32 Papers
19 Citations
Hugh Rand is an academic researcher from Center for Food Safety and Applied Nutrition. The author has contributed to research in topics: Biology & Genome. The author has an hindex of 10, co-authored 24 publications. Previous affiliations of Hugh Rand include Food and Drug Administration.
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Papers
CFSAN SNP Pipeline: an automated method for constructing SNP matrices from next-generation sequence data
TL;DR: CFSAN SNP Pipeline is a robust and accurate tool that it is among the first to combine into a single executable the myriad steps required to produce a SNP matrix from NGS data.
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Interpreting Whole-Genome Sequence Analyses of Foodborne Bacteria for Regulatory Applications and Outbreak Investigations
TL;DR: This work provides a framework for interpreting WGS analyses that combines SNP counts with phylogenetic tree topologies and bootstrap support, and clarifies the roles of WGS, epidemiological, traceback, and other evidence in forming the conclusions of investigations.
GalaxyTrakr: a distributed analysis tool for public health whole genome sequence data accessible to non-bioinformaticians
Jayanthi Gangiredla,Hugh Rand,Daniel Benisatto,Justin Payne,Charles Strittmatter,Jimmy Sanders,William J. Wolfgang,Kevin Libuit,James Bruce Herrick,Melanie Prarat,Magaly Toro,Thomas Farrell,Errol Strain +12 more
TL;DR: GalaxyTrakr as mentioned in this paper is a cloud-based bioinformatics platform for whole-genome sequencing (WGS) that supports coordinated analytic methods and consistent interpretation of results across laboratories.
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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