-
1
-
-
0034897709
-
The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites
-
Anisimova, M., J. P. Bielawski, and Z. Yang. 2001. The accuracy and power of likelihood ratio tests to detect positive selection at amino acid sites. Mol. Biol. Evol. 18:1585-1592.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 1585-1592
-
-
Anisimova, M.1
Bielawski, J.P.2
Yang, Z.3
-
2
-
-
0036272936
-
Accuracy and power of Bayes prediction of amino acid sites under positive selection
-
-. 2002. Accuracy and power of Bayes prediction of amino acid sites under positive selection. Mol. Biol. Evol. 19:950-958.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 950-958
-
-
-
3
-
-
0042208362
-
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites
-
Anisimova, M., R. Nielsen, and Z. Yang. 2003. Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics 164:1229-1236.
-
(2003)
Genetics
, vol.164
, pp. 1229-1236
-
-
Anisimova, M.1
Nielsen, R.2
Yang, Z.3
-
4
-
-
0035061474
-
Positive and negative selection in the DAZ gene family
-
Bielawski, J. P., and Z. Yang. 2001. Positive and negative selection in the DAZ gene family. Mol. Biol. Evol. 18:523-529.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 523-529
-
-
Bielawski, J.P.1
Yang, Z.2
-
5
-
-
3042842589
-
A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution
-
-. 2004. A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J. Mol. Evol. 59:121-132.
-
(2004)
J. Mol. Evol.
, vol.59
, pp. 121-132
-
-
-
6
-
-
0034625046
-
Rapid evolution in plant chitinases: Molecular targets of selection in plant-pathogen coevolution
-
Bishop, J. G., A. M. Dean, and T. Mitchell-Olds. 2000. Rapid evolution in plant chitinases: molecular targets of selection in plant-pathogen coevolution. Proc. Natl. Acad. Sci. USA 97:5322-5327.
-
(2000)
Proc. Natl. Acad. Sci. USA
, vol.97
, pp. 5322-5327
-
-
Bishop, J.G.1
Dean, A.M.2
Mitchell-Olds, T.3
-
8
-
-
0000365503
-
Approaches for empirical Bayes confidence intervals
-
Carlin, B. P., and A. E. Gelfand. 1990. Approaches for empirical Bayes confidence intervals. J. Am. Stat. Assoc. 85:105-114.
-
(1990)
J. Am. Stat. Assoc.
, vol.85
, pp. 105-114
-
-
Carlin, B.P.1
Gelfand, A.E.2
-
10
-
-
3242811414
-
Rapid evolution by positive Darwinian selection in the extracellular domain of the abundant lymphocyte protein CD45 in primates
-
Filip, L. C., and N. I. Mundy. 2004. Rapid evolution by positive Darwinian selection in the extracellular domain of the abundant lymphocyte protein CD45 in primates. Mol. Biol. Evol. 21:1504-1511.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1504-1511
-
-
Filip, L.C.1
Mundy, N.I.2
-
11
-
-
0035057075
-
Molecular evolution of transferrin: Evidence for positive selection in salmonids
-
Ford, M. J. 2001. Molecular evolution of transferrin: evidence for positive selection in salmonids. Mol. Biol. Evol. 18:639-647.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 639-647
-
-
Ford, M.J.1
-
12
-
-
0042573997
-
A codon-based model of host-specific selection in parasites, with an application to the influenza A virus
-
Forsberg, R., and F. B. Christiansen. 2003. A codon-based model of host-specific selection in parasites, with an application to the influenza A virus. Mol. Biol. Evol. 20:1252-1259.
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 1252-1259
-
-
Forsberg, R.1
Christiansen, F.B.2
-
13
-
-
0028168856
-
A codon-based model of nucleotide substitution for protein-coding DNA sequences
-
Goldman, N. and Z. Yang. 1994. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11:725-736.
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 725-736
-
-
Goldman, N.1
Yang, Z.2
-
14
-
-
4444357279
-
Modeling the site-specific variation of selection patterns along lineages
-
Guindon, S., A. G. Rodrigo, K. A. Dyer, and J. P. Huelsenbeck. 2004. Modeling the site-specific variation of selection patterns along lineages. Proc. Natl. Acad. Sci. USA 101:12957-12962.
-
(2004)
Proc. Natl. Acad. Sci. USA
, vol.101
, pp. 12957-12962
-
-
Guindon, S.1
Rodrigo, A.G.2
Dyer, K.A.3
Huelsenbeck, J.P.4
-
15
-
-
0035148533
-
Evidence for positive selection in foot-and-mouth-disease virus capsid genes from field isolates
-
Haydon, D. T., A. D. Bastos, N. J. Knowles, and A. R. Samuel. 2001. Evidence for positive selection in foot-and-mouth-disease virus capsid genes from field isolates. Genetics 157:7-15.
-
(2001)
Genetics
, vol.157
, pp. 7-15
-
-
Haydon, D.T.1
Bastos, A.D.2
Knowles, N.J.3
Samuel, A.R.4
-
16
-
-
2942656772
-
Bayesian estimation of positively selected sites
-
Huelsenbeck, J. P., and K. A. Dyer. 2004. Bayesian estimation of positively selected sites. J. Mol. Evol. 58:661-672.
-
(2004)
J. Mol. Evol.
, vol.58
, pp. 661-672
-
-
Huelsenbeck, J.P.1
Dyer, K.A.2
-
18
-
-
84950461861
-
Empirical Bayes confidence intervals based on bootstrap samples
-
Laird, N. M., and T. A. Louis. 1987. Empirical Bayes confidence intervals based on bootstrap samples. J. Amer. Stat. Assoc. 82:739-750.
-
(1987)
J. Amer. Stat. Assoc.
, vol.82
, pp. 739-750
-
-
Laird, N.M.1
Louis, T.A.2
-
19
-
-
4744358984
-
Species specificity in rodent pheromone receptor repertoires
-
Lane, R. P., J. Young, T. Newman, and B. J. Trask. 2004. Species specificity in rodent pheromone receptor repertoires. Genome Res. 14:603-608.
-
(2004)
Genome Res.
, vol.14
, pp. 603-608
-
-
Lane, R.P.1
Young, J.2
Newman, T.3
Trask, B.J.4
-
20
-
-
0022005270
-
A new method for estimating synonymous and nonsynonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes
-
Li, W.-H., C.-I. Wu, and C.-C. Luo. 1985. A new method for estimating synonymous and nonsynonymous rates of nucleotide substitutions considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2:150-174.
-
(1985)
Mol. Biol. Evol.
, vol.2
, pp. 150-174
-
-
Li, W.-H.1
Wu, C.-I.2
Luo, C.-C.3
-
21
-
-
0018415510
-
Two types of amino acid substitutions in protein evolution
-
Miyata, T., S. Miyazawa, and T. Yasunaga. 1979. Two types of amino acid substitutions in protein evolution. J. Mol. Evol. 12:219-236.
-
(1979)
J. Mol. Evol.
, vol.12
, pp. 219-236
-
-
Miyata, T.1
Miyazawa, S.2
Yasunaga, T.3
-
22
-
-
0036739297
-
Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana
-
Mondragon-Palomino, M., B. C. Meyers, R. W. Michelmore, and B. S. Gaut. 2002. Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res. 12:1305-1315.
-
(2002)
Genome Res.
, vol.12
, pp. 1305-1315
-
-
Mondragon-Palomino, M.1
Meyers, B.C.2
Michelmore, R.W.3
Gaut, B.S.4
-
23
-
-
84950432453
-
Parametric empirical Bayes inference: Theory and applications
-
Morris, C. 1983. Parametric empirical Bayes inference: theory and applications. J. Am. Stat. Assoc. 78:47-65.
-
(1983)
J. Am. Stat. Assoc.
, vol.78
, pp. 47-65
-
-
Morris, C.1
-
24
-
-
3242789545
-
Differential selection of genes of cucumber mosaic virus subgroups
-
Moury, B. 2004. Differential selection of genes of cucumber mosaic virus subgroups. Mol. Biol. Evol. 21:1602-1611.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1602-1611
-
-
Moury, B.1
-
25
-
-
0028024626
-
A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
-
Muse, S. V., and B. S. Gaut. 1994. A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11:715-724.
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 715-724
-
-
Muse, S.V.1
Gaut, B.S.2
-
26
-
-
0031972161
-
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
-
Nielsen, R., and Z. Yang. 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
-
27
-
-
0032849322
-
A method for detecting positive selection at single amino acid sites
-
Suzuki, Y., and T. Gojobori. 1999. A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 16:1315-1328.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 1315-1328
-
-
Suzuki, Y.1
Gojobori, T.2
-
28
-
-
0036855372
-
Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites
-
Suzuki, Y., and M. Nei. 2002. Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 19:1865-1869.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 1865-1869
-
-
Suzuki, Y.1
Nei, M.2
-
29
-
-
1942533483
-
False-positive selection identified by ML-based methods: Examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus
-
-. 2004. False-positive selection identified by ML-based methods: examples from the Sig1 gene of the diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus. Mol. Biol. Evol. 21:914-921.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 914-921
-
-
-
30
-
-
0035957018
-
Positive Darwinian selection in the evolution of mammalian female reproductive proteins
-
Swanson, W. J., Z. Yang, M. F. Wolfner, and C. F. Aquadro. 2001. Positive Darwinian selection in the evolution of mammalian female reproductive proteins. Proc. Natl. Acad. Sci. USA 98:2509-2514.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 2509-2514
-
-
Swanson, W.J.1
Yang, Z.2
Wolfner, M.F.3
Aquadro, C.F.4
-
31
-
-
0242666324
-
Patterns of variation within self-incompatibility loci
-
Takebayashi, N., P. B. Brewer, E. Newbigin, and M. K. Uyenoyama. 2003. Patterns of variation within self-incompatibility loci. Mol. Biol. Evol. 20:1778-1794.
-
(2003)
Mol. Biol. Evol.
, vol.20
, pp. 1778-1794
-
-
Takebayashi, N.1
Brewer, P.B.2
Newbigin, E.3
Uyenoyama, M.K.4
-
32
-
-
0036297139
-
Phylogenetic evidence for adaptive evolution of dengue viruses in nature
-
Twiddy, S. S., C. H. Woelk, and E. C. Holmes. 2002. Phylogenetic evidence for adaptive evolution of dengue viruses in nature. J. Gen. Virol. 83:1679-1689.
-
(2002)
J. Gen. Virol.
, vol.83
, pp. 1679-1689
-
-
Twiddy, S.S.1
Woelk, C.H.2
Holmes, E.C.3
-
33
-
-
8544225780
-
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
-
Wong, W. S. W., Z. Yang, N. Goldman, and R. Nielsen. 2004. Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168:1041-1051.
-
(2004)
Genetics
, vol.168
, pp. 1041-1051
-
-
Wong, W.S.W.1
Yang, Z.2
Goldman, N.3
Nielsen, R.4
-
34
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. Comput. Appl. Biosci. 13:555-556. (http://abacus.gene.ucl. ac.uk/software/paml.html).
-
(1997)
Comput. Appl. Biosci.
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
35
-
-
0033692959
-
Maximum likelihood estimation on large phytogenies and analysis of adaptive evolution in human influenza virus A
-
-. 2000. Maximum likelihood estimation on large phytogenies and analysis of adaptive evolution in human influenza virus A. J. Mol. Evol. 51:423-432.
-
(2000)
J. Mol. Evol.
, vol.51
, pp. 423-432
-
-
-
36
-
-
0036270185
-
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
-
Yang, Z., and R. Nielsen. 2002. Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19:908-917.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 908-917
-
-
Yang, Z.1
Nielsen, R.2
-
37
-
-
0034097381
-
Codon-substitution models for heterogeneous selection pressure at amino acid sites
-
Yang, Z., R. Nielsen, N. Goldman, and A.-M. K. Pedersen. 2000. Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431-449.
-
(2000)
Genetics
, vol.155
, pp. 431-449
-
-
Yang, Z.1
Nielsen, R.2
Goldman, N.3
Pedersen, A.-M.K.4
-
38
-
-
0036134765
-
Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes
-
Yang, Z., and W. J. Swanson. 2002. Codon-substitution models to detect adaptive evolution that account for heterogeneous selective pressures among site classes. Mol. Biol. Evol. 19:49-57.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 49-57
-
-
Yang, Z.1
Swanson, W.J.2
-
39
-
-
0032737463
-
Genealogical evidence for positive selection in the nef gene of HIV-1
-
Zanotto, P. M., E. G. Kallas, R. F. Souza, and E. C. Holmes. 1999. Genealogical evidence for positive selection in the nef gene of HIV-1. Genetics 153:1077-1089.
-
(1999)
Genetics
, vol.153
, pp. 1077-1089
-
-
Zanotto, P.M.1
Kallas, E.G.2
Souza, R.F.3
Holmes, E.C.4
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