AIMC Topic: CpG Islands

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Machine learning unveils an immune-related DNA methylation profile in germline DNA from breast cancer patients.

Clinical epigenetics
BACKGROUND: There is an unmet need for precise biomarkers for early non-invasive breast cancer detection. Here, we aimed to identify blood-based DNA methylation biomarkers that are associated with breast cancer.

Deep learning predicts DNA methylation regulatory variants in the human brain and elucidates the genetics of psychiatric disorders.

Proceedings of the National Academy of Sciences of the United States of America
There is growing evidence for the role of DNA methylation (DNAm) quantitative trait loci (mQTLs) in the genetics of complex traits, including psychiatric disorders. However, due to extensive linkage disequilibrium (LD) of the genome, it is challengin...

Artificial intelligence and leukocyte epigenomics: Evaluation and prediction of late-onset Alzheimer's disease.

PloS one
We evaluated the utility of leucocyte epigenomic-biomarkers for Alzheimer's Disease (AD) detection and elucidates its molecular pathogeneses. Genome-wide DNA methylation analysis was performed using the Infinium MethylationEPIC BeadChip array in 24 l...

Machine learning analysis of DNA methylation in a hypoxia-immune model of oral squamous cell carcinoma.

International immunopharmacology
BACKGROUND: Hypoxia status and immunity are related with the development and prognosis of oral squamous cell carcinoma (OSCC). Here, we constructed a hypoxia-immune model to explore its upstream mechanism and identify potential CpG sites.

Evaluation of marker selection methods and statistical models for chronological age prediction based on DNA methylation.

Legal medicine (Tokyo, Japan)
In forensic investigation, retrieving biological information from DNA evidence is a promising field of interest. One of the applications is on the estimation of the age of the donor based on DNA methylation. A large number of studies focused on age p...

MethylNet: an automated and modular deep learning approach for DNA methylation analysis.

BMC bioinformatics
BACKGROUND: DNA methylation (DNAm) is an epigenetic regulator of gene expression programs that can be altered by environmental exposures, aging, and in pathogenesis. Traditional analyses that associate DNAm alterations with phenotypes suffer from mul...

Mb-level CpG and TFBS islands visualized by AI and their roles in the nuclear organization of the human genome.

Genes & genetic systems
Unsupervised machine learning that can discover novel knowledge from big sequence data without prior knowledge or particular models is highly desirable for current genome study. We previously established a batch-learning self-organizing map (BLSOM) f...

D-GPM: A Deep Learning Method for Gene Promoter Methylation Inference.

Genes
Whole-genome bisulfite sequencing generates a comprehensive profiling of the gene methylation levels, but is limited by a high cost. Recent studies have partitioned the genes into landmark genes and target genes and suggested that the landmark gene e...

Deep Learning/Artificial Intelligence and Blood-Based DNA Epigenomic Prediction of Cerebral Palsy.

International journal of molecular sciences
The etiology of cerebral palsy (CP) is complex and remains inadequately understood. Early detection of CP is an important clinical objective as this improves long term outcomes. We performed genome-wide DNA methylation analysis to identify epigenomic...