Jorma Tarhio

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Publications

Accepted

T. Chhabra, S. Ghuman, J. Tarhio: Improved online algorithms for jumbled matching. To appear in: Discrete Applied Mathematics.

2019

S. Ghuman, E. Giaquinta, J. Tarhio: Lyndon factorization algorithms for small alphabets and run-length encoded strings. Algorithms 12, 6 (2019), 124.

2017

J. Tarhio, J. Holub, E. Giaquinta: Technology beats algorithms (in exact string matching). Software: Practice and Experience 47, 12 (2017), 1877–1885. [pdf]

T. Hirvola, J. Tarhio: Bit-parallel approximate matching of circular strings with k mismatches. Journal of Experimental Algorithmics 22, 1 (2017), 5.

F. J. Fiori, W. Pakalen, J. Tarhio: Counting mismatches with SIMD. In: Proc. PSC '17, The Prague Stringology Conference, 2017.

T. Chhabra, S. Faro, M. O. Külekci, J. Tarhio: Engineering order-preserving pattern matching with SIMD parallelism. Software: Practice and Experience 47, 5 (2017), 731–739. [pdf]

2016

S. Ghuman, J. Tarhio: Jumbled matching with SIMD. In: Proc. PSC '16, The Prague Stringology Conference, 2016, 114–124. [pdf]

T. Chhabra, J. Tarhio: A filtration method for order-preserving matching. Information Processing Letters 116, 2 (2016), 71–74. [pdf]

2015

T. Chhabra, E. Giaquinta, J. Tarhio: Filtration algorithms for approximate order-preserving matching. In: Proc. SPIRE '15, String Processing and Information Retrieval, 22nd International Symposium, Lecture Notes in Computer Science 9309, Springer 2015, 177–187. [pdf]

T. Chhabra, S. Ghuman, J. Tarhio: Tuning algorithms for jumbled matching. In: Proc. PSC '15, 14th Prague Stringology Conference, 2015, 36–46. [pdf]

T. Chhabra, M. O. Külekci, J. Tarhio: Alternative algorithms for order-preserving matching. In: Proc. PSC '15, 14th Prague Stringology Conference, 2015, 57–66. [pdf]

2014

H. Peltola, J. Tarhio: String matching with lookahead. Discrete Applied Mathematics 163, 3 (2014) 352–360. [pdf]

T. Chhabra, J. Tarhio: Order-preserving matching with filtration. In: Proc. SEA '14, 13th International Symposium on Experimental Algorithms. Lecture Notes in Computer Science 8504, Springer, 2014, 307–314. [pdf]

T. Hirvola, J. Tarhio: Approximate online matching of circular strings. In: Proc. SEA '14, 13th International Symposium on Experimental Algorithms. Lecture Notes in Computer Science 8504, Springer, 2014, 315–325. [pdf]

B. Ďurian, T. Chhabra, S. Ghuman, T. Hirvola, H. Peltola, J. Tarhio: Improved two-way bit-parallel search. In: Proc. PSC '14, 13th Prague Stringology Conference, 2014, 71–83. [pdf]

K. Pollari-Malmi, J. Rautio, J. Tarhio: Speeding up compressed matching with SBNDM2. In: Proc. PSC '14, 13th Prague Stringology Conference, 2014, 110–123. [pdf]

S. Ghuman, E. Giaquinta, J. Tarhio: Alternative algorithms for Lyndon factorization. In: Proc. PSC '14, 13th Prague Stringology Conference, 2014, 169–178. [pdf]

2012

F. Claude, G. Navarro, H. Peltola, L. Salmela, J. Tarhio: String matching with alphabet sampling. Journal of Discrete Algorithms 11 (2012), 37–50.

T. Gagie, K. Karhu, J. Kärkkäinen, V. Mäkinen, L. Salmela, J. Tarhio: Indexed multi-pattern matching. In: Proc. LATIN '12, 10th Latin American Theoretical Informatics Symposium (ed. D. Fernández-Baca). Lecture Notes in Computer Science 7256, Springer 2012, 399–407.

2011

H. Peltola, J. Tarhio: Variations of Forward-SBNDM. In: Proc. PSC '11, The Prague Stringology Conference 2011, Czech Technical University, Prague, 2011, 3–14

E. Rivals, L. Salmela, J. Tarhio: Exact search algorithms for biological sequences. In: M. Elloumi, A. Zomaya (eds.): Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications. Wiley, 2011, 91–111.

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. [pdf]

2010

L. Salmela, J. Tarhio: Approximate string matching with reduced alphabet. In: Algorithms and Applications (ed. T. Elomaa, H. Mannila, and P. Orponen). Lecture Notes in Computer Science 6060, Springer, 2010, 210–220. [pdf]

B. Ďurian, H. Peltola, L. Salmela, J. Tarhio: Bit-parallel search algorithms for long patterns. In: Proc. SEA '10, 9th International Symposium on Experimental Algorithms. Lecture Notes in Computer Science 6049, Springer, 2010, 129–140. [pdf]

K. Karhu, S. Khuri, J. Mäkinen, J. Tarhio: Identifying human miRNA targets with a genetic algorithm. In: Proc. ISB '10, International Symposium on Biocomputing (ed. D. Tulpan et al.), ACM, 2010.

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. [pdf]

B. Ďurian, J. Holub, H. Peltola, J. Tarhio: Improving practical exact string matching. Information Processing Letters 110, 4 (2010), 148–152. [pdf]

L. Salmela, J. Tarhio, P. Kalsi: Approximate Boyer-Moore string matching for small alphabets. Algorithmica 58, 3 (2010), 591–609.

J. Tarhio: Twenty years of Journal Tietojenkäsittelytiede (in Finnish). Editorial column. Tietojenkäsittelytiede 31 (2010), p. 4.

2009

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. [pdf]

J. Karlgren, J. Tarhio, H. Hyyrö (eds.): String Processing and Information Retrieval, 16th International Symposium, SPIRE 2009, Saariselkä, Finland, August 2009, Proceedings. Lecture Notes in Computer Science 5721, Springer 2009.

L. Salmela, J. Tarhio, T. Montonen: Towards automated management of compiler assignments. In: Proc. CSEDU '09, Int. Conf. on Computer Supported Education. INSTICC 2009, 243–249. [pdf]

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]

N. Philippe, A. Boureux, L. Bréhélin, J. Tarhio, T. Commes, E. Rivals: Using reads to annotate the genome: influence of length, false locations, and sequence errors on prediction capacity. Nucleic Acids Research 37, 15 (2009), e104.

J. Tarhio: Policies (in Finnish). Editorial column. Tietojenkäsittelytiede 29 (2009), 4–5.

2008

L. Salmela, J. Tarhio: Fast parameterized matching with q-qrams. Journal of Discrete Algorithms 6, 3 (2008), 408–419.

F. Claude, G. Navarro, H. Peltola, L. Salmela, J. Tarhio: Speeding up pattern matching by text sampling. In: Proc. SPIRE '08, String Processing and Information Retrieval. Lecture Notes in Computer Science 5280, Springer 2008, 87–98.

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]

L. Lahti, J. Tarhio: Semi-automated map generation for concept gaming. In: Proc. IADIS International Conference Gaming 2008: Design for Engaging Experience and Social Interaction 2008 (eds. Y. Xiao and E. ten Thij), IADIS Press, 2008, 36–43.

2007

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. [pdf]

P. Kalsi, L. Salmela, J. Tarhio: Tuning approximate Boyer-Moore for gene sequences. In: Proc. SPIRE '07, String Processing and Information Retrieval, Lecture Notes in Computer Science 4726, Springer, 2007, 173–183. [pdf]

H. Peltola, J. Tarhio: On string matching in chunked texts. In: Proc. CIAA '07, Conference on Implementation and Application of Automata, Lecture Notes in Computer Science 4783, Springer, 2007, 157–167.

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.

I. Jormanainen, E. Kärnä-Lin, L. Lahti, K. Pihlainen-Bednarik, E. Sutinen, J. Tarhio, M. Virnes: A framework for research on technology-enhanced special education. In: Proc. ICALT '07, 7th IEEE International Conference on Advanced Learning Technologies, IEEE Computer Society, 2007, 54–55.

J. Litola, A. Korhonen, J. Tarhio: Platform for elaboration of search results. In: Proc. WEBIST '07, Web Information Systems and Technologies. INSTICC and Open University of Catalonia, 2007, 263–269.

2006

L. Salmela, J. Tarhio, J. Kytöjoki: Multi-pattern string matching with q-grams. ACM Journal of Experimental Algorithmics 11, 1 (2006). [pdf]

L. Salmela, J. Tarhio: Sublinear algorithms for parameterized matching. In: Proc. CPM '06, Combinatorial Pattern Matching (ed. M. Lewenstein et al.), Lecture Notes in Computer Science 4009, Springer, 2006, 354–364. [pdf]

J. Tarhio: Thoughts on conference articles (in Finnish). Editorial column. Tietojenkäsittelytiede 25 (2006), 8–9.

2005

G. Navarro, J. Tarhio: LZgrep: a Boyer-Moore string matching tool for Ziv-Lempel compressed text. Software: Practice and Experience 35, 12 (2005), 1107–1130.

G. Navarro, E. Sutinen, J. Tarhio: Indexing text with approximate q-grams. Journal of Discrete Algorithms 3, 2–4 (2005), 157–175.

P. Silander, E. Sutinen, J. Tarhio: Computer aided concept mapping for constructing shared cognitive representations and conceptual artifacts. In: Proc. CELDA '05, The IADIS International Conference on Cognition and Exploratory Learning in Digital Age, 2005, 3–8.

2004

E. Sutinen, J. Tarhio: Approximate string matching with ordered q-grams. Nordic Journal of Computing 11, 4 (2004), 321–343. [pdf]

K. Fredriksson, J. Tarhio: Efficient string matching in Huffman compressed texts. Fundamenta Informaticae 62, 1 (2004), 1–16.

P. Silander, E. Sutinen, J. Tarhio: Mobile collaborative concept mapping — Combining classroom activity with simultaneous field exploration. In: Proc. WMTE '04, 2nd IEEE International Workshop on Wireless and Mobile Technologies in Education, IEEE, 2004, 114–118.

L. Salmela, J. Tarhio: ACE: Automated compiler exercises. In: Proc. 4th Annual Finnish/Baltic Sea Conference on Computer Science Education. Research report TKO-A42. Helsinki University of Technology, Laboratory of Information Processing Science, 2004, 131–135.

V. Meisalo, E. Sutinen, J. Tarhio: The possibilities of information retrieval in education. In: Current research on mathematics and science education, Proc. The XXI annual symposium of The Finnish Association of Mathematics and Science Education Research (eds. A. Laine et al.), University of Helsinki, Department of Applied Sciences of Education, Research Report 253, 2004, 528–549. [pdf]

2003

V. Meisalo, E. Sutinen, J. Tarhio: Modernit oppimisympäristöt — Tieto- ja viestintätekniikka opetuksen ja oppimisen tukena. (Modern Learning Environments: Information and Communication Technology for Supporting Teaching and Learning.) 400 p., Tietosanoma, Helsinki, 2003.

E. Sutinen, J. Tarhio, T. Teräsvirta: Easy algorithm animation on the Web. Multimedia Tools and Applications 19, 2 (2003), 179–194.

J. Kytöjoki, L. Salmela, J. Tarhio: Tuning string matching for huge pattern sets. In: Proc. CPM '03, Combinatorial Pattern Matching (ed. R. Baeza-Yates et al.), Lecture Notes in Computer Science 2676, Springer, 2003, 211–224. [pdf]

M. Lattu, V. Meisalo, J. Tarhio: A visualization tool as a demonstration aid. Computers & Education 41, 2 (2003), 133–148.

A. Korhonen, J. Tarhio (eds.): Tietojenkäsittelytieteen päivät 2003. Tietojenkäsittelytieteen Seura r.y., 2003, 69 p.

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. [pdf]

K. Fredriksson, J. Tarhio: Processing of Huffman compressed texts with a super-alphabet. 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, 108–121.

2002

J. Eskola, J. Tarhio: On visualization of recursion with Excel. In: Proc. Second Program Visualization Workshop (ed. M. Ben-Ari), University of Aarhus, 2002, 45–51.

M. Ben-Ari, N. Myller, E. Sutinen, J. Tarhio: Perspectives on program animation with Jeliot. In: Software Visualization, State-of-the-Art Survey (ed. S. Diehl), Lecture Notes in Computer Science 2269, Springer, 2002, 31–45. [pdf]

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.

J. Rautio, J. Tanninen, J. Tarhio: String matching with stopper compression. In: Proc. DCC '02, Data Compression Conference (ed. J. Storer and M. Cohn), IEEE Computer Society Press, Los Alamitos, California, 2002, p. 469.

J. Rautio, J. Tanninen, J. Tarhio: String matching with stopper encoding and code splitting In: Proc. CPM '02, Combinatorial Pattern Matching (ed. A. Apostolico, M. Takeda), Lecture Notes in Computer Science 2373, Springer, 2002, 42–52. [pdf]

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]

2001

J. Eskola, J. Tarhio: Animation of flowcharts with Excel. In: Proc. First Program Visualization Workshop (ed. E. Sutinen), International Proceedings Series 1, University of Joensuu, Department of Computer Science, 2001, 59–68.

M. Lattu, V. Meisalo, J. Tarhio: On using a visualization tool as a demonstration aid. In: Proc. First Program Visualization Workshop (ed. E. Sutinen), International Proceedings Series 1, University of Joensuu, Department of Computer Science, 2001, 141–157.

A. Karvonen, E. Rautama, 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.

P. Eronen, J.-P. Makkonen, J. Tarhio: Infomediator based network for unifying E-commerce. In: Proc. IAWTIC '01, International Conference on Intelligent Agents, Web Technology and Internet Commerce, Las Vegas, 2001, 285–291.

E. Sutinen, J. Tarhio: Teaching to identify problems in a creative way. In: Proc. FIE '01, 31st ASEE/IEEE Frontiers in Education Conference, IEEE, 2001, p. T1D8–13.

J. Tarhio: On compression of parse trees. In: SPIRE 2001, Eight Symposium on String Processing and Information Retrieval, IEEE Computer Society, 2001, 205–211. [pdf]

V. Meisalo, E. Sutinen, J. Tarhio: Design models for enhancing open learning environments. In: Proc. ICCE '01, Ninth International Conference on Computers in Education, 2001, 520–523.

E. Rautama, E. Sutinen, J. Tarhio: Web tools for creative problem solving. In: Proc. ICCE '01, Nineth International Conference on Computers in Education, 2001, 524–530. [pdf]

J. Eskola, J. Tarhio: Ikoniohjelmointia Excelillä. Dimensio 65, 6 (2001), 52–55.

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. [pdf]

2000

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.

M. Lattu, V. Meisalo, J. Tarhio: How a visualization tool can be used — Evaluating a tool in a research & development project. In: Proc. PPIG '00, 12th Annual Conference of the Psychology of Programming Interest Group (ed. A. Blackwell and E. Bilotta), Memoria, 2000, 19–32.

V. Meisalo, E. Sutinen, J. Tarhio: Modernit oppimisympäristöt — Tietotekniikan käyttö opetuksen ja oppimisen tukena. (Modern Learning Environments: Using Computers to Support Teaching and Learning.) 341 p., Tietosanoma, Helsinki, 2000.

G. Navarro, J. Tarhio: Boyer-Moore string matching over Ziv-Lempel compressed text. In: Combinatorial Pattern Matching, Proceedings of 11th Annual Symposium (ed. R. Giancarlo and D. Sankoff), Lecture Notes in Computer Science 1848, Springer, Berlin, 2000, 166–180. [pdf]

G. Navarro, E. Sutinen, J. Tanninen, J. Tarhio: Indexing text with approximate q-grams. In: Combinatorial Pattern Matching, Proceedings of 11th Annual Symposium (ed. R. Giancarlo and D. Sankoff), Lecture Notes in Computer Science 1848, Springer, Berlin, 2000, 350–363. [pdf]

V. Meisalo, E. Sutinen, J. Tarhio: Miten tietotekniikan opetuksessa ratkaistaan eettisiä ongelmia luovalla tavalla? (How to solve ethical problems in a creative way in Computer Science education) In: Opettaja ja aine (ed. I. Buchberger). Helsingin yliopiston opettajankoulutuslaitos, Tutkimuksia 224. Helsingin yliopisto, 2000, 448–463.

M. Karjunen, E. Sutinen, J. Tarhio: Towards intelligent portfolios on the Web. In: Proc. SSGRR 2000, International Conference on Advances in Infrastructure for Electronic Business, Science, and Education on the Internet (ed. G. Reiss Romoli), Scuola Superiore, Italy, 2000.

J. Tarhio, S. Fincher, D. Joyce (eds.): Proceedings of the 5th Annual SIGCSE Conference on Innovation and Technology in Computer Science Education, ITiCSE 2000, Helsinki, Finland, ACM, 2000.

J. Eskola, J. Tarhio: Flowchart programming with Excel. Report C-2000-52, Department of Computer Science, University of Helsinki, 2000.

1999

J. Kurhila, E. Sutinen, J. Tarhio: Towards meaningful computer uses in education. In: Proc. EUNIS 99: Information Technology Shaping European Universities (ed. K. Sarlin). Espoo, Finland, 1999, 261–264.

V. Meisalo, J. Peltola, J. Tarhio: Reflective evaluation of individual contribution to group work — Problems of evaluation in the context of creative problem solving. In: Proc. Quality Aspects of Mathematics and Science Education (ed. O. Björkqvist). Report 5, Department of Teacher Education, Åbo Akademi University, Vaasa, 1999, 201–210.

M. Lattu, V. Meisalo, J. Tarhio, T. Teräsvirta: Making animations to enhance learning. In: Proc. Quality Aspects of Mathematics and Science Education (ed. O. Björkqvist). Report 5, Department of Teacher Education, Åbo Akademi University, Vaasa, 1999, 217–226.

K. Lemström, J. Tarhio: Detecting monophonic patterns within polyphonic sources. Report C-1999-37, Department of Computer Science, University of Helsinki, 1999.

1998

J. Markkanen, P. Saariluoma, E. Sutinen, J. Tarhio: Visualization and imagery in teaching programming. In: Proc. 10th Annual Meeting of the Psychology of Programming Interest Group (eds. John Domingue and Paul Mulholland). Knowledge Media Institute, Open University, Milton Keynes, 1998, 70–73.

A. Dybdahl, E. Sutinen, J. Tarhio: Excel as teacher's tool (in Finnish). In: Proc. ITK-98, Interaktiivinen teknologia koulutuksessa (ed. V. Kuuliala and E. Suojoki), Hämeenlinnan kesäyliopisto, 1998, p. 110.

E. Sutinen, J. Tarhio: Excel as teacher's and student's tool (in Finnish). Workshop abstract. In: Proc. ITK-98, Interaktiivinen teknologia koulutuksessa (ed. V. Kuuliala and E. Suojoki), Hämeenlinnan kesäyliopisto, 1998, p. 142.

A. Dybdahl, E. Sutinen, J. Tarhio: Excel as a teaching tool. In: Proc. LeTTET '98 and MaTILDA '98 Joint Conference (ed. J. Multisilta and J.-P. Niemi), Porin korkeakouluyksikkö, Pori, 1998, 35–39.

E. Rautama E. Sutinen, J. Tarhio: Everyman's model for collaboration on the Web. In: Proc. LeTTET '98 and MaTILDA '98 Joint Conference (ed. J. Multisilta and J.-P. Niemi), Porin korkeakouluyksikkö, Pori, 1998, 81–85.

S.-P. Lahtinen, E. Sutinen, J. Tarhio: Automated animation of algorithms with Eliot. Journal of Visual Languages and Computing 9, 3 (1998), 337–349.

A. Dybdahl, E. Sutinen, J. Tarhio: On animation features of Excel. In: Proc. ITiCSE '98, Integrating Technology into Computer Science Education, ACM, 1998, 77–80.

V. Meisalo, E. Sutinen, J. Tarhio, T. Teräsvirta: Combining algorithmic and creative problem solving on the Web. In: Proc. Teleteaching '98/IFIP World Computer Congress 1998 (ed. G. Davies). Austrian Computer Society, 1998, 715–724.

V. Meisalo, E. Sutinen, J. Tarhio: Impacts of interdisciplinary dialogue to computer science education. In: Informatics in Higher Education: Views on informatics and non-informatics curricula. Proc. IFIP TC3/WG3.2 International Conference on Informatics (computer science) as a Discipline and in Other Disciplines: what is common? (eds. F. Mulder and T. van Weert), Chapman & Hall, 1998, 241–244.

J. Tarhio: Animointi ongelmanratkaisun apuna. (Animation-aided problem solving.). In: Tuulta purjeisiin: matemaattisten aineiden opetus 2000-luvulle (ed. J. Lavonen, M. Erätuuli). Arena kustannus, 1998, 124–136.

E. Rautama, J. Tarhio: Sharing concept maps on the Web. In: Global Education ON the Net, Proc. ICCE '98, The Sixth International Conference on Computers in Education (ed. T.-W. Chan et al.). Springer, Beijing, 1998, 273–280.

A. Ellis, L. Carswell, A. Bernat, D. Deveaux, P. Frison, V. Meisalo, J. Meyer, U. Nulden, J. Rugelj, J. Tarhio: Resources, tools, and techniques for problem based learning in computing. Report of the ITiCSE '98 Working Group on Problem Based Learning. SIGCSE Bulletin – Inroads 30, 4 (1998), 45b–60b.

1997

E. Sutinen, J. Tarhio: Eliot — what happens inside a program? In: Proc. ITK-97, Interaktiivinen teknologia koulutuksessa (ed. V. Kuuliala et al.), Hämeenlinnan kesäyliopisto, 1997, 94–98.

R. Baeza-Yates, G. Navarro, E. Sutinen, J. Tarhio: Indexing methods for approximate text retrieval. Technical Report TR/DCC-97-2, Dept. of Computer Science, Univ. of Chile.

V. Meisalo, E. Sutinen, J. Tarhio: CLAP: teaching data structures in a creative way. In: Proc. ITiCSE '97, Integrating Technology into Computer Science Education (ed. G. Davies), ACM, Uppsala, 1997, 117–119. Also in: SIGCSE Bulletin 29, 3 (1997).

E. Rautama, E. Sutinen, J. Tarhio: Excel as an algorithm animation environment. In: Proc. ITiCSE '97, Integrating Technology into Computer Science Education (ed. G. Davies), ACM, Uppsala, 1997, 24–26. Also in: SIGCSE Bulletin 29, 3 (1997).

J. Markkanen, E. Rautama, E. Sutinen, J. Tarhio, T. Teräsvirta: Animation of algorithms with Eliot and Jeliot. In: Working Group Reports and Supplementary Proceedings of ITiCSE '97, Integrating Technology into Computer Science Education, ACM, 1997, p. 152.

T. Naps, J. Bergin, R. Jimenez-Peris, M. McNally, M. Patino-Martinez, V. Proulx, J. Tarhio: Using the WWW as the delivery mechanism for interactive, visualization-based instructional modules. In: Working Group Reports and Supplementary Proceedings of ITiCSE '97, Integrating Technology into Computer Science Education, ACM, 1997, 13–26.

S.-P. Lahtinen, E. Sutinen, J. Tarhio: Automated animation of algorithms. Report C-1997-38, Department of Computer Science, University of Helsinki, 1997.

J. Tarhio, H. Peltola: String matching in the DNA alphabet. Software — Practice and Experience 27, 7 (1997), 851–861. [pdf]

S.-P. Lahtinen, E. Sutinen, J. Tarhio, A.-P. Tuovinen: Object-oriented visualization of program logic. In: Proc. Technology of Object-Oriented Languages & Systems TOOLS 23, ISE Inc., Santa Barbara, CA, 1997, 93–107.

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]

E. Sutinen, J. Tarhio, S.-P. Lahtinen, A.-P. Tuovinen, E. Rautama, V. Meisalo: Eliot — an algorithm animation environment. Report A-1997-4, Department of Computer Science, University of Helsinki, 1997.

V. Meisalo, E. Rautama, E. Sutinen, J. Tarhio: Teaching algorithms with animation — a case study using Eliot. In: Proc. LeTTET '96, Learning Technology and Telematics in Education and Training (ed. O. Hatakka). Joensuun yliopistopaino, 1997, 79–84.

E. Rautama, E. Sutinen, J. Tarhio: Supporting learning process with concept map scripts. Journal of Interactive Learning Research 8, 3/4 (1997), 407–420.

A. Valdes, S. McWeeney, H. Salamon, J. Tarhio, K. Ronningen, G. Thomson: The HLA amino acids influencing IDDM predisposition. In: Genetic Diversity of HLA: Functional and Medical Implications, Vol. II (ed. D. Charron). EDK Press, Paris, 1997, 619–627.

1996

S.-P. Lahtinen, T. Lamminjoki, E. Sutinen, J. Tarhio, A.-P. Tuovinen: Towards automated animation of algorithms. In: Proceedings of Fourth International Conference in Central Europe on Computer Graphics and Visualization 96 (ed. N. Thalmann and V. Skala). University of West Bohemia, Department of Computer Science, 1996, 150–161.

K. Lemström, T. Takala, J. Tarhio: Color dithering with n-best algorithm. Proceedings of Fourth International Conference in Central Europe on Computer Graphics and Visualization 96 (ed. N. Thalmann and V. Skala). University of West Bohemia, Department of Computer Science, 1996, 162–170.

J. Tarhio: A sublinear algorithm for two-dimensional string matching. Pattern Recognition Letters 17 (1996), 833–838. [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. [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]

S.-P. Lahtinen, T. Lamminjoki, V. Ollikainen, E. Sutinen, J. Tarhio, A.-P. Tuovinen: Animation technology as a method of learning to write algorithms. In: Opettajakoulutuksen uudet haasteet (ed. M. Ahtee et al.), Report 162, Department of Teacher Education, University of Helsinki, 1996, 147–151.

S.-P. Lahtinen, V. Meisalo, E. Sutinen, J. Tarhio: Unified challenges of algorithm design and problem solving. In: Opettajakoulutuksen uudet haasteet (ed. M. Ahtee et al.), Report 162, Department of Teacher Education, University of Helsinki, 1996, 153–161.

J. Tarhio, M. Tienari (eds.): Computer Science at the University of Helsinki 1996. Report A-1996-3, Department of Computer Science, University of Helsinki, 1996.

E. Rautama, E. Sutinen, J. Tarhio: Opi algoritmi animoiden. (Learn an algorithm by making an animation.) Peda-forum, Korkeakoulupedagoginen tiedotuslehti (Newsletter of a Finnish Network for Developing Instruction and Learning in Higher Education), 2/1996, 21.

E. Rautama, E. Sutinen, J. Tarhio: Algoritmista animaatioksi — mitä, miten ja miksi? (From algorithm to animation — what when, and why?) OTE-lehti, 6/1996, 24–26.

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, 3 (1996), 407–423.

S. McWeeney, A. M. Valdes, H. Salamon, K. Ronningen, J. Tarhio, G. Thomson: HLA class II DR-DQ contribution to IDDM at the amino acid level. Human Immunology 49, Suppl. 1 (1996), p. 41.

1995

J. Tarhio: Context coding of parse trees. In: Proceedings of DCC '95, Data Compression Conference (ed. J. Storer and M. Cohn), IEEE Computer Society Press, Los Alamitos, California, 1995, p. 442.

S.-P. Lahtinen, E. Sutinen, J. Tarhio, A.-P. Tuovinen: Learning and problem solving assisted with animated objects. In: Abstracts of ECER 95, European Conference on Educational Research, University of Bath, England, 1995, p. 153.

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, H. Peltola: String matching in the DNA alphabet. Report C-1995-61, Department of Computer Science, University of Helsinki, 1995.

1994

J. Tarhio: Compilers of programming languages (in Finnish), Report D-1994-339, Department of Computer Science, University of Helsinki, 1994.

P. Orponen, J. Tarhio, E. Ukkonen: Design and analysis of algorithms (in Finnish), Report D-1994-356, Department of Computer Science, University of Helsinki, 1994.

1993

J. Tarhio, E. Ukkonen: Approximate Boyer-Moore string matching. SIAM Journal on Computing 22 (1993), 243–260. [pdf]

E. Sutinen, J. Tarhio: String matching animator SALSA. In: Proceedings of the Third Symposium on Programming Languages and Software Tools (ed. M. Tombak), Department of Computer Science, University of Tartu, 1993, 120–129. [pdf]

J. Tarhio: A Boyer-Moore approach for two-dimensional matching. Report UCB/UCD 93/784, Computer Science Division, University of California, Berkeley, 1993.

1992

K. Pohjonen, J. Tarhio (eds.): Tietojenkäsittelyopin laitoksen tutkimusraportteja 1990-91 — Research reports at the Department of Computer Science 1990-91. Report A-1992-2, Department of Computer Science, University of Helsinki, 1992.

1991

R. op den Akker, B. Melichar, J. Tarhio: The hierarchy of LR-attributed grammars. Memoranda Informatica 91-26. Department of Computer Science, University of Twente, 1991.

R. op den Akker, B. Melichar, J. Tarhio: Attribute evaluation and parsing. Memoranda Informatica 91-31. Department of Computer Science, University of Twente, 1991.

H. Peltola, J. Tarhio: On syntactical data compression. In: Proceedings of the Second Symposium on Programming Languages and Software Tools (ed. K. Koskimies ja K.-J. Räihä), Report A-1991-5, Department of Computer Science, University of Tampere, 1991, 205–214.

R. op den Akker, B. Melichar, J. Tarhio: Attribute evaluation and parsing. Attribute Grammars, Applications and Systems, Proceedings of International Summer School SAGA (ed. H. Alblas and B. Melichar), Lecture Notes in Computer Science 545, Springer-Verlag, Berlin, 1991, 187–214.

J. Tarhio, M. Tienari (eds.): Computer Science at the University of Helsinki 1991. Report A-1991-6, Department of Computer Science, University of Helsinki, 1991.

P. Jokinen, J. Tarhio, E. Ukkonen: A comparison of approximate string matching algorithms. Report A-1991-7, Department of Computer Science, University of Helsinki, 1991.

1990

K. Pohjonen, J. Tarhio (eds.): Tietojenkäsittelyopin laitoksen tutkimusraportteja 1988-89 — Research reports at the Department of Computer Science 1988-89. Report A-1990-1, Department of Computer Science, University of Helsinki, 1990.

J. Tarhio, E. Ukkonen: Approximate Boyer-Moore string macthing. Report A-1990-3, Department of Computer Science, University of Helsinki, 1990.

J. Tarhio: Uncle-attributed grammars. BIT 30 (1990), 437–449.

J. Tarhio, E. Ukkonen: Boyer-Moore approach to approximate string matching. In: Proceedings of 2nd Scandinavian Workshop on Algorithm Theory (ed. J. Gilbert and R. Karlsson), Lecture Notes in Computer Science 447, Springer-Verlag, Berlin, 1990, 348–359.

R. op den Akker, B. Melichar, J. Tarhio: The hierarchy of LR-attributed grammars. In: Proceedings of International Conference WAGA on Attribute Grammars and their Applications (ed. P. Deransart and M. Jourdan), Lecture Notes in Computer Science 461, Springer-Verlag, Berlin, 1990, 13–28.

1989

J. Tarhio: A compiler generator for attribute evaluation during LR parsing. In: Proceedings of the Second Workshop on Compiler Compiler and High Speed Compilation, (ed. D. Hammer), Lecture Notes in Computer Science 371, Springer-Verlag, Berlin, 1989, 146–159.

J. Tarhio, M. Tienari (eds.): Computer Science at the University of Helsinki. Report A-1989-3, Department of Computer Science, University of Helsinki, 1989.

J. Tarhio: ATTE — Editor for attribute grammars. In: Proceedings of the First Finnish-Hungarian Workshop: Symposium on Programming Languages and Software Tools (ed. T. Gyimóthy), Hungarian Academy of Sciences, 1989, 58–64.

1988

E. Soisalon-Soininen, J. Tarhio: Looping LR parsers. Information Processing Letters 26, 5 (1988), 251–253.

J. Tarhio, E. Ukkonen: A greedy approximation algorithm for constructing shortest common superstrings. Theoretical Computer Science 57 (1988), 131–145. [pdf]

O. Peitsalo, J. Tarhio (eds.): Tietojenkäsittelyopin laitoksen tutkimusraportteja 1986-87 — Research reports at the Department of Computer Science 1986-87. Report A-1988-7, Department of Computer Science, University of Helsinki, 1988.

J. Tarhio: The compiler generator Metauncle. Report C-1988-23, Department of Computer Science, University of Helsinki, 1988.

J. Tarhio: Attribute grammars for one-pass compilation. Ph.D. Thesis, Report A-1988-11, Department of Computer Science, University of Helsinki, 1988.

1987

K.-J. Räihä, J. Tarhio: A simplifying transformation for attribute grammars. Report A-1987-4. Department of Computer Science, University of Tampere, 1987.

J. Tarhio, E. Ukkonen: A greedy approximation algorithm for constructing shortest common superstrings. Report C-1987-47, Department of Computer Science, University of Helsinki, 1987.

1986

O. Peitsalo, J. Tarhio (eds.): Tietojenkäsittelyopin laitoksen tutkimusraportteja 1984-85 — Research reports at the Department of Computer Science 1984-85. Report A-1986-1, Department of Computer Science, University of Helsinki, 1986.

K.-J. Räihä, J. Tarhio: A globalizing transformation for attribute grammars. In: Proceedings of the SIGPLAN '86 Symposium on Compiler Construction, SIGPLAN Notices 21, 7 (1986), 74–84.

J. Tarhio, E. Ukkonen: A greedy algorithm for constructing shortest common superstrings. In: Proceedings of Mathematical Foundations of Computer Science 1986 (ed. J. Gruska et al.), Lecture Notes in Computer Science 233, Springer-Verlag, Berlin, 1986, 602–610.

E. Soisalon-Soininen, J. Tarhio: Looping LR parsers. In: Proceedings of 3rd Finnish Symposium on Theoretical Computer Science. Report N:o 15, University of Joensuu, Faculty of Mathematics and Natural Sciences, 1986, 42–48.

1984

J. Tarhio: Bottom-up and top-down attributed grammars. In: Proceedings of the Winter School of Theoretical Computer Science (ed. R. Back et al.), Finnish Society of Information Processing Science, Lammi, 1984, 290–302.

O. Peitsalo, J. Tarhio (eds.): Tietojenkäsittelyopin laitoksen tutkimusraportteja 1983 — Research reports at the Department of Computer Science 1983. Report A-1984-1, Department of Computer Science, University of Helsinki, 1984.

J. Tarhio: Sanatar. Weilin & Göös, Espoo, 1984.

J. Tarhio, E. Ukkonen: On the preprocessing algorithm for the Boyer-Moore string matching. Report C-1984-86, Department of Computer Science, University of Helsinki, 1984.

1983

O. Peitsalo, J. Tarhio (eds.): Tietojenkäsittelyopin laitoksen tutkimusraportteja 1982 — Research reports at the Department of Computer Science 1982. Report A-1983-2, Department of Computer Science, University of Helsinki, 1983.

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. [pdf]

1982

J. Tarhio: LR parsing of some ambiguous grammars. Information Processing Letters 14 (1982), 101–103.

O. Peitsalo, J. Tarhio (eds.): Tietojenkäsittelyopin laitoksen tutkimusraportteja 1981 — Research reports at the Department of Computer Science 1981. Report A-1982-1, Department of Computer Science, University of Helsinki, 1982.

J. Tarhio: Attribute evaluation during LR parsing. Ph.Lic. Thesis, Report A-1982-4, Department of Computer Science, University of Helsinki, 1982.

1981

O. Peitsalo, J. Tarhio (eds.): Tietojenkäsittelyopin laitoksen tutkimusraportteja 1980 — Research reports at the Department of Computer Science 1980. Report A-1981-2, Department of Computer Science, University of Helsinki, 1981.

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