Baculovirus phylogeny based on genome rearrangements

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

Volumn 4751 LNBI, Issue , 2007, Pages 69-82

  Goodman, Daniel ^a   Ollikainen, Noah ^b   Sholley, Chris ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; BIOINFORMATICS; PROBLEM SOLVING; VIRUSES;

BACULOVIRUS PHYLOGENY; GENE-BASED PHYLOGENIES; GENOME REARRANGEMENTS;

GENES;

EID: 38349072117     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-74960-8_6     Document Type: Conference Paper

References (31)

1. Albrecht, J., Nicholas, J., Biller, D., Cameron, K.R., Biesinger, B., Newman, C., Wittmann, S., Craxton, M.A., Coleman, H., Fleckenstein, B., Honess, R.W.: Primary structure of the herpesvirus saimiri genome. J. Virol. 66, 5047-5058 (1992)
2. Belda, E., Moya, A., Silva, F.: Genome Rearrangement Distances and Gene Order Phylogeny in γ-Proteobacteria. Molecular Biology and Evolution. 22, 1456-1467 (2005)
3. Blanchette, M., Bourque, G., Sankoff, D.: Breakpoint phylogenies. In: Miyano, S., Takagi, T. (eds.) Genome Informatics 1997, pp. 25-34. Univ. Academy Press (1997)
4. Bourque, G., Pevzner, P.: Genome-Scale Evolution: Reconstructing Gene Orders in the Ancestral Species. Genome Research. 12(1), 26-36 (2002)
5. Bourque, G., Pevzner, P.A., Tesler, G.: Reconstructing the genomic architecture of ancestral mammals: lessons from human, mouse, and rat genomes. Genome Research. 14, 507-516 (2004)
6. Bryant, D.: The complexity of calculating exemplar distances. In: Sankoff, D., Nadeau, J. (eds.) Comparative Genomics, pp. 207-212. Kluwer Academic Publishers, Dordrecht (2000)
7. Cormen, T.H., Leiserson, C.E., Riverst, R.L, Stein, C.: Introduction to Algorithms. Mc-Graw Hill, New York (2001)
8. El-Mabrouk, N.: Genome rearrangement by reversals and insertions/deletions of contiguous segments. In: Giancarlo, R., Sankoff, D. (eds.) CPM 2000. LNCS, vol. 1848, pp. 222-234. Springer, Heidelberg (2000)
9. Hannenhalli, S., Pevzner, P.: Transforming cabbage into turnip (polynomial algorithm for sorting signed permutations by reversals). In: Theory of Computing STOC 95, pp. 178-189. ACM Press, New York (1995)
10. Hannenhalli, S., Chappey, C., Koonin, E., Pevzner, P.: Genome Sequence Comparison and Scenarios for Gene Rearrangements: A Test Case. Genomics. 30, 299-311 (1995)
11. Hanson, L., Rudis, M., Vasquez-Lee, M., Montgomery, D.: A broadly applicable method to characterize large DNA viruses and adenoviruses based on the DNA polymerase gene. Virology Journal 3, 28 (2006)
12. Herniou, E., Luque, T., Chen, X., Vlak, J., Winstanley, D., Cory, D., O'Reilly, D.: Use of Whole Genome Sequence Data To Infer Baculovirus Phylogeny. Journal of Virology 75(17), 8117-8126 (2001)
13. Herniou, E., lszewski, O., Cory, J., O'Reilly, D.: The Genome Sequence and Evolution of Baculoviruses. Annual Review of Entomology 48, 211-234 (2003)
14. Herniou, E., Olszewski, J., O'Reilly, D., Cory, J.: Ancient Coevolution of Baculoviruses and Their Insect Hosts. Journal of Virology. 78(7), 3244-3251 (2004)
15. Graur, D., Li, W.: Fundamentals of Molecular Evolution. In: Sinauer Associates, Sunderland, Massachusetts (2000)
16. Koonin, E.V., Aravind, L., Kondrashov, A.S.: The impact of comparative genomics on our understanding of evolution. Cell 101(6), 573-576 (2000)
17. Li, L., Stoeckert, C.J., Roos, D.S.: OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes. Genome Res. 13(9), 2178-2189 (2003)
18. Moret, B.M.E., Siepel, A.C., Tang, J., Liu, T.: Inversion medians outperform breakpoint medians in phylogeny reconstruction from gene-order data. In: Guigó, R., Gusfield, D. (eds.) WABI 2002. LNCS, vol. 2452, pp. 521-536. Springer, Heidelberg (2002)
19. Murphy, W.J., Larkin, D.M., van der Wind, A.E., Bourque, G., Tesler, G., Auvil, L., Beever, J.E., Chowdhary, B.P., Galibert, F., Gatzke, L., Hitte, C., Meyers, S.N., Milan, D., Ostrander, E.A., Pape, G., Parker, H.G., Raudsepp, T., Rogatcheva, M.B., Schook, L.B., Skow, L.C., Welge, M., Womack, J.E., O'brien, S.J., Pevzner, P.A., Lewin, H.A.: Dynamics of mammalian chromosome evolution inferred from multispecies comparative maps. Science 309(5734), 613-617 (2005)
20. Murphy, W., Pevzner, P., O'Brien, S.: Mammalian phylogenomics comes of age. Trends in Genetics. 20(12), 631-639 (2004)
21. Olmstead, R., Palmer, J.: Chloroplast DNA systematics: a review of methods and data analysis. Amer. J. Bot. 81, 1205-1224 (1994)
22. Palmer, J., Herbon, L.: Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J. Mol. Evol. 27, 87-97 (1988)
23. Remm, D., Storm, CE.V., Sonnhammer, E.L.L.: Automatic Clustering of Orthologs and In-paralogs from Pairwise Species Comparisons. J. Mol. Biol. 314, 1041-1052
24. Rokas, A., Holland, P.W.H.: Rare genomic changes as a tool for phylogenetics. Trends in Ecology & Evolution 15(11), 454-459 (2000)
25. Sankoff, D.: Genome rearrangement with gene families. Technical Report, Centre de recherches mathématiques, Université de Montréal (1999)
26. Sankoff, D., Blanchette, M.: Multiple genome rearrangement and breakpoint phylogeny. Journal of Computational Biology 5, 555-570 (1998)
27. Snel, B., Bork, P., Huynen, M.: Genome phylogeny based on gene content. Nature Genetics. 21, 108-110 (1999)
28. Snel, B., Bork, P., Huynen, M.: Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene Content. Nature. 417, 399-403 (2002)
29. Tesler, G., Pavel, P.: Genome Rearrangements in Mammalian Evolution: Lessons From Human and Mouse Genomes. Genome Res. 13, 37-45 (2003)
30. Thornton, J.W., DeSalle, R.: Gene family evolution and homology: genomics meets phylogenetics. Annu. Rev. Genomics Hum. Genet. 1, 41-73 (2000)
31. Wang, L., Warnow, T.: Estimating true evolutionary distances between genomes. In: Proceedings of the Thirty-third Symposium on Theory of Computing (STOC'01), pp. 637-646. ACM Press, New York (2001)