Establishing an analytic pipeline for genome-wide DNA methylation

Disentangling the Effects of Colocalizing Genomic Annotations to Functionally Prioritize Non-coding Variants within Complex-Trait Loci

(2015) Gosia Trynka et al.   AMERICAN JOURNAL OF HUMAN GENETICS

MEXPRESS: visualizing expression, DNA methylation and clinical TCGA data

(2015) Alexander Koch et al.   BMC GENOMICS

A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data

(2015) Ting Wang et al.   Epigenetics

Polycomb repressive complex 2 epigenomic signature defines age-associated hypermethylation and gene expression changes

(2015) Mikhail G Dozmorov   Epigenetics

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

(2015) Lee M. Butcher et al.   METHODS

oxBS-450K: A method for analysing hydroxymethylation using 450K BeadChips

(2015) Sabrina K. Stewart et al.   METHODS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Targeted exploration and analysis of large cross-platform human transcriptomic compendia

(2015) Qian Zhu et al.   NATURE METHODS

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

ADMIRE: analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay

(2015) Jens Preussner et al.   Epigenetics & Chromatin

DNA methylation profiling: comparison of genome-wide sequencing methods and the Infinium Human Methylation 450 Bead Chip

(2015) Denise L Walker et al.   Epigenomics

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

(2014) Martin J. Aryee et al.   BIOINFORMATICS

Reference-free cell mixture adjustments in analysis of DNA methylation data

(2014) Eugene Andres Houseman et al.   BIOINFORMATICS

Reducing the risk of false discovery enabling identification of biologically significant genome-wide methylation status using the HumanMethylation450 array

(2014) Haroon Naeem et al.   BMC GENOMICS

Epigenome-wide association studies without the need for cell-type composition

(2014) James Zou et al.   NATURE METHODS

Correction: Klotho Suppresses Cardiomyocyte Apoptosis in Mice with Stress-Induced Cardiac Injury via Downregulation of Endoplasmic Reticulum Stress

(2014) Shuang Song et al.   PLoS One

Novel region discovery method for Infinium 450K DNA methylation data reveals changes associated with aging in muscle and neuronal pathways

(2013) Mei-Lyn Ong et al.   AGING CELL

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

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

(2013) Ruth Pidsley et al.   BMC GENOMICS

Gene set analysis methods: statistical models and methodological differences

(2013) H. Maciejewski   BRIEFINGS IN BIOINFORMATICS

Review of processing and analysis methods for DNA methylation array data

(2013) C S Wilhelm-Benartzi et al.   BRITISH JOURNAL OF CANCER

Batch Effects and Pathway Analysis: Two Potential Perils in Cancer Studies Involving DNA Methylation Array Analysis

(2013) K. N. Harper et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Considerations for normalization of DNA methylation data by Illumina 450K BeadChip assay in population studies

(2013) Paul Yousefi 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

Genome-wide DNA methylation study suggests epigenetic accessibility and transcriptional poising of interferon-regulated genes in naïve CD4+ T cells from lupus patients

(2013) Patrick Coit et al.   JOURNAL OF AUTOIMMUNITY

Recommendations for the design and analysis of epigenome-wide association studies

(2013) Karin B Michels et al.   NATURE METHODS

Low-level processing of Illumina Infinium DNA Methylation BeadArrays

(2013) Timothy J. Triche et al.   NUCLEIC ACIDS RESEARCH

DNA methylation in complex disease: Applications in nursing research, practice, and policy

(2013) Michelle L. Wright et al.   NURSING OUTLOOK

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

(2012) D. Wang et al.   BIOINFORMATICS

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

DNA methylation arrays as surrogate measures of cell mixture distribution

(2012) Eugene Houseman et al.   BMC BIOINFORMATICS

Commentary: The seven plagues of epigenetic epidemiology

(2012) Bastiaan T Heijmans et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies

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

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals

(2012) Takeshi Obayashi et al.   NUCLEIC ACIDS RESEARCH

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

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

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

(2012) Jovana Maksimovic et al.   GENOME BIOLOGY

GenomeRunner: automating genome exploration

(2011) Mikhail G. Dozmorov et al.   BIOINFORMATICS

Significance analysis and statistical dissection of variably methylated regions

(2011) A. E. Jaffe et al.   BIOSTATISTICS

Predicting gene ontology from a global meta-analysis of 1-color microarray experiments

(2011) Mikhail G Dozmorov et al.   BMC BIOINFORMATICS

Genome-wide DNA methylation patterns in CD4+ T cells from patients with systemic lupus erythematosus

(2011) Matlock Jeffries et al.   Epigenetics

How birds of a feather flock together: genetics in autoimmune diseases

(2011) Jasper CA Broen et al.   Expert Review of Clinical Immunology

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

Environmental chemical exposures and human epigenetics

(2011) Lifang Hou et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

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

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Filtering, FDR and power

(2010) Maarten van Iterson et al.   BMC BIOINFORMATICS

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

(2010) Pan Du et al.   BMC BIOINFORMATICS

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

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

NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data

(2010) M. Hackenberg et al.   NUCLEIC ACIDS RESEARCH

Independent filtering increases detection power for high-throughput experiments

(2010) R. Bourgon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets

(2010) Silpa Suthram et al.   PLoS Computational Biology

An operational definition of epigenetics

(2009) S. L. Berger et al.   GENES & DEVELOPMENT

ToppGene Suite for gene list enrichment analysis and candidate gene prioritization

(2009) J. Chen et al.   NUCLEIC ACIDS RESEARCH

Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease

(2009) A. P. Feinberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Epigenetic biomarker development

(2009) Christoph Bock   Epigenomics

Gene-set approach for expression pattern analysis

(2008) D. Nam et al.   BRIEFINGS IN BIOINFORMATICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH