-
1
-
-
33750802977
-
Ancient genomic architecture for mammalian olfactory receptor clusters
-
Aloni, R., Olender, T., and Lancet, D. 2006. Ancient genomic architecture for mammalian olfactory receptor clusters. Genome Biol. 7, R88.
-
(2006)
Genome Biol
, vol.7
-
-
Aloni, R.1
Olender, T.2
Lancet, D.3
-
2
-
-
0029557542
-
Human t-cell receptor variable gene segment families
-
Arden, B., Clark, S., Kabelitz, D., et al. 1995. Human t-cell receptor variable gene segment families. Immunogenetics 42, 455-500.
-
(1995)
Immunogenetics
, vol.42
, pp. 455-500
-
-
Arden, B.1
Clark, S.2
Kabelitz, D.3
-
3
-
-
2442562450
-
Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution
-
Arvestad, L., Berglund, A.-C., Lagergren, J., et al. 2004. Gene tree reconstruction and orthology analysis based on an integrated model for duplications and sequence evolution. Proc. RECOMB 2004 326-335.
-
(2004)
Proc. RECOMB 2004
, pp. 326-335
-
-
Arvestad, L.1
Berglund, A.-C.2
Lagergren, J.3
-
4
-
-
0034767147
-
A linear-time algorithm for computing inversion distance between signed permutations with an experimental study
-
Bader, D., Moret, B., and Yan, M. 2001. A linear-time algorithm for computing inversion distance between signed permutations with an experimental study. J. Comput. Biol. 8, 483-491.
-
(2001)
J. Comput. Biol
, vol.8
, pp. 483-491
-
-
Bader, D.1
Moret, B.2
Yan, M.3
-
5
-
-
35048854107
-
Reversal distance without hurdles and fortresses
-
Bergeron, A., Mixtacki, J., and Stoye, J. 2004. Reversal distance without hurdles and fortresses. Lect. Notes Comput. Sci. 3109, 388-399.
-
(2004)
Lect. Notes Comput. Sci
, vol.3109
, pp. 388-399
-
-
Bergeron, A.1
Mixtacki, J.2
Stoye, J.3
-
6
-
-
19944393218
-
Topological rearrangements and local search method for tandem duplication trees
-
Bertrand, D., and Gascuel, O. 2005. Topological rearrangements and local search method for tandem duplication trees. IEEE Trans. Comput. Biol. Bioinform. 2, 15-28.
-
(2005)
IEEE Trans. Comput. Biol. Bioinform
, vol.2
, pp. 15-28
-
-
Bertrand, D.1
Gascuel, O.2
-
7
-
-
27844468683
-
Reconciling gene trees to a species tree
-
Bonizzoni, P., Vedova, G., and Dondi, R. 2005. Reconciling gene trees to a species tree. Theoret. Comput. Sci. 347, 36-53.
-
(2005)
Theoret. Comput. Sci
, vol.347
, pp. 36-53
-
-
Bonizzoni, P.1
Vedova, G.2
Dondi, R.3
-
8
-
-
0036143403
-
Genome-scale evolution: Reconstructing gene orders in the ancestral species
-
Bourque, G., and Pevzner, P. 2002. Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res. 12, 26-36.
-
(2002)
Genome Res
, vol.12
, pp. 26-36
-
-
Bourque, G.1
Pevzner, P.2
-
9
-
-
3843132934
-
The reversal median problem
-
Caprara, A., 2003. The reversal median problem. J. Comput. 15, 93-113.
-
(2003)
J. Comput
, vol.15
, pp. 93-113
-
-
Caprara, A.1
-
10
-
-
38349011821
-
Inferring a duplication, speciation and loss history from a gene tree
-
Chauve, C., Doyon, J., and El-Mabrouk, N. 2007. Inferring a duplication, speciation and loss history from a gene tree. RECOMB-CG 2007 45-57.
-
(2007)
RECOMB-CG 2007
, pp. 45-57
-
-
Chauve, C.1
Doyon, J.2
El-Mabrouk, N.3
-
11
-
-
0042027896
-
Structural dynamics of eukaryotic chromosome evolution
-
Eichler, E., and Sankoff, D. 2003. Structural dynamics of eukaryotic chromosome evolution. Science 301, 793-797.
-
(2003)
Science
, vol.301
, pp. 793-797
-
-
Eichler, E.1
Sankoff, D.2
-
12
-
-
18544387648
-
A fast and accurate distance-based algorithm to reconstruct tandem duplication trees
-
Elemento, O., and Gascuel, O. 2002. A fast and accurate distance-based algorithm to reconstruct tandem duplication trees. Bioinformatics 18, 92-99.
-
(2002)
Bioinformatics
, vol.18
, pp. 92-99
-
-
Elemento, O.1
Gascuel, O.2
-
13
-
-
0036187352
-
Reconstructing the duplication history of tandemly repeated genes
-
Elemento, O., Gascuel, O., and Lefranc, M.-P. 2002. Reconstructing the duplication history of tandemly repeated genes. Mol. Biol. Evol. 19, 278-288.
-
(2002)
Mol. Biol. Evol
, vol.19
, pp. 278-288
-
-
Elemento, O.1
Gascuel, O.2
Lefranc, M.-P.3
-
14
-
-
0017713284
-
Phylogenies constrained by cross-over process as illustrated by human hemoglobins and a thirteen-cycle, eleven amino-acid repeat in human apolipoprotein A-I
-
Fitch, W. 1977. Phylogenies constrained by cross-over process as illustrated by human hemoglobins and a thirteen-cycle, eleven amino-acid repeat in human apolipoprotein A-I. Genetics 86, 623-644.
-
(1977)
Genetics
, vol.86
, pp. 623-644
-
-
Fitch, W.1
-
15
-
-
33750299036
-
Reconstructing the duplication history of tandemly repeated sequences
-
Gascuel, O, ed, Oxford University Press, New York
-
Gascuel, O., Bertrand, D., and Elemento, O. 2005. Reconstructing the duplication history of tandemly repeated sequences, 205-235. In: Gascuel, O., ed. Mathematics of Evolution and Phylogeny. Oxford University Press, New York.
-
(2005)
Mathematics of Evolution and Phylogeny
, pp. 205-235
-
-
Gascuel, O.1
Bertrand, D.2
Elemento, O.3
-
16
-
-
0242418154
-
The combinatorics of tandem duplication trees
-
Gascuel, O., Hendy, M., Jean-Marie, A., et al. 2003. The combinatorics of tandem duplication trees. Syst. Biol. 52, 110-118.
-
(2003)
Syst. Biol
, vol.52
, pp. 110-118
-
-
Gascuel, O.1
Hendy, M.2
Jean-Marie, A.3
-
17
-
-
0026669901
-
The HLA class I gene family includes at least six genes and twelve pseudogenes and gene fragments
-
Geraghty, D., Koller, B., Hansen, J., et al. 1992. The HLA class I gene family includes at least six genes and twelve pseudogenes and gene fragments. J. Immunol. 149, 1934-1946.
-
(1992)
J. Immunol
, vol.149
, pp. 1934-1946
-
-
Geraghty, D.1
Koller, B.2
Hansen, J.3
-
18
-
-
0000365320
-
Fitting the gene lineage into its species lineage: A parsimony strategy illustrated by cladograms constructed from globin sequences
-
Goodman, M., Czelusniak, J., Moore, G., et al. 1979. Fitting the gene lineage into its species lineage: a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28, 132-168.
-
(1979)
Syst. Zool
, vol.28
, pp. 132-168
-
-
Goodman, M.1
Czelusniak, J.2
Moore, G.3
-
19
-
-
0030253222
-
Reconstruction of ancient molecular phylogeny
-
Guigó, R., Muchnik, I., and Smith, T. 1996. Reconstruction of ancient molecular phylogeny. Mol. Phylogenet. Evol. 6, 189-213.
-
(1996)
Mol. Phylogenet. Evol
, vol.6
, pp. 189-213
-
-
Guigó, R.1
Muchnik, I.2
Smith, T.3
-
20
-
-
0002856077
-
Transforming cabbage into turnip: Polynomial algorithm for sorting signed permutations by reversals
-
Hannenhalli, S., and Pevzner, P.A. 1999. Transforming cabbage into turnip: polynomial algorithm for sorting signed permutations by reversals. J. ACM 48, 1-27.
-
(1999)
J. ACM
, vol.48
, pp. 1-27
-
-
Hannenhalli, S.1
Pevzner, P.A.2
-
21
-
-
33745179207
-
A comprehensive catalogue of human krab-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors
-
Huntley, S., Baggott, D., Hamilton, A., et al. 2006. A comprehensive catalogue of human krab-associated zinc finger genes: insights into the evolutionary history of a large family of transcriptional repressors. Genome Res. 16, 669-677.
-
(2006)
Genome Res
, vol.16
, pp. 669-677
-
-
Huntley, S.1
Baggott, D.2
Hamilton, A.3
-
22
-
-
8444230206
-
Methods for reconstructing the history of tandemrepeats and their application to the human genome
-
Jaitly, D., Kearney, P., Lin, G., et al. 2002.Methods for reconstructing the history of tandemrepeats and their application to the human genome. J. Comput. Syst. Sci. 65, 494-507.
-
(2002)
J. Comput. Syst. Sci
, vol.65
, pp. 494-507
-
-
Jaitly, D.1
Kearney, P.2
Lin, G.3
-
23
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones, D., Taylor, W., and Thornton, J., 1992. The rapid generation of mutation data matrices from protein sequences. Comput. Appl. Biosci. 8, 275-282.
-
(1992)
Comput. Appl. Biosci
, vol.8
, pp. 275-282
-
-
Jones, D.1
Taylor, W.2
Thornton, J.3
-
24
-
-
0033295439
-
A faster and simpler algorithm for sorting signed permutations by reversals
-
Kaplan, H., Shamir, R., and Tarjan, R.E. 2000. A faster and simpler algorithm for sorting signed permutations by reversals. SIAM J. Comput. 29, 880-892.
-
(2000)
SIAM J. Comput
, vol.29
, pp. 880-892
-
-
Kaplan, H.1
Shamir, R.2
Tarjan, R.E.3
-
25
-
-
52449083502
-
Evolution of tandemly arrayed genes in multiple species
-
Lajoie, M., Bertrand, D., and El-Mabrouk, N. 2007a. Evolution of tandemly arrayed genes in multiple species. RECOMB-CG 2007 98-109.
-
(2007)
RECOMB-CG 2007
, pp. 98-109
-
-
Lajoie, M.1
Bertrand, D.2
El-Mabrouk, N.3
-
26
-
-
34250324321
-
Duplication and inversion history of a tandemly repeated genes family
-
Lajoie, M., Bertrand, D., El-Mabrouk, N., et al. 2007b. Duplication and inversion history of a tandemly repeated genes family. J. Comput. Biol. 14, 462-478.
-
(2007)
J. Comput. Biol
, vol.14
, pp. 462-478
-
-
Lajoie, M.1
Bertrand, D.2
El-Mabrouk, N.3
-
27
-
-
0034938644
-
From gene trees to species trees
-
Ma, B., Li, M., and 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
-
28
-
-
33750386912
-
Reconstructing contiguous regions of an ancestral genome
-
Ma, J., Zhang, L., Suh, B.B., et al. 2006. Reconstructing contiguous regions of an ancestral genome. Genome Res. 16, 1557-1565.
-
(2006)
Genome Res
, vol.16
, pp. 1557-1565
-
-
Ma, J.1
Zhang, L.2
Suh, B.B.3
-
29
-
-
23844520968
-
Steps toward accurate reconstructions of phylogenies from gene-order data
-
Moret, B., Tang, J., Wang, L., et al. 2002. Steps toward accurate reconstructions of phylogenies from gene-order data. J. Comput. Syst. Sci. 65, 508-525.
-
(2002)
J. Comput. Syst. Sci
, vol.65
, pp. 508-525
-
-
Moret, B.1
Tang, J.2
Wang, L.3
-
30
-
-
27944477670
-
Concerted and birth-and-death evolution of multigene families
-
Nei, M., and Rooney, A. 2005. Concerted and birth-and-death evolution of multigene families. Annu. Rev. Genet. 39, 121-152.
-
(2005)
Annu. Rev. Genet
, vol.39
, pp. 121-152
-
-
Nei, M.1
Rooney, A.2
-
31
-
-
12044253257
-
Maps between trees and cladistic analysis of historical associations among genes, organisms, and areas
-
Page, R. 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.1
-
32
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist, F., and Huelsenbeck, J. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19, 1572-1574.
-
(2003)
Bioinformatics
, vol.19
, pp. 1572-1574
-
-
Ronquist, F.1
Huelsenbeck, J.2
-
33
-
-
0031721577
-
Multiple genome rearrangement and breakpoint phylogeny
-
Sankoff, D., and Blanchette, M. 1998. Multiple genome rearrangement and breakpoint phylogeny. J. Comput. Biol. 5, 555-570.
-
(1998)
J. Comput. Biol
, vol.5
, pp. 555-570
-
-
Sankoff, D.1
Blanchette, M.2
-
34
-
-
34250380338
-
Primetv: A viewer for reconciled trees
-
Sennblad, B., Schreil, E., Sonnhammer, A.B., et al. 2007. Primetv: a viewer for reconciled trees. BMC Bioinform. 8:148.
-
(2007)
BMC Bioinform
, vol.8
, pp. 148
-
-
Sennblad, B.1
Schreil, E.2
Sonnhammer, A.B.3
-
35
-
-
0038141095
-
Differential expansion of Zinc-Finger transcription factor loci in homologous human and mouse gene clusters
-
Shannon, M., Hamilton, A., Gordon, L., et al. 2003. Differential expansion of Zinc-Finger transcription factor loci in homologous human and mouse gene clusters. Genome Res. 13, 1097-1110.
-
(2003)
Genome Res
, vol.13
, pp. 1097-1110
-
-
Shannon, M.1
Hamilton, A.2
Gordon, L.3
-
36
-
-
33749563310
-
A roadmap of tandemly arrayed genes in the genomes of human, mouse, and rat
-
Shoja, V., and Zhang, L. 2006. A roadmap of tandemly arrayed genes in the genomes of human, mouse, and rat. Mol. Biol. Evol. 23, 2134-2141.
-
(2006)
Mol. Biol. Evol
, vol.23
, pp. 2134-2141
-
-
Shoja, V.1
Zhang, L.2
-
37
-
-
84959066123
-
Finding an optimal inversion median: Experimental results
-
Siepel, A., and Moret, B., 2001. Finding an optimal inversion median: experimental results. Lect. Notes Comput. Sci. 2149, 189-203.
-
(2001)
Lect. Notes Comput. Sci
, vol.2149
, pp. 189-203
-
-
Siepel, A.1
Moret, B.2
-
38
-
-
0036100845
-
Zinc finger gene clusters and tandem gene duplication
-
Tang, M., Waterman, M., and Yooseph, S. 2002. Zinc finger gene clusters and tandem gene duplication. J. Comput. Biol. 9, 429-446.
-
(2002)
J. Comput. Biol
, vol.9
, pp. 429-446
-
-
Tang, M.1
Waterman, M.2
Yooseph, S.3
-
39
-
-
0027968068
-
CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice
-
Thompson, J., Higgins, D., and Gibson, T. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
-
(1994)
Nucleic Acids Res
, vol.22
, pp. 4673-4680
-
-
Thompson, J.1
Higgins, D.2
Gibson, T.3
-
40
-
-
34547844121
-
Automatic genome-wide reconstruction of phylogenetic gene trees
-
Wapinski, I., Pfeffer, A., Friedman, N., et al. 2007. Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics 23, i549-i558.
-
(2007)
Bioinformatics
, vol.23
-
-
Wapinski, I.1
Pfeffer, A.2
Friedman, N.3
-
41
-
-
0029671437
-
Evolution of antennapedia-class homeobox genes
-
Zhang, J., and Nei, M. 1996. Evolution of antennapedia-class homeobox genes. Genetics 142, 295-303.
-
(1996)
Genetics
, vol.142
, pp. 295-303
-
-
Zhang, J.1
Nei, M.2
-
42
-
-
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
-
43
-
-
0041886965
-
Greedy method for inferring tandem duplication history
-
Zhang, L., Ma, B., Wang, L., et al. 2003. Greedy method for inferring tandem duplication history. Bioinformatics 19, 1497-1504.
-
(2003)
Bioinformatics
, vol.19
, pp. 1497-1504
-
-
Zhang, L.1
Ma, B.2
Wang, L.3
|