Evolving genetic networks for synthetic biology

New Generation Computing

Volumn 31, Issue 2, 2013, Pages 71-88

  Noman, Nasimul ^a   Palafox, Leon ^a   Iba, Hitoshi ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

Evolutionary Algorithms; Genetic Network; In Silico Evolution; Synthetic Biology; Systems Biology

Indexed keywords

ARTIFICIAL GENE NETWORKS; BIOLOGICAL NETWORKS; ENGINEERING DISCIPLINES; GENETIC NETWORKS; IN-SILICO; NEAR-OPTIMAL SOLUTIONS; SYNTHETIC BIOLOGY; SYSTEMS BIOLOGY;

ARTIFICIAL INTELLIGENCE; COMPLEX NETWORKS; EVOLUTIONARY ALGORITHMS;

BIOLOGY;

EID: 84880517343     PISSN: 02883635     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00354-013-0201-8     Document Type: Article

References (87)

1. Rawls, R. L.: "Synthetic Biology Makes its Debut," Chem. Eng. News, pp. 49-53 (2000).
2. Hobom, B.; "Gene surgery: on the threshold of synthetic biology," Medizinische Klinik, 75, 24, pp. 834-841, 1980.
3. P. O. of Science and T. (POST), "Synthetic biology," POSTNOTE, 298, pp. 1-4, 2008.
4. Chopra, P. and Kammab, A.; "Engineering life through synthetic biology," In Silico Biology, 6, pp. 401-410, 2006.
5. Anderson, J. C.; Clarke, E. J.; Arkin, A. P. and Voigt, C. A.; "Environmentally controlled invasion of cancer cells by engineered bacteria," Journal of Molecular Biology, 355, 4, pp. 619-627, 2006.
6. Weber, W. and Fussenegger, M.; "Emerging biomedical applications of synthetic biology," Nature Reviews Genetics, 13, pp. 21-35, 2012.
7. Collins, J.; "Synthetic biology: Bits and pieces come to life," Nature, 483, 7387, pp. S8-S10, 2012.
8. Benner, S. A. and Sismour, A. M.; "Synthetic biology," Nature Reviews Genetics, 6, 7, pp. 533-543, 2005.
9. Andrianantoandro, E.; Basu, S.; Karig, D. K. and Weiss, R.; "Synthetic biology: new engineering rules for an emerging discipline," Molecular Systems Biology, 2, 2006.0028, 2006.
10. Karlsson, M. and Weber, W.; "Therapeutic synthetic gene networks," Current Opinion in Biotechnology, 23, 5, pp. 703-711, 2012.
11. Kwok, R.; "Five hard truths for synthetic biology," Nature, 463, pp. 288-290, 2010.
12. Elowitz, M. B. and Leibler, S.; "A synthetic oscillatory network of transcriptional regulators," Nature, 403, 6767, pp. 335-338, 2000.
13. Stricker, J.; Cookson, S.; Bennett, M. R.; Mather, W. H.; Tsimring, L. S. and Hasty, J.; "A fast, robust and tunable synthetic gene oscillator," Nature, 456, 7221, pp. 516-519, 2008.
14. Tigges, M.; Marquez-Lago, T. T.; Stelling, J. and Fussenegger, M.; "A tunable synthetic mammalian oscillator," Nature, 457, 7227, pp. 309-312, 2009.
15. Danino, T.; Mondragòn-Palomino, O.; Tsimring, L. and Hasty, J.; "A synchronized quorum of genetic clocks," Nature, 463, pp. 326-330, 2010.
16. Gardner, T. S.; Cantor, C. R. and Collins, J. J.; "Construction of a genetic toggle switch in escherichia coli," Nature, 403, pp. 339-342, 2000.
17. Deans, T. L.; Cantor, C. R. and Collins, J. J.; "A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells," Cell, 130, 2, pp. 363-372, 2007.
18. Ham, T. S.; Lee, S. K.; Keasling, J. D. and Arkin, A. P.; "Design and construction of a double inversion recombination switch for heritable sequential genetic memory," PLoS ONE, 3, 7, e2815, 2008.
19. Hooshangi, S.; Thiberge, S. and Weiss, R.; "Ultrasensitivity and noise propagation in a synthetic transcriptional cascade," PNAS, 102, 10, pp. 3581-3586, 2005.
20. Sohka, T.; Heins, R. A.; Phelan, R. M.; Greislera, J. M.; Townsend, C. A. and Ostermeier, M.; "An externally tunable bacterial band-pass filter," PNAS, 106, 25, pp. 10135-10140, 2009.
21. Kobayashi, H.; Krn, M.; Araki, M.; Chung, K.; Gardner, T. S.; Cantor, C. R. and Collins, J. J.; "Programmable cells: Interfacing natural and engineered gene networks," PNAS, 101, 22, pp. 8414-8419, 2004.
22. Win, M. N. and Smolke, C. D.; "A modular and extensible rna-based generegulatory platform for engineering cellular function," PNAS, 104, 36, pp. 14283-14288, 2007.
23. Kramer, B. P. and Fussenegger, M.; "Hysteresis in a synthetic mammalian gene network," PNAS, 102, 27, pp. 9517-9522, 2005.
24. You, L.; Cox, R. S.; Weiss, R. and Arnold, F. H.; "Programmed population control by cell-cell communication and regulated killing," Nature, 428, pp. 868-871, 2004.
25. Basu, S.; Gerchman, Y.; Collins, C. H.; Arnold, F. H. and Weiss, R.; "A synthetic multicellular system for programmed pattern formation," Nature, 434, 7037, pp. 1130-1134, 2005.
26. Levskaya, A.; Chevalier, A. A.; Tabor, J. J.; Simpson, Z. B.; Lavery, L. A.; Levy, M.; Davidson, E. A.; Scouras, A.; Ellington, A. D.; Marcotte, E. M. and Voigt, C. A.; "Synthetic biology: engineering escherichia coli to see light," Nature, 438, 7067, pp. 441-442, 2005.
27. Tabor, J. J.; Salis, H. M.; Simpson, Z. B.; Chevalier, A. A.; Levskaya, A.; Marcotte, E. M.; Voigt, C. A. and Ellington, A. D.; "A synthetic genetic edge detection program," Cell, 137, 7, pp. 1272-1281, 2009.
28. Friedland, A. E.; Lu, T. K.; Wang, X.; Shi, D.; Church, G. and Collins, J. J.; "Synthetic gene networks that count," Science, 324, 5931, pp. 1199-1202, 2009.
29. Jakobus, K.; Wend, S. and Weber, W.; "Synthetic mammalian gene networks as a blueprint for the design of interactive biohybrid materials," Chem. Soc. Rev.; 41, pp. 1000-1018, 2012.
30. Nissim, L. and Bar-Ziv, R. H.; "A tunable dual-promoter integrator for targeting of cancer cells," Molecular Systems Biology, 6, p. 4, 2010.
31. Kemmer, C.; Gitzinger, M.; Baba, M. D.-E.; Djonov, V.; Stelling, J. and Fussenegger, M.; "Self-sufficient control of urate homeostasis in mice by a synthetic circuit," Nature Biotechnology, 28, pp. 355-360, 2010.
32. Xie, Z.; Wroblewska, L.; Prochazka, L.; Weiss, R. and Benenson, Y.; "Multi-input rnai-based logic circuit for identification of specific cancer cells," Science, 333, 6047, pp. 1307-1311, 2011.
33. Ye, H.; Baba, M. D.-E.; Peng, R.-W. and Fussenegger, M.; "A synthetic optogenetic transcription device enhances blood-glucose homeostasis in mice," Science, 332, 6037, pp. 1565-1568, 2011.
34. Kemmera, C.; Fluria, D. A.; Witschib, U.; Passeraubb, A.; Gutzwillerc, A. and Fusseneggera, M.; "A designer network coordinating bovine artificial insemination by ovulation-triggered release of implanted sperms," Journal of Controlled Release, 150, 1, pp. 23-29, 2011.
35. Lu, T. K.; Khalil, A. S. and Collins, J. J.; "Next-generation synthetic gene networks," Nature Biotechnology, 27, pp. 1139-1150, 2009.
36. Paladugu, S. R.; Chickarmane, V.; Deckard, A.; Frumkin, J. P.; McCormack, M. and Sauro, H. M.; "In silico evolution of functional modules in biochemical networks," IEEE Proceedings on Systems biology, 153, 4, pp. 223-235, 2006.
37. Alon U.: An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman and Hall/CRC, London (2006)
38. Romero-Campero, F. J.; Jamie, T.; Miguel, C.; Malcolm, B.; Marian, G. and Natalio, K.; "Modular assembly of cell systems biology models using p systems," International Journal of Foundations of Computer Science, 20, pp. 427-442, 2009.
39. Zheng Y.; Sriram G.: "Mathematical modeling: Bridging the gap between concept and realization in synthetic biology,". Journal of Biomedicine and Biotechnology 2010, 541609 (2010)
40. Brandman, O.; J. E. F. Jr.; Li, R. and Meyer, T.; "Interlinked fast and slow positive feedback loops drive reliable cell decisions," Science, 21, pp. 496-498, 2005.
41. Haseltine, E. L. and Arnold, F. H.; "Synthetic gene circuits: Design with directed evolution," Annual Review of Biophysics and Biomolecular Structure, 36, pp. 1-19, 2007.
42. Fung, E.; Wong, W. W.; Suen, J. K.; Bulter, T.; Lee, S.-gu and Liao, J. C.; "A synthetic genemetabolic oscillator," Nature, 435, pp. 118-122, 2005.
43. Montagne, K.; Plasson, R.; Sakai, Y.; Fujii, T. and Rondelez, Y.; "Programming an in vitro dna oscillator using a molecular networking strategy," Molecular systems biology, 7, 1, 2011.
44. Gibson, M. A. and Bruck, J.; "Efficient exact stochastic simulation of chemical systems with many species and many channels," Journal of Physical Chemistry, 104, 9, pp. 1876-1889, 2000.
45. Kampen N. V.: Stochastic Processes in Physics and Chemistry, third ed. Elsevier, Amsterdam (2007)
46. Gillespie, D. T.; "A general method for numerically simulating the stochastic time evolution of coupled chemical reactions," Journal of Computational Physics, 22, 4, pp. 403-434, 1976.
47. Kaznessis Y. N.: "Computational methods in synthetic biology,". Biotechnology Journal 4, 1392-1405 (2009)
48. Salis H.; Kaznessis Y.: "Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions,". Journal of Chemical Physics 112, 054103 (2005)
49. Morelli M.J.; Allen R.J.; Tanase-Nicola S.; Ten Wolde P.R.: "Eliminating fast reactions in stochastic simulations of biochemical networks: A bistable genetic switch,". Journal of Chemical Physics 128, 045105 (2008)
50. Sotiropoulos, V.; Contou-Carrere, M.-N.; Daoutidis, P. and Kaznessis, Y. N.; "Model reduction of multiscale chemical langevin equations: A numerical case study," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 6, 3, pp. 470-482, 2009.
51. Cao, H.; Romero-Campero, F. J.; Heeb, S.; Cámara, M. and Krasnogor, N.; "Evolving cell models for systems and synthetic biology," Systems and synthetic biology, 4, 1, pp. 55-84, 2010.
52. Paun G.: Membrane Computing: An Introduction. Springer, Berlin, Heidelberg (2002)
53. Bernardini, F.; Gheorghe, M.; Krasnogor, N.; Muniyandi, R. C.; Pérez-Jímenez, M. J. and Romero-Campero, F. J.; "On p systems as a modelling tool for biological systems," in Proc. of the 6th international conference on Membrane Computing, pp. 114-133, 2006.
54. Pérez-Jímenez, M. and Romero-Campero, F. J.; "P systems, a new computational modelling tool for systems biology," Transactions on Computational Systems Biology VI, pp. 176-197, 2006.
55. Romero-Campero, F. J. and Pérez-Jímenez, M. J.; "Modelling gene expression control using p systems: The lac operon, a case study," BioSystems, 91, 3, pp. 438-457, 2008.
56. Romero-Campero, F. J. and Pérez-Jímenez M. J.; "A model of the quorum sensing system in vibrio fischeri using p systems," Artificial Life, 14, 1, pp. 95-109, 2008.
57. Fisher, J. and Henzinger, T. A.; "Executable cell biology," Nature Biotechnology, 25, pp. 1239-1249, 2007.
58. Shea, M. A. and Ackers, G. K.; "The OR control system of bacteriophage lambda: A physical-chemical model for gene regulation," Journal of molecular biology, 181, 2, pp. 211-230, 1985.
59. Arkin, A.; Ross, J. and McAdams, H. H.; "Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected escherichia coli cells," Genetics, 149, 4, pp. 1633-1648, 1998.
60. Holland, J. H.; Adaptation in natural and artificial systems: an introductory analysis with applications to biology, control and artificial intelligence, 1st ed.; The University of Michigan Press, 1975.
61. Bäck, T.; Fogel, D. B. and Michalewicz, Z.; Handbook of evolutionary computation, IOP Publishing Ltd.; 1997.
62. Iba, H. and Noman, N.; New Frontier in Evolutionary Algorithms: Theory and Applications, London: Imperial College Press, 2011.
63. Clarke, F. H.; Optimization and nonsmooth analysis, Society for Industrial Mathematics, 5, 1987.
64. Storn, R. Differential Evolution - A Simple and Efficient Heuristic for Global Optimization over Continuous Spaces Journal of Global Optimization, Pp. 341-359, 1997.
65. Trelea, I. C. The particle swarm optimization algorithm: Convergence analysis and parameter selection Information Processing Letters, 85, 6, Pp. 317-325, 2003. [Online]. Available: http://www.sciencedirect.com/science/ article/pii/S0020019002004477
66. Noman, N. and Iba, H.; "Inferring gene regulatory networks using differential evolution with local search heuristics," IEEE/ACM Transaction on Computational Biology and Bioinformatics, 4, 4, pp. 634-647, 2007.
67. Pal, S. K.; Bandyopadhyay, S. and Ray, S. S.; "Evolutionary computation in bioinformatics: a review," IEEE Transactions on Systems, Man and Cybernetics, Part C (Applications and Reviews), 36, 5, pp. 601-615, Sep. 2006. [Online]. Available: http://ieeexplore.ieee.org/xpl/articleDetails.jsp? arnumber=1678036
68. Haupt, R. L. and Haupt, S. E.; Practical genetic algorithms, Wiley-Interscience, 2004.
69. Kitagawa, J. and Iba, H. Identifying metabolic pathways and gene regulation networks with evolutionary algorithms Evolutionary Computation in Bioinformatics, San Francisco: Morgan Kaufmann, Pp. 255-278, 2003.
70. Kuepfer, L.; Peter, M.; Sauer, U. and Stelling, J.; "Ensemble modeling for analysis of cell signaling dynamics," Nature biotechnology, 25, 9, pp. 1001-1006, 2007.
71. Kimura, S.; Ide, K.; Kashihara, A.; Kano, M.; Hatakeyama, M.; Masui, R.; Nakagawa, N.; Yokoyama, S.; Kuramitsu, S. and Konagaya, A.; "Inference of S-system models of genetic networks using cooperative coevolutionary algorithm," Bioinformatics, 21, 7, pp. 1154-1163, 2005.
72. Iba, H.; Sakamoto, E.; "Inferring a system of differential equations for a gene regulatory network by using genetic programming," in Congress on Evolutionary Computation, (CEC2001), 2001, pp. 720-726.
73. Ando, S. and Iba, H.; "Construction of genetic network using evolutionary algorithm and combined fitness function," in Genome Informatics, 14, 2, pp. 94-103, 2003.
74. Kimura, S.; Nakayama, S. and Hatakeyama, M.; "Genetic network inference as a series of discrimination tasks," Bioinformatics, 25, 7, pp. 918-925, 2005.
75. Xu, R.; Wunsch, D. C. II. and Frank, R. L.; "Inference of genetic regulatory networks with recurrent neural network models using particle swarm optimization," IEEE/ACM Transaction on Computational Biology and Bioinformatics, 4, 4, pp. 681-692, 2007.
76. Kabir, M.; Noman, N. and Iba, H.; "Reverse engineering gene regulatory network from microarray data using linear time-variant model," BMC Bioinformatics, 11 (Suppl 1), p. S56, 2010.
77. Ressom, H. W.; Zhang, Y.; Xuan, J.; Wang, Y. J. and Clarke, R.; "Inference of gene regulatory networks from time course gene expression data using neural networks and swarm intelligence," in IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology (CIBCB), pp. 435-442, 2006.
78. Spieth, C.; Streichert, F.; Speer, N. and Zell, A.; "Optimizing topology and parameters of gene regulatory network models from time-series experiments," in Proc. of the Genetic and Evolutionary Computation Conference, pp. 461-470, 2004.
79. Kikuchi, S.; Tominaga, D.; Arita, M.; Takahashi, K. and Tomita, M.; "Dynamic modeling of genetic networks using genetic algorithm and S-system," Bioinformatics, 19, 5, pp. 643-650, 2003.
80. Purcell, O.; Savery, N. J.; Grierson, C. S. and Bernardo, M. D.; "A comparative analysis of synthetic genetic oscillators," Journal of The Royal Society Interface, 7, 52, pp. 1503-1524, 2010.
81. Neri, F.; Cotta, C. and Moscato, P.; Eds.; Handbook of Memetic Algorithms, ser. Studies in Computational Intelligence, 379, Berlin Heidelberg: Springer 2012.
82. Kiga, D. and Yamamura, M. Synthetic biology New Generation Computing, 26, 4, pp. 347-364, 2008.
83. Ma, W.; Trusina, A.; El-Samad, H.; Lim, W. A. and Tang, C.; "Defining network topologies that can achieve biochemical adaptation," Cell, 138, 4, pp. 760-773, 2009.
84. Aldana, M.; Balleza, E.; Kauffman, S. and Resendiz, O.; "Robustness and evolvability in genetic regulatory networks." Journal of theoretical biology, 245, 3, p. 433, 2007.
85. François, P. and Hakim,V.; "Design of genetic networks with specified functions by evolution in silico," Proc. of the National Academy of Sciences of the United States of America, 101, 2, Pp. 580-585, 2004.
86. Drennan, B. and Beer, R. D.; "Evolution of repressilators using a biologically-motivated model of gene expression," in Artificial Life X: Proc. Tenth Intl. Conf. on the Simulation and Synthesis of Living Systems, Citeseer, pp. 22-27, 2006.
87. Komiya, K.; Noman, N. and Iba, H.; "The search for robust topologies of oscillatory gene regulatory networks by evolutionary computation," in Proc. of the fourteenth international conference on Genetic and evolutionary computation conference (GECCO 2012), ACM, pp. 1419-1420, 2012.