An evaluation of the genome-wide false positive rates of common methods for identifying differentially methylated regions using illumina methylation arrays

An epigenome-wide association study of posttraumatic stress disorder in US veterans implicates several new DNA methylation loci

(2020) Mark W. Logue et al.   Clinical Epigenetics

PTSD is associated with increased DNA methylation across regions of HLA-DPB1 and SPATC1L

(2020) Seyma Katrinli et al.   BRAIN BEHAVIOR AND IMMUNITY

mCSEA: detecting subtle differentially methylated regions

(2019) Jordi Martorell-Marugán et al.   BIOINFORMATICS

Nucleotide distance influences co-methylation between nearby CpG sites

(2019) Ornella Affinito et al.   GENOMICS

coMethDMR: accurate identification of co-methylated and differentially methylated regions in epigenome-wide association studies with continuous phenotypes

(2019) Lissette Gomez et al.   NUCLEIC ACIDS RESEARCH

Correction for multiple testing in candidate-gene methylation studies

(2019) Zhenwei Zhou et al.   Epigenomics

Comparison of novel and existing methods for detecting differentially methylated regions

(2018) Samantha Lent et al.   BMC GENETICS

The correlation of methylation levels measured using Illumina 450K and EPIC BeadChips in blood samples

(2017) Mark W Logue et al.   Epigenomics

EPIGENETIC VARIATION ATSKA2PREDICTS SUICIDE PHENOTYPES AND INTERNALIZING PSYCHOPATHOLOGY

(2016) Naomi Sadeh et al.   DEPRESSION AND ANXIETY

Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

(2016) Sebastian Moran et al.   Epigenomics

Probe Lasso: A novel method to rope in differentially methylated regions with 450K DNA methylation data

(2015) Lee M. Butcher et al.   METHODS

SKA2 methylation is associated with decreased prefrontal cortical thickness and greater PTSD severity among trauma-exposed veterans

(2015) N Sadeh et al.   MOLECULAR PSYCHIATRY

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

(2014) Martin J. Aryee et al.   BIOINFORMATICS

De novo detection of differentially bound regions for ChIP-seq data using peaks and windows: controlling error rates correctly

(2014) Aaron T.L. Lun et al.   NUCLEIC ACIDS RESEARCH

A Novel Method for Identification and Quantification of Consistently Differentially Methylated Regions

(2014) Ching-Lin Hsiao et al.   PLoS One

Age-related variations in the methylome associated with gene expression in human monocytes and T cells

(2014) Lindsay M. Reynolds et al.   Nature Communications

Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray

(2013) Yi-an Chen et al.   Epigenetics

Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values

(2012) B. S. Pedersen et al.   BIOINFORMATICS

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data

(2012) Andrew E. Teschendorff et al.   BIOINFORMATICS

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies

(2012) Andrew E Jaffe et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

The Dynamics of DNA Methylation in Schizophrenia and Related Psychiatric Disorders

(2012) Dennis R Grayson et al.   NEUROPSYCHOPHARMACOLOGY

QDMR: a quantitative method for identification of differentially methylated regions by entropy

(2011) Yan Zhang et al.   NUCLEIC ACIDS RESEARCH

Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis

(2010) Pan Du et al.   BMC BIOINFORMATICS

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution

(2010) Hongcang Gu et al.   NATURE METHODS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Generalizing Moving Averages for Tiling Arrays Using Combined P-Value Statistics

(2010) Katerina J Kechris et al.   Statistical Applications in Genetics and Molecular Biology