Journal of Biomedicine and Biotechnology
Volume 2008 (2008), Article ID 472719, 7 pages
doi:10.1155/2008/472719
Research Article

Unsupervised Learning in Detection of Gene Transfer

1Department of Computer Science and Statistics, University of Rhode Island, Kingston, RI 02881, USA
2Department of Molecular and Cell Biology, College of Liberal Arts and Sciences, University of Connecticut, CT 06269, USA
3Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 1X5 , Canada

Received 13 September 2007; Accepted 14 December 2007

Academic Editor: Daniel Howard

Copyright © 2008 L. Hamel et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. J. P. Gogarten, W. F. Doolittle, and J. G. Lawrence, “Prokaryotic evolution in light of gene transfer,” Molecular Biology and Evolution, vol. 19, no. 12, pp. 2226–2238, 2002.
  2. M. D. Hendy and D. Penny, “Spectral analysis of phylogenetic data,” Journal of Classification, vol. 10, pp. 5–24, 1993. View at Publisher · View at Google Scholar
  3. O. Zhaxybayeva, P. Lapierre, and J. P. Gogarten, “Genome mosaicism and organismal lineages,” Trends in Genetics, vol. 20, no. 5, pp. 254–260, 2004. View at Publisher · View at Google Scholar · View at PubMed
  4. T. Kohonen, Self-Organizing Maps, Springer, Berlin, Germany, 3rd edition, 2001.
  5. T. Abe, H. Sugawara, M. Kinouchi, S. Kanaya, and T. Ikemura, “Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples,” DNA Research, vol. 12, no. 5, pp. 281–290, 2005. View at Publisher · View at Google Scholar · View at PubMed
  6. N. Nahar, M. S. Poptsova, L. Hamel, and J. P. Gogarten, “GPX: a tool for the exploration and visualization of genome evolution,” in Proceedings of the 7th IEEE International Symposium on Bioinformatics & Bioengineering (BIBE '07), pp. 1338–1342, Boston, Mass, USA, October 2007. View at Publisher · View at Google Scholar
  7. J. Felsenstein, “Confidence limits on phylogenies: an approach using the bootstrap,” Evolution, vol. 39, no. 4, pp. 783–791, 1985. View at Publisher · View at Google Scholar
  8. G. M. Lento, R. E. Hickson, G. K. Chambers, and D. Penny, “Use of spectral analysis to test hypotheses on the origin of pinnipeds,” Molecular Biology and Evolution, vol. 12, no. 1, pp. 28–52, 1995.
  9. W. M. Fitch, “Homology: a personal view on some of the problems,” Trends in Genetics, vol. 16, no. 5, pp. 227–231, 2000. View at Publisher · View at Google Scholar
  10. S. F. Altschul, W. Gish, W. Miller, E. W. Myers, and D. J. Lipman, “Basic local alignment search tool,” Journal of Molecular Biology, vol. 215, pp. 403–410, 1990.
  11. O. Zhaxybayeva and J. P. Gogarten, “Boostrap, Bayesian probability and maximum likelihood mapping: exploring new tools for comparative genome analyses,” BMC Genomics, vol. 3, p. 4, 2002. View at Publisher · View at Google Scholar
  12. J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, pp. 4673–4680, 1994. View at Publisher · View at Google Scholar
  13. S. Guindon and O. Gascuel, “A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood,” Systematic Biology, vol. 52, no. 5, pp. 696–704, 2003. View at Publisher · View at Google Scholar
  14. R. Jain, M. C. Rivera, J. E. Moore, and J. A. Lake, “Horizontal gene transfer accelerates genome innovation and evolution,” Molecular Biology and Evolution, vol. 20, no. 10, pp. 1598–1602, 2003. View at Publisher · View at Google Scholar · View at PubMed
  15. R. G. Beiko, T. J. Harlow, and M. A. Ragan, “Highways of gene sharing in prokaryotes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 40, pp. 14332–14337, 2005. View at Publisher · View at Google Scholar · View at PubMed
  16. C. Brochier, P. Forterre, and S. Gribaldo, “An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences,” BMC Evolutionary Biology, vol. 5, p. 36, 2005. View at Publisher · View at Google Scholar · View at PubMed
  17. C. R. Woese, “Bacterial evolution,” Microbiology and Molecular Biology Reviews, vol. 51, pp. 221–271, 1987.
  18. O. Zhaxybayeva and J. P. Gogarten, “Cladogenesis, coalescence and the evolution of the three domains of life,” Trends in Genetics, vol. 20, no. 4, pp. 182–187, 2004. View at Publisher · View at Google Scholar · View at PubMed
  19. I. Jolliffe, Principal Component Analysis, Springer, Berlin, Germany, 2002.
  20. L. K. Saul and S. T. Roweis, “Think globally, fit locally: unsupervised learning of low dimensional manifolds,” Journal of Machine Learning Research, vol. 4, no. 2, pp. 119–155, 2004. View at Publisher · View at Google Scholar
  21. C. M. Bishop, M. Svensen, and C. K. I. Williams, “GTM: the generative topographic mapping,” Neural Computation, vol. 10, no. 1, pp. 215–234, 1998. View at Publisher · View at Google Scholar
  22. B. Scholkopf, A. Smola, and K. R. Muller, “Kernel principal component analysis,” in Advances in Kernel Methods-Support Vector Learning, pp. 327–352, MIT press, Cambridge, Mass, USA, 1999.
  23. J. B. Tenenbaum, V. de Silva, and J. C. Langford, “A global geometric framework for nonlinear dimensionality reduction,” Science, vol. 290, no. 5500, pp. 2319–2323, 2000. View at Publisher · View at Google Scholar · View at PubMed