Targeted development of registries of biological parts

PLoS ONE

Volumn 3, Issue 7, 2008, Pages

  Peccoud, Jean ^a   Blauvelt, Megan F ^a   Cai, Yizhi ^a   Cooper, Kristal L ^a   Crasta, Oswald ^a   DeLalla, Emily C ^a   Evans, Clive ^a   Folkerts, Otto ^a   Lyons, Blair M ^a   Mane, Shrinivasrao P ^a   Shelton, Rebecca ^a   Sweede, Matthew A ^a   Waldon, Sally A ^a  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PLASMID DNA; DNA;

ARTICLE; BIOLOGY; CHROMATOGRAPHY; DNA DETERMINATION; GENE AMPLIFICATION; GENE SEQUENCE; GENETIC DATABASE; HUMAN COMPUTER INTERACTION; MOLECULAR CLONING; PLASMID; POLYMERASE CHAIN REACTION; REGISTER; BIOLOGICAL MODEL; CHEMISTRY; GENE LIBRARY; GENE VECTOR; GENETIC PROCEDURES; INFORMATION SYSTEM; METABOLISM; METHODOLOGY; SYSTEMS BIOLOGY; TEMPERATURE;

BIOLOGY; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DNA; GENE LIBRARY; GENETIC TECHNIQUES; GENETIC VECTORS; INFORMATION SYSTEMS; MODELS, BIOLOGICAL; PLASMIDS; POLYMERASE CHAIN REACTION; SYSTEMS BIOLOGY; TEMPERATURE;

EID: 50549090249     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0002671     Document Type: Article

References (28)

1. Wu G, Wolf JB, Ibrahim AF, Vadasz S, Gunasinghe M, et al. (2005) Simplified gene synthesis: A one-step approach to PCR-based gene construction. Journal Of Biotechnology 124: 496-503.
2. Kong DS, Carr PA, Chen L, Zhang SG, Jacobson JM (2007) Parallel gene synthesis in a microfluidic device. Nucleic Acids Research 35.
3. Tian J, Gong H, Sheng N, Zhou X, Gulari E, et al. (2004) Accurate multiplex gene synthesis from programmable DNA microchips. Nature 432: 1050-1054.
4. Villalobos A, Ness JE, Gustafsson C, Minshull J, Govindarajan S (2006) Gene Designer: a synthetic biology tool for constructing artificial DNA segments. BMC Bioinformatics 7: 285.
5. Voigt CA (2006) Genetic parts to program bacteria. Curr Opin Biotechnol 17: 548-557.
6. Cai Y, Hartnett B, Gustafsson C, Peccoud J (2007) A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts. Bioinformatics 23: 2760-2767.
7. Endy D (2005) Foundations for engineering biology. Nature 438: 449-453.
8. Peccoud J, Coulombel L (2007) A competition of synthetic biology or how to create the ≪ Water of E. coli ≫ and nano-barbies. Med Sci (Paris) 23: 551-552.
9. Goodman C (2008) Engineering ingenuity at iGEM. Nat Chem Biol 4: 13.
10. Levskaya A, Chevalier AA, Tabor JJ, Simpson ZB, Lavery LA, et al. (2005) Synthetic biology: Engineering Escherichia coli to see light. Nature 438: 441-442.
11. Chan LY, Kosuri S, Endy D (2005) Refactoring bacteriophage T7. Mol Syst Biol 1: 2005 0018.
12. Ajo-Franklin CM, Drubin DA, Eskin JA, Gee EP, Landgraf D, et al. (2007) Rational design of memory in eukaryotic cells. Genes Dev 21: 2271-2276.
13. Shetty RP, Endy D, Knight TF Jr (2008) Engineering BioBrick vectors from BioBrick parts. J Biol Eng 2: 5.
14. Haynes KA, Broderick ML, Brown AD, Butner TL, Dickson JO, et al. (2008) Engineering bacteria to solve the Burnt Pancake Problem. J Biol Eng 2: 8.
15. Rai A, Boyle J (2007) Synthetic biology: caught between property rights, the public domain, and the commons. PLoS Biol 5: e58.
16. Henkel J, Maurer SM (2007) The economics of synthetic biology. Mol Syst Biol 3: 117.
17. Jabasini M, Zhang L, Dang F, Xu F, Almofli MR, et al. (2002) Analysis of DNA polymorphisms on the human Y-chromosome by microchip electrophoresis. Electrophoresis 23: 1537-1542.
18. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
19. Cox RS 3rd, Surette MG, Elowitz MB (2007) Programming gene expression with combinatorial promoters. Mol Syst Biol 3: 145.
20. Murphy KF, Balazsi G, Collins JJ (2007) Combinatorial promoter design for engineering noisy gene expression. Proc Natl Acad Sci U S A 104: 12726-12731.
21. Gimona M (2006) Protein linguistics - a grammar for modular protein assembly? Nature Reviews Molecular Cell Biology 7: 68-73.
22. Serrano L (2007) Synthetic biology: promises and challenges. Mol Syst Biol 3: 158.
23. Andrianantoandro E, Basu S, Karig DK, Weiss R (2006) Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2: 2006 0028.
24. Arkin AP, Fletcher DA (2006) Fast, cheap and somewhat in control. Genome Biol 7: 114.
25. Ewing B, Green P (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 8: 186-194.
26. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185.
27. Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9: 868-877.
28. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research 13: 2498-2504.