메뉴 건너뛰기




Volumn 16, Issue 3-4, 2012, Pages 318-322

Computational methods in synthetic biology: Towards computer-aided part design

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; RNA; RNA POLYMERASE; TRANSCRIPTION FACTOR;

EID: 84865305634     PISSN: 13675931     EISSN: 18790402     Source Type: Journal    
DOI: 10.1016/j.cbpa.2012.05.003     Document Type: Review
Times cited : (9)

References (48)
  • 1
    • 0038241770 scopus 로고    scopus 로고
    • Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli
    • Atkinson M.R., Savageau M.A., Myers J.T., Ninfa A.J. Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli. Cell 2003, 113:597-607.
    • (2003) Cell , vol.113 , pp. 597-607
    • Atkinson, M.R.1    Savageau, M.A.2    Myers, J.T.3    Ninfa, A.J.4
  • 2
    • 0034212551 scopus 로고    scopus 로고
    • Engineering stability in gene networks by autoregulation
    • Becskei A., Serrano L. Engineering stability in gene networks by autoregulation. Nature 2000, 405:590-593.
    • (2000) Nature , vol.405 , pp. 590-593
    • Becskei, A.1    Serrano, L.2
  • 3
    • 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
  • 4
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • Gardner T.S., Cantor C.R., Collins J.J. 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    Cantor, C.R.2    Collins, J.J.3
  • 7
    • 79955710914 scopus 로고    scopus 로고
    • Eugene - a domain specific language for specifying and constraining synthetic biological parts, devices, and systems
    • Bilitchenko L., Liu A., Cheung S., Weeding E., Xia B., Leguia M., Anderson J.C., Densmore D. 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    Liu, A.2    Cheung, S.3    Weeding, E.4    Xia, B.5    Leguia, M.6    Anderson, J.C.7    Densmore, D.8
  • 8
    • 79961137158 scopus 로고    scopus 로고
    • Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks
    • Beal J., Lu T., Weiss R. Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks. PLoS ONE 2011, 6:e22490.
    • (2011) PLoS ONE , vol.6
    • Beal, J.1    Lu, T.2    Weiss, R.3
  • 9
    • 79952096532 scopus 로고    scopus 로고
    • Computer-aided design of biological circuits using TinkerCell
    • Chandran D., Bergmann F.T., Sauro H.M. Computer-aided design of biological circuits using TinkerCell. Bioeng Bugs 2010, 1:274-281.
    • (2010) Bioeng Bugs , vol.1 , pp. 274-281
    • Chandran, D.1    Bergmann, F.T.2    Sauro, H.M.3
  • 10
    • 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
  • 11
  • 13
    • 84856094936 scopus 로고    scopus 로고
    • Genetic design automation: engineering fantasy or scientific renewal?
    • Lux M.W., Bramlett B.W., Ball D.A., Peccoud J. Genetic design automation: engineering fantasy or scientific renewal?. Trends Biotechnol 2012, 30:120-126.
    • (2012) Trends Biotechnol , vol.30 , pp. 120-126
    • Lux, M.W.1    Bramlett, B.W.2    Ball, D.A.3    Peccoud, J.4
  • 14
    • 0021111879 scopus 로고
    • Compilation and analysis of Escherichia coli promoter DNA sequences
    • Hawley D.K., McClure W.R. Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res 1983, 11:2237-2255.
    • (1983) Nucleic Acids Res , vol.11 , pp. 2237-2255
    • Hawley, D.K.1    McClure, W.R.2
  • 15
    • 0023650609 scopus 로고
    • Analysis of E. coli promoter sequences
    • Harley C.B., Reynolds R.P. Analysis of E. coli promoter sequences. Nucleic Acids Res 1987, 15:2343-2361.
    • (1987) Nucleic Acids Res , vol.15 , pp. 2343-2361
    • Harley, C.B.1    Reynolds, R.P.2
  • 16
    • 0141605202 scopus 로고    scopus 로고
    • Identification and analysis of 'extended -10' promoters in Escherichia coli
    • Mitchell J.E., Zheng D., Busby S.J., Minchin S.D. Identification and analysis of 'extended -10' promoters in Escherichia coli. Nucleic Acids Res 2003, 31:4689-4695.
    • (2003) Nucleic Acids Res , vol.31 , pp. 4689-4695
    • Mitchell, J.E.1    Zheng, D.2    Busby, S.J.3    Minchin, S.D.4
  • 17
    • 0032544080 scopus 로고    scopus 로고
    • Identification of an UP element consensus sequence for bacterial promoters
    • Estrem S.T., Gaal T., Ross W., Gourse R.L. Identification of an UP element consensus sequence for bacterial promoters. Proc Natl Acad Sci USA 1998, 95:9761-9766.
    • (1998) Proc Natl Acad Sci USA , vol.95 , pp. 9761-9766
    • Estrem, S.T.1    Gaal, T.2    Ross, W.3    Gourse, R.L.4
  • 18
    • 44849092251 scopus 로고    scopus 로고
    • Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes
    • Dekhtyar M., Morin A., Sakanyan V. Triad pattern algorithm for predicting strong promoter candidates in bacterial genomes. BMC Bioinform 2008, 9:233.
    • (2008) BMC Bioinform , vol.9 , pp. 233
    • Dekhtyar, M.1    Morin, A.2    Sakanyan, V.3
  • 19
    • 77649254204 scopus 로고    scopus 로고
    • Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE
    • Rhodius V.A., Mutalik V.K. Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE. Proc Natl Acad Sci USA 2010, 107:2854-2859.
    • (2010) Proc Natl Acad Sci USA , vol.107 , pp. 2854-2859
    • Rhodius, V.A.1    Mutalik, V.K.2
  • 20
    • 84860155171 scopus 로고    scopus 로고
    • Predicting the strength of UP-elements and full-length E. coli sigmaE promoters
    • Rhodius V.A., Mutalik V.K., Gross C.A. Predicting the strength of UP-elements and full-length E. coli sigmaE promoters. Nucleic Acids Res 2012, 40:2907-2924.
    • (2012) Nucleic Acids Res , vol.40 , pp. 2907-2924
    • Rhodius, V.A.1    Mutalik, V.K.2    Gross, C.A.3
  • 21
    • 33646581979 scopus 로고    scopus 로고
    • Identifying functionally important mutations from phenotypically diverse sequence data
    • Jensen K., Alper H., Fischer C., Stephanopoulos G. Identifying functionally important mutations from phenotypically diverse sequence data. Appl Environ Microbiol 2006, 72:3696-3701.
    • (2006) Appl Environ Microbiol , vol.72 , pp. 3696-3701
    • Jensen, K.1    Alper, H.2    Fischer, C.3    Stephanopoulos, G.4
  • 22
    • 34547471980 scopus 로고    scopus 로고
    • Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering
    • De Mey M., Maertens J., Lequeux G.J., Soetaert W.K., Vandamme E.J. Construction and model-based analysis of a promoter library for E. coli: an indispensable tool for metabolic engineering. BMC Biotechnol 2007, 7:34.
    • (2007) BMC Biotechnol , vol.7 , pp. 34
    • De Mey, M.1    Maertens, J.2    Lequeux, G.J.3    Soetaert, W.K.4    Vandamme, E.J.5
  • 23
    • 44849090014 scopus 로고    scopus 로고
    • Formation of the open complex by bacterial RNA polymerase - a quantitative model
    • Djordjevic M., Bundschuh R. Formation of the open complex by bacterial RNA polymerase - a quantitative model. Biophys J 2008, 94:4233-4248.
    • (2008) Biophys J , vol.94 , pp. 4233-4248
    • Djordjevic, M.1    Bundschuh, R.2
  • 25
    • 70349964350 scopus 로고    scopus 로고
    • Automated design of synthetic ribosome binding sites to control protein expression
    • Salis H.M., Mirsky E.A., Voigt C.A. 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    Mirsky, E.A.2    Voigt, C.A.3
  • 26
    • 79957534528 scopus 로고    scopus 로고
    • The ribosome binding site calculator
    • Salis H.M. The ribosome binding site calculator. Methods Enzymol 2011, 498:19-42.
    • (2011) Methods Enzymol , vol.498 , pp. 19-42
    • Salis, H.M.1
  • 27
    • 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., Lee S., Lee D. 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    Lee, S.2    Lee, D.3
  • 28
    • 77957797837 scopus 로고    scopus 로고
    • RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression
    • Na D., Lee D. RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression. Bioinformatics 2010, 26:2633-2634.
    • (2010) Bioinformatics , vol.26 , pp. 2633-2634
    • Na, D.1    Lee, D.2
  • 30
    • 64849114915 scopus 로고    scopus 로고
    • Coding-sequence determinants of gene expression in Escherichia coli
    • Kudla G., Murray A.W., Tollervey D., Plotkin J.B. Coding-sequence determinants of gene expression in Escherichia coli. Science 2009, 324:255-258.
    • (2009) Science , vol.324 , pp. 255-258
    • Kudla, G.1    Murray, A.W.2    Tollervey, D.3    Plotkin, J.B.4
  • 31
    • 84862666301 scopus 로고    scopus 로고
    • A computational framework for the design of optimal protein synthesis
    • Racle J., Overney J., Hatzimanikatis V. A computational framework for the design of optimal protein synthesis. Biotechnol Bioeng 2012, 10.1002/bit.24463.
    • (2012) Biotechnol Bioeng
    • Racle, J.1    Overney, J.2    Hatzimanikatis, V.3
  • 32
    • 24044543111 scopus 로고    scopus 로고
    • A network of orthogonal ribosome x mRNA pairs
    • Rackham O., Chin J.W. A network of orthogonal ribosome x mRNA pairs. Nat Chem Biol 2005, 1:159-166.
    • (2005) Nat Chem Biol , vol.1 , pp. 159-166
    • Rackham, O.1    Chin, J.W.2
  • 33
    • 47249126414 scopus 로고    scopus 로고
    • Computational design of orthogonal ribosomes
    • Chubiz L.M., Rao C.V. Computational design of orthogonal ribosomes. Nucleic Acids Res 2008, 36:4038-4046.
    • (2008) Nucleic Acids Res , vol.36 , pp. 4038-4046
    • Chubiz, L.M.1    Rao, C.V.2
  • 35
    • 60149089144 scopus 로고    scopus 로고
    • Regulatory RNAs in bacteria
    • Waters L.S., Storz G. Regulatory RNAs in bacteria. Cell 2009, 136:615-628.
    • (2009) Cell , vol.136 , pp. 615-628
    • Waters, L.S.1    Storz, G.2
  • 36
    • 80052975908 scopus 로고    scopus 로고
    • Engineering biological systems with synthetic RNA molecules
    • Liang J.C., Bloom R.J., Smolke C.D. Engineering biological systems with synthetic RNA molecules. Mol Cell 2011, 43:915-926.
    • (2011) Mol Cell , vol.43 , pp. 915-926
    • Liang, J.C.1    Bloom, R.J.2    Smolke, C.D.3
  • 38
    • 84863226500 scopus 로고    scopus 로고
    • Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals
    • Qi L., Lucks J.B., Liu C.C., Mutalik V.K., Arkin A.P. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Res 2012, 10.1093/nar/gks168.
    • (2012) Nucleic Acids Res
    • Qi, L.1    Lucks, J.B.2    Liu, C.C.3    Mutalik, V.K.4    Arkin, A.P.5
  • 39
    • 79957700542 scopus 로고    scopus 로고
    • Versatile RNA-sensing transcriptional regulators for engineering genetic networks
    • Lucks J.B., Qi L., Mutalik V.K., Wang D., Arkin A.P. Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proc Natl Acad Sci USA 2011, 108:8617-8622.
    • (2011) Proc Natl Acad Sci USA , vol.108 , pp. 8617-8622
    • Lucks, J.B.1    Qi, L.2    Mutalik, V.K.3    Wang, D.4    Arkin, A.P.5
  • 40
    • 66249084560 scopus 로고    scopus 로고
    • Design principles for riboswitch function
    • Beisel C.L., Smolke C.D. Design principles for riboswitch function. PLoS Comput Biol 2009, 5:e1000363.
    • (2009) PLoS Comput Biol , vol.5
    • Beisel, C.L.1    Smolke, C.D.2
  • 41
    • 84455174703 scopus 로고    scopus 로고
    • Model-driven engineering of RNA devices to quantitatively program gene expression
    • Carothers J.M., Goler J.A., Juminaga D., Keasling J.D. Model-driven engineering of RNA devices to quantitatively program gene expression. Science 2011, 334:1716-1719.
    • (2011) Science , vol.334 , pp. 1716-1719
    • Carothers, J.M.1    Goler, J.A.2    Juminaga, D.3    Keasling, J.D.4
  • 42
    • 0034072450 scopus 로고    scopus 로고
    • DNA binding sites: representation and discovery
    • Stormo G.D. DNA binding sites: representation and discovery. Bioinformatics 2000, 16:16-23.
    • (2000) Bioinformatics , vol.16 , pp. 16-23
    • Stormo, G.D.1
  • 43
    • 74549209548 scopus 로고    scopus 로고
    • Inferring binding energies from selected binding sites
    • Zhao Y., Granas D., Stormo G.D. Inferring binding energies from selected binding sites. PLoS Comput Biol 2009, 5:e1000590.
    • (2009) PLoS Comput Biol , vol.5
    • Zhao, Y.1    Granas, D.2    Stormo, G.D.3
  • 44
    • 79958115193 scopus 로고    scopus 로고
    • Quantitative analysis demonstrates most transcription factors require only simple models of specificity
    • Zhao Y., Stormo G.D. Quantitative analysis demonstrates most transcription factors require only simple models of specificity. Nat Biotechnol 2011, 29:480-483.
    • (2011) Nat Biotechnol , vol.29 , pp. 480-483
    • Zhao, Y.1    Stormo, G.D.2
  • 45
    • 65849228838 scopus 로고    scopus 로고
    • Engineering transcription factors with novel DNA-binding specificity using comparative genomics
    • Desai T.A., Rodionov D.A., Gelfand M.S., Alm E.J., Rao C.V. Engineering transcription factors with novel DNA-binding specificity using comparative genomics. Nucleic Acids Res 2009, 37:2493-2503.
    • (2009) Nucleic Acids Res , vol.37 , pp. 2493-2503
    • Desai, T.A.1    Rodionov, D.A.2    Gelfand, M.S.3    Alm, E.J.4    Rao, C.V.5
  • 48
    • 46949091517 scopus 로고    scopus 로고
    • Refinement and standardization of synthetic biological parts and devices
    • Canton B., Labno A., Endy D. 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    Labno, A.2    Endy, D.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.