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Volumn 7, Issue , 2013, Pages

Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model

Author keywords

Budding yeast; Cell cycle; Differential evolution; Latin hypercube sampling; Model reduction; ODE model; Optimization; Phenotype competition; Phenotypic constraints; Sensitivity analysis

Indexed keywords

SACCHAROMYCETALES;

EID: 84879455542     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-7-53     Document Type: Article
Times cited : (26)

References (34)
  • 1
    • 58549110646 scopus 로고    scopus 로고
    • How to deal with large models?
    • 2644176, 19156132
    • Hlavacek WS. How to deal with large models?. Mol Syst Biol 2009, 5:240. 2644176, 19156132.
    • (2009) Mol Syst Biol , vol.5 , pp. 240
    • Hlavacek, W.S.1
  • 3
    • 7444253428 scopus 로고    scopus 로고
    • Systems biology and new technologies enable predictive and preventative medicine
    • 10.1126/science.1104635, 15499008
    • Hood L, Heath J, Phelps M, Lin B. Systems biology and new technologies enable predictive and preventative medicine. Science 2004, 306(5696):640-643. 10.1126/science.1104635, 15499008.
    • (2004) Science , vol.306 , Issue.5696 , pp. 640-643
    • Hood, L.1    Heath, J.2    Phelps, M.3    Lin, B.4
  • 4
    • 0036500993 scopus 로고    scopus 로고
    • Systems biology: a brief overview
    • 10.1126/science.1069492, 11872829
    • Kitano H. Systems biology: a brief overview. Science 2002, 295(5560):1662-1664. 10.1126/science.1069492, 11872829.
    • (2002) Science , vol.295 , Issue.5560 , pp. 1662-1664
    • Kitano, H.1
  • 5
    • 0035656416 scopus 로고    scopus 로고
    • Network dynamics and cell physiology
    • 10.1038/35103078, 11733770
    • Tyson JJ, Chen K, Novak B. Network dynamics and cell physiology. Nat Rev Mol Cell Biol 2001, 2(12):908-916. 10.1038/35103078, 11733770.
    • (2001) Nat Rev Mol Cell Biol , vol.2 , Issue.12 , pp. 908-916
    • Tyson, J.J.1    Chen, K.2    Novak, B.3
  • 7
    • 81455142792 scopus 로고    scopus 로고
    • Parameter estimation using metaheuristics in systems biology: a comprehensive review
    • Sun J, Garibaldi JM, Hodgman C. Parameter estimation using metaheuristics in systems biology: a comprehensive review. IEEE-ACM T Comput Bi 2012, 9(1):185-202.
    • (2012) IEEE-ACM T Comput Bi , vol.9 , Issue.1 , pp. 185-202
    • Sun, J.1    Garibaldi, J.M.2    Hodgman, C.3
  • 9
    • 84862556212 scopus 로고    scopus 로고
    • A cooperative strategy for parameter estimation in large scale systems biology models
    • 10.1186/1752-0509-6-75, 3512509, 22727112
    • Villaverde AF, Egea JA, Banga JR. A cooperative strategy for parameter estimation in large scale systems biology models. BMC Syst Biol 2012, 6:75. 10.1186/1752-0509-6-75, 3512509, 22727112.
    • (2012) BMC Syst Biol , vol.6 , pp. 75
    • Villaverde, A.F.1    Egea, J.A.2    Banga, J.R.3
  • 10
    • 4544246088 scopus 로고    scopus 로고
    • Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis
    • 10.1083/jcb.200404158, 2172102, 15364960
    • Bentele M, Lavrik I, Ulrich M, Stößer S, Heermann DW, Kalthoff H, Krammer PH, Eils R. Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis. J Cell Biol 2004, 166(6):839-851. 10.1083/jcb.200404158, 2172102, 15364960.
    • (2004) J Cell Biol , vol.166 , Issue.6 , pp. 839-851
    • Bentele, M.1    Lavrik, I.2    Ulrich, M.3    Stößer, S.4    Heermann, D.W.5    Kalthoff, H.6    Krammer, P.H.7    Eils, R.8
  • 11
    • 1342265607 scopus 로고    scopus 로고
    • Experimental design in systems biology, based on parameter sensitivity analysis using a Monte Carlo method: A case study for the TNF alpha-mediated NF-kappa B signal transduction pathway
    • Cho K, Shin S, Kolch W, Wolkenhauer O. Experimental design in systems biology, based on parameter sensitivity analysis using a Monte Carlo method: A case study for the TNF alpha-mediated NF-kappa B signal transduction pathway. Simul-T Soc Mod Sim 2003, 79(12):726-739.
    • (2003) Simul-T Soc Mod Sim , vol.79 , Issue.12 , pp. 726-739
    • Cho, K.1    Shin, S.2    Kolch, W.3    Wolkenhauer, O.4
  • 12
    • 33845410054 scopus 로고    scopus 로고
    • Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-base experiments
    • 10.1093/bib/bbl040, 17107967
    • van Riel NAW. Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-base experiments. Brief Bioinform 2006, 7(4):364-374. 10.1093/bib/bbl040, 17107967.
    • (2006) Brief Bioinform , vol.7 , Issue.4 , pp. 364-374
    • van Riel, N.A.W.1
  • 13
    • 77956498018 scopus 로고    scopus 로고
    • Sloppy models, parameter uncertainty, and the role of experimental design
    • 10.1039/b918098b, 3505121, 20556289
    • Apgar JF, Witmer DK, White FM, Tidor B. Sloppy models, parameter uncertainty, and the role of experimental design. Mol Biosyst 2010, 6(10):1890-1900. 10.1039/b918098b, 3505121, 20556289.
    • (2010) Mol Biosyst , vol.6 , Issue.10 , pp. 1890-1900
    • Apgar, J.F.1    Witmer, D.K.2    White, F.M.3    Tidor, B.4
  • 14
    • 2342523297 scopus 로고    scopus 로고
    • Sensitivity analysis for the reduction of complex metabolism models
    • Degenring D, Froemel C, Dikta G, Takors R. Sensitivity analysis for the reduction of complex metabolism models. J Process Contr 2004, 14(7):729-745.
    • (2004) J Process Contr , vol.14 , Issue.7 , pp. 729-745
    • Degenring, D.1    Froemel, C.2    Dikta, G.3    Takors, R.4
  • 15
    • 33846632063 scopus 로고    scopus 로고
    • Oxford: Oxford University Press
    • Morgan D. Cell Cycle 2006, Oxford: Oxford University Press.
    • (2006) Cell Cycle
    • Morgan, D.1
  • 16
    • 3343020085 scopus 로고    scopus 로고
    • Integrative analysis of cell cycle control in budding yeast
    • 10.1091/mbc.E03-11-0794, 491841, 15169868
    • Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, Tyson JJ. Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell 2004, 15(8):3841-3862. 10.1091/mbc.E03-11-0794, 491841, 15169868.
    • (2004) Mol Biol Cell , vol.15 , Issue.8 , pp. 3841-3862
    • Chen, K.C.1    Calzone, L.2    Csikasz-Nagy, A.3    Cross, F.R.4    Novak, B.5    Tyson, J.J.6
  • 18
    • 40749158005 scopus 로고    scopus 로고
    • Complexity reduction of biochemical rate expressions
    • 10.1093/bioinformatics/btn035, 18267948
    • Schmidt H, Madsen MF, Dano S, Cedersund G. Complexity reduction of biochemical rate expressions. Bioinformatics 2008, 24(6):848-854. 10.1093/bioinformatics/btn035, 18267948.
    • (2008) Bioinformatics , vol.24 , Issue.6 , pp. 848-854
    • Schmidt, H.1    Madsen, M.F.2    Dano, S.3    Cedersund, G.4
  • 20
    • 67650760503 scopus 로고    scopus 로고
    • Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood
    • 10.1093/bioinformatics/btp358, 19505944
    • Raue A, Kreutz C, Maiwald T, Bachmann J, Schilling M, Klingmueller U, Timmer J. Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. Bioinformatics 2009, 25(15):1923-1929. 10.1093/bioinformatics/btp358, 19505944.
    • (2009) Bioinformatics , vol.25 , Issue.15 , pp. 1923-1929
    • Raue, A.1    Kreutz, C.2    Maiwald, T.3    Bachmann, J.4    Schilling, M.5    Klingmueller, U.6    Timmer, J.7
  • 21
    • 77949475400 scopus 로고    scopus 로고
    • An iterative identification procedure for dynamic modeling of biochemical networks
    • 10.1186/1752-0509-4-11, 2838808, 20163703
    • Balsa-Canto E, Alonso AA, Banga JR. An iterative identification procedure for dynamic modeling of biochemical networks. BMC Syst Biol 2010, 4:11. 10.1186/1752-0509-4-11, 2838808, 20163703.
    • (2010) BMC Syst Biol , vol.4 , pp. 11
    • Balsa-Canto, E.1    Alonso, A.A.2    Banga, J.R.3
  • 22
    • 81555207959 scopus 로고    scopus 로고
    • Structural Identifiability of Systems Biology Models: A Critical Comparison of Methods
    • 10.1371/journal.pone.0027755, 3222653, 22132135
    • Chis OT, Banga JR, Balsa-Canto E. Structural Identifiability of Systems Biology Models: A Critical Comparison of Methods. PLOS ONE 2011, 6(11):e27755. 10.1371/journal.pone.0027755, 3222653, 22132135.
    • (2011) PLOS ONE , vol.6 , Issue.11
    • Chis, O.T.1    Banga, J.R.2    Balsa-Canto, E.3
  • 23
    • 79952606233 scopus 로고    scopus 로고
    • Addressing parameter identifiability by model-based experimentation
    • 10.1049/iet-syb.2010.0061, 21405200
    • Raue A, Kreutz C, Maiwald T, Klingmueller U, Timmer J. Addressing parameter identifiability by model-based experimentation. IET Syst Biol 2011, 5(2):120-U78. 10.1049/iet-syb.2010.0061, 21405200.
    • (2011) IET Syst Biol , vol.5 , Issue.2
    • Raue, A.1    Kreutz, C.2    Maiwald, T.3    Klingmueller, U.4    Timmer, J.5
  • 25
    • 84880040700 scopus 로고    scopus 로고
    • Mathematical modeling approaches for dynamical analysis of protein regulatory networks with applications to the budding yeast cell cycle and the circadian rhythm in cyanobacteria
    • Laomettachit T. Mathematical modeling approaches for dynamical analysis of protein regulatory networks with applications to the budding yeast cell cycle and the circadian rhythm in cyanobacteria. PhD thesis, Virginia Institute of Technology 2011, [http://scholar.lib.vt.edu/theses/available/etd-11072011-021528/].
    • (2011) PhD thesis, Virginia Institute of Technology
    • Laomettachit, T.1
  • 26
    • 84880046943 scopus 로고    scopus 로고
    • Budding Yeast Cell Cycle Homepage
    • Budding Yeast Cell Cycle Homepage. [http://mpf.biol.vt.edu/research/budding_yeast_model/pp/].
  • 28
    • 33846106739 scopus 로고    scopus 로고
    • Robustness and modular design of the Drosophila segment polarity network
    • Ma W, Lai L, Ouyang Q, Tang C. Robustness and modular design of the Drosophila segment polarity network. Mol Syst Biol 2006, 2:270.
    • (2006) Mol Syst Biol , vol.2 , pp. 270
    • Ma, W.1    Lai, L.2    Ouyang, Q.3    Tang, C.4
  • 29
    • 79955553550 scopus 로고    scopus 로고
    • Origin of bistability underlying mammalian cell cycle entry
    • 3101952, 21525871
    • Yao G, Tan C, West M, Nevins JR, You L. Origin of bistability underlying mammalian cell cycle entry. Mol Syst Biol 2011, 7:485. 3101952, 21525871.
    • (2011) Mol Syst Biol , vol.7 , pp. 485
    • Yao, G.1    Tan, C.2    West, M.3    Nevins, J.R.4    You, L.5
  • 30
    • 4544313613 scopus 로고    scopus 로고
    • The ups and downs of modeling the cell cycle
    • 10.1016/j.cub.2004.09.018, 15380091
    • Ingolia NT, Murray AW. The ups and downs of modeling the cell cycle. Curr Biol 2004, 14(18):R771-R777. 10.1016/j.cub.2004.09.018, 15380091.
    • (2004) Curr Biol , vol.14 , Issue.18
    • Ingolia, N.T.1    Murray, A.W.2
  • 31
    • 49449101097 scopus 로고    scopus 로고
    • High-order combination effects and biological robustness
    • 2538911, 18682705
    • Lehar J, Krueger A, Zimmermann G, Borisy A. High-order combination effects and biological robustness. Mol Syst Biol 2008, 4:215. 2538911, 18682705.
    • (2008) Mol Syst Biol , vol.4 , pp. 215
    • Lehar, J.1    Krueger, A.2    Zimmermann, G.3    Borisy, A.4
  • 32
    • 33746649199 scopus 로고    scopus 로고
    • In vivo robustness analysis of cell division cycle genes in Saccharomyces cerevisiae
    • 10.1371/journal.pgen.0020111, 1500812, 16839182
    • Moriya H, Shimizu-Yoshida Y, Kitano H. In vivo robustness analysis of cell division cycle genes in Saccharomyces cerevisiae. PLoS Genet 2006, 2(7):e111. 10.1371/journal.pgen.0020111, 1500812, 16839182.
    • (2006) PLoS Genet , vol.2 , Issue.7
    • Moriya, H.1    Shimizu-Yoshida, Y.2    Kitano, H.3
  • 33
    • 34547131083 scopus 로고    scopus 로고
    • Phosphorylation of the Sic1 inhibitor of B-type cyclins in Saccharomyces cerevisiae is not essential but contributes to cell cycle robustness
    • 10.1534/genetics.107.073494, 1931548, 17483408
    • Cross FR, Schroeder L, Bean JM. Phosphorylation of the Sic1 inhibitor of B-type cyclins in Saccharomyces cerevisiae is not essential but contributes to cell cycle robustness. Genetics 2007, 176(3):1541-1555. 10.1534/genetics.107.073494, 1931548, 17483408.
    • (2007) Genetics , vol.176 , Issue.3 , pp. 1541-1555
    • Cross, F.R.1    Schroeder, L.2    Bean, J.M.3
  • 34
    • 39749151575 scopus 로고    scopus 로고
    • Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle
    • Panning TD, Watson LT, Allen NA, Chen KC, Shaffer CA, Tyson JJ. Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle. J Global Optim 2008, 40(4):719-738.
    • (2008) J Global Optim , vol.40 , Issue.4 , pp. 719-738
    • Panning, T.D.1    Watson, L.T.2    Allen, N.A.3    Chen, K.C.4    Shaffer, C.A.5    Tyson, J.J.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.