Registry of Standard Biological Models/Sandbox

Sandbox

Synthetic Biology review papers

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 |
2. Endy D. Foundations for engineering biology. Nature. 2005 Nov 24;438(7067):449-53. DOI:10.1038/nature04342 |
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 |
4. Hasty J, McMillen D, and Collins JJ. Engineered gene circuits. Nature. 2002 Nov 14;420(6912):224-30. DOI:10.1038/nature01257 |
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 |

Interesting systems to model in CellML

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 |
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 |
3. 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 |
4. 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 |
5. 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 |

Others

1. Kaznessis YN. Models for synthetic biology. BMC Syst Biol. 2007 Nov 6;1:47. DOI:10.1186/1752-0509-1-47 |
2. Rosenfeld N, Young JW, Alon U, Swain PS, and Elowitz MB. Accurate prediction of gene feedback circuit behavior from component properties. Mol Syst Biol. 2007;3:143. DOI:10.1038/msb4100185 |
3. Sayut DJ, Kambam PK, and Sun L. Engineering and applications of genetic circuits. Mol Biosyst. 2007 Dec;3(12):835-40. DOI:10.1039/b700547d |
4. 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 |
5. Van Regenmortel MH. The rational design of biological complexity: a deceptive metaphor. Proteomics. 2007 Mar;7(6):965-75. DOI:10.1002/pmic.200600407 |
6. Kim J, White KS, and Winfree E. Construction of an in vitro bistable circuit from synthetic transcriptional switches. Mol Syst Biol. 2006;2:68. DOI:10.1038/msb4100099 |