AIMC Topic: CpG Islands

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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...
Humans Artificial Intelligence Genome, Human Binding Sites Centromere Chromosomes, Human Heterochromatin Protein Binding Transcription Factors Oligonucleotides CpG Islands
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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...
CpG Islands Gene Expression Regulation Promoter Regions, Genetic Humans Sequence Analysis, DNA Machine Learning DNA Methylation Gene Expression Profiling Gene Expression Deep Learning Linear Models Computational Biology
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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...
Humans Middle Aged Risk Assessment Disease Progression Diabetes Mellitus, Type 2 Genomics Prognosis Female Risk Factors Male 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...
Epigenesis, Genetic Epigenomics DNA Methylation CpG Islands Cell-Free Nucleic Acids Humans Cerebral Palsy Gene Expression Profiling Artificial Intelligence Case-Control Studies Infant, Newborn Deep Learning ROC Curve Gene Regulatory Networks
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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 ...
Models, Statistical Regression Analysis CpG Islands Genome, Human Genomics Epigenesis, Genetic Sequence Analysis, DNA DNA Methylation Humans Algorithms Deep Learning
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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 DNA Copy Number Variations Breast Survival Analysis Datasets as Topic CpG Islands Promoter Regions, Genetic Receptors, Estrogen Receptors, Progesterone Breast Neoplasms Humans BRCA1 Protein Middle Aged Female Epigenomics Aged Support Vector Machine Adult DNA Methylation
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LogLoss-BERAF: An ensemble-based machine learning model for constructing highly accurate diagnostic sets of methylation sites accounting for heterogeneity in prostate cancer.

PloS one Nov 2, 2018
Although modern methods of whole genome DNA methylation analysis have a wide range of applications, they are not suitable for clinical diagnostics due to their high cost and complexity and due to the large amount of sample DNA required for the analys...
Humans Machine Learning Models, Genetic DNA Methylation Algorithms Prostatic Neoplasms Male CpG Islands Neoplasms Gene Expression Regulation, Neoplastic
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Data mining and machine learning approaches for the integration of genome-wide association and methylation data: methodology and main conclusions from GAW20.

BMC genetics Sep 17, 2018
BACKGROUND: Multiple layers of genetic and epigenetic variability are being simultaneously explored in an increasing number of health studies. We summarize here different approaches applied in the Data Mining and Machine Learning group at the GAW20 t...
Cluster Analysis Humans Machine Learning Data Mining Phenotype CpG Islands Genome-Wide Association Study DNA Methylation
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Using recursive feature elimination in random forest to account for correlated variables in high dimensional data.

BMC genetics Sep 17, 2018
BACKGROUND: Random forest (RF) is a machine-learning method that generally works well with high-dimensional problems and allows for nonlinear relationships between predictors; however, the presence of correlated predictors has been shown to impact it...
Genome-Wide Association Study Polymorphism, Single Nucleotide Genotype Epigenomics Hypoglycemic Agents DNA Methylation CpG Islands Triglycerides Hypertriglyceridemia Humans Machine Learning
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Targeted bisulfite sequencing identified a panel of DNA methylation-based biomarkers for esophageal squamous cell carcinoma (ESCC).

Clinical epigenetics Dec 15, 2017
BACKGROUND: DNA methylation has been implicated as a promising biomarker for precise cancer diagnosis. However, limited DNA methylation-based biomarkers have been described in esophageal squamous cell carcinoma (ESCC).
Pseudogenes Middle Aged Repressor Proteins Logistic Models Esophageal Neoplasms Sequence Analysis, DNA Aged Serine-Threonine Kinase 3 Epigenesis, Genetic Humans CpG Islands DNA Methylation Sensitivity and Specificity Databases, Genetic Machine Learning Promoter Regions, Genetic Early Detection of Cancer Biomarkers, Tumor Female Esophageal Squamous Cell Carcinoma Protein Serine-Threonine Kinases Male Carcinoma, Squamous Cell DNA-Binding Proteins
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