-
2
-
-
0036727869
-
Recreating a functional ancestral archosaur visual pigment
-
Chang, B.S., Jonsson, K., Kazmi, M.A., Donoghue, M.J. and Sakmar, T.P. (2002) Recreating a functional ancestral archosaur visual pigment. Mol. Biol. Evol., 19, 1483-1489.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 1483-1489
-
-
Chang, B.S.1
Jonsson, K.2
Kazmi, M.A.3
Donoghue, M.J.4
Sakmar, T.P.5
-
3
-
-
0141431993
-
Resurrecting the ancestral steroid receptor: Ancient origin of estrogen signaling
-
Thornton, J.W., Need, E. and Crews, D. (2003) Resurrecting the ancestral steroid receptor: ancient origin of estrogen signaling. Science, 301, 1714-1717.
-
(2003)
Science
, vol.301
, pp. 1714-1717
-
-
Thornton, J.W.1
Need, E.2
Crews, D.3
-
4
-
-
79958011043
-
Utilizing natural diversity to evolve protein function: Applications towards thermostability
-
Cole, M.F. and Gaucher, E.A. (2011) Utilizing natural diversity to evolve protein function: applications towards thermostability. Curr. Opin. Chem. Biol., 15, 399-406.
-
(2011)
Curr. Opin. Chem. Biol.
, vol.15
, pp. 399-406
-
-
Cole, M.F.1
Gaucher, E.A.2
-
5
-
-
0037189323
-
Diversity considerations in hiv-1 vaccine selection
-
Gaschen, B., Taylor, J., Yusim, K., Foley, B., Gao, F., Lang, D., Novitsky, V., Haynes, B., Hahn, B.H., Bhattacharya, T. et al. (2002) Diversity considerations in HIV-1 vaccine selection. Science, 296, 2354-2360.
-
(2002)
Science
, vol.296
, pp. 2354-2360
-
-
Gaschen, B.1
Taylor, J.2
Yusim, K.3
Foley, B.4
Gao, F.5
Lang, D.6
Novitsky, V.7
Haynes, B.8
Hahn, B.H.9
Bhattacharya, T.10
-
6
-
-
10944228197
-
Reconstructing large regions of an ancestral mammalian genome in silico
-
Blanchette, M., Green, E.D., Miller, W. and Haussler, D. (2004) Reconstructing large regions of an ancestral mammalian genome in silico. Genome Res., 14, 2412-2423.
-
(2004)
Genome Res.
, vol.14
, pp. 2412-2423
-
-
Blanchette, M.1
Green, E.D.2
Miller, W.3
Haussler, D.4
-
7
-
-
4944223649
-
Ancestral sequence reconstruction in primate mitochondrial DNA: Compositional bias and effect on functional inference
-
Krishnan, N.M., Seligmann, H., Stewart, C.B., De Koning, A.P. and Pollock, D.D. (2004) Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference. Mol. Biol. Evol., 21, 1871-1883.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1871-1883
-
-
Krishnan, N.M.1
Seligmann, H.2
Stewart, C.B.3
De Koning, A.P.4
Pollock, D.D.5
-
8
-
-
38949105667
-
-
Liberles, D. (ed) Oxford University Press, Oxford
-
Pupko, T., Doron-Faigenboim, A., Liberles, D. and Cannarozzi, G. (2007) In: Liberles, D. (ed.), Ancestral sequence reconstruction. Oxford University Press, Oxford.
-
(2007)
Ancestral Sequence Reconstruction
-
-
Pupko, T.1
Doron-Faigenboim, A.2
Liberles, D.3
Cannarozzi, G.4
-
9
-
-
0029881442
-
Probabilistic reconstruction of ancestral protein sequences
-
Koshi, J.M. and Goldstein, R.A. (1996) Probabilistic reconstruction of ancestral protein sequences. J. Mol. Evol., 42, 313-320.
-
(1996)
J. Mol. Evol.
, vol.42
, pp. 313-320
-
-
Koshi, J.M.1
Goldstein, R.A.2
-
10
-
-
0034117082
-
A fast algorithm for joint reconstruction of ancestral amino acid sequences
-
Pupko, T., Pe'er, I., Shamir, R. and Graur, D. (2000) A fast algorithm for joint reconstruction of ancestral amino acid sequences. Mol. Biol. Evol., 17, 890-896.
-
(2000)
Mol. Biol. Evol.
, vol.17
, pp. 890-896
-
-
Pupko, T.1
Pe'Er, I.2
Shamir, R.3
Graur, D.4
-
11
-
-
0036677932
-
A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families
-
Pupko, T., Pe'er, I., Hasegawa, M., Graur, D. and Friedman, N. (2002) A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: application to the evolution of five gene families. Bioinformatics, 18, 1116-1123.
-
(2002)
Bioinformatics
, vol.18
, pp. 1116-1123
-
-
Pupko, T.1
Pe'Er, I.2
Hasegawa, M.3
Graur, D.4
Friedman, N.5
-
12
-
-
0028820333
-
A new method of inference of ancestral nucleotide and amino acid sequences
-
Yang, Z., Kumar, S. and Nei, M. (1995) A new method of inference of ancestral nucleotide and amino acid sequences. Genetics, 141, 1641-1650.
-
(1995)
Genetics
, vol.141
, pp. 1641-1650
-
-
Yang, Z.1
Kumar, S.2
Nei, M.3
-
13
-
-
79551594524
-
Maxalike: Maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences
-
Menzel, P., Stadler, P.F. and Gorodkin, J. (2011) maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences. Bioinformatics, 27, 317-325.
-
(2011)
Bioinformatics
, vol.27
, pp. 317-325
-
-
Menzel, P.1
Stadler, P.F.2
Gorodkin, J.3
-
14
-
-
13244278007
-
GASP: Gapped ancestral sequence prediction for proteins
-
Edwards, R.J. and Shields, D.C. (2004) GASP: gapped ancestral sequence prediction for proteins. BMC Bioinformatics, 5, 123.
-
(2004)
BMC Bioinformatics
, vol.5
, pp. 123
-
-
Edwards, R.J.1
Shields, D.C.2
-
15
-
-
33745605535
-
Assessing the accuracy of ancestral protein reconstruction methods
-
Williams, P.D., Pollock, D.D., Blackburne, B.P. and Goldstein, R.A. (2006) Assessing the accuracy of ancestral protein reconstruction methods. PLoS Comput. Biol., 2, e69.
-
(2006)
PLoS Comput. Biol.
, vol.2
-
-
Williams, P.D.1
Pollock, D.D.2
Blackburne, B.P.3
Goldstein, R.A.4
-
16
-
-
14644397888
-
Raxml-iii: A fast program for maximum likelihood-based inference of large phylogenetic trees
-
Stamatakis, A., Ludwig, T. and Meier, H. (2005) RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics, 21, 456-463.
-
(2005)
Bioinformatics
, vol.21
, pp. 456-463
-
-
Stamatakis, A.1
Ludwig, T.2
Meier, H.3
-
17
-
-
0034350427
-
Gaps as characters in sequence-based phylogenetic analyses
-
Simmons, M.P. and Ochoterena, H. (2000) Gaps as characters in sequence-based phylogenetic analyses. Syst. Biol., 49, 369-381.
-
(2000)
Syst. Biol.
, vol.49
, pp. 369-381
-
-
Simmons, M.P.1
Ochoterena, H.2
-
18
-
-
57149086448
-
A likelihood framework to analyse phyletic patterns
-
Cohen, O., Rubinstein, N.D., Stern, A., Gophna, U. and Pupko, T. (2008) A likelihood framework to analyse phyletic patterns. Philos. Trans. Roy. Soc. Lond. B. Biol. Sci., 363, 3903-3911.
-
(2008)
Philos. Trans. Roy. Soc. Lond. B. Biol. Sci.
, vol.363
, pp. 3903-3911
-
-
Cohen, O.1
Rubinstein, N.D.2
Stern, A.3
Gophna, U.4
Pupko, T.5
-
19
-
-
84857156030
-
Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony - A simulation study
-
Cohen, O. and Pupko, T. (2011) Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony-a simulation study. Genome Biol. Evol., 3, 1265-1275.
-
(2011)
Genome Biol. Evol.
, vol.3
, pp. 1265-1275
-
-
Cohen, O.1
Pupko, T.2
-
20
-
-
0016424695
-
Minimal mutation trees of sequences
-
Sankoff, D. (1975) Minimal mutation trees of sequences. Siam. J. Appl. Math., 28, 35-42.
-
(1975)
Siam J. Appl. Math.
, vol.28
, pp. 35-42
-
-
Sankoff, D.1
-
21
-
-
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
-
22
-
-
0000228203
-
A model of evolutionary change in proteins
-
Dayhoff, M. (ed) National Biomedical Research Foundation, Washington DC
-
Dayhoff, M., Schwartz, R. and Orcutt, B. (1978) A model of evolutionary change in proteins. In: Dayhoff, M. (ed.), Atlas of Protein Sequence and Structure, Vol. 5. National Biomedical Research Foundation, Washington, DC, pp. 345-352.
-
(1978)
Atlas of Protein Sequence and Structure
, vol.5
, pp. 345-352
-
-
Dayhoff, M.1
Schwartz, R.2
Orcutt, B.3
-
23
-
-
0026691182
-
The rapid generation of mutation data matrices from protein sequences
-
Jones, D.T., Taylor, W.R. and Thornton, J.M. (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.T.1
Taylor, W.R.2
Thornton, J.M.3
-
24
-
-
0035031966
-
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach
-
Whelan, S. and Goldman, N. (2001) A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol. Biol. Evol., 18, 691-699.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 691-699
-
-
Whelan, S.1
Goldman, N.2
-
25
-
-
45849154166
-
An improved general amino acid replacement matrix
-
Le, S.Q. and Gascuel, O. (2008) An improved general amino acid replacement matrix. Mol. Biol. Evol., 25, 1307-1320.
-
(2008)
Mol. Biol. Evol.
, vol.25
, pp. 1307-1320
-
-
Le, S.Q.1
Gascuel, O.2
-
26
-
-
0029974748
-
Model of amino acid substitution in proteins encoded by mitochondrial DNA
-
Adachi, J. and Hasegawa, M. (1996) Model of amino acid substitution in proteins encoded by mitochondrial DNA. J. Mol. Evol., 42, 459-468.
-
(1996)
J. Mol. Evol.
, vol.42
, pp. 459-468
-
-
Adachi, J.1
Hasegawa, M.2
-
27
-
-
0033920569
-
Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA
-
Adachi, J., Waddell, P.J., Martin, W. and Hasegawa, M. (2000) Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J. Mol. Evol., 50, 348-358.
-
(2000)
J. Mol. Evol.
, vol.50
, pp. 348-358
-
-
Adachi, J.1
Waddell, P.J.2
Martin, W.3
Hasegawa, M.4
-
28
-
-
0000732090
-
-
Munro, H.N. (ed) New York Academic Press
-
Jukes, T.H. and Cantor, C.R. (1969) In: Munro, H.N. (ed.), Mammalian protein metabolism. New York, Academic Press, pp. 21-123.
-
(1969)
Mammalian Protein Metabolism
, pp. 21-123
-
-
Jukes, T.H.1
Cantor, C.R.2
-
29
-
-
0022376704
-
Dating of the human-ape splitting by a molecular clock of mitochondrial DNA
-
Hasegawa, M., Kishino, H. and Yano, T. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol., 22, 160-174.
-
(1985)
J. Mol. Evol.
, vol.22
, pp. 160-174
-
-
Hasegawa, M.1
Kishino, H.2
Yano, T.3
-
30
-
-
0031972161
-
Likelihood models for detecting positively selected amino acid sites and applications to the hiv-1 envelope gene
-
Nielsen, R. and Yang, Z. (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics, 148, 929-936.
-
(1998)
Genetics
, vol.148
, pp. 929-936
-
-
Nielsen, R.1
Yang, Z.2
-
31
-
-
25444507408
-
Empirical codon substitution matrix
-
Schneider, A., Cannarozzi, G.M. and Gonnet, G.H. (2005) Empirical codon substitution matrix. BMC Bioinformatics, 6, 134.
-
(2005)
BMC Bioinformatics
, vol.6
, pp. 134
-
-
Schneider, A.1
Cannarozzi, G.M.2
Gonnet, G.H.3
-
32
-
-
33846818777
-
A combined empirical and mechanistic codon model
-
Doron-Faigenboim, A. and Pupko, T. (2007) A combined empirical and mechanistic codon model. Mol. Biol. Evol., 24, 388-397.
-
(2007)
Mol. Biol. Evol.
, vol.24
, pp. 388-397
-
-
Doron-Faigenboim, A.1
Pupko, T.2
-
33
-
-
2142738304
-
WebLogo: A sequence logo generator
-
Crooks, G.E., Hon, G., Chandonia, J.M. and Brenner, S.E. (2004) WebLogo: a sequence logo generator. Genome Res., 14, 1188-1190.
-
(2004)
Genome Res.
, vol.14
, pp. 1188-1190
-
-
Crooks, G.E.1
Hon, G.2
Chandonia, J.M.3
Brenner, S.E.4
-
34
-
-
65449188232
-
Jalview version 2-A multiple sequence alignment editor and analysis workbench
-
Waterhouse, A.M., Procter, J.B., Martin, D.M., Clamp, M. and Barton, G.J. (2009) Jalview version 2-a multiple sequence alignment editor and analysis workbench. Bioinformatics, 25, 1189-1191.
-
(2009)
Bioinformatics
, vol.25
, pp. 1189-1191
-
-
Waterhouse, A.M.1
Procter, J.B.2
Martin, D.M.3
Clamp, M.4
Barton, G.J.5
-
35
-
-
34547811379
-
Reconstruction and function of ancestral center-of-tree human immunodeficiency virus type 1 proteins
-
Rolland, M., Jensen, M.A., Nickle, D.C., Yan, J., Learn, G.H., Heath, L., Weiner, D. and Mullins, J.I. (2007) Reconstruction and function of ancestral center-of-tree human immunodeficiency virus type 1 proteins. J. Virol., 81, 8507-8514.
-
(2007)
J. Virol.
, vol.81
, pp. 8507-8514
-
-
Rolland, M.1
Jensen, M.A.2
Nickle, D.C.3
Yan, J.4
Learn, G.H.5
Heath, L.6
Weiner, D.7
Mullins, J.I.8
-
36
-
-
57149084079
-
Evolutionary modeling of rate shifts reveals specificity determinants in hiv-1 subtypes
-
Penn, O., Stern, A., Rubinstein, N.D., Dutheil, J., Bacharach, E., Galtier, N. and Pupko, T. (2008) Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes. PLoS Comput. Biol., 4, e1000214.
-
(2008)
PLoS Comput. Biol.
, vol.4
-
-
Penn, O.1
Stern, A.2
Rubinstein, N.D.3
Dutheil, J.4
Bacharach, E.5
Galtier, N.6
Pupko, T.7
-
37
-
-
13744252890
-
MAFFT version 5: Improvement in accuracy of multiple sequence alignment
-
Katoh, K., Kuma, K., Toh, H. and Miyata, T. (2005) MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res., 33, 511-518.
-
(2005)
Nucleic Acids Res.
, vol.33
, pp. 511-518
-
-
Katoh, K.1
Kuma, K.2
Toh, H.3
Miyata, T.4
|