Recovering true rearrangement events on phylogenetic trees

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4751 LNBI, Issue , 2007, Pages 149-161

  Zhao, Hao ^a   Bourque, Guillaume ^a  

^a GENOME INSTITUTE OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

GENE EXPRESSION; OPTIMAL SYSTEMS; PROBLEM SOLVING;

FRAGILE REARRANGEMENT MODELS; PHYLOGENETIC TREES;

TREES (MATHEMATICS);

EID: 38349105423     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-74960-8_12     Document Type: Conference Paper

References (23)

1. Bafna, V., Pevzner, P.A.: Sorting by transpositions. SIAM Journal on Discrete Mathematics 11(2), 224-240 (1998)
2. Bourque, G., Pevzner, P.A.: Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 12, 26-36 (2002)
3. Bourque, G., Tesler, G., Pevzner, P.A: The convergence of cytogenetics and rearrangement-based models for ancestral genome reconstruction. Genome Res. 16(3), 311-313 (2006)
4. Bourque, G., Zdobnov, E.M., Bork, P., Pevzner, P.A., Tesler, G.: Comparative architectures of mammalian and chicken genomes reveal highly variable rates of genomic rearrangements across different lineages. Genome Res. 15(1), 98-110 (2005)
5. Caprara, A.: Formulations and complexity of multiple sorting by reversals. In: RECOMB 99, pp. 84-93 (1999)
6. Cosner, M., Jansen, R., Moret, B., Raubeson, L., Wang, L., Warnow, T., Wyman, S.: A new fast heuristic for computing the breakpoint phylogeny and experimental phylogenetic analyses of real and synthetic data. In: ISMB00, pp. 104-115 (2000)
7. Froenicke, L., Caldes, M.G., Graphodatsky, A., Muller, S., Lyons, LA, Robinson, T.J, Volleth, M., Yang, F., Wienberg, J.: Are molecular cytogenetics and bioinformatics suggesting diverging models of ancestral mammalian genomes?. Genome Res. 16(3), 306-310 (2006)
8. Hannenhalli, S., Chappey, C., Koonin, E., Pevzner, P.: Genome sequence comparison and scenarios for gene rearrangements: A test case. Genomics 30, 299-311 (1995)
9. Larget, B., Simon, D., Kadane, J., Sweet, D.: A bayesian analysis of metazoan mitochondrial genome arrangements. Mol. Biol. Evol. 22(3), 486-495 (2005)
10. Lin, C.H., Bourque, G., Tan, P.: Comparative analysis of Burkholderia species reveals an association between large-scale and fine-scale divergence in prokaryotes. In: preparation (2007)
11. Ma, J., Zhang, L., Suh, B.B., Raney, B.J., Burhans, R.C, Kent, W J., Blanchette, M., Haussler, D., Miller, W.: Reconstructing contiguous regions of an ancestral genome. Genome Res. 16(12), 1557-1565 (2006)
12. Miklos, I.: MCMC genome rearrangement. Bioinformatics 19(90002), 130ii-137 (2003)
13. Moret, B.M.E., Wyman, S., Bader, D.A., Warnow, T., Yan, M.: A new implementation and detailed study of breakpoint analysis. In: PSB 2001, pp. 583-594 (2001)
14. Murphy, W.J., Larkin, D.M.. van der Wind, A.E.-, Bourque, G.: Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309(5734), 613-617 (2005)
15. Peng, Q., Pevzner, P.A, Tesler, G.: The fragile breakage versus random breakage models of chromosome evolution. PLoS Comput. Biol. 2(2), 14 (2006)
16. Pevzner. P., Tesler, G.: Human and mouse genomic sequences reveal extensive breakpoint reuse in mammalian evolution. Proc. Natl. Acad. Sci. USA 100(13), 7672-7677 (2003)
17. Sankoff, D.: The signal in the genomes. PLoS Comput. Biol. 2(4), e35 (2006)
18. Sankoff, D., Leduc, G., Antoine, N., Paquin, B., Lang, B., Cedergren, R.: Gene order comparisons for phylogenetic inference: Evolution of the mitochondrial genome. Proceedings of the National Academy of Sciences USA 89, 6575-6579 (1992)
19. Sankoff, D., Trinh, P.: Chromosomal breakpoint reuse in genome sequence rearrangement. J. Comput. Biol. 12(6), 812-821 (2005)
20. Savva, G., Dicks, J.L., Roberts, I.N.: Current approaches to whole genome phylogenetic analysis. Briefings in Bioinformatics 4(1), 63-74 (2003)
21. Siepel, A.: An algorithm to find all sorting reversals. In: RECOMB02, pp. 281-290 (2002)
22. Tesler, G.: GRIMM: genome rearrangements web server. Bioinformatics 18(3), 492-493 (2002)
23. Walter, M., Dias, Z., Meidanis, J.: A new approach for approximating the transposition distance. In: De La Fuenta, P. (ed.) SPIRE, pp. 199-208. IEEE Computer Society Press, Los Alamitos (2000)