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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
Computational Biologist

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

BLDG 200 BARC-EAST
BELTSVILLE , MD 20705

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)
Characterization of clostridium perfringens netB+tpel+ type A atrains isolated from necrotic enteritis-afflicted broiler chickens -
Development and characterization of chicken CD127-cpecific antibodies -
Complete genome sequences of two strains of the meat spoilage bacterium Brochothrix thermosphacta isolated from ground chicken -
Paoli, G., Wijey, C., Nguyen, L.T., Chen, C., Yan, X., Irwin, P.L. 2017. Complete genome sequences of two strains of the meat spoilage bacterium Brochothrix thermosphacta isolated from ground chicken. Genome Announcements. 5:47. 10.1128/genomeA.01357-17.
Complete genome sequences of slostridium perfringens strain del1 isolated from necrotic enteritis-afflicted chicken farm -
Li, C.Z., Yan, X., Lillehoj, H.S. 2018. Complete genome sequences of slostridium perfringens strain del1 isolated from necrotic enteritis-afflicted chicken farm. Gut Pathogens. 9:69. https://doi.org/10.1186/s13099-017-0217-6.
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 -
Draft genome sequences of clostridium perfringens strain LLY_N11, a pathogenic isolate of necrotic enteritis from a healthy chicken -
Li, C.Z., Yan, X., Lillehoj, H.S. 2017. Draft genome sequences of clostridium perfringens strain LLY_N11, a pathogenic isolate of necrotic enteritis from a healthy chicken. Genome Announcements. 5:44. https://doi.org/10.1128/genomeA.01225-17.
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.)