Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell
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Johnson, 1981, Lambda repressor and cro — components of an efficient molecular switch, Nature, 294, 217, 10.1038/294217a0
Falke, 1997, The two-component signaling pathway of bacterial chemotaxis: a molecular view of signal transduction by receptors, kinases, and adaptation enzymes, Annu. Rev. Cell Dev. Biol., 13, 457, 10.1146/annurev.cellbio.13.1.457
Mendenhall, 1998, Regulation of Cdc28 cyclin-dependent protein kinase activity during the cell cycle of the yeast Saccharomyces cerevisiae, Microbiol. Mol. Biol. Rev., 62, 1191, 10.1128/MMBR.62.4.1191-1243.1998
DiNardo, 1994, The making of a maggot: patterning the Drosophila embryonic epidermis, Curr. Opin. Genet. Dev., 4, 529, 10.1016/0959-437X(94)90068-E
Lazebnik, 2002, Can a biologist fix a radio? Or, what I learned while studying apoptosis, Cancer Cell, 2, 179, 10.1016/S1535-6108(02)00133-2
Arkin, 1998, Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells, Genetics, 149, 1633, 10.1093/genetics/149.4.1633
Bray, 1993, Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis, Mol. Biol. Cell, 4, 469, 10.1091/mbc.4.5.469
Chen, 2000, Kinetic analysis of a molecular model of the budding yeast cell cycle, Mol. Biol. Cell, 11, 369, 10.1091/mbc.11.1.369
von Dassow, 2000, The segment polarity network is a robust developmental module, Nature, 406, 188, 10.1038/35018085
Sharp, 1998, Prediction of mutant expression patterns using gene circuits, Biosystems, 47, 79, 10.1016/S0303-2647(98)00014-8
Sanchez, 2001, A logical analysis of the Drosophila gap-gene system, J. Theor. Biol., 211, 115, 10.1006/jtbi.2001.2335
Kholodenko, 1999, Quantification of short term signaling by the epidermal growth factor receptor, J. Biol. Chem., 274, 30169, 10.1074/jbc.274.42.30169
Asthagiri, 2000, Bioengineering models of cell signaling, Annu. Rev. Biomed. Eng., 2, 31, 10.1146/annurev.bioeng.2.1.31
Shvartsman, 2002, Autocrine loops with positive feedback enable context-dependent cell signaling, Am. J. Physiol., 282, C545, 10.1152/ajpcell.00260.2001
Ferrell, 2002, Self-perpetuating states in signal transduction: positive feedback, double-negative feedback and bistability, Curr. Opin. Cell Biol., 14, 140, 10.1016/S0955-0674(02)00314-9
Ferrell, 2001, Bistability in cell signaling: how to make continuous processes discontinuous, and reversible processes irreversible, Chaos, 11, 227, 10.1063/1.1349894
Hasty, 2001, Computational studies of gene regulatory networks: in numero molecular biology, Nat. Rev. Genet., 2, 268, 10.1038/35066056
Tyson, 2001, Network dynamics and cell physiology, Nat. Rev. Mol. Cell Biol., 2, 908, 10.1038/35103078
Laurent, 1999, Multistability: a major means of differentiation and evolution in biological systems, Trends Biochem. Sci., 24, 418, 10.1016/S0968-0004(99)01473-5
Brazhnik, 2002, Gene networks: how to put the function in genomics, Trends Biotechnol., 20, 467, 10.1016/S0167-7799(02)02053-X
Savageau, 2001, Design principles for elementary gene circuits: Elements, methods, and examples, Chaos, 11, 142, 10.1063/1.1349892
Thomas, 2001, Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior, Chaos, 11, 170, 10.1063/1.1350439
Iglesias, 2002, Modeling the cell’s guidance system, Sci. STKE, 2002, RE12, 10.1126/stke.2002.148.re12
Segel L: Modeling Dynamic Phenomena in Molecular and Cellular Biology. Cambridge: Cambridge University Press; 1984.
Goldbeter A: Biochemical Oscillations and Cellular Rhythms. Cambridge: Cambridge University Press; 1997.
Fall C, Marland E, Wagner J, Tyson J: Computational Cell Biology. Berlin: Springer; 2002.
Goldbeter, 1981, An amplified sensitivity arising from covalent modification in biological systems, Proc. Natl. Acad. Sci. U.S.A., 78, 6840, 10.1073/pnas.78.11.6840
Levchenko, 2002, Models of eukaryotic gradient sensing: application to chemotaxis of amoebae and neutrophils, Biophys. J., 82, 50, 10.1016/S0006-3495(02)75373-3
Knox, 1986, A molecular mechanism for sensory adaptation based on ligand-induced receptor modification, Proc. Natl. Acad. Sci. U.S.A., 83, 2345, 10.1073/pnas.83.8.2345
Spiro, 1997, A model of excitation and adaptation in bacterial chemotaxis, Proc. Natl. Acad. Sci. U.S.A., 94, 7263, 10.1073/pnas.94.14.7263
Yi, 2000, Robust perfect adaptation in bacterial chemotaxis through integral feedback control, Proc. Natl. Acad. Sci. U.S.A., 97, 4649, 10.1073/pnas.97.9.4649
Ferrell, 1998, The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes, Science, 280, 895, 10.1126/science.280.5365.895
Novak, 1993, Numerical analysis of a comprehensive model of M-phase control in Xenopus oocyte extracts and intact embryos, J. Cell Sci., 106, 1153, 10.1242/jcs.106.4.1153
Kellershohn, 2001, Prion diseases: dynamics of the infection and properties of the bistable transition, Biophys. J., 81, 2517, 10.1016/S0006-3495(01)75897-3
Sha W, Moore J, Chen K, Lassaletta A, Yi C, Tyson J, Sible J: Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. Proc Natl Acad Sci USA 2002, in press.
Cross, 2002, Testing a mathematical model of the yeast cell cycle, Mol. Biol. Cell, 13, 52, 10.1091/mbc.01-05-0265
Gardner, 2000, Construction of a genetic toggle switch in Escherichia coli, Nature, 403, 339, 10.1038/35002131
Becskei, 2001, Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion, EMBO J., 20, 2528, 10.1093/emboj/20.10.2528
Griffith, 1968, Mathematics of cellular control processes. I. Negative feedback to one gene, J. Theor. Biol., 20, 202, 10.1016/0022-5193(68)90189-6
Goodwin, 1966, An entrainment model for timed enzyme syntheses in bacteria, Nature, 209, 479, 10.1038/209479a0
Goldbeter, 1991, A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase, Proc. Natl. Acad. Sci. U.S.A., 88, 9107, 10.1073/pnas.88.20.9107
Kholodenko, 2000, Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades, Eur. J. Biochem., 267, 1583, 10.1046/j.1432-1327.2000.01197.x
Goldbeter, 1995, A model for circadian oscillations in the Drosophila period protein (PER), Proc. R Soc. Lond. Ser. B, 261, 319, 10.1098/rspb.1995.0153
Leloup, 2000, Modeling the molecular regulatory mechanism of circadian rhythms in Drosophila, Bioessays, 22, 84, 10.1002/(SICI)1521-1878(200001)22:1<84::AID-BIES13>3.0.CO;2-I
Smolen, 2001, Modeling circadian oscillations with interlocking positive and negative feedback loops, J. Neurosci., 21, 6644, 10.1523/JNEUROSCI.21-17-06644.2001
Elowitz, 2000, A synthetic oscillatory network of transcriptional regulators, Nature, 403, 335, 10.1038/35002125
Martiel, 1987, A model based on receptor desensitiztion for cyclic-AMP signaling in Dictyostelium cells, Biophys. J., 52, 808, 10.1016/S0006-3495(87)83275-7
Tyson, 1991, Modeling the cell division cycle: cdc2 and cyclin interactions, Proc. Natl. Acad. Sci. U.S.A., 88, 7328, 10.1073/pnas.88.16.7328
Guttman, 1980, Control of repetitive firing in squid axon membrane as a model for a neuron oscillator, J. Physiol., 305, 377, 10.1113/jphysiol.1980.sp013370
Turing, 1952, The chemical basis of morphogenesis, Phil. Trans. R Soc. Lond. B, 237, 37, 10.1098/rstb.1952.0012
Prigogine, 1968, Symmetry-breaking instabilities in dissipative systems, J. Chem. Phys., 48, 1695, 10.1063/1.1668896
Brenner S, Murray J, Wolpert L: Theories of Biological Pattern Formation. London: The Royal Society; 1981.
Tyson, 1989, Cyclic AMP waves during aggregation of Dictyostelium amoebae, Development, 106, 421, 10.1242/dev.106.3.421
Bretschneider, 1995, Three-dimensional scroll waves of cAMP could direct cell movement and gene expression in Dictyostelium slugs, Proc. Natl. Acad. Sci. U.S.A., 92, 4387, 10.1073/pnas.92.10.4387
Meinhardt, 2001, Pattern formation in Escherichia coli: a model for the pole-to-pole oscillations of Min proteins and the localization of the division site, Proc. Natl. Acad. Sci. U.S.A., 98, 14202, 10.1073/pnas.251216598
Hoffmann, 2002, The IκB–NF-κB signaling module: temporal control and selective gene activation, Science, 298, 1241, 10.1126/science.1071914
Kholodenko, 2002, Untangling the wires: a strategy to trace functional interactions in signaling and gene networks, Proc. Nat. Acad. Sci. U.S.A., 99, 12841, 10.1073/pnas.192442699