메뉴 건너뛰기




Volumn 362, Issue 1486, 2007, Pages 1831-1839

A minimal and self-consistent in silico cell model based on macromolecular interactions

Author keywords

Biochemical ordinary differential equation solver; Cooperativity; Genetic regulatory network; Metabolic network; Systems biology markup language

Indexed keywords

ENVIRONMENTAL FACTOR; GENETICS; HOMEOSTASIS; MODELING; OPTIMIZATION;

EID: 35148834742     PISSN: 09628436     EISSN: None     Source Type: Journal    
DOI: 10.1098/rstb.2007.2075     Document Type: Article
Times cited : (7)

References (37)
  • 4
    • 34548104745 scopus 로고    scopus 로고
    • ch. 1. Dordrecht, The Netherlands: Kluwer Academic Publishers
    • Banzhaf, W. & Miller, J. 2004 The challenge of complexity, ch. 1. Dordrecht, The Netherlands: Kluwer Academic Publishers.
    • (2004) The challenge of complexity
    • Banzhaf, W.1    Miller, J.2
  • 7
    • 85020803682 scopus 로고    scopus 로고
    • Biebricher, C. K. 1983 In Darwinian selection of self-replicating RNA molecules, 16 (eds M. K. Hecht, B. Wallace & G. T. Prance) Evolutionary biology, pp. 1-52. New York, NY: Plenum Publishing Corporation.
    • Biebricher, C. K. 1983 In Darwinian selection of self-replicating RNA molecules, vol. 16 (eds M. K. Hecht, B. Wallace & G. T. Prance) Evolutionary biology, pp. 1-52. New York, NY: Plenum Publishing Corporation.
  • 8
    • 0030868829 scopus 로고    scopus 로고
    • Molecular evolution of RNA in vitro
    • doi:10.1016/S0301-4622(97) 00059-8
    • Biebricher, C. K. & Gardiner, W. C. 1997 Molecular evolution of RNA in vitro. Biophys. Chem. 66, 179-192. (doi:10.1016/S0301-4622(97) 00059-8)
    • (1997) Biophys. Chem , vol.66 , pp. 179-192
    • Biebricher, C.K.1    Gardiner, W.C.2
  • 9
    • 0021099437 scopus 로고
    • Kinetics of RNA replication
    • doi:10.1021/bi00279a036
    • Biebricher, C. K., Eigen, M. & Gardiner, W. C. 1983 Kinetics of RNA replication. Biochemistry 22, 2544-2559. (doi:10.1021/bi00279a036)
    • (1983) Biochemistry , vol.22 , pp. 2544-2559
    • Biebricher, C.K.1    Eigen, M.2    Gardiner, W.C.3
  • 13
    • 3042735602 scopus 로고    scopus 로고
    • Prediction of hybridization and melting for double-stranded nucleic acids
    • doi:10.1529/biophysj.103.020743
    • Dimitrov, R. A. & Zuker, M. 2004 Prediction of hybridization and melting for double-stranded nucleic acids. Biophys. J. 87, 215-226. (doi:10.1529/biophysj.103.020743)
    • (2004) Biophys. J , vol.87 , pp. 215-226
    • Dimitrov, R.A.1    Zuker, M.2
  • 14
    • 85040437712 scopus 로고    scopus 로고
    • How neutral networks influence evolvability
    • doi:10.1002/cplx. 10021
    • Ebner, M., Shackleton, M. & Shipman, R. 2001 How neutral networks influence evolvability. Complexity 7, 19-33. (doi:10.1002/cplx. 10021)
    • (2001) Complexity , vol.7 , pp. 19-33
    • Ebner, M.1    Shackleton, M.2    Shipman, R.3
  • 15
    • 85020835115 scopus 로고    scopus 로고
    • Evolving morphologies of simulated 3d organisms based on differential gene expression
    • eds P. Husbands & I. Harvey, Cambridge, MA: MIT Press
    • Eggenberg, P. 1997 Evolving morphologies of simulated 3d organisms based on differential gene expression. In Proc. 4th Eur. Conf. Artificial Life (ECAL'97)London, UK, September 9-13 (eds P. Husbands & I. Harvey). Cambridge, MA: MIT Press.
    • (1997) Proc. 4th Eur. Conf. Artificial Life (ECAL'97)London, UK, September 9-13
    • Eggenberg, P.1
  • 16
    • 0036903361 scopus 로고    scopus 로고
    • Modelling 'Evo-Devo' with RNA
    • doi:10.1002/bies.10190
    • Fontana, W. 2002 Modelling 'Evo-Devo' with RNA. BioEssays 24, 1164-1177. (doi:10.1002/bies.10190)
    • (2002) BioEssays , vol.24 , pp. 1164-1177
    • Fontana, W.1
  • 17
    • 0032577365 scopus 로고    scopus 로고
    • Continuity in evolution: On the nature of transitions
    • doi:10.1126/science.280.5368.1451
    • Fontana, W. & Schuster, P. 1998a Continuity in evolution: on the nature of transitions. Science 280, 145-165. (doi:10.1126/science.280.5368.1451)
    • (1998) Science , vol.280 , pp. 145-165
    • Fontana, W.1    Schuster, P.2
  • 18
    • 0032556237 scopus 로고    scopus 로고
    • Shaping space. The possible and the attainable in RNA genotype-phenotype mapping
    • doi:10.1006/jtbi.1998.0771
    • Fontana, W. & Schuster, P. 1998b Shaping space. The possible and the attainable in RNA genotype-phenotype mapping. J. Theor. Biol. 194, 491-515. (doi:10.1006/jtbi.1998.0771)
    • (1998) J. Theor. Biol , vol.194 , pp. 491-515
    • Fontana, W.1    Schuster, P.2
  • 19
    • 0016527372 scopus 로고
    • Organization of chemical reactions into dividing and metabolizing units: The chemotons
    • doi:10.1016/0303-2647(75)90038-6
    • Gantí, T. 1975 Organization of chemical reactions into dividing and metabolizing units: the chemotons. Biosystems 7, 15-21. (doi:10.1016/0303-2647(75)90038-6)
    • (1975) Biosystems , vol.7 , pp. 15-21
    • Gantí, T.1
  • 20
    • 0037342537 scopus 로고    scopus 로고
    • The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
    • doi:10.1093/bioinformatics/btg015
    • Hucka, M. et al. 2003 The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531. (doi:10.1093/bioinformatics/btg015)
    • (2003) Bioinformatics , vol.19 , pp. 524-531
    • Hucka, M.1
  • 21
    • 0030030533 scopus 로고    scopus 로고
    • Smoothness within ruggedness: The role of neutrality in adaptation
    • doi:10.1073/pnas.93.1.397
    • Huynen, M. A., Stadler, P. F. & Fontana, W. 1996 Smoothness within ruggedness: the role of neutrality in adaptation. Proc. Natl Acad. Sci. USA 93, 397-401. (doi:10.1073/pnas.93.1.397)
    • (1996) Proc. Natl Acad. Sci. USA , vol.93 , pp. 397-401
    • Huynen, M.A.1    Stadler, P.F.2    Fontana, W.3
  • 23
    • 33646163807 scopus 로고    scopus 로고
    • A model of gene expression and regulation in an artificial cellular organism
    • Kennedy, P. J., Osborn, T. R. & model, A. 2001 A model of gene expression and regulation in an artificial cellular organism. Complex Syst. 13, 33-59.
    • (2001) Complex Syst , vol.13 , pp. 33-59
    • Kennedy, P.J.1    Osborn, T.R.2    model, A.3
  • 24
    • 0028836695 scopus 로고
    • The macroworld versus the microworld of biochemical regulation and control
    • doi:10.1016/S0968-0004(00)88955-0
    • Kholodenko, B. N. & Westerhoff, H. V. 1995 The macroworld versus the microworld of biochemical regulation and control. Trends Biochem. Sci. 20, 52-54. (doi:10.1016/S0968-0004(00)88955-0)
    • (1995) Trends Biochem. Sci , vol.20 , pp. 52-54
    • Kholodenko, B.N.1    Westerhoff, H.V.2
  • 25
    • 33746897154 scopus 로고    scopus 로고
    • Evolving dynamics in an artificial regulatory network model
    • Berlin, Germany: Springer
    • Kuo, D. P., Leier, A. & Banzhaf, W. 2004 Evolving dynamics in an artificial regulatory network model. In Proc. Paralell Problem Solving from Nature Conf. vol. LNCS 3242, pp. 571-580. Berlin, Germany: Springer.
    • (2004) Proc. Paralell Problem Solving from Nature Conf , vol.LNCS 3242 , pp. 571-580
    • Kuo, D.P.1    Leier, A.2    Banzhaf, W.3
  • 26
    • 33745631242 scopus 로고    scopus 로고
    • The SBML ODE Solver library: A native API for symbolic and fast numerical analysis of reaction networks
    • doi:10.1093/bioinformatics/btl086
    • Machné, R., Finney, A., Müller, S., Lu, J., Widder, S. & Flamm, C. 2006 The SBML ODE Solver library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinformatics 22, 1406-1407. (doi:10.1093/bioinformatics/btl086)
    • (2006) Bioinformatics , vol.22 , pp. 1406-1407
    • Machné, R.1    Finney, A.2    Müller, S.3    Lu, J.4    Widder, S.5    Flamm, C.6
  • 27
    • 0036788304 scopus 로고    scopus 로고
    • Gene silencing in mammals by small interfering RNAs
    • doi:10.1038/nrg908
    • McManus, M. T. & Sharp, P. A. 2002 Gene silencing in mammals by small interfering RNAs. Nat. Rev. Genet. 3, 737-747. (doi:10.1038/nrg908)
    • (2002) Nat. Rev. Genet , vol.3 , pp. 737-747
    • McManus, M.T.1    Sharp, P.A.2
  • 28
    • 0345849436 scopus 로고    scopus 로고
    • Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press
    • Ptashne, M. & Gann, A. 2002 Genes & signals. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
    • (2002) Genes & signals
    • Ptashne, M.1    Gann, A.2
  • 29
    • 84957670701 scopus 로고
    • Dynamics of gene expression in an artificial genome-implications for biological and artificial ontogeny
    • Reil, T. 1999 Dynamics of gene expression in an artificial genome-implications for biological and artificial ontogeny. Advances in Artificial Life - Proc. 5th Eur. Conf. Artificial Life (ECAL'99), 1674, pp. 457-466.
    • (1674) Advances in Artificial Life - Proc. 5th Eur. Conf. Artificial Life (ECAL'99) , pp. 457-466
    • Reil, T.1
  • 30
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • doi:10.1073/pnas.95.4.1460
    • SantaLucia Jr, J. 1998 A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc. Natl Acad. Sci. USA 95, 1460-1465. (doi:10.1073/pnas.95.4.1460)
    • (1998) Proc. Natl Acad. Sci. USA , vol.95 , pp. 1460-1465
    • SantaLucia Jr, J.1
  • 31
    • 0029968822 scopus 로고    scopus 로고
    • Improved nearest-neighbor parameters for predicting DNA duplex stability
    • doi:10.1021/bi951907q
    • SantaLucia Jr, J., Allawi, H. L. & Seneviratne, P. 1996 Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry 35, 3555-3562. (doi:10.1021/bi951907q)
    • (1996) Biochemistry , vol.35 , pp. 3555-3562
    • SantaLucia Jr, J.1    Allawi, H.L.2    Seneviratne, P.3
  • 32
    • 0034774080 scopus 로고    scopus 로고
    • Evolution in silico and in vitro: The RNA model
    • doi:10.1515/BC.2001.162
    • Schuster, P. 2001 Evolution in silico and in vitro: the RNA model. Biol. Chem. 382, 1301-1314. (doi:10.1515/BC.2001.162)
    • (2001) Biol. Chem , vol.382 , pp. 1301-1314
    • Schuster, P.1
  • 33
    • 27944452645 scopus 로고    scopus 로고
    • A testable genotype-phenotype map: Modeling evolution of RNA molecules
    • eds M. Lässig & A. Valleriani, pp, Berlin, Germany: Springer
    • Schuster, P. 2002 A testable genotype-phenotype map: modeling evolution of RNA molecules. In Biological evolution and statistical physics (eds M. Lässig & A. Valleriani), pp. 56-83. Berlin, Germany: Springer.
    • (2002) Biological evolution and statistical physics , pp. 56-83
    • Schuster, P.1
  • 35
    • 85020783394 scopus 로고    scopus 로고
    • Schuster, P. & Stadler, P. F. 2006 Modelling conformational flexibility and evolution of structure - RNA as an example. In Structural approaches to sequence evolution: molecules, networks, populations (eds U. Blastolla, M. Porto, H. E. Roman & M. Vendruscolo). Biological and medical physics, biomedical engineering, ch. 1, pp. 1-34. Berlin, Germany: Springer.
    • Schuster, P. & Stadler, P. F. 2006 Modelling conformational flexibility and evolution of structure - RNA as an example. In Structural approaches to sequence evolution: molecules, networks, populations (eds U. Blastolla, M. Porto, H. E. Roman & M. Vendruscolo). Biological and medical physics, biomedical engineering, ch. 1, pp. 1-34. Berlin, Germany: Springer.
  • 36
    • 0028196714 scopus 로고
    • From sequences to shapes and back: A case study in RNA secondary structure
    • doi:10.1098/rspb.1994.0040
    • Schuster, P., Fontana, W., Stadler, P. F. & Hofacker, I. L. 1994 From sequences to shapes and back: a case study in RNA secondary structure. Proc. R. Soc. B 255, 279-284. (doi:10.1098/rspb.1994.0040)
    • (1994) Proc. R. Soc. B , vol.255 , pp. 279-284
    • Schuster, P.1    Fontana, W.2    Stadler, P.F.3    Hofacker, I.L.4
  • 37
    • 0041783883 scopus 로고    scopus 로고
    • A taxonomy for artificial embryogeny
    • doi:10.1162/ 106454603322221487
    • Stanley, K. O. & Miikkulainen, R. 2003 A taxonomy for artificial embryogeny. Artif. Life 9, 93-130. (doi:10.1162/ 106454603322221487)
    • (2003) Artif. Life , vol.9 , pp. 93-130
    • Stanley, K.O.1    Miikkulainen, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.