Decoding the dynamic DNA methylation and hydroxymethylation landscapes in endodermal lineage intermediates during pancreatic differentiation of hESC

Engineered Split-TET2 Enzyme for Inducible Epigenetic Remodeling

(2017) Minjung Lee et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Distinct features of H3K4me3 and H3K27me3 chromatin domains in pre-implantation embryos

(2016) Xiaoyu Liu et al.   NATURE

TET-mediated DNA demethylation controls gastrulation by regulating Lefty–Nodal signalling

(2016) Hai-Qiang Dai et al.   NATURE

Nucleation of DNA repair factors by FOXA1 links DNA demethylation to transcriptional pioneering

(2016) Yu Zhang et al.   NATURE GENETICS

DNMT3A and TET2 compete and cooperate to repress lineage-specific transcription factors in hematopoietic stem cells

(2016) Xiaotian Zhang et al.   NATURE GENETICS

Active DNA demethylation at enhancers during the vertebrate phylotypic period

(2016) Ozren Bogdanović et al.   NATURE GENETICS

Transcription factors as readers and effectors of DNA methylation

(2016) Heng Zhu et al.   NATURE REVIEWS GENETICS

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Genome-wide Analysis Identifies Bcl6-Controlled Regulatory Networks during T Follicular Helper Cell Differentiation

(2016) Xindong Liu et al.   Cell Reports

Tet2 and Tet3 cooperate with B-lineage transcription factors to regulate DNA modification and chromatin accessibility

(2016) Chan-Wang Lio et al.   eLife

An Epigenomic Road Map for Endoderm Development

(2015) Klaus H. Kaestner   Cell Stem Cell

Epigenetic Priming of Enhancers Predicts Developmental Competence of hESC-Derived Endodermal Lineage Intermediates

(2015) Allen Wang et al.   Cell Stem Cell

Insulator dysfunction and oncogene activation in IDH mutant gliomas

(2015) William A. Flavahan et al.   NATURE

Broad H3K4me3 is associated with increased transcription elongation and enhancer activity at tumor-suppressor genes

(2015) Kaifu Chen et al.   NATURE GENETICS

Acute loss of TET function results in aggressive myeloid cancer in mice

(2015) Jungeun An et al.   Nature Communications

Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions

(2014) Hao Wu et al.   CELL

CUX1: a modulator of tumour aggressiveness in pancreatic neuroendocrine neoplasms

(2014) Sebastian Krug et al.   ENDOCRINE-RELATED CANCER

Effects of Tet-induced oxidation products of 5-methylcytosine on Dnmt1- and DNMT3a-mediated cytosine methylation

(2014) Debin Ji et al.   Molecular BioSystems

Dissecting the dynamic changes of 5-hydroxymethylcytosine in T-cell development and differentiation

(2014) A. Tsagaratou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA Methylation in Mammals

(2014) E. Li et al.   Cold Spring Harbor Perspectives in Biology

MOABS: model based analysis of bisulfite sequencing data

(2014) Deqiang Sun et al.   GENOME BIOLOGY

BSeQC: quality control of bisulfite sequencing experiments

(2013) Xueqiu Lin et al.   BIOINFORMATICS

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

Dynamic Chromatin Remodeling Mediated by Polycomb Proteins Orchestrates Pancreatic Differentiation of Human Embryonic Stem Cells

(2013) Ruiyu Xie et al.   Cell Stem Cell

TET enzymes, TDG and the dynamics of DNA demethylation

(2013) Rahul M. Kohli et al.   NATURE

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins

(2013) Morgan L Maeder et al.   NATURE BIOTECHNOLOGY

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

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Oxidative bisulfite sequencing of 5-methylcytosine and 5-hydroxymethylcytosine

(2013) Michael J Booth et al.   Nature Protocols

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

PscanChIP: finding over-represented transcription factor-binding site motifs and their correlations in sequences from ChIP-Seq experiments

(2013) Federico Zambelli et al.   NUCLEIC ACIDS RESEARCH

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Enrichment of human embryonic stem cell-derived NKX6.1-expressing pancreatic progenitor cells accelerates the maturation of insulin-secreting cells in vivo

(2013) Alireza Rezania et al.   STEM CELLS

Tet2 Facilitates the Derepression of Myeloid Target Genes during CEBPα-Induced Transdifferentiation of Pre-B Cells

(2012) Eric M. Kallin et al.   MOLECULAR CELL

A unique regulatory phase of DNA methylation in the early mammalian embryo

(2012) Zachary D. Smith et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

The anti-CMS technique for genome-wide mapping of 5-hydroxymethylcytosine

(2012) Yun Huang et al.   Nature Protocols

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Recognition and potential mechanisms for replication and erasure of cytosine hydroxymethylation

(2012) Hideharu Hashimoto et al.   NUCLEIC ACIDS RESEARCH

Tumor development is associated with decrease of TET gene expression and 5-methylcytosine hydroxylation

(2012) H Yang et al.   ONCOGENE

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

(2012) M. J. Booth et al.   SCIENCE

Tet1 and Tet2 Regulate 5-Hydroxymethylcytosine Production and Cell Lineage Specification in Mouse Embryonic Stem Cells

(2011) Kian Peng Koh et al.   Cell Stem Cell

Genome-wide analysis of 5-hydroxymethylcytosine distribution reveals its dual function in transcriptional regulation in mouse embryonic stem cells

(2011) H. Wu et al.   GENES & DEVELOPMENT

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams et al.   NATURE

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

(2011) William A. Pastor et al.   NATURE

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

(2011) Gabriella Ficz et al.   NATURE

Replication-Dependent Loss of 5-Hydroxymethylcytosine in Mouse Preimplantation Embryos

(2011) A. Inoue et al.   SCIENCE

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

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

Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2

(2010) Myunggon Ko et al.   NATURE

Rfx6 directs islet formation and insulin production in mice and humans

(2010) Stuart B. Smith et al.   NATURE

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

Selective chemical labeling reveals the genome-wide distribution of 5-hydroxymethylcytosine

(2010) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

(2010) Yun Huang et al.   PLoS One

DNA methylation and cellular reprogramming

(2010) Daniel D. De Carvalho et al.   TRENDS IN CELL BIOLOGY

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

Dynamic regulation of Pdx1 enhancers by Foxa1 and Foxa2 is essential for pancreas development

(2008) N. Gao et al.   GENES & DEVELOPMENT

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY