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Volumn 8, Issue 3, 2011, Pages 848-850

A note on the fixed parameter tractability of the gene-duplication problem

Author keywords

algorithms; approximability; fixed parameter tractability; gene duplication; Phylogenetics

Indexed keywords

APPROXIMABILITY; FIXED PARAMETERS; FIXED-PARAMETER ALGORITHMS; FIXED-PARAMETER TRACTABILITY; GENE DUPLICATION; GENE DUPLICATIONS; GENE TREE; NP-HARD; PARAMETERIZED; PHYLOGENETICS; ROOTED TRIPLETS;

EID: 79952845540     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2010.74     Document Type: Article
Times cited : (18)

References (20)
  • 1
    • 0000365320 scopus 로고
    • Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences
    • M. Goodman, J. Czelusniak, G. W. Moore, A. E. Romero-Herrera, and G. Matsuda, "Fitting the Gene Lineage into Its Species Lineage, a Parsimony Strategy Illustrated by Cladograms Constructed from Globin Sequences, " Systematic Zoology, vol. 28, pp. 132-163, 1979.
    • (1979) Systematic Zoology , vol.28 , pp. 132-163
    • Goodman, M.1    Czelusniak, J.2    Moore, G.W.3    Romero-Herrera, A.E.4    Matsuda, G.5
  • 2
    • 0034938644 scopus 로고    scopus 로고
    • From gene trees to species trees
    • DOI 10.1137/S0097539798343362, PII S0097539798343362
    • B. Ma, M. Li, and L. Zhang, "From Gene Trees to Species Trees, " SIAM J. Computing, vol. 30, no. 3, pp. 729-752, 2000. (Pubitemid 32644732)
    • (2001) SIAM Journal on Computing , vol.30 , Issue.3 , pp. 729-752
    • Ma, B.1    Li, M.2    Zhang, L.3
  • 3
    • 12044253257 scopus 로고
    • Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas
    • R. D. M. Page, "Maps between Trees and Cladistic Analysis of Historical Associations among Genes, Organisms, and Areas, " Systematic Biology, vol. 43, no. 1, pp. 58-77, 1994. (Pubitemid 24979624)
    • (1994) Systematic Biology , vol.43 , Issue.1 , pp. 58-77
    • Page, R.D.M.1
  • 4
    • 0030253222 scopus 로고    scopus 로고
    • Reconstruction of ancient molecular phylogeny
    • DOI 10.1006/mpev.1996.0071
    • R. Guigó, I. Muchnik, and T. F. Smith, "Reconstruction of Ancient Molecular Phylogeny, " Molecular Phylogenetics and Evolution, vol. 6, no. 2, pp. 189-213, 1996. (Pubitemid 126320615)
    • (1996) Molecular Phylogenetics and Evolution , vol.6 , Issue.2 , pp. 189-213
    • Guigo, R.1    Muchnik, I.2    Smith, T.F.3
  • 5
    • 0029448349 scopus 로고
    • A biologically consistent model for comparing molecular phylogenies
    • B. Mirkin, I. Muchnik, and T. F. Smith, "A Biologically Consistent Model for Comparing Molecular Phylogenies, " J. Computational Biology, vol. 2, no. 4, pp. 493-507, 1995.
    • (1995) J. Computational Biology , vol.2 , Issue.4 , pp. 493-507
    • Mirkin, B.1    Muchnik, I.2    Smith, T.F.3
  • 6
    • 0040714253 scopus 로고    scopus 로고
    • On the equivalence of two tree mapping measures
    • O. Eulenstein and M. Vingron, "On the Equivalence of Two Tree Mapping Measures, " Discrete Applied Math., vol. 88, pp. 101-126, 1998.
    • (1998) Discrete Applied Math. , vol.88 , pp. 101-126
    • Eulenstein, O.1    Vingron, M.2
  • 7
    • 0030762443 scopus 로고    scopus 로고
    • On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies
    • L. Zhang, "On a Mirkin-Muchnik-Smith Conjecture for Comparing Molecular Phylogenies, " J. Computational Biology, vol. 4, no. 2, pp. 177-187, 1997. (Pubitemid 27318314)
    • (1997) Journal of Computational Biology , vol.4 , Issue.2 , pp. 177-187
    • Zhang, L.1
  • 9
    • 0033692378 scopus 로고    scopus 로고
    • Notung: A program for dating gene duplications and optimizing gene family trees
    • K. Chen, D. Durand, and M. Farach-Colton, "Notung: A Program for Dating Gene Duplications and Optimizing Gene Family Trees, " J. Computational Biology, vol. 7, pp. 429-447, 2000.
    • (2000) J. Computational Biology , vol.7 , pp. 429-447
    • Chen, K.1    Durand, D.2    Farach-Colton, M.3
  • 10
    • 27844468683 scopus 로고    scopus 로고
    • Reconciling a gene tree to a species tree under the duplication cost model
    • DOI 10.1016/j.tcs.2005.05.016, PII S030439750500352X
    • P. Bonizzoni, G. D. Vedova, and R. Dondi, "Reconciling a Gene Tree to a Species Tree under the Duplication Cost Model, " Theoretical Computer Science, vol. 347, nos. 1/2, pp. 36-53, 2005. (Pubitemid 41650210)
    • (2005) Theoretical Computer Science , vol.347 , Issue.1-2 , pp. 36-53
    • Bonizzoni, P.1    Della Vedova, G.2    Dondi, R.3
  • 11
    • 33746345337 scopus 로고    scopus 로고
    • DLS-trees: A model of evolutionary scenarios
    • DOI 10.1016/j.tcs.2006.05.019, PII S0304397506003185
    • P. Górecki and J. Tiuryn, "Dls-Trees: A Model of Evolutionary Scenarios, " Theoretical Computer Science, vol. 359, nos. 1-3, pp. 378-399, 2006. (Pubitemid 44119080)
    • (2006) Theoretical Computer Science , vol.359 , Issue.1-3 , pp. 378-399
    • Gorecki, P.1    Tiuryn, J.2
  • 12
    • 52449122374 scopus 로고    scopus 로고
    • Gene family evolution by duplication, speciation, and loss
    • C. Chauve, J.-P. Doyon, and N. El-Mabrouk, "Gene Family Evolution by Duplication, Speciation, and Loss, " J. Computational Biology, vol. 15, no. 8, pp. 1043-1062, 2008.
    • (2008) J. Computational Biology , vol.15 , Issue.8 , pp. 1043-1062
    • Chauve, C.1    Doyon, J.-P.2    El-Mabrouk, N.3
  • 13
    • 67549131988 scopus 로고    scopus 로고
    • The gene-duplication problem: Near-linear time algorithms for NNI-based local searches
    • Apr.-June
    • M. S. Bansal, O. Eulenstein, and A. Wehe, "The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI-Based Local Searches, " IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 6, no. 2, pp. 221-231, Apr.-June 2009.
    • (2009) IEEE/ACM Trans. Computational Biology and Bioinformatics , vol.6 , Issue.2 , pp. 221-231
    • Bansal, M.S.1    Eulenstein, O.2    Wehe, A.3
  • 14
    • 84948965737 scopus 로고    scopus 로고
    • Gene trees and species trees: The gene-duplication problem is fixed-parameter tractable
    • U. Stege, "Gene Trees and Species Trees: The Gene-Duplication Problem Is Fixed-Parameter Tractable, " Proc. Int'l Workshop Algorithms and Data Structures (WADS), pp. 288-293, 1999.
    • (1999) Proc. Int'l Workshop Algorithms and Data Structures (WADS) , pp. 288-293
    • Stege, U.1
  • 17
    • 3543083964 scopus 로고    scopus 로고
    • Constructing the maximum consensus tree from rooted triples
    • B. Y. Wu, "Constructing the Maximum Consensus Tree from Rooted Triples, " J. Combinatorial Optimization, vol. 8, no. 1, pp. 29-39, 2004.
    • (2004) J. Combinatorial Optimization , vol.8 , Issue.1 , pp. 29-39
    • Wu, B.Y.1
  • 18
    • 33845652502 scopus 로고    scopus 로고
    • Using max cut to enhance rooted trees consistency
    • DOI 10.1109/TCBB.2006.58
    • S. Snir and S. Rao, "Using Max Cut to Enhance Rooted Trees Consistency, " IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 3, no. 4, pp. 323-333, Oct.-Dec. 2006. (Pubitemid 44950082)
    • (2006) IEEE/ACM Transactions on Computational Biology and Bioinformatics , vol.3 , Issue.4 , pp. 323-333
    • Snir, S.1    Rao, S.2
  • 19
    • 77951296610 scopus 로고    scopus 로고
    • New results on optimizing rooted triplets consistency
    • J. Byrka, S. Guillemot, and J. Jansson, "New Results on Optimizing Rooted Triplets Consistency, " Discrete Applied Math., vol. 158, pp. 1136-1147, 2010.
    • (2010) Discrete Applied Math. , vol.158 , pp. 1136-1147
    • Byrka, J.1    Guillemot, S.2    Jansson, J.3
  • 20
    • 75149135738 scopus 로고    scopus 로고
    • Efficient genome-scale phylogenetic analysis under the duplication-loss and deep coalescence cost models
    • M. S. Bansal, J. G. Burleigh, and O. Eulenstein, "Efficient Genome-Scale Phylogenetic Analysis under the Duplication-Loss and Deep Coalescence Cost Models, " BMC Bioinformatics, vol. 11, Suppl 1, S42, 2010.
    • (2010) BMC Bioinformatics , vol.11 , Issue.1 SUPPL.
    • Bansal, M.S.1    Burleigh, J.G.2    Eulenstein, O.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.