15.12.2012 Views

Bioinformatics, Volume I Data, Sequence Analysis and Evolution

Bioinformatics, Volume I Data, Sequence Analysis and Evolution

Bioinformatics, Volume I Data, Sequence Analysis and Evolution

SHOW MORE
SHOW LESS

You also want an ePaper? Increase the reach of your titles

YUMPU automatically turns print PDFs into web optimized ePapers that Google loves.

468 Beiko <strong>and</strong> Ragan<br />

8. Nelson, K. E., Clayton, R. A., Gill, S. R., et<br />

al. (1999) Evidence for lateral gene transfer<br />

between Archaea <strong>and</strong> bacteria from genome<br />

sequence of Thermotoga maritima. Nature<br />

399, 323–329.<br />

9. Ragan, M. A. (2001) On surrogate methods<br />

for detecting lateral gene transfer.<br />

FEMS Microbiol Lett 201, 187–191.<br />

10. Ragan, M. A., Harlow, T. J., Beiko, R. G.<br />

(2006) Do different surrogate methods<br />

detect lateral genetic transfer events of different<br />

relative ages? Trends Microbiol 14,<br />

4–8.<br />

11. Ho, S. Y., Jermiin, L. (2004) Tracing the<br />

decay of the historical signal in biological<br />

sequence data. Syst Biol 53, 623–637.<br />

12. Jermiin, L., Ho, S. Y., Ababneh, F., et al.<br />

(2004) The biasing effect of compositional<br />

heterogeneity on phylogenetic estimates<br />

may be underestimated. Syst Biol 53, 638–<br />

643.<br />

13. Tatusov, R. L., Fedorova, N. D., Jackson,<br />

J. D., et al. (2003) The COG database: an<br />

updated version includes eukaryotes. BMC<br />

<strong>Bioinformatics</strong> 4, 41.<br />

14. Peterson, J. D., Umayam, L. A., Dickinson,<br />

T., et al. (2001) The comprehensive<br />

microbial resource. Nucleic Acids Res 29,<br />

123–125.<br />

15. Van Dongen, S. (2000) Graph clustering<br />

by flow simulation. Ph.D. Thesis: University<br />

of Utrecht, Utrecht.<br />

16. Rigoutsos, I., Floratos, A. (1998) Combinatorial<br />

pattern discovery in biological<br />

sequences: the TEIRESIAS algorithm. <strong>Bioinformatics</strong><br />

14, 55–67.<br />

17. Beiko, R. G., Chan, C. X., Ragan, M. A.<br />

(2005) A word-oriented approach to alignment<br />

validation. <strong>Bioinformatics</strong> 21, 2230–<br />

2239.<br />

18. Thompson, J. D., Higgins, D. G., Gibson,<br />

T. J. (1994) CLUSTAL W: improving the<br />

sensitivity of progressive multiple sequence<br />

alignment through sequence weighting,<br />

position-specific gap penalties <strong>and</strong> weight<br />

matrix choice. Nucleic Acids Res 22, 4673–<br />

4680.<br />

19. Notredame, C., Higgins, D. G., Heringa,<br />

J. (2000) T-Coffee: A novel method for fast<br />

<strong>and</strong> accurate multiple sequence alignment.<br />

J Mol Biol 302, 205–217.<br />

20. Lee, C., Grasso, C., Sharlow, M. F. (2002)<br />

Multiple sequence alignment using partial<br />

order graphs. <strong>Bioinformatics</strong> 18, 452–464.<br />

21. Gotoh, O. (1996) Significant improvement<br />

in accuracy of multiple protein sequence<br />

alignments by iterative refinement as<br />

assessed by reference to structural alignments.<br />

J Mol Biol 264, 823–838.<br />

22. Katoh, K., Misawa, K., Kuma, K., et al.<br />

(2002) MAFFT: a novel method for rapid<br />

multiple sequence alignment based on fast<br />

Fourier transform. Nucleic Acids Res 30,<br />

3059–3066.<br />

23. Huelsenbeck, J. P., Ronquist, F. (2001)<br />

MRBAYES: Bayesian inference of phylogenetic<br />

trees. <strong>Bioinformatics</strong> 17, 754–755.<br />

24. Castresana, J. (2000) Selection of conserved<br />

blocks from multiple alignments for<br />

their use in phylogenetic analysis. Mol Biol<br />

Evol 17, 540–552.<br />

25. Creevey, C. J., McInerney, J. O. (2005)<br />

Clann: investigating phylogenetic information<br />

through supertree analyses. <strong>Bioinformatics</strong><br />

21, 390–392.<br />

26. Beiko, R. G., Hamilton, N. H. (2006) Phylogenetic<br />

identification of lateral genetic<br />

transfer events. BMC Evol Biol 6, 15.<br />

27. Altschul, S. F., Madden, T. L., Schaffer, A.<br />

A., et al. (1997) Gapped BLAST <strong>and</strong> PSI-<br />

BLAST: a new generation of protein database<br />

search programs. Nucleic Acids Res 25,<br />

3389–3402.<br />

28. Berman, H. M., Westbrook, J., Feng, Z.,<br />

et al. (2000) The Protein <strong>Data</strong> Bank.<br />

Nucleic Acids Res 28, 235–242.<br />

29. Harlow, T. J., Gogarten, J. P., Ragan, M. A.<br />

(2004) A hybrid clustering approach to recognition<br />

of protein families in 114 microbial<br />

genomes. BMC <strong>Bioinformatics</strong> 5, 45.<br />

30. Sokal, R. R., Sneath, P. H. A. (1963) Principles<br />

of Numerical Taxonomy, W.H. Freeman<br />

& Co, London.<br />

31. Maddison, D. R., Swofford, D. L., Maddison,<br />

W. P. (1997) NEXUS: an extensible<br />

file format for systematic information. Syst<br />

Biol 46, 590–621.<br />

32. Beiko, R. G., Keith, J. M., Harlow, T. J.,<br />

Ragan, M.A. (2006) Searching for convergence<br />

in Markov chain Monte Carlo. Syst<br />

Biol. 55, 553–565.<br />

33. Baum, B. R. (1992) Combining trees as a<br />

way of combining data sets for phylogenetic<br />

inference, <strong>and</strong> the desirability of combining<br />

gene trees. Taxon 41, 3–10.<br />

34. Ragan, M. A. (1992) Phylogenetic inference<br />

based on matrix representation of<br />

trees. Mol Phylogenet Evol 1, 53–58.<br />

35. Geyer, C. J. (1992) Practical Markov chain<br />

Monte Carlo. Stat Sci 7, 473–483.<br />

36. Cowles, M. K., Carlin, B. P. (1996) Markov<br />

chain Monte Carlo convergence diagnostics:<br />

a comparative review. J Amer Statist<br />

Assoc 91, 883–904.

Hooray! Your file is uploaded and ready to be published.

Saved successfully!

Ooh no, something went wrong!