-
1
-
-
71849110893
-
Next-generation synthetic gene networks
-
Dec.
-
T. K. Lu, A. S. Khalil, and J. J. Collins, "Next-generation synthetic gene networks," Nat. Biotechnol., vol. 27, pp. 1139-1150, Dec. 2009.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 1139-1150
-
-
Lu, T.K.1
Khalil, A.S.2
Collins, J.J.3
-
2
-
-
66249088017
-
The second wave of synthetic biology: From modules to systems
-
Jun.
-
P. E. Purnick and R. Weiss, "The second wave of synthetic biology: From modules to systems," Nat. Rev. Mol. Cell Biol., vol. 10, pp. 410-422, Jun. 2009.
-
(2009)
Nat. Rev. Mol. Cell Biol.
, vol.10
, pp. 410-422
-
-
Purnick, P.E.1
Weiss, R.2
-
3
-
-
84890178034
-
Advances in genetic circuit design: Novel biochemistries, deep partmining, precision gene expression
-
A. A. Nielsen, T. H. Segall-Shapiro, and C. A. Voigt, "Advances in genetic circuit design:Novel biochemistries, deep partmining, precision gene expression," Curr. Opin. Chem. Biol., vol. 17, no. 6, pp. 878-892, 2013.
-
(2013)
Curr. Opin. Chem. Biol.
, vol.17
, Issue.6
, pp. 878-892
-
-
Nielsen, A.A.1
Segall-Shapiro, T.H.2
Voigt, C.A.3
-
4
-
-
84899694320
-
Principles of genetic circuit design
-
J. A. Brophy and C. A. Voigt, "Principles of genetic circuit design," Nat. Methods, vol. 11, no. 5, pp. 508-520, 2014.
-
(2014)
Nat. Methods
, vol.11
, Issue.5
, pp. 508-520
-
-
Brophy, J.A.1
Voigt, C.A.2
-
5
-
-
84902159136
-
The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology
-
M. Galdzicki et al., "The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology," Nat. Biotechnol., vol. 32, pp. 545-550, 2014.
-
(2014)
Nat. Biotechnol.
, vol.32
, pp. 545-550
-
-
Galdzicki, M.1
-
6
-
-
84886102271
-
Characterization of a quorum sensing device for synthetic biology design: Experimental and modeling validation
-
N. Saeidi, M. Arshath, M. W. Chang, and C. L. Poh, "Characterization of a quorum sensing device for synthetic biology design: Experimental and modeling validation," Chem. Eng. Sci., vol. 103, pp. 91-99, 2013.
-
(2013)
Chem. Eng. Sci.
, vol.103
, pp. 91-99
-
-
Saeidi, N.1
Arshath, M.2
Chang, M.W.3
Poh, C.L.4
-
7
-
-
78651397316
-
Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'
-
Jan.
-
A. Tamsir, J. J. Tabor, and C. A. Voigt, "Robust multicellular computing using genetically encoded NOR gates and chemical 'wires'," Nature, vol. 469, pp. 212-215, Jan. 2011.
-
(2011)
Nature
, vol.469
, pp. 212-215
-
-
Tamsir, A.1
Tabor, J.J.2
Voigt, C.A.3
-
8
-
-
84868619337
-
Genetic programs constructed from layered logic gates in single cells
-
Nov.
-
T. S. Moon, C. Lou, A. Tamsir, B. C. Stanton, and C. A. Voigt, "Genetic programs constructed from layered logic gates in single cells," Nature, vol. 491, pp. 249-253, Nov. 2012.
-
(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
-
9
-
-
84897096810
-
Genomic mining of prokaryotic repressors for orthogonal logic gates
-
Feb.
-
B. C. Stanton et al., "Genomic mining of prokaryotic repressors for orthogonal logic gates," Nat. Chem. Biol., vol. 10, pp. 99-105, Feb. 2014.
-
(2014)
Nat. Chem. Biol.
, vol.10
, pp. 99-105
-
-
Stanton, B.C.1
-
10
-
-
84868219934
-
Automated selection of synthetic biology parts for genetic regulatory networks
-
F. Yaman, S. Bhatia, A. Adler, D. Densmore, and J. Beal, "Automated selection of synthetic biology parts for genetic regulatory networks," ACS Synth. Biol., vol. 1, no. 8, pp. 332-344, 2012.
-
(2012)
ACS Synth. Biol.
, vol.1
, Issue.8
, pp. 332-344
-
-
Yaman, F.1
Bhatia, S.2
Adler, A.3
Densmore, D.4
Beal, J.5
-
11
-
-
84863322344
-
Contextualizing context for synthetic biology-identifying causes of failure of synthetic biological systems
-
Jul.
-
S. Cardinale and A. P. Arkin, "Contextualizing context for synthetic biology-identifying causes of failure of synthetic biological systems," Biotechnol. J., vol. 7, pp. 856-866, Jul. 2012.
-
(2012)
Biotechnol. J.
, vol.7
, pp. 856-866
-
-
Cardinale, S.1
Arkin, A.P.2
-
12
-
-
84869476328
-
Ribozyme-based insulator parts buffer synthetic circuits from genetic context
-
Nov.
-
C. Lou, B. Stanton, Y. J. Chen, B. Munsky, and C. A. Voigt, "Ribozyme-based insulator parts buffer synthetic circuits from genetic context," Nat. Biotechnol., vol. 30, pp. 1137-1142, Nov. 2012.
-
(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
-
13
-
-
84875720517
-
Precise and reliable gene expression via standard transcription and translation initiation elements
-
V. K. Mutalik et al., "Precise and reliable gene expression via standard transcription and translation initiation elements," Nat. Methods, vol. 10, no. 4, pp. 354-360, 2013.
-
(2013)
Nat. Methods
, vol.10
, Issue.4
, pp. 354-360
-
-
Mutalik, V.K.1
-
14
-
-
84874093664
-
Promoter element arising from the fusion of standard biobrick parts
-
A. I. Yao et al., "Promoter element arising from the fusion of standard biobrick parts," ACS Synth. etic Biol., vol. 2, no. 2, pp. 111-120, 2013.
-
(2013)
ACS Synth. Etic Biol.
, vol.2
, Issue.2
, pp. 111-120
-
-
Yao, A.I.1
-
15
-
-
39149113411
-
Modular cell biology: Retroactivity and insulation
-
D. Del Vecchio, A. J. Ninfa, and E. D. Sontag, "Modular cell biology: Retroactivity and insulation," Mol. Syst. Biol., vol. 4, p. 161, 2008.
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 161
-
-
Del Vecchio, D.1
Ninfa, A.J.2
Sontag, E.D.3
-
16
-
-
84880772006
-
Effects of genetic variation on the e. Coli host-circuit interface
-
S. Cardinale, M. P. Joachimiak, and A. P. Arkin, "Effects of genetic variation on the e. coli host-circuit interface," Cell Reports, vol. 4, no. 2, pp. 231-237, 2013.
-
(2013)
Cell Reports
, vol.4
, Issue.2
, pp. 231-237
-
-
Cardinale, S.1
Joachimiak, M.P.2
Arkin, A.P.3
-
17
-
-
84890217908
-
A wise consistency: Engineering biology for conformity, reliability, predictability
-
A. P. Arkin, "A wise consistency: Engineering biology for conformity, reliability, predictability," Current Opin. Chem. Biol., vol. 17, no. 6, pp. 893-901, 2013.
-
(2013)
Current Opin. Chem. Biol.
, vol.17
, Issue.6
, pp. 893-901
-
-
Arkin, A.P.1
-
18
-
-
84874687019
-
Repurposing crispr as an RNA-guided platform for sequence-specific control of gene expression
-
L. S. Qi et al., "Repurposing crispr as an rna-guided platform for sequence-specific control of gene expression," Cell, vol. 152, no. 5, pp. 1173-1183, 2013.
-
(2013)
Cell
, vol.152
, Issue.5
, pp. 1173-1183
-
-
Qi, L.S.1
-
19
-
-
84882986957
-
Programmable repression and activation of bacterial gene expression using an engineered crispr-cas system
-
D. Bikard et al., "Programmable repression and activation of bacterial gene expression using an engineered crispr-cas system," Nucleic Acids Res., vol. 41, no. 15, pp. 7429-7437, 2013.
-
(2013)
Nucleic Acids Res.
, vol.41
, Issue.15
, pp. 7429-7437
-
-
Bikard, D.1
-
20
-
-
84934936070
-
Multi-input crispr/cas genetic circuits that interface host regulatory networks
-
A. A. Nielsen and C. A. Voigt, "Multi-input crispr/cas genetic circuits that interface host regulatory networks," Mol. Syst. Biol., vol. 10, no. 11, 2014.
-
(2014)
Mol. Syst. Biol.
, vol.10
, Issue.11
-
-
Nielsen, A.A.1
Voigt, C.A.2
-
21
-
-
84862180741
-
A tunable zinc finger-based framework for boolean logic computation in mammalian cells
-
J. J. Lohmueller, T. Z. Armel, and P. A. Silver, "A tunable zinc finger-based framework for boolean logic computation in mammalian cells," Nucleic Acids Res., vol. 40, no. 11, pp. 5180-5187, 2012.
-
(2012)
Nucleic Acids Res.
, vol.40
, Issue.11
, pp. 5180-5187
-
-
Lohmueller, J.J.1
Armel, T.Z.2
Silver, P.A.3
-
22
-
-
84890034375
-
Two-and three-input tale-based and logic computation in embryonic stem cells
-
F. Lienert et al., "Two-and three-input tale-based and logic computation in embryonic stem cells," Nucleic Acids Res., vol. 41, no. 21, pp. 9967-9975, 2013.
-
(2013)
Nucleic Acids Res.
, vol.41
, Issue.21
, pp. 9967-9975
-
-
Lienert, F.1
-
24
-
-
84909963314
-
Toehold switches: De-novo-designed regulators of gene expression
-
A. A. Green, P. A. Silver, J. J. Collins, and P. Yin, "Toehold switches: De-novo-designed regulators of gene expression," Cell, vol. 159, no. 4, pp. 925-939, 2014.
-
(2014)
Cell
, vol.159
, Issue.4
, pp. 925-939
-
-
Green, A.A.1
Silver, P.A.2
Collins, J.J.3
Yin, P.4
-
25
-
-
84876917351
-
-
MIT, Cambridge, MA, USA, Tech. Rep. MIT-CSAIL-TR-2012-008
-
J. Beal, R. Weiss, F. Yaman, N. Davidsohn, and A. Adler, "A method for fast, high-precision characterization of synthetic biology devices," MIT, Cambridge, MA, USA, Tech. Rep. MIT-CSAIL-TR-2012-008, 2012.
-
(2012)
A Method for Fast, High-precision Characterization of Synthetic Biology Devices
-
-
Beal, J.1
Weiss, R.2
Yaman, F.3
Davidsohn, N.4
Adler, A.5
-
26
-
-
66149143984
-
Measuring the activity of biobrick promoters using an in vivo reference standard
-
J. R. Kelly et al., "Measuring the activity of biobrick promoters using an in vivo reference standard," J. Biol. Eng., vol. 3, no. 1, p. 4, 2009.
-
(2009)
J. Biol. Eng.
, vol.3
, Issue.1
, pp. 4
-
-
Kelly, J.R.1
-
27
-
-
0034688174
-
Construction of a genetic toggle switch in Escherichia coli
-
Jan.
-
T. S. Gardner, C. R. Cantor, and J. J. Collins, "Construction of a genetic toggle switch in Escherichia coli," Nature, vol. 403, pp. 339-342, Jan. 2000.
-
(2000)
Nature
, vol.403
, pp. 339-342
-
-
Gardner, T.S.1
Cantor, C.R.2
Collins, J.J.3
-
28
-
-
66349125024
-
Synthetic gene networks that count
-
A. E. Friedland et al., "Synthetic gene networks that count," Science, vol. 324, no. 5931, pp. 1199-1202, 2009.
-
(2009)
Science
, vol.324
, Issue.5931
, pp. 1199-1202
-
-
Friedland, A.E.1
-
29
-
-
84878381909
-
Synthetic analog computation in living cells
-
R. Daniel, J. R. Rubens, R. Sarpeshkar, and T. K. Lu, "Synthetic analog computation in living cells," Nature, vol. 497, no. 7451, pp. 619-623, 2013.
-
(2013)
Nature
, vol.497
, Issue.7451
, pp. 619-623
-
-
Daniel, R.1
Rubens, J.R.2
Sarpeshkar, R.3
Lu, T.K.4
-
30
-
-
84894681034
-
Analog synthetic biology
-
R. Sarpeshkar, "Analog synthetic biology," Philos. T. R. Soc. A., vol. 372, no. 2012, p. 20130110, 2014.
-
(2014)
Philos. T. R. Soc. A.
, vol.372
, Issue.2012
, pp. 20130110
-
-
Sarpeshkar, R.1
-
31
-
-
0022769976
-
Graph-based algorithms for boolean function manipulation
-
Aug.
-
R. E. Bryant, "Graph-based algorithms for boolean function manipulation," IEEE Trans. Comput., vol. C-35, no. 8, pp. 677-691, Aug. 1986.
-
(1986)
IEEE Trans. Comput.
, vol.C-35
, Issue.8
, pp. 677-691
-
-
Bryant, R.E.1
-
33
-
-
84889358019
-
-
New York, NY, USA: Wiley-IEEE Press
-
P. P. Chu, RTL Hardware Design Using VHDL: Coding for Efficiency, Portability, Scalability. New York, NY, USA: Wiley-IEEE Press, 2006.
-
(2006)
RTL Hardware Design Using VHDL: Coding for Efficiency, Portability, Scalability
-
-
Chu, P.P.1
-
35
-
-
0021936756
-
Solving low-density subset sum problems
-
J. C. Lagarias and A. Odlyzko, "Solving low-density subset sum problems," J. ACM, vol. 32, no. 1, pp. 229-246, 1985.
-
(1985)
J. ACM
, vol.32
, Issue.1
, pp. 229-246
-
-
Lagarias, J.C.1
Odlyzko, A.2
-
36
-
-
84897431487
-
Modeling biology with hdl languages: A first step toward a genetic design automation tool inspired from microelectronics
-
Apr.
-
Y. Gendrault, M. Madec, C. Lallement, and J. Haiech, "Modeling biology with hdl languages: A first step toward a genetic design automation tool inspired from microelectronics," IEEE Trans. Bio-Med. Eng., vol. 61, no. 4, pp. 1231-1240, Apr. 2014.
-
(2014)
IEEE Trans. Bio-Med. Eng.
, vol.61
, Issue.4
, pp. 1231-1240
-
-
Gendrault, Y.1
Madec, M.2
Lallement, C.3
Haiech, J.4
-
37
-
-
67650663955
-
Towards programming languages for genetic engineering of living cells
-
M. Pedersen and A. Phillips, "Towards programming languages for genetic engineering of living cells," J. Roy. Soc. Interface, vol. 6, no. Suppl. 4, pp. S437-S450, 2009.
-
(2009)
J. Roy. Soc. Interface
, vol.6
, pp. S437-S450
-
-
Pedersen, M.1
Phillips, A.2
-
38
-
-
79961137158
-
Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks
-
J. Beal, T. Lu, and R. Weiss, "Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks," PLoS ONE, vol. 6, 2011.
-
(2011)
PLoS ONE
, vol.6
-
-
Beal, J.1
Lu, T.2
Weiss, R.3
-
39
-
-
84921345937
-
Proposed data model for the next version of the Synthetic Biology Open Language
-
N. Roehner et al., "Proposed data model for the next version of the Synthetic Biology Open Language," ACS Synth. Biol., vol. 4, pp. 57-71, 2015.
-
(2015)
ACS Synth. Biol.
, vol.4
, pp. 57-71
-
-
Roehner, N.1
-
40
-
-
0037342537
-
The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models
-
M. Hucka et al., "The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models," Bioinformatics, vol. 19, no. 4, pp. 524-531, 2003.
-
(2003)
Bioinformatics
, vol.19
, Issue.4
, pp. 524-531
-
-
Hucka, M.1
-
41
-
-
0037715313
-
Modular modeling of cellular systems with ProMoT/Diva
-
M. Ginkel, A. Kremling, T. Nutsch, R. Rehner, and E. D. Gilles, "Modular modeling of cellular systems with ProMoT/Diva," Bioinformatics, vol. 19, pp. 1169-1176, 2003.
-
(2003)
Bioinformatics
, vol.19
, pp. 1169-1176
-
-
Ginkel, M.1
Kremling, A.2
Nutsch, T.3
Rehner, R.4
Gilles, E.D.5
-
42
-
-
77950327394
-
A language for biochemical systems: Design and formal specification
-
M. Pedersen and G. D. Plotkin, "A language for biochemical systems: Design and formal specification," Proc. CMSB, pp. 77-145, 2010.
-
(2010)
Proc. CMSB
, pp. 77-145
-
-
Pedersen, M.1
Plotkin, G.D.2
-
43
-
-
47149093382
-
Rule-based modelling, symmetries, refinements
-
Berlin, Germany: Springer-Verlag
-
V. Danos, J. Feret, W. Fontana, R. Harmer, and J. Krivine, "Rule-based modelling, symmetries, refinements," in Formal Methods in Systems Biology. Berlin, Germany: Springer-Verlag, 2008, pp. 103-122.
-
(2008)
Formal Methods in Systems Biology
, pp. 103-122
-
-
Danos, V.1
Feret, J.2
Fontana, W.3
Harmer, R.4
Krivine, J.5
-
45
-
-
84874035997
-
Synthesizing biomolecule-based boolean logic gates
-
T. Miyamoto, S. Razavi, R. DeRose, and T. Inoue, "Synthesizing biomolecule-based boolean logic gates," ACS Synth. Biol., vol. 2, no. 2, pp. 72-82, 2012.
-
(2012)
ACS Synth. Biol.
, vol.2
, Issue.2
, pp. 72-82
-
-
Miyamoto, T.1
Razavi, S.2
DeRose, R.3
Inoue, T.4
-
46
-
-
84875230351
-
Synthetic circuits integrating logic and memory in living cells
-
May
-
P. Siuti, J. Yazbek, and T. K. Lu, "Synthetic circuits integrating logic and memory in living cells," Nat. Biotechnol., vol. 31, pp. 448-452, May 2013.
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 448-452
-
-
Siuti, P.1
Yazbek, J.2
Lu, T.K.3
-
47
-
-
84875494939
-
Library of synthetic transcriptional and gates built with split t7 RNA polymerase mutants
-
D. L. Shis and M. R. Bennett, "Library of synthetic transcriptional and gates built with split t7 rna polymerase mutants," PNAS, vol. 110, no. 13, pp. 5028-5033, 2013.
-
(2013)
PNAS
, vol.110
, Issue.13
, pp. 5028-5033
-
-
Shis, D.L.1
Bennett, M.R.2
-
48
-
-
50549095533
-
-
master's thesis, MIT, Cambridge, MA, USA
-
J. Goler, "BioJADE: A design and simulation tools for synthetic biological systems," master's thesis, MIT, Cambridge, MA, USA, 2004.
-
(2004)
BioJADE: A Design and Simulation Tools for Synthetic Biological Systems
-
-
Goler, J.1
-
49
-
-
84878035796
-
AutoBioCAD: Full biodesign automation of genetic circuits
-
G. Rodrigo and A. Jaramillo, "AutoBioCAD: Full biodesign automation of genetic circuits," ACS Synth. Biol., vol. 2, no. 5, pp. 230-236, 2013.
-
(2013)
ACS Synth. Biol.
, vol.2
, Issue.5
, pp. 230-236
-
-
Rodrigo, G.1
Jaramillo, A.2
-
50
-
-
42549159572
-
OptCircuit: An optimization based method for computational design of genetic circuits
-
M. S. Daika and C. D. Maranas, "OptCircuit: An optimization based method for computational design of genetic circuits," BMC Syst. Biol., vol. 2, no. 24, 2008.
-
(2008)
BMC Syst. Biol.
, vol.2
, Issue.24
-
-
Daika, M.S.1
Maranas, C.D.2
-
51
-
-
84868257400
-
An end-to-end workflow for engineering of biological networks from high-level specifications
-
J. Beal et al., "An end-to-end workflow for engineering of biological networks from high-level specifications," ACS Synth. Biol., vol. 1, no. 8, pp. 317-331, 2012.
-
(2012)
ACS Synth. Biol.
, vol.1
, Issue.8
, pp. 317-331
-
-
Beal, J.1
-
52
-
-
84859962781
-
Automatic design of synthetic gene circuits through mixed integer non-linear programming
-
L. Huynh, J. Kececioglu, M. Koppe, and I. Tagkopoulos, "Automatic design of synthetic gene circuits through mixed integer non-linear programming," PloS ONE, vol. 7, no. 4, 2012.
-
(2012)
PloS ONE
, vol.7
, Issue.4
-
-
Huynh, L.1
Kececioglu, J.2
Koppe, M.3
Tagkopoulos, I.4
-
53
-
-
84878026511
-
SBROME: A scalable optimization and module matching framework for automated biosystems design
-
L. Huynh, A. Tsoukalas, M. Koppe, and I. Tagkopoulos, "SBROME: A scalable optimization and module matching framework for automated biosystems design," ACS Synth. Biol., vol. 2, no. 5, pp. 1073-1089, 2013.
-
(2013)
ACS Synth. Biol.
, vol.2
, Issue.5
, pp. 1073-1089
-
-
Huynh, L.1
Tsoukalas, A.2
Koppe, M.3
Tagkopoulos, I.4
-
54
-
-
84906244151
-
Optimal part and module selection for synthetic gene circuit design automation
-
L. Huynh and I. Tagkopoulos, "Optimal part and module selection for synthetic gene circuit design automation," ACS Synth. Biol., vol. 3, no. 8, pp. 556-564, 2014.
-
(2014)
ACS Synth. Biol.
, vol.3
, Issue.8
, pp. 556-564
-
-
Huynh, L.1
Tagkopoulos, I.2
-
55
-
-
84906270297
-
Directed acyclic graph-based technology mapping of genetic circuit models
-
N. Roehner and C. J. Myers, "Directed acyclic graph-based technology mapping of genetic circuit models," ACS Synth. Biol., vol. 3, no. 8, pp. 543-555, 2014.
-
(2014)
ACS Synth. Biol.
, vol.3
, Issue.8
, pp. 543-555
-
-
Roehner, N.1
Myers, C.J.2
-
56
-
-
84994546251
-
Parts & Pools: A framework for modular design of synthetic gene circuits
-
M. A. Marchisio, "Parts & Pools: A framework for modular design of synthetic gene circuits," Front Bioeng. Biotechnol., vol. 2, no. 42, 2014.
-
(2014)
Front Bioeng. Biotechnol.
, vol.2
, Issue.42
-
-
Marchisio, M.A.1
-
57
-
-
84946497311
-
A top-down approach for genetic logic synthesi
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Jun.
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S. M. Laursen, J. J. Boysen, and J. Madsen, "A top-down approach for genetic logic synthesi.," in Proc. IWBDA Con., Jun. 2014, vol. 1, pp. 62-63.
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(2014)
Proc. IWBDA Con.
, vol.1
, pp. 62-63
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Laursen, S.M.1
Boysen, J.J.2
Madsen, J.3
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