ArticleNature communications2021
Cellular Heterogeneity-Adjusted cLonal Methylation (CHALM) improves prediction of gene expression.
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 19 papers.
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Who cites it
19 citing papers in PubMed.
- Decoding coupled epigenetic-fragmentomic signals in circulating cell-free DNA for interpretable cancer diagnosis.Genome medicine · 2026Article
- Pattools‑implemented methylation vector analysis reveals aberrant subtype‑specific methylation in lung cancer across tissue and plasma cfDNA.Clinical and translational medicine · 2026Article
- DNA methylation heterogeneity in complex tumor microenvironment: Quantitative methods, influencing factors, and clinical implications.Genes & diseases · 2026Review
- Article
- Early detection of gastric cancer via multiplex blood assay targeting CfDNA methylation signatures.Gastric cancer : official journal of the International Gastric Cancer Association and the Japanese Gastric Cancer Association · 2026Article
- DNA Methylation, Aging, and Cancer.Epigenomes · 2025Review
- A LTR retrotransposon insertion leads to leafy phenotype in maize by elevating ZmOM66 expression.Nature communications · 2025Article
- Article
- Liquid biopsy in hepatocellular carcinoma: Challenges, advances, and clinical implications.Clinical and molecular hepatology · 2025Review
- An expanded view of cell competition.Development (Cambridge, England) · 2024Review
- BS-clock, advancing epigenetic age prediction with high-resolution DNA methylation bisulfite sequencing data.Bioinformatics (Oxford, England) · 2024Article
- Wemics: A Single-Base Resolution Methylation Quantification Method for Enhanced Prediction of Epigenetic Regulation.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- mHapBrowser: a comprehensive database for visualization and analysis of DNA methylation haplotypes.Nucleic acids research · 2024Article
- DNA methylation profiling to determine the primary sites of metastatic cancers using formalin-fixed paraffin-embedded tissues.Nature communications · 2023Article
- MC profiling: a novel approach to analyze DNA methylation heterogeneity in genome-wide bisulfite sequencing data.NAR genomics and bioinformatics · 2022Article
- Multi-omics pan-cancer study of cuproptosis core geneFrontiers in immunology · 2022Article
- The concurrence of DNA methylation and demethylation is associated with transcription regulation.Nature communications · 2021Article
- Deep learning predicts gene expression as an intermediate data modality to identify susceptibility patterns in Mycobacterium tuberculosis infected Diversity Outbred mice.EBioMedicine · 2021Article
- Integrated Analysis of Omics Data Reveal AP-1 as a Potential Regulation Hub in the Inflammation-Induced Hyperalgesia Rat Model.Frontiers in immunology · 2021Article
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Authors and funding
10 authors.
Funding
Abstract
Promoter DNA methylation is a well-established mechanism of transcription repression, though its global correlation with gene expression is weak. This weak correlation can be attributed to the failure of current methylation quantification methods to consider the heterogeneity among sequenced bulk cells. Here, we introduce Cell Heterogeneity-Adjusted cLonal Methylation (CHALM) as a methylation quantification method. CHALM improves understanding of the functional consequences of DNA methylation, including its correlations with gene expression and H3K4me3. When applied to different methylation datasets, the CHALM method enables detection of differentially methylated genes that exhibit distinct biological functions supporting underlying mechanisms.
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