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Volumn 7, Issue 1, 2012, Pages

Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem

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EID: 84861467760     PISSN: None     EISSN: 17487188     Source Type: Journal    
DOI: 10.1186/1748-7188-7-15     Document Type: Article
Times cited : (22)

References (32)
  • 1
    • 0033982936 scopus 로고    scopus 로고
    • KEGG: Kyoto Encyclopedia of Genes and Genomes
    • 10.1093/nar/28.1.27, 102409, 10592173
    • Kanehisa M, Goto S. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Research 2000, 28:27-30. 10.1093/nar/28.1.27, 102409, 10592173.
    • (2000) Nucleic Acids Research , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 2
    • 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, 12611808
    • Hucka M, et al. The Systems Biology Markup Language (SBML): A Medium for Representation and Exchange of Biochemical Network Models. Bioinformatics 2003, 19(4):524-531. 10.1093/bioinformatics/btg015, 12611808.
    • (2003) Bioinformatics , vol.19 , Issue.4 , pp. 524-531
    • Hucka, M.1
  • 6
    • 0034064689 scopus 로고    scopus 로고
    • A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
    • Schuster S, Fell DA, Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nature Biotechnology 2002, 18:326-332.
    • (2002) Nature Biotechnology , vol.18 , pp. 326-332
    • Schuster, S.1    Fell, D.A.2    Dandekar, T.3
  • 7
    • 33750989365 scopus 로고    scopus 로고
    • Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation
    • 10.1016/j.jtbi.2006.05.013, 16949102
    • Chickarmane V, Kholodenkob BN, Sauro HM. Oscillatory dynamics arising from competitive inhibition and multisite phosphorylation. Journal of Theoretical Biology 2007, 244:68-76. 10.1016/j.jtbi.2006.05.013, 16949102.
    • (2007) Journal of Theoretical Biology , vol.244 , pp. 68-76
    • Chickarmane, V.1    Kholodenkob, B.N.2    Sauro, H.M.3
  • 8
    • 0036212767 scopus 로고    scopus 로고
    • Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors
    • 10.1038/nbt0402-370, 11923843
    • Schoeberl B, Eichler-Jonsson C, Gilles E, Muller G. Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nature Biotechnology 2002, 20(4):370-375. 10.1038/nbt0402-370, 11923843.
    • (2002) Nature Biotechnology , vol.20 , Issue.4 , pp. 370-375
    • Schoeberl, B.1    Eichler-Jonsson, C.2    Gilles, E.3    Muller, G.4
  • 9
    • 33747877324 scopus 로고    scopus 로고
    • BIOCHAM: An Environment for Modeling Biological Systems and Formalizing Experimental Knowledge
    • 10.1093/bioinformatics/btl172, 16672256
    • Calzone L, Fages F, Soliman S. BIOCHAM: An Environment for Modeling Biological Systems and Formalizing Experimental Knowledge. Bioinformatics 2006, 22(14):1805-1807. 10.1093/bioinformatics/btl172, 16672256.
    • (2006) Bioinformatics , vol.22 , Issue.14 , pp. 1805-1807
    • Calzone, L.1    Fages, F.2    Soliman, S.3
  • 10
  • 11
    • 77951956151 scopus 로고    scopus 로고
    • Snoopy - a unifying Petri net framework to investigate biomolecular networks
    • 10.1093/bioinformatics/btq050, 20139470
    • Rohr C, Marwan W, Heiner M. Snoopy - a unifying Petri net framework to investigate biomolecular networks. Bioinformatics 2010, 26(7):974-975. 10.1093/bioinformatics/btq050, 20139470.
    • (2010) Bioinformatics , vol.26 , Issue.7 , pp. 974-975
    • Rohr, C.1    Marwan, W.2    Heiner, M.3
  • 12
    • 0001896749 scopus 로고
    • Convex geometry and semiflows in P/T nets. A comparative study of algorithms for computation of minimal P-semiflows
    • London, UK: Springer-Verlag, Rozenberg G
    • Colom JM, Silva M. Convex geometry and semiflows in P/T nets. A comparative study of algorithms for computation of minimal P-semiflows. Advances in Petri Nets 1990, of Lecture Notes in Computer Science 1991, 483:79-112. London, UK: Springer-Verlag, Rozenberg G.
    • (1991) Advances in Petri Nets 1990, of Lecture Notes in Computer Science , vol.483 , pp. 79-112
    • Colom, J.M.1    Silva, M.2
  • 14
    • 33747856186 scopus 로고    scopus 로고
    • Metatool 5.0: fast and flexible elementary modes analysis
    • 10.1093/bioinformatics/btl267, 16731697
    • von Kamp A, Schuster S. Metatool 5.0: fast and flexible elementary modes analysis. Bioinformatics 2006, 22(15):1930-1931. 10.1093/bioinformatics/btl267, 16731697.
    • (2006) Bioinformatics , vol.22 , Issue.15 , pp. 1930-1931
    • von Kamp, A.1    Schuster, S.2
  • 16
    • 75849164426 scopus 로고    scopus 로고
    • Computing the shortest elementary flux modes in genome-scale metabolic networks
    • 10.1093/bioinformatics/btp564, 19793869
    • de Figueiredo LF, Podhorski A, Rubio A, Kaleta C, Beasley JE, Schuster S, Planes FJ. Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinformatics 2009, 25(23):3158-3165. 10.1093/bioinformatics/btp564, 19793869.
    • (2009) Bioinformatics , vol.25 , Issue.23 , pp. 3158-3165
    • de Figueiredo, L.F.1    Podhorski, A.2    Rubio, A.3    Kaleta, C.4    Beasley, J.E.5    Schuster, S.6    Planes, F.J.7
  • 18
    • 49449120803 scopus 로고
    • Consistency in Networks of Relations
    • Mackworth AK. Consistency in Networks of Relations. Artifcial Intelligence 1977, 8:99-118.
    • (1977) Artifcial Intelligence , vol.8 , pp. 99-118
    • Mackworth, A.K.1
  • 19
    • 84962760644 scopus 로고
    • Constraint satisfaction problems: an overview
    • Meseguer P. Constraint satisfaction problems: an overview. AI Communications 1989, 2:3-17.
    • (1989) AI Communications , vol.2 , pp. 3-17
    • Meseguer, P.1
  • 20
    • 0002514541 scopus 로고
    • Algorithms for Constraint-Satisfaction Problems: A Survey
    • Kumar V. Algorithms for Constraint-Satisfaction Problems: A Survey. AI Magazine 1992, 13:32-44.
    • (1992) AI Magazine , vol.13 , pp. 32-44
    • Kumar, V.1
  • 22
    • 0033848878 scopus 로고    scopus 로고
    • Integrating the MAP kinase signal into the G1 phase cell cycle machinery
    • 10.1002/1521-1878(200009)22:9<818::AID-BIES7>3.0.CO;2-6, 10944584
    • Roovers K, Assoian RK. Integrating the MAP kinase signal into the G1 phase cell cycle machinery. BioEssays 2000, 22(9):818-826. 10.1002/1521-1878(200009)22:9<818::AID-BIES7>3.0.CO;2-6, 10944584.
    • (2000) BioEssays , vol.22 , Issue.9 , pp. 818-826
    • Roovers, K.1    Assoian, R.K.2
  • 23
    • 0034705227 scopus 로고    scopus 로고
    • Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties
    • 10.1073/pnas.97.11.5818, 18517, 10823939
    • Levchenko A, Bruck J, Sternberg PW. Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. PNAS 2000, 97(11):5818-5823. 10.1073/pnas.97.11.5818, 18517, 10823939.
    • (2000) PNAS , vol.97 , Issue.11 , pp. 5818-5823
    • Levchenko, A.1    Bruck, J.2    Sternberg, P.W.3
  • 24
    • 84863195276 scopus 로고    scopus 로고
    • Visualization of the simulation data of biochemical network models: a painted Petri net approach
    • USA: Society for Computer Simulation International, San Diego, CA
    • Hardy S, Robillard PN. Visualization of the simulation data of biochemical network models: a painted Petri net approach. Proceedings of the SCSC'07 summer computer simulation conference 2007, 802-808. USA: Society for Computer Simulation International, San Diego, CA.
    • (2007) Proceedings of the SCSC'07 summer computer simulation conference , pp. 802-808
    • Hardy, S.1    Robillard, P.N.2
  • 25
    • 52949098408 scopus 로고    scopus 로고
    • Large-scale computation of elementary flux modes with bit pattern trees
    • 10.1093/bioinformatics/btn401, 18676417
    • Terzer M, Stelling J. Large-scale computation of elementary flux modes with bit pattern trees. Bioinformatics 2008, 24(19):2229-2235. 10.1093/bioinformatics/btn401, 18676417.
    • (2008) Bioinformatics , vol.24 , Issue.19 , pp. 2229-2235
    • Terzer, M.1    Stelling, J.2
  • 26
    • 0009617613 scopus 로고    scopus 로고
    • Compositional Minimisation of Finite State Systems Using Interface Specifications
    • Graf S, Steffen B, Lüttgen G. Compositional Minimisation of Finite State Systems Using Interface Specifications. Journal of Formal Aspects of Computing 1996, 8(5):607-616.
    • (1996) Journal of Formal Aspects of Computing , vol.8 , Issue.5 , pp. 607-616
    • Graf, S.1    Steffen, B.2    Lüttgen, G.3
  • 29
    • 0345602990 scopus 로고    scopus 로고
    • Topological analysis of metabolic networks based on Petri net theory
    • Zevedei-Oancea I, Schuster S. Topological analysis of metabolic networks based on Petri net theory. In Silico Biology 2003, 3(29).
    • (2003) In Silico Biology , vol.3 , Issue.29
    • Zevedei-Oancea, I.1    Schuster, S.2
  • 32
    • 0032776303 scopus 로고    scopus 로고
    • Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems
    • 25504, 10436023
    • Kohn KW. Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems. Molecular Biology of the Cell 1999, 10(8):2703-2734. 25504, 10436023.
    • (1999) Molecular Biology of the Cell , vol.10 , Issue.8 , pp. 2703-2734
    • Kohn, K.W.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.