ArticlePloS one2019
GenomeGraphR: A user-friendly open-source web application for foodborne pathogen whole genome sequencing data integration, analysis, and visualization.
Article in PloS one, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
15 citing papers in PubMed.
- Prospective modeling and estimating the epidemiologically informative match rate within large foodborne pathogen genomic databases.BMC research notes · 2024Article
- Article
- Use of whole genome sequencing for surveillance and control of foodborne diseases:Frontiers in microbiology · 2024Review
- Human Listeriosis.Clinical microbiology reviews · 2023Review
- Transforming Shiga toxin-producingFrontiers in microbiology · 2023Article
- Salmonella enterica Serovar Typhimurium Isolates from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type.Applied and environmental microbiology · 2022Article
- Salmonella Genomics in Public Health and Food Safety.EcoSal Plus · 2021Article
- Accurate reconstruction of bacterial pan- and core genomes with PEPPAN.Genome research · 2020Article
- Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens.One health outlook · 2020Review
- The EnteroBase user's guide, with case studies onGenome research · 2020Article
- Article
- Listeriosis outbreak likely due to contaminated liver pâté consumed in a tavern, Austria, December 2018.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2019Article
- Whole Genome Sequencing Based Surveillance ofFrontiers in public health · 2019Review
- A Simple and Robust Statistical Method to Define Genetic Relatedness of Samples Related to Outbreaks at the Genomic Scale - Application to RetrospectiveFrontiers in microbiology · 2019Article
- Integrating Whole-Genome Sequencing Data Into Quantitative Risk Assessment of Foodborne Antimicrobial Resistance: A Review of Opportunities and Challenges.Frontiers in microbiology · 2019Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Food safety risk assessments and large-scale epidemiological investigations have the potential to provide better and new types of information when whole genome sequence (WGS) data are effectively integrated. Today, the NCBI Pathogen Detection database WGS collections have grown significantly through improvements in technology, coordination, and collaboration, such as the GenomeTrakr and PulseNet networks. However, high-quality genomic data is not often coupled with high-quality epidemiological or food chain metadata. We have created a set of tools for cleaning, curation, integration, analysis and visualization of microbial genome sequencing data. It has been tested using Salmonella enterica and Listeria monocytogenes data sets provided by NCBI Pathogen Detection (160,000 sequenced isolates in 2018). GenomeGraphR presents foodborne pathogen WGS data and associated curated metadata in a user-friendly interface that allows a user to query a variety of research questions such as, transmission sources and dynamics, global reach, and persistence of genotypes associated with contamination in the food supply and foodborne illness across time or space. The application is freely available (https://fda-riskmodels.foodrisk.org/genomegraphr/).
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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.