Statistical and integrative system-level analysis of DNA methylation data

AE Teschendorff, CL Relton - Nature Reviews Genetics, 2018 - nature.com
Epigenetics plays a key role in cellular development and function. Alterations to the
epigenome are thought to capture and mediate the effects of genetic and environmental risk …

Origins of human disease: the chrono-epigenetic perspective

ES Oh, A Petronis - Nature Reviews Genetics, 2021 - nature.com
Epigenetics has enriched human disease studies by adding new interpretations to disease
features that cannot be explained by genetic and environmental factors. However …

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

EA Houseman, ML Kile, DC Christiani, TA Ince… - BMC …, 2016 - Springer
Background Recent interest in reference-free deconvolution of DNA methylation data has
led to several supervised methods, but these methods do not easily permit the interpretation …

Correlation of an epigenetic mitotic clock with cancer risk

Z Yang, A Wong, D Kuh, DS Paul, VK Rakyan… - Genome biology, 2016 - Springer
Background Variation in cancer risk among somatic tissues has been attributed to variations
in the underlying rate of stem cell division. For a given tissue type, variable cancer risk …

DNA methylation outliers in normal breast tissue identify field defects that are enriched in cancer

AE Teschendorff, Y Gao, A Jones, M Ruebner… - Nature …, 2016 - nature.com
Identifying molecular alterations in normal tissue adjacent to cancer is important for
understanding cancer aetiology and designing preventive measures. Here we analyse the …

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

DS Paul, AE Teschendorff, MAN Dang, R Lowe… - Nature …, 2016 - nature.com
The incidence of type 1 diabetes (T1D) has substantially increased over the past decade,
suggesting a role for non-genetic factors such as epigenetic mechanisms in disease …

Statistical mechanics meets single-cell biology

AE Teschendorff, AP Feinberg - Nature Reviews Genetics, 2021 - nature.com
Single-cell omics is transforming our understanding of cell biology and disease, yet the
systems-level analysis and interpretation of single-cell data faces many challenges. In this …

Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

S Ecker, L Chen, V Pancaldi, FO Bagger… - Genome biology, 2017 - Springer
Background A healthy immune system requires immune cells that adapt rapidly to
environmental challenges. This phenotypic plasticity can be mediated by transcriptional and …

Epigenetic drift, epigenetic clocks and cancer risk

SC Zheng, M Widschwendter, AE Teschendorff - Epigenomics, 2016 - Taylor & Francis
It is well-established that the DNA methylation landscape of normal cells undergoes a
gradual modification with age, termed as 'epigenetic drift'. Here, we review the current state …

Big biological data: challenges and opportunities

Y Li, L Chen - Genomics, Proteomics and Bioinformatics, 2014 - academic.oup.com
In ''Omics''era of the life sciences, data is presented in many forms, which represent the
information at various levels of biological systems, including data about genome …