ArticleNucleic acids research2017
Prediction of genome-wide DNA methylation in repetitive elements.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 65 papers, 1 of them a synthesis that pooled it.
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Who cites it
65 citing papers in PubMed, 1 synthesis or guideline pooled it, 160 citations in OpenAlex.
- Differential methylation as a diagnostic biomarker of rare renal diseases: a systematic review.BMC nephrology · 2019Pooled it
- Combined effects of urine exposure and cryopreservation on sperm quality: an in vitro study of retrograde ejaculation.Asian journal of andrology · 2026Article
- Retroelement Hypomethylation Links Hypoxia Signaling, Immune Phenotypes, and Survival in Clear Cell Renal Cell Carcinoma.bioRxiv : the preprint server for biology · 2026Article
- Epigenome-wide analysis of DNA-methylation signatures following climate-related disasters.BMC medicine · 2026Article
- A Region-Aware Structured Framework Improves Prediction of Gene Expression from DNA Methylation.Computational and structural biotechnology journal · 2026Article
- Epigenetic dysregulation of transposable elements in cognitive impairment and Alzheimer's disease.GeroScience · 2025Article
- Methylation reprogramming associated with aggressive prostate cancer and ancestral disparities.Molecular systems biology · 2025Article
- Methylation reference datasets from quartet DNA materials for benchmarking epigenome sequencing.Nature communications · 2025Article
- Retrotransposon methylation profiles and survival in Black women with high-grade serous ovarian carcinoma.Clinical epigenetics · 2025Article
- Effects of alcohol on the transcriptome, methylome and metabolome of in vitro gastrulating human embryonic cells.Disease models & mechanisms · 2025Article
- Reliable investigation of DNA methylation using Oxford nanopore technologies.Scientific reports · 2025Article
- Identification and Characterization of LINE and SINE Retrotransposons in the African Hedgehog (Genes · 2025Article
- Extensive epigenomic dysregulation is a hallmark of homologous recombination deficiency in triple-negative breast cancer.International journal of cancer · 2025Article
- Evaluation for CpG island methylation of FASN and SREBP promoter in Mongolian gerbil NAFLD model.Archives of medical science : AMS · 2025Article
- Normal gastric tissueEpigenetics reports · 2025Article
- Genome-wide DNA methylation and gene expression in human placentas derived from assisted reproductive technology.Communications medicine · 2024Article
- Understanding the biological processes of kidney carcinogenesis: an integrative multi-omics approach.Molecular systems biology · 2024Article
- Sodium arsenite-induced DNA methylation alterations exacerbated by p53 knockout in MCF7 cells.Heliyon · 2024Article
- Radiogenomic profiling of global DNA methylation associated with molecular phenotypes and immune features in glioma.BMC medicine · 2024Article
- Fetal hemoglobin induction in azacytidine responders enlightens methylation patterns related to blast clearance in higher-risk MDS and CMML.Clinical epigenetics · 2024Article
5 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
Abstract
DNA methylation in repetitive elements (RE) suppresses their mobility and maintains genomic stability, and decreases in it are frequently observed in tumor and/or surrogate tissues. Averaging methylation across RE in genome is widely used to quantify global methylation. However, methylation may vary in specific RE and play diverse roles in disease development, thus averaging methylation across RE may lose significant biological information. The ambiguous mapping of short reads by and high cost of current bisulfite sequencing platforms make them impractical for quantifying locus-specific RE methylation. Although microarray-based approaches (particularly Illumina's Infinium methylation arrays) provide cost-effective and robust genome-wide methylation quantification, the number of interrogated CpGs in RE remains limited. We report a random forest-based algorithm (and corresponding R package, REMP) that can accurately predict genome-wide locus-specific RE methylation based on Infinium array profiling data. We validated its prediction performance using alternative sequencing and microarray data. Testing its clinical utility with The Cancer Genome Atlas data demonstrated that our algorithm offers more comprehensively extended locus-specific RE methylation information that can be readily applied to large human studies in a cost-effective manner. Our work has the potential to improve our understanding of the role of global methylation in human diseases, especially cancer.
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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.