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Volumn 7, Issue 5, 2006, Pages 337-348

An integrated view of protein evolution

Author keywords

[No Author keywords available]

Indexed keywords

ADAPTATION; AMINO ACID SEQUENCE; FUNCTIONAL GENOMICS; GENE EXPRESSION; GENE LOCUS; GENETIC RECOMBINATION; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN EXPRESSION; PROTEIN PURIFICATION; PROTEIN STABILITY; PROTEIN STRUCTURE; REVIEW; STRUCTURAL GENOMICS;

EID: 33646182934     PISSN: 14710056     EISSN: 14710064     Source Type: Journal    
DOI: 10.1038/nrg1838     Document Type: Review
Times cited : (413)

References (142)
  • 1
    • 0041843801 scopus 로고    scopus 로고
    • Molecular phylogenies link rates of evolution and speciation
    • Webster, A. J., Payne, R. J. & Pagel, M. Molecular phylogenies link rates of evolution and speciation. Science 301, 478 (2003).
    • (2003) Science , vol.301 , pp. 478
    • Webster, A.J.1    Payne, R.J.2    Pagel, M.3
  • 2
    • 10344229911 scopus 로고    scopus 로고
    • Sexual and temporal dynamics of molecular evolution in C. elegans development
    • Cutter, A. D. & Ward, S. Sexual and temporal dynamics of molecular evolution in C. elegans development. Mol. Biol. Evol. 22, 178-188 (2005).
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 178-188
    • Cutter, A.D.1    Ward, S.2
  • 3
    • 19644378508 scopus 로고    scopus 로고
    • Sociality and the rate of molecular evolution
    • Bromham, L. & Leys, R. Sociality and the rate of molecular evolution. Mol. Biol. Evol. 22, 1393-1402 (2005).
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1393-1402
    • Bromham, L.1    Leys, R.2
  • 5
    • 0242285634 scopus 로고    scopus 로고
    • Human disease genes: Patterns and predictions
    • Smith, N. G. & Eyre-Walker, A. Human disease genes: patterns and predictions. Gene 318, 169-175 (2003).
    • (2003) Gene , vol.318 , pp. 169-175
    • Smith, N.G.1    Eyre-Walker, A.2
  • 6
    • 0042568725 scopus 로고    scopus 로고
    • Pharmacophylogenomics: Genes, evolution and drug targets
    • Searls, D. B. Pharmacophylogenomics: genes, evolution and drug targets. Nature Rev. Drug Discov. 2, 613-623 (2003). A summary of the potential links between evolutionary genomics and pharmacology.
    • (2003) Nature Rev. Drug Discov. , vol.2 , pp. 613-623
    • Searls, D.B.1
  • 7
    • 0037436412 scopus 로고    scopus 로고
    • Exploiting the co-evolution of interacting proteins to discover interaction specificity
    • Ramani, A. K. & Marcotte, E. M. Exploiting the co-evolution of interacting proteins to discover interaction specificity. J. Mol. Biol. 327, 273-284 (2003).
    • (2003) J. Mol. Biol. , vol.327 , pp. 273-284
    • Ramani, A.K.1    Marcotte, E.M.2
  • 8
    • 0017323923 scopus 로고
    • Biochemical evolution
    • Wilson, A. C., Carlson, S. S. & White, T. J. Biochemical evolution. Annu. Rev. Biochem. 46, 573-639 (1977). A classical early study that recognized several potential determinants of protein evolution.
    • (1977) Annu. Rev. Biochem. , vol.46 , pp. 573-639
    • Wilson, A.C.1    Carlson, S.S.2    White, T.J.3
  • 9
    • 0035546129 scopus 로고    scopus 로고
    • The neutral theory in the genomic era
    • Fay, J. C. & Wu, C. I. The neutral theory in the genomic era. Curr. Opin. Genet. Dev. 11, 642-646 (2001).
    • (2001) Curr. Opin. Genet. Dev. , vol.11 , pp. 642-646
    • Fay, J.C.1    Wu, C.I.2
  • 11
    • 0027020232 scopus 로고
    • The nearly neutral theory of molecular evolution
    • Ohta, T. The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Syst. 23, 263-286 (1992).
    • (1992) Annu. Rev. Ecol. Syst. , vol.23 , pp. 263-286
    • Ohta, T.1
  • 12
    • 0003533590 scopus 로고
    • Oxford Univ. Press, Oxford
    • Gillespie, J. H. The Causes of Molecular Evolution (Oxford Univ. Press, Oxford, 1991). References 10-12 are landmark reviews (frequently with opposing views) on the neutral and nearly neutral theories.
    • (1991) The Causes of Molecular Evolution
    • Gillespie, J.H.1
  • 14
    • 0032714307 scopus 로고    scopus 로고
    • The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents
    • Smith, N. G. C. & Hurst, L. D. The effect of tandem substitutions on the correlation between synonymous and nonsynonymous rates in rodents. Genetics 153, 1395-1402 (1999).
    • (1999) Genetics , vol.153 , pp. 1395-1402
    • Smith, N.G.C.1    Hurst, L.D.2
  • 15
    • 0034748984 scopus 로고    scopus 로고
    • Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: Implications for understanding the mechanistic basis of the male mutation bias
    • Lercher, M. J., Williams, E. J. B. & Hurst, L. D. Local similarity in evolutionary rates extends over whole chromosomes in human-rodent and mouse-rat comparisons: Implications for understanding the mechanistic basis of the male mutation bias. Mol. Biol. Evol. 18, 2032-2039 (2001). An analysis of mutation-rate variation across mammalian genomes and its effect on protein evolution.
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 2032-2039
    • Lercher, M.J.1    Williams, E.J.B.2    Hurst, L.D.3
  • 16
    • 3042616134 scopus 로고    scopus 로고
    • Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile
    • Lercher, M. J., Chamary, J. V. & Hurst, L. D. Genomic regionality in rates of evolution is not explained by clustering of genes of comparable expression profile. Genome Res. 14, 1002-1013 (2004).
    • (2004) Genome Res. , vol.14 , pp. 1002-1013
    • Lercher, M.J.1    Chamary, J.V.2    Hurst, L.D.3
  • 17
    • 0034687371 scopus 로고    scopus 로고
    • The proteins of linked genes evolve at similar rates
    • Williams, E. J. & Hurst, L. D. The proteins of linked genes evolve at similar rates. Nature 407, 900-903 (2000).
    • (2000) Nature , vol.407 , pp. 900-903
    • Williams, E.J.1    Hurst, L.D.2
  • 18
    • 0033615073 scopus 로고    scopus 로고
    • Chromosomal location effects on gene sequence evolution in mammals
    • Matassi, G., Sharp, P. M. & Gautier, C. Chromosomal location effects on gene sequence evolution in mammals. Curr. Biol. 9, 786-791 (1999).
    • (1999) Curr. Biol. , vol.9 , pp. 786-791
    • Matassi, G.1    Sharp, P.M.2    Gautier, C.3
  • 19
    • 0029065571 scopus 로고
    • Association of increased spontaneous mutation-rates with high levels of transcription in yeast
    • Datta, A. & Jinks-Robertson, S. Association of increased spontaneous mutation-rates with high levels of transcription in yeast. Science 268, 1616-1619 (1995).
    • (1995) Science , vol.268 , pp. 1616-1619
    • Datta, A.1    Jinks-Robertson, S.2
  • 20
    • 0036640951 scopus 로고    scopus 로고
    • Human SNP variability and mutation rate are higher in regions of high recombination
    • Lercher, M. J. & Hurst, L. D. Human SNP variability and mutation rate are higher in regions of high recombination. Trends Genet. 18, 337-340 (2002).
    • (2002) Trends Genet. , vol.18 , pp. 337-340
    • Lercher, M.J.1    Hurst, L.D.2
  • 21
    • 0347416710 scopus 로고    scopus 로고
    • Error-prone DNA polymerases: When making a mistake is the only way to get ahead
    • Rattray, A. J. & Strathern, J. N. Error-prone DNA polymerases: when making a mistake is the only way to get ahead. Annu. Rev. Genet. 37, 31-66 (2003).
    • (2003) Annu. Rev. Genet. , vol.37 , pp. 31-66
    • Rattray, A.J.1    Strathern, J.N.2
  • 22
    • 0030020990 scopus 로고    scopus 로고
    • Recent advances in understanding the evolution and maintenance of sex
    • Hurst, L. D. & Peck, J. R. Recent advances in understanding the evolution and maintenance of sex. Trends Ecol. Evol. 11, 46-52 (1996).
    • (1996) Trends Ecol. Evol. , vol.11 , pp. 46-52
    • Hurst, L.D.1    Peck, J.R.2
  • 23
    • 0342383237 scopus 로고
    • Effects of linkage on rates of molecular evolution
    • Birky, C. W. Jr & Walsh, J. B. Effects of linkage on rates of molecular evolution. Proc. Natl Acad. Sci. USA 85, 6414-6418 (1988).
    • (1988) Proc. Natl Acad. Sci. USA , vol.85 , pp. 6414-6418
    • Birky Jr., C.W.1    Walsh, J.B.2
  • 24
    • 20644465818 scopus 로고    scopus 로고
    • A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate
    • Wyckoff, G. J., Malcom, C. M., Vallender, E. J. & Lahn, B. T. A highly unexpected strong correlation between fixation probability of nonsynonymous mutations and mutation rate. Trends Genet. 21, 381-385 (2005). A remarkable study that suggests that up to 40% of the variation in protein evolutionary rates might be attributable to variation in the underlying mutation rate.
    • (2005) Trends Genet. , vol.21 , pp. 381-385
    • Wyckoff, G.J.1    Malcom, C.M.2    Vallender, E.J.3    Lahn, B.T.4
  • 25
    • 31144465926 scopus 로고    scopus 로고
    • Hearing silence: Non-neutral evolution at synonymous sites in mammals
    • Chamary, J. V., Parmley, J. L. & Hurst, L. D. Hearing silence: non-neutral evolution at synonymous sites in mammals. Nature Rev. Genet. 7, 98-108 (2006).
    • (2006) Nature Rev. Genet. , vol.7 , pp. 98-108
    • Chamary, J.V.1    Parmley, J.L.2    Hurst, L.D.3
  • 26
    • 0016220238 scopus 로고
    • The hitch-hiking effect of a favourable gene
    • Smith, J. M. & Haigh, J. The hitch-hiking effect of a favourable gene. Genet. Res. 23, 23-35 (1974).
    • (1974) Genet. Res. , vol.23 , pp. 23-35
    • Smith, J.M.1    Haigh, J.2
  • 27
    • 0037108764 scopus 로고    scopus 로고
    • Linkage limits the power of natural selection in Drosophila
    • Betancourt, A. J. & Presgraves, D. C. Linkage limits the power of natural selection in Drosophila. Proc. Natl Acad. Sci. USA 99, 13616-13620 (2002). This paper claims that regional recombinational differences have a strong influence on the fixation of positively selected mutations.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 13616-13620
    • Betancourt, A.J.1    Presgraves, D.C.2
  • 28
    • 3042544623 scopus 로고    scopus 로고
    • The genomic rate of adaptive amino acid substitution in Drosophila
    • Bierne, N. & Eyre-Walker, A. The genomic rate of adaptive amino acid substitution in Drosophila. Mol. Biol. Evol. 21, 1350-1360 (2004).
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1350-1360
    • Bierne, N.1    Eyre-Walker, A.2
  • 29
    • 24944577454 scopus 로고    scopus 로고
    • Recombination enhances protein adaptation in Drosophila melanogaster
    • Presgraves, D. C. Recombination enhances protein adaptation in Drosophila melanogaster. Curr. Biol. 15, 1651-1656 (2005).
    • (2005) Curr. Biol. , vol.15 , pp. 1651-1656
    • Presgraves, D.C.1
  • 30
    • 5044252972 scopus 로고    scopus 로고
    • Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome
    • Subramanian, S. & Kumar, S. Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome. Genetics 168, 373-381 (2004).
    • (2004) Genetics , vol.168 , pp. 373-381
    • Subramanian, S.1    Kumar, S.2
  • 31
    • 4143122090 scopus 로고    scopus 로고
    • Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata
    • Wright, S. I., Yau, C. B., Looseley, M. & Meyers, B. C. Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol. Biol. Evol. 21, 1719-1726 (2004).
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1719-1726
    • Wright, S.I.1    Yau, C.B.2    Looseley, M.3    Meyers, B.C.4
  • 32
    • 0034978556 scopus 로고    scopus 로고
    • Highly expressed genes in yeast evolve slowly
    • Pal, C., Papp, B. & Hurst, L. D. Highly expressed genes in yeast evolve slowly. Genetics 158, 927-931 (2001). The first identification of protein-expression level as a strong predictor of evolutionary rate in yeast.
    • (2001) Genetics , vol.158 , pp. 927-931
    • Pal, C.1    Papp, B.2    Hurst, L.D.3
  • 33
    • 1242284655 scopus 로고    scopus 로고
    • An analysis of determinants of amino acids substitution rates in bacterial proteins
    • Rocha, E. P. C. & Danchin, A. An analysis of determinants of amino acids substitution rates in bacterial proteins. Mol. Biol. Evol. 21, 108-116 (2004). This work (like reference 48) compares the relative importance of several factors that are implicated in protein evolution, identifying expression level as the most important variable.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 108-116
    • Rocha, E.P.C.1    Danchin, A.2
  • 34
    • 0034633494 scopus 로고    scopus 로고
    • Inaugural article: Global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae
    • Gerton, J. L. et al. Inaugural article: global mapping of meiotic recombination hotspots and coldspots in the yeast Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA 97, 11383-11390 (2000).
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 11383-11390
    • Gerton, J.L.1
  • 35
    • 0035207792 scopus 로고    scopus 로고
    • Does the recombination rate affect the efficiency of purifying selection? The yeast genome provides a partial answer
    • Pal, C., Papp, B. & Hurst, L. D. Does the recombination rate affect the efficiency of purifying selection? The yeast genome provides a partial answer. Mol. Biol. Evol. 18, 2323-2326 (2001).
    • (2001) Mol. Biol. Evol. , vol.18 , pp. 2323-2326
    • Pal, C.1    Papp, B.2    Hurst, L.D.3
  • 36
    • 0346991745 scopus 로고    scopus 로고
    • Protein evolution and codon usage bias on the neo-sex chromosomes of Drosophila miranda
    • Bachtrog, D. Protein evolution and codon usage bias on the neo-sex chromosomes of Drosophila miranda. Genetics 165, 1221-1232 (2003).
    • (2003) Genetics , vol.165 , pp. 1221-1232
    • Bachtrog, D.1
  • 37
    • 2442628547 scopus 로고    scopus 로고
    • Evidence that positive selection drives Y-chromosome degeneration in Drosophila miranda
    • Bachtrog, D. Evidence that positive selection drives Y-chromosome degeneration in Drosophila miranda. Nature Genet. 36, 518-522 (2004).
    • (2004) Nature Genet. , vol.36 , pp. 518-522
    • Bachtrog, D.1
  • 38
    • 0017227120 scopus 로고
    • Evolutionary processes and evolutionary noise at the molecular level. I. Functional density in proteins
    • Zuckerkandl, E. Evolutionary processes and evolutionary noise at the molecular level. I. Functional density in proteins. J. Mol. Evol. 7, 167-183 (1976).
    • (1976) J. Mol. Evol. , vol.7 , pp. 167-183
    • Zuckerkandl, E.1
  • 39
    • 26444621352 scopus 로고    scopus 로고
    • Why highly expressed proteins evolve slowly
    • Drummond, D. A., Bloom, J. D., Adami, C., Wilke, C. O. & Arnold, F. H. Why highly expressed proteins evolve slowly. Proc. Natl Acad. Sci. USA 102, 14338-14343 (2005). Might highly expressed proteins be under strong selection to avoid protein misfolding? Several tests in this remarkable study indicate that this is the case.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 14338-14343
    • Drummond, D.A.1    Bloom, J.D.2    Adami, C.3    Wilke, C.O.4    Arnold, F.H.5
  • 40
    • 0037069428 scopus 로고    scopus 로고
    • Dobzhansky-Muller incompatibilities in protein evolution
    • Kondrashov, A. S., Sunyaev, S. & Kondrashov, F. A. Dobzhansky-Muller incompatibilities in protein evolution. Proc. Natl Acad. Sci. USA 99, 14878-13883 (2002). An original study on the frequency and importance of compensatory substitutions.
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 14878-13883
    • Kondrashov, A.S.1    Sunyaev, S.2    Kondrashov, F.A.3
  • 41
    • 23944490117 scopus 로고    scopus 로고
    • Missense meanderings in sequence space: A biophysical view of protein evolution
    • DePristo, M. A., Weinreich, D. M. & Hartl, D. L. Missense meanderings in sequence space: a biophysical view of protein evolution. Nature Rev. Genet. 6, 678-687 (2005). An original and thought-provoking review that links protein stability and compensatory evolution.
    • (2005) Nature Rev. Genet. , vol.6 , pp. 678-687
    • DePristo, M.A.1    Weinreich, D.M.2    Hartl, D.L.3
  • 42
    • 21044440015 scopus 로고    scopus 로고
    • The coupon collector and the suppressor mutation: Estimating the number of compensatory mutations by maximum likelihood
    • Poon, A., Davis, B. H. & Chao, L. The coupon collector and the suppressor mutation: estimating the number of compensatory mutations by maximum likelihood. Genetics 170, 1323-1332 (2005).
    • (2005) Genetics , vol.170 , pp. 1323-1332
    • Poon, A.1    Davis, B.H.2    Chao, L.3
  • 43
    • 0035963414 scopus 로고    scopus 로고
    • Protein dispensability and rate of evolution
    • Hirsh, A. E. & Fraser, H. B. Protein dispensability and rate of evolution. Nature 411, 1046-1049 (2001). A classical study on the effect of gene 'importance' on protein evolution.
    • (2001) Nature , vol.411 , pp. 1046-1049
    • Hirsh, A.E.1    Fraser, H.B.2
  • 44
    • 0036078078 scopus 로고    scopus 로고
    • Essential genes are more evolutionary conserved than are nonessential genes in bacteria
    • Jordan, I. K., Rogozin, I. B., Wolf, Y. I. & Koonin, E. V. Essential genes are more evolutionary conserved than are nonessential genes in bacteria. Genome Res. 12, 962-968 (2002).
    • (2002) Genome Res. , vol.12 , pp. 962-968
    • Jordan, I.K.1    Rogozin, I.B.2    Wolf, Y.I.3    Koonin, E.V.4
  • 45
    • 10744225908 scopus 로고    scopus 로고
    • Molecular correlates of genes exhibiting RNAi phenotypes in Caenorhabditis elegans
    • Cutter, A. D. et al. Molecular correlates of genes exhibiting RNAi phenotypes in Caenorhabditis elegans. Genome Res. 13, 2651-2657 (2003).
    • (2003) Genome Res. , vol.13 , pp. 2651-2657
    • Cutter, A.D.1
  • 46
    • 0037472928 scopus 로고    scopus 로고
    • Rate of evolution and gene dispensability
    • Pal, C., Papp, B. & Hurst, L. D. Rate of evolution and gene dispensability. Nature 421, 496-497 (2003).
    • (2003) Nature , vol.421 , pp. 496-497
    • Pal, C.1    Papp, B.2    Hurst, L.D.3
  • 47
    • 17244367886 scopus 로고    scopus 로고
    • Functional genomic analysis of the rates of protein evolution
    • Wall, D. P. et al. Functional genomic analysis of the rates of protein evolution. Proc. Natl Acad. Sci. USA 102, 5483-5488 (2005). A sophisticted analysis that aims to disentangle the influences of expression level and dispensability.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 5483-5488
    • Wall, D.P.1
  • 48
    • 30744441602 scopus 로고    scopus 로고
    • A single determinant dominates the rate of yeast protein evolution
    • Drummond, D. A., Raval, A. & Wilke, C. O. A single determinant dominates the rate of yeast protein evolution. Mol. Biol. Evol., 327-337 (2005). This work (like reference 33) compares the relative importance of several factors that are implicated in protein evolution, and identifies expression level as the most important variable.
    • (2005) Mol. Biol. Evol. , pp. 327-337
    • Drummond, D.A.1    Raval, A.2    Wilke, C.O.3
  • 49
    • 16344369543 scopus 로고    scopus 로고
    • Significant impact of protein dispensability on the instantaneous rate of protein evolution
    • Zhang, J. Z. & He, X. L. Significant impact of protein dispensability on the instantaneous rate of protein evolution. Mol. Biol. Evol. 22, 1147-1155 (2005).
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1147-1155
    • Zhang, J.Z.1    He, X.L.2
  • 50
    • 2942624207 scopus 로고    scopus 로고
    • Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast
    • Papp, B., Pal, C. & Hurst, L. D. Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 429, 661-664 (2004). The 'importance' of a gene is highly environment-specific: about half of all 'dispensable' enzymes in the laboratory are essential in specific environments.
    • (2004) Nature , vol.429 , pp. 661-664
    • Papp, B.1    Pal, C.2    Hurst, L.D.3
  • 51
    • 0142124263 scopus 로고    scopus 로고
    • Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution
    • Krylov, D. M., Wolf, Y. I., Rogozin, I. B. & Koonin, E. V. Gene loss, protein sequence divergence, gene dispensability, expression level, and interactivity are correlated in eukaryotic evolution. Genome Res. 13, 2229-2235 (2003).
    • (2003) Genome Res. , vol.13 , pp. 2229-2235
    • Krylov, D.M.1    Wolf, Y.I.2    Rogozin, I.B.3    Koonin, E.V.4
  • 52
    • 0033565762 scopus 로고    scopus 로고
    • Do essential genes evolve slowly?
    • Hurst, L. D. & Smith, N. G. Do essential genes evolve slowly? Curr. Biol. 9, 747-750 (1999).
    • (1999) Curr. Biol. , vol.9 , pp. 747-750
    • Hurst, L.D.1    Smith, N.G.2
  • 53
    • 27744509096 scopus 로고    scopus 로고
    • Sex-specific functional specialization and the evolutionary rates of essential fertility genes
    • Torgerson, D. G., Whitty, B. R. & Singh, R. S. Sex-specific functional specialization and the evolutionary rates of essential fertility genes. J. Mol. Evol. 61, 650-658 (2005). Shows that function-specific positive selection, rather than essentiality, seems to explain the evolution of fertility genes.
    • (2005) J. Mol. Evol. , vol.61 , pp. 650-658
    • Torgerson, D.G.1    Whitty, B.R.2    Singh, R.S.3
  • 54
    • 0024792699 scopus 로고
    • Genetic analysis of protein stability and function
    • Pakula, A. A. & Sauer, R. T. Genetic analysis of protein stability and function. Annu. Rev. Genet. 23, 289-310 (1989).
    • (1989) Annu. Rev. Genet. , vol.23 , pp. 289-310
    • Pakula, A.A.1    Sauer, R.T.2
  • 55
    • 3042681604 scopus 로고    scopus 로고
    • Protein tolerance to random amino acid change
    • Guo, H. H., Choe, J. & Loeb, L. A. Protein tolerance to random amino acid change. Proc. Natl Acad. Sci. USA 101, 9205-9210 (2004).
    • (2004) Proc. Natl Acad. Sci. USA , vol.101 , pp. 9205-9210
    • Guo, H.H.1    Choe, J.2    Loeb, L.A.3
  • 56
    • 0842281551 scopus 로고    scopus 로고
    • Principles of protein folding, misfolding and aggregation
    • Dobson, C. M. Principles of protein folding, misfolding and aggregation. Semin. Cell Dev. Biol. 15, 3-16 (2004).
    • (2004) Semin. Cell Dev. Biol. , vol.15 , pp. 3-16
    • Dobson, C.M.1
  • 57
    • 0033616712 scopus 로고    scopus 로고
    • Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species
    • Haney, P. J. et al. Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species. Proc. Natl Acad. Sci. USA 96, 3578-3583 (1999).
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 3578-3583
    • Haney, P.J.1
  • 59
    • 0035823119 scopus 로고    scopus 로고
    • Understanding hierarchical protein evolution from first principles
    • Dokholyan, N. V. & Shakhnovich, E. I. Understanding hierarchical protein evolution from first principles. J. Mol. Biol. 312, 289-307 (2001).
    • (2001) J. Mol. Biol. , vol.312 , pp. 289-307
    • Dokholyan, N.V.1    Shakhnovich, E.I.2
  • 60
    • 13444305208 scopus 로고    scopus 로고
    • Generality of the structurally constrained protein evolution model: Assessment on representatives of the four main fold classes
    • Parisi, G. & Echave, J. Generality of the structurally constrained protein evolution model: assessment on representatives of the four main fold classes. Gene 345, 45-53 (2005).
    • (2005) Gene , vol.345 , pp. 45-53
    • Parisi, G.1    Echave, J.2
  • 61
    • 0036856289 scopus 로고    scopus 로고
    • The pattern of amino acid replacements in α/β-barrels
    • Dean, A. M., Neuhauser, C., Grenier, E. & Golding, G. B. The pattern of amino acid replacements in α/β-barrels. Mol. Biol. Evol. 19, 1846-1864 (2002).
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 1846-1864
    • Dean, A.M.1    Neuhauser, C.2    Grenier, E.3    Golding, G.B.4
  • 62
    • 0031805465 scopus 로고    scopus 로고
    • Assessing the impact of secondary structure and solvent accessibility on protein evolution
    • Goldman, N., Thorne, J. L. & Jones, D. T. Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics 149, 445-458 (1998).
    • (1998) Genetics , vol.149 , pp. 445-458
    • Goldman, N.1    Thorne, J.L.2    Jones, D.T.3
  • 63
    • 0033969946 scopus 로고    scopus 로고
    • Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica
    • Bustamante, C. D., Townsend, J. P. & Hartl, D. L. Solvent accessibility and purifying selection within proteins of Escherichia coli and Salmonella enterica. Mol. Biol. Evol. 17, 301-308 (2000).
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 301-308
    • Bustamante, C.D.1    Townsend, J.P.2    Hartl, D.L.3
  • 64
    • 0037022286 scopus 로고    scopus 로고
    • Protein topology and stability define the space of allowed sequences
    • Koehl, P. & Levitt, M. Protein topology and stability define the space of allowed sequences. Proc. Natl Acad. Sci. USA 99, 1280-1285 (2002).
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 1280-1285
    • Koehl, P.1    Levitt, M.2
  • 65
    • 12344283074 scopus 로고    scopus 로고
    • Determinants of adaptive evolution at the molecular level: The extended complexity hypothesis
    • Aris-Brosou, S. Determinants of adaptive evolution at the molecular level: the extended complexity hypothesis. Mol. Biol. Evol. 22, 200-209 (2005).
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 200-209
    • Aris-Brosou, S.1
  • 67
    • 13144257707 scopus 로고    scopus 로고
    • The genetic theory of adaptation: A brief history
    • Orr, H. A. The genetic theory of adaptation: a brief history. Nature Rev. Genet. 6, 119-127 (2005). An excellent review on molecular adaptation.
    • (2005) Nature Rev. Genet. , vol.6 , pp. 119-127
    • Orr, H.A.1
  • 68
    • 0037177560 scopus 로고    scopus 로고
    • Evolutionary rate in the protein interaction network
    • Fraser, H. B., Hirsh, A. E., Steinmetz, L. M., Scharfe, C. & Feldman, M. W. Evolutionary rate in the protein interaction network. Science 296, 750-752 (2002). An influential, but controversial study on the effect of protein interactions on evolution.
    • (2002) Science , vol.296 , pp. 750-752
    • Fraser, H.B.1    Hirsh, A.E.2    Steinmetz, L.M.3    Scharfe, C.4    Feldman, M.W.5
  • 69
    • 2942624159 scopus 로고    scopus 로고
    • Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets
    • Bloom, J. D. & Adami, C. Apparent dependence of protein evolutionary rate on number of interactions is linked to biases in protein-protein interactions data sets. BMC Evol. Biol. 3, 21 (2003).
    • (2003) BMC Evol. Biol. , vol.3 , pp. 21
    • Bloom, J.D.1    Adami, C.2
  • 70
    • 0842290925 scopus 로고    scopus 로고
    • Molecular evolution in large genetic networks: Does connectivity equal constraint?
    • Hahn, M. W., Conant, G. C. & Wagner, A. Molecular evolution in large genetic networks: does connectivity equal constraint? J. Mol. Evol. 58, 203-211 (2004).
    • (2004) J. Mol. Evol. , vol.58 , pp. 203-211
    • Hahn, M.W.1    Conant, G.C.2    Wagner, A.3
  • 71
    • 0842291785 scopus 로고    scopus 로고
    • No simple dependence between protein evolution rate and the number of protein-protein interactions: Only the most prolific interactors tend to evolve slowly
    • Jordan, I. K., Wolf, Y. I. & Koonin, E. V. No simple dependence between protein evolution rate and the number of protein-protein interactions: only the most prolific interactors tend to evolve slowly. BMC Evol. Biol. 3, 1 (2003).
    • (2003) BMC Evol. Biol. , vol.3 , pp. 1
    • Jordan, I.K.1    Wolf, Y.I.2    Koonin, E.V.3
  • 72
    • 17444387503 scopus 로고    scopus 로고
    • Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks
    • Agrafioti, I. et al. Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks. BMC Evol. Biol. 5, 23 (2005).
    • (2005) BMC Evol. Biol. , vol.5 , pp. 23
    • Agrafioti, I.1
  • 73
    • 0036443972 scopus 로고    scopus 로고
    • The constraints protein-protein interactions place on sequence divergence
    • Teichmann, S. A. The constraints protein-protein interactions place on sequence divergence. J. Mol. Biol. 324, 399-407 (2002).
    • (2002) J. Mol. Biol. , vol.324 , pp. 399-407
    • Teichmann, S.A.1
  • 74
    • 23344451687 scopus 로고    scopus 로고
    • Structure, function, and evolution of transient and obligate protein-protein interactions
    • Mintseris, J. & Weng, Z. Structure, function, and evolution of transient and obligate protein-protein interactions. Proc. Natl Acad. Sci. USA 102, 10930-10935 (2005).
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 10930-10935
    • Mintseris, J.1    Weng, Z.2
  • 75
    • 33644909094 scopus 로고    scopus 로고
    • The evolutionary rate of a protein is influenced by features of the interacting partners
    • Makino, T. & Gojobori, T. The evolutionary rate of a protein is influenced by features of the interacting partners. Mol. Biol. Evol. 23, 784-789 (2006).
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 784-789
    • Makino, T.1    Gojobori, T.2
  • 76
    • 16844363315 scopus 로고    scopus 로고
    • Modularity and evolutionary constraint on proteins
    • Fraser, H. B. Modularity and evolutionary constraint on proteins. Nature Genet. 37, 351-352 (2005).
    • (2005) Nature Genet. , vol.37 , pp. 351-352
    • Fraser, H.B.1
  • 77
    • 6344241652 scopus 로고    scopus 로고
    • Conservation and coevolution in the scale-free human gene coexpression network
    • Jordan, I. K., Marino-Ramirez, L., Wolf, Y. I. & Koonin, E. V. Conservation and coevolution in the scale-free human gene coexpression network. Mol. Biol. Evol. 21, 2058-2070 (2004).
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 2058-2070
    • Jordan, I.K.1    Marino-Ramirez, L.2    Wolf, Y.I.3    Koonin, E.V.4
  • 78
    • 4344624948 scopus 로고    scopus 로고
    • Molecular evolution in the yeast transcriptional regulation network
    • Evangelisti, A. M. & Wagner, A. Molecular evolution in the yeast transcriptional regulation network. J. Exp. Zool. B 302, 392-411 (2004).
    • (2004) J. Exp. Zool. B , vol.302 , pp. 392-411
    • Evangelisti, A.M.1    Wagner, A.2
  • 79
    • 33644907774 scopus 로고    scopus 로고
    • The effect of multi-functionality on the rate of evolution in yeast
    • Salathe, M., Ackermann, M. & Bonhoeffer, S. The effect of multi-functionality on the rate of evolution in yeast. Mol. Biol. Evol. 23, 721-722 (2006).
    • (2006) Mol. Biol. Evol. , vol.23 , pp. 721-722
    • Salathe, M.1    Ackermann, M.2    Bonhoeffer, S.3
  • 80
    • 0031030479 scopus 로고    scopus 로고
    • Constrained evolution with respect to gene overlap of hepatitis B virus
    • Mizokami, M. et al. Constrained evolution with respect to gene overlap of hepatitis B virus. J. Mol. Evol. 44 (Suppl. 1), 83-90 (1997).
    • (1997) J. Mol. Evol. , vol.44 , Issue.1 SUPPL. , pp. 83-90
    • Mizokami, M.1
  • 81
    • 0004204913 scopus 로고    scopus 로고
    • Univ. Chicago Press, Chicago
    • Raff, R. The Shape of Life (Univ. Chicago Press, Chicago, 1996).
    • (1996) The Shape of Life
    • Raff, R.1
  • 82
    • 21244484614 scopus 로고    scopus 로고
    • Protein evolution in the context of Drosophila development
    • Davis, J. C., Brandman, O. & Petrov, D. A. Protein evolution in the context of Drosophila development. J. Mol. Evol. 60, 774-785 (2005).
    • (2005) J. Mol. Evol. , vol.60 , pp. 774-785
    • Davis, J.C.1    Brandman, O.2    Petrov, D.A.3
  • 83
    • 17844409075 scopus 로고    scopus 로고
    • In search of the vertebrate phylotypic stage: A molecular examination of the developmental hourglass model and von Baer's third law
    • Hazkani-Covo, E., Wool, D. & Graur, D. In search of the vertebrate phylotypic stage: a molecular examination of the developmental hourglass model and von Baer's third law. J. Exp. Zool. B 304, 150-1 58 (2005). In agreement with the 'hourglass' model of animal development, genes that are expressed during the phylotypic stage are under strong stabilizing selection.
    • (2005) J. Exp. Zool. B , vol.304 , pp. 150-158
    • Hazkani-Covo, E.1    Wool, D.2    Graur, D.3
  • 84
    • 2442637669 scopus 로고    scopus 로고
    • The functional genomic distribution of protein divergence in two animal phyla: Coevolution, genomic conflict, and constraint
    • Castillo-Davis, C. I., Kondrashov, F. A., Hartl, D. L. & Kulathinal, R. J. The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint. Genome Res. 14, 802-811 (2004).
    • (2004) Genome Res. , vol.14 , pp. 802-811
    • Castillo-Davis, C.I.1    Kondrashov, F.A.2    Hartl, D.L.3    Kulathinal, R.J.4
  • 85
    • 16344383665 scopus 로고    scopus 로고
    • Rates of protein evolution are positively correlated with developmental timing of expression during mouse spermatogenesis
    • Good, J. M. & Nachman, M. W. Rates of protein evolution are positively correlated with developmental timing of expression during mouse spermatogenesis. Mol. Biol. Evol. 22, 1044-1052 (2005).
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 1044-1052
    • Good, J.M.1    Nachman, M.W.2
  • 86
    • 0033977618 scopus 로고    scopus 로고
    • Determinants of substitution rates in mammalian genes: Expression pattern affects selection intensity but not mutation rate
    • Duret, L. & Mouchiroud, D. Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol. Biol. Evol. 17, 68-74 (2000). The first demonstration of faster evolution of tissue-specific proteins.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 68-74
    • Duret, L.1    Mouchiroud, D.2
  • 87
    • 26444593981 scopus 로고    scopus 로고
    • Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences
    • Xing, Y. & Lee, C. Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc. Natl Acad. Sci. USA 102, 13526-13531 (2005). Shows that exons that are used in minor isoform proteins evolve at higher rates than constitutive exons.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 13526-13531
    • Xing, Y.1    Lee, C.2
  • 88
    • 0037133671 scopus 로고    scopus 로고
    • Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis
    • Akashi, H. & Gojobori, T. Metabolic efficiency and amino acid composition in the proteomes of Escherichia coli and Bacillus subtilis. Proc. Natl Acad. Sci. USA 99, 3695-3700 (2002).
    • (2002) Proc. Natl Acad. Sci. USA , vol.99 , pp. 3695-3700
    • Akashi, H.1    Gojobori, T.2
  • 89
    • 0041817645 scopus 로고    scopus 로고
    • Translational selection and yeast proteome evolution
    • Akashi, H. Translational selection and yeast proteome evolution. Genetics 164, 1291-1303 (2003).
    • (2003) Genetics , vol.164 , pp. 1291-1303
    • Akashi, H.1
  • 90
    • 0037186608 scopus 로고    scopus 로고
    • Testing the neutral theory of molecular evolution with genomic data from Drosophila
    • Fay, J. C., Wyckoff, G. J. & Wu, C. I. Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415, 1024-1026 (2002).
    • (2002) Nature , vol.415 , pp. 1024-1026
    • Fay, J.C.1    Wyckoff, G.J.2    Wu, C.I.3
  • 91
    • 14844325784 scopus 로고    scopus 로고
    • Robustness, evolvability, and neutrality
    • Wagner, A. Robustness, evolvability, and neutrality. FEBS Lett. 579, 1772-1778 (2005).
    • (2005) FEBS Lett. , vol.579 , pp. 1772-1778
    • Wagner, A.1
  • 92
    • 20444430245 scopus 로고    scopus 로고
    • A scan for positively selected genes in the genomes of humans and chimpanzees
    • Nielsen, R. et al. A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol. 3, e170 (2005). A comprehensive overview of the gene classes that were shaped by positive selection in human evolutionary history (see also reference 100).
    • (2005) PLoS Biol. , vol.3
    • Nielsen, R.1
  • 93
    • 20444382446 scopus 로고    scopus 로고
    • Adaptive molecular evolution for 13,000 phage generations: A possible arms race
    • Wichman, H. A., Millstein, J. & Bull, J. J. Adaptive molecular evolution for 13,000 phage generations: a possible arms race. Genetics 170, 19-31 (2005). This work indicates that intraspecies competition might lead to selection for perpetual change.
    • (2005) Genetics , vol.170 , pp. 19-31
    • Wichman, H.A.1    Millstein, J.2    Bull, J.J.3
  • 94
    • 6344272229 scopus 로고    scopus 로고
    • Molecular evolution of sex-biased genes in Drosophila
    • Zhang, Z., Hambuch, T. M. & Parsch, J. Molecular evolution of sex-biased genes in Drosophila. Mol. Biol. Evol. 21, 2130-2139 (2004).
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 2130-2139
    • Zhang, Z.1    Hambuch, T.M.2    Parsch, J.3
  • 95
    • 21044438202 scopus 로고    scopus 로고
    • The rate of compensatory mutation in the DNA bacteriophage φX174
    • Poon, A. & Chao, L. The rate of compensatory mutation in the DNA bacteriophage φX174. Genetics 170, 989-999 (2005).
    • (2005) Genetics , vol.170 , pp. 989-999
    • Poon, A.1    Chao, L.2
  • 96
    • 18544385194 scopus 로고    scopus 로고
    • Adaptive evolution in GroEL from distantly related endosymbiotic bacteria of insects
    • Fares, M. A., Moya, A. & Barrio, E. Adaptive evolution in GroEL from distantly related endosymbiotic bacteria of insects. J. Evol. Biol. 18, 651-660 (2005). This paper (along with others from the same group) indicates that a heat-shock protein might have evolved to mitigate the effect of deleterious substitutions in endosymbionts.
    • (2005) J. Evol. Biol. , vol.18 , pp. 651-660
    • Fares, M.A.1    Moya, A.2    Barrio, E.3
  • 97
    • 28444463255 scopus 로고    scopus 로고
    • Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis
    • Shim Choi, S., Li, W. & Lahn, B. T. Robust signals of coevolution of interacting residues in mammalian proteomes identified by phylogeny-aided structural analysis. Nature Genet. 37, 1367-1371 (2005).
    • (2005) Nature Genet. , vol.37 , pp. 1367-1371
    • Shim Choi, S.1    Li, W.2    Lahn, B.T.3
  • 98
    • 29244467422 scopus 로고    scopus 로고
    • The eloquent ape: Genes, brains and the evolution of language
    • Fisher, S. E. & Marcus, G. F. The eloquent ape: genes, brains and the evolution of language. Nature Rev. Genet. 7, 9-20 (2006).
    • (2006) Nature Rev. Genet. , vol.7 , pp. 9-20
    • Fisher, S.E.1    Marcus, G.F.2
  • 99
    • 24644454655 scopus 로고    scopus 로고
    • Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens
    • Mekel-Bobrov, N. et al. Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens. Science 309, 1720-1722 (2005).
    • (2005) Science , vol.309 , pp. 1720-1722
    • Mekel-Bobrov, N.1
  • 100
    • 27144539145 scopus 로고    scopus 로고
    • Natural selection on protein-coding genes in the human genome
    • Bustamante, C. D. et al. Natural selection on protein-coding genes in the human genome. Nature 437, 1153-1157 (2005). A comprehensive overview of the gene classes that were shaped by positive selection in human evolutionary history (see also reference 92).
    • (2005) Nature , vol.437 , pp. 1153-1157
    • Bustamante, C.D.1
  • 101
    • 33746885883 scopus 로고    scopus 로고
    • Systemic determinants of gene evolution and function
    • 13 Sep doi: 10.1038/msb4100029
    • Koonin, E. V. Systemic determinants of gene evolution and function. Mol. Syst. Biol. 13 Sep 2005 (doi: 10.1038/msb4100029).
    • (2005) Mol. Syst. Biol.
    • Koonin, E.V.1
  • 102
    • 15844364199 scopus 로고    scopus 로고
    • Understanding protein dispensability through machine-learning analysis of high-throughput data
    • Chen, Y. & Xu, D. Understanding protein dispensability through machine-learning analysis of high-throughput data. Bioinformatics 21, 575-581 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 575-581
    • Chen, Y.1    Xu, D.2
  • 104
    • 33646178676 scopus 로고    scopus 로고
    • Unifying measures of gene function and evolution
    • in the press
    • Wolf, Y. I., Carmel, L. & Koonin, E. V. Unifying measures of gene function and evolution. Proc. R. Soc. B (in the press).
    • Proc. R. Soc. B
    • Wolf, Y.I.1    Carmel, L.2    Koonin, E.V.3
  • 105
    • 0038441327 scopus 로고    scopus 로고
    • Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation
    • Elena, S. F. & Lenski, R. E. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nature Rev. Genet. 4, 457-469 (2003).
    • (2003) Nature Rev. Genet. , vol.4 , pp. 457-469
    • Elena, S.F.1    Lenski, R.E.2
  • 106
    • 24644462173 scopus 로고    scopus 로고
    • Accurate multiplex polony sequencing of an evolved bacterial genome
    • Shendure, J. et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309, 1728-1732 (2005).
    • (2005) Science , vol.309 , pp. 1728-1732
    • Shendure, J.1
  • 108
    • 0038157152 scopus 로고    scopus 로고
    • Dosage sensitivity and the evolution of gene families in yeast
    • Papp, B., Pal, C. & Hurst, L. D. Dosage sensitivity and the evolution of gene families in yeast. Nature 424, 194-197. (2003).
    • (2003) Nature , vol.424 , pp. 194-197
    • Papp, B.1    Pal, C.2    Hurst, L.D.3
  • 109
    • 0033616714 scopus 로고    scopus 로고
    • Horizontal gene transfer among genomes: The complexity hypothesis
    • Jain, R., Rivera, M. C. & Lake, J. A. Horizontal gene transfer among genomes: the complexity hypothesis. Proc. Natl Acad. Sci. USA 96, 3801-3806 (1999).
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 3801-3806
    • Jain, R.1    Rivera, M.C.2    Lake, J.A.3
  • 111
    • 0035339920 scopus 로고    scopus 로고
    • Molecular phylogenetics: State-of-the-art methods for looking into the past
    • Whelan, S., Lio, P. & Goldman, N. Molecular phylogenetics: state-of-the-art methods for looking into the past. Trends Genet. 17, 262-272 (2001).
    • (2001) Trends Genet. , vol.17 , pp. 262-272
    • Whelan, S.1    Lio, P.2    Goldman, N.3
  • 112
    • 18744382506 scopus 로고    scopus 로고
    • ProtTest: Selection of best-fit models of protein evolution
    • Abascal, F., Zardoya, R. & Posada, D. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21, 2104-2105 (2005).
    • (2005) Bioinformatics , vol.21 , pp. 2104-2105
    • Abascal, F.1    Zardoya, R.2    Posada, D.3
  • 113
    • 0031773680 scopus 로고    scopus 로고
    • MODELTEST: Testing the model of DNA substitution
    • Posada, D. & Crandall, K. A. MODELTEST: testing the model of DNA substitution. Bioinformatics 14, 817-818 (1998).
    • (1998) Bioinformatics , vol.14 , pp. 817-818
    • Posada, D.1    Crandall, K.A.2
  • 114
    • 0028168856 scopus 로고
    • A codon-based model of nucleotide substitution for protein-coding DNA sequences
    • Goldman, N. & Yang, Z. A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11, 725-736 (1994).
    • (1994) Mol. Biol. Evol. , vol.11 , pp. 725-736
    • Goldman, N.1    Yang, Z.2
  • 115
    • 0035504763 scopus 로고    scopus 로고
    • Understanding human disease mutations through the use of interspecific genetic variation
    • Miller, M. P. & Kumar, S. Understanding human disease mutations through the use of interspecific genetic variation. Hum. Mol. Genet. 10, 2319-2328 (2001).
    • (2001) Hum. Mol. Genet. , vol.10 , pp. 2319-2328
    • Miller, M.P.1    Kumar, S.2
  • 116
    • 0043122919 scopus 로고    scopus 로고
    • SIFT: Predicting amino acid changes that affect protein function
    • Ng, P. C. & Henikoff, S. SIFT: predicting amino acid changes that affect protein function. Nucleic Acids Res. 31, 3812-3814 (2003).
    • (2003) Nucleic Acids Res. , vol.31 , pp. 3812-3814
    • Ng, P.C.1    Henikoff, S.2
  • 117
    • 0036713510 scopus 로고    scopus 로고
    • Human non-synonymous SNPs: Server and survey
    • Ramensky, V., Bork, P. & Sunyaev, S. Human non-synonymous SNPs: server and survey. Nucleic Acids Res. 30, 3894-3900 (2002).
    • (2002) Nucleic Acids Res. , vol.30 , pp. 3894-3900
    • Ramensky, V.1    Bork, P.2    Sunyaev, S.3
  • 118
    • 3442879338 scopus 로고    scopus 로고
    • Assessing the function of genetic variants in candidate gene association studies
    • Rebbeck, T. R., Spitz, M. & Wu, X. F. Assessing the function of genetic variants in candidate gene association studies. Nature Rev. Genet. 5, 589-597 (2004).
    • (2004) Nature Rev. Genet. , vol.5 , pp. 589-597
    • Rebbeck, T.R.1    Spitz, M.2    Wu, X.F.3
  • 119
    • 0041836283 scopus 로고    scopus 로고
    • Estimating the distribution of fitness effects from DNA sequence data: Implications for the molecular clock
    • Piganeau, G. & Eyre-Walker, A. Estimating the distribution of fitness effects from DNA sequence data: implications for the molecular clock. Proc. Natl Acad. Sci. USA 100, 10335-10340 (2003).
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 10335-10340
    • Piganeau, G.1    Eyre-Walker, A.2
  • 120
    • 33644764039 scopus 로고    scopus 로고
    • Estimating selection on non-synonymous mutations
    • Loewe, L., Charlesworth, B., Bartolome, C. & Noel, V. Estimating selection on non-synonymous mutations. Genetics 172, 1079-1092 (2006).
    • (2006) Genetics , vol.172 , pp. 1079-1092
    • Loewe, L.1    Charlesworth, B.2    Bartolome, C.3    Noel, V.4
  • 121
    • 16844369125 scopus 로고    scopus 로고
    • An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus
    • Rokyta, D. R., Joyce, P., Caudle, S. B. & Wichman, H. A. An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus. Nature Genet. 37, 441-444 (2005). References 119-121 attempt to estimate the fitness distribution of mutations; these values are highly relevant to understanding the relative influence of deleterious and advantageous mutations on protein evolution.
    • (2005) Nature Genet. , vol.37 , pp. 441-444
    • Rokyta, D.R.1    Joyce, P.2    Caudle, S.B.3    Wichman, H.A.4
  • 122
    • 11244281311 scopus 로고    scopus 로고
    • The 'evolvability' of promiscuous protein functions
    • Aharoni, A. et al. The 'evolvability' of promiscuous protein functions. Nature Genet. 37, 73-76 (2005).
    • (2005) Nature Genet. , vol.37 , pp. 73-76
    • Aharoni, A.1
  • 123
    • 19344363466 scopus 로고    scopus 로고
    • Preferential duplication of conserved proteins in eukaryotic genomes
    • Davis, J. C. & Petrov, D. A. Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol. 2, 318-326 (2004).
    • (2004) PLoS Biol. , vol.2 , pp. 318-326
    • Davis, J.C.1    Petrov, D.A.2
  • 124
    • 8744268628 scopus 로고    scopus 로고
    • Duplicated genes evolve slower than singletons despite the initial rate increase
    • Jordan, I. K., Wolf, Y. I. & Koonin, E. V. Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol. Biol. 4, 22 (2004).
    • (2004) BMC Evol. Biol. , vol.4 , pp. 22
    • Jordan, I.K.1    Wolf, Y.I.2    Koonin, E.V.3
  • 125
    • 26444473715 scopus 로고    scopus 로고
    • Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons
    • Cusack, B. P. & Wolfe, K. H. Changes in alternative splicing of human and mouse genes are accompanied by faster evolution of constitutive exons. Mol. Biol. Evol. 22, 2198-2208 (2005).
    • (2005) Mol. Biol. Evol. , vol.22 , pp. 2198-2208
    • Cusack, B.P.1    Wolfe, K.H.2
  • 126
    • 0345107239 scopus 로고    scopus 로고
    • Selection in the evolution of gene duplications
    • RESEARCH0008
    • Kondrashov, F. A., Rogozin, I. B., Wolf, Y. I. & Koonin, E. V. Selection in the evolution of gene duplications. Genome Biol. 3, RESEARCH0008 (2002). Shows that selection pressure is relaxed for a short period after gene duplication.
    • (2002) Genome Biol. , vol.3
    • Kondrashov, F.A.1    Rogozin, I.B.2    Wolf, Y.I.3    Koonin, E.V.4
  • 127
    • 22944437097 scopus 로고    scopus 로고
    • Molecular clocks: Four decades of evolution
    • Kumar, S. Molecular clocks: four decades of evolution. Nature Rev. Genet. 6, 654-662 (2005). A comprehensive overview of the reasons for evolutionary rate variation across species.
    • (2005) Nature Rev. Genet. , vol.6 , pp. 654-662
    • Kumar, S.1
  • 128
    • 11844288987 scopus 로고    scopus 로고
    • The rate of DNA evolution: Effects of body size and temperature on the molecular clock
    • Gillooly, J. F., Allen, A. P., West, G. B. & Brown, J. H. The rate of DNA evolution: effects of body size and temperature on the molecular clock. Proc. Natl Acad. Sci. USA 102, 140-145 (2005).
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 140-145
    • Gillooly, J.F.1    Allen, A.P.2    West, G.B.3    Brown, J.H.4
  • 129
    • 0036847064 scopus 로고    scopus 로고
    • Genome evolution in bacterial endosymbionts of insects
    • Wernegreen, J. J. Genome evolution in bacterial endosymbionts of insects. Nature Rev. Genet. 3, 850-861 (2002).
    • (2002) Nature Rev. Genet. , vol.3 , pp. 850-861
    • Wernegreen, J.J.1
  • 130
    • 0033117745 scopus 로고    scopus 로고
    • The role of population size in molecular evolution
    • Gillespie, J. H. The role of population size in molecular evolution. Theor. Popul. Biol. 55, 145-156 (1999).
    • (1999) Theor. Popul. Biol. , vol.55 , pp. 145-156
    • Gillespie, J.H.1
  • 131
    • 0036900082 scopus 로고    scopus 로고
    • Quantifying the slightly deleterious mutation model of molecular evolution
    • Eyre-Walker, A., Keightley, P. D., Smith, N. G. & Gaffney, D. Quantifying the slightly deleterious mutation model of molecular evolution. Mol. Biol. Evol. 19, 2142-2149 (2002).
    • (2002) Mol. Biol. Evol. , vol.19 , pp. 2142-2149
    • Eyre-Walker, A.1    Keightley, P.D.2    Smith, N.G.3    Gaffney, D.4
  • 132
    • 33144483078 scopus 로고    scopus 로고
    • Transitions to asexuality result in excess amino acid substitutions
    • Paland, S. & Lynch, M. Transitions to asexuality result in excess amino acid substitutions. Science 311, 990-992 (2006).
    • (2006) Science , vol.311 , pp. 990-992
    • Paland, S.1    Lynch, M.2
  • 133
    • 0037041421 scopus 로고    scopus 로고
    • The cost of inbreeding in Arabidopsis
    • Bustamante, C. D. et al. The cost of inbreeding in Arabidopsis. Nature 416, 531-534 (2002). References 132 and 133 show the effect of sex and breeding system on the accumulation of deleterious substitutions.
    • (2002) Nature , vol.416 , pp. 531-534
    • Bustamante, C.D.1
  • 134
    • 0037373550 scopus 로고    scopus 로고
    • Connectivity of neutral networks, overdispersion, and structural conservation in protein evolution
    • Bastolla, U., Porto, M., Eduardo Roman, M. H. & Vendruscolo, M. H. Connectivity of neutral networks, overdispersion, and structural conservation in protein evolution. J. Mol. Evol. 56, 243-254 (2003).
    • (2003) J. Mol. Evol. , vol.56 , pp. 243-254
    • Bastolla, U.1    Porto, M.2    Eduardo Roman, M.H.3    Vendruscolo, M.H.4
  • 135
    • 2542445427 scopus 로고    scopus 로고
    • ConSurf: Identification of functional regions in proteins by surface-mapping of phylogenetic information
    • Glaser, F. et al. ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information. Bioinformatics 19, 163-164 (2003).
    • (2003) Bioinformatics , vol.19 , pp. 163-164
    • Glaser, F.1
  • 136
    • 18844407538 scopus 로고    scopus 로고
    • Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast
    • Deutschbauer, A. M. et al. Mechanisms of haploinsufficiency revealed by genome-wide profiling in yeast. Genetics 169, 1915-1925 (2005).
    • (2005) Genetics , vol.169 , pp. 1915-1925
    • Deutschbauer, A.M.1
  • 137
    • 0032567081 scopus 로고    scopus 로고
    • Dissecting the regulatory circuitry of a eukaryotic genome
    • Holstege, F. C. et al. Dissecting the regulatory circuitry of a eukaryotic genome. Cell 95, 717-728 (1998).
    • (1998) Cell , vol.95 , pp. 717-728
    • Holstege, F.C.1
  • 138
    • 0033608998 scopus 로고    scopus 로고
    • Hypermutation in derepressed operons of Escherichia coli K12
    • Wright, B. F., Longacre, A. & Reimers, J. M. Hypermutation in derepressed operons of Escherichia coli K12. Proc. Natl Acad. Sci. USA 96, 5089-5094 (1999).
    • (1999) Proc. Natl Acad. Sci. USA , vol.96 , pp. 5089-5094
    • Wright, B.F.1    Longacre, A.2    Reimers, J.M.3
  • 139
    • 0037371689 scopus 로고    scopus 로고
    • Evidence for co-evolution of gene order and recombination rate
    • Pal, C. & Hurst, L. D. Evidence for co-evolution of gene order and recombination rate. Nature Genet. 33, 392-395 (2003).
    • (2003) Nature Genet. , vol.33 , pp. 392-395
    • Pal, C.1    Hurst, L.D.2
  • 140
    • 0037161731 scopus 로고    scopus 로고
    • Comparative assessment of large-scale data sets of protein-protein interactions
    • von Mering, C. et al. Comparative assessment of large-scale data sets of protein-protein interactions. Nature 417, 399-403 (2002).
    • (2002) Nature , vol.417 , pp. 399-403
    • Von Mering, C.1
  • 141
    • 0035799707 scopus 로고    scopus 로고
    • Lethality and centrality in protein networks
    • Jeong, H., Mason, S. P., Barabasi, A. L. & Oltvai, Z. N. Lethality and centrality in protein networks. Nature 411, 41-42 (2001).
    • (2001) Nature , vol.411 , pp. 41-42
    • Jeong, H.1    Mason, S.P.2    Barabasi, A.L.3    Oltvai, Z.N.4
  • 142
    • 26244440771 scopus 로고    scopus 로고
    • Gene essentiality and the topology of protein interaction networks
    • Coulomb, S., Bauer, M., Bernard, D. & Marsolier-Kergoat, M. C. Gene essentiality and the topology of protein interaction networks. Proc. Biol. Sci. 272, 1721-1725 (2005).
    • (2005) Proc. Biol. Sci. , vol.272 , pp. 1721-1725
    • Coulomb, S.1    Bauer, M.2    Bernard, D.3    Marsolier-Kergoat, M.C.4


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