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Volumn , Issue 9783540888680, 2009, Pages 367-389

Understanding network behavior by structured representations of transition invariants: A petri net perspective on systems and synthetic biology

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EID: 85014438978     PISSN: 16197127     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-3-540-88869-7_19     Document Type: Article
Times cited : (27)

References (52)
  • 2
    • 34548302044 scopus 로고    scopus 로고
    • Petri net modelling of biological networks
    • Chaouiya C (2007) Petri net modelling of biological networks. Brief Bioinform 8(4):210-219
    • (2007) Brief Bioinform , vol.8 , Issue.4 , pp. 210-219
    • Chaouiya, C.1
  • 3
    • 85020050318 scopus 로고    scopus 로고
    • A tool for the analysis of place/transition nets
    • Charlie Website (2008) A tool for the analysis of place/transition nets. BTU Cottbus. http://www-dssz.informatik.tu-cottbus.de/software/charlie/charlie.html
    • (2008) BTU Cottbus
    • Website, C.1
  • 4
    • 0033684774 scopus 로고    scopus 로고
    • Modular analysis of Petri nets
    • Christensen S, Petrucci L (2000) Modular analysis of Petri nets. Comput J 43(3):224-242
    • (2000) Comput J , vol.43 , Issue.3 , pp. 224-242
    • Christensen, S.1    Petrucci, L.2
  • 5
    • 0001896749 scopus 로고
    • Convex geometry and semiflows in P/T nets. In: A comparative study of algorithms for computation ofminimal P-semiflows
    • Springer, Berlin
    • Colom JM, Silva M (1991) Convex geometry and semiflows in P/T nets. In: A comparative study of algorithms for computation ofminimal P-semiflows. LNCS, vol 483. Springer, Berlin, pp 79-112
    • (1991) LNCS , vol.483 , pp. 79-112
    • Colom, J.M.1    Silva, M.2
  • 9
    • 33746061326 scopus 로고    scopus 로고
    • From Petri nets to differential equations—an integrative approach for biochemical network analysis
    • Springer, Berlin
    • Gilbert D, Heiner M (2006) From Petri nets to differential equations—an integrative approach for biochemical network analysis. In: Proceedings of the ICATPN 2006. LNCS, vol 4024. Springer, Berlin, pp 181-200
    • (2006) Proceedings of the ICATPN 2006. LNCS , vol.4024 , pp. 181-200
    • Gilbert, D.1    Heiner, M.2
  • 10
    • 38049136584 scopus 로고    scopus 로고
    • A unifying framework for modelling and analysing biochemical pathways using Petri nets
    • Springer, Berlin
    • Gilbert D, Heiner M, Lehrack S (2007) A unifying framework for modelling and analysing biochemical pathways using Petri nets. In: Proceedings of the CMSB 2007. LNCS/LNBI, vol 4695. Springer, Berlin, pp 200-216
    • (2007) Proceedings of the CMSB 2007. LNCS/LNBI , vol.4695 , pp. 200-216
    • Gilbert, D.1    Heiner, M.2    Lehrack, S.3
  • 13
    • 0037342537 scopus 로고    scopus 로고
    • The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
    • Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H et al (2003) The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. J Bioinform 19:524-531
    • (2003) J Bioinform , vol.19 , pp. 524-531
    • Hucka, M.1    Finney, A.2    Sauro, H.M.3    Bolouri, H.4    Doyle, J.C.5    Kitano, H.6
  • 15
    • 27544485048 scopus 로고    scopus 로고
    • Petri net based model validation in systems biology
    • Springer, Berlin
    • Heiner M, Koch I (2004) Petri net based model validation in systems biology. In: Proceedings of the 25th ICATPN 2004. LNCS, vol 3099. Springer, Berlin, pp 216-237
    • (2004) Proceedings of the 25Th ICATPN 2004. LNCS , vol.3099 , pp. 216-237
    • Heiner, M.1    Koch, I.2
  • 16
    • 3042699469 scopus 로고    scopus 로고
    • Model validation of biological pathways using Petri nets— demonstrated for apoptosis
    • Heiner M, Koch I, Will J (2004) Model validation of biological pathways using Petri nets— demonstrated for apoptosis. Biosystems 75:15-28
    • (2004) Biosystems , vol.75 , pp. 15-28
    • Heiner, M.1    Koch, I.2    Will, J.3
  • 17
    • 0000491652 scopus 로고
    • A Petri net application of metabolic processes
    • Hofestädt R (1994) A Petri net application of metabolic processes. J Syst Anal Model Simul 16:113-122
    • (1994) J Syst Anal Model Simul , vol.16 , pp. 113-122
    • Hofestädt, R.1
  • 20
    • 16344381707 scopus 로고    scopus 로고
    • Application of Petri net theory for modeling and validation of the sucrose breakdown pathway in the potato tuber
    • Koch I, Junker BH, Heiner M (2005) Application of Petri net theory for modeling and validation of the sucrose breakdown pathway in the potato tuber. Bioinformatics 21(7):1219-1226
    • (2005) Bioinformatics , vol.21 , Issue.7 , pp. 1219-1226
    • Koch, I.1    Junker, B.H.2    Heiner, M.3
  • 21
    • 3042808208 scopus 로고    scopus 로고
    • Properties of switch-like bioregulatory networks studied by simulation of the hypoxia response control system
    • Kohn KW, Riss J, Aprelikova O, Weinstein JN, Pommier Y, Barrett JC (2004) Properties of switch-like bioregulatory networks studied by simulation of the hypoxia response control system. Mol Cell Biol 15:3042-3052
    • (2004) Mol Cell Biol , vol.15 , pp. 3042-3052
    • Kohn, K.W.1    Riss, J.2    Aprelikova, O.3    Weinstein, J.N.4    Pommier, Y.5    Barrett, J.C.6
  • 24
    • 57049175092 scopus 로고    scopus 로고
    • On inner and outer descriptions of the steady-state flux cone of a metabolic network
    • Springer, Berlin
    • Larhlimi A, Bockmayr A (2008) On inner and outer descriptions of the steady-state flux cone of a metabolic network. In: Proceedings of the CMSB 2008. LNCS/LNBI, vol 5307. Springer, Berlin, pp 308-327
    • (2008) Proceedings of the CMSB 2008. LNCS/LNBI , vol.5307 , pp. 308-327
    • Larhlimi, A.1    Bockmayr, A.2
  • 25
    • 0027370376 scopus 로고
    • GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems
    • Mendes P (1993) GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput Appl Biosci 9:563-571
    • (1993) Comput Appl Biosci , vol.9 , pp. 563-571
    • Mendes, P.1
  • 26
    • 33845569120 scopus 로고    scopus 로고
    • Petri net based descriptions for systematic understanding of biological pathways
    • Matsuno H, Li C, Miyano S (2006) Petri net based descriptions for systematic understanding of biological pathways. IEICE Trans Fundam Electron Commun Comput Sci E89-A(11):3166-3174
    • (2006) IEICE Trans Fundam Electron Commun Comput Sci , vol.E89-A , Issue.11 , pp. 3166-3174
    • Matsuno, H.1    Li, C.2    Miyano, S.3
  • 28
    • 0024645936 scopus 로고
    • Petri nets: Properties, analysis and applications
    • Murata T (1989) Petri nets: properties, analysis and applications. Proc IEEE 77 4:541-580
    • (1989) Proc IEEE , vol.77 , Issue.4 , pp. 541-580
    • Murata, T.1
  • 32
    • 57049127670 scopus 로고    scopus 로고
    • Compositional definitions of minimal flows in Petri nets
    • Springer, Berlin
    • Pedersen M (2008) Compositional definitions of minimal flows in Petri nets. In: Proceedings of the CMSB 2008. LNCS/LNBI, vol 5307. Springer, Berlin, pp 288-307
    • (2008) Proceedings of the CMSB 2008. LNCS/LNBI , vol.5307 , pp. 288-307
    • Pedersen, M.1
  • 35
    • 8544223537 scopus 로고    scopus 로고
    • Hierarchical thinking in network biology: The unbiased modularization of biochemical networks
    • Papin JA, Reed JL, Palsson PO (2004) Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. Trends Biochem Sci 29(12):641-647
    • (2004) Trends Biochem Sci , vol.29 , Issue.12 , pp. 641-647
    • Papin, J.A.1    Reed, J.L.2    Palsson, P.O.3
  • 37
    • 33645306314 scopus 로고    scopus 로고
    • Time Petri nets for modelling and analysis of biochemical networks
    • Popova-Zeugmann L, Heiner M, Koch I (2005) Time Petri nets for modelling and analysis of biochemical networks. Fundam Inform 67:149-162
    • (2005) Fundam Inform , vol.67 , pp. 149-162
    • Popova-Zeugmann, L.1    Heiner, M.2    Koch, I.3
  • 42
    • 33845417184 scopus 로고    scopus 로고
    • Application of Petri net based analysis techniques to signal transduction pathways
    • Sackmann A, Heiner M, Koch I (2006) Application of Petri net based analysis techniques to signal transduction pathways. BMC Bioinform 7:482
    • (2006) BMC Bioinform , vol.7 , pp. 482
    • Sackmann, A.1    Heiner, M.2    Koch, I.3
  • 43
  • 44
    • 0034615791 scopus 로고    scopus 로고
    • Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective
    • Schilling CH, Letscher D, Palsson BO (2000) Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. Theor Biol 203:229-248
    • (2000) Theor Biol , vol.203 , pp. 229-248
    • Schilling, C.H.1    Letscher, D.2    Palsson, B.O.3
  • 45
    • 85019976541 scopus 로고    scopus 로고
    • A tool to design and animate/simulate graphs
    • Snoopy website (2008) A tool to design and animate/simulate graphs. BTU Cottbus. http://www-dssz.informatik.tu-cottbus.de/software/snoopy.html
    • (2008) BTU Cottbus
  • 46
    • 0036188159 scopus 로고    scopus 로고
    • Exploring the pathway structure of metabolism: Decomposition into subnetworks and application to mycoplasma pneumoniae
    • Schuster S, Pfeiffer T, Moldenhauer F, Koch I, Dandekar T (2002) Exploring the pathway structure of metabolism: decomposition into subnetworks and application to mycoplasma pneumoniae. BioInformatics 18(2):351-361
    • (2002) Bioinformatics , vol.18 , Issue.2 , pp. 351-361
    • Schuster, S.1    Pfeiffer, T.2    Moldenhauer, F.3    Koch, I.4    Dandekar, T.5
  • 49
    • 0020104630 scopus 로고
    • Linear algebra algorithms for the structural analysis of Petri nets
    • (in French)
    • Toudic JM (1982) Linear algebra algorithms for the structural analysis of Petri nets. Rev Tech Thomson CSF (France) 14(1):137-156 (in French)
    • (1982) Rev Tech Thomson CSF (France) , vol.14 , Issue.1 , pp. 137-156
    • Toudic, J.M.1
  • 51
    • 34548381311 scopus 로고    scopus 로고
    • Pathway switching explains the sharp response characteristic of hypoxia response network system
    • Yu Y, Wang G, Simha R, Peng W, Turano F, Zeng C (2007) Pathway switching explains the sharp response characteristic of hypoxia response network system. PLos Comput Biol 8(3):1657-1668
    • (2007) Plos Comput Biol , vol.8 , Issue.3 , pp. 1657-1668
    • Yu, Y.1    Wang, G.2    Simha, R.3    Peng, W.4    Turano, F.5    Zeng, C.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.