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DNA methylation is a well-studied genetic modification crucial to regulate the functioning of the genome. Its alterations play an important role in tumorigenesis and tumor-suppression. Thus, studying DNA methylation data may help biomarker…
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 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,…
Gene expression analysis is a critical method for cancer classification, enabling precise diagnoses through the identification of unique molecular signatures associated with various tumors. Identifying cancer-specific genes from gene…
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…
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…
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…
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…
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…
The prediction plays the important role in detecting efficient protection and therapy of cancer. The prediction of mutations in gene needs a diagnostic and classification, which is based on the whole database (big dataset), to reach…
With the increased affordability and availability of whole-genome sequencing, large-scale and high-throughput gene expression is widely used to characterize diseases, including cancers. However, establishing specificity in cancer diagnosis…
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…
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,…
Late diagnosis and high costs are key factors that negatively impact the care of cancer patients worldwide. Although the availability of biological markers for the diagnosis of cancer type is increasing, costs and reliability of tests…
Pan-cancer classification using transcriptomic (RNA-Seq) data can inform tumor subtyping and therapy selection, but is challenging due to extremely high dimensionality and limited sample sizes. In this study, we propose a novel deep…
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…
Cancer and its subtypes constitute approximately 30% of all causes of death globally and display a wide range of heterogeneity in terms of clinical and molecular responses to therapy. Molecular subtyping has enabled the use of precision…
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…
Determining the primary site of origin for metastatic tumors is one of the open problems in cancer care because the efficacy of treatment often depends on the cancer tissue of origin. Classification methods that can leverage tumor genomic…
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…