M3D: a kernel-based test for spatially correlated changes in methylation profiles

MethylSig: a whole genome DNA methylation analysis pipeline

(2014) Yongseok Park et al.   BIOINFORMATICS

MAGI

(2014) Douglas D Baumann et al.   Epigenetics

Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution

(2014) Michael J. Booth et al.   Nature Chemistry

S-adenosylmethionine Levels Regulate the Schwann Cell DNA Methylome

(2014) Marta Varela-Rey et al.   NEURON

Transcription factor binding predicts histone modifications in human cell lines

(2014) Dan Benveniste et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection of significantly differentially methylated regions in targeted bisulfite sequencing data

(2013) Katja Hebestreit et al.   BIOINFORMATICS

MMDiff: quantitative testing for shape changes in ChIP-Seq data sets

(2013) Gabriele Schweikert et al.   BMC GENOMICS

Dynamic DNA methylation across diverse human cell lines and tissues

(2013) K. E. Varley et al.   GENOME RESEARCH

Accurate detection of differential RNA processing

(2013) Philipp Drewe et al.   NUCLEIC ACIDS RESEARCH

Discovering high-resolution patterns of differential DNA methylation that correlate with gene expression changes

(2013) Nathan D. VanderKraats et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2014

(2013) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

DNA methylome analysis using short bisulfite sequencing data

(2012) Felix Krueger et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

Dnmt3a is essential for hematopoietic stem cell differentiation

(2011) Grant A Challen et al.   NATURE GENETICS

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

DNA Methylation of the First Exon Is Tightly Linked to Transcriptional Silencing

(2011) Fabienne Brenet et al.   PLoS One

Analysis of DNA Methylation in a Three-Generation Family Reveals Widespread Genetic Influence on Epigenetic Regulation

(2011) Jason Gertz et al.   PLoS Genetics

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

Targeting DNA methylation for epigenetic therapy

(2010) Xiaojing Yang et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

The DNA Methylome of Human Peripheral Blood Mononuclear Cells

(2010) Yingrui Li et al.   PLOS BIOLOGY

Epigenetics in cancer

(2009) S. Sharma et al.   CARCINOGENESIS

Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration

(2008) S. Bauer et al.   BIOINFORMATICS

DNA methylation in development and human disease

(2008) Suhasni Gopalakrishnan et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS