Synthesis of programmable biological central processing system

References

• Anderson, J. C., C. A. Voigt, and A. P. Arkin. 2007. “Environmental Signal Integration by a Modular AND Gate.” Molecular Systems Biology 3 (1): 133-138-8. doi:10.1038/msb4100173.
   PubMedGoogle Scholar
• Babu, M. M., and S. A. Teichmann. 2003. “Evolution of Transcription Factors and the Gene Regulatory Network in Escherichia Coli.” Nucleic Acids Research 31 (4): 1234–1244. doi:10.1093/nar/gkg210.
   PubMed Web of Science ®Google Scholar
• Bintu, L., N. E. Buchler, H. G. Garcia, U. Gerland, T. Hwa, J. Kondev, and R. Phillips. 2005. “Transcriptional Regulation by the Numbers: Models.” Current Opinion in Genetics & Development 15 (2): 116–124. doi:10.1016/j.gde.2005.02.007.
   PubMed Web of Science ®Google Scholar
• Bonnet, J., P. Yin, M. E. Ortiz, P. Subsoontorn, and D. Endy. 2013. “Amplifying Genetic Logic Gates.” Science 340 (6132): 599–603. doi:10.1126/science.1232758.
   PubMed Web of Science ®Google Scholar
• Buchler, N. E., U. Gerland, and T. Hwa. 2003. “On Schemes of Combinatorial Transcription Logic.” Proceedings of the National Academy of Sciences of the United States of America 100 (9): 5136–5141. doi:10.1073/pnas.0930314100.
   PubMed Web of Science ®Google Scholar
• Chiu, T. Y., and J. H. R. Jiang. 2017. “Logic Synthesis of Recombinase-Based Genetic Circuits.” Scientific Reports 7: 12873-1-12873-13: doi:10.1038/s41598-017-07386-3.
   Web of Science ®Google Scholar
• Chuang, C. H., and C. L. Lin. 2014a. “Synthesizing Genetic Sequential Logic Circuit with Clock Pulse Generator.” BMC Systems Biology 8: 1–15. doi:10.1186/1752-0509-8-63.
   PubMed Web of Science ®Google Scholar
• Chuang, C. H., and C. L. Lin. 2014b. “A Novel Synthesizing Genetic Logic Circuit: Frequency Multiplier.” IEEE/ACM Transactions on Computational Biology and Bioinformatics 11 (4): 702–713. doi:10.1109/TCBB.2014.2316814.
   PubMed Web of Science ®Google Scholar
• Chuang, C. H., C. L. Lin, Y. C. Chang, T. Jennawasin, and P. K. Chen. 2013. “Design of Synthetic Biological Logic Circuits Based on Evolutionary Algorithm.” IET Systems Biology 7 (4): 89–105. doi:10.1049/iet-syb.2012.0048.
   PubMed Web of Science ®Google Scholar
• Dasika, M. S., and C. D. Maranas. 2008. “OptCircuit: An Optimization Based Method for Computational Design of Genetic Circuits.” BMC Systems Biology 2: 1–19. doi:10.1186/1752-0509-2-24.
   PubMed Web of Science ®Google Scholar
• Davis, P. K., A. Ho, and S. F. Dowdy. 2001. “Biological Methods for Cell-Cycle Synchronization of Mammalian Cells.” Biotechniques 30 (6): 1322–1331. doi:10.2144/01306rv01.
   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. doi:10.1038/35002125.
   PubMed Web of Science ®Google Scholar
• Fernandez-Rodriguez, J., F. Moser, M. Song, and C. A. Voigt. 2017. “Engineering RGB Color Vision into Escherichia Coli.” Nature Chemical Biology 13 (7): 706–708. doi:10.1038/nchembio.2390.
   PubMed Web of Science ®Google Scholar
• Freeman, M. 2017. “Simple CPU.” Simple CPU Design. Accessed 14 October. http://www.simplecpudesign.com/simple_cpu_v1/index.html
   Google Scholar
• Gardner, T. S., C. R. Cantor, and J. J. Collins. 2000. “Construction of a Genetic Toggle Switch in Escherichia Coli.” Nature 403 (6767): 339–342. doi:10.1038/35002131.
   PubMed Web of Science ®Google Scholar
• Halámek, J., V. Bocharova, M. A. Arugula, G. Strack, V. Privman, and E. Katz. 2011. “Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Enzyme Inhibition by a Substrate.” The Journal of Physical Chemistry. B 115 (32): 9838–9845. doi:10.1021/jp2041372.
   PubMed Web of Science ®Google Scholar
• Hasty, J., D. McMillen, and J. J. Collins. 2002. “Engineered Gene Circuits.” Nature 420: 224–230. doi:10.1038/nature01257.
   PubMed Web of Science ®Google Scholar
• Hu, Y. J., C. L. Lin, and W. X. Li. 2017. “Design of Dynamic Genetic Memory.” IET Systems Biology 11 (6): 182–189. doi:10.1049/iet-syb.2017.0021.
   PubMed Web of Science ®Google Scholar
• Kaplan, S., A. Bren, E. Dekel, and U. Alon. 2008. “The Incoherent Feed‐Forward Loop Can Generate Non‐Monotonic Input Functions for Genes.” Molecular Systems Biology 4: 203–211. doi:10.1038/msb.2008.43.
   PubMed Web of Science ®Google Scholar
• Kuo, T. Y., C. L. Lin, N. Charoenkit, Y. Y. Chen, and C. Preuksakarn. 2017. “Toward Theoretical Synthesis of Biocomputer.” IET Systems Biology 11 (1): 36–43. doi:10.1049/iet-syb.2016.0015.
   PubMed Web of Science ®Google Scholar
• Lamaniya, A., and B. Patel. 2014. “Design of Full Adder and Full Subtractor Using DNA Computing.” International Journal of Latest Trends in Engineering and Technology 3 (3): 12–16.
   Google Scholar
• Lauria, M., K. Bhalerao, M. M. Pugalanthiran, and B. Yuan. 2004. “Building Blocks of a Biochemical CPU Based on DNA Transcription Logic.” In 3rd Workshop on Non-Silicon Computation (NSC-3), Munich, German, 19–23 June 2004: 6. University Park, PA: CiteSeerX.
   Google Scholar
• Li, J., H. W. Habbes, J. Eiberger, K. Willecke, R. Dermietzel, and C. Meier. 2007. “Analysis of Connexin Expression during Mouse Schwann Cell Development Identifies Connexin29 as a Novel Marker for the Transition of Neural Crest to Precursor Cells.” Glia 55 (1): 93–103. doi:10.1002/glia.20427.
   PubMed Web of Science ®Google Scholar
• Liebler, D. C. 2001. Introduction to Proteomics: Tools for the New Biology. Totowa, New Jersey: Humana Press.
   Google Scholar
• Lin, C. L., and P. K. Chen. 2014. “Synthesising Periodic Triggering Signals with Genetic Oscillators.” IET Systems Biology 8 (1): 1–12. doi:10.1049/iet-syb.2013.0022.
   PubMed Web of Science ®Google Scholar
• Lin, C. L., P. K. Chen, and Y. Y. Cheng. 2014. “Synthesising Gene Clock with Toggle Switch and Oscillator.” IET Systems Biology 9 (3): 88–94. doi:10.1049/iet-syb.2014.0022.
   Web of Science ®Google Scholar
• Lin, C. L., T. Y. Kuo, and Y. Y. Chen. 2015. “Implementation of a Genetic Logic Circuit: Bio-register.” Systems and Synthetic Biology 9 (S1): 43–48. doi:10.1007/s11693-015-9186-6.
   PubMedGoogle Scholar
• Marchisio, M. A., and J. Stelling. 2011. “Automatic Design of Digital Synthetic Gene Circuits.” PLoS Computational Biology 7 (2): 1–13. doi:10.1371/journal.pcbi.1001083.
   Web of Science ®Google Scholar
• Privman, V. 2011. “Error-Control and Digitalization Concepts for Chemical and Biomolecular Information Processing Systems.” Journal of Computational and Theoretical Nanoscience 8 (3): 490–502. doi:10.1166/jctn.2011.1714.
   Google Scholar
• Privman, V., J. Zhou, J. Halámek, and E. Katz. 2010. “Realization and Properties of Biochemical-Computing Biocatalytic XOR Gate Based on Signal Change.” The Journal of Physical Chemistry B 114 (42): 13601–13608. doi:10.1021/jp107562p.
   PubMed Web of Science ®Google Scholar
• Shen-Orr, S. S., R. Milo, S. Mangan, and U. Alon. 2002. “Network Motifs in the Transcriptional Regulation Network of Escherichia Coli.” Nature Genetics 31 (1): 64–68. doi:10.1038/ng881.
   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: 212–215. doi:10.1038/nature09565.
   PubMed Web of Science ®Google Scholar
• Tu, C. T., and B. S. Chen. 2013. “On the Increase in Network Robustness and Decrease in Network Response Ability During the Aging Process: A Systems Biology Approach via Microarray Data.” IEEE/ACM Transactions on Computational Biology and Bioinformatics 10 (2): 468–480. doi:10.1109/TCBB.2013.23.
   PubMed Web of Science ®Google Scholar
• Wang, B., R. I. Kitney, N. Joly, and M. Buck. 2011. “Engineering Modular and Orthogonal Genetic Logic Gates for Robust Digital-Like Synthetic Biology.” Nature Communications 2: 1–9. doi:10.1038/ncomms1516.
   Web of Science ®Google Scholar
• Weinberg, B. H., N. T. H. Pham, L. D. Caraballo, T. Lozanoski, A. Engel, S. Bhatia, and W. W. Wong. 2017. “Large-Scale Design of Robust Genetic Circuits with Multiple Inputs and Outputs for Mammalian Cells.” Nature Biotechnology 35 (5): 453–462. doi:10.1038/nbt.3805.
   PubMed Web of Science ®Google Scholar
• Weiss, R., and S. Basu. 2002. “The Device Physics of Cellular Logic Gates.” In The First Workshop of Non-Silicon Computation (NSC-1), Cambridge, MA, 3 February 2002: 54–61. University Park, PA: CiteSeerX.
   Google Scholar