Comprehensive evaluation of genome-wide 5-hydroxymethylcytosine profiling approaches in human DNA

A Highly Sensitive and Robust Method for Genome-wide 5hmC Profiling of Rare Cell Populations

(2016) Dali Han et al.   MOLECULAR CELL

Quantitative comparison of DNA methylation assays for biomarker development and clinical applications

(2016) Christoph Bock et al.   NATURE BIOTECHNOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Accurate Measurement of 5-Methylcytosine and 5-Hydroxymethylcytosine in Human Cerebellum DNA by Oxidative Bisulfite on an Array (OxBS-Array)

(2015) Sarah F. Field et al.   PLoS One

Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

(2014) Martin J. Aryee et al.   BIOINFORMATICS

Tet3 and DNA Replication Mediate Demethylation of Both the Maternal and Paternal Genomes in Mouse Zygotes

(2014) Li Shen et al.   Cell Stem Cell

Active and Passive Demethylation of Male and Female Pronuclear DNA in the Mammalian Zygote

(2014) Fan Guo et al.   Cell Stem Cell

Application of a low cost array-based technique — TAB-Array — for quantifying and mapping both 5mC and 5hmC at single base resolution in human pluripotent stem cells

(2014) Kristopher L. Nazor et al.   GENOMICS

Loss of 5-hydroxymethylcytosine in cancer: Cause or consequence?

(2014) Gabriella Ficz et al.   GENOMICS

5-Hydroxymethylcytosine is a predominantly stable DNA modification

(2014) Martin Bachman et al.   Nature Chemistry

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

(2014) Michael J Ziller et al.   NATURE METHODS

5-Hydroxymethylcytosine: generation, fate, and genomic distribution

(2013) Li Shen et al.   CURRENT OPINION IN CELL BIOLOGY

TETonic shift: biological roles of TET proteins in DNA demethylation and transcription

(2013) William A. Pastor et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques

(2013) John P. Thomson et al.   NUCLEIC ACIDS RESEARCH

Dynamic changes in 5-hydroxymethylation signatures underpin early and late events in drug exposed liver

(2013) John P. Thomson et al.   NUCLEIC ACIDS RESEARCH

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

Mining cancer methylomes: prospects and challenges

(2013) Clare Stirzaker et al.   TRENDS IN GENETICS

Dynamics of 5-Hydroxymethylcytosine and Chromatin Marks in Mammalian Neurogenesis

(2013) Maria A. Hahn et al.   Cell Reports

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

(2012) Miao Yu et al.   CELL

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

(2012) Tao Wang et al.   HUMAN MOLECULAR GENETICS

Mapping recently identified nucleotide variants in the genome and transcriptome

(2012) Chun-Xiao Song et al.   NATURE BIOTECHNOLOGY

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine

(2012) Miao Yu et al.   Nature Protocols

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

(2012) M. J. Booth et al.   SCIENCE

Lineage-specific distribution of high levels of genomic

(2011) Alexey Ruzov et al.   CELL RESEARCH

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

High density DNA methylation array with single CpG site resolution

(2011) Marina Bibikova et al.   GENOMICS

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams et al.   NATURE

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

(2011) Jason Ernst 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

5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming

(2011) Mark Wossidlo et al.   Nature Communications

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

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

Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine

(2010) Seung-Gi Jin et al.   NUCLEIC ACIDS RESEARCH

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

(2010) Yun Huang et al.   PLoS One

Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates

(2010) Daniel Globisch et al.   PLoS One

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

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

(2009) M. Tahiliani et al.   SCIENCE

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

Genome-wide DNA methylation profiling using Infinium®assay

(2009) Marina Bibikova et al.   Epigenomics

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY