AIMC Topic: RNA

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DeepRNA-Reg: a deep-learning based approach for comparative analysis of CLIP experiments.

RNA biology Oct 7, 2025
DeepRNA-Reg employs advances in deep learning to enable high-fidelity comparative analysis of paired datasets of high-throughput sequencing of RNA isolated by crosslinking immunoprecipitation (HITS-CLIP). In a HITS-CLIP experimental paradigm where Ag...
Humans MicroRNAs RNA Immunoprecipitation Argonaute Proteins High-Throughput Nucleotide Sequencing Computational Biology Sequence Analysis, RNA Animals Deep Learning
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Partner-RBR: Predicting Multitype RNA-Binding Residues Based on Mutual Learning.

Journal of chemical information and modeling Sep 16, 2025
RNA molecules play diverse and critical roles in various biological processes, including gene expression, post-transcriptional regulation, and disease pathogenesis. Understanding the interaction between proteins and RNA necessitates the precise ident...
Computational Biology RNA-Binding Proteins Machine Learning Protein Binding RNA Binding Sites Sequence Alignment Databases, Protein Models, Molecular
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Advances and Challenges in Machine Learning for RNA-Small Molecule Interaction Modeling: Review.

Journal of chemical theory and computation Sep 8, 2025
RNA plays a pivotal role in biological processes such as gene expression regulation and protein synthesis. Targeting RNA with small molecules offers a novel therapeutic strategy for various diseases by directly modulating these processes. However, th...
Humans Binding Sites Small Molecule Libraries Machine Learning RNA
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Graph Learning-Based Scoring of RNA-Protein Complex Structures.

Journal of chemical theory and computation Aug 29, 2025
Development of suitable scoring functions is essential for the prediction of RNA-protein complex structures. Conventional statistical potential-based scoring functions suffered from deficiencies in handling conformational flexibility. The recent appl...
Nucleic Acid Conformation Models, Molecular RNA Neural Networks, Computer Algorithms Deep Learning Proteins
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GraphVelo allows for accurate inference of multimodal velocities and molecular mechanisms for single cells.

Nature communications Aug 22, 2025
RNA velocities and generalizations emerge as powerful approaches for extracting time-resolved information from high-throughput snapshot single-cell data. Yet, several inherent limitations restrict applying the approaches to genes not suitable for RNA...
Computational Biology RNA Gene Expression Regulation Algorithms Single-Cell Analysis Humans Machine Learning
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GATRsite: RNA-Ligand Binding Site Prediction Using Graph Attention Networks and Pretrained RNA Language Models.

Journal of chemical information and modeling Aug 14, 2025
Identifying functional sites of RNA, particularly those where small molecules bind, is crucial for understanding related biological processes and advancing drug design. Small molecule therapies, compared to traditional protein-targeted therapies, hav...
Ligands Binding Sites Models, Molecular RNA Deep Learning Computational Biology
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Characterizing ssRNA and dsRNA electrophoretic behavior: empirical insights with neural network-aided predictions.

The Analyst Aug 4, 2025
RNA-based therapeutics are currently at the forefront of the biopharmaceutical industry because of their safety, efficacy, and shortened time from disease discovery to therapy development. Microfluidic electrophoresis provides a great analytical plat...
Microfluidic Analytical Techniques RNA, Double-Stranded RNA Electrophoresis Humans Neural Networks, Computer
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m5U-HybridNet: Integrating an RNA Foundation Model with CNN Features for Accurate Prediction of 5-Methyluridine Modification Sites.

Journal of chemical information and modeling Jul 22, 2025
The 5-methyluridine (m5U) modification in RNA is vital for numerous biological processes, making its precise identification a key focus in computational biology. However, traditional wet-lab detection methods are cumbersome and time-consuming, wherea...
Neural Networks, Computer Deep Learning RNA Uridine Computational Biology
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How large is the universe of RNA-like motifs? A clustering analysis of RNA graph motifs using topological descriptors.

PLoS computational biology Jul 15, 2025
Identifying novel and functional RNA structures remains a significant challenge in RNA motif design and is crucial for developing RNA-based therapeutics. Here we introduce a computational topology-based approach with unsupervised machine-learning alg...
Computational Biology Nucleotide Motifs RNA Cluster Analysis Algorithms Nucleic Acid Conformation
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Interpretability-guided RNA N-methyladenosine modification site prediction with invertible neural networks.

Communications biology Jul 8, 2025
As one of the most common and abundant post-transcriptional modifications, N-methyladenosine (mA) has been extensively studied for its essential regulatory role in gene expression and cell functions. The location of mA RNA modification sites, however...
RNA Processing, Post-Transcriptional Computational Biology Methylation RNA Humans Adenosine Animals Neural Networks, Computer Deep Learning
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