Model-based design of synthetic, biological systems

Chemical Engineering Science

Volumn 103, Issue , 2013, Pages 2-11

  Crook, Nathan ^a   Alper, Hal S ^a,b  

^a The University of Texas at Austin   (United States)

^b UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

Biological and biomolecular engineering; Cellular biology and engineering; Mathematical modeling; Metabolism; Molecular biology; Synthetic biology

Indexed keywords

BIOLOGICAL SYSTEMS; CELL ENGINEERING; CHEMICAL ENGINEERING; CHEMICAL PLANTS; CYTOLOGY; MATHEMATICAL MODELS; METABOLISM; MOLECULAR BIOLOGY;

BIOMOLECULAR ENGINEERING; CELLULAR BEHAVIORS; CELLULAR BIOLOGY; CELLULAR METABOLISM; CHEMICAL REACTION NETWORKS; COMPLEX DYNAMIC BEHAVIOR; ENGINEERING FRAMEWORKS; SYNTHETIC BIOLOGY;

DESIGN;

EID: 84886101511     PISSN: 00092509     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ces.2012.12.022     Document Type: Article

References (151)

1. Alper H., Jin Y.-S., Moxley J.F., Stephanopoulos G. Identifying gene targets for the metabolic engineering of lycopene biosynthesis in Escherichia coli. Metab. Eng. 2005, 7:155-164.
2. Amit R., Garcia Hernan G., Phillips R., Fraser Scott E. Building enhancers from the ground up: a synthetic biology approach. Cell 2011, 146:105-118.
3. Antoniewicz M.R., Kelleher J.K., Stephanopoulos G. Determination of confidence intervals of metabolic fluxes estimated from stable isotope measurements. Metab. Eng. 2006, 8:324-337.
4. Antoniewicz M.R., Kelleher J.K., Stephanopoulos G. Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions. Metab. Eng. 2007, 9:68-86.
5. Arnold F.H., Volkov A.A. Directed evolution of biocatalysts. Curr. Opin. Chem. Biol. 1999, 3:54-59.
6. Asadollahi M.A., Maury J., Patil K.R., Schalk M., Clark A., Nielsen J. Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metab. Eng. 2009, 11:328-334.
7. Balagadde F.K., Song H., Ozaki J., Collins C.H., Barnet M., Arnold F.H., Quake S.R., You L. A synthetic Escherichia coli predator-prey ecosystem. Mol. Syst. Biol. 2008, 4:187.
8. Barnes C.P., Silk D., Sheng X., Stumpf M.P.H. Bayesian design of synthetic biological systems. Proc. Natl. Acad. Sci 2011.
9. Basu S., Gerchman Y., Collins C.H., Arnold F.H., Weiss R. A synthetic multicellular system for programmed pattern formation. Nature 2005, 434:1130-1134.
10. Basu S., Mehreja R., Thiberge S., Chen M.-T., Weiss R. Spatiotemporal control of gene expression with pulse-generating networks. Proc. Natl. Acad. Sci. 2004, 101:6355-6360.
11. Bates J.T., Chivian D., Arkin A.P. GLAMM: genome-linked application for metabolic maps. Nucleic Acids Res. 2011, 39:W400-405.
12. Beard D.A., Babson E., Curtis E., Qian H. Thermodynamic constraints for biochemical networks. J. Theor. Biol. 2004, 228:327-333.
13. Becskei A., Seraphin B., Serrano L. Positive feedback in eukaryotic gene networks: cell differentiation by graded to binary response conversion. EMBO J. 2001, 20:2528-2535.
14. Bilitchenko L., Liu A., Cheung S., Weeding E., Xia B., Leguia M., Anderson J.C., Densmore D. Eugene-a domain specific language for specifying and constraining synthetic biological parts, devices, and systems. PLoS ONE 2011, 6:e18882.
15. Blazeck, J., Alper, H.S., 2013. Promoter engineering: recentadvances in controlling transcription at the most fundamental level. Biotechnol. J. 8 (1), 46-58.
16. Blazeck J., Garg R., Reed B., Alper H.S. Controlling promoter strength and regulation in Saccharomyces cerevisiae using synthetic hybrid promoters. Biotechnol. Bioeng 2012.
17. Blazeck J., Liu L., Redden H., Alper H. Tuning gene expression in Yarrowia lipolytica by a hybrid promoter approach. Appl. Environ. Microbiol. 2011, 77:7905-7914.
18. Blazeck J., Reed B., Garg R., Gerstner R., Pan A., Agarwala V., Alper H. Generalizing a hybrid synthetic promoter approach in Yarrowia lipolytica. Appl. Microbiol. Biotechnol. 2012, 1-16.
19. Bonnet J., Subsoontorn P., Endy D. Rewritable digital data storage in live cells via engineered control of recombination directionality. Proc. Natl. Acad. Sci 2012.
20. Brochado A.R., Matos C., Moller B.L., Hansen J., Mortensen U.H., Patil K.R. Improved vanillin production in Baker's yeast through in silico design. Microb. Cell Fact. 2010, 9:84.
21. Brooks B.R., Brooks C.L., Mackerell A.D., Nilsson L., Petrella R.J., Roux B., Won Y., Archontis G., Bartels C., Boresch S., Caflisch A., Caves L., Cui Q., Dinner A.R., Feig M., Fischer S., Gao J., Hodoscek M., Im W., Kuczera K., Lazaridis T., Ma J., Ovchinnikov V., Paci E., Pastor R.W., Post C.B., Pu J.Z., Schaefer M., Tidor B., Venable R.M., Woodcock H.L., Wu X., Yang W., York D.M., Karplus M. CHARMM: the biomolecular simulation program. J. Comput. Chem. 2009, 30:1545-1614.
22. Burgard A.P., Pharkya P., Maranas C.D. Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol. Bioeng. 2003, 84:647-657.
23. Callura J.M., Cantor C.R., Collins J.J. Genetic switchboard for synthetic biology applications. Proc. Natl. Acad. Sci. 2012, 109:5850-5855.
24. Canelas A.B., Ras C., ten Pierick A., van Gulik W.M., Heijnen J.J. An in vivo data-driven framework for classification and quantification of enzyme kinetics and determination of apparent thermodynamic data. Metab. Eng. 2011, 13:294-306.
25. Canton B., Labno A., Endy D. Refinement and standardization of synthetic biological parts and devices. Nat. Biotechnol. 2008, 26:787-793.
26. Carbonell P., Planson A.G., Fichera D., Faulon J.L. A retrosynthetic biology approach to metabolic pathway design for therapeutic production. BMC Syst. Biol. 2011, 5:122.
27. Carothers J.M., Goler J.A., Juminaga D., Keasling J.D. Model-driven engineering of RNA devices to quantitatively program gene expression. Science 2011, 334:1716-1719.
28. Caspi R., Altman T., Dale J.M., Dreher K., Fulcher C.A., Gilham F., Kaipa P., Karthikeyan A.S., Kothari A., Krummenacker M., Latendresse M., Mueller L.A., Paley S., Popescu L., Pujar A., Shearer A.G., Zhang P., Karp P.D. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2010, 38:D473-479.
29. Caspi R., Foerster H., Fulcher C.A., Hopkinson R., Ingraham J., Kaipa P., Krummenacker M., Paley S., Pick J., Rhee S.Y., Tissier C., Zhang P., Karp P.D. MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res. 2010, 34:D511-D516.
30. Chen M.-T., Weiss R. Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana. Nat. Biotechnol. 2005, 23:1551-1555.
31. Cho A., Yun H., Park J.H., Lee S.Y., Park S. Prediction of novel synthetic pathways for the production of desired chemicals. BMC Syst. Biol. 2010, 4:35.
32. Cooper S., Khatib F., Treuille A., Barbero J., Lee J., Beenen M., Leaver-Fay A., Baker D., Popovic Z., Players F. Predicting protein structures with a multiplayer online game. Nature 2010, 466:756-760.
33. Crook N.C., Freeman E.S., Alper H.S. Re-engineering multicloning sites for function and convenience. Nucleic Acids Res. 2011, 39:e92.
34. Curran K.A., Alper H.S. Expanding the chemical palate of cells by combining systems biology and metabolic engineering. Metab. Eng. 2012, 14:289-297.
35. Curran K.A., Crook N.C., Alper H.S. Using flux balance analysis to guide microbial metabolic engineering. Methods Mol. Biol. 2012, 834:197-216.
36. Cvijovic M., Olivares-Hernandez R., Agren R., Dahr N., Vongsangnak W., Nookaew I., Patil K.R., Nielsen J. BioMet Toolbox: genome-wide analysis of metabolism. Nucleic Acids Res. 2010, 38:W144-149.
37. Danino T., Mondragon-Palomino O., Tsimring L., Hasty J. A synchronized quorum of genetic clocks. Nature 2010, 463:326-330.
38. Dasika M.S., Maranas C.D. OptCircuit: an optimization based method for computational design of genetic circuits. BMC Syst. Biol. 2008, 2:24.
39. Davis J.H., Rubin A.J., Sauer R.T. Design, construction and characterization of a set of insulated bacterial promoters. Nucleic Acids Res. 2011, 39:1131-1141.
40. Dobson P.D., Smallbone K., Jameson D., Simeonidis E., Lanthaler K., Pir P., Lu C., Swainston N., Dunn W.B., Fisher P., Hull D., Brown M., Oshota O., Stanford N.J., Kell D.B., King R.D., Oliver S.G., Stevens R.D., Mendes P. Further developments towards a genome-scale metabolic model of yeast. BMC Syst. Biol. 2010, 4:145.
41. Dugar D., Stephanopoulos G. Relative potential of biosynthetic pathways for biofuels and bio-based products. Nat. Biotechnol. 2011, 29:1074-1078.
42. Dunlop M.J., Keasling J.D., Mukhopadhyay A. A model for improving microbial biofuel production using a synthetic feedback loop. Syst. Synth. Biol. 2010, 4:95-104.
43. Edwards J.S., Palsson B.O. Systems properties of the Haemophilus influenzae Rd metabolic genotype. J. Biol. Chem. 1999, 274:17410-17416.
44. Eiben C.B., Siegel J.B., Bale J.B., Cooper S., Khatib F., Shen B.W., Players F., Stoddard B.L., Popovic Z., Baker D. Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nat. Biotechnol. 2012, 30:190-192.
45. Elowitz M.B., Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000, 403:335-338.
46. Endy D. Foundations for engineering biology. Nature 2005, 438:449-453.
47. English B.P., Min W., van Oijen A.M., Lee K.T., Luo G., Sun H., Cherayil B.J., Kou S.C., Xie X.S. Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited. Nat. Chem. Biol. 2006, 2:87-94.
48. Farmer W.R., Liao J.C. Improving lycopene production in Escherichia coli by engineering metabolic control. Nat. Biotechnol. 2000, 18:533-537.
49. Feist A.M., Henry C.S., Reed J.L., Krummenacker M., Joyce A.R., Karp P.D., Broadbelt L.J., Hatzimanikatis V., Palsson B.O. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol. Syst. Biol. 2007, 3.
50. Fischer E., Zamboni N., Sauer U. High-throughput metabolic flux analysis based on gas chromatography-mass spectrometry derived C-13 constraints. Anal. Biochem. 2004, 325:308-316.
51. Fleishman S.J., Whitehead T.A., Ekiert D.C., Dreyfus C., Corn J.E., Strauch E.M., Wilson I.A., Baker D. Computational design of proteins targeting the conserved stem region of influenza hemagglutinin. Science 2011, 332:816-821.
52. Fong S.S., Burgard A.P., Herring C.D., Knight E.M., Blattner F.R., Maranas C.D., Palsson B.O. In silico design and adaptive evolution of Escherichia coli for production of lactic acid. Biotechnol. Bioeng. 2005, 91:643-648.
53. Förster J., Famili I., Fu P., Palsson B.Ø., Nielsen J. Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res. 2003, 13:244-253.
54. François P., Hakim V. Design of genetic networks with specified functions by evolution in silico. Proc. Natl. Acad. Sci. 2004, 101:580-585.
55. Friedland A.E., Lu T.K., Wang X., Shi D., Church G., Collins J.J. Synthetic gene networks that count. Science 2009, 324:1199-1202.
56. Galdzicki M., Rodriguez C., Chandran D., Sauro H.M., Gennari J.H. Standard biological parts knowledgebase. PLoS ONE 2011, 6:e17005.
57. Gama-Castro S., Jimenez-Jacinto V., Peralta-Gil M., Santos-Zavaleta A., Penaloza-Spinola M.I., Contreras-Moreira B., Segura-Salazar J., Muniz-Rascado L., Martinez-Flores I., Salgado H., Bonavides-Martinez C., Abreu-Goodger C., Rodriguez-Penagos C., Miranda-Rios J., Morett E., Merino E., Huerta A.M., Trevino-Quintanilla L., Collado-Vides J. RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation. Nucleic Acids Res. 2008, 36:D120-124.
58. Gardner T.S., Cantor C.R., Collins J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 2000, 403:339-342.
59. Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 1977, 81:2340-2361.
60. Goldberg S.D., Derr P., DeGrado W.F., Goulian M. Engineered single- and multi-cell chemotaxis pathways in E. coli. Mol. Syst. Biol. 2009, 5:283.
61. Goldfless S.J., Belmont B.J., De Paz A.M., Liu J.F., Niles J.C. Direct and specific chemical control of eukaryotic translation with a synthetic RNA-protein interaction. Nucleic Acids Res 2012.
62. Gruber A.R., Lorenz R., Bernhart S.H., Neubock R., Hofacker I.L. The Vienna RNA websuite. Nucleic Acids Res. 2008, 36:W70-74.
63. Gupta, R., Bhattacharyya, A., Agosto-Perez, F.J., Wickramasinghe, P., Davuluri, R.V., 2010. MPromDb update 2010: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-seq experimental data. Nucleic Acids Res.
64. Henry C.S., Broadbelt L.J., Hatzimanikatis V. Thermodynamics-based metabolic flux analysis. Biophys J. 2007, 92:1792-1805.
65. Henry C.S., Broadbelt L.J., Hatzimanikatis V. Discovery and analysis of novel metabolic pathways for the biosynthesis of industrial chemicals: 3-hydroxypropanoate. Biotechnol. Bioeng. 2010, 106:462-473.
66. Henry C.S., DeJongh M., Best A.A., Frybarger P.M., Linsay B., Stevens R.L. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat. Biotechnol. 2010, 28:977-982.
67. Hooshangi S., Thiberge S., Weiss R. Ultrasensitivity and noise propagation in a synthetic transcriptional cascade. Proc. Natl. Acad. Sci. 2005, 102:3581-3586.
68. Hucka M., Finney A., Sauro H.M., Bolouri H., Doyle J.C., Kitano H., Arkin A.P., Bornstein B.J., Bray D., Cornish-Bowden A., Cuellar A.A., Dronov S., Gilles E.D., Ginkel M., Gor V., Goryanin I.I., Hedley W.J., Hodgman T.C., Hofmeyr J.-H., Hunter P.J., Juty N.S., Kasberger J.L., Kremling A., Kummer U., Le Novère N., Loew L.M., Lucio D., Mendes P., Minch E., Mjolsness E.D., Nakayama Y., Nelson M.R., Nielsen P.F., Sakurada T., Schaff J.C., Shapiro B.E., Shimizu T.S., Spence H.D., Stelling J., Takahashi K., Tomita M., Wagner J., Wang J The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19:524-531.
69. Huynh L., Kececioglu J., Köppe M., Tagkopoulos I. Automatic design of synthetic gene circuits through mixed integer non-linear programming. PLoS ONE 2012, 7:e35529.
70. Isaacs F.J., Dwyer D.J., Ding C., Pervouchine D.D., Cantor C.R., Collins J.J. Engineered riboregulators enable post-transcriptional control of gene expression. Nat. Biotechnol. 2004, 22:841-847.
71. Jamshidi N., Palsson B.Ø. Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models. Biophys. J. 2010, 98:175-185.
72. Jiang L., Althoff E.A., Clemente F.R., Doyle L., Röthlisberger D., Zanghellini A., Gallaher J.L., Betker J.L., Tanaka F., Barbas C.F., Hilvert D., Houk K.N., Stoddard B.L., Baker D. De novo computational design of retro-aldol enzymes. Science 2008, 319:1387-1391.
73. Kanehisa M., Goto S., Sato Y., Furumichi M., Tanabe M. KEGG for integration and interpretation of large-scale molecular data sets. Nucleic Acids Res. 2012, 40:D109-114.
74. Kaplan J., DeGrado W.F. De novo design of catalytic proteins. Proc. Natl. Acad. Sci. 2004, 101:11566-11570.
75. Karp P.D., Paley S., Romero P. The Pathway Tools software. Bioinformatics 2002, 18(1):S225-232.
76. Karr Jonathan R., Sanghvi Jayodita C., Macklin Derek N., Gutschow Miriam V., Jacobs Jared M., Bolival B., Assad-Garcia N., Glass John I., Covert Markus W. A whole-cell computational model predicts phenotype from genotype. Cell 2012, 150:389-401.
77. Kennedy, C.J., Boyle, P.M., Waks, Z., Silver, P.A., 2009. Systems-level engineering of non-fermentative metabolism in yeast. Genetics.
78. Kortemme T., Baker D. Computational design of protein-protein interactions. Curr. Opin. Chem. Biol. 2004, 8:91-97.
79. Kramer B.P., Fussenegger M. Hysteresis in a synthetic mammalian gene network. Proc. Natl. Acad. Sci. 2005, 102:9517-9522.
80. Kumar V.S., Maranas C.D. GrowMatch: an automated method for reconciling in silico/in vivo growth predictions. Plos Comput. Biol. 2009, 5:e1000308.
81. Le Fèvre, F., Smidtas, S., Combe, C., Durot, M., d'Alché-Buc, F., Schachter, V., 2009. CycSim-an online tool for exploring and experimenting with genome-scale metabolic models. Bioinformatics.
82. Leaver-Fay A., Tyka M., Lewis S.M., Lange O.F., Thompson J., Jacak R., Kaufman K., Renfrew P.D., Smith C.A., Sheffler W., Davis I.W., Cooper S., Treuille A., Mandell D.J., Richter F., Ban Y.E., Fleishman S.J., Corn J.E., Kim D.E., Lyskov S., Berrondo M., Mentzer S., Popovic Z., Havranek J.J., Karanicolas J., Das R., Meiler J., Kortemme T., Gray J.J., Kuhlman B., Baker D., Bradley P. ROSETTA3: an object-oriented software suite for the simulation and design of macromolecules. Methods Enzymol. 2011, 487:545-574.
83. Lewis N.E., Nagarajan H., Palsson B.O. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat. Rev. Microbiol. 2012, 10:291-305.
84. Lippow S.M., Tidor B. Progress in computational protein design. Curr. Opin. Biotechnol. 2007, 18:305-311.
85. Liu C., Fu X., Liu L., Ren X., Chau C.K.L., Li S., Xiang L., Zeng H., Chen G., Tang L.-H., Lenz P., Cui X., Huang W., Hwa T., Huang J.-D. Sequential establishment of stripe patterns in an expanding cell population. Science 2011, 334:238-241.
86. Looger L.L., Dwyer M.A., Smith J.J., Hellinga H.W. Computational design of receptor and sensor proteins with novel functions. Nature 2003, 423:185-190.
87. Lux M.W., Bramlett B.W., Ball D.A., Peccoud J. Genetic design automation: engineering fantasy or scientific renewal?. Trends Biotechnol. 2012, 30:120-126.
88. Marchisio M.A., Stelling J. Computational design of synthetic gene circuits with composable parts. Bioinformatics 2008, 24:1903-1910.
89. Marchisio M.A., Stelling J. Computational design tools for synthetic biology. Curr. Opin. Biotechnol. 2009, 20:479-485.
90. Marchisio M.A., Stelling J. Automatic design of digital synthetic gene circuits. PLoS Comput. Biol. 2011, 7:e1001083.
91. Mathews D.H., Sabina J., Zuker M., Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 1999, 288:911-940.
92. Mavrovouniotis M.L. Group contributions for estimating standard gibbs energies of formation of biochemical compounds in aqueous solution. Biotechnol. Bioeng. 1990, 36:1070-1082.
93. Morey K.J., Antunes M.S., Barrow M.J., Solorzano F.A., Havens K.L., Smith J.J., Medford J. Crosstalk between endogenous and synthetic components-synthetic signaling meets endogenous components. Biotechnol. J. 2012, 7:846-855.
94. Myers C.J., Barker N., Jones K., Kuwahara H., Madsen C., Nguyen N.P. iBioSim: a tool for the analysis and design of genetic circuits. Bioinformatics 2009, 25:2848-2849.
95. Na D., Lee D. RBSDesigner: software for designing synthetic ribosome binding sites that yields a desired level of protein expression. Bioinformatics 2010, 26:2633-2634.
96. Nannemann D.P., Kaufmann K.W., Meiler J., Bachmann B.O. Design and directed evolution of a dideoxy purine nucleoside phosphorylase. Protein Eng. Des. Sel. 2010, 23:607-616.
97. Nevoigt E. Progress in metabolic engineering of Saccharomyces cerevisiae. Microbiol. Mol. Biol. Rev. 2008, 72:379-412.
98. Nevozhay D., Adams R.M., Murphy K.F., Josić K., Balázsi G. Negative autoregulation linearizes the dose-response and suppresses the heterogeneity of gene expression. Proc. Natl. Acad. Sci 2009.
99. Ng C.Y., Jung M.Y., Lee J., Oh M.K. Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering. Microb. Cell Fact. 2012, 11:68.
100. Nolan R.P., Lee K. Dynamic model of CHO cell metabolism. Metab. Eng. 2011, 13:108-124.
101. Novak B., Tyson J.J. Design principles of biochemical oscillators. Nat. Rev. Mol. Cell Biol. 2008, 9:981-991.
102. Palani S., Sarkar C.A. Synthetic conversion of a graded receptor signal into a tunable, reversible switch. Mol. Syst. Biol. 2011, 7:480.
103. Patil K.R., Rocha I., Forster J., Nielsen J. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinform. 2005, 6:308.
104. Portales-Casamar E., Thongjuea S., Kwon A.T., Arenillas D., Zhao X., Valen E., Yusuf D., Lenhard B., Wasserman W.W., Sandelin A. JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles. Nucleic Acids Res. 2010, 38:D105-110.
105. Pramanik J., Keasling J.D. Stoichiometric model of Escherichia coli metabolism: incorporation of growth-rate dependent biomass composition and mechanistic energy requirements. Biotechnol. Bioeng. 1997, 56:398-421.
106. Puigbò P., Guzmán E., Romeu A., Garcia-Vallvé S. OPTIMIZER: a web server for optimizing the codon usage of DNA sequences. Nucleic Acids Res. 2007, 35:W126-W131.
107. 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.
108. Rialle S., Felicori L., Dias-Lopes C., Peres S., El Atia S., Thierry A.R., Amar P., Molina F. BioNetCAD: design, simulation and experimental validation of synthetic biochemical networks. Bioinformatics 2010, 26:2298-2304.
109. Riccione, K.A., Smith, R.P., Lee, A.J., You, L., 2012. A synthetic biology approach to understanding cellular information processing. ACS Synth. Biol.
110. Rodrigo G., Carrera J., Jaramillo A. Asmparts: assembly of biological model parts. Syst. Synth. Biol. 2007, 1:167-170.
111. Rodrigo G., Carrera J., Jaramillo A. Genetdes: automatic design of transcriptional networks. Bioinformatics 2007, 23:1857-1858.
112. Rodrigo G., Carrera J., Landrain T.E., Jaramillo A. Perspectives on the automatic design of regulatory systems for synthetic biology. FEBS Lett. 2012, 586:2037-2042.
113. Rothlisberger D., Khersonsky O., Wollacott A.M., Jiang L., DeChancie J., Betker J., Gallaher J.L., Althoff E.A., Zanghellini A., Dym O., Albeck S., Houk K.N., Tawfik D.S., Baker D. Kemp elimination catalysts by computational enzyme design. Nature 2008, 453:190-195.
114. Rudge T.J., Steiner P.J., Phillips A., Haseloff J. Computational modeling of synthetic microbial biofilms. ACS Synthetic Biology 2012, 1(8):345-352.
115. Salis H.M., Mirsky E.A., Voigt C.A. Automated design of synthetic ribosome binding sites to control protein expression. Nat. Biotechnol. 2009, 27:946-950.
116. Samish I., MacDermaid C.M., Perez-Aguilar J.M., Saven J.G. Theoretical and computational protein design. Annu. Rev. Phys. Chem. 2011, 62:129-149.
117. Savinell J.M., Palsson B.O. Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism. J. Theor. Biol. 1992, 154:421-454.
118. Scheer M., Grote A., Chang A., Schomburg I., Munaretto C., Rother M., Sohngen C., Stelzer M., Thiele J., Schomburg D. BRENDA, the enzyme information system in 2011. Nucleic Acids Res. 2011, 39:D670-676.
119. Schellenberger J., Park J.O., Conrad T.M., Palsson B.O. BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions. BMC Bioinform. 2010, 11:213.
120. Schellenberger J., Que R., Fleming R.M.T., Thiele I., Orth J.D., Feist A.M., Zielinski D.C., Bordbar A., Lewis N.E., Rahmanian S., Kang J., Hyduke D.R., Palsson B.O. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat. Protoc. 2011, 6:1290-1307.
121. Schilling C.H., Covert M.W., Famili I., Church G.M., Edwards J.S., Palsson B.O. Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 2002, 184:4582-4593.
122. Segrè D., Vitkup D., Church G.M. Analysis of optimality in natural and perturbed metabolic networks. Proc. Natl. Acad. Sci. 2002, 99:15112-15117.
123. Shong J., Jimenez Diaz M.R., Collins C.H. Towards synthetic microbial consortia for bioprocessing. Curr. Opin. Biotechnol. 2012, 23:798-802.
124. Shou W., Ram S., Vilar J.M.G. Synthetic cooperation in engineered yeast populations. Proc. Natl. Acad. Sci. 2007, 104:1877-1882.
125. Siegel J.B., Zanghellini A., Lovick H.M., Kiss G., Lambert A.R., Clair J.L., Gallaher J.L., Hilvert D., Gelb M.H., Stoddard B.L., Houk K.N., Michael F.E., Baker D. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 2010, 329:309-313.
126. Smallbone K., Simeonidis E., Swainston N., Mendes P. Towards a genome-scale kinetic model of cellular metabolism. BMC Syst. Biol. 2010, 4:6.
127. Stricker J., Cookson S., Bennett M.R., Mather W.H., Tsimring L.S., Hasty J. A fast, robust and tunable synthetic gene oscillator. Nature 2008, 456:516-519.
128. Tabor J.J., Salis H.M., Simpson Z.B., Chevalier A.A., Levskaya A., Marcotte E.M., Voigt C.A., Ellington A.D. A synthetic genetic edge detection program. Cell 2009, 137:1272-1281.
129. Tan C., Marguet P., You L. Emergent bistability by a growth-modulating positive feedback circuit. Nat. Chem. Biol. 2009, 5:842-848.
130. Tanouchi Y., Smith R.P., You L. Engineering microbial systems to explore ecological and evolutionary dynamics. Curr. Opin. Biotechnol. 2012, 23:791-797.
131. Tigges M., Marquez-Lago T.T., Stelling J., Fussenegger M. A tunable synthetic mammalian oscillator. Nature 2009, 457:309-312.
132. Topp S., Gallivan J.P. Guiding bacteria with small molecules and RNA. J. Am. Chem. Soc. 2007, 129:6807-6811.
133. Villalobos A., Ness J.E., Gustafsson C., Minshull J., Govindarajan S. Gene Designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinform. 2006, 7:285.
134. Weber W., Stelling J., Rimann M., Keller B., Daoud-El Baba M., Weber C.C., Aubel D., Fussenegger M. A synthetic time-delay circuit in mammalian cells and mice. Proc. Natl. Acad. Sci. 2007, 104:2643-2648.
135. Weeding E., Houle J., Kaznessis Y.N. SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs. Brief Bioinform. 2010, 11:394-402.
136. Win M.N., Liang J.C., Smolke C.D. Frameworks for programming biological function through RNA parts and devices. Chem. Biol. 2009, 16:298-310.
137. Win M.N., Smolke C.D. A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc. Natl. Acad. Sci. 2007, 104:14283-14288.
138. Win M.N., Smolke C.D. Higher-order cellular information processing with synthetic RNA devices. Science 2008, 322:456-460.
139. Yamada T., Letunic I., Okuda S., Kanehisa M., Bork P. iPath2.0: interactive pathway explorer. Nucleic Acids Res. 2011, 39:W412-415.
140. Yamamoto Y.Y., Obokata J. ppdb: a plant promoter database. Nucleic Acids Res. 2008, 36:D977-981.
141. Yaman F., Bhatia S., Adler A., Densmore D., Beal J. Automated selection of synthetic biology parts for genetic regulatory networks. ACS Synth. Biol. 2012, 1:332-344.
142. Yim H., Haselbeck R., Niu W., Pujol-Baxley C., Burgard A., Boldt J., Khandurina J., Trawick J.D., Osterhout R.E., Stephen R., Estadilla J., Teisan S., Schreyer H.B., Andrae S., Yang T.H., Lee S.Y., Burk M.J., Van Dien S. Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol. Nat. Chem. Biol. 2011, 7:445-452.
143. You L., Cox R.S., Weiss R., Arnold F.H. Programmed population control by cell-cell communication and regulated killing. Nature 2004, 428:868-871.
144. Yousofshahi M., Lee K., Hassoun S. Probabilistic pathway construction. Metab. Eng. 2011, 13:435-444.
145. Zadeh J.N., Steenberg C.D., Bois J.S., Wolfe B.R., Pierce M.B., Khan A.R., Dirks R.M., Pierce N.A. NUPACK: analysis and design of nucleic acid systems. J. Comput. Chem. 2011, 32:170-173.
146. Zaslaver A., Mayo A.E., Rosenberg R., Bashkin P., Sberro H., Tsalyuk M., Surette M.G., Alon U. Just-in-time transcription program in metabolic pathways. Nat. Genet. 2004, 36:486-491.
147. Zastrow M.L., PeacockAnna F.A., Stuckey J.A., Pecoraro V.L. Hydrolytic catalysis and structural stabilization in a designed metalloprotein. Nat. Chem. 2012, 4:118-123.
148. Zhang F., Carothers J.M., Keasling J.D. Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat. Biotechnol. 2012, 30:354-359.
149. Zhu J., Zhang M.Q. SCPD: a promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics 1999, 15:607-611.
150. Zomorrodi A.R., Maranas C.D. OptCom: a multi-level optimization framework for the metabolic modeling and analysis of microbial communities. Plos Comput. Biol. 2012, 8:e1002363.
151. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003, 31:3406-3415.