AIMC Topic: DNA Methylation

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Machine Learning-Based Identification of Diagnostic Biomarkers for Korean Male Sarcopenia Through Integrative DNA Methylation and Methylation Risk Score: From the Korean Genomic Epidemiology Study (KoGES).

Journal of Korean medical science
BACKGROUND: Sarcopenia, characterized by a progressive decline in muscle mass, strength, and function, is primarily attributable to aging. DNA methylation, influenced by both genetic predispositions and environmental exposures, plays a significant ro...

Tissue of origin detection for cancer tumor using low-depth cfDNA samples through combination of tumor-specific methylation atlas and genome-wide methylation density in graph convolutional neural networks.

Journal of translational medicine
BACKGROUND: Cell free DNA (cfDNA)-based assays hold great potential in detecting early cancer signals yet determining the tissue-of-origin (TOO) for cancer signals remains a challenging task. Here, we investigated the contribution of a methylation at...

Image-based deep learning model using DNA methylation data predicts the origin of cancer of unknown primary.

Neoplasia (New York, N.Y.)
Cancer of unknown primary (CUP) is a rare type of metastatic cancer in which the origin of the tumor is unknown. Since the treatment strategy for patients with metastatic tumors depends on knowing the primary site, accurate identification of the orig...

Deep learning model integrating cfDNA methylation and fragment size profiles for lung cancer diagnosis.

Scientific reports
Detecting aberrant cell-free DNA (cfDNA) methylation is a promising strategy for lung cancer diagnosis. In this study, our aim is to identify methylation markers to distinguish patients with lung cancer from healthy individuals. Additionally, we soug...

Predicting type 2 diabetes via machine learning integration of multiple omics from human pancreatic islets.

Scientific reports
Type 2 diabetes (T2D) is the fastest growing non-infectious disease worldwide. Impaired insulin secretion from pancreatic beta-cells is a hallmark of T2D, but the mechanisms behind this defect are insufficiently characterized. Integrating multiple la...

A novel blood-based epigenetic biosignature in first-episode schizophrenia patients through automated machine learning.

Translational psychiatry
Schizophrenia (SCZ) is a chronic, severe, and complex psychiatric disorder that affects all aspects of personal functioning. While SCZ has a very strong biological component, there are still no objective diagnostic tests. Lately, special attention ha...

Machine learning and integrative multi-omics network analysis for survival prediction in acute myeloid leukemia.

Computers in biology and medicine
BACKGROUND: Acute myeloid leukemia (AML) is the most common malignant myeloid disorder in adults and the fifth most common malignancy in children, necessitating advanced technologies for outcome prediction.

Effective training of nanopore callers for epigenetic marks with limited labelled data.

Open biology
Nanopore sequencing platforms combined with supervised machine learning (ML) have been effective at detecting base modifications in DNA such as 5-methylcytosine (5mC) and N6-methyladenine (6mA). These ML-based nanopore callers have typically been tra...

Using a hybrid neural network architecture for DNA sequence representation: A study on N-methylcytosine sites.

Computers in biology and medicine
N-methylcytosine (4mC) is a modified form of cytosine found in DNA, contributing to epigenetic regulation. It exists in various genomes, including the Rosaceae family encompassing significant fruit crops like apples, cherries, and roses. Previous inv...

Prediction of DNA methylation-based tumor types from histopathology in central nervous system tumors with deep learning.

Nature medicine
Precision in the diagnosis of diverse central nervous system (CNS) tumor types is crucial for optimal treatment. DNA methylation profiles, which capture the methylation status of thousands of individual CpG sites, are state-of-the-art data-driven mea...