Parallel networks: Synthetic biology and artificial intelligence

ACM Journal on Emerging Technologies in Computing Systems

Volumn 11, Issue 3, 2014, Pages

  Deans, Tara L ^a  

^a UNIVERSITY OF UTAH   (United States)

Author keywords

Artificial intelligence; DNA; Gene control; Genetic circuits; Synthetic biology

Indexed keywords

ARTIFICIAL INTELLIGENCE; CELL ENGINEERING; DNA; GENETIC ALGORITHMS;

COMPUTER SCIENTISTS; ENGINEERING CELLS; GENE CONTROL; GENETIC CIRCUITS; MODERN TECHNOLOGIES; NOVEL FUNCTIONS; PARALLEL NETWORK; SCIENCE COMMUNITY;

SYNTHETIC BIOLOGY;

EID: 84920692542     PISSN: 15504832     EISSN: 15504840     Source Type: Journal    
DOI: 10.1145/2667229     Document Type: Article

References (178)

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.
2. B. Alberts. 2002. Molecular Biology of the Cell. Garland Science, New York.
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.
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.
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.
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.
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.
8. S. Auslander, D. Auslander, M. Muller, M. Wieland, and M. Fussenegger. 2012. Programmable single-cell mammalian biocomputers. Nature 487, 123-127.
9. S. Auslander and M. Fussenegger. 2013. From gene switches to mammalian designer cells: Present and future prospects. Trends Biotechnol 31, 155-168.
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.
11. G. Balazsi and J. J. Collins. 2007. Taking the inventory inside single cells. Nat. Chem. Biol. 3, 141-142.
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.
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.
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.
15. T. S. Bayer and C. D. Smolke. 2005. Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol 23, 337-343.
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.
17. A. Becskei and L. Serrano. 2000. Engineering stability in gene networks by autoregulation. Nature 405, 590-593.
18. M. A. Bedau. 2003. Artificial life: Organization, adaptation and complexity from the bottom up. Trends Cogn. Sci. 7, 505-512.
19. Y. Benenson. 2012. Biomolecular computing systems: principles, progress and potential. Nat. Rev. Genet. 13, 455-468.
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.
21. J. Bonnet, P. Yin, M. E. Ortiz, P. Subsoontorn, and D. Endy. 2013. Amplifying genetic logic gates. Science 340, 599-603.
22. C. G. Bowsher and P. S. Swain. 2014. Environmental sensing, information transfer, and cellular decisionmaking. Curr. Opin. Biotechnol. 28C, 149-155.
23. H. Breithaupt. 2006. The engineer's approach to biology. EMBO Rep 7, 21-23.
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.
25. J. A. Brophy and C. A. Voigt. 2014. Principles of genetic circuit design. Nat Methods 11, 508-520.
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.
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.
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.
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.
30. D. E. Cameron, C. J. Bashor, and J. J. Collins. 2014. A brief history of synthetic biology. Nat. Rev. Microbiol. 12, 381-390.
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.
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.
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.
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.
35. A. A. Cheng and T. K. Lu. 2012. Synthetic biology: An emerging engineering discipline. Annu. Rev. Biomed. Eng. 14, 155-178.
36. J. W. Chin. 2006a. Modular approaches to expanding the functions of living matter. Nat. Chem. Biol. 2, 304-311.
37. J. W. Chin. 2006b. Programming and engineering biological networks. Curr. Opin. Struct. Biol. 16, 551-556.
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.
39. J. Collins. 2012. Synthetic Biology: Bits and pieces come to life. Nature 483, S8-10.
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.
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.
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.
43. R. Daniel, J. R. Rubens, R. Sarpeshkar, and T. K. Lu. 2013. Synthetic analog computation in living cells. Nature 497, 619-623.
44. T. Danino, O. Mondragon-Palomino, L. Tsimring, and J. Hasty. 2010. A synchronized quorum of genetic clocks. Nature 463, 326-330.
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.
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.
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.
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.
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.
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.
51. M. B. Elowitz and S. Leibler. 2000. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338.
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.
53. D. Endy. 2005. Foundations for engineering biology. Nature 438, 449-453.
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.
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.
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.
57. J. A. Fischer, E. Giniger, T. Maniatis, and M. Ptashne. 1988. GAL4 activates transcription in Drosophila. Nature 332, 853-856.
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.
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.
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.
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.
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.
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.
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.
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.
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.
67. C. C. Guet, M. B. Elowitz, W. Hsing, and S. Leibler. 2002. Combinatorial synthesis of genetic networks. Science 296, 1466-1470.
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.
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.
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.
71. J. Hemphill and A. Deiters. 2013. DNA computation in mammalian cells: microRNA logic operations. J Am. Chem. Soc. 135, 10512-10518.
72. W. J. Holtz and J. D. Keasling. 2010. Engineering static and dynamic control of synthetic pathways. Cell 140, 19-23.
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.
74. P. D. Hsu, E. S. Lander, and F. Zhang. 2014. Development and applications of CRISPR-Cas9 for genome engineering. Cell 157, 1262-1278.
75. M. C. Hu and N. Davidson. 1987. The inducible lac operator-repressor system is functional in mammalian cells. Cell 48, 555-566.
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.
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.
78. F. J. Isaacs, W. J. Blake, and J. J. Collins. 2005. Molecular biology. Signal processing in single cells. Science 307, 1886-1888.
79. F. J. Isaacs, D. J. Dwyer, and J. J. Collins. 2006. RNA synthetic biology. Nat. Biotechnol. 24, 545-554.
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.
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.
82. E. M. Judd, M. T. Laub, and H. H. Mcadams. 2000. Toggles and oscillators: New genetic circuit designs. Bioessays 22, 507-509.
83. M. Kaern, W. J. Blake, and J. J. Collins. 2003. The engineering of gene regulatory networks. Ann. Rev. Biomed. Eng. 5, 179-206.
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.
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.
86. M. Karlsson and W. Weber. 2012. Therapeutic synthetic gene networks. Curr. Opin. Biotechnol. 23, 703-711.
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.
88. A. S. Khalil and J. J. Collins. 2010. Synthetic biology: Applications come of age. Nat. Rev. Genet. 11, 367-379.
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.
90. D. H. Kim and J. J. Rossi. 2007. Strategies for silencing human disease using RNA interference. Nat. Rev. Genet. 8, 173-184.
91. H. Kitano. 2002. Computational systems biology. Nature 420, 206-210.
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.
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.
94. M. A. Kohanski and J. J. Collins. 2008. Rewiring bacteria, two components at a time. Cell 133, 947-948.
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.
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.
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.
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.
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.
100. J. Layton. 2005. How robotic vacuums work. In HowStuffWorks.com.
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.
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.
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.
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.
105. M. Lewandoski. 2001. Conditional control of gene expression in the mouse. Nat. Rev. Genet. 2, 743-755.
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.
107. W. A. Lim. 2010. Designing customized cell signalling circuits. Nat. Rev. Mol. Cell Biol. 11, 393-403.
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.
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.
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.
111. T. K. Lu and J. J. Collins. 2007. Dispersing biofilms with engineered enzymatic bacteriophage. Proc. Natl. Acad. Sci. USA 104, 11197-11202.
112. T. K. Lu, A. S. Khalil, and J. J. Collins. 2009. Next-generation synthetic gene networks. Nat. Biotechnol 27, 1139-1150.
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.
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.
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.
116. N. J. Mckenna and B. W. O'Malley. 2002. Combinatorial control of gene expression by nuclear receptors and coregulators. Cell 108, 465-474.
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.
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.
119. J. Minker. 2000. Introduction to Logic-Based Artificial Intelligence. Kluwer Academic Publishers Dordrecht.
120. T. Miyamoto, S. Razavi, R. Derose, and T. Inoue. 2013. Synthesizing biomolecule-based Boolean logic gates. ACS Synthet. Biol. 2, 72-82.
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.
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.
123. S. Mukherji and A. Van Oudenaarden. 2009. Synthetic biology: Understanding biological design from synthetic circuits. Nat. Rev. Genet. 10, 859-871.
124. C. J. Myers. 2010. Engineering Genetic Circuits. CRC Press, Boca Raton, FL.
125. N. Nandagopal and M. B. Elowitz. 2011. Synthetic biology: Integrated gene circuits. Science 333, 1244-1248.
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.
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.
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.
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.
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.
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.
132. S. Payne and L. You. 2013. Engineered cell-cell communication and its applications. Adv. Biochem. Eng. Biotechnol.
133. R. Pfeifer, M. Lungarella, and F. Iida. 2007. Self-organization, embodiment, and biologically inspired robotics. Science 318, 1088-1093.
134. M. Ptashne. 1992. A Genetic Switch: Phage [Lambda] and Higher Organisms 2nd Ed. Cell Press, Blackwell Scientific Publications, Cambridge, MA.
135. O. Purcell and T. K. Lu. 2014. Synthetic analog and digital circuits for cellular computation and memory. Curr. Opin. Biotechnol. 29C, 146-155.
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.
137. O. Rackham and J. W. Chin. 2005. A network of orthogonal ribosome x mRNA pairs. Nat. Chem. Biol. 1, 159-166.
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.
139. R. Reddy 2006. Robotics and intelligent systems in support of society. Intell. Syst. IEEE 21, 24-31.
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.
141. N. Roehner and C. J. Myers. 2014a. Directed acyclic graph-based technology mapping of genetic circuit models. ACS Synthet. Biol. 3, 543-555.
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.
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.
144. N. Roquet and T. K. Lu. 2014. Digital and analog gene circuits for biotechnology. Biotechnol. J. 9, 597-608.
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.
146. W C. Ruder, T. Lu, and J. J. Collins. 2011. Synthetic biology moving into the clinic. Science 333, 1248-1252.
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.
148. J. D. Sander and J. K. Joung. 2014. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat. Biotechnol. 32, 347-355.
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.
150. P. A. Sharp. 2001. RNA interference-2001. Genes Dev. 15, 485-490.
151. A. Singh, T. L. Deans, and J. H. Elisseeff. 2013. Photomodulation of cellular gene expression in hydrogels. Acs Macro. Letter 2, 269-272.
152. P. Siuti, J. Yazbek, and T. K. Lu. 2013. Synthetic circuits integrating logic and memory in living cells. Nat. Biotechnol. 31, 448-452.
153. P. Siuti, J. Yazbek, and T. K. Lu. 2014. Engineering genetic circuits that compute and remember. Nat. Protoc. 9, 1292-1300.
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.
155. D. Sprinzak and M. B. Elowitz. 2005. Reconstruction of genetic circuits. Nature 438, 443-448.
156. N Sternberg and D. Hamilton. 1981. Bacteriophage P1 site-specific recombination. I. Recombination between loxP sites. J. Mol. Biol. 150, 467-486.
157. J. T. Stevens and C. J. Myers. 2013. Dynamic modeling of cellular populations within iBioSim. ACS Synthet. Biol. 2, 223-229.
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.
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.
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.
161. C. A. Voigt. 2006. Genetic parts to program bacteria. Curr. Opin. Biotechnol. 17, 548-557.
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.
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.
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.
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.
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.
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.
168. H. V. Westerhoff and B. O. Palsson. 2004. The evolution of molecular biology into systems biology. Nat. Biotechnol. 22, 1249-1252.
169. N. Wiener. 1948. Cybernetics. Wiley, New York.
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.
171. M. N. Win and C. D. Smolke. 2008. Higher-order cellular information processing with synthetic RNA devices. Science 322, 456-460.
172. P. J. Wittkopp, B. K. Haerum, and A. G. Clark. 2004. Evolutionary changes in cis and trans gene regulation. Nature 430, 85-88.
173. J. B. Xavier. 2011. Social interaction in synthetic and natural microbial communities. Mol. Syst. Biol. 7, 483.
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.
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.
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.
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.
178. H. Youk and W. A. Lim. 2014. Secreting and sensing the same molecule allows cells to achieve versatile social behaviors. Science 343, 1242782.