-
1
-
-
0037079054
-
Computational systems biology
-
Kitano H (2002) Computational systems biology. Nature 420: 206-210.
-
(2002)
Nature
, vol.420
, pp. 206-210
-
-
Kitano, H.1
-
2
-
-
29544448913
-
Extension of a genetic network model by iterative experimentation and mathematical analysis
-
Locke JCW, Southern MM, Kozma-Bognr L, Hibberd V, Brown PE, et al. (2005) Extension of a genetic network model by iterative experimentation and mathematical analysis. Mol Syst Biol 1: 0013.
-
(2005)
Mol Syst Biol
, vol.1
, pp. 0013
-
-
Locke, J.C.W.1
Southern, M.M.2
Kozma-Bognr, L.3
Hibberd, V.4
Brown, P.E.5
-
5
-
-
33745780500
-
Network motifs: Structure does not determine function
-
Ingram PJ, Stumpf MPH, Stark J (2006) Network motifs: Structure does not determine function. BMC Genomics 7: 108.
-
(2006)
BMC Genomics
, vol.7
, pp. 108
-
-
Ingram, P.J.1
Stumpf, M.P.H.2
Stark, J.3
-
6
-
-
33646167129
-
Plasticity of the cis-regulatory input function of a gene
-
doi:10.1371/journal. pbio.0040045
-
Mayo AE, Setty Y, Shavit S, Zaslaver A, Alon U (2006) Plasticity of the cis-regulatory input function of a gene. PLoS Biol 4: e45. doi:10.1371/journal. pbio.0040045
-
(2006)
PLoS Biol
, vol.4
-
-
Mayo, A.E.1
Setty, Y.2
Shavit, S.3
Zaslaver, A.4
Alon, U.5
-
7
-
-
17644427718
-
Causal protein-signaling networks derived from multiparameter single-cell data
-
Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP (2005) Causal protein-signaling networks derived from multiparameter single-cell data. Science 308: 523-529.
-
(2005)
Science
, vol.308
, pp. 523-529
-
-
Sachs, K.1
Perez, O.2
Pe'er, D.3
Lauffenburger, D.A.4
Nolan, G.P.5
-
8
-
-
33846467150
-
A systems approach to measuring the binding energy landscapes of transcription factors
-
Maerkl SJ, Quake SR (2007) A systems approach to measuring the binding energy landscapes of transcription factors. Science 315: 233-237.
-
(2007)
Science
, vol.315
, pp. 233-237
-
-
Maerkl, S.J.1
Quake, S.R.2
-
9
-
-
0035815743
-
The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media
-
Minton AP (2001) The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media. J Biol Chem 276: 10577-10580.
-
(2001)
J Biol Chem
, vol.276
, pp. 10577-10580
-
-
Minton, A.P.1
-
10
-
-
0033857139
-
Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry
-
Teusink B, Passarge J, Reijenga CA, Esgalhado E, van der Weijden CC, et al. (2000) Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur J Biochem 267: 5313-5329.
-
(2000)
Eur J Biochem
, vol.267
, pp. 5313-5329
-
-
Teusink, B.1
Passarge, J.2
Reijenga, C.A.3
Esgalhado, E.4
van der Weijden, C.C.5
-
11
-
-
0032406131
-
Nonlinear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation
-
Mendes P, Kell D (1998) Nonlinear optimization of biochemical pathways: Applications to metabolic engineering and parameter estimation. Bioinformatics 14: 869-883.
-
(1998)
Bioinformatics
, vol.14
, pp. 869-883
-
-
Mendes, P.1
Kell, D.2
-
12
-
-
33750374139
-
Linking data to models: Data regression
-
Jaqaman K, Danuser G (2006) Linking data to models: Data regression. Nat Rev Mol Cell Biol 7: 813-819.
-
(2006)
Nat Rev Mol Cell Biol
, vol.7
, pp. 813-819
-
-
Jaqaman, K.1
Danuser, G.2
-
13
-
-
0023657252
-
Characterization of binding equilibrium data by a variety of fitted isotherms
-
Brodersen R, Nielsen F, Christiansen JC, Andersen K (1987) Characterization of binding equilibrium data by a variety of fitted isotherms. Eur J Biochem 169: 487-495.
-
(1987)
Eur J Biochem
, vol.169
, pp. 487-495
-
-
Brodersen, R.1
Nielsen, F.2
Christiansen, J.C.3
Andersen, K.4
-
14
-
-
32044474451
-
A hybrid approach for efficient and robust parameter estimation in biochemical pathways
-
Rodriguez-Fernandez M, Mendes P, Banga JR (2006) A hybrid approach for efficient and robust parameter estimation in biochemical pathways. Biosystems 83: 248-265.
-
(2006)
Biosystems
, vol.83
, pp. 248-265
-
-
Rodriguez-Fernandez, M.1
Mendes, P.2
Banga, J.R.3
-
15
-
-
1342265607
-
Experimental design in systems biology, based on parameter sensitivity analysis using a Monte Carlo method: A case study for the TNFα mediated NF-κB signal transduction pathway
-
Cho KH, Shin SY, Kolch W, Wolkenhauer O (2003) Experimental design in systems biology, based on parameter sensitivity analysis using a Monte Carlo method: A case study for the TNFα mediated NF-κB signal transduction pathway. Simulation 79: 726-739.
-
(2003)
Simulation
, vol.79
, pp. 726-739
-
-
Cho, K.H.1
Shin, S.Y.2
Kolch, W.3
Wolkenhauer, O.4
-
17
-
-
2642513030
-
Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space
-
Wiback S, Famili I, Greenberg HJ, Palsson BØ (2004) Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space. J Theor Biol 228: 437-447.
-
(2004)
J Theor Biol
, vol.228
, pp. 437-447
-
-
Wiback, S.1
Famili, I.2
Greenberg, H.J.3
Palsson, B.4
-
18
-
-
21244477594
-
k-Cone analysis: Determining all candidate values for kinetic parameters on a network scale
-
Wiback S, Famili I, Mahadevan R, Palsson BØ (2005) k-Cone analysis: Determining all candidate values for kinetic parameters on a network scale. Biophys J 88: 1616-1625.
-
(2005)
Biophys J
, vol.88
, pp. 1616-1625
-
-
Wiback, S.1
Famili, I.2
Mahadevan, R.3
Palsson, B.4
-
19
-
-
0034995375
-
Complex biology with no parameters
-
Bailey JE (2001) Complex biology with no parameters. Nat Biotechnol 19: 503-504.
-
(2001)
Nat Biotechnol
, vol.19
, pp. 503-504
-
-
Bailey, J.E.1
-
20
-
-
42749109054
-
Statistical mechanical approaches to models with many poorly known parameters
-
Brown KS, Sethna JP (2003) Statistical mechanical approaches to models with many poorly known parameters. Phys Rev E 68: 021904.
-
(2003)
Phys Rev E
, vol.68
, pp. 021904
-
-
Brown, K.S.1
Sethna, J.P.2
-
21
-
-
33748557777
-
The statistical mechanics of complex signaling networks: Nerve growth factor signaling
-
Brown KS, Hill CC, Calero GA, Myers CR, Lee KH, et al. (2004) The statistical mechanics of complex signaling networks: Nerve growth factor signaling. Phys Biol 1: 184-195.
-
(2004)
Phys Biol
, vol.1
, pp. 184-195
-
-
Brown, K.S.1
Hill, C.C.2
Calero, G.A.3
Myers, C.R.4
Lee, K.H.5
-
23
-
-
33750016873
-
Sloppy-model universality class and the Vandermonde matrix
-
Waterfall JJ, Casey FP, Gutenkunst RN, Brown KS, Myers CR, et al. (2006) Sloppy-model universality class and the Vandermonde matrix. Phys Rev Lett 97: 150601.
-
(2006)
Phys Rev Lett
, vol.97
, pp. 150601
-
-
Waterfall, J.J.1
Casey, F.P.2
Gutenkunst, R.N.3
Brown, K.S.4
Myers, C.R.5
-
24
-
-
1342286938
-
Simulation methods for optimal experimental design in systems biology
-
Faller D, Klingmuller U, Timmer J (2003) Simulation methods for optimal experimental design in systems biology. Simulation 79: 717-725.
-
(2003)
Simulation
, vol.79
, pp. 717-725
-
-
Faller, D.1
Klingmuller, U.2
Timmer, J.3
-
25
-
-
0242490789
-
Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: Insights from an identifiability analysis of an in silico network
-
Zak DE, Gonye GE, Schwaber JS, Doyle FJ III (2003) Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: Insights from an identifiability analysis of an in silico network. Genome Res 13: 2396-2405.
-
(2003)
Genome Res
, vol.13
, pp. 2396-2405
-
-
Zak, D.E.1
Gonye, G.E.2
Schwaber, J.S.3
Doyle III, F.J.4
-
26
-
-
21644489637
-
Model identification of signal transduction networks from data using a state regulator problem
-
Gadkar KG, Varner J, Doyle FJ III (2005) Model identification of signal transduction networks from data using a state regulator problem. IEEE Syst Biol 2: 17-30.
-
(2005)
IEEE Syst Biol
, vol.2
, pp. 17-30
-
-
Gadkar, K.G.1
Varner, J.2
Doyle III, F.J.3
-
27
-
-
34249744604
-
Optimal experimental design in an epidermal growth factor receptor signalling and downregulation model. IET
-
Casey FP, Baird D, Feng Q, Gutenkunst RN, Waterfall JJ, et al. (2007) Optimal experimental design in an epidermal growth factor receptor signalling and downregulation model. IET Syst Biol 1: 190-202.
-
(2007)
Syst Biol
, vol.1
, pp. 190-202
-
-
Casey, F.P.1
Baird, D.2
Feng, Q.3
Gutenkunst, R.N.4
Waterfall, J.J.5
-
28
-
-
0025826876
-
Modeling the cell division cycle: Cdc2 and cyclin interactions
-
Tyson JJ (1991) Modeling the cell division cycle: cdc2 and cyclin interactions. Proc Natl Acad Sci U S A 88: 7328-7332.
-
(1991)
Proc Natl Acad Sci U S A
, vol.88
, pp. 7328-7332
-
-
Tyson, J.J.1
-
29
-
-
22144476845
-
Globally optimised parameters for a model of mitotic control in frog egg extracts
-
Zwolak JW, Tyson JJ, Watson LT (2005) Globally optimised parameters for a model of mitotic control in frog egg extracts. Syst Biol (Stevenage) 152: 81-92.
-
(2005)
Syst Biol (Stevenage)
, vol.152
, pp. 81-92
-
-
Zwolak, J.W.1
Tyson, J.J.2
Watson, L.T.3
-
30
-
-
0026006671
-
A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase
-
Goldbeter A (1991) A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase. Proc Natl Acad Sci U S A 88: 9107-9111.
-
(1991)
Proc Natl Acad Sci U S A
, vol.88
, pp. 9107-9111
-
-
Goldbeter, A.1
-
32
-
-
0030281174
-
A kinetic mechanism for nicotinic acetylcholine receptors based on multiple allosteric transitions
-
Edelstein SJ, Schaad O, Henry E, Bertrand D, Changeux JP (1996) A kinetic mechanism for nicotinic acetylcholine receptors based on multiple allosteric transitions. Biol Cybern 75: 361-379.
-
(1996)
Biol Cybern
, vol.75
, pp. 361-379
-
-
Edelstein, S.J.1
Schaad, O.2
Henry, E.3
Bertrand, D.4
Changeux, J.P.5
-
33
-
-
0034019315
-
Negative feedback and ultrasensitivity can bring about oscillations in the mitogen activated protein kinase cascades
-
Kholodenko BN (2000) Negative feedback and ultrasensitivity can bring about oscillations in the mitogen activated protein kinase cascades. Eur J Biochem 267: 1583-1588.
-
(2000)
Eur J Biochem
, vol.267
, pp. 1583-1588
-
-
Kholodenko, B.N.1
-
34
-
-
4243067196
-
The roles of APC and Axin derived from experimental and theoretical analysis of the Wnt pathway
-
doi:10.1371/journal.pbio.0000010
-
Lee E, Salic A, Kruger R, Heinrich R, Kirschner MW (2003) The roles of APC and Axin derived from experimental and theoretical analysis of the Wnt pathway. PLoS Biol 1: e10. doi:10.1371/journal.pbio.0000010
-
(2003)
PLoS Biol
, vol.1
-
-
Lee, E.1
Salic, A.2
Kruger, R.3
Heinrich, R.4
Kirschner, M.W.5
-
35
-
-
0033532569
-
Chaos and birhythmicity in a model for circadian oscillations of the PER and TIM proteins in drosophila
-
Leloup JC, Goldbeter A (1999) Chaos and birhythmicity in a model for circadian oscillations of the PER and TIM proteins in drosophila. J Theor Biol 198: 445-459.
-
(1999)
J Theor Biol
, vol.198
, pp. 445-459
-
-
Leloup, J.C.1
Goldbeter, A.2
-
36
-
-
0034644270
-
The segment polarity network is a robust developmental module
-
von Dassow G, Meir E, Munro EM, Odell GM (2000) The segment polarity network is a robust developmental module. Nature 406: 188-192.
-
(2000)
Nature
, vol.406
, pp. 188-192
-
-
von Dassow, G.1
Meir, E.2
Munro, E.M.3
Odell, G.M.4
-
37
-
-
0035927611
-
Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm
-
Ueda HR, Hagiwara M, Kitano H (2001) Robust oscillations within the interlocked feedback model of Drosophila circadian rhythm. J Theor Biol 210: 401-406.
-
(2001)
J Theor Biol
, vol.210
, pp. 401-406
-
-
Ueda, H.R.1
Hagiwara, M.2
Kitano, H.3
-
39
-
-
0037025146
-
Dynamic modeling of the central carbon metabolism of Escherichia coli
-
Chassagnole C, Noisommit-Rizzi N, Schmid JW, Mauch K, Reuss M (2002) Dynamic modeling of the central carbon metabolism of Escherichia coli. Biotechnol Bioeng 79: 53-73.
-
(2002)
Biotechnol Bioeng
, vol.79
, pp. 53-73
-
-
Chassagnole, C.1
Noisommit-Rizzi, N.2
Schmid, J.W.3
Mauch, K.4
Reuss, M.5
-
40
-
-
3343020085
-
Integrative analysis of cell cycle control in budding yeast
-
Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, et al. (2004) Integrative analysis of cell cycle control in budding yeast. Mol Biol Cell 15: 3841-3862.
-
(2004)
Mol Biol Cell
, vol.15
, pp. 3841-3862
-
-
Chen, K.C.1
Calzone, L.2
Csikasz-Nagy, A.3
Cross, F.R.4
Novak, B.5
-
41
-
-
17344362384
-
Prediction and validation of the distinct dynamics of transient and sustained ERK activation
-
Sasagawa S, Ozaki Y, Fujita K, Kuroda S (2005) Prediction and validation of the distinct dynamics of transient and sustained ERK activation. Nat Cell Biol 7: 365-373.
-
(2005)
Nat Cell Biol
, vol.7
, pp. 365-373
-
-
Sasagawa, S.1
Ozaki, Y.2
Fujita, K.3
Kuroda, S.4
-
42
-
-
33644877164
-
BioModels Database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
-
Le Novere N, Bornstein B, Broicher A, Courtot M, Donizelli M, et al. (2006) BioModels Database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 34: D689-D691.
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Le Novere, N.1
Bornstein, B.2
Broicher, A.3
Courtot, M.4
Donizelli, M.5
-
43
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, et al. (2003) The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19: 524-531.
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
-
44
-
-
34548383316
-
-
Available:, Accessed 5 September
-
Gutenkunst RN, Casey FP, Waterfall JJ, Atlas JC, Kuczenski RS, et al. SloppyCell. Available: http://sloppycell.sourceforge.net. Accessed 5 September 2007.
-
(2007)
SloppyCell
-
-
Gutenkunst, R.N.1
Casey, F.P.2
Waterfall, J.J.3
Atlas, J.C.4
Kuczenski, R.S.5
-
45
-
-
0004163930
-
-
3rd edition. Amsterdam: Academic Press. 706 p
-
Mehta ML (2004) Random Matrices. 3rd edition. Amsterdam: Academic Press. 706 p.
-
(2004)
Random Matrices
-
-
Mehta, M.L.1
|