Mathematical modeling as a tool for investigating cell cycle control networks

Methods : a Companion to Methods in Enzymology
Jill C Sible, John J Tyson

Abstract

Although not a traditional experimental "method," mathematical modeling can provide a powerful approach for investigating complex cell signaling networks, such as those that regulate the eukaryotic cell division cycle. We describe here one modeling approach based on expressing the rates of biochemical reactions in terms of nonlinear ordinary differential equations. We discuss the steps and challenges in assigning numerical values to model parameters and the importance of experimental testing of a mathematical model. We illustrate this approach throughout with the simple and well-characterized example of mitotic cell cycles in frog egg extracts. To facilitate new modeling efforts, we describe several publicly available modeling environments, each with a collection of integrated programs for mathematical modeling. This review is intended to justify the place of mathematical modeling as a standard method for studying molecular regulatory networks and to guide the non-expert to initiate modeling projects in order to gain a systems-level perspective for complex control systems.

References

Oct 15, 1991·Proceedings of the National Academy of Sciences of the United States of America·A Goldbeter
Nov 30, 1990·Cell·M J SolomonM W Kirschner
Jan 1, 1996·Biophysical Chemistry·C Dennis Thron
Sep 25, 1997·Trends in Biochemical Sciences·Pedro Mendes
Sep 29, 1999·Proceedings of the National Academy of Sciences of the United States of America·B D Aguda
Dec 3, 1999·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·A Hershko
Jan 19, 2000·Molecular Biology of the Cell·K C ChenJohn J Tyson
Jan 26, 2002·Molecular Biology of the Cell·Frederick R CrossMartha Klovstad
Oct 22, 2002·American Journal of Physiology. Cell Physiology·Zhilin QuW Robb MacLellan
Jan 2, 2003·Proceedings of the National Academy of Sciences of the United States of America·Wei ShaJill C Sible
Mar 12, 2003·Nature Cell Biology·Joseph R PomereningJames E Ferrell
Mar 22, 2003·Current Opinion in Cell Biology·John J TysonBela Novak
Apr 16, 2003·Cell Cycle·Shaochun BaiMandri Obeyesekere
Oct 30, 2003·Omics : a Journal of Integrative Biology·Nicholas AllenJason Zwolak
Dec 20, 2003·Omics : a Journal of Integrative Biology·Herbert M SauroHiroaki Kitano
Jun 1, 2004·Molecular Biology of the Cell·Katherine C ChenJohn J Tyson
Jun 23, 2004·Biology of the Cell·Narat J Eungdamrong, Ravi Iyengar
Jul 27, 2004·Bioinformatics·Marc VassJohn J Tyson
Jul 29, 2004·Journal of Cell Science·Zhilin QuW Robb MacLellan
Feb 18, 2005·Molecular Biology of the Cell·Frederick R CrossKatherine C Chen
Feb 24, 2005·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jason ZwolakLayne T Watson
Oct 19, 2006·Systems Biology·Jason ZwolakLayne T Watson

Citations

May 3, 2011·Annual Review of Biomedical Engineering·Thomas S DeisboeckVittorio Cristini
Aug 13, 2009·Journal of Mathematical Biology·Fusheng Tang, Weijiu Liu
Mar 10, 2009·Briefings in Bioinformatics·Attila Csikasz-Nagy
Sep 29, 2011·Science Signaling·Eric A Sobie
Sep 19, 2009·Molecular BioSystems·Adrien Fauré, Denis Thieffry
Jan 1, 2008·Biotechnology & Genetic Engineering Reviews·Rui AlvesAlbert Sorribas
Jul 5, 2011·Journal of Theoretical Biology·Maria-Grazia AscenziGeorge Mohler
Dec 21, 2010·Methods : a Companion to Methods in Enzymology·Brandon S Razooky, Leor S Weinberger
Jul 16, 2014·ACS Synthetic Biology·Jason G Lomnitz, Michael A Savageau
Aug 19, 2008·Trends in Cell Biology·David C Clarke, Xuedong Liu
Aug 16, 2008·Journal of Theoretical Biology·Ivan Mura, Attila Csikasz-Nagy
Sep 4, 2012·Scientific Reports·Myong-Hee Sung, Gordon L Hager
Nov 9, 2010·Journal of Neuroendocrinology·J TabakG Leng
Feb 22, 2011·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·Imtiaz A KhanRachel J Errington
May 1, 2010·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Ranjit RandhawaJohn J Tyson
Sep 25, 2015·BMC Biology·H Frederik NijhoutMichael C Reed
Jan 8, 2011·BMC Systems Biology·John H Gauthier, Phillip I Pohl
Jul 9, 2013·Drug Discovery Today·Zhihui Wang, Thomas S Deisboeck
Dec 2, 2011·Molecular Biology of the Cell·Qing Kang, Joseph R Pomerening
May 4, 2012·Gene Regulation and Systems Biology·Clark D JeffriesWilliam K Kaufmann
Jun 2, 2018·Integrative Biology : Quantitative Biosciences From Nano to Macro·Yasmin Z PatersonJasmin Fisher
Mar 10, 2010·Biochemistry. Biokhimii︠a︡·A A TerentievK V Shaitan
Nov 22, 2016·Integrative Biology : Quantitative Biosciences From Nano to Macro·M SumitJ J Linderman
Sep 17, 2008·Essays in Biochemistry·Padmini Rangamani, Ravi Iyengar
Jul 16, 2019·Simulation·Thomas C JonesClifford A Shaffer

Related Concepts

Cell Cycle
Cell-Free System
In Silico
Ovum
Xenopus laevis
Signal Transduction

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