This list is by no means complete. We will be adding papers as we go, and you are welcome to help.
Note: Think of this Wiki as an encyclopedia of BioCircuits. Also, think of your instructor (that's Eric) as a micro-managing editor-in-chief. Thus, if you would like to add a paper to this list, please correspond Eric via email to make sure I approve.
- Micklos, Freyer and Crothy, DNA Science Cold Spring Harbor Laboratory Press, 2003.
- Murray, Mathematial Biology, Springer, 3rd Edition, 2005.
- Klipp, Herwig, Kowald, Wierling and Lehrach, Systems Biology in Practice, Wiley-VCH, 2006.
- Snyder and Champness, Molecular Genetics of Bacteria, ASM Press, 2002.
- Kutter and Sulakvelidze (editors), Bacteriophages: Biology and Applications, CRC Press, 2004.
- Nelson and Cox, Principles of Biochemistry, 4th Edition, Freeman, 2004.
- Ptashne, Genetic Switch: Phage Lambda and Higher Organisms, Blackwell, 1992.
- Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits, Chapman & Hall/CRC, 2006]
- Feinberg, Lectures on Reaction Networks. Freely available book on the web.
- Lazebnik, Can a biologist fix a radio?. Cancer Cell 2(3), 179-182, 2003.
- Ramsey, Orrel and Bolouri, Dizzy: Stochastic simulatios of large scale genetic regulatory networks. J. of Bioinformatics and Computational Biology, 3(2), 2005.
- Ronen, Rosenberg, Shraiman and Alon, Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics. PNAS 99(16), 10555-10560, 2002.
- Braun, Basu, and Weiss, Parameter Estimation for Two Synthetic Gene Networks: A Case Study. IEEE International Conference on Acoustics, Speech, and Signal Processing, March 2005.
- Arkin, Ross and McAdams Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics 149(4), 1633-48, 1998.
- Gally, Bogan, Eisenstein and Blomfield, Environmental regulation of the fim switch controlling type 1 fimbrial phase variation in Escherichia coli K-12: effects of temperature and media. J. Bacteriol. 175(19), 6186-6193, 1993.
- Gibson and Bruck, Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels. J. Phys. Chem. A 104(9), 1876-1889, 2000.
- Gillespie, Exact Stochastic Simulation of Coupled Chemical Reactions. J. Chem. Phys. 81(25), 2340-2361, 1977.
- Gillespie, Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 115(4), 1716-1733, 2001.
- Rathinam, Petzold, Cao and Gillespie, Stiffness in stochastic chemically reacting systems: The implicit tau-leaping method. J. Chemical Physics, 119(23), 12784-12794, 2003.
- McAdams and Arkin, Stochastic mechanisms in gene expression. PNAS 94, 814-819, 1997.
- Munsky and Khammash, The finite state projection algorithm for the solution of the chemical master equation. J. Chem. Phys. 124, 044104, 2006.
- Spuddich and Koshland, Quantitation of the Sensory Response in Bacterial Chemotaxis. PNAS 72(2), 710-713, 1975.
- J. T. Mettetal and A. van Oudenaarden, Necessary noise (review), Science 317, 463 (2007).
- Santillán and Mackey, Dynamic regulation of the tryptophan operon: A modeling study and comparison with experimental data. PNAS 98(4), 1364-1369, 2001.
- Bhartiya, Rawool1 and Venkatesh, Dynamic model of Escherichia coli tryptophan operon shows an optimal structural design. Eur. J. Biochem. 270, 2644-2651, 2003.
- Wilson and Murray, Restriction and Modification Systems. Annual Review of Genetics 25, 585-627, 1991.
- Tian, Gong, Sheng, Zhou, Gulari, Gao and Church, Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432, 1050-1054, 2004.
- This is the basis for how Codon Devices can make custom made genes up to 15kbp long.
- Arkin and Fletcher, Fast, Cheap and Somewhat in Control. Genome Biology 7(8), 114, 2006.
- Atkinson, Savageau, Myers and Ninfa, Development of Genetic Circuitry Exhibiting Toggle Switch or Oscillatory Behavior in Escherichia coli. Cell 113(5), 597-607, 2003.
- Ball, Synthetic Biology: Starting From Scratch. Nature 431, 624-626, 2004.
- Basu, Gerchman, Collins, Arnold and Weiss, A synthetic multicellular system for programmed pattern formation. Nature 434, 1130-1134, 2005.
- Basu, Karig and Weiss, Synthetic biology: new engineering rules for an emerging discipline. Molecular Systems Biology 2, 2006.
- Bayer and Smolke. Programmable ligand controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol .23, 337-343.
- Cherry and Adler, How to make a bistable switch. Journal of Theoretical Biology 203(2), 117-133, 2000.
- Elowitz and Leibler, A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338, 2000.
- Endy, Deese and Wadey, Adventures in Synthetic Biology. The cartoon version.
- Isaacs, Dwyer and Collins, RNA Synthetic Biology. Nature Biotechnology 24, 545-554, 2006.
- Voigt, Synthetic Parts to Program Bacteria. Current Opinion in Biotechnology 17, 548-557, 2006.
- Wall, Hlavacek and Savageau, Design of Gene Circuits: Lessions from Bacteria. Nature Reviews Genetics 5, 34-42, 2004.
- Thorn, Inhibition by malonate of succinic dehydrogenase in heart-muscle preparations. Biochem J. 54(4), 540–547, 1953.
- Dennis, Regulation of Synthesis and Activity of a Mutant RNA Polymerase in Escherichia coli. Proc. Nat. Acad. Sci. 74(12), 5416-5420, 1977.
- Errington, Glass, Hayward, and Scaife, Structure and Orientation of an RNA Polymerase operon in Escherichia coli. Nature 249, 519-522, 1974.
- Jishage and Ishihama, Regulation of RNA Polymerase Sigma Subunit Synthesis in Escherichia coli: Intracellular Levels of σ-70 and σ-38. J. Bacteriology 177(23), 6832–6835, 1995.
In Vitro Circuits
- Kim, White and Winfree, Construction of an in vitro bistable circuit from synthetic transcriptional switches, Molecular Systems Biology 2 (2006).
- Ellington and Szostak, In vitro selection of RNA molecules that bind specific ligands, Nature 346, 818 - 822 (30 August 1990).