AIMC Topic: Enhancer Elements, Genetic
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eRFSVM: a hybrid classifier to predict enhancers-integrating random forests with support vector machines.
Hereditas
Jun 30, 2016
BACKGROUND: Enhancers are tissue specific distal regulation elements, playing vital roles in gene regulation and expression. The prediction and identification of enhancers are important but challenging issues for bioinformatics studies. Existing comp...
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...
Machine learning identification of enhancers in the rhesus macaque genome.
Neuron
May 21, 2025
Nonhuman primate (NHP) neuroanatomy and cognitive complexity make NHPs ideal models to study human neurobiology and disease. However, NHP circuit-function investigations are limited by the availability of molecular reagents that are effective in NHPs...
CREATE: cell-type-specific cis-regulatory element identification via discrete embedding.
Nature communications
May 17, 2025
Cis-regulatory elements (CREs), including enhancers, silencers, promoters and insulators, play pivotal roles in orchestrating gene regulatory mechanisms that drive complex biological traits. However, current approaches for CRE identification are pred...
AI-Driven Drug Target Screening Platform Identified Oncogene CACNA2D1 Activated by Enhancer Infestation in Epstein-Barr Virus-Associated Nasopharyngeal Carcinoma.
International journal of molecular sciences
May 14, 2025
The management of nasopharyngeal cancer (NPC) is rapidly evolving, with immune checkpoint inhibitors emerging as a prominent treatment approach. However, drug development targeting specific molecular and cellular abnormalities in NPC has slowed. Rece...
Endometrial tumorigenesis involves epigenetic plasticity demarcating non-coding somatic mutations and 3D-genome alterations.
Genome biology
May 9, 2025
BACKGROUND: The incidence and mortality of endometrial cancer (EC) is on the rise. Eighty-five percent of ECs depend on estrogen receptor alpha (ERĪ±) for proliferation, but little is known about its transcriptional regulation in these tumors.
EPIPDLF: a pretrained deep learning framework for predicting enhancer-promoter interactions.
Bioinformatics (Oxford, England)
May 6, 2025
MOTIVATION: Enhancers and promoters, as regulatory DNA elements, play pivotal roles in gene expression, homeostasis, and disease development across various biological processes. With advancing research, it has been uncovered that distal enhancers may...
EnsembleSE: identification of super-enhancers based on ensemble learning.
Briefings in functional genomics
Jan 15, 2025
Super-enhancers (SEs) are typically located in the regulatory regions of genes, driving high-level gene expression. Identifying SEs is crucial for a deeper understanding of gene regulatory networks, disease mechanisms, and the development and physiol...
Machine and Deep Learning Methods for Predicting 3D Genome Organization.
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2025
Three-dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, topologically associating domains (TADs), and A/B compartments, play critical roles in a wide range of cellular processes by regulating gene expressi...
A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity.
Nucleic acids research
Nov 27, 2024
Enhancers play a critical role in dynamically regulating spatial-temporal gene expression and establishing cell identity, underscoring the significance of designing them with specific properties for applications in biosynthetic engineering and gene t...
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