IGEM:Harvard/2010/Background Reading

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Contents

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 pmid:16978856. PubMed HubMed [1]
  2. Serrano L. Synthetic biology: promises and challenges. Mol Syst Biol 2007; 3 158. doi:10.1038/msb4100202 pmid:18091727. 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. 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 [4]
  5. Agapakis CM and Silver PA. Synthetic biology: exploring and exploiting genetic modularity through the design of novel biological networks. Mol Biosyst 2009 Jul; 5(7) 704-13. doi:10.1039/b901484e pmid:19562109. PubMed HubMed [5]
  6. Boyle PM and Silver PA. Harnessing nature's toolbox: regulatory elements for synthetic biology. J R Soc Interface 2009 Aug 6; 6 Suppl 4 S535-46. doi:10.1098/rsif.2008.0521.focus pmid:19324675. PubMed HubMed [6]
  7. Haynes KA and Silver PA. Eukaryotic systems broaden the scope of synthetic biology. J Cell Biol 2009 Nov 30; 187(5) 589-96. doi:10.1083/jcb.200908138 pmid:19948487. PubMed HubMed [7]
All Medline abstracts: PubMed HubMed

Circuits

  1. Ajo-Franklin CM, Drubin DA, Eskin JA, Gee EP, Landgraf D, Phillips I, and Silver PA. Rational design of memory in eukaryotic cells. Genes Dev 2007 Sep 15; 21(18) 2271-6. doi:10.1101/gad.1586107 pmid:17875664. PubMed HubMed [8]
  2. 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 [9]
  3. 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 [10]
All Medline abstracts: PubMed HubMed

Computation

  1. Stojanovic MN and Stefanovic D. A deoxyribozyme-based molecular automaton. Nat Biotechnol 2003 Sep; 21(9) 1069-74. doi:10.1038/nbt862 pmid:12923549. PubMed HubMed [11]
  2. Haynes KA, Broderick ML, Brown AD, Butner TL, Dickson JO, Harden WL, Heard LH, Jessen EL, Malloy KJ, Ogden BJ, Rosemond S, Simpson S, Zwack E, Campbell AM, Eckdahl TT, Heyer LJ, and Poet JL. Engineering bacteria to solve the Burnt Pancake Problem. J Biol Eng 2008 May 20; 2 8. doi:10.1186/1754-1611-2-8 pmid:18492232. PubMed HubMed [12]
  3. Baumgardner J, Acker K, Adefuye O, Crowley ST, Deloache W, Dickson JO, Heard L, Martens AT, Morton N, Ritter M, Shoecraft A, Treece J, Unzicker M, Valencia A, Waters M, Campbell AM, Heyer LJ, Poet JL, and Eckdahl TT. Solving a Hamiltonian Path Problem with a bacterial computer. J Biol Eng 2009 Jul 24; 3 11. doi:10.1186/1754-1611-3-11 pmid:19630940. PubMed HubMed [13]
  4. Savage DF, Way J, and Silver PA. Defossiling fuel: how synthetic biology can transform biofuel production. ACS Chem Biol 2008 Jan 18; 3(1) 13-6. doi:10.1021/cb700259j pmid:18205286. PubMed HubMed [14]
  5. Lovley DR. Bug juice: harvesting electricity with microorganisms. Nat Rev Microbiol 2006 Jul; 4(7) 497-508. doi:10.1038/nrmicro1442 pmid:16778836. PubMed HubMed [15]
  6. Lovley DR. Microbial fuel cells: novel microbial physiologies and engineering approaches. Curr Opin Biotechnol 2006 Jun; 17(3) 327-32. doi:10.1016/j.copbio.2006.04.006 pmid:16679010. PubMed HubMed [16]
  7. Reguera G, McCarthy KD, Mehta T, Nicoll JS, Tuominen MT, and Lovley DR. Extracellular electron transfer via microbial nanowires. Nature 2005 Jun 23; 435(7045) 1098-101. doi:10.1038/nature03661 pmid:15973408. PubMed HubMed [17]
  8. Cho YK, Donohue TJ, Tejedor I, Anderson MA, McMahon KD, and Noguera DR. Development of a solar-powered microbial fuel cell. J Appl Microbiol 2008 Mar; 104(3) 640-50. doi:10.1111/j.1365-2672.2007.03580.x pmid:17927750. PubMed HubMed [18]
  9. Walter JM, Greenfield D, Bustamante C, and Liphardt J. Light-powering Escherichia coli with proteorhodopsin. Proc Natl Acad Sci U S A 2007 Feb 13; 104(7) 2408-12. doi:10.1073/pnas.0611035104 pmid:17277079. PubMed HubMed [19]
  10. Reguera G, Nevin KP, Nicoll JS, Covalla SF, Woodard TL, and Lovley DR. Biofilm and nanowire production leads to increased current in Geobacter sulfurreducens fuel cells. Appl Environ Microbiol 2006 Nov; 72(11) 7345-8. doi:10.1128/AEM.01444-06 pmid:16936064. PubMed HubMed [20]
  11. Gorby YA, Yanina S, McLean JS, Rosso KM, Moyles D, Dohnalkova A, Beveridge TJ, Chang IS, Kim BH, Kim KS, Culley DE, Reed SB, Romine MF, Saffarini DA, Hill EA, Shi L, Elias DA, Kennedy DW, Pinchuk G, Watanabe K, Ishii S, Logan B, Nealson KH, and Fredrickson JK. Electrically conductive bacterial nanowires produced by Shewanella oneidensis strain MR-1 and other microorganisms. Proc Natl Acad Sci U S A 2006 Jul 25; 103(30) 11358-63. doi:10.1073/pnas.0604517103 pmid:16849424. PubMed HubMed [21]
All Medline abstracts: PubMed HubMed

Chemistry

  1. 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 [22]
  2. 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 [23]
  3. Kennedy CJ, Boyle PM, Waks Z, and Silver PA. Systems-level engineering of nonfermentative metabolism in yeast. Genetics 2009 Sep; 183(1) 385-97. doi:10.1534/genetics.109.105254 pmid:19564482. PubMed HubMed [24]
  4. Withers ST and Keasling JD. Biosynthesis and engineering of isoprenoid small molecules. Appl Microbiol Biotechnol 2007 Jan; 73(5) 980-90. doi:10.1007/s00253-006-0593-1 pmid:17115212. PubMed HubMed [25]
All Medline abstracts: PubMed HubMed

Light

  1. Shimizu-Sato S, Huq E, Tepperman JM, and Quail PH. A light-switchable gene promoter system. Nat Biotechnol 2002 Oct; 20(10) 1041-4. doi:10.1038/nbt734 pmid:12219076. PubMed HubMed [26]
  2. Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, Levy M, Davidson EA, Scouras A, Ellington AD, Marcotte EM, and Voigt CA. Synthetic biology: engineering Escherichia coli to see light. Nature 2005 Nov 24; 438(7067) 441-2. doi:10.1038/nature04405 pmid:16306980. PubMed HubMed [27]
  3. Tyszkiewicz AB and Muir TW. Activation of protein splicing with light in yeast. Nat Methods 2008 Apr; 5(4) 303-5. doi:10.1038/nmeth.1189 pmid:18272963. PubMed HubMed [28]
All Medline abstracts: PubMed HubMed

Human Practices

  1. de Lorenzo V and Danchin A. Synthetic biology: discovering new worlds and new words. EMBO Rep 2008 Sep; 9(9) 822-7. doi:10.1038/embor.2008.159 pmid:18724274. PubMed HubMed [19]
  2. Maurer SM. Before it's too late. Why synthetic biologists need an open-parts collaboration--and how to build one. EMBO Rep 2009 Aug; 10(8) 806-9. doi:10.1038/embor.2009.165 pmid:19648956. PubMed HubMed [30]
  3. Kelle A. Synthetic biology and biosecurity. From low levels of awareness to a comprehensive strategy. EMBO Rep 2009 Aug; 10 Suppl 1 S23-7. doi:10.1038/embor.2009.119 pmid:19636299. PubMed HubMed [31]
  4. Potthast T. Paradigm shifts versus fashion shifts? Systems and synthetic biology as new epistemic entities in understanding and making 'life'. EMBO Rep 2009 Aug; 10 Suppl 1 S42-5. doi:10.1038/embor.2009.130 pmid:19636303. PubMed HubMed [32]
  5. Moya A, Krasnogor N, Peretó J, and Latorre A. Goethe's dream. Challenges and opportunities for synthetic biology. EMBO Rep 2009 Aug; 10 Suppl 1 S28-32. doi:10.1038/embor.2009.120 pmid:19636300. PubMed HubMed [33]
  6. Morange M. A new revolution? The place of systems biology and synthetic biology in the history of biology. EMBO Rep 2009 Aug; 10 Suppl 1 S50-3. doi:10.1038/embor.2009.156 pmid:19636306. PubMed HubMed [34]
  7. Deamer D. On the origin of systems. Systems biology, synthetic biology and the origin of life. EMBO Rep 2009 Aug; 10 Suppl 1 S1-4. doi:10.1038/embor.2009.117 pmid:19636296. PubMed HubMed [35]
  8. Deplazes A. Piecing together a puzzle. An exposition of synthetic biology. EMBO Rep 2009 May; 10(5) 428-32. doi:10.1038/embor.2009.76 pmid:19415076. PubMed HubMed [36]
  9. What's in a name?. Nat Biotechnol 2009 Dec; 27(12) 1071-3. doi:10.1038/nbt1209-1071 pmid:20010573. PubMed HubMed [37]
  10. Bennett G, Gilman N, Stavrianakis A, and Rabinow P. From synthetic biology to biohacking: are we prepared?. Nat Biotechnol 2009 Dec; 27(12) 1109-11. doi:10.1038/nbt1209-1109 pmid:20010587. PubMed HubMed [38]
  11. Kaebnick GE. Should moral objections to synthetic biology affect public policy?. Nat Biotechnol 2009 Dec; 27(12) 1106-8. doi:10.1038/nbt1209-1106 pmid:20010586. PubMed HubMed [39]
  12. Dabrock P. Playing God? Synthetic biology as a theological and ethical challenge. Syst Synth Biol 2009 Dec; 3(1-4) 47-54. doi:10.1007/s11693-009-9028-5 pmid:19816799. PubMed HubMed [40]
  13. Wellhausen R and Mukunda G. Aspects of the political economy of development and synthetic biology. Syst Synth Biol 2009 Dec; 3(1-4) 115-23. doi:10.1007/s11693-009-9032-9 pmid:19816807. PubMed HubMed [41]
  14. Rabinow P and Bennett G. Synthetic biology: ethical ramifications 2009. Syst Synth Biol 2009 Dec; 3(1-4) 99-108. doi:10.1007/s11693-009-9042-7 pmid:19816805. PubMed HubMed [42]
  15. Marliere P. The farther, the safer: a manifesto for securely navigating synthetic species away from the old living world. Syst Synth Biol 2009 Dec; 3(1-4) 77-84. doi:10.1007/s11693-009-9040-9 pmid:19816802. PubMed HubMed [43]
  16. Bedau MA, Parke EC, Tangen U, and Hantsche-Tangen B. Social and ethical checkpoints for bottom-up synthetic biology, or protocells. Syst Synth Biol 2009 Dec; 3(1-4) 65-75. doi:10.1007/s11693-009-9039-2 pmid:19816801. PubMed HubMed [44]
  17. Schmidt M, Ganguli-Mitra A, Torgersen H, Kelle A, Deplazes A, and Biller-Andorno N. A priority paper for the societal and ethical aspects of synthetic biology. Syst Synth Biol 2009 Dec; 3(1-4) 3-7. doi:10.1007/s11693-009-9034-7 pmid:19816794. PubMed HubMed [45]
  18. Kronberger N, Holtz P, Kerbe W, Strasser E, and Wagner W. Communicating Synthetic Biology: from the lab via the media to the broader public. Syst Synth Biol 2009 Dec; 3(1-4) 19-26. doi:10.1007/s11693-009-9031-x pmid:19816796. PubMed HubMed [46]
  19. Pauwels E. Review of quantitative and qualitative studies on U.S. public perceptions of synthetic biology. Syst Synth Biol 2009 Dec; 3(1-4) 37-46. doi:10.1007/s11693-009-9035-6 pmid:19816798. PubMed HubMed [47]
All Medline abstracts: PubMed HubMed
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