Robust synthetic gene network design via library-based search method

Bioinformatics

Volumn 27, Issue 19, 2011, Pages 2700-2706

  Wu, Chih Hung ^a   Lee, Hsiao Ching ^b   Chen, Bor Sen ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^b Department of Biological Science and Technology ^*  (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

SYNTHETIC DNA;

ARTICLE; BIOLOGICAL MODEL; GENE EXPRESSION REGULATION; GENE LIBRARY; GENE REGULATORY NETWORK; GENETICS; PROMOTER REGION; SYNTHETIC BIOLOGY;

GENE EXPRESSION REGULATION; GENE LIBRARY; GENE REGULATORY NETWORKS; GENES, SYNTHETIC; MODELS, GENETIC; PROMOTER REGIONS, GENETIC; SYNTHETIC BIOLOGY;

EID: 80052526091     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr465     Document Type: Article

References (44)

1. Alon,U. (2007) An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman & Hall/CRC, London.
2. Arkin,A. et al. (1998) Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected Escherichia coli cells. Genetics, 149, 1633-1648.
3. Atkinson,M.R. et al. (2003) Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell, 113, 597-607.
4. Basu,S. et al. (2005)Asynthetic multicellular system for programmed pattern formation. Nature, 434, 1130-1134.
5. Basu,S. et al. (2004) Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl Acad. Sci. USA, 101, 6355-6360.
6. Braun,D. et al. (2005) Parameter estimation for two synthetic gene networks: a case study. IEEE Int. Conf. Acoustics Speech Signal Process., 5, 769-772.
7. Canton,B. et al. (2008) Refinement and standardization of synthetic biological parts and devices. Nat. Biotechnol., 26, 787-794.
8. Chatterjee,R. and Yuan,L. (2006) Directed evolution of metabolic pathways. Trends Biotechnol., 24, 28-38.
9. Chen,B.S. and Chen,P.W. (2010) GA-based Design Algorithms for the Robust Synthetic Genetic Oscillators with Prescribed Amplitude, Period and Phase. Gene Regul. Syst. Biol, 4, 35-52.
10. Chen,B.S. andWu,C.H. (2009)Asystematic design method for robust synthetic biology to satisfy design specifications. BMC Syst. Biol., 3, 66.
11. Chen,B.S. andWu,C.H. (2010) Robust Optimal Reference-Tracking DesignMethod for Stochastic Synthetic Biology Systems: T-S Fuzzy Approach. IEEE T Fuzzy Syst., 18, 1144-1159.
12. Ellis,T. et al. (2009) Diversity-based, model-guided construction of synthetic gene networks with predicted functions. Nat. Biotechnol., 27, 465-471.
13. Elowitz,M.B. and Leibler,S. (2000) A synthetic oscillatory network of transcriptional regulators. Nature, 403, 335-338.
14. Friedland,A.E. et al. (2009) Synthetic gene networks that count. Science, 324, 1199-1202.
15. Gardner,T.S. et al. (2000) Construction of a genetic toggle switch in Escherichia coli. Nature, 403, 339-342.
16. Goh,K.I. et al. (2008) Sustained oscillations in extended genetic oscillatory systems. Biophys. J., 94, 4270-4276.
17. Goldberg,D. (1989) Genetic Algorithms in Search, Optimization, and Machine Learning. 1989. Addision Wesley, MA, USA.
18. Grefenstette,J.J. (1986) Optimization of control parameters for genetic algorithms. IEEE Trans. Syst. Man Cybernet., 16, 122-128.
19. Guet,C.C. et al. (2002) Combinatorial synthesis of genetic networks. Science, 296, 1466-1470.
20. Holland,J.H. (1992) Adaptation in Natural and Artificial Systems: an Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence. Bradford Book, Cambridge.
21. Hooshangi,S. et al. (2005) Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc. Natl Acad. Sci. USA, 102, 3581-3586.
22. Iadevaia,S. and Mantzaris,N.V. (2006) Genetic network driven control of PHBV copolymer composition. J. Biotechnol., 122, 99-121.
23. Katayama,K. and Narihisa,H. (2000) An efficient hybrid genetic algorithm for the traveling salesman problem. Electron. Commun. Jpn, 84, 76-83.
24. Kelly,J.R. et al. (2009) Measuring the activity of BioBrick promoters using an in vivo reference standard. J. Biol. Eng., 3, 4.
25. Kobayashi,T. et al. (2003) Modeling genetic switches with positive feedback loops. J. Theor. Biol., 221, 379-399.
26. Kobayashi,H. et al. (2004) Programmable cells: interfacing natural and engineered gene networks. Proc. Natl Acad. Sci. USA, 101, 8414-8419.
27. Kramer,B.P. et al. (2004) An engineered epigenetic transgene switch in mammalian cells. Nat. Biotechnol., 22, 867-870.
28. Leveau,J.H. and Lindow,S.E. (2001) Predictive and interpretive simulation of green fluorescent protein expression in reporter bacteria. J. Bacteriol., 183, 6752-6762.
29. Lu,T.K. et al. (2009) Next-generation synthetic gene networks. Nat. Biotechnol., 27, 1139-1150.
30. Murphy,K.F. et al. (2007) Combinatorial promoter design for engineering noisy gene expression. Proc. Natl Acad. Sci. USA, 104, 12726-12731.
31. Nakanishi,H. et al. (2008) Dynamical analysis on gene activity in the presence of repressors and an interfering promoter. Biophys. J., 95, 4228-4240.
32. Pai,A. et al. (2009) Engineering multicellular systems by cell-cell communication. Curr. Opin. Biotechnol., 20, 461-470.
33. Renders,J.M. and Flasse,S.P. (1996) Hybrid methods using genetic algorithms for global optimization. IEEE Trans. Syst. Man Cybernet., 26, 243-258.
34. Rinaudo,K. et al. (2007) A universal RNAi-based logic evaluator that operates in mammalian cells. Nat. Biotechnol., 25, 795-801.
35. Semsey,S. et al. (2009) Dominant negative autoregulation limits steady-state repression levels in gene networks. J. Bacteriol., 191, 4487-4491.
36. Sohka,T. et al. (2009a) Morphogen-defined patterning of Escherichia coli enabled by an externally tunable band-pass filter. J. Biol. Eng., 3, 10.
37. Sohka,T. et al. (2009b)An externally tunable bacterial band-pass filter. Proc. Natl Acad. Sci. USA, 106, 10135-10140.
38. Stricker,J. et al. (2008)Afast, robust and tunable synthetic gene oscillator. Nature, 456, 516-519.
39. Tigges,M. et al. (2009)Atunable synthetic mammalian oscillator. Nature, 457, 309-312.
40. Tuttle,L.M. et al. (2005) Model-Driven Designs of an Oscillating Gene Network. Biophy. J., 89, 3873-3883.
41. Win,M.N. and Smolke,C.D. (2007) A modular and extensible RNA-based generegulatory platform for engineering cellular function. Proc. Natl Acad. Sci. USA, 104, 14283-14288.
42. Win,M.N. and Smolke,C.D. (2008) Higher-order cellular information processing with synthetic RNA devices. Science, 322, 456-460.
43. Wu,C.H. et al. (2011) Multiobjective H2/H∞ synthetic gene network design based on promoter libraries. Math. Biosci. [Epub ahead of print, doi.org/10.1016/j.mbs.2011.07.001].
44. Yokobayashi,Y. et al. (2002) Directed evolution of a genetic circuit. Proc. Natl Acad. Sci. USA, 99, 16587-16591.