Evolutioanry Bioinformatics Laboratory

Publications

• Wywial E, Haven J, Casjens SR, Hernandez YA, Singh S, Mongodin EF, Fraser-Liggett CM, Luft BJ, Schutzer SE, Qiu WG. 2009. Fast, adaptive evolution at a bacterial host-resistance locus: The PFam54 gene array in Borrelia burgdorferi. Gene. 445:26-37.

• Tran D, Haven J, Qiu WG, Polle JE. 2009. An update on carotenoid biosynthesis in algae: phylogenetic evidence for the existence of two classes of phytoene synthase. Planta. 229(3):723-9.

• Arva NC, Talbott KE, Okoro DR, Brekman A, Qiu WG, Bargonetti J. 2008. Disruption of the p53-Mdm2 complex by Nutlin-3 reveals different cancer cell phenotypes. Ethnicity and Disease. 18(S2):1-8.

• Qiu, WG; Bruno, JF; McCaig, WD; Xu, Y.; Livey, I.; Schriefer, ME; Luft, BJ. 2008. Wide distribution of a high-virulence borrelia burgdorferi clone in Europe and North America. Emerging Infectious Diseases. 14(7):1097-1104. [Open Access]

• Otoo HN; Lee KG; Qiu WG; Lipke PN. 2008. Candia albicans Als adhesins have conserved amyloid-forming sequences. Eukaryotic Cell. 7 (5):776-82.

• Coronado JE; Mneimneh S; Epstein SL; Qiu WG; Lipke PN. 2007. Conserved processes and lineage-specific proteins in fungal cell wall evolution. Eukaryotic Cell. 6 (12):2269-77. [ASM Abstract]

• Lapp, H.; Bala, S; Balhoff, J. P.; et al. (24 authors) 2007. The 2006 NESCent Phyloinformatics Hackathon: A Field Report. Evolutionary Bioinformatics. 3:357-366. [Open Access]

• Hladish, T.; Gopalan, V.; Liang, C. Z.; Qiu, W. G.; Yang, P.; Stoltzfus, A. 2007. Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data. BMC Bioinformatics. 8:191. [Open Access ]

• Attie, O.; Bruno, J. F.; Xu, Y.; Qiu, D.; Luft, B. J.; Qiu, W. G. 2007. Co-evolution of the outer surface protein C gene (ospC) and intraspecific lineages of Borrelia burgdorferi sensu stricto in the northeastern United States. Infection, Genetics and Evolution. 7 (1):1-12. [ PubMed ] [ PDF ]

• Casjens, S., Huang, W., Gilcrease, E., Qiu, W., McCaig, W., Luft, B., Schutzer, S., and Fraser, C. 2006. Comparative genomics of Borrelia burgdorferi. In: The Moelcular Biology of Spirochetes , Cabello, F., Hulinska, D., and Godfrey, H. (Eds.), IOS Press, Amsterdam, pp. 79-96.

• Romov, P. A.; Li, F. B.; Lipke, L. N.; Epstein, S. L.; Qiu, W. G.. 2006. Comparative genomics reveals long, evolutionarily-conserved, low-complexity islands in yeast proteins. Journal of Molecular Evolution. 63 (3):415-425 [ PubMed ] [ PDF ]

• Coronado, J. E.; Attie, O.; Epstein, S. L.; Qiu, W. G.; Lipke, P. N. 2006. Composition-modified matrices improve identification of homologs of Saccharomyces cerevisiae low-complexity glycoporteins. Eukaryotic Cell. 5 (4): 628-637 [PubMed] [Application website]
  

• Goplan, V. , Qiu, W. G.; Chen, M. Z.; Stolzfus, A. 2006. Nexplorer: Phylogeny-based exploration of sequence family data. Bioinformatics. 22: 120-121 [Open Access]
  

• Qiu W. G.; Schutzer S. E., Bruno J. F., Attie O., Xu Y., Dunn J. J., Fraser C. M., Casjens S. R., and Luft B. J.. 2004. Genetic exchange and plasmid transfers in Borrelia burgdorferi sensu stricto revealed by three-way genome comparisons and multilocus sequence typing. PNAS 101 (39): 14150-14155. [Open Access] [Data Posting]

• Qiu, W. G.; Schisler, N. J.; Stoltzfus, A. 2004. The evolutionary gain of splicesomal introns: Sequence and phase preferences. Molecular Biology and Evolution 21:1252-1263. [PubMed Abstract] [PDF]

• Qiu, W. G.; Dykhuizen, D. E.; Acosta, M. S.; Luft, B. J. 2002. Geographic Uniformity of the Lyme Disease Spirochete (Borrelia burgdorferi) and Its Shared History With Tick Vector (Ixodes scapularis) in the Northeastern United States. Genetics 160: 833-49. [PubMed Abstract] [PDF]

• Rannala, B.; Qiu, W. G.; Dykhuizen, D. E. 2000. Methods for estimating gene frequencies and detecting selection in bacterial populations. Genetics 155: 499-508. [PubMed Abstract] [PDF]

• Wang, I. N.; Dykhuizen, D. E.; Qiu, W. G.; Dunn, J. J.; Bosler, E. M.; Luft, B. J.1999. Genetic diversity of ospC in a local population of Borrelia burgdorferi sensu stricto. Genetics 151: 15-30. [PubMed Abstract] [PDF]

• Qiu, W. G.; Bosler, E. M.; Campbell, J. R.; Ugine, G. D.; Wang, I. N.; Luft, B. J.; Dykhuizen, D. E. 1997. A population genetic study of Borrelia burgdorferi sensu stricto from eastern Long Island, New York, suggested frequency-dependent selection, gene flow and host adaptation. Hereditas 127:203-16. [PubMed Abstract] [Reprint available from WGQ]