Steven Davis
Center for Food Safety and Applied Nutrition
5 Papers
2 Citations
Steven Davis is an academic researcher from Center for Food Safety and Applied Nutrition. The author has contributed to research in topics: Pipeline (software) & Tree (data structure). The author has an hindex of 4, co-authored 5 publications. Previous affiliations of Steven Davis include Food and Drug Administration.
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Papers
Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance
Ruth Timme,Hugh Rand,Martin Shumway,Eija Trees,Mustafa Simmons,Richa Agarwala,Steven Davis,Glenn E. Tillman,Stephanie Defibaugh-Chavez,Heather A. Carleton,William Klimke,Lee S. Katz,Lee S. Katz +12 more
TL;DR: This work has identified four well-documented foodborne pathogen events in which the epidemiology was concordant with routine phylogenomic analyses (reference-based SNP and wgMLST approaches), and proposed five benchmark datasets to help standardize comparison of current and future phylogenomic pipelines, and facilitate important cross-institutional collaborations.
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Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance.
Ruth Timme,Errol Strain,Joseph D. Baugher,Steven Davis,Narjol Gonzalez-Escalona,Maria Sanchez Leon,Marc W. Allard,Eric W. Brown,Sandra M. Tallent,Hugh Rand +9 more
TL;DR: A historical perspective on the use of WGS for pathogen tracking is provided and the efforts underway to ensure the major steps in phylogenomic pipelines used for pathogenic disease surveillance can be readily validated are summarized.
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TreeToReads - a pipeline for simulating raw reads from phylogenies
Emily Jane McTavish,James B. Pettengill,Steven Davis,Hugh Rand,Errol Strain,Marc W. Allard,Ruth Timme +6 more
TL;DR: A simulation approach to generate raw read data from mutated genomes simulated under a known phylogeny (TreeToReads) to assess the robustness of a given result, which is critical within both research and applied settings.
An evaluation of alternative methods for constructing phylogenies from whole genome sequence data: a case study with Salmonella
James B. Pettengill,Yan Luo,Steven Davis,Yi Chen,Narjol Gonzalez-Escalona,Andrea Ottesen,Hugh Rand,Marc W. Allard,Errol Strain +8 more
TL;DR: This investigation into the robustness of clustering patterns illustrates the importance of carefully considering how data from different platforms are combined and analyzed, and clear differences in the topologies inferred are found.
TreeToReads - a pipeline for simulating raw reads from phylogenies.
Emily Jane McTavish,Emily Jane McTavish,James B. Pettengill,Steven Davis,Hugh Rand,Errol Strain,Marc W. Allard,Ruth Timme +7 more
TL;DR: A program, TreeToReads, is offered, which can generate raw read data from mutated genomes simulated under a known phylogeny, which allows direct comparisons of simulated and observed data in a controlled environment.