Electronic versions are available for your personal use only. For a complete list, see the chronological list of publications.
B. Ďurian, J. Holub, H. Peltola, J. Tarhio: Tuning BNDM with q-grams. In: Proc. ALENEX '09, Tenth Workshop on Algorithm Engineering and Experiments. SIAM, 2009, 29–37. [pdf]
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.
J. Mäkinen, J. Tarhio, S. Khuri: PMSGA: A fast DNA fragment assembler. In: Proc. BIOINFORMATICS 2010, First International Conference on Bioinformatics (ed. A. Fred et al.), INSTICC, 2010, 77–82.
L. Salmela, J. Tarhio: Algorithms for weighted matching. In: Proc. SPIRE '07, String Processing and Information Retrieval, Lecture Notes in Computer Science 4726, Springer, 2007, 276–286.
L. Salmela, J. Tarhio, J. Kytöjoki: Multi-pattern string matching with q-grams. ACM Journal of Experimental Algorithmics 11, 1 (2006). [pdf]
K. Lemström, J. Tarhio: Transposition invariant pattern matching for multi-track strings. Nordic Journal of Computing 10, 3 (2003), 185–205.
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. [ps.gz]
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. [ps.gz]
J. Tarhio, H. Peltola: String matching in the DNA alphabet. Software — Practice and Experience 27, 7 (1997), 851–861. [pdf]
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. [ps.gz]
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. [ps.gz]
P. Kalsi, H. Peltola, J. Tarhio: Comparison of exact string matching algorithms for biological sequences. In: Proc. BIRD '08, 2nd International Conference on Bioinformatics Research and Development (ed. M. Elloumi et al.). Communications in Computer and Information Science 13, Springer 2008, 417–426. [pdf]
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.
H. Salamon, J. Tarhio, K. Ronningen, G. Thomson: On distinguishing unique combinations in biological sequences. Journal of Computational Biology 3 (1996), 407-423.
A. Korhonen, E. Sutinen, J. Tarhio: Understanding algorithms by means of visualized path testing. In: Software Visualization, State-of-the-Art Survey (ed. S. Diehl), Lecture Notes in Computer Science 2269, Springer, 2002, 256-268.
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. [ps.gz]
M. Lattu, V. Meisalo, J. Tarhio: A visualization tool as a demonstration aid. Computers & Education 41, 2 (2003), 133–148.
P. Eronen, J. Nuutinen, E. Rautama, E. Sutinen, J. Tarhio: Concept gaming. In: Proc. ICCE Tenth International Conference on Computers in Education. IEEE Computer Society Press, Los Alamitos, California, 2002, 997-1001. [pdf]
E. Rautama, A. Karvonen, J. Tarhio, J. Turkia: Versatile concept map viewing on the Web. In: Proc. ITiCSE '01, Innovation and Technology in Computer Science Education, ACM, 2001, 105-108.