AIMC Topic: Enhancer Elements, Genetic
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Learning the sequence code of protein expression in human immune cells.
Science advances
Jul 23, 2025
Accurate protein expression in human immune cells is essential for appropriate cellular function. The mechanisms that define protein abundance are complex and are executed on transcriptional, posttranscriptional, and posttranslational levels. Here, w...
Diff-SE: A Diffusion-Augmented Contrastive Learning Framework for Super-Enhancer Prediction.
Journal of chemical information and modeling
Jul 4, 2025
Super-enhancers (SEs) are cis-regulatory elements that play crucial roles in gene expression and are implicated in diseases such as cancer and Alzheimer's. Traditional identification methods rely on ChIP-seq experiments, which are costly and time-con...
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...
Lineage-specific regulatory evolution: insights from massively parallel reporter assays.
Current opinion in genetics & development
Jun 20, 2025
Lineage-specific genetic variants play a key role in evolutionary divergence, particularly through changes in cis-regulatory elements that fine-tune gene expression. Massively parallel reporter assays (MPRAs) provide a powerful approach to characteri...
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
Muscle Proteins
Hippo Signaling Pathway
Protein Binding
DNA-Binding Proteins
YAP-Signaling Proteins
Transcription Factors
Mice
Molecular Dynamics Simulation
Animals
Protein Serine-Threonine Kinases
Trophoblasts
Signal Transduction
Phosphoproteins
Deep Learning
Adaptor Proteins, Signal Transducing
Enhancer Elements, Genetic
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...
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