• Cai Z., Y. Duan, Y.-S. Li, G. Lin, M. Ozden, and X.-F. Wan. IPMiner: a progenitor identifier for influenza A virus. Proceedings of OPTIONS VII, Hong Kong, 2010. In press.

CCV for Genetic Distance Calculation in Bacteria

  • Wu, X., X.-F. Wan, G. Wu, D. Xu, and G. Lin. 2006. Phylogenetic analysis using complete signature information of whole genomes and clustered neighbor-joining method. International Journal of Bioinformatics Research and Applications, 2: 219-248.

CCV for Genetic Distance Calculation in Influenza Viruses

  • Wan, X.-F. , X. Wu, G. Lin, S. B. Holton, R. A. Desmone, C.-R. Shyu, M. Emch, and Y. Guan. 2007. Computational Identification of reassortments in avian influenza viruses. Avian Diseases, 51: 434-439.

CCV-MST for Influenza Reassortment Identification

  • Wan, X.F., M. Ozden, and G. Lin. 2008. Ubiquitous reassortments in influenza A viruses, Journal of Bioinformatics and Computational Biology, 6: 981-99.

Applications of CCV and MST in Influenza Viruses

  • Wan, X.-F. , G. Chen, F. Luo, M. Emch, and R. Donis. 2007. A quantitative genotype algorithm reflecting H5N1 Avian Influenza niches. Bioinformatics, 23: 2368-2375.
  • Wan, X.-F., T. Nguyen, C.T. Davis, C.B. Smith, Z. Zhao, M. Carrel, K. Inui, H. T. Do, D. T. Mai, S. Jadhao, A. Balish, F. Luo, M. Emch, Y. Matsuoka, N. J. Cox, C.V. Nguyen, A. Klimov, and R. Donis. 2008. Evolution of highly pathogenic H5N1 avian influenza viruses in Vietnam between 2001 and 2007. PLoS ONE, 3(10): e3462.
  • Zhao, Z., K. Shortridge, M. Garcia, Y. Guan, and X.-F. Wan. 2008. Genotypic diversity of highly pathogenic H5N1 avian influenza viruses. Journal of General Virology, 89: 2182-2193.
  • Wan, X.-F., M. Emch, and Z.-M. Zhao. 2009. Advances in molecular evolution of influenza A viruses. In Global View at Fight against Influenza, edited by Mitrasinovic, Chapter 4, pp. 31-48, Nova Publisher, Inc.

Applications of CCV in HIV and FMDV

  • Wu, X., 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, 23:1744-52.
  • Lin, G. Z. Cai, J. Wu, X.-F. Wan, L. Xu, and R. Goebel. 2008. Identifying signature composition strings for Foot-and-Mouth disease virus serotype recognition. BMC Bioinformatics, 9: 279.