Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers

MeQA: a pipeline for MeDIP-seq data quality assessment and analysis

(2011) J. Huang et al.   BIOINFORMATICS

hmChIP: a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data

(2011) Li Chen et al.   BIOINFORMATICS

Thymine DNA Glycosylase Is Essential for Active DNA Demethylation by Linked Deamination-Base Excision Repair

(2011) Salvatore Cortellino et al.   CELL

Human non-CG methylation

(2011) Olga V. Dyachenko et al.   Epigenetics

Comparative methylome analysis of benign and malignant peripheral nerve sheath tumors

(2011) A. Feber et al.   GENOME RESEARCH

Embryonic lethal phenotype reveals a function of TDG in maintaining epigenetic stability

(2011) Daniel Cortázar et al.   NATURE

The Polycomb complex PRC2 and its mark in life

(2011) Raphaël Margueron et al.   NATURE

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

(2011) Gabriella Ficz et al.   NATURE

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

A comparative analysis of DNA methylation across human embryonic stem cell lines

(2011) Pao-Yang Chen et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Combinatorial Transcriptional Control In Blood Stem/Progenitor Cells: Genome-wide Analysis of Ten Major Transcriptional Regulators

(2010) Nicola K. Wilson et al.   Cell Stem Cell

Jarid2 and PRC2, partners in regulating gene expression

(2010) G. Li et al.   GENES & DEVELOPMENT

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

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

Whole-genome DNA methylation profiling using MethylCap-seq

(2010) Arie B. Brinkman et al.   METHODS

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Ensembl 2011

(2010) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Jumonji Modulates Polycomb Activity and Self-Renewal versus Differentiation of Stem Cells

(2009) Xiaohua Shen et al.   CELL

SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state

(2009) S. Bilodeau et al.   GENES & DEVELOPMENT

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

(2008) David A Nix et al.   BMC BIOINFORMATICS

Connecting microRNA Genes to the Core Transcriptional Regulatory Circuitry of Embryonic Stem Cells

(2008) Alexander Marson et al.   CELL

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

Ezh1 and Ezh2 Maintain Repressive Chromatin through Different Mechanisms

(2008) Raphael Margueron et al.   MOLECULAR CELL

EZH1 Mediates Methylation on Histone H3 Lysine 27 and Complements EZH2 in Maintaining Stem Cell Identity and Executing Pluripotency

(2008) Xiaohua Shen et al.   MOLECULAR CELL

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY

The methylome: approaches for global DNA methylation profiling

(2008) Stephan Beck et al.   TRENDS IN GENETICS