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Nadia Pisanti, Maxime Crochemore, Roberto Grossi, MarieFrance Sagot, "Bases of Motifs for Generating Repeated Patterns with Wild Cards," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 2, no. 1, pp. 4050, JanuaryMarch, 2005.  
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@article{ 10.1109/TCBB.2005.5, author = {Nadia Pisanti and Maxime Crochemore and Roberto Grossi and MarieFrance Sagot}, title = {Bases of Motifs for Generating Repeated Patterns with Wild Cards}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {2}, number = {1}, issn = {15455963}, year = {2005}, pages = {4050}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2005.5}, 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  Bases of Motifs for Generating Repeated Patterns with Wild Cards IS  1 SN  15455963 SP40 EP50 EPD  4050 A1  Nadia Pisanti, A1  Maxime Crochemore, A1  Roberto Grossi, A1  MarieFrance Sagot, PY  2005 KW  Motifs basis KW  repeated motifs. VL  2 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] A. Aho and M. Corasick, “Efficient String Matching: An Aid to Bibliographic Search,” Comm. ACM, vol. 18, no. 6, pp. 333340, 1975.
[2] A. Apostolico and L. Parida, “Incremental Paradigms of Motif Discovery,” J. Computational Biology, vol. 11, no. 1, pp. 1525, 2004.
[3] R. BaezaYates and G. Gonnet, “A New Approach to Text Searching,” Comm. ACM, vol. 35, pp. 7482, 1992.
[4] 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.
[5] M. Crochemore and W. Rytter, Jewels of Stringology. World Scientific Publishing, 2002.
[6] E. Eskin, “From Profiles to Patterns and Back Again: A Branch and Bound Algorithm for Finding Near Optimal Motif Profiles,” RECOMB'04: Proc. Eighth Ann. Int'l Conf. Computational Molecular Biology, pp. 115124, 2004.
[7] E. Eskin, U. Keich, M. Gelfand, and P. Pevzner, “GenomeWide Analysis of Bacterial Promoter Regions,” Proc. Pacific Symp. Biocomputing, pp. 2940, 2003.
[8] M. Fischer and M. Paterson, “String Matching and Other Products,” SIAM AMS Complexity of Computation, R. Karp, ed., pp. 113125, 1974.
[9] M. Gribskov, A. McLachlan, and D. Eisenberg, “Profile Analysis: Detection of Distantly Related Proteins,” Proc. Nat'l Academy of Sciences, vol. 84, no. 13, pp. 43554358, 1987.
[10] D. Gusfield, Algorithms on Strings, Trees and Sequences: Computer Science and Computational Biology. Cambridge Univ. Press, 1997.
[11] G.Z. Hertz and G.D. Stormo, “Escherichia Coli Promoter Sequences: Analysis and Prediction,” Methods in Enzymology, vol. 273, pp. 3042, 1996.
[12] C.E. Lawrence, S.F. Altschul, M.S. Boguski, J.S. Liu, A.F. Neuwald, and J.C. Wooton, “Detecting Subtle Sequence Signals: A Gibbs Sampling Strategy for Multiple Alignment,” Science, vol. 262, pp. 208214, 1993.
[13] C.E. Lawrence and A.A. Reilly, “An Expectation Maximization (EM) Algorithm for the Identification and Characterization of Common Sites in Unaligned Biopolymer Sequences,” Proteins: Structure, Function, and Genetics, vol. 7, pp. 4151, 1990.
[14] 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. 345362, 2000.
[15] W. Miller, “Comparison of Genomic DNA Sequences: Solved and Unsolved Problems,” Bioinformatics, vol. 17, pp. 391397, 2001.
[16] G. Myers, “A Fast BitVector Algorithm for Approximate String Matching Based on Dynamic Programming,” J. ACM, vol. 46, no. 3, pp. 395415, 1999.
[17] L. Parida, I. Rigoutsos, A. Floratos, D. Platt, and Y. Gao, “Pattern Discovery on Character Sets and RealValued Data: Linear Bound on Irredundant Motifs and Efficient Polynomial Time Algorithm,” Proc. SIAM Symp. Discrete Algorithms (SODA), 2000.
[18] L. Parida, I. Rigoutsos, and D. Platt, “An OutputSensitive Flexible Pattern Discovery Algorithm,” Combinatorial Pattern Matching, A. Amir and G. Landau, eds., pp. 131142, SpringerVerlag, 2001.
[19] J. Pelfrêne, S. Abdeddaïm, and J. Alexandre, “Extracting Approximate Patterns,” Combinatorial Pattern Matching, pp. 328347, SpringerVerlag, 2003.
[20] N. Pisanti, M. Crochemore, R. Grossi, and M.F. Sagot, “A Basis for Repeated Motifs in Pattern Discovery and Text Mining,” Technical Report IGM 200210, Institut GaspardMonge, Univ. of MarnelaVallée, July 2002.
[21] N. Pisanti, M. Crochemore, R. Grossi, and M.F. Sagot, “A Basis of Tiling Motifs for Generating Repeated Patterns and Its Complexity for Higher Quorum,” Math. Foundations of Computer Science (MFCS), B. Rovan and P. Vojtás, eds., pp. 622631, SpringerVerlag, 2003.
[22] N. Pisanti, M. Crochemore, R. Grossi, and M.F. Sagot, String Algorithmics, chapter: A Comparative Study of Bases for Motif Inference, pp. 195225, KCL Press, 2004.
[23] D. Pollard, C. Bergman, J. Stoye, S. Celniker, and M. Eisen, “Benchmarking Tools for the Alignment of Functional Noncoding DNA,” BMC Bioinformatics, vol. 5, pp. 623, 2004.
[24] A. Vanet, L. Marsan, and M.F. Sagot, “Promoter Sequences and Algorithmical Methods for Identifying Them,” Research in Microbiology, vol. 150, pp. 779799, 1999.
[25] S. Wu and U. Manber, “PathMatching Problems,” Algorithmica, vol. 8, no. 2, pp. 89101, 1992.