Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources
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Title
Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources
Authors
Keywords
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Journal
BMC GENOMICS
Volume 19, Issue 1, Pages -
Publisher
Springer Nature America, Inc
Online
2018-11-06
DOI
10.1186/s12864-018-5137-4
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- (2016) Kristi L. Helke et al. CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
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- (2016) Alison H Holmes et al. LANCET
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- (2016) Hattie E Webb et al. LANCET INFECTIOUS DISEASES
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- (2016) Suchawan Pornsukarom et al. PLoS One
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- (2016) Helen M. Sancheza et al. WATER AIR AND SOIL POLLUTION
- The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies
- (2016) Catherine E. Yoshida et al. PLoS One
- Practical considerations of surveillance of Salmonella serovars other than Enteridis and Typhimurium
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- (2014) Pimlapas Leekitcharoenphon et al. PLoS One
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- SRST2: Rapid genomic surveillance for public health and hospital microbiology labs
- (2014) Michael Inouye et al. Genome Medicine
- QUAST: quality assessment tool for genome assemblies
- (2013) Alexey Gurevich et al. BIOINFORMATICS
- The Scourge of Antibiotic Resistance: The Important Role of the Environment
- (2013) R. L. Finley et al. CLINICAL INFECTIOUS DISEASES
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- (2013) Annaëlle Kerouanton et al. Foodborne Pathogens and Disease
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- (2013) A. E. Mather et al. SCIENCE
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- (2011) Margaret A. Davis et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
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- Alignment-free genome comparison with feature frequency profiles (FFP) and optimal resolutions
- (2009) Gregory E. Sims et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
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