-
1
-
-
54949133752
-
SynBioSS: the synthetic biology modeling suite
-
Hill A.D., et al. SynBioSS: the synthetic biology modeling suite. Bioinformatics 2008, 24:2551-2553.
-
(2008)
Bioinformatics
, vol.24
, pp. 2551-2553
-
-
Hill, A.D.1
-
2
-
-
71849095864
-
TinkerCell: modular CAD tool for synthetic biology
-
Chandran D., et al. TinkerCell: modular CAD tool for synthetic biology. J. Biol. Eng. 2009, 3:19.
-
(2009)
J. Biol. Eng.
, vol.3
, pp. 19
-
-
Chandran, D.1
-
3
-
-
67849130568
-
Writing DNA with GenoCAD™
-
Czar M.J., et al. Writing DNA with GenoCAD™. Nucleic Acids Res. 2009, 37:W40-W47.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Czar, M.J.1
-
4
-
-
50549103571
-
Computational design of synthetic gene circuits with composable parts
-
Marchisio M.A., Stelling J. Computational design of synthetic gene circuits with composable parts. Bioinformatics 2008, 24:1903-1910.
-
(2008)
Bioinformatics
, vol.24
, pp. 1903-1910
-
-
Marchisio, M.A.1
Stelling, J.2
-
5
-
-
46249085749
-
Asmparts: assembly of biological model parts
-
Rodrigo G., et al. Asmparts: assembly of biological model parts. Syst. Synth. Biol. 2007, 1:167-170.
-
(2007)
Syst. Synth. Biol.
, vol.1
, pp. 167-170
-
-
Rodrigo, G.1
-
6
-
-
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 2009, 25:2848-2849.
-
(2009)
Bioinformatics
, vol.25
, pp. 2848-2849
-
-
Myers, C.J.1
-
7
-
-
77956517750
-
BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks
-
Rialle S., et al. BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks. Bioinformatics 2010, 26:2298-2304.
-
(2010)
Bioinformatics
, vol.26
, pp. 2298-2304
-
-
Rialle, S.1
-
8
-
-
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 2011, 6:e18882.
-
(2011)
PLoS ONE
, vol.6
-
-
Bilitchenko, L.1
-
9
-
-
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. 2011, 498:97-135.
-
(2011)
Methods Enzymol.
, vol.498
, pp. 97-135
-
-
Xia, B.1
-
10
-
-
67650663955
-
Towards programming languages for genetic engineering of living cells
-
Pedersen M., Phillips A. Towards programming languages for genetic engineering of living cells. J. R. Soc. Interface 2009, 6(Suppl. 4):S437-S450.
-
(2009)
J. R. Soc. Interface
, vol.6
, Issue.SUPPL. 4
-
-
Pedersen, M.1
Phillips, A.2
-
11
-
-
66249088017
-
The second wave of synthetic biology: from modules to systems
-
Purnick P.E.M., Weiss R. The second wave of synthetic biology: from modules to systems. Nat. Rev. Mol. Cell Biol. 2009, 10:410-422.
-
(2009)
Nat. Rev. Mol. Cell Biol.
, vol.10
, pp. 410-422
-
-
Purnick, P.E.M.1
Weiss, R.2
-
12
-
-
75149167486
-
Five hard truths for synthetic biology
-
Kwok R. Five hard truths for synthetic biology. Nature 2010, 463:288-290.
-
(2010)
Nature
, vol.463
, pp. 288-290
-
-
Kwok, R.1
-
13
-
-
70349782009
-
Computational design tools for synthetic biology
-
Marchisio M.A., Stelling J. Computational design tools for synthetic biology. Curr. Opin. Biotechnol. 2009, 20:479-485.
-
(2009)
Curr. Opin. Biotechnol.
, vol.20
, pp. 479-485
-
-
Marchisio, M.A.1
Stelling, J.2
-
14
-
-
77956652264
-
Programming cells: towards an automated 'genetic compiler'
-
Clancy K., Voigt C.A. Programming cells: towards an automated 'genetic compiler'. Curr. Opin. Biotechnol. 2010, 21:572-581.
-
(2010)
Curr. Opin. Biotechnol.
, vol.21
, pp. 572-581
-
-
Clancy, K.1
Voigt, C.A.2
-
15
-
-
79951497643
-
Computational design approaches and tools for synthetic biology
-
MacDonald J.T., et al. Computational design approaches and tools for synthetic biology. Integr. Biol. 2011, 3:97-108.
-
(2011)
Integr. Biol.
, vol.3
, pp. 97-108
-
-
MacDonald, J.T.1
-
16
-
-
77950347143
-
The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms
-
Alterovitz G., et al. The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. Brief Bioinform. 2010, 11:80-95.
-
(2010)
Brief Bioinform.
, vol.11
, pp. 80-95
-
-
Alterovitz, G.1
-
18
-
-
0034688173
-
A synthetic oscillatory network of transcriptional regulators
-
Elowitz M.B., Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403:335-338.
-
(2000)
Nature
, vol.403
, pp. 335-338
-
-
Elowitz, M.B.1
Leibler, S.2
-
19
-
-
57049159362
-
A fast, robust and tunable synthetic gene oscillator
-
Stricker J., et al. A fast, robust and tunable synthetic gene oscillator. Nature 2008, 456:516-519.
-
(2008)
Nature
, vol.456
, pp. 516-519
-
-
Stricker, J.1
-
20
-
-
75149191906
-
A synchronized quorum of genetic clocks
-
Danino T., et al. A synchronized quorum of genetic clocks. Nature 2010, 463:326-330.
-
(2010)
Nature
, vol.463
, pp. 326-330
-
-
Danino, T.1
-
21
-
-
77951107086
-
Synthetic biology: applications come of age
-
Khalil A.S., Collins J.J. Synthetic biology: applications come of age. Nat. Rev. Genet. 2010, 11:367-379.
-
(2010)
Nat. Rev. Genet.
, vol.11
, pp. 367-379
-
-
Khalil, A.S.1
Collins, J.J.2
-
22
-
-
77951909023
-
Co-design in synthetic biology: a system-level analysis of the development of an environmental sensing device
-
Ball D.A., et al. Co-design in synthetic biology: a system-level analysis of the development of an environmental sensing device. Pac. Symp. Biocomput. 2010, 2010:385-396.
-
(2010)
Pac. Symp. Biocomput.
, vol.2010
, pp. 385-396
-
-
Ball, D.A.1
-
23
-
-
42549129218
-
From genotype to phenotype: systems biology meets natural variation
-
Benfey P.N., Mitchell-Olds T. From genotype to phenotype: systems biology meets natural variation. Science 2008, 320:495-497.
-
(2008)
Science
, vol.320
, pp. 495-497
-
-
Benfey, P.N.1
Mitchell-Olds, T.2
-
26
-
-
79959933199
-
Synthetic biology methodology and model refinement based on microelectronic modeling tools and languages
-
Gendrault Y., et al. Synthetic biology methodology and model refinement based on microelectronic modeling tools and languages. Biotechnol. J. 2011, 6:796-806.
-
(2011)
Biotechnol. J.
, vol.6
, pp. 796-806
-
-
Gendrault, Y.1
-
28
-
-
73349101023
-
Modeling structure-function relationships in synthetic DNA sequences using attribute grammars
-
Cai Y., et al. Modeling structure-function relationships in synthetic DNA sequences using attribute grammars. PLoS Comput. Biol. 2009, 5:e1000529.
-
(2009)
PLoS Comput. Biol.
, vol.5
-
-
Cai, Y.1
-
29
-
-
46949091517
-
Refinement and standardization of synthetic biological parts and devices
-
Canton B., et al. Refinement and standardization of synthetic biological parts and devices. Nat. Biotechnol. 2008, 26:787-793.
-
(2008)
Nat. Biotechnol.
, vol.26
, pp. 787-793
-
-
Canton, B.1
-
30
-
-
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. 2009, 3:4.
-
(2009)
J. Biol. Eng.
, vol.3
, pp. 4
-
-
Kelly, J.R.1
-
31
-
-
0025166089
-
Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis
-
de Smit M.H., van Duin J. Secondary structure of the ribosome binding site determines translational efficiency: a quantitative analysis. Proc. Natl. Acad. Sci. U.S.A. 1990, 87:7668-7672.
-
(1990)
Proc. Natl. Acad. Sci. U.S.A.
, vol.87
, pp. 7668-7672
-
-
de Smit, M.H.1
van Duin, J.2
-
32
-
-
70349964350
-
Automated design of synthetic ribosome binding sites to control protein expression
-
Salis H.M., et al. Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 2009, 27:946-950.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 946-950
-
-
Salis, H.M.1
-
33
-
-
77952611328
-
Mathematical modeling of translation initiation for the estimation of its efficiency to computationally design mRNA sequences with desired expression levels in prokaryotes
-
Na D., et al. 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. 2010, 4:71.
-
(2010)
BMC Syst. Biol.
, vol.4
, pp. 71
-
-
Na, D.1
-
34
-
-
77951589688
-
Cooperation between translating ribosomes and RNA polymerase in transcription elongation
-
Proshkin S., et al. Cooperation between translating ribosomes and RNA polymerase in transcription elongation. Science 2010, 328:504-508.
-
(2010)
Science
, vol.328
, pp. 504-508
-
-
Proshkin, S.1
-
36
-
-
39149113411
-
Modular cell biology: retroactivity and insulation
-
Del Vecchio D., et al. Modular cell biology: retroactivity and insulation. Mol. Syst. Biol. 2008, 4:161.
-
(2008)
Mol. Syst. Biol.
, vol.4
, pp. 161
-
-
Del Vecchio, D.1
-
37
-
-
79953903095
-
Measuring retroactivity from noise in gene regulatory networks
-
Kim K.H., Sauro H.M. Measuring retroactivity from noise in gene regulatory networks. Biophys. J. 2011, 100:1167-1177.
-
(2011)
Biophys. J.
, vol.100
, pp. 1167-1177
-
-
Kim, K.H.1
Sauro, H.M.2
-
38
-
-
59149092285
-
Gene synthesis demystified
-
Czar M.J., et al. Gene synthesis demystified. Trends Biotechnol. 2009, 27:63-72.
-
(2009)
Trends Biotechnol.
, vol.27
, pp. 63-72
-
-
Czar, M.J.1
-
39
-
-
51449095986
-
Genetic design: rising above the sequence
-
Goler J.A., et al. Genetic design: rising above the sequence. Trends Biotechnol. 2008, 26:538-544.
-
(2008)
Trends Biotechnol.
, vol.26
, pp. 538-544
-
-
Goler, J.A.1
-
40
-
-
28544451327
-
Foundations for engineering biology
-
Endy D. Foundations for engineering biology. Nature 2005, 438:449-453.
-
(2005)
Nature
, vol.438
, pp. 449-453
-
-
Endy, D.1
-
42
-
-
77649305316
-
BglBricks: a flexible standard for biological part assembly
-
Anderson J.C., et al. BglBricks: a flexible standard for biological part assembly. J. Biol. Eng. 2010, 4:1.
-
(2010)
J. Biol. Eng.
, vol.4
, pp. 1
-
-
Anderson, J.C.1
-
43
-
-
79957471219
-
Enzymatic assembly of overlapping DNA fragments
-
Gibson D.G. Enzymatic assembly of overlapping DNA fragments. Methods Enzymol. 2011, 498:349-361.
-
(2011)
Methods Enzymol.
, vol.498
, pp. 349-361
-
-
Gibson, D.G.1
-
44
-
-
68749104564
-
Structural instability of plasmid biopharmaceuticals: challenges and implications
-
Oliveira P.H., et al. Structural instability of plasmid biopharmaceuticals: challenges and implications. Trends Biotechnol. 2009, 27:503-511.
-
(2009)
Trends Biotechnol.
, vol.27
, pp. 503-511
-
-
Oliveira, P.H.1
-
45
-
-
77952526654
-
GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs
-
Cai Y., et al. GenoCAD for iGEM: a grammatical approach to the design of standard-compliant constructs. Nucleic Acids Res. 2010, 38:2637-2644.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 2637-2644
-
-
Cai, Y.1
-
46
-
-
77952521393
-
Algorithms for automated DNA assembly
-
Densmore D., et al. Algorithms for automated DNA assembly. Nucleic Acids Res. 2010, 38:2607-2616.
-
(2010)
Nucleic Acids Res.
, vol.38
, pp. 2607-2616
-
-
Densmore, D.1
-
48
-
-
58849137994
-
Systems biology: experimental design
-
Kreutz C., Timmer J. Systems biology: experimental design. FEBS J. 2009, 276:923-942.
-
(2009)
FEBS J.
, vol.276
, pp. 923-942
-
-
Kreutz, C.1
Timmer, J.2
-
49
-
-
77956498018
-
Sloppy models, parameter uncertainty, and the role of experimental design
-
Apgar J.F., et al. Sloppy models, parameter uncertainty, and the role of experimental design. Mol. Biosyst. 2010, 6:1890-1900.
-
(2010)
Mol. Biosyst.
, vol.6
, pp. 1890-1900
-
-
Apgar, J.F.1
-
50
-
-
44049088216
-
Mathematical analysis and quantification of fluorescent proteins as transcriptional reporters
-
Wang X., et al. Mathematical analysis and quantification of fluorescent proteins as transcriptional reporters. Biophys. J. 2008, 94:2017-2026.
-
(2008)
Biophys. J.
, vol.94
, pp. 2017-2026
-
-
Wang, X.1
-
51
-
-
64749116742
-
Using movies to analyse gene circuit dynamics in single cells
-
Locke J.C.W., Elowitz M.B. Using movies to analyse gene circuit dynamics in single cells. Nat. Rev. Microbiol. 2009, 7:383-392.
-
(2009)
Nat. Rev. Microbiol.
, vol.7
, pp. 383-392
-
-
Locke, J.C.W.1
Elowitz, M.B.2
-
52
-
-
68949215494
-
Microfluidic devices for measuring gene network dynamics in single cells
-
Bennett M.R., Hasty J. Microfluidic devices for measuring gene network dynamics in single cells. Nat. Rev. Genet. 2009, 10:628-638.
-
(2009)
Nat. Rev. Genet.
, vol.10
, pp. 628-638
-
-
Bennett, M.R.1
Hasty, J.2
-
53
-
-
75749143909
-
Origin of irreversibility of cell cycle start in budding yeast
-
Charvin G., et al. Origin of irreversibility of cell cycle start in budding yeast. PLoS Biol. 2010, 8:e1000284.
-
(2010)
PLoS Biol.
, vol.8
-
-
Charvin, G.1
-
54
-
-
78650334784
-
Build life to understand it
-
Elowitz M., Lim W.A. Build life to understand it. Nature 2010, 468:889-890.
-
(2010)
Nature
, vol.468
, pp. 889-890
-
-
Elowitz, M.1
Lim, W.A.2
-
55
-
-
77952903892
-
Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems
-
Bashor C.J., et al. Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. Annu. Rev. Biophys. 2010, 39:515-537.
-
(2010)
Annu. Rev. Biophys.
, vol.39
, pp. 515-537
-
-
Bashor, C.J.1
-
56
-
-
0345743608
-
Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era
-
Kell D.B., Oliver S.G. Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. Bioessays 2004, 26:99-105.
-
(2004)
Bioessays
, vol.26
, pp. 99-105
-
-
Kell, D.B.1
Oliver, S.G.2
-
57
-
-
1642336155
-
Functional genomic hypothesis generation and experimentation by a robot scientist
-
King R.D., et al. Functional genomic hypothesis generation and experimentation by a robot scientist. Nature 2004, 427:247-252.
-
(2004)
Nature
, vol.427
, pp. 247-252
-
-
King, R.D.1
-
58
-
-
77954839098
-
Machine science
-
Evans J., Rzhetsky A. Machine science. Science 2010, 329:399-400.
-
(2010)
Science
, vol.329
, pp. 399-400
-
-
Evans, J.1
Rzhetsky, A.2
-
59
-
-
79952638264
-
Cellular decision making and biological noise: from microbes to mammals
-
Balazsi G., et al. Cellular decision making and biological noise: from microbes to mammals. Cell 2011, 144:910-925.
-
(2011)
Cell
, vol.144
, pp. 910-925
-
-
Balazsi, G.1
-
60
-
-
46449120581
-
Virus attenuation by genome-scale changes in codon pair bias
-
Coleman J.R., et al. Virus attenuation by genome-scale changes in codon pair bias. Science 2008, 320:1784-1787.
-
(2008)
Science
, vol.320
, pp. 1784-1787
-
-
Coleman, J.R.1
-
61
-
-
77954482089
-
Live attenuated influenza virus vaccines by computer-aided rational design
-
Mueller S., et al. Live attenuated influenza virus vaccines by computer-aided rational design. Nat. Biotechnol. 2010, 28:723-1729.
-
(2010)
Nat. Biotechnol.
, vol.28
, pp. 723-1729
-
-
Mueller, S.1
-
62
-
-
78650304100
-
Synonymous but not the same: the causes and consequences of codon bias
-
Plotkin J.B., Kudla G. Synonymous but not the same: the causes and consequences of codon bias. Nat. Rev. Genet. 2011, 12:32-42.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 32-42
-
-
Plotkin, J.B.1
Kudla, G.2
-
63
-
-
28544433105
-
Refactoring bacteriophage T7
-
2005.0018
-
Chan L.Y., et al. Refactoring bacteriophage T7. Mol. Syst. Biol. 2005, 1. 2005.0018.
-
(2005)
Mol. Syst. Biol.
, vol.1
-
-
Chan, L.Y.1
-
64
-
-
0037041888
-
Synthetic gene network for entraining and amplifying cellular oscillations
-
Hasty J., et al. Synthetic gene network for entraining and amplifying cellular oscillations. Phys. Rev. Lett. 2002, 88:148101.
-
(2002)
Phys. Rev. Lett.
, vol.88
, pp. 148101
-
-
Hasty, J.1
-
65
-
-
0037154293
-
Synchronizing genetic relaxation oscillators by intercell signaling
-
McMillen D., et al. Synchronizing genetic relaxation oscillators by intercell signaling. Proc. Natl. Acad. Sci. U.S.A. 2002, 99:679-684.
-
(2002)
Proc. Natl. Acad. Sci. U.S.A.
, vol.99
, pp. 679-684
-
-
McMillen, D.1
-
67
-
-
79952074324
-
Standard biological parts knowledgebase
-
Galdzicki M., et al. Standard biological parts knowledgebase. PLoS ONE 2011, 6:e17005.
-
(2011)
PLoS ONE
, vol.6
-
-
Galdzicki, M.1
-
68
-
-
78651292737
-
Essential information for synthetic DNA sequences
-
Peccoud J., et al. Essential information for synthetic DNA sequences. Nat. Biotechnol. 2011, 29:22.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 22
-
-
Peccoud, J.1
-
69
-
-
33748796893
-
Open source tools and toolkits for bioinformatics: significance, and where are we?
-
Stajich J.E., Lapp H. Open source tools and toolkits for bioinformatics: significance, and where are we?. Brief Bioinform. 2006, 7:287-296.
-
(2006)
Brief Bioinform.
, vol.7
, pp. 287-296
-
-
Stajich, J.E.1
Lapp, H.2
-
70
-
-
59849087643
-
Scientific workflow design for mere mortals
-
McPhillips T., et al. Scientific workflow design for mere mortals. Future Gener. Comput. Syst. 2009, 25:541-551.
-
(2009)
Future Gener. Comput. Syst.
, vol.25
, pp. 541-551
-
-
McPhillips, T.1
-
71
-
-
42449138783
-
Scientific workflows as productivity tools for drug discovery
-
Shon J., et al. Scientific workflows as productivity tools for drug discovery. Curr. Opin. Drug Discov. Dev. 2008, 11:381-388.
-
(2008)
Curr. Opin. Drug Discov. Dev.
, vol.11
, pp. 381-388
-
-
Shon, J.1
-
72
-
-
0034688174
-
Construction of a genetic toggle switch in Escherichia coli
-
Gardner T.S., et al. 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
|