-
1
-
-
0000122278
-
Statistical construction of chemical reaction mechanisms from measured time-series
-
Arkin,A. and Ross,J. (1995) Statistical construction of chemical reaction mechanisms from measured time-series. J. Phys. Chem., 99, 970-979.
-
(1995)
J. Phys. Chem.
, vol.99
, pp. 970-979
-
-
Arkin, A.1
Ross, J.2
-
2
-
-
0030848624
-
A test case of correlation metric construction of a reaction pathway from measurements
-
Arkin,A., Shen,P. and Ross,J. (1997) A test case of correlation metric construction of a reaction pathway from measurements. Science, 277, 1275-1279.
-
(1997)
Science
, vol.277
, pp. 1275-1279
-
-
Arkin, A.1
Shen, P.2
Ross, J.3
-
3
-
-
0035822634
-
Bistability in the JNK cascade
-
Bagowski,C.P. and Ferrell,J.E.,Jr. (2001) Bistability in the JNK cascade. Curr. Biol., 11, 1176-1182.
-
(2001)
Curr. Biol.
, vol.11
, pp. 1176-1182
-
-
Bagowski, C.P.1
Ferrell Jr., J.E.2
-
4
-
-
0036856356
-
A duplication growth model of gene expression networks
-
Bhan,A., Galas,D.J. and Dewey,T.G. (2002) A duplication growth model of gene expression networks. Bioinformatics, 18, 1486-1493.
-
(2002)
Bioinformatics
, vol.18
, pp. 1486-1493
-
-
Bhan, A.1
Galas, D.J.2
Dewey, T.G.3
-
5
-
-
0031203337
-
Why do protein kinase cascades have more than one level?
-
Brown,G.C., Hoek,J.B. and Kholodenko,B.N. (1997) Why do protein kinase cascades have more than one level? Trends Biochem. Sci., 22, 288.
-
(1997)
Trends Biochem. Sci.
, vol.22
, pp. 288
-
-
Brown, G.C.1
Hoek, J.B.2
Kholodenko, B.N.3
-
6
-
-
0036406361
-
Modular response analysis of cellular regulatory networks
-
Bruggeman,F.J., Westerhoff,H.V., Hoek,J.B. and Kholodenko,B.N. (2002) Modular response analysis of cellular regulatory networks. J. Theor. Biol., 218, 507-520.
-
(2002)
J. Theor. Biol.
, vol.218
, pp. 507-520
-
-
Bruggeman, F.J.1
Westerhoff, H.V.2
Hoek, J.B.3
Kholodenko, B.N.4
-
8
-
-
0024673575
-
Use of implicit methods from general sensitivity theory to develop a systematic approach to metabolic control. II. Complex systems
-
Cascante,M., Franco,R. and Canela,E.I. (1989) Use of implicit methods from general sensitivity theory to develop a systematic approach to metabolic control. II. Complex systems. Math. Biosci., 94, 289-309.
-
(1989)
Math. Biosci.
, vol.94
, pp. 289-309
-
-
Cascante, M.1
Franco, R.2
Canela, E.I.3
-
9
-
-
0035282334
-
Mammalian MAP kinase signalling cascades
-
Chang,L. and Karin,M. (2001) Mammalian MAP kinase signalling cascades. Nature, 410, 37-40.
-
(2001)
Nature
, vol.410
, pp. 37-40
-
-
Chang, L.1
Karin, M.2
-
10
-
-
0001622226
-
Toward a systematic determination of complex reaction mechanisms
-
Chevalier,T., Schreiber,T. and Ross,J. (1993) Toward a systematic determination of complex reaction mechanisms. J. Phys. Chem., 97, 6776-6787.
-
(1993)
J. Phys. Chem.
, vol.97
, pp. 6776-6787
-
-
Chevalier, T.1
Schreiber, T.2
Ross, J.3
-
11
-
-
0032837252
-
Computational methods for the identification of differential and coordinated gene expression
-
Claverie,J.M. (1999) Computational methods for the identification of differential and coordinated gene expression. Hum. Mol. Genet., 8, 1821-1832.
-
(1999)
Hum. Mol. Genet.
, vol.8
, pp. 1821-1832
-
-
Claverie, J.M.1
-
12
-
-
0036683181
-
Linking the genes: Inferring quantitative gene networks from microarray data
-
de la Fuente,A., Brazhnik,P. and Mendes,P. (2002) Linking the genes: inferring quantitative gene networks from microarray data. Trends Genet., 18, 395-398.
-
(2002)
Trends Genet.
, vol.18
, pp. 395-398
-
-
de la Fuente, A.1
Brazhnik, P.2
Mendes, P.3
-
13
-
-
0033736476
-
Genetic network inference: From co-expression clustering to reverse engineering
-
D'Haeseleer,P., Liang,S. and Somogyi,R. (2000) Genetic network inference: from co-expression clustering to reverse engineering. Bioinformatics, 16, 707-726.
-
(2000)
Bioinformatics
, vol.16
, pp. 707-726
-
-
D'Haeseleer, P.1
Liang, S.2
Somogyi, R.3
-
14
-
-
0035125986
-
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
-
Edwards,J.S., Ibarra,R.U. and Palsson,B.O. (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat. Biotechnol., 19, 125-130.
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 125-130
-
-
Edwards, J.S.1
Ibarra, R.U.2
Palsson, B.O.3
-
15
-
-
0032496358
-
The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes
-
Ferrell,J.E.,Jr. and Machleder,E.M. (1998) The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science, 280, 895-898.
-
(1998)
Science
, vol.280
, pp. 895-898
-
-
Ferrell Jr., J.E.1
Machleder, E.M.2
-
16
-
-
3242882981
-
Chain functions and scoring functions in genetic networks
-
Gat-Viks,I. and Shamir,R. (2003) Chain functions and scoring functions in genetic networks. Bioinformatics, 19, I108-I117.
-
(2003)
Bioinformatics
, vol.19
-
-
Gat-Viks, I.1
Shamir, R.2
-
17
-
-
0026287765
-
The kinetics of mammalian gene expression
-
Hargrove,J.L., Hulsey,M.G. and Beale,E.G. (1991) The kinetics of mammalian gene expression. Bioessays, 13, 667-674.
-
(1991)
Bioessays
, vol.13
, pp. 667-674
-
-
Hargrove, J.L.1
Hulsey, M.G.2
Beale, E.G.3
-
18
-
-
0344464762
-
Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks
-
Husmeier,D. (2003) Sensitivity and specificity of inferring genetic regulatory interactions from microarray experiments with dynamic Bayesian networks. Bioinformatics, 19, 2271-2282.
-
(2003)
Bioinformatics
, vol.19
, pp. 2271-2282
-
-
Husmeier, D.1
-
19
-
-
0033642067
-
Discovery of regulatory interactions through perturbation: Inference and experimental design
-
Ideker,T.E., Thorsson,V. and Karp,R.M. (2000) Discovery of regulatory interactions through perturbation: inference and experimental design. Pac. Symp. Biocomput., 305-316.
-
(2000)
Pac. Symp. Biocomput.
, pp. 305-316
-
-
Ideker, T.E.1
Thorsson, V.2
Karp, R.M.3
-
20
-
-
0037466509
-
Sensitivity analysis of stoichiometric networks: An extension of metabolic control analysis to non-steady state trajectories
-
Ingalls,B.P. and Sauro,H.M. (2003) Sensitivity analysis of stoichiometric networks: an extension of metabolic control analysis to non-steady state trajectories. J. Theor. Biol., 222, 23-36.
-
(2003)
J. Theor. Biol.
, vol.222
, pp. 23-36
-
-
Ingalls, B.P.1
Sauro, H.M.2
-
21
-
-
0033667580
-
Dynamics of gene expression in rat hepatocytes under stress
-
Jayaraman,A., Yarmush,M.L. and Roth,C.M. (2000) Dynamics of gene expression in rat hepatocytes under stress. Metab. Eng., 2, 239-251.
-
(2000)
Metab. Eng.
, vol.2
, pp. 239-251
-
-
Jayaraman, A.1
Yarmush, M.L.2
Roth, C.M.3
-
22
-
-
0034019315
-
Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades
-
Kholodenko,B.N. (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
-
23
-
-
0033570090
-
Quantification of short term signaling by the epidermal growth factor receptor
-
Kholodenko,B.N., Demin,O.V., Moehren,G. and Hoek,J.B. (1999) Quantification of short term signaling by the epidermal growth factor receptor. J. Biol. Chem., 274, 30169-30181.
-
(1999)
J. Biol. Chem.
, vol.274
, pp. 30169-30181
-
-
Kholodenko, B.N.1
Demin, O.V.2
Moehren, G.3
Hoek, J.B.4
-
24
-
-
0031099173
-
Control analysis of periodic phenomena in biological systems
-
Kholodenko,B.N., Demin,O.V. and Westerhoff,H.V. (1997a) Control analysis of periodic phenomena in biological systems. J. Phys. Chem., 101, 2070-2081.
-
(1997)
J. Phys. Chem.
, vol.101
, pp. 2070-2081
-
-
Kholodenko, B.N.1
Demin, O.V.2
Westerhoff, H.V.3
-
25
-
-
0031559933
-
Quantification of information transfer via cellular signal transduction pathways
-
[Erratum (1997) FEBS Lett. 419 150.]
-
Kholodenko,B.N., Hoek,J.B., Westerhoff,H.V. and Brown,G.C. (1997b) Quantification of information transfer via cellular signal transduction pathways [Erratum (1997) FEBS Lett. 419 150.] FEBS Lett., 414, 430-434.
-
(1997)
FEBS Lett.
, vol.414
, pp. 430-434
-
-
Kholodenko, B.N.1
Hoek, J.B.2
Westerhoff, H.V.3
Brown, G.C.4
-
26
-
-
0036789922
-
Untangling the wires: A strategy to trace functional interactions in signaling and gene networks
-
Kholodenko,B.N., Kiyatkin,A., Bruggeman,F.J., Sontag,E., Westerhoff,H.V. and Hoek,J.B. (2002) Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. Proc. Natl Acad. Sci., USA, 99, 12841-12846.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 12841-12846
-
-
Kholodenko, B.N.1
Kiyatkin, A.2
Bruggeman, F.J.3
Sontag, E.4
Westerhoff, H.V.5
Hoek, J.B.6
-
27
-
-
3242704801
-
Determination of Functional Network Structure from Local Parameter Dependence Data
-
arXiv: physics/0205003
-
Kholodenko,B.N. and Sontag,E.D. (2002) Determination of Functional Network Structure from Local Parameter Dependence Data. arXiv: physics/0205003.
-
(2002)
-
-
Kholodenko, B.N.1
Sontag, E.D.2
-
28
-
-
0028836695
-
The macroworld versus the microworld of biochemical regulation and control
-
Kholodenko,B.N. and Westerhoff,H.V. (1995) The macroworld versus the microworld of biochemical regulation and control. Trends Biochem. Sci., 20, 52-54.
-
(1995)
Trends Biochem. Sci.
, vol.20
, pp. 52-54
-
-
Kholodenko, B.N.1
Westerhoff, H.V.2
-
29
-
-
0028898474
-
Control in channelled pathways. A matrix method calculating the enzyme control coefficients
-
Kholodenko,B.N., Westerhoff,H.V., Puigjaner,J. and Cascante,M. (1995) Control in channelled pathways. A matrix method calculating the enzyme control coefficients. Biophys. Chem., 53, 247-258.
-
(1995)
Biophys. Chem.
, vol.53
, pp. 247-258
-
-
Kholodenko, B.N.1
Westerhoff, H.V.2
Puigjaner, J.3
Cascante, M.4
-
30
-
-
0028829346
-
Negative feedback regulation and desensitization of insulin- and epidermal growth factor-stimulated p21ras activation
-
Langlois,W.J., Sasaoka,T., Saltiel,A.R. and Olefsky,J.M. (1995) Negative feedback regulation and desensitization of insulin- and epidermal growth factor-stimulated p21ras activation. J. Biol. Chem., 270, 25320-25323.
-
(1995)
J. Biol. Chem.
, vol.270
, pp. 25320-25323
-
-
Langlois, W.J.1
Sasaoka, T.2
Saltiel, A.R.3
Olefsky, J.M.4
-
32
-
-
0034705227
-
Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties
-
Levchenko,A., Bruck,J. and Sternberg,P.W. (2000) Scaffold proteins may biphasically affect the levels of mitogen-activated protein kinase signaling and reduce its threshold properties. Proc. Natl Acad. Sci., USA, 97, 5818-5823.
-
(2000)
Proc. Natl Acad. Sci. USA
, vol.97
, pp. 5818-5823
-
-
Levchenko, A.1
Bruck, J.2
Sternberg, P.W.3
-
33
-
-
0037069697
-
The Molecule Pages database
-
Li,J., Ning,Y., Hedley,W., Saunders,B., Chen,Y., Tindill,N., Hannay,T. and Subramaniam,S. (2002) The Molecule Pages database. Nature, 420, 716-717.
-
(2002)
Nature
, vol.420
, pp. 716-717
-
-
Li, J.1
Ning, Y.2
Hedley, W.3
Saunders, B.4
Chen, Y.5
Tindill, N.6
Hannay, T.7
Subramaniam, S.8
-
35
-
-
0037039289
-
Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model
-
Moehren,G., Markevich,N., Demin,O., Kiyatkin,A., Goryanin,I., Hoek,J.B. and Kholodenko,B.N. (2002) Temperature dependence of the epidermal growth factor receptor signaling network can be accounted for by a kinetic model. Biochemistry, 41, 306-320.
-
(2002)
Biochemistry
, vol.41
, pp. 306-320
-
-
Moehren, G.1
Markevich, N.2
Demin, O.3
Kiyatkin, A.4
Goryanin, I.5
Hoek, J.B.6
Kholodenko, B.N.7
-
36
-
-
0033518256
-
Synexpression groups in eukaryotes
-
Niehrs,C. and Pollet,N. (1999) Synexpression groups in eukaryotes. Nature, 402, 483-487.
-
(1999)
Nature
, vol.402
, pp. 483-487
-
-
Niehrs, C.1
Pollet, N.2
-
37
-
-
0028897360
-
Mechanism of eve stripe formation
-
Reinitz,J. and Sharp,D.H. (1995) Mechanism of eve stripe formation. Mech. Dev., 49, 133-158.
-
(1995)
Mech. Dev.
, vol.49
, pp. 133-158
-
-
Reinitz, J.1
Sharp, D.H.2
-
38
-
-
0036627676
-
Reverse engineering of regulatory networks: Simulation studies on a genetic algorithm approach for ranking hypotheses
-
Repsilber,D., Liljenstrom,H. and Andersson,S.G.E. (2002) Reverse engineering of regulatory networks: simulation studies on a genetic algorithm approach for ranking hypotheses. Biosystems, 66, 31-41.
-
(2002)
Biosystems
, vol.66
, pp. 31-41
-
-
Repsilber, D.1
Liljenstrom, H.2
Andersson, S.G.E.3
-
40
-
-
0041744850
-
On the deduction of chemical reaction pathways from measurements of time series of concentrations
-
Samoilov,M., Arkin,A. and Ross,J. (2001) On the deduction of chemical reaction pathways from measurements of time series of concentrations. Chaos, 11, 108-114.
-
(2001)
Chaos
, vol.11
, pp. 108-114
-
-
Samoilov, M.1
Arkin, A.2
Ross, J.3
-
41
-
-
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. and Muller,G. (2002) Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nat. Biotechnol., 20, 370-375.
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 370-375
-
-
Schoeberl, B.1
Eichler-Jonsson, C.2
Gilles, E.D.3
Muller, G.4
-
42
-
-
0034064689
-
A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks
-
Schuster,S., Fell,D.A. and Dandekar,T. (2000) A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol., 18, 326-332.
-
(2000)
Nat. Biotechnol.
, vol.18
, pp. 326-332
-
-
Schuster, S.1
Fell, D.A.2
Dandekar, T.3
-
43
-
-
0003012587
-
Neural networks for control
-
Trentelman,H.L. and Willems,J.C. (eds), Birkhauser, Boston
-
Sontag,E.D. (1993) Neural networks for control. In Trentelman,H.L. and Willems,J.C. (eds), Essays on Control: Perspectives in the Theory and its Applications. Birkhauser, Boston, pp. 339-380.
-
(1993)
Essays on Control: Perspectives in the Theory and Its Applications
, pp. 339-380
-
-
Sontag, E.D.1
-
44
-
-
0038094430
-
From the top down: Towards a predictive biology of signalling networks
-
Stark,J., Callard,R. and Hubank,M. (2003) From the top down: towards a predictive biology of signalling networks. Trends Biotechnol., 21, 290-293.
-
(2003)
Trends Biotechnol.
, vol.21
, pp. 290-293
-
-
Stark, J.1
Callard, R.2
Hubank, M.3
-
45
-
-
0037687416
-
Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling
-
Tegner,J., Yeung,M.K., Hasty,J. and Collins,J.J. (2003) Reverse engineering gene networks: integrating genetic perturbations with dynamical modeling. Proc. Natl Acad. Sci., USA, 100, 5944-5949.
-
(2003)
Proc. Natl Acad. Sci. USA
, vol.100
, pp. 5944-5949
-
-
Tegner, J.1
Yeung, M.K.2
Hasty, J.3
Collins, J.J.4
-
46
-
-
36749108213
-
Classification of instabilities in chemical reaction systems
-
Tyson,J.J. (1975) Classification of instabilities in chemical reaction systems. J. Chem. Phys., 62, 1010-1015.
-
(1975)
J. Chem. Phys.
, vol.62
, pp. 1010-1015
-
-
Tyson, J.J.1
-
47
-
-
0035656416
-
Network dynamics and cell physiology
-
Tyson,J.J., Chen,K. and Novak,B. (2001) Network dynamics and cell physiology. Nat. Rev. Mol. Cell. Biol., 2, 908-916.
-
(2001)
Nat. Rev. Mol. Cell. Biol.
, vol.2
, pp. 908-916
-
-
Tyson, J.J.1
Chen, K.2
Novak, B.3
-
48
-
-
0029979217
-
Chemical kinetic theory: Understanding cell-cycle regulation
-
Tyson,J.J., Novak,B., Odell,G.M., Chen,K. and Thron,C.D. (1996) Chemical kinetic theory: understanding cell-cycle regulation. Trends Biochem. Sci., 21, 89-96.
-
(1996)
Trends Biochem. Sci.
, vol.21
, pp. 89-96
-
-
Tyson, J.J.1
Novak, B.2
Odell, G.M.3
Chen, K.4
Thron, C.D.5
-
49
-
-
0037197832
-
Determination of causal connectivities of species in reaction networks
-
Vance,W., Arkin,A. and Ross,J. (2002) Determination of causal connectivities of species in reaction networks. Proc. Natl Acad. Sci., USA, 99, 5816-5821.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 5816-5821
-
-
Vance, W.1
Arkin, A.2
Ross, J.3
-
50
-
-
0034644270
-
The segment polarity network is a robust developmental module
-
von Dassow,G., Meir,E., Munro,E.M. and Odell,G.M. (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
-
51
-
-
0034104824
-
Coarse-grained reverse engineering of genetic regulatory networks
-
Wahde,M. and Hertz,J. (2000) Coarse-grained reverse engineering of genetic regulatory networks. Biosystems, 55, 129-136.
-
(2000)
Biosystems
, vol.55
, pp. 129-136
-
-
Wahde, M.1
Hertz, J.2
-
52
-
-
0028234589
-
Getting to the inside of cells using metabolic control analysis
-
Westerhoff,H.V., Hofmeyr,J.H. and Kholodenko,B.N. (1994) Getting to the inside of cells using metabolic control analysis. Biophys. Chem., 50, 273-283.
-
(1994)
Biophys. Chem.
, vol.50
, pp. 273-283
-
-
Westerhoff, H.V.1
Hofmeyr, J.H.2
Kholodenko, B.N.3
-
53
-
-
0141925279
-
Process pathway inference via time series analysis
-
Wiggins,C. and Nemenman,I. (2003) Process pathway inference via time series analysis. Exp. Mechan., 43, 361-370.
-
(2003)
Exp. Mechan.
, vol.43
, pp. 361-370
-
-
Wiggins, C.1
Nemenman, I.2
-
54
-
-
0037197936
-
Reverse engineering gene networks using singular value decomposition and robust regression
-
Yeung,M.K., Tegner,J. and Collins,J.J. (2002) Reverse engineering gene networks using singular value decomposition and robust regression. Proc. Natl Acad. Sci., USA, 99, 6163-6168.
-
(2002)
Proc. Natl Acad. Sci. USA
, vol.99
, pp. 6163-6168
-
-
Yeung, M.K.1
Tegner, J.2
Collins, J.J.3
-
55
-
-
0037205479
-
ERK negatively regulates the epidermal growth factor-mediated interaction of Gab 1 and the phosphatidylinositol 3-kinase
-
Yu,C.F., Liu,Z.X. and Cantley,L.G. (2002) ERK negatively regulates the epidermal growth factor-mediated interaction of Gab 1 and the phosphatidylinositol 3-kinase. J. Biol. Chem., 277, 19382-19388.
-
(2002)
J. Biol. Chem.
, vol.277
, pp. 19382-19388
-
-
Yu, C.F.1
Liu, Z.X.2
Cantley, L.G.3
|