AIMC Topic: Enhancer Elements, Genetic
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Machine learning-assisted decoding of temporal transcriptional dynamics via fluorescent timer.
Nature communications
Jul 1, 2025
Investigating the temporal dynamics of gene expression is crucial for understanding gene regulation across various biological processes. Using the Fluorescent Timer protein, the Timer-of-cell-kinetics-and-activity system enables analysis of transcrip...
Evaluating methods for the prediction of cell-type-specific enhancers in the mammalian cortex.
Cell genomics
May 21, 2025
Identifying cell-type-specific enhancers is critical for developing genetic tools to study the mammalian brain. We organized the "Brain Initiative Cell Census Network (BICCN) Challenge: Predicting Functional Cell Type-Specific Enhancers from Cross-Sp...
iEnhancer-DS: Attention-based improved densenet for identifying enhancers and their strength.
Computational biology and chemistry
May 5, 2025
Enhancers are short DNA fragments that enhance gene expression by binding to transcription factors. Accurately identifying enhancers and their strength is crucial for understanding gene regulation mechanisms. However, traditional enhancer sequencing ...
High-resolution dynamic imaging of chromatin DNA communication using Oligo-LiveFISH.
Cell
Apr 15, 2025
Three-dimensional (3D) genome dynamics are crucial for cellular functions and disease. However, real-time, live-cell DNA visualization remains challenging, as existing methods are often confined to repetitive regions, suffer from low resolution, or r...
Utilizing a deep learning model based on BERT for identifying enhancers and their strength.
PloS one
Apr 9, 2025
An enhancer is a specific DNA sequence typically located within a gene at upstream or downstream position and serves as a pivotal element in the regulation of eukaryotic gene transcription. Therefore, the recognition of enhancers is highly significan...
Interpreting regulatory mechanisms of Hippo signaling through a deep learning sequence model.
Cell genomics
Apr 1, 2025
Signaling pathway components are well studied, but how they mediate cell-type-specific transcription responses is an unresolved problem. Using the Hippo pathway in mouse trophoblast stem cells as a model, we show that the DNA binding of signaling eff...
TEA Domain Transcription Factors
Hippo Signaling Pathway
YAP-Signaling Proteins
Molecular Dynamics Simulation
Phosphoproteins
Transcription Factors
Mice
Enhancer Elements, Genetic
Deep Learning
DNA-Binding Proteins
Protein Serine-Threonine Kinases
Signal Transduction
Muscle Proteins
Protein Binding
Animals
Trophoblasts
Adaptor Proteins, Signal Transducing
DeepEnhancerPPO: An Interpretable Deep Learning Approach for Enhancer Classification.
International journal of molecular sciences
Dec 2, 2024
Enhancers are short genomic segments located in non-coding regions of the genome that play a critical role in regulating the expression of target genes. Despite their importance in transcriptional regulation, effective methods for classifying enhance...
A multi-perspective deep learning framework for enhancer characterization and identification.
Computational biology and chemistry
Nov 19, 2024
Enhancers are vital elements in the genome that boost the transcriptional activity of neighboring genes and are essential in regulating cell-specific gene expression. Therefore, accurately identifying and characterizing enhancers is essential for com...
RAEPI: Predicting Enhancer-Promoter Interactions Based on Restricted Attention Mechanism.
Interdisciplinary sciences, computational life sciences
Nov 15, 2024
Enhancer-promoter interactions (EPIs) are crucial in gene transcription regulation and cell differentiation. Traditional biological experiments are costly and time-consuming, motivating the development of computational prediction methods. However, ex...
MuSE: A deep learning model based on multi-feature fusion for super-enhancer prediction.
Computational biology and chemistry
Nov 15, 2024
Although bioinformatics-based methods accurately identify SEs (Super-enhancers), the results depend on feature design. It is foundational to representing biological sequences and automatically extracting their key features for improving SE identifica...
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