-
2
-
-
84883467711
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
-
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
-
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
|