ArticleBioinformatics (Oxford, England)2015
Curation, integration and visualization of bacterial virulence factors in PATRIC.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 60 papers.
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Who cites it
60 citing papers in PubMed.
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- Genomic and Immunoinformatics Insights Into a Bovine-Derived Brucella abortus S19 Field Strain: Adaptations Impacting Vaccine Efficacy.Veterinary medicine and science · 2025Article
- Seasonal Variations of the Nebraska Salt Marsh Microbiome: Environmental Impact, Antibiotic Resistance, and Unique Species.Microorganisms · 2025Article
- Hybrid Genome and Clinical Impact of Emerging Extensively Drug-Resistant Priority Bacterial PathogenLife (Basel, Switzerland) · 2025Article
- Accurate prediction of virulence factors using pre-train protein language model and ensemble learning.BMC genomics · 2025Article
- Article
- Comparative Analysis of Virulence Genes in Non-Tuberculosis Mycobacteria (NTM) Isolated from Kenyan Camel Milk Suggests Potential Pathogenicity.Current microbiology · 2025Article
- Review
- Salmonella enterica virulence databases and bioinformatic analysis tools development.Scientific reports · 2024Article
- Whole-genome sequencing and analysis ofMicrobiology resource announcements · 2024Article
- Determinants of Antibiotic Resistance and Virulence Factors in the Genome ofAntibiotics (Basel, Switzerland) · 2024Article
- Transient colonizing microbes promote gut dysbiosis and functional impairment.NPJ biofilms and microbiomes · 2024Article
- Global compositional and functional states of the human gut microbiome in health and disease.Genome research · 2024Article
- Draft genome sequence data ofData in brief · 2024Article
- Partial genomic characterization of Chromobacterium piscinae from India reveals multi drug resistance.Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] · 2024Article
- Genome Sequence Comparisons between Small and Large Colony Phenotypes of Equine Clinical Isolates ofAnimals : an open access journal from MDPI · 2024Article
- Genotypic analyses of IncHI2 plasmids from enteric bacteria.Scientific reports · 2024Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
motivationWe've developed a highly curated bacterial virulence factor (VF) library in PATRIC (Pathosystems Resource Integration Center, www.patricbrc.org) to support infectious disease research. Although several VF databases are available, there is still a need to incorporate new knowledge found in published experimental evidence and integrate these data with other information known for these specific VF genes, including genomic and other omics data. This integration supports the identification of VFs, comparative studies and hypothesis generation, which facilitates the understanding of virulence and pathogenicity.
resultsWe have manually curated VFs from six prioritized NIAID (National Institute of Allergy and Infectious Diseases) category A-C bacterial pathogen genera, Mycobacterium, Salmonella, Escherichia, Shigella, Listeria and Bartonella, using published literature. This curated information on virulence has been integrated with data from genomic functional annotations, trancriptomic experiments, protein-protein interactions and disease information already present in PATRIC. Such integration gives researchers access to a broad array of information about these individual genes, and also to a suite of tools to perform comparative genomic and transcriptomics analysis that are available at PATRIC. AVAILABILITY AND IMPLEMENTATION: All tools and data are freely available at PATRIC (http://patricbrc.org). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.