相关论文: Higher order methylation features for clustering a…
We make use of ideas from the theory of complex networks to implement a machine learning classification of human DNA methylation data, that carry signatures of cancer development. The data were obtained from patients with various kinds of…
DNA methylation is a significant driver of cell-type heterogeneity and has been implicated in various regulatory processes ranging from cell differentiation to imprinting. As the methyl group is embedded in the DNA molecule, assessing DNA…
Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder characterized by progressive cognitive decline and widespread epigenetic dysregulation in the brain. DNA methylation, as a stable yet dynamic epigenetic modification,…
High-throughput genetic and epigenetic data are often screened for associations with an observed phenotype. For example, one may wish to test hundreds of thousands of genetic variants, or DNA methylation sites, for an association with…
A common problem in bioinformatics is related to identifying gene regulatory regions marked by relatively high frequencies of motifs, or deoxyribonucleic acid sequences that often code for transcription and enhancer proteins. Predicting…
In DNA computing, it is impossible to decide whether a specific hybridization among complex DNA molecules is effective or not within acceptable time. In order to address this common problem, we introduce a new method based on the machine…
This study investigates the correlation between dairy farm characteristics and methane concentrations as derived from satellite observations in Eastern Canada. Utilizing data from 11 dairy farms collected between January 2020 and December…
Motivation: Methods are needed to test pre-defined genomic regions such as promoters for differential methylation in genome-wide association studies, where the number of samples is limited and the data have large amounts of measurement…
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…
A deeper understanding of the drivers of evapotranspiration and the modelling of its constituent parts (evaporation and transpiration) could be of significant importance to the monitoring and management of water resources globally over the…
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…
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…
DNA methylation datasets in cancer studies are comprised of measurements on a large number of genomic locations called cytosine-phosphate-guanine (CpG) sites with complex correlation structures. A fundamental goal of these studies is the…
Cancer is a term that denotes a group of diseases caused by abnormal growth of cells that can spread in different parts of the body. According to the World Health Organization (WHO), cancer is the second major cause of death after…
We develop Bayesian inference methods for a recently-emerging type of epigenetic data to study the transmission fidelity of DNA methylation patterns over cell divisions. The data consist of parent-daughter double-stranded DNA methylation…
Artificial intelligence methods including deep neural networks (DNN) can provide rapid molecular classification of tumors from routine histology with accuracy that matches or exceeds human pathologists. Discerning how neural networks make…
Gene expression can be used to subtype breast cancer with improved prediction of risk of recurrence and treatment responsiveness over that obtained using routine immunohistochemistry (IHC). However, in the clinic, molecular profiling is…
Gene expression profiles obtained through DNA microarray have proven successful in providing critical information for cancer detection classifiers. However, the limited number of samples in these datasets poses a challenge to employ complex…
Identifying disease-associated changes in DNA methylation can help to gain a better understanding of disease etiology. Bisulfite sequencing technology allows the generation of methylation profiles at single base of DNA. We previously…
Background: The analysis of DNA methylation is a key component in the development of personalized treatment approaches. A common way to measure DNA methylation is the calculation of beta values, which are bounded variables of the form M =…