Reference-free deconvolution of DNA methylation data and mediation by cell composition effects

Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies

(2016) Elior Rahmani et al.   NATURE METHODS

Mathematical modelling of transcriptional heterogeneity identifies novel markers and subpopulations in complex tissues

(2016) Niya Wang et al.   Scientific Reports

Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective

(2015) E Andres Houseman et al.   BMC BIOINFORMATICS

Inuteroarsenic exposure and epigenome-wide associations in placenta, umbilical artery, and human umbilical vein endothelial cells

(2015) Andres Cardenas et al.   Epigenetics

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

DNA methylation changes in the placenta are associated with fetal manganese exposure

(2015) Jennifer Z.J. Maccani et al.   REPRODUCTIVE TOXICOLOGY

A varying T cell subtype explains apparent tobacco smoking induced single CpG hypomethylation in whole blood

(2015) Mario Bauer et al.   Clinical Epigenetics

Independent genomewide screens identify the tumor suppressor VTRNA2-1 as a human epiallele responsive to periconceptional environment

(2015) Matt J Silver et al.   GENOME BIOLOGY

Epigenetic signatures of alcohol abuse and hepatitis infection during human hepatocarcinogenesis

(2015) Ryan A. Hlady et al.   Oncotarget

DNA extracted from saliva for methylation studies of psychiatric traits: Evidence tissue specificity and relatedness to brain

(2014) Alicia K. Smith et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART B-NEUROPSYCHIATRIC GENETICS

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

(2014) Eugene Andres Houseman et al.   BIOINFORMATICS

Effect of prenatal arsenic exposure on DNA methylation and leukocyte subpopulations in cord blood

(2014) Molly L Kile et al.   Epigenetics

Adiposity is associated with DNA methylation profile in adipose tissue

(2014) Golareh Agha et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Taxonomy of breast cancer based on normal cell phenotype predicts outcome

(2014) Sandro Santagata et al.   JOURNAL OF CLINICAL INVESTIGATION

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

(2014) James Zou et al.   NATURE METHODS

The Dynamics of DNA Methylation Covariation Patterns in Carcinogenesis

(2014) Andrew E. Teschendorff et al.   PLoS Computational Biology

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

(2014) Andrew E Jaffe et al.   GENOME BIOLOGY

Computational deconvolution: extracting cell type-specific information from heterogeneous samples

(2013) Shai S Shen-Orr et al.   CURRENT OPINION IN IMMUNOLOGY

Differential DNA Methylation in Umbilical Cord Blood of Infants Exposed to Low Levels of Arsenic in Utero

(2013) Devin C. Koestler et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Human metastable epiallele candidates link to common disorders

(2013) R. Alan Harris et al.   Epigenetics

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

(2013) Yi-an Chen et al.   Epigenetics

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

(2013) Yun Liu et al.   NATURE BIOTECHNOLOGY

Predictors and Consequences of Global DNA Methylation in Cord Blood and at Three Years

(2013) Julie B. Herbstman et al.   PLoS One

Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction

(2013) Gerald Quon et al.   Genome Medicine

DNA methylation regulates lineage-specifying genes in primary lymphatic and blood endothelial cells

(2012) Simone Brönneke et al.   ANGIOGENESIS

A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data

(2012) Andrew E. Teschendorff et al.   BIOINFORMATICS

DNA methylation arrays as surrogate measures of cell mixture distribution

(2012) Eugene Houseman et al.   BMC BIOINFORMATICS

CTen: a web-based platform for identifying enriched cell types from heterogeneous microarray data

(2012) Jason E Shoemaker et al.   BMC GENOMICS

Decreased NK Cells in Patients with Head and Neck Cancer Determined in Archival DNA

(2012) W. P. Accomando et al.   CLINICAL CANCER RESEARCH

Peripheral blood DNA methylation profiles are indicative of head and neck squamous cell carcinoma: An epigenome-wide association study

(2012) Scott M. Langevin et al.   Epigenetics

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

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

Methylation Subtypes and Large-Scale Epigenetic Alterations in Gastric Cancer

(2012) H. Zouridis et al.   Science Translational Medicine

Correction: The Dynamics and Prognostic Potential of DNA Methylation Changes at Stem Cell Gene Loci in Women's Cancer

(2012) Joanna Zhuang et al.   PLoS Genetics

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

(2011) Andrew E. Teschendorff et al.   BIOINFORMATICS

Genome-wide Methylation Analysis Identifies Genes Specific to Breast Cancer Hormone Receptor Status and Risk of Recurrence

(2011) M. J. Fackler et al.   CANCER RESEARCH

DNA methylation profiling reveals a predominant immune component in breast cancers

(2011) Sarah Dedeurwaerder et al.   EMBO Molecular Medicine

Infant growth restriction is associated with distinct patterns of DNA methylation in human placentas

(2011) Carolyn E. Banister et al.   Epigenetics

Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: A case study

(2011) Renaud Gaujoux et al.   INFECTION GENETICS AND EVOLUTION

Probabilistic analysis of gene expression measurements from heterogeneous tissues

(2010) Timo Erkkilä et al.   BIOINFORMATICS

DNA methylation and epigenetic control of cellular differentiation

(2010) David A. Khavari et al.   CELL CYCLE

Arsenic-Associated Oxidative Stress, Inflammation, and Immune Disruption in Human Placenta and Cord Blood

(2010) Sultan Ahmed et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Maintaining Cell Identity through Global Control of Genomic Organization

(2010) Gioacchino Natoli   IMMUNITY

Comprehensive methylome map of lineage commitment from haematopoietic progenitors

(2010) Hong Ji et al.   NATURE

Effect of Arsenic on Regulatory T Cells

(2009) B. Hernández-Castro et al.   JOURNAL OF CLINICAL IMMUNOLOGY

An Epigenetic Signature in Peripheral Blood Predicts Active Ovarian Cancer

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

Aging and Environmental Exposures Alter Tissue-Specific DNA Methylation Dependent upon CpG Island Context

(2009) Brock C. Christensen et al.   PLoS Genetics