User:NKuldell/Q/A working reference list

Running reference list: incomplete and unorganized

from Part 1, Q2

• Sci Am Fab group
• Pam's G&D paper
• Voigt's TIBS paper
• Voigt,Keasling Nat Chem Biol. 2005 Nov;1(6):304-7
• Paras Chopra and Akhil Kamma "Engineering Life through Synthetic Biology"

[1]

Reviews that focus on implications of the technology are

• Synthetic Biologists face up to security risks Nature 436, 894-895 (18 Aug 2005) News File:Presentation material-synthbiolrisks Nat05.pdf
• From Understanding to Action: Community-Based Options for Improving Safety and Security in Synthetic Biology, Stephen M. Maurer, Keith V. Lucas & Starr Terrell, Goldman School of Public Policy, University of California at Berkeley PDF link
• Draft Declaration of the Second International Meeting on Synthetic Biology, Attendees of SB2.0, University of California at Berkeley, May 2006. pdf article
• (AJ) Bhutkar's article in The Journal of Biolaw & Business analyzing patentability, ethical and regulatory challenges in Synthetic Biology.

Reviews in the lay press include

• Tucker & Zilinskas, The New Atlantis, Spring 2006 link
• Custom-Made Microbes, at Your Service by A Pollack NYT Science section January 17, 2006 link

from Part1, Q3

add [2]

1. Chan LY, Kosuri S, and Endy D. Refactoring bacteriophage T7. Mol Syst Biol. 2005;1:2005.0018. DOI:10.1038/msb4100025 |
2. Itaya M, Tsuge K, Koizumi M, and Fujita K. Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proc Natl Acad Sci U S A. 2005 Nov 1;102(44):15971-6. DOI:10.1073/pnas.0503868102 |
3. Pósfai G, Plunkett G 3rd, Fehér T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, and Blattner FR. Emergent properties of reduced-genome Escherichia coli. Science. 2006 May 19;312(5776):1044-6. DOI:10.1126/science.1126439 |
4. Ro DK, Paradise EM, Ouellet M, Fisher KJ, Newman KL, Ndungu JM, Ho KA, Eachus RA, Ham TS, Kirby J, Chang MC, Withers ST, Shiba Y, Sarpong R, and Keasling JD. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature. 2006 Apr 13;440(7086):940-3. DOI:10.1038/nature04640 |
5. Giesecke AV, Fang R, and Joung JK. Synthetic protein-protein interaction domains created by shuffling Cys2His2 zinc-fingers. Mol Syst Biol. 2006;2:2006.2011. DOI:10.1038/msb4100053 |
6. Chen IA, Salehi-Ashtiani K, and Szostak JW. RNA catalysis in model protocell vesicles. J Am Chem Soc. 2005 Sep 28;127(38):13213-9. DOI:10.1021/ja051784p |

from Part1, Q4

7. Knight TF. Engineering novel life. Mol Syst Biol. 2005;1:2005.0020. DOI:10.1038/msb4100028 |
8. Endy D. Foundations for engineering biology. Nature. 2005 Nov 24;438(7067):449-53. DOI:10.1038/nature04342 |

from Part1, Q5

6. Chen IA, Salehi-Ashtiani K, and Szostak JW. RNA catalysis in model protocell vesicles. J Am Chem Soc. 2005 Sep 28;127(38):13213-9. DOI:10.1021/ja051784p |
9. Cello J, Paul AV, and Wimmer E. Chemical synthesis of poliovirus cDNA: generation of infectious virus in the absence of natural template. Science. 2002 Aug 9;297(5583):1016-8. DOI:10.1126/science.1072266 |
10. Smith HO, Hutchison CA 3rd, Pfannkoch C, and Venter JC. Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides. Proc Natl Acad Sci U S A. 2003 Dec 23;100(26):15440-5. DOI:10.1073/pnas.2237126100 |
11. Tumpey TM, Basler CF, Aguilar PV, Zeng H, Solórzano A, Swayne DE, Cox NJ, Katz JM, Taubenberger JK, Palese P, and García-Sastre A. Characterization of the reconstructed 1918 Spanish influenza pandemic virus. Science. 2005 Oct 7;310(5745):77-80. DOI:10.1126/science.1119392 |
12. van Aken J. Risks of resurrecting 1918 flu virus outweigh benefits. Nature. 2006 Jan 19;439(7074):266. DOI:10.1038/439266a |
13. Johnston WK, Unrau PJ, Lawrence MS, Glasner ME, and Bartel DP. RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science. 2001 May 18;292(5520):1319-25. DOI:10.1126/science.1060786 |

from Part 1, Q6

14. Carlson R. The pace and proliferation of biological technologies. Biosecur Bioterror. 2003;1(3):203-14. DOI:10.1089/153871303769201851 |

Zwick (2005) Technology: a genome sequencing center in every lab. Eur. J. Hum. Genet. 13:1167-1168.

from Part 2, Q2

15. 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 |
16. Sprinzak D and Elowitz MB. Reconstruction of genetic circuits. Nature. 2005 Nov 24;438(7067):443-8. DOI:10.1038/nature04335 |
17. 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 |
18. Isaacs FJ, Dwyer DJ, and Collins JJ. RNA synthetic biology. Nat Biotechnol. 2006 May;24(5):545-54. DOI:10.1038/nbt1208 |
19. 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 |
20. Endy D. Foundations for engineering biology. Nature. 2005 Nov 24;438(7067):449-53. DOI:10.1038/nature04342 |
21. Voigt CA and Keasling JD. Programming cellular function. Nat Chem Biol. 2005 Nov;1(6):304-7. DOI:10.1038/nchembio1105-304 |

from Part 3, Q3

4. Ro DK, Paradise EM, Ouellet M, Fisher KJ, Newman KL, Ndungu JM, Ho KA, Eachus RA, Ham TS, Kirby J, Chang MC, Withers ST, Shiba Y, Sarpong R, and Keasling JD. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature. 2006 Apr 13;440(7086):940-3. DOI:10.1038/nature04640 |
22. 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 |