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Molecular Biology and Pooling Design

  • Weili Wu
  • Yingshu Li
  • Chih-hao Huang
  • Ding-Zhu Du
Part of the Springer Optimization and Its Applications book series (SOIA, volume 7)

Abstract

The study of gene functions requires a high-quality DNA library. A large amount of testing and screening needs to be performed to obtain a high-quality DNA library. Therefore, the efficiency of testing and screening becomes very important. Pooling design is a very helpful tool, which has developed a lot of applications in molecular biology. In this chapter, we introduce recent developments in this research direction.

Keywords

Group Testing Positive Clone Simplicial Complex Discrete Apply Mathematic Pooling Design 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    A. De Bonis and U. Vaccari. Improved algorithms for group testing with inhibitors. Information Processing Letters, 65: 57–64, 1998.CrossRefGoogle Scholar
  2. 2.
    D. Z. Du and F. K. Hwang. Combinatorial Group Testing and Its Applications (2nd ed.), World Scientific, Singapore, 1999.Google Scholar
  3. 3.
    D. Z. Du and F. K. Hwang. Pooling Designs: Group Testing in Biology, manuscript.Google Scholar
  4. 4.
    D. Z. Du and F. K. Hwang. Identifying d positive clones in the presence of inhibitors, manuscript.Google Scholar
  5. 5.
    A. G. D’ychkov, A. J. Macula, D. C. Torney, and P. A. Vilenkin. Two models of nonadaptive group testing for designing screening experiments. In Proceedings of the 6th International Workshop on Model-Oriented Designs and Analysis, pages 63–75, 2001.Google Scholar
  6. 6.
    M. Farach, S. Kannan, E. Knill, and S. Muthukrishnan. Group testing problem with sequences in experimental molecular biology. In Proceedings of the Compression and Complexity of Sequences, pages 357–367, 1997.Google Scholar
  7. 7.
    H. Q. Ngo and D.-Z. Du. New constructions of non-adaptive and error-tolerance pooling designs. Discrete Mathematics, 243: 161–170, 2002.CrossRefGoogle Scholar
  8. 8.
    H. Q. Ngo and D.-Z. Du. A survey on combinatorial group testing algorithms with applications to DNA library screening. In D.-Z. Du, P.M. Pardalos, and J. Wang, editors, Discrete Mathematical Problems with Medical Applications, pages 171–182. American Mathematical Society, Providence, RI, 2000.Google Scholar
  9. 9.
    F. K. Hwang and Y. C. Liu. Error tolerant pooling designs with inhibitors. Journal of Computational Biology, 10: 231–236, 2003.PubMedCrossRefGoogle Scholar
  10. 10.
    T. Huang and C.-W. Weng. A note on decoding of superimposed codes. Journal of Combinatorial Optimization, 7: 381–384, 2003.CrossRefGoogle Scholar
  11. 11.
    F.K. Hwang. On Macula’s error-correcting pooling design, to appear in Discrete Mathematics, 268: 311–314, 2003.CrossRefGoogle Scholar
  12. 12.
    A.J. Macula. A simple construction of (d-disjunct matrices with certain constant weights. Discrete Mathematics 162: 311–312, 1996.CrossRefGoogle Scholar
  13. 13.
    A. J. Macula. Error correcting nonadaptive group testing with d e-disjunct matrices. Discrete Applied Mathematics, 80: 217–222, 1997.CrossRefGoogle Scholar
  14. 14.
    M. V. Marathe, A. G. Percus, and D. C. Torney. Combinatorial optimization in biology, manuscript, 2000.Google Scholar
  15. 15.
    H. Park, W. Wu, Z. Liu, X. Wu, and H. Zhao, DNA screening, pooling designs, and simplicial complex. Journal of Combinatorial Optimization, 7(4): 389–394, 2003.CrossRefGoogle Scholar
  16. 16.
    W. W. Paterson. Error Correcting Codes, MIT Press, Cambridge, MA, 1961.Google Scholar
  17. 17.
    W. Wu, C. Li, X. Wu, and X. Huang. Decoding in pooling designs. Journal of Combinatorial Optimization, 7(4): 385–388, 2003.CrossRefGoogle Scholar
  18. 18.
    W. Wu, C. Li, and X. Huang. On error-tolerant DNA screening, submitted to Discrete Applied Mathematics.Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2007

Authors and Affiliations

  • Weili Wu
    • 1
  • Yingshu Li
    • 2
  • Chih-hao Huang
    • 2
  • Ding-Zhu Du
    • 1
  1. 1.Department of Computer ScienceUniversity of Texas at DallasRichardsonUSA
  2. 2.Department of Computer Science and EngineeringUniversity of MinnesotaMinneapolisUSA

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