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Volumn 12, Issue SUPPL. 9, 2011, Pages

Structural properties of the reconciliation space and their applications in enumerating nearly-optimal reconciliations between a gene tree and a species tree

Author keywords

[No Author keywords available]

Indexed keywords

GENE DUPLICATIONS; GENE FAMILIES; GENE LOSS; GENE TREE; GRAPH-THEORETIC; INFERENCE PROBLEM; LEAST COMMON ANCESTORS;

EID: 80053506758     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-12-S9-S7     Document Type: Article
Times cited : (16)

References (22)
  • 1
    • 72849144434 scopus 로고    scopus 로고
    • Sequencing technologies - the next generation
    • 10.1038/nrg2626, 19997069
    • Metzker M. Sequencing technologies - the next generation. Nature Reviews Genetics 2010, 11:31-46. 10.1038/nrg2626, 19997069.
    • (2010) Nature Reviews Genetics , vol.11 , pp. 31-46
    • Metzker, M.1
  • 2
    • 0023822631 scopus 로고
    • Relationship between gene trees and species trees
    • Pamilo P, Nei M. Relationship between gene trees and species trees. Mol. Biol. Evol 1988, 5:568-583.
    • (1988) Mol. Biol. Evol , vol.5 , pp. 568-583
    • Pamilo, P.1    Nei, M.2
  • 3
    • 0031504952 scopus 로고    scopus 로고
    • Gene trees in species trees
    • Maddison W. Gene trees in species trees. Syst. Biol 1997, 46:523-536.
    • (1997) Syst. Biol , vol.46 , pp. 523-536
    • Maddison, W.1
  • 4
    • 0000365320 scopus 로고
    • Fitting the gene lineage into its species lineage: A parsimony strategy illustrated by cladograms constructed from globin sequences
    • 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. Syst. Zool 1979, 28:132-168.
    • (1979) Syst. Zool , vol.28 , pp. 132-168
    • Goodman, M.1    Czelusniak, J.2    Moore, G.3    Romero-Herrera, A.4    Matsuda, G.5
  • 5
    • 12044253257 scopus 로고
    • Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas
    • Page R. Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst. Biol 1994, 43:58-77.
    • (1994) Syst. Biol , vol.43 , pp. 58-77
    • Page, R.1
  • 6
    • 0034938644 scopus 로고    scopus 로고
    • From gene trees to species trees
    • Ma B, Li M, Zhang L. From gene trees to species trees. SIAM J. Comput 2010, 30:729-752.
    • (2010) SIAM J. Comput , vol.30 , pp. 729-752
    • Ma, B.1    Li, M.2    Zhang, L.3
  • 7
    • 80052886059 scopus 로고    scopus 로고
    • From gene trees to species trees II: species tree inference by minimizing deep coalescence event
    • accepted
    • Zhang L. From gene trees to species trees II: species tree inference by minimizing deep coalescence event. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2011, accepted.
    • (2011) IEEE/ACM Transactions on Computational Biology and Bioinformatics
    • Zhang, L.1
  • 8
    • 27844468683 scopus 로고    scopus 로고
    • Reconciling a gene tree to a species tree under the duplication cost model
    • Bonizzoni P, Della Vedova G, Dondi R. Reconciling a gene tree to a species tree under the duplication cost model. Theoretical Computer Science 2005, 347:36-53.
    • (2005) Theoretical Computer Science , vol.347 , pp. 36-53
    • Bonizzoni, P.1    Della Vedova, G.2    Dondi, R.3
  • 9
    • 33746345337 scopus 로고    scopus 로고
    • DLS-trees: A model of evolutionary scenario
    • Gorecki P, Tiuryn J. DLS-trees: A model of evolutionary scenario. Theoretical Computer Science 2006, 359:378-399.
    • (2006) Theoretical Computer Science , vol.359 , pp. 378-399
    • Gorecki, P.1    Tiuryn, J.2
  • 10
    • 70349414048 scopus 로고    scopus 로고
    • The gene evolution model and computing its associated probabilities
    • Arvestad L, Lagergren J, Sennblad B. The gene evolution model and computing its associated probabilities. J. ACM 2009, 56(2):1-44.
    • (2009) J. ACM , vol.56 , Issue.2 , pp. 1-44
    • Arvestad, L.1    Lagergren, J.2    Sennblad, B.3
  • 11
    • 0033692378 scopus 로고    scopus 로고
    • Notung: A program for dating gene duplications and optimizing gene family trees
    • 10.1089/106652700750050871, 11108472
    • Chen K, Durand D, Farach-Colton M. Notung: A program for dating gene duplications and optimizing gene family trees. Journal of Computational Biology 2000, 7:429-447. 10.1089/106652700750050871, 11108472.
    • (2000) Journal of Computational Biology , vol.7 , pp. 429-447
    • Chen, K.1    Durand, D.2    Farach-Colton, M.3
  • 12
    • 0031949306 scopus 로고    scopus 로고
    • Duplication-based measures of difference between gene and species trees
    • 10.1089/cmb.1998.5.135, 9541877
    • Eulenstein O, Mirkin B, Vingron M. Duplication-based measures of difference between gene and species trees. Journal of Computational Biology 1998, 5:135-148. 10.1089/cmb.1998.5.135, 9541877.
    • (1998) Journal of Computational Biology , vol.5 , pp. 135-148
    • Eulenstein, O.1    Mirkin, B.2    Vingron, M.3
  • 13
    • 46249107577 scopus 로고    scopus 로고
    • The multiple gene duplication problem revisited
    • Bansal M, Eulenstein O. The multiple gene duplication problem revisited. Bioinformatics 2008, 23:132-138.
    • (2008) Bioinformatics , vol.23 , pp. 132-138
    • Bansal, M.1    Eulenstein, O.2
  • 14
    • 68049099068 scopus 로고    scopus 로고
    • Coalescent methods for estimating phylogenetic trees
    • 10.1016/j.ympev.2009.05.033, 19501178
    • Liu L, Yu L, Kubatko L, Pearl D, Edwards S. Coalescent methods for estimating phylogenetic trees. Mol. Phylogenet. Evol 2009, 53:320-328. 10.1016/j.ympev.2009.05.033, 19501178.
    • (2009) Mol. Phylogenet. Evol , vol.53 , pp. 320-328
    • Liu, L.1    Yu, L.2    Kubatko, L.3    Pearl, D.4    Edwards, S.5
  • 15
    • 67650324396 scopus 로고    scopus 로고
    • New perspectives on gene family evolution: Losses in reconciliation and a link with supertrees
    • Springer Berlin / Heidelberg, Batzoglou S
    • Chauve C, El-Mabrouk N. New perspectives on gene family evolution: Losses in reconciliation and a link with supertrees. Research in Computational Molecular Biology, LNCS 5541 2009, 46-58. Springer Berlin / Heidelberg, Batzoglou S.
    • (2009) Research in Computational Molecular Biology, LNCS 5541 , pp. 46-58
    • Chauve, C.1    El-Mabrouk, N.2
  • 16
    • 65649131928 scopus 로고    scopus 로고
    • Gene tree discordance, phylogenetic inference, and the multispecies coalescent
    • 10.1016/j.tree.2009.01.009, 19307040
    • Degnan J, Rosenberg N. Gene tree discordance, phylogenetic inference, and the multispecies coalescent. Trends in Ecology and Evolution 2009, 24:332-340. 10.1016/j.tree.2009.01.009, 19307040.
    • (2009) Trends in Ecology and Evolution , vol.24 , pp. 332-340
    • Degnan, J.1    Rosenberg, N.2
  • 17
    • 78651298101 scopus 로고    scopus 로고
    • Consistency properties of species tree inference by minimizing deep coalescences
    • 10.1089/cmb.2010.0102, 21210728
    • Than C, Rosenberg N. Consistency properties of species tree inference by minimizing deep coalescences. Journal of Computational Biology 2011, 18:1-15. 10.1089/cmb.2010.0102, 21210728.
    • (2011) Journal of Computational Biology , vol.18 , pp. 1-15
    • Than, C.1    Rosenberg, N.2
  • 18
    • 70349658769 scopus 로고    scopus 로고
    • Species tree inference by minimizing deep coalescences
    • 10.1371/journal.pcbi.1000501, 2729383, 19749978
    • Than C, Nakhleh L. Species tree inference by minimizing deep coalescences. PLoS Computational Biology 2009, 5(9):e1000501. 10.1371/journal.pcbi.1000501, 2729383, 19749978.
    • (2009) PLoS Computational Biology , vol.5 , Issue.9
    • Than, C.1    Nakhleh, L.2
  • 19
    • 0034530345 scopus 로고    scopus 로고
    • Origins of the coalescent. 1974-1982
    • 1461350, 11102348
    • Kingman J. Origins of the coalescent. 1974-1982. Genetics 2000, 156:1461-1463. 1461350, 11102348.
    • (2000) Genetics , vol.156 , pp. 1461-1463
    • Kingman, J.1
  • 20
    • 70349820532 scopus 로고    scopus 로고
    • Space of gene/species trees reconciliations and parsimonious models
    • 10.1089/cmb.2009.0095, 19754270
    • Doyon J, Chauve C, Hamel S. Space of gene/species trees reconciliations and parsimonious models. Journal of Computational Biology 2009, 16:1399-1418. 10.1089/cmb.2009.0095, 19754270.
    • (2009) Journal of Computational Biology , vol.16 , pp. 1399-1418
    • Doyon, J.1    Chauve, C.2    Hamel, S.3
  • 21
    • 84888282532 scopus 로고    scopus 로고
    • An efficient method for exploring the space of gene tree/species tree reconciliations in a probabilistic framework
    • Doyon J, Hamel S, Chauve C. An efficient method for exploring the space of gene tree/species tree reconciliations in a probabilistic framework. preprint 2010,
    • (2010) preprint
    • Doyon, J.1    Hamel, S.2    Chauve, C.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.