On the interplay between the evolvability and network robustness in an evolutionary biological network: A systems biology approach

Evolutionary Bioinformatics

Volumn 2011, Issue 7, 2011, Pages 201-223

  Chen, Bor Sen ^a   Lin, Ying Po ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

Author keywords

Antagonistic pleiotropy of gene network; Bias variance dilemma; Biochemical network; Evolutionary adaptability; Evolvability; Gene network; Natural selection; Network robustness; Robustness; Sensitivity; Stability; Stochastic system

Indexed keywords

ARTICLE; BIOCHEMISTRY; ENVIRONMENTAL FACTOR; GENE REGULATORY NETWORK; GENETIC STABILITY; MOLECULAR BIOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NETWORK ROBUSTNESS; NONLINEAR SYSTEM; PHENOTYPE; PLEIOTROPY; SENSITIVITY ANALYSIS; STATISTICS; SYSTEMS BIOLOGY;

EID: 83455194714     PISSN: None     EISSN: 11769343     Source Type: Journal    
DOI: 10.4137/EBO.S8123     Document Type: Article

References (90)

1. Hartwell LH, Hopfield JJ, Leibler S, Murray AW. From molecular to modular cell biology. Nature. 1999;402(6761):47-52.
2. Eisenberg D, Marcotte EM, Xenarios I, Yeates TO. Protein function in the post-genomic era. Nature. 2000;405(6788):823-6.
3. von Dassow G, Meir E, Munro EM, Odell GM. The segment polarity network is a robust developmental module. Nature. 2000;406(6792):188-92.
4. Klipp E. Systems Biology in Practice: Concepts, Implementation and Application: Wiley-Vch; 2005.
5. Kitano H. Biological robustness. Nature Reviews Genetics. 2004;5(11): 826-37.
6. Chen BS, Wang YC, Wu WS, Li WH. A new measure of the robustness of biochemical networks. Bioinformatics. 2005;21(11):2698-705.
7. Freeman S, Herron JC, Payton M. Evolutionary Analysis 3rd ed.: Pearson/ Prentice Hall Upper Saddle River, NJ. USA; 2004.
8. Chen BS, Wu WS. Underlying principles of natural selection in network evolution: systems biology approach. Evolutionary Bioinformatics Online. 2007;3:245-62.
9. Tawfik DS. Messy biology and the origins of evolutionary innovations. Nature Chemical Biology. 2010;6(10):692-6.
10. Lenski RE, Barrick JE, Ofria C. Balancing robustness and evolvability. PLoS Biol. 2006;4(12):2190-2.
11. Waddington CH. Canalization of development and the inheritance of acquired characters. Nature. 1942;150(3811):563.
12. Gibson G, Wagner G. Canalization in evolutionary genetics: a stabilizing theory? BioEssays. 2000;22(4):372-80.
13. Draghi JA, Parsons TL, Wagner GP, Plotkin JB. Mutational robustness can facilitate adaptation. Nature. 2010;463(7279):353-5.
14. Wagner A. Robustness and evolvability: a paradox resolved. Proceedings of the Royal Society B: Biological Sciences. 2008;275(1630):91.
15. Szollsi GJ, Derenyi I. Congruent evolution of genetic and environmental robustness in micro-RNA. Molecular Biology and Evolution. 2009;26(4):867
16. Hillenmeyer ME, Fung E, Wildenhain J, et al. The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science. 2008;320(5874):362.
17. Dudley AM, Janse DM, Tanay A, Shamir R, Church GMD. A global view of pleiotropy and phenotypically derived gene function in yeast. Molecular Systems Biology. 2005;1:1.
18. Pan X, Ye P, Yuan DS, Wang X, Bader JS, Boeke JD. A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell. 2006;124(5):1069-81.
19. Tong AHY, Lesage G, Bader GD, et al. Global mapping of the yeast genetic interaction network. Science. 2004;303(5659):808.
20. Levy SF, Siegal ML. Network hubs buffer environmental variation in Saccharomyces cerevisiae. PLoS Biology. 2008;6(11):e264.
21. Ohya Y, Sese J, Yukawa M, et al. High-dimensional and large-scale phenotyping of yeast mutants. Proceedings of the National Academy of Sciences of the United States of America. 2005;102(52):19015.
22. Lehner B. Genes confer similar robustness to environmental, stochastic, and genetic perturbations in yeast. PloS One. 2010;5(2):e9035.
23. Franklin GF, Powell JD, Emami-Naeini A. Feedback Control of Dynamic Systems. New York: Addison-Wesley; 1994.
24. Doyle JC, Francis BA, Tannenbaum A. Feedback Control Theory. New York: Maxwell Macmillan International; 1992.
25. Freeman S, Herron J, Payton M. Evolutionary Analysis: Prentice Hall Upper Saddle River, NJ; 1998.
26. Conant GC, Wagner A. Convergent evolution of gene circuits. Nat Genet. 2003;34(3):264-6.
27. Dekel E, Alon U. Optimality and evolutionary tuning of the expression level of a protein. Nature. 2005;436(7050):588-92.
28. Doolittle RF. Evolutionary aspects of whole-genome biology. Curr Opin Struct Biol. 2005;15(3):248-53.
29. Chen BS, Wang YC. On the attenuation and amplification of molecular noise in genetic regulatory networks. BMC Bioinformatics. 2006;7(1):52.
30. Krawitz P, Shmulevich I. Entropy of complex relevant components of Boolean networks. Phys Rev E. 2007;76(3):36115.
31. Lezon TR, Banavar JR, Cieplak M, Maritan A, Fedoroff NV. Using the principle of entropy maximization to infer genetic interaction networks from gene expression patterns. Proc Natl Acad Sci. 2006;103(50): 19033-8.
32. Stoll G, Rougemont J, Naef F. Representing perturbed dynamics in biological network models. Phys Rev E. 2007;76(1):11917.
33. Zhang WH, Chen BS, Tseng CS. Robust H filtering for nonlinear stochastic systems. IEEE Trans. Signal Processing. 2005;53(2):589-98.
34. Boyd S, El Ghaoui L, Feron E, Balakrishnan V. Linear Matrix Inequalities in System and Control Theory: Society for Industrial Mathematics; 1994.
35. Visser J, Hermisson J, Wagner GP, et al. Perspective: evolution and detection of genetic robustness. Evolution. 2003;57(9):1959-72.
36. Voit EO. Computational Analysis of Biochemical Systems: A Practical Guide for Biochemists and Molecular Biologists. Cambridge: Cambridge University Press; 2000.
37. Voit EO. Design principles and operating principles: the yin and yang of optimal functioning. Math Biosci. 2003;182(1):81-92.
38. Campisi J. Aging, tumor suppression and cancer: high wire-act! Mechanisms of Ageing and Development. 2005;126(1):51-58.
39. Zhang WH, Chen BS. State Feedback H2/H∞ Control for a Class of Nonlinear Stochastic Systems. SIAM J on Control and Optimization. 2006;44:1973-91.
40. Chen BS, Chen WH, Wu HL. Robust H2/H∞ global linearization filter design for nonlinear stochastic systems. IEEE Trans. Circuits and Systems I. 2009;56(7):1441-54.
41. Hood L. Systems biology: integrating technology, biology, and computation. Mech Ageing Dev. 2003;124(1):9-16.
42. Chen BS, Chang YT, Wang YC. Robust H∞ stabilization design in gene networks under stochastic molecular noises: fuzzy-interpolation approach. IEEE Trans Syst Man Cybern B. Cybernetic. 2008;38(1):25-42.
43. Chen BS, Chang YT. A systematic molecular circuit design method for gene networks under biochemical time delays and molecular noises. BMC Systems Biology. 2008;2(1):103.
44. Chen BS, Chen PW. Robust engineered circuit design principles for stochastic biochemical networks with parameter uncertainties and disturbances. IEEE Trans Biomed Circ Syst. 2008;2(2):114-32.
45. Chen BS, Chen PW. On the estimation of robustness and filtering ability of dynamic biochemical networks under process delays, internal parametric perturbations and external disturbances. Mathematical Biosciences. 2009;222(2):92-108.
46. Chen BS, Chang CH, Lee HC. Robust synthetic biology design: stochastic game theory approach. Bioinformatics. 2009;25(14):1822-30.
47. Chen BS, Wu CH. A systematic design method for robust synthetic biology to satisfy design specifications. BMC Systems Biology. 2009;3(1):66.
48. Li CW, Chen BS. Stochastic Spatio-Temporal Dynamic Model for Gene/ Protein Interaction Network in Early Drosophila Development. Gene Regul Syst Biol. 2009;3:191.
49. Chen BS, Wu WS, Li WH. On the adaptive design rules of biochemical networks in evolution. Evol Bioinform. 2007;3:27-39.
50. Badyaev AV. Stress-induced variation in evolution: from behavioural plasticity to genetic assimilation. Proc Biol Sci. 2005;272(1566):877-86.
51. Cucker F, Smale S. Best Choices for Regularization Parameters in Learning Theory: On the Bias-Variance Problem. Foundations of Computational Mathematics. 2008;2(4):413-28.
52. Denic S, Vasic B, Charalambous C, Palanivelu R. Robust control of uncertain context-sensitive probabilistic Boolean networks. Systems Biology, IET. 2009;3(4):279-95.
53. Tsai KY, Wang FS. Evolutionary optimization with data collocation for reverse engineering of biological networks. Bioinformatics. 2005;21(7):1180-8.
54. Liu PK, Wang FS. Inference of biochemical network models in S-system using multiobjective optimization approach. Bioinformatics. 2008;24(8):1085-92.
55. Freeman S, Herron J, Payton M. Evolutionary Analysis. 2nd ed. New Jersey: Prentice Hall; 2001.
56. Chen BS, Li CW. On the Interplay between Entropy and Robustness of Gene Regulatory Networks. Entropy. 2010;12(5):1071-101.
57. Madan Babu M, Teichmann SA. Evolution of transcription factors and the gene regulatory network in Escherichia coli. Nucleic Acids Research. 2003;31(4):1234.
58. Babu MM, Aravind L. Adaptive evolution by optimizing expression levels in different environments. Trends Microbiol. 2006;14(1):11-4.
59. Madan Babu M, Teichmann SA, Aravind L. Evolutionary dynamics of prokaryotic transcriptional regulatory networks. Journal of Molecular Biology. 2006;358(2):614-33.
60. Kobayashi H, Karn M, Araki M, et al. Programmable cells: interfacing natural and engineered gene networks. Proceedings of the National Academy of Sciences of the United States of America. 2004;101(22):8414-9.
61. Li WH, Olmstead R. Molecular evolution: Sinauer Associates Sunderland, MA; 1997.
62. Kitano H. Biological robustness in complex host-pathogen systems. Progress in drug research. Fortschritte der Arzneimittelforschung. Progres des recherches pharmaceutiques. 2007;64:239, 241.
63. Barkai N, Shilo BZ. Variability and robustness in biomolecular systems. Molecular Cell. 2007;28(5):755-60.
64. Felix MA, Wagner A. Robustness and evolution: concepts, insights and challenges from a developmental model system. Heredity. 2006;100(2):132-40.
65. Graur D, Li WH. Fundamentals of Molecular Evolution. Massachusetts: Sinauer Associates Inc.; 2000.
66. McAdams HH, Arkin A. It's a noisy business! Genetic regulation at the nanomolar scale. Trend Genet. 1999;15(2):65-9.
67. Ideker T, Galitski T, Hood L. A New Approach to Decoding Life. Annu Rev Genomics Hum Genet. 2001;2:343-72.
68. Hasty J, McMillen D, Collins JJ. Engineered gene circuits. Nature. 2002;420(6912):224-30.
69. Chen BS, Wu WS. Robust filtering circuit design for stochastic gene networks under intrinsic and extrinsic molecular noises. Math Biosci. 2008;211(2):342-55.
70. Batt G, Yordanov B, Weiss R, Belta C. Robustness analysis and tuning of synthetic gene networks. Bioinformatics. 2007;23(18):2415-22.
71. Setty Y, Mayo AE, Surette MG, Alon U. Detailed map of a cis-regulatory input function. Proceedings of the National Academy of Sciences of the United States of America. 2003;100(13):7702-7.
72. Basu S, Gerchman Y, Collins CH, Arnold FH, Weiss R. A synthetic multicellular system for programmed pattern formation. Nature. 2005;434(7037):1130-4.
73. Hasty J, Dolnik M, Rottschafer V, Collins JJ. Synthetic gene network for entraining and amplifying cellular oscillations. Physical Review Letters. 2002;88(14):148101.
74. Nagarajan R, Aubin JE, Peterson CA. Robust dependencies and structures in stem cell differentiation. INT J Bifurcation Chao. 2005;15(4):1503-14.
75. Edwards JS, Palsson BO. Robustness analysis of the escherichiacoli metabolic network. Biotech Progr. 2000;16(6):927-39.
76. Lenz P, Swain PS. An entropic mechanism to generate highly cooperative and specific binding from protein phosphorylations. Curr Biol. 2006;16(21):2150-5.
77. Denic SZ, Vasic B, Charalambous CD, Palanivelu R. Robust control of uncertain context-sensitive probabilistic Boolean networks. IET Syst Biol. 2009;3(4):279-95.
78. Lapidus S, Han B, Wang J. Intrinsic noise, dissipation cost, and robustness of cellular networks: The underlying energy landscape of MAPK signal transduction. Proc Natl Acad Sci. 2008;105(16):6039-44.
79. Gelfand MS. Evolution of transcriptional regulatory networks in microbial genomes. Curr Opini Struct Biol. 2006;16(3):420-9.
80. Freeman M. Feedback control of intercellular signalling in development. Nature. 2000;408(6810):313-9.
81. Kitano H. Systems biology: a brief overview. Science. 2002;295(5560): 1662-4.
82. Karn M, Elston TC, Blake WJ, Collins JJ. Stochasticity in gene expression: from theories to phenotypes. Nat Rev Genet. 2005;6(6):451-64.
83. Basu S, Mehreja R, Thiberge S, Chen MT, Weiss R. Spatiotemporal control of gene expression with pulse-generating networks. Proceedings of the National Academy of Sciences of the United States of America. 2004;101(17):6355-60.
84. Isaacs FJ, Hasty J, Cantor CR, Collins JJ. Prediction and measurement of an autoregulatory genetic module. Proceedings of the National Academy of Sciences of the United States of America. 2003;100(13):7714-9.
85. Kaern M, Blake WJ, Collins JJ. The engineering of gene regulatory networks. Annual Review of Biomedical Engineering. 2003;5(1):179-206.
86. Chen BS, Hsu CY, Liou JJ. Robust design of biological circuits: Evolutionary System Biology approach. Journal of Biomedicine and Biotechnology (in press). 2011.
87. Chen BS, Wu CH. Robust Optimal Reference-Tracking Design Method for Stochastic Synthetic Biology Systems: T-S Fuzzy Approach. Fuzzy Systems, IEEE Transactions on. 2010;18(6):1144-59.
88. Wu CH, Lee HC, Chen BS. Robust synthetic gene network design via library-based search method. Bioinformatics (in press). 2011.
89. Chen BS, Chen PW. GA-based design algorithms for the robust synthetic genetic oscillators with prescribed amplitude, period and phase. Gene Regulation and Systems Biology. 2010;4:35-52.
90. Bickel PJ, Li B, Tsybakov AB, et al. Regularization in statistics. Test. 2006;15(2):271-344.