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

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Spring 2008 - Introduction to Synthetic Biology

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General Reviews on Synthetic Biology

  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 | PubMed ID:16978856 | HubMed [1]
  2. Endy D. Foundations for engineering biology. Nature. 2005 Nov 24;438(7067):449-53. DOI:10.1038/nature04342 | PubMed ID:16306983 | 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 | PubMed ID:16738572 | 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 | PubMed ID:12432407 | 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 | PubMed ID:17289915 | 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 | PubMed ID:17710092 | HubMed [6]
  7. Keasling JD. Synthetic biology for synthetic chemistry. ACS Chem Biol. 2008 Jan 18;3(1):64-76. DOI:10.1021/cb7002434 | PubMed ID:18205292 | HubMed [7]
  8. Serrano L. Synthetic biology: promises and challenges. Mol Syst Biol. 2007;3:158. DOI:10.1038/msb4100202 | PubMed ID:18091727 | HubMed [8]
  9. McDaniel R and Weiss R. Advances in synthetic biology: on the path from prototypes to applications. Curr Opin Biotechnol. 2005 Aug;16(4):476-83. DOI:10.1016/j.copbio.2005.07.002 | PubMed ID:16019200 | HubMed [9]
  10. Heinemann M and Panke S. Synthetic biology--putting engineering into biology. Bioinformatics. 2006 Nov 15;22(22):2790-9. DOI:10.1093/bioinformatics/btl469 | PubMed ID:16954140 | HubMed [10]
  11. Sismour AM and Benner SA. Synthetic biology. Expert Opin Biol Ther. 2005 Nov;5(11):1409-14. DOI:10.1517/14712598.5.11.1409 | PubMed ID:16255644 | HubMed [11]
  12. Forster AC and Church GM. Synthetic biology projects in vitro. Genome Res. 2007 Jan;17(1):1-6. DOI:10.1101/gr.5776007 | PubMed ID:17151344 | HubMed [12]
  13. Sprinzak D and Elowitz MB. Reconstruction of genetic circuits. Nature. 2005 Nov 24;438(7067):443-8. DOI:10.1038/nature04335 | PubMed ID:16306982 | HubMed [13]
  14. Lucks JB, Qi L, Whitaker WR, and Arkin AP. Toward scalable parts families for predictable design of biological circuits. Curr Opin Microbiol. 2008 Dec;11(6):567-73. DOI:10.1016/j.mib.2008.10.002 | PubMed ID:18983935 | HubMed [14]
  15. Fu P. A perspective of synthetic biology: assembling building blocks for novel functions. Biotechnol J. 2006 Jun;1(6):690-9. DOI:10.1002/biot.200600019 | PubMed ID:16892318 | HubMed [15]
  16. Marguet P, Balagadde F, Tan C, and You L. Biology by design: reduction and synthesis of cellular components and behaviour. J R Soc Interface. 2007 Aug 22;4(15):607-23. DOI:10.1098/rsif.2006.0206 | PubMed ID:17251159 | HubMed [16]
  17. Tan C, Song H, Niemi J, and You L. A synthetic biology challenge: making cells compute. Mol Biosyst. 2007 May;3(5):343-53. DOI:10.1039/b618473c | PubMed ID:17460793 | HubMed [17]
  18. Pleiss J. The promise of synthetic biology. Appl Microbiol Biotechnol. 2006 Dec;73(4):735-9. DOI:10.1007/s00253-006-0664-3 | PubMed ID:17269152 | HubMed [18]
  19. Meyer A, Pellaux R, and Panke S. Bioengineering novel in vitro metabolic pathways using synthetic biology. Curr Opin Microbiol. 2007 Jun;10(3):246-53. DOI:10.1016/j.mib.2007.05.009 | PubMed ID:17548240 | HubMed [19]
  20. Michalodimitrakis K and Isalan M. Engineering prokaryotic gene circuits. FEMS Microbiol Rev. 2009 Jan;33(1):27-37. DOI:10.1111/j.1574-6976.2008.00139.x | PubMed ID:19016883 | HubMed [20]
  21. Kaern M, Blake WJ, and Collins JJ. The engineering of gene regulatory networks. Annu Rev Biomed Eng. 2003;5:179-206. DOI:10.1146/annurev.bioeng.5.040202.121553 | PubMed ID:14527313 | HubMed [21]
All Medline abstracts: PubMed | HubMed

Seminal Papers

  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 | PubMed ID:10659856 | 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 | PubMed ID:10659857 | HubMed [2]
All Medline abstracts: PubMed | HubMed

Foundational technologies / Standardisation effort

  1. Arkin A. Setting the standard in synthetic biology. Nat Biotechnol. 2008 Jul;26(7):771-4. DOI:10.1038/nbt0708-771 | PubMed ID:18612298 | HubMed [1]
  2. Canton B, Labno A, and Endy D. Refinement and standardization of synthetic biological parts and devices. Nat Biotechnol. 2008 Jul;26(7):787-93. DOI:10.1038/nbt1413 | PubMed ID:18612302 | HubMed [2]
  3. Lucks JB, Qi L, Whitaker WR, and Arkin AP. Toward scalable parts families for predictable design of biological circuits. Curr Opin Microbiol. 2008 Dec;11(6):567-73. DOI:10.1016/j.mib.2008.10.002 | PubMed ID:18983935 | HubMed [3]
  4. Peccoud J, Blauvelt MF, Cai Y, Cooper KL, Crasta O, DeLalla EC, Evans C, Folkerts O, Lyons BM, Mane SP, Shelton R, Sweede MA, and Waldon SA. Targeted development of registries of biological parts. PLoS One. 2008 Jul 16;3(7):e2671. DOI:10.1371/journal.pone.0002671 | PubMed ID:18628824 | HubMed [4]
  5. Goler JA, Bramlett BW, and Peccoud J. Genetic design: rising above the sequence. Trends Biotechnol. 2008 Oct;26(10):538-44. DOI:10.1016/j.tibtech.2008.06.003 | PubMed ID:18687496 | HubMed [5]
  6. Czar MJ, Anderson JC, Bader JS, and Peccoud J. Gene synthesis demystified. Trends Biotechnol. 2009 Feb;27(2):63-72. DOI:10.1016/j.tibtech.2008.10.007 | PubMed ID:19111926 | HubMed [6]
  7. Bio FAB Group, Baker D, Church G, Collins J, Endy D, Jacobson J, Keasling J, Modrich P, Smolke C, and Weiss R. Engineering life: building a fab for biology. Sci Am. 2006 Jun;294(6):44-51. DOI:10.1038/scientificamerican0606-44 | PubMed ID:16711359 | HubMed [7]
All Medline abstracts: PubMed | HubMed

Cool/Inspiring Synthetic Biology Projects

  1. Chan LY, Kosuri S, and Endy D. Refactoring bacteriophage T7. Mol Syst Biol. 2005;1:2005.0018. DOI:10.1038/msb4100025 | PubMed ID:16729053 | 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 | PubMed ID:17700541 | 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 | PubMed ID:17662949 | 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 | PubMed ID:16330045 | 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 | PubMed ID:17592147 | 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 | PubMed ID:17652177 | 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 | PubMed ID:15858574 | 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 | PubMed ID:15064770 | 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 | PubMed ID:12451174 | 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 | PubMed ID:15096621 | 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 | PubMed ID:17675429 | 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 | PubMed ID:15994559 | 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 | PubMed ID:15875027 | 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 | PubMed ID:17652177 | HubMed [14]
All Medline abstracts: PubMed | HubMed

Expression Chassis Related

  1. Luisi PL. Toward the engineering of minimal living cells. Anat Rec. 2002 Nov 1;268(3):208-14. DOI:10.1002/ar.10155 | PubMed ID:12382319 | 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 | PubMed ID:17850764 | HubMed [2]
  3. Forster AC and Church GM. Towards synthesis of a minimal cell. Mol Syst Biol. 2006;2:45. DOI:10.1038/msb4100090 | PubMed ID:16924266 | 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 | PubMed ID:17668286 | 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 | PubMed ID:16224117 | 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 | PubMed ID:15591347 | 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 | PubMed ID:15498568 | 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 | PubMed ID:16351070 | 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 | PubMed ID:16408021 | HubMed [9]
All Medline abstracts: PubMed | HubMed

DNA Assembly Related

  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)

Modelling Related

Synthetic Biology: Ethics and Impact on Society

  1. Check E. Synthetic biologists face up to security issues. Nature. 2005 Aug 18;436(7053):894-5. DOI:10.1038/436894a | PubMed ID:16107798 | HubMed [1]
  2. Check E. Synthetic biologists try to calm fears. Nature. 2006 May 25;441(7092):388-9. DOI:10.1038/441388a | PubMed ID:16724023 | 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 | PubMed ID:17355173 | HubMed [3]
  4. Henkel J and Maurer SM. The economics of synthetic biology. Mol Syst Biol. 2007;3:117. DOI:10.1038/msb4100161 | PubMed ID:17551512 | 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 | PubMed ID:17557094 | HubMed [5]
All Medline abstracts: PubMed | HubMed