Related papers: Modeling DNA methylation dynamics with approaches …
Background: Recent assays for individual-specific genome-wide DNA methylation profiles have enabled epigenome-wide association studies to identify specific CpG sites associated with a phenotype. Computational prediction of CpG site-specific…
DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in…
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…
Cell-free DNA (cfDNA) analysis is a powerful, minimally invasive tool for monitoring disease progression, treatment response, and early detection. A major challenge, however, is accurately determining the tissue of origin, especially in…
We introduce a model of DNA sequence evolution which can account for biases in mutation rates that depend on the identity of the neighboring bases. An analytic solution for this class of non-equilibrium models is developed by adopting…
We perform a statistical study of the distances between successive occurrencies of a given dinucleotide in the DNA sequence for a number of organisms of different complexity. Our analysis highlights peculiar features of the dinucleotide CG…
DNA methylation is an epigenetic mechanism whose important role in development has been widely recognized. This epigenetic modification results in heritable changes in gene expression not encoded by the DNA sequence. The underlying…
DNA methylation is an important epigenetic mark that has been studied extensively for its regulatory role in biological processes and diseases. WGBS allows for genome-wide measurements of DNA methylation up to single-base resolutions, yet…
Motivation: DNA methylation is an intensely studied epigenetic mark, yet its functional role is incompletely understood. Attempts to quantitatively associate average DNA methylation to gene expression yield poor correlations outside of the…
Interrogating the evolution of biological changes at early stages of life requires longitudinal profiling of molecules, such as DNA methylation, which can be challenging with children. We introduce a probabilistic and longitudinal machine…
DNA methylation is an important biological mechanism to regulate gene expression and control cell development. Mechanistic modeling has become a popular approach to enhance our understanding of the dynamics of methylation pattern formation…
During mammalian embryo development, reprogramming of DNA methylation plays important roles in the erasure of parental epigenetic memory and the establishment of na\"{i}ve pluripogent cells. Multiple enzymes that regulate the processes of…
This paper explores the transgenerational DNA methylation pattern (DNA methylation transmitted from one generation to the next) via a clustering approach. Beta regression is employed to model the transmission pattern from parents to their…
Identifying differentially methylated cytosine-guanine dinucleotide (CpG) sites between benign and tumour samples can assist in understanding disease. However, differential analysis of bounded DNA methylation data often requires data…
A novel method to classify human cells is presented in this work based on the transform-domain method on DNA methylation data. DNA methylation profile variations are observed in human cells with the progression of disease stages, and the…
DNA methylation plays a pivotal role in the genetic evolution of both embryonic and adult cells. For adult somatic cells, location and dynamics of methylation has been very precisely pinned down with the 5-cytosine markers on…
DNA methylation is an epigenetic mechanism that regulates gene expression by adding methyl groups to DNA. Abnormal methylation patterns can disrupt gene expression and have been linked to cancer development. To quantify DNA methylation,…
The methylation of DNA regulates gene expression. On cell division the methylation state of the DNA is typically inherited from parent to daughter cells. While the chemical bond between the methyl group and the DNA is very strong, changes…
The presence of neighbor dependencies generated a specific pattern of dinucleotide frequencies in all organisms. Especially, the CpG-methylation-deamination process is the predominant substitution process in vertebrates and needs to be…
A Deep Autoencoder based content retrieval algorithm is proposed for prediction and differentiation of cancer types based on the presence of epigenetic patterns of DNA methylation identified in genetic regions known as CpG islands. The…