AIMC Topic: Computational Biology

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DRAMMA: a multifaceted machine learning approach for novel antimicrobial resistance gene detection in metagenomic data.

Microbiome Mar 7, 2025
BACKGROUND: Antibiotics are essential for medical procedures, food security, and public health. However, ill-advised usage leads to increased pathogen resistance to antimicrobial substances, posing a threat of fatal infections and limiting the benefi...
Bacteria Metagenome Anti-Bacterial Agents Computational Biology Humans Drug Resistance, Bacterial Metagenomics Machine Learning Genes, Bacterial
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DHUpredET: A comparative computational approach for identification of dihydrouridine modification sites in RNA sequence.

Analytical biochemistry Mar 6, 2025
Laboratory-based detection of D sites is laborious and expensive. In this study, we developed effective machine learning models employing efficient feature encoding methods to identify D sites. Initially, we explored various state-of-the-art feature ...
Machine Learning RNA Base Sequence Computational Biology Uridine Sequence Analysis, RNA
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EVlncRNA-net: A dual-channel deep learning approach for accurate prediction of experimentally validated lncRNAs.

International journal of biological macromolecules Mar 6, 2025
Long non-coding RNAs (lncRNAs) play key roles in numerous biological processes and are associated with various human diseases. High-throughput RNA sequencing (HTlncRNAs) has identified tens of thousands of lncRNAs across species, but only a small fra...
RNA, Long Noncoding High-Throughput Nucleotide Sequencing Neural Networks, Computer Computational Biology Animals Humans Deep Learning Sequence Analysis, RNA Mice
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GRATCR: Epitope-Specific T Cell Receptor Sequence Generation With Data-Efficient Pre-Trained Models.

IEEE journal of biomedical and health informatics Mar 6, 2025
T cell receptors (TCRs) play a crucial role in numerous immunotherapies targeting tumor cells. However, their acquisition and optimization present significant challenges, involving laborious and time-consuming wet lab experimental resource. Deep gene...
Deep Learning Receptors, Antigen, T-Cell Computational Biology Sequence Analysis, Protein Humans Epitopes, T-Lymphocyte
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CardiOT: Towards Interpretable Drug Cardiotoxicity Prediction Using Optimal Transport and Kolmogorov--Arnold Networks.

IEEE journal of biomedical and health informatics Mar 6, 2025
Investigating the inhibitory effects of compounds on cardiac ion channels is essential for assessing cardiac drug safety. Consequently, researchers have developed computational models to evaluate combined cardiotoxicity (CCT) on cardiac ion channels....
Cardiotoxicity Ion Channels Computational Biology Humans Models, Cardiovascular Neural Networks, Computer
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NPENN: A Noise Perturbation Ensemble Neural Network for Microbiome Disease Phenotype Prediction.

IEEE journal of biomedical and health informatics Mar 6, 2025
With advances in microbiomics, the crucial role of microbes in disease progression is increasingly recognized. However, predicting disease phenotypes using microbiome data remains challenging due to data complexity, heterogeneity, and limited model g...
Computational Biology Microbiota Neural Networks, Computer Humans Phenotype
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Drug Repositioning via Multi-View Representation Learning With Heterogeneous Graph Neural Network.

IEEE journal of biomedical and health informatics Mar 6, 2025
Exploring simple and efficient computational methods for drug repositioning has emerged as a popular and compelling topic in the realm of comprehensive drug development. The crux of this technology lies in identifying potential drug-disease associati...
Algorithms Computational Biology Drug Repositioning Graph Neural Networks Humans Neural Networks, Computer
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Knowledge Graph Neural Network With Spatial-Aware Capsule for Drug-Drug Interaction Prediction.

IEEE journal of biomedical and health informatics Mar 6, 2025
Uncovering novel drug-drug interactions (DDIs) plays a pivotal role in advancing drug development and improving clinical treatment. The outstanding effectiveness of graph neural networks (GNNs) has garnered significant interest in the field of DDI pr...
Algorithms Computational Biology Humans Neural Networks, Computer Drug Interactions Graph Neural Networks
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Multimodal Drug Target Binding Affinity Prediction Using Graph Local Substructure.

IEEE journal of biomedical and health informatics Mar 6, 2025
Predicting the binding affinity of drug target is essential to reduce drug development costs and cycles. Recently, several deep learning-based methods have been proposed to utilize the structural or sequential information of drugs and targets to pred...
Humans Algorithms Drug Discovery Pharmaceutical Preparations Computational Biology Deep Learning Proteins Protein Binding
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BINDTI: A Bi-Directional Intention Network for Drug-Target Interaction Identification Based on Attention Mechanisms.

IEEE journal of biomedical and health informatics Mar 6, 2025
The identification of drug-target interactions (DTIs) is an essential step in drug discovery. In vitro experimental methods are expensive, laborious, and time-consuming. Deep learning has witnessed promising progress in DTI prediction. However, how t...
Proteins Humans Neural Networks, Computer Deep Learning Drug Discovery Computational Biology
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