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Volumn 2013, Issue 9, 2013, Pages 43-68

A unifying mathematical framework for genetic robustness, environmental robustness, network robustness and their trade-off on phenotype robustness in biological networks part I: Gene regulatory networks in systems and evolutionary biology

Author keywords

Evolutionary biology; Evolvability; Network robustness; Network sensitivity; Phenotype robustness; Systems biology

Indexed keywords

ARTICLE; COMPUTER SIMULATION; EVOLUTIONARY ADAPTATION; GENE REGULATORY NETWORK; GENE SEQUENCE; GENETIC VARIABILITY; GENOTYPE ENVIRONMENT INTERACTION; LINEAR SYSTEM; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; MONTE CARLO METHOD; NONLINEAR SYSTEM; PHENOTYPE; SYSTEM ANALYSIS; SYSTEMS BIOLOGY;

EID: 84874513506     PISSN: 11769343     EISSN: None     Source Type: Journal    
DOI: 10.4137/EBO.S10080     Document Type: Article
Times cited : (12)

References (43)
  • 1
    • 84947634865 scopus 로고
    • A nonlinear H control design in robotic systems under parameter perturbation and external disturbance
    • Chen BS, Lee TS, Feng TH. A nonlinear H control design in robotic systems under parameter perturbation and external disturbance. Int J Control. 1994;59(2):439-461.
    • (1994) Int J Control , vol.59 , Issue.2 , pp. 439-461
    • Chen, B.S.1    Lee, T.S.2    Feng, T.H.3
  • 2
    • 0033205006 scopus 로고    scopus 로고
    • Robustness design of nonlinear dynamic systems via fuzzy linear control
    • Chen BS, Tseng CS, Uang HJ. Robustness design of nonlinear dynamic systems via fuzzy linear control. IEEE Trans Fuzzy Systems. 1999;7(5):571-585.
    • (1999) IEEE Trans Fuzzy Systems , vol.7 , Issue.5 , pp. 571-585
    • Chen, B.S.1    Tseng, C.S.2    Uang, H.J.3
  • 3
    • 0742269301 scopus 로고    scopus 로고
    • Stochastic H2/H∞ control with state-dependent noise
    • Chen BS, Zhang W. Stochastic H2/H∞ control with state-dependent noise. IEEE Trans Automatic Control. 2004;49(1):45-57.
    • (2004) IEEE Trans Automatic Control , vol.49 , Issue.1 , pp. 45-57
    • Chen, B.S.1    Zhang, W.2
  • 4
    • 33645831442 scopus 로고    scopus 로고
    • State feedback H∞ control for a class of nonlinear stochastic systems
    • Zhang W, Chen BS. State feedback H∞ control for a class of nonlinear stochastic systems. SIAM J on Control and Optimization. 2006;44:1973-1991.
    • (2006) SIAM J On Control and Optimization , vol.44 , pp. 1973-1991
    • Zhang, W.1    Chen, B.S.2
  • 5
    • 13244258477 scopus 로고    scopus 로고
    • Robust H∞ fltering for nonlinear stochastic systems
    • Zhang W, Chen BS, Tseng CS. Robust H∞ fltering for nonlinear stochastic systems. IEEE Trans. Signal Processing. 2005;53(2):589-598.
    • (2005) IEEE Trans Signal Processing , vol.53 , Issue.2 , pp. 589-598
    • Zhang, W.1    Chen, B.S.2    Tseng, C.S.3
  • 6
    • 0037863109 scopus 로고    scopus 로고
    • Robust H∞ and mixed H2/H∞ flters for equalization designs of nonlinear communication systems: Fuzzy interpolation approach
    • Chen BS, Tsai CL, Chen DS. Robust H∞ and mixed H2/H∞ flters for equalization designs of nonlinear communication systems: fuzzy interpolation approach. IEEE Trans Fuzzy Systems. 2003;11(3):384-398.
    • (2003) IEEE Trans Fuzzy Systems , vol.11 , Issue.3 , pp. 384-398
    • Chen, B.S.1    Tsai, C.L.2    Chen, D.S.3
  • 7
    • 39649116670 scopus 로고    scopus 로고
    • Robust H∞ stabilization design in gene networks under stochastic molecular noises: Fuzzy-interpolation approach
    • Chen BS, Chang YT, Wang YC. Robust H∞ stabilization design in gene networks under stochastic molecular noises: Fuzzy-interpolation approach. IEEE Trans Syst, Man, and Cyber. 2008;38(1):25-42.
    • (2008) IEEE Trans Syst, Man, and Cyber , vol.38 , Issue.1 , pp. 25-42
    • Chen, B.S.1    Chang, Y.T.2    Wang, Y.C.3
  • 8
    • 38349082134 scopus 로고    scopus 로고
    • Robust fltering circuit design for stochastic gene networks under intrinsic and extrinsic molecular noises
    • Chen BS, Wu WS. Robust fltering circuit design for stochastic gene networks under intrinsic and extrinsic molecular noises. Math Biosci. 2008;211(2):342-355.
    • (2008) Math Biosci , vol.211 , Issue.2 , pp. 342-355
    • Chen, B.S.1    Wu, W.S.2
  • 9
    • 0034667684 scopus 로고    scopus 로고
    • Plasticity, evolvability, and modularity in RNA
    • Ancel LW, Fontana W. Plasticity, evolvability, and modularity in RNA. J Exp Zool. 2000;288(3):242-283.
    • (2000) J Exp Zool , vol.288 , Issue.3 , pp. 242-283
    • Ancel, L.W.1    Fontana, W.2
  • 10
    • 34548511143 scopus 로고    scopus 로고
    • New structural variation in evolutionary searches of RNA neutral networks
    • Martin OC, Wagner A. New structural variation in evolutionary searches of RNA neutral networks. Biosystems. 2007;90(2):475-485.
    • (2007) Biosystems , vol.90 , Issue.2 , pp. 475-485
    • Martin, O.C.1    Wagner, A.2
  • 11
    • 0036436325 scopus 로고    scopus 로고
    • Best choices for regularization parameters in learning theory: On the bias-variance problem
    • Cucker F, Smale S. Best choices for regularization parameters in learning theory: on the bias-variance problem. Foundations of Computational Mathematics. 2002;2(4):413-428.
    • (2002) Foundations of Computational Mathematics , vol.2 , Issue.4 , pp. 413-428
    • Cucker, F.1    Smale, S.2
  • 13
    • 2442537233 scopus 로고    scopus 로고
    • Gene regulatory network growth by duplication
    • Teichmann SA, Babu MM. Gene regulatory network growth by duplication. Nat Genet. 2004;36(5):492-496.
    • (2004) Nat Genet , vol.36 , Issue.5 , pp. 492-496
    • Teichmann, S.A.1    Babu, M.M.2
  • 14
    • 83455194714 scopus 로고    scopus 로고
    • On the interplay between the evolvability and network robustness in an evolutionary biological network: A systems biology approach
    • Epub Nov 1, 2011
    • Chen BS, Lin YP. On the interplay between the evolvability and network robustness in an evolutionary biological network: a systems biology approach. Evol Bioinform Online. 2011;7:201-233. Epub Nov 1, 2011.
    • (2011) Evol Bioinform Online , vol.7 , pp. 201-233
    • Chen, B.S.1    Lin, Y.P.2
  • 15
    • 0035823775 scopus 로고    scopus 로고
    • Complexity and fragility in ecological networks
    • Sole RV, Montoya M. Complexity and fragility in ecological networks. Proc Biol Sci. 2001;268(1480):2039-2045.
    • (2001) Proc Biol Sci , vol.268 , Issue.1480 , pp. 2039-2045
    • Sole, R.V.1    Montoya, M.2
  • 16
    • 0030030533 scopus 로고    scopus 로고
    • Smoothness within ruggedness: The role of neutrality in adaptation
    • Huynen MA, Stadler PF, Fontana W. Smoothness within ruggedness: The role of neutrality in adaptation. Proc Nat Acad Sci U S A. 1996;93(1):397.
    • (1996) Proc Nat Acad Sci U S A , vol.93 , Issue.1 , pp. 397
    • Huynen, M.A.1    Stadler, P.F.2    Fontana, W.3
  • 17
    • 0038668776 scopus 로고    scopus 로고
    • The evolutionary origin of complex
    • Lenski RE, Ofria C, Pennock RT, Adami C. The evolutionary origin of complex. Nature. 2003;423(6936):139-144.
    • (2003) Nature , vol.423 , Issue.6936 , pp. 139-144
    • Lenski, R.E.1    Ofria, C.2    Pennock, R.T.3    Adami, C.4
  • 18
    • 33645299807 scopus 로고    scopus 로고
    • On the attenuation and amplifcation of molecular noise in genetic regulatory networks
    • Chen BS, Wang YC. On the attenuation and amplifcation of molecular noise in genetic regulatory networks. BMC Bioinformatics. 2006;7(52): 1-14.
    • (2006) BMC Bioinformatics , vol.7 , Issue.52 , pp. 1-14
    • Chen, B.S.1    Wang, Y.C.2
  • 20
    • 36348946191 scopus 로고    scopus 로고
    • On the robust circuit design schemes of biochemical networks: Steady-state approach
    • Chen BS, Wu WS, Wang YC, H LW. On the robust circuit design schemes of biochemical networks: steady-state approach. IEEE Trans Biomed Circuits and Systems. 2007;1(2):91-104.
    • (2007) IEEE Trans Biomed Circuits and Systems , vol.1 , Issue.2 , pp. 91-104
    • Chen, B.S.1    Wu, W.S.2    Wang, Y.C.3    Lw, H.4
  • 21
    • 0030002954 scopus 로고    scopus 로고
    • Rules for coupled expression of regulator and effector genes in inducible circuits
    • Hlavacek WS, Savageau MA. Rules for coupled expression of regulator and effector genes in inducible circuits. J Mol Biol. 1996;255(1):121-139.
    • (1996) J Mol Biol , vol.255 , Issue.1 , pp. 121-139
    • Hlavacek, W.S.1    Savageau, M.A.2
  • 23
    • 0035487293 scopus 로고    scopus 로고
    • Recombineering: A powerful new tool for mouse functional genomics
    • Copeland NG, Jenkins NA, Court D. Recombineering: a powerful new tool for mouse functional genomics. Nat Rev Genet. 2001;2(10):769-779.
    • (2001) Nat Rev Genet , vol.2 , Issue.10 , pp. 769-779
    • Copeland, N.G.1    Jenkins, N.A.2    Court, D.3
  • 24
    • 0036953835 scopus 로고    scopus 로고
    • Genetic engineering using homologous recombination
    • Sawitzke J, Thomason L. Genetic engineering using homologous recombination. Annu Rev Genet. 2002;36:361-388.
    • (2002) Annu Rev Genet , vol.36 , pp. 361-388
    • Sawitzke, J.1    Thomason, L.2
  • 25
    • 52249111600 scopus 로고    scopus 로고
    • Robust engineered circuit design principles for stochastic biochemical networks with parameter uncertainties and disturbances
    • Chen BS, Chen PW. Robust engineered circuit design principles for stochastic biochemical networks with parameter uncertainties and disturbances. IEEE Trans Biomedical Circuits and Systems. 2008;2(2):114-132.
    • (2008) IEEE Trans Biomedical Circuits and Systems , vol.2 , Issue.2 , pp. 114-132
    • Chen, B.S.1    Chen, P.W.2
  • 27
    • 0035690920 scopus 로고    scopus 로고
    • H∞ decentralized fuzzy model reference tracking control design for nonlinear interconnected systems
    • Tseng CS, Chen BS. H∞ decentralized fuzzy model reference tracking control design for nonlinear interconnected systems. IEEE Trans Fuzzy Systems. 2001;9(6):795-809.
    • (2001) IEEE Trans Fuzzy Systems , vol.9 , Issue.6 , pp. 795-809
    • Tseng, C.S.1    Chen, B.S.2
  • 28
    • 0035360942 scopus 로고    scopus 로고
    • Fuzzy tracking control design for nonlinear dynamic systems via TS fuzzy model
    • Tseng CS, Chen BS, Uang HJ. Fuzzy tracking control design for nonlinear dynamic systems via TS fuzzy model. IEEE Trans Fuzzy Systems. 2001;9(3):381-392.
    • (2001) IEEE Trans Fuzzy Systems , vol.9 , Issue.3 , pp. 381-392
    • Tseng, C.S.1    Chen, B.S.2    Uang, H.J.3
  • 30
    • 10744228524 scopus 로고    scopus 로고
    • Perspective: Evolution and detection of genetic robustness
    • Visser J, Hermisson J, Wagner GP, et al. Perspective: evolution and detection of genetic robustness. Evolution. 2003;57(9):1959-1972.
    • (2003) Evolution , vol.57 , Issue.9 , pp. 1959-1972
    • Visser, J.1    Hermisson, J.2    Wagner, G.P.3
  • 32
    • 7644238181 scopus 로고    scopus 로고
    • Biological robustness
    • Kitano H. Biological robustness. Nat Rev Genet. 2004;5(11):826-837.
    • (2004) Nat Rev Genet , vol.5 , Issue.11 , pp. 826-837
    • Kitano, H.1
  • 33
    • 15244340261 scopus 로고    scopus 로고
    • Priming nonlinear searches for pathway identifcation
    • Vefingstad S, Almeida J, Voit E. Priming nonlinear searches for pathway identifcation. Theor Biol Med Model. 2004;1(1):8.
    • (2004) Theor Biol Med Model , vol.1 , Issue.1 , pp. 8
    • Vefingstad, S.1    Almeida, J.2    Voit, E.3
  • 34
    • 0037461033 scopus 로고    scopus 로고
    • Dynamic modeling of genetic networks using genetic algorithm and S-system
    • Kikuchi S, Tominaga D, Arita M, Takahashi K, Tomita M. Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics. 2003;19(5):643-650.
    • (2003) Bioinformatics , vol.19 , Issue.5 , pp. 643-650
    • Kikuchi, S.1    Tominaga, D.2    Arita, M.3    Takahashi, K.4    Tomita, M.5
  • 35
    • 51149203927 scopus 로고
    • Canalization of development and the inheritance of acquired characters
    • Waddington CH. Canalization of development and the inheritance of acquired characters. Nature. 1942;150(3811):563-565.
    • (1942) Nature , vol.150 , Issue.3811 , pp. 563-565
    • Waddington, C.H.1
  • 36
    • 77949386270 scopus 로고    scopus 로고
    • Genes confer similar robustness to environmental, stochastic, and genetic perturbations in yeast
    • Lehner B. Genes confer similar robustness to environmental, stochastic, and genetic perturbations in yeast. PLoS One. 2010;5(2):e9035.
    • (2010) PLoS One , vol.5 , Issue.2
    • Lehner, B.1
  • 38
    • 77953528177 scopus 로고    scopus 로고
    • On the interplay between entropy and robustness of gene regulatory networks
    • Chen BS, Li CW. On the interplay between entropy and robustness of gene regulatory networks. Entropy. 2010;12(5):1071-1101.
    • (2010) Entropy , vol.12 , Issue.5 , pp. 1071-1101
    • Chen, B.S.1    Li, C.W.2
  • 39
    • 10944272639 scopus 로고    scopus 로고
    • Aging, tumor suppression and cancer: High wire-act!
    • Campisi J. Aging, tumor suppression and cancer: high wire-act! Mech Ageing Dev. 2005;126(1):51-58.
    • (2005) Mech Ageing Dev , vol.126 , Issue.1 , pp. 51-58
    • Campisi, J.1
  • 40
    • 0029394561 scopus 로고
    • A genetic approach to mixed H2/H∞ optimal PID control
    • Chen BS, Cheng YM, Lee CH. A genetic approach to mixed H2/H∞ optimal PID control. IEEE Control Systems Magazine. 1995;15(5):51-60.
    • (1995) IEEE Control Systems Magazine , vol.15 , Issue.5 , pp. 51-60
    • Chen, B.S.1    Cheng, Y.M.2    Lee, C.H.3
  • 41
    • 0032204112 scopus 로고    scopus 로고
    • A structure-specifed H∞ optimal control design for practical applications: A genetic approach
    • Chen BS, Cheng YM. A structure-specifed H∞ optimal control design for practical applications: a genetic approach. IEEE Trans Control Systems Technology. 1998;6(6):707-718.
    • (1998) IEEE Trans Control Systems Technology , vol.6 , Issue.6 , pp. 707-718
    • Chen, B.S.1    Cheng, Y.M.2
  • 42
    • 84862908629 scopus 로고    scopus 로고
    • Robust design of biological circuits: Evolutionary systems biology approach
    • Chen BS, Hsu CY, Liou JJ. Robust design of biological circuits: evolutionary systems biology approach. J Biomed Biotech. 2011;2011.
    • (2011) J Biomed Biotech , pp. 2011
    • Chen, B.S.1    Hsu, C.Y.2    Liou, J.J.3
  • 43
    • 70450224938 scopus 로고    scopus 로고
    • Underlying principles of natural selection in network evolution: Systems biology approach
    • Chen BS, Wu WS. Underlying principles of natural selection in network evolution: systems biology approach. Evol Bioinform Online. 2007;3:245.
    • (2007) Evol Bioinform Online , vol.3 , pp. 245
    • Chen, B.S.1    Wu, W.S.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.