AIMC Topic: Host-Pathogen Interactions

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Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions.

Briefings in bioinformatics
In recent years, high-throughput experimental techniques have significantly enhanced the accuracy and coverage of protein-protein interaction identification, including human-pathogen protein-protein interactions (HP-PPIs). Despite this progress, expe...

Machine Learning Methods for Predicting Human-Adaptive Influenza A Viruses Based on Viral Nucleotide Compositions.

Molecular biology and evolution
Each influenza pandemic was caused at least partly by avian- and/or swine-origin influenza A viruses (IAVs). The timing of and the potential IAVs involved in the next pandemic are currently unpredictable. We aim to build machine learning (ML) models ...

PVsiRNAPred: Prediction of plant exclusive virus-derived small interfering RNAs by deep convolutional neural network.

Journal of bioinformatics and computational biology
Plant exclusive virus-derived small interfering RNAs (vsiRNAs) regulate various biological processes, especially important in antiviral immunity. The identification of plant vsiRNAs is important for understanding the biogenesis and function mechanism...

Victors: a web-based knowledge base of virulence factors in human and animal pathogens.

Nucleic acids research
Virulence factors (VFs) are molecules that allow microbial pathogens to overcome host defense mechanisms and cause disease in a host. It is critical to study VFs for better understanding microbial pathogenesis and host defense mechanisms. Victors (ht...

Targeting Virus-host Protein Interactions: Feature Extraction and Machine Learning Approaches.

Current drug metabolism
BACKGROUND: Targeting critical viral-host Protein-Protein Interactions (PPIs) has enormous application prospects for therapeutics. Using experimental methods to evaluate all possible virus-host PPIs is labor-intensive and time-consuming. Recent growt...

Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes.

Science (New York, N.Y.)
Identifying the animal origins of RNA viruses requires years of field and laboratory studies that stall responses to emerging infectious diseases. Using large genomic and ecological datasets, we demonstrate that animal reservoirs and the existence an...

High Mobility Group Box 1 Protein Enhances HIV Replication in Newly Infected Primary T Cells.

Clinical laboratory
BACKGROUND: High-mobility group box 1 (HMGB1), a DNA-binding protein, has recently been shown to have effects on HIV replication, but the effects are dependent on the cell type and the timing of infection. Using human primary T cells, this study aime...