Literature DB >> 15725733

Parameter estimation for a mathematical model of the cell cycle in frog eggs.

Jason W Zwolak1, John J Tyson, Layne T Watson.   

Abstract

Parameter values for a kinetic model of the nuclear replication-division cycle in frog eggs are estimated by fitting solutions of the kinetic equations (nonlinear ordinary differential equations) to a suite of experimental observations. A set of optimal parameter values is found by minimizing an objective function defined as the orthogonal distance between the data and the model. The differential equations are solved by LSODAR and the objective function is minimized by ODRPACK. The optimal parameter values are close to the "guesstimates" of the modelers who first studied this problem. These tools are sufficiently general to attack more complicated problems, where guesstimation is impractical or unreliable.

Mesh:

Year:  2005        PMID: 15725733     DOI: 10.1089/cmb.2005.12.48

Source DB:  PubMed          Journal:  J Comput Biol        ISSN: 1066-5277            Impact factor:   1.479


  11 in total

Review 1.  Mathematical modeling as a tool for investigating cell cycle control networks.

Authors:  Jill C Sible; John J Tyson
Journal:  Methods       Date:  2007-02       Impact factor: 3.608

2.  Modeling Dose-response at Low Dose: A Systems Biology Approach for Ionization Radiation.

Authors:  Yuchao Zhao; Paolo F Ricci
Journal:  Dose Response       Date:  2010-03-18       Impact factor: 2.658

3.  When the optimal is not the best: parameter estimation in complex biological models.

Authors:  Diego Fernández Slezak; Cecilia Suárez; Guillermo A Cecchi; Guillermo Marshall; Gustavo Stolovitzky
Journal:  PLoS One       Date:  2010-10-25       Impact factor: 3.240

4.  A quantitative model of the effect of unreplicated DNA on cell cycle progression in frog egg extracts.

Authors:  Jason Zwolak; Nassiba Adjerid; Elife Z Bagci; John J Tyson; Jill C Sible
Journal:  J Theor Biol       Date:  2009-05-31       Impact factor: 2.691

5.  Modeling molecular regulatory networks with JigCell and PET.

Authors:  Clifford A Shaffer; Jason W Zwolak; Ranjit Randhawa; John J Tyson
Journal:  Methods Mol Biol       Date:  2009

6.  Toward a Logic of the Organism: A Process Philosophical Consideration.

Authors:  Spyridon A Koutroufinis
Journal:  Entropy (Basel)       Date:  2021-12-30       Impact factor: 2.524

7.  Simulating quantitative cellular responses using asynchronous threshold Boolean network ensembles.

Authors:  John Jack; John F Wambaugh; Imran Shah
Journal:  BMC Syst Biol       Date:  2011-07-11

8.  Optimal experiment selection for parameter estimation in biological differential equation models.

Authors:  Mark K Transtrum; Peng Qiu
Journal:  BMC Bioinformatics       Date:  2012-07-27       Impact factor: 3.169

9.  A framework for scalable parameter estimation of gene circuit models using structural information.

Authors:  Hiroyuki Kuwahara; Ming Fan; Suojin Wang; Xin Gao
Journal:  Bioinformatics       Date:  2013-07-01       Impact factor: 6.937

10.  Dynamical modeling of syncytial mitotic cycles in Drosophila embryos.

Authors:  Laurence Calzone; Denis Thieffry; John J Tyson; Bela Novak
Journal:  Mol Syst Biol       Date:  2007-07-31       Impact factor: 11.429

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