Module locking in biochemical synthesis

IEEE/ACM International Conference on Computer-Aided Design, Digest of Technical Papers, ICCAD

Volumn , Issue , 2008, Pages 758-764

  Fett, Brian ^a   Riedel, Marc D ^a  

^a University of Minnesota   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ASYNCHRONOUS CIRCUIT DESIGNS; BIO-CHEMICALS; BIOCHEMICAL REACTIONS; BIOCHEMICAL SYNTHESES; HANDSHAKING; INPUT QUANTITIES; LOGIC SYNTHESES; MOLECULAR TYPES; ORDERS OF MAGNITUDES; PROBABILISTIC COMPUTATIONS; RELATIVE RATES; ROBUST COMPUTATIONS; STOCHASTIC MODULES;

COMMERCE; COMPUTER AIDED DESIGN; MACHINE DESIGN; PROBABILITY; REACTION RATES;

PROBABILITY DISTRIBUTIONS;

EID: 57849133481     PISSN: 10923152     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/ICCAD.2008.4681661     Document Type: Conference Paper

References (26)

1. A. Arkin, J. Ross, and H. McAdams, "Stochastic Kinetic Analysis of Developmental Pathway Bifurcation in Phage λ-Infected E. Coli Cells," Genetics, Vol. 149, No. 1633, 1998.
2. Y. Benenson, B. Gil, U. Ben-Dor, R. Adar, and E. Shapiro, "An Autonomous Molecular Computer for Logical Control of Gene Expression," Nature, Vol. 429, pp. 423-429, 2004.
3. BioBricks Parts List, MIT Registry of Standard Biological Parts, http://parts.mit.edu.
4. D. Endy and R. Brent, "Modelling Cellular Behaviour," Nature, Vol. 409, pp. 391-395, 2001.
5. D. Endy, "Foundations for Engineering Biology," Nature, Vol. 438, pp. 449-453, 2005.
6. B. Fett, J. Bruck, and M. Riedel, "Synthesizing Stochasticity in Biochemical Systems," Design Automation Conference, pp. 640-645, 2007.
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. D. Gillespie, "Exact Stochastic Simulation of Coupled Chemical Reactions," Journal of Physical Chemistry, Vol. 81, No. 25, pp. 2340-2361, 1977.
9. C. Goble, S. Pettifer, R. Stevens, and C. Greenhalgh, "Knowledge Integration: in silico Experiments in Bioinformatics," in The Grid: Blueprint for a New Computing Infrastructure, 2nd Edition, eds. Ian Foster and Carl Kesselman, Morgan Kaufman, 2003.
10. R. Heinrich and S. Shuster, "The Regulation of Cellular Systems," Chapman and Hall, 1996.
11. 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.
12. I. Herskowitz, "Life Cycle of the Budding Yeast Saccharomyces cerevisiae," Microbiological Reviews, Vol. 52, No. 4, pp. 536-553, 1988.
13. E. Libby, T. Perkins, and P. Swain, "Noisy Information processing through transcriptional regulation," Pmceedings of the National Academy of Sciences, Vol. 104, No. 17, pp. 7151-7156, 2007.
14. L. Lok and R. Brent, "Automatic Generation of Cellular Reaction Networks with Moleculizer 1.0," Nature Biotechnology, Vol. 23, No. 1, pp. 131-136, 2005.
15. C. Myers, "Asynchronous Circuit Design," John Wiley and Sons, 2001.
16. L. Nagel and D. Pederson, "Simulation Program with Integrated Circuit Emphasis," Midwest Symposium on Circuit Theory, 1973.
17. S. Paliwal, P. Iglesias, K. Hilioti, A. Groisman, and A. Levchenko, "MAPK-mediated bimodal Gene Expression and Adaptive Gradient Sensing in Yeast," Nature, Vol. 446, Issue 7131, pp. 46-51, 2007.
18. W. Qian and M. Riedel, "Robust Polynomial Arithmetic with Stochastic Logic," Design Automation Conference, 2008.
19. J. Rabaey, "Design without Borders - A Tribute to the Legacy of A. Richard Newton," Design Automation Conference, 2007.
20. M. Riedel, "The Computer-Aided Synthesis of Stochasticity in Biochemical Systems," Advances in Synthetic Biology, 2008.
21. D. Ro, E. Paradise, M. Ouellet, K. Fisher, K. Newman, J. Ndungu, K. Ho, R. Eachus, T. Ham, M. Chang, S. Withers, Y. Shiba, R. Sarpong, and J. Keasling, "Production of the Antimalarial Drug Precursor Artemisinic Acid in Engineered Yeast," Nature, Vol. 440, pp. 940-943, 2006.
22. 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.
23. H. Smith, C. Hutchinson III, C. Pfannkoch, and J. Venter, "Generating a Synthetic Genome by Whole Genome Assembly: ΦX174 Bacteriophage from Synthetic Oligonucleotides," Proceedings of the National Academy of Sciences, Vol. 100, pp. 15440-15445, 2003.
24. J. Glass, et al., "Essential Genes of a Minimal Bacterium," Proceedings of the National Academy of Sciences, Vol. 103, pp. 425-430, 2006.
25. L. Weinberger, J. Burnett, J. Toettcher, A. Arkin, and D. Schaffer, "Stochastic Gene Expression in a Lentiviral Positive-Feedback Loop: HIV-I Tat Fluctuations Drive Phenotypic Diversity," Cell, Vol. 122, pp. 169-182, 2005.
26. E. Zielinska, "Chris Voigt: Biology's Toy Maker," The Scientist, Vol. 21, No. 9, 2007.