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| SeqSero2: Rapid and Improved Salmonella Serotype Determination Using Whole-Genome Sequencing Data S Zhang, HC den Bakker, S Li, J Chen, BA Dinsmore, C Lane, AC Lauer, ... Applied and environmental microbiology 85 (23), e01746-19, 2019 | 210 | 2019 |
| Genomic epidemiology: whole-genome-sequencing–powered surveillance and outbreak investigation of foodborne bacterial pathogens X Deng, HC den Bakker, RS Hendriksen Annual review of food science and technology 7, 353-374, 2016 | 195 | 2016 |
| Transcriptomic response of Escherichia coli O157: H7 to oxidative stress S Wang, K Deng, S Zaremba, X Deng, C Lin, Q Wang, ML Tortorello, ... Applied and environmental microbiology 75 (19), 6110-6123, 2009 | 193 | 2009 |
| Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings NA Feasey, J Hadfield, KH Keddy, TJ Dallman, J Jacobs, X Deng, ... Nature genetics 48 (10), 1211-1217, 2016 | 188 | 2016 |
| Transcriptome sequencing of Salmonella enterica serovar Enteritidis under desiccation and starvation stress in peanut oil X Deng, Z Li, W Zhang Food microbiology 30 (1), 311-315, 2012 | 169 | 2012 |
| Mashtree: a rapid comparison of whole genome sequence files LS Katz, T Griswold, SS Morrison, JA Caravas, S Zhang, HC den Bakker, ... Journal of Open Source Software 4 (44), 2019 | 142 | 2019 |
| Comparative analysis of subtyping methods against a whole-genome-sequencing standard for Salmonella enterica serotype Enteritidis X Deng, N Shariat, EM Driebe, CC Roe, B Tolar, E Trees, P Keim, ... Journal of clinical microbiology 53 (1), 212-218, 2015 | 133 | 2015 |
| A comparative analysis of the Lyve-SET phylogenomics pipeline for genomic epidemiology of foodborne pathogens LS Katz, T Griswold, AJ Williams-Newkirk, D Wagner, A Petkau, C Sieffert, ... Frontiers in Microbiology 8, 375, 2017 | 123 | 2017 |
| Genomic epidemiology of Salmonella enterica serotype Enteritidis based on population structure of prevalent lineages X Deng, PT Desai, HC den Bakker, M Mikoleit, B Tolar, RS Hendriksen, JG Frye ... Emerging Infectious Diseases 20 (9), 1481, 2014 | 103 | 2014 |
| Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification X Deng, AM Phillippy, Z Li, SL Salzberg, W Zhang BMC genomics 11, 1-21, 2010 | 101 | 2010 |
| Zoonotic source attribution of Salmonella enterica serotype Typhimurium using genomic surveillance data, United States S Zhang, S Li, W Gu, H den Bakker, D Boxrud, A Taylor, C Roe, E Driebe, ... Emerging Infectious Diseases 25 (1), 82, 2019 | 83 | 2019 |
| Global spread of Salmonella Enteritidis via centralized sourcing and international trade of poultry breeding stocks S Li, Y He, DA Mann, X Deng Nature communications 12 (1), 5109, 2021 | 75 | 2021 |
| Emerging applications of machine learning in food safety X Deng, S Cao, AL Horn Annual Review of Food Science and Technology 12, 513-538, 2021 | 73 | 2021 |
| Salmonella Serotyping; Comparison of the Traditional Method to a Microarray-Based Method and an in silico Platform Using Whole Genome Sequencing Data B Diep, C Barretto, AC Portmann, C Fournier, A Karczmarek, G Voets, S Li, ... Frontiers in microbiology 10, 2554, 2019 | 68 | 2019 |
| Quasimetagenomics-based and real-time-sequencing-aided detection and subtyping of Salmonella enterica from food samples JY Hyeon, S Li, DA Mann, S Zhang, Z Li, Y Chen, X Deng Applied and environmental microbiology 84 (4), e02340-17, 2018 | 60 | 2018 |
| Rapid detection of Salmonella in raw chicken breast using real-time PCR combined with immunomagnetic separation and whole genome amplification JY Hyeon, X Deng Food microbiology 63, 111-116, 2017 | 57 | 2017 |
| The food industry's current and future role in preventing microbial foodborne illness within the United States MP Doyle, MC Erickson, W Alali, J Cannon, X Deng, Y Ortega, MA Smith, ... Clinical Infectious Diseases 61 (2), 252-259, 2015 | 54 | 2015 |
| Prevalence, serotype diversity, biofilm-forming ability and eradication of Listeria monocytogenes isolated from diverse foods in Shanghai, China W Wang, X Zhou, Y Suo, X Deng, M Cheng, C Shi, X Shi Food Control 73, 1068-1073, 2017 | 40 | 2017 |
| The Mobile Colistin Resistance Gene, mcr-1.1, Is Carried on IncX4 Plasmids in Multidrug Resistant E. coli Isolated from Rainbow Trout Aquaculture J Hassan, RZ Eddine, D Mann, S Li, X Deng, IP Saoud, II Kassem Microorganisms 8 (11), 1636, 2020 | 37 | 2020 |
