methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data

fastcluster: Fast Hierarchical, Agglomerative Clustering Routines forRandPython

(2015) Daniel Müllner   Journal of Statistical Software

MethylSig: a whole genome DNA methylation analysis pipeline

(2014) Yongseok Park et al.   BIOINFORMATICS

Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments

(2014) Egor Dolzhenko et al.   BMC BIOINFORMATICS

Deciphering the heterogeneity in DNA methylation patterns during stem cell differentiation and reprogramming

(2014) Xiaojian Shao et al.   BMC GENOMICS

WBSA: Web Service for Bisulfite Sequencing Data Analysis

(2014) Fang Liang et al.   PLoS One

Methy-Pipe: An Integrated Bioinformatics Pipeline for Whole Genome Bisulfite Sequencing Data Analysis

(2014) Peiyong Jiang et al.   PLoS One

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

(2014) Andrea Riebler et al.   GENOME BIOLOGY

Detection of significantly differentially methylated regions in targeted bisulfite sequencing data

(2013) Katja Hebestreit et al.   BIOINFORMATICS

Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues

(2013) Jiang Zhu et al.   CELL

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

(2013) M. Stevens et al.   GENOME RESEARCH

Patterns of population epigenomic diversity

(2013) Robert J. Schmitz et al.   NATURE

Subtelomeric hotspots of aberrant 5-hydroxymethylcytosine-mediated epigenetic modifications during reprogramming to pluripotency

(2013) Tao Wang et al.   NATURE CELL BIOLOGY

A Reference Methylome Database and Analysis Pipeline to Facilitate Integrative and Comparative Epigenomics

(2013) Qiang Song et al.   PLoS One

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Detection of allele-specific methylation through a generalized heterogeneous epigenome model

(2012) Q. Peng et al.   BIOINFORMATICS

A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data

(2012) H. Wu et al.   BIOSTATISTICS

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

Widespread dynamic DNA methylation in response to biotic stress

(2012) R. H. Dowen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification of a specific reprogramming-associated epigenetic signature in human induced pluripotent stem cells

(2012) S. Ruiz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

Hydroxylation of 5-Methylcytosine by TET1 Promotes Active DNA Demethylation in the Adult Brain

(2011) Junjie U. Guo et al.   CELL

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

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

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

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

The DNA methylome

(2010) Mattia Pelizzola et al.   FEBS LETTERS

Genome-wide screen of promoter methylation identifies novel markers in melanoma

(2009) Y. Koga et al.   GENOME RESEARCH

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY