AIMC Topic: RNA-Binding Proteins

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Predicting Long Noncoding RNA and Protein Interactions Using Heterogeneous Network Model.

BioMed research international Dec 29, 2015
Recent study shows that long noncoding RNAs (lncRNAs) are participating in diverse biological processes and complex diseases. However, at present the functions of lncRNAs are still rarely known. In this study, we propose a network-based computational...
RNA-Binding Proteins Neural Networks, Computer Databases, Genetic Computer Simulation RNA, Long Noncoding
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RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

Science (New York, N.Y.) Dec 18, 2014
To facilitate precision medicine and whole-genome annotation, we developed a machine-learning technique that scores how strongly genetic variants affect RNA splicing, whose alteration contributes to many diseases. Analysis of more than 650,000 intron...
RNA Splice Sites Exons Genetic Code MutL Protein Homolog 1 DNA Colorectal Neoplasms, Hereditary Nonpolyposis Genetic Markers Humans Muscular Atrophy, Spinal Genome-Wide Association Study Genetic Variation Models, Genetic Artificial Intelligence Molecular Sequence Annotation Computer Simulation Nuclear Proteins Quantitative Trait Loci Polymorphism, Single Nucleotide Introns Adaptor Proteins, Signal Transducing RNA Splicing RNA-Binding Proteins Mutation, Missense Child Development Disorders, Pervasive
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DRBP-EDP: classification of DNA-binding proteins and RNA-binding proteins using ESM-2 and dual-path neural network.

NAR genomics and bioinformatics Jun 1, 2025
Regulation of DNA or RNA at the transcriptional, post-transcriptional, and translational levels are key steps in the central dogma of molecular biology. DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs) play pivotal roles in the precise reg...
Databases, Protein DNA-Binding Proteins Software Deep Learning RNA-Binding Proteins Humans Neural Networks, Computer
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CR-deal: Explainable Neural Network for circRNA-RBP Binding Site Recognition and Interpretation.

Interdisciplinary sciences, computational life sciences Jun 1, 2025
circRNAs are a type of single-stranded non-coding RNA molecules, and their unique feature is their closed circular structure. The interaction between circRNAs and RNA-binding proteins (RBPs) plays a key role in biological functions and is crucial for...
Humans RNA-Binding Proteins Binding Sites RNA, Circular Neural Networks, Computer Deep Learning Computational Biology
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ASiDentify (ASiD): a machine learning model to predict new autism spectrum disorder risk genes.

Genetics May 8, 2025
Autism spectrum disorder (ASD) is a neurodevelopmental disorder that affects nearly 3% of children and has a strong genetic component. While hundreds of ASD risk genes have been identified through sequencing studies, the genetic heterogeneity of ASD ...
Autism Spectrum Disorder Genetic Predisposition to Disease RNA-Binding Proteins Neurons Humans Machine Learning
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Structure-Based Prediction of lncRNA-Protein Interactions by Deep Learning.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2025
The interactions between long noncoding RNA (lncRNA) and protein play crucial roles in various biological processes. Computational methods are essential for predicting lncRNA-protein interactions and deciphering their mechanisms. In this chapter, we ...
Software Deep Learning Protein Binding Humans Neural Networks, Computer Proteins Computational Biology RNA-Binding Proteins RNA, Long Noncoding
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Study of prognostic splicing factors in cancer using machine learning approaches.

Human molecular genetics Jun 21, 2024
Splicing factors (SFs) are the major RNA-binding proteins (RBPs) and key molecules that regulate the splicing of mRNA molecules through binding to mRNAs. The expression of splicing factors is frequently deregulated in different cancer types, causing ...
Gene Expression Regulation, Neoplastic RNA Splicing Alternative Splicing Computational Biology RNA, Messenger RNA-Binding Proteins RNA Splicing Factors Machine Learning Prognosis Biomarkers, Tumor Neoplasms Liver Neoplasms Carcinoma, Hepatocellular Humans
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Improved prediction of DNA and RNA binding proteins with deep learning models.

Briefings in bioinformatics May 23, 2024
Nucleic acid-binding proteins (NABPs), including DNA-binding proteins (DBPs) and RNA-binding proteins (RBPs), play important roles in essential biological processes. To facilitate functional annotation and accurate prediction of different types of NA...
RNA-Binding Proteins DNA-Binding Proteins Deep Learning Humans Computational Biology Neural Networks, Computer
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DeepLocRNA: an interpretable deep learning model for predicting RNA subcellular localization with domain-specific transfer-learning.

Bioinformatics (Oxford, England) Feb 1, 2024
MOTIVATION: Accurate prediction of RNA subcellular localization plays an important role in understanding cellular processes and functions. Although post-transcriptional processes are governed by trans-acting RNA binding proteins (RBPs) through intera...
RNA, Messenger RNA-Binding Proteins RNA Nucleotide Motifs Deep Learning Mice Computational Biology Humans Animals
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ResidualBind: Uncovering Sequence-Structure Preferences of RNA-Binding Proteins with Deep Neural Networks.

Methods in molecular biology (Clifton, N.J.) Jan 1, 2023
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...
Neural Networks, Computer Protein Binding RNA-Binding Proteins DNA RNA Position-Specific Scoring Matrices
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