Genetic–epigenetic interactions in cis: a major focus in the post-GWAS era

C Do, A Shearer, M Suzuki, MB Terry, J Gelernter… - Genome biology, 2017 - Springer
Studies on genetic–epigenetic interactions, including the mapping of methylation
quantitative trait loci (mQTLs) and haplotype-dependent allele-specific DNA methylation …

Simultaneous sequencing of genetic and epigenetic bases in DNA

J Füllgrabe, WS Gosal, P Creed, S Liu, CK Lumby… - Nature …, 2023 - nature.com
DNA comprises molecular information stored in genetic and epigenetic bases, both of which
are vital to our understanding of biology. Most DNA sequencing approaches address either …

Bioinformatics tools for genome-wide epigenetic research

VE Angarica, A Del Sol - Neuroepigenomics in Aging and Disease, 2017 - Springer
Epigenetics play a central role in the regulation of many important cellular processes, and
dysregulations at the epigenetic level could be the source of serious pathologies, such as …

CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data

W Guo, P Zhu, M Pellegrini, MQ Zhang, X Wang… - …, 2018 - academic.oup.com
Motivation DNA methylation is important for gene silencing and imprinting in both plants and
animals. Recent advances in bisulfite sequencing allow detection of single nucleotide …

Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

J Xu, G Chen, PJ Hermanson, Q Xu, C Sun, W Chen… - Genome biology, 2019 - Springer
Background DNA methylation can provide a source of heritable information that is
sometimes entirely uncoupled from genetic variation. However, the extent of this uncoupling …

Rapid recovery gene downregulation during excess-light stress and recovery in Arabidopsis

PA Crisp, DR Ganguly, AB Smith, KD Murray… - The Plant …, 2017 - academic.oup.com
Stress recovery may prove to be a promising approach to increase plant performance and,
theoretically, mRNA instability may facilitate faster recovery. Transcriptome (RNA-seq …

Direct haplotype-resolved 5-base HiFi sequencing for genome-wide profiling of hypermethylation outliers in a rare disease cohort

WA Cheung, AF Johnson, WJ Rowell, E Farrow… - Nature …, 2023 - nature.com
Long-read HiFi genome sequencing allows for accurate detection and direct phasing of
single nucleotide variants, indels, and structural variants. Recent algorithmic development …

Hemispheric asymmetry in the human brain and in Parkinson's disease is linked to divergent epigenetic patterns in neurons

P Li, E Ensink, S Lang, L Marshall, M Schilthuis… - Genome biology, 2020 - Springer
Background Hemispheric asymmetry in neuronal processes is a fundamental feature of the
human brain and drives symptom lateralization in Parkinson's disease (PD), but its …

[HTML][HTML] Comparative hepatotoxicity of novel lithium bis (trifluoromethanesulfonyl) imide (LiTFSI, ie. HQ-115) and legacy Perfluorooctanoic acid (PFOA) in male mice …

M Sands, X Zhang, M Laws, M Spinella… - Environment …, 2024 - Elsevier
Abstract Lithium Bis (trifluoromethanesulfonyl) imide (LiTFSI ie. HQ-115), a polymer
electrolyte used in energy applications, has been detected in the environment, yet its health …

Long-term environmental metal exposure is associated with hypomethylation of CpG sites in NFKB1 and other genes related to oncogenesis

A Stepanyan, A Petrackova, S Hakobyan, J Savara… - Clinical …, 2023 - Springer
Background Long-term environmental exposure to metals leads to epigenetic changes and
may increase risks to human health. The relationship between the type and level of metal …