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Articles

A synthetic biology approach for the design of genetic algorithms with bacterial agents

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Pages 275-292 | Received 17 Dec 2020, Accepted 18 Jan 2021, Published online: 28 Jan 2021

References

  • Hatwágner MF, Horváth A. Maintaining genetic diversity in bacterial evolutionary algorithm. Annales Univ. Sci. Budapest., Sect. Comp. 2012;37:175–194.
  • Harvey I. The microbial genetic algorithm,” in 10th European Conference, ECAL 2009, Advances in Artificial Life. Darwin Meets von Neumann, Lecture Notes in Computer Science, Part II. LNCS 5778, Berlin. Springer Verlag, G. Kampis, I. Karsai, and E. Szathmáry, Eds., Budapest, Hungary, 2011, pp. 126–133.
  • Anandaraman C, Madurai Sankar AV, Natarajan R. A new evolutionary algorithm based on bacterial evolution and its application for scheduling a flexible manufacturing system. Jurnal Teknik Industri. 2012;14:1–12.
  • Perales-Gravan C, Lahoz-Beltra R. An AM radio receiver designed with a genetic algorithm based on a bacterial conjugation genetic operator. IEEE Trans Evol Comput. 2008;12:129–142.
  • Mehrafsa A, Sokhandan A, Karimian G. A high performance genetic algorithm using bacterial conjugation operator (HPGA). Genet. Program. Evolvable Mach. 2013;14:395–427.
  • Singh PK, Mondal SK, Maiti M. A hybridized chemotactic genetic algorithm for optimization. J Comp Sci Sys Biol. 2016;9:45–50.
  • Passino KM. Biomimicry of bacterial foraging for distributed optimization and control. IEEE Control Syst Mag. 2002;22:52–67.
  • Botzheim J, Cabrita C, Kóczy LT, et al. Fuzzy rule extraction by bacterial memetic algorithms. Int J Intell Syst. 2009;24:312–339.
  • Cameron E, Bashor CJ, Collins JJ. A brief history of synthetic biology. Nat Rev Microbiol. 2014;12:381–390.
  • MacDonald IC, Deans TL. Tools and applications in synthetic biology. Adv Drug Del Rev. 2016;105:20–34.
  • Xie M, Fussenegger M. Designing cell function: assembly of synthetic gene circuits for cell biology applications. Nat. Rev. Mol. Cell. Biol. 2018;19:507–525. doi:10.1038/s41580-018-0024-z.
  • Lahoz-Beltra R, Navarro J, Marijuan PC. Bacterial computing: a form of natural computing and its applications. Front Microbiol. 2014;5:101, DOI: 10.3389/fmicb.2014.00101,.
  • Jang SS, Oishi KT, Egbert RG, et al. Specification and simulation of synthetic multicelled behaviors. ACS Synth Biol. 2012;1:365–374.
  • Oishi K, Klavins E. A framework for implementing finite state machines in gene regulatory networks. ACS Synth Biol. 2014;3:652–665.
  • Gutiérrez M, Gregorio-Godoy P, Pérez Del Pulgar G, et al. A new improved and extended version of the multicell bacterial simulator gro. ACS Synth Biol. 2017;6:1496–1508.
  • Gorochowski TE. Agent-based modelling in synthetic biology. Essays Biochem. 2016;60:325–336.
  • Matyjaszkiewicz A, Fiore G, Annunziata F, et al. BSim 2.0: An advanced agent-based cell simulator. ACS Synth Biol. 2017;6:1969–1972.
  • Allen RJ, Waclaw B. Bacterial growth: a statistical physicist’s guide. Rep Prog Phys. 2019;82:016601; doi:10.1088/1361-6633/aae546.
  • Norris V, Zemirline A, Amar P, et al. Computing with bacterial constituents, cells and populations: from bioputing to bactoputing. Theory Biosci 2011;130:211–228.
  • Dekel E, Alon U. Optimality and evolutionary tuning of the expression level of a protein. Nature. 2005;436:588–592.
  • Hariharan P, Balasubramaniam D, Peterkofsky A, et al. Thermodynamic mechanism for inhibition of lactose permease by the phosphotransferase protein IIAGlc. PNAS. 2015;112:2407–2412.
  • Baumgardner J, Acker K, Adefuye O, et al. Solving a Hamiltonian path problem with a bacterial computer. J Biol Eng. 2009;3:1–11.
  • Poet JL, Campbell AM, Eckdahl TT, et al. Bacterial computing. XRDS. 2010;17:10–15.
  • Kari L, Kitto R, Gloor G. A computer scientist’s guide to molecular biology. Soft comput. 2001;5:95–101.
  • Hunter L. Molecular biology for computer scientists. In: L Hunter, editor. Artificial Intelligence and molecular biology. Menlo Park, CA: AAAI Press/MIT Press; 1993. p. 1–46.
  • Lahoz-Beltra R, Gargantilla Becerra A. “A genetic algorithm designed with bacterial agents (BAGA)”. figshare. Software. https://doi.org/10.6084/m9.figshare.13396544.v1, 2020.
  • Villa TG, Feijoo-Siota L, Sánchez-Pérez A, et al. Horizontal gene transfer in bacteria, an overview of the mechanisms involved. In: T Villa, M Viñas, editor. Horizontal gene transfer. Cham: Springer; 2019. p. 3–76.
  • Gresham D, Hong J. The functional basis of adaptive evolution in chemostats. FEMS Microbiol Rev. 2015;39:2–16.
  • Dykhuizen DE. Experimental studies of natural selection in bacteria. Annu Rev Ecol Syst 1990;21:373–398.
  • Santos-Moreno J, Schaerli Y. Using synthetic biology to engineer spatial patterns. Advanced Biosystems. 2019;3(4). 1800280.
  • Umesh P, Naveen F, Maheswara Rao CU, et al. Programming language for synthetic biology. Syst Synth Biol 2010;4:265–269.
  • Condon A, Kirchner H, Larivière D, et al. Will biologists become computer scientists? EMBO Rep. 2018;19:e46628:1–6.
  • Schwille P, Sundmacher K. “Synthetic Biology: Life, Remixed,” Available: https://www.mpg.de/8219292/synthetic_biology, Accessed on: Mar. 6, 2020.
  • Peisajovich SG. Evolutionary synthetic biology. ACS Synth Biol. 2012;1:199–210.
  • Nielsen AAK, Der BS, Shin J, et al. Genetic circuit design automation. Science. 2016;352(6281), aac7341, doi:10.1126/science.aac7341.
  • Dragosits M, Mattanovich D. Adaptive laboratory evolution – principles and applications for biotechnology. Microb. Cell. Fact. 2013;12:64), doi:10.1186/1475-2859-12-64.
  • Wakabayashi K, Yamamura M. A design for cellular evolutionary computation by using bacteria. Nat Comput. 2005;4:275–292.

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