Grasping nettles: cellular heterogeneity and other confounders in epigenome-wide association studies

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

(2014) Eugene Andres Houseman et al.   BIOINFORMATICS

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

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

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

(2014) James Zou et al.   NATURE METHODS

Reconstructing the DNA Methylation Maps of the Neandertal and the Denisovan

(2014) D. Gokhman et al.   SCIENCE

The relationship between DNA methylation, genetic and expression inter-individual variation in untransformed human fibroblasts

(2014) James R Wagner et al.   GENOME BIOLOGY

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

(2014) Andrew E Jaffe et al.   GENOME BIOLOGY

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

(2013) Devin C Koestler et al.   Epigenetics

A cross-platform analysis of 14,177 expression quantitative trait loci derived from lymphoblastoid cell lines

(2013) L. Liang et al.   GENOME RESEARCH

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis

(2013) Yun Liu et al.   NATURE BIOTECHNOLOGY

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

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

(2013) Karin B Michels et al.   NATURE METHODS

Surrogate variable analysis using partial least squares (SVA-PLS) in gene expression studies

(2012) Sutirtha Chakraborty et al.   BIOINFORMATICS

DNA methylation arrays as surrogate measures of cell mixture distribution

(2012) Eugene Houseman et al.   BMC BIOINFORMATICS

Genetic analysis of DNA methylation and gene expression levels in whole blood of healthy human subjects

(2012) Kristel R van Eijk et al.   BMC GENOMICS

Peripheral Blood Immune Cell Methylation Profiles Are Associated with Nonhematopoietic Cancers

(2012) D. C. Koestler et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Age-associated DNA methylation in pediatric populations

(2012) R. S. Alisch et al.   GENOME RESEARCH

Periconceptional maternal micronutrient supplementation is associated with widespread gender related changes in the epigenome: a study of a unique resource in the Gambia

(2012) Batbayar Khulan et al.   HUMAN MOLECULAR GENETICS

Cigarette smoking behaviors and time since quitting are associated with differential DNA methylation across the human genome

(2012) Emily S. Wan et al.   HUMAN MOLECULAR GENETICS

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

Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates

(2012) Gregory Hannum et al.   MOLECULAR CELL

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

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Differential DNA Methylation in Purified Human Blood Cells: Implications for Cell Lineage and Studies on Disease Susceptibility

(2012) Lovisa E. Reinius 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

Gene-Environment Interactions in Genome-Wide Association Studies: A Comparative Study of Tests Applied to Empirical Studies of Type 2 Diabetes

(2011) M. C. Cornelis et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Tobacco-Smoking-Related Differential DNA Methylation: 27K Discovery and Replication

(2011) Lutz P. Breitling et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies

(2011) Andrew E. Teschendorff et al.   BIOINFORMATICS

Direct and Indirect Effects in a Survival Context

(2011) Theis Lange et al.   EPIDEMIOLOGY

Cell type-specific DNA methylation at intragenic CpG islands in the immune system

(2011) A. M. Deaton et al.   GENOME RESEARCH

Chromosome-wide DNA methylation analysis predicts human tissue-specific X inactivation

(2011) Allison M. Cotton et al.   HUMAN GENETICS

Eosinophils: multifaceted biological properties and roles in health and disease

(2011) Hirohito Kita   IMMUNOLOGICAL REVIEWS

A promoter DNA demethylation landscape of human hematopoietic differentiation

(2011) Vincenzo Calvanese et al.   NUCLEIC ACIDS RESEARCH

Odds Ratios for Mediation Analysis for a Dichotomous Outcome

(2010) T. J. VanderWeele et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer

(2010) A. E. Teschendorff et al.   GENOME RESEARCH

Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains

(2010) V. K. Rakyan et al.   GENOME RESEARCH

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

A Study of the Influence of Sex on Genome Wide Methylation

(2010) Jingyu Liu et al.   PLoS One

A Bayesian Framework to Account for Complex Non-Genetic Factors in Gene Expression Levels Greatly Increases Power in eQTL Studies

(2010) Oliver Stegle et al.   PLoS Computational Biology

Molecular networks as sensors and drivers of common human diseases

(2009) Eric E. Schadt   NATURE

The transcriptional network for mesenchymal transformation of brain tumours

(2009) Maria Stella Carro et al.   NATURE

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

The Relationship of DNA Methylation with Age, Gender and Genotype in Twins and Healthy Controls

(2009) Marco P. Boks et al.   PLoS One

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Variations in DNA elucidate molecular networks that cause disease

(2008) Yanqing Chen et al.   NATURE

Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation

(2008) Kristi Kerkel et al.   NATURE GENETICS