Journal Publications


    2017

  1. Xie H., L. Li, Z. Ye, X. Li, E. P. Plant, O. Zoueva, Y. Zhao, X. Jing, Z. Lin, T. Kawano, M.-J. Chiang, C. Finch, M. Kosikova, A. Zhang, Y. Zhu, and X.-F. Wan. 2017. Differential Effects of Prior Influenza Exposures on H3N2 Cross-reactivity of Human Post-vaccination Sera. Clinical Infectious Diseases, [Epub ahead of print].
  2. Xu, Y., A. M. Ramey, A. S. Bowman, T. J. DeLiberto, M. L. Killian, S. Krauss, J. M. Nolting, M. K. Torchetti, A. B. Reeves, R. J. Webby, D. E. Stallknecht, X.-F. Wan. 2017. Low Pathogenic Influenza A Viruses in North American Diving Ducks Contribute to the Emergence of a Novel Highly Pathogenic Influenza A(H7N8) Virus. Journal of Virology, in press.
  3. Martin, B., A. S. Bowman, L. Li, J. Nolting, D. R. Smith, L. Hanson, and X.-F. Wan. 2017. Detection of Antigenic Variants of Swine Subtype H3 Influenza A Viruses from Clinical Samples. J Clin Microbiol, Epub ahead: JCM.02049-16.
  4. Wang C, Liu H, Luo J, Chen L, Li M, Su W, Zhao N, Liu S, Xie L, Jia Y, Ding H, Wan X, He H. 2017. HA Triggers the Switch from MEK1 SUMOylation to Phosphorylation of the ERK Pathway in Influenza A Virus-Infected Cells and Facilitates Its Infection. Frontiers in cellular and infection microbiology, 7(27).
  5. Sun, H., B.S. Kaplan, M. Guan, G. Zhang, J. Ye, L.-P. Long, S. Blackmon, C.-K. Yang, M.-J. Chiang, H. Xie, N. Zhao, J. Cooley, D. F. Smith, M. Liao, C. Cardona, L. Li, G.P. Wang, R. Webby, and X.-F. Wan. 2017. Pathogenicity and Transmission of a Swine Influenza A(H6N6) Virus. Emerging Microbes and Infections, 6(e16).
  6. Luo, J., L. Ferguson, D.R. Smith, A. R. Woolums, W. B. Epperson, and X.-F. Wan. 2017. Serological evidence for high prevalence of Influenza D Viruses in Bovine, Nebraska, United States, 2003–2004. Virology, 501: 88-91.
  7. Krishnavajala, A., P.J. Muire, L. Hanson, H. Wan, F. McCarthy, N. Zhou and L. Petrie-Hanson. 2017. Transcriptome changes associated with protective immunity in T and B cell-deficient rag1-/- mutant zebrafish. International Journal of Immunology, 5(2): 20-36.

  8. 2016

  9. L. Ferguson, A. K. Olivier, S. Genova, W.B. Epperson, D. R. Smith, L. Schneider, K. Barton, K. McCuan, R. J. Webby, and X.-F. Wan. 2016. Pathogenesis of Influenza D virus in Cattle. Journal of Virology, 91(12): 5636-5642.
  10. Bailey, E., L.-P. Long, N. Zhao, J. S. Hall, J.A. Baroch, J. Nolting, L. Senter, F. L. Cunningham, T. Pharr, L. Hanson, R. Slemons, T. J. DeLiberto, and X.-F. Wan. 2016. Antigenic characterization of H3 subtypes of avian influenza viruses in North America. Avian Diseases, 60(1s): 346-353.
  11. Li, Y., X.-M. Huang, D.-M. Zhao, Y.-Z. Liu, K.-W. He, Y.-X. Liu, C.-H. Chen, L.-P. Long, Y. Xu, X.-X. Xie, K.-K. Han, X.-Y. Liu, J. Yang, Y.-F. Zhang, F. Fan, R. Webby, and X.-F. Wan. 2016. Perspective on the origin and spread of avian H7N9 influenza A viruses in the Yangtze Delta Region of China. Avian Diseases, 60(1s): 118-125.
  12. Y. Xu, E. Bailey, E. Spackman, T. Li, H. Wang, L.-P. Long, J. A. Baroch, F. L. Cunningham, X. Lin, R. G. Jarman, T. J. DeLiberto, and X.-F. Wan. 2016. Limited Antigenic Diversity in Contemporary H7 Avian-Origin Influenza A Viruses from North America. Scientific Reports, 6(20688).
  13. Sun, H., J.-L. Xue, E. Bailey, Y. Xu, G. Hu, J. Baroch, Y. Zhang, L. Pace, T. J. DeLiberto, and X.-F. Wan. 2016. A quantitative RT-PCR assay for rapid detection of Eurasia lineage H10 subtype influenza A virus infection. Virologica Sinica, 31(5): 444-447.

  14. 2015

  15. H. Xie, X.-F. Wan, Z. Ye, E. Plant, Y. Zhao, Y. Xu, X. Li, C. Finch, N. Zhao, T. Kawano, O. Zoueva, X. Jing, Z. Lin, Z. Zhang, and Y. Zhu. 2015. Cross-Reactivity of 2014/15 Northern Hemisphere Seasonal Influenza Vaccines and Antigenic Maps Derived from Human and Ferret Serological Data. Scientific Reports, 5(15279).
  16. L. Ferguson, L. Eckard, W. B. Epperson, L.-P. Long, D. Smith, C. Huston, S. Genova, R. Webby, X.-F. Wan. 2015. Influenza D virus Infection in Mississippi Beef Cattle. Virology, 486: 28-34.
  17. N. Zhao, B. Martin, C.-K. Yang, F. Luo, and X.-F. Wan. 2015. Association analyses of large-scale glycan microarray data reveal unusual host-specific substructures of influenza A virus binding glycans. Scientific Reports, 5: 15778.
  18. H. Sun, F. L. Cunningham, J. Harris, Y. Xu, L.-P. Long, K. Hanson-Dorr, J. A. Baroch, P. Fioranelli, M. W. Lutman, T. Li, K. Pedersen, B. S. Schmit, J. Cooley, X. Lin, R. G. Jarman, T. J. DeLiberto and X.-F. Wan. 2015. Dynamics of virus shedding and antibody responses in influenza A virus-infected feral swine. Journal of General Virology, 96(9): 2569-2578.
  19. W. Su, Y. Zhao, C. Wang, Y. Wu, J. Luo, L. Chen, N. Zhao, M. Li, C. Xing, H. Liu, H. Zhang, Y.-F. Chang, H. Ding, X.-F. Wan, and H. He. 2015. Genes of wild bird-origin avian influenza A(H9N2) virus confer high pathogenicity to H7N9 virus. Cell Reports, 12(12): 1-12.
  20. J. Ye, F. Wen, Y. Xu, N. Zhao, L. Long, H. Sun, J. Yang, J. Cooley, G. T. Pharr, R. Webby, and X.-F. Wan. 2015. Error-prone PCR-based mutagenesis strategy for rapidly generating high-yield influenza vaccine candidates. Virology, 482: 234--243.
  21. S. Kumar, E. A. Driskell, A. J. Cooley, K. Jia, S. Blackmon, X.- F. Wan, E. W. Uhl, J. T. Saliki, S. Sanchez, P. M. Krimer, and R. J. Hogan. 2015. Fatal Canid herpesvirus 1 Respiratory Infections in Four Apparently Healthy Adult Dogs. Veterinary Pathology, 52(4): 681--687.
  22. Y. Xu, H. Cao, H. Liu, H. Sun, B. Martin, Y. Zhao, Q. Wang, G. Deng, J. Xue, Y. Zong, J. Zhu, F. Wen, L.-P. Long, S.-S. Wong, N. Zhao, X. Fu, M. Liao, G. Hu, R. Webby, G. F. Gao, and X.-F. Wan. 2015. Identification of the source of A (H10N8) virus causing human infection. Infection, Genetics and Evolution, 30: 159--163.
  23. B. E. Martin, K. Jia, H. Sun, J. Ye, C. Hall, D. Ware, and X.-F. Wan. 2015. Detection of influenza antigenic variants directly from clinical samples using polyclonal antibody based proximity ligation assays. Virology, 476: 151--158.
  24. S.D. Collier, S.L. Branton, J.D. Evans, S.A. Leigh, X.F. Wan, A.M. Cooksey, H.A. Olanrewaju, and G.T. Pharr. 2015. Proteomic Analysis of Mycoplasma gallisepticum Vaccine Strain F. International Journal of Poultry Science, 14(1): 1--12.

  25. 2014

  26. E. Spackman, D. E. Swayne, M. J. Pantin-jackwood, X.-F. Wan, M. K. Torchetti, M. Hassan, D. L. Suarez, and M. S. E. Silva. 2014. Variation in protection of four divergent avian influenza virus vaccine seed strains against eight clade 2.2.1 and 2.2.1.1. Egyptian H5N1 high pathogenicity variants in poultry. Influenza Other Respi Viruses, 8(6): 654--662.
  27. Z.-X. Feng, Y. Bai, J.-T. Yao, G. T. Pharr, X.-F. Wan, S.-B. Xiao, L.-Z. Chi, Y. Gan, H.-Y. Wang, Y.-N. Wei, M.-J. Liu, Q.-Y. Xiong, F.-F. Bai, B. Li, X.-S. Wu, and G.-Q. Shao. 2014. Use of serological and mucosal immune responses to Mycoplasma hyopneumoniae antigens P97R1, P46 and P36 in the diagnosis of infection. The Veterinary Journal, 202(1): 128--133.
  28. E. Spackman, X.-F. Wan, D. Kapczynski, Y. Xu, M. Pantin-jackwood, D. L. Suarez, and D. Swayne. 2014. Potency, Efficacy, and Antigenic Mapping of H7 Avian Influenza Virus Vaccines Against the 2012 H7N3 Highly Pathogenic Avian Influenza Virus from Mexico. Avian Diseases, 58(3): 359--366.
  29. J. Yang, T. Zhang, and X.-F. Wan. 2014. Sequence-Based Antigenic Change Prediction by a Sparse Learning Method Incorporating Co-Evolutionary Information. PLoS ONE, 9(9): e106660.
  30. Z. Feng, J. A. Baroch, L.-P. Long, Y. Xu, F. L. Cunningham, K. Pedersen, M. W. Lutman, B. S. Schmit, A. S. Bowman, T. J. Deliberto, and X.-F. Wan. 2014. Influenza A Subtype H3 Viruses in Feral Swine, United States, 2011-2012. Emerg. Infect. Dis., 20(5): 839--842.
  31. J. Yang, S. Grünewald, Y. Xu, and X.-F. Wan. 2014. Quartet-based methods to reconstruct phylogenetic networks. BMC Systems Biology, 8(1): 21.
  32. M. S. Beato, Y. Xu, L.-P. Long, I. Capua, and X.-F. Wan. 2014. Antigenic and Genetic Evolution of Low-Pathogenicity Avian Influenza Viruses of Subtype H7N3 following Heterologous Vaccination. Clinical and Vaccine Immunology, 21(5): 603--612.

  33. 2013

  34. G. Yang, S. Li, S. Blackmon, J. Ye, K. C. Bradley, J. Cooley, D. Smith, L. Hanson, C. Cardona, D. A. Steinhauer, R. Webby, M. Liao, and X.-F. Wan. 2013. Mutation tryptophan to leucine at position 222 of haemagglutinin could facilitate H3N2 influenza A virus infection in dogs. Journal of General Virology, 94: 2599--2608.
  35. X.-F. Wan, M. Carrel, L.-P. Long, A. P. Alker, and M. Emch. 2013. Perspective on emergence and re-emergence of amantadine resistant influenza A viruses in domestic animals in China. Infection, Genetics and Evolution, 20: 298--303.
  36. Z.-X. Feng, Y.-N. Wei, G.-L. Li, X.-M. Lu, X.-F. Wan, G. T. Pharr, Z.-W. Wang, M. Kong, Y. Gan, F.-F. Bai, M.-J. Liu, Q.-Y. Xiong, X.-S. Wu, and G.-Q. Shao. 2013. Development and validation of an attenuated Mycoplasma hyopneumoniae aerosol vaccine. Veterinary Microbiology, 167(3-4): 417--424.
  37. S. Warren, X.-F. Wan, G. Conant, and D. Korkin. 2013. Extreme Evolutionary Conservation of Functionally Important Regions in H1N1 Influenza Proteome. PLoS ONE, 8(11): e81027.
  38. J. Ye, Y. Xu, J. Harris, H. Sun, A. S. Bowman, F. Cunningham, C. Cardona, K. J. Yoon, R. D. Slemons, and X.-F. Wan. 2013. Mutation from arginine to lysine at the position 189 of hemagglutinin contributes to the antigenic drift in H3N2 swine influenza viruses. Virology, 446(1-2): 225--229.
  39. J. Yang, J. Li, S. Grünewald, and X.-F. Wan. 2013. BinAligner: a heuristic method to align biological networks. BMC Bioinformatics, 14(Suppl 14): S8.
  40. X.-T. Yuan, T. Zhang, and X.-F. Wan. 2013. A Joint Matrix Completion and Filtering Model for Influenza Serological Data Integration. PLoS ONE, 8(7): e69842.
  41. H. Wan, J. Gao, K. Xu, H. Chen, L. K. Couzens, K. H. Rivers, J. D. Easterbrook, K. Yang, L. Zhong, M. Rajabi, J. Ye, I. Sultana, X.-F. Wan, X. Liu, D. R. Perez, J. K. Taubenberger, and M. C. Eichelberger. 2013. Molecular Basis for Broad Neuraminidase Immunity: Conserved Epitopes in Seasonal and Pandemic H1N1 as Well as H5N1 Influenza Viruses. Journal of Virology, 87(16): 9290--9300.
  42. H. Sun, J. Yang, T. Zhang, L.-P. Long, K. Jia, G. Yang, R. J. Webby, and X.-F. Wan. 2013. Using Sequence Data To Infer the Antigenicity of Influenza Virus. mBio, 4(4).
  43. Z. Feng, J. Gomez, A. S. Bowman, J. Ye, L.-P. Long, S. W. Nelson, J. Yang, B. Martin, K. Jia, J. M. Nolting, F. Cunningham, C. Cardona, J. Zhang, K.-J. Yoon, R. D. Slemons, and X.-F. Wan. 2013. Antigenic Characterization of H3N2 Influenza A Viruses from Ohio Agricultural Fairs. Journal of Virology, 87(13): 7655--7667.
  44. A. Mummert, H. Weiss, L.-P. Long, J. M. Amigo, and X.-F. Wan. 2013. A Perspective on Multiple Waves of Influenza Pandemics. PLoS ONE, 8(4): e60343.
  45. J. Yang, S. Grunewald, and X.-F. Wan. 2013. Quartet-Net: A Quartet-Based Method to Reconstruct Phylogenetic Networks. Molecular Biology and Evolution, 30(5): 1206--1217.
  46. X.-F. Wan, J. L. Barnett, F. Cunningham, S. Chen, G. Yang, S. Nash, L.-P. Long, L. Ford, S. Blackmon, Y. Zhang, L. Hanson, and Q. He. 2013. Detection of African swine fever virus-like sequences in ponds in the Mississippi Delta through metagenomic sequencing. Virus Genes, 46(3): 441--446.
  47. M. S. Beato, M. Mancin, J. Yang, A. Buratin, M. Ruffa, S. Maniero, A. Fusaro, C. Terregino, X.-F. Wan, and I. Capua. 2013. Antigenic characterization of recent H5N1 highly pathogenic avian influenza viruses circulating in Egyptian poultry. Virology, 435(2): 350--356.

  48. 2012

  49. Z. Cai, M. F. Ducatez, J. Yang, T. Zhang, L.-P. Long, A. C. Boon, R. J. Webby, and X.-F. Wan. 2012. Identifying Antigenicity-Associated Sites in Highly Pathogenic H5N1 Influenza Virus Hemagglutinin by Using Sparse Learning. Journal of Molecular Biology, 422(1): 145--155.
  50. M. A. Carrel, M. Emch, T. Nguyen, R. T. Jobe, and X.-F. Wan. 2012. Population-environment drivers of H5N1 avian influenza molecular change in Vietnam. Health & Place, 18(5): 1122--1131.
  51. X.F. Wan. 2012. Lessons from Emergence of A/Goose/Guangdong/1996-Like H5N1 Highly Pathogenic Avian Influenza Viruses and Recent Influenza Surveillance Efforts in Southern China. Zoonoses and Public Health, 59: 32--42.
  52. L.-P. Long, C. Yuan, Z. Cai, H. Xu, and X.-F. Wan. 2012. Mixture model analysis reflecting dynamics of the population diversity of 2009 pandemic H1N1 influenza virus. In Silico Biology, 11(5,6): 225–236.
  53. F. Zhou, G. Wang, P. Buchy, Z. Cai, H. Chen, Z. Chen, G. Cheng, X.-F. Wan, V. Deubel, and P. Zhou. 2012. A Triclade DNA Vaccine Designed on the Basis of a Comprehensive Serologic Study Elicits Neutralizing Antibody Responses against All Clades and Subclades of Highly Pathogenic Avian Influenza H5N1 Viruses. Journal of Virology, 86(12): 6970--6978.
  54. P. Xuan, Y. Zhang, T.-r. J. Tzeng, X.-F. Wan, and F. Luo. 2012. A quantitative structure-activity relationship (QSAR) study on glycan array data to determine the specificities of glycan-binding proteins. Glycobiology, 22(4): 552--560.
  55. J. L. Barnett, J. Yang, Z. Cai, T. Zhang, and X.-F. Wan. 2012. AntigenMap 3D: an online antigenic cartography resource. Bioinformatics, 28(9): 1292--1293.
  56. M. Carrel, X.-F. Wan, T. Nguyen, and M. Emch. 2012. Highly Pathogenic H5N1 Avian Influenza Viruses Exhibit Few Barriers to Gene Flow in Vietnam. EcoHealth, 9(1): 60--69.
  57. Z. Cai, T. Zhang, and X.-F. Wan. 2012. Antigenic distance measurements for seasonal influenza vaccine selection. Vaccine, 30(2): 448--453.

  58. 2011

  59. M. Carrel, X.-F. Wan, T. Nguyen, and M. Emch. 2011. Genetic Variation of Highly Pathogenic H5N1 Avian Influenza Viruses in Vietnam Shows Both Species-Specific and Spatiotemporal Associations. Avian Diseases, 55(4): 659--666.
  60. X.-F. Wan, L. Dong, Y. Lan, L.-P. Long, C. Xu, S. Zou, Z. Li, L. Wen, Z. Cai, W. Wang, X. Li, F. Yuan, H. Sui, Y. Zhang, J. Dong, S. Sun, Y. Gao, M. Wang, T. Bai, L. Yang, D. Li, W. Yang, H. Yu, S. Wang, Z. Feng, Y. Wang, Y. Guo, R. J. Webby, and Y. Shu. 2011. Indications that Live Poultry Markets Are a Major Source of Human H5N1 Influenza Virus Infection in China. Journal of Virology, 85(24): 13432--13438.
  61. M. F. Ducatez, Z. Cai, M. Peiris, Y. Guan, Z. Ye, X.-F. Wan, and R. J. Webby. 2011. Extent of Antigenic Cross-Reactivity among Highly Pathogenic H5N1 Influenza Viruses. Journal of Clinical Microbiology, 49(10): 3531--3536.
  62. G. Zhang, W. Kong, W. Qi, L.-P. Long, Z. Cao, L. Huang, H. Qi, N. Cao, W. Wang, F. Zhao, Z. Ning, M. Liao, and X.-F. Wan. 2011. Identification of an H6N6 swine influenza virus in southern China. Infection, Genetics and Evolution, 11(5): 1174--1177.
  63. K. L. Henne, X.-F. Wan, W. Wei, and D. K. Thompson. 2011. SO2426 is a positive regulator of siderophore expression in Shewanella oneidensis MR-1. BMC Microbiology, 11(1): 125.
  64. Z. Cai, T. Zhang, and X.-F. Wan. 2011. Concepts and applications for influenza antigenic cartography. Influenza and Other Respiratory Viruses, 5(Suppl 1): 204--207.
  65. Z. Cai, Y. Duan, Y. Li, G. Lin, M. Ozden, and X.-F. Wan. 2011. IPMiner: a progenitor gene identifier for influenza A virus. Influenza and Other Respiratory Viruses, 5(Suppl 1): 413--415.
  66. L. Yan, S. Zhang, L. Pace, F. Wilson, H. Wan, and M. Zhang. 2011. Combination of Reverse Transcription Real-Time Polymerase Chain Reaction and Antigen Capture Enzyme-Linked Immunosorbent Assay for the Detection of Animals Persistently Infected with Bovine Viral Diarrhea Virus. Journal of Veterinary Diagnostic Investigation, 23(1): 16--25.

  67. 2010

  68. S. Li, Z. Shi, P. Jiao, G. Zhang, Z. Zhong, W. Tian, L.-P. Long, Z. Cai, X. Zhu, M. Liao, and X.-F. Wan. 2010. Avian-origin H3N2 canine influenza A viruses in Southern China. Infection, Genetics and Evolution, 10(8): 1286--1288.
  69. Z. Cai, T. Zhang, and X.-F. Wan. 2010. A Computational Framework for Influenza Antigenic Cartography. PLoS Comput Biol, 6(10): e1000949.
  70. X.-F. Wan, S. L. Branton, S. D. Collier, J. D. Evans, S. A. Leigh, and G. T. Pharr. 2010. Proteomics inference of genes involved in host adaptation of Mycoplasma gallinarum. Veterinary Microbiology, 145(1-2): 177--184.
  71. Y. Jang and X. F. Wan. 2010. Development of Chemical Bond based Elastic Network Model and its application in identifying functional motions in H5N1 highly pathogenic avian influenza viruses. International Journal of Bioinformatics Research and Applications, 6(1): 1.
  72. M. A. Carrel, M. Emch, R. T. Jobe, A. Moody, and X.-F. Wan. 2010. Spatiotemporal Structure of Molecular Evolution of H5N1 Highly Pathogenic Avian Influenza Viruses in Vietnam. PLoS ONE, 5(1): e8631.

  73. 2009

  74. T. Nguyen, C. T. Davis, W. Stembridge, B. Shu, A. Balish, K. Inui, H. T. Do, H. T. Ngo, X.-F. Wan, M. Mccarron, S. E. Lindstrom, N. J. Cox, C. V. Nguyen, A. I. Klimov, and R. O. Donis. 2009. Characterization of a highly pathogenic avian influenza H5N1 virus sublineage in poultry seized at ports of entry into Vietnam. Virology, 387(2): 250--256.
  75. F. Luo, B. Li, X.-F. Wan, and R. H. Scheuermann. 2009. Core and periphery structures in protein interaction networks. BMC Bioinformatics, 10(Suppl 4): S8.

  76. 2008

  77. T. Z. Salem, C. M. Turney, L. Wang, J. Xue, X.-F. Wan, and X.-W. Cheng. 2008. Transcriptional analysis of a major capsid protein gene from Spodoptera exigua ascovirus 5a. Arch Virol, 153(1): 149--162.
  78. X.-F. Wan, T. Nguyen, C. T. Davis, C. B. Smith, Z.-M. Zhao, M. Carrel, K. Inui, H. T. Do, D. T. Mai, S. Jadhao, A. Balish, B. Shu, F. Luo, M. Emch, Y. Matsuoka, S. E. Lindstrom, N. J. Cox, C. V. Nguyen, A. Klimov, and R. O. Donis. 2008. Evolution of Highly Pathogenic H5N1 Avian Influenza Viruses in Vietnam between 2001 and 2007. PLoS ONE, 3(10): e3462.
  79. X.-F. Wan, M. Ozden, and G. Lin. 2008. Ubiquitous reassortments in influenza A viruses. Journal of Bioinformatics and Computational Biology, 06(05): 981--999.
  80. X.-F. Wan, P. P. Dempsey, and D. Xu. 2008. RnallViewer: A Tool for Prediction, Localization and Visualization of RNA Local Secondary Structure. International Journal of Computational Science, (5): 607-612.
  81. Z.-M. Zhao, K. F. Shortridge, M. Garcia, Y. Guan, and X.-F. Wan. 2008. Genotypic diversity of H5N1 highly pathogenic avian influenza viruses. Journal of General Virology, 89(9): 2182--2193.
  82. K. Chourey, W. Wei, X.-F. Wan, and D. K. Thompson. 2008. Transcriptome analysis reveals response regulator SO2426-mediated gene expression in Shewanella oneidensis MR-1 under chromate challenge. BMC Genomics, 9(1): 395.
  83. H. Gao, D. Pattison, T. Yan, D. M. Klingeman, X. Wang, J. Petrosino, L. Hemphill, X. Wan, A. B. Leaphart, G. M. Weinstock, T. Palzkill, and J. Zhou. 2008. Generation and Validation of a Shewanella oneidensis MR-1 Clone Set for Protein Expression and Phage Display. PLoS ONE, 3(8): e2983.
  84. G. Lin, Z. Cai, J. Wu, X.-F. Wan, L. Xu, and R. Goebel. 2008. Identifying a few foot-and-mouth disease virus signature nucleotide strings for computational genotyping. BMC Bioinformatics, 9(1): 279.

  85. 2007

  86. X.-F. Wan, G. Chen, F. Luo, M. Emch, and R. Donis. 2007. A quantitative genotype algorithm reflecting H5N1 Avian influenza niches. Bioinformatics, 23(18): 2368--2375.
  87. C.H. Kang, Y.D. Nam, W.H. Chung, Z.X. Quan, Y.H. Park, S.J. Park, R. Desmone, X.F. Wan,, and S.K. Rhee. 2007. Relationship between genome similarity and DNA-DNA hybridization among closely related bacteria. Journal of Microbiology and Biotechnology, 17(6): 945--951.
  88. X. Wu, Z. Cai, X.-F. Wan, T. Hoang, R. Goebel, and G. Lin. 2007. Nucleotide composition string selection in HIV-1 subtyping using whole genomes. Bioinformatics, 23(14): 1744--1752.
  89. M. C. Angellotti, S. B. Bhuiyan, G. Chen, and X.-F. Wan. 2007. CodonO: codon usage bias analysis within and across genomes. Nucleic Acids Research, 35(Web Server): W132--W136.
  90. X.-W. Cheng, X.-F. Wan, J. Xue, and R. C. Moore. 2007. Ascovirus and its evolution. Virol. Sin., 22(2): 137--147.
  91. X.-F. Wan, X. Wu, G. Lin, S. B. Holton, R. A. Desmone, C.-R. Shyu, Y. Guan, and M. E. Emch. 2007. Computational Identification of Reassortments in Avian Influenza Viruses. Avian Diseases, 51(s1): 434--439.
  92. Z. Song, L. Chen, A. Ganapathy, X.-F. Wan, L. Brechenmacher, N. Tao, D. Emerich, G. Stacey, and D. Xu. 2007. Development and assessment of scoring functions for protein identification using PMF data. Electrophoresis, 28(5): 864--870.

  93. 2006

  94. X.-F. Wan, G. Lin, and D. Xu. 2006. Rnall: An efficient algorithm for predicting RNA local secondary structural landscape in genomes. Journal of Bioinformatics and Computational Biology, 04(05): 1015--1031.
  95. X. Wu, X. F. Wan, G. Wu, D. Xu, and G. Lin. 2006. Phylogenetic analysis using complete signature information of whole genomes and clustered Neighbour-Joining method. International Journal of Bioinformatics Research and Applications, 2(3): 219.
  96. M. E. Clark, Q. He, Z. He, K. H. Huang, E. J. Alm, X.-F. Wan, T. C. Hazen, A. P. Arkin, J. D. Wall, J.-Z. Zhou, and M. W. Fields. 2006. Temporal Transcriptomic Analysis as Desulfovibrio vulgaris Hildenborough Transitions into Stationary Phase during Electron Donor Depletion. Applied and Environmental Microbiology, 72(8): 5578--5588.
  97. M. Shababi, J. Bourque, K. Palanichelvam, A. Cole, D. Xu, X.-F. Wan, and J. Schoelz. 2006. The Ribosomal Shunt Translation Strategy of Cauliflower Mosaic Virus Has Evolved from Ancient Long Terminal Repeats. Journal of Virology, 80(8): 3811--3822.
  98. A. B. Leaphart, D. K. Thompson, K. Huang, E. Alm, X.-F. Wan, A. Arkin, S. D. Brown, L. Wu, T. Yan, X. Liu, G. S. Wickham, and J. Zhou. 2006. Transcriptome Profiling of Shewanella oneidensis Gene Expression following Exposure to Acidic and Alkaline pH. Journal of Bacteriology, 188(4): 1633--1642.
  99. X.-F. Wan, J. Zhou, and D. Xu. 2006. CodonO: a new informatics method for measuring synonymous codon usage bias within and across genomes. International Journal of General Systems, 35(1): 109--125.

  100. 2005

  101. X.-F. Wan and D. Xu. 2005. Computational Methods for Remote Homolog Identification. Current Protein & Peptide Science, 6(6): 527--546.
  102. W.-H. Chung, S.-K. Rhee, X.-F. Wan, J.-W. Bae, Z.-X. Quan, and Y.-H. Park. 2005. Design of long oligonucleotide probes for functional gene detection in a microbial community. Bioinformatics, 21(22): 4092--4100.
  103. X.-F. Wan and D. Xu. 2005. Intrinsic Terminator Prediction and Its Application in Synechococcus sp. WH8102. Journal of Computer Science and Technology, 20(4): 465--482.
  104. X.-F. Wan, T. Ren, K.-J. Luo, M. Liao, G.-H. Zhang, J.-D. Chen, W.-S. Cao, Y. Li, N.-Y. Jin, D. Xu, and C.-A. Xin. 2005. Genetic characterization of H5N1 avian influenza viruses isolated in southern China during the 2003-04 avian influenza outbreaks. Arch Virol, 150(6): 1257--1266.

  105. 2004

  106. X.-F. Wan, N. C. Verberkmoes, L. A. Mccue, D. Stanek, H. Connelly, L. J. Hauser, L. Wu, X. Liu, T. Yan, A. Leaphart, R. L. Hettich, J. Zhou, and D. K. Thompson. 2004. Transcriptomic and Proteomic Characterization of the Fur Modulon in the Metal-Reducing Bacterium Shewanella oneidensis. Journal of Bacteriology, 186(24): 8385--8400.
  107. S.-K. Rhee, X. Liu, L. Wu, S. C. Chong, X. Wan, and J. Zhou. 2004. Detection of Genes Involved in Biodegradation and Biotransformation in Microbial Communities by Using 50-Mer Oligonucleotide Microarrays. Applied and Environmental Microbiology, 70(7): 4303--4317.
  108. X.-F. Wan, D. Xu, A. Kleinhofs, and J. Zhou. 2004. Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes. BMC Evol Biol, 4(1): 19.
  109. X.-F. Wan, SusanM. Bridges, and JohnA. Boyle. 2004. Revealing gene transcription and translation initiation patterns in archaea, using an interactive clustering model. Extremophiles, 8(4).
  110. X. Wan, S. L. Branton, L. A. Hanson, and G. T. Pharr. 2004. Identification and Initial Characterization of a Putative Mycoplasma gallinarum Leucine Aminopeptidase Gene. Current Microbiology, 48(1): 32--38.
  111. X. Wan, S.L. Branton, M.B. Hughlett, L.A. Hanson, and G.T. Pharr. 2004. Expression and Subcellular Location of a Leucine Aminopeptidase of Mycoplasma Gallinarum. International Journal of Poultry Science, 3(1): 70--74.

  112. Before 2004

  113. G. T. Pharr, S. L. Branton, L. A. Hanson, F. C. Minion, M. B. Hughlett, and X. Wan. 2002. Characterization of pMGA Genes from the F - Strain (Vaccine Strain) of Mycoplasma Gallisepticum. International Journal of Poultry Science, 1(4): 63--73.
  114. Y. Guo, M. Wang, X. Xu, X. Wan, J. Guo, J. Dong, and Y. Zhang. 1999. Nucleotide sequence of A/Goose/Guangdong/2/96(H5N1) virus M and NS RNA. Chinese Journal of Experimental and Clinical Virology, 13(4): 305--309.
  115. Y. Guo, X. Xu, and X. Wan. 1998. Genetic characterization of an avian influenza A (H5N1) virus isolated from a sick goose in China. Chinese Journal of Experimental and Clinical Virology, 12(4): 322--325.
  116. X. Wan and C. Xin. 1998. Prevention and control of Avian Influenza. Journal of Poultry Husbandry and Diseases Control, 6: 5--6.
  117. C. Xin, M. Liao, G. Huang, and X. Wan. 1996. Avian Influenza. Journal of Poultry Husbandry and Diseases Control, 12: 4--5.
  118. M.W. Hu and X. Wan. 1996. Current status of sturgeon aquaculture. Freshwater Fisheries, 26(5): 28--30.
  119. C. Xin, M. Liao, G. Huang, and X. Wan. 1995. Fluoride and soft leg symptom in poultry. Journal of Poultry Husbandry and Diseases Control, 12: 13--14.

Referred Conference Proceedings


  1. L. Han, Y. Zhang, X.-F. Wan, and T. Zhang. 2016. Generalized hierarchical square model for arbitrary-order interactive antigenic sites identification in influenza virus data. ACM SIGKDD 2016 Conference on Knowledge Discovery & Data Mining. 13-17 August, San Francisco, USA.
  2. T. Grindinger, F. Luo, X.-F. Wan, and R. H. Scheuermann. 2008. Exploring Core/Periphery Structures in Protein Interaction Networks Provides Structure-Property Relation Insights. The 8th IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Philadelphia, PA, November, 2008, pp. 179--186.
  3. X. Wu, R. Goebel, X.-F. Wan, and G. Lin. 2006. Whole genome composition distance for HIV-1 genotyping. Computational Systems Bioinformatics - Proceedings of the Conference, CSB 2006, pp. 179--190.
  4. X. Wu, R. G. Goebel, X.-F. Wan, and G. Lin. 2006. Weighted Composition Distance for HIV Genotyping. In Proceedings of the 2006 Computational Systems Bioinformatics Conference. Stanford, California, 14-18 August 2006, pp. 179--190.
  5. X. Wu, G. Lin, X.-F. Wan, and D. Xu. 2005. Whole genome phylogeny based on clustered signature string composition. IEEE Computational Systems Bioinformatics Conference - Workshops (CSBW '05), pp. 53--54.
  6. A. Ganapathy, X.-F. Wan, J. Wan, J. Thelen, D.W. Emerich, G. Stacey, and D. Xu. 2004. Statistical assessment for mass-spec protein identification using peptide fingerprinting approach. In Proceedings of the 26th Annual International Conference IEEE Engineering in Medicine and Biology Society (EMBS'04), Bioinformatics and Computational Biology, San Francisco, CA, pp. 3051--3054.
  7. X. Wan, S. M. Bridges, J. A. Boyle, and A. P. Boyle. 2002. Interactive clustering for exploration of genomic data. Intelligent engineering systems through artificial neural networks eds., pp. 753--758.

Book Chapters


  1. Z. Wang, T. Liu, J. Wang, X.-F. Wan, and D. Xu. 2015. Remote homology identification for protein structure prediction and function study. Handbook of Computational Molecular Biology, CRC Press, in press.
  2. X.-F. Wan and D. K. Thompson. 2009. High-Throughput Technologies and Functional Genomics. Systems Biology and Synthetic Biology, edited by P. Fu and S. Panke, Chapter 3, pp. 67--113, John Wiley & Sons, Inc., Hoboken, NJ, USA.
  3. X.-F. Wan, M. Emch, and Z.-M. Zhao. 2009. Advances in molecular evolution of influenza A viruses. Global View at Fight Against Influenza, edited by Mitrasinovic, Chapter 4, pp. 31--48, Nova Publisher, Inc..
  4. D. Xu, O. Duzlevski, and X.-F. Wan. 2005. In Search of Remote Homolog. Handbook of Computational Molecular Biology, edited by Aluru, Chapter 33, pp. 1--27, CRC Press.
  5. X.-F. Wan, D. Ataman, and D. Xu. 2005. Application of computational biology in understanding emerging infectious diseases: inferring the biological function for S-M complex of SARS-CoV. In Progress in Bioinformatics, pp. 55--80, Nova Publisher, Inc..