Minimum leaf removal for reconciliation: Complexity and algorithms

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

Volumn 7354 LNCS, Issue , 2012, Pages 399-412

  Dondi, Riccardo ^a   El Mabrouk, Nadia ^b  

^a UNIVERSITY OF BERGAMO   (Italy)

^b UNIVERSITÉ DE MONTRÉAL   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

COMBINATORIAL PROBLEM; FIXED-PARAMETER ALGORITHMS; GENE FAMILIES; GENE TREE; LEAF REMOVAL; MULTIPLE GENES; PREPROCESS;

ALGORITHMS; FORESTRY; PATTERN MATCHING;

GENES;

ALGORITHMS; FORESTRY; GENES;

EID: 84863110624     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-31265-6_32     Document Type: Conference Paper

References (30)

1. Alimonti, P., Kann, V.: Some APX-completeness results for cubic graphs. Theor. Comput. Sci. 237(1-2), 123-134 (2000)
2. Altschul, S., Gish, W., Miller, W., Myers, E., Lipman, D.: Basic local alignment search tool. J. Mol. Biol. 215(3), 403-410 (1990)
3. Arvestad, L., Berglung, A.C., Lagergren, J., Sennblad, B.: Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. In: Gusfield, D. (ed.) RECOMB 2004, pp. 326-335. ACM, New York (2004)
4. Blin, G., Bonizzoni, P., Dondi, R., Rizzi, R., Sikora, F.: Complexity Insights of the Minimum Duplication Problem. In: Bieliková, M., Friedrich, G., Gottlob, G., Katzenbeisser, S., Turán, G. (eds.) SOFSEM 2012. LNCS, vol. 7147, pp. 153-164. Springer, Heidelberg (2012)
5. Blomme, T., Vandepoele, K., Bodt, S.D., Silmillion, C., Maere, S., van de Peer, Y.: The gain and loss of genes during 600 millions years of vertebrate evolution. Genome Biology 7, R43 (2006)
6. Bonizzoni, P., Della Vedova, G., Dondi, R.: Reconciling a gene tree to a species tree under the duplication cost model. Theoretical Computer Science 347, 36-53 (2005)
7. Chang, W.-C., Eulenstein, O.: Reconciling Gene Trees with Apparent Polytomies. In: Chen, D.Z., Lee, D.T. (eds.) COCOON 2006. LNCS, vol. 4112, pp. 235-244. Springer, Heidelberg (2006)
8. Chauve, C., El-Mabrouk, N.: New Perspectives on Gene Family Evolution: Losses in Reconciliation and a Link with Supertrees. In: Batzoglou, S. (ed.) RECOMB 2009. LNCS, vol. 5541, pp. 46-58. Springer, Heidelberg (2009)
9. Chen, K., Durand, D., Farach-Colton, M.: Notung: Dating gene duplications using gene family trees. Journal of Computational Biology 7, 429-447 (2000)
10. Cotton, J., Page, R.: Rates and patterns of gene duplication and loss in the human genome. Proceedings of the Royal Society of London. Series B 272, 277-283 (2005)
11. Demuth, J., Bie, T.D., Stajich, J., Cristianini, N., Hahn, M.: The evolution of mammalian gene families. PLoS ONE 1, e85 (2006)
12. Doroftei, A., El-Mabrouk, N.: Removing Noise from Gene Trees. In: Przytycka, T.M., Sagot, M.-F. (eds.) WABI 2011. LNCS (LNBI), vol. 6833, pp. 76-91. Springer, Heidelberg (2011)
13. Durand, D., Haldórsson, B., Vernot, B.: A hybrid micro-macroevolutionary approach to gene tree reconstruction. Journal of Computational Biology 13, 320-335 (2006)
14. Eichler, E., Sankoff, D.: Structural dynamics of eukaryotic chromosome evolution. Science 301, 793-797 (2003)
15. Goodman, M., Czelusniak, J., Moore, G., Romero-Herrera, A., Matsuda, G.: Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Systematic Zoology 28, 132-163 (1979)
16. Górecki, P., Eulenstein, O.: A Linear Time Algorithm for Error-Corrected Reconciliation of Unrooted Gene Trees. In: Chen, J., Wang, J., Zelikovsky, A. (eds.) ISBRA 2011. LNCS, vol. 6674, pp. 148-159. Springer, Heidelberg (2011)
17. Gorecki, P., Tiuryn, J.: DLS-trees: a model of evolutionary scenarios. Theoretical Computer Science 359, 378-399 (2006)
18. Guigó, R., Muchnik, I., Smith, T.: Reconstruction of ancient molecular phylogeny. Molecular Phylogenetics and Evolution 6, 189-213 (1996)
19. Hahn, M.: Bias in phylogenetic tree reconciliation methods: implications for vertebrate genome evolution. Genome Biology 8(R141) (2007)
20. Hahn, M., Han, M., Han, S.G.: Gene family evolution across 12 drosophilia genomes. PLoS Genetics 3, e197 (2007)
21. Kristensen, D., Wolf, Y., Mushegian, A., Koonin, E.: Computational methods for gene orthology inference. Briefings in Bioinformatics 12(5), 379-391 (2011)
22. Ma, B., Li, M., Zhang, L.: From gene trees to species trees. SIAM J. on Comput. 30, 729-752 (2000)
23. Niedermeier, R.: Invitation to Fixed-Parameter Algorithms. Oxford University Press, Oxford (2006)
24. Ohno, S.: Evolution by gene duplication. Springer, Berlin (1970)
25. Page, R.: Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Systematic Biology 43, 58-77 (1994)
26. Page, R.: Genetree: comparing gene and species phylogenies using reconciled trees. Bioinformatics 14, 819-820 (1998)
27. Page, R., Charleston, M.: Reconciled trees and incongruent gene and species trees. DIMACS Series in Discrete Mathematics and Theoretical Computer Science 37, 57-70 (1997)
28. Page, R., Cotton, J.: Vertebrate phylogenomics: reconciled trees and gene duplications. In: Pacific Symposium on Biocomputing, pp. 536-547 (2002)
29. Sanderson, M., McMahon, M.: Inferring angiosperm phylogeny from EST data with widespread gene duplication. BMC Evolutionary Biology 7, S3 (2007)
30. Vernot, B., Stolzer, M., Goldman, A., Durand, D.: Reconciliation with non-binary species trees. Journal of Computational Biology 15, 981-1006 (2008)