Imperial College/Courses/Spring2008/Synthetic Biology/Resources/Literature

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1. Voigt CA. Genetic parts to program bacteria. Curr Opin Biotechnol 2006 Oct; 17(5) 548-57. doi:10.1016/j.copbio.2006.09.001 pmid:16978856. PubMed HubMed [1]
2. Endy D. Foundations for engineering biology. Nature 2005 Nov 24; 438(7067) 449-53. doi:10.1038/nature04342 pmid:16306983. PubMed HubMed [2]
3. Andrianantoandro E, Basu S, Karig DK, and Weiss R. Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2006; 2 2006.0028. doi:10.1038/msb4100073 pmid:16738572. PubMed HubMed [3]
4. Hasty J, McMillen D, and Collins JJ. Engineered gene circuits. Nature 2002 Nov 14; 420(6912) 224-30. doi:10.1038/nature01257 pmid:12432407. PubMed HubMed [4]
5. Drubin DA, Way JC, and Silver PA. Designing biological systems. Genes Dev 2007 Feb 1; 21(3) 242-54. doi:10.1101/gad.1507207 pmid:17289915. PubMed HubMed [5]
6. Yeh BJ and Lim WA. Synthetic biology: lessons from the history of synthetic organic chemistry. Nat Chem Biol 2007 Sep; 3(9) 521-5. doi:10.1038/nchembio0907-521 pmid:17710092. PubMed HubMed [6]
7. Keasling JD. Synthetic biology for synthetic chemistry. ACS Chem Biol 2008 Jan 18; 3(1) 64-76. doi:10.1021/cb7002434 pmid:18205292. PubMed HubMed [7]
8. Serrano L. Synthetic biology: promises and challenges. Mol Syst Biol 2007; 3 158. doi:10.1038/msb4100202 pmid:18091727. PubMed HubMed [8]

• 'Cellular Gate Technology', 1998, Knight, Thomas F. Sussman, Gerald Jay
• 'A Standard Parts List for Biological Circuitry', 1999, Arkin, Adam Endy, Drew
• 'Cellular computation and communications using engineered genetic regulatory networks', 2001, Ron Weiss

1. Elowitz MB and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 2000 Jan 20; 403(6767) 335-8. doi:10.1038/35002125 pmid:10659856. PubMed HubMed [1]
2. Gardner TS, Cantor CR, and Collins JJ. Construction of a genetic toggle switch in Escherichia coli. Nature 2000 Jan 20; 403(6767) 339-42. doi:10.1038/35002131 pmid:10659857. PubMed HubMed [2]

1. Chan LY, Kosuri S, and Endy D. Refactoring bacteriophage T7. Mol Syst Biol 2005; 1 2005.0018. doi:10.1038/msb4100025 pmid:16729053. PubMed HubMed [1]
2. Anderson JC, Voigt CA, and Arkin AP. Environmental signal integration by a modular AND gate. Mol Syst Biol 2007; 3 133. doi:10.1038/msb4100173 pmid:17700541. PubMed HubMed [2]
3. Deans TL, Cantor CR, and Collins JJ. A tunable genetic switch based on RNAi and repressor proteins for regulating gene expression in mammalian cells. Cell 2007 Jul 27; 130(2) 363-72. doi:10.1016/j.cell.2007.05.045 pmid:17662949. PubMed HubMed [3]
4. Anderson JC, Clarke EJ, Arkin AP, and Voigt CA. Environmentally controlled invasion of cancer cells by engineered bacteria. J Mol Biol 2006 Jan 27; 355(4) 619-27. doi:10.1016/j.jmb.2005.10.076 pmid:16330045. PubMed HubMed [4]
5. Lu TK and Collins JJ. Dispersing biofilms with engineered enzymatic bacteriophage. Proc Natl Acad Sci U S A 2007 Jul 3; 104(27) 11197-202. doi:10.1073/pnas.0704624104 pmid:17592147. PubMed HubMed [5]
6. Murphy KF, Balázsi G, and Collins JJ. Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci U S A 2007 Jul 31; 104(31) 12726-31. doi:10.1073/pnas.0608451104 pmid:17652177. PubMed HubMed [6]
7. Basu S, Gerchman Y, Collins CH, Arnold FH, and Weiss R. A synthetic multicellular system for programmed pattern formation. Nature 2005 Apr 28; 434(7037) 1130-4. doi:10.1038/nature03461 pmid:15858574. PubMed HubMed [7]
8. You L, Cox RS 3rd, Weiss R, and Arnold FH. Programmed population control by cell-cell communication and regulated killing. Nature 2004 Apr 22; 428(6985) 868-71. doi:10.1038/nature02491 pmid:15064770. PubMed HubMed [8]
9. Yokobayashi Y, Weiss R, and Arnold FH. Directed evolution of a genetic circuit. Proc Natl Acad Sci U S A 2002 Dec 24; 99(26) 16587-91. doi:10.1073/pnas.252535999 pmid:12451174. PubMed HubMed [9]
10. Basu S, Mehreja R, Thiberge S, Chen MT, and Weiss R. Spatiotemporal control of gene expression with pulse-generating networks. Proc Natl Acad Sci U S A 2004 Apr 27; 101(17) 6355-60. doi:10.1073/pnas.0307571101 pmid:15096621. PubMed HubMed [10]
11. Hawkins AC, Arnold FH, Stuermer R, Hauer B, and Leadbetter JR. Directed evolution of Vibrio fischeri LuxR for improved response to butanoyl-homoserine lactone. Appl Environ Microbiol 2007 Sep; 73(18) 5775-81. doi:10.1128/AEM.00060-07 pmid:17675429. PubMed HubMed [11]
12. Balagaddé FK, You L, Hansen CL, Arnold FH, and Quake SR. Long-term monitoring of bacteria undergoing programmed population control in a microchemostat. Science 2005 Jul 1; 309(5731) 137-40. doi:10.1126/science.1109173 pmid:15994559. PubMed HubMed [12]
13. Fung E, Wong WW, Suen JK, Bulter T, Lee SG, and Liao JC. A synthetic gene-metabolic oscillator. Nature 2005 May 5; 435(7038) 118-22. doi:10.1038/nature03508 pmid:15875027. PubMed HubMed [13]
14. Murphy KF, Balázsi G, and Collins JJ. Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci U S A 2007 Jul 31; 104(31) 12726-31. doi:10.1073/pnas.0608451104 pmid:17652177. PubMed HubMed [14]

1. Luisi PL. Toward the engineering of minimal living cells. Anat Rec 2002 Nov 1; 268(3) 208-14. doi:10.1002/ar.10155 pmid:12382319. PubMed HubMed [1]
2. Murtas G, Kuruma Y, Bianchini P, Diaspro A, and Luisi PL. Protein synthesis in liposomes with a minimal set of enzymes. Biochem Biophys Res Commun 2007 Nov 9; 363(1) 12-7. doi:10.1016/j.bbrc.2007.07.201 pmid:17850764. PubMed HubMed [2]
3. Forster AC and Church GM. Towards synthesis of a minimal cell. Mol Syst Biol 2006; 2 45. doi:10.1038/msb4100090 pmid:16924266. PubMed HubMed [3]
4. Murtas G. Question 7: construction of a semi-synthetic minimal cell: a model for early living cells. Orig Life Evol Biosph 2007 Oct; 37(4-5) 419-22. doi:10.1007/s11084-007-9090-5 pmid:17668286. PubMed HubMed [4]
5. Noireaux V, Bar-Ziv R, Godefroy J, Salman H, and Libchaber A. Toward an artificial cell based on gene expression in vesicles. Phys Biol 2005 Sep 15; 2(3) P1-8. doi:10.1088/1478-3975/2/3/P01 pmid:16224117. PubMed HubMed [5]
6. Noireaux V and Libchaber A. A vesicle bioreactor as a step toward an artificial cell assembly. Proc Natl Acad Sci U S A 2004 Dec 21; 101(51) 17669-74. doi:10.1073/pnas.0408236101 pmid:15591347. PubMed HubMed [6]
7. Ishikawa K, Sato K, Shima Y, Urabe I, and Yomo T. Expression of a cascading genetic network within liposomes. FEBS Lett 2004 Oct 22; 576(3) 387-90. doi:10.1016/j.febslet.2004.09.046 pmid:15498568. PubMed HubMed [7]
8. Rackham O and Chin JW. Cellular logic with orthogonal ribosomes. J Am Chem Soc 2005 Dec 21; 127(50) 17584-5. doi:10.1021/ja055338d pmid:16351070. PubMed HubMed [8]
9. Rackham O and Chin JW. A network of orthogonal ribosome x mRNA pairs. Nat Chem Biol 2005 Aug; 1(3) 159-66. doi:10.1038/nchembio719 pmid:16408021. PubMed HubMed [9]

1. Idempotent Vector Design for Standard Assembly of Biobricks, Knight T. et al (2003)
2. A New Biobrick Assembly Strategy Designed for Facile Protein Engineering, Phillips, Silver (2006)

• Dynamics and Control of Synthetic Bio-molecular Networks (Del Vecchio and Sontag, 2007)
• Modular cell biology: retroactivity and insulation (Del Vecchio et al, 2007)
• An Introduction to Systems Biology (Uri Alon)

1. Check E. Synthetic biologists face up to security issues. Nature 2005 Aug 18; 436(7053) 894-5. doi:10.1038/436894a pmid:16107798. PubMed HubMed [1]
2. Check E. Synthetic biologists try to calm fears. Nature 2006 May 25; 441(7092) 388-9. doi:10.1038/441388a pmid:16724023. PubMed HubMed [2]
3. Rai A and Boyle J. Synthetic biology: caught between property rights, the public domain, and the commons. PLoS Biol 2007 Mar; 5(3) e58. doi:10.1371/journal.pbio.0050058 pmid:17355173. PubMed HubMed [3]
4. Henkel J and Maurer SM. The economics of synthetic biology. Mol Syst Biol 2007; 3 117. doi:10.1038/msb4100161 pmid:17551512. PubMed HubMed [4]
5. Bügl H, Danner JP, Molinari RJ, Mulligan JT, Park HO, Reichert B, Roth DA, Wagner R, Budowle B, Scripp RM, Smith JA, Steele SJ, Church G, and Endy D. DNA synthesis and biological security. Nat Biotechnol 2007 Jun; 25(6) 627-9. doi:10.1038/nbt0607-627 pmid:17557094. PubMed HubMed [5]