메뉴 건너뛰기




Volumn 4, Issue , 2004, Pages

Gene family evolution: An in-depth theoretical and simulation analysis of non-linear birth-death-innovation models

Author keywords

[No Author keywords available]

Indexed keywords

EUKARYOTA;

EID: 8744283816     PISSN: 14712148     EISSN: None     Source Type: Journal    
DOI: 10.1186/1471-2148-4-32     Document Type: Article
Times cited : (46)

References (55)
  • 1
    • 0035039580 scopus 로고    scopus 로고
    • Scale invariance in biology: Coincidence or footprint of a universal mechanism?
    • Gisiger T: Scale invariance in biology: coincidence or footprint of a universal mechanism? Biol Rev Camb Philos Soc 2001, 76:161-209.
    • (2001) Biol Rev Camb Philos Soc , vol.76 , pp. 161-209
    • Gisiger, T.1
  • 4
    • 33748756571 scopus 로고    scopus 로고
    • From gene families and genera to incomes and internet file sizes: Why power laws are so common in nature
    • Reed WJ, Hughes BD: From gene families and genera to incomes and internet file sizes: why power laws are so common in nature. Phys Rev E Stat Nonlin Soft Matter Phys 2002, 66:67103.
    • (2002) Phys Rev E Stat Nonlin Soft Matter Phys , vol.66 , pp. 67103
    • Reed, W.J.1    Hughes, B.D.2
  • 5
    • 0242713700 scopus 로고    scopus 로고
    • The dominance of the population by a selected few: Power-law behaviour applies to a wide variety of genomic properties
    • research0040.1-40.7.
    • Luscombe N,, Qian J, Zhang Z, Johnson T, Gerstein M: The dominance of the population by a selected few: power-law behaviour applies to a wide variety of genomic properties. Genome Biol 2002, 3:research0040.1-40.7.
    • (2002) Genome Biol , vol.3
    • Luscombe, N.1    Qian, J.2    Zhang, Z.3    Johnson, T.4    Gerstein, M.5
  • 6
    • 0035798398 scopus 로고    scopus 로고
    • Protein family and fold occurrence in genomes: Power-law behaviour and evolutionary model
    • Qian J, Luscombe NM, Gerstein M: Protein family and fold occurrence in genomes: power-law behaviour and evolutionary model. J Mol Biol 2001, 313:673-681.
    • (2001) J Mol Biol , vol.313 , pp. 673-681
    • Qian, J.1    Luscombe, N.M.2    Gerstein, M.3
  • 9
    • 0742305866 scopus 로고    scopus 로고
    • Network biology: Understanding the cell's functional organization
    • Barabasi AL, Oltvai ZN: Network biology: understanding the cell's functional organization. Nat Rev Genet 2004, 5:101-113.
    • (2004) Nat Rev Genet , vol.5 , pp. 101-113
    • Barabasi, A.L.1    Oltvai, Z.N.2
  • 10
    • 0035555690 scopus 로고    scopus 로고
    • Distribution associated with stochastic processes of gene expression in a single eukariotic cell
    • Kuznetsov VA: Distribution associated with stochastic processes of gene expression in a single eukariotic cell. EUROSIP Journal on Applied Signal Processing 2001, 4:285-296.
    • (2001) EUROSIP Journal on Applied Signal Processing , vol.4 , pp. 285-296
    • Kuznetsov, V.A.1
  • 11
    • 0003111370 scopus 로고    scopus 로고
    • Statistics of the numbers of transcripts and protein sequences encoded in the genome
    • Edited by: Zhang W and Shmulevich I. Boston, Kluwer
    • Kuznetsov VA: Statistics of the numbers of transcripts and protein sequences encoded in the genome. Computational and Statistical Approaches to Genomics Edited by: Zhang W and Shmulevich I. Boston, Kluwer; 2002:125-171.
    • (2002) Computational and Statistical Approaches to Genomics , pp. 125-171
    • Kuznetsov, V.A.1
  • 12
  • 13
    • 0037079014 scopus 로고    scopus 로고
    • The structure of the protein universe and genome evolution
    • Koonin EV, Wolf YI, Karev GP: The structure of the protein universe and genome evolution. Nature 2002, 420:218-223.
    • (2002) Nature , vol.420 , pp. 218-223
    • Koonin, E.V.1    Wolf, Y.I.2    Karev, G.P.3
  • 14
    • 0038483826 scopus 로고    scopus 로고
    • Emergence of scaling in random networks
    • Barabasi AL, Albert R: Emergence of scaling in random networks. Science 1999, 286:509-512.
    • (1999) Science , vol.286 , pp. 509-512
    • Barabasi, A.L.1    Albert, R.2
  • 15
    • 0000357469 scopus 로고
    • The possible modification of the response of the wild type to recurrent mutations
    • Fisher RA: The possible modification of the response of the wild type to recurrent mutations. Am Nat 1928, 62:115-126.
    • (1928) Am Nat , vol.62 , pp. 115-126
    • Fisher, R.A.1
  • 16
  • 19
    • 0036066765 scopus 로고    scopus 로고
    • The role of lineagespecific gene family expansion in the evolution of eukaryotes
    • Lespinet O, Wolf YI, Koonin EV, Aravind L: The role of lineagespecific gene family expansion in the evolution of eukaryotes. Genome Res 2002, 12:1048-1059.
    • (2002) Genome Res , vol.12 , pp. 1048-1059
    • Lespinet, O.1    Wolf, Y.I.2    Koonin, E.V.3    Aravind, L.4
  • 20
    • 1942452749 scopus 로고    scopus 로고
    • Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae
    • Kellis M, Birren BW, Lander ES: Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature 2004, 428:617-624.
    • (2004) Nature , vol.428 , pp. 617-624
    • Kellis, M.1    Birren, B.W.2    Lander, E.S.3
  • 23
    • 0033972072 scopus 로고    scopus 로고
    • The probability of duplicate gene preservation by subfunctionalization
    • Lynch M, Force A: The probability of duplicate gene preservation by subfunctionalization. Genetics 2000, 154:459-473.
    • (2000) Genetics , vol.154 , pp. 459-473
    • Lynch, M.1    Force, A.2
  • 24
    • 0034634395 scopus 로고    scopus 로고
    • The evolutionary fate and consequences of duplicate genes
    • Lynch M, Conery JS: The evolutionary fate and consequences of duplicate genes. Science 2000, 290:1151-1155.
    • (2000) Science , vol.290 , pp. 1151-1155
    • Lynch, M.1    Conery, J.S.2
  • 25
    • 0034633626 scopus 로고    scopus 로고
    • Lineage-specific loss and divergence of functionally linked genes in eukaryotes
    • Aravind L, Watanabe H, Lipman DJ, Koonin EV: Lineage-specific loss and divergence of functionally linked genes in eukaryotes. Proc Natl Acad Sci U S A 2000, 97:11319-11324.
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 11319-11324
    • Aravind, L.1    Watanabe, H.2    Lipman, D.J.3    Koonin, E.V.4
  • 29
    • 0034084865 scopus 로고    scopus 로고
    • Who's your neighbor? New computational approaches for functional genomics
    • Galperin MY, Koonin EV: Who's your neighbor? new computational approaches for functional genomics. Nat Biotechnol 2000, 18:609-613.
    • (2000) Nat Biotechnol , vol.18 , pp. 609-613
    • Galperin, M.Y.1    Koonin, E.V.2
  • 30
    • 0033832615 scopus 로고    scopus 로고
    • Predicting protein function by genomic context: Quantitative evaluation and qualitative inferences
    • Huynen M, Snel B, Lathe W., 3rd, Bork P: Predicting protein function by genomic context: quantitative evaluation and qualitative inferences. Genome Res 2000, 10:1204-1210.
    • (2000) Genome Res , vol.10 , pp. 1204-1210
    • Huynen, M.1    Snel, B.2    Lathe III, W.3    Bork, P.4
  • 32
    • 0041828241 scopus 로고    scopus 로고
    • Scaling laws in the functional content of genomes
    • van Nimwegen E: Scaling laws in the functional content of genomes. Trends Genet 2003, 19:479-484.
    • (2003) Trends Genet , vol.19 , pp. 479-484
    • Van Nimwegen, E.1
  • 34
    • 0034777716 scopus 로고    scopus 로고
    • Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome
    • Rzhetsky A, Gomez SM: Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinformatics 2001, 17:988-996.
    • (2001) Bioinformatics , vol.17 , pp. 988-996
    • Rzhetsky, A.1    Gomez, S.M.2
  • 36
    • 0037460091 scopus 로고    scopus 로고
    • Evolving protein interaction networks through gene duplication
    • Pastor-Satorras R, Smith E, Sole RV: Evolving protein interaction networks through gene duplication. J Theor Biol 2003, 222:199-210.
    • (2003) J Theor Biol , vol.222 , pp. 199-210
    • Pastor-Satorras, R.1    Smith, E.2    Sole, R.V.3
  • 37
    • 0037423828 scopus 로고    scopus 로고
    • How the global structure of protein interaction networks evolves
    • Wagner A: How the global structure of protein interaction networks evolves. Proc R Soc Lond B Biol Sci 2003, 270:457-466.
    • (2003) Proc R Soc Lond B Biol Sci , vol.270 , pp. 457-466
    • Wagner, A.1
  • 42
    • 1842631448 scopus 로고    scopus 로고
    • Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control
    • Yanai I, Graur D, Ophir R: Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. Omics 2004, 8:15-24.
    • (2004) Omics , vol.8 , pp. 15-24
    • Yanai, I.1    Graur, D.2    Ophir, R.3
  • 43
    • 0142148213 scopus 로고    scopus 로고
    • Simple stochastic birth and death models of genome evolution: Was there enough time for us to evolve?
    • Karev GP, Wolf YI, Koonin EV: Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve? Bioinformatics 2003, 19:1889-1900.
    • (2003) Bioinformatics , vol.19 , pp. 1889-1900
    • Karev, G.P.1    Wolf, Y.I.2    Koonin, E.V.3
  • 49
    • 0036739709 scopus 로고    scopus 로고
    • Extinction dynamics in mainland-island metapopulations: An N-patch stochastic model
    • Alonso D, McKane A: Extinction dynamics in mainland-island metapopulations: an N-patch stochastic model. Bull Math Biol 2002, 64:913-958.
    • (2002) Bull Math Biol , vol.64 , pp. 913-958
    • Alonso, D.1    McKane, A.2
  • 50
    • 8744270389 scopus 로고    scopus 로고
    • Mathematical modeling of the evolution of domain composition of proteomes: A birth-anddeath process with innovation
    • Edited by: Galperin M Y Koonin E V. Amsterdam, Horizon Press
    • Karev GP, Wolf YI, Koonin EV: Mathematical modeling of the evolution of domain composition of proteomes: A birth-anddeath process with innovation. Computational genomics: from sequence to function Volume 3. Edited by: Galperin M Y Koonin E V. Amsterdam, Horizon Press; 2002:261-314.
    • (2002) Computational Genomics: From Sequence to Function Volume 3 , vol.3 , pp. 261-314
    • Karev, G.P.1    Wolf, Y.I.2    Koonin, E.V.3
  • 51
    • 1642340045 scopus 로고    scopus 로고
    • A model explaining the size distribution of gene and protein families
    • Reed WJ, Hughes BD: A model explaining the size distribution of gene and protein families. Math Biosci 2004, 189:97-102.
    • (2004) Math Biosci , vol.189 , pp. 97-102
    • Reed, W.J.1    Hughes, B.D.2
  • 52
    • 0031924363 scopus 로고    scopus 로고
    • The frequency distribution of gene family sizes in complete genomes
    • Huynen MA, van Nimwegen E: The frequency distribution of gene family sizes in complete genomes. Mol Biol Evol 1998, 15:583-589.
    • (1998) Mol Biol Evol , vol.15 , pp. 583-589
    • Huynen, M.A.1    Van Nimwegen, E.2
  • 53
    • 0002339389 scopus 로고
    • Salivary chromosome maps
    • Bridges CA: Salivary chromosome maps. J Hered 1935, 26:60-64.
    • (1935) J Hered , vol.26 , pp. 60-64
    • Bridges, C.A.1
  • 54
    • 19344363466 scopus 로고    scopus 로고
    • Preferential duplication of conserved proteins in eukaryotic genomes
    • Davis JC, Petrov DA: Preferential duplication of conserved proteins in eukaryotic genomes. PLoS Biol 2004, 2:E55.
    • (2004) PLoS Biol , vol.2
    • Davis, J.C.1    Petrov, D.A.2
  • 55
    • 8744268628 scopus 로고    scopus 로고
    • Duplicated genes evolve slower than singletons despite the initial rate increase
    • Jordan IK, Wolf YI, Koonin EV: Duplicated genes evolve slower than singletons despite the initial rate increase. BMC Evol Biol 2004, 4:22.
    • (2004) BMC Evol Biol , vol.4 , pp. 22
    • Jordan, I.K.1    Wolf, Y.I.2    Koonin, E.V.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.