Latest techniques to study DNA methylation

A High-Quality De novo Genome Assembly from a Single Mosquito Using PacBio Sequencing

(2019) Sarah Kingan et al.   Genes

Single-molecule sequencing detection of N6-methyladenine in microbial reference materials

(2019) Alexa B. R. McIntyre et al.   Nature Communications

Using long-read sequencing to detect imprinted DNA methylation

(2019) Scott Gigante et al.   NUCLEIC ACIDS RESEARCH

NanoMod: a computational tool to detect DNA modifications using Nanopore long-read sequencing data

(2019) Qian Liu et al.   BMC GENOMICS

Using local alignment to enhance single-cell bisulfite sequencing data efficiency

(2019) Peng Wu et al.   BIOINFORMATICS

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

(2019) Peng Ni et al.   BIOINFORMATICS

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads

(2019) Carolin A. Müller et al.   NATURE METHODS

DNAmod: the DNA modification database

(2019) Ankur Jai Sood et al.   Journal of Cheminformatics

Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data

(2019) Qian Liu et al.   Nature Communications

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Dynamics and function of DNA methylation in plants

(2018) Huiming Zhang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

“Same difference”: comprehensive evaluation of four DNA methylation measurement platforms

(2018) Thadeous J. Kacmarczyk et al.   Epigenetics & Chromatin

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

(2018) Stephen J. Clark et al.   Nature Communications

Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

(2018) Haotian Teng et al.   GigaScience

Deciphering bacterial epigenomes using modern sequencing technologies

(2018) John Beaulaurier et al.   NATURE REVIEWS GENETICS

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Mapping DNA methylation with high-throughput nanopore sequencing

(2017) Arthur C Rand et al.   NATURE METHODS

TET-mediated active DNA demethylation: mechanism, function and beyond

(2017) Xiaoji Wu et al.   NATURE REVIEWS GENETICS

Single-cell epigenomics: Recording the past and predicting the future

(2017) Gavin Kelsey et al.   SCIENCE

Single-Cell Multiomics: Multiple Measurements from Single Cells

(2017) Iain C. Macaulay et al.   TRENDS IN GENETICS

Bisulfite oligonucleotide-capture sequencing for targeted base- and strand-specific absolute 5-methylcytosine quantitation

(2016) Dustin R. Masser et al.   AGE

Parallel single-cell sequencing links transcriptional and epigenetic heterogeneity

(2016) Christof Angermueller et al.   NATURE METHODS

Multi-Omics of Single Cells: Strategies and Applications

(2016) Christoph Bock et al.   TRENDS IN BIOTECHNOLOGY

Profiling genome-wide DNA methylation

(2016) Wai-Shin Yong et al.   Epigenetics & Chromatin

DNA methylation in bacteria: from the methyl group to the methylome

(2015) María A Sánchez-Romero et al.   CURRENT OPINION IN MICROBIOLOGY

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

(2015) Hongshan Guo et al.   Nature Protocols

Post-conversion targeted capture of modified cytosines in mammalian and plant genomes

(2015) Qing Li et al.   NUCLEIC ACIDS RESEARCH

Defining the sequence requirements for the positioning of base J in DNA using SMRT sequencing

(2015) Paul-Andre Genest et al.   NUCLEIC ACIDS RESEARCH

Single molecule-level detection and long read-based phasing of epigenetic variations in bacterial methylomes

(2015) John Beaulaurier et al.   Nature Communications

Targeted DNA Methylation Analysis by Next-generation Sequencing

(2015) Dustin R. Masser et al.   Jove-Journal of Visualized Experiments

Abnormalities in human pluripotent cells due to reprogramming mechanisms

(2014) Hong Ma et al.   NATURE

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

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

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

(2014) Michael J Ziller et al.   NATURE METHODS

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

(2014) Sébastien A Smallwood et al.   NATURE METHODS

DNA Methylation in Mammals

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

Haplotype Estimation Using Sequencing Reads

(2013) Olivier Delaneau et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Enhanced 5-methylcytosine detection in single-molecule, real-time sequencing via Tet1 oxidation

(2013) Tyson A Clark et al.   BMC BIOLOGY

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

(2013) Chun-Xiao Song et al.   CELL

Chemical Modification-Assisted Bisulfite Sequencing (CAB-Seq) for 5-Carboxylcytosine Detection in DNA

(2013) Xingyu Lu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain

(2013) Junjie U Guo et al.   NATURE NEUROSCIENCE

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

Focused, high accuracy 5-methylcytosine quantitation with base resolution by benchtop next-generation sequencing

(2013) Dustin R Masser et al.   Epigenetics & Chromatin

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

(2012) Miao Yu et al.   CELL

Going beyond five bases in DNA sequencing

(2012) Jonas Korlach et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

(2012) E. E. Schadt et al.   GENOME RESEARCH

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

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

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

(2012) Fumihito Miura et al.   NUCLEIC ACIDS RESEARCH

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

(2012) M. J. Booth et al.   SCIENCE

Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia

(2012) Altuna Akalin et al.   PLoS Genetics

Differential DNA methylation in discrete developmental stages of the parasitic nematode Trichinella spiralis

(2012) Fei Gao et al.   GENOME BIOLOGY

Gel-free multiplexed reduced representation bisulfite sequencing for large-scale DNA methylation profiling

(2012) Patrick Boyle et al.   GENOME BIOLOGY

Strategies for discovery and validation of methylated and hydroxymethylated DNA biomarkers

(2012) Ekaterina Olkhov-Mitsel et al.   Cancer Medicine

CpG islands and the regulation of transcription

(2011) A. M. Deaton et al.   GENES & DEVELOPMENT

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

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

(2011) Hongcang Gu et al.   Nature Protocols

Uncovering the role of 5-hydroxymethylcytosine in the epigenome

(2011) Miguel R. Branco et al.   NATURE REVIEWS GENETICS

Repetitive DNA and next-generation sequencing: computational challenges and solutions

(2011) Todd J. Treangen et al.   NATURE REVIEWS GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Characterization of DNA methyltransferase specificities using single-molecule, real-time DNA sequencing

(2011) Tyson A. Clark et al.   NUCLEIC ACIDS RESEARCH

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing

(2011) Eun-Joon Lee et al.   NUCLEIC ACIDS RESEARCH

Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types

(2011) Michael J. Ziller et al.   PLoS Genetics

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

(2010) Yun Huang et al.   PLoS One

Epigenetic Reprogramming in Plant and Animal Development

(2010) Suhua Feng et al.   SCIENCE

High-throughput bisulfite sequencing in mammalian genomes

(2009) Zachary D. Smith et al.   METHODS

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

(2009) Akiko Doi et al.   NATURE GENETICS

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

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

(2008) Ryan Lister et al.   CELL

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE