-
2
-
-
34249079154
-
Network motifs: Theory and experimental approaches
-
U. Alon. 2007. Network motifs: theory and experimental approaches. Nat. Rev. Genet. 8, 450-461.
-
(2007)
Nat. Rev. Genet.
, vol.8
, pp. 450-461
-
-
Alon, U.1
-
3
-
-
33344463375
-
Developing applications using model-driven design environments
-
K. Balasubramanian, A. Gokhale, G. Karsai, J. Sztipanovits, and S. Neema. 2006. Developing applications using model-driven design environments. Computer 39, 33-40.
-
(2006)
Computer
, vol.39
, pp. 33-40
-
-
Balasubramanian, K.1
Gokhale, A.2
Karsai, G.3
Sztipanovits, J.4
Neema, S.5
-
4
-
-
79961137158
-
Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks
-
J. Beal, T. Lu, and R. Weiss. 2011. Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks. PLoS ONE 6, e22490.
-
(2011)
PLoS ONE
, vol.6
, pp. e22490
-
-
Beal, J.1
Lu, T.2
Weiss, R.3
-
5
-
-
84879778973
-
Pigeon: A design visualizer for synthetic biology
-
S. Bhatia and D. Densmore. 2013. Pigeon: A design visualizer for synthetic biology. ACS Synthet. Biol. 2, 348-350.
-
(2013)
ACS Synthet. Biol.
, vol.2
, pp. 348-350
-
-
Bhatia, S.1
Densmore, D.2
-
6
-
-
15744387380
-
Transcriptional regulation by the numbers: Models
-
L. Bintu, N. E. Buchler, H. G. Garcia, U. Gerland, T. Hwa, J. Kondev, and R. Phillips. 2005. Transcriptional regulation by the numbers: Models. Curr. Opin. Genet. Develop. 15, 116-124.
-
(2005)
Curr. Opin. Genet. Develop.
, vol.15
, pp. 116-124
-
-
Bintu, L.1
Buchler, N.E.2
Garcia, H.G.3
Gerland, U.4
Hwa, T.5
Kondev, J.6
Phillips, R.7
-
7
-
-
29144508806
-
Development and characterization of a subtilin-regulated expression system in Bacillus subtilis: Strict control of gene expression by addition of subtilin
-
R. S. Bongers, J.-W. Veening, M. Van Wieringen, O. P. Kuipers, and M. Kleerebezem. 2005. Development and characterization of a subtilin-regulated expression system in Bacillus subtilis: Strict control of gene expression by addition of subtilin. Appl. Environ. Microbiol. 71, 8818-8824.
-
(2005)
Appl. Environ. Microbiol.
, vol.71
, pp. 8818-8824
-
-
Bongers, R.S.1
Veening, J.-W.2
Van Wieringen, M.3
Kuipers, O.P.4
Kleerebezem, M.5
-
9
-
-
0027231876
-
Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis
-
D. Bray, R. B. Bourret, andM. I. Simon. 1993. Computer simulation of the phosphorylation cascade controlling bacterial chemotaxis. Molec. Biol. Cell 4, 469-482.
-
(1993)
Molec. Biol. Cell
, vol.4
, pp. 469-482
-
-
Bray, D.1
Bourret, R.B.2
Simon, A.I.3
-
10
-
-
0037965981
-
On schemes of combinatorial transcription logic
-
N. E. Buchler, U. Gerland, and T. Hwa. 2003. On schemes of combinatorial transcription logic. Proc. Nat. Acad. Sci. 100, 5136-5141.
-
(2003)
Proc. Nat. Acad. Sci.
, vol.100
, pp. 5136-5141
-
-
Buchler, N.E.1
Gerland, U.2
Hwa, T.3
-
11
-
-
35748938455
-
A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts
-
Y. Cai, B. Hartnett, C. Gustafsson, and J. Peccoud. 2007. A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 23, 2760-2767.
-
(2007)
Bioinformatics
, vol.23
, pp. 2760-2767
-
-
Cai, Y.1
Hartnett, B.2
Gustafsson, C.3
Peccoud, J.4
-
12
-
-
1342329447
-
An overview of CellML 1. 1, a biological model description language
-
A. A. Cuellar, C. M. Lloyd, P. F. Nielsen, D. P. Bullivant, D. P. Nickerson, and P. J. Hunter. 2003. An overview of CellML 1. 1, a biological model description language. Simulation 79, 740-747.
-
(2003)
Simulation
, vol.79
, pp. 740-747
-
-
Cuellar, A.A.1
Lloyd, C.M.2
Nielsen, P.F.3
Bullivant, D.P.4
Nickerson, D.P.5
Hunter, P.J.6
-
13
-
-
71849095864
-
TinkerCell: Modular CAD tool for synthetic biology
-
D. Chandran, F. T. Bergmann, and H. M. Sauro. 2009. TinkerCell: Modular CAD tool for synthetic biology. J. Biol. Eng. 3, 19.
-
(2009)
J. Biol. Eng.
, vol.3
, pp. 19
-
-
Chandran, D.1
Bergmann, F.T.2
Sauro, H.M.3
-
14
-
-
77956652264
-
Programming cells: Towards an automated 'Genetic Compiler'
-
K. Clancy and C. A. Voigt. 2010. Programming cells: Towards an automated 'Genetic Compiler'. Curr. Opin. Biotechnol. 21, 572-581.
-
(2010)
Curr. Opin. Biotechnol.
, vol.21
, pp. 572-581
-
-
Clancy, K.1
Voigt., C.A.2
-
15
-
-
77951969603
-
Standard virtual biological parts: A repository of modular modeling components for synthetic biology
-
M. T. Cooling, V. Rouilly, G. Misirli, J. Lawson, T. Yu, J. Hallinan, and A. Wipat. 2010. Standard virtual biological parts: A repository of modular modeling components for synthetic biology. Bioinformatics 26, 925-931.
-
(2010)
Bioinformatics
, vol.26
, pp. 925-931
-
-
Cooling, M.T.1
Rouilly, V.2
Misirli, G.3
Lawson, J.4
Yu, T.5
Hallinan, J.6
Wipat, A.7
-
16
-
-
0036328418
-
Unraveling the Web services web: An introduction to SOAP, WSDL, and UDDI
-
F. Curbera, M. Duftler, R. Khalaf, W. Nagy, N. Mukhi, and S. Weerawarana. 2002. Unraveling the Web services web: An introduction to SOAP, WSDL, and UDDI. IEEE Internet Comput. 6, 86-93.
-
(2002)
IEEE Internet Comput.
, vol.6
, pp. 86-93
-
-
Curbera, F.1
Duftler, M.2
Khalaf, R.3
Nagy, W.4
Mukhi, N.5
Weerawarana, S.6
-
17
-
-
42549159572
-
OptCircuit: An optimization based method for computational design of genetic circuits
-
M. Dasika and C. Maranas. 2008. OptCircuit: An optimization based method for computational design of genetic circuits. BMC Syst. Biol. 2, 24.
-
(2008)
BMC Syst. Biol.
, vol.2
, pp. 24
-
-
Dasika, M.1
Maranas, C.2
-
18
-
-
79951565301
-
Design, construction and characterization of a set of insulated bacterial promoters
-
J. H. Davis, A. J. Rubin, and R. T. Sauer. 2010. Design, construction and characterization of a set of insulated bacterial promoters. Nucl. Acids Res. 39, 1131-1141.
-
(2010)
Nucl. Acids Res.
, vol.39
, pp. 1131-1141
-
-
Davis, J.H.1
Rubin, A.J.2
Sauer, R.T.3
-
19
-
-
77955138108
-
Engineering input/output nodes in prokaryotic regulatory circuits
-
A. De Las Heras, C. A. Carreño, E. Martnez-Garca, and V. De Lorenzo. 2010. Engineering input/output nodes in prokaryotic regulatory circuits. FEMS Microbiol. Rev. 34, 842-865.
-
(2010)
FEMS Microbiol. Rev.
, vol.34
, pp. 842-865
-
-
De Heras Las, A.1
Carreño, C.A.2
Martnez-Garca, E.3
De Lorenzo, V.4
-
21
-
-
84867823155
-
Design automation for synthetic biological systems
-
D. Densmore and S. Hassoun. 2012. Design automation for synthetic biological systems. Des. Test Comput. IEEE 1-1.
-
(2012)
Des. Test Comput. IEEE
, pp. 1
-
-
Densmore, D.1
Hassoun, S.2
-
22
-
-
77956000821
-
Rule based constraints for the construction of genetic devices
-
D. Densmore, J. T. Kittleson, L. Bilitchenko, A. Liu, and J. C. Anderson. 2010. Rule based constraints for the construction of genetic devices. In Proceedings of the IEEE International Symposium on Circuits and Systems (ISCAS'10). 557-560.
-
(2010)
Proceedings of the IEEE International Symposium on Circuits and Systems (ISCAS'10)
, pp. 557-560
-
-
Densmore, D.1
Kittleson, J.T.2
Bilitchenko, L.3
Liu, A.4
Anderson, J.C.5
-
23
-
-
79960423002
-
JSBML: A flexible Java library for working with SBML
-
A. Dräger, N. Rodriguez, M. Dumousseau, A. Dörr, C. Wrzodek, N. Le Novere, A. Zell, and M. Hucka. 2011. JSBML: A flexible Java library for working with SBML. Bioinformatics 27, 2167-2168.
-
(2011)
Bioinformatics
, vol.27
, pp. 2167-2168
-
-
Dräger, A.1
Rodriguez, N.2
Dumousseau, M.3
Dörr, A.4
Wrzodek, C.5
Le Novere, N.6
Zell, A.7
Hucka, M.8
-
24
-
-
22044443709
-
The sequence ontology: A tool for the unification of genome annotations
-
K. Eilbeck, S. Lewis, C. Mungall, M. Yandell, L. Stein, R. Durbin, and M. Ashburner. 2005. The sequence ontology: A tool for the unification of genome annotations. Genome Biol. 6, R44.
-
(2005)
Genome Biol.
, vol.6
, pp. R44
-
-
Eilbeck, K.1
Lewis, S.2
Mungall, C.3
Yandell, M.4
Stein, L.5
Durbin, R.6
Ashburner, M.7
-
25
-
-
0034688173
-
A synthetic oscillatory network of transcriptional regulators
-
M. B. Elowitz and S. Leibler. 2000. A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338.
-
(2000)
Nature
, vol.403
, pp. 335-338
-
-
Elowitz, M.B.1
Leibler, S.2
-
26
-
-
67650674074
-
Designing and encoding models for synthetic biology
-
L. Endler, N. Rodriguez, N. Juty, V. Chelliah, C. Laibe, C. Li, and N. Le Novere. 2009. Designing and encoding models for synthetic biology. J. Roy. Soc. Interf. 6, S405-S417.
-
(2009)
J. Roy. Soc. Interf.
, vol.6
, pp. S405-S417
-
-
Endler, L.1
Rodriguez, N.2
Juty, N.3
Chelliah, V.4
Laibe, C.5
Li, C.6
Le Novere, N.7
-
27
-
-
84902479181
-
An overview of the SAE architecture analysis & design language (AADL) standard: A basis formodel-based architecture-driven embedded systems engineering
-
Springer
-
P. H. Feiler, B. Lewis, S. Vestal, and E. Colbert. 2005. An overview of the SAE architecture analysis & design language (AADL) standard: A basis formodel-based architecture-driven embedded systems engineering. In Architecture Description Languages, Springer, 3-15.
-
(2005)
Architecture Description Languages
, pp. 3-15
-
-
Feiler, P.H.1
Lewis, B.2
Vestal, S.3
Colbert, E.4
-
29
-
-
9444266171
-
CellDesigner: A process diagram editor for gene-regulatory and biochemical networks
-
A. Funahashi, M. Morohashi, H. Kitano, and N. Tanimura. 2003. CellDesigner: A process diagram editor for gene-regulatory and biochemical networks. BIOSILICO 1, 159-162.
-
(2003)
BIOSILICO
, vol.1
, pp. 159-162
-
-
Funahashi, A.1
Morohashi, M.2
Kitano, H.3
Tanimura, N.4
-
30
-
-
84902159136
-
The synthetic biology open language (sbol) provides a community standard for communicating designs in synthetic biology
-
M. Galdzicki, K. P. Clancy, E. Oberortner, M. Pocock, J. Y. Quinn, C. A. Rodriguez, N. Roehner, M. L. Wilson, L. Adam, J. C. Anderson, B. A. Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. Grunberg, J. Hallinan, N. J. Hillson, J. D. Johnson, A. Kuchinsky, M. Lux, G. Misirli, J. Peccoud, H. A. Plahar, E. Sirin, G.-B. Stan, A. Villalobos, A. Wipat, J. H. Gennari, C. J. Myers, and H. M. Sauro. 2014. The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology. Nat. Biotech. 32, 545-550.
-
(2014)
Nat. Biotech.
, vol.32
, pp. 545-550
-
-
Galdzicki, M.1
Clancy, K.P.2
Oberortner, E.3
Pocock, M.4
Quinn, J.Y.5
Rodriguez, C.A.6
Roehner, N.7
Wilson, M.L.8
Adam, L.9
Anderson, J.C.10
Bartley, B.A.11
Beal, J.12
Chandran, D.13
Chen, J.14
Densmore, D.15
Endy, D.16
Grunberg, R.17
Hallinan, J.18
Hillson, N.J.19
Johnson, J.D.20
Kuchinsky, A.21
Lux, M.22
Misirli, G.23
Peccoud, J.24
Plahar, H.A.25
Sirin, E.26
Stan, G.-B.27
Villalobos, A.28
Wipat, A.29
Gennari, J.H.30
Myers, C.J.31
Sauro, H.M.32
more..
-
31
-
-
0034887203
-
Creating the gene ontology resource: Design and implementation
-
The Gene Ontology Consortium.
-
The Gene Ontology Consortium. 2001. Creating the gene ontology resource: Design and implementation. Gen. Res. 11, 1425-1433. http://genome. cshlp. org/citmgr?gca=genome%3B11%2F8%2F1425.
-
(2001)
Gen. Res.
, vol.11
, pp. 1425-1433
-
-
-
34
-
-
84861970231
-
Bridging the gap between design and reality-A dual evolutionary strategy for the design of synthetic genetic circuits
-
February 1-4, J. Schier, C. M. B. A. Correia, A. L. N. Fred, and H. Gamboa, Eds., SciTePress
-
J. Hallinan, S. Park, and A. Wipat. 2012. Bridging the gap between design and reality-A dual evolutionary strategy for the design of synthetic genetic circuits. In Proceedings of the (Bioinformatics'12)-International Conference on Bioinformatics Models, Methods and Algorithms, February 1-4, J. Schier, C. M. B. A. Correia, A. L. N. Fred, and H. Gamboa, Eds., SciTePress, 263-268.
-
(2012)
Proceedings of the (Bioinformatics'12)-International Conference on Bioinformatics Models, Methods and Algorithms
, pp. 263-268
-
-
Hallinan, J.1
Park, S.2
Wipat, A.3
-
36
-
-
54949133752
-
SynBioSS: The synthetic biology modeling suite
-
A. D. Hill, J. R. Tomshine, E. M. B. Weeding, V. Sotiropoulos, and Y. N. Kaznessis. 2008. SynBioSS: The synthetic biology modeling suite. Bioinformatics 24, 2551-2553.
-
(2008)
Bioinformatics
, vol.24
, pp. 2551-2553
-
-
Hill, A.D.1
Tomshine, J.R.2
Weeding, E.M.B.3
Sotiropoulos, V.4
Kaznessis, Y.N.5
-
37
-
-
33845368513
-
COPASI-a COmplex pathway simulator
-
S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus, M. Singhal, L. Xu, P. Mendes, and U. Kummer. 2006. COPASI-a COmplex PAthway SImulator. Bioinformatics 22, 3067-3074.
-
(2006)
Bioinformatics
, vol.22
, pp. 3067-3074
-
-
Hoops, S.1
Sahle, S.2
Gauges, R.3
Lee, C.4
Pahle, J.5
Simus, N.6
Singhal, M.7
Xu, L.8
Mendes, P.9
Kummer, U.10
-
38
-
-
0037342537
-
The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models
-
M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle, H. Kitano, A. P. Arkin, B. J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, S. Dronov, E. D. Gilles, M. Ginkel, V. Gor, I. I. Goryanin, W. J. Hedley, T. C. Hodgman, J. H. Hofmeyr, P. J. Hunter, N. S. Juty, J. L. Kasberger, A. Kremling, U. Kummer, N. Le Novere, L. M. Loew, D. Lucio, P. Mendes, E. Minch, E. D. Mjolsness, Y. Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, J. C. Schaff, B. E. Shapiro, T. S. Shimizu, H. D. Spence, J. Stelling, K. Takahashi, M. Tomita, J. Wagner, and W. J. 2003. The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531.
-
(2003)
Bioinformatics
, vol.19
, pp. 524-531
-
-
Hucka, M.1
Finney, A.2
Sauro, H.M.3
Bolouri, H.4
Doyle, J.C.5
Kitano, H.6
Arkin, A.P.7
Bornstein, B.J.8
Bray, D.9
Cornish-Bowden, A.10
Cuellar, A.A.11
Dronov, S.12
Gilles, E.D.13
Ginkel, M.14
Gor, V.15
Goryanin, I.I.16
Hedley, W.J.17
Hodgman, T.C.18
Hofmeyr, J.H.19
Hunter, P.J.20
Juty, N.S.21
Kasberger, J.L.22
Kremling, A.23
Kummer, U.24
Le Novere, N.25
Loew, L.M.26
Lucio, D.27
Mendes, P.28
Minch, E.29
Mjolsness, E.D.30
Nakayama, Y.31
Nelson, M.R.32
Nielsen, P.F.33
Sakurada, T.34
Schaff, J.C.35
Shapiro, B.E.36
Shimizu, T.S.37
Spence, H.D.38
Stelling, J.39
Takahashi, K.40
Tomita, M.41
Wagner, J.W.J.42
more..
-
39
-
-
84878026511
-
SBROME: A scalable optimization and module matching framework for automated biosystems design
-
L. Huynh, A. Tsoukalas, M. Köppe, and I. Tagkopoulos. 2013. SBROME: A scalable optimization and module matching framework for automated biosystems design. ACS Synthet. Biol. 2, 263-273.
-
(2013)
ACS Synthet. Biol.
, vol.2
, pp. 263-273
-
-
Huynh, L.1
Tsoukalas, A.2
Köppe, M.3
Tagkopoulos, I.4
-
40
-
-
38149049951
-
Models for synthetic biology
-
Y. Kaznessis. 2007. Models for synthetic biology. BMC Syst. Biol. 1, 47.
-
(2007)
BMC Syst. Biol.
, vol.1
, pp. 47
-
-
Kaznessis, Y.1
-
41
-
-
79953903095
-
Measuring retroactivity from noise in gene regulatory networks
-
Kyung H. Kim and HerbertM. Sauro. 2011. Measuring retroactivity from noise in gene regulatory networks. Biophys. J. 100, 1167-1177.
-
(2011)
Biophys. J.
, vol.100
, pp. 1167-1177
-
-
Kim, K.H.1
Sauro2
-
42
-
-
0027392580
-
Biosynthesis of the lantibiotic subtilin is regulated by a histidine kinase/response regulator system
-
C. Klein, C. Kaletta, and K. D. Entian. 1993. Biosynthesis of the lantibiotic subtilin is regulated by a histidine kinase/response regulator system. Appl. Environ. Microbiol. 59, 296-303.
-
(1993)
Appl. Environ. Microbiol.
, vol.59
, pp. 296-303
-
-
Klein, C.1
Kaletta, C.2
Entian, K.D.3
-
43
-
-
77953934646
-
BioModels database: An enhanced, curated and annotated resource for published quantitative kinetic models
-
C. Li, M. Donizelli, N. Rodriguez, H. Dharuri, L. Endler, V. Chelliah, L. Li, E. He, A. Henry, M. Stefan, J. Snoep, M. Hucka, N. Le Novere, and C. Laibe. 2010. BioModels database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst. Biol. 4, 92.
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. 92
-
-
Li, C.1
Donizelli, M.2
Rodriguez, N.3
Dharuri, H.4
Endler, L.5
Chelliah, V.6
Li, L.7
He, E.8
Henry, A.9
Stefan, M.10
Snoep, J.11
Hucka, M.12
Le Novere, N.13
Laibe, C.14
-
45
-
-
78651264001
-
Annotation of SBML models through rule-based semantic integration
-
A. Lister, P. Lord, M. Pocock, and A. Wipat. 2010. Annotation of SBML models through rule-based semantic integration. J. Biomed. Semant. 1, S3.
-
(2010)
J. Biomed. Semant.
, vol.1
, pp. S3
-
-
Lister, A.1
Lord, P.2
Pocock, M.3
Wipat, A.4
-
46
-
-
0034428916
-
An industrial view of electronic design automation
-
D. MacMillen, R. Camposano, D. Hill, and T. W. Williams. 2000. An industrial view of electronic design automation. IEEE Trans. Comput.-Aided Des. Integ. Circ. Syst. 19, 1428-1448.
-
(2000)
IEEE Trans. Comput.-Aided Des. Integ. Circ. Syst.
, vol.19
, pp. 1428-1448
-
-
MacMillen, D.1
Camposano, R.2
Hill, D.3
Williams, T.W.4
-
47
-
-
50549103571
-
Computational design of synthetic gene circuits with composable parts
-
M. A. Marchisio and J. Stelling. 2008. Computational design of synthetic gene circuits with composable parts. Bioinformatics 24, 1903-1910.
-
(2008)
Bioinformatics
, vol.24
, pp. 1903-1910
-
-
Marchisio, M.A.1
Stelling, J.2
-
48
-
-
70349782009
-
Computational design tools for synthetic biology
-
M. A. Marchisio and J. Stelling. 2009. Computational design tools for synthetic biology. Curr. Opin. Biotechnol. 20, 479-485.
-
(2009)
Curr. Opin. Biotechnol.
, vol.20
, pp. 479-485
-
-
Marchisio, M.A.1
Stelling, J.2
-
50
-
-
79953323650
-
Model annotation for synthetic biology: Automating model to nucleotide sequence conversion
-
G. Misirli, J. S. Hallinan, T. Yu, J. R. Lawson, S. M. Wimalaratne, M. T. Cooling, and A. Wipat. 2011. Model annotation for synthetic biology: Automating model to nucleotide sequence conversion. Bioinformatics 27, 973-979.
-
(2011)
Bioinformatics
, vol.27
, pp. 973-979
-
-
Misirli, G.1
Hallinan, J.S.2
Yu, T.3
Lawson, J.R.4
Wimalaratne, S.M.5
Cooling, M.T.6
Wipat, A.7
-
51
-
-
84887344613
-
BacillOndex: An integrated data resource for systems and synthetic biology
-
G. Misirli, A. Wipat, J. Mullen, K. James, M. Pocock, W. Smith, N. Allenby, and J. Hallinan. 2013. BacillOndex: An integrated data resource for systems and synthetic biology. J. Integrat. Bioinf. 10, 224.
-
(2013)
J. Integrat. Bioinf.
, vol.10
, pp. 224
-
-
Misirli, G.1
Wipat, A.2
Mullen, J.3
James, K.4
Pocock, M.5
Smith, W.6
Allenby, N.7
Hallinan, J.8
-
52
-
-
70350669878
-
IBioSim: A tool for the analysis and design of genetic circuits
-
C. J. Myers, N. Barker, K. Jones, H. Kuwahara, C. Madsen, and N.-P. D. Nguyen. 2009. iBioSim: A tool for the analysis and design of genetic circuits. Bioinformatics 25, 2848-2849.
-
(2009)
Bioinformatics
, vol.25
, pp. 2848-2849
-
-
Myers, C.J.1
Barker, N.2
Jones, K.3
Kuwahara, H.4
Madsen, C.5
Nguyen, N.-P.D.6
-
53
-
-
77957797837
-
RBSDesigner: Software for designing synthetic ribosome binding sites that yields a desired level of protein expression
-
D. Na and D. Lee. 2010. RBSDesigner: Software for designing synthetic ribosome binding sites that yields a desired level of protein expression. Bioinformatics 26, 2633-2634.
-
(2010)
Bioinformatics
, vol.26
, pp. 2633-2634
-
-
Na, D.1
Lee, D.2
-
54
-
-
77952611328
-
Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes
-
D. Na, S. Lee, and D. Lee. 2010. 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. 4, 71.
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. 71
-
-
Na, D.1
Lee, S.2
Lee, D.3
-
55
-
-
0036578645
-
Regulation of noise in the expression of a single gene
-
E. M. Ozbudak, M. Thattai, I. Kurtser, A. D. Grossman, and A. van Oudenaarden. 2002. Regulation of noise in the expression of a single gene. Nat. Genet. 31, 69-73.
-
(2002)
Nat. Genet.
, vol.31
, pp. 69-73
-
-
Ozbudak, E.M.1
Thattai, M.2
Kurtser, I.3
Grossman, A.D.4
Van A.Oudenaarden.5
-
56
-
-
67650663955
-
Towards programming languages for genetic engineering of living cells
-
M. Pedersen and A. Phillips. 2009. Towards programming languages for genetic engineering of living cells. J. Roy. Soc. Interf. 6, S437-S450.
-
(2009)
J. Roy. Soc. Interf.
, vol.6
, pp. S437-S450
-
-
Pedersen, M.1
Phillips, A.2
-
58
-
-
34547861255
-
Genetdes: Automatic design of transcriptional networks
-
G. Rodrigo, J. Carrera, and A. Jaramillo. 2007b. Genetdes: Automatic design of transcriptional networks. Bioinformatics 23, 1857-1858.
-
(2007)
Bioinformatics
, vol.23
, pp. 1857-1858
-
-
Rodrigo, G.1
Carrera, J.2
Jaramillo, A.3
-
59
-
-
80455124085
-
Computational design of synthetic regulatory networks from a genetic library to characterize the designability of dynamical behaviors
-
G. Rodrigo, J. Carrera, and A. Jaramillo. 2011. Computational design of synthetic regulatory networks from a genetic library to characterize the designability of dynamical behaviors. Nucl. Acids Res. 39, e138.
-
(2011)
Nucl. Acids Res.
, vol.39
, pp. e138
-
-
Rodrigo, G.1
Carrera, J.2
Jaramillo, A.3
-
60
-
-
70349964350
-
Automated design of synthetic ribosome binding sites to control protein expression
-
H. M. Salis, E. A. Mirsky, and C. A. Voigt. 2009. Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 27, 946-950.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 946-950
-
-
Salis, H.M.1
Mirsky, E.A.2
Voigt., C.A.3
-
61
-
-
77955155615
-
Noise and robustness in prokaryotic regulatory networks
-
R. Silva-Rocha and V. de Lorenzo. 2010. Noise and robustness in prokaryotic regulatory networks. Ann. Rev. Microbiol. 64, 257-275.
-
(2010)
Ann. Rev. Microbiol.
, vol.64
, pp. 257-275
-
-
Silva-Rocha, R.1
De Lorenzo, V.2
-
62
-
-
79952645848
-
Informing biological design by integration of systems and synthetic biology
-
C. D. Smolke and P. A. Silver. 2011. Informing biological design by integration of systems and synthetic biology. Cell 144, 855-859.
-
(2011)
Cell
, vol.144
, pp. 855-859
-
-
Smolke, C.D.1
Silver, P.A.2
-
63
-
-
77953383994
-
Measurement of single-cell dynamics
-
D. G. Spiller, C. D. Wood, D. A. Rand, and M. R. H. White. 2010. Measurement of single-cell dynamics. Nat. 465, 736-745.
-
(2010)
Nat.
, vol.465
, pp. 736-745
-
-
Spiller, D.G.1
Wood, C.D.2
Rand, D.A.3
White, M.R.H.4
-
64
-
-
4644268555
-
Mathematical models in microbial systems biology
-
J. Stelling. 2004. Mathematical models in microbial systems biology. Curr. Opin. Microbiol. 7, 513-518.
-
(2004)
Curr. Opin. Microbiol.
, vol.7
, pp. 513-518
-
-
Stelling, J.1
-
65
-
-
33645293152
-
An excitable gene regulatory circuit induces transient cellular differentiation
-
G. M. Süel, J. Garcia-Ojalvo, L. M. Liberman, and M. B. Elowitz. 2006. An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440, 545-550.
-
(2006)
Nature
, vol.440
, pp. 545-550
-
-
Süel, G.M.1
Garcia-Ojalvo, J.2
Liberman, L.M.3
Elowitz, M.B.4
-
66
-
-
0035162592
-
The COG database: New developments in phylogenetic classification of proteins from complete genomes
-
R. L. Tatusov, D. A. Natale, I. V. Garkavtsev, T. A. Tatusova, U. T. Shankavaram, B. S. Rao, B. Kiryutin, M. Y. Galperin, N. D. Fedorova, and E. V. Koonin. 2001. The COG database: New developments in phylogenetic classification of proteins from complete genomes. Nucl. Acids Res. 29, 22-28.
-
(2001)
Nucl. Acids Res.
, vol.29
, pp. 22-28
-
-
Tatusov, R.L.1
Natale, D.A.2
Garkavtsev, I.V.3
Tatusova, T.A.4
Shankavaram, U.T.5
Rao, B.S.6
Kiryutin, B.7
Galperin, M.Y.8
Fedorova, N.D.9
Koonin, E.V.10
-
67
-
-
17444387728
-
The bacillus subtilis sin operon: An evolvable network
-
C. A. Voigt, D. M. Wolf, and A. P. Arkin. 2005. The bacillus subtilis sin operon: An evolvable network. Motif. Genet. 169, 1187-1202.
-
(2005)
Motif. Genet.
, vol.169
, pp. 1187-1202
-
-
Voigt, C.A.1
Wolf, D.M.2
Arkin, A.P.3
-
68
-
-
5044227742
-
The evolution of molecular biology into systems biology
-
H. V. Westerhoff and B. O. Palsson. 2004. The evolution of molecular biology into systems biology. Nat. Biotechnol. 22, 1249-1252.
-
(2004)
Nat. Biotechnol.
, vol.22
, pp. 1249-1252
-
-
Westerhoff, H.V.1
Palsson, B.O.2
-
69
-
-
84868219934
-
Automated selection of synthetic biology parts for genetic regulatory networks
-
F. Yaman, S. Bhatia, A. Adler, D. Densmore, and J. Beal. 2012. Automated selection of synthetic biology parts for genetic regulatory networks. ACS Synthet. Biol. 1, 332-344.
-
(2012)
ACS Synthet. Biol.
, vol.1
, pp. 332-344
-
-
Yaman, F.1
Bhatia, S.2
Adler, A.3
Densmore, D.4
Beal, J.5
-
70
-
-
77951925139
-
Synthetic biology: Tools to design, build, and optimize cellular processes
-
E. Young and H. Alper. 2010. Synthetic biology: Tools to design, build, and optimize cellular processes. J. Biomed. Biotechnol.
-
(2010)
J. Biomed. Biotechnol
-
-
Young, E.1
Alper, H.2
-
71
-
-
84899436101
-
Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits
-
A. R. Zomorrodi and C. D. Maranas. 2014. Coarse-grained optimization-driven design and piecewise linear modeling of synthetic genetic circuits. Europ. J. Oper. Res.
-
(2014)
Europ. J. Oper. Res
-
-
Zomorrodi, A.R.1
Maranas, C.D.2
|