20002019

Research output per year

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Research Output

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Conference contribution
2017

Counting mismatches with SIMD

Fiori, F., Pakalén, W. & Tarhio, J., 2017, Proceedings of the Prague Stringology Conference 2017. Holub, J. & Zdarek, J. (eds.). Czech Technical University, p. 51-61

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2016

Jumbled matching with SIMD

Ghuman, S. & Tarhio, J., 2016, Prague Stringology Conference 2016, August 29-31, 2016. Holub, J. & Zdarek, J. (eds.). Prague, Czech Republic: Czech Technical University, p. 114-124

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2015

Alternative Algorithms for Order-Preserving Matching

Chhabra, T., Kulekci, M. O. & Tarhio, J., 2015, Prague Stringology Conference 2015, Prague, Czech Republic, August 24-26, 2015. Jan Holub, J. Z. (ed.). p. 36-46

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

12 Citations (Scopus)

Filtration Algorithms for Approximate Order-Preserving Matching

Chhabra, T., Giaquinta, E. & Tarhio, J., 2015, 22nd International Symposium on String Processing and Information Retrieval, London, UK, September 1-4, 2015. p. 177-187

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

9 Citations (Scopus)

Tuning Algorithms for Jumbled Matching

Chhabra, T., Ghuman, S. S. & Tarhio, J., 2015, Prague Stringology Conference 2015, August 24-26, 2015Prague, Czech Republic,. Holub, J. & Zdarek, J. (eds.). p. 57-66

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2 Citations (Scopus)
2014

Alternative algorithms for Lyndon factorization

Ghuman, S. S., Giaquinta, E. & Tarhio, J., 2014, 13th Prague Stringology Conference, Prague, Czech Republic, September 1-3, 2014. p. 169-178 12 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

5 Citations (Scopus)

Approximate online matching of circular strings.

Hirvola, T. & Tarhio, J., 2014, Symposium on Experimental Algorithms, Copenhagen, Denmark, 29 June - 1 July, 2014. p. 315-325

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

6 Citations (Scopus)

Improved Two-Way Bit-parallel Search

Durian, B., Chhabra, T., Ghuman, S. S., Hirvola, T., Peltola, H. & Tarhio, J., 2014, PSC 2014, the Prague Stringology Conference 2014, Prague, Czech Republic; September 13, 2014. Holub, J. & Zdárek, J. (eds.). Prague, p. 7183

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

7 Citations (Scopus)

Order-preserving matching with filtration.

Chhabra, T. & Tarhio, J., 2014, Symposium on Experimental Algorithms, Copenhagen, Denmark, June 29 - July 1, 2014. p. 307-314

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

17 Citations (Scopus)

Speeding up Compressed Matching with SBNDM2

Pollari-Malmi, K., Rautio, J. & Tarhio, J., 2014, Prague Stringology Conference, Prague, Czech Republic, September 1-3, 2014. Holub, J. & Zdárek, J. (eds.). Prague, p. 110-123

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2012

Indexed Multi-Pattern Matching

Gagie, T., Karhu, K., Kärkkäinen, J., Mäkinen, V., Salmela, L. & Tarhio, J., 2012, 10th Latin American Theoretical Informatics Symposium (LATIN); Arequipa, Peru; April 16-20, 2012. Fernandez-Baca, D. (ed.). Heidelberg, Germany, p. 399-407

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

4 Citations (Scopus)
2011

GAST, a Genomic Alignment Search Tool

Karhu, K., Mäkinen, J., Rautio, J., Salamon, H. & Tarhio, J., 2011, International Conference on Bioinformatics Models, Methods and Algorithms. Rome, Italy, 28-29 January, 2011. SciTePress, p. 82-90

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Variations of Forward-SBNDM

Peltola, H. & Tarhio, J., 2011, PSC 2011, the Prague Stringology Conference 2011, Prague, Czech Republicon August 2931, 2011. Holub, J. & Zdárek, J. (eds.). Prague, Czech Republic, p. 3-14

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

20 Citations (Scopus)
2010

Bit-Parallel Search Algorithms for Long Patterns

Durian, B., Peltola, H., Salmela, L. & Tarhio, J., 2010, 9th International Symposium on Experimental Algorithms.Ischia Island, Naples, Italy.May 20-22, 2010. Festa, P. (ed.). Berlin, Heidelberg, Germany, p. 129-140

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

26 Citations (Scopus)

Identifying human miRNA targets with a genetic algorithm

Karhu, K., Khuri, S., Mäkinen, J. & Tarhio, J., 2010, International Symposium on Biocomputing, Calicut, Kerala, India, February 15-17, 2010. Tulpan, D., Palakal, M., Abdul Nazeer, K. & Aswati Nair, R. (eds.). New York, NY, USA: ACM, p. Article No. 30

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

1 Citation (Scopus)

PMSGA: A fast DNA fragment assembler

Mäkinen, J., Tarhio, J. & Khuri, S., 2010, International Conference on Bioinformatics, Valencia, Spain, January 20-23, 2010. Fred, A. E. A. (ed.). INSTICC, p. 7782

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2009

MPSCAN: fast localisation of multiple reads in genomes

Rivals, E., Salmela, L., Kiiskinen, P., Kalsi, P. & Tarhio, J., 2009, WABI 2009, 9th Workshop on Algorithms in Bioinformatics, Philadelphia, USA, September 12-13. Salzberg, S. L. & Warnow, T. (eds.). Berlin, Germany, p. 246-260

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

16 Citations (Scopus)

Towards automated management of compiler assignments

Salmela, L., Tarhio, J. & Montonen, T., 2009, International Conference on Computer Supported Education (CSEDU 2009), March 23-26, Lisboa, Portugal. Cordeiro, J., Shishkov, B., Verbraeck, A. & Helfert, M. (eds.). INSTICC, p. 243-249

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

1 Citation (Scopus)

Tuning BNDM with q-Grams

Durian, B., Holub, J., Peltola, H. & Tarhio, J., 2009, ALENEX09, Tenth Workshop on Algorithm Engineering and Experiments; 3.1.2009; New York Marriott Downtown, New York, New York, U.S.A.. Philadelphia, PA, USA: Society for Industrial and Applied Mathematics (SIAM), p. 29-37

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

29 Citations (Scopus)
2008

Exact string matching algorithms for biological sequences

Kalsi, P., Peltola, H. & Tarhio, J., 2008, BIRD'08, 2nd International Conference on Bioinformatics Research and Development / ALBIO'08, Workshop on Algorithms in Molecular Biology; July 7-9, 2008; Vienna, Austria. Mourad Elloumi, J. K., Michal Linial, R. F. M. & Kristan Schneider, C. T. (eds.). Berlin, p. pages 417-426

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Semi-automated map generation for concept gaming

Lahti, L. & Tarhio, J., 2008, IADIS International Conference Gaming 2008 (part of MCCSIS 2008): Design for Engaging Experience and Social Interaction, 25-27 July 2008, Amsterdam, the Netherlands. Xiao, Y. & ten Thij, E. (eds.). p. 36-43

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Speeding up pattern matching by text sampling

Claude, F., Navarro, G., Peltola, H., Salmela, L. & Tarhio, J., 2008, SPIRE 2008, 15th International Symposium on String Processing and Information Retrieval, Melbourne, Australia, November 10-12. Amir, A., Turpin, A. & Moffat, A. (eds.). Berlin, Germany, p. 87-98

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2 Citations (Scopus)
2007

Algorithms for Weighted Matching

Salmela, L. & Tarhio, J., 2007, String Processing and Information Retrieval, Santiago, Chile, October 2007. Ziviani, N. & Baeza-Yates, R. (eds.). Germany, p. 276-286

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

6 Citations (Scopus)

On String Matching in Chunked Texts

Peltola, H. & Tarhio, J., 2007, Implementation and Application of Automata, 12th International Conference, CIAA 2007; July 16-18, 2007; Prague, Czech Republic. Holub, J. & Zdárek, J. (eds.). Heidelberg, p. 157-167

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

1 Citation (Scopus)

Platform for Elaboration of Search Results

Korhonen, A., Litola, J. & Tarhio, J., 2007, Web Information Systems and Technologies, March 3-6, Barcelona, Spain. Joaquim Filipe, J. C. (ed.). Portugal, p. 263-269

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

1 Citation (Scopus)

Tuning Approximate Boyer-Moore for Gene Sequences

Kalsi, P., Salmela, L. & Tarhio, J., 2007, String Processing and Information Retrieval, Santiago, Chile, October 2007. Ziviani, N. & Baeza-Yates, R. (eds.). Germany, p. 173-183

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2006

Sublinear algorithms for parameterized matching

Salmela, L. & Tarhio, J., 2006, Combinatorial Pattern Matching, Barcelona, Spain, July 2006. Lewenstein, M. & Valiente, G. (eds.). Germany, p. p. 354-364

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

4 Citations (Scopus)
2005

Computer aided concept mapping for constructing shared cognitive representations and conceptual artifacts

Silander, P., Sutinen, E. & Tarhio, J., 2005, ADIS International Conference Cognition and Exploratory Learning in Digital Age (CELDA 2005), Dec. 14-16 2005, Porto, Portugal. Isaias, P. & Sampson, D. G. (eds.). p. 3-8

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2004

ACE: Automated Compiler Exercises

Salmela, L. & Tarhio, J., 2004, Kolin Kolistelut-Koli Calling 2004. Fourth Finnish/Baltic Sea Conference on Computer Science Education, Koli, Finland, October 1-3,2004. Korhonen, A. & Malmi, L. (eds.). Espoo: Helsinki University of Technology, Department of Computer Science and Engineering, Laboratory of Information Processing Science, p. 131-135

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Mobile collaborative concept mapping - Combining classroom activity with simultaneous field exploration

Silander, P., Sutinen, E. & Tarhio, J., 2004, 2nd IEEE International Workshop on Wireless and Mobile Technologies in Education, March 23-25, 2004, Jhongli, Taiwan. Los Alamitos: IEEE Computer Society, p. 114-118

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

16 Citations (Scopus)

The Possibilities of Information Retrieval in Education

Meisalo, V., Sutinen, E. & Tarhio, J., 2004, Proceedings of the XXI annual symposium of tthe Finnish Association of Mathematics and Science Education Research. Laine, A., Lavonen, J. & Meisalo, V. (eds.). Helsinki: University of Helsinki, Department of Applied Sciences of Education, p. 528-549

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2003

Alternative Algorithms for Bit-Parallel String Matching

Peltola, H. & Tarhio, J., 2003, String Processing and Information Retrieval, 10th International Symposium, SPIRE 2003; October 8-10, 2003; Manaus, Brazil. Nascimento, M., Moura E. S., D. & Oliveira, A. L. (eds.). Heidelberg, p. 80-94

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

49 Citations (Scopus)

Processing of Huffman Compressed Texts with a Super-Alphabet

Fredriksson, K. & Tarhio, J., 2003, String Processing and Information Retrieval, 10th International Symposium, SPIRE 2003; October 8-10, 2003; Manaus, Brazil. Nascimento, M., Moura E. S., D. & Oliveira, A. L. (eds.). Heidelberg, p. 108-121

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2 Citations (Scopus)

Tuning string matching for huge pattern sets

Kytöjoki, J., Salmela, L. & Tarhio, J., 2003, Combinatorial Pattern Matching, 14th Annual Symposium, June 25-27, 2003, Morelia, Mexico. Baeza-Yates, R., Chavez, E. & Crochemore, M. (eds.). Berlin, p. 211-224

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

9 Citations (Scopus)
2002

Concept gaming

Eronen, P., Nuutinen, J., Rautama, E., Sutinen, E. & Tarhio, J., 2002, International Conference on Computers in Education (ICCE2002), December 3-6, 2002, Auckland, New Zealand. et al., K. (ed.). Los Alamitos, California: IEEE Computer Society, p. 997-1001

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2 Citations (Scopus)

On visualization of recursion with Excel

Eskola, J. & Tarhio, J., 2002, Second Program Visualization Workshop, June 27-28, HornstrupCentret, Denmark. Ben-Ari, M. (ed.). Aarhus: University of Aarhus, Dept. of Computer Science, p. 45-51

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Perspectives on program animation with Jeliot

Ben-Ari, M., Myller, N., Sutinen, E. & Tarhio, J., 2002, Software Visualization. International Seminar, Dagstuhl Castle, Germany, May 20-25, 2001. Diehl, S. (ed.). Berlin, p. 31-45

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

String matching with stopper encoding and code splitting.

Rautio, J., Tanninen, J. & Tarhio, J., 2002, Combinatorial Pattern Matching, 13th Annual Symposium, July 3-5, 2002, Fukuoka, Japan. Apostolico, A. & Takeda, M. (eds.). Berlin, p. 42-52

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

18 Citations (Scopus)
2001

Animation of flowcharts with Excel

Eskola, J. & Tarhio, J., 2001, The First Program Visualization Workshop. Sutinen, E. (ed.). Joensuu: Joensuun yliopisto, p. 59-68

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Design models for enhancing open learning environments

Meisalo, V., Sutinen, E. & Tarhio, J., 2001, 9th International Conference on Computers in Education (ICCE/SchoolNet2001), Seoul, Korea, 12.-15.11.2001. Seoul, Korea, p. 520-523

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Infomediator based network for unifying E-commerce

Eronen, P., Makkonen, J-P. & Tarhio, J., 2001, International Conference on Intelligent Agents, Web Technology and Internet Commerce, Las Vegas, 9.-11.7.2001. Las Vegas, USA, p. 285-291

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

On compression of parse trees

Tarhio, J., 2001, 8th International Symposium on String Processing and Information Retrieval, Laguna San Rafel, Chile, 13.-15.11.2001,. Los Alamitos, California: IEEE Computer Society, p. 205-211

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

On using a visualization tool as a demonstration aid.

Lattu, M., Meisalo, V. & Tarhio, J., 2001, The First Program Visualization Workshop, July 7-8, 2000, Porvoo. Sutinen, E. (ed.). Joensuu: Joensuun yliopisto, p. 141-162

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Teaching to identify problems in a creative way

Sutinen, E. & Tarhio, J., 2001, 31st ASEE/IEEEE Frontiers in Education Conference, Reno, Nevada, 10.-13.10.2001. Reno, Nevada, U.S.A.: IEEE, p. p. T1D8-13

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Versatile concept map viewing on the Web

Rautama, E., Karvonen, A., Tarhio, J. & Turkia, J., 2001, The 6th Annual Conference on Innovation and Technology in Computer Science Education, June 25-27, 2001, England. Finkel, D. (ed.). Canterbury: ACM/SIGCSE, p. 105-108

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Web tools for creative problem solving

Rautama, E., Sutinen, E. & Tarhio, J., 2001, 9th International Conference on Computers in Education (ICCE/SchoolNet2001), Seoul, Korea, 12.-15.11.2001. Seoul, Korea, p. 524-530

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2000

Boyer-Moore string matching over Ziv-Lempel compressed text

Navarro, G. & Tarhio, J., 2000, CPM '00, 11th Annual Symposium on Combinatorial Pattern Matching, June 21-23, 2000, Montreal. Giancarlo, R. & Sankoff, D. (eds.). Berlin, p. 166-180

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

How a visualization tool can be used - Evaluating a tool in a research & development project

Lattu, M., Meisalo, V. & Tarhio, J., 2000, PPIG '00, 12th Annual Meeting of the Psychology of Programming Interest Group, April 11-13, 2000, Calabro, Italy. Blackwell, A. & Bilotta, E. (eds.). Cosenza: PPIG, p. 19-32

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Indexing text with approximate q-grams

Navarro, G., Sutinen, E., Tanninen, J. & Tarhio, J., 2000, CPM '00, 11th Annual Symposium on Combinatorial Pattern Matching, June 21-23, 2000, Montreal. Giancarlo, R. & Sankoff, D. (eds.). Berlin, p. 350-363

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

20 Citations (Scopus)

Searching monophonic patterns within polyphonic sources

Lemström, K. & Tarhio, J., 2000, RIAO '00, Conf. of Content-Based Multimedia Information Access, April 12-14, 2000, Paris. Paris: C.I.D., p. 1261-1279

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review