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F. Claude, G. Navarro, H. Peltola, L. Salmela, J. Tarhio: String matching with alphabet sampling. To appear in: Journal of Discrete Algorithms.
T. Gagie, K. Karhu, J. Kärkkäinen, V. Mäkinen, L. Salmela, J. Tarhio: Indexed multi-pattern matching. To appear in: Proc. LATIN '12, 10th Latin American Theoretical Informatics Symposium.
H. Peltola, J. Tarhio: Variations of Forward-SBNDM. In: Proc. PSC '11, The Prague Stringology Conference 2011, Czech Technical University, Prague, 2011, 3–14
K. Karhu, J. Mäkinen, J. Rautio, H. Salamon, J. Tarhio: GAST, a genomic alignment search tool. In: Proc. International Conference on Bioinformatics Models, Methods and Algorithms, SciTePress, 2011, 82-90.
B. Ďurian, J. Holub, H. Peltola, J. Tarhio: Improving practical exact string matching. Information Processing Letters 110, 4 (2010), 148–152.
L. Salmela, J. Tarhio, P. Kalsi: Approximate Boyer-Moore string matching for small alphabets. Algorithmica 58, 3 (2010), 591–609.
E. Rivals, L. Salmela, P. Kiiskinen, P. Kalsi, J. Tarhio: MPSCAN: fast localisation of multiple reads in genomes. In: Proc. WABI '09, 9th Workshop on Algorithms in Bioinformatics (ed. S.L. Salzberg and T. Warnow), Lecture Notes in Bioinformatics 5724, Springer, 2009, 246–260.
E. Rivals, A. Boureux, M. Lejeune, F. Ottones, O. Pérez, J. Tarhio, F. Pierrat, F. Ruffle, T. Commes, J. Marti: Transcriptome annotation using tandem SAGE tags. Nucleic Acids Research 35, 17 (2007), e108.
L. Salmela, J. Tarhio, J. Kytöjoki: Multi-pattern string matching with q-grams. ACM Journal of Experimental Algorithmics 11, 1 (2006). [pdf]
G. Navarro, E. Sutinen, J. Tarhio: Indexing text with approximate q-grams. Journal of Discrete Algorithms 3, 2–4 (2005), 157–175.
H. Peltola, J. Tarhio: Alternative algorithms for bit-parallel string matching. In: Proc. SPIRE '03, 10th Symposium on String Processing and Information Retrieval (ed. M. Nascimento et al.), Lecture Notes in Computer Science 2857, Springer, 2003, 80–94. [pdf]
G. Navarro, R. Baeza-Yates, E. Sutinen, J. Tarhio: Indexing methods for approximate string matching. Bulletin of the Technical Committee on Data Engineering 24, 4 (2001), 19–27.
J. Tarhio: On compression of parse trees. In: Proc. SPIRE '01, Eight Symposium on String Processing and Information Retrieval, IEEE Computer Society, 2001, 205-211. [pdf]
K. Lemström, J. Tarhio: Searching monophonic patterns within polyphonic sources. In: Proc. RIAO '00, Content-Based Multimedia Information Access (Vol. 2), C.I.D., Paris, 2000, 1261–1279.
S.-P. Lahtinen, E. Sutinen, J. Tarhio: Automated animation of algorithms with Eliot. Journal of Visual Languages and Computing 9, 3 (1998), 337-349.
J. Haajanen, M. Pesonius, E. Sutinen, J. Tarhio, T. Teräsvirta, P. Vanninen: Animation of user algorithms on the Web. In: Proc. VL '97, IEEE Symposium on Visual Languages, IEEE, 1997, 360-367. [pdf]
J. Tarhio, H. Peltola: String matching in the DNA alphabet. Software — Practice and Experience 27, 7 (1997), 851–861. [pdf]
E. Sutinen, J. Tarhio: Filtration with q-samples in approximate string matching. In: Combinatorial Pattern Matching, Proceedings of 7th Annual Symposium (ed. D. Hirschberg and G. Myers), Lecture Notes in Computer Science 1075, Springer, Berlin, 1996, 50–63.
O. Lehtinen, E. Sutinen, J. Tarhio: Experiments on block indexing. In: Proceedings of Third South American Workshop on String Processing (ed. N. Ziviani et al.), Carleton University Press, 1996, 183–193. [pdf]
P. Jokinen, J. Tarhio, E. Ukkonen: A comparison of approximate string matching algorithms. Software - Practice and Experience 26, 12 (1996), 1439-1458. [pdf]
H. Salamon, J. Tarhio, K. Ronningen, G. Thomson: On distinguishing unique combinations in biological sequences. Journal of Computational Biology 3 (1996), 407-423.
E. Sutinen, J. Tarhio: On using q-gram locations in approximate string matching. In: Algorithms - ESA '95, Proceedings of Third Annual European Symposium (ed. P. Spirakis), Lecture Notes in Computer Science 979, Springer, Berlin, 1995, 327-340. [pdf]
J. Tarhio, E. Ukkonen: Approximate Boyer-Moore string matching. SIAM Journal on Computing 22, 2 (1993), 243-260. [pdf]
J. Tarhio, E. Ukkonen: A greedy approximation algorithm for constructing shortest common superstrings. Theoretical Computer Science 57 (1988), 131–145.
H. Peltola, H. Söderlund, J. Tarhio, E. Ukkonen: Algorithms for some string matching problems arising in molecular genetics. In: Information Processing 83 (ed. R. Mason), North-Holland, 1983, 59–64.