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                    U.S. DEPARTMENT OF AGRICULTURE
 Characterization and Interventions for Foodborne Pathogens: Wyndmoor, PA
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ARS Home Northeast Area Wyndmoor, Pennsylvania Eastern Regional Research Center Characterization and Interventions for Foodborne Pathogens People & Locations







Yiping  He
                        Characterization and Interventions for Foodborne Pathogens

                        




                        
                        Research Molecular Biologist
                        Phone: (215) 233-6422
                        
                        
                        Fax: (215) 233-6581(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            ProjectsDetection, Quantification and Characterization Technologies for Foodborne Pathogens
                                                    In-House Appropriated
                                                                    (D)Accession Number: 440529**Publications**
                                                (Clicking on the reprint icon
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                                                    will take you to the publication reprint.)Whole genome sequences, de novo assembly, and annotation of antibiotic resistant Campylobacter jejuni strains S27, S33, and S36 newly isolated from chicken meat
                                                        

- (Peer Reviewed Journal)He, Y., Kanrar, S., Reed, S., Lee, J., Capobianco Jr, J.A. 2024. Whole genome sequences, de novo assembly, and annotation of Campylobacter jejuni strains S27, S33, and S36 newly isolated from chicken meat. Microorganisms. 12(1):159. https://doi.org/10.3390/microorganisms12010159.Detection and isolation of Campylobacter spp. from raw meat

- (Peer Reviewed Journal)High-yield and high-throuhput delamination of multilayer MXene via high-pressure homogenization
                                                        

- (Peer Reviewed Journal)Inman, C.A., Shevchuk, K., Anayee, M., Hammill, B., Lee, J., Saraf, M., Shuck, C., Armstrong, C.M., He, Y., Jin, Z.T., Shekhirev, M., Capobianco Jr, J.A., Gogotsi1, Y. 2023. High-yield and high-throuhput delamination of multilayer MXene via high-pressure homogenization. Chemical Engineering Journal. 475:146089. https://doi.org/10.1016/j.cej.2023.146089.Complete genome sequence of Campylobacter jejuni BSD5, a multidrug-resistant isolate from a poultry processing facility in the United States
                                                        

- (Peer Reviewed Journal)He, Y., Reed, S.A., Gunther, N.W., Armstrong, C.M., Capobianco Jr, J.A. 2023. Complete genome sequence of Campylobacter jejuni BSD5, a multidrug-resistant isolate from a poultry processing facility in the United States. Microbiology Resource Announcements. 12(6). https://doi.org/10.1128/mra.00284-23.Use of a commercial tissue dissociation system to detect Salmonella-contaminated poultry products
                                                        

- (Peer Reviewed Journal)Armstrong, C.M., He, Y., Chen, C., Counihan, K.L., Lee, J., Reed, S.A., Capobianco Jr, J.A. 2023. Use of a commercial tissue dissociation system to detect Salmonella-contaminated poultry products. Analytical and Bioanalytical Chemistry. https://doi.org/10.1007/s00216-023-04668-w.Enhancing detection of Listeria monocytogenes in food products using an enzyme
                                                        

- (Peer Reviewed Journal)Felton, S., Armstrong, C.M., Chen, C., He, Y., Lee, J., Reed, S.A., Akula, N., Walker, S., Berger, B., Capobianco Jr, J.A. 2022. Enhancing detection of Listeria monocytogenes in food products using an enzyme. Food Control. https://doi.org/10.1016/j.foodcont.2022.109445.Complete genome sequences of multidrug-resistant Campylobacter coli strains YH501, YH503, and YH504 from retail chicken
                                                        

- (Peer Reviewed Journal)He, Y., Reed, S.A., Yan, X., Zhang, D., Strobaugh Jr, T.P., Capobianco Jr, J.A., Gehring, A.G. 2022. Complete genome sequences of multidrug-resistant Campylobacter coli strains YH501, YH503, and YH504 from retail chicken. Microbiology Resource Announcements. Available online: https://www.researchgate.net/journal/Microbiology-Resource-Announcements-2576-098X. https://doi.org/10.1128%2Fmra.00237-22.Antimicrobial effect of zinc oxide nanoparticles on Campylobacter jejuni and Salmonella enterica serovar Enteritidis
                                                        

- (Peer Reviewed Journal)He, Y., Capobianco Jr, J.A., Irwin, P., Reed, S.A., Lee, J. 2022. Antimicrobial effect of zinc oxide nanoparticles on Campylobacter jejuni and Salmonella enterica serovar Enteritidis. Journal of Food Safety. https://doi/10.1111/jfs.12979.Comparative transcriptome analysis reveals differentially expressed genes related to antimicrobial properties of lysostaphin in Staphylococcus aureus
                                                        

- (Peer Reviewed Journal)Yan, X., Xie, Y., Li, C.C., Donovan, D.M., Gehring, A.G., Irwin, P.L., He, Y. 2022. Comparative transcriptome analysis reveals differentially expressed genes related to antimicrobial properties of lysostaphin in Staphylococcus aureus. Applied Microbiology and Biotechnology. 11(2):125. https://doi.org/10.3390/antibiotics11020125.DsrA modulates central carbon metabolism and redox balance by directly repressing pflB expression in Salmonella Typhimurium
                                                        

- (Peer Reviewed Journal)Dong, R., Liang, Y., He, S., Cui, Y., Shi, C., He, Y., Shi, X. 2022. DsrA modulates central carbon metabolism and redox balance by directly repressing pflB expression in Salmonella Typhimurium. Microbiology Spectrum. 10(1):1. Article e01522-21. https://doi.org/10.1128%2Fspectrum.01522-21.Comparative methylome analysis of Campylobacter jejuni strain YH002 reveals a putative novel motif and diverse epigenetic regulations of virulence genes
                                                        

- (Peer Reviewed Journal)Ghatak, S., Armstrong, C.M., Reed, S.A., He, Y. 2020. Comparative methylome analysis of Campylobacter jejuni strain YH002 reveals a putative novel motif and diverse epigenetic regulations of virulence genes. Frontiers in Microbiology. https://doi.org/10.3389/fmicb.2020.610395.Bacterial cell recovery after hollow fiber microfiltration sample concentration and washing: most probable bacterial composition in frozen vegetables
                                                        

- (Peer Reviewed Journal)Irwin, P., He, Y., Nguyen, L.T., Gehring, M., Gehring, A.G., Chen, C., Capobianco Jr, J.A. 2020. Bacterial cell recovery after hollow fiber microfiltration sample concentration and washing: Most probable bacterial composition in frozen vegetables. LWT - Food Science and Technology. 140:110. https://doi.org/10.1016/j.lwt.2020.110640.DsrA stimulates the oxidative stress resistance in Salmonella enterica serovar Typhimurium
                                                        

- (Peer Reviewed Journal)Dong, R., Qin, X., He, S., Zhou, X., Cui, Y., Shi, C., He, Y., Shi, X. 2020. DsrA stimulates the oxidative stress resistance in Salmonella enterica serovar Typhimurium. Food Control. Available online:science/journal/09567135. https://doi.org/10.1016/j.foodcont.2020.107571.Comparative analysis of genomic and functional characteristics of a multidrug resistant Campylobacter jejuni strain YH002 isolated from retail beef liver
                                                        

- (Peer Reviewed Journal)Ghatak, S., He, Y., Reed, S.A., Irwin, P.L. 2020. Comparative analysis of genomic and functional characteristics of a multidrug resistant Campylobacter jejuni strain YH002 isolated from retail beef liver. Foodborne Pathogens and Disease. https://doi.org/10.1089/fpd.2019.2770.Complete genome sequence and annotation of Campylobacter jejuni YH003 isolated from retail chicken
                                                        

- (Peer Reviewed Journal)He, Y., Reed, S.A., Strobaugh Jr, T.P. 2020. Complete genome sequence and annotation of Campylobacter jejuni YH003 isolated from retail chicken. Microbiology Resource Announcements. https://doi.org/10.1128/MRA.01307-19.Impacts of clarification techniques on sample constituents and pathogen retention
                                                        

- (Peer Reviewed Journal)Armstrong, C.M., Gehring, A.G., Paoli, G., Chen, C., He, Y., Capobianco Jr, J.A. 2019. Impacts of clarification techniques on sample constituents and pathogen retention. Foods. https://doi.org/10.3390/foods8120636.Pulsed-field gel electrophoresis typing of Staphylococcus aureus strains
                                                        

- (Book / Chapter)He, Y., Reed, S.A. 2019. Pulsed-field gel electrophoresis typing of Staphylococcus aureus strains. In: Walker, J.M., editor. Methods in Molecular Biology. New York, NY: Springer. 2069:78-88. https://doi.org/10.1007/978-1-4939-9849-4_5.A comprehensive multilocus sequence typing scheme for identification and genotyping of Staphylococcus strains
                                                        

- (Peer Reviewed Journal)Song, M., Li, Q., He, Y., Feng, Z., Lan, L., Fan, Y., Liu, H., Chen, D., Yang, M. 2019. A comprehensive multilocus sequence typing scheme for identification and genotyping of Staphylococcus strains. Foodborne Pathogens and Disease. 16(5):331-338. https://doi.org/10.1089/fpd.2018.2565.Whole genome sequencing and annotation of Staphylococcus aureus strain SJTUF_J27 isolated from seaweed
                                                        

- (Peer Reviewed Journal)Xie, Y., He, Y., Ghatak, S., Irwin, P.L., Yan, X., Strobaugh Jr, T.P., Gehring, A.G. 2018. Whole genome sequencing and annotation of Staphylococcus aureus strain SJTUF_J27 isolated from seaweed. Data in Brief. 20:894-898. https://doi.org/10.1016/j.dib.2018.08.084.Rapid and potentially portable detection and quantification technologies for foodborne pathogens

- (Proceedings)Gehring, A.G., Armstrong, C.M., Capobianco Jr, J.A., He, Y., Paoli, G., Fratamico, P.M. 2017. Rapid and potentially portable detection and quantification technologies for foodborne pathogens . United States-Japan Cooperative Program in Natural Resources (UJNR). p.12.Genetic basis for the resistance of Staphylococcus aureus to peptidoglycan hydrolase by comparative transcriptome and whole genome sequence analysis

- (Abstract Only)Whole genome sequencing and analysis of Campylobacter coli YH502 from retail chicken reveals a plasmid-borne type VI secretion system
                                                        

- (Peer Reviewed Journal)Ghatak, S., He, Y., Reed, S.A., Strobaugh Jr, T.P., Irwin, P.L. 2017. Whole genome sequencing and analysis of Campylobacter coli YH502 from retail chicken reveals a plasmid-borne type VI secretion system. Genomics Data. 11:128-131.Evaluation of ELISA tests specific for Shiga toxin 1 and 2 in food and water samples
                                                        

- (Peer Reviewed Journal)Gehring, A.G., Fratamico, P.M., Lee, J., Ruth, L., He, X., He, Y., Paoli, G., Stanker, L.H., Rubio, F.M. 2017. Evaluation of ELISA tests specific for Shiga toxin 1 and 2 in food and water samples. Food Control. 77:145-149.Study on the mechanism of antibacterial action of magnesium oxide nanoparticles against foodborne pathogens
                                                        

- (Peer Reviewed Journal)He, Y., Ingudam, S., Reed, S.A., Gehring, A.G., Strobaugh Jr, T.P., Irwin, P.L. 2016. Study on the mechanism of antibacterial action of magnesium oxide nanoparticles against foodborne pathogens. Journal of Nanobiotechnology (Biomed Central Open Access). DOI:10.1186/s12951-016-0202-0.Antimicrobial properties and mechanism of magnesium oxide nanoparticles on Campylobacter, E. coli O157:H7, and Salmonella

- (Abstract Only)Reed, S.A., Ingudum, S., Irwin, P.L., He, Y. 2015. Antimicrobial properties and mechanism of magnesium oxide nanoparticles on Campylobacter, E. coli O157:H7, and Salmonella. Meeting Abstract. meeting abstract.An improved method to simultaneously detect Salmonella enteritidis, Escherichia coli O157 and Listeria monocytogenes in ground black pepper using multiplex real-time PCR

- (Abstract Only)Complete genome sequence of Campylobacter jejuni YH001 from beef liver which contains a novel plasmid

- (Peer Reviewed Journal)He, Y., Yan, X., Reed, S.A., Xie, Y., Chen, C., Irwin, P.L. 2015. Complete genome sequence of Campylobacter jejuni YH001 from beef liver which contains a novel plasmid. Genome Announcements. 3(1):e01492-14.Near-quantitative extraction of genomic DNA from various food-borne eubacteria

- (Peer Reviewed Journal)Irwin, P.L., Nguyen, L.T., He, Y., Paoli, G., Gehring, A.G., Chen, C. 2014. Near-quantitative extraction of genomic DNA from various food-borne eubacteria. BMC Microbiology. DOI: 10.1186/s12866-014-0326-z.Rapid identification and classification of Campylobacter spp. using laser optical scattering technology
                                                        

- (Peer Reviewed Journal)He, Y., Reed, S.A., Bhunia, A.K., Gehring, A.G., Nguyen, L.T., Irwin, P.L. 2015. Rapid identification and classification of Campylobacter spp. using laser optical scattering technology. Food Microbiology. 47:28-35.Variability in DNA polymerase efficiency: effects of random error, DNA extraction method, and isolate type

- (Peer Reviewed Journal)Irwin, P.L., Nguyen, L.T., Chen, C., He, Y. 2014. Variability in DNA polymerase efficiency: effects of random error, DNA extraction method, and isolate type. JSM Mathematics & Statistics. 1(1):1003.A high-throughput, precipitating colorimetric sandwich ELISA microarray for shiga toxins
                                                        

- (Peer Reviewed Journal)Gehring, A.G., He, X., Fratamico, P.M., Lee, J., Bagi, L.K., Brewster, J.D., Paoli, G., He, Y., Xie, Y., Skinner, C.B., Barnett, C., Harris, D. 2014. A high-throughput, precipitating colorimetric sandwich ELISA microarray for shiga toxins. Toxins. 6:1855-1872.A robust multiplex real-time PCR method for simultaneous detection of Salmonella spp., Escherichia coli O157 and Listeria monocytogenes in fresh fruits and vegetables

- (Abstract Only)Simultaneous detection of Salmonella spp., Escherichia coli O157 and Listeria monocytogenes in a variety of cheeses and spinach using a multiplex real-time PCR method

- (Abstract Only)Pulsed-field gel electrophoresis typing of Staphylococcus aureus isolates

- (Book / Chapter)He, Y., Xie, Y., Reed, S.A. 2013. Pulsed-field gel electrophoresis typing of Staphylococcus aureus isolates. In: Walker, John M. Methods in Molecular Biology. New York, NY:Humana Press. p. 103-111.High-throughput antibody microarray for bacteria and toxins

- (Abstract Only)Optimization and application of a custom microarray for the detection and genotyping of E. coli O157:H7 in fresh meat samples
                                                        

- (Peer Reviewed Journal)Suo, B., He, Y., Irwin, P.L., Gehring, A.G. 2013. Optimization and application of a custom microarray for the detection and genotyping of E. coli O157:H7 in fresh meat samples. Journal of Food Analytical Methods. 6:1477-1484.Non-stochastic sampling error in quantal analyses for Campylobacter species on poultry products

- (Peer Reviewed Journal)Irwin, P.L., Reed, S.A., Brewster, J.D., Nguyen, L.T., He, Y. 2013. Non-stochastic sampling error in quantal analyses for Campylobacter species on poultry products. Analytical and Bioanalytical Chemistry. 405(7):2353-2369.A multiplex real-time PCR method for simultaneous detection of Salmonella spp., Escherichia coli O157 and Listeria monocytogenes in soft cheese

- (Abstract Only)Rapid identification and classification of Staphylococcus aureus by attenuated total reflectance fourier transform infrared spectroscopy

- (Peer Reviewed Journal)Xie, Y., Xu, S., Hu, Y., Chen, W., He, Y., Shi, X. 2012. Rapid identification and classification of Staphylococcus aureus by attenuated total reflectance fourier transform infrared spectroscopy. Journal of Food Safety. 32(2):176-183.Genotypes and enterotoxin gene profiles of Staphylococcus aureus clinical isolates from China

- (Peer Reviewed Journal)Xie, Y., He, Y., Gehring, A.G., Hu, Y., Tu, S., Shi, X. 2011. Genotypes and enterotoxin gene profiles of Staphylococcus aureus clinical isolates from China. PLoS One. DOI: 10.1371/journal.pone.0028276.Antibacterial activities of magnesium oxide (MgO) nanoparticles against foodborne pathogens

- (Peer Reviewed Journal)Jin, Z.T., He, Y. 2012. Antibacterial activities of magnesium oxide (MgO) nanoparticles against foodborne pathogens. Journal of Nanoparticle Research. 13:6877-6885.Antimicrobial activity of spherical silver nanoparticles: evidence for induction of a prolonged bacterial lag phase

- (Abstract Only)Effects of polyphosphate additives on the pH of processed chicken exudates and the survival of Campylobacter

- (Peer Reviewed Journal)Gunther, N.W., He, Y., Fratamico, P.M. 2011. Effects of polyphosphate additives on the pH of processed chicken exudates and the survival of Campylobacter. Journal of Food Protection. 74:1735-1740.Antibacterial activity and mechanism of action of zinc oxide nanoparticles against Campylobacter jejuni

- (Peer Reviewed Journal)Xie, Y., He, Y., Irwin, P.L., Jin, Z.T., Shi, X. 2011. Antibacterial activity and mechanism of action of zinc oxide nanoparticles against Campylobacter jejuni. Applied and Environmental Microbiology. 77:2325-2331.Antimicrobial activity of spherical silver nanoparticles prepared using a biocompatible macromolecular capping agent: evidence for induction of a greatly prolonged bacterial lag phase

- (Peer Reviewed Journal)Irwin, P.L., Martin, J., Nguyen, L.T., He, Y., Gehring, A.G., Chen, C. 2010. Antimicrobial activity of spherical silver nanoparticles prepared using a biocompatible macromolecular capping agent: evidence for induction of a greatly prolonged bacterial lag phase. Journal of Nanobiotechnology (Biomed Central Open Access). 34:1-12.Simultaneous detection of Escherichia coli O157:H7 and Salmonella Typhimurium:  The use of magnetic beads conjugated with multiple capture antibodies

- (Peer Reviewed Journal)Tu, S., Reed, S.A., Gehring, A.G., He, Y. 2010. Simultaneous detection of Escherichia coli O157:H7 and Salmonella Typhimurium:  The use of magnetic beads conjugated with multiple capture antibodies. Journal of Food Analytical Methods. DOI 10.1007/s12161-010-9175-z.Simultaneous detection and differentiation of Campylobacter jejuni, C. coli, and C. lari in chickens by multiplex real-time PCR

- (Peer Reviewed Journal)He, Y., Yao, X., Gunther, N.W., Tu, S., Shi, X. 2010. Simultaneous detection and differentiation of Campylobacter jejuni, C. coli, and C. lari in chickens by multiplex real-time PCR. Journal of Food Analytical Methods. 137:168-174.A multiplex real-time PCR for simultaneous detection of Salmonella spp., E. coli O157 and L. monocytogenes in meat products

- (Peer Reviewed Journal)Suo, B., He, Y., Tu, S., Shi, X. 2010. A multiplex real-time PCR for simultaneous detection of Salmonella spp., E. coli O157 and L. monocytogenes in meat products. Foodborne Pathogens and Disease. 7(6):619-628.QUANTIFICATIVE ANALYSIS OF VIABLE, STRESSED AND DEAD CELLS OF CAMPYLOBACTER JEJUNI STRAIN 81-176

- (Peer Reviewed Journal)He, Y., Chen, C. 2010. QUANTIFICATIVE ANALYSIS OF VIABLE, STRESSED AND DEAD CELLS OF CAMPYLOBACTER JEJUNI STRAIN 81-176. Food Microbiology. 27:439-446.Development of an oligonucleotide-based microarray to detect multiple foodborne pathogens

- (Peer Reviewed Journal)Suo, B., He, Y., Paoli, G., Gehring, A.G., Tu, S., Shi, X. 2009. Development of an oligonucleotide-based microarray to detect multiple foodborne pathogens. Molecular and Cellular Probes. 24:77-86.A microarray approach for simultaneous detection of multiple pathogens in food

- (Abstract Only)Development of an oligonucleotide-based microarray to detect multiple foodborne pathogens

- (Abstract Only)Suo, B., He, Y., Paoli, G., Gehring, A.G., Tu, S. 2009. Development of an oligonucleotide-based microarray to detect multiple foodborne pathogens. Meeting Abstract. 1:100.Production of Shiga-like toxins by Escherichia coli O157:H7: Effects of other bacteria and analogues of quorum sensing molecules

- (Peer Reviewed Journal)Tu, S., Uknalis, J., Paoli, G., He, Y., Gehring, A.G. 2009. Production of Shiga-like toxins by Escherichia coli O157:H7: Effects of other bacteria and analogues of quorum sensing molecules. Journal of Rapid Methods and Automation in Microbiology.17(4):420-437.Capture of E. coli O157:H7 using immunomagnetic beads of different size and  antibody conjugating chemistry

- (Peer Reviewed Journal)Tu, S., Reed, S.A., Gehring, A.G., He, Y., Paoli, G. 2009. Capture of E. coli O157:H7 using immunomagnetic beads of different size and  antibody conjugating chemistry. Sensors. 9:717-730.Detection of Salmonella Enteriditis from Egg Components Using Different Immunomagnetic Beads and Time-resolved Fluorescence

- (Peer Reviewed Journal)Tu, S., Reed, S.A., Gehring, A.G., He, Y. 2008. Detection of Salmonella Enteriditis from Egg Components Using Different Immunomagnetic Beads and Time-resolved Fluorescence. Journal of Food Analytical Methods. Available:http://www.springerlink.com/content/68381p3740355j10/Detection of Salmonella Enteriditis from egg components using different immunomagnetic beads and time–resolved fluorescence

- (Abstract Only)Tu, S., Reed, S.A., He, Y., Gehring, A.G. 2008. Detection of Salmonella Enteriditis from egg components using different immunomagnetic beads and time–resolved fluorescence. [Abstract]p.2-42.Analysis of AI-2/LuxS dependent transcriptional profiling in Campylobacter jejuni 81-176

- (Peer Reviewed Journal)He, Y., Frye, J.G., Strobaugh Jr, T.P., Chen, C. 2008. Ai-2/luxs dependent transcriptional profiling in campylobacter jejuni 81-176. Foodborne Pathogens and Disease. 5(4):399-415.Application of horse-radish peroxidase linked chemiluminescence to determine the production mechanism of Shiga-like toxins by E. coli O157:H7

- (Proceedings)Tu, S., Uknalis, J., Gehring, A.G., He, Y. 2007. Application of horse-radish peroxidase linked chemiluminescence to determine the production mechanism of Shiga-like toxins by E. coli O157:H7. Proceedings of SPIE.#6761Application of horse-radish peroxidase linked chemiluminescence to determine the production mechanism of Shiga-like toxins by E. coli O157:H7

- (Proceedings)Tu, S., Uknalis, J., Gehring, A.G., He, Y. 2007. Application of horse-radish peroxidase linked chemiluminescence to determine the production mechanism of Shiga-like toxins by E. coli O157:H7. Proceedings of SPIE.6761:67610C-1-67610C-9.Microarray Analysis of Quorum-Sensing Regulated Gene Expression in Campylobacter jejuni

- (Abstract Only)He, Y., Frye, J.G., Chen, C. 2007. Microarray Analysis of Quorum-Sensing Regulated Gene Expression in Campylobacter jejuni. Meeting Abstract.Comparison of methods for detecting live, stressed, and dead cells of Campylobacter jejuni

- (Abstract Only)Chen, C., He, Y. 2007. Comparison of methods for detecting live, stressed, and dead cells of Campylobacter jejuni. Abstract. International Association for Food Protection. P3-50.Detection of live/dead Campylobacter jejuni cells by real-time PCR

- (Abstract Only)Chen, C., He, Y. 2006. Detection of live/dead Campylobacter jejuni cells by real-time PCR. Abstract. p.3-1.AI-2 Quorum Sensing in Campylobacter jejuni

- (Abstract Only)He, Y., Chen, C. 2006. Ai-2 quorum sensing in campylobacter jejuni. Meeting Abstract.


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