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Issue No.03 - March (2012 vol.45)
pp: 47-53
Steven S. Skiena , Stony Brook University
ABSTRACT
The advent of low-cost, large-scale DNA synthesis, coupled with advanced algorithmic tools, opens the door to a host of exciting new biotechnology applications, including vaccines.
INDEX TERMS
computational biology, biology and genetics, algorithm analysis
CITATION
Steven S. Skiena, "Redesigning Viral Genomes", Computer, vol.45, no. 3, pp. 47-53, March 2012, doi:10.1109/MC.2012.41
REFERENCES
1. D.G. Gibson et al., "Creation of a Bacterial Cell Controlled by a Chemically Synthesized Genome," Science,2 July 2010, pp. 52-56.
2. E. Wimmer et al., "Synthetic Viruses: A New Opportunity to Understand and Prevent Viral Disease," Nature Biotechnology, Dec. 2009, pp. 1163-1172.
3. J.B. Plotkin and G. Kudla, "Synonymous but Not the Same: The Causes and Consequences of Codon Bias," Nature Reviews Genetics, Jan. 2011, pp. 32-42.
4. J.R. Coleman et al., "Virus Attenuation by Genome-Scale Changes in Codon-Pair Bias," Science, June 2008, pp. 1784-1787.
5. S. Mueller et al., "Live Attenuated Influenza Vaccines by Computer-Aided Rational Design," Nature Biotechnology, July 2010, pp. 723-726.
6. V. Sitaraman et al., "Computationally Designed Adeno-Associated Virus (AAV) Rep 78 Is Efficiently Maintained within an Adenovirus Vector," Proc. National Academy of Sciences,23 Aug. 2011, pp. 14294-14299.
7. D.-Z. Du and F.K. Hwang, Pooling Designs and Nonadaptive Group Testing: Important Tools for DNA Sequencing, World Scientific, 2006.
8. Y.-L. Lin, C. Ward, and S. Skiena, "Synthetic Sequence Design for Signal Location Search," Proc. 16th Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB 12), Springer, 2012; http:/recomb2012.crg.eu.
9. F.J. Isaacs et al., "Precise Manipulation of Chromosomes in Vivo Enables Genome-Wide Codon Replacement," Science,15 July 2011, pp. 348-353.
10. J.S. Dymond et al., "Synthetic Chromosome Arms Function in Yeast and Generate Phenotypic Diversity by Design," Nature,22 Sept. 2011, pp. 471-476.
11. M.J. Czar, Y. Cai, and J. Peccoud, "Writing DNA with GenoCAD," Nucleic Acids Research, July 2009, pp. W40-W47.
12. P. Montes et al., "Optimizing Restriction Site Placement for Synthetic Genomes," Proc. 21st Ann. Conf. Combinatorial Pattern Matching (CPM 10), LNCS 6129, Springer, 2010, pp. 323-337.
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