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9.6 Bibliographic Notes
A. Apostolico, M. E. Bock, S. Lonardi, and X. Xu: Efficient detection of unusual words. Journal of Computational Biology 7(1/2), 2000, pp. 71–94.
P. Baldi and S. Brunak: Bioinformatics — The Machine Learning Approach, 2nd edition. MIT Press, 2001.
L. E. Baum and T. Petrie: Statistical inference for probabilistic functions of finite state Markov chains. Annals of Mathematical Statistics 37, 1966, pp. 1554–1563.
G. Benson: Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Research 27(2), 1999, pp. 573–580.
G. Churchill: Stochastic models for heterogeneous DNA sequences. Bulletin of Mathematical Biology 51, 1989, pp. 79–94.
P. Clote and R. Backofen: Computational Molecular Biology — An Introduction. Wiley, 2000.
M. Crochemore: An optimal algorithm for computing the repetitions in a word. Information Processing Letters 12(5), 1981, pp. 244–250.
R. Durbin, S. Eddy, A. Krogh, and G. Mitchinson: Biological Sequence Analysis — Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, 1998.
W. J. Ewens and G. R. Grant: Statistical Methods in Bioinformatics — An Introduction. Springer, 2002.
J. F. Gentleman and R. C. Mullin: The distribution of the frequency of occurrence of nucleotide subsequences, based on their overlap capability. Biometrics 45, 1989, pp. 35–52.
L. J. Guibas and A. M. Odlyzko: String overlaps, pattern matching and nontransitive games. Journal of Combinatorial Theory, Series A 30, 1981, pp. 183–208.
D. Gusfield: Algorithms on Strings, Trees, and Sequences. Cambridge University Press, 1997.
D. Harel and R. E. Tarjan: Fast algorithms for finding nearest common ancestors. SIAM Journal on Computing 13, 1984, pp. 338–355.
S. Karlin, C. Burge, and A. M. Campbell: Statistical analyses of counts and distributions of restriction sites in DNA sequences. Nucleic Acids Research 20(6), 1992, pp. 1363–1370.
G. M. Landau and J. P. Schmidt: An algorithm for approximate tandem repeats. Proceedings of the Fourth Annual Symposium on Combinatorial Pattern Matching (CPM’93), Springer LNCS 684, 1993, pp. 120–133.
M. Y. Leung, G. M. Marsh, and T. P. Speed: Over and underrepresentation of short DNA words in herpes virus genomes. Journal of Computational Biology 3, 1996, pp. 345–360.
M. Li, B. Ma, and L. Wang: Finding similar regions in many strings. Proceedings of the 31st ACM Annual Symposium on the Theory of Computing (STOC’99), 1999, pp. 473–482.
M. Li, B. Ma, and L. Wang: Finding similar regions in many sequences. Journal of Computer and System Sciences 65(1), 2002, pp. 73–96.
M. G. Main and R. J. Lorentz: An O(n log n) algorithm for finding all repetitions in a string. Journal of Algorithms 5, 1984, pp. 422–432.
P. A. Pevzner: Computational Molecular Biology — An Algorithmic Approach. MIT Press, 2000.
P. A. Pevzner, M. Y. Borodovsky, and A. A. Mironov: Linguistics of nucleotide sequences. I: The significance of deviations from mean statistical characteristics and prediction of the frequencies of occurence of words. Journal of Biomolecular Structure and Dynamics 6, 1989, pp. 1013–1026.
L. R. Rabiner: A tutorial on Hidden Markov Models and selected applications in speech recognition. Proceedings of the IEEE 77(2), 1989, pp. 257–286.
G. Reinert, S. Schbath, and M. S. Waterman: Probabilistic and statistical properties of words: An overview. Journal of Computational Biology 7(1/2), 2000, pp. 1–46.
S. M. Ross: Introduction to Probability Models, 8th edition. Academic Press 2002.
B. Schieber and U. Vishkin: On finding lowest common ancestors: simplification and parallelization. SIAM Journal on Computing 17, 1988, pp. 1253–1262.
J. van Helden, B. André, and J. Collado-Vides: Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies. Journal of Molecular Biology 281, 1998, pp. 827–842.
A. J. Viterbi: Error bounds for convolutional codes and an asymptotically optimal decoding algorithm. IEEE Transactions on Information Theory IT-13, 1967, pp. 260–269.
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(2007). Finding Signals in DNA Sequences. In: Algorithmic Aspects of Bioinformatics. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71913-7_9
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