AIMC Topic: DNA Methylation

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DeepMethylation: a deep learning based framework with GloVe and Transformer encoder for DNA methylation prediction.

PeerJ
DNA methylation is a crucial topic in bioinformatics research. Traditional wet experiments are usually time-consuming and expensive. In contrast, machine learning offers an efficient and novel approach. In this study, we propose DeepMethylation, a no...

Precision epigenetics provides a scalable pathway for improving coronary heart disease care globally.

Epigenomics
Coronary heart disease (CHD) is the world's leading cause of death. Up to 90% of all CHD deaths are preventable, but effective prevention of this mortality requires more scalable, precise methods for assessing CHD status and monitoring treatment resp...

Prediction of DNA Methylation based on Multi-dimensional feature encoding and double convolutional fully connected convolutional neural network.

PLoS computational biology
DNA methylation takes on critical significance to the regulation of gene expression by affecting the stability of DNA and changing the structure of chromosomes. DNA methylation modification sites should be identified, which lays a solid basis for gai...

Comprehensive tissue deconvolution of cell-free DNA by deep learning for disease diagnosis and monitoring.

Proceedings of the National Academy of Sciences of the United States of America
Plasma cell-free DNA (cfDNA) is a noninvasive biomarker for cell death of all organs. Deciphering the tissue origin of cfDNA can reveal abnormal cell death because of diseases, which has great clinical potential in disease detection and monitoring. D...

Development of a model for the prediction of biological age.

Computer methods and programs in biomedicine
BACKGROUND AND OBJECTIVE: Rates of aging vary markedly among individuals, and biological age serves as a more reliable predictor of current health status than does chronological age. As such, the ability to predict biological age can support appropri...

EpiTEAmDNA: Sequence feature representation via transfer learning and ensemble learning for identifying multiple DNA epigenetic modification types across species.

Computers in biology and medicine
Methylation is a major DNA epigenetic modification for regulating the biological processes without altering the DNA sequence, and multiple types of DNA methylations have been discovered, including 6mA, 5hmC, and 4mC. Multiple computational approaches...

I-DNAN6mA: Accurate Identification of DNA N-Methyladenine Sites Using the Base-Pairing Map and Deep Learning.

Journal of chemical information and modeling
The recent discovery of numerous DNA N-methyladenine (6mA) sites has transformed our perception about the roles of 6mA in living organisms. However, our ability to understand them is hampered by our inability to identify 6mA sites rapidly and cost-ef...

A Comparison of Three Different Deep Learning-Based Models to Predict the MGMT Promoter Methylation Status in Glioblastoma Using Brain MRI.

Journal of digital imaging
Glioblastoma (GBM) is the most common primary malignant brain tumor in adults. The standard treatment for GBM consists of surgical resection followed by concurrent chemoradiotherapy and adjuvant temozolomide. O-6-methylguanine-DNA methyltransferase (...

Fused deep learning paradigm for the prediction of o6-methylguanine-DNA methyltransferase genotype in glioblastoma patients: A neuro-oncological investigation.

Computers in biology and medicine
BACKGROUND: The O6-methylguanine-DNA methyltransferase (MGMT) is a deoxyribonucleic acid (DNA) repairing enzyme that has been established as an essential clinical brain tumor biomarker for Glioblastoma Multiforme (GBM). Knowing the status of MGMT met...

Application of Feature Selection and Deep Learning for Cancer Prediction Using DNA Methylation Markers.

Genes
DNA methylation is a process that can affect gene accessibility and therefore gene expression. In this study, a machine learning pipeline is proposed for the prediction of breast cancer and the identification of significant genes that contribute to t...