Referred Publications

1. Wan, X.-F., P. P. Dempsey, and D. Xu. BioAnalyzer: A tool for RNA local secondary structure prediction, localization, and visualization. Submitted.
2. Cheng, X.-W.,  J. Xue, L. Wang, C. Seaborn, and X.-F. Wan. Transcriptional analysis of a major capsid protein gene from Spodoptera exigua Ascovirus. Submitted.
3. Lin, G. Z. Cai, J. Wu, X.-F. Wan, L. Xu, and R. Goebel. Identifying Signature Composition Strings for Foot-and-Mouth Disease Virus Serotype Recognition. Submitted.
4. Luo, F., X.-F. Wan, C-F Chen, and R. Scheuermann. Functional modules from protein interaction network via local optimization. Submitted.
5. Wang, X., H. Gao, X.-F. Wan, J. Zhou, and T. Palzkill. DNA binding specificity of the Shewanella oneidensis MR-1 response regulatory protein ArcA. Submitted.
6. Wan, X.-F., G. Chen, F. Luo, M. Emch, and R. Donis. A quantitative genotype algorithm reflecting H5N1 Avian Influenza niches. Bioinformatics, accept for publication.
7. Wu, X., Z. Cai, X.-F. Wan, T. Hoang, R. Goebel, and G. Lin. Nucleotide composition string selection in HIV-1 subtyping using whole genomes. Bioinformatics, accept for publication.
8. Angellotti, M.C., S.B. Bhuiyan, G. Chen, and X.-F. Wan.  CodonO: codon usage analysis within and across genomes.  Nucleic Acid Research, accept for publication.
9. Kang, C.-H., Y.-D. Nam, W.-H. Chung, Z.-X. Quan, Y.-H. Park, S.-J. Park, R. A. Desmone, X.-F. Wan, and S.-K. Rhee. Relationship between genome similarity and DNA-DNA hybridization among closely related bacteria. .Journal of Microbiology and Biotechnology, in press.
10. Cheng, X.-W., X.-F. Wan, J. Xue, and R. Moore. 2007. Ascovirus and its evolution. Virologica Sinica, 22: 19.
11. Wan, X.-F., X. Wu, G. Lin, S.B. Holton, R.A. Desmone, C.-R. Shyu, Y. Guan, and M. Emch. 2007. Computational Identification of reassortments in avian influenza viruses. Avian Diseases, 51: 434-439.
12. Song, Z, L. Chen, A. Ganapathy, X.-F. Wan, N. Tao, D. Emerich, G. Stacey, and D. Xu. 2007. Development and assement of scoring functions for protein identification using peptide mass fingerprinting data. Electrophoresis, 28: 864-870.
13. Wan, X.-F., 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, 4: 1015-1031.
14. Wu, X., 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. Pages 179-190.
15. Clark, M.E., Q. He, Z. He, K.H. Huang, E.J. Alm, X.-F. Wan, T.C. Hazen, A.P. Arkin, J.D. Wall, J. Zhou, and M.W. Fields. 2006. Temporal transcriptomic analysis of Desulfovibrio vulgaris Hildenborough transition into stationary phase growth during electron donor depletion. Applied Environmental Microbiology, 72:5578-5588.
16. Wu, X., X.-F. Wan, G. Wu, D. Xu, and G. Lin. Phylogenetic analysis using complete signature information of whole genomes and clustered neighbor-joining method. International Journal of Bioinformatics Research and Applications, 2:219-248.
17. Shababi, M., J. Bourque, P. Karuppaiah, 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, 80:3811-3822 .
18. Wan, X.-F., J. Zhou, and D. Xu. 2006. CodonO: a new informatics method measuring synonymous codon usage bias. International Journal of General Systems, 35: 109-125.
19. Leaphart, A. B, D. K. Thompson, K. Huang, E. Alm, X.-F. Wan, A. Arkin, S. D. Brown, L. Wu, and J. Zhou.  2006. Transcriptome analysis of Shewanella oneidensis gene expression in response to acidic and alkaline pH stress. Journal of Bacteriology, 188: 1633-1642.
20. Wan, X.-F. and D. Xu. 2005. Computational detection of remote homology. Current Protein and Peptide Science, 6: 527-546.
21. Chung, W. H., S. K. Rhee, X.-F. Wan, J.-W. Bae, Z.-X. Quan, and Y.-H. Park. 2005. Design of long oligonucleotide probe for detection of functional gene in microbial community. Bioinformatics, 21: 4092-4100.
22. Wan, X.-F. and D. Xu. 2005. Intrinsic terminator prediction and its application in Synechococcus sp. WH8102. Journal of Computer Science and Technology, 20: 465-482.
23. Wan, X.-F., 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 pandemic. Archives of Virology, 150: 1257-1266.
24. X. Wu, X.-F. Wan, D. Xu, and G. Lin.Whole Genome Phylogeny Based on Clustered Signature String Composition. 2005. In Posters in 2005 IEEE Computational Systems Bioinformatics Conference (CSB 2005). Stanford University, California. August 8-11, pp. 53-54.
25. Wan, X.-F., N.C. VerBerkmoes, L. A. McCue, D. Stanek, H. Connelly, 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: 8385-8400.
26. Rhee, S. K., X. Liu, L. Wu, S. C. Chong, X. Wan, and J. Zhou. 2004. Detection of biodegradation and biotransformation genes in microbial communities using 50-mer oligonucleotide microarrays. Applied and Environmental Microbiology, 70: 4303-4317.
27. Wan, X.-F., S. M. Bridges, and J. A. Boyle. 2004. Revealing different transcription initiation and translation initiation patterns in archaea using an interactive clustering model. Extremophiles, 8: 291-299.
28. Ganapathy, A., X.-F. Wan, B. D. Gue, 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.
29. Wan, X.-F., D. Xu, A. Kleinhofs, and J. Zhou. 2004. Quantitative relationship between codon usage bias and GC composition across the unicellular genomes. BMC Evolutionary Biology, 4: 19 (http://www.biomedcentral.com/1471-2148/4/19/).
30. Wan, X., S. L. Branton, L. A. Hanson, and G. T. Pharr. 2004. Identification and initial characterization of an aminopeptidase gene in M. gallinarum. Current Microbiology, 48: 32-38.
31. Wan, X., 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.
32. Wan, X.-F. , D. Xu, and J. Zhou. 2003. A new informatics method measuring synonymous codon usage bias. In Intelligent engineering systems through artificial neural networks, vol 13, eds. Dagli et al., 1101-1018. New York, NY: ASME Press.
33. Pharr, G. T., 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.
34. Wan, X., S. M. Bridges, J. A. Boyle, and A. P. Boyle. 2002. Interactive clustering for exploration of genomic data. In Intelligent engineering systems through artificial neural networks, vol 12, eds. Dagli et al., 753-758. New York, NY: ASME Press.
35. Guo, Y., 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, 4 (13): 305-309.
36. Guo, Y., 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.
37. Wan, X. and C. Xin. 1998. Prevention and control of Avian Influenza. Journal of Poultry Husbandry and Diseases Control, 6: 5-6.
38. Xin, C., M. Liao, G. Huang, and X. Wan. 1996. Avian Influenza. Journal of Poultry Husbandry and Diseases Control, 12: 4-5.
39. Hu, M.W. and X. Wan. 1996. Current status of sturgeon aquaculture. Freshwater Fisherie, 26(5): 28-30.
40. Xin, C., 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.

    Book Chapters

41. Wan, X.-F., 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 Bioinformatics: New Research , edited by Peter V. Yan, pp. 55-80, Nova Publisher, Inc..
42. Xu, D., O. Duzlevski, and X.-F. Wan. 2005. In search of remote homolog. In Handbook of Computational Molecular Biology, edited by Aluru, Chapter 33, pp.1-27, CRC Press.
43. Wan, X.-F. and D.K. Thompson. High-throughput technologies and functional genomics. In Systems biology and synthetic biology, Fu ed. John Wiley & Son, Inc., in press.