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Volumn 19, Issue 4, 2008, Pages 389-395

Sloppiness, robustness, and evolvability in systems biology

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMICAL NETWORKS; COLLECTIVE BEHAVIOR; EVOLVABILITY; EXTERNAL CONDITIONING; MULTI-PARAMETER MODELS; REACTION PARAMETERS; ROBUST SY STEMS; SYSTEM BEHAVIORS; SYSTEMS BIOLOGY;

EID: 49549094042     PISSN: 09581669     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.copbio.2008.06.008     Document Type: Review
Times cited : (159)

References (48)
  • 5
    • 38549096995 scopus 로고    scopus 로고
    • Robustness and evolution: concepts, insights and challenges from a developmental model system
    • Felix M.A., and Wagner A. Robustness and evolution: concepts, insights and challenges from a developmental model system. Heredity 100 (2008) 132-140
    • (2008) Heredity , vol.100 , pp. 132-140
    • Felix, M.A.1    Wagner, A.2
  • 6
    • 34548825690 scopus 로고    scopus 로고
    • Towards a theory of biological robustness
    • Kitano H. Towards a theory of biological robustness. Mol Syst Biol 3 (2007) 137
    • (2007) Mol Syst Biol , vol.3 , pp. 137
    • Kitano, H.1
  • 7
    • 2142640522 scopus 로고    scopus 로고
    • Stable or robust? What's the difference?
    • Jen E. Stable or robust? What's the difference?. Complexity 8 (2003) 12-18
    • (2003) Complexity , vol.8 , pp. 12-18
    • Jen, E.1
  • 8
    • 36348992094 scopus 로고    scopus 로고
    • Robustness and evolvability: a paradox resolved
    • Introduces the notion of phenotype robustness and phenotype evolvability in which the apparent tension between robustness and evolvability is resolved, and applies these ideas to the study of RNA secondary structures.
    • Wagner A. Robustness and evolvability: a paradox resolved. Proc R Soc Lond B Biol Sci 275 (2008) 91-100. Introduces the notion of phenotype robustness and phenotype evolvability in which the apparent tension between robustness and evolvability is resolved, and applies these ideas to the study of RNA secondary structures.
    • (2008) Proc R Soc Lond B Biol Sci , vol.275 , pp. 91-100
    • Wagner, A.1
  • 10
    • 0001757026 scopus 로고
    • On temperature independence in the clock system controlling emergence time in Drosophila
    • Pittendrigh C.S. On temperature independence in the clock system controlling emergence time in Drosophila. Proc Natl Acad Sci U S A 40 (1954) 1018-1029
    • (1954) Proc Natl Acad Sci U S A , vol.40 , pp. 1018-1029
    • Pittendrigh, C.S.1
  • 11
    • 12244296161 scopus 로고    scopus 로고
    • No transcription-translation feedback in circadian rhythm of KaiC phosphorylation
    • Tomita J., Nakajima M., Kondo T., and Iwasaki H. No transcription-translation feedback in circadian rhythm of KaiC phosphorylation. Science 307 (2005) 251-254
    • (2005) Science , vol.307 , pp. 251-254
    • Tomita, J.1    Nakajima, M.2    Kondo, T.3    Iwasaki, H.4
  • 12
    • 34250637942 scopus 로고    scopus 로고
    • An allosteric model of circadian KaiC phosphorylation
    • Presents a model of circadian rhythms in cyanobacteria, from which we extracted the submodel for KaiC phosphorylation dynamics.
    • van Zon J.S., Lubensky D.K., Altena PRH, and ten Wolde P.R. An allosteric model of circadian KaiC phosphorylation. Proc Natl Acad Sci U S A 104 (2007) 7420-7425. Presents a model of circadian rhythms in cyanobacteria, from which we extracted the submodel for KaiC phosphorylation dynamics.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 7420-7425
    • van Zon, J.S.1    Lubensky, D.K.2    Altena PRH3    ten Wolde, P.R.4
  • 13
    • 0034644270 scopus 로고    scopus 로고
    • The segment polarity network is a robust developmental module
    • von Dassow G., Meir E., Munro E.M., and Odell G.M. The segment polarity network is a robust developmental module. Nature 406 (2000) 188-192
    • (2000) Nature , vol.406 , pp. 188-192
    • von Dassow, G.1    Meir, E.2    Munro, E.M.3    Odell, G.M.4
  • 14
    • 49549088420 scopus 로고    scopus 로고
    • Chaves M, Sontag ED, Sengupta AM: Shape, size and robustness: feasible regions in the parameter space of biochemical networks 2007. URL: http://arXiv.org/abs/0710.4269.
    • Chaves M, Sontag ED, Sengupta AM: Shape, size and robustness: feasible regions in the parameter space of biochemical networks 2007. URL: http://arXiv.org/abs/0710.4269.
  • 15
    • 0030797355 scopus 로고    scopus 로고
    • Robustness in simple biochemical networks
    • Barkai N., and Leibler S. Robustness in simple biochemical networks. Nature 387 (1997) 913-917
    • (1997) Nature , vol.387 , pp. 913-917
    • Barkai, N.1    Leibler, S.2
  • 16
  • 17
    • 0034712843 scopus 로고    scopus 로고
    • Robust perfect adaptation in bacterial chemotaxis through integral feedback control
    • Yi T.M., Huang Y., Simon M.I., and Doyle J. Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc Natl Acad Sci U S A 97 (2000) 4649-4653
    • (2000) Proc Natl Acad Sci U S A , vol.97 , pp. 4649-4653
    • Yi, T.M.1    Huang, Y.2    Simon, M.I.3    Doyle, J.4
  • 18
    • 27844574799 scopus 로고    scopus 로고
    • Motifs, control, and stability
    • Doyle J., and Csete M. Motifs, control, and stability. PLoS Biol 3 (2005) e392
    • (2005) PLoS Biol , vol.3
    • Doyle, J.1    Csete, M.2
  • 19
    • 1842558252 scopus 로고    scopus 로고
    • Robust control in bacterial regulatory circuits
    • Goulian M. Robust control in bacterial regulatory circuits. Curr Opin Microbiol 7 (2004) 198-202
    • (2004) Curr Opin Microbiol , vol.7 , pp. 198-202
    • Goulian, M.1
  • 21
    • 0040357165 scopus 로고    scopus 로고
    • Chance and necessity in evolution: lessons from RNA
    • Schuster P., and Fontana W. Chance and necessity in evolution: lessons from RNA. Physica D 133 (1999) 427-452
    • (1999) Physica D , vol.133 , pp. 427-452
    • Schuster, P.1    Fontana, W.2
  • 22
    • 0036903361 scopus 로고    scopus 로고
    • Modelling 'evo-devo' with RNA
    • Fontana W. Modelling 'evo-devo' with RNA. Bioessays 24 (2002) 1164-1177
    • (2002) Bioessays , vol.24 , pp. 1164-1177
    • Fontana, W.1
  • 23
    • 34548511143 scopus 로고    scopus 로고
    • New structural variation in evolutionary searches of RNA neutral networks
    • Sumedha, Martin O.C., and Wagner A. New structural variation in evolutionary searches of RNA neutral networks. Biosystems 90 (2007) 475-485
    • (2007) Biosystems , vol.90 , pp. 475-485
    • Sumedha1    Martin, O.C.2    Wagner, A.3
  • 24
    • 33847268619 scopus 로고    scopus 로고
    • Robustness can evolve gradually in complex regulatory gene networks with varying topology
    • Ciliberti S., Martin O.C., and Wagner A. Robustness can evolve gradually in complex regulatory gene networks with varying topology. PLoS Comput Biol 3 (2007) e15
    • (2007) PLoS Comput Biol , vol.3
    • Ciliberti, S.1    Martin, O.C.2    Wagner, A.3
  • 25
    • 35348892535 scopus 로고    scopus 로고
    • Innovation and robustness in complex regulatory gene networks
    • Examines the structure of neutral networks and connections between robustness and evolvability in a simple model of gene regulatory networks.
    • Ciliberti S., Martin O.C., and Wagner A. Innovation and robustness in complex regulatory gene networks. Proc Natl Acad Sci U S A 104 (2007) 13591-13596. Examines the structure of neutral networks and connections between robustness and evolvability in a simple model of gene regulatory networks.
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 13591-13596
    • Ciliberti, S.1    Martin, O.C.2    Wagner, A.3
  • 26
    • 0042154192 scopus 로고    scopus 로고
    • Evolutionary capacitance as a general feature of complex gene networks
    • Bergman A., and Siegal M.L. Evolutionary capacitance as a general feature of complex gene networks. Nature 424 (2003) 549-552
    • (2003) Nature , vol.424 , pp. 549-552
    • Bergman, A.1    Siegal, M.L.2
  • 27
    • 54049134468 scopus 로고    scopus 로고
    • Myers CR: Satisfiability, sequence niches, and molecular codes in cellular signaling. IET Systems Biology 2008, in press. URL: http://arXiv.org/abs/q-bio/0702042.
    • Myers CR: Satisfiability, sequence niches, and molecular codes in cellular signaling. IET Systems Biology 2008, in press. URL: http://arXiv.org/abs/q-bio/0702042. Explores the nontrivial structure of neutral spaces that arise from the satisfaction of conflicting constraints in a genotype-to-phenotype map relating protein sequences to the avoidance of crosstalk.
  • 28
    • 0035923604 scopus 로고    scopus 로고
    • Degeneracy and complexity in biological systems
    • Edelman G.M., and Gally J.A. Degeneracy and complexity in biological systems. Proc Natl Acad Sci U S A 98 (2001) 13763-13768
    • (2001) Proc Natl Acad Sci U S A , vol.98 , pp. 13763-13768
    • Edelman, G.M.1    Gally, J.A.2
  • 29
    • 49549109676 scopus 로고    scopus 로고
    • Gutenkunst RN, Sethna JP: Adaptive mutation in a geometrical model of chemotype evolution 2007. URL: http://arXiv.org/abs/0712.3240.
    • Gutenkunst RN, Sethna JP: Adaptive mutation in a geometrical model of chemotype evolution 2007. URL: http://arXiv.org/abs/0712.3240.
  • 30
    • 42749109054 scopus 로고    scopus 로고
    • Statistical mechanical approaches to models with many poorly known parameters
    • Brown K.S., and Sethna J.P. Statistical mechanical approaches to models with many poorly known parameters. Phys Rev E 68 (2003) 021904
    • (2003) Phys Rev E , vol.68 , pp. 021904
    • Brown, K.S.1    Sethna, J.P.2
  • 32
    • 35748977901 scopus 로고    scopus 로고
    • Universally sloppy parameter sensitivities in systems biology models
    • Demonstrates the universality of sloppy eigenvalue spectra in chemical kinetic network models from systems biology, and highlights the inefficiency of constraining models by direct parameter measurement because of this sloppy structure.
    • Gutenkunst R.N., Waterfall J.J., Casey F.P., Brown K.S., Myers C.R., and Sethna J.P. Universally sloppy parameter sensitivities in systems biology models. PLoS Comput Biol 3 (2007) e189. Demonstrates the universality of sloppy eigenvalue spectra in chemical kinetic network models from systems biology, and highlights the inefficiency of constraining models by direct parameter measurement because of this sloppy structure.
    • (2007) PLoS Comput Biol , vol.3
    • Gutenkunst, R.N.1    Waterfall, J.J.2    Casey, F.P.3    Brown, K.S.4    Myers, C.R.5    Sethna, J.P.6
  • 34
    • 33750016873 scopus 로고    scopus 로고
    • Sloppy-model universality class and the Vandermonde matrix
    • Discusses the mathematical origins of sloppy behavior in multiparameter models, with examples of sloppy model behavior outside of biology.
    • Waterfall J.J., Casey F.P., Gutenkunst R.N., Brown K.S., Myers C.R., Brouwer P.W., Elser V., and Sethna J.P. Sloppy-model universality class and the Vandermonde matrix. Phys Rev Lett 97 (2006) 150601. Discusses the mathematical origins of sloppy behavior in multiparameter models, with examples of sloppy model behavior outside of biology.
    • (2006) Phys Rev Lett , vol.97 , pp. 150601
    • Waterfall, J.J.1    Casey, F.P.2    Gutenkunst, R.N.3    Brown, K.S.4    Myers, C.R.5    Brouwer, P.W.6    Elser, V.7    Sethna, J.P.8
  • 36
    • 27244440301 scopus 로고    scopus 로고
    • Biochemical networks with uncertain parameters
    • Liebermeister W., and Klipp E. Biochemical networks with uncertain parameters. IEE Proc Syst Biol 152 (2005) 97-107
    • (2005) IEE Proc Syst Biol , vol.152 , pp. 97-107
    • Liebermeister, W.1    Klipp, E.2
  • 38
    • 36248952170 scopus 로고    scopus 로고
    • The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks
    • Grimbs S., Selbig J., Bulik S., Holzhutter H.G., and Steuer R. The stability and robustness of metabolic states: identifying stabilizing sites in metabolic networks. Mol Syst Biol 3 (2007) 146
    • (2007) Mol Syst Biol , vol.3 , pp. 146
    • Grimbs, S.1    Selbig, J.2    Bulik, S.3    Holzhutter, H.G.4    Steuer, R.5
  • 39
    • 21244477594 scopus 로고    scopus 로고
    • k-cone analysis: determining all candidate values for kinetic parameters on a network scale
    • Famili I., Mahadevan R., and Palsson B.O. k-cone analysis: determining all candidate values for kinetic parameters on a network scale. Biophys J 88 (2005) 1616-1625
    • (2005) Biophys J , vol.88 , pp. 1616-1625
    • Famili, I.1    Mahadevan, R.2    Palsson, B.O.3
  • 41
    • 41049095598 scopus 로고    scopus 로고
    • Diverse metabolic model parameters generate similar methionine cycle dynamics
    • Piazza M., Feng X.J., Rabinowitz J.D., and Rabitz H. Diverse metabolic model parameters generate similar methionine cycle dynamics. J Theor Biol 251 (2008) 628-639
    • (2008) J Theor Biol , vol.251 , pp. 628-639
    • Piazza, M.1    Feng, X.J.2    Rabinowitz, J.D.3    Rabitz, H.4
  • 42
    • 0037108539 scopus 로고    scopus 로고
    • Ingeneue: a versatile tool for reconstituting genetic networks, with examples from the segment polarity network
    • Meir E., Munro E.M., Odell G.M., and Dassow G.V. Ingeneue: a versatile tool for reconstituting genetic networks, with examples from the segment polarity network. J Exp Zool 294 (2002) 216-251
    • (2002) J Exp Zool , vol.294 , pp. 216-251
    • Meir, E.1    Munro, E.M.2    Odell, G.M.3    Dassow, G.V.4
  • 44
    • 0030758944 scopus 로고    scopus 로고
    • Modeling temperature compensation in chemical and biological oscillators
    • Ruoff P., Rensing L., Kommedal R., and Mohsenzadeh S. Modeling temperature compensation in chemical and biological oscillators. Chronobiol Int 14 (1997) 499-510
    • (1997) Chronobiol Int , vol.14 , pp. 499-510
    • Ruoff, P.1    Rensing, L.2    Kommedal, R.3    Mohsenzadeh, S.4
  • 45
    • 33846568101 scopus 로고    scopus 로고
    • A proposal for robust temperature compensation of circadian rhythms
    • Hong C.I., Conrad E.D., and Tyson J.J. A proposal for robust temperature compensation of circadian rhythms. Proc Natl Acad Sci U S A 104 (2007) 1195-1200
    • (2007) Proc Natl Acad Sci U S A , vol.104 , pp. 1195-1200
    • Hong, C.I.1    Conrad, E.D.2    Tyson, J.J.3
  • 46
    • 33645523760 scopus 로고    scopus 로고
    • How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: a theoretical study
    • Cheng Y., Zhang Y., and McCammon J.A. How does activation loop phosphorylation modulate catalytic activity in the cAMP-dependent protein kinase: a theoretical study. Protein Sci 15 (2006) 672-683
    • (2006) Protein Sci , vol.15 , pp. 672-683
    • Cheng, Y.1    Zhang, Y.2    McCammon, J.A.3
  • 47
    • 33846106739 scopus 로고    scopus 로고
    • Robustness and modular design of the Drosophila segment polarity network
    • Ma W., Lai L., Ouyang Q., and Tang C. Robustness and modular design of the Drosophila segment polarity network. Mol Syst Biol 2 (2006) 70
    • (2006) Mol Syst Biol , vol.2 , pp. 70
    • Ma, W.1    Lai, L.2    Ouyang, Q.3    Tang, C.4
  • 48
    • 3142517462 scopus 로고    scopus 로고
    • Topology and robustness in the Drosophila segment polarity network
    • Ingolia N.T. Topology and robustness in the Drosophila segment polarity network. PLoS Biol 2 (2004) e123
    • (2004) PLoS Biol , vol.2
    • Ingolia, N.T.1


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