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Hideo Bannai, Heikki Hyyr?, Ayumi Shinohara, Masayuki Takeda, Kenta Nakai, Satoru Miyano, "An O(N^2) Algorithm for Discovering Optimal Boolean Pattern Pairs," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, no. 4, pp. 159170, OctoberDecember, 2004.  
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@article{ 10.1109/TCBB.2004.36, author = {Hideo Bannai and Heikki Hyyr? and Ayumi Shinohara and Masayuki Takeda and Kenta Nakai and Satoru Miyano}, title = {An O(N^2) Algorithm for Discovering Optimal Boolean Pattern Pairs}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {1}, number = {4}, issn = {15455963}, year = {2004}, pages = {159170}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2004.36}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
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TY  JOUR JO  IEEE/ACM Transactions on Computational Biology and Bioinformatics TI  An O(N^2) Algorithm for Discovering Optimal Boolean Pattern Pairs IS  4 SN  15455963 SP159 EP170 EPD  159170 A1  Hideo Bannai, A1  Heikki Hyyr?, A1  Ayumi Shinohara, A1  Masayuki Takeda, A1  Kenta Nakai, A1  Satoru Miyano, PY  2004 KW  Pattern discovery KW  Boolean patterns KW  suffix tree KW  suffix array. VL  1 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
Abstract—We consider the problem of finding the optimal
[1] A. Brazma, I. Jonassen, I. Eidhammer, and D. Gilbert, “Approaches to the Automatic Discovery of Patterns in Biosequences,” J. Computational Biology, vol. 5, pp. 279305, 1998.
[2] L. Marsan and M.F. Sagot, “Algorithms for Extracting Structured Motifs Using a Suffix Tree with an Application to Promoter and Regulatory Site Consensus Identification,” J. Computational Biology, vol. 7, pp. 345360, 2000.
[3] H. Arimura, A. Wataki, R. Fujino, and S. Arikawa, “A Fast Algorithm for Discovering Optimal String Patterns in Large Text Databases,” Proc. Int'l Workshop Algorithmic Learning Theory, pp. 247261, 1998.
[4] E. Eskin and P.A. Pevzner, “Finding Composite Regulatory Patterns in DNA Sequences,” Bioinformatics, vol. 18, pp. S354S363, 2002.
[5] X. Liu, D. Brutlag, and J. Liu, “BioProspector: Discovering Conserved DNA Motifs in Upstream Regulatory Regions of CoExpressed Genes,” Proc. Pacific Symp. Biocomputing, pp. 127138, 2001.
[6] O. Maruyama, H. Bannai, Y. Tamada, S. Kuhara, and S. Miyano, “Fast Algorithm for Extracting Multiple Unordered Short Motifs Using Bit Operations,” Information Sciences, vol. 146, pp. 115126, 2002.
[7] S. Shimozono, A. Shinohara, T. Shinohara, S. Miyano, S. Kuhara, and S. Arikawa, “Knowledge Acquisition from Amino Acid Sequences by Machine Learning System BONSAI,” Trans. Information Processing Soc. Japan, vol. 35, no. 10, pp. 20092018, 1994.
[8] A. Shinohara, M. Takeda, S. Arikawa, M. Hirao, H. Hoshino, and S. Inenaga, “Finding Best Patterns Practically,” Progress in Discovery Science, pp. 307317, 2002.
[9] M. Takeda, S. Inenaga, H. Bannai, A. Shinohara, and S. Arikawa, “Discovering Most Classificatory Patterns for Very Expressive Pattern Classes,” Proc. Sixth Int'l Conf. Discovery Science, pp. 486493, 2003.
[10] D. Shinozaki, T. Akutsu, and O. Maruyama, “Finding Optimal Degenerate Patterns in DNA Sequences,” Bioinformatics, vol. 19, pp. 206ii214ii, 2003.
[11] H.J. Bussemaker, H. Li, and E.D. Siggia, “Regulatory Element Detection Using Correlation with Expression,” Nature Genetics, vol. 27, pp. 167171, 2001.
[12] H. Bannai, S. Inenaga, A. Shinohara, M. Takeda, and S. Miyano, “A String Pattern Regression Algorithm and Its Application to Pattern Discovery in Long Introns,” Genome Informatics, vol. 13, pp. 311, 2002.
[13] E.M. Conlon, X.S. Liu, J.D. Lieb, and J.S. Liu, “Integrating Regulatory Motif Discovery and GenomeWide Expression Analysis,” Proc. US Nat'l Academy Sciences, vol. 100, no. 6, pp. 33393344, 2003.
[14] H. Bannai, S. Inenaga, A. Shinohara, M. Takeda, and S. Miyano, “Efficiently Finding Regulatory Elements Using Correlation with Gene Expression,” J. Bioinformatics and Computational Biology, vol. 2, no. 2, pp. 273288, 2004.
[15] C.B. Z. Zilberstein, E. Eskin, and Z. Yakhini, “Using Expression Data to Discover RNA and DNA Regulatory Sequence Motifs,” First Ann. RECOMB Satellite Workshop on Regulatory Genomics, 2004.
[16] D. Gusfield, Algorithms on Strings, Trees, and Sequences. Cambridge Univ. Press, 1997.
[17] Y. Wang, C. Liu, J. Storey, R. Tibshirani, D. Herschlag, and P. Brown, “Precision and Functional Specificity in mRNA Decay,” Proc. US Nat'l Academy of Sciences, vol. 99, no. 9, pp. 58605865, 2002.
[18] E. Yang, E. van Nimwegen, M. Zavolan, N. Rajewsky, M. Schroeder, M. Magnasco, and J. Darnell Jr., “Decay Rates of Human mRNAs: Correlation with Functional Characteristics and Sequence Attributes,” Genome Research, vol. 13, no. 8, pp. 18631872, 2003.
[19] H. Bannai, H. Hyyrö, A. Shinohara, M. Takeda, K. Nakai, and S. Miyano, “Finding Optimal Pairs of Patterns,” Proc. Fourth Int'l Workshop Algorithms in Bioinformatics, pp. 450462, 2004.
[20] U. Manber and G. Myers, “Suffix Arrays: A New Method for OnLine String Searches,” SIAM J. Computing, vol. 22, no. 5, pp. 935948, 1993.
[21] D.K. Kim, J.S. Sim, H. Park, and K. Park, “LinearTime Construction of Suffix Arrays,” Proc. 14th Ann. Symp. Combinatorial Pattern Matching, pp. 186199, 2003.
[22] P. Ko and S. Aluru, “Space Efficient Linear Time Construction of Suffix Arrays,” Proc. 14th Ann. Symp. Combinatorial Pattern Matching, pp. 200210, 2003.
[23] J. Kärkkäinen and P. Sanders, “Simple Linear Work Suffix Array Construction,” Proc. 30th Int'l Colloquium Automata, Languages and Programming, pp. 943955, 2003.
[24] T. Kasai, H. Arimura, and S. Arikawa, “Efficient Substring Traversal with Suffix Arrays,” Technical Report 185, Dept. of Informatics, Kyushu Univ., 2001.
[25] M.I. Abouelhoda, S. Kurtz, and E. Ohlebusch, “The Enhanced Suffix Array and Its Applications to Genome Analysis,” Proc. Second Int'l Workshop Algorithms in Bioinformatics, pp. 449463, 2002.
[26] M.A. Bender and M. FarachColton, “The LCA Problem Revisited,” Proc. Latin American Theoretical Informatics, pp. 8894, 2000.
[27] S. Alstrup, C. Gavoille, H. Kaplan, and T. Rauhe, “Nearest Common Ancestors: A Survey and a New Distributed Algorithm,” Proc. 14th Ann. ACM Symp. Parallel Algorithms and Architectures, pp. 258264, 2002.
[28] L. Hui, “Color Set Size Problem with Applications to String Matching,” Proc. Third Ann. Symp. Combinatorial Pattern Matching, pp. 230243, 1992.
[29] T. Kasai, G. Lee, H. Arimura, S. Arikawa, and K. Park, “LinearTime LongestCommonPrefix Computation in Suffix Arrays and Its Applications,” Proc. 12th Ann. Symp. Combinatorial Pattern Matching, pp. 181192, 2001.
[30] C.J. Wilusz, M. Wormington, and S.W. Peltz, “The CaptoTail Guide to mRNA Turnover,” Nature Reviews: Molecular Cell Biology, vol. 2, pp. 237246, 2001.
[31] J. Graber, “Variations in Yeast 3'Processing CisElements Correlate with Transcript Stability,” Trends in Genetetics, vol. 19, no. 9, pp. 473476, , 2003.
[32] M. Wickens, D.S. Bernstein, J. Kimble, and R. Parker, “A PUF Family Portrait: 3' UTR Regulation as a Way of Life,” Trends in Genetics, vol. 18, no. 3, pp. 150157, 2002.
[33] M.J. RuizEchevarria, R. Munshi, J. Tomback, T.G. Kinzy, and S.W. Peltz, “Characterization of a General Stabilizer Element that Block DeadenylationDependent mRNA Decay,” J. Biological Chemistry, vol. 276, no. 33, pp. 3099531003, 2001.
[34] A. Kasprzyk, D. Keefe, D. Smedley, D. London, W. Spooner, C. Melsopp, M. Hammond, P. RoccaSerra, T. Cox, and E. Birney, “EnsMart: A Generic System for Fast and Flexible Access to Biological Data,” Genome Research, vol. 14, pp. 160169, 2004.
[35] S. Inenaga, H. Bannai, H. Hyyrö, A. Shinohara, M. Takeda, K. Nakai, and S. Miyano, “Finding Optimal Pairs of Cooperative and Competing Patterns with Bounded Distance,” Proc. Seventh Int'l Conf. Discovery Science, pp. 3246, 2004.