Population-based microbial computing: a third wave of synthetic biology?

References

• Amos, M. 2006. Genesis Machines: The New Science of Biocomputing. London: Atlantic Books.
   Google Scholar
• Andrianantoandro, E., S. Basu, D. K. Karig, and R. Weiss. 2006. “Synthetic Biology: New Engineering Rules for an Emerging Discipline.” Molecular Systems Biology 2 (1). doi:10.1038/msb4100073.
   PubMed Web of Science ®Google Scholar
• Atkinson, S., and P. Williams. 2009. “Quorum Sensing and Social Networking in the Microbial World.” Journal of the Royal Society Interface 6 (40): 959–978.
   PubMed Web of Science ®Google Scholar
• Attiya, H., and J. Welch. 2004. Distributed Computing: Fundamentals, Simulations and Advanced Topics. Hoboken, NJ: John Wiley and Sons.
   Google Scholar
• Bacchus, W., M. Fussenegger. 2013. “Engineering of Synthetic Intercellular Communication Systems.” Metabolic Engineering 16: 33–41. doi:10.1016/j.ymben.2012.12.001.
   PubMed Web of Science ®Google Scholar
• Balagaddé, F. K., H. Song, J. Ozaki, C. H. Collins, M. Barnet, F. H. Arnold, S. R. Quake, and L. You. 2008. “A Synthetic Escherichia coli Predator-prey Ecosystem.” Molecular Systems Biology 4: 187. doi:10.1038/msb.2008.24.
   PubMed Web of Science ®Google Scholar
• Ball, P. 1999. The Self-Made Tapestry: Pattern Formation in Nature. Oxford: Oxford University Press.
   Google Scholar
• Basu, S., Y. Gerchman, C. H. Collins, F. H. Arnold, and R. Weiss. 2005. “A Synthetic Multicellular System for Programmed Pattern Formation.” Nature 434 (7037): 1130–1134.
   PubMed Web of Science ®Google Scholar
• Becskei, A., and L. Serrano. 2000. “Engineering Stability in Gene Networks by Autoregulation.” Nature 405 (6786): 590–593.
   PubMed Web of Science ®Google Scholar
• Benner, S. A., and A. M. Sismour. 2005. “Synthetic Biology.” Nature Reviews Genetics 6 (7): 533–543.
   PubMed Web of Science ®Google Scholar
• Bray, D. 2009. Wetware: A Computer in Every Living Cell. New Haven, CT: Yale University Press.
   Google Scholar
• Brenner, K., L. You, and F. H. Arnold. 2008. “Engineering Microbial Consortia: A New Frontier in Synthetic Biology.” Trends in Biotechnology 26 (9): 483–489.
   PubMed Web of Science ®Google Scholar
• Church, G., and E. Regis. 2012. Regenesis: How Synthetic Biology will Reinvent Nature and Ourselves. New York: Basic Books.
   Google Scholar
• Danino, T., O. Mondragǹ-Palomino, L. Tsimring, and J. Hasty. 2010. “A Synchronized Quorum of Genetic Clocks.” Nature 463 (7279): 326–330.
   PubMed Web of Science ®Google Scholar
• Dorrian, H., J. Borresen, and M. Amos. 2013. “Community Structure and Multi-modal Oscillations in Complex Networks.” PLOS ONE 8 (10): e75569.
   PubMed Web of Science ®Google Scholar
• Elowitz, M. B., and S. Leibler. 2000. “A Synthetic Oscillatory Network of Transcriptional Regulators.” Nature 403 (6767): 335–338.
   PubMed Web of Science ®Google Scholar
• Forster, A. C., and G. M. Church. 2006. “Towards Synthesis of a Minimal Cell.” Molecular Systems Biology 2: 45. doi:10.1038/msb4100090.
   PubMed Web of Science ®Google Scholar
• Gardner, T. S., C. R. Cantor, and J. J. Collins. 2000. “Construction of a Genetic Toggle Switch in Escherichia coli.” Nature 403: 339–342.
   PubMed Web of Science ®Google Scholar
• Goñi-Moreno, A., and M. Amos. 2012. “A Reconfigurable NAND/NOR Genetic Logic Gate.” BMC Syst Biol 6 (1): 126. doi:10.1186/1752-0509-6-126.
   PubMed Web of Science ®Google Scholar
• Goñi-Moreno, A., M. Amos, and F. de la Cruz. 2013. “Multicellular Computing using Conjugation for Wiring.” PLOS ONE 8 (6): e65986.
   PubMed Web of Science ®Google Scholar
• Goodwin, B. C. 1965. “Oscillatory Behaviour in Enzymatic Control Processes.” In Advances in Enzyme Regulation, Vol. 3, edited by G. Weber, 425–438. Oxford: Pergamon Press.
   Google Scholar
• Hasty, J., D. McMillen, and J. J. Collins. 2002. “Engineered Gene Circuits.” Nature 420 (6912): 224–230.
   PubMed Web of Science ®Google Scholar
• Heinemann, M., and S. Panke. 2006. “Synthetic Biology – Putting Engineering into Biology.” Bioinformatics 22 (22): 2790–2799.
   PubMed Web of Science ®Google Scholar
• Khalil, A. S., and J. J. Collins. 2010. “Synthetic Biology: Applications Come of Age.” Nature Reviews Genetics 11 (5): 367–379.
   PubMed Web of Science ®Google Scholar
• Levy, S. 1992. Artificial Life: The Quest for a New Creation. London: Jonathan Cape.
   Google Scholar
• Li, B., and L. You. 2011. “Division of Logic Labour.” Nature 469 (4): 171–172.
   PubMed Web of Science ®Google Scholar
• Likic, V. A., M. J. McConville, T. Lithgow, and A. Bacic. 2010. “Systems Biology: The Next Frontier for Bioinformatics.” Advances in Bioinformatics. doi:10.1155/2010/268925.
   PubMedGoogle Scholar
• Llosa, M., F. X. Gomis-Rüth, M. Coll, and F. D. L. Cruz. 2002. “Bacterial Conjugation: A Two-step Mechanism for DNA Transport.” Molecular Microbiology 45 (1): 1–8.
   PubMed Web of Science ®Google Scholar
• Lou, C., X. Liu, M. Ni, Y. Huang, Q. Huang, J. Huang, L. Jiang. 2010. “Synthesizing a Novel Genetic Sequential Logic Circuit: A Push-on Push-off Switch.” Molecular Systems Biology 6: 350. doi:10.1038/msb.2010.2.
   PubMed Web of Science ®Google Scholar
• Macía, J., F. Posas, and R. V. Solé. 2012. “Distributed Computation: The New Wave of Synthetic Biology Devices.” Trends in Biotechnology 30 (6): 342–349.
   PubMed Web of Science ®Google Scholar
• McDaniel, R., and R. Weiss. 2005. “Advances in Synthetic Biology: On the Path from Prototypes to Applications.” Current Opinion in Biotechnology 16 (4): 476–483.
   PubMed Web of Science ®Google Scholar
• Monod, J. 1971. Chance and Necessity. New York, NY: Alfred A. Knopf.
   Google Scholar
• von Neumann, J. 1961. “The General and Logical Theory of Automata.” In Collected Works of John von Neumann, Vol. 5, edited by A. H. Taub, 289–326. Oxford: Pergamon Press.
   Google Scholar
• Noireaux, V., and A. Libchaber. 2004. “A Vesicle Bioreactor as a Step Toward an Artificial Cell Assembly.” Proceedings of the National Academy of Sciences of the United States of America 101 (51): 17669–17674.
   PubMed Web of Science ®Google Scholar
• O’Malley, M. A., and J. Dupré. 2005. “Fundamental Issues in Systems Biology.” BioEssays 27: 1270–1276.
   PubMed Web of Science ®Google Scholar
• Ortiz, M. E., and D. Endy. 2012. “Engineered Cell-cell Communication via DNA Messaging.” Journal of Biological Engineering 6 (1): 16. doi:10.1186/1754-1611-6-16.
   PubMed Web of Science ®Google Scholar
• Payne, S., B. Li, Y. Cao, S. Schaeffer, M. D. Ryser, and L. You. 2013. “Temporal Control of Self-organized Pattern Formation without Morphogen Gradients in Bacteria.” Molecular Systems Biology 9: 697. doi:10.1038/msb.2013.55.
   PubMed Web of Science ®Google Scholar
• Pohorille, A., and D. Deamer. 2002. “Artificial Cells: Prospects for Biotechnology.” Trends in Biotechnology 20 (3): 123–128.
   PubMed Web of Science ®Google Scholar
• Purnick, P. E., and R. Weiss. 2009. “The Second Wave of Synthetic Biology: From Modules to Systems.” Nature Reviews Molecular Cell Biology 10 (6): 410–422.
   PubMed Web of Science ®Google Scholar
• Rasmussen, S., L. Chen, M. Nilsson, and S. Abe. 2003. “Bridging Nonliving and Living Matter.” Artificial Life 9 (3): 269–316.
   PubMed Web of Science ®Google Scholar
• Regot, S., J. Macia, N. Conde, K. Furukawa, J. Kjellén, T. Peeters, S. Hohmann, E. de Nadal, F. Posas, and R. Solé. 2011. “Distributed Biological Computation with Multicellular Engineered Networks.” Nature 469 (7329): 207–211.
   PubMed Web of Science ®Google Scholar
• Rinaudo, K., L. Bleris, R. Maddamsetti, S. Subramanian, R. Weiss, and Y. Benenson. 2007. “A Universal RNAi-based Logic Evaluator that Operates in Mammalian Cells.” Nature Biotechnology 25 (7): 795–801.
   PubMed Web of Science ®Google Scholar
• Ruoff, P., M. Vinsjevik, C. Monnerjah, and L. Rensing. 1999. “The Goodwin Oscillator: On the Importance of Degradation Reactions in the Circadian Clock.” Journal of Biological Rhythms 14 (6): 469–479.
   PubMed Web of Science ®Google Scholar
• Russel, M. 1995. “Moving through the Membrane with Filamentous Phages.” Trends in Microbiology 3 (6): 223–228.
   PubMed Web of Science ®Google Scholar
• Serrano, L. 2007. “Synthetic Biology: Promises and Challenges.” Molecular Systems Biology 3: 158. doi:10.1038/msb4100202.
   PubMed Web of Science ®Google Scholar
• Slusarczyk, A. L., A. Lin, and R. Weiss. 2012. “Foundations for the Design and Implementation of Synthetic Genetic Circuits.” Nature Reviews Genetics 13 (6): 406–420.
   PubMed Web of Science ®Google Scholar
• Solé, R. V., and J. Macia. 2013. “Expanding the Landscape of Biological Computation with Synthetic Multicellular Consortia.” Natural Computing 12 (4): 485–497. doi:10.1007/s11047-013-9380-y.
   Web of Science ®Google Scholar
• Strogatz, S. 2003. Sync: The Emerging Science of Spontaneous Order. London: Penguin Books.
   Google Scholar
• Szybalksi, W.1974. “Contribution to Eighteenth OHOLO Biological Conference Panel Discussion.” In Control of Gene Expression, edited by A. Kohn and A. Shatkay, 405. New York: Plenum Press.
   Google Scholar
• Tabor, J. J., H. M. Salis, Z. B. Simpson, A. A. Chevalier, A. Levskaya, E. M. Marcotte, C. A. Voigt, and A. D. Ellington. 2009. “A Synthetic Genetic Edge Detection Program.” Cell 137 (7): 1272–1281.
   PubMed Web of Science ®Google Scholar
• Tamsir, A., J. J. Tabor, and C. A. Voigt. 2011. “Robust Multicellular Computing using Genetically Encoded NOR Gates and Chemical ‘Wires.” Nature 469 (7329): 212–215.
   PubMed Web of Science ®Google Scholar
• Wall, M. E., W. S. Hlavacek, and M. A. Savageau. 2004. “Design of Gene Circuits: Lessons from Bacteria.” Nature Review Genetics 5 (1): 34–42.
   PubMed Web of Science ®Google Scholar