메뉴 건너뛰기




Volumn , Issue , 2010, Pages 81-98

Pseudaptations and the emergence of beneficial traits

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84887652058     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-3-642-12340-5_5     Document Type: Chapter
Times cited : (5)

References (70)
  • 1
    • 0036013593 scopus 로고    scopus 로고
    • Statistical mechanics of complex networks
    • Albert R, Barabasi AL (2002) Statistical mechanics of complex networks. Rev Modern Phy 74:47-94
    • (2002) Rev Modern Phy , vol.74 , pp. 47-94
    • Albert, R.1    Barabasi, A.L.2
  • 2
    • 0034721164 scopus 로고    scopus 로고
    • Error and attack tolerance of complex networks
    • Albert R, Jeong H, Barabási AL (2000) Error and attack tolerance of complex networks. Nature 406:378-382
    • (2000) Nature , vol.406 , pp. 378-382
    • Albert, R.1    Jeong, H.2    Barabási, A.L.3
  • 3
    • 0014581827 scopus 로고
    • 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
  • 4
    • 36749042777 scopus 로고    scopus 로고
    • Latent evolutionary potentials under the neutral mutational drift of an enzyme
    • Amitai G, Devi Gupta R, Tawfik DS (2007) Latent evolutionary potentials under the neutral mutational drift of an enzyme. HFSP J 1:67-78
    • (2007) HFSP J , vol.1 , pp. 67-78
    • Amitai, G.1    Devi Gupta, R.2    Tawfik, D.S.3
  • 5
    • 0031777847 scopus 로고    scopus 로고
    • On error minimization in a sequential origin of the standard genetic code
    • Ardell DH (1998) On error minimization in a sequential origin of the standard genetic code. J Mol Evol 47:1-13
    • (1998) J Mol Evol , vol.47 , pp. 1-13
    • Ardell, D.H.1
  • 6
    • 0030625954 scopus 로고    scopus 로고
    • Neutral networks in protein space: A computational study based on knowledge-based potentials of mean force
    • Babjide A, Hofacker IL, Sippl MJ, Stadler PF (1997) Neutral networks in protein space: a computational study based on knowledge-based potentials of mean force. Fold Des 2:261-269
    • (1997) Fold Des , vol.2 , pp. 261-269
    • Babjide, A.1    Hofacker, I.L.2    Sippl, M.J.3    Stadler, P.F.4
  • 7
    • 33745242506 scopus 로고    scopus 로고
    • Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks
    • Balaji S, Iyer LM, Aravind L, Babu MM (2006) Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks. J Mol Biol 360:204-212
    • (2006) J Mol Biol , vol.360 , pp. 204-212
    • Balaji, S.1    Iyer, L.M.2    Aravind, L.3    Babu, M.M.4
  • 8
    • 0038483826 scopus 로고    scopus 로고
    • Emergence of scaling in random networks
    • Barabasi AL, Albert R (1999) Emergence of scaling in random networks. Science 286:509-512
    • (1999) Science , vol.286 , pp. 509-512
    • Barabasi, A.L.1    Albert, R.2
  • 9
    • 12444301754 scopus 로고    scopus 로고
    • Structure and evolution of protein in interaction networks: A statistical model for link dynamics
    • Berg J, Lassig M, Wagner A (2004) Structure and evolution of protein in interaction networks: a statistical model for link dynamics. BMC Evol Biol 4:51
    • (2004) BMC Evol Biol , vol.4 , pp. 51
    • Berg, J.1    Lassig, M.2    Wagner, A.3
  • 11
    • 13044269058 scopus 로고    scopus 로고
    • Modeling evolutionary landscapes: Mutational stability, topology and superfunnels in sequence space
    • Bornberg-Bauer E, Chan HS (1999) Modeling evolutionary landscapes: mutational stability, topology and superfunnels in sequence space. Proc Natl Acad Sci USA 96:10689-10694
    • (1999) Proc Natl Acad Sci USA , vol.96 , pp. 10689-10694
    • Bornberg-Bauer, E.1    Chan, H.S.2
  • 12
    • 33646240072 scopus 로고    scopus 로고
    • Direct evolution of genetic robustness in microRNA
    • Borenstein E, Ruppin E (2006) Direct evolution of genetic robustness in microRNA. Proc Natl Acad Sci USA 103:6593-6598
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 6593-6598
    • Borenstein, E.1    Ruppin, E.2
  • 13
    • 0014378880 scopus 로고
    • The origin of the genetic code
    • Crick FHC (1968) The origin of the genetic code. J Mol Biol 38:367-379
    • (1968) J Mol Biol , vol.38 , pp. 367-379
    • Crick, F.H.C.1
  • 14
    • 0024745336 scopus 로고
    • The extension reached by the minimization of polarity distances during the evolution of the genetic code
    • Di Giulio M (1989) The extension reached by the minimization of polarity distances during the evolution of the genetic code. J Mol Evol 29:288-293
    • (1989) J Mol Evol , vol.29 , pp. 288-293
    • Di Giulio, M.1
  • 15
    • 0033580813 scopus 로고    scopus 로고
    • Systems properties of the Haemophilus influenzae Rd metabolic genotype
    • Edwards JS, Palsson BO (1999) Systems properties of the Haemophilus influenzae Rd metabolic genotype. J Biol Chem 274:17410-17416
    • (1999) J Biol Chem , vol.274 , pp. 17410-17416
    • Edwards, J.S.1    Palsson, B.O.2
  • 16
    • 0034519221 scopus 로고    scopus 로고
    • Robustness analysis of the Escherichia coli metabolic network
    • Edwards JS, Palsson BO (2000) Robustness analysis of the Escherichia coli metabolic network. Biotech Prog 16:927-939
    • (2000) Biotech Prog , vol.16 , pp. 927-939
    • Edwards, J.S.1    Palsson, B.O.2
  • 19
    • 0035233646 scopus 로고    scopus 로고
    • Optimality of the genetic code with respect to protein stability and amino-acid frequencies
    • Gilis D, Massar S, Cerf NJ, Rooman M (2001) Optimality of the genetic code with respect to protein stability and amino-acid frequencies. Genome Biol 2:11
    • (2001) Genome Biol , vol.2 , pp. 11
    • Gilis, D.1    Massar, S.2    Cerf, N.J.3    Rooman, M.4
  • 21
    • 65549084298 scopus 로고    scopus 로고
    • Potential role of phenotypic mutations in the evolution of protein expression and stability
    • Goldsmith M, Tawfik DS (2009) Potential role of phenotypic mutations in the evolution of protein expression and stability. Proc Natl Acad Sci USA 106:6197-6202
    • (2009) Proc Natl Acad Sci USA , vol.106 , pp. 6197-6202
    • Goldsmith, M.1    Tawfik, D.S.2
  • 22
    • 7544235210 scopus 로고    scopus 로고
    • On the optimality of the genetic code, with consideration of termination codons
    • Goodarzi H, Nejad HA, Torabi N (2004) On the optimality of the genetic code, with consideration of termination codons. BioSystems 77:163-173
    • (2004) BioSystems , vol.77 , pp. 163-173
    • Goodarzi, H.1    Nejad, H.A.2    Torabi, N.3
  • 23
    • 0030963745 scopus 로고    scopus 로고
    • The exaptive excellence of spandrels as a term and prototype
    • Gould SG (1997) The exaptive excellence of spandrels as a term and prototype. Proc Natl Acad Sci USA 94:10750-10755
    • (1997) Proc Natl Acad Sci USA , vol.94 , pp. 10750-10755
    • Gould, S.G.1
  • 24
    • 0018692402 scopus 로고
    • The spandrels of San Marco and the panglossian paradigm: A critique of the adaptionist program
    • Gould SG, Lewontin RC (1979) The spandrels of San Marco and the panglossian paradigm: a critique of the adaptionist program. Proc R Soc Lond B 205:581-598
    • (1979) Proc R Soc Lond B , vol.205 , pp. 581-598
    • Gould, S.G.1    Lewontin, R.C.2
  • 25
    • 0030691734 scopus 로고    scopus 로고
    • Evolution of model proteins on a foldability landscape
    • Govindarajan S, Goldstein RA (1997) Evolution of model proteins on a foldability landscape. Proteins 29:461-464
    • (1997) Proteins , vol.29 , pp. 461-464
    • Govindarajan, S.1    Goldstein, R.A.2
  • 26
    • 0016197604 scopus 로고
    • 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
  • 27
    • 41049083886 scopus 로고    scopus 로고
    • Comparative analysis of the transcription-factor gene regulatory networks of E.coli and S.cerevisiae
    • Guzman-Vargas L, Santillan M (2008) Comparative analysis of the transcription-factor gene regulatory networks of E.coli and S.cerevisiae. BMC Syst Biol 2:13
    • (2008) BMC Syst Biol , vol.2 , pp. 13
    • Guzman-Vargas, L.1    Santillan, M.2
  • 28
    • 0842290925 scopus 로고    scopus 로고
    • Molecular evolution in large genetic networks: Does connectivity equal constraint
    • Hahn MW, Conant GC, Wagner A (2004) Molecular evolution in large genetic networks: does connectivity equal constraint. J Mol Evol 58:203-211
    • (2004) J Mol Evol , vol.58 , pp. 203-211
    • Hahn, M.W.1    Conant, G.C.2    Wagner, A.3
  • 29
    • 0026327996 scopus 로고
    • A quantitative measure of error minimization in the genetic code
    • Haig D, Hurst LD (1992) A quantitative measure of error minimization in the genetic code. J Mol Evol 33:412-417
    • (1992) J Mol Evol , vol.33 , pp. 412-417
    • Haig, D.1    Hurst, L.D.2
  • 31
    • 0027377681 scopus 로고
    • Multiple coding and the evolutionary properties of RNA secondary structure
    • Huynen MA, Konings DAM, Hogeweg P (1993) Multiple coding and the evolutionary properties of RNA secondary structure. J Theor Biol 185:251-267
    • (1993) J Theor Biol , vol.185 , pp. 251-267
    • Huynen, M.A.1    Konings, D.A.M.2    Hogeweg, P.3
  • 33
    • 38349032624 scopus 로고    scopus 로고
    • Evolution of gene regulatory networks: Robustness as an emergent property of evolution
    • Krishnan A, Tomita M, Giuliani A (2007) Evolution of gene regulatory networks: robustness as an emergent property of evolution. Phys Stat Mech Appl 387:2170-2186
    • (2007) Phys Stat Mech Appl , vol.387 , pp. 2170-2186
    • Krishnan, A.1    Tomita, M.2    Giuliani, A.3
  • 35
    • 32144441867 scopus 로고    scopus 로고
    • Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: Large-scale organization and robustness
    • Li D, Li J, Ouyang S, Wang J, Wu S, Wan P, Zhu Y, Xu X, He F (2006) Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: Large-scale organization and robustness. Proteomics 6:456-461
    • (2006) Proteomics , vol.6 , pp. 456-461
    • Li, D.1    Li, J.2    Ouyang, S.3    Wang, J.4    Wu, S.5    Wan, P.6    Zhu, Y.7    Xu, X.8    He, F.9
  • 36
    • 27944470116 scopus 로고    scopus 로고
    • Preferential attachment in the evolution of metabolic networks
    • Light S, Kraulis P, Elofsson A (2005) Preferential attachment in the evolution of metabolic networks. BMC Genom 6:159
    • (2005) BMC Genom , vol.6 , pp. 159
    • Light, S.1    Kraulis, P.2    Elofsson, A.3
  • 37
    • 84900294191 scopus 로고    scopus 로고
    • Large-scale topological properties of molecular networks
    • Koonin E, Wolf Y, Karev G eds, Springer, New York
    • Maslov S, Sneppen K (2006) Large-scale topological properties of molecular networks. In: Koonin E, Wolf Y, Karev G (eds) Power laws, scale-free networks and genome biology. Springer, New York
    • (2006) Power Laws, Scale-free Networks and Genome Biology
    • Maslov, S.1    Sneppen, K.2
  • 38
    • 33744914840 scopus 로고    scopus 로고
    • A sequential "2-1-3" model of genetic code evolution that explains codon constraints
    • Massey SE (2006) A sequential "2-1-3" model of genetic code evolution that explains codon constraints. J Mol Evol 62:809-810
    • (2006) J Mol Evol , vol.62 , pp. 809-810
    • Massey, S.E.1
  • 39
    • 34247880393 scopus 로고    scopus 로고
    • A comparative genomics analysis of codon reassignments reveals a link with mitochondrial proteome size and a mechanism of genetic code change via suppressor tRNAs
    • Massey SE, Garey JR (2007) A comparative genomics analysis of codon reassignments reveals a link with mitochondrial proteome size and a mechanism of genetic code change via suppressor tRNAs. J Mol Evol 64:399-410
    • (2007) J Mol Evol , vol.64 , pp. 399-410
    • Massey, S.E.1    Garey, J.R.2
  • 40
    • 55949110334 scopus 로고    scopus 로고
    • A neutral origin of error minimization in the genetic code
    • Massey SE (2008a) A neutral origin of error minimization in the genetic code. J Mol Evol 67:510-516
    • (2008) J Mol Evol , vol.67 , pp. 510-516
    • Massey, S.E.1
  • 41
    • 56449115405 scopus 로고    scopus 로고
    • The proteomic constraint and its role in molecular evolution
    • Massey SE (2008b) The proteomic constraint and its role in molecular evolution. Mol Biol Evol 25:2557-2565
    • (2008) Mol Biol Evol , vol.25 , pp. 2557-2565
    • Massey, S.E.1
  • 42
    • 76749163630 scopus 로고    scopus 로고
    • Searching of code space for an error minimized genetic code via Codon Capture leads to failure, or requires at least 20 improving codon reassignments via the Ambiguous Intermediate mechanism
    • Massey SE (2010) Searching of code space for an error minimized genetic code via Codon Capture leads to failure, or requires at least 20 improving codon reassignments via the Ambiguous Intermediate mechanism. J Mol Evol 70:106-115
    • (2010) J Mol Evol , vol.70 , pp. 106-115
    • Massey, S.E.1
  • 43
    • 0014935646 scopus 로고
    • Natural selection and the concept of a protein space
    • Maynard Smith J (1970) Natural selection and the concept of a protein space. Nature 225:563-564
    • (1970) Nature , vol.225 , pp. 563-564
    • Maynard Smith, J.1
  • 45
    • 0002254841 scopus 로고    scopus 로고
    • Why won't the group selection controversy go away?
    • Okasha S (2001) Why won't the group selection controversy go away? Brit J Phil Sci 52:25-50
    • (2001) Brit J Phil Sci , vol.52 , pp. 25-50
    • Okasha, S.1
  • 46
    • 0024583607 scopus 로고
    • Codon reassignment (codon capture) in evolution
    • Osawa S, Jukes TH (1989) Codon reassignment (codon capture) in evolution. J Mol Evol 28:271-278
    • (1989) J Mol Evol , vol.28 , pp. 271-278
    • Osawa, S.1    Jukes, T.H.2
  • 47
    • 0036209507 scopus 로고    scopus 로고
    • Resolving the paradox of sex and recombination
    • Otto SP, Lenormand T (2002) Resolving the paradox of sex and recombination. Nat Rev Gen 3:252-261
    • (2002) Nat Rev Gen , vol.3 , pp. 252-261
    • Otto, S.P.1    Lenormand, T.2
  • 49
    • 29144470990 scopus 로고    scopus 로고
    • Topology, tinkering and evolution of the human transcription factor network
    • Rodriguez-Caso C, Medina MA, Sole RV (2005) Topology, tinkering and evolution of the human transcription factor network. FEBS J 272:6423-6434
    • (2005) FEBS J , vol.272 , pp. 6423-6434
    • Rodriguez-Caso, C.1    Medina, M.A.2    Sole, R.V.3
  • 50
    • 33745614283 scopus 로고    scopus 로고
    • In silico predicted robustness of viroids RNA secondary structures. I. The effect of single mutations
    • Sanjuan R, Forment J, Elena SF (2006) In silico predicted robustness of viroids RNA secondary structures. I. The effect of single mutations. Mol Biol Evol 23:1427-1436
    • (2006) Mol Biol Evol , vol.23 , pp. 1427-1436
    • Sanjuan, R.1    Forment, J.2    Elena, S.F.3
  • 51
    • 0028332057 scopus 로고
    • Transfer RNA mutation and the malleability of the genetic code
    • Schultz DW, Yarus M (1994) Transfer RNA mutation and the malleability of the genetic code. J Mol Biol 235:1377-1380
    • (1994) J Mol Biol , vol.235 , pp. 1377-1380
    • Schultz, D.W.1    Yarus, M.2
  • 52
    • 0023811909 scopus 로고
    • Stationary mutant distributions and evolutionary optimization
    • Schuster P, Swetina J (1988) Stationary mutant distributions and evolutionary optimization. Bull Math Biol 50:635-660
    • (1988) Bull Math Biol , vol.50 , pp. 635-660
    • Schuster, P.1    Swetina, J.2
  • 53
    • 0028196714 scopus 로고
    • From sequences to shapes and back: A case study in RNA secondary structures
    • Schuster P, Fontana W, Stadler PF, Hofacker IL (1994) From sequences to shapes and back: a case study in RNA secondary structures. Proc Roy Soc Lond B 255:279-284
    • (1994) Proc Roy Soc Lond B , vol.255 , pp. 279-284
    • Schuster, P.1    Fontana, W.2    Stadler, P.F.3    Hofacker, I.L.4
  • 54
    • 55949087147 scopus 로고    scopus 로고
    • In silico genetic robustness analysis of secondary structural elements in the miRNA gene
    • Shu W, Ni M, Bo X, Zheng Z, Wang S (2008) In silico genetic robustness analysis of secondary structural elements in the miRNA gene. J Mol Evol 67:560-569
    • (2008) J Mol Evol , vol.67 , pp. 560-569
    • Shu, W.1    Ni, M.2    Bo, X.3    Zheng, Z.4    Wang, S.5
  • 55
    • 25144498379 scopus 로고    scopus 로고
    • A human protein-protein interaction network: A resource for annotating the proteome
    • Stelzl U et al (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell 122:957-968
    • (2005) Cell , vol.122 , pp. 957-968
    • Stelzl, U.1
  • 56
    • 47549100994 scopus 로고    scopus 로고
    • The effect of recombination on the neutral evolution of genetic robustness
    • Szollosi GJ, Derenyi I (2008) The effect of recombination on the neutral evolution of genetic robustness. Math Biosci 214:58-62
    • (2008) Math Biosci , vol.214 , pp. 58-62
    • Szollosi, G.J.1    Derenyi, I.2
  • 58
    • 0036306115 scopus 로고    scopus 로고
    • Why are proteins so robust to site mutations?
    • Taverna DM, Goldstein RA (2002) Why are proteins so robust to site mutations? J Mol Biol 315:479-484
    • (2002) J Mol Biol , vol.315 , pp. 479-484
    • Taverna, D.M.1    Goldstein, R.A.2
  • 60
    • 0034943378 scopus 로고    scopus 로고
    • The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes
    • Wagner A (2001) The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol Biol Evol 18:1283-1292
    • (2001) Mol Biol Evol , vol.18 , pp. 1283-1292
    • Wagner, A.1
  • 61
    • 0037423828 scopus 로고    scopus 로고
    • How the global structure of protein interaction networks evolves
    • Wagner A (2003) How the global structure of protein interaction networks evolves. Proc R Soc Lond B 270:457-466
    • (2003) Proc R Soc Lond B , vol.270 , pp. 457-466
    • Wagner, A.1
  • 63
    • 84900165584 scopus 로고    scopus 로고
    • The connectivity of large genetic networks. Design, history or mere chemistry?
    • Koonin E, Wolf Y, Karev G eds, Springer, New York
    • Wagner A (2006) The connectivity of large genetic networks. Design, history or mere chemistry? In: Koonin E, Wolf Y, Karev G (eds) Power laws, scale-free networks and genome biology. Springer, New York
    • (2006) Power Laws, Scale-free Networks and Genome Biology
    • Wagner, A.1
  • 64
    • 36348992094 scopus 로고    scopus 로고
    • Robustness and evolvability: A paradox resolved
    • Wagner A (2008) Robustness and evolvability: a paradox resolved. Proc R Soc B 275:91-100
    • (2008) Proc R Soc B , vol.275 , pp. 91-100
    • Wagner, A.1
  • 65
    • 0033567123 scopus 로고    scopus 로고
    • Viral RNA and evolved mutational robustness
    • Wagner A, Stadler PF (1999) Viral RNA and evolved mutational robustness. J Exp Zool 285:119-127
    • (1999) J Exp Zool , vol.285 , pp. 119-127
    • Wagner, A.1    Stadler, P.F.2
  • 66
    • 23644454631 scopus 로고    scopus 로고
    • Network motifs are enriched with transcription factors whose transcripts have short half-lifes
    • Wang E, Purisima E (2005) Network motifs are enriched with transcription factors whose transcripts have short half-lifes. Trends Gen 21:492-495
    • (2005) Trends Gen , vol.21 , pp. 492-495
    • Wang, E.1    Purisima, E.2
  • 67
    • 0034895529 scopus 로고    scopus 로고
    • Adaptive evolution on neutral network
    • Wilke CO (2001) Adaptive evolution on neutral network. Bull Math Sci 63:715-730
    • (2001) Bull Math Sci , vol.63 , pp. 715-730
    • Wilke, C.O.1
  • 68
    • 0035913336 scopus 로고    scopus 로고
    • Evolution of digital organisms at high mutation rates leads to survival of the flattest
    • Wilke CO, Wang JL, Ofria C, Lenski RE, Adami C (2001) Evolution of digital organisms at high mutation rates leads to survival of the flattest. Nature 412:331-333
    • (2001) Nature , vol.412 , pp. 331-333
    • Wilke, C.O.1    Wang, J.L.2    Ofria, C.3    Lenski, R.E.4    Adami, C.5
  • 69
    • 0036678845 scopus 로고    scopus 로고
    • Roles of mutation and recombination in the evolution of protein thermodynamics
    • Xia Y, Levitt M (2002) Roles of mutation and recombination in the evolution of protein thermodynamics. Proc Natl Acad Sci USA 99:10382-10387
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 10382-10387
    • Xia, Y.1    Levitt, M.2
  • 70
    • 32144446421 scopus 로고    scopus 로고
    • The standard genetic code enhances adaptive evolution of proteins
    • Zhu W, Freeland S (2006) The standard genetic code enhances adaptive evolution of proteins. J Theor Biol 239:63-70
    • (2006) J Theor Biol , vol.239 , pp. 63-70
    • Zhu, W.1    Freeland, S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.