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Volumn 1, Issue 8, 2012, Pages 375-384

A data-Driven framework for identifying nonlinear dynamic models of genetic parts

Author keywords

Biochemical models; Dynamic; Genetic parts; NARMAX; Nonlinear system identification

Indexed keywords

ACCURACY; ARTICLE; CELL POPULATION; CHEMICAL MODEL; CONCEPTUAL FRAMEWORK; ENZYME MECHANISM; GENETIC VARIABILITY; MOLECULAR DYNAMICS; NONLINEAR DYNAMIC MODELING; PRIORITY JOURNAL; SIMULATION; STATISTICAL MODEL;

EID: 84868230984     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb300009t     Document Type: Article
Times cited : (16)

References (60)
  • 1
    • 66249088017 scopus 로고    scopus 로고
    • The second wave of synthetic biology: From modules to systems
    • Purnick, P. E. M., and Weiss, R. (2009) The second wave of synthetic biology: From modules to systems. Nat. Rev. Mol. Cell Biol. 10, 410-422.
    • (2009) Nat. Rev. Mol. Cell Biol. , vol.10 , pp. 410-422
    • Purnick, M.P.E.1    Weiss, R.2
  • 3
    • 0016074488 scopus 로고
    • In vivo and in vitro initiation of transcription
    • Szybalski, W. (1974) In vivo and in vitro initiation of transcription. Adv. Exp. Med. Biol. 44, 23-24.
    • (1974) Adv. Exp. Med. Biol. , vol.44 , pp. 23-24
    • Szybalski, W.1
  • 4
    • 0018032871 scopus 로고
    • Nobel prizes and restriction enzymes
    • Szybalski, W., and Skalka, A. (1978) Nobel prizes and restriction enzymes. Gene 4, 181-182.
    • (1978) Gene , vol.4 , pp. 181-182
    • Szybalski, W.1    Skalka, A.2
  • 5
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • DOI 10.1038/35002125
    • Elowitz, M. B., and Leibler, S. (2000) A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338. (Pubitemid 30062393)
    • (2000) Nature , vol.403 , Issue.6767 , pp. 335-338
    • Elowitz, M.B.1    Leibier, S.2
  • 6
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • DOI 10.1038/35002131
    • Gardner, T. S., Cantor, C. R., and Collins, J. J. (2000) Construction of a genetic toggle switch in Escherichia coli. Nature 403, 339-342. (Pubitemid 30062394)
    • (2000) Nature , vol.403 , Issue.6767 , pp. 339-342
    • Gardner, T.S.1    Cantor, C.R.2    Collins, J.J.3
  • 9
    • 33847378479 scopus 로고    scopus 로고
    • Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids
    • DOI 10.1016/j.ymben.2006.10.005, PII S1096717606001042
    • Shiba, Y., Paradise, E. M., Kirby, J., Ro, D. K., and Keasling, J. D. (2007) Engineering of the pyruvate dehydrogenase bypass in Saccharomyces cerevisiae for high-level production of isoprenoids. Metab. Eng. 9, 160-168. (Pubitemid 46331877)
    • (2007) Metabolic Engineering , vol.9 , Issue.2 , pp. 160-168
    • Shiba, Y.1    Paradise, E.M.2    Kirby, J.3    Ro, D.-K.4    Keasling, J.D.5
  • 12
    • 77951107086 scopus 로고    scopus 로고
    • Synthetic biology: Applications come of age
    • Khalil, A. S., and Collins, J. J. (2010) Synthetic biology: Applications come of age. Nat. Rev. Genet. 11, 367-379.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 367-379
    • Khalil, A.S.1    Collins, J.J.2
  • 13
    • 63849290890 scopus 로고    scopus 로고
    • Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy
    • Lu, T. K.; Collins, J. J. Engineered bacteriophage targeting gene networks as adjuvants for antibiotic therapy. Proc. Natl. Acad. Sci. U.S.A.2009,
    • (2009) Proc. Natl. Acad. Sci. U.S.A.
    • Lu, T.K.1    Collins, J.J.2
  • 15
    • 0142027136 scopus 로고    scopus 로고
    • Development of a set of simple bacterial biosensors for quantitative and rapid measurements of arsenite and arsenate in potable water
    • DOI 10.1021/es034258b
    • Stocker, J., Balluch, D., Gsell, M., Harms, H., Feliciano, J., Daunert, S., Malik, K. A., and van der Meer, J. R. (2003) Development of a set of simple bacterial biosensors for quantitative and rapid measurements of arsenite and arsenate in potable Water. Environ. Sci. Technol. 37, 4743-4750. (Pubitemid 37266395)
    • (2003) Environmental Science and Technology , vol.37 , Issue.20 , pp. 4743-4750
    • Stocker, J.1    Balluch, D.2    Gsell, M.3    Harms, H.4    Feliciano, J.5    Daunert, S.6    Malik, K.A.7    Van Der Meer, J.R.8
  • 16
    • 77953622209 scopus 로고    scopus 로고
    • Where microbiology meets microengineering: Design and applications of reporter bacteria
    • van der Meer, J. R., and Belkin, S. (2010) Where microbiology meets microengineering: Design and applications of reporter bacteria. Nat. Rev. Microbiol. 8, 511-522.
    • (2010) Nat. Rev. Microbiol. , vol.8 , pp. 511-522
    • Van Der Meer, J.R.1    Belkin, S.2
  • 17
    • 70349281876 scopus 로고    scopus 로고
    • Engineering for biofuels: Exploiting innate microbial capacity or importing biosynthetic potential?
    • Alper, H., and Stephanopoulos, G. (2009) Engineering for biofuels: Exploiting innate microbial capacity or importing biosynthetic potential? Nat. Rev. Microbiol. 7, 715-723.
    • (2009) Nat. Rev. Microbiol. , vol.7 , pp. 715-723
    • Alper, H.1    Stephanopoulos, G.2
  • 18
    • 38049001166 scopus 로고    scopus 로고
    • Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
    • Atsumi, S., Hanai, T., and Liao, J. C. (2008) Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 451, 86-89.
    • (2008) Nature , vol.451 , pp. 86-89
    • Atsumi, S.1    Hanai, T.2    Liao, J.C.3
  • 19
    • 40449119329 scopus 로고    scopus 로고
    • Metabolic engineering delivers next-generation biofuels
    • DOI 10.1038/nbt0308-298, PII NBT0308298
    • Keasling, J. D., and Chou, H. (2008) Metabolic engineering delivers next-generation biofuels. Nat. Biotechnol. 26, 298-299. (Pubitemid 351355120)
    • (2008) Nature Biotechnology , vol.26 , Issue.3 , pp. 298-299
    • Keasling, J.D.1    Chou, H.2
  • 20
    • 75149167486 scopus 로고    scopus 로고
    • Five hard truths for synthetic biology
    • Kwok, R. (2010) Five hard truths for synthetic biology. Nature 463, 288-290.
    • (2010) Nature , vol.463 , pp. 288-290
    • Kwok, R.1
  • 21
    • 46949110597 scopus 로고    scopus 로고
    • Setting the standard in synthetic biology
    • Arkin, A. (2008) Setting the standard in synthetic biology. Nat. Biotechnol. 26, 771-773.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 771-773
    • Arkin, A.1
  • 22
    • 28544451327 scopus 로고    scopus 로고
    • Foundations for engineering biology
    • DOI 10.1038/nature04342, PII N04342
    • Endy, D. (2005) Foundations for engineering biology. Nature 438, 449-453. (Pubitemid 41742010)
    • (2005) Nature , vol.438 , Issue.7067 , pp. 449-453
    • Endy, D.1
  • 24
    • 46949091517 scopus 로고    scopus 로고
    • Refinement and standardization of synthetic biological parts and devices
    • DOI 10.1038/nbt1413, PII NBT1413
    • Canton, B., Labno, A., and Endy, D. (2008) Refinement and standardization of synthetic biological parts and devices. Nat. Biotechnol. 26, 787-793. (Pubitemid 351961452)
    • (2008) Nature Biotechnology , vol.26 , Issue.7 , pp. 787-793
    • Canton, B.1    Labno, A.2    Endy, D.3
  • 27
    • 58149354385 scopus 로고    scopus 로고
    • Analysis of combinatorial cis-regulation in synthetic and genomic promoters
    • Gertz, J., Siggia, E. D., and Cohen, B. A. (2008) Analysis of combinatorial cis-regulation in synthetic and genomic promoters. Nature 457, 215-218.
    • (2008) Nature , vol.457 , pp. 215-218
    • Gertz, J.1    Siggia, E.D.2    Cohen, B.A.3
  • 28
    • 33846116559 scopus 로고    scopus 로고
    • Construction of an in vitro bistable circuit from synthetic transcriptional switches
    • Kim, J.; White, K. S.; Winfree, E. Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol. Syst. Biol. 2006, 2.
    • (2006) Mol. Syst. Biol. , vol.2
    • Kim, J.1    White, K.S.2    Winfree, E.3
  • 29
    • 0034105896 scopus 로고    scopus 로고
    • In vitro-in vivo scaling of CYP kinetic data not consistent with the classical Michaelis-Menten model
    • Houston, J. B., and Kenworthy, K. E. (2000) In vitro-in vivo scaling of CYP kinetic data not consistent with the classical Michaelis-Menten model. Drug Metab. Dispos. 28, 246.
    • (2000) Drug Metab. Dispos. , vol.28 , pp. 246
    • Houston, J.B.1    Kenworthy, K.E.2
  • 30
    • 0020286666 scopus 로고
    • On the practical identifiability of microbial growth models incorporating Michaelis-Menten type nonlinearities
    • DOI 10.1016/0025-5564(82)90061-X
    • Holmberg, A. (1982) On the practical identifiability of microbial growth models incorporating Michaelis-Menten type nonlinearities. Math. Biosci. 62, 23-43. (Pubitemid 13136364)
    • (1982) Mathematical Biosciences , vol.62 , Issue.1 , pp. 23-43
    • Holmberg, A.1
  • 32
    • 51749113592 scopus 로고    scopus 로고
    • Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli
    • Covert, M. W., Xiao, N., Chen, T. J., and Karr, J. R. (2008) Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics 24, 2044-2050.
    • (2008) Bioinformatics , vol.24 , pp. 2044-2050
    • Covert, M.W.1    Xiao, N.2    Chen, T.J.3    Karr, J.R.4
  • 34
    • 52649087274 scopus 로고    scopus 로고
    • Modelling and analysis of gene regulatory networks
    • Karlebach, G., and Shamir, R. (2008) Modelling and analysis of gene regulatory networks. Nat. Rev. Mol. Cell Biol. 9, 770-780.
    • (2008) Nat. Rev. Mol. Cell Biol. , vol.9 , pp. 770-780
    • Karlebach, G.1    Shamir, R.2
  • 35
    • 58549110252 scopus 로고    scopus 로고
    • Stochastic modelling for quantitative description of heterogeneous biological systems
    • Wilkinson, D. J. (2009) Stochastic modelling for quantitative description of heterogeneous biological systems. Nat. Rev. Genet. 10, 122-133.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 122-133
    • Wilkinson, D.J.1
  • 36
    • 0022011031 scopus 로고
    • Input-output parametric models for non-linear systems. Part I: Deterministic non-linear systems
    • Leontaritis, I. J., and Billings, S. A. (1985) Input-output parametric models for non-linear systems. Part 1: Deterministic nonlinear systems. Int. J. Control 41, 303-328. (Pubitemid 15476363)
    • (1985) International Journal of Control , vol.41 , Issue.2 , pp. 303-328
    • Leontaritis, I.J.1    Billings, S.A.2
  • 37
    • 0022011215 scopus 로고
    • Input-output parametric models for non-linear systems. Part II: Stochastic non-linear systems
    • Leontaritis, I. J., and Billings, S. A. (1985) Input-output parametric models for nonlinear systems. Part 2: Stochastic nonlinear systems. Int. J. Control 41, 329-344. (Pubitemid 15476364)
    • (1985) International Journal of Control , vol.41 , Issue.2 , pp. 329-344
    • Leontaritis, I.J.1    Billings, S.A.2
  • 38
    • 0024771664 scopus 로고
    • Orthogonal least squares methods and their application to non-linear system identification
    • Chen, S., Billings, S. A., and Luo, W. (1989) Orthogonal least squares methods and their application to non-linear system identification. Int. J. Control 50, 1873-1896. (Pubitemid 20636409)
    • (1989) International Journal of Control , vol.50 , Issue.5 , pp. 1873-1896
    • Chen, S.1    Billings, S.A.2    Luo, W.3
  • 39
    • 35348876164 scopus 로고    scopus 로고
    • Modelling and identification of non-linear deterministic systems in the delta-domain
    • DOI 10.1016/j.automatica.2007.03.020, PII S0005109807002506
    • Anderson, S. R., and Kadirkamanathan, V. (2007) Modelling and identification of non-linear deterministic systems in the deltadomain. Automatica 43, 1859-1868. (Pubitemid 47576056)
    • (2007) Automatica , vol.43 , Issue.11 , pp. 1859-1868
    • Anderson, S.R.1    Kadirkamanathan, V.2
  • 40
    • 77953772177 scopus 로고    scopus 로고
    • Nonlinear dynamic modeling of isometric force production in primate eye muscle
    • Anderson, S. R., Lepora, N. F., Porrill, J., and Dean, P. (2010) Nonlinear dynamic modeling of isometric force production in primate eye muscle. IEEE Trans. Biomed. Eng. 57, 1554-1567.
    • (2010) IEEE Trans. Biomed. Eng. , vol.57 , pp. 1554-1567
    • Anderson, S.R.1    Lepora, N.F.2    Porrill, J.3    Dean, P.4
  • 42
    • 28844494949 scopus 로고    scopus 로고
    • Past, present and future of nonlinear system identification in structural dynamics
    • DOI 10.1016/j.ymssp.2005.04.008, PII S0888327005000828
    • Kerschen, G., Worden, K., Vakakis, A., and Golinval, J. (2006) Past, present and future of nonlinear system identification in structural dynamics. Mech. Syst. Signal Process. 20, 505-592. (Pubitemid 41766672)
    • (2006) Mechanical Systems and Signal Processing , vol.20 , Issue.3 , pp. 505-592
    • Kerschen, G.1    Worden, K.2    Vakakis, A.F.3    Golinval, J.-C.4
  • 43
    • 0003054377 scopus 로고
    • Identification of loudspeaker nonlinearities using the NARMAX modeling technique
    • Jang, H. K., and Kim, K. J. (1994) Identification of loudspeaker nonlinearities using the NARMAX modeling technique. J. Audio Eng. Soc. 42, 50-60.
    • (1994) J. Audio Eng. Soc. , vol.42 , pp. 50-60
    • Jang, H.K.1    Kim, K.J.2
  • 45
    • 0035414889 scopus 로고    scopus 로고
    • Nonlinear gas turbine modeling using NARMAX structures
    • DOI 10.1109/19.948295, PII S0018945601060181, Selected Papers IMTC 2000
    • Chiras, N., Evans, C., and Rees, D. (2001) Nonlinear gas turbine modeling using NARMAX structures. IEEE Trans. Instrum. Meas. 50, 893-898. (Pubitemid 32945746)
    • (2001) IEEE Transactions on Instrumentation and Measurement , vol.50 , Issue.4 , pp. 893-898
    • Chiras, N.1    Evans, C.2    Rees, D.3
  • 47
    • 0024631931 scopus 로고
    • Representations of non-linear systems: The NARMAX model
    • Chen, S., and Billings, S. A. (1989) Representations of nonlinear systems: The NARMAX model. Int. J. Control 49, 1013-1032. (Pubitemid 20610988)
    • (1989) International Journal of Control , vol.49 , Issue.3 , pp. 1013-1032
    • Chen, S.1    Billings, S.A.2
  • 50
    • 0033340605 scopus 로고    scopus 로고
    • Direct approach to identification of nonlinear differential models from discrete data
    • DOI 10.1006/mssp.1999.1230
    • Coca, D., and Billings, S. A. (1999) A direct approach to identification of nonlinear differential models from discrete data. Mech. Syst. Signal Process. 13, 739-755. (Pubitemid 30507799)
    • (1999) Mechanical Systems and Signal Processing , vol.13 , Issue.5 , pp. 739-755
    • Coca, D.1    Billings, S.A.2
  • 51
    • 80055035853 scopus 로고    scopus 로고
    • Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology
    • Wang, B., Kitney, R. I., Joly, N., and Buck, M. (2011) Engineering modular and orthogonal genetic logic gates for robust digital-like synthetic biology. Nat. Commun. 2, 508.
    • (2011) Nat. Commun. , vol.2 , pp. 508
    • Wang, B.1    Kitney, R.I.2    Joly, N.3    Buck, M.4
  • 52
    • 78651397316 scopus 로고    scopus 로고
    • Robust Multicellular Computing Using Genetically Encoded NOR Gates And Chemical 'wires'
    • Tamsir, A., Tabor, J. J., and Voigt, C. A. (2011) Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Nature 469, 212-215.
    • (2011) Nature , vol.469 , pp. 212-215
    • Tamsir, A.1    Tabor, J.J.2    Voigt, C.A.3
  • 54
    • 0742304416 scopus 로고    scopus 로고
    • Term and variable selection for nonlinear models
    • Wei, H., Billings, S. A., and Lui, J. (2004) Term and variable selection for nonlinear models. Int. J. Control 77, 86-110.
    • (2004) Int. J. Control , vol.77 , pp. 86-110
    • Wei, H.1    Billings, S.A.2    Lui, J.3
  • 55
    • 84859774286 scopus 로고    scopus 로고
    • Structure detection and parameter estimation for NARX models in a unified EM framework
    • DOI: 10.1016/j.automatica.2012.02.021
    • Baldacchino, T., Anderson, S. R., and Kadirkamanathan, V. (2012) Structure detection and parameter estimation for NARX models in a unified EM framework. Automatica, DOI: 10.1016/j.automatica.2012.02.021.
    • (2012) Automatica
    • Baldacchino, T.1    Anderson, S.R.2    Kadirkamanathan, V.3
  • 56
    • 0023169857 scopus 로고
    • On the dynamics of the irreversible Michaelis-Menten reaction mechanism
    • Palsson, B. O. (1987) On the dynamics of the irreversible Michaelis-Menten reaction mechanism. Chem Eng. Sci. 42, 447-458.
    • (1987) Chem Eng. Sci. , vol.42 , pp. 447-458
    • Palsson, B.O.1
  • 57
    • 0037390670 scopus 로고    scopus 로고
    • Separable nonlinear least squares: The variable projection method and its applications
    • Golub, G., and Pereyra, V. (2003) Separable nonlinear least squares: The variable projection method and its applications. Inverse Problems 19, R1.
    • (2003) Inverse Problems , vol.19
    • Golub, G.1    Pereyra, V.2
  • 58
    • 0032624479 scopus 로고    scopus 로고
    • Linear and non-linear system identification using separable least-squares
    • Bruls, J., Chou, C. T., Haverkamp, B. R. J., and Verhaegen, M. (1999) Linear and non-linear system identification using separable least-squares. Eur. J. Control 5, 116-128.
    • (1999) Eur. J. Control , vol.5 , pp. 116-128
    • Bruls, J.1    Chou, C.T.2    Haverkamp, B.R.J.3    Verhaegen, M.4
  • 59
    • 0024480612 scopus 로고
    • Accurate derivative estimation from noisy data: A state-space approach
    • Fioretti, S., and Jetto, L. (1989) Accurate derivative estimation from noisy data: A state-space approach. Int. J. Syst. Sci. 20, 33-53.
    • (1989) Int. J. Syst. Sci. , vol.20 , pp. 33-53
    • Fioretti, S.1    Jetto, L.2


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