-
1
-
-
77957240693
-
Multifactorial determinants of protein expression in prokaryotic open reading frames
-
Allert, M., Cox, J.C. and Hellinga, H.W. (2010) Multifactorial determinants of protein expression in prokaryotic open reading frames. J. Mol. Biol., 402, 905-918.
-
(2010)
J. Mol. Biol.
, vol.402
, pp. 905-918
-
-
Allert, M.1
Cox, J.C.2
Hellinga, H.W.3
-
2
-
-
0030801002
-
Gapped BLAST and PSI-BLAST: A new generation of protein database search programs
-
Altschul, S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
-
(1997)
Nucleic Acids Res.
, vol.25
, pp. 3389-3402
-
-
Altschul, S.F.1
-
3
-
-
79959991126
-
Building enhancers from the ground up: A synthetic biology approach
-
Amit, R. et al. (2011) Building enhancers from the ground up: a synthetic biology approach. Cell, 146, 105-118.
-
(2011)
Cell
, vol.146
, pp. 105-118
-
-
Amit, R.1
-
5
-
-
67849122320
-
MEME SUITE: Tools for motif discovery and searching
-
Bailey, T.L. et al. (2009) MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res., 37, W202-W208.
-
(2009)
Nucleic Acids Res.
, vol.37
-
-
Bailey, T.L.1
-
6
-
-
0028303468
-
Quantitative analysis of ribosome binding sites in E.coli
-
Barrick, D. et al. (1994) Quantitative analysis of ribosome binding sites in E.coli. Nucleic Acids Res., 22, 1287-1295.
-
(1994)
Nucleic Acids Res.
, vol.22
, pp. 1287-1295
-
-
Barrick, D.1
-
7
-
-
84877294439
-
Measurement and modeling of intrinsic transcription terminators
-
Cambray, G. et al. (2013) Measurement and modeling of intrinsic transcription terminators. Nucleic Acids Res., 41, 5139-5148.
-
(2013)
Nucleic Acids Res.
, vol.41
, pp. 5139-5148
-
-
Cambray, G.1
-
8
-
-
57149092385
-
Synonymous genes explore different evolutionary landscapes
-
Cambray, G. and Mazel, D. (2008) Synonymous genes explore different evolutionary landscapes. PLoS Genet., 4, e1000256.
-
(2008)
PLoS Genet.
, vol.4
-
-
Cambray, G.1
Mazel, D.2
-
9
-
-
80053926913
-
Toward rational design of bacterial genomes, Curr
-
Cambray, G., Mutalik, V.K. and Arkin, A.P. (2011) Toward rational design of bacterial genomes, Curr. Opin. Microbiol., 14, 624-630.
-
(2011)
Opin. Microbiol.
, vol.14
, pp. 624-630
-
-
Cambray, G.1
Mutalik, V.K.2
Arkin, A.P.3
-
11
-
-
84867615847
-
Computational codon optimization of synthetic gene for protein expression
-
Chung, B.K. and Lee, D.Y. (2012) Computational codon optimization of synthetic gene for protein expression. BMC Syst. Biol., 6, 134.
-
(2012)
BMC Syst. Biol.
, vol.6
, pp. 134
-
-
Chung, B.K.1
Lee, D.Y.2
-
12
-
-
59149092285
-
Gene synthesis demystified
-
Czar, M.J. et al. (2009) Gene synthesis demystified. Trends Biotechnol., 27, 63-72.
-
(2009)
Trends Biotechnol.
, vol.27
, pp. 63-72
-
-
Czar, M.J.1
-
13
-
-
84856740693
-
Efficient manipulations of synonymous mutations for controlling translation rate: An analytical approach
-
Dana, A. and Tuller, T. (2012) Efficient manipulations of synonymous mutations for controlling translation rate: an analytical approach. J. Comput. Biol., 19, 200-231.
-
(2012)
J. Comput. Biol.
, vol.19
, pp. 200-231
-
-
Dana, A.1
Tuller, T.2
-
14
-
-
79951565301
-
Design, construction and characterization of a set of insulated bacterial promoters
-
Davis, J.H., Rubin, A.J. and Sauer, R.T. (2011) Design, construction and characterization of a set of insulated bacterial promoters. Nucleic Acids Res., 39, 1131-1141.
-
(2011)
Nucleic Acids Res.
, vol.39
, pp. 1131-1141
-
-
Davis, J.H.1
Rubin, A.J.2
Sauer, R.T.3
-
15
-
-
0028036559
-
Control of translation by mRNA secondary structure in Escherichia coli. A quantitative analysis of literature data
-
de Smit, M.H. and van Duin, J. (1994) Control of translation by mRNA secondary structure in Escherichia coli. A quantitative analysis of literature data. J. Mol. Biol., 244, 144-150.
-
(1994)
J. Mol. Biol.
, vol.244
, pp. 144-150
-
-
De Smit, M.H.1
Van Duin, J.2
-
16
-
-
84880652281
-
Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast
-
Dvir, S. et al. (2013) Deciphering the rules by which 5'-UTR sequences affect protein expression in yeast. Proc. Natl Acad. Sci. USA, 110, E2792-E2801.
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
-
-
Dvir, S.1
-
17
-
-
28544451327
-
Foundations for engineering biology
-
Endy, D. (2005) Foundations for engineering biology. Nature, 438, 449-453.
-
(2005)
Nature
, vol.438
, pp. 449-453
-
-
Endy, D.1
-
18
-
-
84864318077
-
Operator sequence alters gene expression independently of transcription factor occupancy in bacteria
-
Garcia, H.G. et al. (2012) Operator sequence alters gene expression independently of transcription factor occupancy in bacteria. Cell Rep., 2, 150-161.
-
(2012)
Cell Rep.
, vol.2
, pp. 150-161
-
-
Garcia, H.G.1
-
19
-
-
84876044227
-
MRNA secondary structure optimization using a correlated stem-loop prediction
-
Gaspar, P. et al. (2013) mRNA secondary structure optimization using a correlated stem-loop prediction. Nucleic Acids Res, 41, e73.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Gaspar, P.1
-
20
-
-
84870439703
-
EuGene: Maximizing synthetic gene design for heterologous expression
-
Gaspar, P. et al. (2012) EuGene: maximizing synthetic gene design for heterologous expression. Bioinformatics, 28, 2683-2684.
-
(2012)
Bioinformatics
, vol.28
, pp. 2683-2684
-
-
Gaspar, P.1
-
21
-
-
25844449770
-
Galaxy: A platform for interactive large-scale genome analysis
-
Giardine, B. et al. (2005) Galaxy: a platform for interactive large-scale genome analysis. Genome Res., 15, 1451-1455.
-
(2005)
Genome Res.
, vol.15
, pp. 1451-1455
-
-
Giardine, B.1
-
22
-
-
77953584054
-
Creation of a bacterial cell controlled by a chemically synthesized genome
-
Gibson, D.G. et al. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science, 329, 52-56.
-
(2010)
Science
, vol.329
, pp. 52-56
-
-
Gibson, D.G.1
-
23
-
-
77649198142
-
A universal trend of reduced mRNA stability near the translation- initiation site in prokaryotes and eukaryotes
-
Gu, W., Zhou, T. and Wilke, C.O. (2010) A universal trend of reduced mRNA stability near the translation-initiation site in prokaryotes and eukaryotes. PLoS Comput. Biol., 6, e1000664.
-
(2010)
PLoS Comput. Biol.
, vol.6
-
-
Gu, W.1
Zhou, T.2
Wilke, C.O.3
-
24
-
-
3042782585
-
Codon bias and heterol-ogous protein expression
-
Gustafsson, C., Govindarajan, S. and Minshull, J. (2004) Codon bias and heterol-ogous protein expression. Trends Biotechnol., 22, 346-353.
-
(2004)
Trends Biotechnol.
, vol.22
, pp. 346-353
-
-
Gustafsson, C.1
Govindarajan, S.2
Minshull, J.3
-
25
-
-
0020486135
-
A role for mRNA secondary structure in the control of translation initiation
-
Hall, M.N. et al. (1982) A role for mRNA secondary structure in the control of translation initiation. Nature, 295, 616-618.
-
(1982)
Nature
, vol.295
, pp. 616-618
-
-
Hall, M.N.1
-
26
-
-
0043123153
-
Vienna RNA secondary structure server
-
Hofacker, I.L. (2003) Vienna RNA secondary structure server. Nucleic Acids Res., 31, 3429-3431.
-
(2003)
Nucleic Acids Res.
, vol.31
, pp. 3429-3431
-
-
Hofacker, I.L.1
-
27
-
-
0021958933
-
Codon usage and tRNA content in unicellular and multicellular organisms
-
Ikemura, T. (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol., 2, 13-34.
-
(1985)
Mol. Biol. Evol.
, vol.2
, pp. 13-34
-
-
Ikemura, T.1
-
28
-
-
0028804911
-
Effects of rare codon clusters on high-level expression of heterol-ogous proteins in Escherichia coli
-
Kane, J.F. (1995) Effects of rare codon clusters on high-level expression of heterol-ogous proteins in Escherichia coli. Curr. Opin. Biotechnol., 6, 494-500.
-
(1995)
Curr. Opin. Biotechnol.
, vol.6
, pp. 494-500
-
-
Kane, J.F.1
-
29
-
-
34447499141
-
Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake
-
Kingsford, C.L., Ayanbule, K. and Salzberg, S.L. (2007) Rapid, accurate, computational discovery of Rho-independent transcription terminators illuminates their relationship to DNA uptake. Genome Biol., 8, R22.
-
(2007)
Genome Biol.
, vol.8
-
-
Kingsford, C.L.1
Ayanbule, K.2
Salzberg, S.L.3
-
30
-
-
77952706498
-
Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence
-
Kinney, J.B. et al. (2010) Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc. Natl Acad. Sci. USA, 107, 9158-9163.
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 9158-9163
-
-
Kinney, J.B.1
-
31
-
-
26444479778
-
Optimization by simulated annealing
-
Kirkpatrick, S., Gelatt, C.D. Jr and Vecchi, M.P. (1983) Optimization by simulated annealing. Science, 220, 671-680.
-
(1983)
Science
, vol.220
, pp. 671-680
-
-
Kirkpatrick, S.1
Gelatt Jr., C.D.2
Vecchi, M.P.3
-
32
-
-
84882777421
-
Composability of regulatory sequences controlling transcription and translation in Escherichia coli
-
Kosuri, S. et al. (2013) Composability of regulatory sequences controlling transcription and translation in Escherichia coli. Proc. Natl Acad. Sci. USA, 110, 14024-14029.
-
(2013)
Proc. Natl Acad. Sci. USA
, vol.110
, pp. 14024-14029
-
-
Kosuri, S.1
-
33
-
-
64849114915
-
Coding-sequence determinants of gene expression in Escherichia coli
-
Kudla, G. et al. (2009) Coding-sequence determinants of gene expression in Escherichia coli. Science, 324, 255-258.
-
(2009)
Science
, vol.324
, pp. 255-258
-
-
Kudla, G.1
-
34
-
-
0348013051
-
Hierarchy of sequence-dependent features associated with prokaryotic translation
-
Lithwick, G. and Margalit, H. (2003) Hierarchy of sequence-dependent features associated with prokaryotic translation. Genome Res., 13, 2665-2673.
-
(2003)
Genome Res.
, vol.13
, pp. 2665-2673
-
-
Lithwick, G.1
Margalit, H.2
-
35
-
-
84865283376
-
DNA synthesis, assembly and applications in synthetic biology
-
Ma, S., Tang, N. and Tian, J. (2012) DNA synthesis, assembly and applications in synthetic biology. Curr. Opin. Chem. Biol., 16, 260-267.
-
(2012)
Curr. Opin. Chem. Biol.
, vol.16
, pp. 260-267
-
-
Ma, S.1
Tang, N.2
Tian, J.3
-
36
-
-
84934438960
-
UNAFold: Software for nucleic acid folding and hybridization
-
Markham, N.R. and Zuker, M. (2008) UNAFold: software for nucleic acid folding and hybridization. Methods Mol. Biol., 453, 3-31.
-
(2008)
Methods Mol. Biol.
, vol.453
, pp. 3-31
-
-
Markham, N.R.1
Zuker, M.2
-
37
-
-
84875725658
-
Quantitative estimation of activity and quality for collections of functional genetic elements
-
Mutalik, V.K. et al. (2013) Quantitative estimation of activity and quality for collections of functional genetic elements. Nat. Methods, 10, 347-353.
-
(2013)
Nat. Methods
, vol.10
, pp. 347-353
-
-
Mutalik, V.K.1
-
38
-
-
84859842558
-
Rationally designed families of orthogonal RNA regulators of translation
-
Mutalik, V.K. et al. (2012) Rationally designed families of orthogonal RNA regulators of translation. Nat. Chem. Biol., 8, 447-454.
-
(2012)
Nat. Chem. Biol.
, vol.8
, pp. 447-454
-
-
Mutalik, V.K.1
-
39
-
-
84873596341
-
Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs
-
Na, D. et al. (2013) Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat. Biotechnol., 31, 170-174.
-
(2013)
Nat. Biotechnol.
, vol.31
, pp. 170-174
-
-
Na, D.1
-
40
-
-
84863230316
-
Massively parallel functional dissection of mammalian enhancers in vivo
-
Patwardhan, R.P. et al. (2012) Massively parallel functional dissection of mammalian enhancers in vivo. Nat. Biotechnol., 30, 265-270.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 265-270
-
-
Patwardhan, R.P.1
-
41
-
-
71849118573
-
High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis
-
Patwardhan, R.P. et al. (2009) High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis. Nat. Biotechnol., 27, 1173-1175.
-
(2009)
Nat. Biotechnol.
, vol.27
, pp. 1173-1175
-
-
Patwardhan, R.P.1
-
42
-
-
78650304100
-
Synonymous but not the same: The causes and consequences of codon bias
-
Plotkin, J.B. and Kudla, G. (2011) Synonymous but not the same: the causes and consequences of codon bias. Nat. Rev. Genet., 12, 32-42.
-
(2011)
Nat. Rev. Genet.
, vol.12
, pp. 32-42
-
-
Plotkin, J.B.1
Kudla, G.2
-
43
-
-
79955773387
-
Parallel on-chip gene synthesis and application to optimization of protein expression
-
Quan, J. et al. (2011) Parallel on-chip gene synthesis and application to optimization of protein expression. Nat. Biotechnol., 29, 449-452.
-
(2011)
Nat. Biotechnol.
, vol.29
, pp. 449-452
-
-
Quan, J.1
-
44
-
-
77958499566
-
The GeneOptimizer Algorithm: Using a sliding window approach to cope with the vast sequence space in multiparameter DNA sequence optimization
-
Raab, D. et al. (2010) The GeneOptimizer Algorithm: using a sliding window approach to cope with the vast sequence space in multiparameter DNA sequence optimization. Syst. Synth. Biol., 4, 215-225.
-
(2010)
Syst. Synth. Biol.
, vol.4
, pp. 215-225
-
-
Raab, D.1
-
45
-
-
84862666301
-
A computational framework for the design of optimal protein synthesis
-
Racle, J., Overney, J. and Hatzimanikatis, V. (2012) A computational framework for the design of optimal protein synthesis. Biotechnol. Bioeng., 109, 2127-2133.
-
(2012)
Biotechnol. Bioeng.
, vol.109
, pp. 2127-2133
-
-
Racle, J.1
Overney, J.2
Hatzimanikatis, V.3
-
46
-
-
77649254204
-
Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE
-
Rhodius, V.A. and Mutalik, V.K. (2010) Predicting strength and function for promoters of the Escherichia coli alternative sigma factor, sigmaE. Proc. Natl Acad. Sci. USA, 107, 2854-2859.
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 2854-2859
-
-
Rhodius, V.A.1
Mutalik, V.K.2
-
47
-
-
84866559567
-
De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells
-
Rodrigo, G., Landrain, T.E. and Jaramillo, A. (2012) De novo automated design of small RNA circuits for engineering synthetic riboregulation in living cells. Proc. Natl Acad. Sci. USA, 109, 15271-15276.
-
(2012)
Proc. Natl Acad. Sci. USA
, vol.109
, pp. 15271-15276
-
-
Rodrigo, G.1
Landrain, T.E.2
Jaramillo, A.3
-
48
-
-
70349964350
-
Automated design of synthetic ribosome binding sites to control protein expression
-
Salis, H.M., Mirsky, E.A. and Voigt, C.A. (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
-
49
-
-
33845411737
-
Enzyme-free nucleic acid logic circuits
-
Seelig, G. et al. (2006) Enzyme-free nucleic acid logic circuits. Science, 314, 1585-1588.
-
(2006)
Science
, vol.314
, pp. 1585-1588
-
-
Seelig, G.1
-
50
-
-
84862002321
-
Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters
-
Sharon, E. et al. (2012) Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat. Biotechnol., 30, 521-530.
-
(2012)
Nat. Biotechnol.
, vol.30
, pp. 521-530
-
-
Sharon, E.1
-
51
-
-
0023650543
-
The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications
-
Sharp, P.M. and Li, W.H. (1987) The codon Adaptation Index-a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res., 15, 1281-1295.
-
(1987)
Nucleic Acids Res.
, vol.15
, pp. 1281-1295
-
-
Sharp, P.M.1
Li, W.H.2
-
52
-
-
0016610995
-
Determinant of cistron specificity in bacterial ribosomes
-
Shine, J. and Dalgarno, L. (1975) Determinant of cistron specificity in bacterial ribosomes. Nature, 254, 34-38.
-
(1975)
Nature
, vol.254
, pp. 34-38
-
-
Shine, J.1
Dalgarno, L.2
-
53
-
-
84883457107
-
Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model
-
Smith, R.P. et al. (2013) Massively parallel decoding of mammalian regulatory sequences supports a flexible organizational model. Nat. Genet., 45, 1021-1028.
-
(2013)
Nat. Genet.
, vol.45
, pp. 1021-1028
-
-
Smith, R.P.1
-
54
-
-
79959954386
-
RSAT 2011: Regulatory sequence analysis tools
-
Thomas-Chollier, M. et al. (2011) RSAT 2011: regulatory sequence analysis tools. Nucleic Acids Res., 39, W86-W91.
-
(2011)
Nucleic Acids Res.
, vol.39
-
-
Thomas-Chollier, M.1
-
55
-
-
77649245858
-
Translation efficiency is determined by both codon bias and folding energy
-
Tuller, T. et al. (2010) Translation efficiency is determined by both codon bias and folding energy. Proc. Natl Acad. Sci. USA, 107, 3645-3650.
-
(2010)
Proc. Natl Acad. Sci. USA
, vol.107
, pp. 3645-3650
-
-
Tuller, T.1
-
56
-
-
36348992094
-
Robustness and evolvability: A paradox resolved
-
Wagner, A. (2008) Robustness and evolvability: a paradox resolved. Proc. Biol. Sci., 275, 91-100.
-
(2008)
Proc. Biol. Sci.
, vol.275
, pp. 91-100
-
-
Wagner, A.1
-
57
-
-
70349199628
-
Design parameters to control synthetic gene expression in Escherichia coli
-
Welch, M. et al. (2009) Design parameters to control synthetic gene expression in Escherichia coli. PLoS One, 4, e7002.
-
(2009)
PLoS One
, vol.4
-
-
Welch, M.1
-
58
-
-
79957518680
-
Designing genes for successful protein expression
-
Welch, M. et al. (2011) Designing genes for successful protein expression. Methods Enzymol., 498, 43-66.
-
(2011)
Methods Enzymol.
, vol.498
, pp. 43-66
-
-
Welch, M.1
|