Analysing and interpreting DNA methylation data

C Bock - Nature Reviews Genetics, 2012 - nature.com
DNA methylation is an epigenetic mark that has suspected regulatory roles in a broad range
of biological processes and diseases. The technology is now available for studying DNA …

Ecological plant epigenetics: Evidence from model and non‐model species, and the way forward

CL Richards, C Alonso, C Becker, O Bossdorf… - Ecology …, 2017 - Wiley Online Library
Growing evidence shows that epigenetic mechanisms contribute to complex traits, with
implications across many fields of biology. In plant ecology, recent studies have attempted to …

A compendium of genetic regulatory effects across pig tissues

J Teng, Y Gao, H Yin, Z Bai, S Liu, H Zeng… - Nature …, 2024 - nature.com
Abstract The Farm Animal Genotype-Tissue Expression (FarmGTEx) project has been
established to develop a public resource of genetic regulatory variants in livestock, which is …

The DNA methylation landscape of human early embryos

H Guo, P Zhu, L Yan, R Li, B Hu, Y Lian, J Yan, X Ren… - Nature, 2014 - nature.com
DNA methylation is a crucial element in the epigenetic regulation of mammalian embryonic
development,,,,. However, its dynamic patterns have not been analysed at the genome scale …

Comprehensive analysis of DNA methylation data with RnBeads

Y Assenov, F Müller, P Lutsik, J Walter, T Lengauer… - Nature …, 2014 - nature.com
RnBeads is a software tool for large-scale analysis and interpretation of DNA methylation
data, providing a user-friendly analysis workflow that yields detailed hypertext reports …

DNA methylation loss in late-replicating domains is linked to mitotic cell division

W Zhou, HQ Dinh, Z Ramjan, DJ Weisenberger… - Nature …, 2018 - nature.com
DNA methylation loss occurs frequently in cancer genomes, primarily within lamina-
associated, late-replicating regions termed partially methylated domains (PMDs). We …

Lentiviral gene therapy for X-linked chronic granulomatous disease

DB Kohn, C Booth, EM Kang, SY Pai, KL Shaw… - Nature medicine, 2020 - nature.com
Chronic granulomatous disease (CGD) is a rare inherited disorder of phagocytic cells,. We
report the initial results of nine severely affected X-linked CGD (X-CGD) patients who …

Single-cell DNA methylome sequencing of human preimplantation embryos

P Zhu, H Guo, Y Ren, Y Hou, J Dong, R Li, Y Lian… - Nature …, 2018 - nature.com
DNA methylation is a crucial layer of epigenetic regulation during mammalian embryonic
development,–. Although the DNA methylome of early human embryos has been analyzed …

DNA methylation in Arabidopsis has a genetic basis and shows evidence of local adaptation

MJ Dubin, P Zhang, D Meng, MS Remigereau… - elife, 2015 - elifesciences.org
Epigenome modulation potentially provides a mechanism for organisms to adapt, within and
between generations. However, neither the extent to which this occurs, nor the mechanisms …

BISCUIT: an efficient, standards-compliant tool suite for simultaneous genetic and epigenetic inference in bulk and single-cell studies

W Zhou, BK Johnson, J Morrison… - Nucleic Acids …, 2024 - academic.oup.com
Data from both bulk and single-cell whole-genome DNA methylation experiments are under-
utilized in many ways. This is attributable to inefficient map** of methylation sequencing …