-
1
-
-
41249097444
-
Interaction networks for systems biology
-
Bader S, Kühner S, Gavin AC (2008) Interaction networks for systems biology. FEBS Letter 582(8): 1220-4.
-
(2008)
FEBS Letter
, vol.582
, Issue.8
, pp. 1220-1224
-
-
Bader, S.1
Kühner, S.2
Gavin, A.C.3
-
2
-
-
0037417886
-
Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by data based modeling
-
Swameye I, Muller TG, Timmer J, Sandra O, Klingmuller U (2002) Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by data based modeling. Proc Natl Acad Sci USA 100(3): 1028-1033.
-
(2002)
Proc Natl Acad Sci USA
, vol.100
, Issue.3
, pp. 1028-1033
-
-
Swameye, I.1
Muller, T.G.2
Timmer, J.3
Sandra, O.4
Klingmuller, U.5
-
3
-
-
36248952170
-
The stability and robustness of metabolic states: Identifying stabilizihg sites in metabolic networks
-
Grimbs S, Selbig J, Bulik S, Holzhütter HG, Steuer R (2007) The stability and robustness of metabolic states: identifying stabilizihg sites in metabolic networks. Mol Syst Biol 3: 146.
-
(2007)
Mol Syst Biol
, vol.3
, pp. 146
-
-
Grimbs, S.1
Selbig, J.2
Bulik, S.3
Holzhütter, H.G.4
Steuer, R.5
-
4
-
-
34548049053
-
Mathematical modeling of intracellular signaling pathways
-
Klipp E, Liebermeister W (2006) Mathematical modeling of intracellular signaling pathways. BMC Neurosci 2006; 7(Suppl 1): S10.
-
(2006)
BMC Neurosci
, vol.7
, Issue.SUPPL. 1
-
-
Klipp, E.1
Liebermeister, W.2
-
5
-
-
33845410054
-
Dynamic modeling and analysis of biochemical networks: Mechanism-based models and model-based experiments
-
Natal AW, Riel V (2006) Dynamic modeling and analysis of biochemical networks: mechanism-based models and model-based experiments. Briefings in Bioinformatics 7: 364-374.
-
(2006)
Briefings in Bioinformatics
, vol.7
, pp. 364-374
-
-
Natal, A.W.1
Riel, V.2
-
6
-
-
0036789922
-
Untangling the wires: A strategy to trace functional interactions in signaling and gene networks
-
Kholodenko BN, Kiyatkin A, Bruggeman FJ, Sontag E, Westerhoff HV, et al. (2002) Untangling the wires: a strategy to trace functional interactions in signaling and gene networks. Proc Natl Acad Sci USA 99(20): 12841-12846.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, Issue.20
, pp. 12841-12846
-
-
Kholodenko, B.N.1
Kiyatkin, A.2
Bruggeman, F.J.3
Sontag, E.4
Westerhoff, H.V.5
-
7
-
-
48549086662
-
automatically generated model of a metabolic network
-
Borger S, Liebermeister W, Uhlendorf J, Klipp E (2007) automatically generated model of a metabolic network. Genome Informatics Series 18 (1): 215-224.
-
(2007)
Genome Informatics Series
, vol.18
, Issue.1
, pp. 215-224
-
-
Borger, S.1
Liebermeister, W.2
Uhlendorf, J.3
Klipp, E.4
-
8
-
-
33747061013
-
Structural kinetic modeling of metabolic networks
-
Steuer R, Gross T, Selbig J, Blasius B (2006) Structural kinetic modeling of metabolic networks. Proc Natl Acad Sci USA 103(32): 11868-11873.
-
(2006)
Proc Natl Acad Sci USA
, vol.103
, Issue.32
, pp. 11868-11873
-
-
Steuer, R.1
Gross, T.2
Selbig, J.3
Blasius, B.4
-
9
-
-
20444411533
-
the silicon cell initiative: Working towards a detailed kinetic description at the cellular level
-
Snoep JL (2005) the silicon cell initiative: working towards a detailed kinetic description at the cellular level. Curr Opin Biotechnol 16: 336-343.
-
(2005)
Curr Opin Biotechnol
, vol.16
, pp. 336-343
-
-
Snoep, J.L.1
-
10
-
-
22344438058
-
Electronic Data Sources for Kinetic Models of Cell Signaling
-
HarshaRani GV, Vayttaden SJ, Bhalla US (2005) Electronic Data Sources for Kinetic Models of Cell Signaling. J Biochem 137: 653-657.
-
(2005)
J Biochem
, vol.137
, pp. 653-657
-
-
HarshaRani, G.V.1
Vayttaden, S.J.2
Bhalla, U.S.3
-
11
-
-
36248943011
-
Dynamic pathway modeling: Feasibility analysis and optimal experimental design
-
Maiwald T, Kreutz C, Pfeifer AC, Bohl S, Klingymüller U, et al. (2007) Dynamic pathway modeling: feasibility analysis and optimal experimental design. Ann N Y Acad Sci 1115: 212-220.
-
(2007)
Ann N Y Acad Sci
, vol.1115
, pp. 212-220
-
-
Maiwald, T.1
Kreutz, C.2
Pfeifer, A.C.3
Bohl, S.4
Klingymüller, U.5
-
12
-
-
40149110264
-
Parameter estimate of signal transduction pathways
-
Arisi I, Cattaneo A, Rosato V (2006) Parameter estimate of signal transduction pathways. BMC Neurosci 7(Suppl 1): S6.
-
(2006)
BMC Neurosci
, vol.7
, Issue.SUPPL. 1
-
-
Arisi, I.1
Cattaneo, A.2
Rosato, V.3
-
13
-
-
0242574982
-
Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods
-
Moles CG, Mendes, P, Banga JR (2003) Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods. Genome Res 13: 2467-2474.
-
(2003)
Genome Res
, vol.13
, pp. 2467-2474
-
-
Moles, C.G.1
Mendes, P.2
Banga, J.R.3
-
14
-
-
33751423943
-
Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems
-
Rodriguez-Fernandez M, Egea JA. Banga JR (2006) Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems. BMC Bioinformatics 7: 483.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 483
-
-
Rodriguez-Fernandez, M.1
Egea, J.A.2
Banga, J.R.3
-
15
-
-
33845875759
-
Simulated maximum likelihood method for estimating kinetic rates in gene expression
-
Tian T, Xu S, Gao J, Burrage K (2006) Simulated maximum likelihood method for estimating kinetic rates in gene expression. Bioinformatics 23(1): 84-91.
-
(2006)
Bioinformatics
, vol.23
, Issue.1
, pp. 84-91
-
-
Tian, T.1
Xu, S.2
Gao, J.3
Burrage, K.4
-
16
-
-
17044395470
-
Reverse engineering of biochemical equations from time-course data by means of genetic programming
-
Sugimoto M, Kikuchi S, Tomita M (2005) Reverse engineering of biochemical equations from time-course data by means of genetic programming. Biosystems 80(2): 155-164.
-
(2005)
Biosystems
, vol.80
, Issue.2
, pp. 155-164
-
-
Sugimoto, M.1
Kikuchi, S.2
Tomita, M.3
-
17
-
-
33751418323
-
a simplified method for power-law modeling of metabolic pathways from time-course data and steady-state flux profiles
-
Kitayama T, Kinoshita A, Sugimoto M, Nakayama Y, Tomita M (2006) a simplified method for power-law modeling of metabolic pathways from time-course data and steady-state flux profiles. Theory Biology Med Model 3: 24.
-
(2006)
Theory Biology Med Model
, vol.3
, pp. 24
-
-
Kitayama, T.1
Kinoshita, A.2
Sugimoto, M.3
Nakayama, Y.4
Tomita, M.5
-
18
-
-
33749340654
-
Parameter estimation in biochemical systems models with alternating regression
-
Chou IC, Martens H, Voit EO (2006) Parameter estimation in biochemical systems models with alternating regression. Theor Biol Med Model 3: 25.
-
(2006)
Theor Biol Med Model
, vol.3
, pp. 25
-
-
Chou, I.C.1
Martens, H.2
Voit, E.O.3
-
19
-
-
36549012683
-
Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference
-
Quach M, Brunel N, d'Alché-Buc F (2007) Estimating parameters and hidden variables in non-linear state-space models based on ODEs for biological networks inference. Bioinformatics 23(23): 3209-3216.
-
(2007)
Bioinformatics
, vol.23
, Issue.23
, pp. 3209-3216
-
-
Quach, M.1
Brunel, N.2
d'Alché-Buc, F.3
-
20
-
-
0028409736
-
Adaptive model architecture and extended Kalman-Bucy filters
-
Costa PJ (1994) Adaptive model architecture and extended Kalman-Bucy filters. IEEE Trans. Aerospace Electron System 30: 525-533.
-
(1994)
IEEE Trans. Aerospace Electron System
, vol.30
, pp. 525-533
-
-
Costa, P.J.1
-
21
-
-
84899008192
-
Learning nonlinear dynamical systems using an EM algorithm
-
NIPS'98, 431-437
-
Ghahramani Z, Roweis S (1999) Learning nonlinear dynamical systems using an EM algorithm. Neural Information Processing Systems 11 (NIPS'98): 431-437.
-
(1999)
Neural Information Processing Systems
, vol.11
-
-
Ghahramani, Z.1
Roweis, S.2
-
22
-
-
84889830739
-
-
Simon D (2006) optimal state estimation-Kalman, H∞, and nonlinear approaches. New Jersey: A John Wiley & Sons, Inc. Hoboken. 552 p.
-
Simon D (2006) optimal state estimation-Kalman, H∞, and nonlinear approaches. New Jersey: A John Wiley & Sons, Inc. Hoboken. 552 p.
-
-
-
-
23
-
-
21244437999
-
Unscented filtering and nonlinear estimation
-
Julier SJ, Uhlmann JK (2004) Unscented filtering and nonlinear estimation. Proceedings of the IEEE 92: 401-422.
-
(2004)
Proceedings of the IEEE
, vol.92
, pp. 401-422
-
-
Julier, S.J.1
Uhlmann, J.K.2
-
25
-
-
0001460136
-
On sequential Monte Carlo sampling methods for Bayesian filtering
-
Doucet A, Godsill S, Andrieu C (2000) On sequential Monte Carlo sampling methods for Bayesian filtering. Statistics and Computing 10: 197-208.
-
(2000)
Statistics and Computing
, vol.10
, pp. 197-208
-
-
Doucet, A.1
Godsill, S.2
Andrieu, C.3
-
26
-
-
34547583106
-
Bayesian estimation via sequential Monte Carlo sampling - Constrained dynamic systems
-
Lang L, Chen W, Bakshi BR, Goel PK, Ungarala S (2007) Bayesian estimation via sequential Monte Carlo sampling - Constrained dynamic systems. Automatica 3: 1615-1622.
-
(2007)
Automatica
, vol.3
, pp. 1615-1622
-
-
Lang, L.1
Chen, W.2
Bakshi, B.R.3
Goel, P.K.4
Ungarala, S.5
-
27
-
-
30344486983
-
Recursive Monte Carlo filters: Algorithms and theoretical analysis
-
Künsch HR (2005) Recursive Monte Carlo filters: algorithms and theoretical analysis. Annals of Statistics 33: 1983-2021.
-
(2005)
Annals of Statistics
, vol.33
, pp. 1983-2021
-
-
Künsch, H.R.1
-
30
-
-
33847335120
-
A genetic network for the clock of neurospora crassa
-
Yu Y, Dong W, Altimus C, Tang X, Griffith J, et al. (2007) A genetic network for the clock of neurospora crassa. Proc Natl Acad Sci USA 104: 2809-2814.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 2809-2814
-
-
Yu, Y.1
Dong, W.2
Altimus, C.3
Tang, X.4
Griffith, J.5
-
31
-
-
33750845118
-
TGF-â concentration dependence of Smad phosphorylation kinetics: A systems perspective
-
Clarke DC, Betterton MD, Liu X (2006) TGF-â concentration dependence of Smad phosphorylation kinetics: a systems perspective. IEEE Systems Biology 153: 412-424.
-
(2006)
IEEE Systems Biology
, vol.153
, pp. 412-424
-
-
Clarke, D.C.1
Betterton, M.D.2
Liu, X.3
-
32
-
-
41449088987
-
â2-Adrenergic Receptor Signaling and Desensitization Elucidated by Quantitative Modeling of Real Time cAMP Dynamics
-
ViolinD, DiPilato LM, Yildirim N, Elston TC, Zhang J, et al. (2008) â2-Adrenergic Receptor Signaling and Desensitization Elucidated by Quantitative Modeling of Real Time cAMP Dynamics. J Biol Chem 283: 2949-2961.
-
(2008)
J Biol Chem
, vol.283
, pp. 2949-2961
-
-
Violin, D.1
DiPilato, L.M.2
Yildirim, N.3
Elston, T.C.4
Zhang, J.5
-
33
-
-
13844298920
-
Modeling the nonlinear dynamics of cellular signal transduction
-
Timmer J, Muller TGM, Swameye I, Sandra O, Klingmuller U (2004) Modeling the nonlinear dynamics of cellular signal transduction. International Journal of Bifurcation and Chaos 14: 2069-2079.
-
(2004)
International Journal of Bifurcation and Chaos
, vol.14
, pp. 2069-2079
-
-
Timmer, J.1
Muller, T.G.M.2
Swameye, I.3
Sandra, O.4
Klingmuller, U.5
-
34
-
-
0037138370
-
Signaling through the JAK/STAT pathway, recent advances and future Challenges
-
Kisseleva T, Bhattacharya S, Braunstein J, Schindler CW (2002) Signaling through the JAK/STAT pathway, recent advances and future Challenges. Gene 285: 1-24.
-
(2002)
Gene
, vol.285
, pp. 1-24
-
-
Kisseleva, T.1
Bhattacharya, S.2
Braunstein, J.3
Schindler, C.W.4
-
35
-
-
0034667593
-
Meaningful relationships: The regulation of the Ras/Raf/ MEK/ ERK pathway by protein interaction
-
Kolch W (2000) Meaningful relationships: the regulation of the Ras/Raf/ MEK/ ERK pathway by protein interaction. Biochem J 351: 289-305.
-
(2000)
Biochem J
, vol.351
, pp. 289-305
-
-
Kolch, W.1
-
36
-
-
0004237102
-
-
Third edition. New Jersey: Prentice Hall, Upper Saddle River
-
Ogata K (1998) System Dynamics. Third edition. New Jersey: Prentice Hall, Upper Saddle River.
-
(1998)
System Dynamics
-
-
Ogata, K.1
-
37
-
-
42949164125
-
Formulating genome-scale kinetic models in the post-genome era
-
Jamshidi N, Palsson BØ (2008) Formulating genome-scale kinetic models in the post-genome era. Molecular Systems Biology 4: 171.
-
(2008)
Molecular Systems Biology
, vol.4
, pp. 171
-
-
Jamshidi, N.1
Palsson, B.2
-
39
-
-
10944253539
-
Estimation of parameters in a linear state space model using a Rao-Blackwellised particle filter
-
Li P, Goodall R, Kadirkamanathan V (2004) Estimation of parameters in a linear state space model using a Rao-Blackwellised particle filter. IEE Proc Control Theory Appl 151: 727-738.
-
(2004)
IEE Proc Control Theory Appl
, vol.151
, pp. 727-738
-
-
Li, P.1
Goodall, R.2
Kadirkamanathan, V.3
-
40
-
-
1542329124
-
Polynomial extended kalman filtering for discrete-time nonlinear stochastic systems
-
Maui, Hawii, USA, December
-
Germani A, Manes C, Palumbo P (2003) Polynomial extended kalman filtering for discrete-time nonlinear stochastic systems. Proceedings of the 42nd IEEE Conference on Decision and Control Maui, Hawii, USA, December 2003 1: 886-891.
-
(2003)
Proceedings of the 42nd IEEE Conference on Decision and Control
, vol.1
, pp. 886-891
-
-
Germani, A.1
Manes, C.2
Palumbo, P.3
-
42
-
-
84958662607
-
Mathematical Modeling of the influence of RKIP on the ERK Signaling Pathway
-
Cho KH, Shin SY, Kim HW, Wolkenhauer O, McFerran B, et al. (2003) Mathematical Modeling of the influence of RKIP on the ERK Signaling Pathway. Lecture Notes in Computer Science 2602: 127-141.
-
(2003)
Lecture Notes in Computer Science
, vol.2602
, pp. 127-141
-
-
Cho, K.H.1
Shin, S.Y.2
Kim, H.W.3
Wolkenhauer, O.4
McFerran, B.5
-
43
-
-
37649031765
-
Estimation of parameters and unobserved components for nonlinear systems from noisy time series
-
Sitz A, Schwarz U, Kurths J, Voss HU (2002) Estimation of parameters and unobserved components for nonlinear systems from noisy time series. Physical Review E 66: 016210.
-
(2002)
Physical Review E
, vol.66
, pp. 016210
-
-
Sitz, A.1
Schwarz, U.2
Kurths, J.3
Voss, H.U.4
-
44
-
-
41349094363
-
Freedom of expression Introduction to special issue
-
Riddihough G, Purnell BA, Travis J (2008) Freedom of expression Introduction to special issue. Science 319(5871): 1781.
-
(2008)
Science
, vol.319
, Issue.5871
, pp. 1781
-
-
Riddihough, G.1
Purnell, B.A.2
Travis, J.3
-
45
-
-
14844307159
-
Inferring quantitative models of regulatory networks from expression data
-
Nachman I, Regev A, Friedman N (2004) Inferring quantitative models of regulatory networks from expression data. Bioinformatics 20 (Suppl. 1): 248-256.
-
(2004)
Bioinformatics
, vol.20
, Issue.SUPPL. 1
, pp. 248-256
-
-
Nachman, I.1
Regev, A.2
Friedman, N.3
-
46
-
-
0018435192
-
asymptotic behavior of the extended Kalman filter as a parameter estimator for linear systems
-
Ljung L. (1979) asymptotic behavior of the extended Kalman filter as a parameter estimator for linear systems. IEEE Trans on Automatic Control AC-2: 36-50.
-
(1979)
IEEE Trans on Automatic Control
, vol.AC-2
, pp. 36-50
-
-
Ljung, L.1
|