A syntactic model to design and verify synthetic genetic constructs derived from standard biological parts

Bioinformatics

Volumn 23, Issue 20, 2007, Pages 2760-2767

  Cai, Yizhi ^a   Hartnett, Brian ^a   Gustafsson, Claes ^b   Peccoud, Jean ^a  

^a VIRGINIA BIOINFORMATICS INSTITUTE   (United States)

^b DNA20 Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENETICS; BIOINFORMATICS; CONTROLLED STUDY; DNA SEQUENCE; ESCHERICHIA COLI; GENE CONSTRUCT; GENE FUNCTION; GENE LIBRARY; GENETIC ALGORITHM; NONHUMAN; PRIORITY JOURNAL;

ESCHERICHIA COLI;

EID: 35748938455     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btm446     Document Type: Article

References (50)

1. Appel,A.W. and Palsberg,J. (2002) Modern Compiler Implementation in Java. Cambridge University Press, Cambridge, UK; New York, USA.
2. Baker,D. et al. (2006) Engineering life: Building a fab for biology. Sci. Am., 294, 44-51.
3. Bayer,T.S. and Smolke,C.D. (2005) Programmable ligand-controlled riboregulators of eukaryotic gene expression. Nat. Biotechnol., 23, 337-343.
4. Benner,S.A. and Sismour,A.M. (2005) Synthetic biology. Nat. Rev. Genet., 6, 533-543.
5. Berens,C. and Hillen,W. (2003) Gene regulation by tetracyclines. Eur. J. Biochem., 270, 3109-3121.
6. Brendel,V. and Busse,H.G. (1984) Genome structure described by formal languages. Nucleic Acids Res., 12, 2561-2568.
7. Brendel,V. et al. (1986) Linguistics of nucleotide sequences: morphology and comparison of vocabularies. J. Biomol. Struct. Dyn. 4, 11-21.
8. Cavin Perier,R. et al. (1998) The Eukaryotic, Promoter Database EPD. Nucleic Acids Res., 26, 353-357.
9. Chen,M.T. and Weiss,R. (2005) Artificial cell-cell communication in yeast Saccharomyces cerevisiae using signaling elements from Arabidopsis thaliana. Nat. Biotechnol., 23, 1551-1555.
10. Chin,J.W. (2006) Programming and engineering biological networks. Curr. Opin. Struct. Biol., 16, 551-556.
11. Collado-Vides,J. (1992) Grammatical model of the regulation of gene expression. Proc. Natl Acad. Sci. USA, 89, 9405-9409.
12. Dong,S. and Searls,D.B. (1994) Gene structure prediction by linguistic methods. Genomics, 23, 540-551.
13. Elowitz,M.B. and Leibler,S. (2000) A synthetic oscillatory network of transcriptional regulators. Nature, 403, 335-338.
14. Endy,D. (2005) Foundations for engineering biology. Nature, 438 449-453.
15. Finn,J. et al. (2004) An enhanced autogene-based dual-promoter cytoplasmic expression system yields increased gene expression. Gene Ther., 11, 276-283.
16. Gardner,T.S. et al. (2000) Construction of a genetic toggle switch in Escherichia coli. Nature, 403, 339-342.
17. Gimona,M. (2006) Protein linguistics - a grammar for modular protein assembly? Nat. Rev. Mol. Cell Biol., 7, 68-73.
18. Goeddel,D.V. et al. (1979) Direct expression in Escherichia coli of a DNA sequence coding for human growth hormone. Nature, 281 544-548.
19. Gonzalez-Nicolini,V. and Fussenegger,M. (2005) A novel binary adenovirus-based dual-regulated expression system for independent transcription control of two different transgenes. J. Gene Med., 7, 1573-1585.
20. Gossen,M. and Bujard,H. (1992) Tight control of gene-expression in mammalian-cells by tetracychne-responsive promoters. Proc. Natl Acad. Sci. USA, 89, 5547-5551.
21. Guet,C.C. et al. (2002) Combinatorial synthesis of genetic networks. Science, 296, 1466-1470.
22. Guido,N.J. et al. (2006) A bottom-up approach to gene regulation. Nature, 439, 856-860.
23. Heinemann,M. and Panke,S. (2006) Synthetic biology - putting engineering into biology. Bioinformatics, 22, 2790-2799.
24. Knudsen,B. and Hein,J. (1999) RNA secondary structure prediction using stochastic context-free grammars and evolutionary history. Bioinformatics, 15, 446-454.
25. Knudsen,B. and Hein,J. (2003) Pfold: RNA secondary structure prediction using stochastic context-free grammars. Nucleic Acids Res., 31 3423-3428.
26. Kobayashi,H. et al. (2004) Programmable cells: Interfacing natural and engineered gene networks. Proc. Natl Acad. Sci. USA, 101 8414-8419.
27. Landthaler,M. and Shub,D.A. (1999) Unexpected abundance of self-splicing introns in the genome of bacteriophage Twort: Introns in multiple genes, a single gene with three introns, and exon skipping by group I ribozymes. Proc. Natl Acad. Sci. USA, 96, 7005-7010.
28. Linz,P. (2006) An Introduction to Formal Languages and Automata. Jones and Bartlett Publishers, Sudbury, MA.
29. Loose,C. et al. (2006) A linguistic model for the rational design of antimicrobial peptides. Nature, 443, 867-869.
30. Matsui,H. et al. (2005) Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures. Bioinformatics 21, 2611-2617.
31. McDaniel,R. and Weiss,R. (2005) Advances in synthetic biology: On the path from prototypes to applications. Curr. Opin. Biotechnol., 16, 476-483.
32. Meyer-Ficca,M.L. et al. (2004) Comparative analysis of inducible expression systems in transient transfection studies. Anal. Biochem. 334, 9-19.
33. Miller,E.S. et al. (2003) Bacteriophage T4 genome. Microbiol. Mol. Biol. Rev., 67, 86-156, table of contents.
34. Munch,R. et al. (2003) PRODORIC: Prokaryotic database of gene regulation. Nucleic Acids Res., 31, 266-269.
35. Padidam,M. (2003) Chemically regulated gene expression in plants. Curr. Opin. Plant Biol., 6, 169-177.
36. Pavesi,A. (2006) Origin and evolution of overlapping genes in the family Microviridae. J. Gen. Virol., 87, 1013-1017.
37. Rigoutsos,I. and Floratos,A. (1998) Combinatorial pattern discovery in biological sequences: The TEIRESIAS algorithm. Bioinformatics, 14, 55-67.
38. Rivas,E. and Eddy,S.R. (2000) The language of RNA: A formal grammar that includes pseudoknots. Bioinformatics, 16, 334-340.
39. Rodger,S.H. and Finley,T.W. (2006) JFLAP-an Interactive Formal Languages and Automata Package. Jones and Bartlett, Sudbury, MA.
40. Sakakibara,Y. (2005) Grammatical inference in bioinformatics. IEEE Trans. Pattern Anal. Mach. Intell., 27, 1051-1062.
41. Sakakibara,Y. et al. (1994) Stochastic context-free grammars for transfer-Rna modeling. Nucleic Acids Res., 22, 5112-5120.
42. Searls,D.B. (1992) The Linguistics of DNA. Am. Sci., 80, 579-591.
43. Searls,D.B. (1993) The computational linguistics of biological sequences. In Artificial Intelligence and Molecular Biology. American Association for Artificial Intelligence, Menlo Park, CA, USA, pp. 47-120.
44. Searls,D.B. (1997) Linguistic approaches to biological sequences. Comput. Appl. Biosci., 13, 333-344.
45. Searls,D.B. (2002) The language of genes. Nature, 420, 211-217.
46. Searls,D.B. and Noordewier,M.O. (1991) Pattern-matching search of DNA sequences using logic grammars. In Seventh IEEE Conference on Artificial Intelligence Applications. Vol. 1, pp. 3-9.
47. Villalobos,A. et al. (2006) Gene Designer: A synthetic biology tool for constructing artificial DNA segments. BMC Bioinformatics [electronic resource], 7, 285.
48. Voigt,C.A. (2006) Genetic parts to program bacteria. Curr. Opin. Biotechnol., 17, 548-557.
49. Wang,R. et al. (2003) Chemically regulated expression systems and their applications in transgenic plants. Transgenic Res., 12 529-540.
50. Zhu,J. and Zhang,M.Q. (1999) SCPD: A promoter database of the yeast Saccharomyces cerevisiae. Bioinformatics, 15, 607-611.