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Cited by 49Gene Regulatory Network AnalysisMathematical Biology Tumor GrowthMicrotubule and mitosis dynamics

The DOI matches its Crossref record.

Globally optimised parameters for a model of mitotic control in frog egg extracts.

Zwolak, J.W., Tyson, J.J., Watson, L.T.·2005·IEE Proceedings - Systems Biology
DOI 10.1049/ip-syb:20045032
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Abstract

DNA synthesis and nuclear division in the developing frog egg are controlled by fluctuations in the activity of M-phase promoting factor (MPF). The biochemical mechanism of MPF regulation is most easily studied in cytoplasmic extracts of frog eggs, for which careful experimental studies of the kinetics of phosphorylation and dephosphorylation of MPF and its regulators have been made. In 1998 Marlovits et al. used these data sets to estimate the kinetic rate constants in a mathematical model of the control system originally proposed by Novak & Tyson. In a recent publication, we showed that a gradient-based optimisation algorithm finds a locally optimal parameter set quite close to the 'Marlovits' estimates. In this paper, we combine global and local optimisation strategies to show that the 'refined Marlovits' parameter set, with one minor but significant modification to the Novak & Tyson equations, is the unique, best-fitting solution to the parameter estimation problem.

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  • By examining 17 models from the systems biology literature, the paper showed that their parameter sensitivities all share striking common features deemed "sloppiness".

    “By examining 17 models from the systems biology literature [2,21,25,28–41], we showed that their parameter sensitivities all share striking common features deemed “sloppiness””

    From Universally Sloppy Parameter Sensitivities in Systems Biology Models (2007) · cites this paper as [29]

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Research works printed but not linked: 45

  1. Bray, 1995, 376, 307, 10.1038/376307a0 · DOI
  2. Hanahan, 2000, 100, 57
  3. Kohn, 1999, 10, 2703
  4. Hartwell, 1999, 402, C47, 10.1038/35011540 · DOI · Paper page
  5. Brent, 2000, 100, 169
  6. Hasty, 2001, 2, 268
  7. Tyson, 2001, 2, 908
  8. Martiel, 1987, 52, 808, 10.1016/S0006-3495(87)83275-7 · DOI
  9. Bray, 1993, 4, 469
  10. McAdams, 1995, 269, 650, 10.1126/science.7624793 · DOI
  11. Arkin, 1998, 149, 1633
  12. Sharp, 1998, 47, 79
  13. von Dassow, 2000, 188, 10.1038/35018085 · DOI · Paper page
  14. Asthagiri, 2001, 17, 227
  15. Meinhardt, 2001, 98, 14202, 10.1073/pnas.251216598 · DOI
  16. Chen, 2004, 15, 3841
  17. Cross, 2002, 13, 52
  18. Hoffmann, 2002, 298, 1241, 10.1126/science.1071914 · DOI
  19. Pomerening, 2003, 5, 346
  20. Sha, 2003, 100, 975
  21. Eissing, 2004, 279, 36892
  22. Barkai, 1997, 913, 10.1038/43199 · DOI · Paper page
  23. Zwolak, 2005, 12, 48
  24. Marlovits, 1998, 72, 169
  25. Novak, 1993, 106, 1153
  26. Kumagai, 1992, 70, 139
  27. Kumagai, 1995, 6, 199
  28. Tang, 1993, 12, 3427
  29. Solomon, 1990, 63, 1013
  30. He, 2002, 23, 5, 10.1023/A:1019992822938 · DOI
  31. Boggs, 1989, 4, 348
  32. Hindmarsh, 1980, 4, 10
  33. He, 2004, 3, 10.1109/TWC.2004.837454 · DOI
  34. Watson, 2001, 18, 155
  35. Jones, 1993, 79, 157
  36. Meza, 1996, 17, 1142, 10.1002/(SICI)1096-987X(19960715)17:9<1142::AID-JCC6>3.0.CO;2-S · DOI
  37. Moles, 2003, 13, 2467
  38. Lewis, R.M., Torczon, V., and Trosset, M.W.: ‘Direct search methods: then and now’, Numerical analysis: optimization and non-linear equations, (North-Holland 2000),4, p. 191–208 · DOI
  39. Kolda, 2003, 45, 385, 10.1137/S003614450242889 · DOI
  40. Boggs, P.T., Byrd, R.H., Rogers, J.E., and Schnabel, R.B.: User's reference guide for ODRPACK version 2.01: software for weighted orthogonal distance regression, (Center for Computing and Applied Mathematics, U.S. Department of Commerce, Gaithersburg, MD, 1992) · DOI
  41. Boggs, 1987, 6, 1052
  42. Radhakrishnan, K., and Hindmarsh, A.C.: Description and use of LSODE, the Livermore solver for ordinary differential equations, (NASA Reference Publication 1327. Lawrence Livermore National Laboratory Livermore, CA, Dec 1993) · DOI
  43. Petzold, 1983, 4, 136, 10.1137/0904010 · DOI
  44. Shampine, L.F., and Allen, R.C.: ‘Numerical computing: an introduction’, (W. B. Saunders Company, Philadelphia, PA 1973)
  45. Dekker, T.J.: ‘Finding a zero by means of successive linear interpolation’, Constructive aspects of the fundamental theorem of algebra, (Wiley-Interscience, London 1969)

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Metadata

Authors
Zwolak, J. W., Tyson, J. J., & Watson, L. T.
Affiliations
Virginia Tech (US)
ORCID
Tyson, J.J.
Venue
IEE Proceedings - Systems Biology
Publisher
Institution of Engineering and Technology (IET)
Published
2005
Volume
152
Issue
2
Pages
81
ISSN
1741-2471 (ISSN-L)
DOI
10.1049/ip-syb:20045032
OpenAlex
W2071026449
Cited by
49
References
0
Citations by year
2022: 2 · 2020: 2 · 2016: 2 · 2015: 1 · 2014: 1 · 2012: 1
FWCI
2.49
Type
journal article
Language
en
Open access
closed
Locations
  • Systems Biology (publishedVersion)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
  • Physical Sciences › Mathematics › Modeling and Simulation › Mathematical Biology Tumor Growth
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Microtubule and mitosis dynamics
Keywords
mitotic control, M-phase promoting factor, parameter estimation, global optimization, gradient-based optimization, nuclear division, DNA synthesis
MeSH terms
Animals, Cell Extracts, Computer Simulation, Cytoplasm, Feedback, Mitosis, Models, Biological, Ranidae, Signal Transduction, Cell Cycle Proteins

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