Computer methods and programs in biomedicine
Dec 30, 2016
BACKGROUND AND OBJECTIVE: The O-methylguanine-DNA-methyltransferase (MGMT) promoter methylation has been shown to be associated with improved outcomes in patients with glioblastoma (GBM) and may be a predictive marker of sensitivity to chemotherapy. ...
As the number of sequenced bacterial genomes increases, the need for rapid and reliable tools for the annotation of functional elements (e.g., transcriptional regulatory elements) becomes more desirable. Promoters are the key regulatory elements, whi...
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...
MOTIVATION: Advances in bacterial promoter predictors based on machine learning have greatly improved identification metrics. However, existing models overlooked the impact of negative datasets, previously identified in GC-content discrepancies betwe...
Sheng wu gong cheng xue bao = Chinese journal of biotechnology
Mar 25, 2025
Synthetic biology is an emerging interdisciplinary field at the convergence of biology, engineering, and computer science. It employs a bottom-up approach to progressively design biological parts, devices, and circuits, aiming to create artificial bi...
Sheng wu gong cheng xue bao = Chinese journal of biotechnology
Mar 25, 2025
Nucleic acid elements are essential functional sequences that play critical roles in regulating gene expression, optimizing pathways, and enabling gene editing to enhance the production of target products in biomanufacturing. Therefore, the design an...
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...
Long non-coding RNAs (lncRNAs) are closely associated with the regulation of gene expression, whose promoters play a crucial role in comprehensively understanding lncRNA regulatory mechanisms, functions and their roles in diseases. Due to limitations...
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...
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...