Review of processing and analysis methods for DNA methylation array data

A data-driven approach to preprocessing Illumina 450K methylation array data

(2013) Ruth Pidsley et al.   BMC GENOMICS

A genome-wide methylation study on obesity

(2013) Xiaojing Xu et al.   Epigenetics

Blood-based profiles of DNA methylation predict the underlying distribution of cell types

(2013) Devin C Koestler et al.   Epigenetics

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

(2013) Yi-an Chen et al.   Epigenetics

An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform

(2013) Francesco Marabita et al.   Epigenetics

Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis

(2013) Yun Liu et al.   NATURE BIOTECHNOLOGY

An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways

(2013) James West et al.   Scientific Reports

Differential variability improves the identification of cancer risk markers in DNA methylation studies profiling precursor cancer lesions

(2012) A. E. Teschendorff et al.   BIOINFORMATICS

IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data

(2012) D. Wang et al.   BIOINFORMATICS

CpGassoc: an R function for analysis of DNA methylation microarray data

(2012) Richard T. Barfield 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

A comparison of feature selection and classification methods in DNA methylation studies using the Illumina Infinium platform

(2012) Joanna J Zhuang et al.   BMC BIOINFORMATICS

DNA methylation arrays as surrogate measures of cell mixture distribution

(2012) Eugene Houseman et al.   BMC BIOINFORMATICS

Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects

(2012) Kristel R van Eijk et al.   BMC GENOMICS

Measuring the methylome in clinical samples: Improved processing of the Infinium Human Methylation450 BeadChip Array

(2012) Hong Pan et al.   Epigenetics

MethLAB: A graphical user interface package for the analysis of array-based DNA methylation data

(2012) Varun Kilaru et al.   Epigenetics

Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates

(2012) Gregory Hannum et al.   MOLECULAR CELL

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

Factors underlying variable DNA methylation in a human community cohort

(2012) L. L. Lam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Complete pipeline for Infinium® Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation

(2012) Nizar Touleimat et al.   Epigenomics

Population-specificity of human DNA methylation

(2012) Hunter B Fraser et al.   GENOME BIOLOGY

SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips

(2012) Jovana Maksimovic et al.   GENOME BIOLOGY

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies

(2011) Andrew E. Teschendorff et al.   BIOINFORMATICS

Batch effect correction for genome-wide methylation data with Illumina Infinium platform

(2011) Zhifu Sun et al.   BMC Medical Genomics

DNA methylation profiling reveals a predominant immune component in breast cancers

(2011) Sarah Dedeurwaerder et al.   EMBO Molecular Medicine

High density DNA methylation array with single CpG site resolution

(2011) Marina Bibikova et al.   GENOMICS

Statistical approaches for the analysis of DNA methylation microarray data

(2011) Kimberly D. Siegmund   HUMAN GENETICS

Epigenome-wide association studies for common human diseases

(2011) Vardhman K. Rakyan et al.   NATURE REVIEWS GENETICS

Evaluation of the Infinium Methylation 450K technology

(2011) Sarah Dedeurwaerder et al.   Epigenomics

Preprocessing differential methylation hybridization microarray data

(2011) Shuying Sun et al.   BioData Mining

Semi-supervised recursively partitioned mixture models for identifying cancer subtypes

(2010) Devin C. Koestler et al.   BIOINFORMATICS

A statistical framework for Illumina DNA methylation arrays

(2010) Pei Fen Kuan et al.   BIOINFORMATICS

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

(2010) Pan Du et al.   BMC BIOINFORMATICS

Subset Quantile Normalization Using Negative Control Features

(2010) Zhijin Wu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Epigenetics as a unifying principle in the aetiology of complex traits and diseases

(2010) Arturas Petronis   NATURE

Integrating common and rare genetic variation in diverse human populations

(2010)   NATURE

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

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

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Hunting for the 5th base: Techniques for analyzing DNA methylation

(2009) Ole Ammerpohl et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

An Epigenetic Signature in Peripheral Blood Predicts Active Ovarian Cancer

(2009) Andrew E. Teschendorff et al.   PLoS One

lumi: a pipeline for processing Illumina microarray

(2008) P. Du et al.   BIOINFORMATICS

Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions

(2008) E Andres Houseman et al.   BMC BIOINFORMATICS