Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies

DNA methylation shows genome-wide association ofNFIX,RAPGEF2andMSRB3with gestational age at birth

(2012) Hwajin Lee et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

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

(2011) Andrew E. Teschendorff et al.   BIOINFORMATICS

Significance analysis and statistical dissection of variably methylated regions

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

High density DNA methylation array with single CpG site resolution

(2011) Marina Bibikova et al.   GENOMICS

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

Epigenome-wide association studies for common human diseases

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

Accurate genome-scale percentage DNA methylation estimates from microarray data

(2010) M. J. Aryee et al.   BIOSTATISTICS

Comprehensive methylome map of lineage commitment from haematopoietic progenitors

(2010) Hong Ji et al.   NATURE

Epigenetic memory in induced pluripotent stem cells

(2010) K. Kim et al.   NATURE

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

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

Epigenetics in cancer

(2009) S. Sharma et al.   CARCINOGENESIS

Methylation matters

(2009) Dirk Schübeler   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

(2009) Akiko Doi et al.   NATURE GENETICS

Multiple loci associated with indices of renal function and chronic kidney disease

(2009) Anna Köttgen et al.   NATURE GENETICS

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

(2009) Rafael A Irizarry et al.   NATURE GENETICS

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

Comprehensive high-throughput arrays for relative methylation (CHARM)

(2008) R. A. Irizarry et al.   GENOME RESEARCH

An integrated software system for analyzing ChIP-chip and ChIP-seq data

(2008) Hongkai Ji et al.   NATURE BIOTECHNOLOGY

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY