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Volumn 29, Issue 1, 2014, Pages 146-155

Synthetic analog and digital circuits for cellular computation and memory

Author keywords

[No Author keywords available]

Indexed keywords

ANALOG COMPUTERS; BIOLOGY; COMPLEX NETWORKS; GENES;

EID: 84899838922     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2014.04.009     Document Type: Review
Times cited : (80)

References (48)
  • 1
    • 84863980696 scopus 로고    scopus 로고
    • Biomolecular computing systems: principles, progress and potential
    • Benenson Y. Biomolecular computing systems: principles, progress and potential. Nat Rev Genet 2012, 13:455-468.
    • (2012) Nat Rev Genet , vol.13 , pp. 455-468
    • Benenson, Y.1
  • 2
    • 34347389431 scopus 로고    scopus 로고
    • Mammalian synthetic biology: engineering of sophisticated gene networks
    • Greber D., Fussenegger M. Mammalian synthetic biology: engineering of sophisticated gene networks. J Biotechnol 2007, 130:329-345.
    • (2007) J Biotechnol , vol.130 , pp. 329-345
    • Greber, D.1    Fussenegger, M.2
  • 3
    • 84883820704 scopus 로고    scopus 로고
    • Building synthetic memory
    • Inniss M.C., Silver P.A. Building synthetic memory. Curr Biol 2013, 23:R812-R816.
    • (2013) Curr Biol , vol.23
    • Inniss, M.C.1    Silver, P.A.2
  • 4
    • 0037165942 scopus 로고    scopus 로고
    • Combinatorial synthesis of genetic networks
    • Guet C.C., Elowitz M.B., Hsing W., Leibler S. Combinatorial synthesis of genetic networks. Science 2002, 296:1466-1470.
    • (2002) Science , vol.296 , pp. 1466-1470
    • Guet, C.C.1    Elowitz, M.B.2    Hsing, W.3    Leibler, S.4
  • 5
    • 4344703213 scopus 로고    scopus 로고
    • BioLogic gates enable logical transcription control in mammalian cells
    • Kramer B.P., Fischer C., Fussenegger M. BioLogic gates enable logical transcription control in mammalian cells. Biotechnol Bioeng 2004, 87:478-484.
    • (2004) Biotechnol Bioeng , vol.87 , pp. 478-484
    • Kramer, B.P.1    Fischer, C.2    Fussenegger, M.3
  • 6
    • 34547916832 scopus 로고    scopus 로고
    • Environmental signal integration by a modular AND gate
    • Anderson J.C., Voigt C.A., Arkin A.P. Environmental signal integration by a modular AND gate. Mol Syst Biol 2007, 3:133.
    • (2007) Mol Syst Biol , vol.3 , pp. 133
    • Anderson, J.C.1    Voigt, C.A.2    Arkin, A.P.3
  • 7
    • 84862180741 scopus 로고    scopus 로고
    • A tunable zinc finger-based framework for Boolean logic computation in mammalian cells
    • Lohmueller J.J., Armel T.Z., Silver P.A. A tunable zinc finger-based framework for Boolean logic computation in mammalian cells. Nucleic Acids Res 2012.
    • (2012) Nucleic Acids Res
    • Lohmueller, J.J.1    Armel, T.Z.2    Silver, P.A.3
  • 8
    • 84890034375 scopus 로고    scopus 로고
    • Two- and three-input TALE-based AND logic computation in embryonic stem cells
    • Lienert F., et al. Two- and three-input TALE-based AND logic computation in embryonic stem cells. Nucleic Acids Res 2013.
    • (2013) Nucleic Acids Res
    • Lienert, F.1
  • 9
    • 34447310821 scopus 로고    scopus 로고
    • A universal RNAi-based logic evaluator that operates in mammalian cells
    • Rinaudo K., et al. A universal RNAi-based logic evaluator that operates in mammalian cells. Nat Biotechnol 2007, 25:795-801.
    • (2007) Nat Biotechnol , vol.25 , pp. 795-801
    • Rinaudo, K.1
  • 10
    • 77956431677 scopus 로고    scopus 로고
    • Rationally designed logic integration of regulatory signals in mammalian cells
    • Leisner M., Bleris L., Lohmueller J., Xie Z., Benenson Y. Rationally designed logic integration of regulatory signals in mammalian cells. Nature Nano 2010, 5:666-670.
    • (2010) Nature Nano , vol.5 , pp. 666-670
    • Leisner, M.1    Bleris, L.2    Lohmueller, J.3    Xie, Z.4    Benenson, Y.5
  • 11
    • 80052456127 scopus 로고    scopus 로고
    • Multi-input RNAi-based logic circuit for identification of specific cancer cells
    • Xie Z., Wroblewska L., Prochazka L., Weiss R., Benenson Y. Multi-input RNAi-based logic circuit for identification of specific cancer cells. Science 2011, 333:1307-1311.
    • (2011) Science , vol.333 , pp. 1307-1311
    • Xie, Z.1    Wroblewska, L.2    Prochazka, L.3    Weiss, R.4    Benenson, Y.5
  • 12
    • 54249113318 scopus 로고    scopus 로고
    • Higher-order cellular information processing with synthetic RNA devices
    • Win M.N., Smolke C.D. Higher-order cellular information processing with synthetic RNA devices. Science 2008, 322:456-460.
    • (2008) Science , vol.322 , pp. 456-460
    • Win, M.N.1    Smolke, C.D.2
  • 13
    • 29344453148 scopus 로고    scopus 로고
    • Cellular logic with orthogonal ribosomes
    • Rackham O., Chin J.W. Cellular logic with orthogonal ribosomes. J Am Chem Soc 2005, 127:17584-17585.
    • (2005) J Am Chem Soc , vol.127 , pp. 17584-17585
    • Rackham, O.1    Chin, J.W.2
  • 14
    • 0141757323 scopus 로고    scopus 로고
    • Reprogramming control of an allosteric signaling switch through modular recombination
    • Dueber J.E., Yeh B.J., Chak K., Lim W.A. Reprogramming control of an allosteric signaling switch through modular recombination. Science 2003, 301:1904-1908.
    • (2003) Science , vol.301 , pp. 1904-1908
    • Dueber, J.E.1    Yeh, B.J.2    Chak, K.3    Lim, W.A.4
  • 16
    • 84868619337 scopus 로고    scopus 로고
    • Genetic programs constructed from layered logic gates in single cells
    • Moon T.S., Lou C., Tamsir A., Stanton B.C., Voigt C.A. Genetic programs constructed from layered logic gates in single cells. Nature 2012, 491:249-253.
    • (2012) Nature , vol.491 , pp. 249-253
    • Moon, T.S.1    Lou, C.2    Tamsir, A.3    Stanton, B.C.4    Voigt, C.A.5
  • 17
    • 67549145283 scopus 로고    scopus 로고
    • A synthetic genetic edge detection program
    • Tabor J.J., et al. A synthetic genetic edge detection program. Cell 2009, 137:1272-1281.
    • (2009) Cell , vol.137 , pp. 1272-1281
    • Tabor, J.J.1
  • 18
    • 78651406505 scopus 로고    scopus 로고
    • Distributed biological computation with multicellular engineered networks
    • Regot S., et al. Distributed biological computation with multicellular engineered networks. Nature 2011, 469:207-211.
    • (2011) Nature , vol.469 , pp. 207-211
    • Regot, S.1
  • 19
    • 78651397316 scopus 로고    scopus 로고
    • Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'
    • Tamsir A., Tabor J.J., Voigt C.A. Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'. Nature 2011, 469:212-215.
    • (2011) Nature , vol.469 , pp. 212-215
    • Tamsir, A.1    Tabor, J.J.2    Voigt, C.A.3
  • 21
    • 61949434787 scopus 로고    scopus 로고
    • Deterministic limit of stochastic chemical kinetics
    • Gillespie D.T. Deterministic limit of stochastic chemical kinetics. J Phys Chem B 2009, 113:1640-1644.
    • (2009) J Phys Chem B , vol.113 , pp. 1640-1644
    • Gillespie, D.T.1
  • 22
    • 34249950625 scopus 로고    scopus 로고
    • Stochastic simulation of chemical kinetics
    • Gillespie D.T. Stochastic simulation of chemical kinetics. Annu Rev Phys Chem 2007, 58:35-55.
    • (2007) Annu Rev Phys Chem , vol.58 , pp. 35-55
    • Gillespie, D.T.1
  • 23
    • 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
  • 24
    • 34447505900 scopus 로고    scopus 로고
    • A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells
    • Deans T.L., Cantor C.R., Collins J.J. A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell 2007, 130:363-372.
    • (2007) Cell , vol.130 , pp. 363-372
    • Deans, T.L.1    Cantor, C.R.2    Collins, J.J.3
  • 25
    • 84879520478 scopus 로고    scopus 로고
    • Engineering of regulated stochastic cell fate determination
    • Wu M., et al. Engineering of regulated stochastic cell fate determination. Proc Natl Acad Sci U S A 2013, 110:10610-10615.
    • (2013) Proc Natl Acad Sci U S A , vol.110 , pp. 10610-10615
    • Wu, M.1
  • 26
    • 22144452865 scopus 로고    scopus 로고
    • Hysteresis in a synthetic mammalian gene network
    • Kramer B.P., Fussenegger M. Hysteresis in a synthetic mammalian gene network. Proc Natl Acad Sci U S A 2005, 102:9517-9522.
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 9517-9522
    • Kramer, B.P.1    Fussenegger, M.2
  • 27
    • 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
  • 28
    • 34548856538 scopus 로고    scopus 로고
    • Rational design of memory in eukaryotic cells
    • Ajo-Franklin C.M., et al. Rational design of memory in eukaryotic cells. Genes Dev 2007, 21:2271-2276.
    • (2007) Genes Dev , vol.21 , pp. 2271-2276
    • Ajo-Franklin, C.M.1
  • 29
    • 79952214973 scopus 로고    scopus 로고
    • Synthetic circuit identifies subpopulations with sustained memory of DNA damage
    • Burrill D.R., Silver P.A. Synthetic circuit identifies subpopulations with sustained memory of DNA damage. Genes Dev 2011, 25:434-439.
    • (2011) Genes Dev , vol.25 , pp. 434-439
    • Burrill, D.R.1    Silver, P.A.2
  • 30
    • 22644434444 scopus 로고    scopus 로고
    • Novel gene switches for targeted and timed expression of proteins of interest
    • Vilaboa N., Fenna M., Munson J., Roberts S.M., Voellmy R. Novel gene switches for targeted and timed expression of proteins of interest. Mol Ther 2005, 12:290-298.
    • (2005) Mol Ther , vol.12 , pp. 290-298
    • Vilaboa, N.1    Fenna, M.2    Munson, J.3    Roberts, S.M.4    Voellmy, R.5
  • 31
    • 84863644753 scopus 로고    scopus 로고
    • Synthetic memory circuits for tracking human cell fate
    • Burrill D.R., Inniss M.C., Boyle P.M., Silver P.A. Synthetic memory circuits for tracking human cell fate. Genes Dev 2012, 26:1486-1497.
    • (2012) Genes Dev , vol.26 , pp. 1486-1497
    • Burrill, D.R.1    Inniss, M.C.2    Boyle, P.M.3    Silver, P.A.4
  • 32
    • 0037018930 scopus 로고    scopus 로고
    • Rational design of artificial zinc-finger proteins using a nondegenerate recognition code table
    • Sera T., Uranga C. Rational design of artificial zinc-finger proteins using a nondegenerate recognition code table. Biochemistry 2002, 41:7074-7081.
    • (2002) Biochemistry , vol.41 , pp. 7074-7081
    • Sera, T.1    Uranga, C.2
  • 33
    • 56649114274 scopus 로고    scopus 로고
    • A one pot, one step, precision cloning method with high throughput capability
    • Engler C., Kandzia R., Marillonnet S. A one pot, one step, precision cloning method with high throughput capability. PLoS ONE 2008, 3:e3647.
    • (2008) PLoS ONE , vol.3
    • Engler, C.1    Kandzia, R.2    Marillonnet, S.3
  • 34
    • 84860585919 scopus 로고    scopus 로고
    • Site-specific integration with bacteriophage φC31 integrase
    • Hillman R.T., Calos M.P. Site-specific integration with bacteriophage φC31 integrase. Cold Spring Harb Protoc 2012, 2012.
    • (2012) Cold Spring Harb Protoc , vol.2012
    • Hillman, R.T.1    Calos, M.P.2
  • 35
    • 50949122967 scopus 로고    scopus 로고
    • Design and construction of a double inversion recombination switch for heritable sequential genetic memory
    • Ham T.S., Lee S.K., Keasling J.D., Arkin A.P. Design and construction of a double inversion recombination switch for heritable sequential genetic memory. PLoS ONE 2008, 3:e2815.
    • (2008) PLoS ONE , vol.3
    • Ham, T.S.1    Lee, S.K.2    Keasling, J.D.3    Arkin, A.P.4
  • 36
    • 66349125024 scopus 로고    scopus 로고
    • Synthetic gene networks that count
    • Friedland A.E., et al. Synthetic gene networks that count. Science 2009, 324:1199-1202.
    • (2009) Science , vol.324 , pp. 1199-1202
    • Friedland, A.E.1
  • 37
    • 84861865655 scopus 로고    scopus 로고
    • Rewritable digital data storage in live cells via engineered control of recombination directionality
    • Bonnet J., Subsoontorn P., Endy D. Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc Natl Acad Sci U S A 2012, 109:8884-8889.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 8884-8889
    • Bonnet, J.1    Subsoontorn, P.2    Endy, D.3
  • 38
    • 77949405661 scopus 로고    scopus 로고
    • Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch
    • Lou C., et al. Synthesizing a novel genetic sequential logic circuit: a push-on push-off switch. Mol Syst Biol 2010, 6:350.
    • (2010) Mol Syst Biol , vol.6 , pp. 350
    • Lou, C.1
  • 39
    • 84875230351 scopus 로고    scopus 로고
    • Synthetic circuits integrating logic and memory in living cells
    • Siuti P., Yazbek J., Lu T.K. Synthetic circuits integrating logic and memory in living cells. Nat Biotechnol 2013.
    • (2013) Nat Biotechnol
    • Siuti, P.1    Yazbek, J.2    Lu, T.K.3
  • 41
    • 71849110893 scopus 로고    scopus 로고
    • Next-generation synthetic gene networks
    • Lu T.K., Khalil A.S., Collins J.J. Next-generation synthetic gene networks. Nat Biotechnol 2009, 27:1139-1150.
    • (2009) Nat Biotechnol , vol.27 , pp. 1139-1150
    • Lu, T.K.1    Khalil, A.S.2    Collins, J.J.3
  • 42
    • 84886488970 scopus 로고    scopus 로고
    • Tunable and multifunctional eukaryotic transcription factors based on CRISPR/Cas
    • Farzadfard F., Perli S.D., Lu T.K. Tunable and multifunctional eukaryotic transcription factors based on CRISPR/Cas. ACS Synth Biol 2013, 2:604-613.
    • (2013) ACS Synth Biol , vol.2 , pp. 604-613
    • Farzadfard, F.1    Perli, S.D.2    Lu, T.K.3
  • 43
    • 84874687019 scopus 로고    scopus 로고
    • Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression
    • Qi L.S., et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 2013, 152:1173-1183.
    • (2013) Cell , vol.152 , pp. 1173-1183
    • Qi, L.S.1
  • 44
    • 84864634066 scopus 로고    scopus 로고
    • A synthetic biology framework for programming eukaryotic transcription functions
    • Khalil A.S., et al. A synthetic biology framework for programming eukaryotic transcription functions. Cell 2012, 150:647-658.
    • (2012) Cell , vol.150 , pp. 647-658
    • Khalil, A.S.1
  • 45
    • 84858609338 scopus 로고    scopus 로고
    • Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology
    • Blount B.A., Weenink T., Vasylechko S., Ellis T. Rational diversification of a promoter providing fine-tuned expression and orthogonal regulation for synthetic biology. PLoS ONE 2012, 7:e33279.
    • (2012) PLoS ONE , vol.7
    • Blount, B.A.1    Weenink, T.2    Vasylechko, S.3    Ellis, T.4
  • 46
    • 84869476328 scopus 로고    scopus 로고
    • Ribozyme-based insulator parts buffer synthetic circuits from genetic context
    • Lou C., Stanton B., Chen Y.-J., Munsky B., Voigt C.A. Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nat Biotechnol 2012, 30:1137-1142.
    • (2012) Nat Biotechnol , vol.30 , pp. 1137-1142
    • Lou, C.1    Stanton, B.2    Chen, Y.-J.3    Munsky, B.4    Voigt, C.A.5
  • 47
    • 84880371084 scopus 로고    scopus 로고
    • Towards a whole-cell modeling approach for synthetic biology
    • Purcell O., Jain B., Karr J.R., Covert M.W., Lu T.K. Towards a whole-cell modeling approach for synthetic biology. CHAOS 2013, 23:25112.
    • (2013) CHAOS , vol.23 , pp. 25112
    • Purcell, O.1    Jain, B.2    Karr, J.R.3    Covert, M.W.4    Lu, T.K.5
  • 48
    • 84899713900 scopus 로고    scopus 로고
    • Digital and analog gene circuits for biotechnology
    • Roquet N., Lu T.K. Digital and analog gene circuits for biotechnology. Biotechnol J 2014.
    • (2014) Biotechnol J
    • Roquet, N.1    Lu, T.K.2


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