Systematic identification and annotation of human methylation marks based on bisulfite sequencing methylomes reveals distinct roles of cell type-specific hypomethylation in the regulation of cell identity genes

Integrative Analyses of Human Reprogramming Reveal Dynamic Nature of Induced Pluripotency

(2015) Davide Cacchiarelli et al.   CELL

Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin

(2015) Xiaofei Yang et al.   HUMAN MOLECULAR GENETICS

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

Transcription factor binding dynamics during human ES cell differentiation

(2015) Alexander M. Tsankov et al.   NATURE

Modeling the relationship of epigenetic modifications to transcription factor binding

(2015) Liang Liu et al.   NUCLEIC ACIDS RESEARCH

Deconstruction of DNA Methylation Patterns During Myogenesis Reveals Specific Epigenetic Events in the Establishment of the Skeletal Muscle Lineage

(2015) Elvira carrió et al.   STEM CELLS

Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics

(2015) Matthias Farlik et al.   Cell Reports

Effects of cytosine methylation on transcription factor binding sites

(2014) Yulia A Medvedeva et al.   BMC GENOMICS

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

MetaImprint: an information repository of mammalian imprinted genes

(2014) Y. Wei et al.   DEVELOPMENT

Genome-wide parent-of-origin DNA methylation analysis reveals the intricacies of human imprinting and suggests a germline methylation-independent mechanism of establishment

(2014) F. Court et al.   GENOME RESEARCH

Promiscuous MYC locus rearrangements hijack enhancers but mostly super-enhancers to dysregulate MYC expression in multiple myeloma

(2014) M Affer et al.   LEUKEMIA

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers

(2013) Jakob Lovén et al.   CELL

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Super-Enhancers in the Control of Cell Identity and Disease

(2013) Denes Hnisz et al.   CELL

Mapping Human Epigenomes

(2013) Chloe M. Rivera et al.   CELL

Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells

(2013) Wei Xie et al.   CELL

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm

(2013) B. Zhang et al.   GENOME RESEARCH

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Large conserved domains of low DNA methylation maintained by Dnmt3a

(2013) Mira Jeong et al.   NATURE GENETICS

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

(2013) Gary C Hon et al.   NATURE GENETICS

Quantitative epigenetic co-variation in CpG islands and co-regulation of developmental genes

(2013) Hongbo Liu et al.   Scientific Reports

DNA methylation presents distinct binding sites for human transcription factors

(2013) Shaohui Hu et al.   eLife

Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development

(2013) Yi-An Ko et al.   GENOME BIOLOGY

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data

(2012) Jianzhong Su et al.   NUCLEIC ACIDS RESEARCH

DNA methylation status predicts cell type-specific enhancer activity

(2011) Malgorzata Wiench et al.   EMBO JOURNAL

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

DiseaseMeth: a human disease methylation database

(2011) J. Lv et al.   NUCLEIC ACIDS RESEARCH

QDMR: a quantitative method for identification of differentially methylated regions by entropy

(2011) Yan Zhang et al.   NUCLEIC ACIDS RESEARCH

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

(2011) Jordana T Bell et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

CpG islands influence chromatin structure via the CpG-binding protein Cfp1

(2010) John P. Thomson et al.   NATURE

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

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

Identifying novel constrained elements by exploiting biased substitution patterns

(2009) Manuel Garber et al.   BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

(2009) Rafael A Irizarry et al.   NATURE GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

A census of human transcription factors: function, expression and evolution

(2009) Juan M. Vaquerizas et al.   NATURE REVIEWS GENETICS

DNA hypomethylation in cancer cells

(2009) Melanie Ehrlich   Epigenomics

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

(2008) Ryan Lister et al.   CELL

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

(2008) V. K. Rakyan et al.   GENOME RESEARCH

Epigenetics in Cancer

(2008) Manel Esteller   NEW ENGLAND JOURNAL OF MEDICINE

Errors in the bisulfite conversion of DNA: modulating inappropriate- and failed-conversion frequencies

(2008) D. P. Genereux et al.   NUCLEIC ACIDS RESEARCH

On the nature of human housekeeping genes

(2008) Jiang Zhu et al.   TRENDS IN GENETICS