AIMC Topic: CpG Islands

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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...
Neoplasms Gene Expression Regulation, Neoplastic Models, Genetic DNA Methylation Prostatic Neoplasms Humans Machine Learning Algorithms Male CpG Islands
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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...
CpG Islands Genome-Wide Association Study DNA Methylation Cluster Analysis Data Mining Humans Machine Learning Phenotype
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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...
CpG Islands Triglycerides Hypertriglyceridemia Humans Machine Learning Genome-Wide Association Study Epigenomics Polymorphism, Single Nucleotide Hypoglycemic Agents Genotype DNA Methylation
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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 Repressor Proteins Middle Aged Serine-Threonine Kinase 3 Esophageal Neoplasms Aged Early Detection of Cancer Sequence Analysis, DNA Logistic Models CpG Islands Sensitivity and Specificity Epigenesis, Genetic DNA Methylation Protein Serine-Threonine Kinases Promoter Regions, Genetic Humans Databases, Genetic Biomarkers, Tumor DNA-Binding Proteins Esophageal Squamous Cell Carcinoma Machine Learning Male Female Carcinoma, Squamous Cell
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DNA methylation-based forensic age prediction using artificial neural networks and next generation sequencing.

Forensic science international. Genetics Feb 28, 2017
The ability to estimate the age of the donor from recovered biological material at a crime scene can be of substantial value in forensic investigations. Aging can be complex and is associated with various molecular modifications in cells that accumul...
High-Throughput Nucleotide Sequencing CpG Islands Forensic Genetics Twins, Monozygotic Epigenomics DNA Methylation DNA Saliva Humans Neural Networks, Computer Adult Aging Middle Aged Machine Learning Aged
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DMAK: A curated pan-cancer DNA methylation annotation knowledgebase.

Bioengineered Aug 12, 2016
Pan-cancer analysis can identify cell- and tissue-specific genomic loci and regions with underlying biological functions. Here we present an online curated DNA Methylation Annotation Knowledgebase, DMAK, which includes the pan-cancer analysis results...
Knowledge Bases CpG Islands Humans Neoplasms DNA Methylation
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Genome-Wide Locations of Potential Epimutations Associated with Environmentally Induced Epigenetic Transgenerational Inheritance of Disease Using a Sequential Machine Learning Prediction Approach.

PloS one Nov 16, 2015
Environmentally induced epigenetic transgenerational inheritance of disease and phenotypic variation involves germline transmitted epimutations. The primary epimutations identified involve altered differential DNA methylation regions (DMRs). Differen...
Computational Biology Epigenesis, Genetic Databases, Genetic Sequence Analysis, DNA Bayes Theorem Mutation Spermatozoa DNA Methylation Cluster Analysis Reproducibility of Results Male Genome-Wide Association Study Genetic Predisposition to Disease Humans Machine Learning Phenotype Female DDT Environmental Exposure Methoxychlor Granulosa Cells Sertoli Cells CpG Islands Chromosomes
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Characterization and machine learning prediction of allele-specific DNA methylation.

Genomics Sep 25, 2015
A large collection of Single Nucleotide Polymorphisms (SNPs) has been identified in the human genome. Currently, the epigenetic influences of SNPs on their neighboring CpG sites remain elusive. A growing body of evidence suggests that locus-specific ...
Exons Machine Learning Brain CpG Islands Animals Species Specificity Epigenomics Humans Mice Promoter Regions, Genetic DNA Methylation Binding Sites Alleles Polymorphism, Single Nucleotide Logistic Models
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Development and validation of a machine learning prognostic model based on an epigenomic signature in patients with pancreatic ductal adenocarcinoma.

International journal of medical informatics Jul 1, 2025
BACKGROUND: In Pancreatic Ductal Adenocarcinoma (PDAC), current prognostic scores are unable to fully capture the biological heterogeneity of the disease. While some approaches investigating the role of multi-omics in PDAC are emerging, the analysis ...
Machine Learning Prognosis Female Male Humans Mutation Carcinoma, Pancreatic Ductal Tumor Suppressor Protein p53 CpG Islands Proto-Oncogene Proteins p21(ras) Middle Aged Epigenomics DNA Methylation Pancreatic Neoplasms
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Temporally discordant chromatin accessibility and DNA demethylation define short- and long-term enhancer regulation during cell fate specification.

Cell reports May 27, 2025
Chromatin and DNA modifications mediate the transcriptional activity of lineage-specifying enhancers, but recent work challenges the dogma that joint chromatin accessibility and DNA demethylation are prerequisites for transcription. To understand thi...
Animals Cell Lineage Enhancer Elements, Genetic Mice Chromatin DNA Methylation Neural Stem Cells Cell Differentiation DNA Demethylation CpG Islands
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