AIMC Topic: Host-Pathogen Interactions

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Expanding the drug discovery space with predicted metabolite-target interactions.

Communications biology Mar 5, 2021
Metabolites produced in the human gut are known modulators of host immunity. However, large-scale identification of metabolite-host receptor interactions remains a daunting challenge. Here, we employed computational approaches to identify 983 potenti...
Protein Interaction Maps Bacteria Signal Transduction Humans Gastrointestinal Microbiome Machine Learning Inflammatory Bowel Diseases Cells, Cultured Drug Discovery Databases, Factual Gene Expression Profiling Transcriptome Data Mining Ligands Molecular Targeted Therapy Metabolomics Host-Pathogen Interactions Metabolome Anti-Inflammatory Agents Gastrointestinal Agents
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Utilizing Computational Machine Learning Tools to Understand Immunogenic Breadth in the Context of a CD8 T-Cell Mediated HIV Response.

Frontiers in immunology Feb 18, 2021
Predictive models are becoming more and more commonplace as tools for candidate antigen discovery to meet the challenges of enabling epitope mapping of cohorts with diverse HLA properties. Here we build on the concept of using two key parameters, div...
HIV Infections Proteome CD8-Positive T-Lymphocytes HLA Antigens Humans Machine Learning Epitopes, T-Lymphocyte Peptides Viral Proteins Antigens, Viral HIV Genetic Variation Host-Pathogen Interactions Genome, Viral
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A new resource on artificial intelligence powered computer automated detection software products for tuberculosis programmes and implementers.

Tuberculosis (Edinburgh, Scotland) Jan 4, 2021
Recently, the number of artificial intelligence powered computer-aided detection (CAD) products that detect tuberculosis (TB)-related abnormalities from chest X-rays (CXR) available on the market has increased. Although CXR is a relatively effective ...
Humans Software Diffusion of Innovation Automation Host-Pathogen Interactions Reproducibility of Results Predictive Value of Tests Radiography, Thoracic Lung Radiographic Image Interpretation, Computer-Assisted Diagnosis, Computer-Assisted Tuberculosis, Pulmonary Deep Learning Mycobacterium tuberculosis
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IL6-mediated HCoV-host interactome regulatory network and GO/Pathway enrichment analysis.

PLoS computational biology Sep 30, 2020
During these days of global emergency for the COVID-19 disease outbreak, there is an urgency to share reliable information able to help worldwide life scientists to get better insights and make sense of the large amount of data currently available. I...
Betacoronavirus Pneumonia, Viral Host-Pathogen Interactions Gene Ontology Humans Viral Proteins Pandemics Genes, Viral COVID-19 Interleukin-6 SARS-CoV-2 Coronavirus Infections
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Mimicry Embedding Facilitates Advanced Neural Network Training for Image-Based Pathogen Detection.

mSphere Sep 9, 2020
The use of deep neural networks (DNNs) for analysis of complex biomedical images shows great promise but is hampered by a lack of large verified data sets for rapid network evolution. Here, we present a novel strategy, termed "mimicry embedding," for...
Animals Deep Learning Image Processing, Computer-Assisted Toxoplasma Zebrafish Microscopy Host-Pathogen Interactions Vaccinia virus Neural Networks, Computer Artificial Intelligence
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Target Identification Using Homopharma and Network-Based Methods for Predicting Compounds Against Dengue Virus-Infected Cells.

Molecules (Basel, Switzerland) Apr 18, 2020
Drug target prediction is an important method for drug discovery and design, can disclose the potential inhibitory effect of active compounds, and is particularly relevant to many diseases that have the potential to kill, such as dengue, but lack any...
Humans Neural Networks, Computer Protein Interaction Mapping Dengue Lipids Drug Discovery Antiviral Agents Dengue Virus Protein Interaction Maps Host-Pathogen Interactions Computational Biology Virus Replication
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A generalizable 29-mRNA neural-network classifier for acute bacterial and viral infections.

Nature communications Mar 4, 2020
Improved identification of bacterial and viral infections would reduce morbidity from sepsis, reduce antibiotic overuse, and lower healthcare costs. Here, we develop a generalizable host-gene-expression-based classifier for acute bacterial and viral ...
Support Vector Machine Bacterial Infections Acute Disease Datasets as Topic Host-Pathogen Interactions Virus Diseases Sepsis Hospital Mortality ROC Curve RNA, Messenger Adult Male Middle Aged Intensive Care Units Gene Expression Profiling Female Humans Neural Networks, Computer Aged Aged, 80 and over
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OHMI: the ontology of host-microbiome interactions.

Journal of biomedical semantics Dec 30, 2019
BACKGROUND: Host-microbiome interactions (HMIs) are critical for the modulation of biological processes and are associated with several diseases. Extensive HMI studies have generated large amounts of data. We propose that the logical representation o...
Microbiota Biological Ontologies Host-Pathogen Interactions
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mSphere of Influence: the Rise of Artificial Intelligence in Infection Biology.

mSphere Jun 26, 2019
Artur Yakimovich works in the field of computational virology and applies machine learning algorithms to study host-pathogen interactions. In this mSphere of Influence article, he reflects on two papers "Holographic Deep Learning for Rapid Optical Sc...
Toxoplasma Host-Pathogen Interactions Bacillus Algorithms Deep Learning Computational Biology
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Machine-Learning-Based Predictor of Human-Bacteria Protein-Protein Interactions by Incorporating Comprehensive Host-Network Properties.

Journal of proteome research Apr 22, 2019
The large-scale identification of protein-protein interactions (PPIs) between humans and bacteria remains a crucial step in systematically understanding the underlying molecular mechanisms of bacterial infection. Computational prediction approaches a...
Francisella tularensis Gene Expression Bacterial Proteins Host-Pathogen Interactions Proteome Protein Interaction Mapping Humans Models, Statistical Bacillus anthracis Yersinia pestis Machine Learning Databases, Protein Protein Binding Eukaryotic Cells Area Under Curve Molecular Mimicry
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