ArticleFrontiers in genetics2021
GMQN: A Reference-Based Method for Correcting Batch Effects and Probe Bias in HumanMethylation BeadChip.
Article in Frontiers in genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- TiSMeD: A tissue-specific methylation and expression database for biomarker and translational applications.Molecular therapy. Nucleic acids · 2026Article
- When complexity does not pay: benchmarking deep learning and ensemble methods for biomarker discovery.Briefings in bioinformatics · 2026Article
- Epigenetic analyses suggest different pathways during pregnancy for development of type 1 diabetes in children with high versus low-neutral human leukocyte antigen-risk.Journal of internal medicine · 2026Article
- A robust computational framework for methylation age and disease-risk prediction based on pairwise learning.Nature computational science · 2026Article
- Database resources of the National Genomics Data Center, China National Center for Bioinformation in 2026.Nucleic acids research · 2026Article
- EWAS Open Platform 2026: a deeply integrated resource for epigenome-wide association studies.Nucleic acids research · 2026Article
- Article
- Unveiling the epigenetic impact of vegan vs. omnivorous diets on aging: insights from the Twins Nutrition Study (TwiNS).BMC medicine · 2024Article
- Alternative polyadenylation quantitative trait methylation mapping in human cancers provides clues into the molecular mechanisms of APA.American journal of human genetics · 2024Article
- Kidney-specific methylation patterns correlate with kidney function and are lost upon kidney disease progression.Clinical epigenetics · 2024Article
- Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2024.Nucleic acids research · 2024Article
- Precise and interpretable neural networks reveal epigenetic signatures of aging across youth in health and disease.Frontiers in aging · 2024Article
- NCAE: data-driven representations using a deep network-coherent DNA methylation autoencoder identify robust disease and risk factor signatures.Briefings in bioinformatics · 2023Article
- Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2023.Nucleic acids research · 2023Article
- MethBank 4.0: an updated database of DNA methylation across a variety of species.Nucleic acids research · 2023Article
- Article
- Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022.Nucleic acids research · 2022Article
- EWAS Open Platform: integrated data, knowledge and toolkit for epigenome-wide association study.Nucleic acids research · 2022Article
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5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The Illumina HumanMethylation BeadChip is one of the most cost-effective methods to quantify DNA methylation levels at single-base resolution across the human genome, which makes it a routine platform for epigenome-wide association studies. It has accumulated tens of thousands of DNA methylation array samples in public databases, providing great support for data integration and further analysis. However, the majority of public DNA methylation data are deposited as processed data without background probes which are widely used in data normalization. Here, we present Gaussian mixture quantile normalization (GMQN), a reference based method for correcting batch effects as well as probe bias in the HumanMethylation BeadChip. Availability and implementation: https://github.com/MengweiLi-project/gmqn.
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