Predicting genome-wide DNA methylation using methylation marks, genomic position, and DNA regulatory elements

A thiol switch opens the gate

(2014) Haike Antelmann   Nature Chemical Biology

Predicting DNA methylation level across human tissues

(2014) Baoshan Ma et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Andrew E Jaffe et al.   GENOME BIOLOGY

CpGIMethPred: computational model for predicting methylation status of CpG islands in human genome

(2013) Hao Zheng et al.   BMC Medical Genomics

Early de novo DNA methylation and prolonged demethylation in the muscle lineage

(2013) Koji Tsumagari et al.   Epigenetics

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

A statin-dependent QTL for GATM expression is associated with statin-induced myopathy

(2013) Lara M. Mangravite et al.   NATURE

Programming of DNA Methylation Patterns

(2012) Howard Cedar et al.   Annual Review of Biochemistry

DNA methylation profiling in breast cancer discordant identical twins identifies DOK7 as novel epigenetic biomarker

(2012) H. Heyn et al.   CARCINOGENESIS

Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites

(2012) A. Hogart et al.   GENOME RESEARCH

DNA Methylation Profiling Identifies Global Methylation Differences and Markers of Adrenocortical Tumors

(2012) Nesrin S. Rechache et al.   JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

Fast and accurate genotype imputation in genome-wide association studies through pre-phasing

(2012) Bryan Howie et al.   NATURE GENETICS

Conditional and joint multiple-SNP analysis of GWAS summary statistics identifies additional variants influencing complex traits

(2012) Jian Yang et al.   NATURE GENETICS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

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

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

The Contribution of RNA Decay Quantitative Trait Loci to Inter-Individual Variation in Steady-State Gene Expression Levels

(2012) Athma A. Pai et al.   PLoS Genetics

Dissecting the regulatory architecture of gene expression QTLs

(2012) Daniel J Gaffney et al.   GENOME BIOLOGY

A Genome-wide Comparison of the Functional Properties of Rare and Common Genetic Variants in Humans

(2011) Qianqian Zhu et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Prediction of methylation CpGs and their methylation degrees in human DNA sequences

(2011) Xuan Zhou et al.   COMPUTERS IN BIOLOGY AND MEDICINE

Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome

(2011) Juan Sandoval et al.   Epigenetics

CpG islands and the regulation of transcription

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

A DNA methylation fingerprint of 1628 human samples

(2011) A. F. Fernandez et al.   GENOME RESEARCH

High density DNA methylation array with single CpG site resolution

(2011) Marina Bibikova et al.   GENOMICS

Directional DNA Methylation Changes and Complex Intermediate States Accompany Lineage Specificity in the Adult Hematopoietic Compartment

(2011) Emily Hodges et al.   MOLECULAR CELL

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

Identification of genetic elements that autonomously determine DNA methylation states

(2011) Florian Lienert et al.   NATURE GENETICS

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

(2011) Jordana T Bell et al.   GENOME BIOLOGY

Genetic Control of Individual Differences in Gene-Specific Methylation in Human Brain

(2010) Dandan Zhang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genome-wide conserved consensus transcription factor binding motifs are hyper-methylated

(2010) Mun-Kit Choy et al.   BMC GENOMICS

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

Genetic Heterogeneity in Human Disease

(2010) Jon McClellan et al.   CELL

Distinct Epigenomic Landscapes of Pluripotent and Lineage-Committed Human Cells

(2010) R. David Hawkins et al.   Cell Stem Cell

Epigenetic Mechanisms that Regulate Cell Identity

(2010) María J. Barrero et al.   Cell Stem Cell

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

Conserved role of intragenic DNA methylation in regulating alternative promoters

(2010) Alika K. Maunakea et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

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

RUNX3 is multifunctional in carcinogenesis of multiple solid tumors

(2010) L S H Chuang et al.   ONCOGENE

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

VEZF1 Elements Mediate Protection from DNA Methylation

(2010) Jacqueline Dickson et al.   PLoS Genetics

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

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

Profile analysis and prediction of tissue-specific CpG island methylation classes

(2009) Christopher Previti et al.   BMC BIOINFORMATICS

Learning from Imbalanced Data

(2009) Haibo He et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

DNA Methylation: An Introduction to the Biology and the Disease-Associated Changes of a Promising Biomarker

(2009) Jörg Tost   MOLECULAR BIOTECHNOLOGY

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

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

An Epigenetic Signature in Peripheral Blood Predicts Active Ovarian Cancer

(2009) Andrew E. Teschendorff et al.   PLoS One

A Flexible and Accurate Genotype Imputation Method for the Next Generation of Genome-Wide Association Studies

(2009) Bryan N. Howie et al.   PLoS Genetics

Histone methylation marks play important roles in predicting the methylation status of CpG islands

(2008) Shicai Fan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS