Profiling genome-wide DNA methylation

DNA methylation of cord blood cell types: Applications for mixed cell birth studies

(2016) Kelly M. Bakulski et al.   Epigenetics

DNA methylation on N6-adenine in mammalian embryonic stem cells

(2016) Tao P. Wu et al.   NATURE

Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences

(2016) Sebastian Moran et al.   Epigenomics

methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data

(2015) Kamal Kishore et al.   BMC BIOINFORMATICS

BSPAT: a fast online tool for DNA methylation co-occurrence pattern analysis based on high-throughput bisulfite sequencing data

(2015) Ke Hu et al.   BMC BIOINFORMATICS

MethGo: a comprehensive tool for analyzing whole-genome bisulfite sequencing data

(2015) Wen-Wei Liao et al.   BMC GENOMICS

Genome-wide analysis of DNA methylation in subjects with type 1 diabetes identifies epigenetic modifications associated with proliferative diabetic retinopathy

(2015) Elisabet Agardh et al.   BMC Medicine

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

DNA Demethylation Dynamics in the Human Prenatal Germline

(2015) Sofia Gkountela et al.   CELL

Epigenome-Wide Association of Liver Methylation Patterns and Complex Metabolic Traits in Mice

(2015) Luz D. Orozco et al.   Cell Metabolism

DNA methylation and application in forensic sciences

(2015) Farzeen Kader et al.   FORENSIC SCIENCE INTERNATIONAL

DNA methylation changes induced by long and short photoperiods in Nasonia

(2015) Mirko Pegoraro et al.   GENOME RESEARCH

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

(2015) Daofeng Li et al.   METHODS

Genome-wide signature of local adaptation linked to variable CpG methylation in oak populations

(2015) Alexander Platt et al.   MOLECULAR ECOLOGY

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing

(2015) Mark A Urich et al.   Nature Protocols

Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing

(2015) Hongshan Guo et al.   Nature Protocols

Single-cell epigenomics: techniques and emerging applications

(2015) Omer Schwartzman et al.   NATURE REVIEWS GENETICS

Charting oxidized methylcytosines at base resolution

(2015) Hao Wu 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

Reading the unique DNA methylation landscape of the brain: Non-CpG methylation, hydroxymethylation, and MeCP2

(2015) Benyam Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Base resolution methylome profiling: considerations in platform selection, data preprocessing and analysis

(2015) Zhifu Sun et al.   Epigenomics

Charting oxidized methylcytosines at base resolution

(2015) Hao Wu 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

A preliminary exploration on DNA methylation of transgene across generations in transgenic rats

(2015) Qiling Li et al.   Scientific Reports

Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics

(2015) Matthias Farlik et al.   Cell Reports

Whole-genome bisulfite sequencing of cell-free DNA identifies signature associated with metastatic breast cancer

(2015) Christophe Legendre et al.   Clinical Epigenetics

5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer

(2015) Santiago Uribe-Lewis et al.   GENOME BIOLOGY

SMAP: a streamlined methylation analysis pipeline for bisulfite sequencing

(2015) Shengjie Gao et al.   GigaScience

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Genome-Wide Epigenetic Regulation of Gene Transcription in Maize Seeds

(2015) Xiaoduo Lu et al.   PLoS One

MethylSig: a whole genome DNA methylation analysis pipeline

(2014) Yongseok Park et al.   BIOINFORMATICS

Accessing epigenetic variation in the plant methylome

(2014) K. D. Kim et al.   Briefings in Functional Genomics

Methylated DNA Immunoprecipitation and High-Throughput Sequencing (MeDIP-seq) Using Low Amounts of Genomic DNA

(2014) Ming-Tao Zhao et al.   Cellular Reprogramming

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

5-Hydroxymethylcytosine is a predominantly stable DNA modification

(2014) Martin Bachman et al.   Nature Chemistry

Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Advances in the profiling of DNA modifications: cytosine methylation and beyond

(2014) Nongluk Plongthongkum et al.   NATURE REVIEWS GENETICS

WBSA: Web Service for Bisulfite Sequencing Data Analysis

(2014) Fang Liang et al.   PLoS One

Statistical methods for detecting differentially methylated loci and regions

(2014) Mark D. Robinson et al.   Frontiers in Genetics

Detection of significantly differentially methylated regions in targeted bisulfite sequencing data

(2013) Katja Hebestreit et al.   BIOINFORMATICS

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

(2013) Weilong Guo et al.   BMC GENOMICS

Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition

(2013) Alika K Maunakea et al.   CELL RESEARCH

Genome-wide DNA methylation assay reveals novel candidate biomarker genes in cervical cancer

(2013) Sanja A Farkas et al.   Epigenetics

Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing

(2013) Aniruddha Chatterjee et al.   Epigenetics

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA

(2013) M. Regulski et al.   GENOME RESEARCH

The DNA Methyltransferase Dnmt1 Directly Interacts with the SET and RING Finger-associated (SRA) Domain of the Multifunctional Protein Uhrf1 to Facilitate Accession of the Catalytic Center to Hemi-methylated DNA

(2013) Ahmet Can Berkyurek et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Patterns of population epigenomic diversity

(2013) Robert J. Schmitz et al.   NATURE

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

Comparison of Methods for Quantification of Global DNA Methylation in Human Cells and Tissues

(2013) Sofia Lisanti et al.   PLoS One

Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA

(2013) A. H. Laszlo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mining cancer methylomes: prospects and challenges

(2013) Clare Stirzaker et al.   TRENDS IN GENETICS

BRAT-BW: efficient and accurate mapping of bisulfite-treated reads

(2012) Elena Y. Harris et al.   BIOINFORMATICS

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing

(2012) Zhifu Sun et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

CHH islands: de novo DNA methylation in near-gene chromatin regulation in maize

(2012) J. I. Gent et al.   GENOME RESEARCH

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Mapping recently identified nucleotide variants in the genome and transcriptome

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

BLUEPRINT to decode the epigenetic signature written in blood

(2012) David Adams et al.   NATURE BIOTECHNOLOGY

Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine

(2012) Miao Yu et al.   Nature Protocols

Methylome analysis using MeDIP-seq with low DNA concentrations

(2012) Oluwatosin Taiwo et al.   Nature Protocols

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

GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data

(2012) Touati Benoukraf et al.   NUCLEIC ACIDS RESEARCH

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging

(2012) Fumihito Miura et al.   NUCLEIC ACIDS RESEARCH

DNA methylation dynamics during the mammalian life cycle

(2012) J. A. Hackett et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

A Comparison of the Whole Genome Approach of MeDIP-Seq to the Targeted Approach of the Infinium HumanMethylation450 BeadChip® for Methylome Profiling

(2012) Christine Clark et al.   PLoS One

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Resources for methylome analysis suitable for gene knockout studies of potential epigenome modifiers

(2012) Gareth A Wilson et al.   GigaScience

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

(2011) Felix Krueger et al.   BIOINFORMATICS

MethylCoder: software pipeline for bisulfite-treated sequences

(2011) B. Pedersen et al.   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

A novel approach identifies new differentially methylated regions (DMRs) associated with imprinted genes

(2011) S. Choufani et al.   GENOME RESEARCH

High density DNA methylation array with single CpG site resolution

(2011) Marina Bibikova et al.   GENOMICS

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

A comparative analysis of DNA methylation across human embryonic stem cell lines

(2011) Pao-Yang Chen et al.   GENOME BIOLOGY

Quantification of Fetal DNA by Use of Methylation-Based DNA Discrimination

(2010) A. O. H. Nygren et al.   CLINICAL CHEMISTRY

Evaluation of affinity-based genome-wide DNA methylation data: Effects of CpG density, amplification bias, and copy number variation

(2010) M. D. Robinson et al.   GENOME RESEARCH

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Whole-genome DNA methylation profiling using MethylCap-seq

(2010) Arie B. Brinkman et al.   METHODS

Conserved role of intragenic DNA methylation in regulating alternative promoters

(2010) Alika K. Maunakea et al.   NATURE

Quantitative comparison of genome-wide DNA methylation mapping technologies

(2010) Christoph Bock et al.   NATURE BIOTECHNOLOGY

Single base–resolution methylome of the silkworm reveals a sparse epigenomic map

(2010) Hui Xiang et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

The UCSC Genome Browser database: update 2011

(2010) P. A. Fujita et al.   NUCLEIC ACIDS RESEARCH

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

(2010) Yun Huang et al.   PLoS One

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

High-throughput bisulfite sequencing in mammalian genomes

(2009) Zachary D. Smith et al.   METHODS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

(2009) Rafael A Irizarry et al.   NATURE GENETICS

MBD-isolated Genome Sequencing provides a high-throughput and comprehensive survey of DNA methylation in the human genome

(2009) David Serre et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Demethylation of Arabidopsis Endosperm

(2009) T.-F. Hsieh et al.   SCIENCE

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Comprehensive high-throughput arrays for relative methylation (CHARM)

(2008) R. A. Irizarry et al.   GENOME RESEARCH

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE