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Items: 1 to 20 of 206


Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model.

Oguz C, Laomettachit T, Chen KC, Watson LT, Baumann WT, Tyson JJ.

BMC Syst Biol. 2013 Jun 28;7:53. doi: 10.1186/1752-0509-7-53.


Predicting network modules of cell cycle regulators using relative protein abundance statistics.

Oguz C, Watson LT, Baumann WT, Tyson JJ.

BMC Syst Biol. 2017 Feb 28;11(1):30. doi: 10.1186/s12918-017-0409-1.


Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies.

Dräger A, Kronfeld M, Ziller MJ, Supper J, Planatscher H, Magnus JB, Oldiges M, Kohlbacher O, Zell A.

BMC Syst Biol. 2009 Jan 14;3:5. doi: 10.1186/1752-0509-3-5.


Parameter estimation with bio-inspired meta-heuristic optimization: modeling the dynamics of endocytosis.

Tashkova K, Korošec P, Silc J, Todorovski L, Džeroski S.

BMC Syst Biol. 2011 Oct 11;5:159. doi: 10.1186/1752-0509-5-159.


Integrative analysis of cell cycle control in budding yeast.

Chen KC, Calzone L, Csikasz-Nagy A, Cross FR, Novak B, Tyson JJ.

Mol Biol Cell. 2004 Aug;15(8):3841-62. Epub 2004 May 28.


Parameter estimation of dynamic biological network models using integrated fluxes.

Liu Y, Gunawan R.

BMC Syst Biol. 2014 Nov 18;8:127. doi: 10.1186/s12918-014-0127-x.


Recent developments in parameter estimation and structure identification of biochemical and genomic systems.

Chou IC, Voit EO.

Math Biosci. 2009 Jun;219(2):57-83. doi: 10.1016/j.mbs.2009.03.002. Epub 2009 Mar 25. Review.


Bayesian parameter estimation for nonlinear modelling of biological pathways.

Ghasemi O, Lindsey ML, Yang T, Nguyen N, Huang Y, Jin YF.

BMC Syst Biol. 2011;5 Suppl 3:S9. doi: 10.1186/1752-0509-5-S3-S9. Epub 2011 Dec 23.


An improved swarm optimization for parameter estimation and biological model selection.

Abdullah A, Deris S, Mohamad MS, Anwar S.

PLoS One. 2013 Apr 11;8(4):e61258. doi: 10.1371/journal.pone.0061258. Print 2013. Erratum in: PLoS One. 2013;8(5). doi:10.1371/annotation/0e890aa4-232d-4fd3-bb82-675dd9fc33ff.


A data integration approach for cell cycle analysis oriented to model simulation in systems biology.

Alfieri R, Merelli I, Mosca E, Milanesi L.

BMC Syst Biol. 2007 Aug 1;1:35.


Differential simulated annealing: a robust and efficient global optimization algorithm for parameter estimation of biological networks.

Dai Z, Lai L.

Mol Biosyst. 2014 Jun;10(6):1385-92. doi: 10.1039/c4mb00100a. Epub 2014 Apr 9.


A simple work flow for biologically inspired model reduction--application to early JAK-STAT signaling.

Quaiser T, Dittrich A, Schaper F, Mönnigmann M.

BMC Syst Biol. 2011 Feb 21;5:30. doi: 10.1186/1752-0509-5-30.


A Model of Yeast Cell-Cycle Regulation Based on a Standard Component Modeling Strategy for Protein Regulatory Networks.

Laomettachit T, Chen KC, Baumann WT, Tyson JJ.

PLoS One. 2016 May 17;11(5):e0153738. doi: 10.1371/journal.pone.0153738. eCollection 2016.


An improved hybrid of particle swarm optimization and the gravitational search algorithm to produce a kinetic parameter estimation of aspartate biochemical pathways.

Ismail AM, Mohamad MS, Abdul Majid H, Abas KH, Deris S, Zaki N, Mohd Hashim SZ, Ibrahim Z, Remli MA.

Biosystems. 2017 Dec;162:81-89. doi: 10.1016/j.biosystems.2017.09.013. Epub 2017 Sep 23.


Parameter optimization by using differential elimination: a general approach for introducing constraints into objective functions.

Nakatsui M, Horimoto K, Okamoto M, Tokumoto Y, Miyake J.

BMC Syst Biol. 2010 Sep 13;4 Suppl 2:S9. doi: 10.1186/1752-0509-4-S2-S9.


Investigating dynamics of inhibitory and feedback loops in ERK signalling using power-law models.

Vera J, Rath O, Balsa-Canto E, Banga JR, Kolch W, Wolkenhauer O.

Mol Biosyst. 2010 Nov;6(11):2174-91. doi: 10.1039/c0mb00018c. Epub 2010 Aug 18.


Estimating a predator-prey dynamical model with the parameter cascades method.

Cao J, Fussmann GF, Ramsay JO.

Biometrics. 2008 Sep;64(3):959-67. Epub 2007 Nov 19.


An integrative and practical evolutionary optimization for a complex, dynamic model of biological networks.

Maeda K, Fukano Y, Yamamichi S, Nitta D, Kurata H.

Bioprocess Biosyst Eng. 2011 May;34(4):433-46. doi: 10.1007/s00449-010-0486-7. Epub 2010 Nov 27.


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