Statistical and integrative system-level analysis of DNA methylation data

AE Teschendorff, CL Relton - Nature Reviews Genetics, 2018 - nature.com
Epigenetics plays a key role in cellular development and function. Alterations to the
epigenome are thought to capture and mediate the effects of genetic and environmental risk …

An evaluation of methods correcting for cell-type heterogeneity in DNA methylation studies

K McGregor, S Bernatsky, I Colmegna, M Hudson… - Genome biology, 2016 - Springer
Background Many different methods exist to adjust for variability in cell-type mixture
proportions when analyzing DNA methylation studies. Here we present the result of an …

Analysing and interpreting DNA methylation data

C Bock - Nature Reviews Genetics, 2012 - nature.com
DNA methylation is an epigenetic mark that has suspected regulatory roles in a broad range
of biological processes and diseases. The technology is now available for studying DNA …

An overview of DNA methylation-derived trait score methods and applications

MF Nabais, DA Gadd, E Hannon, J Mill, AF McRae… - Genome Biology, 2023 - Springer
Microarray technology has been used to measure genome-wide DNA methylation in
thousands of individuals. These studies typically test the associations between individual …

DNA methylation-based predictors of health: applications and statistical considerations

PD Yousefi, M Suderman, R Langdon… - Nature Reviews …, 2022 - nature.com
DNA methylation data have become a valuable source of information for biomarker
development, because, unlike static genetic risk estimates, DNA methylation varies …

MeDeCom: discovery and quantification of latent components of heterogeneous methylomes

P Lutsik, M Slawski, G Gasparoni, N Vedeneev, M Hein… - Genome biology, 2017 - Springer
It is important for large-scale epigenomic studies to determine and explore the nature of
hidden confounding variation, most importantly cell composition. We developed MeDeCom …

Statistical methods for detecting differentially methylated loci and regions

MD Robinson, A Kahraman, CW Law, H Lindsay… - Frontiers in …, 2014 - frontiersin.org
DNA methylation, the reversible addition of methyl groups at CpG dinucleotides, represents
an important regulatory layer associated with gene expression. Changed methylation status …

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm

B Zhang, Y Zhou, N Lin, RF Lowdon, C Hong… - Genome …, 2013 - genome.cshlp.org
DNA methylation plays key roles in diverse biological processes such as X chromosome
inactivation, transposable element repression, genomic imprinting, and tissue-specific gene …

Introduction to epigenomics and epigenome-wide analysis

MJ Fazzari, JM Greally - Statistical Methods in Molecular Biology, 2010 - Springer
Epigenetics is the study of heritable change other than those encoded in DNA sequence.
Cytosine methylation of DNA at CpG dinucleotides is the most well-studied epigenetic …

Genome‐wide DNA methylation profiling

M Bibikova, JB Fan - Wiley Interdisciplinary Reviews: Systems …, 2010 - Wiley Online Library
DNA methylation plays a critical role in the regulation of gene expression. The ability to
access the methylation status for a large number of genes or the entire genome should …