메뉴 건너뛰기




Volumn , Issue , 2009, Pages 604-637

Petri nets and GRN models

Author keywords

[No Author keywords available]

Indexed keywords


EID: 84885938752     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.4018/978-1-60566-685-3.ch025     Document Type: Chapter
Times cited : (5)

References (75)
  • 1
    • 3042996554 scopus 로고    scopus 로고
    • Continuous and hybrid petri nets
    • 10.1142/S0218126698000079
    • Alla, H., & David, R. (1998). Continuous and hybrid Petri nets. Journal of Circuits, Systems, and Computers, 8(1), 159-188. doi:10.1142/S0218126698000079
    • (1998) Journal of circuits Systems, and Computers , vol.8 , Issue.1 , pp. 159-188
    • Alla, H.1    David, R.2
  • 6
    • 34548302044 scopus 로고    scopus 로고
    • Petri net modelling of biological networks
    • 10.1093/bib/bbm029
    • Chaouiya, C. (2007). Petri net modelling of biological networks. Briefings in Bioinformatics, 8(4), 210-219. doi:10.1093/bib/bbm029
    • (2007) Briefings in Bioinformatics , vol.8 , Issue.4 , pp. 210-219
    • Chaouiya, C.1
  • 7
    • 0345170901 scopus 로고    scopus 로고
    • Quantitative petri net model of gene regulated metabolic networks in the cell
    • Chen, M., & Hofestädt, R. (2003). Quantitative Petri net model of gene regulated metabolic networks in the cell. In Silico Biology, 3.
    • (2003) In Silico Biology , pp. 3
    • Chen, M.1    Hofestädt, R.2
  • 9
    • 2642527148 scopus 로고    scopus 로고
    • Genomic object net ii: How to model biopathways with hybrid functional petri net with extension
    • Doi, A., Masao Nagasaki, M., Matsuno, H., & Satoru Miyano, S. (2003). Genomic object net II: How to model biopathways with hybrid functional Petri net with extension. Applied Bioinformatics, 2(3), 185-188.
    • (2003) Applied Bioinformatics , vol.2 , Issue.3 , pp. 185-188
    • Doi, A.1    Masao Nagasaki, M.2    Matsuno, H.3    Satoru Miyano, S.4
  • 10
    • 0034625143 scopus 로고    scopus 로고
    • The escherichia coli mg1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
    • P.B.O. 10.1073/pnas.97.10.5528
    • Edwards, J. S., P. B. O. (2000). The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proceedings of the National Academy of Sciences of the United States of America, 97(10), 5528-5533. doi:10.1073/pnas.97.10.5528
    • (2000) Proceedings of the National Academy of Sciences of the United States of America , vol.97 , Issue.10 , pp. 5528-5533
    • Edwards, J.S.1
  • 11
    • 0038127128 scopus 로고    scopus 로고
    • Transfection of normal primary human skeletal myoblasts with p21 and p57 antisense oligonucleotides to improve their proliferation: A first step towards an alternative molecular therapy approach of duchenne muscular dystrophy
    • Endesfelder, S., Bucher, S., Kliche, A., Reszka, R., & Speer, A. (2003). Transfection of normal primary human skeletal myoblasts with p21 and p57 antisense oligonucleotides to improve their proliferation: A first step towards an alternative molecular therapy approach of Duchenne muscular dystrophy. Journal of Molecular Medicine, 81, 355-362.
    • (2003) Journal of Molecular Medicine , vol.81 , pp. 355-362
    • Endesfelder, S.1    Bucher, S.2    Kliche, A.3    Reszka, R.4    Speer, A.5
  • 12
    • 12844282811 scopus 로고    scopus 로고
    • Antisense oligonucleotides and short interfering rnas silencing the cyclin-dependent kinase inhibitor p21 improve proliferation of duchenne muscular dystrophy patients' primary skeletal myoblasts
    • 10.1007/s00109-004-0607-3
    • Endesfelder, S., Kliche, A., Lochmüller, H., von Moers, A., & Speer, A. (2005).Antisense oligonucleotides and short interfering RNAs silencing the cyclin-dependent kinase inhibitor p21 improve proliferation of Duchenne muscular dystrophy patients' primary skeletal myoblasts. Journal of Molecular Medicine, 83, 64-71. doi:10.1007/s00109-004-0607-3
    • (2005) Journal of Molecular Medicine , vol.83 , pp. 64-71
    • Endesfelder, S.1    Kliche, A.2    Lochmüller, H.3    von Moers, A.4    Speer, A.5
  • 15
    • 0032499741 scopus 로고    scopus 로고
    • Quantitative modeling of stochastic systems in moldecular biology by using stochstic petri nets
    • 10.1073/pnas.95.12.6750
    • Goss, P. J. E., & Peccoud, J. (1998). Quantitative modeling of stochastic systems in moldecular biology by using stochstic Petri nets. Proceedings of the National Academy of Sciences of the United States of America, 95, 6750-6755. doi:10.1073/pnas.95.12.6750
    • (1998) Proceedings of the National Academy of Sciences of the United States of America , vol.95 , pp. 6750-6755
    • Goss, P.J.E.1    Peccoud, J.2
  • 18
    • 41549107955 scopus 로고    scopus 로고
    • Modularization of biochemical networks based on classification of petri net t-invariants
    • 10.1186/1471-2105-9-90
    • Grafahrend-Belau, E., Schreiber, F., Heiner, M., Sackmann, A., Junker, B. H., & Grunwald, S. (2008). Modularization of biochemical networks based on classification of Petri net t-invariants. Journal, 9, 90. doi:10.1186/1471-2105-9-90
    • (2008) Journal , vol.9 , Issue.90
    • Grafahrend-Belau, E.1    Schreiber, F.2    Heiner, M.3    Sackmann, A.4    Junker, B.H.5    Grunwald, S.6
  • 19
    • 41549085829 scopus 로고    scopus 로고
    • Petri net modelling of gene regulation of the duchenne muscular dystrophy
    • 10.1016/j.biosystems.2008.02.005
    • Grunwald, S., Speer, A., Ackermann, J., & Koch, I. (2008). Petri net modelling of gene regulation of the Duchenne muscular dystrophy. Bio Systems, 92, 189-205. doi:10.1016/j.biosystems.2008.02.005
    • (2008) Bio Systems , vol.92 , pp. 189-205
    • Grunwald, S.1    Speer, A.2    Ackermann, J.3    Koch, I.4
  • 22
    • 21644439156 scopus 로고    scopus 로고
    • R.P.N. 10.1142/S0219720004000764
    • Hardy, S., R. P. N. (2004). J. Bioinform. Comput. Biol.,2(4), 595-613 doi:10.1142/S0219720004000764
    • (2004) J. Bioinform. Comput. Biol , vol.2 , Issue.4 , pp. 595-613
    • Hardy, S.1
  • 23
    • 10944244598 scopus 로고    scopus 로고
    • Modeling and simulation of molecular biology systems using petri nets: Modeling goals of various approaches
    • 10.1142/S0219720004000764
    • Hardy, S., & Robillard, P. N. (2004). Modeling and simulation of molecular biology systems using Petri nets: Modeling goals of various approaches. Journal of Bioinformatics and Computational Biology, 2(4), 619-637. doi:10.1142/S0219720004000764
    • (2004) Journal of Bioinformatics and Computational Biology , vol.2 , Issue.4 , pp. 619-637
    • Hardy, S.1    Robillard, P.N.2
  • 26
    • 0032229446 scopus 로고    scopus 로고
    • Quantitative modeling of biochemical networks
    • Hofestädt, R., & Thelen, S. (1998). Quantitative modeling of biochemical networks. In Silico Biology, 1(1), 39-53.
    • (1998) In Silico Biology , vol.1 , Issue.1 , pp. 39-53
    • Hofestädt, R.1    Thelen, S.2
  • 27
    • 0037342537 scopus 로고    scopus 로고
    • The systems biology markup language (sbml): A medium for representation and exchange of biochemical network models
    • 10.1093/bioinformatics/btg015
    • Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., & Kitano, H. (2003). The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics (Oxford, England), 19(4), 524-531. doi:10.1093/bioinformatics/btg015
    • (2003) Bioinformatics (Oxford, England , vol.19 , Issue.4 , pp. 524-531
    • Hucka, M.1    Finney, A.2    Sauro, H.M.3    Bolouri, H.4    Doyle, J.C.5    Kitano, H.6
  • 30
    • 84898504100 scopus 로고    scopus 로고
    • Retrieved from
    • Koch, I. (2008b). Supplementary material. Retrieved from http://www.molgen.mpg.de/~koch_i/
    • (2008) Supplementary Material
    • Koch, I.1
  • 31
    • 67651223375 scopus 로고    scopus 로고
    • Petri nets in biological network analysis
    • In B. Junker & F. Schreiber (Eds.), Wiley & Sons
    • Koch, I., & Heiner, M. (2008). Petri nets in biological network analysis. In B. Junker & F. Schreiber (Eds.), Analysis of biological networks (pp. 139-179). Wiley & Sons.
    • (2008) Analysis of Biological Networks , pp. 139-179
    • Koch, I.1    Heiner, M.2
  • 32
    • 16344381707 scopus 로고    scopus 로고
    • Application of petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber
    • 10.1093/bioinformatics/bti145
    • Koch, I., Junker, B., & Heiner, M. (2005). Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber. Bioinformatics (Oxford, England), 21(7), 1219-1226. doi:10.1093/bioinformatics/bti145
    • (2005) Bioinformatics (Oxford, England , vol.21 , Issue.7 , pp. 1219-1226
    • Koch, I.1    Junker, B.2    Heiner, M.3
  • 34
    • 33244465693 scopus 로고    scopus 로고
    • Knowledge representation model for systems-level analysis of signal transduction networks
    • Lee, D.-Y., Zimmer, R., Lee, D.-Y., Hanisch, D., & Sunwon, P. (2004). Knowledge representation model for systems-level analysis of signal transduction networks. Genome Informatics, 15(2), 234-243.
    • (2004) Genome Informatics , vol.15 , Issue.2 , pp. 234-243
    • Lee, D.-Y.1    Zimmer, R.2    Lee, D.-Y.3    Hanisch, D.4    Sunwon, P.5
  • 35
    • 23744463967 scopus 로고    scopus 로고
    • Reconstructing the regulatory network controlling commitment and sporulation in physarum polycephalum based on hierarchical petri net modeling and simulation
    • 10.1016/j.jtbi.2005.03.018
    • Marwan, W., Sujathab, A., & Starostzik, C. (2005). Reconstructing the regulatory network controlling commitment and sporulation in Physarum polycephalum based on hierarchical Petri net modeling and simulation. Journal of Theoretical Biology, 236, 349-365. doi:10.1016/j.jtbi.2005.03.018
    • (2005) Journal of Theoretical Biology , vol.236 , pp. 349-365
    • Marwan, W.1    Sujathab, A.2    Starostzik, C.3
  • 38
    • 0345170900 scopus 로고    scopus 로고
    • Biopathways representation and simulation on hybrid functional petri net
    • Matsuno, H., Tanaka, Y., Aoshima, H., Doi, A., Matsui, M., & Miyano, S. (2003). Biopathways representation and simulation on hybrid functional Petri net. In Silico Biology, 3(3), 389-404.
    • (2003) In Silico Biology , vol.3 , Issue.3 , pp. 389-404
    • Matsuno, H.1    Tanaka, Y.2    Aoshima, H.3    Doi, A.4    Matsui, M.5    Miyano, S.6
  • 39
    • 84898498550 scopus 로고
    • Paper presented at the ieeeinternational conference on consumer electronics
    • Digest of Technical Papers
    • Murata, T. (1989). Petri Nets: Properties, analysis, and applications. Paper presented at the IEEEInternational Conference on Consumer Electronics. Digest of Technical Papers.
    • (1989) Petri Nets: Properties, Analysis, and Applications
    • Murata, T.1
  • 40
    • 2642533799 scopus 로고    scopus 로고
    • Genomic object net i: A platform for modeling and simulating biopathways
    • Nagasaki, M., Atsushi Doi, A., Matsuno, H., & Miyano, S. (2003). Genomic object net I: A platform for modeling and simulating biopathways. Applied Bioinformatics, 2(3), 181-184.
    • (2003) Applied Bioinformatics , vol.2 , Issue.3 , pp. 181-184
    • Nagasaki, M.1    Atsushi Doi, A.2    Matsuno, H.3    Miyano, S.4
  • 41
    • 25844525601 scopus 로고    scopus 로고
    • A quantitative model of the switch cycle of an archaeal flagellar motor and its sensory control
    • 10.1529/ biophysj.104.057570
    • Nutsch, T., Oesterhelt, D., Gilles, E. D., & Marwan, W. (2005). A quantitative model of the switch cycle of an archaeal flagellar motor and its sensory control. Biophysical Journal, 89, 2307-2323. doi:10.1529/ biophysj.104.057570
    • (2005) Biophysical Journal , vol.89 , pp. 2307-2323
    • Nutsch, T.1    Oesterhelt, D.2    Gilles, E.D.3    Marwan, W.4
  • 44
    • 14544306029 scopus 로고    scopus 로고
    • Using petri net tools to study properties and dynamics of biological systems
    • 10.1197/jamia.M1637
    • Peleg, M., Rubin, D., & Altman, R. B. (2005). Using Petri net tools to study properties and dynamics of biological systems. Journal of the American Medical Informatics Association, 12(2), 181-199. doi:10.1197/jamia.M1637
    • (2005) Journal of the American Medical Informatics Association , vol.12 , Issue.2 , pp. 181-199
    • Peleg, M.1    Rubin, D.2    Altman, R.B.3
  • 47
    • 79958858403 scopus 로고    scopus 로고
    • Retrieved from
    • Poland, F. (2008). Cell illustrator. Retrieved from http://www.fqs.pl/life_science/cell_illustrator
    • (2008) Cell Illustrator
    • Poland, F.1
  • 48
    • 33645306314 scopus 로고    scopus 로고
    • Modelling and analysis of biochemical networks with time petri nets
    • Popova-Zeugmann, L., Heiner, M., & Koch, I. (2005). Modelling and analysis of biochemical networks with time Petri nets. Fundamenta Informaticae, 67, 149-163.
    • (2005) Fundamenta Informaticae , vol.67 , pp. 149-163
    • Popova-Zeugmann, L.1    Heiner, M.2    Koch, I.3
  • 52
    • 0030026495 scopus 로고    scopus 로고
    • Qualitative analysis of biochemical reaction systems
    • 10.1016/0010-4825(95)00042-9
    • Reddy, V. N., Mavrovouniotis, M. L., & Liebman, M. N. (1996). Qualitative analysis of biochemical reaction systems. Computers in Biology and Medicine, 26(1), 9-24. doi:10.1016/0010-4825(95)00042-9
    • (1996) Computers in Biology and Medicine , vol.26 , Issue.1 , pp. 9-24
    • Reddy, V.N.1    Mavrovouniotis, M.L.2    Liebman, M.N.3
  • 54
    • 0023453329 scopus 로고
    • Silhouettes:A graphical aid to the interpretation and validation of cluster analysis
    • 10.1016/0377-0427(87)90125-7
    • Rousseeuw, P. J. (1987). Silhouettes:A graphical aid to the interpretation and validation of cluster analysis. Journal of Computational and Applied Mathematics, 20, 53-65. doi:10.1016/0377-0427(87)90125-7
    • (1987) Journal of Computational and Applied Mathematics , vol.20 , pp. 53-65
    • Rousseeuw, P.J.1
  • 56
    • 33846851564 scopus 로고    scopus 로고
    • An analysis of the petri net based model of the human body iron homeostasis process
    • 10.1016/j.compbiolchem.2006.09.005
    • Sackmann, A., Formanowicz, D., Formanowicz, P., Koch, I., & Blazewicz, J. (2007). An analysis of the Petri net based model of the human body iron homeostasis process. Computational Biology and Chemistry, 31, 1-10. doi:10.1016/j.compbiolchem.2006.09.005
    • (2007) Computational Biology and Chemistry , vol.31 , pp. 1-10
    • Sackmann, A.1    Formanowicz, D.2    Formanowicz, P.3    Koch, I.4    Blazewicz, J.5
  • 57
    • 33845417184 scopus 로고    scopus 로고
    • Application of petri net based analysis techniques to signal transduction pathways
    • 10.1186/1471-2105-7-482
    • Sackmann, A., Heiner, M., & Koch, I. (2006). Application of Petri net based analysis techniques to signal transduction pathways. Journal, 7, 482. doi:10.1186/1471-2105-7-482
    • (2006) Journal , vol.7 , Issue.482
    • Sackmann, A.1    Heiner, M.2    Koch, I.3
  • 58
    • 33947371802 scopus 로고    scopus 로고
    • Cell fate simulation model of gustatory neurons with micrornas double-negative feedback loop by hybrid functional petri net with extension
    • Saito, A., Nagasaki, M., Doi, A., Ueno, K., & Miyano, M. (2006). Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loop by hybrid functional Petri net with extension. Genome Informatics, 17(1), 100-111.
    • (2006) Genome Informatics , vol.17 , Issue.1 , pp. 100-111
    • Saito, A.1    Nagasaki, M.2    Doi, A.3    Ueno, K.4    Miyano, M.5
  • 59
    • 0023375195 scopus 로고
    • The neighbor-joining method: A new method for reconstructing phylogenetic trees
    • Saitou, N., & Nei, M. (1987). The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4, 406-425.
    • (1987) Molecular Biology and Evolution , vol.4 , pp. 406-425
    • Saitou, N.1    Nei, M.2
  • 60
    • 0036330798 scopus 로고    scopus 로고
    • Genome-scale metabolic model of helicobacter pylori 26695
    • C.M.W. 10.1128/JB.184.16.4582-4593.2002
    • Schilling, C. H., C. M. W., Famili, I., Church, G. M., Edwards, J. S., & Palsson, B.O. (2002). Genome-scale metabolic model of Helicobacter pylori 26695. Journal of Bacteriology, 184, 4582-4593. doi:10.1128/JB.184.16.4582-4593.2002
    • (2002) Journal of Bacteriology , vol.184 , pp. 4582-4593
    • Schilling, C.H.1    Famili, I.2    Church, G.M.3    Edwards, J.S.4    Palsson, B.O.5
  • 61
    • 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
    • 10.1006/jtbi.2000.1073
    • Schilling, C. H., Letscher, D., & Palsson, B. O. (2000). Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway oriented perspective. Journal of Theoretical Biology, 203, 229-248. doi:10.1006/jtbi.2000.1073
    • (2000) Journal of Theoretical Biology , vol.203 , pp. 229-248
    • Schilling, C.H.1    Letscher, D.2    Palsson, B.O.3
  • 63
    • 27544501653 scopus 로고    scopus 로고
    • Qualitative modelling of regulated metabolic pathways: Application to the tryptophan biosynthesis in e.coli
    • 10.1093/bioinformatics/bti1130 (Oxford, England
    • Simao, E., Remy, E., Thieffry, D., & Chaouiya, C. (2005). Qualitative modelling of regulated metabolic pathways: application to the tryptophan biosynthesis in E.Coli. Bioinformatics (Oxford, England), 21(Suppl. 2), ii190-ii196. doi:10.1093/bioinformatics/bti1130
    • (2005) Bioinformatics , vol.21 , Issue.SUPPL. 2
    • Simao, E.1    Remy, E.2    Thieffry, D.3    Chaouiya, C.4
  • 66
    • 33847304166 scopus 로고    scopus 로고
    • Qualitatively modelling and analysing genetic regulatory networks: A petri net approach
    • 10.1093/bioinformatics/btl596
    • Steggles, L. J., Banks, R., & Wipat, A. (2007). Qualitatively modelling and analysing genetic regulatory networks: A Petri net approach. Bioinformatics (Oxford, England), 23(3), 336-343. doi:10.1093/bioinformatics/btl596
    • (2007) Bioinformatics (Oxford, England , vol.23 , Issue.3 , pp. 336-343
    • Steggles, L.J.1    Banks, R.2    Wipat, A.3
  • 68
    • 0024114801 scopus 로고
    • A note on the neighbor-joining algorithm of saitou and nei
    • Studier, J. A., & Keppler, K. J. (1988). A note on the neighbor-joining algorithm of Saitou and Nei. Molecular Biology and Evolution, 5, 729-731.
    • (1988) Molecular Biology and Evolution , vol.5 , pp. 729-731
    • Studier, J.A.1    Keppler, K.J.2
  • 70
    • 84898527626 scopus 로고    scopus 로고
    • Ontology based standardization of petri net modeling for signalling pathways
    • Takai-Igarashi, T. (2005). Ontology based standardization of Petri net modeling for signalling pathways. Journal, 5, 0047
    • (2005) Journal , vol.5 , pp. 0047
    • Takai-Igarashi, T.1
  • 71
    • 58149293242 scopus 로고    scopus 로고
    • TGI-group, Retrieved from
    • TGI-group. (2008). Petri Nets World. Retrieved from http://www.informatik.uni-hamburg.de./TGI/PetriNets
    • (2008) Petri Nets World
  • 72
    • 0029267491 scopus 로고
    • Dynamical behaviour of biological regulatory networks-i. Biological role of feedback loops and practical use of the concept of the loop-characteristic state
    • Thomas, R., Thieffry, D., & Kaufman, M. (1995). Dynamical behaviour of biological regulatory networks-I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state. Bulletin of Mathematical Biology, 57, 247-276.
    • (1995) Bulletin of Mathematical Biology , vol.57 , pp. 247-276
    • Thomas, R.1    Thieffry, D.2    Kaufman, M.3
  • 75
    • 0345096675 scopus 로고    scopus 로고
    • Steady state analysis of metabolic pathways using petri nets
    • Voss, K., Heiner, M., & Koch, I. (2003). Steady state analysis of metabolic pathways using Petri nets. In Silico Biology, 3(3), 367-387.
    • (2003) In Silico Biology , vol.3 , Issue.3 , pp. 367-387
    • Voss, K.1    Heiner, M.2    Koch, I.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.