-
1
-
-
0037079054
-
Computational Systems Biology
-
Kitano H: Computational Systems Biology. Nature 2002, 420:206-210.
-
(2002)
Nature
, vol.420
, pp. 206-210
-
-
Kitano, H.1
-
2
-
-
0035805255
-
Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Network
-
Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L: Integrated Genomic and Proteomic Analyses of a Systematically Perturbed Network. Science 2001, 292(5518):929-934.
-
(2001)
Science
, vol.292
, Issue.5518
, pp. 929-934
-
-
Ideker, T.1
Thorsson, V.2
Ranish, J.A.3
Christmas, R.4
Buhler, J.5
Eng, J.K.6
Bumgarner, R.7
Goodlett, D.R.8
Aebersold, R.9
Hood, L.10
-
3
-
-
0347004632
-
The Next Step in Systems Biology: Simulating the Temporospatial Dynamics of Molecular Networks
-
Zhu H, Huang S, Dhar P: The Next Step in Systems Biology: Simulating the Temporospatial Dynamics of Molecular Networks. Bioessays 2003, 26:68-72.
-
(2003)
Bioessays
, vol.26
, pp. 68-72
-
-
Zhu, H.1
Huang, S.2
Dhar, P.3
-
4
-
-
1342265607
-
Experimental Design in Systems Biology, Based on Parameter Sensitivity Analysis Using a Monte-Carlo Method: A Case Study for the TNF α-Mediated NF- κB Signal Transduction Pathway
-
Cho KH, Shin SY, Kolch W, Wolkenhauer O: Experimental Design in Systems Biology, Based on Parameter Sensitivity Analysis Using a Monte-Carlo Method: A Case Study for the TNF α-Mediated NF- κB Signal Transduction Pathway. Simulation 2003, 79:726-739.
-
(2003)
Simulation
, vol.79
, pp. 726-739
-
-
Cho, K.H.1
Shin, S.Y.2
Kolch, W.3
Wolkenhauer, O.4
-
5
-
-
0035125986
-
In silico Predictions of Escherichia coli Metabolic Capabilities are Consistent with Experimental Data
-
Edwards JS, Ibarra RU, Palsson BO: In silico Predictions of Escherichia coli Metabolic Capabilities are Consistent with Experimental Data. Nat Biotechnol 2001, 19:125-130.
-
(2001)
Nat. Biotechnol.
, vol.19
, pp. 125-130
-
-
Edwards, J.S.1
Ibarra, R.U.2
Palsson, B.O.3
-
6
-
-
0036212767
-
Computational Modeling of the Dynamics of the MAP Kinase Cascade Activated by Surface and Internalized EGF Receptors
-
Schöberl B, Jonsson CE, Gilles ED, Müller G: Computational Modeling of the Dynamics of the MAP Kinase Cascade Activated by Surface and Internalized EGF Receptors. Nat Biotechnol 2002, 20:370-375.
-
(2002)
Nat. Biotechnol.
, vol.20
, pp. 370-375
-
-
Schöberl, B.1
Jonsson, C.E.2
Gilles, E.D.3
Müller, G.4
-
8
-
-
0033985570
-
Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle
-
Chen KC, Csikasz-Nagy A, Gyorffy B, Val J, Novak B, Tyson JJ: Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle. Mol Bio Cell 2000, 11:369-391.
-
(2000)
Mol. Bio. Cell
, vol.11
, pp. 369-391
-
-
Chen, K.C.1
Csikasz-Nagy, A.2
Gyorffy, B.3
Val, J.4
Novak, B.5
Tyson, J.J.6
-
9
-
-
1542375741
-
Optimal identification of biochemical reaction networks
-
Feng XJ, Rabitz H: Optimal identification of biochemical reaction networks. Biophys J 2004, 86(3):1270-1281.
-
(2004)
Biophys. J.
, vol.86
, Issue.3
, pp. 1270-1281
-
-
Feng, X.J.1
Rabitz, H.2
-
10
-
-
0242574982
-
Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods
-
Moles CG, Mendes P, Banga JR: Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods. Genome Res 2003, 13:2467-2474.
-
(2003)
Genome Res.
, vol.13
, pp. 2467-2474
-
-
Moles, C.G.1
Mendes, P.2
Banga, J.R.3
-
11
-
-
0034102942
-
Global Optimization for the Parameter Estimation of Differential-Algebraic Systems
-
Esposito WR, Floudas CA: Global Optimization for the Parameter Estimation of Differential-Algebraic Systems. Ind Eng Chem Res 2000, 39:1291-1310.
-
(2000)
Ind. Eng. Chem. Res.
, vol.39
, pp. 1291-1310
-
-
Esposito, W.R.1
Floudas, C.A.2
-
13
-
-
31244435059
-
A Rigorous Global Optimization Algorithm for Problems with Ordinary Differential Equations
-
Papamichail I, Adjiman CS: A Rigorous Global Optimization Algorithm for Problems with Ordinary Differential Equations. J Global Optim 2002, 24:1-33.
-
(2002)
J. Global Optim.
, vol.24
, pp. 1-33
-
-
Papamichail, I.1
Adjiman, C.S.2
-
14
-
-
0002017426
-
-
Dordrecht, Netherlands: Kluwer Academic Publishers chap. Stochastic methods
-
Guss C, Boender E, Romeijn HE: Handbook of Global Optimization Dordrecht, Netherlands: Kluwer Academic Publishers 1995 chap. Stochastic methods:829-869.
-
(1995)
Handbook of Global Optimization
, pp. 829-869
-
-
Guss, C.1
Boender, E.2
Romeijn, H.E.3
-
15
-
-
0031316575
-
Application of Stochastic Global Optimization Algorithms to Practical Problems
-
Ali MM, Storey C, Törn A: Application of Stochastic Global Optimization Algorithms to Practical Problems. J Optim Theory Appl 1997, 95:545-563.
-
(1997)
J. Optim. Theory Appl.
, vol.95
, pp. 545-563
-
-
Ali, M.M.1
Storey, C.2
Törn, A.3
-
16
-
-
0001591529
-
Stochastic Global Optimzation: Problem Classes and Solution Techniques
-
Törn A, Ali MM, Viitanen S: Stochastic Global Optimzation: Problem Classes and Solution Techniques. J Global Optim 1999, 14:437-447.
-
(1999)
J. Global Optim.
, vol.14
, pp. 437-447
-
-
Törn, A.1
Ali, M.M.2
Viitanen, S.3
-
17
-
-
0035113215
-
Global Identifiability of Nonlinear Models of Biological Systems
-
Audoly S, Bellu G, D'Angio L, Saccomani MP, Cobelli C: Global Identifiability of Nonlinear Models of Biological Systems. IEEE Trans Biomed Eng 2001, 48:55-65.
-
(2001)
IEEE Trans. Biomed. Eng.
, vol.48
, pp. 55-65
-
-
Audoly, S.1
Bellu, G.2
D'Angio, L.3
Saccomani, M.P.4
Cobelli, C.5
-
18
-
-
0025343801
-
Parameter estimation: Local identifiability of parameters
-
Jacquez JA, Perry T: Parameter estimation: local identifiability of parameters. Amer J Physiol 1990, 258:E727-E736.
-
(1990)
Amer. J. Physiol.
, vol.258
-
-
Jacquez, J.A.1
Perry, T.2
-
19
-
-
0141606905
-
Modeling Ethylene/Butene Copolymerization with Multi-Site Catalysts: Parameter Estimability and Experimental Design
-
Yao KZ, Shaw BM, Kou B, McAuley KB, Bacon DW: Modeling Ethylene/Butene Copolymerization with Multi-Site Catalysts: Parameter Estimability and Experimental Design. Polymer Reaction Eng 2003, 11:563-588.
-
(2003)
Polymer Reaction Eng.
, vol.11
, pp. 563-588
-
-
Yao, K.Z.1
Shaw, B.M.2
Kou, B.3
McAuley, K.B.4
Bacon, D.W.5
-
20
-
-
0021431509
-
Multiexponential, Multicompartmental, and Noncompartmental Modeling. II. Data Analysis and Statistical Considerations
-
Landaw EM, DiStefano III JJ: Multiexponential, Multicompartmental, and Noncompartmental Modeling. II. Data Analysis and Statistical Considerations. Amer J Physiol 1984, 246:R665-R677.
-
(1984)
Amer. J. Physiol.
, vol.246
-
-
Landaw, E.M.1
DiStefano III, J.J.2
-
21
-
-
0035000446
-
Practical Identifiability of Model Parameters by Combined Respirometric-Titrimetric Measurements
-
Petersen B, Gernaey K, Vanrolleghem PA: Practical Identifiability of Model Parameters by Combined Respirometric-Titrimetric Measurements. Water Science Tech 2001, 43:347-355.
-
(2001)
Water Science Tech.
, vol.43
, pp. 347-355
-
-
Petersen, B.1
Gernaey, K.2
Vanrolleghem, P.A.3
-
22
-
-
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 J, Doyle III FJ: 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 2003, 13:2396-2405.
-
(2003)
Genome Res.
, vol.13
, pp. 2396-2405
-
-
Zak, D.E.1
Gonye, G.E.2
Schwaber, J.3
Doyle III, F.J.4
-
23
-
-
0034661129
-
Statistical Tools for Optimal Dynamic Model Building
-
Asprey SP, Macchietto S: Statistical Tools for Optimal Dynamic Model Building. Comput Chem Eng 2000, 24:1261-1267.
-
(2000)
Comput. Chem. Eng.
, vol.24
, pp. 1261-1267
-
-
Asprey, S.P.1
Macchietto, S.2
-
24
-
-
4644301730
-
A Benchmark for Methods in Reverse Engineering and Model Discrimination: Problem Formulation and Solutions
-
Kremling A, Fischer S, Gadkar K, Doyle III FJ, Sauter T, Bullinger E, Allgower F, Gilles ED: A Benchmark for Methods in Reverse Engineering and Model Discrimination: Problem Formulation and Solutions. Genome Res 2004, 14:1773-1785.
-
(2004)
Genome Res.
, vol.14
, pp. 1773-1785
-
-
Kremling, A.1
Fischer, S.2
Gadkar, K.3
Doyle III, F.J.4
Sauter, T.5
Bullinger, E.6
Allgower, F.7
Gilles, E.D.8
-
25
-
-
0037092884
-
Computation of Optimal Identification Experiments for Nonlinear Dynamic Process Models: A Stochastic Global Optimization Approach
-
Banga JR, Versyck KJ, Impe JFV: Computation of Optimal Identification Experiments for Nonlinear Dynamic Process Models: A Stochastic Global Optimization Approach. Ind Eng Chem Res 2002, 41:2425-2430.
-
(2002)
Ind. Eng. Chem. Res.
, vol.41
, pp. 2425-2430
-
-
Banga, J.R.1
Versyck, K.J.2
Impe, J.F.V.3
-
28
-
-
0031235724
-
The Role of Model Validation for Assessing the Size of the Unmodeled Dynamics
-
Ljung L, Guo L: The Role of Model Validation for Assessing the Size of the Unmodeled Dynamics. IEEE Trans Automat Contr 1997, 42:1230-1239.
-
(1997)
IEEE Trans. Automat. Contr.
, vol.42
, pp. 1230-1239
-
-
Ljung, L.1
Guo, L.2
-
29
-
-
0028436875
-
A Time-Domain Approach to Model Validation
-
Poolla K, Khargonekar P, Tikku A, Krause J, Nagpal K: A Time-Domain Approach to Model Validation. IEEE Trans Automat Contr 1994, 39:951-959.
-
(1994)
IEEE Trans. Automat. Contr.
, vol.39
, pp. 951-959
-
-
Poolla, K.1
Khargonekar, P.2
Tikku, A.3
Krause, J.4
Nagpal, K.5
-
31
-
-
84950062346
-
Qualitative and Quantitative Indentifiability Analysis of Non-Linear Chemical Kinetic Models
-
Vajda S, Rabitz H, Walter E, Lecourtier Y: Qualitative and Quantitative Indentifiability Analysis of Non-Linear Chemical Kinetic Models. Chem Eng Commun 1989, 83:191-219.
-
(1989)
Chem. Eng. Commun.
, vol.83
, pp. 191-219
-
-
Vajda, S.1
Rabitz, H.2
Walter, E.3
Lecourtier, Y.4
-
34
-
-
21644484269
-
Heuristic Methods for Measurement Selection for Identification of Biological Systems
-
Heidelberg, Germany
-
Gadkar KG, Gunawan R, Doyle III FJ: Heuristic Methods for Measurement Selection for Identification of Biological Systems. Int Conf Systems Biology, Heidelberg, Germany 2004.
-
(2004)
Int. Conf. Systems Biology
-
-
Gadkar, K.G.1
Gunawan, R.2
Doyle III, F.J.3
-
36
-
-
0027552335
-
Biomass Estimation in Plant Cell Cultures Using Extended Kalman Filter
-
Albiol J, Robusté J, Casas C, Poch M: Biomass Estimation in Plant Cell Cultures Using Extended Kalman Filter. Biotechnol Prog 1993, 9:174-178.
-
(1993)
Biotechnol. Prog.
, vol.9
, pp. 174-178
-
-
Albiol, J.1
Robusté, J.2
Casas, C.3
Poch, M.4
-
37
-
-
0030062541
-
On-Line State Estimation and Parameter Identification for Batch Fermentation
-
Gee DA, Ramirez WF: On-Line State Estimation and Parameter Identification for Batch Fermentation. Biotechnol Prog 1996, 12:132-140.
-
(1996)
Biotechnol. Prog.
, vol.12
, pp. 132-140
-
-
Gee, D.A.1
Ramirez, W.F.2
-
38
-
-
0021507444
-
Studies on on-Line Biorector Identification. I. Theory
-
Stephanopoulos G, San KY: Studies on on-Line Biorector Identification. I. Theory. Biotechnol Bioeng 1984, 26:1176-1188.
-
(1984)
Biotechnol. Bioeng.
, vol.26
, pp. 1176-1188
-
-
Stephanopoulos, G.1
San, K.Y.2
-
39
-
-
0030994705
-
Bioprocess Supervision: Neural Networks and Knowledge Based Systems
-
Glassey J, Ignova M, Ward AC, Montague GA, Morris AJ: Bioprocess Supervision: Neural Networks and Knowledge Based Systems. J Biotechnol 1997, 52:201-205.
-
(1997)
J. Biotechnol.
, vol.52
, pp. 201-205
-
-
Glassey, J.1
Ignova, M.2
Ward, A.C.3
Montague, G.A.4
Morris, A.J.5
-
40
-
-
0026449753
-
Comparision of Feed-Forward and Recurrent Neural Networks for Bioprocess State Estimation
-
Karim MN, Rivera SL: Comparision of Feed-Forward and Recurrent Neural Networks for Bioprocess State Estimation. Comp Chem Eng 1992, 16(Suppl):S369-S377.
-
(1992)
Comp. Chem. Eng.
, vol.16
, Issue.SUPPL.
-
-
Karim, M.N.1
Rivera, S.L.2
-
41
-
-
0342981802
-
Exploratory Analysis of Bioprocesses Using Artificial Neural Network-Based Methods
-
Simutis R, Lübbert A: Exploratory Analysis of Bioprocesses Using Artificial Neural Network-Based Methods. Biotechnol Prog 1997, 13:479-487.
-
(1997)
Biotechnol. Prog.
, vol.13
, pp. 479-487
-
-
Simutis, R.1
Lübbert, A.2
-
42
-
-
0043240532
-
Maximum a Posteriori Estimation of Transient Enhanced Diffusion Energetics
-
Gunawan R, Jung MYL, Seebauer EG, Braatz RD: Maximum a Posteriori Estimation of Transient Enhanced Diffusion Energetics. AIChE J 2003, 49:2114-2123.
-
(2003)
AIChE J.
, vol.49
, pp. 2114-2123
-
-
Gunawan, R.1
Jung, M.Y.L.2
Seebauer, E.G.3
Braatz, R.D.4
-
44
-
-
21644489637
-
Model Identification of Signal Transduction Networks from Data Using a State Regulator Problem
-
Gadkar KG, Varner J, Doyle III FJ: Model Identification of Signal Transduction Networks from Data Using a State Regulator Problem. IEE Systems Biology 2005, 2:.
-
(2005)
IEE Systems Biology
, vol.2
-
-
Gadkar, K.G.1
Varner, J.2
Doyle III, F.J.3
-
45
-
-
0036138322
-
2 easy steps
-
2 easy steps. Bioinformatics 2001, 17(12):1183-1197.
-
(2001)
Bioinformatics
, vol.17
, Issue.12
, pp. 1183-1197
-
-
Wagner, A.1
-
46
-
-
0038048325
-
Inferring genetic networks and identifying compound model of action via expression profiling
-
Gardner TS, Bernardo DD, Lorenz D, Collins JJ: Inferring genetic networks and identifying compound model of action via expression profiling. Science 2003, 301:102-105.
-
(2003)
Science
, vol.301
, pp. 102-105
-
-
Gardner, T.S.1
Bernardo, D.D.2
Lorenz, D.3
Collins, J.J.4
-
47
-
-
16844376909
-
Reverse engineering of regulatory networks in human B cells
-
Basso K, Margolin AA, Stolovitzky G, Klein U, Dalla-Favera R, Califano A: Reverse engineering of regulatory networks in human B cells. Nat Genet 2005, 37(4382-390 [http://dx.doi.org/10.1038/ng1532].
-
(2005)
Nat. Genet.
, vol.37
, Issue.4382-4390
-
-
Basso, K.1
Margolin, A.A.2
Stolovitzky, G.3
Klein, U.4
Dalla-Favera, R.5
Califano, A.6
-
48
-
-
0041846841
-
On the Design of Optimally Informative Deynamic Experiments for Model Discrimination in Multiresponse Nonlinear Situations
-
Chen BH, Asprey SP: On the Design of Optimally Informative Deynamic Experiments for Model Discrimination in Multiresponse Nonlinear Situations. Ind Eng Chem Res 2003, 42:1379-1390.
-
(2003)
Ind. Eng. Chem. Res.
, vol.42
, pp. 1379-1390
-
-
Chen, B.H.1
Asprey, S.P.2
-
50
-
-
25444512982
-
BioSens 2.0: Sensitivity Analysis Toolkit
-
Taylor S, Gunawan R, Doyle III FJ: BioSens 2.0: Sensitivity Analysis Toolkit. 2005 [http://www.chemengr.ucsb.edu/~ceweb/faculty/doyle/biosens/BioSens.htm].
-
(2005)
-
-
Taylor, S.1
Gunawan, R.2
Doyle III, F.J.3
|