On the tandem duplication-random loss model of genome rearrangement

Proceedings of the Annual ACM-SIAM Symposium on Discrete Algorithms

Volumn , Issue , 2006, Pages 564-570

  Chaudhuri, Kamalika ^a   Chen, Kevin ^a   Mihaescu, Radu ^a   Rao, Satish ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DUPLICATED GENES; MITOCHONDRIAL GENOMES; RANK AGGREGATION PROBLEM; TANDEM DUPLICATION;

ALGORITHMS; APPROXIMATION THEORY; GENES; MATHEMATICAL MODELS; PROBLEM SOLVING;

GENETIC ENGINEERING;

EID: 33244458846     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/1109557.1109619     Document Type: Conference Paper

References (25)

1. B. Moret, J. Tang, and T. Warnow. Reconstructing phytogenies from gene-content and gene-order data. In O. Gascuel, editor, Mathematics of Evolution and Phylogeny. Oxford Univ. Press, 2004.
2. D. Sankoff and J. Nadeau, editors. Comparative Genomics. Kluwer Academic Publishers, 2000.
3. N. El-Mabrouk. Genome rearrangements by reverals and insertions/deletions of contiguous segments. In CPM, 2000.
4. M. Marron, K.M. Swenson, and B.M.E. Moret. Genomic distances under deletions and insertions. In COCOON, 2003.
5. J. Tang, B. Moret, L. Cui, and C. dePamphilis. Phylogenetic reconstruction from arbitrary gene-order data. In BIBE, pages 592-599, 2004.
6. K.M. Swenson, M. Marron, J.V. Earnest-DeYoung, and B.M.E. Moret. Approximating the true evolutionary distance between two genomes. Tech. Report TRCS-2004-15, Univ. of New Mexico, 2004.
7. J. L. Boore. The duplication/random loss model for gene rearrangement exemplified by mitochondrial genomes of deuterostome animals. In D. Sankoff and J. Nadeau, editors, Comparative Genomics. Kluwer, 2000.
8. R. L. Mueller and J. L. Boore. Molecular mechanisms of extensive mitochondrial gene rearrangement in plethodontid salamanders. Mol. Bio. Evol., 22(10):2104-2112, 2005.
9. C. Moritz, T. E. Dowling, and W. M. Brown. Evolution of animal mitochondrial DNA: relvance for population biology and systematics. Annu. Rev. Ecol. Syst., 18:269-292, 1987.
10. S. Bensch and A. Härlid. Mitochondrial genomic rearrangements in songbirds. Mol. Biol. Evol., 17:107-113, 2000.
11. D. V. Lavrov, J. L. Boore, and W. M. Brown. Complete mtDN A sequences of two millipedes suggest a new model for mitochondrial gene rearrangements: duplication and nonrandom loss. Mol. Biol. Evol., 19(2):163-169, 2002.
12. J. G. Inoue, M. Miya, K. Tsukamoto, and M. Nishida. Evolution of the deep-sea guiper eel mitochondrial genomes: large-scale gene rearrangements originated within the eels. Mol. Biol. Evol., 20:1917-1924, November 2003.
13. I. Miklos and J. Hein. Genome rearrangement in mitochondria and its computational biology. In J. Lager-gren, editor, Comparative Genomics: RECOMB 2004 Int. Workshop, volume 3388. Springer-Verlag, 2005.
14. S. Ohno. Evolution by Gene Duplication. Springer, New York, 1970.
15. M. Kellis, B. Birren, and E. Lander. Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature, 428:617-624, 2004.
16. O. Jaillon, J. Aury, F. Brunet, J. Petit, N. Stange-Thomann, et al. Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature, 431:946-957, October 2004.
17. J. Felsenstein. Inferring Phylogenies. Sinauer Associates, 2004.
18. C. Dwork, R. Kumar, M. Naor, and D. Sivakumar. Rank aggregation methods for the web. In WWW, 2001.
19. N. Ailon, M. Charikar, and A. Newman. Aggregating inconsistent information: Ranking and clustering. In STOC, 2005.
20. S. Arora, A. Frieze, and H. Kaplan. A new rounding procedure for the assignment problem with applications to dense graph arrangement problems. In FOCS, 1996.
21. I. Pe'er and R. Shamir. The median, problem for breakpoints are NP-complete. Technical Report TR98-071, ECCC, 1998.
22. A. Caprara. Formulations and hardness of multiple sorting by reversals. In RECOMB, 1999.
23. I. Pe'er and R. Shamir. Approximation algorithms for the permutations median problem in the breakpoint model. In D. Sankoff and J. Nadeau, editors, Comparative Genomics, pages 225-241. Kluwer Academic Press, 2000.
24. G. Even, J. Naor, B. Schieber, and M. Sudan. Approximating minimum feedback sets and multi-cuts in directed graphs. In Proc. 4th Int. Conf. on Integer Prog. and Combinational Optimization, 1995.
25. K. G. Helfenbein, W. M. Brown, and J. L. Boore. The complete mitochondrial genome of the articulate brachiopod Terebratalia transversa. Mol. Biol. Evol., 18(9):1734-1744, September 2001.