AIMC Topic: CpG Islands

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

PloS one Mar 31, 2021
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...
Aged Aged, 80 and over Sensitivity and Specificity Male Case-Control Studies Humans Biomarkers Prognosis Female DNA Methylation Leukocytes Alzheimer Disease CpG Islands Late Onset Disorders Deep Learning Genome-Wide Association Study Epigenesis, Genetic Epigenomics Signal Transduction
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Machine learning analysis of DNA methylation in a hypoxia-immune model of oral squamous cell carcinoma.

International immunopharmacology Oct 19, 2020
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.
Computational Biology Humans Gene Expression Regulation, Neoplastic Machine Learning Squamous Cell Carcinoma of Head and Neck Prognosis Head and Neck Neoplasms Tumor Microenvironment Databases, Genetic DNA Methylation Models, Biological Hypoxia CpG Islands
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Evaluation of marker selection methods and statistical models for chronological age prediction based on DNA methylation.

Legal medicine (Tokyo, Japan) Jul 1, 2020
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...
Humans Machine Learning Algorithms Adult Male Aging Middle Aged Sequence Analysis, DNA Forecasting Female Aged Aged, 80 and over Young Adult Forensic Genetics DNA Methylation Models, Statistical Linear Models CpG Islands
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MethylNet: an automated and modular deep learning approach for DNA methylation analysis.

BMC bioinformatics Mar 17, 2020
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...
Deep Learning User-Computer Interface DNA Methylation CpG Islands Humans Aging Neoplasms
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Mb-level CpG and TFBS islands visualized by AI and their roles in the nuclear organization of the human genome.

Genes & genetic systems Mar 12, 2020
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...
Chromosomes, Human Heterochromatin CpG Islands Genome, Human Binding Sites Centromere Humans Artificial Intelligence Protein Binding Transcription Factors Oligonucleotides
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D-GPM: A Deep Learning Method for Gene Promoter Methylation Inference.

Genes Oct 14, 2019
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...
Gene Expression Regulation Promoter Regions, Genetic DNA Methylation Gene Expression Linear Models CpG Islands Machine Learning Humans Gene Expression Profiling Deep Learning Computational Biology Sequence Analysis, DNA
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Machine-learning to stratify diabetic patients using novel cardiac biomarkers and integrative genomics.

Cardiovascular diabetology Jun 11, 2019
BACKGROUND: Diabetes mellitus is a chronic disease that impacts an increasing percentage of people each year. Among its comorbidities, diabetics are two to four times more likely to develop cardiovascular diseases. While HbA1c remains the primary dia...
Prognosis Female Risk Factors Male Middle Aged Risk Assessment Disease Progression Diabetes Mellitus, Type 2 Genomics Humans CpG Islands Support Vector Machine Systems Integration DNA Methylation Genetic Predisposition to Disease Mitochondria, Heart Glycated Hemoglobin Polymorphism, Single Nucleotide Diabetic Cardiomyopathies Genetic Markers Epigenesis, Genetic DNA, Mitochondrial Models, Genetic
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Deep Learning/Artificial Intelligence and Blood-Based DNA Epigenomic Prediction of Cerebral Palsy.

International journal of molecular sciences Apr 27, 2019
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...
Gene Expression Profiling Case-Control Studies Deep Learning ROC Curve Gene Regulatory Networks CpG Islands Humans Epigenesis, Genetic Artificial Intelligence Epigenomics Cerebral Palsy Infant, Newborn DNA Methylation Cell-Free Nucleic Acids
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MRCNN: a deep learning model for regression of genome-wide DNA methylation.

BMC genomics Apr 4, 2019
BACKGROUND: Determination of genome-wide DNA methylation is significant for both basic research and drug development. As a key epigenetic modification, this biochemical process can modulate gene expression to influence the cell differentiation which ...
Humans Algorithms Models, Statistical Deep Learning Genomics Regression Analysis Epigenesis, Genetic CpG Islands Sequence Analysis, DNA Genome, Human DNA Methylation
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Molecular and epigenetic profiles of BRCA1-like hormone-receptor-positive breast tumors identified with development and application of a copy-number-based classifier.

Breast cancer research : BCR Jan 25, 2019
BACKGROUND: BRCA1-mutated cancers exhibit deficient homologous recombination (HR) DNA repair, resulting in extensive copy number alterations and genome instability. HR deficiency can also arise in tumors without a BRCA1 mutation. Compared with other ...
Homologous Recombination CpG Islands Humans DNA Copy Number Variations Breast Neoplasms Promoter Regions, Genetic Female Breast Middle Aged Receptors, Estrogen Aged Survival Analysis Epigenomics Receptors, Progesterone Adult Datasets as Topic Support Vector Machine BRCA1 Protein DNA Methylation
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