Updates to data versions and analytic methods influence the reproducibility of results from epigenome-wide association studies

Childhood DNA methylation as a marker of early life rapid weight gain and subsequent overweight

(2021) N. Robinson et al.   Clinical Epigenetics

An effective processing pipeline for harmonizing DNA methylation data from Illumina’s 450K and EPIC platforms for epidemiological studies

(2021) Lauren A. Vanderlinden et al.   BMC Research Notes

CoMeBack: DNA methylation array data analysis for co-methylated regions

(2020) Evan Gatev et al.   BIOINFORMATICS

Childhood maltreatment and DNA methylation: A systematic review

(2020) Charlotte A.M. Cecil et al.   NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS

Central and peripheral stress-induced epigenetic mechanisms of resilience

(2020) Katarzyna Anna Dudek et al.   CURRENT OPINION IN PSYCHIATRY

Sensitive periods for the effect of childhood adversity on DNA methylation: Results from a prospective, longitudinal study

(2019) Erin C. Dunn et al.   BIOLOGICAL PSYCHIATRY

Integration of DNA methylation patterns and genetic variation in human pediatric tissues help inform EWAS design and interpretation

(2019) Sumaiya A. Islam et al.   Epigenetics & Chromatin

Moving to a World Beyond “p 

(2019) Ronald L. Wasserstein et al.   AMERICAN STATISTICIAN

A systematic review of smoking-related epigenetic alterations

(2019) Gagandeep Kaur et al.   ARCHIVES OF TOXICOLOGY

The diverse roles of DNA methylation in mammalian development and disease

(2019) Maxim V. C. Greenberg et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

DNA methylation as a marker for prenatal smoke exposure in adults

(2018) Rebecca C Richmond et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

What life course theoretical models best explain the relationship between exposure to childhood adversity and psychopathology symptoms: recency, accumulation, or sensitive periods?

(2018) Erin C. Dunn et al.   PSYCHOLOGICAL MEDICINE

Socioeconomic position during pregnancy and DNA methylation signatures at three stages across early life: epigenome-wide association studies in the ALSPAC birth cohort

(2018) Rossella Alfano et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

A survey of inter-individual variation in DNA methylation identifies environmentally responsive co-regulated networks of epigenetic variation in the human genome

(2018) Paras Garg et al.   PLoS Genetics

DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis

(2016) Bonnie R. Joubert et al.   AMERICAN JOURNAL OF HUMAN GENETICS

The ASA's Statement onp-Values: Context, Process, and Purpose

(2016) Ronald L. Wasserstein et al.   AMERICAN STATISTICIAN

An evaluation of processing methods for HumanMethylation450 BeadChip data

(2016) Jie Liu et al.   BMC GENOMICS

The Frisch–Waugh–Lovell theorem for the lasso and the ridge regression

(2016) Hiroshi Yamada   COMMUNICATIONS IN STATISTICS-THEORY AND METHODS

Exact Post-Selection Inference for Sequential Regression Procedures

(2016) Ryan J. Tibshirani et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Increased DNA methylation variability in type 1 diabetes across three immune effector cell types

(2016) Dirk S. Paul et al.   Nature Communications

Comparison of pre-processing methodologies for Illumina 450k methylation array data in familial analyses

(2016) Emma Cazaly et al.   Clinical Epigenetics

Model Selection of the Effect of Binary Exposures over the Life Course

(2015) Andrew D. A. C. Smith et al.   EPIDEMIOLOGY

Data Resource Profile: Accessible Resource for Integrated Epigenomic Studies (ARIES)

(2015) Caroline L Relton et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Between-array normalization for 450K data

(2015) Jonathan A. Heiss et al.   Frontiers in Genetics

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

A significance test for the lasso

(2014) Richard Lockhart et al.   ANNALS OF STATISTICS

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

(2014) Eugene Andres Houseman et al.   BIOINFORMATICS

Genomic distribution and possible functions of DNA hydroxymethylation in the brain

(2014) Lu Wen et al.   GENOMICS

Low-level processing of Illumina Infinium DNA Methylation BeadArrays

(2013) Timothy J. Triche et al.   NUCLEIC ACIDS RESEARCH

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

Cohort Profile: The Avon Longitudinal Study of Parents and Children: ALSPAC mothers cohort

(2012) A. Fraser et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Cohort Profile: The ‘Children of the 90s’—the index offspring of the Avon Longitudinal Study of Parents and Children

(2012) Andy Boyd et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

Complete pipeline for Infinium® Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation

(2012) Nizar Touleimat et al.   Epigenomics

SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips

(2012) Jovana Maksimovic et al.   GENOME BIOLOGY

Subset Quantile Normalization Using Negative Control Features

(2010) Zhijin Wu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Epigenetics as a unifying principle in the aetiology of complex traits and diseases

(2010) Arturas Petronis   NATURE

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

(2009) S. Kriaucionis et al.   SCIENCE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

A structured approach to modelling the effects of binary exposure variables over the life course

(2008) Gita Mishra et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY