-
1
-
-
0034614334
-
A long twentieth century of the cell cycle and beyond
-
Nurse, P. A long twentieth century of the cell cycle and beyond. Cell 100, 71-78 (2000).
-
(2000)
Cell
, vol.100
, pp. 71-78
-
-
Nurse, P.1
-
2
-
-
0037727678
-
Metabolic pathways in the post-genome era
-
Papin, J. A., Price, N. D., Wiback, S. J., Fell, D. A. & Palsson, B. O. Metabolic pathways in the post-genome era. Trends Biochem. Sci. 28, 250-258 (2003).
-
(2003)
Trends Biochem. Sci.
, vol.28
, pp. 250-258
-
-
Papin, J.A.1
Price, N.D.2
Wiback, S.J.3
Fell, D.A.4
Palsson, B.O.5
-
3
-
-
0344328817
-
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)
-
Reed, J. L., Vo, T. D., Schilling, C. H. & Palsson, B. O. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 4, R54 (2003).
-
(2003)
Genome Biol.
, vol.4
-
-
Reed, J.L.1
Vo, T.D.2
Schilling, C.H.3
Palsson, B.O.4
-
4
-
-
0037047611
-
MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network
-
Bhalla, U. S., Ram, P. T. & Iyengar, R. MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 297, 1018-1023 (2002).
-
(2002)
Science
, vol.297
, pp. 1018-1023
-
-
Bhalla, U.S.1
Ram, P.T.2
Iyengar, R.3
-
5
-
-
0037044575
-
The IκB-NF-κB signaling module: Temporal control and selective gene activation
-
Hoffmann, A., Levchenko, A., Scott, M. L. & Baltimore, D. The IκB-NF-κB signaling module: Temporal control and selective gene activation. Science 298, 1241-1245 (2002).
-
(2002)
Science
, vol.298
, pp. 1241-1245
-
-
Hoffmann, A.1
Levchenko, A.2
Scott, M.L.3
Baltimore, D.4
-
6
-
-
0029790351
-
Ultrasensitivity in the mitogen-activated protein kinase cascade
-
Huang, C. Y. & Ferrell, J. E., Jr. Ultrasensitivity in the mitogen-activated protein kinase cascade. Proc. Natl Acad. Sci. USA 93, 10078-10083 (1996).
-
(1996)
Proc. Natl Acad. Sci. USA
, vol.93
, pp. 10078-10083
-
-
Huang, C.Y.1
Ferrell Jr., J.E.2
-
7
-
-
0842288229
-
Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades
-
Markevich, N. I., Hoek, J. B. & Kholodenko, B. N. Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J. Cell Biol. 164, 353-359 (2004).
-
(2004)
J. Cell Biol.
, vol.164
, pp. 353-359
-
-
Markevich, N.I.1
Hoek, J.B.2
Kholodenko, B.N.3
-
8
-
-
0036212767
-
Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors
-
Schoeberl, B., Eichler-Jonsson, C., Gilles, E. D. & Muller, G. Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nature Biotechnol. 20, 370-375 (2002).
-
(2002)
Nature Biotechnol.
, vol.20
, pp. 370-375
-
-
Schoeberl, B.1
Eichler-Jonsson, C.2
Gilles, E.D.3
Muller, G.4
-
9
-
-
33746889808
-
A comprehensive pathway map of epidermal growth factor receptor signaling
-
Oda, K., Matsuoka, Y., Funahashi, A. & Kitano, H. A comprehensive pathway map of epidermal growth factor receptor signaling. Mol. Syst. Biol. 1, 0010 (2005).
-
(2005)
Mol. Syst. Biol.
, vol.1
, pp. 0010
-
-
Oda, K.1
Matsuoka, Y.2
Funahashi, A.3
Kitano, H.4
-
11
-
-
33745027397
-
Quantitative fluorescent speckle microscopy of cytoskeleton dynamics
-
Danuser, G. & Waterman-Storer, C. M. Quantitative fluorescent speckle microscopy of cytoskeleton dynamics. Annu. Rev. Biophys. Biomol. Struct. 35, 361-387 (2006).
-
(2006)
Annu. Rev. Biophys. Biomol. Struct.
, vol.35
, pp. 361-387
-
-
Danuser, G.1
Waterman-Storer, C.M.2
-
12
-
-
0032825265
-
Regulated actin cytoskeleton assembly at filopodium tips controls their extension and retraction
-
Mallavarapu, A. & Mitchison, T. Regulated actin cytoskeleton assembly at filopodium tips controls their extension and retraction. J. Cell Biol. 146, 1097-1106 (1999).
-
(1999)
J. Cell Biol.
, vol.146
, pp. 1097-1106
-
-
Mallavarapu, A.1
Mitchison, T.2
-
13
-
-
0029000524
-
Time series characterization of simulated microtubule dynamics in the nerve growth cone
-
Odde, D. J. & Buettner, H. M. Time series characterization of simulated microtubule dynamics in the nerve growth cone. Ann. Biomed. Eng. 23, 268-286 (1995).
-
(1995)
Ann. Biomed. Eng.
, vol.23
, pp. 268-286
-
-
Odde, D.J.1
Buettner, H.M.2
-
14
-
-
4544309783
-
Two distinct actin networks drive the protrusion of migrating cells
-
Ponti, A., Machacek, M., Gupton, S. L., Waterman-Storer, C. M. & Danuser, G. Two distinct actin networks drive the protrusion of migrating cells. Science 305, 1782-1786 (2004).
-
(2004)
Science
, vol.305
, pp. 1782-1786
-
-
Ponti, A.1
Machacek, M.2
Gupton, S.L.3
Waterman-Storer, C.M.4
Danuser, G.5
-
15
-
-
0031029852
-
Stochastic mechanisms in gene expression
-
McAdams, H. H. & Arkin, A. Stochastic mechanisms in gene expression. Proc. Natl Acad. Sci. USA 94, 814-819 (1997).
-
(1997)
Proc. Natl Acad. Sci. USA
, vol.94
, pp. 814-819
-
-
McAdams, H.H.1
Arkin, A.2
-
16
-
-
0842285841
-
Summing up the noise in gene networks
-
Paulsson, J. Summing up the noise in gene networks. Nature 427, 415-418 (2004).
-
(2004)
Nature
, vol.427
, pp. 415-418
-
-
Paulsson, J.1
-
17
-
-
33645238574
-
A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks
-
Conzelmann, H., Saez-Rodriguez, J., Sauter, T., Kholodenko, B. N. & Gilles, E. D. A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks. BMC Bioinformatics 7, 34 (2006).
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 34
-
-
Conzelmann, H.1
Saez-Rodriguez, J.2
Sauter, T.3
Kholodenko, B.N.4
Gilles, E.D.5
-
18
-
-
32044469862
-
A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity
-
Blinov, M. L., Faeder, J. R., Goldstein, B. & Hlavacek, W. S. A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity. Biosystems 83, 136-151 (2006).
-
(2006)
Biosystems
, vol.83
, pp. 136-151
-
-
Blinov, M.L.1
Faeder, J.R.2
Goldstein, B.3
Hlavacek, W.S.4
-
19
-
-
33747366698
-
Rules for modeling signal-transduction systems
-
Hlavacek, W. S. et al. Rules for modeling signal-transduction systems. Sci. STKE re6 (2006).
-
(2006)
Sci. STKE
-
-
Hlavacek, W.S.1
-
20
-
-
33846027696
-
Particle-Based Stochastic Simulation in Systems Biology
-
Tolle, D. P. & Le Novere, N. Particle-Based Stochastic Simulation in Systems Biology. Current Bioinformatics 1, 1-6 (2006).
-
(2006)
Current Bioinformatics
, vol.1
, pp. 1-6
-
-
Tolle, D.P.1
Le Novere, N.2
-
21
-
-
0034688174
-
Construction of a genetic toggle switch in Escherichia coli
-
Gardner, T. S., Cantor, C. R. & Collins, J. J. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339-342 (2000).
-
(2000)
Nature
, vol.403
, pp. 339-342
-
-
Gardner, T.S.1
Cantor, C.R.2
Collins, J.J.3
-
22
-
-
0037376655
-
Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell
-
Tyson, J. J., Chen, K. C. & Novak, B. Sniffers, buzzers, toggles and blinkers: Dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 15, 221-231 (2003).
-
(2003)
Curr. Opin. Cell Biol.
, vol.15
, pp. 221-231
-
-
Tyson, J.J.1
Chen, K.C.2
Novak, B.3
-
23
-
-
0034644270
-
The segment polarity network is a robust developmental module
-
von Dassow, G., Meir, E., Munro, E. M. & Odell, G. M. The segment polarity network is a robust developmental module. Nature 406, 188-192 (2000).
-
(2000)
Nature
, vol.406
, pp. 188-192
-
-
von Dassow, G.1
Meir, E.2
Munro, E.M.3
Odell, G.M.4
-
24
-
-
52949112270
-
-
in (eds. Szallasi, Z., Stelling, J. & Periwal, V.) (MIT Press, Cambridge
-
Conrad, E. D. & Tyson, J. J. in System Modeling in Cellular Biology (eds. Szallasi, Z., Stelling, J. & Periwal, V.) 97-123 (MIT Press, Cambridge, 2006).
-
(2006)
System Modeling in Cellular Biology
, pp. 97-123
-
-
Conrad, E.D.1
Tyson, J.J.2
-
25
-
-
33750501661
-
The steady-state assumption: Fact or fiction?
-
Farrow, L. A. & Edelson, D. The steady-state assumption: Fact or fiction? Int. J. Chem. Kin. 1, 309-322 (1974).
-
(1974)
Int. J. Chem. Kin.
, vol.1
, pp. 309-322
-
-
Farrow, L.A.1
Edelson, D.2
-
26
-
-
33746626536
-
Use and abuse of the quasi-steady-state approximation
-
Flach, E. H. & Schnell, S. Use and abuse of the quasi-steady-state approximation. IEE Proc. Syst. Biol. 153, 187-191 (2006).
-
(2006)
IEE Proc. Syst. Biol.
, vol.153
, pp. 187-191
-
-
Flach, E.H.1
Schnell, S.2
-
27
-
-
0023734558
-
On the validity of the steady state assumption of enzyme kinetics
-
Segel, L. A. On the validity of the steady state assumption of enzyme kinetics. Bull. Math. Biol. 50, 579-593 (1988).
-
(1988)
Bull. Math. Biol.
, vol.50
, pp. 579-593
-
-
Segel, L.A.1
-
30
-
-
33746604865
-
Parametric estimation in models combining signal transduction and metabolic pathways: The dependent input approach
-
van Riel, N. A. W. & Sontag, E. D. Parametric estimation in models combining signal transduction and metabolic pathways: The dependent input approach. IEE Proc.Syst. Biol. 153, 263-274 (2006).
-
(2006)
IEE Proc.Syst. Biol.
, vol.153
, pp. 263-274
-
-
van Riel, N.A.W.1
Sontag, E.D.2
-
31
-
-
33745451921
-
Oscillations and variability in the p53 system
-
Geva-Zatorsky, N. et al. Oscillations and variability in the p53 system. Mol. Syst. Biol. 2, 0033 (2006).
-
(2006)
Mol. Syst. Biol.
, vol.2
, pp. 0033
-
-
Geva-Zatorsky, N.1
-
32
-
-
33750809764
-
Direct Lyaponov exponent analysis enables parametric study of transient signalling governing cell behaviour
-
Aldridge, B. B., Haller, G., Sorger, P. K. & Lauffenburger, D. A. Direct Lyaponov exponent analysis enables parametric study of transient signalling governing cell behaviour. IEE Proc. Syst. Biol. 153, (2006).
-
(2006)
IEE Proc. Syst. Biol.
, pp. 153
-
-
Aldridge, B.B.1
Haller, G.2
Sorger, P.K.3
Lauffenburger, D.A.4
-
33
-
-
4544246088
-
Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis
-
Bentele, M. et al. Mathematical modeling reveals threshold mechanism in CD95-induced apoptosis. J. Cell Biol. 166, 839-851 (2004).
-
(2004)
J. Cell Biol.
, vol.166
, pp. 839-851
-
-
Bentele, M.1
-
35
-
-
33750505067
-
-
in (eds. Marsden, J. E., Sirovich, L. & Antman, S. S.) (Springer-Verlag, New York
-
Wiggins, S. in Introduction to Applied Nonlinear Dynamical Systems and Chaos (eds. Marsden, J. E., Sirovich, L. & Antman, S. S.) 356 (Springer-Verlag, New York, 2003).
-
(2003)
Introduction to Applied Nonlinear Dynamical Systems and Chaos
, pp. 356
-
-
Wiggins, S.1
-
37
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
Hucka, M. et al. The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
-
38
-
-
17844408690
-
A cell-centered approach to developmental biology
-
Merks, R. M. H. & Glazier, J. A. A cell-centered approach to developmental biology. Physica A 352, 113-130 (2005).
-
(2005)
Physica A
, vol.352
, pp. 113-130
-
-
Merks, R.M.H.1
Glazier, J.A.2
-
39
-
-
1642580788
-
A meeting with Enrico Fermi
-
Dyson, F. A meeting with Enrico Fermi. Nature 427, 297 (2004).
-
(2004)
Nature
, vol.427
, pp. 297
-
-
Dyson, F.1
-
40
-
-
23444439817
-
Using process diagrams for the graphical representation of biological networks
-
Kitano, H., Funahashi, A., Matsuoka, Y. & Oda, K. Using process diagrams for the graphical representation of biological networks. Nature Biotechnol. 23, 961-966 (2005).
-
(2005)
Nature Biotechnol.
, vol.23
, pp. 961-966
-
-
Kitano, H.1
Funahashi, A.2
Matsuoka, Y.3
Oda, K.4
-
41
-
-
0242574982
-
Parameter estimation in biochemical pathways: A comparison of global optimization methods
-
Moles, C. G., Mendes, P. & Banga, J. R. Parameter estimation in biochemical pathways: A comparison of global optimization methods. Genome Res. 13, 2467-2474 (2003).
-
(2003)
Genome Res.
, vol.13
, pp. 2467-2474
-
-
Moles, C.G.1
Mendes, P.2
Banga, J.R.3
-
42
-
-
33745075591
-
Tools for kinetic modeling of biochemical networks
-
Alves, R., Antunes, F. & Salvador, A. Tools for kinetic modeling of biochemical networks. Nature Biotechnol. 24, 667-672 (2006).
-
(2006)
Nature Biotechnol.
, vol.24
, pp. 667-672
-
-
Alves, R.1
Antunes, F.2
Salvador, A.3
-
43
-
-
28644433993
-
Minimum information requested in the annotation of biochemical models (MIRIAM)
-
Le Novere, N. et al. Minimum information requested in the annotation of biochemical models (MIRIAM). Nature Biotechnol 23, 1509-1515 (2005).
-
(2005)
Nature Biotechnol
, vol.23
, pp. 1509-1515
-
-
Le Novere, N.1
-
44
-
-
44049109914
-
A Rigorous Derivation of the Chemical Master Equation
-
Gillespie, D. T. A Rigorous Derivation of the Chemical Master Equation. Physica A 188, 404-425 (1992).
-
(1992)
Physica A
, vol.188
, pp. 404-425
-
-
Gillespie, D.T.1
-
45
-
-
9744247592
-
Reducing a chemical master equation by invariant manifold methods
-
Roussel, M. R. & Zhu, R. Reducing a chemical master equation by invariant manifold methods. J. Chem. Phys. 121, 8716-8730 (2004).
-
(2004)
J. Chem. Phys.
, vol.121
, pp. 8716-8730
-
-
Roussel, M.R.1
Zhu, R.2
|