Genome-wide assays that identify and quantify modified cytosines in human disease studies

Unusual Characteristics of the DNA Binding Domain of Epigenetic Regulatory Protein MeCP2 Determine Its Binding Specificity

(2014) Sergei Khrapunov et al.   BIOCHEMISTRY

Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation

(2014) M. Ronnerblad et al.   BLOOD

Comparative DNA methylome analysis of endometrial carcinoma reveals complex and distinct deregulation of cancer promoters and enhancers

(2014) Bo Zhang et al.   BMC GENOMICS

Kidney Cancer Is Characterized by Aberrant Methylation of Tissue-Specific Enhancers That Are Prognostic for Overall Survival

(2014) C. Y. Hu et al.   CLINICAL CANCER RESEARCH

Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer

(2014) Phillippa C. Taberlay et al.   GENOME RESEARCH

Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization

(2014) N. Bonhoure et al.   GENOME RESEARCH

Genome-Wide DNA Methylation as an Epigenetic Consequence of Epstein-Barr Virus Infection of Immortalized Keratinocytes

(2014) C. E. Birdwell et al.   JOURNAL OF VIROLOGY

Tet oxidizes thymine to 5-hydroxymethyluracil in mouse embryonic stem cell DNA

(2014) Toni Pfaffeneder et al.   Nature Chemical Biology

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

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

Obesity accelerates epigenetic aging of human liver

(2014) S. Horvath et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Expanding the Epigenetic Landscape: Novel Modifications of Cytosine in Genomic DNA

(2014) S. Kriaucionis et al.   Cold Spring Harbor Perspectives in Biology

Mosaic Epigenetic Dysregulation of Ectodermal Cells in Autism Spectrum Disorder

(2014) Esther R. Berko et al.   PLoS Genetics

Accounting for cellular heterogeneity is critical in epigenome-wide association studies

(2014) Andrew E Jaffe et al.   GENOME BIOLOGY

DMEAS: DNA methylation entropy analysis software

(2013) Jianlin He et al.   BIOINFORMATICS

Quantification of 5-Methylcytosine and 5-Hydroxymethylcytosine in Genomic DNA from Hepatocellular Carcinoma Tissues by Capillary Hydrophilic-Interaction Liquid Chromatography/Quadrupole TOF Mass Spectrometry

(2013) M.-L. Chen et al.   CLINICAL CHEMISTRY

Blood-based profiles of DNA methylation predict the underlying distribution of cell types

(2013) Devin C Koestler et al.   Epigenetics

Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray

(2013) Yi-an Chen et al.   Epigenetics

De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements

(2013) F. Schlesinger et al.   GENOME RESEARCH

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

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

Widespread DNA hypomethylation at gene enhancer regions in placentas associated with early-onset pre-eclampsia

(2013) J. D. Blair et al.   MOLECULAR HUMAN REPRODUCTION

Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues

(2013) Gary C Hon et al.   NATURE GENETICS

Recommendations for the design and analysis of epigenome-wide association studies

(2013) Karin B Michels et al.   NATURE METHODS

Comparative annotation of functional regions in the human genome using epigenomic data

(2013) Kyoung-Jae Won et al.   NUCLEIC ACIDS RESEARCH

A new insight into the 5-carboxycytosine and 5-formylcytosine under typical bisulfite conditions: a deamination mechanism study

(2013) Lingxia Jin et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands

(2013) J. Schreiber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes

(2013) Dvir Aran et al.   GENOME BIOLOGY

A screen for hydroxymethylcytosine and formylcytosine binding proteins suggests functions in transcription and chromatin regulation

(2013) Mario Iurlaro et al.   GENOME BIOLOGY

Cytosine methylation changes in enhancer regions of core pro-fibrotic genes characterize kidney fibrosis development

(2013) Yi-An Ko et al.   GENOME BIOLOGY

IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data

(2012) D. Wang et al.   BIOINFORMATICS

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

(2012) Miao Yu et al.   CELL

Inflammation-Associated Cancer Development in Digestive Organs: Mechanisms and Roles for Genetic and Epigenetic Modulation

(2012) Tsutomu Chiba et al.   GASTROENTEROLOGY

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies

(2012) Andrew E Jaffe et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Unsupervised pattern discovery in human chromatin structure through genomic segmentation

(2012) Michael M Hoffman et al.   NATURE METHODS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Integrative annotation of chromatin elements from ENCODE data

(2012) Michael M. Hoffman et al.   NUCLEIC ACIDS RESEARCH

5-Aza-2′-deoxycytidine-induced genome rearrangements are mediated by DNMT1

(2012) A Y Maslov et al.   ONCOGENE

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

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

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

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

(2012) Yaping Liu et al.   GENOME BIOLOGY

Genome-wide distribution of 5-formylcytosine in embryonic stem cells is associated with transcription and depends on thymine DNA glycosylase

(2012) Eun-Ang Raiber et al.   GENOME BIOLOGY

Variable DNA Methylation Is Associated with Chronic Obstructive Pulmonary Disease and Lung Function

(2011) Weiliang Qiu et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

DNA Demethylation Dynamics

(2011) Nidhi Bhutani et al.   CELL

DNA methylation status predicts cell type-specific enhancer activity

(2011) Malgorzata Wiench et al.   EMBO JOURNAL

Epigenetic changes in B lymphocytes associated with house dust mite allergic asthma

(2011) Marien Pascual et al.   Epigenetics

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

Late-replicating heterochromatin is characterized by decreased cytosine methylation in the human genome

(2011) M. Suzuki et al.   GENOME RESEARCH

DNA methylation profiles of human active and inactive X chromosomes

(2011) A. J. Sharp et al.   GENOME RESEARCH

High density DNA methylation array with single CpG site resolution

(2011) Marina Bibikova et al.   GENOMICS

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

(2011) William A. Pastor et al.   NATURE

Targeted bisulfite sequencing by solution hybrid selection and massively parallel sequencing

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

Correction of PCR-bias in quantitative DNA methylation studies by means of cubic polynomial regression

(2011) Evgeny A. Moskalev et al.   NUCLEIC ACIDS RESEARCH

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

(2011) S. Ito et al.   SCIENCE

Analysis of DNA Methylation in a Three-Generation Family Reveals Widespread Genetic Influence on Epigenetic Regulation

(2011) Jason Gertz et al.   PLoS Genetics

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

(2011) Jordana T Bell et al.   GENOME BIOLOGY

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

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

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

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Protocol matters: which methylome are you actually studying?

(2010) Mark D Robinson et al.   Epigenomics

Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain

(2010) J. Raphael Gibbs et al.   PLoS Genetics

Optimized design and data analysis of tag-based cytosine methylation assays

(2010) Masako Suzuki et al.   GENOME BIOLOGY

High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing

(2009) E. Hodges et al.   GENOME RESEARCH

Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity

(2009) C. Schmidl et al.   GENOME RESEARCH

EBV transformation and cell culturing destabilizes DNA methylation in human lymphoblastoid cell lines

(2009) D. Grafodatskaya et al.   GENOMICS

Epigenetic mechanisms in neurological diseases: genes, syndromes, and therapies

(2009) Rocio G Urdinguio et al.   LANCET NEUROLOGY

Targeted bisulfite sequencing reveals changes in DNA methylation associated with nuclear reprogramming

(2009) Jie Deng et al.   NATURE BIOTECHNOLOGY

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

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

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

Genome-wide DNA methylation profiling

(2009) Marina Bibikova et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

High-Throughput Quantitative Polymerase Chain Reaction in Picoliter Droplets

(2008) Margaret Macris Kiss et al.   ANALYTICAL CHEMISTRY

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

(2008) Ryan Lister et al.   CELL

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

A Novel CpG Island Set Identifies Tissue-Specific Methylation at Developmental Gene Loci

(2008) Robert Illingworth et al.   PLOS BIOLOGY