Related papers: Methylator: A Modular Framework for DNA Methylatio…
Motivation: Bisulphite sequencing enables the detection of cytosine methylation. The sequence of the methylation states of cytosines on any given read forms a methylation pattern that carries substantially more information than merely…
Among the different biomarkers of aging based on omics and clinical data, DNA methylation clocks stand apart providing unmatched accuracy in assessing the biological age of both humans and animal models of aging. Here, we discuss robustness…
Methylation and hydroxylation of cytosines to form 5-methylcytosine (5mC) and 5-droxymethylcytosine (5hmC) belong to the most important epigenetic modifications and their vital role in the regulation of gene expression has been widely…
In aiming to explain the establishment, maintenance and stability of methylation pattern in gene body of Arabidopsis we propose here a theoretical framework for understanding how the methylated and unmethylated states of cytosine residues…
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…
DNA methylation is a crucial regulator of gene transcription and has been linked to various diseases, including autoimmune diseases and cancers. However, diagnostics based on DNA methylation face challenges due to large feature sets and…
Medulloblastoma is a malignant pediatric brain cancer, and the discovery of molecular subgroups is enabling personalized treatment strategies. In 2019, a consensus identified eight novel subtypes within Groups 3 and 4, each displaying…
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…
DNA methylation is a well-studied genetic modification that regulates gene transcription of Eukaryotes. Its alternations have been recognized as a significant component of cancer development. In this study, we use the DNA methylation 450k…
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…
Sensitive and reliable methylation assay is important for oncogentic studies and clinical applications. Here, a new methylation assay was developed by the use of adapter-dependent adapter in library preparation. This new assay avoids 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…
Genetic algorithms are a well-known example of bio-inspired heuristic methods. They mimic natural selection by modeling several operators such as mutation, crossover, and selection. Recent discoveries about Epigenetics regulation processes…
In this paper we propose network methodology to infer prognostic cancer biomarkers based on the epigenetic pattern DNA methylation. Epigenetic processes such as DNA methylation reflect environmental risk factors, and are increasingly…
DNA methylation is usually treated as an epigenetic memory mark: transcriptional history is written into regulatory DNA and later stabilizes a chosen cell identity. This picture explains persistence, but it makes memory passive. Here we…
DNA methylation is an intensely studied epigenetic mark implicated in many biological processes of direct clinical relevance. While sequencing based technologies are increasingly allowing high resolution measurements of DNA methylation,…
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,…
In many fields, researchers are interested in large and complex biological processes. Two important examples are gene expression and DNA methylation in genetics. One key problem is to identify aberrant patterns of these processes and…
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…
Colorectal cancer remains a major global health concern, with early detection being pivotal for improving patient outcomes. In this study, we leveraged high throughput methylation profiling of cellfree DNA to identify and validate…