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Volumn 13, Issue 1, 2012, Pages 3-31

The evolution of higher-level biochemical reaction models

Author keywords

Biochemical modeling; Genetic programming; Grammar guided; Process algebra; Statistical features; Time series

Indexed keywords

BIOCHEMICAL PHENOMENA; BIOCHEMICAL REACTIONS; CANDIDATE SOLUTION; COMPLEX REACTIONS; COMPUTATIONAL TOOLS; FITNESS EVALUATIONS; FORMAL MODELING; GENETIC PROGRAMMING SYSTEM; GENETIC PROGRAMS; GRAMMAR-GUIDED; PROCESS ALGEBRAS; PROGRAMMING INTERFACE; STATISTICAL FEATURES; THEORETICAL COMPUTER SCIENCE;

EID: 84861100278     PISSN: 13892576     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10710-011-9144-3     Document Type: Article
Times cited : (2)

References (79)
  • 1
    • 0036749170 scopus 로고    scopus 로고
    • Evolutionary modeling and inference of gene network
    • DOI 10.1016/S0020-0255(02)00235-9, PII S0020025502002359
    • S. Ando, E. Sakamoto, H. Iba, Evolutionary modeling and inference of gene network. Inf. Sci. 145(3-4), 237-259 (2002) (Pubitemid 35152041)
    • (2002) Information Sciences , vol.145 , Issue.3-4 , pp. 237-259
    • Ando, S.1    Sakamoto, E.2    Iba, H.3
  • 3
    • 78649903919 scopus 로고    scopus 로고
    • Petri nets for modelling metabolic pathways: A survey
    • P. Baldan, N. Cocco, A. Marin, M. Simeoni, Petri nets for modelling metabolic pathways: a survey. Nat. Comput. 9(4), 955-989 (2010)
    • (2010) Nat. Comput. , vol.9 , Issue.4 , pp. 955-989
    • Baldan, P.1    Cocco, N.2    Marin, A.3    Simeoni, M.4
  • 4
    • 23144460685 scopus 로고    scopus 로고
    • ed. by R. Riolo, B. Worzel. Artificial Regulatory Networks and Genetic Programming Kluwer, Dordrecht
    • W. Banzhaf, in Genetic Programming Theory and Practice, ed. by R. Riolo, B. Worzel. Artificial Regulatory Networks and Genetic Programming (Kluwer, Dordrecht, 2003), pp. 43-61.
    • (2003) Genetic Programming Theory and Practice , pp. 43-61
    • Banzhaf, W.1
  • 5
    • 84861096385 scopus 로고    scopus 로고
    • ed. by P.K. Chawdhry et al. Finding Acceptable Solutions in the Pareto-Optimal Range Using Multiobjective Genetic Algorithms Springer, Berlin
    • P. Bentley, J. Wakefield, in Soft Computing in Engineering Design and Manufacturing, ed. by P.K. Chawdhry et al. Finding Acceptable Solutions in the Pareto-Optimal Range Using Multiobjective Genetic Algorithms (Springer, Berlin, 1997)
    • (1997) Soft Computing in Engineering Design and Manufacturing
    • Bentley, P.1    Wakefield, J.2
  • 6
    • 84861097148 scopus 로고    scopus 로고
    • BioSPI: The biospi project Last accessed July 9 2010
    • BioSPI: The biospi project (2010). http://www.wisdom.weizmann.ac.il/ biospi. Last accessed July 9, 2010
    • (2010)
  • 11
    • 72749112070 scopus 로고    scopus 로고
    • ed. by A.I. Esparcia et al. Learning Regulation Functions of Metabolic Systems by Artificial Neural Networks ACM Press, New york
    • A. Castellini, V. Manca, in Proceedings of the GECCO 2009, ed. by A.I. Esparcia et al. Learning Regulation Functions of Metabolic Systems by Artificial Neural Networks (ACM Press, New york, 2009), pp. 193-200
    • (2009) Proceedings of the GECCO 2009 , pp. 193-200
    • Castellini, A.1    Manca, V.2
  • 12
    • 34548302044 scopus 로고    scopus 로고
    • Petri net modelling of biological networks
    • C. Chaoulya, Petri net modelling of biological networks. Brief Bioinform 8(4), 210-219 (2007)
    • (2007) Brief Bioinform , vol.8 , Issue.4 , pp. 210-219
    • Chaoulya, C.1
  • 13
    • 33745616528 scopus 로고    scopus 로고
    • Identification of biochemical networks by S-tree based genetic programming
    • D.Y. Cho, K.H. Cho, B.T. Zhang, Identification of biochemical networks by S-tree based genetic programming. Bioinformatics 22(13), 1631-1640 (2006)
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1631-1640
    • Cho, D.Y.1    Cho, K.H.2    Zhang, B.T.3
  • 14
    • 65649102679 scopus 로고    scopus 로고
    • Recent developments in parameter estimation and structure identification of biochemical and genomic systems
    • I. Chou, E. Voit, Recent developments in parameter estimation and structure identification of biochemical and genomic systems. Math. Biosci. 219, 57-83 (2009)
    • (2009) Math. Biosci. , vol.219 , pp. 57-83
    • Chou, I.1    Voit, E.2
  • 15
    • 55749101417 scopus 로고    scopus 로고
    • ed. by D. Srinivasan, L. Wang. Evolving Genetic Regulatory Networks for Systems Biology IEEE Press, Singapore
    • D. Chu, in Proceedings of the CEC 2007, ed. by D. Srinivasan, L. Wang. Evolving Genetic Regulatory Networks for Systems Biology (IEEE Press, Singapore, 2007), pp. 875-882
    • (2007) Proceedings of the CEC 2007 , pp. 875-882
    • Chu, D.1
  • 19
    • 45749111042 scopus 로고    scopus 로고
    • ed. by M. Bernardo, P. Degano, G. Zavattaro. The BlenX Language: A Tutorial. LNCS 5016 Springer, Berline
    • L. Dematte, C. Priami, A. Romanel, in SFM 2008, ed. by M. Bernardo, P. Degano, G. Zavattaro. The BlenX Language: A Tutorial. LNCS 5016 (Springer, Berline, 2008), pp. 313-365
    • (2008) SFM 2008 , pp. 313-365
    • Dematte, L.1    Priami, C.2    Romanel, A.3
  • 22
    • 0027415226 scopus 로고
    • Cellular automata approaches to biological modeling
    • G. Ermentrout, L. Edelstein-Keshet, Cellular automata approaches to biological modeling. J. Theor. Biol. 160, 97-133 (1993)
    • (1993) J. Theor. Biol. , vol.160 , pp. 97-133
    • Ermentrout, G.1    Edelstein-Keshet, L.2
  • 23
    • 36049044199 scopus 로고    scopus 로고
    • Executable cell biology
    • DOI 10.1038/nbt1356, PII NBT1356
    • J. Fisher, T. Henzinger, Executable cell biology. Nat. Biotechnol. 25(11), 1239-1249 (2007) (Pubitemid 350089829)
    • (2007) Nature Biotechnology , vol.25 , Issue.11 , pp. 1239-1249
    • Fisher, J.1    Henzinger, T.A.2
  • 25
    • 0033707946 scopus 로고    scopus 로고
    • Using Bayesian networks to analyze expression data
    • N. Friedman, M. Linial, I. Nachman, D. Pe'er, Using Bayesian networks to analyze expression data. J. Comput. Biol. 7(3-4), 601-620 (2000)
    • (2000) J. Comput. Biol. , vol.7 , Issue.3-4 , pp. 601-620
    • Friedman, N.1    Linial, M.2    Nachman, I.3    Pe'er, D.4
  • 26
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • D. Gillespie, Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem 81, 2340-2361 (1977)
    • (1977) J. Phys. Chem , vol.81 , pp. 2340-2361
    • Gillespie, D.1
  • 29
    • 61349180117 scopus 로고    scopus 로고
    • Gene regulatory network inference: Data integration in dynamic models-A review
    • M. Hecker, S. Lambeck, S. Toepfer, van E. Someren, R. Guthke, Gene regulatory network inference: data integration in dynamic models-a review. Biosystems 96(1), 86-103 (2009)
    • (2009) Biosystems , vol.96 , Issue.1 , pp. 86-103
    • Hecker, M.1    Lambeck, S.2    Toepfer, S.3    Van Someren, E.4    Guthke, R.5
  • 31
    • 0344464762 scopus 로고    scopus 로고
    • Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks
    • DOI 10.1093/bioinformatics/btg313
    • D. Husmeier, Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks. Bioinformatics 19(17), 2271-2282 (2003) (Pubitemid 37483983)
    • (2003) Bioinformatics , vol.19 , Issue.17 , pp. 2271-2282
    • Husmeier, D.1
  • 33
    • 84861100915 scopus 로고    scopus 로고
    • Evolutionary synthesis of stochastic gene network models using feature-based search spaces
    • in press
    • J. Imada, B. Ross, Evolutionary synthesis of stochastic gene network models using feature-based search spaces. New Generation Computing (2010, in press)
    • (2010) New Generation Computing
    • Imada, J.1    Ross, B.2
  • 34
    • 84861101294 scopus 로고    scopus 로고
    • INRIA: OCAML Last accessed July 1 2010
    • INRIA: OCAML (2010). http://caml.inria.fr/ocaml/. Last accessed July 1, 2010
    • (2010)
  • 35
    • 21044438483 scopus 로고    scopus 로고
    • Evolutionary optimization in uncertain environments - A survey
    • DOI 10.1109/TEVC.2005.846356
    • Y. Jin, J. Branke, Evolutionary optimization in uncertain environments-a survey. IEEE Trans. Evol. Comput. 9(3), 303-317 (2005) (Pubitemid 40871134)
    • (2005) IEEE Transactions on Evolutionary Computation , vol.9 , Issue.3 , pp. 303-317
    • Jin, Y.1    Branke, J.2
  • 36
    • 84861100916 scopus 로고    scopus 로고
    • Last accessed July 12 2011
    • O. Kahramanogullari, Pim-spim (2010). http://sites.google.com/site/ ozankahramanogullari/software/pim. Last accessed July 12, 2011
    • (2010) Pim-spim
    • Kahramanogullari, O.1
  • 37
    • 84861096481 scopus 로고    scopus 로고
    • ed. by S.B. Cooper, V. Danos. An Intuitive Automated Modelling Interface for Systems Biology EPTCS
    • O. Kahramanogullari, L. Cardelli, in DCM'09, ed. by S.B. Cooper, V. Danos. An Intuitive Automated Modelling Interface for Systems Biology (EPTCS, 2009), pp. 1-18
    • (2009) DCM'09 , pp. 1-18
    • Kahramanogullari, O.1    Cardelli, L.2
  • 38
    • 0037461033 scopus 로고    scopus 로고
    • Dynamics modeling of genetic networks using genetic algorithm and S-system
    • DOI 10.1093/bioinformatics/btg027
    • S. Kikuchi, D. Tominaga, M. Arita, K. Takahashi, M. Tomita, Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics 19(5), 643-650 (2003) (Pubitemid 36417059)
    • (2003) Bioinformatics , vol.19 , Issue.5 , pp. 643-650
    • Kikuchi, S.1    Tominaga, D.2    Arita, M.3    Takahashi, K.4    Tomita, M.5
  • 39
    • 0344113807 scopus 로고    scopus 로고
    • Identifying metabolic pathways and gene regulation networks with evolutionary algorithms
    • G. Fogel, D. Corne (eds) Morgan Kaufmann, Los Altos
    • J. Kitagawa, H. Iba, Identifying Metabolic Pathways and Gene Regulation Networks with Evolutionary Algorithms. In: G. Fogel, D. Corne (eds) Evolutionary Computation in Bioinformatics, (Morgan Kaufmann, Los Altos, 2003) pp. 255-278.
    • (2003) Evolutionary Computation in Bioinformatics , pp. 255-278
    • Kitagawa, J.1    Iba, H.2
  • 43
    • 54849411117 scopus 로고    scopus 로고
    • Applying intelligent computing techniques to modeling biologial networks from expression data
    • W.P. Lee, K.C. Yang, Applying intelligent computing techniques to modeling biologial networks from expression data. Genomics Proteomics Bioinf. 6(2), 111-120 (2008)
    • (2008) Genomics Proteomics Bioinf. , vol.6 , Issue.2 , pp. 111-120
    • Lee, W.P.1    Yang, K.C.2
  • 45
    • 33846884998 scopus 로고    scopus 로고
    • Evolving fuzzy rules to model gene expression
    • DOI 10.1016/j.biosystems.2006.04.006, PII S0303264706000864
    • R. Linden, A. Bhaya, Evolving fuzzy rules to model gene expression. Biosystems 88(1-2), 76-91 (2007) (Pubitemid 46217904)
    • (2007) BioSystems , vol.88 , Issue.1-2 , pp. 76-91
    • Linden, R.1    Bhaya, A.2
  • 48
    • 38449088751 scopus 로고    scopus 로고
    • Inferring cellular networks-A review
    • F. Markowetz, R. Spang, Inferring cellular networks-a review. BMC Bioinf. 8, 1-17 (2007)
    • (2007) BMC Bioinf. , vol.8 , pp. 1-17
    • Markowetz, F.1    Spang, R.2
  • 50
    • 35048848525 scopus 로고    scopus 로고
    • ed. by K. Deb et al. Systems Biology Modeling in Human Genetic Using Petri Nets and Grammatical Evolution. LNCS 3102 Springer, Berlin
    • J. Moore, L. Hahn, In: Proceeding of the GECCO 2004, ed. by K. Deb et al. Systems Biology Modeling in Human Genetic Using Petri Nets and Grammatical Evolution. LNCS 3102 (Springer, Berlin, 2004), pp. 392-401
    • (2004) Proceeding of the GECCO 2004 , pp. 392-401
    • Moore, J.1    Hahn, L.2
  • 51
    • 33744973448 scopus 로고    scopus 로고
    • ed. by N. Mastorakis, S.D. Nikolopoulos. Feature-Based Classification of Time-Series Data. Nova Science Publishers, Inc., Commack
    • A. Nanopoulos, R. Alcock, Y. Manolopoulos, in Information Processing and Technology, ed. by N. Mastorakis, S.D. Nikolopoulos. Feature-Based Classification of Time-Series Data. (Nova Science Publishers, Inc., Commack, 2001), pp. 49-61
    • (2001) Information Processing and Technology , pp. 49-61
    • Nanopoulos, A.1    Alcock, R.2    Manolopoulos, Y.3
  • 53
    • 32444451211 scopus 로고    scopus 로고
    • ed. by H.-G. Beyer et al. Evolving Petri Nets to Represent Metabolic Pathways ACM, New York
    • J. Nummela, B. Julstrom, in Proceedings of the GECCO 2005, ed. by H.-G. Beyer et al. Evolving Petri Nets to Represent Metabolic Pathways (ACM, New York, 2005), pp. 2133-2139
    • (2005) Proceedings of the GECCO 2005 , pp. 2133-2139
    • Nummela, J.1    Julstrom, B.2
  • 57
    • 38049104446 scopus 로고    scopus 로고
    • Last accessed Dec 9, 2008
    • A. Phillips, The stochastic pi machine (2008). http://research.microsoft. com/aphillip/spim. Last accessed Dec 9, 2008
    • (2008) The Stochastic Pi Machine
    • Phillips, A.1
  • 59
    • 84974715948 scopus 로고
    • Stochastic pi-calculus
    • C. Priami, Stochastic pi-calculus. Comput. J. 38(7), 579-589 (1995)
    • (1995) Comput. J. , vol.38 , Issue.7 , pp. 579-589
    • Priami, C.1
  • 60
    • 46649107949 scopus 로고    scopus 로고
    • Inference of noisy nonlinear differential equation models for gene regulatory networks using genetic programming and kalman filtering
    • L. Qian, H. Wang, E. Dougherty, Inference of noisy nonlinear differential equation models for gene regulatory networks using genetic programming and kalman filtering. IEEE Trans. Signal Process. 56(7), 3327-3339 (2008)
    • (2008) IEEE Trans. Signal Process. , vol.56 , Issue.7 , pp. 3327-3339
    • Qian, L.1    Wang, H.2    Dougherty, E.3
  • 61
    • 53549123008 scopus 로고    scopus 로고
    • Nature, nurture, or chance: Stochastic gene expression and its consequences
    • A. Raj, A. van Oudenaarden, Nature, nurture, or chance: stochastic gene expression and its consequences. Cell 135, 216-226 (2008)
    • (2008) Cell , vol.135 , pp. 216-226
    • Raj, A.1    Van Oudenaarden, A.2
  • 63
    • 21844459472 scopus 로고    scopus 로고
    • Evolution of mathematical models of chaotic systems based on multiobjective genetic programming
    • DOI 10.1007/s10115-004-0184-3
    • K. Rodriguez-Vazquez, P.J. Fleming, Evolution of mathematical models of chaotic systems based on multiobjective genetic programming. Knowl. Inf. Syst. 8(2), 235-256 (2005) (Pubitemid 40951992)
    • (2005) Knowledge and Information Systems , vol.8 , Issue.2 , pp. 235-256
    • Rodriguez-Vazquez, K.1    Fleming, P.J.2
  • 64
    • 0034804539 scopus 로고    scopus 로고
    • Logic-based genetic programming with definite clause translation grammars
    • B. Ross, Logic-based genetic programming with definite clause translation grammars. New Gener. Comput. 19(4), 313-337 (2001) (Pubitemid 32933468)
    • (2001) New Generation Computing , vol.19 , Issue.4 , pp. 313-337
    • Ross, B.J.1
  • 65
    • 84861097145 scopus 로고    scopus 로고
    • ed. by R. Andonie. Using Genetic Programming to Synthesize Monotonic Stochastic Processes ACTA Press
    • B. Ross, in Proceedings CI-2007, ed. by R. Andonie. Using Genetic Programming to Synthesize Monotonic Stochastic Processes (ACTA Press, 2007)
    • (2007) Proceedings CI-2007
    • Ross, B.1
  • 68
    • 84861099034 scopus 로고    scopus 로고
    • ed. by R. Riolo et al. Using Multiobjective Genetic Programming to Synthesize Stochastic Processes Springer
    • B. Ross, J. Imada, in Genetic Programming-Theory and Practice, ed. by R. Riolo et al. Using Multiobjective Genetic Programming to Synthesize Stochastic Processes (Springer, 2009)
    • (2009) Genetic Programming-Theory and Practice
    • Ross, B.1    Imada, J.2
  • 72
    • 84861101293 scopus 로고    scopus 로고
    • SICS: SICStus Prolog 4 Last accessed July 1 2010
    • SICS: SICStus Prolog 4 (2010). http://www.sics.se/isl/sicstuswww/site/ index.htm. Last accessed July 1, 2010.
    • (2010)
  • 74
  • 76
    • 33749012790 scopus 로고    scopus 로고
    • Characteristic-based clustering for time series data
    • DOI 10.1007/s10618-005-0039-x
    • X. Wang, K. Smith, R. Hyndman, Characteristic-based clustering for time series data. Data Min. Knowl. Discov. 13(3), 335-364. (2006). doi:10.1007/s10618-005-0039-x (Pubitemid 44455024)
    • (2006) Data Mining and Knowledge Discovery , vol.13 , Issue.3 , pp. 335-364
    • Wang, X.1    Smith, K.2    Hyndman, R.3
  • 77
    • 84861100913 scopus 로고    scopus 로고
    • Last accessed July 2 2010
    • Wikipedia: Phagocytosis (2010). http://en.wikipedia.org/wiki/Phagocytosi. Last accessed July 2, 2010
    • (2010) Wikipedia: Phagocytosis
  • 78
    • 12344259602 scopus 로고    scopus 로고
    • Advances to Bayesian network inference for generating causal networks from observational biological data
    • DOI 10.1093/bioinformatics/bth448
    • J. Yu, V. Smith, P. Wang, A. Hartemink, E. Jarvis, Advances to Bayesian network inference for generating causal networks from observational biological data. Bioinformatics 20(18), 3594-3603 (2004) (Pubitemid 40136795)
    • (2004) Bioinformatics , vol.20 , Issue.18 , pp. 3594-3603
    • Yu, J.1    Smith, V.A.2    Wang, P.P.3    Hartemink, A.J.4    Jarvis, E.D.5


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