioRxiv : the preprint server for biology · 2024Article
- Toward Mapping Spatiotemporally Resolved Transcriptomes and RNA-Protein Interactions.Wiley interdisciplinary reviews. RNAReview
Corrections and comments
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Authors and funding
12 authors.
Funding
Abstract
Genomic DNA is under constant oxidative damage, with 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxo-dG) being the prominent lesion linked to mutagenesis, epigenetics, and gene regulation. Existing methods to detect 8-oxo-dG rely on indirect approaches, while nanopore sequencing enables direct detection of base modifications. A model for 8-oxo-dG detection is currently missing due to the lack of training data. Here, we develop a strategy using synthetic oligos to generate long, 8-oxo-dG context-variable DNA molecules for deep learning and nanopore sequencing. Our training approach addresses the rarity of 8-oxo-dG relative to guanine, enabling specific detection. Applied to a tissue culture model of oxidative damage, our method reveals uneven genomic 8-oxo-dG distribution, dissimilar context pattern to C>A mutations, and local 5-mC depletion. This dual measurement of 5-mC and 8-oxo-dG at single-molecule resolution uncovers new insights into their interplay. Our approach also provides a general framework for detecting other rare DNA modifications using synthetic DNA and nanopore sequencing.
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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.