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Volumn 22, Issue 3, 2014, Pages 463-493

Modeling and Analyzing Biological Systems Using Colored Hierarchical Petri Nets Illustrated by C. Elegans Vulval Development

Author keywords

C. elegans Vulval Development; Colored Hierarchical Petri Nets; Modeling Approach; Modeling Framework

Indexed keywords


EID: 84940263170     PISSN: 02183390     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0218339014500181     Document Type: Article
Times cited : (9)

References (54)
  • 1
    • 60649097295 scopus 로고    scopus 로고
    • Computational challenges in systems biology
    • Heath AP, Kavraki LE, Computational challenges in systems biology, Comput Sci Rev 3(1):1-17, 2009.
    • (2009) Comput Sci Rev , vol.3 , Issue.1 , pp. 1-17
    • Heath, A.P.1    Kavraki, L.E.2
  • 3
    • 79958020937 scopus 로고    scopus 로고
    • Petri nets as a framework for the reconstruction and analysis of signal transduction pathways and regulatory networks
    • Marwan W, Wagler A, Weismantel R, Petri nets as a framework for the reconstruction and analysis of signal transduction pathways and regulatory networks, Nat Comput 10(2):639-654, 2011.
    • (2011) Nat Comput , vol.10 , Issue.2 , pp. 639-654
    • Marwan, W.1    Wagler, A.2    Weismantel, R.3
  • 4
    • 78649903919 scopus 로고    scopus 로고
    • Petri nets for modelling metabolic pathways: A survey
    • Baldan P, Cocco N, Marin A, Simeoni M, 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
  • 5
    • 34548302044 scopus 로고    scopus 로고
    • Petri net modelling of biological networks
    • Chaouiya C, Petri net modelling of biological networks, Briefings Bioinform 8(4):210-219, 2007.
    • (2007) Briefings Bioinform , vol.8 , Issue.4 , pp. 210-219
    • Chaouiya, C.1
  • 6
    • 0042828946 scopus 로고    scopus 로고
    • Modeling transmission of directly transmitted infectious diseases using colored stochastic Petri nets
    • Bahi-Jaber N, Pontier D, Modeling transmission of directly transmitted infectious diseases using colored stochastic Petri nets, Math Biosci 185:1-13, 2003.
    • (2003) Math Biosci , vol.185 , pp. 1-13
    • Bahi-Jaber, N.1    Pontier, D.2
  • 7
    • 84878362183 scopus 로고    scopus 로고
    • A high-level Petri net framework for genetic regulatory networks
    • Banks R, Steggles LJ, A high-level Petri net framework for genetic regulatory networks, J Integr Bioinform 4(3):1-12, 2007.
    • (2007) J Integr Bioinform , vol.4 , Issue.3 , pp. 1-12
    • Banks, R.1    Steggles, L.J.2
  • 10
    • 84896689115 scopus 로고    scopus 로고
    • Executable Petri net models for the analysis of metabolic pathways
    • Genrich H, Küffner R, Voss K, Executable Petri net models for the analysis of metabolic pathways, Int J Softw Tools Technol Transf 3(4):394-404, 2001.
    • (2001) Int J Softw Tools Technol Transf , vol.3 , Issue.4 , pp. 394-404
    • Genrich, H.1    Küffner, R.2    Voss, K.3
  • 11
    • 33644817463 scopus 로고    scopus 로고
    • Colored Petri net modeling and simulation of signal transduction pathways
    • Lee D, Zimmer R, Lee S, Park S, Colored Petri net modeling and simulation of signal transduction pathways, Metab Eng 8(2):112-122, 2006.
    • (2006) Metab Eng , vol.8 , Issue.2 , pp. 112-122
    • Lee, D.1    Zimmer, R.2    Lee, S.3    Park, S.4
  • 12
    • 0345983652 scopus 로고    scopus 로고
    • Qualitative models of molecular function: Linking genetic polymorphisms of trna to their functional sequelae
    • Peleg M, Gabashvili IS, Altman RB, Qualitative models of molecular function: Linking genetic polymorphisms of trna to their functional sequelae, Proc IEEE 90(12):1875-1886, 2002.
    • (2002) Proc. IEEE , vol.90 , Issue.12 , pp. 1875-1886
    • Peleg, M.1    Gabashvili, I.S.2    Altman, R.B.3
  • 15
    • 0345096675 scopus 로고    scopus 로고
    • Steady state analysis of metabolic pathways using Petri nets
    • Voss K, Heiner M, Koch I, Steady state analysis of metabolic pathways using Petri nets, In Silico Biol 3:0031, 2003.
    • (2003) Silico Biol , vol.3 , pp. 31
    • Voss, K.1    Heiner, M.2    Koch, I.3
  • 18
    • 77951956151 scopus 로고    scopus 로고
    • Snoopy-a unifying Petri net framework to investigate biomolecular networks
    • Rohr C, Marwan W, Heiner M, Snoopy-a unifying Petri net framework to investigate biomolecular networks, Bioinformatics 26(7):974-975, 2010.
    • (2010) Bioinformatics , vol.26 , Issue.7 , pp. 974-975
    • Rohr, C.1    Marwan, W.2    Heiner, M.3
  • 20
    • 84862493851 scopus 로고    scopus 로고
    • PhD Thesis, Department of Computer Science, Brandenburg University of Technology Cottbus
    • Liu F, Colored Petri nets for systems biology, PhD Thesis, Department of Computer Science, Brandenburg University of Technology Cottbus, 2012.
    • (2012) Colored Petri Nets for Systems Biology
    • Liu, F.1
  • 22
    • 84883056967 scopus 로고    scopus 로고
    • Multiscale modelling and analysis of planar cell polarity in the drosophila wing
    • online 1 August 2012
    • Gao Q, Gilbert D, Heiner M, Liu F, Maccagnola D, Tree D, Multiscale modelling and analysis of planar cell polarity in the drosophila wing, IEEE/ACM Trans Comput Biol Bioinform 10(2):337-351, 2013, online 1 August 2012.
    • (2013) IEEE/ACM Trans Comput Biol Bioinform , vol.10 , Issue.2 , pp. 337-351
    • Gao, Q.1    Gilbert, D.2    Heiner, M.3    Liu, F.4    MacCagnola, D.5    Tree, D.6
  • 24
    • 84879642133 scopus 로고    scopus 로고
    • Colouring space-A coloured framework for spatial modelling in systems biology
    • in Colom JM, Desel J (eds.) Springer
    • Gilbert D, Heiner M, Liu F, Saunders N, Colouring space-A coloured framework for spatial modelling in systems biology, in Colom JM, Desel J (eds.), Proc PETRI NETS 2013, Lecture Notes in Computer Science, Vol. 7927, Springer, pp. 230-249, 2013.
    • (2013) Proc PETRI NETS 2013, Lecture Notes in Computer Science , vol.7927 , pp. 230-249
    • Gilbert, D.1    Heiner, M.2    Liu, F.3    Saunders, N.4
  • 25
    • 84885999784 scopus 로고    scopus 로고
    • Modelling and analysis of phase variation in bacterial colony growth
    • in Gupta A, Henzinger TA (eds.) Springer
    • Parvu O, Gilbert D, Heiner M, Liu F, Saunders N, Modelling and analysis of phase variation in bacterial colony growth, in Gupta A, Henzinger TA (eds.), Proc CMSB 2013, Lecture Notes in Computer Science, Vol. 8130, Springer, pp. 78-91, 2013.
    • (2013) Proc CMSB 2013, Lecture Notes in Computer Science , vol.8130 , pp. 78-91
    • Parvu, O.1    Gilbert, D.2    Heiner, M.3    Liu, F.4    Saunders, N.5
  • 28
    • 0000098171 scopus 로고
    • Coloured Petri nets and the invariant-method
    • Jensen K, Coloured Petri nets and the invariant-method, Theor Comput Sci 14(3):317-336, 1981.
    • (1981) Theor Comput Sci , vol.14 , Issue.3 , pp. 317-336
    • Jensen, K.1
  • 31
    • 49149133038 scopus 로고
    • The temporal semantics of concurrent programs
    • Pnueli A, The temporal semantics of concurrent programs, Theor Comput Sci 13(1):45-60, 1981.
    • (1981) Theor Comput Sci , vol.13 , Issue.1 , pp. 45-60
    • Pnueli, A.1
  • 35
    • 84862491494 scopus 로고    scopus 로고
    • Technical report, Technical report 02-12, Department of Computer Science, Brandenburg University of Technology Cottbus, March
    • Liu F, Heiner M, Rohr C, Manual for colored Petri nets in Snoopy, Technical report, Technical report 02-12, Department of Computer Science, Brandenburg University of Technology Cottbus, March 2012, Available at http://www-dssz.informatik.tucottbus. de/publications/btu-reports/Manual for colored Petri nets 2012 03.pdf.
    • (2012) Manual for Colored Petri Nets in Snoopy
    • Liu, F.1    Heiner, M.2    Rohr, C.3
  • 36
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie DT, Exact stochastic simulation of coupled chemical reactions, J Phys Chem 81(25):2340-2361, 1977.
    • (1977) J Phys Chem , vol.81 , Issue.25 , pp. 2340-2361
    • Gillespie, D.T.1
  • 40
    • 84879619513 scopus 로고    scopus 로고
    • MARCIE-Model checking and reachability analysis done efficiently
    • Colom JM, Desel J (eds.) Springer June
    • Heiner M, Rohr C, Schwarick M, MARCIE-Model checking and reachability analysis done efficiently, Colom JM, Desel J (eds.), Proc PETRI NETS 2013, Lecture Notes in Computer Science, Vol. 7927, Springer, pp. 389-399, June 2013.
    • (2013) Proc PETRI NETS 2013, Lecture Notes in Computer Science , vol.7927 , pp. 389-399
    • Heiner, M.1    Rohr, C.2    Schwarick, M.3
  • 42
    • 0442272485 scopus 로고    scopus 로고
    • Crosstalk between the EGFR and LIN-12/Notch pathways in C. Elegans vulval development
    • Yoo A, Bais C, Greenwald I, Crosstalk between the EGFR and LIN-12/Notch pathways in C. elegans vulval development, Science 303(5658):663-666, 2004.
    • (2004) Science , vol.303 , Issue.5658 , pp. 663-666
    • Yoo, A.1    Bais, C.2    Greenwald, I.3
  • 43
    • 34249725570 scopus 로고    scopus 로고
    • Predictive modeling of signaling crosstalk during C. Elegans vulval development
    • Fisher J, Piterman N, Hajnal A, Henzinger TA, Predictive modeling of signaling crosstalk during C. elegans vulval development, PLoS Comput Biol 3(5):e92, 2007.
    • (2007) PLoS Comput Biol , vol.3 , Issue.5 , pp. e92
    • Fisher, J.1    Piterman, N.2    Hajnal, A.3    Henzinger, T.A.4
  • 44
    • 0024309272 scopus 로고
    • The combined action of two intercellular signaling pathways specifies three cell fates during vulval induction in C. Elegans
    • Sternberg PW, Horvitz HR, The combined action of two intercellular signaling pathways specifies three cell fates during vulval induction in C. elegans, Cell 58(4):679-693, 1989.
    • (1989) Cell , vol.58 , Issue.4 , pp. 679-693
    • Sternberg, P.W.1    Horvitz, H.R.2
  • 45
    • 31944451493 scopus 로고    scopus 로고
    • Intercellular coupling amplifies fate segregation during Caenorhabditis elegans vulval development
    • Giurumescu CA, Sternberg PW, Asthagiri AR, Intercellular coupling amplifies fate segregation during Caenorhabditis elegans vulval development, Proc Nat Acad Sci USA 103(5):1331-1336, 2006.
    • (2006) Proc Nat Acad Sci USA , vol.103 , Issue.5 , pp. 1331-1336
    • Giurumescu, C.A.1    Sternberg, P.W.2    Asthagiri, A.R.3
  • 46
    • 68549085469 scopus 로고    scopus 로고
    • Executing multicellular differentiation: Quantitative predictive modelling of C. Elegans vulval development
    • Bonzanni N, Krepska E, Feenstra1 KA, Fokkink W, Kielmann T, Bal H, Heringa1 J, Executing multicellular differentiation: Quantitative predictive modelling of C. elegans vulval development, Bioinformatics 25(16):2049-2056, 2009.
    • (2009) Bioinformatics , vol.25 , Issue.16 , pp. 2049-2056
    • Bonzanni, N.1    Krepska, E.2    Feenstra, K.A.3    Fokkink, W.4    Kielmann, T.5    Bal, H.6    Heringa, J.7
  • 47
    • 67651062669 scopus 로고    scopus 로고
    • Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension
    • Li C, Nagasaki M, Ueno K, Miyano S, Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension, BMC Syst Biol 3:42, 2009.
    • (2009) BMC Syst Biol , vol.3 , pp. 42
    • Li, C.1    Nagasaki, M.2    Ueno, K.3    Miyano, S.4
  • 49
    • 0002112447 scopus 로고
    • The statistical analysis of simulation results
    • in Lavenberg SS (ed.) Academic Press, New York
    • Welch PD, The statistical analysis of simulation results, in Lavenberg SS (ed.), The Computer Performance Modeling Handbook, Academic Press, New York, 1983.
    • (1983) The Computer Performance Modeling Handbook
    • Welch, P.D.1
  • 50
    • 70349352585 scopus 로고    scopus 로고
    • On the statistical accuracy of stochastic simulation algorithms implemented in Dizzy
    • SandmannW, Maier C, On the statistical accuracy of stochastic simulation algorithms implemented in Dizzy, Proc 5th Int Workshop on Computational Systems Biology, pp. 153-157, 2008.
    • (2008) Proc 5th Int Workshop On Computational Systems Biology , pp. 153-157
    • SandmannW Maier, C.1
  • 52
    • 84878161581 scopus 로고    scopus 로고
    • Biomodel engineering for multiscale systems biology
    • online available 12-October-2012
    • Heiner M, Gilbert D, Biomodel engineering for multiscale systems biology, Prog Biophys Mol Biol 111(2-3):119-128, 2013, online available 12-October-2012.
    • (2013) Prog Biophys Mol Biol , vol.111 , Issue.2-3 , pp. 119-128
    • Heiner, M.1    Gilbert, D.2
  • 53
    • 84890562030 scopus 로고    scopus 로고
    • Modeling membrane systems using colored stochastic Petri nets
    • Liu F, Heiner M, Modeling membrane systems using colored stochastic Petri nets, Nat Comput 12(4):617-629, 2013.
    • (2013) Nat Comput , vol.12 , Issue.4 , pp. 617-629
    • Liu, F.1    Heiner, M.2
  • 54
    • 84879629991 scopus 로고    scopus 로고
    • Multiscale modelling of coupled Ca2+ channels using coloured stochastic Petri nets
    • Liu F, Heiner M, Multiscale modelling of coupled Ca2+ channels using coloured stochastic Petri nets, IET Syst Biol 7(4):106-113, 2013
    • (2013) IET Syst Biol , vol.7 , Issue.4 , pp. 106-113
    • Liu, F.1    Heiner, M.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.