-
1
-
-
42749109054
-
Statistical mechanical approaches to models with many poorly known parameters
-
Brown K, Sethna J. Statistical mechanical approaches to models with many poorly known parameters. Phys Rev E 2003, 68(2):21904.
-
(2003)
Phys Rev E
, vol.68
, Issue.2
, pp. 21904
-
-
Brown, K.1
Sethna, J.2
-
2
-
-
33748557777
-
The statistical mechanics of complex signaling networks: nerve growth factor signaling
-
10.1088/1478-3967/1/3/006, 16204838
-
Brown K, Hill C, Calero G, Myers C, Lee K, Sethna J, Cerione R. The statistical mechanics of complex signaling networks: nerve growth factor signaling. Phys Biol 2004, 1(3):184-195. 10.1088/1478-3967/1/3/006, 16204838.
-
(2004)
Phys Biol
, vol.1
, Issue.3
, pp. 184-195
-
-
Brown, K.1
Hill, C.2
Calero, G.3
Myers, C.4
Lee, K.5
Sethna, J.6
Cerione, R.7
-
3
-
-
13444270529
-
Parameter estimation for a mathematical model of the cell cycle in frog eggs
-
10.1089/cmb.2005.12.48, 15725733
-
Zwolak J, Tyson J, Watson L. Parameter estimation for a mathematical model of the cell cycle in frog eggs. J Comput Biol 2005, 12:48-63. 10.1089/cmb.2005.12.48, 15725733.
-
(2005)
J Comput Biol
, vol.12
, pp. 48-63
-
-
Zwolak, J.1
Tyson, J.2
Watson, L.3
-
4
-
-
58849106769
-
Systems biology: parameter estimation for biochemical models
-
10.1111/j.1742-4658.2008.06844.x, 19215296
-
Ashyraliyev M, Fomekong-Nanfack Y, Kaandorp J, Blom J. Systems biology: parameter estimation for biochemical models. FEBS J 2009, 276(4):886-902. 10.1111/j.1742-4658.2008.06844.x, 19215296.
-
(2009)
FEBS J
, vol.276
, Issue.4
, pp. 886-902
-
-
Ashyraliyev, M.1
Fomekong-Nanfack, Y.2
Kaandorp, J.3
Blom, J.4
-
5
-
-
78149457680
-
When the optimal is not the best: Parameter estimation in complex biological models
-
10.1371/journal.pone.0013283, 2963600, 21049094
-
Slezak D, Suárez C, Cecchi G, Marshall G, Stolovitzky G. When the optimal is not the best: Parameter estimation in complex biological models. PloS One 2010, 5(10):e13283. 10.1371/journal.pone.0013283, 2963600, 21049094.
-
(2010)
PloS One
, vol.5
, Issue.10
-
-
Slezak, D.1
Suárez, C.2
Cecchi, G.3
Marshall, G.4
Stolovitzky, G.5
-
6
-
-
81555207959
-
Structural Identifiability of Systems Biology Models: A Critical Comparison of Methods
-
10.1371/journal.pone.0027755, 3222653, 22132135
-
Chis O, Banga J, Balsa-Canto E. Structural Identifiability of Systems Biology Models: A Critical Comparison of Methods. PloS One 2011, 6(11):e27755. 10.1371/journal.pone.0027755, 3222653, 22132135.
-
(2011)
PloS One
, vol.6
, Issue.11
-
-
Chis, O.1
Banga, J.2
Balsa-Canto, E.3
-
7
-
-
79952606233
-
Addressing parameter identifiability by model-based experimentation
-
Raue A, Kreutz C, Maiwald T, Klingmuller U, Timmer J. Addressing parameter identifiability by model-based experimentation. Syst Biol, IET 2011, 5(2):120-130.
-
(2011)
Syst Biol, IET
, vol.5
, Issue.2
, pp. 120-130
-
-
Raue, A.1
Kreutz, C.2
Maiwald, T.3
Klingmuller, U.4
Timmer, J.5
-
8
-
-
84871923785
-
Parameter Estimation Using Meta-Heuristics in Systems Biology: A Comprehensive Review
-
Sun J, Garibaldi J, Hodgman C. Parameter Estimation Using Meta-Heuristics in Systems Biology: A Comprehensive Review. Comput Biol and Bioinf, IEEE/ACM Trans on 2011, 99:1-1.
-
(2011)
Comput Biol and Bioinf, IEEE/ACM Trans on
, vol.99
, pp. 1-1
-
-
Sun, J.1
Garibaldi, J.2
Hodgman, C.3
-
9
-
-
79952293516
-
Signal Transduction, Sloppy Models, and Statistical Mechanics
-
Cornell University 2003
-
Brown KS. Signal Transduction, Sloppy Models, and Statistical Mechanics. PhD thesis Cornell University 2003.
-
PhD thesis
-
-
Brown, K.S.1
-
10
-
-
33750016873
-
Sloppy-Model Universality Class and the Vandermonde Matrix
-
Waterfall J, Casey F, Gutenkunst R, Brown K, Myers C, Brouwer P, Elser V, Sethna J. Sloppy-Model Universality Class and the Vandermonde Matrix. Phys Rev Lett 2006, 97(15):150601.
-
(2006)
Phys Rev Lett
, vol.97
, Issue.15
, pp. 150601
-
-
Waterfall, J.1
Casey, F.2
Gutenkunst, R.3
Brown, K.4
Myers, C.5
Brouwer, P.6
Elser, V.7
Sethna, J.8
-
11
-
-
35748977901
-
Universally sloppy parameter sensitivities in systems biology models
-
Gutenkunst R, Waterfall J, Casey F, Brown K, Myers C, Sethna J. Universally sloppy parameter sensitivities in systems biology models. PLoS Comput Biol 2007, 3(10):e189.
-
(2007)
PLoS Comput Biol
, vol.3
, Issue.10
-
-
Gutenkunst, R.1
Waterfall, J.2
Casey, F.3
Brown, K.4
Myers, C.5
Sethna, J.6
-
12
-
-
77956498018
-
Sloppy models, parameter uncertainty, and the role of experimental design
-
10.1039/b918098b, 3505121, 20556289
-
Apgar J, Witmer D, White F, Tidor B. Sloppy models, parameter uncertainty, and the role of experimental design. Mol BioSyst 2010, 6(10):1890-1900. 10.1039/b918098b, 3505121, 20556289.
-
(2010)
Mol BioSyst
, vol.6
, Issue.10
, pp. 1890-1900
-
-
Apgar, J.1
Witmer, D.2
White, F.3
Tidor, B.4
-
13
-
-
79960347744
-
Comment on Sloppy models, parameter uncertainty, and the role of experimental design
-
Chachra R, Transtrum M, Sethna J. Comment on Sloppy models, parameter uncertainty, and the role of experimental design. Mol BioSyst 2011, 4.
-
(2011)
Mol BioSyst
, pp. 4
-
-
Chachra, R.1
Transtrum, M.2
Sethna, J.3
-
14
-
-
58849137994
-
Systems biology: experimental design
-
10.1111/j.1742-4658.2008.06843.x, 19215298
-
Kreutz C, Timmer J. Systems biology: experimental design. FEBS J 2009, 276(4):923-942. 10.1111/j.1742-4658.2008.06843.x, 19215298.
-
(2009)
FEBS J
, vol.276
, Issue.4
, pp. 923-942
-
-
Kreutz, C.1
Timmer, J.2
-
15
-
-
77953839617
-
Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species
-
Xu T, Vyshemirsky V, Gormand A, von Kriegsheim A, Girolami M, Baillie G, Ketley D, Dunlop A, Milligan G, Houslay M, et al. Inferring signaling pathway topologies from multiple perturbation measurements of specific biochemical species. Sci's STKE 2010, 3(113):ra20.
-
(2010)
Sci's STKE
, vol.3
, Issue.113
-
-
Xu, T.1
Vyshemirsky, V.2
Gormand, A.3
von Kriegsheim, A.4
Girolami, M.5
Baillie, G.6
Ketley, D.7
Dunlop, A.8
Milligan, G.9
Houslay, M.10
-
16
-
-
3042702377
-
Optimal sampling time selection for parameter estimation in dynamic pathway modeling
-
10.1016/j.biosystems.2004.03.007, 15245803
-
Kutalik Z, Cho K, Wolkenhauer O. Optimal sampling time selection for parameter estimation in dynamic pathway modeling. Biosystems 2004, 75:43-55. 10.1016/j.biosystems.2004.03.007, 15245803.
-
(2004)
Biosystems
, vol.75
, pp. 43-55
-
-
Kutalik, Z.1
Cho, K.2
Wolkenhauer, O.3
-
17
-
-
77956289955
-
Classic and contemporary approaches to modeling biochemical reactions
-
10.1101/gad.1945410, 23281480
-
Chen W, Niepel M, Sorger P. Classic and contemporary approaches to modeling biochemical reactions. Genes & Dev 2010, 24(17):1861-1875. 10.1101/gad.1945410, 23281480.
-
(2010)
Genes & Dev
, vol.24
, Issue.17
, pp. 1861-1875
-
-
Chen, W.1
Niepel, M.2
Sorger, P.3
-
18
-
-
84859749049
-
An Integrated Strategy for Prediction Uncertainty Analysis
-
10.1093/bioinformatics/bts088, 3324512, 22355081
-
Vanlier J, Tiemann C, Hilbers P, van Riel N. An Integrated Strategy for Prediction Uncertainty Analysis. Bioinformatics 2012, 28(8):1130-1135. 10.1093/bioinformatics/bts088, 3324512, 22355081.
-
(2012)
Bioinformatics
, vol.28
, Issue.8
, pp. 1130-1135
-
-
Vanlier, J.1
Tiemann, C.2
Hilbers, P.3
van Riel, N.4
-
19
-
-
84859739489
-
A Bayesian Approach to Targeted Experiment Design
-
10.1093/bioinformatics/bts092, 3324513, 22368245
-
Vanlier J, Tiemann C, Hilbers P, van Riel N. A Bayesian Approach to Targeted Experiment Design. Bioinformatics 2012, 28(8):1136-1142. 10.1093/bioinformatics/bts092, 3324513, 22368245.
-
(2012)
Bioinformatics
, vol.28
, Issue.8
, pp. 1136-1142
-
-
Vanlier, J.1
Tiemann, C.2
Hilbers, P.3
van Riel, N.4
-
20
-
-
84871921477
-
Dialogue for Reverse Engineering Assessments and Methods
-
Dialogue for Reverse Engineering Assessments and Methods. , http://www.the-dream-project.org/
-
-
-
-
21
-
-
76649138302
-
Why are Nonlinear Fits to Data So Challenging?
-
060210, 1060201
-
Transtrum MK, Machta BB, Sethna JP. Why are Nonlinear Fits to Data So Challenging?. Phys Rev Lett 2010, 104(060210):1060201.
-
(2010)
Phys Rev Lett
, vol.104
-
-
Transtrum, M.K.1
Machta, B.B.2
Sethna, J.P.3
-
22
-
-
79953156419
-
Geometry of nonlinear least squares with applications to sloppy models and optimization
-
Transtrum MK, Machta BB, Sethna JP. Geometry of nonlinear least squares with applications to sloppy models and optimization. Phys Rev E 2011, 83(3):036701.
-
(2011)
Phys Rev E
, vol.83
, Issue.3
, pp. 036701
-
-
Transtrum, M.K.1
Machta, B.B.2
Sethna, J.P.3
-
23
-
-
0000718866
-
Modeling large scale biological systems from functional genomic data: parameter estimation
-
Mendes P. Modeling large scale biological systems from functional genomic data: parameter estimation. Found Syst Biol 2001, 163-186.
-
(2001)
Found Syst Biol
, pp. 163-186
-
-
Mendes, P.1
-
24
-
-
0242574982
-
Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods
-
10.1101/gr.1262503, 403766, 14559783
-
Moles C, Mendes P, Banga J. Parameter Estimation in Biochemical Pathways: A Comparison of Global Optimization Methods. Genome Res 2003, 13(11):2467-2474. 10.1101/gr.1262503, 403766, 14559783.
-
(2003)
Genome Res
, vol.13
, Issue.11
, pp. 2467-2474
-
-
Moles, C.1
Mendes, P.2
Banga, J.3
-
25
-
-
32044474451
-
A hybrid approach for efficient and robust parameter estimation in biochemical pathways
-
10.1016/j.biosystems.2005.06.016, 16236429
-
Rodriguez-Fernandez M, Mendes P, Banga J. A hybrid approach for efficient and robust parameter estimation in biochemical pathways. BioSystems 2006, 83(2-3):248-265. 10.1016/j.biosystems.2005.06.016, 16236429.
-
(2006)
BioSystems
, vol.83
, Issue.2-3
, pp. 248-265
-
-
Rodriguez-Fernandez, M.1
Mendes, P.2
Banga, J.3
-
26
-
-
84966204312
-
Numerical methods for computing angles between linear subspaces
-
Björck A, Golub G. Numerical methods for computing angles between linear subspaces. Mathematics Comput 1973, 27(123):579-594.
-
(1973)
Mathematics Comput
, vol.27
, Issue.123
, pp. 579-594
-
-
Björck, A.1
Golub, G.2
-
27
-
-
34249744604
-
Optimal experimental design in an epidermal growth factor receptor signalling and down-regulation model
-
Casey F, Baird D, Feng Q, Gutenkunst R, Waterfall J, Myers C, Brown K, Cerione R, Sethna J. Optimal experimental design in an epidermal growth factor receptor signalling and down-regulation model. Syst Biol, IET 2007, 1(3):190-202.
-
(2007)
Syst Biol, IET
, vol.1
, Issue.3
, pp. 190-202
-
-
Casey, F.1
Baird, D.2
Feng, Q.3
Gutenkunst, R.4
Waterfall, J.5
Myers, C.6
Brown, K.7
Cerione, R.8
Sethna, J.9
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