AIMC Topic: Computational Biology

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Mammalian piRNA target prediction using a hierarchical attention model.

BMC bioinformatics Feb 11, 2025
BACKGROUND: Piwi-interacting RNAs (piRNAs) are well established for monitoring and protecting the genome from transposons in germline cells. Recently, numerous studies provided evidence that piRNAs also play important roles in regulating mRNA transcr...
Mammals Piwi-Interacting RNA Animals Deep Learning Computational Biology RNA, Small Interfering Mice Humans
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SHASI-ML: a machine learning-based approach for immunogenicity prediction in vaccine development.

Frontiers in cellular and infection microbiology Feb 11, 2025
INTRODUCTION: Accurate prediction of immunogenic proteins is crucial for vaccine development and understanding host-pathogen interactions in bacterial diseases, particularly for Salmonella infections which remain a significant global health challenge...
Salmonella Infections Salmonella Vaccines Immunogenicity, Vaccine Antigens, Bacterial Computational Biology Algorithms Salmonella typhimurium Proteome Humans Vaccine Development Salmonella Machine Learning Bacterial Proteins
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Recent advances and future challenges in predictive modeling of metalloproteins by artificial intelligence.

Molecules and cells Feb 10, 2025
Metal coordination is essential for structural/catalytic functions of metalloproteins that mediate a wide range of biological processes in living organisms. Advances in bioinformatics have significantly enhanced our understanding of metal-binding sit...
Metalloproteins Models, Molecular Binding Sites Humans Metals Artificial Intelligence Computational Biology
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Deep learning for RNA structure prediction.

Current opinion in structural biology Feb 10, 2025
Predicting RNA structures from sequences with computational approaches is of vital importance in RNA biology considering the high costs of experimental determination. AI methods have revolutionized this field in recent years, enabling RNA structure p...
Deep Learning Computational Biology RNA Nucleic Acid Conformation
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Feature gene selection and functional validation of SH3KBP1 in infantile hemangioma using machine learning.

Biochemical and biophysical research communications Feb 10, 2025
BACKGROUND: Infantile hemangioma (IH) is a prevalent vascular tumor in infancy with a complex pathogenesis that remains unclear. This study aimed to investigate the underlying mechanisms of IH using comprehensive bioinformatics analyses and in vitro ...
Male Infant Child, Preschool Hemangioma Gene Regulatory Networks MicroRNAs Gene Expression Profiling Machine Learning Adaptor Proteins, Signal Transducing Female Computational Biology Gene Expression Regulation, Neoplastic Humans
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Deep Learning for Antimicrobial Peptides: Computational Models and Databases.

Journal of chemical information and modeling Feb 10, 2025
Antimicrobial peptides are a promising strategy to combat antimicrobial resistance. However, the experimental discovery of antimicrobial peptides is both time-consuming and laborious. In recent years, the development of computational technologies (es...
Computational Biology Antimicrobial Peptides Deep Learning
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SEGT-GO: a graph transformer method based on PPI serialization and explanatory artificial intelligence for protein function prediction.

BMC bioinformatics Feb 10, 2025
BACKGROUND: A massive amount of protein sequences have been obtained, but their functions remain challenging to discern. In recent research on protein function prediction, Protein-Protein Interaction (PPI) Networks have played a crucial role. Uncover...
Artificial Intelligence Algorithms Protein Interaction Maps Databases, Protein Protein Interaction Mapping Computational Biology Proteins
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DSANIB: Drug-Target Interaction Predictions With Dual-View Synergistic Attention Network and Information Bottleneck Strategy.

IEEE journal of biomedical and health informatics Feb 10, 2025
Prediction of drug-target interactions (DTIs) is one of the crucial steps for drug repositioning. Identifying DTIs through bio-experimental manners is always expensive and time-consuming. Recently, deep learning-based approaches have shown promising ...
Drug Interactions Deep Learning Computational Biology Drug Repositioning Humans Algorithms
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Mapping the learning curves of deep learning networks.

PLoS computational biology Feb 10, 2025
There is an important challenge in systematically interpreting the internal representations of deep neural networks (DNNs). Existing techniques are often less effective for non-tabular tasks, or they primarily focus on qualitative, ad-hoc interpretat...
Learning Curve Humans Neural Networks, Computer Deep Learning Computational Biology Computer Simulation
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CellCircLoc: Deep Neural Network for Predicting and Explaining Cell Line-Specific CircRNA Subcellular Localization.

IEEE journal of biomedical and health informatics Feb 10, 2025
The subcellular localization of circular RNAs (circRNAs) is crucial for understanding their functional relevance and regulatory mechanisms. CircRNA subcellular localization exhibits variations across different cell lines, demonstrating the diversity ...
Humans Computational Biology Cell Line RNA, Circular Neural Networks, Computer Deep Learning
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