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Volumn 29, Issue 3, 2012, Pages 7-20

Design automation for synthetic biological systems

Author keywords

Electronic design automation; Genetic regulatory network; Metabolic engineering; Parts devices; Pathways; Synthetic biology; Systems; Systems biology

Indexed keywords

ELECTRONIC DESIGN AUTOMATION; GENETIC REGULATORY NETWORKS; PARTS DEVICES; PATHWAYS; SYNTHETIC BIOLOGY; SYSTEMS BIOLOGY;

EID: 84867823155     PISSN: 07407475     EISSN: None     Source Type: Journal    
DOI: 10.1109/MDT.2012.2193370     Document Type: Article
Times cited : (20)

References (40)
  • 2
    • 29144482539 scopus 로고    scopus 로고
    • Environmentally controlled invasion of cancer cells by engineered bacteria
    • Apr. [Online].
    • J. C. Anderson, E. J. Clarke, A. P. Arkin, and C. A. Voigt. (2012, Apr.). Environmentally controlled invasion of cancer cells by engineered bacteria. J. Mol. Biol. [Online]. 355(4), pp. 619-627. Available: http://dx.doi.org/10.1016/ j.jmb.2005.10.076.
    • (2012) J. Mol. Biol. , vol.355 , Issue.4 , pp. 619-627
    • Anderson, J.C.1    Clarke, E.J.2    Arkin, A.P.3    Voigt, C.A.4
  • 3
    • 77952515515 scopus 로고    scopus 로고
    • Synthetic biology: Designer bacteria degrades toxin
    • Apr. [Online].
    • J. R. Kirby. (2012, Apr.). Synthetic biology: Designer bacteria degrades toxin. Nature Chemical Biology. [Online]. 6(6), pp. 398-399. Available: http://dx.doi.org/10.1038/nchembio.378.
    • (2012) Nature Chemical Biology , vol.6 , Issue.6 , pp. 398-399
    • Kirby, J.R.1
  • 4
    • 38049001166 scopus 로고    scopus 로고
    • Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels
    • Jan.
    • S. Atsumi, T. Hanai, and J. C. Liao, "Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels," Nature, vol. 451, pp. 86-89, Jan. 2008.
    • (2008) Nature , vol.451 , pp. 86-89
    • Atsumi, S.1    Hanai, T.2    Liao, J.C.3
  • 5
    • 67651219110 scopus 로고    scopus 로고
    • Engineering bacterial signals and sensors
    • H. Salis, A. Tamsir, and C. Voigt, "Engineering bacterial signals and sensors," Contrib. Microbiol. vol. 16, pp. 194-225, 2009.
    • (2009) Contrib. Microbiol. , vol.16 , pp. 194-225
    • Salis, H.1    Tamsir, A.2    Voigt, C.3
  • 6
    • 68949161807 scopus 로고    scopus 로고
    • Programming cells by multiplex genome engineering and accelerated evolution
    • Apr. [Online].
    • H. H. Wang, F. J. Isaacs, P. A. Carr, Z. Z. Sun, G. Xu, C. R. Forest, and G. M. Church. (2012, Apr.). Programming cells by multiplex genome engineering and accelerated evolution. Nature. [Online]. 460(7257), pp. 894-898. Available: http://dx.doi.org/10.1038/nature08187.
    • (2012) Nature , vol.460 , Issue.7257 , pp. 894-898
    • Wang, H.H.1    Isaacs, F.J.2    Carr, P.A.3    Sun, Z.Z.4    Xu, G.5    Forest, C.R.6    Church, G.M.7
  • 8
    • 78651397316 scopus 로고    scopus 로고
    • Robust multicellular computing using genetically encoded NOR gates and chemical/'wires/'
    • Apr. [Online].
    • A. Tamsir, J. J. Tabor, and C. A. Voigt. (2012, Apr.). Robust multicellular computing using genetically encoded NOR gates and chemical/'wires/'. Nature. [Online]. 469(7329), pp. 212-215. Available: http://dx.doi.org/10.1038/nature09565.
    • (2012) Nature , vol.469 , Issue.7329 , pp. 212-215
    • Tamsir, A.1    Tabor, J.J.2    Voigt, C.A.3
  • 9
    • 77649305316 scopus 로고    scopus 로고
    • BglBricks: A flexible standard for biological part assembly
    • Apr. [Online].
    • J. C. Anderson, J. E. Dueber, M. Leguia, G. C. Wu, J. A. Goler, A. P. Arkin, and J. D. Keasling. (2012, Apr.). BglBricks: A flexible standard for biological part assembly. J. Biol. Eng. [Online]. 4(1), pp. 1+. Available: http://dx.doi.org/10.1186/1754-1611-4-1.
    • (2012) J. Biol. Eng. , vol.4 , Issue.1
    • Anderson, J.C.1    Dueber, J.E.2    Leguia, M.3    Wu, G.C.4    Goler, J.A.5    Arkin, A.P.6    Keasling, J.D.7
  • 10
    • 67349270900 scopus 로고    scopus 로고
    • Enzymatic assembly of DNA molecules up to several hundred kilobases
    • Apr. [Online].
    • D. G. Gibson, L. Young, R.-Y. Y. Chuang, J. C. Venter, C. A. Hutchison, and H. O. Smith. (2012, Apr.). Enzymatic assembly of DNA molecules up to several hundred kilobases. Nature Meth. [Online]. 6(5), pp. 343-345. Available: http://dx.doi.org/10.1038/nmeth.1318.
    • (2012) Nature Meth. , vol.6 , Issue.5 , pp. 343-345
    • Gibson, D.G.1    Young, L.2    Chuang, R.-Y.Y.3    Venter, J.C.4    Hutchison, C.A.5    Smith, H.O.6
  • 11
    • 79961137158 scopus 로고    scopus 로고
    • Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks
    • Apr. [Online].
    • J. Beal, T. Lu, and R. Weiss. (2012, Apr.). Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks. PLoS ONE. [Online]. 6(8), pp. e22490+. Available: http://dx.doi.org/ 10.1371/journal.pone.0022490.
    • (2012) PLoS ONE. , vol.6 , Issue.8
    • Beal, J.1    Lu, T.2    Weiss, R.3
  • 12
    • 79955710914 scopus 로고    scopus 로고
    • Eugene A domain specific language for specifying and constraining synthetic biological parts, devices, and systems
    • Apr. [Online].
    • L. Bilitchenko, A. Liu, S. Cheung, E. Weeding, B. Xia, M. Leguia, J. C. Anderson, and D. Densmore. (2012, Apr.). Eugene A domain specific language for specifying and constraining synthetic biological parts, devices, and systems. PLoS ONE. [Online]. 6(4), pp. e18882+. Available: http://dx.doi.org/10.1371/ journal.pone.0018882.
    • (2012) PLoS ONE. , vol.6 , Issue.4
    • 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
  • 13
    • 67650663955 scopus 로고    scopus 로고
    • Towards programming languages for genetic engineering of living cells
    • Apr. [Online].
    • M. Pedersen and A. Phillips. (2012, Apr.). Towards programming languages for genetic engineering of living cells. J. Roy. Soc. Interface. [Online]. 6(Suppl 4), pp. S437-S450. Available: http://dx.doi.org/10.1098/rsif.2008.0516. focus.
    • (2012) J. Roy. Soc. Interface. , vol.6 , Issue.SUPPL. 4
    • Pedersen, M.1    Phillips, A.2
  • 14
    • 79953769431 scopus 로고    scopus 로고
    • Retroactivity attenuation in bio-molecular systems based on timescale separation
    • S. Jayanthi and D. D. Vecchio, "Retroactivity attenuation in bio-molecular systems based on timescale separation," IEEE Trans. Automat. Control, vol. 56, no. 4, pp. 748-761, 2011.
    • (2011) IEEE Trans. Automat. Control , vol.56 , Issue.4 , pp. 748-761
    • Jayanthi, S.1    Vecchio, D.D.2
  • 15
    • 62949154042 scopus 로고    scopus 로고
    • Design and performance of in vitro transcription rate regulatory circuits
    • Dec.
    • E. Franco and R. Murray, "Design and performance of in vitro transcription rate regulatory circuits," in Proc. 47th IEEE Conf. Dec. Contr., 2008. CDC 2008., Dec. 2008, pp. 161-166.
    • (2008) Proc. 47th IEEE Conf. Dec. Contr., 2008. CDC 2008. , pp. 161-166
    • Franco, E.1    Murray, R.2
  • 17
    • 75149186930 scopus 로고    scopus 로고
    • Design and characterization of a three-terminal transcriptional device through polymerase per second
    • Sep
    • P. A. Varadarajan and D. Del Vecchio, "Design and characterization of a three-terminal transcriptional device through polymerase per second," IEEE Trans. Nanobiosci., vol. 8, pp. 281-289, Sep. 2009.
    • (2009) IEEE Trans. Nanobiosci. , vol.8 , pp. 281-289
    • Varadarajan, P.A.1    Del Vecchio, D.2
  • 18
    • 46949091517 scopus 로고    scopus 로고
    • Refinement and standardization of synthetic biological parts and devices
    • DOI 10.1038/nbt1413, PII NBT1413
    • B. Canton, A. Labno, and D. Endy. (2012, Apr.). Refinement and standardization of synthetic biological parts and devices. Nature Biotechnol. [Online]. 26(7), pp. 787-793. Available: http://dx.doi.org/10.1038/nbt1413. (Pubitemid 351961452)
    • (2008) Nature Biotechnology , vol.26 , Issue.7 , pp. 787-793
    • Canton, B.1    Labno, A.2    Endy, D.3
  • 19
    • 71849095864 scopus 로고    scopus 로고
    • TinkerCell: Modular CAD tool for synthetic biology
    • Apr. [Online].
    • D. Chandran, F. Bergmann, and H. Sauro. (2012, Apr.). TinkerCell: Modular CAD tool for synthetic biology. J. Biol. Eng. [Online]. 3(1), pp. 19+. Available: http://dx.doi.org/10.1186/1754-1611-3-19
    • (2012) J. Biol. Eng. , vol.3 , Issue.1
    • Chandran, D.1    Bergmann, F.2    Sauro, H.3
  • 20
    • 79957523391 scopus 로고    scopus 로고
    • SynBioSS-aided design of synthetic biological constructs
    • Apr. [Online].
    • Y. N. Kaznessis. (2012, Apr.). SynBioSS-aided design of synthetic biological constructs. Methods Enzymol. [Online]. 498, pp. 137-152. Available: http://dx.doi.org/10.1016/B978-0-12-385120-8.00006-1.
    • (2012) Methods Enzymol. , vol.498 , pp. 137-152
    • Kaznessis, Y.N.1
  • 21
    • 67849130568 scopus 로고    scopus 로고
    • Writing DNA with genoCADTM
    • Apr. [Online].
    • M. J. Czar, Y. Cai, and J. Peccoud. (2012, Apr.).Writing DNA with GenoCADTM. Nucl. Acids Res. [Online]. 37(suppl 2), pp. W40-W47. Available: http://dx.doi.org/10.1093/nar/gkp361.
    • (2012) Nucl. Acids Res. , vol.37 , Issue.SUPPL. 2
    • Czar, M.J.1    Cai, Y.2    Peccoud, J.3
  • 22
    • 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
    • B. Xia, S. Bhatia, B. Bubenheim, M. Dadgar, D. Densmore, and J. Anderson, "Developer's and user's guide to clotho v2.0 a software platform for the creation of synthetic biological systems," Methods Enzymol., vol. 498, 2011.
    • (2011) Methods Enzymol. , vol.498
    • Xia, B.1    Bhatia, S.2    Bubenheim, B.3    Dadgar, M.4    Densmore, D.5    Anderson, J.6
  • 23
    • 70350669878 scopus 로고    scopus 로고
    • IBioSim: A tool for the analysis and design of genetic circuits
    • Apr. [Online].
    • C. J. Myers, N. Barker, K. Jones, H. Kuwahara, C. Madsen, and N.-P. P. Nguyen. (2012, Apr.). iBioSim: A tool for the analysis and design of genetic circuits. Bioinformatics. [Online]. 25(21), pp. 2848-2849. Available: http://dx.doi.org/10.1093/bioinformatics/btp457.
    • (2012) Bioinformatics. , vol.25 , Issue.21 , pp. 2848-2849
    • Myers, C.J.1    Barker, N.2    Jones, K.3    Kuwahara, H.4    Madsen, C.5    Nguyen, N.-P.P.6
  • 24
    • 84859320316 scopus 로고    scopus 로고
    • J5 dna assembly design automation software
    • Apr. [Online].
    • N. J. Hillson, R. D. Rosengarten, and J. D. Keasling. (2012, Apr.). j5 dna assembly design automation software. ACS Synthetic Biol. [Online]. 1(1), pp. 14-21. Available: http://pubs.acs.org/doi/abs/10.1021/sb2000116.
    • (2012) ACS Synthetic Biol. , vol.1 , Issue.1 , pp. 14-21
    • Hillson, N.J.1    Rosengarten, R.D.2    Keasling, J.D.3
  • 25
    • 61449140264 scopus 로고    scopus 로고
    • Promot: Modular modeling for systems biology
    • Apr. [Online].
    • S. Mirschel, K. Steinmetz, M. Rempel, M. Ginkel, and E. D. Gilles. (2012, Apr.). Promot: Modular modeling for systems biology. Bioinformatics. [Online]. 25(5), pp. 687-689. Available: http://bioinformatics. oxfordjournals.org/ content/25/5/687.abstract.
    • (2012) Bioinformatics. , vol.25 , Issue.5 , pp. 687-689
    • Mirschel, S.1    Steinmetz, K.2    Rempel, M.3    Ginkel, M.4    Gilles, E.D.5
  • 26
    • 45749137679 scopus 로고    scopus 로고
    • Minimal Eschenchia coli cell for the most efficient production of ethanol from hexoses and pentoses
    • DOI 10.1128/AEM.02708-07
    • C. T. Trinh, P. Unrean, and F. Srienc, "Minimal Escherichia coli cell for the most efficient production of ethanol from hexoses and pentoses," Appl. Environ. Microbiol., vol. 74, pp. 3634-3643, Jun. 2008. (Pubitemid 351874892)
    • (2008) Applied and Environmental Microbiology , vol.74 , Issue.12 , pp. 3634-3643
    • Trinh, C.T.1    Unrean, P.2    Srienc, F.3
  • 28
    • 79960414910 scopus 로고    scopus 로고
    • Systems metabolic engineering for chemicals and materials
    • Aug.
    • J. W. Lee, T. Y. Kim, Y. S. Jang, S. Choi, and S. Y. Lee, "Systems metabolic engineering for chemicals and materials," Trends Biotechnol., vol. 29, pp. 370-378, Aug. 2011.
    • (2011) Trends Biotechnol. , vol.29 , pp. 370-378
    • Lee, J.W.1    Kim, T.Y.2    Jang, Y.S.3    Choi, S.4    Lee, S.Y.5
  • 29
    • 80053394442 scopus 로고    scopus 로고
    • The original Michaelis constant: Translation of the 1913 Michaelis-Menten paper
    • Apr. [Online]
    • L. Michaelis, M. L. Menten, K. A. Johnson, and R. S. Goody. (2012, Apr.). The original Michaelis constant: Translation of the 1913 Michaelis-Menten paper. Biochemistry. [Online]. 50(39), pp. 8264-8269. Available: http://www.ncbi.nlm.nih.gov/pubmed/21888353.
    • (2012) Biochemistry. , vol.50 , Issue.39 , pp. 8264-8269
    • Michaelis, L.1    Menten, M.L.2    Johnson, K.A.3    Goody, R.S.4
  • 30
    • 0022493181 scopus 로고
    • Fat synthesis in adipose tissue. An examination of stoichiometric constraints
    • D. A. Fell and J. Small, "Fat synthesis in adipose tissue. An examination of stoichiometric constraints," Biochem. J., vol. 238, no. 3, pp. 781-786, Sep. 1986. (Pubitemid 16004713)
    • (1986) Biochemical Journal , vol.238 , Issue.3 , pp. 781-786
    • Fell, D.A.1    Small, J.R.2
  • 31
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: Evaluating the consequences of constraints
    • DOI 10.1038/nrmicro1023
    • N. Price, J. Reed, and B. Palsson, "Genome-scale models of microbial cells: Evaluating the consequences of constraints," Nature Rev. Microbiol., vol. 2, no. 11, pp. 886-897, 2004. (Pubitemid 39567269)
    • (2004) Nature Reviews Microbiology , vol.2 , Issue.11 , pp. 886-897
    • Price, N.D.1    Reed, J.L.2    Palsson, B.O.3
  • 32
    • 0000029295 scopus 로고    scopus 로고
    • On elementary flux modes in biochemical reaction systems at steady state
    • Apr. [Online].
    • S. Schuster and C. Hlgetag. (2012, Apr.). On elementary flux modes in biochemical reaction systems at steady state. J. Biol. Syst. [Online]. 2(2), pp. 165-182. Available: http://wwwback.jacobs-university.de/imperia/md/content/ groups/schools/ses/chilgetag/schusterhilgetagjbiolsyst1994.pdf.
    • (2012) J. Biol. Syst. , vol.2 , Issue.2 , pp. 165-182
    • Schuster, S.1    Hlgetag, C.2
  • 36
    • 8744224466 scopus 로고    scopus 로고
    • Optstrain: A computational framework for redesign of microbial production systems
    • Apr. [Online].
    • P. Pharkya, A. P. Burgard, and C. D. Maranas. (2012, Apr.). Optstrain: A computational framework for redesign of microbial production systems. Genome Research. [Online]. 14(11), pp. 2367-2376. Available: http://genome.cshlp.org/ content/14/11/2367.abstract.
    • (2012) Genome Research. , vol.14 , Issue.11 , pp. 2367-2376
    • Pharkya, P.1    Burgard, A.P.2    Maranas, C.D.3
  • 37
    • 79958753912 scopus 로고    scopus 로고
    • Probabilistic pathway construction
    • Jul.
    • M. Yousofshahi, K. Lee, and S. Hassoun, "Probabilistic pathway construction," Metab. Eng., vol. 13, no. 4, pp. 435-44, Jul. 2011.
    • (2011) Metab. Eng. , vol.13 , Issue.4 , pp. 435-444
    • Yousofshahi, M.1    Lee, K.2    Hassoun, S.3
  • 38
    • 0037199968 scopus 로고    scopus 로고
    • Hierarchical organization of modularity in metabolic networks
    • DOI 10.1126/science.1073374
    • E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltvai, and A.-L. Barabasi, "Hierarchical organization of modularity in metabolic networks," Science, vol. 297, no. 5586, pp. 1551-1555, 2002. (Pubitemid 34971002)
    • (2002) Science , vol.297 , Issue.5586 , pp. 1551-1555
    • Ravasz, E.1    Somera, A.L.2    Mongru, D.A.3    Oltvai, Z.N.4    Barabasi, A.-L.5
  • 39
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • DOI 10.1038/35002131
    • T. S. Gardner, C. R. Cantor, and J. J. Collins, "Construction of a genetic toggle switch in Escherichia coli," Nature, vol. 403, no. 6767, pp. 339-42, Jan. 2000. (Pubitemid 30062394)
    • (2000) Nature , vol.403 , Issue.6767 , pp. 339-342
    • Gardner, T.S.1    Cantor, C.R.2    Collins, J.J.3
  • 40
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • Apr. [Online].
    • M. B. Elowitz and S. Leibler. (2012, Apr.). A synthetic oscillatory network of transcriptional regulators. Nature. [Online]. 403(6767), pp. 335-338. Available: http://dx.doi.org/10.1038/35002125.
    • (2012) Nature , vol.403 , Issue.6767 , pp. 335-338
    • Elowitz, M.B.1    Leibler, S.2


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