-
1
-
-
77951107086
-
Synthetic biology: Applications come of age
-
Khalil, A.S. & Collins, J.J. Synthetic biology: applications come of age. Nat. Rev. Genet. 11, 367-379 (2010).
-
(2010)
Nat. Rev. Genet
, vol.11
, pp. 367-379
-
-
Khalil, A.S.1
Collins, J.J.2
-
2
-
-
33745442792
-
The promise of synthetic biology
-
Keasling, J. The promise of synthetic biology. The Bridge 35, 18-21 (2005).
-
(2005)
The Bridge
, vol.35
, pp. 18-21
-
-
Keasling, J.1
-
3
-
-
84863980696
-
Biomolecular computing systems: Principles, progress and potential
-
Benenson, Y. Biomolecular computing systems: principles, progress and potential. Nat. Rev. Genet. 13, 455-468 (2012).
-
(2012)
Nat. Rev. Genet
, vol.13
, pp. 455-468
-
-
Benenson, Y.1
-
4
-
-
84884586013
-
Metabolic engineering: Past and future
-
Woolston, B.M., Edgar, S. & Stephanopoulos, G. Metabolic engineering: past and future. Annu. Rev. Chem. Biomol. Eng. 4, 259-288 (2013).
-
(2013)
Annu. Rev. Chem. Biomol. Eng
, vol.4
, pp. 259-288
-
-
Woolston, B.M.1
Edgar, S.2
Stephanopoulos, G.3
-
5
-
-
80052493200
-
Synthetic biology: Integrated gene circuits
-
Nandagopal, N. & Elowitz, M.B. Synthetic biology: integrated gene circuits. Science 333, 1244-1248 (2011).
-
(2011)
Science
, vol.333
, pp. 1244-1248
-
-
Nandagopal, N.1
Elowitz, M.B.2
-
6
-
-
70450223309
-
Synthetic biology: Understanding biological design from synthetic circuits
-
Mukherji, S. & van Oudenaarden, A. Synthetic biology: understanding biological design from synthetic circuits. Nat. Rev. Genet. 10, 859-871 (2009).
-
(2009)
Nat. Rev. Genet
, vol.10
, pp. 859-871
-
-
Mukherji, S.1
Van Oudenaarden, A.2
-
7
-
-
84902143991
-
-
United States. National Bureau of Standards. Office of Engineering Standards Services
-
Slattery, W.J. An Index of US Voluntary Engineering Standards; Covering Those Standards, Specifications, Test Methods, and Recommended Practices Issued by National Standardization Organizations in the United States. vol. 329 (United States. National Bureau of Standards. Office of Engineering Standards Services, 1971).
-
(1971)
An Index of US Voluntary Engineering Standards; Covering Those Standards, Specifications, Test Methods, and Recommended Practices Issued by National Standardization Organizations in the United States
, vol.329
-
-
Slattery, W.J.1
-
8
-
-
84868257400
-
An end-to-end workflow for engineering of biological networks from high-level specifications
-
Beal, J. et al. An end-to-end workflow for engineering of biological networks from high-level specifications. ACS Synth. Biol. 1, 317-331 (2012).
-
(2012)
ACS Synth. Biol
, vol.1
, pp. 317-331
-
-
Beal, J.1
-
9
-
-
78651292737
-
Essential information for synthetic DNA sequences
-
Peccoud, J. et al. Essential information for synthetic DNA sequences. Nat. Biotechnol. 29, 22 (2011).
-
(2011)
Nat. Biotechnol
, vol.29
, pp. 22
-
-
Peccoud, J.1
-
10
-
-
84876917351
-
A method for fast, high-precision characterization of synthetic biology devices
-
Beal, J., Weiss, R., Yaman, F., Davidsohn, N. & Adler, A. A method for fast, high-precision characterization of synthetic biology devices. MIT CSAIL Tech Report 2012-008 (2012).
-
(2012)
MIT CSAIL Tech Report
, pp. 2012-3008
-
-
Beal, J.1
Weiss, R.2
Yaman, F.3
Davidsohn, N.4
Adler, A.5
-
11
-
-
46949091517
-
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. 26, 787-793 (2008).
-
(2008)
Nat. Biotechnol
, vol.26
, pp. 787-793
-
-
Canton, B.1
Labno, A.2
Endy, D.3
-
12
-
-
66149143984
-
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. 3, 4 (2009).
-
(2009)
J. Biol. Eng
, vol.3
, pp. 4
-
-
Kelly, J.R.1
-
13
-
-
82355181974
-
Synthetic gene networks: Methods and protocols
-
(eds. Wilfried Weber W. & Fussenegger M.)
-
Müller, K.M. & Arndt, K.M. in Synthetic Gene Networks: Methods and Protocols (eds. Wilfried Weber, W. & Fussenegger, M.) Methods in Molecular Biology, vol. 813, 23-43 (2012).
-
(2012)
Methods in Molecular Biology
, vol.813
, pp. 23-43
-
-
Müller, K.M.1
Arndt, K.M.2
-
14
-
-
0023989064
-
Improved tools for biological sequence comparison
-
Pearson, W.R. & Lipman, D.J. Improved tools for biological sequence comparison. Proc. Natl. Acad. Sci. USA 85, 2444-2448 (1988).
-
(1988)
Proc. Natl. Acad. Sci. USA
, vol.85
, pp. 2444-2448
-
-
Pearson, W.R.1
Lipman, D.J.2
-
15
-
-
84877258311
-
A survey of enabling technologies in synthetic biology
-
Kahl, L.J. & Endy, D. A survey of enabling technologies in synthetic biology. J. Biol. Eng. 7, 13 (2013).
-
(2013)
J. Biol. Eng
, vol.7
, pp. 13
-
-
Kahl, L.J.1
Endy, D.2
-
16
-
-
84883385638
-
-
United States Standards Strategy Committee, American National Standards Institute
-
United States Standards Strategy Committee. United States Standards Strategy (American National Standards Institute, 2010).
-
(2010)
United States Standards Strategy
-
-
-
17
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
Hucka, M. et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531 (2003).
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
-
18
-
-
22044443709
-
The Sequence Ontology: A tool for the unification of genome annotations
-
Eilbeck, K. et al. The Sequence Ontology: a tool for the unification of genome annotations. Genome Biol. 6, R44 (2005).
-
(2005)
Genome Biol
, vol.6
-
-
Eilbeck, K.1
-
19
-
-
79952015982
-
Evolution of the Sequence Ontology terms and relationships
-
Mungall, C.J., Batchelor, C. & Eilbeck, K. Evolution of the Sequence Ontology terms and relationships. J. Biomed. Inform. 44, 87-93 (2011).
-
(2011)
J. Biomed. Inform
, vol.44
, pp. 87-93
-
-
Mungall, C.J.1
Batchelor, C.2
Eilbeck, K.3
-
21
-
-
0034688174
-
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 403, 339-342 (2000).
-
(2000)
Nature
, vol.403
, pp. 339-342
-
-
Gardner, T.S.1
Cantor, C.R.2
Collins, J.J.3
-
22
-
-
79952074324
-
Standard biological parts knowledgebase
-
Galdzicki, M., Rodriguez, C., Chandran, D., Sauro, H.M. & Gennari, J.H. Standard Biological Parts Knowledgebase. PLoS ONE 6, e17005 (2011).
-
(2011)
PLoS ONE
, vol.6
-
-
Galdzicki, M.1
Rodriguez, C.2
Chandran, D.3
Sauro, H.M.4
Gennari, J.H.5
-
23
-
-
79955710914
-
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 6, e18882 (2011).
-
(2011)
PLoS ONE
, vol.6
-
-
Bilitchenko, L.1
-
24
-
-
84857388023
-
DeviceEditor visual biological CAD canvas
-
Chen, J., Densmore, D., Ham, T.S., Keasling, J.D. & Hillson, N.J. DeviceEditor visual biological CAD canvas. J. Biol. Eng. 6, 1 (2012).
-
(2012)
J. Biol. Eng
, vol.6
, Issue.1
-
-
Chen, J.1
Densmore, D.2
Ham, T.S.3
Keasling, J.D.4
Hillson, N.J.5
-
25
-
-
70349964350
-
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. 27, 946-950 (2009).
-
(2009)
Nat. Biotechnol
, vol.27
, pp. 946-950
-
-
Salis, H.M.1
Mirsky, E.A.2
Voigt, C.A.3
-
26
-
-
79957442875
-
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. 498, 97-135 (2011).
-
(2011)
Methods Enzymol
, vol.498
, pp. 97-135
-
-
Xia, B.1
-
27
-
-
70350669878
-
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 25, 2848-2849 (2009).
-
(2009)
Bioinformatics
, vol.25
, pp. 2848-2849
-
-
Myers, C.J.1
-
28
-
-
84867488931
-
Design, implementation and practice of JBEI-ICE: An open source biological part registry platform and tools
-
Ham, T.S. et al. Design, implementation and practice of JBEI-ICE: an open source biological part registry platform and tools. Nucleic Acids Res. 40, e141 (2012).
-
(2012)
Nucleic Acids Res
, vol.40
-
-
Ham, T.S.1
-
29
-
-
73349101023
-
Modeling structure-function relationships in synthetic DNA sequences using attribute grammars
-
Cai, Y., Lux, M.W., Adam, L. & Peccoud, J. Modeling structure-function relationships in synthetic DNA sequences using attribute grammars. PLoS Comput. Biol. 5, e1000529 (2009).
-
(2009)
PLoS Comput. Biol
, vol.5
-
-
Cai, Y.1
Lux, M.W.2
Adam, L.3
Peccoud, J.4
-
30
-
-
77956664073
-
The BioPAX community standard for pathway data sharing
-
Demir, E. et al. The BioPAX community standard for pathway data sharing. Nat. Biotechnol. 28, 935-942 (2010).
-
(2010)
Nat. Biotechnol
, vol.28
, pp. 935-942
-
-
Demir, E.1
-
31
-
-
68449103579
-
The systems biology graphical notation
-
Le Novère, N. et al. The Systems Biology Graphical Notation. Nat. Biotechnol. 27, 735-741 (2009).
-
(2009)
Nat. Biotechnol
, vol.27
, pp. 735-741
-
-
Le Novère, N.1
-
32
-
-
33644877164
-
BioModels Database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
-
Le Novère, N. et al. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34, D689-D691 (2006).
-
(2006)
Nucleic Acids Res
, vol.34
-
-
Le Novère, N.1
-
33
-
-
2442595958
-
CellML: Its future, present and past
-
Lloyd, C.M., Halstead, M.D.B. & Nielsen, P.F. CellML: its future, present and past. Prog. Biophys. Mol. Biol. 85, 433-450 (2004).
-
(2004)
Prog. Biophys. Mol. Biol
, vol.85
, pp. 433-450
-
-
Lloyd, C.M.1
Halstead, M.D.B.2
Nielsen, P.F.3
-
34
-
-
65649154507
-
Rule-based modeling of biochemical systems with BioNetGen
-
Faeder, J.R., Blinov, M.L. & Hlavacek, W.S. Rule-based modeling of biochemical systems with BioNetGen. Methods Mol. Biol. 500, 113-167 (2009).
-
(2009)
Methods Mol. Biol
, vol.500
, pp. 113-167
-
-
Faeder, J.R.1
Blinov, M.L.2
Hlavacek, W.S.3
-
35
-
-
33746788103
-
Gene Designer: A synthetic biology tool for constructing artificial DNA segments
-
Villalobos, A., Ness, J., Gustafsson, C., Minshull, J. & Govindarajan, S. Gene Designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinformatics 7, 285 (2006).
-
(2006)
BMC Bioinformatics
, vol.7
, pp. 285
-
-
Villalobos, A.1
Ness, J.2
Gustafsson, C.3
Minshull, J.4
Govindarajan, S.5
-
36
-
-
84859320316
-
J5 DNA assembly design automation software
-
Hillson, N.J., Rosengarten, R.D. & Keasling, J.D. j5 DNA Assembly Design Automation Software. ACS Synth. Biol. 1, 14-21 (2012).
-
(2012)
ACS Synth. Biol
, vol.1
, pp. 14-21
-
-
Hillson, N.J.1
Rosengarten, R.D.2
Keasling, J.D.3
-
37
-
-
79953323650
-
Model annotation for synthetic biology: Automating model to nucleotide sequence conversion
-
Misirli, G. et al. Model annotation for synthetic biology: automating model to nucleotide sequence conversion. Bioinformatics 27, 973-979 (2011).
-
(2011)
Bioinformatics
, vol.27
, pp. 973-979
-
-
Misirli, G.1
-
38
-
-
79961137158
-
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 6, e22490 (2011).
-
(2011)
PLoS ONE
, vol.6
-
-
Beal, J.1
Lu, T.2
Weiss, R.3
-
39
-
-
71849095864
-
TinkerCell: Modular CAD tool for synthetic biology
-
Chandran, D., Bergmann, F.T. & Sauro, H.M. TinkerCell: modular CAD tool for synthetic biology. J. Biol. Eng. 3, 19 (2009).
-
(2009)
J. Biol. Eng
, vol.3
, pp. 19
-
-
Chandran, D.1
Bergmann, F.T.2
Sauro, H.M.3
|