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Enhancer Elements, Genetic

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Deciphering the regulatory syntax of genomic DNA with deep learning.

Journal of biosciences
An organism's genome contains many sequence regions that perform diverse functions. Examples of such regions include genes, promoters, enhancers, and binding sites for regulatory proteins and RNAs. One of biology's most important open problems is how...

iEnhancer-DCLA: using the original sequence to identify enhancers and their strength based on a deep learning framework.

BMC bioinformatics
Enhancers are small regions of DNA that bind to proteins, which enhance the transcription of genes. The enhancer may be located upstream or downstream of the gene. It is not necessarily close to the gene to be acted on, because the entanglement struc...

A deep learning based two-layer predictor to identify enhancers and their strength.

Methods (San Diego, Calif.)
The enhancer is a DNA sequence that can increase the activity of promoters and thus speed up the frequency of gene transcription. The enhancer plays an essential role in activating gene expression. Currently, gene sequencing technology has been devel...

Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.

Science (New York, N.Y.)
Protein-coding differences between species often fail to explain phenotypic diversity, suggesting the involvement of genomic elements that regulate gene expression such as enhancers. Identifying associations between enhancers and phenotypes is challe...

Analysis of super-enhancer using machine learning and its application to medical biology.

Briefings in bioinformatics
The analysis of super-enhancers (SEs) has recently attracted attention in elucidating the molecular mechanisms of cancer and other diseases. SEs are genomic structures that strongly induce gene expression and have been reported to contribute to the o...

SENet: A deep learning framework for discriminating super- and typical enhancers by sequence information.

Computational biology and chemistry
Super-enhancers are large domains on the genome where multiple short typical enhancers within a specific genomic distance are stitched together. Typically, they are cell type-specific and responsible for defining cell identity and regulating gene tra...

DeepITEH: a deep learning framework for identifying tissue-specific eRNAs from the human genome.

Bioinformatics (Oxford, England)
MOTIVATION: Enhancers are vital cis-regulatory elements that regulate gene expression. Enhancer RNAs (eRNAs), a type of long noncoding RNAs, are transcribed from enhancer regions in the genome. The tissue-specific expression of eRNAs is crucial in th...

Modeling islet enhancers using deep learning identifies candidate causal variants at loci associated with T2D and glycemic traits.

Proceedings of the National Academy of Sciences of the United States of America
Genetic association studies have identified hundreds of independent signals associated with type 2 diabetes (T2D) and related traits. Despite these successes, the identification of specific causal variants underlying a genetic association signal rema...

HEAP: a task adaptive-based explainable deep learning framework for enhancer activity prediction.

Briefings in bioinformatics
Enhancers are crucial cis-regulatory elements that control gene expression in a cell-type-specific manner. Despite extensive genetic and computational studies, accurately predicting enhancer activity in different cell types remains a challenge, and t...

Improving Enhancer Identification with a Multi-Classifier Stacked Ensemble Model.

Journal of molecular biology
Enhancers are DNA regions that are responsible for controlling the expression of genes. Enhancers are usually found upstream or downstream of a gene, or even inside a gene's intron region, but are normally located at a distant location from the genes...