ArticleBriefings in bioinformatics2025
MambaCpG: an accurate model for single-cell DNA methylation status imputation using mamba.
Article in Briefings in bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- A systematic benchmarking framework and dual-view optimization strategy for single-cell DNA methylation imputation.Briefings in bioinformatics · 2026Article
- Dissecting epigenetic heterogeneity in single-cell DNA methylomes with a unified framework.Nature communications · 2026Article
- Mamba6mA: a Mamba-based DNA N6-methyladenine site prediction model.Bioinformatics (Oxford, England) · 2026Article
- Artificial intelligence for comprehensive DNA methylation analysis: overview, challenges, and future directions.Briefings in bioinformatics · 2025Review
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Authors and funding
8 authors.
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Abstract
DNA methylation is a key epigenetic modification involved in biological processes and disease development. The accurate analysis of DNA methylation site information is of significant biological importance. Despite advances in single-cell sequencing, data sparsity due to low cytosine-phosphate-guanine (CpG) coverage remains a challenge. To address this, we introduce MambaCpG, a single-cell DNA methylation state imputation model based on the Mamba block. MambaCpG integrates the methylation matrix and DNA sequence context and uses bidirectional Mamba blocks to obtain embeddings, effectively capturing the long-range dependencies between CpG sites within DNA methylation patterns. Experiments on seven datasets of various scales demonstrate that MambaCpG outperforms existing models on large, highly sparse datasets while showing competitive performance on smaller datasets. MambaCpG has lower parameter and memory requirements, making it suitable for practical applications. MambaCpG also reveals ultra-long-range dependencies and provides new insights into DNA methylation patterning.
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Registered trials
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