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Interpreting Whole-Genome Sequence Analyses of Foodborne Bacteria for Regulatory Applications and Outbreak Investigations

Frontiers in microbiology, 2018-07, Vol.9, p.1482

2018

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Cross-study homogeneity of psoriasis gene expression in skin across a large expression range

PloS one, 2013-01, Vol.8 (1), p.e52242-e52242

2013

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GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians

BMC genomics, 2021-02, Vol.22 (1), p.114-11, Article 114

2021

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Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates

BMC genomics, 2024-07, Vol.25 (1), p.679-17, Article 679

2024

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CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data

PeerJ. Computer science, 2015-08, Vol.1, p.e20

2015

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Using Evolutionary Analyses to Refine Whole-Genome Sequence Match Criteria

Frontiers in microbiology, 2022-06, Vol.13, p.797997-797997

2022

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Transient and resident pathogens: Intra-facility genetic diversity of Listeria monocytogenes and Salmonella from food production environments

PloS one, 2022-09, Vol.17 (9), p.e0268470-e0268470

2022

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RIPS (rapid intuitive pathogen surveillance): a tool for surveillance of genome sequence data from foodborne bacterial pathogens

Frontiers in bioinformatics, 2024-08, Vol.4, p.1415078

2024

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Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination

Genome Biology, 2019-12, Vol.20 (1), p.286-286, Article 286

2019

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Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation

BMC genomics, 2023-04, Vol.24 (1), p.165-165, Article 165

2023

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Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

BMC genomics, 2021-05, Vol.22 (1), p.389-18, Article 389

2021

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Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples

PeerJ (San Francisco, CA), 2023-01, Vol.11, p.e14596, Article e14596

2023

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Whole-Genome Assessment of Clinical Acinetobacter baumannii Isolates Uncovers Potentially Novel Factors Influencing Carbapenem Resistance

Frontiers in microbiology, 2021-10, Vol.12, p.714284-714284

2021

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Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples

PloS one, 2016-11, Vol.11 (11), p.e0166162-e0166162

2016

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Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance

PeerJ (San Francisco, CA), 2017-10, Vol.5, p.e3893, Article e3893

2017

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Segal's Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project

PeerJ (San Francisco, CA), 2017-06, Vol.5, p.e3480-e3480, Article e3480

2017

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Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities

Microbiology spectrum, 2023-12, Vol.11 (6), p.e0148223-e0148223

2023

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Gen-FS coordinated proficiency test data for genomic foodborne pathogen surveillance, 2017 and 2018 exercises

Scientific data, 2020-11, Vol.7 (1), p.402, Article 402

2020

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A multinational listeriosis outbreak and the importance of sharing genomic data

The Lancet. Microbe, 2020-10, Vol.1 (6), p.e233-e234

2020

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An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella

PeerJ (San Francisco, CA), 2014-10, Vol.2, p.e620-e620

2014

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PRAWNS: compact pan-genomic features for whole-genome population genomics

Bioinformatics (Oxford, England), 2023-01, Vol.39 (1)

2023

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Numerical simulations and a conceptual model of the stratocumulus to trade cumulus transition

Journal of the atmospheric sciences, 1997, Vol.54 (1), p.168-192

1997

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Interpretative Labor and the Bane of Nonstandardized Metadata in Public Health Surveillance and Food Safety

Clinical infectious diseases, 2021-10, Vol.73 (8), p.1537-1539

2021

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Gene expression profiles normalized in psoriatic skin by treatment with brodalumab, a human anti-IL-17 receptor monoclonal antibody

The Journal of immunology (1950), 2014-04, Vol.192 (8), p.3828-3836

2014

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Genomic diversity of Salmonella enterica isolated from papaya samples collected during multiple outbreaks in 2017

Microbiology (Society for General Microbiology), 2020-05, Vol.166 (5), p.453-459

2020

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Interpreting Whole-Genome Sequence Analyses of Foodborne Bacteria for Regulatory Applications and Outbreak Investigations

Cross-study homogeneity of psoriasis gene expression in skin across a large expression range

GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians

Benchmarking short and long read polishing tools for nanopore assemblies: achieving near-perfect genomes for outbreak isolates

CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data

Using Evolutionary Analyses to Refine Whole-Genome Sequence Match Criteria

Transient and resident pathogens: Intra-facility genetic diversity of Listeria monocytogenes and Salmonella from food production environments

RIPS (rapid intuitive pathogen surveillance): a tool for surveillance of genome sequence data from foodborne bacterial pathogens

Within-species contamination of bacterial whole-genome sequence data has a greater influence on clustering analyses than between-species contamination

Assessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation

Evaluating the accuracy of Listeria monocytogenes assemblies from quasimetagenomic samples using long and short reads

Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples

Whole-Genome Assessment of Clinical Acinetobacter baumannii Isolates Uncovers Potentially Novel Factors Influencing Carbapenem Resistance

Real-Time Pathogen Detection in the Era of Whole-Genome Sequencing and Big Data: Comparison of k-mer and Site-Based Methods for Inferring the Genetic Distances among Tens of Thousands of Salmonella Samples

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance

Segal's Law, 16S rRNA gene sequencing, and the perils of foodborne pathogen detection within the American Gut Project

Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities

Gen-FS coordinated proficiency test data for genomic foodborne pathogen surveillance, 2017 and 2018 exercises

A multinational listeriosis outbreak and the importance of sharing genomic data

An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella

PRAWNS: compact pan-genomic features for whole-genome population genomics

Numerical simulations and a conceptual model of the stratocumulus to trade cumulus transition

Interpretative Labor and the Bane of Nonstandardized Metadata in Public Health Surveillance and Food Safety

Gene expression profiles normalized in psoriatic skin by treatment with brodalumab, a human anti-IL-17 receptor monoclonal antibody

Genomic diversity of Salmonella enterica isolated from papaya samples collected during multiple outbreaks in 2017

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