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Parallel Networks: Synthetic Biology and Artificial Intelligence

Published:30 December 2014Publication History
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Abstract

Synthetic biology has emerged as an important technology for engineering cells to behave in controllable and predictable ways. The promise of this modern technology is dependent on our understanding of cellular complexity to allow us to engineer cells with novel function. In this regard, the fields of computer science and synthetic biology are critical for accelerating both our understanding of biological systems, and our ability to quantitatively engineer cells. Thus, advances in biology and biotechnology are arising at the intersection of computer science and synthetic biology approaches. This review seeks to introduce the field of synthetic biology to the computer science community, and to ignite a curiosity and interest in fostering a unique synergy for possible collaborations between synthetic biologists and computer scientists.

References

  1. C. M. Ajo-Franklin, D. A. Drubin, J. A. Eskin, E. P. Gee, D. Landgraf, I. Phillips, and P. A. Silver. 2007. Rational design of memory in eukaryotic cells. Genes Dev 21, 2271--2276.Google ScholarGoogle ScholarCross RefCross Ref
  2. B. Alberts. 2002. Molecular Biology of the Cell. Garland Science, New York.Google ScholarGoogle Scholar
  3. J. C. Anderson, E. J. Clarke, A. P. Arkin, and C. A. Voigt. 2006. Environmentally controlled invasion of cancer cells by engineered bacteria. J. Molec. Biol. 355, 619--627.Google ScholarGoogle ScholarCross RefCross Ref
  4. E. Andrianantoandro, S. Basu, D. K. Karig, and R. Weiss. 2006. Synthetic biology: New engineering rules for an emerging discipline. Molec. Syst. Biol. 2, 2006 0028.Google ScholarGoogle ScholarCross RefCross Ref
  5. N. Anesiadis, H. Kobayashi, W. R. Cluett, and R. Mahadevan. 2013. Analysis and design of a genetic circuit for dynamic metabolic engineering. ACS Synthet. Biol. 2, 442--452.Google ScholarGoogle ScholarCross RefCross Ref
  6. M. S. Antunes, K. J. Morey, J. J. Smith, K. D. Albrecht, T. A. Bowen, J. K. Zdunek, J. F. Troupe, M. J. Cuneo, C. T. Webb, H. W. Hellinga, and J. I. Medford. 2011. Programmable ligand detection system in plants through a synthetic signal transduction pathway. PLoS One 6, e16292.Google ScholarGoogle ScholarCross RefCross Ref
  7. J. A. Arpino, E. J. Hancock, J. Anderson, M. Barahona, G. B. Stan, A. Papachristodoulou, and K. Polizzi. 2013. Tuning the dials of Synthetic Biology. Microbiology 159, 1236--1253.Google ScholarGoogle ScholarCross RefCross Ref
  8. S. Auslander, D. Auslander, M. Muller, M. Wieland, and M. Fussenegger. 2012. Programmable single-cell mammalian biocomputers. Nature 487, 123--127.Google ScholarGoogle ScholarCross RefCross Ref
  9. S. Auslander and M. Fussenegger. 2013. From gene switches to mammalian designer cells: Present and future prospects. Trends Biotechnol 31, 155--168.Google ScholarGoogle ScholarCross RefCross Ref
  10. S. Ayukawa, M. Takinoue, and D. Kiga. 2011. RTRACS: A modularized RNA-dependent RNA transcription system with high programmability. Acc. Chem. Res. 44, 1369--1379.Google ScholarGoogle ScholarCross RefCross Ref
  11. G. Balazsi and J. J. Collins. 2007. Taking the inventory inside single cells. Nat. Chem. Biol. 3, 141--142.Google ScholarGoogle ScholarCross RefCross Ref
  12. C. J. Bashor, N. C. Helman, S. Yan, and W. A. Lim. 2008. Using engineered scaffold interactions to reshape MAP kinase pathway signaling dynamics. Science 319, 1539--1543.Google ScholarGoogle ScholarCross RefCross Ref
  13. S. Basu, Y. Gerchman, C. H. Collins, F. H. Arnold, and R. Weiss. 2005. A synthetic multicellular system for programmed pattern formation. Nature 434, 1130--1134.Google ScholarGoogle ScholarCross RefCross Ref
  14. S. Basu, R. Mehreja, S. Thiberge, M. T. Chen, and R. Weiss. 2004. Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl. Acad. Sci. USA 101, 6355--6360.Google ScholarGoogle ScholarCross RefCross Ref
  15. T. S. Bayer and C. D. Smolke. 2005. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol 23, 337--343.Google ScholarGoogle ScholarCross RefCross Ref
  16. A. Becskei, B. Seraphin, and L. Serrano. 2001. Positive feedback in eukaryotic gene networks: Cell differentiation by graded to binary response conversion. EMBO J 20, 2528--2535.Google ScholarGoogle ScholarCross RefCross Ref
  17. A. Becskei and L. Serrano. 2000. Engineering stability in gene networks by autoregulation. Nature 405, 590--593.Google ScholarGoogle ScholarCross RefCross Ref
  18. M. A. Bedau. 2003. Artificial life: Organization, adaptation and complexity from the bottom up. Trends Cogn. Sci. 7, 505--512.Google ScholarGoogle ScholarCross RefCross Ref
  19. Y. Benenson. 2012. Biomolecular computing systems: principles, progress and potential. Nat. Rev. Genet. 13, 455--468.Google ScholarGoogle ScholarCross RefCross Ref
  20. F. A. B. G. Bio, D. Baker, G. Church, J. Collins, D. Endy, J. Jacobson, J. Keasling, P. Modrich, C. Smolke, and R. Weiss. 2006. Engineering life: Building a fab for biology. Sci. Am. 294, 44--51.Google ScholarGoogle Scholar
  21. J. Bonnet, P. Yin, M. E. Ortiz, P. Subsoontorn, and D. Endy. 2013. Amplifying genetic logic gates. Science 340, 599--603.Google ScholarGoogle ScholarCross RefCross Ref
  22. C. G. Bowsher and P. S. Swain. 2014. Environmental sensing, information transfer, and cellular decision-making. Curr. Opin. Biotechnol. 28C, 149--155.Google ScholarGoogle ScholarCross RefCross Ref
  23. H. Breithaupt. 2006. The engineer's approach to biology. EMBO Rep 7, 21--23.Google ScholarGoogle ScholarCross RefCross Ref
  24. E. H. Bromley, K. Channon, E. Moutevelis, and D. N. Woolfson. 2008. Peptide and protein building blocks for synthetic biology: From programming biomolecules to self-organized biomolecular systems. ACS Chem. Biol. 3, 38--50.Google ScholarGoogle ScholarCross RefCross Ref
  25. J. A. Brophy and C. A. Voigt. 2014. Principles of genetic circuit design. Nat Methods 11, 508--520.Google ScholarGoogle ScholarCross RefCross Ref
  26. T. Bulter, S. G. Lee, W. W. Wong, E. Fung, M. R. Connor, and J. C. Liao. 2004. Design of artificial cell-cell communication using gene and metabolic networks. Proc. Nat. Acad. Sci. USA 101, 2299--2304.Google ScholarGoogle ScholarCross RefCross Ref
  27. D. R. Burrill, M. C. Inniss, P. M. Boyle, and P. A. Silver. 2012. Synthetic memory circuits for tracking human cell fate. Genes Dev. 26, 1486--1497.Google ScholarGoogle ScholarCross RefCross Ref
  28. J. M. Callura, C. R. Cantor, and J. J. Collins. 2012. Genetic switchboard for synthetic biology applications. Proc. Natl. Acad. Sci. USA 109, 5850--5855.Google ScholarGoogle ScholarCross RefCross Ref
  29. J. M. Callura, D. J. Dwyer, F. J. Isaacs, C. R. Cantor, and J. J. Collins. 2010. Tracking, tuning, and terminating microbial physiology using synthetic riboregulators. Proc. Natl. Acad. Sci. USA 107, 15898--15903.Google ScholarGoogle ScholarCross RefCross Ref
  30. D. E. Cameron, C. J. Bashor, and J. J. Collins. 2014. A brief history of synthetic biology. Nat. Rev. Microbiol. 12, 381--390.Google ScholarGoogle ScholarCross RefCross Ref
  31. K. Channon, E. H. Bromley, and D. N. Woolfson. 2008. Synthetic biology through biomolecular design and engineering. Curr. Opin. Struct. Biol. 18, 491--498.Google ScholarGoogle ScholarCross RefCross Ref
  32. A. Y. Chen, Z. Deng, A. N. Billings, U. O. Seker, M. Y. Lu, R. J. Citorik, B. Zakeri, and T. K. Lu. 2014. Synthesis and patterning of tunable multiscale materials with engineered cells. Nat. Mater. 13, 515--523.Google ScholarGoogle ScholarCross RefCross Ref
  33. M. T. Chen and R. Weiss. 2005. Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana. Nat. Biotechnol. 23, 1551--1555.Google ScholarGoogle ScholarCross RefCross Ref
  34. Y. Y. Chen, M. C. Jensen, and C. D. Smolke. 2010. Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems. Proc. Natl. Acad. Sci. USA 107, 8531--8536.Google ScholarGoogle ScholarCross RefCross Ref
  35. A. A. Cheng and T. K. Lu. 2012. Synthetic biology: An emerging engineering discipline. Annu. Rev. Biomed. Eng. 14, 155--178.Google ScholarGoogle ScholarCross RefCross Ref
  36. J. W. Chin. 2006a. Modular approaches to expanding the functions of living matter. Nat. Chem. Biol. 2, 304--311.Google ScholarGoogle ScholarCross RefCross Ref
  37. J. W. Chin. 2006b. Programming and engineering biological networks. Curr. Opin. Struct. Biol. 16, 551--556.Google ScholarGoogle ScholarCross RefCross Ref
  38. G. M. Church, M. B. Elowitz, C. D. Smolke, C. A. Voigt, and R. Weiss. 2014. Realizing the potential of synthetic biology. Nat. Rev. Mol. Cell. Biol. 15, 289--294.Google ScholarGoogle ScholarCross RefCross Ref
  39. J. Collins. 2012. Synthetic Biology: Bits and pieces come to life. Nature 483, S8--10.Google ScholarGoogle ScholarCross RefCross Ref
  40. J. J. Collins, M. Maxon, A. Ellington, M. Fussenegger, R. Weiss, and H. Sauro. 2014. Synthetic biology: How best to build a cell. Nature 509, 155--157.Google ScholarGoogle ScholarCross RefCross Ref
  41. C. A. Cronin, W. Gluba. and H. Scrable. 2001. The lac operator-repressor system is functional in the mouse. Genes Dev. 15, 1506--1517.Google ScholarGoogle ScholarCross RefCross Ref
  42. R. H. Dahl, F. Zhang, J. Alonso-Gutierrez, E. Baidoo, T. S. Batth, A. M. Redding-Johanson, C. J. Petzold, A. Mukhopadhyay, T. S. Lee, P. D. Adams, and J. D. Keasling. 2013. Engineering dynamic pathway regulation using stress-response promoters. Nat. Biotechnol. 31, 1039--1046.Google ScholarGoogle ScholarCross RefCross Ref
  43. R. Daniel, J. R. Rubens, R. Sarpeshkar, and T. K. Lu. 2013. Synthetic analog computation in living cells. Nature 497, 619--623.Google ScholarGoogle ScholarCross RefCross Ref
  44. T. Danino, O. Mondragon-Palomino, L. Tsimring, and J. Hasty. 2010. A synchronized quorum of genetic clocks. Nature 463, 326--330.Google ScholarGoogle ScholarCross RefCross Ref
  45. T. L. Deans, C. R. Cantor, and J. J. Collins. 2007. A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell 130, 363--372.Google ScholarGoogle ScholarCross RefCross Ref
  46. T. L. Deans and J. H. Elisseeff. 2010. The life of a cell: Probing the complex relationships with the world. Cell Stem Cell 6, 499--501.Google ScholarGoogle ScholarCross RefCross Ref
  47. T. L. Deans, A. Singh, M. Gibson, and J. H. Elisseeff. 2012. Regulating synthetic gene networks in 3D materials. Proc. Natl. Acad. Sci. USA 109, 15217--15222.Google ScholarGoogle ScholarCross RefCross Ref
  48. J. E. Dueber, B. J. Yeh, K. Chak, and W. A. Lim. 2003. Reprogramming control of an allosteric signaling switch through modular recombination. Science 301, 1904--1908.Google ScholarGoogle ScholarCross RefCross Ref
  49. M. A. Dwyer, L. L. Looger, and H. W. Hellinga. 2003. Computational design of a Zn2+ receptor that controls bacterial gene expression. Proc. Natl. Acad. Sci. USA 100, 11255--11260.Google ScholarGoogle ScholarCross RefCross Ref
  50. T. Ellis, X. Wang, and J. J. Collins. 2009. Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat. Biotechnol. 27, 465--471.Google ScholarGoogle ScholarCross RefCross Ref
  51. M. B. Elowitz and S. Leibler. 2000. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335--338.Google ScholarGoogle ScholarCross RefCross Ref
  52. K. Endo, K. Hayashi, T. Inoue, and H. Saito. 2013. A versatile cis-acting inverter module for synthetic translational switches. Nat. Commun 4, 2393.Google ScholarGoogle ScholarCross RefCross Ref
  53. D. Endy. 2005. Foundations for engineering biology. Nature 438, 449--453.Google ScholarGoogle ScholarCross RefCross Ref
  54. F. Farzadfard, S. D. Perli, and T. K. Lu. 2013. Tunable and multifunctional eukaryotic transcription factors based on CRISPR/Cas. ACS Synth. Biol. 2, 604--613.Google ScholarGoogle ScholarCross RefCross Ref
  55. A. Fire, S. Xu, M. K. Montgomery, S. A. Kostas, S. E. Driver, and C. C. Mello. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391, 806--811.Google ScholarGoogle ScholarCross RefCross Ref
  56. M. A. Fischbach, J. A. Bluestone, and W. A. Lim. 2013. Cell-based therapeutics: The next pillar of medicine. Sci. Trans. Med. 5, 179ps177.Google ScholarGoogle Scholar
  57. J. A. Fischer, E. Giniger, T. Maniatis, and M. Ptashne. 1988. GAL4 activates transcription in Drosophila. Nature 332, 853--856.Google ScholarGoogle ScholarCross RefCross Ref
  58. A. E. Friedland, T. K. Lu, X. Wang, D. Shi, G. Church, and J. J. Collins. 2009. Synthetic gene networks that count. Science 324, 1199--1202.Google ScholarGoogle ScholarCross RefCross Ref
  59. Y. Fu, J. D. Sander, D. Reyon, V. M. Cascio, and J. K. Joung. 2014. Improving CRISPR-Cas nuclease specificity using truncated guide RNAs. Nat. Biotechnol. 32, 279--284.Google ScholarGoogle ScholarCross RefCross Ref
  60. T. R. Fuerst, M. P. Fernandez, and B. Moss. 1989. Transfer of the inducible lac repressor/operator system from Escherichia coli to a vaccinia virus expression vector. Proc. Natl. Acad. Sci. USA 86, 2549--2553.Google ScholarGoogle ScholarCross RefCross Ref
  61. E. Fung, W. W. Wong, J. K. Suen, T. Bulter, S. G. Lee, and J. C. Liao. 2005. A synthetic gene-metabolic oscillator. Nature 435, 118--122.Google ScholarGoogle ScholarCross RefCross Ref
  62. R. Gaber, T. Lebar, A. Majerle, B. Ster, A. Dobnikar, M. Bencina, and R. Jerala. 2014. Designable DNA-binding domains enable construction of logic circuits in mammalian cells. Nat. Chem. Biol. 10, 203--208.Google ScholarGoogle ScholarCross RefCross Ref
  63. J. R. Garcia, H. J. Cha, G. Rao, M. R. Marten, and W. E. Bentley. 2009. Microbial nar-GFP cell sensors reveal oxygen limitations in highly agitated and aerated laboratory-scale fermentors. Microb. Cell Fact 8, 6.Google ScholarGoogle ScholarCross RefCross Ref
  64. T. S. Gardner, C. R. Cantor, and J. J. Collins. 2000. Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339--342.Google ScholarGoogle ScholarCross RefCross Ref
  65. D. G. Gibson, G. A. Benders, C. Andrews-Pfannkoch, E. A. Denisova, H. Baden-Tillson, J. Zaveri, T. B. Stockwell, A. Brownley, D. W. Thomas, M. A. Algire, C. Merryman, L. Young, V. N. Noskov, J. I. Glass, J. C. Venter, C. A. 3rd Hutchison, and H. O. Smith. 2008. Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319, 1215--1220.Google ScholarGoogle ScholarCross RefCross Ref
  66. X. Guan, L. Q. Gu, S. Cheley, O. Braha, and H. Bayley. 2005. Stochastic sensing of TNT with a genetically engineered pore. Chembiochem 6, 1875--1881.Google ScholarGoogle ScholarCross RefCross Ref
  67. C. C. Guet, M. B. Elowitz, W. Hsing, and S. Leibler. 2002. Combinatorial synthesis of genetic networks. Science 296, 1466--1470.Google ScholarGoogle ScholarCross RefCross Ref
  68. N. J. Guido, P. Lee, X. Wang, T. C. Elston, and J. J. Collins. 2007. A pathway and genetic factors contributing to elevated gene expression noise in stationary phase. Biophys J. 93, L55--57.Google ScholarGoogle ScholarCross RefCross Ref
  69. N. J. Guido, X. Wang, D. Adalsteinsson, D. Mcmillen, J. Hasty, C. R. Cantor, T. C. Elston, and J. J. Collins. 2006. A bottom-up approach to gene regulation. Nature 439, 856--860.Google ScholarGoogle ScholarCross RefCross Ref
  70. J. Hasty, D. Mcmillen, F. Isaacs, and J. J. Collins. 2001. Computational studies of gene regulatory networks: In numero molecular biology. Nat. Rev. Genet. 2, 268--279.Google ScholarGoogle ScholarCross RefCross Ref
  71. J. Hemphill and A. Deiters. 2013. DNA computation in mammalian cells: microRNA logic operations. J Am. Chem. Soc. 135, 10512--10518.Google ScholarGoogle ScholarCross RefCross Ref
  72. W. J. Holtz and J. D. Keasling. 2010. Engineering static and dynamic control of synthetic pathways. Cell 140, 19--23.Google ScholarGoogle ScholarCross RefCross Ref
  73. C. Hsu, S. Scherrer, A. Buetti-Dinh, P. Ratna, J. Pizzolato, V. Jaquet, and A. Becskei. 2012. Stochastic signalling rewires the interaction map of a multiple feedback network during yeast evolution. Nat. Commun. 3, 682.Google ScholarGoogle ScholarCross RefCross Ref
  74. P. D. Hsu, E. S. Lander, and F. Zhang. 2014. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157, 1262--1278.Google ScholarGoogle ScholarCross RefCross Ref
  75. M. C. Hu and N. Davidson. 1987. The inducible lac operator-repressor system is functional in mammalian cells. Cell 48, 555--566.Google ScholarGoogle ScholarCross RefCross Ref
  76. I. Y. Hwang, M. H. Tan, E. Koh, C. L. Ho, C. L. Poh, and M. W. Chang. 2014. Reprogramming microbes to be pathogen-seeking killers. ACS Synthet. Biol. 3, 228--237.Google ScholarGoogle ScholarCross RefCross Ref
  77. T. Ideker, V. Thorsson, J. A. Ranish, R. Christmas, J. Buhler, J. K. Eng, R. Bumgarner, D. R. Goodlett, R. Aebersold, and L. Hood. 2001. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292, 929--934.Google ScholarGoogle ScholarCross RefCross Ref
  78. F. J. Isaacs, W. J. Blake, and J. J. Collins. 2005. Molecular biology. Signal processing in single cells. Science 307, 1886--1888.Google ScholarGoogle ScholarCross RefCross Ref
  79. F. J. Isaacs, D. J. Dwyer, and J. J. Collins. 2006. RNA synthetic biology. Nat. Biotechnol. 24, 545--554.Google ScholarGoogle ScholarCross RefCross Ref
  80. F. J. Isaacs, D. J. Dwyer, C. Ding, D. D. Pervouchine, C. R. Cantor, and J. J. Collins. 2004. Engineered riboregulators enable post-transcriptional control of gene expression. Nat. Biotechnol. 22, 841--847.Google ScholarGoogle ScholarCross RefCross Ref
  81. H. Jeong, B. Tombor, R. Albert, Z. N. Oltvai, and A. L. Barabasi. 2000. The large-scale organization of metabolic networks. Nature 407, 651--654.Google ScholarGoogle ScholarCross RefCross Ref
  82. E. M. Judd, M. T. Laub, and H. H. Mcadams. 2000. Toggles and oscillators: New genetic circuit designs. Bioessays 22, 507--509.Google ScholarGoogle ScholarCross RefCross Ref
  83. M. Kaern, W. J. Blake, and J. J. Collins. 2003. The engineering of gene regulatory networks. Ann. Rev. Biomed. Eng. 5, 179--206.Google ScholarGoogle ScholarCross RefCross Ref
  84. M. Kaern, T. C. Elston, W. J. Blake, and J. J. Collins. 2005. Stochasticity in gene expression: From theories to phenotypes. Nat. Rev. Genet. 6, 451--464.Google ScholarGoogle ScholarCross RefCross Ref
  85. T. Kalmar, C. Lim, C. Hayward, S. Munoz-Descalzo, J. Nichols, J. Garcia-Ojalvo, and A. Martinez Arias. 2009. Regulated fluctuations in nanog expression mediate cell fate decisions in embryonic stem cells. PLoS Biol 7, e1000149.Google ScholarGoogle ScholarCross RefCross Ref
  86. M. Karlsson and W. Weber. 2012. Therapeutic synthetic gene networks. Curr. Opin. Biotechnol. 23, 703--711.Google ScholarGoogle ScholarCross RefCross Ref
  87. A. J. Keung, C. J. Bashor, S. Kiriakov, J. J. Collins, and A. S. Khalil. 2014. Using targeted chromatin regulators to engineer combinatorial and spatial transcriptional regulation. Cell 158, 110--120.Google ScholarGoogle ScholarCross RefCross Ref
  88. A. S. Khalil and J. J. Collins. 2010. Synthetic biology: Applications come of age. Nat. Rev. Genet. 11, 367--379.Google ScholarGoogle ScholarCross RefCross Ref
  89. A. S. Khalil, T. K. Lu, C. J. Bashor, C. L. Ramirez, N. C. Pyenson, J. K. Joung, and J. J. Collins. 2012. A synthetic biology framework for programming eukaryotic transcription functions. Cell 150, 647--658.Google ScholarGoogle ScholarCross RefCross Ref
  90. D. H. Kim and J. J. Rossi. 2007. Strategies for silencing human disease using RNA interference. Nat. Rev. Genet. 8, 173--184.Google ScholarGoogle ScholarCross RefCross Ref
  91. H. Kitano. 2002. Computational systems biology. Nature 420, 206--210.Google ScholarGoogle ScholarCross RefCross Ref
  92. J. Klein, J. R. Heal, W. D. Hamilton, T. Boussemghoune, T. O. Tange, F. Delegrange, G. Jaeschke, A. Hatsch, and J. Heim. 2014. Yeast synthetic biology platform generates novel chemical structures as scaffolds for drug discovery. ACS Synth. Biol. 3, 314--323.Google ScholarGoogle ScholarCross RefCross Ref
  93. H. Kobayashi, M. Kaern, M. Araki, K. Chung, T. S. Gardner, C. R. Cantor, and J. J. Collins. 2004. Programmable cells: interfacing natural and engineered gene networks. Proc. Natl. Acad. Sci. USA 101, 8414--8419.Google ScholarGoogle ScholarCross RefCross Ref
  94. M. A. Kohanski and J. J. Collins. 2008. Rewiring bacteria, two components at a time. Cell 133, 947--948.Google ScholarGoogle ScholarCross RefCross Ref
  95. S. Kok, L. H. Stanton, T. Slaby, M. Durot, V. F. Holmes, K. G. Patel, D. Platt, E. B. Shapland, Z. Serber, J. Dean, J. D. Newman, and S. S. Chandran. 2014. Rapid and Reliable DNA Assembly via Ligase Cycling Reaction. ACS Synthet. Biol. 3, 97--106.Google ScholarGoogle ScholarCross RefCross Ref
  96. J. W. Kotula, S. J. Kerns, L. A. Shaket, L. Siraj, J. J. Collins, J. C. Way, and P. A. Silver. 2014. Programmable bacteria detect and record an environmental signal in the mammalian gut. Proc. Natl. Acad. Sci. USA 111, 4838--4843.Google ScholarGoogle ScholarCross RefCross Ref
  97. B. P. Kramer, A. U. Viretta, M. Daoud-El-Baba, D. Aubel, W. Weber, and M. Fussenegger. 2004. An engineered epigenetic transgene switch in mammalian cells. Nat. Biotechnol. 22, 867--870.Google ScholarGoogle ScholarCross RefCross Ref
  98. A. M. Lanza, N. C. Crook, and H. S. Alper. 2012. Innovation at the intersection of synthetic and systems biology. Curr. Opin. Biotechnol. 23, 712--717.Google ScholarGoogle ScholarCross RefCross Ref
  99. M. H. Larson, L. A. Gilbert, X. Wang, W. A. Lim, J. S. Weissman, and L. S. Qi. 2013. CRISPR interference (CRISPRi) for sequence-specific control of gene expression. Nat. Protoc. 8, 2180--2196.Google ScholarGoogle ScholarCross RefCross Ref
  100. J. Layton. 2005. How robotic vacuums work. In HowStuffWorks.com.Google ScholarGoogle Scholar
  101. I. Lee and E. M. Marcotte. 2009. Effects of functional bias on supervised learning of a gene network model. Meth. Mol. Biol. 541, 463--475.Google ScholarGoogle ScholarCross RefCross Ref
  102. S. K. Lee, H. Chou, T. S. Ham, T. S. Lee, and J. D. Keasling. 2008. Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels. Curr. Opin. Biotechnol. 19, 556--563.Google ScholarGoogle ScholarCross RefCross Ref
  103. S. Y. Lee, H. U. Kim, J. H. Park, J. M. Park, and T. Y. Kim. 2009. Metabolic engineering of microorganisms: general strategies and drug production. Drug Discov. Today 14, 78--88.Google ScholarGoogle ScholarCross RefCross Ref
  104. A. Levskaya, O. D. Weiner, W. A. Lim, and C. A. Voigt. 2009. Spatiotemporal control of cell signalling using a light-switchable protein interaction. Nature 461, 997--1001.Google ScholarGoogle ScholarCross RefCross Ref
  105. M. Lewandoski. 2001. Conditional control of gene expression in the mouse. Nat. Rev. Genet. 2, 743--755.Google ScholarGoogle ScholarCross RefCross Ref
  106. F. Lienert, J. J. Lohmueller, A. Garg, and P. A. Silver. 2014. Synthetic biology in mammalian cells: Next generation research tools and therapeutics. Nat. Rev. Mol. Cell Biol. 15, 95--107.Google ScholarGoogle ScholarCross RefCross Ref
  107. W. A. Lim. 2010. Designing customized cell signalling circuits. Nat. Rev. Mol. Cell Biol. 11, 393--403.Google ScholarGoogle ScholarCross RefCross Ref
  108. K. D. Litcofsky, R. B. Afeyan, R. J. Krom, A. S. Khalil, and J. J. Collins. 2012. Iterative plug-and-play methodology for constructing and modifying synthetic gene networks. Nat. Meth. 9, 1077--1080.Google ScholarGoogle ScholarCross RefCross Ref
  109. H. S. Liu, C. H. Lee, C. F. Lee, I. J. Su, and T. Y. Chang. 1998. Lac/Tet dual-inducible system functions in mammalian cell lines. Biotechniques 24, 624--628, 630--622.Google ScholarGoogle ScholarCross RefCross Ref
  110. L. L. Looger, M. A. Dwyer, J. J. Smith, and H. W. Hellinga. 2003. Computational design of receptor and sensor proteins with novel functions. Nature 423, 185--190.Google ScholarGoogle ScholarCross RefCross Ref
  111. T. K. Lu and J. J. Collins. 2007. Dispersing biofilms with engineered enzymatic bacteriophage. Proc. Natl. Acad. Sci. USA 104, 11197--11202.Google ScholarGoogle ScholarCross RefCross Ref
  112. T. K. Lu, A. S. Khalil, and J. J. Collins. 2009. Next-generation synthetic gene networks. Nat. Biotechnol 27, 1139--1150.Google ScholarGoogle ScholarCross RefCross Ref
  113. R. Lutz and H. Bujard. 1997. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucl. Acids Res. 25, 1203--1210.Google ScholarGoogle ScholarCross RefCross Ref
  114. M. S. Magaraci, A. Veerakumar, P. Qiao, A. Amurthur, J. Y. Lee, J. S. Miller, M. Goulian, and C. A. Sarkar. 2014. Engineering Escherichia coli for light-activated cytolysis of mammalian cells. ACS Synthet. Biol.Google ScholarGoogle Scholar
  115. V. J. Martin, D. J. Pitera, S. T. Withers, J. D. Newman, and J. D. Keasling. 2003. Engineering a mevalonate pathway in Escherichia coli for production of terpenoids. Nat. Biotechnol. 21, 796--802.Google ScholarGoogle ScholarCross RefCross Ref
  116. N. J. Mckenna and B. W. O'Malley. 2002. Combinatorial control of gene expression by nuclear receptors and coregulators. Cell 108, 465--474.Google ScholarGoogle ScholarCross RefCross Ref
  117. M. T. Mee, J. J. Collins, G. M. Church, and H. H. Wang. 2014. Syntrophic exchange in synthetic microbial communities. Proc. Natl. Acad. Sci. USA 111, E2149--2156.Google ScholarGoogle ScholarCross RefCross Ref
  118. J. T. Mettetal, D. Muzzey, C. Gomez-Uribe, and A. Van Oudenaarden. 2008. The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae. Science 319, 482--484.Google ScholarGoogle ScholarCross RefCross Ref
  119. J. Minker. 2000. Introduction to Logic-Based Artificial Intelligence. Kluwer Academic Publishers Dordrecht. Google ScholarGoogle ScholarDigital LibraryDigital Library
  120. T. Miyamoto, S. Razavi, R. Derose, and T. Inoue. 2013. Synthesizing biomolecule-based Boolean logic gates. ACS Synthet. Biol. 2, 72--82.Google ScholarGoogle ScholarCross RefCross Ref
  121. T. S. Moon, C. Lou, A. Tamsir, B. C. Stanton, and C. A. Voigt. 2012. Genetic programs constructed from layered logic gates in single cells. Nature 491, 249--253.Google ScholarGoogle ScholarCross RefCross Ref
  122. F. Moser, N. J. Broers, S. Hartmans, A. Amsir, R. Erkman, J. A. Roubos, R. Bovenberg, and C. A. Voigt. 2012. Genetic circuit performance under conditions relevant for industrial bioreactors. ACS Synthet. Biol. 1, 555--564.Google ScholarGoogle ScholarCross RefCross Ref
  123. S. Mukherji and A. Van Oudenaarden. 2009. Synthetic biology: Understanding biological design from synthetic circuits. Nat. Rev. Genet. 10, 859--871.Google ScholarGoogle ScholarCross RefCross Ref
  124. C. J. Myers. 2010. Engineering Genetic Circuits. CRC Press, Boca Raton, FL.Google ScholarGoogle Scholar
  125. N. Nandagopal and M. B. Elowitz. 2011. Synthetic biology: Integrated gene circuits. Science 333, 1244--1248.Google ScholarGoogle ScholarCross RefCross Ref
  126. D. Nevozhay, R. M. Adams, E. Van Itallie, M. R. Bennett, and G. Balazsi. 2012. Mapping the environmental fitness landscape of a synthetic gene circuit. PLoS Comput. Biol. 8, e1002480.Google ScholarGoogle ScholarCross RefCross Ref
  127. L. Nissim, S. D. Perli, A. Fridkin, P. Perez-Pinera, and T. K. Lu. 2014. Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. Molec. Cell 54, 698--710.Google ScholarGoogle ScholarCross RefCross Ref
  128. V. Noireaux, Y. T. Maeda, and A. Libchaber. 2011. Development of an artificial cell, from self-organization to computation and self-reproduction. Proc. Natl. Acad. Sci. USA 108, 3473--3480.Google ScholarGoogle ScholarCross RefCross Ref
  129. S. O'Gorman, D. T. Fox, and G. M. Wahl. 1991. Recombinase-mediated gene activation and site-specific integration in mammalian cells. Science 251, 1351--1355.Google ScholarGoogle ScholarCross RefCross Ref
  130. E. J. Olson, L. A. Hartsough, B. P. Landry, R. Shroff, and J. J. Tabor. 2014. Characterizing bacterial gene circuit dynamics with optically programmed gene expression signals. Nat. Meth. 11, 449--455.Google ScholarGoogle ScholarCross RefCross Ref
  131. J. H. Park and S. Y. Lee. 2008. Towards systems metabolic engineering of microorganisms for amino acid production. Curr. Opin. Biotechnol. 19, 454--460.Google ScholarGoogle ScholarCross RefCross Ref
  132. S. Payne and L. You. 2013. Engineered cell-cell communication and its applications. Adv. Biochem. Eng. Biotechnol.Google ScholarGoogle Scholar
  133. R. Pfeifer, M. Lungarella, and F. Iida. 2007. Self-organization, embodiment, and biologically inspired robotics. Science 318, 1088--1093.Google ScholarGoogle ScholarCross RefCross Ref
  134. M. Ptashne. 1992. A Genetic Switch: Phage {Lambda} and Higher Organisms 2nd Ed. Cell Press, Blackwell Scientific Publications, Cambridge, MA.Google ScholarGoogle Scholar
  135. O. Purcell and T. K. Lu. 2014. Synthetic analog and digital circuits for cellular computation and memory. Curr. Opin. Biotechnol. 29C, 146--155.Google ScholarGoogle ScholarCross RefCross Ref
  136. P. E. Purnick and R. Weiss. 2009. The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 10, 410--422.Google ScholarGoogle ScholarCross RefCross Ref
  137. O. Rackham and J. W. Chin. 2005. A network of orthogonal ribosome x mRNA pairs. Nat. Chem. Biol. 1, 159--166.Google ScholarGoogle ScholarCross RefCross Ref
  138. S. Rasmussen, M. J. Raven, G. N. Keating, and M. A. Bedau. 2003. Collective intelligence of the artificial life community on its own successes, failures, and future. Artif. Life 9, 207--235. Google ScholarGoogle ScholarDigital LibraryDigital Library
  139. R. Reddy. 2006. Robotics and intelligent systems in support of society. Intell. Syst. IEEE 21, 24--31. Google ScholarGoogle ScholarDigital LibraryDigital Library
  140. D. K. Ro, E. M. Paradise, M. Ouellet, K. J. Fisher, K. L. Newman, J. M. Ndungu, K. A. Ho, R. A. Eachus, T. S. Ham, J. Kirby, M. C. Chang, S. T. Withers, Y. Shiba, R. Sarpong, and J. D. Keasling. 2006. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440, 940--943.Google ScholarGoogle ScholarCross RefCross Ref
  141. N. Roehner and C. J. Myers. 2014a. Directed acyclic graph-based technology mapping of genetic circuit models. ACS Synthet. Biol. 3, 543--555.Google ScholarGoogle ScholarCross RefCross Ref
  142. N. Roehner and C. J. Myers. 2014b. A methodology to annotate systems biology markup language models with the synthetic biology open language. ACS Synthet. Biol. 3, 57--66.Google ScholarGoogle ScholarCross RefCross Ref
  143. N. Roehner, E. Oberortner, M. Pocock, J. Beal, K. Clancy, C. Madsen, G. Misirli, A. Wipat, H. Sauro, and C. J. Myers. 2014. Proposed data model for the next version of the synthetic biology open language. ACS Synthet. Biol.Google ScholarGoogle Scholar
  144. N. Roquet and T. K. Lu. 2014. Digital and analog gene circuits for biotechnology. Biotechnol. J. 9, 597--608.Google ScholarGoogle ScholarCross RefCross Ref
  145. N. Rosenfeld, M. B. Elowitz, and U. Alon. 2002. Negative autoregulation speeds the response times of transcription networks. J. Mol. Biol. 323, 785--793.Google ScholarGoogle ScholarCross RefCross Ref
  146. W. C. Ruder, T. Lu, and J. J. Collins. 2011. Synthetic biology moving into the clinic. Science 333, 1248--1252.Google ScholarGoogle ScholarCross RefCross Ref
  147. M. Ruzzi, K. D. Breunig, A. G. Ficca, and C. P. Hollenberg. 1987. Positive regulation of the beta-galactosidase gene from Kluyveromyces lactis is mediated by an upstream activation site that shows homology to the GAL upstream activation site of Saccharomyces cerevisiae. Molec. Cell. Biol. 7, 991--997.Google ScholarGoogle ScholarCross RefCross Ref
  148. J. D. Sander and J. K. Joung. 2014. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 32, 347--355.Google ScholarGoogle ScholarCross RefCross Ref
  149. B. Sauer and N. Henderson. 1989. Cre-stimulated recombination at loxP-containing DNA sequences placed into the mammalian genome. Nucl. Acids Res. 17, 147--161.Google ScholarGoogle ScholarCross RefCross Ref
  150. P. A. Sharp. 2001. RNA interference--2001. Genes Dev. 15, 485--490.Google ScholarGoogle ScholarCross RefCross Ref
  151. A. Singh, T. L. Deans, and J. H. Elisseeff. 2013. Photomodulation of cellular gene expression in hydrogels. Acs Macro. Letter 2, 269--272.Google ScholarGoogle Scholar
  152. P. Siuti, J. Yazbek, and T. K. Lu. 2013. Synthetic circuits integrating logic and memory in living cells. Nat. Biotechnol. 31, 448--452.Google ScholarGoogle ScholarCross RefCross Ref
  153. P. Siuti, J. Yazbek, and T. K. Lu. 2014. Engineering genetic circuits that compute and remember. Nat. Protoc. 9, 1292--1300.Google ScholarGoogle ScholarCross RefCross Ref
  154. R. V. Sole, A. Munteanu, C. Rodriguez-Caso, and J. Macia. 2007. Synthetic protocell biology: From reproduction to computation. Philos Trans. Roy. Soc Lond B Biol. Sci. 362, 1727--1739.Google ScholarGoogle ScholarCross RefCross Ref
  155. D. Sprinzak and M. B. Elowitz. 2005. Reconstruction of genetic circuits. Nature 438, 443--448.Google ScholarGoogle ScholarCross RefCross Ref
  156. N. Sternberg and D. Hamilton. 1981. Bacteriophage P1 site-specific recombination. I. Recombination between loxP sites. J. Mol. Biol. 150, 467--486.Google ScholarGoogle ScholarCross RefCross Ref
  157. J. T. Stevens and C. J. Myers. 2013. Dynamic modeling of cellular populations within iBioSim. ACS Synthet. Biol. 2, 223--229.Google ScholarGoogle ScholarCross RefCross Ref
  158. J. Szulc, M. Wiznerowicz, M. O. Sauvain, D. Trono, and P. Aebischer. 2006. A versatile tool for conditional gene expression and knockdown. Nat. Meth. 3, 109--116.Google ScholarGoogle ScholarCross RefCross Ref
  159. A. Tamsir, J. J. Tabor, and C. A. Voigt. 2011. Robust multicellular computing using genetically encoded NOR gates and chemical ‘wires’. Nature 469, 212--215.Google ScholarGoogle ScholarCross RefCross Ref
  160. F. J. Vizeacoumar, Y. Chong, C. Boone, and B. J. Andrews. 2009. A picture is worth a thousand words: genomics to phenomics in the yeast Saccharomyces cerevisiae. FEBS Lett 583, 1656--1661.Google ScholarGoogle ScholarCross RefCross Ref
  161. C. A. Voigt. 2006. Genetic parts to program bacteria. Curr. Opin. Biotechnol. 17, 548--557.Google ScholarGoogle ScholarCross RefCross Ref
  162. M. Wakiyama, R. Muramatsu, Y. Kaitsu, M. Ikeda, and S. Yokoyama. 2011. Inducible protein expression in Drosophila Schneider 2 cells using the lac operator-repressor system. Biotechnol. Lett. 33, 2361--2366.Google ScholarGoogle ScholarCross RefCross Ref
  163. Y. Wang, Y. Y. Yau, D. Perkins-Balding, and J. G. Thomson. 2011. Recombinase technology: Applications and possibilities. Plant. Cell. Rep. 30, 267--285.Google ScholarGoogle ScholarCross RefCross Ref
  164. J. C. Way, J. J. Collins, J. D. Keasling, and P. A. Silver. 2014. Integrating biological redesign: Where synthetic biology came from and where it needs to go. Cell. 157, 151--161.Google ScholarGoogle ScholarCross RefCross Ref
  165. W. Weber, R. Schoenmakers, B. Keller, M. Gitzinger, T. Grau, M. Daoud-El Baba, P. Sander, and M. Fussenegger. 2008. A synthetic mammalian gene circuit reveals antituberculosis compounds. Proc. Natl. Acad. Sci. USA 105, 9994--9998.Google ScholarGoogle ScholarCross RefCross Ref
  166. W. Weber, J. Stelling, M. Rimann, B. Keller, M. Daoud-El Baba, C. C. Weber, D. Aubel, and M. Fussenegger. 2007. A synthetic time-delay circuit in mammalian cells and mice. Proc. Natl. Acad. Sci. USA 104, 2643--2648.Google ScholarGoogle ScholarCross RefCross Ref
  167. N. Webster, J. R. Jin, S. Green, M. Hollis, and P. Chambon. 1988. The yeast UASG is a transcriptional enhancer in human HeLa cells in the presence of the GAL4 trans-activator. Cell 52, 169--178.Google ScholarGoogle ScholarCross RefCross Ref
  168. H. V. Westerhoff and B. O. Palsson. 2004. The evolution of molecular biology into systems biology. Nat. Biotechnol. 22, 1249--1252.Google ScholarGoogle ScholarCross RefCross Ref
  169. N. Wiener. 1948. Cybernetics. Wiley, New York.Google ScholarGoogle Scholar
  170. M. N. Win and C. D. Smolke. 2007. A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc. Natl. Acad. Sci. USA 104, 14283--14288.Google ScholarGoogle ScholarCross RefCross Ref
  171. M. N. Win and C. D. Smolke. 2008. Higher-order cellular information processing with synthetic RNA devices. Science 322, 456--460.Google ScholarGoogle ScholarCross RefCross Ref
  172. P. J. Wittkopp, B. K. Haerum, and A. G. Clark. 2004. Evolutionary changes in cis and trans gene regulation. Nature 430, 85--88.Google ScholarGoogle ScholarCross RefCross Ref
  173. J. B. Xavier. 2011. Social interaction in synthetic and natural microbial communities. Mol. Syst. Biol. 7, 483.Google ScholarGoogle ScholarCross RefCross Ref
  174. Z. Xie, L. Wroblewska, L. Prochazka, R. Weiss, and Y. Benenson. 2011. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 333, 1307--1311.Google ScholarGoogle ScholarCross RefCross Ref
  175. B. J. Yeh, R. J. Rutigliano, A. Deb, D. Bar-Sagi, and W. A. Lim. 2007. Rewiring cellular morphology pathways with synthetic guanine nucleotide exchange factors. Nature 447, 596--600.Google ScholarGoogle ScholarCross RefCross Ref
  176. C. Yoo, L. Ramirez, and J. Liuzzi. 2014. Big data analysis using modern statistical and machine learning methods in medicine. Int. Neurourol. J. 18, 50--57.Google ScholarGoogle ScholarCross RefCross Ref
  177. L. You, R. S. 3rd Cox, R. Weiss, and F. H. Arnold. 2004. Programmed population control by cell-cell communication and regulated killing. Nature 428, 868--871.Google ScholarGoogle ScholarCross RefCross Ref
  178. H. Youk and W. A. Lim. 2014. Secreting and sensing the same molecule allows cells to achieve versatile social behaviors. Science 343, 1242782.Google ScholarGoogle ScholarCross RefCross Ref

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  1. Parallel Networks: Synthetic Biology and Artificial Intelligence

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          cover image ACM Journal on Emerging Technologies in Computing Systems
          ACM Journal on Emerging Technologies in Computing Systems  Volume 11, Issue 3
          Special Issue on Computational Synthetic Biology and Regular Papers
          December 2014
          219 pages
          ISSN:1550-4832
          EISSN:1550-4840
          DOI:10.1145/2711453
          Issue’s Table of Contents

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          Publication History

          • Published: 30 December 2014
          • Accepted: 1 August 2014
          • Received: 1 July 2014
          Published in jetc Volume 11, Issue 3

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