AIMC Topic: Epigenomics

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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...
CpG Islands Cerebral Palsy Epigenesis, Genetic Epigenomics DNA Methylation Cell-Free Nucleic Acids Humans Artificial Intelligence Infant, Newborn Gene Expression Profiling Case-Control Studies Deep Learning ROC Curve Gene Regulatory Networks
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DeepHistone: a deep learning approach to predicting histone modifications.

BMC genomics Apr 4, 2019
MOTIVATION: Quantitative detection of histone modifications has emerged in the recent years as a major means for understanding such biological processes as chromosome packaging, transcriptional activation, and DNA damage. However, high-throughput exp...
Humans Deep Learning Histones Chromosome Mapping Chromatin Chromatin Immunoprecipitation Polymorphism, Single Nucleotide Epigenomics Protein Processing, Post-Translational Gene Expression Regulation
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Deep-learning augmented RNA-seq analysis of transcript splicing.

Nature methods Mar 25, 2019
A major limitation of RNA sequencing (RNA-seq) analysis of alternative splicing is its reliance on high sequencing coverage. We report DARTS (https://github.com/Xinglab/DARTS), a computational framework that integrates deep-learning-based predictions...
Alternative Splicing Gene Expression Regulation K562 Cells RNA Splicing Exons Sequence Analysis, RNA Epigenomics Hep G2 Cells Models, Statistical Bayes Theorem Signal Processing, Computer-Assisted RNA High-Throughput Nucleotide Sequencing Algorithms Reproducibility of Results Gene Expression Profiling Deep Learning Humans
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Enhancer prediction with histone modification marks using a hybrid neural network model.

Methods (San Diego, Calif.) Mar 21, 2019
Enhancer is a DNA sequence of a genome that controls transcription of downstream target genes. Enhancers are known to be associated with certain epigenetic signatures. Machine learning tools, such as CSI-ANN, ChromHMM, and RFECS, were developed for p...
Humans Neural Networks, Computer Machine Learning Chromatin Histone Code Computational Biology Epigenomics Histones Enhancer Elements, Genetic
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Machine learning polymer models of three-dimensional chromatin organization in human lymphoblastoid cells.

Methods (San Diego, Calif.) Mar 7, 2019
We present machine learning models of human genome three-dimensional structure that combine one dimensional (linear) sequence specificity, epigenomic information, and transcription factor binding profiles, with the polymer-based biophysical simulatio...
Humans Machine Learning Gene Expression Regulation Genome, Human Computer Simulation Promoter Regions, Genetic Protein Binding Chromatin Epigenomics Polymers
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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 ...
BRCA1 Protein Humans Homologous Recombination DNA Copy Number Variations Middle Aged Female Breast Epigenomics CpG Islands Aged Survival Analysis Support Vector Machine Adult Datasets as Topic Promoter Regions, Genetic DNA Methylation Breast Neoplasms Receptors, Estrogen Receptors, Progesterone
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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...
Genotype Epigenomics Hypoglycemic Agents DNA Methylation CpG Islands Triglycerides Hypertriglyceridemia Humans Machine Learning Genome-Wide Association Study Polymorphism, Single Nucleotide
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Epigenetic machine learning: utilizing DNA methylation patterns to predict spastic cerebral palsy.

BMC bioinformatics Jun 21, 2018
BACKGROUND: Spastic cerebral palsy (CP) is a leading cause of physical disability. Most people with spastic CP are born with it, but early diagnosis is challenging, and no current biomarker platform readily identifies affected individuals. The aim of...
Pattern Recognition, Automated Genome, Human Cerebral Palsy Humans Machine Learning Biomarkers Genetic Predisposition to Disease Female Epigenomics Male Sequence Analysis, DNA Case-Control Studies DNA Methylation Adolescent
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Sequential regulatory activity prediction across chromosomes with convolutional neural networks.

Genome research Mar 27, 2018
Models for predicting phenotypic outcomes from genotypes have important applications to understanding genomic function and improving human health. Here, we develop a machine-learning system to predict cell-type-specific epigenetic and transcriptional...
Regulatory Sequences, Nucleic Acid Models, Genetic Gene Expression Regulation Promoter Regions, Genetic Neural Networks, Computer Humans Genomics Chromosomes Machine Learning Polymorphism, Single Nucleotide Animals Gene Expression Profiling Computational Biology Epigenomics
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Machine learning for epigenetics and future medical applications.

Epigenetics May 19, 2017
Understanding epigenetic processes holds immense promise for medical applications. Advances in Machine Learning (ML) are critical to realize this promise. Previous studies used epigenetic data sets associated with the germline transmission of epigene...
Epigenesis, Genetic Humans Epigenomics Machine Learning Genetics, Medical Animals
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