Xiangyu Deng

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Genomic Epidemiology of Salmonella enterica Serotype Enteritidis based on Population Structure of Prevalent Lineages

Rene S. Hendriksen, Martin Wiedmann, Prerak T. Desai, 2014, Emerging infectious diseases.

Comparative Analysis of Subtyping Methods against a Whole-Genome-Sequencing Standard for Salmonella enterica Serotype Enteritidis

D. Engelthaler, P. Keim, E. Trees, 2014, Journal of Clinical Microbiology.

TITLE: Comparative analysis of subtyping methods against a whole genome sequencing

P. Keim, P. Fields, Xiangyu Deng, 2014 .

Probing the pan-genome of Listeria monocytogenes: new insights into intraspecific niche expansion and genomic diversification

S. Salzberg, A. Phillippy, Xiangyu Deng, 2010, BMC Genomics.

Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens.

Henk C den Bakker, Xiangyu Deng, Xiangyu Deng, 2016, Annual review of food science and technology.

Implications of Mobile Genetic Elements for Salmonella enterica Single-Nucleotide Polymorphism Subtyping and Source Tracking Investigations

L. Baert, H. Carleton, L. Katz, 2019, Applied and Environmental Microbiology.

Prevalence, serotype diversity, biofilm-forming ability and eradication of Listeria monocytogenes isolated from diverse foods in Shanghai, China

Xiangyu Deng, C. Shi, Xianming Shi, 2017 .

Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes

Xiangyu Deng, R. Meinersmann, D. Mann, 2020, mSystems.

Bioinformatics Aspects of Foodborne Pathogen Research

Xiangyu Deng, L. Strawn, Henk Bakker, 2017 .

Molecular Source Tracking and Molecular Subtyping

Xiangyu Deng, Heather Carleton, Peter Gerner-Smidt, 2019, Food Microbiology.

Simultaneous removal of multidrug-resistant Salmonella enterica serotype typhimurium, antibiotics and antibiotic resistance genes from water by electrooxidation on a Magnéli phase Ti4O7 anode

Qingguo Huang, Xiangyu Deng, Ying Teng, 2020 .

Evaluation of real-time nanopore sequencing for Salmonella serotype prediction.

M. Wiedmann, Xiangyu Deng, Hao Luo, 2020, Food microbiology.

Zoonotic Source Attribution of Salmonella enterica Serotype

B. Bruce, P. McDermott, Shaohua Zhao, 2021 .

The food industry's current and future role in preventing microbial foodborne illness within the United States.

Xiangyu Deng, M. Doyle, M. Erickson, 2015, Clinical infectious diseases : an official publication of the Infectious Diseases Society of America.

Salmonella enterica Serovar Typhimurium Isolates from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type

Xiangyu Deng, N. Shariat, E. Dudley, 2022, Applied and environmental microbiology.

Salmonella enterica serovar Typhimurium from Wild Birds in the United States Represent 1 Distinct Lineages Defined by Bird Type 2 3 Running title : S . Typhimurium lineages from U . S . wild birds 4 5

Xiangyu Deng, N. Shariat, E. Dudley, 2021 .

A quasimetagenomics method for concerted detection and subtyping of Salmonella enterica and E. coli O157:H7 from romaine lettuce.

Xiangyu Deng, D. Mann, Shaoting Li, 2020, Food microbiology.

Pathogen Identification Using High-Density Microarrays

K. Allen, Xiangyu Deng, Wei Zhang, 2010 .

Integrative Assessment of Reduced Listeria monocytogenes Susceptibility to Benzalkonium Chloride in Produce Processing Environments

Xiangyu Deng, H. D. den Bakker, H. Oliver, 2022, Applied and environmental microbiology.

Mashtree: a rapid comparison of whole genome sequence files

Lee S. Katz, Henk C. den Bakker, Heather A. Carleton, 2019, J. Open Source Softw..

The Dissemination of Multidrug Resistant E. coli Harboring the Mobile Colistin Resistance Gene, mcr-1.1, on Transmissible Plasmids to the Mediterranean Sea.

Xiangyu Deng, I. Kassem, H. Jaafar, 2020, Journal of global antimicrobial resistance.

Salmonella Serotype Determination Utilizing High-Throughput Genome Sequencing Data

Yanlong Yin, Xiangyu Deng, Yanlong Yin, 2015, Journal of Clinical Microbiology.

Salmonella Serotyping; Comparison of the Traditional Method to a Microarray-Based Method and an in silico Platform Using Whole Genome Sequencing Data

Xiangyu Deng, C. Barretto, A. Karczmarek, 2019, Front. Microbiol..

The Mobile Colistin Resistance Gene, mcr-1.1, Is Carried on IncX4 Plasmids in Multidrug Resistant E. coli Isolated from Rainbow Trout Aquaculture

Xiangyu Deng, I. Kassem, I. Saoud, 2020, Microorganisms.

Transcriptome sequencing of Salmonella enterica serovar Enteritidis under desiccation and starvation stress in peanut oil.

Xiangyu Deng, Wei Zhang, Zengxin Li, 2012, Food microbiology.

Whole-Genome Sequencing Analysis of Salmonella Enterica Serotype Enteritidis Isolated from Poultry Sources in South Korea, 2010–2017

Xiangyu Deng, Chang-Seon Song, Dong‐Hun Lee, 2021, Pathogens.

Salmonella enterica and Escherichia coli in Wheat Flour: Detection and Serotyping by a Quasimetagenomic Approach Assisted by Magnetic Capture, Multiple-Displacement Amplification, and Real-Time Sequencing

Xiangyu Deng, H. D. den Bakker, F. Diez-Gonzalez, 2020, Applied and Environmental Microbiology.

Survival and transcriptomic response of Salmonella enterica on fresh-cut fruits.

Xiangyu Deng, Wei Zhang, M. Tortorello, 2021, International journal of food microbiology.

SeqSero2: Rapid and Improved Salmonella Serotype Determination Using Whole-Genome Sequencing Data

Jessica C. Chen, P. Fields, Xiangyu Deng, 2019, Applied and Environmental Microbiology.

Zoonotic Source Attribution of Salmonella enterica Serotype Typhimurium Using Genomic Surveillance Data, United States

Beau B. Bruce, B. Bruce, P. McDermott, 2019, Emerging infectious diseases.

Efficient oligonucleotide probe selection for pan-genomic tiling arrays

Adam M. Phillippy, Steven Salzberg, Xiangyu Deng, 2009, BMC Bioinformatics.

High-Throughput Sequencing

Lee S. Katz, Wei Zhang, Xiangyu Deng, 2014, Encyclopedia of Autism Spectrum Disorders.

Salmonella enterica serovar Typhimurium from Wild Birds in the United States Represent Distinct Lineages Defined by Bird Type

Xiangyu Deng, N. Shariat, E. Dudley, 2021, bioRxiv.

Global spread of Salmonella Enteritidis via centralized sourcing and international trade of poultry breeding stocks

Xiangyu Deng, D. Mann, Shaoting Li, 2021, Nature Communications.

Rapid detection of Salmonella in poultry environmental samples using real-time PCR coupled with immunomagnetic separation and whole genome amplification

Xiangyu Deng, D. Mann, Jinquan Wang, 2019, Poultry science.

Rapid detection of Salmonella in raw chicken breast using real-time PCR combined with immunomagnetic separation and whole genome amplification.

Xiangyu Deng, Ji-Yeon Hyeon, 2017, Food microbiology.

A Comparative Analysis of the Lyve-SET Phylogenomics Pipeline for Genomic Epidemiology of Foodborne Pathogens

Gary Van Domselaar, Lee S. Katz, Xiangyu Deng, 2017, Front. Microbiol..

Applied Genomics of Foodborne Pathogens

Xiangyu Deng, R. Hendriksen, H. Bakker, 2017 .

Salmonella Levels Associated with Skin of Turkey Parts.

Xiangyu Deng, W. Alali, M. Harrison, 2016, Journal of food protection.

Draft Genome Sequences of Multidrug-Resistant and mcr-1.1-Harboring Escherichia coli Isolated from Drinking and Well Waters Used in Syrian Refugee Camps

Xiangyu Deng, I. Kassem, D. Mann, 2021, Microbiology Resource Announcements.

Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income 1 settings and invasive disease in low-income settings

Gemma C. Langridge, S. Nair, T. Dallman, 2016 .

Transcriptomic Response of Escherichia coli O157:H7 to Oxidative Stress

S. Zaremba, Siyun Wang, Xiangyu Deng, 2009, Applied and Environmental Microbiology.

PRAP: Pan Resistome analysis pipeline

Xiujuan Zhou, Xiangyu Deng, Andrew Gehring, 2020, BMC Bioinformatics.

Emerging Applications of Machine Learning in Food Safety.

Xiangyu Deng, Shuhao Cao, A. Horn, 2021, Annual review of food science and technology.

Transcriptomic Response of Listeria monocytogenes during the Transition to the Long-Term-Survival Phase

R. Anantheswaran, Xiangyu Deng, Wei Zhang, 2011, Applied and Environmental Microbiology.

Quasimetagenomics-Based and Real-Time-Sequencing-Aided Detection and Subtyping of Salmonella enterica from Food Samples

Yi Chen, Xiangyu Deng, Shaoting Li, 2017, Applied and Environmental Microbiology.

Glove-mediated transfer of Listeria monocytogenes on fresh-cut cantaloupe.

Xiangyu Deng, Wei Zhang, L. Beuchat, 2020, Food microbiology.

Draft genome sequences and resistome analysis of multidrug-resistant and mcr-1-harboring E. coli isolated from preharvest poultry in Lebanon.

Xiangyu Deng, I. Kassem, D. Mann, 2021, Journal of Global Antimicrobial Resistance.

Emergence of the Mobile Colistin Resistance Gene mcr-1 in Multidrug-Resistant Escherichia coli Isolated from the Fecal Matter of Toddlers in a Community

Xiangyu Deng, I. Kassem, D. Mann, 2021, Antimicrobial Agents and Chemotherapy.

Letter to the Editor: First Report of the Detection of the Plasmid-Borne Colistin Resistance Gene, mcr-1.26, in Multidrug-Resistant Escherichia coli Isolated from a Domesticated Pigeon.

Xiangyu Deng, I. Kassem, D. Mann, 2022, Microbial drug resistance.

Comparison between qPCR, VIDAS immunoassays, and agar streaking for the detection of Listeria monocytogenes from food and environmental surfaces containing and not containing Listeria innocua.

Han Yang, T. Hammack, Yi Chen, 2022, Journal of food protection.

Genome Sequence of Salmonella enterica Serotype Tennessee Strain CDC07-0191, Implicated in the 2006-2007 Multistate Food-Borne Outbreak Linked to Peanut Butter in the United States

W. F. Fricke, D. MacCannell, P. Fields, 2013, Genome Announcements.

Salmonella survival during thermal dehydration of fresh garlic and storage of dehydrated garlic products.

Xiangyu Deng, Shaokang Zhang, Yan Qi, 2017, International journal of food microbiology.

Evaluation of nanopore sequencing technology to identify Salmonella enterica Choleraesuis var. Kunzendorf and Orion var. 15+, 34.

Xiangyu Deng, Hao Luo, R. Baker, 2021, International journal of food microbiology.

GC Content-Associated Sequencing Bias Caused by Library Preparation Method May Infrequently Affect Salmonella Serotype Prediction Using SeqSero2

Xiangyu Deng, Shaoting Li, Shaokang Zhang, 2020, Applied and Environmental Microbiology.

Impact of library preparation-induced low GC sequencing bias on Salmonella serotype prediction using SeqSero2

Xiangyu Deng, Shaoting Li, Shaokang Zhang, 2020, bioRxiv.

Evaluation of multiplex nanopore sequencing for Salmonella serotype prediction and antimicrobial resistance gene and virulence gene detection

M. Wiedmann, Xiangyu Deng, Hao Luo, 2023, Frontiers in Microbiology.

Distinct Salmonella Enteritidis lineages associated with enterocolitis in high-income settings and invasive disease in low-income settings

S. Nair, T. Dallman, G. Dougan, 2016, Nature Genetics.

Running Title : Emergence of distinct lineages of S . Enteritidis 66

Langridge, S. Nair, T. Dallman, 2016 .

Evaluation of Nanopore sequencing technology to differentiate Salmonella serotypes and serotype variants with the same or closely related antigenic formulae

Xiangyu Deng, Hao Luo, R. Baker, 2020, bioRxiv.

Proteomic analysis of Aspergillus niger 3.316 under heat stress

Xiangyu Deng, B. Du, Jun Li, 2020, MicrobiologyOpen.

Evaluation of Salmonella Serotype Prediction With Multiplex Nanopore Sequencing

M. Wiedmann, Xiangyu Deng, Hao Luo, 2021, Frontiers in Microbiology.

Subtyping Evaluation of Salmonella Enteritidis Using Single Nucleotide Polymorphism and Core Genome Multilocus Sequence Typing with Nanopore Reads

Xiangyu Deng, D. Mann, Shaoting Li, 2022, Applied and environmental microbiology.

TITLE: Comparative analysis of subtyping methods against a whole genome sequencing

P. Keim, P. Fields, Xiangyu Deng, 2014 .

First Report of the Mobile Colistin Resistance Gene, mcr-1.26, in Multidrug-Resistant Escherichia coli Isolated from Retail Chicken Meat.

T. Naas, M. Esseili, Xiangyu Deng, 2023, Journal of global antimicrobial resistance.

Draft Genome Sequences of Antibiotic-Resistant Serratia sp. Strains Isolated from Raw Sewage and Sediment Sludge in Georgia, USA

M. Esseili, Xiangyu Deng, I. Kassem, 2022, Microbiology resource announcements.

Genomic characterization of Salmonella isolated from retail chicken and humans with diarrhea in Qingdao, China

Xiangyu Deng, Shaoting Li, Wei Wang, 2023, Frontiers in microbiology.

Comparative genomics unveils extensive genomic variation between populations of Listeria species in natural and food-associated environments

M. Wiedmann, Xiangyu Deng, D. Weller, 2023, ISME communications.

Distributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century

Xiangyu Deng, Heng Li, Zhemin Zhou, 2023, Nature communications.