AIMC Topic: Enhancer Elements, Genetic
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DeepDualEnhancer: A Dual-Feature Input DNABert Based Deep Learning Method for Enhancer Recognition.
International journal of molecular sciences
Nov 1, 2024
Enhancers are cis-regulatory DNA sequences that are widely distributed throughout the genome. They can precisely regulate the expression of target genes. Since the features of enhancer segments are difficult to detect, we propose DeepDualEnhancer, a ...
Development of a novel prognostic signature derived from super-enhancer-associated gene by machine learning in head and neck squamous cell carcinoma.
Oral oncology
Sep 7, 2024
Dysregulated super-enhancer (SE) results in aberrant transcription that drives cancer initiation and progression. SEs have been demonstrated as novel promising diagnostic/prognostic biomarkers and therapeutic targets across multiple human cancers. He...
EPI-Trans: an effective transformer-based deep learning model for enhancer promoter interaction prediction.
BMC bioinformatics
Jun 18, 2024
BACKGROUND: Recognition of enhancer-promoter Interactions (EPIs) is crucial for human development. EPIs in the genome play a key role in regulating transcription. However, experimental approaches for classifying EPIs are too expensive in terms of eff...
Identification of drug responsive enhancers by predicting chromatin accessibility change from perturbed gene expression profiles.
NPJ systems biology and applications
May 30, 2024
Individual may response to drug treatment differently due to their genetic variants located in enhancers. These variants can alter transcription factor's (TF) binding strength, affect enhancer's chromatin activity or interaction, and eventually chang...
Cell-type-directed design of synthetic enhancers.
Nature
Dec 12, 2023
Transcriptional enhancers act as docking stations for combinations of transcription factors and thereby regulate spatiotemporal activation of their target genes. It has been a long-standing goal in the field to decode the regulatory logic of an enhan...
Targeted design of synthetic enhancers for selected tissues in the Drosophila embryo.
Nature
Dec 12, 2023
Enhancers control gene expression and have crucial roles in development and homeostasis. However, the targeted de novo design of enhancers with tissue-specific activities has remained challenging. Here we combine deep learning and transfer learning t...
Improving Enhancer Identification with a Multi-Classifier Stacked Ensemble Model.
Journal of molecular biology
Oct 16, 2023
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...
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
Aug 21, 2023
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...
SENet: A deep learning framework for discriminating super- and typical enhancers by sequence information.
Computational biology and chemistry
Jun 11, 2023
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...
Relating enhancer genetic variation across mammals to complex phenotypes using machine learning.
Science (New York, N.Y.)
Apr 28, 2023
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...
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