-
1
-
-
77950841799
-
Parameter estimation and model selection in computational biology
-
Lillacci G, Khammash M, (2010) Parameter estimation and model selection in computational biology. PLoS Comput Biol 6: e1000696.
-
(2010)
PLoS Comput Biol
, vol.6
-
-
Lillacci, G.1
Khammash, M.2
-
2
-
-
78149457680
-
When the optimal is not the best: parameter estimation in complex biological models
-
Slezak DF, Suarez C, Cecchi GA, Marshall G, Stolovitzky G, (2010) When the optimal is not the best: parameter estimation in complex biological models. PloS ONE 5: e13283.
-
(2010)
PloS ONE
, vol.5
-
-
Slezak, D.F.1
Suarez, C.2
Cecchi, G.A.3
Marshall, G.4
Stolovitzky, G.5
-
4
-
-
0001362410
-
The Levenberg-Marquardt algorithm: implementation and theory
-
More J, (1978) The Levenberg-Marquardt algorithm: implementation and theory. Numer Anal 630: 105-116.
-
(1978)
Numer Anal
, vol.630
, pp. 105-116
-
-
More, J.1
-
5
-
-
77958577251
-
Gradient descent optimization in gene regulatory pathways
-
Das M, Mukhopadhyay S, De RK, (2010) Gradient descent optimization in gene regulatory pathways. PloS ONE 5: e12475.
-
(2010)
PloS ONE
, vol.5
-
-
Das, M.1
Mukhopadhyay, S.2
De, R.K.3
-
6
-
-
0016473731
-
The Nelder-Mead simplex procedure for function minimization
-
Olsson DM, Nelson LS, (1975) The Nelder-Mead simplex procedure for function minimization. Technometrics 17: 45-51.
-
(1975)
Technometrics
, vol.17
, pp. 45-51
-
-
Olsson, D.M.1
Nelson, L.S.2
-
7
-
-
58149415047
-
Least squares fitting of a straight line with correlated errors, Earth Planet Sci Lett
-
York D, (1968) Least squares fitting of a straight line with correlated errors, Earth Planet Sci Lett. 5: 320-324.
-
(1968)
, vol.5
, pp. 320-324
-
-
York, D.1
-
8
-
-
84861648926
-
A distribution-matching method for parameter estimation and model selection in computational biology
-
Lillacci G, Khammash M, (2012) A distribution-matching method for parameter estimation and model selection in computational biology. Int J Robust Nonlinear Control 22(10): 1065-1081.
-
(2012)
Int J Robust Nonlinear Control
, vol.22
, Issue.10
, pp. 1065-1081
-
-
Lillacci, G.1
Khammash, M.2
-
9
-
-
81455142792
-
Parameter estimation using meta-heuristics in systems biology: a comprehensive review
-
Sun J, Garibaldi J, Hodgman C, (2012) Parameter estimation using meta-heuristics in systems biology: a comprehensive review. IEEE/ACM Trans Comput Biol Bioinform 9: 185-202.
-
(2012)
IEEE/ACM Trans Comput Biol Bioinform
, vol.9
, pp. 185-202
-
-
Sun, J.1
Garibaldi, J.2
Hodgman, C.3
-
10
-
-
77955187053
-
Global parameter estimation methods for stochastic biochemical systems
-
Poovathingal SK, Gunawan R, (2010) Global parameter estimation methods for stochastic biochemical systems. BMC Bioinformatics 11: 414-426.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 414-426
-
-
Poovathingal, S.K.1
Gunawan, R.2
-
11
-
-
41549140160
-
Bayesian inference for a discretely observed stochastic kinetic model
-
Golightly A, Wilkinson DJ, (2008) Bayesian inference for a discretely observed stochastic kinetic model. Stat Comput 18: 125-135.
-
(2008)
Stat Comput
, vol.18
, pp. 125-135
-
-
Golightly, A.1
Wilkinson, D.J.2
-
12
-
-
44649137397
-
Particle swarm optimization and differential evolution algorithms: technical analysis, applications and hybridization perspectives
-
Das S, Abraham A, Konar A (2008) Particle swarm optimization and differential evolution algorithms: technical analysis, applications and hybridization perspectives. Adv Comput Intell Ind Syst: 1-38.
-
(2008)
Adv Comput Intell Ind Syst
, pp. 1-38
-
-
Das, S.1
Abraham, A.2
Konar, A.3
-
14
-
-
84855981944
-
Global optimization in systems biology: stochastic methods and their applications
-
Balsa-Canto E, Banga JR, Egea JA, Fernandez-Villaverde A, de Hijas-Liste GM, (2012) Global optimization in systems biology: stochastic methods and their applications. Adv Exp Med Biol 736: 409-24.
-
(2012)
Adv Exp Med Biol
, vol.736
, pp. 409-424
-
-
Balsa-Canto, E.1
Banga, J.R.2
Egea, J.A.3
Fernandez-Villaverde, A.4
de Hijas-Liste, G.M.5
-
16
-
-
73449088381
-
Interactions between connected half-sarcomeres produce emergent mechanical behavior in a mathematical model of muscle
-
Campbell KS, (2009) Interactions between connected half-sarcomeres produce emergent mechanical behavior in a mathematical model of muscle. PLoS Comput Biol 5: e1000560.
-
(2009)
PLoS Comput Biol
, vol.5
-
-
Campbell, K.S.1
-
17
-
-
34250092221
-
Genetic algorithms and machine learning
-
Goldberg DE, (1988) Genetic algorithms and machine learning. Mach Learn 3: 95-99.
-
(1988)
Mach Learn
, vol.3
, pp. 95-99
-
-
Goldberg, D.E.1
-
18
-
-
67650679629
-
A comparison of genetic algorithms and particle swarm optimization for parameter estimation in stochastic biochemical systems, Evolutionary Computation
-
Besozzi D, Cazzaniga P, Mauri G, Pescini D, Vanneschi L (2009) A comparison of genetic algorithms and particle swarm optimization for parameter estimation in stochastic biochemical systems, Evolutionary Computation. Mach Learn Data Min Bioinformatics: 116-127.
-
(2009)
Mach Learn Data Min Bioinformatics
, pp. 116-127
-
-
Besozzi, D.1
Cazzaniga, P.2
Mauri, G.3
Pescini, D.4
Vanneschi, L.5
-
20
-
-
84862556212
-
A cooperative strategy for parameter estimation in large scale systems biology models, BMC Syst Biol
-
Villaverde AF, Egea JA, Banga JR, (2012) A cooperative strategy for parameter estimation in large scale systems biology models, BMC Syst Biol. 6: 75.
-
(2012)
, vol.6
, pp. 75
-
-
Villaverde, A.F.1
Egea, J.A.2
Banga, J.R.3
-
21
-
-
0347899800
-
Fundamentals of scatter search and path relinking
-
Glover F, Laguna M, Marti R, (2000) Fundamentals of scatter search and path relinking. Control Cybern 39: 653-684.
-
(2000)
Control Cybern
, vol.39
, pp. 653-684
-
-
Glover, F.1
Laguna, M.2
Marti, R.3
-
22
-
-
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: 483-501.
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 483-501
-
-
Rodriguez-Fernandez, M.1
Egea, J.A.2
Banga, J.R.3
-
23
-
-
0142000477
-
Differential evolution - a simple and efficient heuristic for global optimization over continuous spaces
-
Storn R, Price K, (1997) Differential evolution - a simple and efficient heuristic for global optimization over continuous spaces. J Glob Optim 11: 341-359.
-
(1997)
J Glob Optim
, vol.11
, pp. 341-359
-
-
Storn, R.1
Price, K.2
-
24
-
-
65649138437
-
Computational modeling of biochemical networks using COPASI, Methods Mol Biol
-
Mendes P, Hoops S, Sahle S, Gauges R, Dada J, et al. (2009) Computational modeling of biochemical networks using COPASI, Methods Mol Biol. 500: 17-59.
-
(2009)
, vol.500
, pp. 17-59
-
-
Mendes, P.1
Hoops, S.2
Sahle, S.3
Gauges, R.4
Dada, J.5
-
25
-
-
41849104688
-
Hybrid optimization method with general switching strategy for parameter estimation, BMC Syst Biol
-
Balsa-Canto E, Peifer M, Banga JR, Timmer J, Fleck C, (2008) Hybrid optimization method with general switching strategy for parameter estimation, BMC Syst Biol. 2: 26.
-
(2008)
, vol.2
, pp. 26
-
-
Balsa-Canto, E.1
Peifer, M.2
Banga, J.R.3
Timmer, J.4
Fleck, C.5
-
27
-
-
78650776100
-
Hybrid particle swarm optimization algorithms based on differential evolution and local search
-
Fu W, Johnston M, Zhang M, (2010) Hybrid particle swarm optimization algorithms based on differential evolution and local search. Adv Artif Intell 6464: 313-322.
-
(2010)
Adv Artif Intell
, vol.6464
, pp. 313-322
-
-
Fu, W.1
Johnston, M.2
Zhang, M.3
-
28
-
-
84864320135
-
A new hybrid firefly algorithm for complex and nonlinear problem
-
Abdullah A, Deris S, Mohamad MS, Hashim SZM, (2012) A new hybrid firefly algorithm for complex and nonlinear problem. Distrib Comput Artif Intell 151: 678-680.
-
(2012)
Distrib Comput Artif Intell
, vol.151
, pp. 678-680
-
-
Abdullah, A.1
Deris, S.2
Mohamad, M.S.3
Hashim, S.Z.M.4
-
29
-
-
77957863557
-
Firefly algorithms for multimodal optimization
-
Yang XS (2009) Firefly algorithms for multimodal optimization. Stoch Algorithms Found Appl: 169-178.
-
(2009)
Stoch Algorithms Found Appl
, pp. 169-178
-
-
Yang, X.S.1
-
30
-
-
40149112059
-
Stimulus design for model selection and validation in cell signaling
-
Apgar JF, Toettcher JE, Endy D, White FM, Tidor B, (2008) Stimulus design for model selection and validation in cell signaling. PLoS Comput Biol 4: e30.
-
(2008)
PLoS Comput Biol
, vol.4
-
-
Apgar, J.F.1
Toettcher, J.E.2
Endy, D.3
White, F.M.4
Tidor, B.5
-
31
-
-
34249744604
-
Optimal experimental design in an epidermal growth factor receptor signalling and down-regulation model
-
Casey FP, Baird D, Feng Q, Gutenkunst RN, Waterfall JJ, et al. (2007) Optimal experimental design in an epidermal growth factor receptor signalling and down-regulation model. IET Syst Biol 1: 190-202.
-
(2007)
IET 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
-
32
-
-
81555207959
-
Structural Identifiability of Systems Biology Models: A Critical Comparison of Methods
-
Chis OT, Banga JR, Balsa-Canto E, (2011) Structural Identifiability of Systems Biology Models: A Critical Comparison of Methods. PLoS ONE 6: e27755.
-
(2011)
PLoS ONE
, vol.6
-
-
Chis, O.T.1
Banga, J.R.2
Balsa-Canto, E.3
-
33
-
-
0000025874
-
On structural identifiability
-
Bellman R, Åström KJ, (1970) On structural identifiability. MathBiosci 7: 329-339.
-
(1970)
MathBiosci
, vol.7
, pp. 329-339
-
-
Bellman, R.1
Åström, K.J.2
-
34
-
-
79952606233
-
Addressing parameter identifiability by model-based experimentation
-
Raue A, Kreutz C, Maiwald T, Klingmüller U, Timmer J, (2011) Addressing parameter identifiability by model-based experimentation. IET Syst Biol 5: 120-130.
-
(2011)
IET Syst Biol
, vol.5
, pp. 120-130
-
-
Raue, A.1
Kreutz, C.2
Maiwald, T.3
Klingmüller, U.4
Timmer, J.5
-
35
-
-
79551552677
-
Model-based inference of biochemical parameters and dynamic properties of microbial signal transduction networks
-
Schaber J, Klipp E, (2011) Model-based inference of biochemical parameters and dynamic properties of microbial signal transduction networks. Curr Opin Biotechnol 22: 109-116.
-
(2011)
Curr Opin Biotechnol
, vol.22
, pp. 109-116
-
-
Schaber, J.1
Klipp, E.2
-
36
-
-
80051962319
-
Firefly algorithm for continuous constrained optimization tasks, Comput Collect Intell
-
Lukasik S, Zak S (2009) Firefly algorithm for continuous constrained optimization tasks, Comput Collect Intell. Semantic Web Soc Netw Multiagent Syst: 197-107.
-
(2009)
Semantic Web Soc Netw Multiagent Syst
, pp. 107-197
-
-
Lukasik, S.1
Zak, S.2
-
37
-
-
77954398160
-
Stress-specific response of the p53-Mdm2 feedback loop
-
Hunziker A, Jensen MH, Sandeep K, (2010) Stress-specific response of the p53-Mdm2 feedback loop. BMC Syst Biol 4: 94-102.
-
(2010)
BMC Syst Biol
, vol.4
, pp. 94-102
-
-
Hunziker, A.1
Jensen, M.H.2
Sandeep, K.3
-
38
-
-
39049111481
-
In silico analysis of arginine catabolism as a source of nitric oxide or polyamines in endothelial cells
-
Montanez R, Rodriguez-Caso C, Sanchez-Jimenez F, Medina MA, (2008) In silico analysis of arginine catabolism as a source of nitric oxide or polyamines in endothelial cells. Amino Acids 34: 223-229.
-
(2008)
Amino Acids
, vol.34
, pp. 223-229
-
-
Montanez, R.1
Rodriguez-Caso, C.2
Sanchez-Jimenez, F.3
Medina, M.A.4
-
39
-
-
80053629073
-
Parameter estimation with bio-inspired meta-heuristic optimization: modeling the dynamics of endocytosis
-
Tashkova K, Korosec P, Silc J, Todorovski L, Dzeroski S, (2011) Parameter estimation with bio-inspired meta-heuristic optimization: modeling the dynamics of endocytosis. BMC Syst Biol 5: 159-185.
-
(2011)
BMC Syst Biol
, vol.5
, pp. 159-185
-
-
Tashkova, K.1
Korosec, P.2
Silc, J.3
Todorovski, L.4
Dzeroski, S.5
-
40
-
-
73449142148
-
Optimal experimental design for parameter estimation of a cell signaling model, PLoS Comp Biol
-
Bandara S, Schlöder JP, Eils R, Bock HG, Meyer T, (2009) Optimal experimental design for parameter estimation of a cell signaling model, PLoS Comp Biol. 5: e1000558.
-
(2009)
, vol.5
-
-
Bandara, S.1
Schlöder, J.P.2
Eils, R.3
Bock, H.G.4
Meyer, T.5
-
41
-
-
62749173565
-
Differential equation modeling of HIV viral fitness experiments: model identification, model selection, and multimodel inference
-
Miao H, Dykes C, Demeter LM, Wu H, (2009) Differential equation modeling of HIV viral fitness experiments: model identification, model selection, and multimodel inference. Biometrics 65: 292-300.
-
(2009)
Biometrics
, vol.65
, pp. 292-300
-
-
Miao, H.1
Dykes, C.2
Demeter, L.M.3
Wu, H.4
-
42
-
-
0000501656
-
Information theory and an extension of the maximum likelihood principle
-
Akaike H, (1973) Information theory and an extension of the maximum likelihood principle. Int Symp Inf theory 1: 267-281.
-
(1973)
Int Symp Inf Theory
, vol.1
, pp. 267-281
-
-
Akaike, H.1
-
43
-
-
58849162806
-
Systems biology: model based evaluation and comparison of potential explanations for given biological data
-
Cedersund G, Roll J, (2009) Systems biology: model based evaluation and comparison of potential explanations for given biological data. FEBS J 276: 903-922.
-
(2009)
FEBS J
, vol.276
, pp. 903-922
-
-
Cedersund, G.1
Roll, J.2
-
44
-
-
33646807832
-
The P53 pathway: what questions remain to be explored?
-
Levine AJ, Hu W, Feng Z, (2006) The P53 pathway: what questions remain to be explored? Cell Death Differ 13: 1027-36.
-
(2006)
Cell Death Differ
, vol.13
, pp. 1027-1036
-
-
Levine, A.J.1
Hu, W.2
Feng, Z.3
-
45
-
-
67349091738
-
The ups and downs of p53: understanding protein dynamics in single cells
-
Batchelor E, Loewer A, Lahav G, (2009) The ups and downs of p53: understanding protein dynamics in single cells. Nat Rev Cancer 9: 371-377.
-
(2009)
Nat Rev Cancer
, vol.9
, pp. 371-377
-
-
Batchelor, E.1
Loewer, A.2
Lahav, G.3
-
46
-
-
0030941458
-
p53, the cellular gatekeeper for growth and division
-
Levine AJ, (1997) p53, the cellular gatekeeper for growth and division. Cell 88: 323-331.
-
(1997)
Cell
, vol.88
, pp. 323-331
-
-
Levine, A.J.1
-
47
-
-
18344377030
-
The p53 pathway: positive and negative feedback loops
-
Harris SL, Levine AJ, (2005) The p53 pathway: positive and negative feedback loops. Oncogene 24: 2899.
-
(2005)
Oncogene
, vol.24
, pp. 2899
-
-
Harris, S.L.1
Levine, A.J.2
-
48
-
-
53149144701
-
Explaining oscillations and variability in the p53-Mdm2 system
-
Proctor CJ, Gray DA, (2008) Explaining oscillations and variability in the p53-Mdm2 system. BMC Syst Biol 2: 75-95.
-
(2008)
BMC Syst Biol
, vol.2
, pp. 75-95
-
-
Proctor, C.J.1
Gray, D.A.2
-
49
-
-
77953508699
-
Mathematical modeling: bridging the gap between concept and realization in synthetic biology
-
doi: 10.1155/2010/541609
-
Yuting Z, Ganesh S (2010) Mathematical modeling: bridging the gap between concept and realization in synthetic biology. J Biomed Biotechnol, doi: 10.1155/2010/541609.
-
(2010)
J Biomed Biotechnol
-
-
Yuting, Z.1
Ganesh, S.2
-
50
-
-
23444456772
-
Regulation of immune responses by L-arginine metabolism
-
Bronte V, Zanovello P, (2005) Regulation of immune responses by L-arginine metabolism. Nat Rev Immunol 5: 641-654.
-
(2005)
Nat Rev Immunol
, vol.5
, pp. 641-654
-
-
Bronte, V.1
Zanovello, P.2
-
51
-
-
14844321288
-
Space in systems biology of signaling pathways-towards intracellular molecular crowding in silico
-
Takahashi K, Arjunan SN, Tomita M, (2005) Space in systems biology of signaling pathways-towards intracellular molecular crowding in silico. FEBS Lett 579: 1783-8.
-
(2005)
FEBS Lett
, vol.579
, pp. 1783-1788
-
-
Takahashi, K.1
Arjunan, S.N.2
Tomita, M.3
-
52
-
-
83755203610
-
Stochastic simulation for spatial modelling of dynamic processes in a living cell
-
In: Koeppl H, Setti G, di Bernardo M, Densmore D, editors Springer Verlag
-
Burrage K, Burrage P, Leier A, Marquez-Lago TT, Nicolau DV (2011) Stochastic simulation for spatial modelling of dynamic processes in a living cell. In: Koeppl H, Setti G, di Bernardo M, Densmore D, editors. Design and Analysis of Bio-molecular Circuits. Springer Verlag. 43-62.
-
(2011)
Design and Analysis of Bio-molecular Circuits
, pp. 43-62
-
-
Burrage, K.1
Burrage, P.2
Leier, A.3
Marquez-Lago, T.T.4
Nicolau, D.V.5
-
53
-
-
84863088389
-
Dynamic optimization of distributed biological systems using robust and efficient numerical techniques
-
Vilas C, Balsa-Canto E, García SG, Banga JR, Alonso AA, (2012) Dynamic optimization of distributed biological systems using robust and efficient numerical techniques. BMC Syst Biol. 6: 79.
-
(2012)
BMC Syst Biol
, vol.6
, pp. 79
-
-
Vilas, C.1
Balsa-Canto, E.2
García, S.G.3
Banga, J.R.4
Alonso, A.A.5
|