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pycoMeth: a toolbox for differential methylation testing from Nanopore methylation calls
We present pycoMeth , a toolbox to store, manage and analyze DNA methylation calls from long-read sequencing data obtained using the Oxford Nanopore...
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Transcriptome- and DNA methylation-based cell-type deconvolutions produce similar estimates of differential gene expression and differential methylation
BackgroundChanging cell-type proportions can confound studies of differential gene expression or DNA methylation (DNAm) from peripheral blood...
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Differential methylation analysis in neuropathologically confirmed dementia with Lewy bodies
Dementia with Lewy bodies (DLB) is a common form of dementia in the elderly population. We performed genome-wide DNA methylation mapping of...
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Differential DNA methylation landscape of miRNAs genes in mice liver fibrosis
BackgroundPatients with chronic liver disease were found nearly all to have liver fibrosis, which is characterized by excess accumulation of...
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DNA Methylation in Ctenophores
Epigenomic regulation and dynamic DNA methylation, in particular, are widespread mechanisms orchestrating the genome operation across time and...
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Phasing DNA Methylation
Haplotyping enables the study of allele-specific events. Heterozygous variants, primarily single nucleotide variants (SNVs), enable the assignment of...
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Heterogeneity of increased biological age in type 2 diabetes correlates with differential tissue DNA methylation, biological variables, and pharmacological treatments
Biological age (BA) closely depicts age-related changes at a cellular level. Type 2 diabetes mellitus (T2D) accelerates BA when calculated using...
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Contribution of RdDM to the ecotype-specific differential methylation on conserved as well as highly variable regions between Arabidopsis ecotypes
BackgroundSeveral studies showed genome-wide DNA methylation during Arabidopsis embryogenesis and germination. Although it has been known that the...
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Differential DNA methylation and CTCF binding between the ESR1 promoter a of MCF-7 and MDA-MB-231 breast cancer cells
BackgroundESR1 is expressed by 60–70% of breast tumours. it’s a good prognosis factor and the target of hormone therapy. Optimization of ESR1...
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Estimating genome-wide DNA methylation heterogeneity with methylation patterns
BackgroundIn a heterogeneous population of cells, individual cells can behave differently and respond variably to the environment. This cellular...
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Evolution and Diversity of DNA Methylation in Eukaryotes
DNA methylation (DNAm) is an important and well characterized epigenetic process which regulates gene expression, plays a vital role in embryonic...
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DMRscaler: a scale-aware method to identify regions of differential DNA methylation spanning basepair to multi-megabase features
BackgroundPathogenic mutations in genes that control chromatin function have been implicated in rare genetic syndromes. These chromatin modifiers...
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Differential DNA methylation in Pacific oyster reproductive tissue in response to ocean acidification
BackgroundThere is a need to investigate mechanisms of phenotypic plasticity in marine invertebrates as negative effects of climate change, like...
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Cloning and differential methylation of 28 S rRNA gene from two wing phenotypes of Sogatella furcifera, an important pest in rice
Sogatella furcifera is an important rice pest with wing dimorphism. We previously demonstrated that differentially methylated DNA fragments obtained...
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Associations between DNA methylation and gene regulation depend on chromatin accessibility during transgenerational plasticity
BackgroundEpigenetic processes are proposed to be a mechanism regulating gene expression during phenotypic plasticity. However, environmentally...
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Single-molecule long-read methylation profiling reveals regional DNA methylation regulated by Elongator Complex Subunit 2 in Arabidopsis roots experiencing spaceflight
BackgroundThe Advanced Plant Experiment-04 - Epigenetic Expression (APEX-04-EpEx) experiment onboard the International Space Station examined the...
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Small RNA and DNA Methylation of Tea Plants
Small RNAs are a category of short noncoding RNAs (ncRNAs) with 18–30 nt lengths. Based on their function and mechanisms of biogenesis, these small...
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Interactive DNA Methylation Array Analysis with ShinyÉPICo
Arrays provide a cost-effective platform for the analysis of human DNA methylation. ShinyÉPICo is an interactive, web-based, and graphical tool that...
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LuxHMM: DNA methylation analysis with genome segmentation via hidden Markov model
BackgroundDNA methylation plays an important role in studying the epigenetics of various biological processes including many diseases. Although...
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Epigenetic differences between wild and cultivated grapevines highlight the contribution of DNA methylation during crop domestication
The domestication process in grapevines has facilitated the fixation of desired traits. Nowadays, vegetative propagation through cuttings enables...
