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  • Selected papers

He Y, Xu T, Li S, Mann DA, Britton B, Oliver H, den Bakker HC, Deng X. 2022 Integrative assessment of reduced Listeria monocytogenes susceptibility to benzalkonium chloride in produce processing environments. Applied and Environmental Microbiology

Li S, He Y, Mann DA, Deng X. 2021. Global spread of Salmonella Enteritidis via centralized sourcing and international trade of breeding stocks. Nature Communications 

Deng X, Chao S, Horn A. 2021. Emerging applications of machine learning in food safety. Annual Review of Food Science and Technology 

Li S, Mann DA, Zhang S, Yan Q, Meinersmann J, Deng X. 2020. Microbiome-informed food safety and quality: longitudinal consistency and cross-sectional distinctiveness of retail chicken breast microbiomes. mSystems 

Zhang S, den Bakker H, Li S, Chen J, Dinsmore BA, Lane C, Lauer AC, Fields PI, Deng X. 2019. SeqSero2: Rapid and improved Salmonella serotype determination using whole genome sequencing data. Applied and Environmental Microbiology

Zhang S, Li S, Gu W, den Bakker H, Boxrud D, Taylor A, Roe C, Driebe E, Engelthaler DM, Allard M, Brown E, McDermott P, Zhao S, Bruce BB, Trees Eija, Fields PI, Deng X. 2019. Zoonotic Source Attribution of Salmonella enterica Serotype Typhimurium using genomic surveillance data, United States. Emerging Infectious Diseases 

Hyeon J, Li S, Mann DA, Zhang S, Li Z, Chen Y, Deng X. 2018. Quasimetagenomics-based and real-time-sequencing-aided detection and subtyping of Salmonella enterica from food samples. Applied and Environmental Microbiology

Feasey AN, Hadfield J, Keddy KH, Dallman TJ, Jacobs J, Deng X et al (47 co-authors). 2016. Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings. Nature Genetics 48:1211-1217

Deng X, den Bakker HC, Hendriksen RS. 2016. Genomic epidemiology: Whole-genome Sequencing-powered surveillance and outbreak investigation of foodborne bacterial pathogens. Annual Review of Food Science and Technology 

Zhang S, Yin Y, Jones MB, Zhang Z, Kaiser BLD, Dinsmore BA, Fitzgerald C, Fields PI, Deng X. 2015. Salmonella serotype determination utilizing high-throughput genome sequencing. Journal of Clinical Microbiology


Deng X, Desai PT, den Bakker HC, Mikoleit M, Tolar B, Trees E, Hendriksen RS, Frye, JG, Porwolik S, Weimer BC, Wiedmann M, Weinstock GM, Fields PI, McClelland. 2014. Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages. Emerging Infectious Diseases


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