Subtraction-free and bisulfite-free specific sequencing of 5-methylcytosine and its oxidized derivatives at base resolution

DNA 5-Methylcytosine-Specific Amplification and Sequencing

(2020) Chang Liu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Mapping the epigenetic modifications of DNA and RNA

(2020) Lin-Yong Zhao et al.   Protein & Cell

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

(2020) Yu He et al.   Science Advances

Bisulfite-free direct detection of 5-methylcytosine and 5-hydroxymethylcytosine at base resolution

(2019) Yibin Liu et al.   NATURE BIOTECHNOLOGY

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

Bisulfite-Free, Nanoscale Analysis of 5-Hydroxymethylcytosine at Single Base Resolution

(2018) Hu Zeng et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Nondestructive, base-resolution sequencing of 5-hydroxymethylcytosine using a DNA deaminase

(2018) Emily K Schutsky et al.   NATURE BIOTECHNOLOGY

Mapping and elucidating the function of modified bases in DNA

(2017) Eun-Ang Raiber et al.   Nature Reviews Chemistry

Base-resolution profiling of active DNA demethylation using MAB-seq and caMAB-seq

(2016) Hao Wu et al.   Nature Protocols

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

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics

(2015) Xingyu Lu et al.   CELL RESEARCH

Chromatin and RNA Maps Reveal Regulatory Long Noncoding RNAs in Mouse

(2015) Gireesh K. Bogu et al.   MOLECULAR AND CELLULAR BIOLOGY

5-Formylcytosine can be a stable DNA modification in mammals

(2015) Martin Bachman et al.   Nature Chemical Biology

Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale

(2015) Bo Xia et al.   NATURE METHODS

High-throughput single nucleotide variant discovery in E14 mouse embryonic stem cells provides a new reference genome assembly

(2014) Danny Incarnato et al.   GENOMICS

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Single-base resolution analysis of active DNA demethylation using methylase-assisted bisulfite sequencing

(2014) Hao Wu et al.   NATURE BIOTECHNOLOGY

Quantitative sequencing of 5-formylcytosine in DNA at single-base resolution

(2014) Michael J. Booth et al.   Nature Chemistry

DNA Methylation in Mammals

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

MLML: consistent simultaneous estimates of DNA methylation and hydroxymethylation

(2013) Jianghan Qu et al.   BIOINFORMATICS

Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming

(2013) Chun-Xiao Song et al.   CELL

MeCP2 Binds to 5hmC Enriched within Active Genes and Accessible Chromatin in the Nervous System

(2012) Marian Mellén et al.   CELL

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

(2012) Miao Yu et al.   CELL

A map of the cis-regulatory sequences in the mouse genome

(2012) Yin Shen et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

5-formylcytosine and 5-carboxylcytosine reduce the rate and substrate specificity of RNA polymerase II transcription

(2012) Matthew W Kellinger et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

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

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

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

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

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

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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