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Volumn 29, Issue 18, 2013, Pages 2327-2334

A computational method to preclude multistationarity in networks of interacting species

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGICAL MODEL; BIOLOGY; PHOSPHORYLATION; PROCEDURES; RNA INTERFERENCE; SYSTEMS BIOLOGY; ARTICLE; METHODOLOGY;

EID: 84883480592     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btt400     Document Type: Article
Times cited : (34)

References (46)
  • 2
    • 84883467711 scopus 로고    scopus 로고
    • Qualitative inference in dynamical systems
    • John Wiley and Sons, Chichester
    • Atay,F.M. and Jost,J. (2011) Qualitative inference in dynamical systems. In: Handbook of Statistics in Systems Biology. John Wiley and Sons, Chichester, pp. 339-358.
    • (2011) Handbook of Statistics in Systems Biology , pp. 339-358
    • Atay, F.M.1    Jost, J.2
  • 3
    • 50049105002 scopus 로고    scopus 로고
    • Mathematical analysis of models for reaction kinetics in intracellular environments
    • Bajzer,Z. et al. (2008) Mathematical analysis of models for reaction kinetics in intracellular environments. Math. Biosci., 215, 35-47.
    • (2008) Math. Biosci. , vol.215 , pp. 35-47
    • Bajzer, Z.1
  • 4
    • 77649244142 scopus 로고    scopus 로고
    • Graph-theoretic approaches to injectivity and multiple equilibria in systems of interacting elements
    • Banaji,M. and Craciun,G. (2009) Graph-theoretic approaches to injectivity and multiple equilibria in systems of interacting elements. Commun. Math. Sci., 7, 867-900.
    • (2009) Commun. Math. Sci. , vol.7 , pp. 867-900
    • Banaji, M.1    Craciun, G.2
  • 5
    • 72049099058 scopus 로고    scopus 로고
    • Graph-theoretic criteria for injectivity and unique equilibria in general chemical reaction systems
    • Banaji,M. and Craciun,G. (2010) Graph-theoretic criteria for injectivity and unique equilibria in general chemical reaction systems. Adv. Appl. Math., 44, 168-184.
    • (2010) Adv. Appl. Math. , vol.44 , pp. 168-184
    • Banaji, M.1    Craciun, G.2
  • 6
    • 37849018685 scopus 로고    scopus 로고
    • P matrix properties, injectivity, and stability in chemical reaction systems
    • Banaji,M. et al. (2007) P matrix properties, injectivity, and stability in chemical reaction systems. SIAM J. Appl. Math., 67, 1523-1547.
    • (2007) SIAM J. Appl. Math. , vol.67 , pp. 1523-1547
    • Banaji, M.1
  • 7
    • 0347444723 scopus 로고    scopus 로고
    • Micrornas: Genomics, biogenesis, mechanism, and function
    • Bartel,D. (2004) Micrornas: Genomics, biogenesis, mechanism, and function. Cell, 116, 281-97.
    • (2004) Cell , vol.116 , pp. 281-297
    • Bartel, D.1
  • 8
    • 84861626253 scopus 로고    scopus 로고
    • Switching in mass action networks based on linear inequalities
    • Conradi,C. and Flockerzi,D. (2012) Switching in mass action networks based on linear inequalities. SIAM J. Appl. Dyn. Syst., 11, 110-134.
    • (2012) SIAM J Appl. Dyn. Syst. , vol.11 , pp. 110-134
    • Conradi, C.1    Flockerzi, D.2
  • 9
    • 37649013307 scopus 로고    scopus 로고
    • Subnetwork analysis reveals dynamic features of complex (bio)chemical networks
    • Conradi,C. et al. (2007) Subnetwork analysis reveals dynamic features of complex (bio)chemical networks. Proc. Natl Acad. Sci. USA, 104, 19175-19180.
    • (2007) Proc. Natl Acad. Sci. USA , vol.104 , pp. 19175-19180
    • Conradi, C.1
  • 10
    • 27844475135 scopus 로고    scopus 로고
    • Multiple equilibria in complex chemical reaction networks. I The injectivity property
    • Craciun,G. and Feinberg,M. (2005) Multiple equilibria in complex chemical reaction networks. I. The injectivity property. SIAM J. Appl. Math., 65, 1526-1546.
    • (2005) SIAM J. Appl. Math. , vol.65 , pp. 1526-1546
    • Craciun, G.1    Feinberg, M.2
  • 11
    • 33745027709 scopus 로고    scopus 로고
    • Multiple equilibria in complex chemical reaction networks. II. The species-reaction graph
    • Craciun,G. and Feinberg,M. (2006) Multiple equilibria in complex chemical reaction networks. II. The species-reaction graph. SIAM J. Appl. Math., 66, 1321-1338.
    • (2006) SIAM J. Appl. Math. , vol.66 , pp. 1321-1338
    • Craciun, G.1    Feinberg, M.2
  • 12
    • 77951199596 scopus 로고    scopus 로고
    • Multiple equilibria in complex chemical reaction networks: Semiopen mass action systems
    • Craciun,G. and Feinberg,M. (2010) Multiple equilibria in complex chemical reaction networks: Semiopen mass action systems. SIAM J. Appl. Math., 70, 1859-1877.
    • (2010) SIAM J Appl. Math. , vol.70 , pp. 1859-1877
    • Craciun, G.1    Feinberg, M.2
  • 13
    • 79251538918 scopus 로고    scopus 로고
    • Modeling RNA interference in mammalian cells
    • Cuccato,G. et al. (2011) Modeling RNA interference in mammalian cells. BMC Syst. Biol., 5, 19.
    • (2011) BMC Syst. Biol. , vol.5 , pp. 19
    • Cuccato, G.1
  • 14
    • 27644465844 scopus 로고    scopus 로고
    • Rnai the natural way
    • Cullen,B. (2005) Rnai the natural way. Nat. Genet., 37, 1163-1165.
    • (2005) Nat. Genet. , vol.37 , pp. 1163-1165
    • Cullen, B.1
  • 15
    • 84883484291 scopus 로고    scopus 로고
    • 30 July 2013, date last accessed)
    • Donnell,P et al. (2013) CoNtRol. http://reaction-networks.net/control/ (30 July 2013, date last accessed).
    • (2013) CoNtRol.
    • Donnell, P.1
  • 16
    • 0041631740 scopus 로고    scopus 로고
    • version 2.2. (30 July 2013, date last accessed)
    • Ellison,P. et al. (2012) Chemical reaction network toolbox. version 2.2. http://www. crnt.osu.edu/CRNTWin (30 July 2013, date last accessed).
    • (2012) Chemical reaction network toolbox
    • Ellison, P.1
  • 17
    • 0023531427 scopus 로고
    • Chemical reaction network structure and the stability of complex isothermal reactors I The deficiency zero and deficiency one theorems
    • Feinberg,M. (1987) Chemical reaction network structure and the stability of complex isothermal reactors I. The deficiency zero and deficiency one theorems. Chem. Eng. Sci., 42, 2229-68.
    • (1987) Chem. Eng. Sci. , vol.42 , pp. 2229-2268
    • Feinberg, M.1
  • 18
    • 84867575860 scopus 로고    scopus 로고
    • Preclusion of switch behavior in reaction networks with mass-action kinetics
    • Feliu,E. andWiuf,C. (2012) Preclusion of switch behavior in reaction networks with mass-action kinetics. Appl. Math. Comput., 219, 1449-1467.
    • (2012) Appl. Math. Comput. , vol.219 , pp. 1449-1467
    • Feliu, E.1    Wiuf, C.2
  • 19
    • 84861101520 scopus 로고    scopus 로고
    • A Jacobian criterion for the simultaneous injectivity on positive variables of linearly parameterized polynomials maps
    • Gnacadja,G. (2012) A Jacobian criterion for the simultaneous injectivity on positive variables of linearly parameterized polynomials maps. Linear Algebra Appl., 437, 612-622.
    • (2012) Linear Algebra Appl. , vol.437 , pp. 612-622
    • Gnacadja, G.1
  • 20
    • 84865683792 scopus 로고    scopus 로고
    • Simplifying the Jacobian criterion for precluding multistationarity in chemical reaction networks
    • Joshi,B. and Shiu,A. (2012) Simplifying the Jacobian criterion for precluding multistationarity in chemical reaction networks. SIAM J. Appl. Math., 72, 857-876.
    • (2012) SIAM J Appl. Math. , vol.72 , pp. 857-876
    • Joshi, B.1    Shiu, A.2
  • 21
    • 84871696692 scopus 로고    scopus 로고
    • Atoms of multistationarity in chemical reaction networks
    • Joshi,B. and Shiu,A. (2013) Atoms of multistationarity in chemical reaction networks. J. Math. Chem., 51, 153-178.
    • (2013) J. Math. Chem. , vol.51 , pp. 153-178
    • Joshi, B.1    Shiu, A.2
  • 22
    • 0033982936 scopus 로고    scopus 로고
    • Kegg: Kyoto encyclopedia of genes and genomes
    • Kanehisa,M. and Goto,S. (2000) Kegg: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res., 28, 27-30.
    • (2000) Nucleic Acids Res. , vol.28 , pp. 27-30
    • Kanehisa, M.1    Goto, S.2
  • 23
    • 34548729774 scopus 로고    scopus 로고
    • A new necessary condition on interaction graphs for multistationarity
    • Kaufman,M. et al. (2007) A new necessary condition on interaction graphs for multistationarity. J. Theor. Biol., 248, 675-685.
    • (2007) J. Theor. Biol. , vol.248 , pp. 675-685
    • Kaufman, M.1
  • 24
    • 33744544180 scopus 로고    scopus 로고
    • Fractal reaction kinetics
    • Kopelman,R. (1998) Fractal reaction kinetics. Science, 241, 1620-1626.
    • (1998) Science , vol.241 , pp. 1620-1626
    • Kopelman, R.1
  • 25
    • 77953934646 scopus 로고    scopus 로고
    • BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
    • Li,C. et al. (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst. Biol., 4, 92.
    • (2010) BMC Syst. Biol. , vol.4 , pp. 92
    • Li, C.1
  • 26
    • 79952754267 scopus 로고    scopus 로고
    • Bistability and oscillations in gene regulation mediated by small noncoding rnas
    • Liu,D. et al. (2011) Bistability and oscillations in gene regulation mediated by small noncoding rnas. PLoS One, 6, e17029.
    • (2011) PLoS One , vol.6
    • Liu, D.1
  • 27
    • 0842288229 scopus 로고    scopus 로고
    • Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades
    • Markevich,N.I. et al. (2004) Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J. Cell Biol., 164, 353-359.
    • (2004) J. Cell Biol. , vol.164 , pp. 353-359
    • Markevich, N.I.1
  • 29
    • 35248861103 scopus 로고    scopus 로고
    • Efficient degradation and expression prioritization with small RNAs
    • Mitarai,N. et al. (2007) Efficient degradation and expression prioritization with small RNAs. Phys. Biol., 4, 164-71.
    • (2007) Phys. Biol. , vol.4 , pp. 164-171
    • Mitarai, N.1
  • 31
    • 84863623375 scopus 로고    scopus 로고
    • Characterizing multistationarity regimes in biochemical reaction networks
    • Otero-Muras,I. et al. (2012) Characterizing multistationarity regimes in biochemical reaction networks. PLoS One, 7, e39194.
    • (2012) PLoS One , vol.7
    • Otero-Muras, I.1
  • 32
    • 84859211122 scopus 로고    scopus 로고
    • Chemical reaction systems with toric steady states
    • Pérez Millá n,M. et al. (2012) Chemical reaction systems with toric steady states. Bull. Math. Biol., 74, 1027-1065.
    • (2012) Bull. Math. Biol. , vol.74 , pp. 1027-1065
    • Pérez Millán, M.1
  • 33
    • 84883486238 scopus 로고    scopus 로고
    • Pocab: A software infrastructure to explore algebraic methods for bio-chemical reaction networks
    • Samal,S.S. et al. (2012) Pocab: A software infrastructure to explore algebraic methods for bio-chemical reaction networks. Lect. Notes Comput. Sci., 7442, 294-307.
    • (2012) Lect. Notes Comput. Sci. , vol.7442 , pp. 294-307
    • Samal, S.S.1
  • 34
    • 0031853923 scopus 로고    scopus 로고
    • Development of fractal kinetic theory for enzyme-catalyzed reactions and implications for the design of biochemical pathways
    • Savageau,M.A. (1998) Development of fractal kinetic theory for enzyme-catalyzed reactions and implications for the design of biochemical pathways. BioSystems, 47, 9-36.
    • (1998) BioSystems , vol.47 , pp. 9-36
    • Savageau, M.A.1
  • 35
    • 2442543316 scopus 로고    scopus 로고
    • Reaction kinetics in intracellular environments with macromolecular crowding: Simulations and rate laws
    • Schnell,S. and Turner,T.E. (2004) Reaction kinetics in intracellular environments with macromolecular crowding: Simulations and rate laws. Progr. Biophys. Mol. Biol., 85, 235-260.
    • (2004) Progr. Biophys. Mol. Biol. , vol.85 , pp. 235-260
    • Schnell, S.1    Turner, T.E.2
  • 36
    • 84867854824 scopus 로고    scopus 로고
    • Concordant chemical reaction networks
    • Shinar,G. and Feinberg,M. (2012) Concordant chemical reaction networks. Math. Biosci., 240, 92-113.
    • (2012) Math. Biosci. , vol.240 , pp. 92-113
    • Shinar, G.1    Feinberg, M.2
  • 37
    • 80055040254 scopus 로고    scopus 로고
    • Designing attractive models via automated identification of chaotic and oscillatory dynamical regimes
    • Silk,D. et al. (2011) Designing attractive models via automated identification of chaotic and oscillatory dynamical regimes. Nat. Comm., 2, 489.
    • (2011) Nat. Comm. , vol.2 , pp. 489
    • Silk, D.1
  • 38
    • 70350672602 scopus 로고    scopus 로고
    • ERNEST: A toolbox for chemical reaction network theory
    • Soranzo,N. and Altafini,C. (2009) ERNEST: A toolbox for chemical reaction network theory. Bioinformatics, 25, 2853-2854.
    • (2009) Bioinformatics , vol.25 , pp. 2853-2854
    • Soranzo, N.1    Altafini, C.2
  • 39
    • 7744230024 scopus 로고    scopus 로고
    • Graphic requirements for multistationarity
    • Soulé,C. (2003) Graphic requirements for multistationarity. ComPlexUs, 1, 123-133.
    • (2003) ComPlexUs , vol.1 , pp. 123-133
    • Soulé, C.1
  • 40
    • 84861734149 scopus 로고    scopus 로고
    • CRNreals: A toolbox for distinguishability and identifiability analysis of biochemical reaction networks
    • Szederkényi,G. et al. (2012) CRNreals: A toolbox for distinguishability and identifiability analysis of biochemical reaction networks. Bioinformatics, 28, 1549-1550.
    • (2012) Bioinformatics , vol.28 , pp. 1549-1550
    • Szederkényi, G.1
  • 42
    • 42149099412 scopus 로고    scopus 로고
    • On the number of steady states in a multiple futile cycle
    • Wang,L. and Sontag,E.D. (2008) On the number of steady states in a multiple futile cycle. J. Math. Biol., 57, 29-52.
    • (2008) J. Math. Biol. , vol.57 , pp. 29-52
    • Wang, L.1    Sontag, E.D.2
  • 43
    • 84883473729 scopus 로고    scopus 로고
    • Power-law kinetics and determinant criteria for the preclusion of multistationarity in networks of interacting species
    • to appear
    • Wiuf,C. and Feliu,E. (2013) Power-law kinetics and determinant criteria for the preclusion of multistationarity in networks of interacting species. SIAM J. Appl. Dyn. Syst., to appear.
    • (2013) SIAM J Appl. Dyn. Syst.
    • Wiuf, C.1    Feliu, E.2
  • 44
    • 44649094594 scopus 로고    scopus 로고
    • Kinetic oscillations in the expression of messenger RNA regulatory protein, and nonprotein coding RNA
    • Zhdanov,V.P. (2008) Kinetic oscillations in the expression of messenger RNA, regulatory protein, and nonprotein coding RNA. Chem. Phys. Lett., 458, 359-362.
    • (2008) Chem. Phys. Lett. , vol.458 , pp. 359-362
    • Zhdanov, V.P.1
  • 45
    • 56949102344 scopus 로고    scopus 로고
    • Bistability in gene transcription: Interplay of messenger RNA, protein, and nonprotein coding RNA
    • Zhdanov,V.P. (2009) Bistability in gene transcription: Interplay of messenger RNA, protein, and nonprotein coding RNA. Biosystems, 95, 75-81.
    • (2009) Biosystems , vol.95 , pp. 75-81
    • Zhdanov, V.P.1
  • 46
    • 79959975090 scopus 로고    scopus 로고
    • Kinetic models of the interference of gene transcription to ncRNA and mRNA
    • Zhdanov,V.P. (2011) Kinetic models of the interference of gene transcription to ncRNA and mRNA. Chaos, 21, 023135.
    • (2011) Chaos , vol.21 , pp. 023135
    • Zhdanov, V.P.1


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