Difference between revisions of "IGEM:Harvard/2010/Background Reading"

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== Synthetic Biology ==
 
== Synthetic Biology ==

Latest revision as of 06:40, 22 January 2010

Harvard2010backgroundreading.png

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. Serrano L. Synthetic biology: promises and challenges. Mol Syst Biol. 2007;3:158. DOI:10.1038/msb4100202 | PubMed ID:18091727 | 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. 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 [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 | PubMed ID:19562109 | 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 | PubMed ID:19324675 | 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 | PubMed ID:19948487 | 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 | PubMed ID:17875664 | 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 | PubMed ID:10659856 | 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 | PubMed ID:10659857 | 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 | PubMed ID:12923549 | 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 | PubMed ID:18492232 | 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 | PubMed ID:19630940 | 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 | PubMed ID:18205286 | HubMed [14]
  5. Lovley DR. Bug juice: harvesting electricity with microorganisms. Nat Rev Microbiol. 2006 Jul;4(7):497-508. DOI:10.1038/nrmicro1442 | PubMed ID:16778836 | 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 | PubMed ID:16679010 | 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 | PubMed ID:15973408 | 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 | PubMed ID:17927750 | 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 | PubMed ID:17277079 | 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 | PubMed ID:16936064 | 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 | PubMed ID:16849424 | 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 | PubMed ID:18205292 | 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 | PubMed ID:17710092 | 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 | PubMed ID:19564482 | 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 | PubMed ID:17115212 | 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 | PubMed ID:12219076 | 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 | PubMed ID:16306980 | 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 | PubMed ID:18272963 | 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 | PubMed ID:18724274 | 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 | PubMed ID:19648956 | 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 | PubMed ID:19636299 | 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 | PubMed ID:19636303 | 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 | PubMed ID:19636300 | 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 | PubMed ID:19636306 | 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 | PubMed ID:19636296 | 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 | PubMed ID:19415076 | HubMed [36]
  9. What's in a name?. Nat Biotechnol. 2009 Dec;27(12):1071-3. DOI:10.1038/nbt1209-1071 | PubMed ID:20010573 | 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 | PubMed ID:20010587 | 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 | PubMed ID:20010586 | 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 | PubMed ID:19816799 | 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 | PubMed ID:19816807 | 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 | PubMed ID:19816805 | 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 | PubMed ID:19816802 | 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 | PubMed ID:19816801 | 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 | PubMed ID:19816794 | 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 | PubMed ID:19816796 | 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 | PubMed ID:19816798 | HubMed [47]
All Medline abstracts: PubMed | HubMed