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RESEARCH ARTICLES 2007 2006 2005 2004 2003 2002 2001 2000 & EARLIER |
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Original Research Articles
2007
Ciliberto A, Capuani F, Tyson JJ. Modeling Networks of Coupled Enzymatic Reactions
Using the Total Quasi-Steady State Approximation. PLoS Comput Biol 2007 Mar 17; 3(3): e45 [Epub
ahead of print] Csikasz-Nagy A, Kapuy O, Gyorffy B, Tyson JJ,
Novak B. Modeling the septation initiation network (SIN) in
fission yeast cells. Curr Genet. 2007 Mar 6; [Epub ahead of print] Sible JC, Tyson JJ. Mathematical modeling as a tool for investigating
cell cycle control networks. Methods. 2007 Feb;41(2):238-47. Hong CI, Conrad ED, Tyson JJ. A proposal for robust temperature compensation of
circadian rhythms. Proc Natl Acad Sci U S A. 2007 Jan
23;104(4):1195-200. Zhang T, Brazhnik P, Tyson JJ. Cell Cycle. 2007 Jan;6(1):85-94. |
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2006
Analysis of a generic model of eukaryotic cell-cycle
regulation. Biophys J. 2006 Jun 15;90(12):4361-79. Battogtokh D, Aihara K, Tyson JJ. Synchronization of eukaryotic cells by periodic
forcing. Phys Rev Lett. 2006 Apr 14;96(14):148102. Vass MT, Shaffer CA, Ramakrishnan N, Watson LT,
Tyson JJ. The JigCell model builder: a spreadsheet interface
for creating biochemical reaction network models. IEEE/ACM Trans Comput Biol Bioinform. 2006
Apr-Jun;3(2):155-64. Brazhnik P, Tyson JJ. Cell cycle control in bacteria and yeast: a case of
convergent evolution? Cell Cycle. 2006 Mar;5(5):522-9. Tyson JJ. Another turn for p53. Mol Syst Biol. 2006;2:2006.0032. Battogtokh D, Tyson JJ. Periodic forcing of a mathematical model of the
eukaryotic cell cycle. Phys Rev E Stat Nonlin Soft Matter Phys. 2006
Jan;73(1 Pt 1):011910. Allen NA, Chen KC, Shaffer CA, Tyson JJ, Watson
LT. Syst Biol (Stevenage). 2006 Jan;153(1):13-21. |
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2005
Rewiring the exit from mitosis. Cell Cycle. 2005 Aug;4(8):1107-12. Zwolak JW, Tyson JJ, Watson LT. Globally optimised parameters for a model of
mitotic control in frog egg extracts. Syst Biol (Stevenage). 2005 Jun;152(2):81-92. Ciliberto A, Novak B, Tyson JJ. Steady states and oscillations in the p53/Mdm2
network. Cell Cycle. 2005 Mar;4(3):488-93. Zwolak JW, Tyson JJ, Watson LT. Parameter estimation for a mathematical model of
the cell cycle in frog eggs. J Comput Biol. 2005;12(1):48-63. |
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2004
The JigCell model builder and run manager. Bioinformatics. 2004 Dec 12;20(18):3680-1. Zwolak JW, Tyson JJ, Watson LT. Finding all steady state solutions of chemical
kinetic models Nonlinear Analysis: Real World Applications,
Volume 5, Issue 5, December 2004, Pages 801-814 Novak B, Tyson JJ. A model for restriction point control of the
mammalian cell cycle. J Theor Biol. 2004 Oct 21;230(4):563-79. Battogtokh D, Tyson JJ. Bifurcation analysis of a model of the budding
yeast cell cycle. Chaos. 2004 Sep;14(3):653-61. Chen KC, Calzone L, Csikasz-Nagy A, Cross FR,
Novak B, Tyson JJ. Integrative analysis of cell cycle control in
budding yeast. Mol Biol Cell. 2004 Aug;15(8):3841-62. Sveiczer A, Tyson JJ and Novak B. Modelling the fission yeast cell cycle. Brief. Funct. Genomics Proteomics 2004 2:298-307. Battogtokh D, Tyson JJ. Turbulence near cyclic fold bifurcations in
birhythmic media. Phys Rev E Stat Nonlin Soft Matter Phys. 2004
Aug;70(2 Pt 2):026212. Thornton BR, Chen KC, Cross FR, Tyson JJ,
Toczyski DP. Cycling without the cyclosome: modeling a yeast
strain lacking the APC. Cell Cycle. 2004 May;3(5):629-33. |
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2003
Ciliberto A, Novak B, Tyson JJ. Mathematical model of the morphogenesis
checkpoint in budding yeast. J Cell Biol. 2003 Dec 22;163(6):1243-54. Novak B, Tyson JJ. Modelling the controls of the eukaryotic cell
cycle. Biochem Soc Trans. 2003 Dec;31(Pt 6):1526-9. Ciliberto A, Petrus MJ, Tyson JJ, Sible JC. A kinetic model of the cyclin E/Cdk2
developmental timer in Xenopus laevis embryos. Biophys Chem. 2003 Jul 1;104(3):573-89. Sha W, Moore J, Chen KC, Lassaletta AD, Yi CS,
Tyson JJ, Sible JC. Hysteresis drives cell-cycle transitions in Xenopus
laevis egg extracts.Proc Natl Acad Sci U S A. 2003 Feb
4;100(3):975-80. |
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2002
Novak B, Sible JC, Tyson JJ. Checkpoints in the cell cycle. Encyclopedia of Life Sciences. London: Nature
Publishing Group. http://www.els.net/ 2002 [doi:10.1038/npg.els.0001355],
pp.1-8. |
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2001
Sveiczer A, Tyson JJ,
Novak B A stochastic, molecular
model of the fission yeast cell cycle: role of the nucleocytoplasmic ratio in
cycle time regulation. Biophys Chem. 2001 Aug
30;92(1-2):1-15. Tyson JJ, Novak B. Regulation of the
eukaryotic cell cycle: molecular antagonism, hysteresis, and irreversible
transitions. J Theor Biol. 2001 May
21;210(2):249-63. Novak B, Pataki Z,
Ciliberto A, Tyson JJ. Mathematical model of the
cell division cycle of fission yeast. Chaos. 2001
Mar;11(1):277-286. Tyson JJ, Mackey MC. Molecular, metabolic, and
genetic control: An introduction. Chaos. 2001
Mar;11(1):81-83. |
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2000
and earlier
Sveiczer A, Csikasz-Nagy
A, Gyorffy B, Tyson JJ, Novak B. Modeling the fission
yeast cell cycle: quantized cycle times in wee1- cdc25Delta mutant
cells. Proc Natl Acad Sci U S A.
2000 Jul 5;97(14):7865-70. Ciliberto A, Tyson JJ. Mathematical model for
early development of the sea urchin embryo. Bull Math Biol. 2000
Jan;62(1):37-59. Chen KC, Csikasz-Nagy A,
Gyorffy B, Val J, Novak B, Tyson JJ. Kinetic analysis of a molecular model of the budding
yeast cell cycle. Mol Biol Cell. 2000 Jan;11(1):369-91.
Tyson JJ, Hong CI, Thron
CD, Novak B. A simple model of
circadian rhythms based on dimerization and proteolysis of PER and TIM Biophys J. 1999
Nov;77(5):2411-7. Novak B, Toth A,
Csikasz-Nagy A, Gyorffy B, Tyson JJ, Nasmyth K. Finishing the cell cycle. J Theor Biol. 1999 Jul
21;199(2):223-33. Brazhnik P,Tyson JJ. On Traveling Wave Solutions of Fisher's Equation in
Two Spatial Dimensions. SIAP.1999 Vol 60 Iss 2,
371-391 Borisuk MT, Tyson JJ. Bifurcation analysis of a
model of mitotic control in frog eggs. J Theor Biol. 1998 Nov
7;195(1):69-85. Novak B, Csikasz-Nagy A,
Gyorffy B, Chen KC, Tyson JJ. Biophys Chem. 1998 May
5;72(1-2):185-200. Marlovits G, Tyson CJ,
Novak B, Tyson JJ. Modeling M-phase control
in Xenopus oocyte extracts: the surveillance mechanism for unreplicated DNA. Biophys Chem. 1998 May
5;72(1-2):169-84. Novak B, Tyson JJ. Modeling the control of
DNA replication in fission yeast. Proc Natl Acad Sci U S A.
1997 Aug 19;94(17):9147-52. Brazhnik P, Tyson JJ. Physica D: Nonlinear
Phenomena, Volume 102, Issues 3-4, 1 April 1997, Pages 300-312. Brazhnik P, Tyson JJ. Nonspiral excitation waves beyond the eikonal
approximation. Phys Rev E Stat Phys
Plasmas Fluids Relat Interdiscip Topics. 1996 Oct;54(4):4338-4346. Brazhnik P, Tyson JJ. Phys Rev E Stat Phys
Plasmas Fluids Relat Interdiscip Topics. 1996 Aug;54(2):1958-1968. Tyson JJ, Novak B, Odell
GM, Chen KC, Thron CD. Chemical kinetic theory
as a tool for understanding the regulation of M-phase promoting factor in the
cell cycle. Trends Biochem. Sci.
1996. 21: 89-96. Novak B, and Tyson JJ. Quantitative analysis of
a molecular model of mitotic control in fission yeast. J. Theor. Biol.
1995.173:283-305. Novak B, Tyson JJ. Numerical analysis of a
comprehensive model of M-phase control in Xenopus oocyte extracts and intact
embryos. J Cell Sci. 1993 Dec;106
( Pt 4):1153-68. Novak B, Tyson JJ. Modeling the cell
division cycle: M-phase trigger, oscillations and size control. J. Theor. Biol. 1993.
165:101-134. Segel L, Tyson JJ. Law of mass action. Nature. 1992 May
14;357(6374):106. Weimar JR, Tyson JJ,
Watson LT. Diffusion and wave
propagation in cellular automaton models of excitable media Physica D: Nonlinear
Phenomena, Volume 55, Issues 3-4, March 1992, Pages 309-327 Weimar JR, Tyson JJ, Watson
LT. Third generation cellular
automaton for modeling excitable media Physica D: Nonlinear
Phenomena, Volume 55, Issues 3-4, March 1992, Pages 328-339 Keener JP, Tyson JJ. The dynamics of helical
scroll waves in excitable media Physica D: Nonlinear
Phenomena, Volume 53, Issue 1, October 1991, Pages 151-161 Gerhardt M, Schuster H,
Tyson JJ. A cellular automaton
model of excitable media IV. Untwisted scroll rings Physica D: Nonlinear
Phenomena, Volume 50, Issue 2, June 1991, Pages 189-206 Tyson JJ. Modeling the cell
division cycle: cdc2 and cyclin interactions. Proc Natl Acad Sci U S A.
1991 Aug 15;88(16):7328-32. Gerhardt M, Schuster H,
Tyson JJ. A cellular automaton
model of excitable media : II. Curvature, dispersion, rotating waves and
meandering waves Physica D: Nonlinear
Phenomena, Volume 46, Issue 3, December 1990, Pages 392-415 Gerhardt M, Schuster H,
Tyson JJ. A cellular automaton
model of excitable media : III. Fitting the Belousov-Zhabotinskii reaction Physica D: Nonlinear
Phenomena, Volume 46, Issue 3, December 1990, Pages 416-426 Tyson JJ, Keener JP. Helical and circular
scroll wave filaments Physica D: Nonlinear
Phenomena, Volume 44, Issues 1-2, August 1990, Pages 191-202 Tyson JJ, Chen KC,
Lederman M, Bates RC. Analysis of the kinetic
hairpin transfer model for parvoviral DNA replication. J Theor Biol. 1990 May
22;144(2):155-69. Gerhardt M, Schuster H,
Tyson JJ. A cellular automation
model of excitable media including curvature and dispersion. Science. 1990 Mar
30;247(4950):1563-6. Tyson JJ. Effects of asymmetric
division on a stochastic model of the cell division cycle. Math Biosci. 1989
Oct;96(2):165-84. |