J. W. Dubendorff and F. W. Studier, Controlling basal expression in an inducible T7 expression system by blocking the target T7 promoter with lac repressor, J. Mol. Biol, vol.219, pp.45-59, 1991.

N. Mertens, E. Remaut, and W. Fiers, Tight transcriptional control mechanism ensures stable high-level expression from T7 promoter-based expression plasmids, Bio/Technology, vol.13, pp.175-179, 1995.

Z. Xie, L. Wroblewska, L. Prochazka, R. Weiss, and Y. Benenson, Multi-input RNAi-based logic circuit for identification of specific cancer cells, Science, vol.333, pp.1307-1311, 2011.

Y. Y. Chen, M. C. Jensen, and C. D. Smolke, Genetic control of mammalian T-cell proliferation with synthetic RNA regulatory systems, Proc. Natl. Acad. Sci. USA, vol.107, pp.8531-8536, 2010.

J. C. Anderson, E. J. Clarke, A. P. Arkin, and C. A. Voigt, Environmentally controlled invasion of cancer cells by engineered bacteria, J. Mol. Biol, vol.355, pp.619-627, 2006.

N. Saeidi, Engineering microbes to sense and eradicate Pseudomonas aeruginosa, a human pathogen, Mol. Syst. Biol, vol.7, p.521, 2011.

D. M. Widmaier, Engineering the Salmonella type III secretion system to export spider silk monomers, Mol. Syst. Biol, vol.5, p.309, 2009.

J. Bonnet, P. Subsoontorn, and D. Endy, Rewritable digital data storage in live cells via engineered control of recombination directionality, Proc. Natl. Acad. Sci. USA, vol.109, pp.8884-8889, 2012.

W. C. Ruder, T. Lu, and J. J. Collins, Synthetic biology moving into the clinic, Science, vol.333, pp.1248-1252, 2011.

J. Sinha, S. J. Reyes, and J. P. Gallivan, Reprogramming bacteria to seek and destroy an herbicide, Nat. Chem. Biol, vol.6, pp.464-470, 2010.

J. D. Keasling, Manufacturing molecules through metabolic engineering, Science, vol.330, pp.1355-1358, 2010.

P. A. Carr and G. M. Church, Genome engineering, Nat. Biotechnol, vol.27, pp.1151-1162, 2009.

D. Endy, Foundations for engineering biology, Nature, vol.438, pp.449-453, 2005.

G. Cambray, V. K. Mutalik, and A. P. Arkin, Toward rational design of bacterial genomes, Curr. Opin. Microbiol, vol.14, pp.624-630, 2011.
URL : https://hal.archives-ouvertes.fr/hal-02650917

S. Cardinale and A. P. Arkin, Contextualizing context for synthetic biologyidentifying causes of failure of synthetic biological systems, Biotechnol. J, vol.7, pp.856-866, 2012.

B. Wilkinson and J. Micklefield, Mining and engineering natural-product biosynthetic pathways, Nat. Chem. Biol, vol.3, pp.379-386, 2007.

B. Canton, A. Labno, and D. Endy, Refinement and standardization of synthetic biological parts and devices, Nat. Biotechnol, vol.26, pp.787-793, 2008.

C. D. Smolke, Building outside of the box: iGEM and the BioBricks Foundation, Nat. Biotechnol, vol.27, pp.1099-1102, 2009.

H. Gulvanessian and M. Holicky, Eurocodes: using reliability analysis to combine action effects, Proceedings of the ICE -Structures and Buildings, vol.158, pp.243-252, 2005.

V. K. Mutalik, G. Nonaka, S. E. Ades, V. A. Rhodius, and C. A. Gross, Promoter strength properties of the complete sigma E regulon of Escherichia coli and Salmonella enterica, J. Bacteriol, vol.191, pp.7279-7287, 2009.

I. G. Hook-barnard and D. M. Hinton, Transcription initiation by mix and match elements: flexibility for polymerase binding to bacterial promoters, Gene Regul. Syst. Bio, vol.1, pp.275-293, 2007.

T. Shimada, Classification and strength measurement of stationaryphase promoters by use of a newly developed promoter cloning vector, J. Bacteriol, vol.186, pp.7112-7122, 2004.

A. Zaslaver, A comprehensive library of fluorescent transcriptional reporters for Escherichia coli, Nat. Methods, vol.3, pp.623-628, 2006.

A. H. Babiskin and C. D. Smolke, Synthetic RNA modules for fine-tuning gene expression levels in yeast by modulating RNase III activity, Nucleic Acids Res, vol.39, pp.8651-8664, 2011.

O. Yarchuk, N. Jacques, J. Guillerez, and M. Dreyfus, Interdependence of translation, transcription and mRNA degradation in the lacZ gene, J. Mol. Biol, vol.226, pp.581-596, 1992.

K. O. Cho and C. Yanofsky, Sequence changes preceding a Shine-Dalgarno region influence trpE mRNA translation and decay, J. Mol. Biol, vol.204, pp.51-60, 1988.

A. P. Telesnitsky and M. J. Chamberlin, Sequences linked to prokaryotic promoters can affect the efficiency of downstream termination sites, J. Mol. Biol, vol.205, pp.315-330, 1989.

T. Ellinger, D. Behnke, R. Knaus, H. Bujard, and J. D. Gralla, Contextdependent effects of upstream A-tracts -stimulation or inhibition of Escherichia coli promoter function, J. Mol. Biol, vol.239, pp.466-475, 1994.

D. Stueber and H. Bujard, Transcription from efficient promoters can interfere with plasmid replication and diminish expression of plasmid specified genes, EMBO J, vol.1, pp.1399-1404, 1982.

D. Barrick, Quantitative analysis of ribosome binding sites in E.coli, Nucleic Acids Res, vol.22, pp.1287-1295, 1994.

R. S. Cox, . Iii, M. G. Surette, and M. Elowitz, Programming gene expression with combinatorial promoters, Mol. Syst. Biol, vol.3, p.145, 2007.

H. Alper, C. Fischer, E. Nevoigt, and G. Stephanopoulos, Tuning genetic control through promoter engineering, Proc. Natl. Acad. Sci. USA, vol.102, pp.12678-12683, 2005.

T. Ellis, X. Wang, and J. J. Collins, Diversity-based, model-guided construction of synthetic gene networks with predicted functions, Nat. Biotechnol, vol.27, pp.465-471, 2009.

R. Reynolds and M. J. Chamberlin, Parameters affecting transcription termination by Escherichia coli RNA: II. Construction and analysis of hybrid terminators, J. Mol. Biol, vol.224, pp.53-63, 1992.

T. A. Carrier and J. D. Keasling, Library of synthetic 5? secondary structures to manipulate mRNA stability in Escherichia coli, Biotechnol. Prog, vol.15, pp.58-64, 1999.

H. M. Salis, E. A. Mirsky, and C. A. Voigt, Automated design of synthetic ribosome binding sites to control protein expression, Nat. Biotechnol, vol.27, pp.946-950, 2009.

V. K. Mutalik, L. Qi, J. C. Guimaraes, J. B. Lucks, and A. P. Arkin, Rationally designed families of orthogonal RNA regulators of translation, Nat. Chem. Biol, vol.8, pp.447-454, 2012.

A. S. Khalil, A synthetic biology framework for programming eukaryotic transcription functions, Cell, vol.150, pp.647-658, 2012.

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, 2009.

M. H. De-smit and J. Van-duin, Control of translation by mRNA secondary structure in Escherichia coli. A quantitative analysis of literature data, J. Mol. Biol, vol.244, pp.144-150, 1994.

J. Jonsson, T. Norberg, L. Carlsson, C. Gustafsson, and S. Wold, Quantitative sequence-activity models (QSAM)-tools for sequence design, Nucleic Acids Res, vol.21, pp.733-739, 1993.

T. D. Yager and P. H. Hippel, A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli, Biochemistry, vol.30, pp.1097-1118, 1991.

J. H. Davis, A. J. Rubin, and R. T. Sauer, Design, construction and characterization of a set of insulated bacterial promoters, Nucleic Acids Res, vol.39, pp.1131-1141, 2011.

L. Qi, R. E. Haurwitz, W. Shao, J. A. Doudna, and A. P. Arkin, RNA processing enables predictable programming of gene expression, Nat. Biotechnol, vol.30, pp.1002-1006, 2012.

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, 2012.

S. Klumpp, Z. Zhang, and T. Hwa, Growth rate-dependent global effects on gene expression in bacteria, Cell, vol.139, pp.1366-1375, 2009.

V. K. Mutalik, Precise and reliable gene expression via standard transcription and translation initiation elements, Nat. Methods advance online publication, 2013.
URL : https://hal.archives-ouvertes.fr/hal-02652723

J. R. Kelly, Measuring the activity of BioBrick promoters using an in vivo reference standard, J. Biol. Eng, vol.3, p.4, 2009.

J. T. Kittleson, G. C. Wu, and J. C. Anderson, Successes and failures in modular genetic engineering, Curr. Opin. Chem. Biol, vol.16, pp.329-336, 2012.

C. F. Wu and M. S. Hamada, Experiments: Planning, Analysis, and Optimization, 2009.

F. M. Ausubel, Short Protocols in Molecular Biology, 2002.

C. Engler, R. Kandzia, and S. Marillonnet, A one pot, one step, precision cloning method with high throughput capability, PLoS ONE, vol.3, p.3647, 2008.

N. J. Hillson, R. D. Rosengarten, and J. Keasling, j5 DNA assembly design automation software, ACS Synth. Biol, vol.1, pp.14-21, 2012.

J. D. Pédelacq, S. Cabantous, T. Tran, T. C. Terwilliger, and G. S. Waldo, Engineering and characterization of a superfolder green fluorescent protein, Nat. Biotechnol, vol.24, pp.79-88, 2006.

R. E. Campbell, A monomeric red fluorescent protein, Proc. Natl. Acad. Sci. USA, vol.99, pp.7877-7882, 2002.

T. S. Lee, BglBrick vectors and datasheets: a synthetic biology platform for gene expression, J. Biol. Eng, vol.5, p.12, 2011.

A. Haldimann and B. L. Wanner, Conditional-replication, integration, excision, and retrieval plasmid-host systems for gene structure-function studies of bacteria, J. Bacteriol, vol.183, pp.6384-6393, 2001.

R. Lutz and H. Bujard, Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I 1 -I 2 regulatory elements, Nucleic Acids Res, vol.25, pp.1203-1210, 1997.

T. Baba, Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection, Mol. Syst. Biol, vol.2, p.8, 2006.

J. H. Leveau and S. E. Lindow, Predictive and interpretive simulation of green fluorescent protein expression in reporter bacteria, J. Bacteriol, vol.183, pp.6752-6762, 2001.

R. Iizuka, M. Yamagishi-shirasaki, and T. Funatsu, Kinetic study of de novo chromophore maturation of fluorescent proteins, Anal. Biochem, vol.414, pp.173-178, 2011.

K. Lo, F. Hahne, R. R. Brinkman, and R. Gottardo, flowClust: a Bioconductor package for automated gating of flow cytometry data, BMC Bioinformatics, vol.10, p.145, 2009.

M. K. Kerr and G. A. Churchill, Experimental design for gene expression microarrays, Biostatistics, vol.2, pp.183-201, 2001.

M. K. Kerr, M. Martin, and G. A. Churchill, Analysis of variance for gene expression microarray data, J. Comput. Biol, vol.7, pp.819-837, 2000.

S. Ringquist, Translation initiation in Escherichia coli: sequences within the ribosome-binding site, Mol. Microbiol, vol.6, pp.1219-1229, 1992.

K. E. Shearwin, B. P. Callen, and J. B. Egan, Transcriptional interference-a crash course, Trends Genet, vol.21, pp.339-345, 2005.