AIMC Topic: Promoter Regions, Genetic
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Deep learning deciphers the related role of master regulators and G-quadruplexes in tissue specification.
Scientific reports
Jul 2, 2025
G-quadruplexes (GQs) are non-canonical DNA structures encoded by G-flipons with potential roles in gene regulation and chromatin structure. Here, we explore the role of G-flipons in tissue specification. We present a deep learning-based framework for...
Rapid diagnosis of TERT promoter mutation using Terahertz absorption spectroscopy in glioblastoma.
Scientific reports
May 27, 2025
Glioblastoma (GBM) is a highly aggressive brain tumor with poor outcomes and limited treatment options. The telomerase reverse transcriptase (TERT) promoter mutation, one of the key biomarkers in GBM, is linked to tumor progression and prognosis. Thi...
A KAN-based hybrid deep neural networks for accurate identification of transcription factor binding sites.
PloS one
May 7, 2025
BACKGROUND: Predicting protein-DNA binding sites in vivo is a challenging but urgent task in many fields such as drug design and development. Most promoters contain many transcription factor (TF) binding sites, yet only a few have been identified thr...
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...
A predictive model for MGMT promoter methylation status in glioblastoma based on terahertz spectral data.
Analytical biochemistry
Mar 29, 2025
O-methylguanine-DNA methyltransferase (MGMT) promoter methylation is a crucial biomarker in glioblastoma (GBM) that influences response to temozolomide. Traditional detection methods, such as gene sequencing, are time-consuming and limited to postope...
Combining diffusion and transformer models for enhanced promoter synthesis and strength prediction in deep learning.
mSystems
Mar 19, 2025
UNLABELLED: In the field of synthetic biology, the engineering of synthetic promoters that outperform their natural counterparts is of paramount importance, which can optimize the expression of exogenous genes, enhance the efficiency of metabolic pat...
HybProm: An attention-assisted hybrid CNN-BiLSTM model for the interpretable prediction of DNA promoter.
Methods (San Diego, Calif.)
Feb 8, 2025
Promoter prediction is essential for analyzing gene structures, understanding regulatory networks, transcription mechanisms, and precisely controlling gene expression. Recently, computational and deep learning methods for promoter prediction have gai...
PmiProPred: A novel method towards plant miRNA promoter prediction based on CNN-Transformer network and convolutional block attention mechanism.
International journal of biological macromolecules
Feb 3, 2025
It is crucial to understand the transcription mechanisms of miRNAs, especially considering the presence of peptides encoded by miRNAs. Since promoters function as the switch for gene transcription, precisely identifying these regions is essential for...
Detecting IDH and TERTp mutations in diffuse gliomas using H-MRS with attention deep-shallow networks.
Computers in biology and medicine
Jan 27, 2025
BACKGROUND: Preoperative and noninvasive detection of isocitrate dehydrogenase (IDH) and telomerase reverse transcriptase gene promoter (TERTp) mutations in glioma is critical for prognosis and treatment planning. This study aims to develop deep lear...
ProPr54 web server: predicting σ promoters and regulon with a hybrid convolutional and recurrent deep neural network.
NAR genomics and bioinformatics
Jan 7, 2025
σ serves as an unconventional sigma factor with a distinct mechanism of transcription initiation, which depends on the involvement of a transcription activator. This unique sigma factor σ is indispensable for orchestrating the transcription of genes ...
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