A reassessment of DNA-immunoprecipitation-based genomic profiling

Combinatorial DNA methylation codes at repetitive elements

(2017) Christophe Papin et al.   GENOME RESEARCH

The chemistries and consequences of DNA and RNA methylation and demethylation

(2017) Franziska R. Traube et al.   RNA Biology

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

(2017) Ksenia Skvortsova et al.   Epigenetics & Chromatin

TFBSTools: an R/bioconductor package for transcription factor binding site analysis

(2016) Ge Tan et al.   BIOINFORMATICS

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

DNA methylation on N6-adenine in mammalian embryonic stem cells

(2016) Tao P. Wu et al.   NATURE

Active DNA demethylation at enhancers during the vertebrate phylotypic period

(2016) Ozren Bogdanović et al.   NATURE GENETICS

DNA Methylation on N6-Adenine in C. elegans

(2015) Eric Lieberman Greer et al.   CELL

N6-Methyladenine DNA Modification in Drosophila

(2015) Guoqiang Zhang et al.   CELL

N6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas

(2015) Ye Fu et al.   CELL

Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications

(2015) Magdalena J Koziol et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Identification of methylated deoxyadenosines in vertebrates reveals diversity in DNA modifications

(2015) Magdalena J Koziol et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Loss of Tet Enzymes Compromises Proper Differentiation of Embryonic Stem Cells

(2014) Meelad M. Dawlaty et al.   DEVELOPMENTAL CELL

Aptamers in immunological research

(2014) Roald Nezlin   IMMUNOLOGY LETTERS

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Genome-wide Analysis Reveals TET- and TDG-Dependent 5-Methylcytosine Oxidation Dynamics

(2013) Li Shen et al.   CELL

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

(2013) Chun-Xiao Song et al.   CELL

Whole-Genome Bisulfite Sequencing of Two Distinct Interconvertible DNA Methylomes of Mouse Embryonic Stem Cells

(2013) Ehsan Habibi et al.   Cell Stem Cell

Predicting the molecular complexity of sequencing libraries

(2013) Timothy Daley et al.   NATURE METHODS

Comparative analysis of affinity-based 5-hydroxymethylation enrichment techniques

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

Comprehensive Methylome Characterization of Mycoplasma genitalium and Mycoplasma pneumoniae at Single-Base Resolution

(2013) Maria Lluch-Senar et al.   PLoS Genetics

Chromatin and epigenetic regulation of pre-mRNA processing

(2012) S. J. Brown et al.   HUMAN MOLECULAR GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The GLIB technique for genome-wide mapping of 5-hydroxymethylcytosine

(2012) William A Pastor et al.   Nature Protocols

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees

(2012) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Comparison of methyl-DNA immunoprecipitation (MeDIP) and methyl-CpG binding domain (MBD) protein capture for genome-wide DNA methylation analysis reveal CpG sequence coverage bias

(2011) Shalima S. Nair et al.   Epigenetics

Genome-wide Regulation of 5hmC, 5mC, and Gene Expression by Tet1 Hydroxylase in Mouse Embryonic Stem Cells

(2011) Yufei Xu et al.   MOLECULAR CELL

5-Hydroxymethylcytosine: a new kid on the epigenetic block?

(2011) F. Matarese et al.   Molecular Systems Biology

TET1 and hydroxymethylcytosine in transcription and DNA methylation fidelity

(2011) Kristine Williams 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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

General Transcription Factor Binding at CpG Islands in Normal Cells Correlates with Resistance to De novo DNA Methylation in Cancer Cells

(2010) C. Gebhard et al.   CANCER RESEARCH

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

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

(2010) R Alan Harris et al.   NATURE BIOTECHNOLOGY

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Orphan CpG Islands Identify Numerous Conserved Promoters in the Mammalian Genome

(2010) Robert S. Illingworth et al.   PLoS Genetics