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Xiangyu Deng
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Salmonella serotype determination utilizing high-throughput genome sequencing data
S Zhang, Y Yin, MB Jones, Z Zhang, BL Deatherage Kaiser, BA Dinsmore, ...
Journal of clinical microbiology 53 (5), 1685-1692, 2015
3312015
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
1722009
Genomic epidemiology: whole-genome-sequencing-powered surveillance and outbreak investigation of foodborne bacterial pathogens
X Deng, HC den Bakker, RS Hendriksen
Annu Rev Food Sci Technol 7 (1), 353-374, 2016
1562016
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
1452016
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
1382012
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
1142015
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
982019
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
962017
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), 1-21, 2010
902010
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, E Trees, ...
Emerging Infectious Diseases 20 (9), 1481, 2014
872014
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), 1762, 2019
642019
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
622019
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
492018
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
432017
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
372015
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
362019
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
312017
Efficient oligonucleotide probe selection for pan-genomic tiling arrays
AM Phillippy, X Deng, W Zhang, SL Salzberg
BMC bioinformatics 10 (1), 1-11, 2009
312009
Transcriptomic response of Listeria monocytogenes during the transition to the long-term-survival phase
J Wen, X Deng, Z Li, EG Dudley, RC Anantheswaran, SJ Knabel, ...
Applied and environmental microbiology 77 (17), 5966-5972, 2011
242011
Emerging applications of machine learning in food safety
X Deng, S Cao, AL Horn
Annual Review of Food Science and Technology 12 (1), 513-538, 2021
212021
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