DeepH&M: Estimating single-CpG hydroxymethylation and methylation levels from enrichment and restriction enzyme sequencing methods

DNA (Hydroxy)Methylation in T Helper Lymphocytes

(2019) Silvia Monticelli   TRENDS IN BIOCHEMICAL SCIENCES

Transposable elements drive widespread expression of oncogenes in human cancers

(2019) Hyo Sik Jang et al.   NATURE GENETICS

The role of TET-mediated DNA hydroxymethylation in prostate cancer

(2018) E. Smeets et al.   MOLECULAR AND CELLULAR ENDOCRINOLOGY

Profiling DNA Methylation Based on Next-Generation Sequencing Approaches: New Insights and Clinical Applications

(2018) Daniela Barros-Silva et al.   Genes

A unique role for DNA (hydroxy)methylation in epigenetic regulation of human inhibitory neurons

(2018) Alexey Kozlenkov et al.   Science Advances

The role of DNA methylation in epigenetics of aging

(2018) Archana Unnikrishnan et al.   PHARMACOLOGY & THERAPEUTICS

Mouse olfactory bulb methylome and hydroxymethylome maps reveal noncanonical active turnover of DNA methylation

(2017) Qin Ma et al.   Epigenetics

5-hydroxymethylcytosine accumulation in postmitotic neurons results in functional demethylation of expressed genes

(2017) Marian Mellén et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2017) Ksenia Skvortsova et al.   Epigenetics & Chromatin

Portraits of TET-mediated DNA hydroxymethylation in cancer

(2016) Jana Jeschke et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Whole-genome analysis of the methylome and hydroxymethylome in normal and malignant lung and liver

(2016) Xin Li et al.   GENOME RESEARCH

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

(2016) Dali Han et al.   MOLECULAR CELL

Absence of genomic hypomethylation or regulation of cytosine-modifying enzymes with aging in male and female mice

(2016) Niran Hadad et al.   Epigenetics & Chromatin

The elusive role of 5′-hydroxymethylcytosine

(2016) Moshe Szyf   Epigenomics

DNA hydroxymethylation controls cardiomyocyte gene expression in development and hypertrophy

(2016) Carolina M. Greco et al.   Nature Communications

Combining MeDIP-seq and MRE-seq to investigate genome-wide CpG methylation

(2015) Daofeng Li et al.   METHODS

Charting oxidized methylcytosines at base resolution

(2015) Hao Wu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Charting oxidized methylcytosines at base resolution

(2015) Hao Wu et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MeSiC: A Model-Based Method for Estimating 5 mC Levels at Single-CpG Resolution from MeDIP-seq

(2015) Yun Xiao et al.   Scientific Reports

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Programming and Inheritance of Parental DNA Methylomes in Mammals

(2014) Lu Wang et al.   CELL

The role of 5-hydroxymethylcytosine in human cancer

(2014) Gerd P. Pfeifer et al.   CELL AND TISSUE RESEARCH

Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain

(2014) Lu Wen et al.   GENOME BIOLOGY

MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation

(2013) Jianghan Qu et al.   BIOINFORMATICS

Mapping Human Epigenomes

(2013) Chloe M. Rivera et al.   CELL

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods

(2013) M. Stevens et al.   GENOME RESEARCH

Chromatin modifiers and remodellers: regulators of cellular differentiation

(2013) Taiping Chen et al.   NATURE REVIEWS GENETICS

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data

(2012) H. Wu et al.   BIOSTATISTICS

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

(2012) Miao Yu et al.   CELL

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

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

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

(2012) M. J. Booth et al.   SCIENCE

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

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

(2011) Gabriella Ficz et al.   NATURE

5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging

(2011) Keith E Szulwach et al.   NATURE NEUROSCIENCE

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

(2011) S. Ito et al.   SCIENCE

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

Conserved role of intragenic DNA methylation in regulating alternative promoters

(2010) Alika K. Maunakea et al.   NATURE

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

(2010) R Alan Harris et al.   NATURE BIOTECHNOLOGY

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

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li 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

DNA methylation landscapes: provocative insights from epigenomics

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