AIMC Topic: Computational Biology

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RNA-protein interaction prediction using network-guided deep learning.

Communications biology Feb 16, 2025
Accurate computational determination of RNA-protein interactions remains challenging, particularly when encountering unknown RNAs and proteins. The limited number of RNAs and their flexibility constrained the effectiveness of the deep-learning models...
RNA-Binding Proteins RNA, Viral RNA SARS-CoV-2 Deep Learning Humans Computational Biology Neural Networks, Computer COVID-19
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Identifying RNA-small Molecule Binding Sites Using Geometric Deep Learning with Language Models.

Journal of molecular biology Feb 15, 2025
RNAs are emerging as promising therapeutic targets, yet identifying small molecules that bind to them remains a significant challenge in drug discovery. This underscores the crucial role of computational modeling in predicting RNA-small molecule bind...
Computational Biology Nucleic Acid Conformation Drug Discovery Models, Molecular Binding Sites Deep Learning RNA Small Molecule Libraries
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Identification of biomarkers associated with phagocytosis regulatory factors in coronary artery disease using machine learning and network analysis.

Mammalian genome : official journal of the International Mammalian Genome Society Feb 14, 2025
BACKGROUND: Coronary artery disease (CAD) is the leading cause of death worldwide, and aberrant phagocytosis may be involved in its development. Understanding this aspect may provide new avenues for prompt CAD diagnosis.
Biomarkers Gene Expression Profiling Protein Interaction Maps Humans Machine Learning Interleukin-1beta Coronary Artery Disease Phagocytosis Receptors, IgG Toll-Like Receptor 2 Syk Kinase Transcription Factors Databases, Genetic MicroRNAs Gene Regulatory Networks Polymorphism, Single Nucleotide Computational Biology
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Artificial Intuition and accelerating the process of antimicrobial drug discovery.

Computers in biology and medicine Feb 14, 2025
New drug development is a very challenging, expensive, and usually time-consuming process. This issue is very important with regard to antimicrobials, which are affected by the global issue of the development and spread of resistance. This framework ...
Antitubercular Agents Molecular Dynamics Simulation Mycobacterium tuberculosis Anti-Infective Agents Drug Discovery Computational Biology Humans Artificial Intelligence
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Interpretable AI for inference of causal molecular relationships from omics data.

Science advances Feb 14, 2025
The discovery of molecular relationships from high-dimensional data is a major open problem in bioinformatics. Machine learning and feature attribution models have shown great promise in this context but lack causal interpretation. Here, we show that...
Algorithms Gene Regulatory Networks Computational Biology Alzheimer Disease Humans Machine Learning
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Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases.

Genome research Feb 14, 2025
Metagenomics, particularly genome-resolved metagenomics, have significantly deepened our understanding of microbes, illuminating their taxonomic and functional diversity and roles in ecology, physiology, and evolution. However, eukaryotic populations...
Rumen Eukaryota Metagenome Databases, Protein Fungi Metagenomics Ruminants Animals Deep Learning Computational Biology Gastrointestinal Microbiome
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Using a multi-strain infectious disease model with physical information neural networks to study the time dependence of SARS-CoV-2 variants of concern.

PLoS computational biology Feb 14, 2025
With the ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its increasing adaptation to humans, several variants of concern (VOCs) and variants of interest (VOIs) have been identified since late 2020. These include...
Models, Biological Humans British Columbia Computer Simulation Neural Networks, Computer COVID-19 SARS-CoV-2 Algorithms Computational Biology
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Simpler Protein Domain Identification Using Spectral Clustering.

Proteins Feb 13, 2025
The decomposition of a biomolecular complex into domains is an important step to investigate biological functions and ease structure determination. A successful approach to do so is the SPECTRUS algorithm, which provides a segmentation based on spect...
Cluster Analysis Proteins Databases, Protein Algorithms Deep Learning Computational Biology Protein Conformation Sequence Alignment Sequence Analysis, Protein Models, Molecular Protein Domains Amino Acid Sequence
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A Perspective on Artificial Intelligence for Molecular Pathologists.

The Journal of molecular diagnostics : JMD Feb 13, 2025
The widespread adoption of next-generation sequencing technology in molecular pathology has enabled us to interrogate the genome as never before. The huge quantities of data generated by sequencing, the enormous complexity of human and microbial gene...
Pathology, Molecular Computational Biology Pathologists High-Throughput Nucleotide Sequencing Humans Artificial Intelligence Machine Learning
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PhageDPO: A machine-learning based computational framework for identifying phage depolymerases.

Computers in biology and medicine Feb 13, 2025
Bacteriophages (phages) are the most predominant and genetically diverse biological entities on Earth. Phages are viruses that infect bacteria and encode numerous proteins with potential biotechnological application. However, most phage-encoded prote...
Machine Learning Software Viral Proteins Computational Biology Support Vector Machine Genome, Viral Bacteriophages
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