메뉴 건너뛰기




Volumn 31, Issue 18, 2015, Pages 2999-3007

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BACTERIUM; BIOLOGICAL MODEL; COMPUTER SIMULATION; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; HUMAN; LIVER TUMOR; LOGIC; PROCEDURES; SIGNAL TRANSDUCTION; STANDARDS; STATISTICAL MODEL; SYSTEMS BIOLOGY;

EID: 84941769665     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btv314     Document Type: Article
Times cited : (21)

References (46)
  • 1
    • 0032616683 scopus 로고    scopus 로고
    • Identification of genetic networks from a small number of gene expression patterns under the Boolean network model
    • Akutsu, T. et al. (1999) Identification of genetic networks from a small number of gene expression patterns under the Boolean network model. Pac. Symp. Biocomput., 5, 17-28.
    • (1999) Pac. Symp. Biocomput , vol.5 , pp. 17-28
    • Akutsu, T.1
  • 2
    • 84906242439 scopus 로고    scopus 로고
    • Boolean modeling: A logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions
    • Wiley Interdisc
    • Albert, R. and Thakar, J. (2014) Boolean modeling: a logic-based dynamic approach for understanding signaling and regulatory networks and for making useful predictions. Wiley Interdisc. Rev. Syst. Biol. Med., 6, 353-369.
    • (2014) Rev. Syst. Biol. Med. , vol.6 , pp. 353-369
    • Albert, R.1    Thakar, J.2
  • 3
    • 65349179556 scopus 로고    scopus 로고
    • Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/Insulin-induced signaling
    • Aldridge, B. B. et al. (2009) Fuzzy logic analysis of kinase pathway crosstalk in TNF/EGF/Insulin-induced signaling. PLoS Comput. Biol., 5, e1000340.
    • (2009) PLoS Comput. Biol , vol.5 , pp. e1000340
    • Aldridge, B.B.1
  • 4
    • 77956554551 scopus 로고    scopus 로고
    • Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes
    • Alexopoulos, L. G. et al. (2010) Networks inferred from biochemical data reveal profound differences in toll-like receptor and inflammatory signaling between normal and transformed hepatocytes. Mol. Cell Proteomics, 9, 1849-1865.
    • (2010) Mol. Cell Proteomics , vol.9 , pp. 1849-1865
    • Alexopoulos, L.G.1
  • 5
    • 79961185589 scopus 로고    scopus 로고
    • AMIGO, a toolbox for advanced model identification in systems biology using global optimization
    • Balsa-Canto, E. and Banga, J. R. (2011) AMIGO, a toolbox for advanced model identification in systems biology using global optimization. Bioinformatics, 27, 2311-2313.
    • (2011) Bioinformatics , vol.27 , pp. 2311-2313
    • Balsa-Canto, E.1    Banga, J.R.2
  • 6
    • 46349105936 scopus 로고    scopus 로고
    • Optimization in computational systems biology
    • Banga, J. R. (2008) Optimization in computational systems biology. BMC Syst. Biol., 2, 47.
    • (2008) BMC Syst. Biol , vol.2 , pp. 47
    • Banga, J.R.1
  • 7
    • 18244399035 scopus 로고    scopus 로고
    • Global optimization of bioprocesses using stochastic and hybrid methods
    • Floudas C. A. and Pardalos, P. (eds. ) kluwer academic publishers, norwell, MA
    • Banga, J. R. et al. (2004) Global optimization of bioprocesses using stochastic and hybrid methods. In: Floudas, C. A. and Pardalos, P. (eds. ) Frontiers in global optimization. kluwer academic publishers, norwell, MA, pp. 45-70.
    • (2004) Frontiers in Global Optimization , pp. 45-70
    • Banga, J.R.1
  • 8
    • 84907588582 scopus 로고    scopus 로고
    • Data-derived modeling characterizes plasticity of MAPK signaling in melanoma
    • Bernardo-Faura, M. et al. (2014) Data-derived modeling characterizes plasticity of MAPK signaling in melanoma. PLoS Comput. Biol., 10, e1003795.
    • (2014) PLoS Comput. Biol. , vol.10 , pp. e1003795
    • Bernardo-Faura, M.1
  • 9
  • 10
    • 84869219619 scopus 로고    scopus 로고
    • Logic modeling and the ridiculome under the rug
    • Blinov, M. and Moraru, I. (2012) Logic modeling and the ridiculome under the rug. BMC Biol., 10, 92.
    • (2012) BMC Biol. , vol.10 , pp. 92
    • Blinov, M.1    Moraru, I.2
  • 11
    • 33747813561 scopus 로고    scopus 로고
    • The inferelator: An algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo
    • Bonneau, R. et al. (2006) The inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo. Genome Biol., 7, R36.
    • (2006) Genome Biol , vol.7 , pp. R36
    • Bonneau, R.1
  • 12
    • 24944488392 scopus 로고    scopus 로고
    • Global mixed-integer dynamic optimization
    • Chachuat, B. et al. (2005) Global mixed-integer dynamic optimization. AIChE J., 51, 2235-2253.
    • (2005) AIChE J , vol.51 , pp. 2235-2253
    • Chachuat, B.1
  • 14
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: A literature review
    • de Jong, H. (2002) Modeling and simulation of genetic regulatory systems: a literature review. J. Comput. Biol. J. Comput. Mol. Cell Biol., 9, 67-103.
    • (2002) J. Comput. Biol. J. Comput. Mol. Cell Biol , vol.9 , pp. 67-103
    • De Jong, H.1
  • 15
    • 69549124230 scopus 로고    scopus 로고
    • An evolutionary method for complex-process optimization
    • Egea, J. A. et al. (2010) An evolutionary method for complex-process optimization. Comput. Oper. Res., 37, 315-324.
    • (2010) Comput. Oper. Res. , vol.37 , pp. 315-324
    • Egea, J.A.1
  • 16
    • 44349104095 scopus 로고    scopus 로고
    • A TABU search-based algorithm for mixed-integer nonlinear problems and its application to integrated process and control system design
    • Exler, O. et al. (2008) A TABU search-based algorithm for mixed-integer nonlinear problems and its application to integrated process and control system design. Comput. Chem. Eng., 32, 1877-1891.
    • (2008) Comput. Chem. Eng , vol.32 , pp. 1877-1891
    • Exler, O.1
  • 17
    • 84869237089 scopus 로고    scopus 로고
    • A comparative study of sqp-type algorithms for nonlinear and nonconvex mixed-integer optimization
    • Exler, O. et al. (2012) A comparative study of sqp-type algorithms for nonlinear and nonconvex mixed-integer optimization. Math. Program. Comput., 4, 383-412.
    • (2012) Math. Program. Comput. , vol.4 , pp. 383-412
    • Exler, O.1
  • 19
    • 2342517433 scopus 로고    scopus 로고
    • Part II. Future perspective on optimization
    • Grossmann, I. E. and Biegler, L. T. (2004) Part II. Future perspective on optimization. Comput. Chem. Eng., 28, 1193-1218.
    • (2004) Comput. Chem. Eng , vol.28 , pp. 1193-1218
    • Grossmann, I.E.1    Biegler, L.T.2
  • 20
    • 84886735391 scopus 로고    scopus 로고
    • Identification of regulatory structure and kinetic parameters of biochemical networks via mixed-integer dynamic optimization
    • Guillén-Gosálbez, G. et al. (2013) Identification of regulatory structure and kinetic parameters of biochemical networks via mixed-integer dynamic optimization. BMC Syst. Biol., 7, 113.
    • (2013) BMC Syst. Biol. , vol.7 , pp. 113
    • Guillén-Gosálbez, G.1
  • 21
    • 77149153391 scopus 로고    scopus 로고
    • The complexity of the simple two-component system KdpD/KdpE in Escherichia coli
    • Heermann, R. and Jung, K. (2010) The complexity of the simple two-component system KdpD/KdpE in Escherichia coli. FEMS Microbiol. Lett., 304, 97-106.
    • (2010) FEMS Microbiol. Lett. , vol.304 , pp. 97-106
    • Heermann, R.1    Jung, K.2
  • 22
    • 84904210610 scopus 로고    scopus 로고
    • Branch-and-lift algorithm for deterministic global optimization in nonlinear optimal control
    • Houska, B. and Chachuat, B. (2014) Branch-and-lift algorithm for deterministic global optimization in nonlinear optimal control. J. Optim. Theory Appl., 162, 208-248.
    • (2014) J. Optim. Theory Appl. , vol.162 , pp. 208-248
    • Houska, B.1    Chachuat, B.2
  • 23
    • 84861826804 scopus 로고    scopus 로고
    • Histidine kinases and response regulators in networks
    • Jung, K. et al. (2012) Histidine kinases and response regulators in networks. Curr. Opin. Microbiol., 15, 118-124.
    • (2012) Curr. Opin. Microbiol. , vol.15 , pp. 118-124
    • Jung, K.1
  • 24
    • 0014489272 scopus 로고
    • Metabolic stability and epigenesis in randomly constructed genetic nets
    • Kauffman, S. A. (1969) Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol., 22, 437-467.
    • (1969) J. Theor. Biol , vol.22 , pp. 437-467
    • Kauffman, S.A.1
  • 25
    • 77951962279 scopus 로고    scopus 로고
    • Odefy-from discrete to continuous models
    • Krumsiek, J. et al. (2010) Odefy-from discrete to continuous models. BMC Bioinformatics, 11, 233.
    • (2010) BMC Bioinformatics , vol.11 , pp. 233
    • Krumsiek, J.1
  • 26
    • 34948840834 scopus 로고    scopus 로고
    • Ensemble modeling for analysis of cell signaling dynamics
    • Kuepfer, L. et al. (2007) Ensemble modeling for analysis of cell signaling dynamics. Nat. Biotechnol., 25, 1001-1006.
    • (2007) Nat. Biotechnol , vol.25 , pp. 1001-1006
    • Kuepfer, L.1
  • 27
    • 84879029281 scopus 로고    scopus 로고
    • The sensor kinase KdpD of Escherichia coli senses external K\+
    • Laermann, V. et al. (2013) The sensor kinase KdpD of Escherichia coli senses external K\+. Mol. Microbiol., 88, 1194-1204.
    • (2013) Mol. Microbiol. , vol.88 , pp. 1194-1204
    • Laermann, V.1
  • 29
    • 84864952677 scopus 로고    scopus 로고
    • State-time spectrum of signal transduction logic models
    • MacNamara, A. et al. (2012) State-time spectrum of signal transduction logic models. Phys. Biol., 9, 045003.
    • (2012) Phys. Biol. , vol.9 , pp. 045003
    • MacNamara, A.1
  • 30
    • 33646346114 scopus 로고    scopus 로고
    • A method for the generation of standardized qualitative dynamical systems of regulatory networks
    • Mendoza, L. and Xenarios, I. (2006) A method for the generation of standardized qualitative dynamical systems of regulatory networks. Theor. Biol. Med. Model, 3, 13.
    • (2006) Theor. Biol. Med. Model , vol.3 , pp. 13
    • Mendoza, L.1    Xenarios, I.2
  • 31
    • 0242574982 scopus 로고    scopus 로고
    • Parameter estimation in biochemical pathways: A comparison of global optimization methods
    • Moles, C. G. et al. (2003) Parameter estimation in biochemical pathways: a comparison of global optimization methods. Genome Res., 13, 2467-2474.
    • (2003) Genome Res , vol.13 , pp. 2467-2474
    • Moles, C.G.1
  • 32
    • 79953668247 scopus 로고    scopus 로고
    • Training signaling pathway maps to biochemical data with constrained fuzzy logic: Quantitative analysis of liver cell responses to inflammatory stimuli
    • Morris, M. K. et al. (2011) Training signaling pathway maps to biochemical data with constrained fuzzy logic: quantitative analysis of liver cell responses to inflammatory stimuli. PLoS Comput. Biol., 7, e1001099.
    • (2011) PLoS Comput. Biol. , vol.7 , pp. e1001099
    • Morris, M.K.1
  • 33
    • 32044474451 scopus 로고    scopus 로고
    • A hybrid approach for efficient and robust parameter estimation in biochemical pathways
    • Rodriguez-Fernandez, M. et al. (2006a). A hybrid approach for efficient and robust parameter estimation in biochemical pathways. Biosystems, 83, 248-265.
    • (2006) Biosystems , vol.83 , pp. 248-265
    • Rodriguez-Fernandez, M.1
  • 34
    • 33751423943 scopus 로고    scopus 로고
    • Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems
    • Rodriguez-Fernandez, M. et al. (2006b). Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems. BMC Bioinformatics, 7, 483.
    • (2006) BMC Bioinformatics , vol.7 , pp. 483
    • Rodriguez-Fernandez, M.1
  • 35
    • 84881269024 scopus 로고    scopus 로고
    • Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems
    • Rodriguez-Fernandez, M. et al. (2013) Simultaneous model discrimination and parameter estimation in dynamic models of cellular systems. BMC Syst. Biol., 7, 76.
    • (2013) BMC Syst. Biol. , vol.7 , pp. 76
    • Rodriguez-Fernandez, M.1
  • 36
    • 71449120701 scopus 로고    scopus 로고
    • Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction
    • Saez-Rodriguez, J. et al. (2009) Discrete logic modelling as a means to link protein signalling networks with functional analysis of mammalian signal transduction. Mol. Syst. Biol., 5, 331.
    • (2009) Mol. Syst. Biol , vol.5 , pp. 331
    • Saez-Rodriguez, J.1
  • 37
    • 84879452903 scopus 로고    scopus 로고
    • Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks
    • Samaga, R. and Klamt, S. (2013) Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks. Cell Commun. Signal, 11, 43.
    • (2013) Cell Commun. Signal , vol.11 , pp. 43
    • Samaga, R.1    Klamt, S.2
  • 38
    • 84864932570 scopus 로고    scopus 로고
    • More: Mixed optimization for reverse engineering-an application to modeling biological networks response via sparse systems of nonlinear differential equations
    • Sambo, F. et al. (2012) More: Mixed optimization for reverse engineering-an application to modeling biological networks response via sparse systems of nonlinear differential equations. IEEE/ACM Trans. Comput. Biol. Bioinf., 9, 1459-1471
    • (2012) IEEE/ACM Trans. Comput. Biol. Bioinf. , vol.9 , pp. 1459-1471
    • Sambo, F.1
  • 39
    • 57649176899 scopus 로고    scopus 로고
    • Extended ant colony optimization for non-convex mixed integer nonlinear programming
    • Schlü ter, M. et al. (2009) Extended ant colony optimization for non-convex mixed integer nonlinear programming. Comput. Oper. Res., 36, 2217-2229.
    • (2009) Comput. Oper. Res. , vol.36 , pp. 2217-2229
    • Schlü Ter, M.1
  • 40
    • 84941794373 scopus 로고    scopus 로고
    • Stochastic global optimization: Stopping rules
    • Floudas C. A. and Pardalos, P. (eds) Springer, NY, US
    • Schoen, F. (2009) Stochastic global optimization: stopping rules. In: Floudas, C. A. and Pardalos, P. (eds. ) Encyclopedia of Optimization. Springer, NY, US, pp. 3743-3746.
    • (2009) Encyclopedia of Optimization , pp. 3743-3746
    • Schoen, F.1
  • 42
    • 84897389995 scopus 로고    scopus 로고
    • Assessment of network inference methods: How to cope with an underdetermined problem
    • Siegenthaler, C. and Gunawan, R. (2014) Assessment of network inference methods: how to cope with an underdetermined problem. PloS One, 9, e90481.
    • (2014) PloS One , vol.9 , pp. e90481
    • Siegenthaler, C.1    Gunawan, R.2
  • 43
    • 84855997910 scopus 로고    scopus 로고
    • Inference of complex biological networks: Distinguishability issues and optimization-based solutions
    • Szederkényi, G. et al. (2011) Inference of complex biological networks: distinguishability issues and optimization-based solutions. BMC Syst. Biol., 5, 177.
    • (2011) BMC Syst. Biol. , vol.5 , pp. 177
    • Szederkényi, G.1
  • 44
    • 84867537553 scopus 로고    scopus 로고
    • CellNOptR: A flexible toolkit to train protein signaling networks to data using multiple logic formalisms
    • Terfve, C. et al. (2012) CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Syst. Biol., 6, 133.
    • (2012) BMC Syst. Biol. , vol.6 , pp. 133
    • Terfve, C.1
  • 45
    • 84891892050 scopus 로고    scopus 로고
    • Reverse engineering and identification in systems biology: Strategies, perspectives and challenges
    • Villaverde, A. F. and Banga, J. R. (2014) Reverse engineering and identification in systems biology: strategies, perspectives and challenges. J. R. Soc. Interface, 11, 20130505.
    • (2014) J. R. Soc. Interface , vol.11 , pp. 20130505
    • Villaverde, A.F.1    Banga, J.R.2
  • 46
    • 70449481350 scopus 로고    scopus 로고
    • Transforming boolean models to continuous models: Methodology and application to t-cell receptor signaling
    • Wittmann, D. M. et al. (2009) Transforming boolean models to continuous models: methodology and application to t-cell receptor signaling. BMC Syst. Biol., 3, 98.
    • (2009) BMC Syst. Biol , vol.3 , pp. 98
    • Wittmann, D.M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.