-
1
-
-
0014581827
-
The genetic code and error transmission
-
Alff-Steinberger, C. 1969. The genetic code and error transmission. Proc. Natl. Acad. Sci. USA 64:584-591.
-
(1969)
Proc. Natl. Acad. Sci. USA
, vol.64
, pp. 584-591
-
-
Alff-Steinberger, C.1
-
2
-
-
0031714828
-
Accelerated evolution of cytochrome b in simian primates: Adaptive evolution in concert with other mitochondrial proteins?
-
Andrews, T. D., L. S. Jermiin, and S. Easteal. 1998. Accelerated evolution of cytochrome b in simian primates: adaptive evolution in concert with other mitochondrial proteins? J. Mol. Evol. 47:249-257.
-
(1998)
J. Mol. Evol.
, vol.47
, pp. 249-257
-
-
Andrews, T.D.1
Jermiin, L.S.2
Easteal, S.3
-
3
-
-
0030026404
-
Cytochrome b nucleotide sequences and the identification of five primary lineages of extant cetaceans
-
Arnason, U., and A. Gullberg. 1996. Cytochrome b nucleotide sequences and the identification of five primary lineages of extant cetaceans. Mol. Biol. Evol. 13:407-417.
-
(1996)
Mol. Biol. Evol.
, vol.13
, pp. 407-417
-
-
Arnason, U.1
Gullberg, A.2
-
4
-
-
0031966661
-
The structural basis of molecular adaptation
-
Golding, G. B., and A. M. Dean. 1998. The structural basis of molecular adaptation. Mol. Biol. Evol. 15:355-369.
-
(1998)
Mol. Biol. Evol.
, vol.15
, pp. 355-369
-
-
Golding, G.B.1
Dean, A.M.2
-
5
-
-
0027168787
-
Mitochondrial cytochrome b: Evolution and structure of the protein
-
Degli Esposti, M., S. De Vries, M. Crimi, A. Ghelli, T. Paternello, and A. Meyer. 1993. Mitochondrial cytochrome b: evolution and structure of the protein. Biochim. Biophys. Acta 1143:243-271.
-
(1993)
Biochim. Biophys. Acta
, vol.1143
, pp. 243-271
-
-
Degli Esposti, M.1
De Vries, S.2
Crimi, M.3
Ghelli, A.4
Paternello, T.5
Meyer, A.6
-
6
-
-
0027658301
-
Phylogenetic relationships of pocket gophers (Cratogeomys and Pappogeomys) based on mitochondrial DNA cytochrome b sequences
-
DeWalt, T. S., P. D. Sudman, M. S. Hafner, and S. K. Davis. 1993. Phylogenetic relationships of pocket gophers (Cratogeomys and Pappogeomys) based on mitochondrial DNA cytochrome b sequences. Mol. Phylogenet. Evol. 2:193-204.
-
(1993)
Mol. Phylogenet. Evol.
, vol.2
, pp. 193-204
-
-
DeWalt, T.S.1
Sudman, P.D.2
Hafner, M.S.3
Davis, S.K.4
-
7
-
-
0036840569
-
A sliding-window method to detect selective constraints in protein-coding genes and its application to RNA viruses
-
Fares, M. A., S. F. Elena, J. Ortiz, A. Moya, and E. Barrio. 2002. A sliding-window method to detect selective constraints in protein-coding genes and its application to RNA viruses. J. Mol. Evol. 55:509-521.
-
(2002)
J. Mol. Evol.
, vol.55
, pp. 509-521
-
-
Fares, M.A.1
Elena, S.F.2
Ortiz, J.3
Moya, A.4
Barrio, E.5
-
8
-
-
0242516028
-
Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein
-
Gaucher, E. A., M. M. Miyamoto, and S. A. Benner. 2003. Evolutionary, structural and biochemical evidence for a new interaction site of the leptin obesity protein. Genetics 163:1549-1553.
-
(2003)
Genetics
, vol.163
, pp. 1549-1553
-
-
Gaucher, E.A.1
Miyamoto, M.M.2
Benner, S.A.3
-
9
-
-
0016197604
-
Amino acid difference formula to help explain protein evolution
-
Grantham, R. 1974. Amino acid difference formula to help explain protein evolution. Science 185:862-864.
-
(1974)
Science
, vol.185
, pp. 862-864
-
-
Grantham, R.1
-
10
-
-
0031157173
-
Correlation of functional domains and rates of nucleotide substitution in cytochrome b
-
Griffiths, C. S. 1997. Correlation of functional domains and rates of nucleotide substitution in cytochrome b. Mol. Phylogenet. Evol. 7:352-365.
-
(1997)
Mol. Phylogenet. Evol.
, vol.7
, pp. 352-365
-
-
Griffiths, C.S.1
-
11
-
-
0027377540
-
Relationship between amino acid properties and protein compressibility
-
Gromiha, M. M., and P. K. Ponnuswamy. 1993. Relationship between amino acid properties and protein compressibility. J. Theoret. Biol. 165:87-100.
-
(1993)
J. Theoret. Biol.
, vol.165
, pp. 87-100
-
-
Gromiha, M.M.1
Ponnuswamy, P.K.2
-
12
-
-
0035147609
-
Molecular evolution of aerobic energy metabolism in primates
-
Grossman, L. I., T. R. Schmidt, D. E. Wildman, and M. Goodman. 2001. Molecular evolution of aerobic energy metabolism in primates. Mol. Phylogenet. Evol. 18:26-36.
-
(2001)
Mol. Phylogenet. Evol.
, vol.18
, pp. 26-36
-
-
Grossman, L.I.1
Schmidt, T.R.2
Wildman, D.E.3
Goodman, M.4
-
13
-
-
0025764044
-
Evolution of the cytochrome b gene of mammals
-
Irwin, D. M., T. D. Kocher, and A. C. Wilson. 1991. Evolution of the cytochrome b gene of mammals. J. Mol. Evol. 32: 128-144.
-
(1991)
J. Mol. Evol.
, vol.32
, pp. 128-144
-
-
Irwin, D.M.1
Kocher, T.D.2
Wilson, A.C.3
-
14
-
-
0032479524
-
1 complex
-
1 complex. Science 281:64-71.
-
(1998)
Science
, vol.281
, pp. 64-71
-
-
Iwata, S.1
Lee, J.W.2
Okada, K.3
Lee, J.K.4
Iwata, M.5
Rasmussen, B.6
Link, T.A.7
Ramaswamy, S.8
Jap, B.K.9
-
15
-
-
0033026624
-
Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes
-
Koshi, J. M., D. P. Mindell, and R. A. Goldstein. 1999. Using physical-chemistry-based substitution models in phylogenetic analyses of HIV-1 subtypes. Mol. Biol. Evol. 16:173-179.
-
(1999)
Mol. Biol. Evol.
, vol.16
, pp. 173-179
-
-
Koshi, J.M.1
Mindell, D.P.2
Goldstein, R.A.3
-
16
-
-
0020475449
-
A simple method for displaying the hydropathic character of a protein
-
Kyte, J., and R. F. Doolittle. 1982. A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157:105-132.
-
(1982)
J. Mol. Biol.
, vol.157
, pp. 105-132
-
-
Kyte, J.1
Doolittle, R.F.2
-
17
-
-
1942469391
-
Evidence of positively selected sites in mammalian α-defensins
-
Lynn, D. J., A. T. Lloyd, M. A. Fares, and C. O'Farrelly. 2004. Evidence of positively selected sites in mammalian α-defensins. Mol. Biol. Evol. 21:819-827.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 819-827
-
-
Lynn, D.J.1
Lloyd, A.T.2
Fares, M.A.3
O'Farrelly, C.4
-
18
-
-
0033947771
-
The codon-degeneracy model of molecular evolution
-
McClellan, D. A. 2000. The codon-degeneracy model of molecular evolution. J. Mol. Evol. 50:131-140.
-
(2000)
J. Mol. Evol.
, vol.50
, pp. 131-140
-
-
McClellan, D.A.1
-
19
-
-
0034982702
-
Estimating the influence of selection on the variable amino acid sites of the cytochrome b protein functional domains
-
McClellan, D. A., and K. G. McCracken. 2001. Estimating the influence of selection on the variable amino acid sites of the cytochrome b protein functional domains. Mol. Biol. Evol. 18:917-925.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 917-925
-
-
McClellan, D.A.1
McCracken, K.G.2
-
20
-
-
0842317930
-
-
Brigham Young University, Provo, Utah
-
McClellan, D. A., J. K. Sailsbery, and R. G. Christensen. 2003. CDM: codon-degeneracy model. Version 2.0. Brigham Young University, Provo, Utah.
-
(2003)
CDM: Codon-Degeneracy Model. Version 2.0
-
-
McClellan, D.A.1
Sailsbery, J.K.2
Christensen, R.G.3
-
21
-
-
0842305096
-
Genetic codes as evolutionary filters: Subtle differences in the structure of genetic codes result in significant differences in patterns of nucleotide substitution
-
McClellan, D. A., D. G. Whiting, R. G. Christensen, and J. K. Sailsbery. 2004. Genetic codes as evolutionary filters: subtle differences in the structure of genetic codes result in significant differences in patterns of nucleotide substitution. J. Theoret. Biol. 226:393-400.
-
(2004)
J. Theoret. Biol.
, vol.226
, pp. 393-400
-
-
McClellan, D.A.1
Whiting, D.G.2
Christensen, R.G.3
Sailsbery, J.K.4
-
22
-
-
0028151699
-
Phylogeny of all major groups of cetaceans based on DNA sequences from three mitochondrial genes
-
Milinkovitch, M. C., A. Meyer, and J. R. Powell. 1994. Phylogeny of all major groups of cetaceans based on DNA sequences from three mitochondrial genes. Mol. Biol. Evol. 11:939-948.
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 939-948
-
-
Milinkovitch, M.C.1
Meyer, A.2
Powell, J.R.3
-
23
-
-
0033819550
-
Measuring shifts in function and evolutionary opportunity using variability profiles: A case study of the globins
-
Naylor, G. J. P., and M. Gerstein. 2000. Measuring shifts in function and evolutionary opportunity using variability profiles: a case study of the globins. J. Mol. Evol. 51:223-233.
-
(2000)
J. Mol. Evol.
, vol.51
, pp. 223-233
-
-
Naylor, G.J.P.1
Gerstein, M.2
-
24
-
-
0036366690
-
Detecting positively selected amino acid sites using posterior predictive P-values
-
Nielsen, R., and J. P. Huelsenbeck. 2002. Detecting positively selected amino acid sites using posterior predictive P-values. Pac. Symp. Biocomput. 2002:576-588.
-
(2002)
Pac. Symp. Biocomput.
, vol.2002
, pp. 576-588
-
-
Nielsen, R.1
Huelsenbeck, J.P.2
-
25
-
-
0035912816
-
Retroposon analysis of major cetacean lineages: The monophyly of toothed whales and the paraphyly of river dolphins
-
Nikaido, M., F. Matsuno, H. Hamilton, R. L. Brownell Jr., Y. Cao, W. Ding, Z. Zuoyan, A. M. Shedlock, R. E. Fordyce, M. Hasagawa, and N. Okada. 2001. Retroposon analysis of major cetacean lineages: the monophyly of toothed whales and the paraphyly of river dolphins. Proc. Natl. Acad. Sci. USA 98:7384-7389.
-
(2001)
Proc. Natl. Acad. Sci. USA
, vol.98
, pp. 7384-7389
-
-
Nikaido, M.1
Matsuno, F.2
Hamilton, H.3
Brownell Jr., R.L.4
Cao, Y.5
Ding, W.6
Zuoyan, Z.7
Shedlock, A.M.8
Fordyce, R.E.9
Hasagawa, M.10
Okada, N.11
-
26
-
-
0033621101
-
Phylogenetic relationships among cetartiodactyls based on insertions of short and long interspersed elements: Hippopotamuses are the closest extant relatives of whales
-
Nikaido, M., A. P. Rooney, and N. Okada. 1999. Phylogenetic relationships among cetartiodactyls based on insertions of short and long interspersed elements: hippopotamuses are the closest extant relatives of whales. Proc. Natl. Acad. Sci. USA 96:10261-10266.
-
(1999)
Proc. Natl. Acad. Sci. USA
, vol.96
, pp. 10261-10266
-
-
Nikaido, M.1
Rooney, A.P.2
Okada, N.3
-
27
-
-
0031773680
-
MODELTEST: Testing the model of DNA substitution
-
Posada, D., and K. A. Crandall. 1998. MODELTEST: testing the model of DNA substitution. Bioinformatics 14:817-818.
-
(1998)
Bioinformatics
, vol.14
, pp. 817-818
-
-
Posada, D.1
Crandall, K.A.2
-
28
-
-
0018635651
-
The spatial distribution of physical, chemical, energetic and conformational properties of amino acid residues in globular proteins
-
Prabhakaran, M., and P. K. Ponnuswamy. 1979. The spatial distribution of physical, chemical, energetic and conformational properties of amino acid residues in globular proteins. J. theoret. Biol. 80:485-504.
-
(1979)
J. Theoret. Biol.
, vol.80
, pp. 485-504
-
-
Prabhakaran, M.1
Ponnuswamy, P.K.2
-
29
-
-
0041386108
-
MrBayes 3: Bayesian phylogenetic inference under mixed models
-
Ronquist, F., and J. P. Huelsenbeck. 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.P.2
-
30
-
-
0035056971
-
Evolution of nuclear- and mitochondrial-encoded subunit interaction in cytochrome c oxidase
-
Schmidt, T. R., W. Wu, M. Goodman, and L. I. Grossman. 2001. Evolution of nuclear- and mitochondrial-encoded subunit interaction in cytochrome c oxidase. Mol. Biol. Evol. 18: 563-569.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 563-569
-
-
Schmidt, T.R.1
Wu, W.2
Goodman, M.3
Grossman, L.I.4
-
31
-
-
0036313499
-
A simple covarion-based approach to analyze nucleotide substitution rates
-
Siltberg, J., and D. A. Liberles. 2002. A simple covarion-based approach to analyze nucleotide substitution rates. J. Evol. Biol. 15:588-594.
-
(2002)
J. Evol. Biol.
, vol.15
, pp. 588-594
-
-
Siltberg, J.1
Liberles, D.A.2
-
32
-
-
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
-
34
-
-
14544276715
-
On the fundamental nature and evolution of the genetic code
-
Woese, C. R., D. H. Dugre, S. A. Dugre, M. Kondo, and W. C. Saxinger. 1966. On the fundamental nature and evolution of the genetic code. Cold Spring Harb. Symp. Quant. Biol. 403:304-308.
-
(1966)
Cold Spring Harb. Symp. Quant. Biol.
, vol.403
, pp. 304-308
-
-
Woese, C.R.1
Dugre, D.H.2
Dugre, S.A.3
Kondo, M.4
Saxinger, W.C.5
-
35
-
-
0037461034
-
TreeSAAP: Selection on amino acid properties using phylogenetic trees
-
Woolley, S., J. Johnson, M. J. Smith, K. A. Crandall, and D. A. McClellan. 2003. TreeSAAP: selection on amino acid properties using phylogenetic trees. Bioinformatics 19: 671-672.
-
(2003)
Bioinformatics
, vol.19
, pp. 671-672
-
-
Woolley, S.1
Johnson, J.2
Smith, M.J.3
Crandall, K.A.4
McClellan, D.A.5
-
36
-
-
0031766244
-
What amino acid properties affect protein evolution?
-
Xia, X., and W.-H. Li. 1998. What amino acid properties affect protein evolution? J. Mol. Evol. 47:557-564.
-
(1998)
J. Mol. Evol.
, vol.47
, pp. 557-564
-
-
Xia, X.1
Li, W.-H.2
-
37
-
-
0030683599
-
PAML: A program package for phylogenetic analysis by maximum likelihood
-
Yang, Z. 1997. PAML: a program package for phylogenetic analysis by maximum likelihood. CABIOS 13:555-556.
-
(1997)
CABIOS
, vol.13
, pp. 555-556
-
-
Yang, Z.1
-
38
-
-
0033639150
-
Statistical methods for detecting molecular adaptation
-
Yang, Z., and J. P. Bielawski. 2000. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. 15: 496-503.
-
(2000)
Trends Ecol. Evol.
, vol.15
, pp. 496-503
-
-
Yang, Z.1
Bielawski, J.P.2
-
39
-
-
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
-
40
-
-
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
-
41
-
-
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
-
42
-
-
0032537117
-
1
-
1. Nature 392:677-684.
-
(1998)
Nature
, vol.392
, pp. 677-684
-
-
Zhang, Z.1
Huang, L.2
Shulmeister, V.M.3
Chi, Y.-I.4
Kim, K.K.5
Hung, L.-W.6
Crofts, A.R.7
Berry, E.A.8
Kim, S.-H.9
|