ArticleNature communications2021
Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning.
Article in Nature communications, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
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Who cites it
73 citing papers in PubMed, 125 citations in OpenAlex.
- Sperm AluY Epimutations in Male Partners of Couples with Unexplained Recurrent Pregnancy Loss.bioRxiv : the preprint server for biology · 2026Article
- Methionine overaccumulation reinforces heterochromatic non-CG hypermethylation and transposon silencing in Arabidopsis.Plant physiology · 2026Article
- Revolutionizing drug discovery from natural products: The roles of artificial intelligence and multi-omics in accelerating innovation.Acta pharmaceutica Sinica. B · 2026Article
- Epigenetic orchestration of sugar signaling in plant development and stress adaptation.Horticulture research · 2026Article
- CMA-Nano: A DNA Methylation Detection Method for Nanopore Sequencing Data Based on a Cross-Modal Attention Mechanism.ACS omega · 2026Article
- Haplotype-resolved genome assembly sheds light on the evolutionary history of autohexaploid Tripidium arundinaceum.Nature communications · 2026Article
- Gapless and phased genome assembly reveals post-allopolyploidization subgenomic diversification of tobacco centromeres.Genome biology · 2026Article
- Long-read sequencing technologies and bioinformatics: a new perspective for decoding DNA methylation modifications.Journal of translational medicine · 2026Review
- An improved Solanum verrucosum genome provides insight into potato centromeres and epigenetic regulation.G3 (Bethesda, Md.) · 2026Article
- MethyNano: supervised contrastive pretraining enables robust and generalizable methylation detection from nanopore sequencing.Bioinformatics (Oxford, England) · 2026Article
- Bioinformatics insights into plant genomic imprinting: approaches, challenges, and future perspectives.Briefings in functional genomics · 2026Review
- Bream: an open-source deep learning framework for simultaneous base calling and DNA methylation detection on novel nanopore sequencing platforms.Frontiers in genetics · 2026Article
- Integrated genomic and DNA methylome analyses reveal epigenetic regulation of stevia glycoside biosynthesis inHorticulture research · 2025Article
- Pan-centromere landscape and dynamic evolution in Brassica plants.Nature plants · 2025Article
- DNA methylation landscape of Nautilus Pompilius.BMC genomics · 2025Article
- Non-CG DNA methylation in animal genomes.Nature genetics · 2025Review
- Computational analysis of DNA methylation from long-read sequencing.Nature reviews. Genetics · 2025Review
- Artificial intelligence for comprehensive DNA methylation analysis: overview, challenges, and future directions.Briefings in bioinformatics · 2025Review
- PlantDeepMeth: A Deep Learning Model for Predicting DNA Methylation States in Plants.Plants (Basel, Switzerland) · 2025Article
- Accurate cross-species 5mC detection for Oxford Nanopore sequencing in plants with DeepPlant.Nature communications · 2025Article
13 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 4 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In plants, cytosine DNA methylations (5mCs) can happen in three sequence contexts as CpG, CHG, and CHH (where H = A, C, or T), which play different roles in the regulation of biological processes. Although long Nanopore reads are advantageous in the detection of 5mCs comparing to short-read bisulfite sequencing, existing methods can only detect 5mCs in the CpG context, which limits their application in plants. Here, we develop DeepSignal-plant, a deep learning tool to detect genome-wide 5mCs of all three contexts in plants from Nanopore reads. We sequence Arabidopsis thaliana and Oryza sativa using both Nanopore and bisulfite sequencing. We develop a denoising process for training models, which enables DeepSignal-plant to achieve high correlations with bisulfite sequencing for 5mC detection in all three contexts. Furthermore, DeepSignal-plant can profile more 5mC sites, which will help to provide a more complete understanding of epigenetic mechanisms of different biological processes.
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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.