ArticleGenome biology2014
Dynamic evolution of clonal epialleles revealed by methclone.
Article in Genome biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- DNA Methylation Stochasticity Is Linked to Transcriptional Variability and Convergent Epigenetic Disruption across Genetic Subtypes of Acute Myeloid Leukemia.Cancer research · 2026Article
- DNA methylation patterns re-establish during clonal expansion restoring cell-to-cell epialleles heterogeneity.Biology direct · 2026Article
- DNA methylation heterogeneity in complex tumor microenvironment: Quantitative methods, influencing factors, and clinical implications.Genes & diseases · 2026Review
- DNA methylation cooperates with genomic alterations during non-small cell lung cancer evolution.Nature genetics · 2025Article
- Evidence of DNA methylation heterogeneity and epipolymorphism in kidney cancer tissue samples.Oncogene · 2025Article
- DNA methylation heterogeneity attributable to a complex tumor immune microenvironment prompts prognostic risk in glioma.Epigenetics · 2024Article
- Specific Methyl-CpG Configurations Define Cell Identity through Gene Expression Regulation.International journal of molecular sciences · 2023Article
- Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments.PLoS computational biology · 2023Article
- Tracking the evolution of esophageal squamous cell carcinoma under dynamic immune selection by multi-omics sequencing.Nature communications · 2023Article
- DNA methylation entropy as a measure of stem cell replication and aging.Genome biology · 2023Article
- Inferring the Cancer Cellular Epigenome Heterogeneity via DNA Methylation Patterns.Cancer treatment and research · 2023Article
- epialleleR: an R/Bioconductor package for sensitive allele-specific methylation analysis in NGS data.GigaScience · 2022Article
- MC profiling: a novel approach to analyze DNA methylation heterogeneity in genome-wide bisulfite sequencing data.NAR genomics and bioinformatics · 2022Article
- Epialleles and epiallelic heterogeneity in hematological malignancies.Medical oncology (Northwood, London, England) · 2022Review
- A novel workflow for the qualitative analysis of DNA methylation data.Computational and structural biotechnology journal · 2022Article
- DNA methylation-calling tools for Oxford Nanopore sequencing: a survey and human epigenome-wide evaluation.Genome biology · 2021Article
- Review
- Genomic and epigenomic evolution of acquired resistance to combination therapy in esophageal squamous cell carcinoma.JCI insight · 2021Article
- Epigenetic Forensics for Suspect Identification and Age Prediction.Forensic genomics · 2021Article
- The DNA methylation landscape of multiple myeloma shows extensive inter- and intrapatient heterogeneity that fuels transcriptomic variability.Genome medicine · 2021Article
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
We describe methclone, a novel method to identify epigenetic loci that harbor large changes in the clonality of their epialleles (epigenetic alleles). Methclone efficiently analyzes genome-wide DNA methylation sequencing data. We quantify the changes using a composition entropy difference calculation and also introduce a new measure of global clonality shift, loci with epiallele shift per million loci covered, which enables comparisons between different samples to gauge overall epiallelic dynamics. Finally, we demonstrate the utility of methclone in capturing functional epiallele shifts in leukemia patients from diagnosis to relapse. Methclone is open-source and freely available at https://code.google.com/p/methclone.
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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.