Precise identification of target sites of RNA-binding proteins (RBP) is important to understand their biochemical and cellular functions. A large amount of experimental data is generated by in vivo and in vitro approaches. The binding preferences det...
Journal of bioinformatics and computational biology
35451938
RNA-binding proteins (RBPs) have crucial roles in various cellular processes such as alternative splicing and gene regulation. Therefore, the analysis and identification of RBPs is an essential issue. However, although many computational methods have...
MOTIVATION: Protein-RNA interactions play essential roles in many biological processes, including pre-mRNA processing, post-transcriptional gene regulation and RNA degradation. Accurate identification of binding sites on RNA-binding proteins (RBPs) i...
BACKGROUND: Addressing the laborious nature of traditional biological experiments by using an efficient computational approach to analyze RNA-binding proteins (RBPs) binding sites has always been a challenging task. RBPs play a vital role in post-tra...
Circular RNA (circRNA) can exert biological functions by interacting with RNA-binding protein (RBP), and some deep learning-based methods have been developed to predict RBP binding sites on circRNA. However, most of these methods identify circRNA-RBP...
DNA methylation is a process that can affect gene accessibility and therefore gene expression. In this study, a machine learning pipeline is proposed for the prediction of breast cancer and the identification of significant genes that contribute to t...
Proteins interact with nucleic acids to regulate the life activities of organisms. Therefore, how to accurately and efficiently identify nucleic acid-binding proteins (NABPs) is particularly significant. Some sequence-based computational methods have...
RNA-binding proteins (RBPs) are key co- and post-transcriptional regulators of gene expression, playing a crucial role in many biological processes. Experimental methods like CLIP-seq have enabled the identification of transcriptome-wide RNA-protein ...
Methods in molecular biology (Clifton, N.J.)
36705906
Deep neural networks have demonstrated improved performance at predicting sequence specificities of DNA- and RNA-binding proteins. However, it remains unclear why they perform better than previous methods that rely on k-mers and position weight matri...
RNA-binding proteins (RBPs) play significant roles in many biological life activities, many algorithms and tools are proposed to predict RBPs for researching biological mechanisms of RNA-protein binding sites. Deep learning algorithms based on tradit...