Effects of cytosine methylation on transcription factor binding sites

Epigenetics: The missing link to understanding β-cell dysfunction in the pathogenesis of type 2 diabetes

(2012) Elizabeth R. Gilbert et al.   Epigenetics

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Genome-wide DNA hydroxymethylation changes are associated with neurodevelopmental genes in the developing human cerebellum

(2012) Tao Wang et al.   HUMAN MOLECULAR GENETICS

A differentially methylated single CpG-site is correlated with estrogen receptor alpha transcription

(2012) Rainer W. Fürst et al.   JOURNAL OF STEROID BIOCHEMISTRY AND MOLECULAR BIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Evaluation of single CpG sites as proxies of CpG island methylation states at the genome scale

(2012) Víctor Barrera et al.   NUCLEIC ACIDS RESEARCH

HOCOMOCO: a comprehensive collection of human transcription factor binding sites models

(2012) Ivan V. Kulakovskiy et al.   NUCLEIC ACIDS RESEARCH

Quantitative Sequencing of 5-Methylcytosine and 5-Hydroxymethylcytosine at Single-Base Resolution

(2012) M. J. Booth et al.   SCIENCE

Epigenetic Islands in a Genetic Ocean

(2012) D. Schubeler   SCIENCE

Widespread Site-Dependent Buffering of Human Regulatory Polymorphism

(2012) Matthew T. Maurano et al.   PLoS Genetics

Unamplified cap analysis of gene expression on a single-molecule sequencer

(2011) M. Kanamori-Katayama et al.   GENOME RESEARCH

Identification of genetic elements that autonomously determine DNA methylation states

(2011) Florian Lienert et al.   NATURE GENETICS

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

(2011) Hongcang Gu et al.   Nature Protocols

5-Hydroxymethylcytosine is associated with enhancers and gene bodies in human embryonic stem cells

(2011) Hume Stroud et al.   GENOME BIOLOGY

Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated

(2010) Mun-Kit Choy et al.   BMC GENOMICS

Intergenic, gene terminal, and intragenic CpG islands in the human genome

(2010) Yulia A Medvedeva et al.   BMC GENOMICS

General Transcription Factor Binding at CpG Islands in Normal Cells Correlates with Resistance to De novo DNA Methylation in Cancer Cells

(2010) C. Gebhard et al.   CANCER RESEARCH

Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains

(2010) V. K. Rakyan et al.   GENOME RESEARCH

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications

(2010) R Alan Harris et al.   NATURE BIOTECHNOLOGY

Targets and dynamics of promoter DNA methylation during early mouse development

(2010) Julie Borgel et al.   NATURE GENETICS

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Dinucleotide Weight Matrices for Predicting Transcription Factor Binding Sites: Generalizing the Position Weight Matrix

(2010) Rahul Siddharthan   PLoS One

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

(2010) Yun Huang et al.   PLoS One

CpG methylation of half-CRE sequences creates C/EBP  binding sites that activate some tissue-specific genes

(2010) V. Rishi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Role of epigenetics in Alzheimer’s and Parkinson’s disease

(2010) John BJ Kwok   Epigenomics

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Motif discovery and motif finding from genome-mapped DNase footprint data

(2009) Ivan V. Kulakovskiy et al.   BIOINFORMATICS

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

Developmental programming of CpG island methylation profiles in the human genome

(2009) Ravid Straussman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DNA hypomethylation in cancer cells

(2009) Melanie Ehrlich   Epigenomics

Aging and Environmental Exposures Alter Tissue-Specific DNA Methylation Dependent upon CpG Island Context

(2009) Brock C. Christensen et al.   PLoS Genetics

G9a/GLP complexes independently mediate H3K9 and DNA methylation to silence transcription

(2008) Makoto Tachibana et al.   EMBO JOURNAL

Cyclical DNA methylation of a transcriptionally active promoter

(2008) Raphaël Métivier et al.   NATURE

Transient cyclical methylation of promoter DNA

(2008) Sara Kangaspeska et al.   NATURE

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS

DNA methylation landscapes: provocative insights from epigenomics

(2008) Miho M. Suzuki et al.   NATURE REVIEWS GENETICS

Nutritional Control of Reproductive Status in Honeybees via DNA Methylation

(2008) R. Kucharski et al.   SCIENCE

Global Mapping of DNA Methylation in Mouse Promoters Reveals Epigenetic Reprogramming of Pluripotency Genes

(2008) Cassandra R. Farthing et al.   PLoS Genetics