Phylogenetic reconstruction from complete gene orders of whole genomes

Series on Advances in Bioinformatics and Computational Biology

Volumn 6, Issue , 2008, Pages 241-250

  Swenson, K M ^a   Arndt, W ^b   Tang, J ^b   Moret, B M E ^a,c  

^a EPFL   (Switzerland)

^b University of South Carolina   (United States)

^c SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

Author keywords

Gene duplication; Gene inversion; Gene loss; Genomic distance; Phylogenetic reconstruction; Whole genome data

Indexed keywords

GENE DUPLICATIONS; GENE LOSS; GENOMIC DISTANCE; PHYLOGENETIC RECONSTRUCTION; WHOLE-GENOME DATA;

BIOINFORMATICS; BIOLOGY; FORESTRY;

GENES;

EID: 84856946215     PISSN: 17516404     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (35)

1. J.R. Brown, C.J. Douady, M.J. Italia,W.E.Marshall and M.J. Stanhope, Nature Genetics 28, 281 (2001).
2. E. Lerat, V. Daubin and N. Moran, PLoS Biology 1 (2003).
3. A. Rokas, B.L. Williams, N. King and S.B. Carroll, Nature 425, 798 (2003).
4. S.T. Fitz-Gibbon and C.H. House, Nucleic Acids Res. 27, 4218 (1999).
5. X. Gu and H. Zhang, Mol. Biol. Evol. 21, 1401 (2004).
6. A. Rokas and P. Holland, Trends in Ecol. and Evol. 15, 454 (2000).
7. B.M.E. Moret and T. Warnow, Advances in phylogeny reconstruction from gene order and content data, in Molecular Evolution: Producing the Biochemical Data, Part B, eds. E. Zimmer and E. Roalson, Methods in Enzymology 395, 673 (Elsevier, 2005).
8. J.L. Boore and W.M. Brown, Curr. Opinion Genet. Dev. 8, 668 (1998).
9. M.E. Cosner, R.K. Jansen, B.M.E. Moret, L.A. Raubeson, L.-S. Wang, T. Warnow and S.K.Wyman, An empirical comparison of phylogenetic methods on chloroplast gene order data in Campanulaceae, in Comparative Genomics, eds. D. Sankoff and J.H. Nadeau, 99 (Kluwer Academic Publishers, 2000).
10. S.R. Downie and J.D. Palmer, Use of chloroplast DNA rearrangements in reconstructing plant phylogeny, in Molecular Systematics of Plants, eds. D. Soltis, P. Soltis and J.J. Doyle, 14 (Chapman and Hall, New York, 1992).
11. D. Sankoff, G. Leduc, N. Antoine, B. Paquin, B.F. Lang and R. Cedergren, Proc. Nat'l Acad. Sci., USA 89, 6575 (1992).
12. D.B. Stein, D.S. Conant, M.E. Ahearn, E.T. Jordan, S.A. Kirch, M. Hasebe, K. Iwatsuki, M.K. Tan and J.A. Thomson, Proc. Nat'l Acad. Sci., USA 89, 1856 (1992).
13. Y.I. Wolf, I.B. Rogozin, A.S. Kondrashov and E.V. Koonin, BMC Evol. Biol. 1 (2001).
14. L.-S. Wang, R.K. Jansen, B.M.E. Moret, L.A. Raubeson and T. Warnow, J. Mol. Evol. 63, 473 (2006).
15. T. Kunisawa, J. Theor. Biol. 213, 9 (2001).
16. T. Kunisawa, J. Theor. Biol. 222, 495 (2003).
17. T. Kunisawa, J. Theor. Biol. 239, 367 (2006).
18. E. Belda, A. Moya and F.J. Silva, Mol. Biol. Evol. 22, 1456 (2005).
19. B.M.E. Moret, S.K. Wyman, D.A. Bader, T. Warnow and M. Yan, A new implementation and detailed study of breakpoint analysis, in Proc. 6th Pacific Symp. on Biocomputing (PSB'01), 583 (World Scientific Pub., 2001).
20. G. Tesler, J. Comp. Syst. Sci. 65, 587 (2002).
21. G. Blin, C. Chauve and G. Fertin, Genes order and phylogenetic reconstruction: Application to gamma-proteobacteria, in Proc. 3rd RECOMB Workshop on Comparative Genomics (RECOMBCG' 05), LNCS 3678, 11 (Springer Verlag, 2005).
22. B. Larget, D.L. Simon, J.B. Kadane and D. Sweet, Mol. Biol. Evol. 22, 486 (2005).
23. M. Marron, K.M. Swenson and B.M.E. Moret, Theor. Comp. Sci. 325, 347 (2004).
24. K.M. Swenson, M. Marron, J.V. Earnest-DeYoung and B.M.E. Moret, Approximating the true evolutionary distance between two genomes, in Proc. 7th SIAM Workshop on Algorithm Engineering & Experiments (ALENEX'05), 121 (SIAM Press, Philadelphia, 2005).
25. S. Angibaud, G. Fertin, I. Rusu and S. Vialette, J. Comp. Biol. 14, 379 (2007).
26. J. Earnest-DeYoung, Reversing gene erosion: Reconstructing ancestral bacterial gene orders, Master's thesis, University of New Mexico (2004).
27. J. Tang and B.M.E. Moret, Linear programming for phylogenetic reconstruction based on gene rearrangements, in Proc. 16th Ann. Symp. Combin. Pattern Matching (CPM'05), LNCS 3537, 406 (Springer Verlag, 2005).
28. J. Tang and B.M.E. Moret, Scaling up accurate phylogenetic reconstruction from gene-order data, in Proc. 11th Int'l Conf. on Intelligent Systems for Mol. Biol. (ISMB'03), Bioinformatics 19, i305 (2003).
29. B.M.E. Moret, J. Tang, L.-S.Wang and T. Warnow, J. Comp. Syst. Sci. 65, 508 (2002).
30. A. Bachrach, K. Chen, C. Harrelson, R. Mihaescu, S. Rao and A. Shah, Lower bounds for maximum parsimony with gene order data, in Proc. 3rd RECOMB Workshop on Comparative Genomics (RECOMBCG'05), LNCS 3678, 1 (Springer Verlag, 2005).
31. J.V. Earnest-DeYoung, E. Lerat and B.M.E. Moret, Reversing gene erosion: reconstructing ancestral bacterial genomes from gene-content and gene-order data, in Proc. 4th Int'l Workshop Algs. in Bioinformatics (WABI'04), LNCS 3240, 1 (Springer Verlag, 2004).
32. S. Yancopoulos, O. Attie and R. Friedberg, Bioinformatics 21, 3340 (2005).
33. B.M.E. Moret, L.-S.Wang, T. Warnow and S. Wyman, New approaches for reconstructing phylogenies from gene-order data, in Proc. 9th Int'l Conf. on Intelligent Systems for Mol. Biol. (ISMB'01), Bioinformatics 17, S165 (2001).
34. D. Aldous, Stat. Sci. 16, 23 (2001).
35. D. Robinson and L. Foulds, Math. Biosci. 53, 131 (1981).