Associating cellular epigenetic models with human phenotypes

Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells

(2016) Lu Chen et al.   CELL

Mechanisms of DNA-binding specificity and functional gene regulation by transcription factors

(2016) Ngaio C Smith et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

DNA Methylation and BMI: Investigating Identified Methylation Sites atHIF3Ain a Causal Framework

(2016) Rebecca C. Richmond et al.   DIABETES

Molecular basis of PRC1 targeting to Polycomb response elements by PhoRC

(2016) Felice Frey et al.   GENES & DEVELOPMENT

Epigenome-wide association study of body mass index and the adverse outcomes of adiposity

(2016) Simone Wahl et al.   NATURE

Transition states and cell fate decisions in epigenetic landscapes

(2016) Naomi Moris et al.   NATURE REVIEWS GENETICS

Epigenome-wide Association Studies and the Interpretation of Disease -Omics

(2016) Ewan Birney et al.   PLoS Genetics

Distinct epigenomes in CD4+ T cells of newborns, middle-ages and centenarians

(2016) Ming Zhao et al.   Scientific Reports

The Effects ofIn UteroVitamin D Deficiency on Airway Smooth Muscle Mass and Lung Function

(2015) Rachel E. Foong et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

(2015) Franziska Paul et al.   CELL

Functional genomics bridges the gap between quantitative genetics and molecular biology

(2015) Tuuli Lappalainen   GENOME RESEARCH

CETCh-seq: CRISPR epitope tagging ChIP-seq of DNA-binding proteins

(2015) Daniel Savic et al.   GENOME RESEARCH

Influence of environmental exposure on human epigenetic regulation

(2015) C. J. Marsit   JOURNAL OF EXPERIMENTAL BIOLOGY

Competition between DNA methylation and transcription factors determines binding of NRF1

(2015) Silvia Domcke et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

RNA-mediated epigenetic regulation of gene expression

(2015) Daniel Holoch et al.   NATURE REVIEWS GENETICS

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

Targeting Polycomb systems to regulate gene expression: modifications to a complex story

(2015) Neil P. Blackledge et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

ZFP57 recognizes multiple and closely spaced sequence motif variants to maintain repressive epigenetic marks in mouse embryonic stem cells

(2015) Zahra Anvar et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Netha Ulahannan et al.   Epigenetics & Chromatin

The Genetic and Mechanistic Basis for Variation in Gene Regulation

(2015) Athma A. Pai et al.   PLoS Genetics

Noncoding RNAs and Epigenetic Mechanisms During X-Chromosome Inactivation

(2014) Anne-Valerie Gendrel et al.   Annual Review of Cell and Developmental Biology

Reference-free cell mixture adjustments in analysis of DNA methylation data

(2014) Eugene Andres Houseman et al.   BIOINFORMATICS

High-resolution mapping defines the cooperative architecture of Polycomb response elements

(2014) G. A. Orsi et al.   GENOME RESEARCH

Prenatal retinoid deficiency leads to airway hyperresponsiveness in adult mice

(2014) Felicia Chen et al.   JOURNAL OF CLINICAL INVESTIGATION

Principles of regulatory information conservation between mouse and human

(2014) Yong Cheng et al.   NATURE

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

(2014) Sébastien A Smallwood et al.   NATURE METHODS

Epigenome-wide association studies without the need for cell-type composition

(2014) James Zou et al.   NATURE METHODS

Diversity and clonal selection in the human T-cell repertoire

(2014) Q. Qi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

In vitro and in vivo testing methods of epigenomic endpoints for evaluating endocrine disruptors

(2014) John Greally   ALTEX-Alternatives to Animal Experimentation

The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences

(2014) N. Ari Wijetunga et al.   Nature Communications

Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

(2014) Nicholas E. Banovich et al.   PLoS Genetics

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

(2014) Andrew E Jaffe et al.   GENOME BIOLOGY

Global Analysis of DNA Methylation Variation in Adipose Tissue from Twins Reveals Links to Disease-Associated Variants in Distal Regulatory Elements

(2013) Elin Grundberg et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2013) Yi-an Chen et al.   Epigenetics

Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing

(2013) H. Guo et al.   GENOME RESEARCH

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

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

(2013) Karin B Michels et al.   NATURE METHODS

Transcriptional regulation by Polycomb group proteins

(2013) Luciano Di Croce et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Transcription Factors That Convert Adult Cell Identity Are Differentially Polycomb Repressed

(2013) Fred P. Davis et al.   PLoS One

YY1TargetDB: an integral information resource for Yin Yang 1 target loci

(2013) Andy M. Guo et al.   Database-The Journal of Biological Databases and Curation

Sequence analysis of T-cell repertoires in health and disease

(2013) Daniel J Woodsworth et al.   Genome Medicine

Transcription Factor Occupancy Can Mediate Active Turnover of DNA Methylation at Regulatory Regions

(2013) Angelika Feldmann et al.   PLoS Genetics

Passive and active DNA methylation and the interplay with genetic variation in gene regulation

(2013) Maria Gutierrez-Arcelus et al.   eLife

Disentangling the Many Layers of Eukaryotic Transcriptional Regulation

(2012) Katherine M. Lelli et al.   Annual Review of Genetics

DNA methylation arrays as surrogate measures of cell mixture distribution

(2012) Eugene Houseman et al.   BMC BIOINFORMATICS

Commentary: The seven plagues of epigenetic epidemiology

(2012) Bastiaan T Heijmans et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Two-step epigenetic Mendelian randomization: a strategy for establishing the causal role of epigenetic processes in pathways to disease

(2012) Caroline L Relton et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

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

(2012) Jacob F. Degner et al.   NATURE

Heterogeneity in White Blood Cells Has Potential to Confound DNA Methylation Measurements

(2012) Bjorn T. Adalsteinsson et al.   PLoS One

Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population

(2012) Jordana T. Bell et al.   PLoS Genetics

Genomic imprinting in mammals: its life cycle, molecular mechanisms and reprogramming

(2011) Yufeng Li et al.   CELL RESEARCH

DNA methylation profiles of human active and inactive X chromosomes

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

Commentary: The epidemiology of epigenetics: Figure 1

(2011) David Haig   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

The Epigenotype

(2011) C. H. Waddington   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Epigenome-wide association studies for common human diseases

(2011) Vardhman K. Rakyan et al.   NATURE REVIEWS GENETICS

Prenatal environmental exposures, epigenetics, and disease

(2011) Frederica Perera et al.   REPRODUCTIVE TOXICOLOGY

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

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

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

Prenatal Exposure to the Environmental Obesogen Tributyltin Predisposes Multipotent Stem Cells to Become Adipocytes

(2010) Séverine Kirchner et al.   MOLECULAR ENDOCRINOLOGY

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Molecular Signals of Epigenetic States

(2010) Roberto Bonasio et al.   SCIENCE

Replication in Genome-Wide Association Studies

(2010) Peter Kraft et al.   STATISTICAL SCIENCE

Polycomb Proteins Remain Bound to Chromatin and DNA during DNA Replication In Vitro

(2009) Nicole J. Francis et al.   CELL

Evolution of the RNA-dependent RNA polymerase (RdRP) genes: Duplications and possible losses before and after the divergence of major eukaryotic groups

(2009) Jie Zong et al.   GENE

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

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

A Maternal-Zygotic Effect Gene, Zfp57, Maintains Both Maternal and Paternal Imprints

(2008) Xiajun Li et al.   DEVELOPMENTAL CELL

Replacement of a Drosophila Polycomb response element core, and in situ analysis of its DNA motifs

(2008) Gabriella Kozma et al.   MOLECULAR GENETICS AND GENOMICS