AIMC Topic: Computational Biology

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BPFun: a deep learning framework for bioactive peptide function prediction using multi-label strategy by transformer-driven and sequence rich intrinsic information.

BMC bioinformatics Jul 21, 2025
Bioactive peptides are beneficial or have physiological effects on the life activities of biological organisms. The functions of bioactive peptides are diverse, usually with one or more, so accurately detecting the multiple functions of multi-functio...
Computational Biology Amino Acid Sequence Peptides Deep Learning
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A deep ensemble framework for human essential gene prediction by integrating multi-omics data.

Scientific reports Jul 21, 2025
Essential genes are necessary for the survival or reproduction of a living organism. The prediction and analysis of gene essentiality can advance our understanding of basic life and human diseases, and further boost the development of new drugs. We p...
Multiomics Genes, Essential Humans Gene Ontology Neural Networks, Computer Genomics Deep Learning Computational Biology Protein Interaction Maps Machine Learning
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Exploration of common pathogenic genes between cerebral amyloid angiopathy and insomnia based on bioinformatics and experimental validation.

Scientific reports Jul 20, 2025
Cerebral amyloid angiopathy (CAA) and insomnia are age-related neurological disorders increasingly recognized as being closely associated. However, research on the shared genes and their biological mechanisms remains limited. This study aims to ident...
Cerebral Amyloid Angiopathy Male Humans Gene Expression Profiling Machine Learning Protein Interaction Maps Female Computational Biology Gene Expression Regulation Gene Regulatory Networks Animals Sleep Initiation and Maintenance Disorders
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DTIP-WINDGRU a novel drug-target interaction prediction with wind-enhanced gated recurrent unit.

BMC bioinformatics Jul 20, 2025
BACKGROUND: Identification of drug target interactions (DTI) is an important part of the drug discovery process. Since prediction of DTI using laboratory tests is time consuming and laborious, automated tools using computational intelligence (CI) tec...
Drug Discovery Deep Learning Computational Biology Humans Machine Learning Algorithms
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Ecosystem-based reservoir computing. Hypothesis paper.

Bio Systems Jul 19, 2025
Reservoir computing (RC) has emerged as a powerful computational paradigm, leveraging the intrinsic dynamics of complex systems to process temporal data efficiently. Here we propose to extend RC into ecological domains, where the ecosystems themselve...
Ecosystem Computational Biology Ecology Humans Computer Simulation
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MultiRepPI: a cross-modal feature fusion-based multiple characterization framework for plant peptide-protein interaction prediction.

BMC plant biology Jul 19, 2025
Plant peptide-protein interactions (PepPI) play a crucial role in plant growth, development, immune regulation, and environmental adaptation. However, existing computational methods still face several challenges in PepPI prediction. First, most metho...
Neural Networks, Computer Peptides Protein Interaction Mapping Computational Biology Plant Proteins
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Prediction of hub genes in pulpal inflammation and regeneration using autoencoders and a generative AI approach.

Scientific reports Jul 19, 2025
Pulpal inflammation and regeneration are crucial for enhancing endodontic treatment outcomes. Transcriptomic studies highlight the involvement of proinflammatory cytokines, NF-κB signaling, and stem cell activity. This study employs a generative AI a...
Regeneration Gene Ontology Autoencoder Pulpitis Inflammation Dental Pulp Gene Regulatory Networks Artificial Intelligence Computational Biology Software Humans Transcriptome Gene Expression Profiling Protein Interaction Maps
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Artificial intelligence-driven computational methods for antibody design and optimization.

mAbs Jul 18, 2025
Antibodies play a crucial role in our immune system. Their ability to bind to and neutralize pathogens opens opportunities to develop antibodies for therapeutic and diagnostic use. Computational methods capable of designing antibodies for a target an...
Computational Biology Animals Humans Protein Engineering Antibodies Drug Design Artificial Intelligence
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A new approach for microbe-disease association prediction: incorporating representation learning of latent relationships.

BMC medical informatics and decision making Jul 18, 2025
BACKGROUND: Predicting associations between microbes and diseases is crucial for clinical diagnosis and therapy. However, biological experiments are time-intensive, necessitating efficient computational models. Traditional models rely on existing mic...
Deep Learning Computational Biology Humans
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A densely connected framework for cancer subtype classification.

BMC bioinformatics Jul 18, 2025
BACKGROUND: Reliable identification of cancer subtypes is crucial for devising personalized treatment strategies. Integrating multi-omics data has proven to be an effective method for analyzing cancer subtypes. By combining molecular information acro...
Humans Machine Learning Deep Learning Computational Biology Kidney Neoplasms Algorithms Neoplasms
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