AIMC Topic: RNA-Binding Proteins

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Uncertainty Quantification and Temperature Scaling Calibration for Protein-RNA Binding Site Prediction.

Journal of chemical information and modeling Jun 2, 2025
The black-box nature of deep learning has increasingly drawn attention to the reliability and uncertainty of predictive models. Currently, several uncertainty quantification (UQ) methods have been proposed and successfully applied in the fields of mo...
Neural Networks, Computer Temperature Calibration Binding Sites Uncertainty Protein Binding RNA-Binding Proteins RNA
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Artificial intelligence-assisted RNA-binding protein signature for prognostic stratification and therapeutic guidance in breast cancer.

Frontiers in immunology Apr 16, 2025
BACKGROUND: Breast cancer is the most common malignancy in women globally, with significant heterogeneity affecting prognosis and treatment. RNA-binding proteins play vital roles in tumor progression, yet their prognostic potential remains unclear. T...
Machine Learning Prognosis Humans Female RNA-Binding Proteins Artificial Intelligence Gene Expression Profiling Breast Neoplasms Gene Expression Regulation, Neoplastic Transcriptome Tumor Microenvironment Single-Cell Analysis Biomarkers, Tumor
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RPI-GGCN: Prediction of RNA-Protein Interaction Based on Interpretability Gated Graph Convolution Neural Network and Co-Regularized Variational Autoencoders.

IEEE transactions on neural networks and learning systems Apr 4, 2025
RNA-protein interactions (RPIs) play an important role in several fundamental cellular physiological processes, including cell motility, chromosome replication, transcription and translation, and signaling. Predicting RPI can guide the exploration of...
Autoencoder RNA-Binding Proteins Proteins RNA Humans Neural Networks, Computer Algorithms Computational Biology
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RBPsuite 2.0: an updated RNA-protein binding site prediction suite with high coverage on species and proteins based on deep learning.

BMC biology Mar 11, 2025
BACKGROUND: RNA-binding proteins (RBPs) play crucial roles in many biological processes, and computationally identifying RNA-RBP interactions provides insights into the biological mechanism of diseases associated with RBPs.
Binding Sites Computational Biology Humans RNA, Circular RNA-Binding Proteins Software RNA Deep Learning
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Key RNA-binding proteins in renal fibrosis: a comprehensive bioinformatics and machine learning framework for diagnostic and therapeutic insights.

Renal failure Feb 16, 2025
BACKGROUND: Renal fibrosis is a critical factor in chronic kidney disease progression, with limited diagnostic and therapeutic options. Emerging evidence suggests RNA-binding proteins (RBPs) are pivotal in regulating cellular mechanisms underlying fi...
Disease Models, Animal Fibrosis Ureteral Obstruction Single-Cell Analysis Mice Computational Biology RNA-Binding Proteins Kidney Renal Insufficiency, Chronic Machine Learning Biomarkers Animals Humans
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RNA-protein interaction prediction using network-guided deep learning.

Communications biology Feb 16, 2025
Accurate computational determination of RNA-protein interactions remains challenging, particularly when encountering unknown RNAs and proteins. The limited number of RNAs and their flexibility constrained the effectiveness of the deep-learning models...
Humans Neural Networks, Computer COVID-19 RNA-Binding Proteins RNA, Viral RNA SARS-CoV-2 Deep Learning Computational Biology
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ZeRPI: A graph neural network model for zero-shot prediction of RNA-protein interactions.

Methods (San Diego, Calif.) Jan 30, 2025
RNA-protein interactions are crucial for biological functions across multiple levels. RNA binding proteins (RBPs) intricately engage in diverse biological processes through specific RNA molecule interactions. Previous studies have revealed the indisp...
RNA Graph Neural Networks Neural Networks, Computer Machine Learning Algorithms Protein Binding Humans Computational Biology RNA-Binding Proteins
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Assessing donor kidney function: the role of CIRBP in predicting delayed graft function post-transplant.

Frontiers in immunology Jan 17, 2025
INTRODUCTION: Delayed graft function (DGF) shortens the survival time of transplanted kidneys and increases the risk of rejection. Current methods are inadequate in predicting DGF. More precise tools are required to assess kidney suitability for tran...
Tissue Donors Aged Graft Survival Biomarkers Adult Middle Aged Kidney Female Delayed Graft Function Male Humans Risk Factors RNA-Binding Proteins Kidney Transplantation
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DeepMiRBP: a hybrid model for predicting microRNA-protein interactions based on transfer learning and cosine similarity.

BMC bioinformatics Dec 18, 2024
BACKGROUND: Interactions between microRNAs and RNA-binding proteins are crucial for microRNA-mediated gene regulation and sorting. Despite their significance, the molecular mechanisms governing these interactions remain underexplored, apart from sequ...
Binding Sites Computational Biology RNA-Binding Proteins MicroRNAs Neural Networks, Computer Deep Learning
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AGML: Adaptive Graph-Based Multi-Label Learning for Prediction of RBP and as Event Associations During EMT.

IEEE/ACM transactions on computational biology and bioinformatics Dec 10, 2024
Increasing evidence has indicated that RNA-binding proteins (RBPs) play an essential role in mediating alternative splicing (AS) events during epithelial-mesenchymal transition (EMT). However, due to the substantial cost and complexity of biological ...
Humans Machine Learning Algorithms Alternative Splicing Computational Biology RNA-Binding Proteins Epithelial-Mesenchymal Transition
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