Synthesizing stochasticity in biochemical systems

Proceedings - Design Automation Conference

Volumn , Issue , 2007, Pages 640-645

  Fett, Brian ^a   Bruck, Jehoshua ^b   Riedel, Marc D ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Biochemical reactions; Computational biology; Markov processes; Random processes; Stochasticity; Synthesis; Synthetic biology

Indexed keywords

BIOCHEMICAL SENSING; COMPUTATIONAL BIOLOGY; FUNCTIONAL DEPENDENCIES; STOCHASTICITY; SYNTHETIC BIOLOGY;

BIOCHEMISTRY; DRUG PRODUCTS; MOLECULAR DYNAMICS; NATURAL SCIENCES COMPUTING; PROBABILITY DISTRIBUTIONS;

RANDOM PROCESSES;

EID: 34547268025     PISSN: 0738100X     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/DAC.2007.375244     Document Type: Conference Paper

References (14)

1. D. Endy and R. Brent, "Modelling Cellular Behaviour," Nature, Vol. 409, pp. 391-395, 2001.
2. D. Endy, "Foundations For Engineering Biology," Nature, Vol. 438, pp. 449-453, 2005.
3. M. Sedlak and N. Ho, "Production of Ethanol from Cellulosic Biomass Hydrolysate Using Genetically Engineered Yeast," Applied Biochemistry & Biotechnology, Vol. 114, No. 1-3, pp. 403-416, 2004.
4. D.-K. Ro et al., "Production of the Antimalarial Drug Precursor Artemisinic Acid in Engineered Yeast," Nature, Vol. 440, pp. 940-943, 2006.
5. J. Anderson, E. Clarke, A. Arkin, and C. Voigt, "Environmentally Controlled Invasion of Cancer Cells by Engineered Bacteria," Journal of Molecular Biology, Vol. 355, No. 4, pp. 619-627, 2006.
6. D. Gillespie, "Exact Stochastic Simulation of Coupled Chemical Reactions," Journal of Physical Chemistry, Vol. 81, No. 25, pp. 2340-2361, 1977.
7. M. Gibson and J. Bruck, "Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels," Journal of Physical Chemistry A, No. 104, pp. 1876-1889, 2000.
8. M. Cook, "Networks of Relations," Ph.D. Dissertation, Advisor J. Bruck, Caltech, 2005.
9. M. Samoilov, A. Arkin, and J. Ross, "Signal Processing by Simple Chemical Systems," Journal of Physical Chemistry, Vol. 106, pp. 10205-10221, 2002.
10. A. Hernday, B. Braaten, and D. Low," The Intricate Workings of a Bacterial Epigenetic Switch," Advances in Experimental Medicine & Biology, Vol. 547, No. 83-9, 2004.
11. L. Weinberger, J. Burnett, J. Toettcher, A. Arkin, and D. Schaffer, "Stochastic Gene Expression in a Lentiviral Positive-Feedback Loop: HIV-1 Tat Fluctuations Drive Phenotypic Diversity," Cell, Vol. 122, pp. 169-182, 2005.
12. A. Arkin, J. Ross, and H. McAdams, "Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage A-Infected E. Coli Cells," Genetics, Vol. 149, No. 1633, 1998.
13. BioBricks Parts List, MIT Registry of Standard Biological Parts,http://parts.mit.edu.
14. I. Herskowitz, "Life Cycle of the Budding Yeast Saccharomyces cerevisiae," Microbiological Reviews, Vol. 52, No. 4, pp. 536-553, 1988.