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ChE 154/255, BMSE 255 |
Supplemental reading |
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Journal Articles |
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A. Arkin, J. Ross and H. H. McAdams, “Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage l-Infected Escherichia coli Cells” Genetics 149: 1633-1648 (1998). [pdf] |
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A. Asthagiri and D. Lauffenburger, “Bioengineering
models of cell signaling”, Annu.
Rev. Biomed. |
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H. Bolouri and E.H. Davidson, “Modeling transcriptional regulatory networks”, BioEssays, 24:1118-1129 (2002). [pdf] |
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H. DeJong, “Modeling and simulation of gene
regulatory systems: a literature review”, J. Comp. Biol., 9:67-103
(2002). [pdf] |
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D. Faller, U. Klingmueller, and J. Timmer, “Simulation methods for optimal experimental design in systems biology”, Simulation, 79:717-725 (2003). [pdf] |
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D. Forger and C. Peskin, “A detailed predictive model of the mammalian circadian clock”, Proc. Natl. Acad. Sci. USA, 100, 14806-14811 (2003). [pdf] |
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M. Fussenegger, J.E. Bailey, and J. Varner, “A mathematical model of caspase function in apoptosis”, Nat. Biotechnol., 18(7): 768-774 (2000). [pdf] |
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D.T. Gillespie, “Exact stochastic simulation of coupled chemical reactions”, J. Phys. Chem., 81:2340-2361 (1977). [pdf] |
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A. Gilman and A. Arkin, “Genetic code: representations and dynamical models of genetic components and networks”, Annu. Rev. Genomics Hum. Genet., 3:341-369 (2002). [pdf] |
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L. Giot et al., “A Protein Interaction Map of Drosophila melanogaster”, Science, 302, 1727-1736 (2003). |
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J. Hasty, D. McMillen, F. Isaacs and J.J. Collins, “Computational studies of gene regulatory networks: in numero molecular biology”, Nature Rev. Genetics, 2:268-279 (2001). [pdf] |
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J. Hasty, D. McMillen and J.J. Collins, “Engineered gene circuits”, Nature, 420:224-230 (2002). [pdf] |
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T. Ideker, T. Galitski, and L. Hood, “A new approach to decoding life: systems biology”, Annu. Rev. Genomics Hum. Genet., 2: 343-372 (2001). [pdf] |
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J.-C. Leloup and A. Goldbeter, “Modeling the molecular regulatory mechanism of circadian rhythms in Drosophila”, BioEssays, 22: 84-93 (2000). [pdf] |
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J.-C. Leloup and A. Goldbeter, “Toward a detailed computational model for the mammalian circadian clock”, Proc. Natl. Acad. Sci. USA, 100: 7051-7056 (2003). [pdf] |
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S. Li et al., “A Map of the Interactome Network of the Metazoan C. Elegans”, Science., 303: 540-543 (2004). [pdf] |
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H. McAdams and A. Arkin, “Simulation of prokaryotic genetic circuits”, Annu. Rev. Biophys. Biomol. Struct., 27:199-224 (1998). [pdf] |
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H. McAdams and A. Arkin, “Towards a circuit engineering discipline”, Curr. Biol., 10:R318-R320 (2000). [pdf] |
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S. Neves and R. Iyengar, “Modeling of signaling networks”, BioEssays, 24:1110-1117 (2002). [pdf] |
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R. Prill, P. Iglesias, and A. Levchenko, “Dynamic Properties of Network Motifs Contribute to Biological Network Organization”, PLoS Biology, 3, 1881-1892 (2005). [pdf] |
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C. Rao
and A. Arkin, “Control motifs for intracellular regulatory
networks”, Annu. Rev. Biomed. |
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C. Rao, J. Kirby, and A. Arkin, “Design and Diversity in Bacterial Chemotaxis: A Comparative Study in Escherichia coli and Bacillus subtilis”, PLoS Biology, 2: 239-252 (2004). [pdf] |
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M. Savageau, “Design principles for elementary gene circuits: Elements, methods, and examples”, Chaos, 11:142-159 (2001). [pdf] |
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P. Smolen, D.A. Baxter, and J.H. Byrne, “Modeling transcriptional control in gene networks – methods, recent results, and future directions”, Bull. Math. Biol., 62:247-292 (2000). [pdf] |
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J.J. Tyson, A. Csikasz-Nagy, and B. Novak, “The dynamics of cell cycle regulation”, Bioessays, 24(12):1095-1109 (2002). [pdf] |
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T.-M. Yi, Y. Huang, M.I. Simon, and J. Doyle, “Robust perfect adaptation in bacterial chemotaxis through integral feedback control”, PNAS, 97:4649-4653 (2000). [pdf] |
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Books |
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J.M. Bower and H. Bolouri (eds.), Computational Modeling of Genetic and Biochemical Networks (Computational Molecular Biology), MIT Press (2001). |
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A.M. Campbell and L.J. Heyer, Discovering Genomics, Proteomics, and Bioinformatics, CSHL Press (2003). |
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J. Gerhart and M. Kirschner, Cells, Embryos, and Evolution: Toward a Cellular and Developmental Understanding of Phenotypic Variation and Evolutionary Adaptability, Blackwell Science (1997). |
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H. Kitano, Foundations of Systems Biology, MIT Press (2001). |
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M. Ptashne and A. Gann, Genes & Signals, CSHL Press (2002). |
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E.O.
Voit, Computational Analysis of
Biochemical Systems: A Practical Guide for Biochemists and Molecular
Biologists, |
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Relevent WWW sites |
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