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Description of Research Interests
Genomics and molecular biology of foodborne pathogens; pathogen subtyping and genomic epidemiology; bioinformatics; microbial phylogenetics and evolution; food microbiology.
Selected Publications
Deng X, Chao S, Horn A. 2021. Emerging applications of machine learning in food safety. Annual Review of Food Science and Technology 12
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 DOI:10.1128/mSystems.00589-20
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. 2019. Applied and Environmental Microbiology 85:e01746-19. DOI: 1128/AEM.01746-19. (Featured by AEM spotlight)
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 25(1): 82-91 (Featured by Nature Reviews Microbiology - Genome Watch, The Verge, and EID podcast)
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 84 e02340-17 (Featured by AEM spotlight)
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 7:353-374.
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 53:1685-1692
Deng X, Shariat N, Driebe E, Roe C, Tolar B, Trees E, Keim PS, Zhang W, Dudley EG, Fields PI, Engelthaler DM. 2015. Comparative analysis of subtyping methods against a whole genome sequencing standard in Salmonella enterica serotype Enteritidis. Journal of Clinical Microbiology 53:212-218
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 20:1481-1489