Complexity insights of the minimum duplication problem

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

Volumn 7147 LNCS, Issue , 2012, Pages 153-164

  Blin, Guillaume ^a   Bonizzoni, Paola ^b   Dondi, Riccardo ^c   Rizzi, Romeo ^d   Sikora, Florian ^a,e  

^a UNIVERSITÉ PARIS EST   (France)

^b UNIVERSITY OF MILANO BICOCCA   (Italy)

^c UNIVERSITY OF BERGAMO   (Italy)

^d UNIVERSITY OF UDINE   (Italy)

^e FRIEDRICH SCHILLER UNIVERSITY JENA   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

COMPARATIVE GENOMICS; GENE DUPLICATIONS; GENE TREE; PHYLOGENETICS; RANDOMIZED ALGORITHMS;

COMPUTER SCIENCE; FORESTRY; GENES;

TREES (MATHEMATICS);

FORESTRY; GENETIC ENGINEERING; PROBLEM SOLVING;

EID: 84856052181     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-27660-6_13     Document Type: Conference Paper

References (16)

1. Alimonti, P., Kann, V.: Some APX-completeness results for cubic graphs. Theoretical Comput. Sci. 237(1-2), 123-134 (2000)
2. Bansal, M.S., Burleigh, J.G., Eulenstein, O., Wehe, A.: Heuristics for the Gene-Duplication Problem: A θ(n) Speed-Up for the Local Search. In: Speed, T.P., Huang, H. (eds.) RECOMB 2007. LNCS (LNBI), vol. 4453, pp. 238-252. Springer, Heidelberg (2007) (Pubitemid 47164544)
3. Bansal, M.S., Eulenstein, O., Wehe, A.: The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches. IEEE/ACM Trans. Comput. Biology Bioinform. 6(2), 221-231 (2009)
4. Bansal, M.S., Shamir, R.: A Note on the Fixed Parameter Tractability of the Gene-Duplication Problem. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 8(3), 848-850 (2011)
5. Byrka, J., Guillemot, S., Jansson, J.: New results on optimizing rooted triplets consistency. Discrete Appl. Math. 158(11), 1136-1147 (2010)
6. Chang, W.-C., Burleigh, J.G., Fernández-Baca, D.F., Eulenstein, O.: An ILP solution for the gene duplication problem. BMC Bioinformatics (suppl. 1), S14(12) (2011)
7. 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)
8. Eichler, E.F., Sankoff, D.: Structural dynamics of eukaryotic chromosome evolution. Science 301(5634), 521-565 (2003)
9. Felsenstein, J.: Phylogenies from molecular sequences: Inference and reliability. Ann. Review Genet. 22, 521-565 (1988)
10. Fitch,W.M.: Homology a personal view on some of the problems. Trends Genet. 16, 227-231 (2000)
11. Hallett, M.T., Lagergren, J.: New algorithms for the duplication-loss model. In: RECOMB, pp. 138-146 (2000)
12. Kleinberg, J., Tardos, E.: Algorithm Design. Pearson Education (2006)
13. Ma, B., Li, M., Zhang, L.: From Gene Trees to Species Trees. SIAM J. Comput. 30(3), 729-752 (2000)
14. Ouangraoua, A., Swenson, K.M., Chauve, C.: An Approximation Algorithm for Computing a Parsimonious First Speciation in the Gene Duplication Model. In: Tannier, E. (ed.) RECOMB-CG 2010. LNCS, vol. 6398, pp. 290-301. Springer, Heidelberg (2010)
15. Stege, U.: Gene Trees and Species Trees: The Gene-Duplication Problem in Fixed- Parameter Tractable. In: Dehne, F.K.H.A., Gupta, A., Sack, J.-R., Tamassia, R. (eds.) WADS 1999. LNCS, vol. 1663, pp. 288-293. Springer, Heidelberg (1999)
16. Welsh, D.J.A., Powell, M.B.: An upper bound for the chromatic number of a graph and its application to timetabling problems. The Computer Journal 10(1), 85-86 (1967)