-
3
-
-
2442562450
-
Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution
-
Arvestad L, Berglund AC, Lagergren J, Sennblad B. 2004. Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. In Bourne PE, Gusfield D. (eds.), Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, San Diego, CA, Mar. 27-31, 2004, pp. 326-335.
-
(2004)
In Bourne PE, Gusfield D. (eds.), Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, San Diego, CA, Mar. 27-31
, vol.2004
-
-
Arvestad, L.1
Berglund, A.C.2
Lagergren, J.3
Sennblad, B.4
-
4
-
-
70349414048
-
The gene evolution model and computing its associated probabilities
-
Arvestad L, Lagergren J, Sennblad B. 2009. The gene evolution model and computing its associated probabilities. J ACM 56: 7.
-
(2009)
J ACM
, vol.56
, pp. 7
-
-
Arvestad, L.1
Lagergren, J.2
Sennblad, B.3
-
5
-
-
49949102302
-
The gene-duplication problem: near-linear time algorithms for N.N.I based local searches
-
Mandoiu I.I., Sunderraman R, Zelikovsky A (eds.). ISBRA. New York: Springer-Verlag
-
Bansal MS, Eulenstein O. 2008a. The gene-duplication problem: near-linear time algorithms for NNI based local searches. In Mandoiu II, Sunderraman R, Zelikovsky A (eds.), ISBRA, Vol. 4983 of Lecture Notes in Computer Science. New York: Springer-Verlag, pp. 14-25.
-
(2008)
of Lecture Notes in Computer Science
, vol.4983
, pp. 14-25
-
-
Bansal, M.S.1
Eulenstein, O.2
-
6
-
-
46249107577
-
The multiple gene duplication problem revisited
-
Bansal MS, Eulenstein O. 2008b. The multiple gene duplication problem revisited. Bioinformatics 24 i132-i1328.
-
(2008)
Bioinformatics
, vol.24
-
-
Bansal, M.S.1
Eulenstein, O.2
-
8
-
-
34547428923
-
Heuristics for the gene-duplication problem: a Θ (n) speed-up for the local search
-
Speed TP, Huang H (eds.). New York: Springer-Verlag
-
Bansal MS, Burleigh JG, Eulenstein O, Wehe A. 2007. Heuristics for the gene-duplication problem: a Θ (n) speed-up for the local search. In Speed TP, Huang H (eds.), RECOMB, Vol. 4453 of Lecture Notes in Computer Science. New York: Springer-Verlag, pp. 238-252.
-
(2007)
RECOMB, Vol. 4453 of Lecture Notes in Computer Science
, pp. 238-252
-
-
Bansal, M.S.1
Burleigh, J.G.2
Eulenstein, O.3
Wehe, A.4
-
9
-
-
84885514777
-
Submitted for publication. A note on the fixed parameter tractability of the gene-duplication problem
-
Bansal MS, Shamir R. Submitted for publication. A note on the fixed parameter tractability of the gene-duplication problem. IEEE/ACM Trans Comput Biol Bioninf.
-
IEEE/ACM Trans Comput Biol Bioninf.
-
-
Bansal, M.S.1
Shamir, R.2
-
10
-
-
22844448185
-
Bounding the number of hybridisation events for a consistent evolutionary history
-
Baroni M, Grünewald S, Moulton V, Semple C. 2005. Bounding the number of hybridisation events for a consistent evolutionary history. J Math Biol 51: 171-182.
-
(2005)
J Math Biol
, vol.51
, pp. 171-182
-
-
Baroni, M.1
Grünewald, S.2
Moulton, V.3
Semple, C.4
-
11
-
-
33746088446
-
An improved algorithm for the macro-evolutionary phylogeny problem
-
Lewenstein M, Valiente G (eds.). New York: Springer-Verlag
-
Behzadi B, Vingron M. 2006a. An improved algorithm for the macro-evolutionary phylogeny problem. In Lewenstein M, Valiente G (eds.), CPM, Vol. 4009 of Lecture Notes in Computer Science. New York: Springer-Verlag, pp. 177-187.
-
(2006)
CPM, Vol. 4009 of Lecture Notes in Computer Science
, pp. 177-187
-
-
Behzadi, B.1
Vingron, M.2
-
12
-
-
33750360816
-
Reconstructing domain compositions of ancestral multi-domain proteins
-
Bourque G, El-Mabrouk N (eds.), New York: Springer-Verlag
-
Behzadi B, Vingron M. 2006b. Reconstructing domain compositions of ancestral multi-domain proteins. In Bourque G, El-Mabrouk N (eds.), Comparative Genomics Vol. 4205 of Lecture Notes in Computer Science. New York: Springer-Verlag, pp. 1-10.
-
(2006)
Comparative Genomics Vol. 4205 of Lecture Notes in Computer Science
, pp. 1-10
-
-
Behzadi, B.1
Vingron, M.2
-
13
-
-
84896788505
-
The LCA problem revisited
-
Gonnet GH, Panario D, Viola A (eds.), New York: Springer-Verlag
-
Bender MA, Farach-Colton M. 2000. The LCA problem revisited. In Gonnet GH, Panario D, Viola A (eds.), LATIN , Vol. 1776 of Lecture Notes in Computer Science. New York: Springer-Verlag, pp. 88-94.
-
(2000)
LATIN , Vol. 1776 of Lecture Notes in Computer Science
, pp. 88-94
-
-
Bender, M.A.1
Farach-Colton, M.2
-
14
-
-
33746433923
-
Optimal gene trees from sequences and species trees using a soft interpretation of parsimony
-
Berglund-Sonnhammer AC, Steffansson P, Betts MJ, Liberles DA. 2006. Optimal gene trees from sequences and species trees using a soft interpretation of parsimony. J Mol Evol 63: 240-250.
-
(2006)
J Mol Evol
, vol.63
, pp. 240-250
-
-
Berglund-Sonnhammer, A.C.1
Steffansson, P.2
Betts, M.J.3
Liberles, D.A.4
-
16
-
-
0036931408
-
The (super)tree of life: procedures, problems, and prospects
-
Bininda-Emonds ORP, Gittleman JL, Steel MA. 2002. The (super)tree of life: procedures, problems, and prospects. Annu Rev Ecol Syst 33: 265-289.
-
(2002)
Annu Rev Ecol Syst
, vol.33
, pp. 265-289
-
-
Bininda-Emonds, O.R.P.1
Gittleman, J.L.2
Steel, M.A.3
-
17
-
-
34047108602
-
The delayed rise of present-day mammals
-
Bininda-Emonds ORP, Cardillo M, Jones KE, MacPhee RDE, Beck RMD, Grenyer R, Price SA, Vos RA, Gittleman JL, Purvis A. 2007. The delayed rise of present-day mammals. Nature 446: 507-512.
-
(2007)
Nature
, vol.446
, pp. 507-512
-
-
Bininda-Emonds, O.R.P.1
Cardillo, M.2
Jones, K.E.3
MacPhee, R.D.E.4
Beck, R.M.D.5
Grenyer, R.6
Price, S.A.7
Vos, R.A.8
Gittleman, J.L.9
Purvis, A.10
-
18
-
-
3142700743
-
Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes
-
Blanc G, Wolfe KH. 2004. Widespread paleopolyploidy in model plant species inferred from age distributions of duplicate genes. Plant Cell 16: 1667-1678.
-
(2004)
Plant Cell
, vol.16
, pp. 1667-1678
-
-
Blanc, G.1
Wolfe, K.H.2
-
19
-
-
0037313579
-
A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome
-
Blanc G, Hokamp K, Wolfe KH. 2003. A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res 13: 137-144.
-
(2003)
Genome Res
, vol.13
, pp. 137-144
-
-
Blanc, G.1
Hokamp, K.2
Wolfe, K.H.3
-
20
-
-
27844468683
-
Reconciling a gene tree to a species tree under the duplication cost model
-
Bonizzoni P, Della Vedova G, Dondi R. 2005. Reconciling a gene tree to a species tree under the duplication cost model. Theor Comput Sci 347: 36-53.
-
(2005)
Theor Comput Sci
, vol.347
, pp. 36-53
-
-
Bonizzoni, P.1
Della Vedova, G.2
Dondi, R.3
-
21
-
-
84885541065
-
On the computational complexity of the rooted subtree prune and regraft distance
-
Bordewich M, Semple C. 2004. On the computational complexity of the rooted subtree prune and regraft distance. Ann Combinatorics 8409-423.
-
(2004)
Ann Combinatorics
, pp. 8409-423
-
-
Bordewich, M.1
Semple, C.2
-
22
-
-
0037468758
-
Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events
-
Bowers JE, Chapman BA, Rong J, Paterson AH. 2003. Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433-438.
-
(2003)
Nature
, vol.422
, pp. 433-438
-
-
Bowers, J.E.1
Chapman, B.A.2
Rong, J.3
Paterson, A.H.4
-
23
-
-
46249105952
-
-
In Vingron M, Wong L (eds.), RECOMB, Vol. 4955 of Lecture Notes in Computer Science. New York: Springer-Verlag, pp. 273-284
-
Burleigh JG, Bansal MS, Wehe A, Eulenstein O. 2008. Locating multiple gene duplications through reconciled trees. In Vingron M, Wong L (eds.), RECOMB, Vol. 4955 of Lecture Notes in Computer Science. New York: Springer-Verlag, pp. 273-284.
-
(2008)
Locating multiple gene duplications through reconciled trees
-
-
Burleigh, J.G.1
Bansal, M.S.2
Wehe, A.3
Eulenstein, O.4
-
24
-
-
70349193234
-
Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy events in plants
-
Burleigh J, Bansal M, Wehe A, Eulenstein O. 2009. Locating large-scale gene duplication events through reconciled trees: implications for identifying ancient polyploidy events in plants. J Comput Biol 16: 1071-1083.
-
(2009)
J Comput Biol
, vol.16
, pp. 1071-1083
-
-
Burleigh, J.1
Bansal, M.2
Wehe, A.3
Eulenstein, O.4
-
25
-
-
33749532842
-
Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes
-
Cannon SB, Sterck L, Rombauts S, Sato S, Cheung F, Gouzy J, Wang X, Mudge J, Vasdewani J, Schiex T, et al. 2006. Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc Nat Acad Sci USA 103: 14959-14964.
-
(2006)
Proc Nat Acad Sci USA
, vol.103
, pp. 14959-14964
-
-
Cannon, S.B.1
Sterck, L.2
Rombauts, S.3
Sato, S.4
Cheung, F.5
Gouzy, J.6
Wang, X.7
Mudge, J.8
Vasdewani, J.9
Schiex, T.10
-
26
-
-
33749574597
-
-
In Chen DZ, Lee DT (eds.), COCOON, Vol. 4112 of Lecture Notes in Computer Science. New York: Springer-Verlag, pp. 235-244
-
Chang WC, Eulenstein O. 2006. Reconciling gene trees with apparent polytomies. In Chen DZ, Lee DT (eds.), COCOON, Vol. 4112 of Lecture Notes in Computer Science. New York: Springer-Verlag, pp. 235-244.
-
(2006)
Reconciling gene trees with apparent polytomies
-
-
Chang, W.C.1
Eulenstein, O.2
-
27
-
-
0033692378
-
NOTUNG: a program for dating gene duplications and optimizing gene family trees
-
Chen K, Durand D, Farach-Colton M. 2000. NOTUNG: a program for dating gene duplications and optimizing gene family trees. J Comput Biol 7: 429-447.
-
(2000)
J Comput Biol
, vol.7
, pp. 429-447
-
-
Chen, K.1
Durand, D.2
Farach-Colton, M.3
-
28
-
-
1242264357
-
Darwin's abominable mystery: insights from a supertree of the angiosperms
-
Davies TJ, Barraclough TG, Chase MW, Soltis PS, Soltis DE, Savolainen V. 2004. Darwin's abominable mystery: insights from a supertree of the angiosperms. Proc Natl Acad Sci USA 101: 1904-1909.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 1904-1909
-
-
Davies, T.J.1
Barraclough, T.G.2
Chase, M.W.3
Soltis, P.S.4
Soltis, D.E.5
Savolainen, V.6
-
29
-
-
33645981936
-
A hybrid micro-macroevolutionary approach to gene tree reconstruction
-
Durand D, Halldórsson BV, Vernot B. 2006. A hybrid micro-macroevolutionary approach to gene tree reconstruction. J Comput Biol 13: 320-335.
-
(2006)
J Comput Biol
, vol.13
, pp. 320-335
-
-
Durand, D.1
Halldórsson, B.V.2
Vernot, B.3
-
30
-
-
33749579169
-
Vorhersage von Genduplikationen und deren Entwicklung in der Evolution
-
Ph.D. dissertation, Rheinische Friedrich-Wilhelms-Universität Bonn
-
Eulenstein O. 1998. Vorhersage von Genduplikationen und deren Entwicklung in der Evolution. Ph.D. dissertation, Rheinische Friedrich-Wilhelms-Universität Bonn.
-
(1998)
-
-
Eulenstein, O.1
-
32
-
-
84867451275
-
-
In Chwa KY, Ibarra OH (eds.), ISAAC Vol. 1533 of Lecture Notes in Computer Science. New York: Springer-Verlag, pp. 347-356
-
Fellows MR, Hallett MT, Stege U. 1998. On the multiple gene duplication problem. In Chwa KY, Ibarra OH (eds.), ISAAC Vol. 1533 of Lecture Notes in Computer Science. New York: Springer-Verlag, pp. 347-356.
-
(1998)
On the multiple gene duplication problem
-
-
Fellows, M.R.1
Hallett, M.T.2
Stege, U.3
-
33
-
-
0242583637
-
Analogs and duals of the MAST problem for sequences and trees
-
Fellows MR, Hallett MT, Stege U. 2003. Analogs and duals of the MAST problem for sequences and trees. J Algorithms 49: 192-216.
-
(2003)
J Algorithms
, vol.49
, pp. 192-216
-
-
Fellows, M.R.1
Hallett, M.T.2
Stege, U.3
-
34
-
-
0003991673
-
-
Sunderland, MA: Sinauer Associates
-
Felsenstein J. 2004. Inferring Phylogenies. Sunderland, MA: Sinauer Associates. www.loc.gov/catdir/toc/ecip043/2003008942.html.
-
(2004)
Inferring Phylogenies
-
-
Felsenstein, J.1
-
35
-
-
0014860857
-
An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution
-
Fitch WM, Markowitz E. 1970. An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution. Biochem Genet 4: 579-593.
-
(1970)
Biochem Genet
, vol.4
, pp. 579-593
-
-
Fitch, W.M.1
Markowitz, E.2
-
36
-
-
0003603813
-
Computers and Intractability: A Guide to the Theory of NPCompleteness. San Francisco: W.H
-
Freeman
-
Garey MR, Johnson DS. 1979. Computers and Intractability: A Guide to the Theory of NPCompleteness. San Francisco: W.H. Freeman.
-
(1979)
-
-
Garey, M.R.1
Johnson, D.S.2
-
37
-
-
0000365320
-
Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences
-
Goodman M, Czelusniak J, Moore GW, Romero-Herrera AE, Matsuda G. 1979. Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst Zool 28: 132-163.
-
(1979)
Syst Zool
, vol.28
, pp. 132-163
-
-
Goodman, M.1
Czelusniak, J.2
Moore, G.W.3
Romero-Herrera, A.E.4
Matsuda, G.5
-
38
-
-
0000803938
-
Consensus supertrees: the synthesis of rooted trees containing overlapping sets of labelled leaves
-
Gordon AD. 1986. Consensus supertrees: the synthesis of rooted trees containing overlapping sets of labelled leaves. J Classification 3: 335-348.
-
(1986)
J Classification
, vol.3
, pp. 335-348
-
-
Gordon, A.D.1
-
40
-
-
26444580983
-
-
In Lagergren J (ed.), Comparative Genomics, Vol. 3388 of Lecture Notes in Computer Science. New York: Springer-Verlag, pp. 42-54
-
Górecki P, Tiuryn J. 2004. On the structure of reconciliations. In Lagergren J (ed.), Comparative Genomics, Vol. 3388 of Lecture Notes in Computer Science. New York: Springer-Verlag, pp. 42-54.
-
(2004)
On the structure of reconciliations
-
-
Górecki, P.1
Tiuryn, J.2
-
41
-
-
33846667953
-
Inferring phylogeny from whole genomes
-
10.1093/bioinformatics/btl296.
-
Górecki P, Tiuryn J. 2007a. Inferring phylogeny from whole genomes. Bioinformatics 23: e116-e122. 10.1093/bioinformatics/btl296.
-
(2007)
Bioinformatics
, vol.23
-
-
Górecki, P.1
Tiuryn, J.2
-
42
-
-
33847295811
-
Urec: a system for unrooted reconciliation
-
Górecki P, Tiuryn J. 2007b. Urec: a system for unrooted reconciliation. Bioinformatics 23: 511-512.
-
(2007)
Bioinformatics
, vol.23
, pp. 511-512
-
-
Górecki, P.1
Tiuryn, J.2
-
43
-
-
0004042690
-
-
New York: Columbia University Press
-
Grant V. 1981. Plant Speciation. New York: Columbia University Press.
-
(1981)
Plant Speciation
-
-
Grant, V.1
-
45
-
-
4143051590
-
Ancestral genome duplication in rice
-
Guyot R, Keller B. 2004. Ancestral genome duplication in rice. Genome 47: 610-614.
-
(2004)
Genome
, vol.47
, pp. 610-614
-
-
Guyot, R.1
Keller, B.2
-
46
-
-
23744452485
-
Estimating the tempo and mode of gene family evolution from comparative genomic data
-
Hahn MW, De Bie T, Stajich JE, Nguyen C, Cristianini N. 2005. Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res 15: 1153-1160.
-
(2005)
Genome Res
, vol.15
, pp. 1153-1160
-
-
Hahn, M.W.1
De Bie, T.2
Stajich, J.E.3
Nguyen, C.4
Cristianini, N.5
-
48
-
-
2442573762
-
Simultaneous identification of duplications and lateral transfers
-
Hallett MT, Lagergren J, Tofigh A. 2004. Simultaneous identification of duplications and lateral transfers. In Bourne PE, Gusfield D. (eds.), Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, San Diego, CA, Mar. 27-31, 2004, pp. 347-356.
-
(2004)
In Bourne PE, Gusfield D. (eds.), Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, San Diego, CA, Mar. 27-31
, vol.2004
-
-
Hallett, M.T.1
Lagergren, J.2
Tofigh, A.3
-
49
-
-
0001996348
-
The probabilities of rooted tree-shapes generated by random bifurcation
-
Harding EF. 1971. The probabilities of rooted tree-shapes generated by random bifurcation. Adv Appl Prob 3: 44-77.
-
(1971)
Adv Appl Prob
, vol.3
, pp. 44-77
-
-
Harding, E.F.1
-
50
-
-
36148960409
-
The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo- than subfunctionalisation
-
Hughes T, Liberles DA. 2007. The pattern of evolution of smaller-scale gene duplicates in mammalian genomes is more consistent with neo- than subfunctionalisation. J Mol Evol 65: 574-588.
-
(2007)
J Mol Evol
, vol.65
, pp. 574-588
-
-
Hughes, T.1
Liberles, D.A.2
-
51
-
-
54349113511
-
A characterisation of the effects of speciation and whole genome duplication on the distribution of gene family sizes and its application to detecting large scale duplication
-
Hughes T, Liberles D. 2008. A characterisation of the effects of speciation and whole genome duplication on the distribution of gene family sizes and its application to detecting large scale duplication. J Mol Evol 67: 343-357.
-
(2008)
J Mol Evol
, vol.67
, pp. 343-357
-
-
Hughes, T.1
Liberles, D.2
-
52
-
-
84885546187
-
Linear-time algorithms for the multiple gene duplication problems
-
Luo CW, Chen MC, Chen YC, Yang RW, Liu HF, Chao KM. 2009. Linear-time algorithms for the multiple gene duplication problems. IEEE/ACM Trans Comput Biol Bioinf 15: 1545-5963.
-
(2009)
IEEE/ACM Trans Comput Biol Bioinf
, vol.15
, pp. 1545-5963
-
-
Luo, C.W.1
Chen, M.C.2
Chen, Y.C.3
Yang, R.W.4
Liu, H.F.5
Chao, K.M.6
-
53
-
-
0037270015
-
The evolutionary demography of duplicate genes
-
Lynch M, Conery JS. 2003. The evolutionary demography of duplicate genes. J Struct Funct Genom 3: 35-44.
-
(2003)
J Struct Funct Genom
, vol.3
, pp. 35-44
-
-
Lynch, M.1
Conery, J.S.2
-
54
-
-
0034938644
-
From gene trees to species trees
-
Ma B, Li M, Zhang L. 2000. From gene trees to species trees. SIAM J Comput 30: 729-752.
-
(2000)
SIAM J Comput
, vol.30
, pp. 729-752
-
-
Ma, B.1
Li, M.2
Zhang, L.3
-
55
-
-
0024940670
-
Reconstructing character evolution on polytomous cladograms
-
Maddison WP. 1989. Reconstructing character evolution on polytomous cladograms. Cladistics Int J Willi Hennig Soc 5: 365-377.
-
(1989)
Cladistics Int J Willi Hennig Soc
, vol.5
, pp. 365-377
-
-
Maddison, W.P.1
-
56
-
-
0029448349
-
A biologically consistent model for comparing molecular phylogenies
-
Mirkin B, Muchnik IB, Smith TF. 1995. A biologically consistent model for comparing molecular phylogenies. J Comput Biol 2: 493-507.
-
(1995)
J Comput Biol
, vol.2
, pp. 493-507
-
-
Mirkin, B.1
Muchnik, I.B.2
Smith, T.F.3
-
57
-
-
33748795802
-
Biological applications of the theory of birthand-death processes
-
Novozhilov AS, Karev GP, Koonin EV. 2006. Biological applications of the theory of birthand-death processes. Brief Bioinf 7: 70-85.
-
(2006)
Brief Bioinf
, vol.7
, pp. 70-85
-
-
Novozhilov, A.S.1
Karev, G.P.2
Koonin, E.V.3
-
58
-
-
12044253257
-
Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas
-
Page RDM. 1994. Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas. Syst Biol 43: 58-77.
-
(1994)
Syst Biol
, vol.43
, pp. 58-77
-
-
Page, R.D.M.1
-
59
-
-
0031774059
-
GeneTree: comparing gene and species phylogenies using reconciled trees
-
Page RDM. 1998. GeneTree: comparing gene and species phylogenies using reconciled trees. Bioinformatics 14: 819-820.
-
(1998)
Bioinformatics
, vol.14
, pp. 819-820
-
-
Page, R.D.M.1
-
60
-
-
0036365666
-
Vertebrate phylogenomics: reconciled trees and gene duplications
-
Pacific Symposium on Biocomputing
-
Page RDM, Cotton JA. 2002. Vertebrate phylogenomics: reconciled trees and gene duplications. Pacific Symposium on Biocomputing, pp. 536-547.
-
(2002)
, pp. 536-547
-
-
Page, R.D.M.1
Cotton, J.A.2
-
61
-
-
3042836334
-
Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics
-
Paterson AH, Bowers JE, Chapman BA. 2004. Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics. Proc Natl Acad Sci USA 101: 9903-9908.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 9903-9908
-
-
Paterson, A.H.1
Bowers, J.E.2
Chapman, B.A.3
-
62
-
-
34548202141
-
An ancient genome duplication contributed to the abundance of metabolic genes in the moss physcomitrella patens
-
Rensing SA, Ick J, Fawcett JA, Lang D, Zimmer A, Van de Peer Y, Reski R. 2007. An ancient genome duplication contributed to the abundance of metabolic genes in the moss physcomitrella patens. BMC Evol Biol 7130.
-
(2007)
B.M.C Evol Biol
, pp. 7130
-
-
Rensing, S.A.1
Ick, J.2
Fawcett, J.A.3
Lang, D.4
Zimmer, A.5
Van de Peer, Y.6
Reski, R.7
-
63
-
-
0003080472
-
Comparison of labeled trees with valency three
-
Robinson DF. 1971 Comparison of labeled trees with valency three. J Comb Theory 11: 105-119.
-
(1971)
J Comb Theory
, vol.11
, pp. 105-119
-
-
Robinson, D.F.1
-
64
-
-
33748126145
-
Assessing site-interdependent phylogenetic models of sequence evolution
-
Rodrigue N, Philippe H, Lartillot N. 2006. Assessing site-interdependent phylogenetic models of sequence evolution. Mol Biol Evol 23: 1762-1775.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 1762-1775
-
-
Rodrigue, N.1
Philippe, H.2
Lartillot, N.3
-
65
-
-
12144290265
-
A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (gossypium)
-
Rong J, Abbey C, Bowers JE, Brubaker CL, Chang C, Chee PW, Delmonte TA, Ding X, Garza JJ, Marler BS, et al. 2004. A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (gossypium). Genetics 166: 389-417.
-
(2004)
Genetics
, vol.166
, pp. 389-417
-
-
Rong, J.1
Abbey, C.2
Bowers, J.E.3
Brubaker, C.L.4
Chang, C.5
Chee, P.W.6
Delmonte, T.A.7
Ding, X.8
Garza, J.J.9
Marler, B.S.10
-
66
-
-
0032030505
-
Phylogenetic supertrees: assembling the trees of life
-
Sanderson MJ, Purvis A, Henze C. 1998. Phylogenetic supertrees: assembling the trees of life. Trends Ecol Evol 13: 105-109.
-
(1998)
Trends Ecol Evol
, vol.13
, pp. 105-109
-
-
Sanderson, M.J.1
Purvis, A.2
Henze, C.3
-
67
-
-
2442712340
-
Mining EST databases to resolve evolutionary events in major crop species
-
Schlueter JA, Dixon P, Granger C, Grant D, Clark L, Doyle JJ, Shoemaker RC. 2004. Mining EST databases to resolve evolutionary events in major crop species. Genome 47: 868-876.
-
(2004)
Genome
, vol.47
, pp. 868-876
-
-
Schlueter, J.A.1
Dixon, P.2
Granger, C.3
Grant, D.4
Clark, L.5
Doyle, J.J.6
Shoemaker, R.C.7
-
68
-
-
33745478966
-
Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae
-
Schranz ME, Mitchell-Olds T. 2006. Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae. Plant Cell 18: 1152-1165.
-
(2006)
Plant Cell
, vol.18
, pp. 1152-1165
-
-
Schranz, M.E.1
Mitchell-Olds, T.2
-
69
-
-
0037109058
-
The hidden duplication past of Arabidopsis thaliana
-
Simillion C, Vandepoele K, Van Montagu MCE, Zabeau M, Van de Peer Y. 2002. The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci USA 99: 13627-13632.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 13627-13632
-
-
Simillion, C.1
Vandepoele, K.2
Van Montagu, M.C.E.3
Zabeau, M.4
Van de Peer, Y.5
-
72
-
-
21244483590
-
EST data suggest that poplar is an ancient polyploid
-
Sterck L, Rombauts S, Jansson S, Sterky F, Rouze P, Van de Peer Y. 2005. EST data suggest that poplar is an ancient polyploid. New Phytol 167: 165-170.
-
(2005)
New Phytol
, vol.167
, pp. 165-170
-
-
Sterck, L.1
Rombauts, S.2
Jansson, S.3
Sterky, F.4
Rouze, P.5
Van de Peer, Y.6
-
73
-
-
30744435826
-
An evolutionary space-time model with varying among-site dependencies
-
Stern A, and Pupko T. 2006. An evolutionary space-time model with varying among-site dependencies. Mol Biol Evol 23: 392-400.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 392-400
-
-
Stern, A.1
Pupko, T.2
-
74
-
-
0141564555
-
Evidence that rice and other cereals are ancient aneuploids
-
Vandepoele K, Simillion C, Van de Peer Y. 2003. Evidence that rice and other cereals are ancient aneuploids. Plant Cell 15: 2192-2202.
-
(2003)
Plant Cell
, vol.15
, pp. 2192-2202
-
-
Vandepoele, K.1
Simillion, C.2
Van de Peer, Y.3
-
76
-
-
0034671866
-
The origins of genomic duplications in arabidopsis
-
Vision TJ, Brown DG, Tanksley SD. 2000. The origins of genomic duplications in arabidopsis. Science 290: 2114-2117.
-
(2000)
Science
, vol.290
, pp. 2114-2117
-
-
Vision, T.J.1
Brown, D.G.2
Tanksley, S.D.3
-
77
-
-
14244250895
-
Duplication and DNA segmental loss in the rice genome: implications for diploidization
-
Wang X, Shi X, Hao B, Ge S, Luo J. 2005. Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol 165: 937-946.
-
(2005)
New Phytol
, vol.165
, pp. 937-946
-
-
Wang, X.1
Shi, X.2
Hao, B.3
Ge, S.4
Luo, J.5
-
78
-
-
46249126320
-
DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony
-
Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. DupTree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24: 1540-154.
-
(2008)
Bioinformatics
, vol.24
, pp. 1540-154
-
-
Wehe, A.1
Bansal, M.S.2
Burleigh, J.G.3
Eulenstein, O.4
-
80
-
-
0028064845
-
Maximum likelihood phylogenetic estimation from dna sequences with variable rates over sites: approximate methods
-
Yang Z. 1994. Maximum likelihood phylogenetic estimation from dna sequences with variable rates over sites: approximate methods. J Mol Evol 39: 306-314.
-
(1994)
J Mol Evol
, vol.39
, pp. 306-314
-
-
Yang, Z.1
-
81
-
-
20144366003
-
The genomes of Oryza sativa: a history of duplications
-
Yu J, Wang J, Lin W, Li S, Li H, Zhou J, Ni P, Dong W, Hu S, Zeng C, et al. 2005. The genomes of Oryza sativa: a history of duplications. PLoS Biol 3 e38.
-
(2005)
P.LoS Biol
, vol.3
-
-
Yu, J.1
Wang, J.2
Lin, W.3
Li, S.4
Li, H.5
Zhou, J.6
Ni, P.7
Dong, W.8
Hu, S.9
Zeng, C.10
-
82
-
-
0030762443
-
On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies
-
Zhang L. 1997. On a Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies. J Comput Biol 4: 177-187.
-
(1997)
J Comput Biol
, vol.4
, pp. 177-187
-
-
Zhang, L.1
-
83
-
-
1642337027
-
Inferring a species tree from gene trees under the deep coalescence cost
-
R.E.C.O.M.B 2000 poster.
-
Zhang L. 2000. Inferring a species tree from gene trees under the deep coalescence cost. RECOMB 2000 poster.
-
(2000)
-
-
Zhang, L.1
-
84
-
-
0034791426
-
A simple algorithm to infer gene duplication and speciation events on a gene tree
-
Zmasek CM, Eddy SR. 2001. A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics 17: 821-828.
-
(2001)
Bioinformatics
, vol.17
, pp. 821-828
-
-
Zmasek, C.M.1
Eddy, S.R.2
|