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United States Department of Agriculture

Agricultural Research Service

Related Topics

Xianghe Yan
Molecular Characterization of Foodborne Pathogens
Computational Biologist

Phone: (215) 233-6732
Fax: (215) 233-6581
Room 1026

600 E MERMAID LN
WYNDMOOR, PA, 19038-8598

Projects
GENOMIC AND PROTEOMIC ANALYSIS OF FOODBORNE PATHOGENS
Appropriated (D)
  Accession Number: 420999

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Molecular serotyping of Escherichia coli: A verification and reclassification - (Abstract Only)
Yan, X., Fratamico, P.M., Tebbs, R., O'Connell, C., Baranzoni, G., Allred, A., Swimley, M., Debroy, C. 2014. Molecular serotyping of Escherichia coli: A verification and reclassification. Meeting Abstract. MA.
Complete genome sequence and comparison of two Shiga toxin-producing Escherichia coli O104 isolates - (Abstract Only)
Yan, X., Fratamico, P.M., Bono, J.L., Baranzoni, G., Tebbs, R., O'Connell, C. 2014. Complete genome sequence and comparison of two Shiga toxin-producing Escherichia coli O104 isolates. Meeting Abstract. MA.
DNA sequence and analysis of the O-antigen gene clusters of Escherichia coli serogroups O62, O68, O131, O140, O142, and O163 and serogroup-specific PCR assays - (Abstract Only)
Liu, Y., Fratamico, P.M., Debroy, C., Yan, X., Needleman, D.S., Li, R.W., Wang, W., Losada, L., Brinkac, L., Rodune, D., Toro, M., Meng, J. 2014. DNA sequence and analysis of the O-antigen gene clusters of Escherichia coli serogroups O62, O68, O131, O140, O142, and O163 and serogroup-specific PCR assays. Meeting Abstract. March 22-25, 2014.
Phenotypic and genotypic characterization of biofilm forming capability in non-O157 Shiga toxin-producing Escherichia coli strains - (Peer Reviewed Journal)
Chen, C., Hofmann, C.S., Cottrell, B.J., Strobaugh Jr, T.P., Paoli, G., Nguyen, L.T., Yan, X., Uhlich, G.A. 2013. Phenotypic and genotypic characterization of biofilm forming capability in non-O157 Shiga toxin-producing Escherichia coli strains. PLoS One. 8(12):e84863.
A simulated metagenomic approach for bacterial serotyping using shotgun genome sequences coupled with O-Antigen gene cluster analysis - (Abstract Only)
Yan, X., Chen, C., Hu, J., Fratamico, P.M. 2013. A simulated metagenomic approach for bacterial serotyping using shotgun genome sequences coupled with O-Antigen gene cluster analysis. Meeting Abstract. MA.
Cronobacter (Enterobacter) sakazakii - (Book / Chapter)
Yan, X., Gurtler, J. 2014. Cronobacter (Enterobacter) sakazakii. Encyclopedia of Food Microbiology. vol 1. In: Batt, C.A., Tortorello, M.L. (Eds.), Elsevier Ltd, Academic Press. pp. 528-532.
Phylogenetic identification of bacterial MazF toxin protein motifs among probiotic strains and foodborne pathogens and potential implications of engineered probiotic intervention in food Reprint Icon - (Peer Reviewed Journal)
Yan, X., Gurtler, J., Fratamico, P.M., Hu, J., Juneja, V.K. 2012. Phylogenetic identification of bacterial MazF toxin protein motifs among probiotic strains and foodborne pathogens and potential implications of engineered probiotic intervention in food. BioMed Central(BMC) Cell & Bioscience. 2:39.
DNA sequence and analysis of a 90.1 kb virulence plasmid in shiga toxin-producing Escherichia coli (STEC) O145:NM 83-75 - (Peer Reviewed Journal)
Yan, X., Fratamico, P.M., Needleman, D.S., Bayles, D.O. 2012. DNA sequence and analysis of a 90.1 kb virulence plasmid in shiga toxin-producing Escherichia coli (STEC) O145:NM 83-75. Plasmid Journal. 68:25-32.
Bs-Knn: An Effective Algorithm for Predicting Protein Subchloroplast Localization - (Peer Reviewed Journal)
Hu, J., Yan, X. 2012. BS-KNN: an effective algorithm for predicting protein subchloroplast localization. Evolutionary Bioinformatics. 8:79-87.
Omics, microbial modeling, and food safety information infrastructure: a food safety perspective - (Book / Chapter)
Yan, X., Juneja, V.K., Fratamico, P.M., Smith, J.L. 2012. Omics, microbial modeling, and food safety information infrastructure: a food safety perspective. In: Yan, X., Juneja, V., Fratamico, P., Smith, J., editors. Omics Technologies and Microbial Modeling in Food-borne Pathogens. Lancaster, PA: DESTech Publication. p. 3-16.
Rfid Technologies for Imported Foods Inspection - (Book / Chapter)
Bai, L., Yan, X., Biswas, S., Fratamico, P.M. 2012. RFID technologies for imported foods inspection. In: Yan, X., Juneja, V., Fratamico, P., Smith, J., editors. Omics Technologies and Microbial Modeling in Food-borne Pathogens. Lancaster, PA: DEStech Publishers. p. 603-614.
Thermal inactivation of foodborne pathogens and the USDA pathogen modeling program - (Peer Reviewed Journal)
Juneja, V.K., Huang, L., Yan, X. 2011. Thermal inactivation of foodborne pathogens and the USDA pathogen modeling program. Journal of Thermal Analysis. 106(1):191-198.
Sensitive detection of multiple hepatitis A virus genotypes with a single polony-based assay - (Abstract Only) - (04-Mar-11)
A comparative genomics approach for biomarker candidate discovery among shiga toxin-producing Escherichia coli - (Abstract Only) - (01-Mar-11)
Comprehensive approaches for molecular biomarker discovery for the detection and identification of Cronobacter spp. (Enterobacter sakazakii), Salmonella, and other foodborne pathogens Reprint Icon - (Peer Reviewed Journal)
Yan, X., Gurtler, J., Fratamico, P.M., Hu, J., Gunther, N.W., Juneja, V.K., Huang, L. 2011. Comprehensive approaches for molecular biomarker discovery for the detection and identification of Cronobacter spp. (Enterobacter sakazakii), Salmonella, and other foodborne pathogens. Applied and Environmental Microbiology. 77:1833-1843.
Detection by multiplex real-time PCR assays and isolation of Shiga toxin-producing Escherichia coli serogroups O26, O45, O103, O111, O121, and O145 in ground beef - (Peer Reviewed Journal)
Fratamico, P.M., Bagi, L.K., Cray Jr, W.C., Narang, N., Medina, M.B., Liu, Y. 2011. Detection by multiplex real-time PCR assays and isolation of Shiga toxin-producing Escherichia coli serogroups O26, O45, O103, O111, O121, and O145 in ground beef. Foodborne Pathogens and Disease. DOI: 10.1089=fpd.2010.0773.
Eavesdropping by bacteria: the role of SdiA in Escherichia coli and Salmonella enterica serovar Typhimurium quorum sensing - (Review Article)
Smith, J.L., Fratamico, P.M., Yan, X. 2011. Eavesdropping by bacteria: the role of SdiA in Escherichia coli and Salmonella enterica serovar Typhimurium quorum sensing. Foodborne Pathogens and Disease. 8:169-178.
Differential gene expression of Escherichia coli O157:H7 in ground beef extract compared to tryptic soy broth Reprint Icon - (Peer Reviewed Journal)
Fratamico, P.M., Yan, X., Li, Y. 2011. Differential gene expression of Escherichia coli O157:H7 in ground beef extract compared to tryptic soy broth. Journal of Food Science. 76:79-87.
The complete DNA sequence and analysis of the virulence plasmid and of five additional plasmids carried by Shiga toxin-producing Escherichia coli O26:H11 strain H30 Reprint Icon - (Peer Reviewed Journal)
Fratamico, P.M., Yan, X., Caprioli, A., Esposito, G., Needleman, D.S., Pepe, T., Tozzoli, R., Cortesi, M.L., Morabito, S. 2011. The complete DNA sequence and analysis of the virulence plasmid and of five additional plasmids carried by Shiga toxin-producing Escherichia coli O26:H11 strain H30. Journal of Medical Microbiology. 301:192-203.
Gyr B versus 16s rDNA sequencing for the identification of Campylobacter jejuni, Campylobacter coli, and Campylobacter lari - (Peer Reviewed Journal)
Gunther, N.W., Almond, J.T., Yan, X., Needleman, D.S. 2011. Gyr B versus 16s rDNA sequencing for the identification of Campylobacter jejuni, Campylobacter coli, and Campylobacter lari. Journal of Nucleic Acids Investigation. DOI: 101089/fpd.2010.0773.
Sustainable wireless sensing technologies for imported foods inspection - (Proceedings) - (08-Apr-10)
From ontology selection and semantic web to the integrated information system of food-borne diseases and food safety - (Peer Reviewed Journal)
Yan, X., Peng, Y., Meng, J., Rusante, J., Fratamico, P.M., Huang, L., Juneja, V.K., Needleman, D.S. 2011. From ontology selection and semantic web to the integrated information system of food-borne diseases and food safety. Software Tools and Algorithms for Biological Systems. 26-34.
Improved efficiency in amplification of Escherichia coli o-antigen gene clusters using genome-wide sequence comparison - (Abstract Only) - (01-Mar-10)
Escherichia coli serogroup O2 and O28ac O-antigen gene cluster sequences and detection of pathogenic E. coli O2 and O28ac by PCR - (Peer Reviewed Journal)
Fratamico, P.M., Yan, X., Debroy, C., Bryne, B., Monaghan, A., Liu, Y., Bolton, D., Fanning, S. 2010. Escherichia coli serogroup O2 and O28ac O-antigen gene cluster sequences and detection of pathogenic E. coli O2 and O28ac by PCR. Canadian Journal of Microbiology. 56:308-316.
Microbial profiling, neural network and semantic web: an integrated information system for human pathogen risk management, prevention and surveillance in food safety - (Proceedings)
Yan, X., Peng, Y., Meng, J., Ruzante, J., Fratamico, P.M., Huang, L., Juneja, V.K. 2009. Microbial profiling, neural network and semantic web: an integrated information system for human pathogen risk management, prevention and surveillance in food safety. International Conference on Predictive Modeling in Foods. 1:11-12.
MicroBQs: a centralized database for use in studying bacterial biofilms and quorum sensing - (Book / Chapter)
Yan, X., Gui, J., Fratamico, P.M. 2009. MicroBQs: a centralized database for use in studying bacterial biofilms and quorum sensing. Book Chapter. Oxford, UK: Woodhead Publishing Ltd. p. 152-166. Biofilms in the Food and Beverage Industries, P.M. Fratamico, B.A. Annous, and N.W. Gunther (Ed.)
ARS News Articles
Last Modified: 11/22/2014
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