BACKGROUND: Alternative splicing is a pivotal mechanism of post-transcriptional modification that contributes to the transcriptome plasticity and proteome diversity in metazoan cells. Although many splicing regulations around the exon/intron regions ...
Interdisciplinary sciences, computational life sciences
39546160
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...
International journal of molecular sciences
39519295
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 ...
Invertible promoters (invertons) are crucial regulatory elements in bacteria, facilitating gene expression changes under stress. Despite their importance, their prevalence and the range of regulated gene functions are largely unknown. We introduced D...
Cancer imaging : the official publication of the International Cancer Imaging Society
39716317
OBJECTIVE: This study aims to evaluate the effectiveness of deep learning features derived from multi-sequence magnetic resonance imaging (MRI) in determining the O-methylguanine-DNA methyltransferase (MGMT) promoter methylation status among glioblas...
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...
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 ...
Promoters are essential DNA sequences that initiate transcription and regulate gene expression. Precisely identifying promoter sites is crucial for deciphering gene expression patterns and the roles of gene regulatory networks. Recent advancements in...
Methods in molecular biology (Clifton, N.J.)
39283464
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...
To understand the complex relationship between histone mark activity and gene expression, recent advances have used in silico predictions based on large-scale machine learning models. However, these approaches have omitted key contributing factors li...