Related papers: Next Generation Epigenetic Detection Technique:Ide…
Cytosine methylation has been found to play a crucial role in various biological processes, including a number of human diseases. The detection of this small modification remains challenging. In this work, we computationally explore the…
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…
Methylation of CpG dinucleotides is a prevalent epigenetic modification that is required for proper development in vertebrates, and changes in CpG methylation are essential to cellular differentiation. Genome-wide DNA methylation assays…
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…
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…
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…
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…
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…
Epigenetic alterations have an important role in the development of several types of cancer. Epigenetic studies generate a large amount of data, which makes it essential to develop novel models capable of dealing with large-scale data. In…
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…
Nanopore based sequencing has demonstrated significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multi-layered…
A key focus in current cancer research is the discovery of cancer biomarkers that allow earlier detection with high accuracy and lower costs for both patients and hospitals. Blood samples have long been used as a health status indicator,…
Accurate computational identification of DNA methylation is essential for understanding epigenetic regulation. Although deep learning excels in this binary classification task, its "black-box" nature impedes biological insight. We address…
Nanopores -- nanosized holes that can transport ions and molecules -- are very promising devices for genomic screening, in particular DNA sequencing. Both solid-state and biological pores suffer from the drawback, however, that the channel…
DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…
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…
DNA cytosine methylation is a critical epigenetic mark regulating gene expression and thus playing an important role in development and differentiation across eukaryotes. Existing tools for high-throughput methylation analysis often lack…
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 a crucial epigenetic marker used in various clocks to predict epigenetic age. However, many existing clocks fail to account for crucial information about CpG sites and their interrelationships, such as co-methylation…
The research reported in this paper identifies the epigenetic biomarker (methylation beta pattern) of breast cancer. Many cancers are triggered by abnormal gene expression levels caused by aberrant methylation of CpG sites in the DNA. In…