메뉴 건너뛰기




Volumn 30, Issue 2, 2012, Pages 120-126

Genetic design automation: Engineering fantasy or scientific renewal?

Author keywords

[No Author keywords available]

Indexed keywords

CAD TOOL; COMPLEX RELATIONSHIPS; COMPUTER AIDED DESIGN TOOLS; DOMAIN SPECIFIC; GENETIC DESIGN; GENETIC SYSTEMS; PRODUCTIVITY GAIN; REAL VALUES; SYNTHETIC BIOLOGY; WORK-FLOWS;

EID: 84856094936     PISSN: 01677799     EISSN: 18793096     Source Type: Journal    
DOI: 10.1016/j.tibtech.2011.09.001     Document Type: Review
Times cited : (42)

References (72)
  • 1
    • 54949133752 scopus 로고    scopus 로고
    • SynBioSS: the synthetic biology modeling suite
    • Hill A.D., et al. SynBioSS: the synthetic biology modeling suite. Bioinformatics 2008, 24:2551-2553.
    • (2008) Bioinformatics , vol.24 , pp. 2551-2553
    • Hill, A.D.1
  • 2
    • 71849095864 scopus 로고    scopus 로고
    • TinkerCell: modular CAD tool for synthetic biology
    • Chandran D., et al. TinkerCell: modular CAD tool for synthetic biology. J. Biol. Eng. 2009, 3:19.
    • (2009) J. Biol. Eng. , vol.3 , pp. 19
    • Chandran, D.1
  • 3
    • 67849130568 scopus 로고    scopus 로고
    • Writing DNA with GenoCAD™
    • Czar M.J., et al. Writing DNA with GenoCAD™. Nucleic Acids Res. 2009, 37:W40-W47.
    • (2009) Nucleic Acids Res. , vol.37
    • Czar, M.J.1
  • 4
    • 50549103571 scopus 로고    scopus 로고
    • Computational design of synthetic gene circuits with composable parts
    • Marchisio M.A., Stelling J. Computational design of synthetic gene circuits with composable parts. Bioinformatics 2008, 24:1903-1910.
    • (2008) Bioinformatics , vol.24 , pp. 1903-1910
    • Marchisio, M.A.1    Stelling, J.2
  • 5
    • 46249085749 scopus 로고    scopus 로고
    • Asmparts: assembly of biological model parts
    • Rodrigo G., et al. Asmparts: assembly of biological model parts. Syst. Synth. Biol. 2007, 1:167-170.
    • (2007) Syst. Synth. Biol. , vol.1 , pp. 167-170
    • Rodrigo, G.1
  • 6
    • 70350669878 scopus 로고    scopus 로고
    • IBioSim: a tool for the analysis and design of genetic circuits
    • Myers C.J., et al. iBioSim: a tool for the analysis and design of genetic circuits. Bioinformatics 2009, 25:2848-2849.
    • (2009) Bioinformatics , vol.25 , pp. 2848-2849
    • Myers, C.J.1
  • 7
    • 77956517750 scopus 로고    scopus 로고
    • BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks
    • Rialle S., et al. BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks. Bioinformatics 2010, 26:2298-2304.
    • (2010) Bioinformatics , vol.26 , pp. 2298-2304
    • Rialle, S.1
  • 8
    • 79955710914 scopus 로고    scopus 로고
    • Eugene - a domain specific language for specifying and constraining synthetic biological parts, devices, and systems
    • Bilitchenko L., et al. Eugene - a domain specific language for specifying and constraining synthetic biological parts, devices, and systems. PLoS ONE 2011, 6:e18882.
    • (2011) PLoS ONE , vol.6
    • Bilitchenko, L.1
  • 9
    • 79957442875 scopus 로고    scopus 로고
    • Developer's and user's guide to Clotho v2.0. A software platform for the creation of synthetic biological systems
    • Xia B., et al. Developer's and user's guide to Clotho v2.0. A software platform for the creation of synthetic biological systems. Methods Enzymol. 2011, 498:97-135.
    • (2011) Methods Enzymol. , vol.498 , pp. 97-135
    • Xia, B.1
  • 10
    • 67650663955 scopus 로고    scopus 로고
    • Towards programming languages for genetic engineering of living cells
    • Pedersen M., Phillips A. Towards programming languages for genetic engineering of living cells. J. R. Soc. Interface 2009, 6(Suppl. 4):S437-S450.
    • (2009) J. R. Soc. Interface , vol.6 , Issue.SUPPL. 4
    • Pedersen, M.1    Phillips, A.2
  • 11
    • 66249088017 scopus 로고    scopus 로고
    • The second wave of synthetic biology: from modules to systems
    • Purnick P.E.M., Weiss R. The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 2009, 10:410-422.
    • (2009) Nat. Rev. Mol. Cell Biol. , vol.10 , pp. 410-422
    • Purnick, P.E.M.1    Weiss, R.2
  • 12
    • 75149167486 scopus 로고    scopus 로고
    • Five hard truths for synthetic biology
    • Kwok R. Five hard truths for synthetic biology. Nature 2010, 463:288-290.
    • (2010) Nature , vol.463 , pp. 288-290
    • Kwok, R.1
  • 13
    • 70349782009 scopus 로고    scopus 로고
    • Computational design tools for synthetic biology
    • Marchisio M.A., Stelling J. Computational design tools for synthetic biology. Curr. Opin. Biotechnol. 2009, 20:479-485.
    • (2009) Curr. Opin. Biotechnol. , vol.20 , pp. 479-485
    • Marchisio, M.A.1    Stelling, J.2
  • 14
    • 77956652264 scopus 로고    scopus 로고
    • Programming cells: towards an automated 'genetic compiler'
    • Clancy K., Voigt C.A. Programming cells: towards an automated 'genetic compiler'. Curr. Opin. Biotechnol. 2010, 21:572-581.
    • (2010) Curr. Opin. Biotechnol. , vol.21 , pp. 572-581
    • Clancy, K.1    Voigt, C.A.2
  • 15
    • 79951497643 scopus 로고    scopus 로고
    • Computational design approaches and tools for synthetic biology
    • MacDonald J.T., et al. Computational design approaches and tools for synthetic biology. Integr. Biol. 2011, 3:97-108.
    • (2011) Integr. Biol. , vol.3 , pp. 97-108
    • MacDonald, J.T.1
  • 16
    • 77950347143 scopus 로고    scopus 로고
    • The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms
    • Alterovitz G., et al. The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. Brief Bioinform. 2010, 11:80-95.
    • (2010) Brief Bioinform. , vol.11 , pp. 80-95
    • Alterovitz, G.1
  • 18
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • Elowitz M.B., Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403:335-338.
    • (2000) Nature , vol.403 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2
  • 19
    • 57049159362 scopus 로고    scopus 로고
    • A fast, robust and tunable synthetic gene oscillator
    • Stricker J., et al. A fast, robust and tunable synthetic gene oscillator. Nature 2008, 456:516-519.
    • (2008) Nature , vol.456 , pp. 516-519
    • Stricker, J.1
  • 20
    • 75149191906 scopus 로고    scopus 로고
    • A synchronized quorum of genetic clocks
    • Danino T., et al. A synchronized quorum of genetic clocks. Nature 2010, 463:326-330.
    • (2010) Nature , vol.463 , pp. 326-330
    • Danino, T.1
  • 21
    • 77951107086 scopus 로고    scopus 로고
    • Synthetic biology: applications come of age
    • Khalil A.S., Collins J.J. Synthetic biology: applications come of age. Nat. Rev. Genet. 2010, 11:367-379.
    • (2010) Nat. Rev. Genet. , vol.11 , pp. 367-379
    • Khalil, A.S.1    Collins, J.J.2
  • 22
    • 77951909023 scopus 로고    scopus 로고
    • Co-design in synthetic biology: a system-level analysis of the development of an environmental sensing device
    • Ball D.A., et al. Co-design in synthetic biology: a system-level analysis of the development of an environmental sensing device. Pac. Symp. Biocomput. 2010, 2010:385-396.
    • (2010) Pac. Symp. Biocomput. , vol.2010 , pp. 385-396
    • Ball, D.A.1
  • 23
    • 42549129218 scopus 로고    scopus 로고
    • From genotype to phenotype: systems biology meets natural variation
    • Benfey P.N., Mitchell-Olds T. From genotype to phenotype: systems biology meets natural variation. Science 2008, 320:495-497.
    • (2008) Science , vol.320 , pp. 495-497
    • Benfey, P.N.1    Mitchell-Olds, T.2
  • 26
    • 79959933199 scopus 로고    scopus 로고
    • Synthetic biology methodology and model refinement based on microelectronic modeling tools and languages
    • Gendrault Y., et al. Synthetic biology methodology and model refinement based on microelectronic modeling tools and languages. Biotechnol. J. 2011, 6:796-806.
    • (2011) Biotechnol. J. , vol.6 , pp. 796-806
    • Gendrault, Y.1
  • 28
    • 73349101023 scopus 로고    scopus 로고
    • Modeling structure-function relationships in synthetic DNA sequences using attribute grammars
    • Cai Y., et al. Modeling structure-function relationships in synthetic DNA sequences using attribute grammars. PLoS Comput. Biol. 2009, 5:e1000529.
    • (2009) PLoS Comput. Biol. , vol.5
    • Cai, Y.1
  • 29
    • 46949091517 scopus 로고    scopus 로고
    • Refinement and standardization of synthetic biological parts and devices
    • Canton B., et al. Refinement and standardization of synthetic biological parts and devices. Nat. Biotechnol. 2008, 26:787-793.
    • (2008) Nat. Biotechnol. , vol.26 , pp. 787-793
    • Canton, B.1
  • 30
    • 66149143984 scopus 로고    scopus 로고
    • Measuring the activity of BioBrick promoters using an in vivo reference standard
    • Kelly J.R., et al. Measuring the activity of BioBrick promoters using an in vivo reference standard. J. Biol. Eng. 2009, 3:4.
    • (2009) J. Biol. Eng. , vol.3 , pp. 4
    • Kelly, J.R.1
  • 31
    • 0025166089 scopus 로고
    • Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis
    • de Smit M.H., van Duin J. Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis. Proc. Natl. Acad. Sci. U.S.A. 1990, 87:7668-7672.
    • (1990) Proc. Natl. Acad. Sci. U.S.A. , vol.87 , pp. 7668-7672
    • de Smit, M.H.1    van Duin, J.2
  • 32
    • 70349964350 scopus 로고    scopus 로고
    • Automated design of synthetic ribosome binding sites to control protein expression
    • Salis H.M., et al. Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 2009, 27:946-950.
    • (2009) Nat. Biotechnol. , vol.27 , pp. 946-950
    • Salis, H.M.1
  • 33
    • 77952611328 scopus 로고    scopus 로고
    • Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes
    • Na D., et al. Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes. BMC Syst. Biol. 2010, 4:71.
    • (2010) BMC Syst. Biol. , vol.4 , pp. 71
    • Na, D.1
  • 34
    • 77951589688 scopus 로고    scopus 로고
    • Cooperation between translating ribosomes and RNA polymerase in transcription elongation
    • Proshkin S., et al. Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science 2010, 328:504-508.
    • (2010) Science , vol.328 , pp. 504-508
    • Proshkin, S.1
  • 36
    • 39149113411 scopus 로고    scopus 로고
    • Modular cell biology: retroactivity and insulation
    • Del Vecchio D., et al. Modular cell biology: retroactivity and insulation. Mol. Syst. Biol. 2008, 4:161.
    • (2008) Mol. Syst. Biol. , vol.4 , pp. 161
    • Del Vecchio, D.1
  • 37
    • 79953903095 scopus 로고    scopus 로고
    • Measuring retroactivity from noise in gene regulatory networks
    • Kim K.H., Sauro H.M. Measuring retroactivity from noise in gene regulatory networks. Biophys. J. 2011, 100:1167-1177.
    • (2011) Biophys. J. , vol.100 , pp. 1167-1177
    • Kim, K.H.1    Sauro, H.M.2
  • 38
    • 59149092285 scopus 로고    scopus 로고
    • Gene synthesis demystified
    • Czar M.J., et al. Gene synthesis demystified. Trends Biotechnol. 2009, 27:63-72.
    • (2009) Trends Biotechnol. , vol.27 , pp. 63-72
    • Czar, M.J.1
  • 39
    • 51449095986 scopus 로고    scopus 로고
    • Genetic design: rising above the sequence
    • Goler J.A., et al. Genetic design: rising above the sequence. Trends Biotechnol. 2008, 26:538-544.
    • (2008) Trends Biotechnol. , vol.26 , pp. 538-544
    • Goler, J.A.1
  • 40
    • 28544451327 scopus 로고    scopus 로고
    • Foundations for engineering biology
    • Endy D. Foundations for engineering biology. Nature 2005, 438:449-453.
    • (2005) Nature , vol.438 , pp. 449-453
    • Endy, D.1
  • 42
    • 77649305316 scopus 로고    scopus 로고
    • BglBricks: a flexible standard for biological part assembly
    • Anderson J.C., et al. BglBricks: a flexible standard for biological part assembly. J. Biol. Eng. 2010, 4:1.
    • (2010) J. Biol. Eng. , vol.4 , pp. 1
    • Anderson, J.C.1
  • 43
    • 79957471219 scopus 로고    scopus 로고
    • Enzymatic assembly of overlapping DNA fragments
    • Gibson D.G. Enzymatic assembly of overlapping DNA fragments. Methods Enzymol. 2011, 498:349-361.
    • (2011) Methods Enzymol. , vol.498 , pp. 349-361
    • Gibson, D.G.1
  • 44
    • 68749104564 scopus 로고    scopus 로고
    • Structural instability of plasmid biopharmaceuticals: challenges and implications
    • Oliveira P.H., et al. Structural instability of plasmid biopharmaceuticals: challenges and implications. Trends Biotechnol. 2009, 27:503-511.
    • (2009) Trends Biotechnol. , vol.27 , pp. 503-511
    • Oliveira, P.H.1
  • 45
    • 77952526654 scopus 로고    scopus 로고
    • GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs
    • Cai Y., et al. GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs. Nucleic Acids Res. 2010, 38:2637-2644.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 2637-2644
    • Cai, Y.1
  • 46
    • 77952521393 scopus 로고    scopus 로고
    • Algorithms for automated DNA assembly
    • Densmore D., et al. Algorithms for automated DNA assembly. Nucleic Acids Res. 2010, 38:2607-2616.
    • (2010) Nucleic Acids Res. , vol.38 , pp. 2607-2616
    • Densmore, D.1
  • 48
    • 58849137994 scopus 로고    scopus 로고
    • Systems biology: experimental design
    • Kreutz C., Timmer J. Systems biology: experimental design. FEBS J. 2009, 276:923-942.
    • (2009) FEBS J. , vol.276 , pp. 923-942
    • Kreutz, C.1    Timmer, J.2
  • 49
    • 77956498018 scopus 로고    scopus 로고
    • Sloppy models, parameter uncertainty, and the role of experimental design
    • Apgar J.F., et al. Sloppy models, parameter uncertainty, and the role of experimental design. Mol. Biosyst. 2010, 6:1890-1900.
    • (2010) Mol. Biosyst. , vol.6 , pp. 1890-1900
    • Apgar, J.F.1
  • 50
    • 44049088216 scopus 로고    scopus 로고
    • Mathematical analysis and quantification of fluorescent proteins as transcriptional reporters
    • Wang X., et al. Mathematical analysis and quantification of fluorescent proteins as transcriptional reporters. Biophys. J. 2008, 94:2017-2026.
    • (2008) Biophys. J. , vol.94 , pp. 2017-2026
    • Wang, X.1
  • 51
    • 64749116742 scopus 로고    scopus 로고
    • Using movies to analyse gene circuit dynamics in single cells
    • Locke J.C.W., Elowitz M.B. Using movies to analyse gene circuit dynamics in single cells. Nat. Rev. Microbiol. 2009, 7:383-392.
    • (2009) Nat. Rev. Microbiol. , vol.7 , pp. 383-392
    • Locke, J.C.W.1    Elowitz, M.B.2
  • 52
    • 68949215494 scopus 로고    scopus 로고
    • Microfluidic devices for measuring gene network dynamics in single cells
    • Bennett M.R., Hasty J. Microfluidic devices for measuring gene network dynamics in single cells. Nat. Rev. Genet. 2009, 10:628-638.
    • (2009) Nat. Rev. Genet. , vol.10 , pp. 628-638
    • Bennett, M.R.1    Hasty, J.2
  • 53
    • 75749143909 scopus 로고    scopus 로고
    • Origin of irreversibility of cell cycle start in budding yeast
    • Charvin G., et al. Origin of irreversibility of cell cycle start in budding yeast. PLoS Biol. 2010, 8:e1000284.
    • (2010) PLoS Biol. , vol.8
    • Charvin, G.1
  • 54
    • 78650334784 scopus 로고    scopus 로고
    • Build life to understand it
    • Elowitz M., Lim W.A. Build life to understand it. Nature 2010, 468:889-890.
    • (2010) Nature , vol.468 , pp. 889-890
    • Elowitz, M.1    Lim, W.A.2
  • 55
    • 77952903892 scopus 로고    scopus 로고
    • Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems
    • Bashor C.J., et al. Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. Annu. Rev. Biophys. 2010, 39:515-537.
    • (2010) Annu. Rev. Biophys. , vol.39 , pp. 515-537
    • Bashor, C.J.1
  • 56
    • 0345743608 scopus 로고    scopus 로고
    • Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era
    • Kell D.B., Oliver S.G. Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. Bioessays 2004, 26:99-105.
    • (2004) Bioessays , vol.26 , pp. 99-105
    • Kell, D.B.1    Oliver, S.G.2
  • 57
    • 1642336155 scopus 로고    scopus 로고
    • Functional genomic hypothesis generation and experimentation by a robot scientist
    • King R.D., et al. Functional genomic hypothesis generation and experimentation by a robot scientist. Nature 2004, 427:247-252.
    • (2004) Nature , vol.427 , pp. 247-252
    • King, R.D.1
  • 58
    • 77954839098 scopus 로고    scopus 로고
    • Machine science
    • Evans J., Rzhetsky A. Machine science. Science 2010, 329:399-400.
    • (2010) Science , vol.329 , pp. 399-400
    • Evans, J.1    Rzhetsky, A.2
  • 59
    • 79952638264 scopus 로고    scopus 로고
    • Cellular decision making and biological noise: from microbes to mammals
    • Balazsi G., et al. Cellular decision making and biological noise: from microbes to mammals. Cell 2011, 144:910-925.
    • (2011) Cell , vol.144 , pp. 910-925
    • Balazsi, G.1
  • 60
    • 46449120581 scopus 로고    scopus 로고
    • Virus attenuation by genome-scale changes in codon pair bias
    • Coleman J.R., et al. Virus attenuation by genome-scale changes in codon pair bias. Science 2008, 320:1784-1787.
    • (2008) Science , vol.320 , pp. 1784-1787
    • Coleman, J.R.1
  • 61
    • 77954482089 scopus 로고    scopus 로고
    • Live attenuated influenza virus vaccines by computer-aided rational design
    • Mueller S., et al. Live attenuated influenza virus vaccines by computer-aided rational design. Nat. Biotechnol. 2010, 28:723-1729.
    • (2010) Nat. Biotechnol. , vol.28 , pp. 723-1729
    • Mueller, S.1
  • 62
    • 78650304100 scopus 로고    scopus 로고
    • Synonymous but not the same: the causes and consequences of codon bias
    • Plotkin J.B., Kudla G. Synonymous but not the same: the causes and consequences of codon bias. Nat. Rev. Genet. 2011, 12:32-42.
    • (2011) Nat. Rev. Genet. , vol.12 , pp. 32-42
    • Plotkin, J.B.1    Kudla, G.2
  • 63
    • 28544433105 scopus 로고    scopus 로고
    • Refactoring bacteriophage T7
    • 2005.0018
    • Chan L.Y., et al. Refactoring bacteriophage T7. Mol. Syst. Biol. 2005, 1. 2005.0018.
    • (2005) Mol. Syst. Biol. , vol.1
    • Chan, L.Y.1
  • 64
    • 0037041888 scopus 로고    scopus 로고
    • Synthetic gene network for entraining and amplifying cellular oscillations
    • Hasty J., et al. Synthetic gene network for entraining and amplifying cellular oscillations. Phys. Rev. Lett. 2002, 88:148101.
    • (2002) Phys. Rev. Lett. , vol.88 , pp. 148101
    • Hasty, J.1
  • 65
    • 0037154293 scopus 로고    scopus 로고
    • Synchronizing genetic relaxation oscillators by intercell signaling
    • McMillen D., et al. Synchronizing genetic relaxation oscillators by intercell signaling. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:679-684.
    • (2002) Proc. Natl. Acad. Sci. U.S.A. , vol.99 , pp. 679-684
    • McMillen, D.1
  • 67
    • 79952074324 scopus 로고    scopus 로고
    • Standard biological parts knowledgebase
    • Galdzicki M., et al. Standard biological parts knowledgebase. PLoS ONE 2011, 6:e17005.
    • (2011) PLoS ONE , vol.6
    • Galdzicki, M.1
  • 68
    • 78651292737 scopus 로고    scopus 로고
    • Essential information for synthetic DNA sequences
    • Peccoud J., et al. Essential information for synthetic DNA sequences. Nat. Biotechnol. 2011, 29:22.
    • (2011) Nat. Biotechnol. , vol.29 , pp. 22
    • Peccoud, J.1
  • 69
    • 33748796893 scopus 로고    scopus 로고
    • Open source tools and toolkits for bioinformatics: significance, and where are we?
    • Stajich J.E., Lapp H. Open source tools and toolkits for bioinformatics: significance, and where are we?. Brief Bioinform. 2006, 7:287-296.
    • (2006) Brief Bioinform. , vol.7 , pp. 287-296
    • Stajich, J.E.1    Lapp, H.2
  • 70
    • 59849087643 scopus 로고    scopus 로고
    • Scientific workflow design for mere mortals
    • McPhillips T., et al. Scientific workflow design for mere mortals. Future Gener. Comput. Syst. 2009, 25:541-551.
    • (2009) Future Gener. Comput. Syst. , vol.25 , pp. 541-551
    • McPhillips, T.1
  • 71
    • 42449138783 scopus 로고    scopus 로고
    • Scientific workflows as productivity tools for drug discovery
    • Shon J., et al. Scientific workflows as productivity tools for drug discovery. Curr. Opin. Drug Discov. Dev. 2008, 11:381-388.
    • (2008) Curr. Opin. Drug Discov. Dev. , vol.11 , pp. 381-388
    • Shon, J.1
  • 72
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • Gardner T.S., et al. Construction of a genetic toggle switch in Escherichia coli. Nature 2000, 403:339-342.
    • (2000) Nature , vol.403 , pp. 339-342
    • Gardner, T.S.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.