BayMeth: improved DNA methylation quantification for affinity capture sequencing data using a flexible Bayesian approach

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods

(2013) M. Stevens et al.   GENOME RESEARCH

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Quality Evaluation of Methyl Binding Domain Based Kits for Enrichment DNA-Methylation Sequencing

(2013) Tim De Meyer et al.   PLoS One

Removing technical variability in RNA-seq data using conditional quantile normalization

(2012) K. D. Hansen et al.   BIOSTATISTICS

Analyzing the cancer methylome through targeted bisulfite sequencing

(2012) Eun-Joon Lee et al.   CANCER LETTERS

Minireview: Epigenetics of Obesity and Diabetes in Humans

(2012) Howard Slomko et al.   ENDOCRINOLOGY

Copy-number-aware differential analysis of quantitative DNA sequencing data

(2012) M. D. Robinson et al.   GENOME RESEARCH

Methylome analysis using MeDIP-seq with low DNA concentrations

(2012) Oluwatosin Taiwo et al.   Nature Protocols

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

A Comparison of the Whole Genome Approach of MeDIP-Seq to the Targeted Approach of the Infinium HumanMethylation450 BeadChip® for Methylome Profiling

(2012) Christine Clark et al.   PLoS One

Genome-wide DNA methylation profiling of non-small cell lung carcinomas

(2012) Rejane Carvalho et al.   Epigenetics & Chromatin

MBD-seq as a cost-effective approach for methylome-wide association studies: demonstration in 1500 case–control samples

(2012) Karolina A Aberg et al.   Epigenomics

False positive peaks in ChIP-seq and other sequencing-based functional assays caused by unannotated high copy number regions

(2011) Joseph K. Pickrell et al.   BIOINFORMATICS

Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias

(2011) Shalima S. Nair et al.   Epigenetics

Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors

(2011) A. Feber et al.   GENOME RESEARCH

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

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing

(2011) Eun-Joon Lee et al.   NUCLEIC ACIDS RESEARCH

Statistical Quantification of Methylation Levels by Next-Generation Sequencing

(2011) Guodong Wu et al.   PLoS One

High Resolution Detection and Analysis of CpG Dinucleotides Methylation Using MBD-Seq Technology

(2011) Xun Lan et al.   PLoS One

Repitools: an R package for the analysis of enrichment-based epigenomic data

(2010) A. L. Statham et al.   BIOINFORMATICS

Genome-wide analysis of aberrant methylation in human breast cancer cells using methyl-DNA immunoprecipitation combined with high-throughput sequencing

(2010) Yoshinao Ruike et al.   BMC GENOMICS

Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage

(2010) L. Chavez et al.   GENOME RESEARCH

Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation

(2010) M. D. Robinson et al.   GENOME RESEARCH

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

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

(2010) Hongcang Gu et al.   NATURE METHODS

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Protocol matters: which methylome are you actually studying?

(2010) Mark D Robinson et al.   Epigenomics

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Copy number variation has little impact on bead-array-based measures of DNA methylation

(2009) E. Andrés Houseman et al.   BIOINFORMATICS

PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data

(2009) C. D. Greenman et al.   BIOSTATISTICS

Finding the fifth base: Genome-wide sequencing of cytosine methylation

(2009) R. Lister et al.   GENOME RESEARCH

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome

(2009) David Serre et al.   NUCLEIC ACIDS RESEARCH

MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment

(2008) M. Pelizzola et al.   GENOME RESEARCH

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY