AIMC Topic: Genome, Viral
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Pathogenicity and virulence of lumpy skin disease virus: A comprehensive update.
Virulence
Apr 27, 2025
Lumpy skin disease (LSD), which was confined to the Africa for many decades, has expanded its geographical distribution to numerous countries across Asia and Europe in recent years. The LSD virus (LSDV) is a relatively poorly studied virus. Its 151 K...
Genome evolution of Kaposi sarcoma-associated herpesvirus (KSHV).
Journal of virology
Apr 16, 2025
UNLABELLED: Kaposi sarcoma (KS) is the most common cancer in people living with HIV (PLWH), particularly in sub-Saharan Africa (SSA), where Kaposi sarcoma herpesvirus (KSHV or human herpesvirus 8 [HHV-8]) is endemic. In KSHV endemic areas, the overal...
Predicting viral host codon fitness and path shifting through tree-based learning on codon usage biases and genomic characteristics.
Scientific reports
Apr 10, 2025
Viral codon fitness (VCF) of the host and the VCF shifting has seldom been studied under quantitative measurements, although they could be concepts vital to understand pathogen epidemiology. This study demonstrates that the relative synonymous codon ...
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...
Pathogen genomic surveillance and the AI revolution.
Journal of virology
Jan 29, 2025
The unprecedented sequencing efforts during the COVID-19 pandemic paved the way for genomic surveillance to become a powerful tool for monitoring the evolution of circulating viruses. Herein, we discuss how a state-of-the-art artificial intelligence ...
Identification of patient demographic, clinical, and SARS-CoV-2 genomic factors associated with severe COVID-19 using supervised machine learning: a retrospective multicenter study.
BMC infectious diseases
Jan 28, 2025
BACKGROUND: Drivers of COVID-19 severity are multifactorial and include multidimensional and potentially interacting factors encompassing viral determinants and host-related factors (i.e., demographics, pre-existing conditions and/or genetics), thus ...
Evaluating Neural Network Performance in Predicting Disease Status and Tissue Source of JC Polyomavirus from Patient Isolates Based on the Hypervariable Region of the Viral Genome.
Viruses
Dec 25, 2024
JC polyomavirus (JCPyV) establishes a persistent, asymptomatic kidney infection in most of the population. However, JCPyV can reactivate in immunocompromised individuals and cause progressive multifocal leukoencephalopathy (PML), a fatal demyelinatin...
Machine Learning Early Detection of SARS-CoV-2 High-Risk Variants.
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Oct 14, 2024
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved many high-risk variants, resulting in repeated COVID-19 waves over the past years. Therefore, accurate early warning of high-risk variants is vital for epidemic prevention a...
Improving viral annotation with artificial intelligence.
mBio
Sep 4, 2024
Viruses of bacteria, "phages," are fundamental, poorly understood components of microbial community structure and function. Additionally, their dependence on hosts for replication positions phages as unique sensors of ecosystem features and environme...
Machine Learning Using Template-Based-Predicted Structure of Haemagglutinin Predicts Pathogenicity of Avian Influenza.
Journal of microbiology and biotechnology
Aug 6, 2024
Deep learning presents a promising approach to complex biological classifications, contingent upon the availability of well-curated datasets. This study addresses the challenge of analyzing three-dimensional protein structures by introducing a novel ...
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