AIMC Topic: CpG Islands

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ReQuant: improved base modification calling by k-mer value imputation.

Nucleic acids research May 10, 2025
Nanopore sequencing allows identification of base modifications, such as methylation, directly from raw current data. Prevailing approaches, including deep learning (DL) methods, require training data covering all possible sequence contexts. These da...
Software Algorithms Deep Learning Humans CpG Islands Bacteriophage lambda Nanopore Sequencing Sequence Analysis, DNA DNA Methylation DNA
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Leveraging molecular-QTL co-association to predict novel disease-associated genetic loci using a graph convolutional neural network.

PloS one Jan 1, 2025
Genome-wide association studies (GWAS) have successfully uncovered numerous associations between genetic variants and disease traits to date. Yet, identifying significantly associated loci remains a considerable challenge due to the concomitant multi...
Quantitative Trait Loci Genome-Wide Association Study Genetic Predisposition to Disease Humans Polymorphism, Single Nucleotide Neural Networks, Computer DNA Methylation Convolutional Neural Networks CpG Islands
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Imputing missing RNA-sequencing data from DNA methylation by using a transfer learning-based neural network.

GigaScience Jul 1, 2020
BACKGROUND: Gene expression plays a key intermediate role in linking molecular features at the DNA level and phenotype. However, owing to various limitations in experiments, the RNA-seq data are missing in many samples while there exist high-quality ...
Algorithms Prognosis Reproducibility of Results Neural Networks, Computer Machine Learning Epigenomics DNA Methylation High-Throughput Nucleotide Sequencing Neoplasms Computational Biology Epigenesis, Genetic Humans CpG Islands Gene Expression Regulation
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[Methylation level of MEG3 and semen quality].

Zhonghua nan ke xue = National journal of andrology Nov 1, 2019
OBJECTIVE: To study the relationship between semen quality and the methylation level of maternally expressed gene 3 (MEG3) in sperm.
Sperm Motility CpG Islands RNA, Long Noncoding Genomic Imprinting Semen Analysis Humans Spermatozoa Methylation Male
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Outgroup Machine Learning Approach Identifies Single Nucleotide Variants in Noncoding DNA Associated with Autism Spectrum Disorder.

Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing Jan 1, 2019
Autism spectrum disorder (ASD) is a heritable neurodevelopmental disorder affecting 1 in 59 children. While noncoding genetic variation has been shown to play a major role in many complex disorders, the contribution of these regions to ASD susceptibi...
CpG Islands RNA, Untranslated Microsatellite Repeats Supranuclear Palsy, Progressive DNA Whole Genome Sequencing Genetic Variation Logistic Models MicroRNAs Humans Machine Learning Phenotype Child Gene Regulatory Networks Polymorphism, Single Nucleotide Male Autism Spectrum Disorder Genetic Predisposition to Disease Genetic Association Studies Case-Control Studies Female Computational Biology Cohort Studies
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DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes.

Bioinformatics (Oxford, England) Oct 1, 2017
MOTIVATION: 5-Methylcytosine and 5-Hydroxymethylcytosine in DNA are major epigenetic modifications known to significantly alter mammalian gene expression. High-throughput assays to detect these modifications are expensive, labor-intensive, unfeasible...
CpG Islands 5-Methylcytosine DNA Methylation DNA Mammals Machine Learning Animals Humans Software Epigenesis, Genetic Algorithms
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Higher order methylation features for clustering and prediction in epigenomic studies.

Bioinformatics (Oxford, England) Sep 1, 2016
MOTIVATION: DNA methylation is an intensely studied epigenetic mark, yet its functional role is incompletely understood. Attempts to quantitatively associate average DNA methylation to gene expression yield poor correlations outside of the well-under...
DNA Methylation Machine Learning Gene Expression Promoter Regions, Genetic CpG Islands Forecasting Genome Epigenomics
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