Consistency of sequence-based gene clusters

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

Volumn 6398 LNBI, Issue , 2010, Pages 252-263

  Wittler, Roland ^a,b   Stoye, Jens ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

^b BIELEFELD UNIVERSITY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

CO-LOCATED; COMBINATORIAL MODELS; COMMON INTERVALS; COMPARATIVE GENOMICS; COMPLEX MODEL; CONSISTENCY PROBLEMS; GENE CLUSTERS; GENE ORDERS; LINEAR-TIME ALGORITHMS; NP-COMPLETENESS; RECONSTRUCTION CRITERIA; SIMPLE MODELING;

CLUSTERING ALGORITHMS;

GENES;

EID: 78649967415     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-16181-0_21     Document Type: Conference Paper

References (22)

1. Adam, Z., Turmel, M., Lemieux, C., Sankoff, D.: Common intervals and symmetric difference in a model-free phylogenomics, with an application to streptophyte evolution. J. Comp. Biol. 14(4), 436-445 (2007)
2. Bergeron, A., Blanchette, M., Chateau, A., Chauve, C.: Reconstructing ancestral gene order using conserved intervals. In: Jonassen, I., Kim, J. (eds.) WABI 2004. LNCS (LNBI), vol. 3240, pp. 14-25. Springer, Heidelberg (2004)
3. Bergeron, A., Stoye, J.: On the similarity of sets of permutations and its applications to genome comparison. J. Comp. Biol. 13(7), 1340-1354 (2006)
4. Bhutkar, A., Gelbart, W.M., Smith, T.F.: Inferring genome-scale rearrangement phylogeny and ancestral gene order: A drosophila case study. Genome Biol. 8(11), R236 (2007) (Pubitemid 351935869)
5. Blin, G., Stoye, J.: Finding nested common intervals efficiently. J. Comp. Biol. (to appear 2010);
6. A preliminary version appeared in Proc. of RECOMB-CG 2009. LNCS (LNBI), vol. 5817, pp. 59-69 (2009)
7. Böcker, S., Jahn, K., Mixtacki, J., Stoye, J.: Computation of median gene clusters. J. Comp. Biol. 16(8), 1085-1099 (2009)
8. Chauve, C., Tannier, E.: A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes. PLoS Comput. Biol. 4(11), e1000234 (2008)
9. Csucombining double acute accentrös, M., Miklós, I.: Mathematical framework for phylogenetic birth-and-death models. Arxiv preprint arXiv:0902.0970 (2009)
10. Hoberman, R., Durand, D.: The Incompatible Desiderata of Gene Cluster Properties. In: McLysaght, A., Huson, D.H. (eds.) RECOMB 2005. LNCS (LNBI), vol. 3678, pp. 73-87. Springer, Heidelberg (2005)
11. Hsu, W.-L., McConnell, R.: PQ-trees, PC-trees, and planar graphs. In: Mehta, D.P., Sahni, S. (eds.) Handbook of Data Structures and Applications (2004)
12. Huynen, M.A., Snel, B., Bork, P.: Inversions and the dynamics of eukaryotic gene order. Trends Genet. 17(6), 304-306 (2001)
13. Itai, A., Papadimitriou, C.H., Szwarcfiter, J.L.: Hamilton paths in grid graphs. SIAM J. Computing 11(4), 676-686 (1982)
14. Jaillon, O., Aury, J.-M., Brunet, F., Petit, J.-L., Stange-Thomann, N., et al.: Genome duplication in the teleost fish tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431(7011), 946-957 (2004)
15. Lawrence, J.G., Roth, J.R.: Selfish operons: Horizontal transfer drive the evolution of gene clusters. Genetics 143(4), 1843-1860 (1996)
16. Ma, J., Zhang, L., Suh, B.B., Raney, B.J., Burhans, R.C., Kent, J.W., Blanchette, M., Haussler, D., Miller, W.Z.: Reconstructing contiguous regions of an ancestral genome. Genome Res. 16(12), 1557-1565 (2006)
17. Overbeek, R., Fonstein, M., D'Souza, M., Pusch, G.D., Maltsev, N.: The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA 96(6), 2896-2901 (1999)
18. Page, R.D.M., Charleston, M.A.: From gene to organismal phylogeny: Reconciled trees and the gene tree/species tree problem. Mol. Phyl. and Evol. 7(2), 231-240 (1997)
19. Rahmann, S., Klau, G.W.: Integer linear programs for discovering approximate gene clusters. In: Bücher, P., Moret, B.M.E. (eds.) WABI 2006. LNCS (LNBI), vol. 4175, pp. 298-306. Springer, Heidelberg (2006)
20. Stoye, J., Wittler, R.: A unified approach for reconstructing ancient gene clusters. IEEE/ACM Trans. Comput. Biol. Bioinf. 6(3), 387-400 (2009)
21. Uno, T., Yagiura, M.: Fast algorithms to enumerate all common intervals of two permutations. Algorithmica 26(2), 290-309 (2000)
22. Wittler, R.: Phylogeny-based Analysis of Gene Clusters. Ph.D. Thesis, Faculty of Technology, Bielefeld University (2010), http://bieson.ub.uni- bielefeld.de/ volltexte/2010/1627/