MEDIPS: genome-wide differential coverage analysis of sequencing data derived from DNA enrichment experiments

DNA–Methylome Analysis of Mouse Intestinal Adenoma Identifies a Tumour-Specific Signature That Is Partly Conserved in Human Colon Cancer

(2013) Christina Grimm et al.   PLoS Genetics

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

(2011) William A. Pastor et al.   NATURE

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY