Epigenetic regulation of gene expression in cancer: techniques, resources and analysis
LT Kagohara, GL Stein-O'Brien, D Kelley… - Briefings in …, 2018 - academic.oup.com
Cancer is a complex disease, driven by aberrant activity in numerous signaling pathways in
even individual malignant cells. Epigenetic changes are critical mediators of these functional …
even individual malignant cells. Epigenetic changes are critical mediators of these functional …
[HTML][HTML] Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450k) data
TJ Morris, S Beck - Methods, 2015 - Elsevier
Abstract The Illumina HumanMethylation450 BeadChip has become a popular platform for
interrogating DNA methylation in epigenome-wide association studies (EWAS) and related …
interrogating DNA methylation in epigenome-wide association studies (EWAS) and related …
Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi
The minfi package is widely used for analyzing Illumina DNA methylation array data. Here
we describe modifications to the minfi package required to support the …
we describe modifications to the minfi package required to support the …
Functional normalization of 450k methylation array data improves replication in large cancer studies
We propose an extension to quantile normalization that removes unwanted technical
variation using control probes. We adapt our algorithm, functional normalization, to the …
variation using control probes. We adapt our algorithm, functional normalization, to the …
Meffil: efficient normalization and analysis of very large DNA methylation datasets
Motivation DNA methylation datasets are growing ever larger both in sample size and
genome coverage. Novel computational solutions are required to efficiently handle these …
genome coverage. Novel computational solutions are required to efficiently handle these …
Reconstructing A/B compartments as revealed by Hi-C using long-range correlations in epigenetic data
Abstract Analysis of Hi-C data has shown that the genome can be divided into two
compartments called A/B compartments. These compartments are cell-type specific and are …
compartments called A/B compartments. These compartments are cell-type specific and are …
Lifetime stress accelerates epigenetic aging in an urban, African American cohort: relevance of glucocorticoid signaling
Background Chronic psychological stress is associated with accelerated aging and
increased risk for aging-related diseases, but the underlying molecular mechanisms are …
increased risk for aging-related diseases, but the underlying molecular mechanisms are …
[HTML][HTML] The early-life exposome and epigenetic age acceleration in children
P de Prado-Bert, C Ruiz-Arenas, M Vives-Usano… - Environment …, 2021 - Elsevier
The early-life exposome influences future health and accelerated biological aging has been
proposed as one of the underlying biological mechanisms. We investigated the association …
proposed as one of the underlying biological mechanisms. We investigated the association …
Epigenetic prediction of complex traits and death
Background Genome-wide DNA methylation (DNAm) profiling has allowed for the
development of molecular predictors for a multitude of traits and diseases. Such predictors …
development of molecular predictors for a multitude of traits and diseases. Such predictors …
Novel DNA methylation signatures of tobacco smoking with trans-ethnic effects
C Christiansen, JE Castillo-Fernandez… - Clinical …, 2021 - Springer
Background Smoking remains one of the leading preventable causes of death. Smoking
leaves a strong signature on the blood methylome as shown in multiple studies using the …
leaves a strong signature on the blood methylome as shown in multiple studies using the …