AIMC Topic: RNA-Binding Proteins

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An Integrated TCN-CrossMHA Model for Predicting circRNA-RBP Binding Sites.

Interdisciplinary sciences, computational life sciences Nov 6, 2024
Circular RNA (circRNA) has the capacity to bind with RNA binding protein (RBP), thereby exerting a substantial impact on diseases. Predicting binding sites aids in comprehending the interaction mechanism, thereby offering insights for disease treatme...
Protein Binding Computational Biology RNA-Binding Proteins Neural Networks, Computer Algorithms RNA, Circular Binding Sites Humans
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Data-augmented machine learning scoring functions for virtual screening of YTHDF1 mA reader protein.

Computers in biology and medicine Oct 12, 2024
Machine learning is rapidly advancing the drug discovery process, significantly enhancing speed and efficiency. Innovation in computer-aided drug design is primarily driven by structure- and ligand-based approaches. When the number of known inhibitor...
Machine Learning Drug Discovery RNA-Binding Proteins Humans
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Capture of RNA-binding proteins across mouse tissues using HARD-AP.

Nature communications Sep 28, 2024
RNA-binding proteins (RBPs) modulate all aspects of RNA metabolism, but a comprehensive picture of RBP expression across tissues is lacking. Here, we describe our development of the method we call HARD-AP that robustly retrieves RBPs and tightly asso...
Mice Machine Learning RNA-Binding Proteins Animals Humans RNA Protein Binding Binding Sites
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Deciphering colorectal cancer radioresistance and immune microrenvironment: unraveling the role of EIF5A through single-cell RNA sequencing and machine learning.

Frontiers in immunology Sep 3, 2024
BACKGROUND: Radiotherapy (RT) is a critical component of treatment for locally advanced rectal cancer (LARC), though patient response varies significantly. The variability in treatment outcomes is partly due to the resistance conferred by cancer stem...
Eukaryotic Translation Initiation Factor 5A Peptide Initiation Factors Neoplastic Stem Cells Radiation Tolerance Cell Line, Tumor Single-Cell Analysis Colorectal Neoplasms Tumor Microenvironment Mice RNA-Binding Proteins Animals Gene Expression Regulation, Neoplastic Humans Machine Learning
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iCRBP-LKHA: Large convolutional kernel and hybrid channel-spatial attention for identifying circRNA-RBP interaction sites.

PLoS computational biology Aug 22, 2024
Circular RNAs (circRNAs) play vital roles in transcription and translation. Identification of circRNA-RBP (RNA-binding protein) interaction sites has become a fundamental step in molecular and cell biology. Deep learning (DL)-based methods have been ...
Humans Neural Networks, Computer Computational Biology RNA-Binding Proteins Binding Sites Algorithms Deep Learning RNA, Circular
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pyRBDome: a comprehensive computational platform for enhancing RNA-binding proteome data.

Life science alliance Jul 30, 2024
High-throughput proteomics approaches have revolutionised the identification of RNA-binding proteins (RBPome) and RNA-binding sequences (RBDome) across organisms. Yet, the extent of noise, including false positives, associated with these methodologie...
Binding Sites Databases, Protein RNA Protein Binding Computational Biology Proteomics Proteome RNA-Binding Proteins Humans Machine Learning Software
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MAHyNet: Parallel Hybrid Network for RNA-Protein Binding Sites Prediction Based on Multi-Head Attention and Expectation Pooling.

IEEE/ACM transactions on computational biology and bioinformatics Jun 5, 2024
RNA-binding proteins (RBPs) can regulate biological functions by interacting with specific RNAs, and play an important role in many life activities. Therefore, the rapid identification of RNA-protein binding sites is crucial for functional annotation...
RNA Binding Sites Neural Networks, Computer Computational Biology RNA-Binding Proteins Algorithms
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Deep Learning for Elucidating Modifications to RNA-Status and Challenges Ahead.

Genes May 15, 2024
RNA-binding proteins and chemical modifications to RNA play vital roles in the co- and post-transcriptional regulation of genes. In order to fully decipher their biological roles, it is an essential task to catalogue their precise target locations al...
Nucleic Acid Conformation Deep Learning RNA Humans RNA, Messenger RNA-Binding Proteins
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CRIECNN: Ensemble convolutional neural network and advanced feature extraction methods for the precise forecasting of circRNA-RBP binding sites.

Computers in biology and medicine Apr 10, 2024
Circular RNAs (circRNAs) have surfaced as important non-coding RNA molecules in biology. Understanding interactions between circRNAs and RNA-binding proteins (RBPs) is crucial in circRNA research. Existing prediction models suffer from limited availa...
Humans Neural Networks, Computer RNA-Binding Proteins Binding Sites Computational Biology RNA, Circular
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EPDRNA: A Model for Identifying DNA-RNA Binding Sites in Disease-Related Proteins.

The protein journal Mar 16, 2024
Protein-DNA and protein-RNA interactions are involved in many biological processes and regulate many cellular functions. Moreover, they are related to many human diseases. To understand the molecular mechanism of protein-DNA binding and protein-RNA b...
DNA-Binding Proteins Humans RNA Binding Sites Protein Binding Machine Learning Databases, Protein Computational Biology Algorithms DNA RNA-Binding Proteins
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