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Unformatted text preview: Int. J. Bioinformatics Research and Applications, Vol. x, No. x, xxxx 1 Decoding Algorithms in Pooling Designs with Inhibitors and Error-Tolerance My T. Thai * , David MacCallum † , Ping Deng ‡ , and Weili Wu ‡ * Department of Computer and Information Science and Engineer- ing, University of Florida, P.O. Box 116120, Gainesville, FL 32611. † Department of Computer Science, University of Minnesota, Twin Cities, 200 Union Street S.E., Minneapolis, MN 55455. ‡ Department of Computer Science, University of Texas at Dallas, Richardson, TX 75083. E-mail: [email protected] [email protected] [email protected] [email protected] Abstract: Pooling designs are used in DNA library screening to ef- ficiently distinguish positive clones from negative clones, which is of fundamental importance in studying gene functions and many other ap- plications in biology. One of the challenges of pooling designs is to design decoding algorithms for determining whether a clone is positive based on the test outcomes and a binary matrix representing the pools. This problem becomes more difficult in practice due to errors in biological ex- periments. More challenging, in some applications, besides positive and negative clones, there is a third category of clones called ”inhibitors” whose effect is to neutralize positives. In this paper, we present a novel decoding algorithm identifying all positive clones with the presence of inhibitors and experimental errors. Keywords: Decoding Algorithms, Pooling Designs, Group Testing, Inhibitors. Reference to this paper should be made as follows: M. T. Thai, D. MacCallum, P. Deng, and W. Wu (2006) ‘Decoding Algorithms in Pool- ing Designs with Inhibitors and Fault Tolerance’, Int. J. Bioinformatics Research and Applications , Vol. x, No. x, pp.xxx–xxx. Biographical notes: My T. Thai received her Ph.D. degree in Com- puter Science from the University of Minnesota in 2005. She is an assis- tant professor at the Department of Computer and Information Science and Engineering, the University of Florida. Her research interests in- clude Wireless Networks, Computational Biology, Applied Algorithms, and Combinatorics. She is a member of the IEEE Computer Society. David MacCallum is scheduled to receive his PhD in Computer Science from the University of Minnesota in August 2006. He received his PhD in Philosophy from the University of Maryland in 1992. He is an asso- Copyright c 200x Inderscience Enterprises Ltd. 2 M. T. Thai et al. ciate professor in the Philosophy Department at Carleton College. His research interests include computational biology, sensor networks, quan- tum computation and logic. Ping Deng received her Master degree in Computer Science from the University of Texas at Dallas in August, 2003. She is a Ph.D candidate in Computer Science at the same university. Her research interests in- clude data mining, intrusion detection, bioinformatics....
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This note was uploaded on 05/20/2011 for the course CAP 5515 taught by Professor Ungor during the Spring '08 term at University of Florida.
- Spring '08