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Best of 2006-2007

Best of 2007-2008

Past Reading




Papers that at least one of us has read and enjoyed, with a short summary and explanation of relevance.

  • Important mathematical background that underlies transcriptional regulation, the most prevalent feedback system in biology. I find it interesting that biology separates (to some degree) the amount of protein expressed from a protein's function, and this separation allows for control over the number of proteins in the cell. -Kelsic [1]
  • Modular functional modeling of feedback mechanisms in the heat shock response. An example of how protein numbers can be controlled via feedback vs. parameter tuning. [2]
  • Experiment and modelling that demonstrate how negative transcriptional regulation can change the time-response of a genetic circuit.[3]
  • Engineeging implementation of negative transcriptional feedback for control over the variance of protein distributions. An example of how transcriptional feedback can be used for precise gene control.[4]
  • Theoretical paper discussing the minimum number of molecules required to perform stable switching. It's article #74 on his publications page -Milo
  • A quorum sensing system regulates a gene that causes cell death. The result is a population control circuit. They're able to generate step-response-like plots of cell growth vs. time and show that with control the cells grow to a lower steady state value. [5] --Mary 17:52, 14 November 2006 (EST)
  • This paper uses the population control circuit from the paper above, but runs the reactions in a microfluidic bioreactor. Since they're feeding in fresh media and they can take measurements for ~8 days straight. Under the microfluidic conditions they observe oscillatory behavior from genetic circuits that maintained a constant steady state under the bulk growing conditions. [6] --Mary 18:11, 14 November 2006 (EST)


papers that no one has read, but that might be interesting.


  1. Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, and Phillips R. . pmid:15797194. PubMed HubMed [Phillips1]
  2. El-Samad H, Kurata H, Doyle JC, Gross CA, and Khammash M. . pmid:15668395. PubMed HubMed [Doyle]
  3. Rosenfeld N, Elowitz MB, and Alon U. . pmid:12417193. PubMed HubMed [Elowitz]
  4. El-Samad H, Kurata H, Doyle JC, Gross CA, and Khammash M. . pmid:15668395. PubMed HubMed [Becskei]
  5. You L, Cox RS 3rd, Weiss R, and Arnold FH. . pmid:15064770. PubMed HubMed [You_Nature2004]
  6. Balagaddé FK, You L, Hansen CL, Arnold FH, and Quake SR. . pmid:15994559. PubMed HubMed [Balagadde_Science2005]
All Medline abstracts: PubMed HubMed
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