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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Environmental Microbial & Food Safety Laboratory » People & Locations » Xianghe Yan

Xianghe Yan
Environmental Microbial & Food Safety Laboratory
General Biological Science

Phone: (301) 504-9292
Fax:
Room 125A

BLDG 200 BARC-EAST
BELTSVILLE , MD 20705
Projects
Identification of Plant-Derived Bioactive Compounds for their Potential as Alternatives to Conventional Antimicrobials
In-House Appropriated (D)
  Accession Number: 431059

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Effects of Eimeria maxima and Clostridium perfringens infections on Cecal Microbiome in Broiler Chickens Analyzed by 16S rRNA Sequencing -
Genetic basis for the resistance of Staphylococcus aureus to peptidoglycan hydrolase by comparative transcriptome and whole genome sequence analysis -
Intestinal meta-transcriptome comparison reveals disparate antiviral transcriptional response and its association with Mitochondria in chicken immunity development -
Comparative genomic analysis of full genome sequences of two closely related isolates of Clostridium perfringens reveals regions of genome plasticity with prevention potential -
Genome sequences of Ralstonia insidiosa type strain ATCC 49129 and strain FC1138, a strong biofilm producer isolated from a fresh-cut produce-processing plant -
Xu, Y., Nagy, A., Liu, N., Nou, X., Yan, X., Haley, B.J., Kim, S. 2016. Genome sequences of Ralstonia insidiosa type strain ATCC 49129 and strain FC1138, a strong biofilm producer isolated from a fresh-cut produce-processing plant. American Society for Microbiology, Genome Announcements. 4(4):e00847-17.
Whole-genome sequence of Escherichia coli serotype O157:H7 strain EDL932 (ATCC 43894) -
Uhlich, G.A., Paoli, G., Chen, C., Cottrell, B.J., Zhang, X., Yan, X. 2016. Whole-genome sequence of Escherichia coli serotype O157:H7 strain EDL932 (ATCC 43894). Genome Announcements. doi: 10.1128/genomeA.00647-16.
Stx1 prophage excision in Escherichia coli strain PA20 confers strong curli and biofilm formation by restoring native mlrA Reprint Icon -
Uhlich, G.A., Chen, C., Cottrell, B.J., Yan, X., Hofmann, C.S., Nguyen, L.T. 2016. Stx1 prophage excision in Escherichia coli strain PA20 confers strong curli and biofilm formation by restoring native mlrA. FEMS Microbiology Letters. doi: 10.1093/femsle/fnw123.
Comparison of O-antigen gene clusters of all O-serogroups of Escherichia coli and proposal for adopting a new nomenclature for O-typing -
Needleman, D.S., Debroy, C., Fratamico, P.M., Yan, X., Baranzoni, G., Liu, Y., Tebbs, R., O'Connell, C.D., Allred, A., Swimley, M., Mwangi, M., Kapur, V., Garay, J., Roberts, E.L., Katani, R. 2016. Comparison of O-antigen gene clusters of all O-serogroups of Escherichia coli and proposal for adopting a new nomenclature for O-typing. Meeting Abstract. [abstract] Association of Biomolecular Resources Facilities Meeting.
Understanding the host-adapted state of Citrobacter rodentium by transcriptomic analysis -
Smith, A.D., Yan, X., Chen, C.T., Dawson, H.D., Bhagwat, A.A. 2016. Understanding the host-adapted state of Citrobacter rodentium by transcriptomic analysis. Archives Of Microbiology. 198:353-362.
Comparison of O-Antigen gene clusters of all O-Serogroups of Escherichia coli and proposal for adopting a new nomenclature for O-Typing -
Debroy, C., Fratamico, P.M., Yan, X., Baranzoni, G., Liu, Y., Needleman, D.S., Tebbs, R., O'Connell, C.D., Allred, A., Swimley, M., Mwangi, M., Kapur, V., Raygoza Garay, J., Katani, R., Roberts, E.L. 2016. Comparison of O-Antigen gene clusters of all O-Serogroups of Escherichia coli and proposal for adopting a new nomenclature for O-Typing. PLoS One. DOI:10.1371/journal.pone.0147434.
Genome sequencing and comparative genomics provides insights on the evolutionary dynamics and pathogenic potential of different H-Types of Shiga toxin-producing Escherichia coli O104 -
Yan, X., Fratamico, P.M., Bono, J.L., Baranzoni, G., Chen, C. 2015. Genome sequencing and comparative genomics provides insights on the evolutionary dynamics and pathogenic potential of different H-Types of Shiga toxin-producing Escherichia coli O104. BMC Microbiology. DOI: 10.1186/s12866-015-0413-9.
Application of metagenomics technologies for antimicrobial resistance and food safety research and beyond -
Chen, C., Yan, X., Wang, S., Jackson, C.R. 2015. Application of metagenomics technologies for antimicrobial resistance and food safety research and beyond. In: Chen, C.Y., Yan, X., and Jackson, C.R., editors. Antimicrobial Resistance and Food Safety-Methods and Techniques. New York, NY: Elsevier B.V. p. 401-422.
Escherichia coli O-antigen gene clusters of serogroups O62, O68, O131, O140, O142, and O163: DNA sequences and similarity between O62 and O68, and PCR-based serogrouping -
Liu, Y., Fratamico, P.M., Debroy, C., Yan, X., Needleman, D.S., Li, R.W., Wang, W., Losada, L., Brinkac, L., Radune, D., Toro, M., Meng, J. 2015. Escherichia coli O-antigen gene clusters of serogroups O62, O68, O131, O140, O142, and O163: DNA sequences and similarity between O62 and O68, and PCR-based serogrouping. Biosensors. 5:51-68.
Complete genome sequence of Campylobacter jejuni YH001 from beef liver which contains a novel plasmid -
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.
Predicting protein submitochondrial locations using a K-Nearest neighbor method based on the Bit-Score weighted euclidean distance -
Hu, J., Yan, X. 2014. Predicting protein submitochondrial locations using a K-Nearest neighbor method based on the Bit-Score weighted euclidean distance. Bioinformatics Research and Applications International Symposium Proceedings Series. DOI: 10:1007/9783-319.
Molecular serotyping of Escherichia coli: A verification and reclassification -
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 -
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 -
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 -
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.
Sequencing and genome annotation of honey bee microsporidia parasite, Nosema apis and comparative genome analysis with its sympatric congener, N. ceranae Reprint Icon -
Chen, Y., Pettis, J.S., Zhao, Y., Cornman, R.S., Tallon, L.L., Sadzewicz, L.L., Ye, J., Li, R., Zhang, X., Hamilton, M.C., Pernal, S., Melathopoulos, A., Yan, X., Evans, J.D. 2013. Sequencing and genome annotation of honey bee microsporidia parasite, Nosema apis and comparative genome analysis with its sympatric congener, N. ceranae. Biomed Central (BMC) Genomics. 14:451. DOI: 10.1186/1471-2164-14-451.
A simulated metagenomic approach for bacterial serotyping using shotgun genome sequences coupled with O-Antigen gene cluster analysis -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
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 -
A comparative genomics approach for biomarker candidate discovery among shiga toxin-producing Escherichia coli -
Comprehensive approaches for molecular biomarker discovery for the detection and identification of Cronobacter spp. (Enterobacter sakazakii), Salmonella, and other foodborne pathogens Reprint Icon -
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 -
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 -
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 -
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 -
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 -
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 -
From ontology selection and semantic web to the integrated information system of food-borne diseases and food safety -
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 -
Escherichia coli serogroup O2 and O28ac O-antigen gene cluster sequences and detection of pathogenic E. coli O2 and O28ac by PCR -
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 -
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 -
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.)