Jorma Tarhio

Research outputs

  1. 2018
  2. E-pub ahead of print

    Improved online algorithms for jumbled matching

    Ghuman, S. S., Tarhio, J. & Chhabra, T., 1 Jan 2018, In : Discrete Applied Mathematics. p. 1-13

    Research output: Contribution to journalArticleScientificpeer-review

  3. 2017
  4. Published

    Bit-parallel approximate matching of circular strings with k mismatches

    Hirvola, T. & Tarhio, J., Dec 2017, In : ACM Journal of Experimental Algorithmics. 22, 1, p. 1-12 12 p., 1.5.

    Research output: Contribution to journalArticleScientificpeer-review

  5. Published

    Engineering order-preserving pattern matching with SIMD parallelism

    Chhabra, T., Faro, S., Külekci, M. O. & Tarhio, J., May 2017, In : SOFTWARE-PRACTICE AND EXPERIENCE. 47, 5, p. 731–739

    Research output: Contribution to journalArticleScientificpeer-review

  6. Published

    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

  7. Published

    Technology beats algorithms (in exact string matching)

    Tarhio, J., Holub, J. & Giaquinta, E., 2017, In : SOFTWARE-PRACTICE AND EXPERIENCE. 47, 12, p. 1877–1885

    Research output: Contribution to journalArticleScientificpeer-review

  8. 2016
  9. Published

    A filtration method for order-preserving matching

    Chhabra, T. & Tarhio, J., 1 Feb 2016, In : Information Processing Letters. 116, 2, p. 71-74 4 p.

    Research output: Contribution to journalArticleScientificpeer-review

  10. Published

    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

  11. 2015
  12. Published

    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

  13. Published

    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

  14. Published

    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

  15. 2014
  16. Published

    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

  17. Published

    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

  18. Published

    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

  19. Published

    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

  20. Published

    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

  21. Published

    String Matching with Lookahead

    Peltola, H. & Tarhio, J., 2014, In : Discrete Applied Mathematics. 163, 3, p. 352-360

    Research output: Contribution to journalArticleScientificpeer-review

  22. 2012
  23. Published

    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

  24. Published

    String matching with alphabet sampling

    Claude, F., Navarro, G., Peltola, H., Salmela, L. & Tarhio, J., 2012, In : Journal of Discrete Algorithms. 11, p. 37-50

    Research output: Contribution to journalArticleScientificpeer-review

  25. 2011
  26. Published

    Exact search algorithms for biological sequences

    Rivals, E., Salmela, L. & Tarhio, J., 2011, Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications. Elloumi, M. Z. (ed.). Hoboken, New Jersey: JOHN WILEY & SONS, p. 91-111

    Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

  27. Published

    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

  28. Published

    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

  29. 2010
  30. Published

    Approximate Boyer-Moore string matching for small alphabets

    Salmela, L., Tarhio, J. & Kalsi, P., 2010, In : Algorithmica. 58, 3, p. 591609

    Research output: Contribution to journalArticleScientificpeer-review

  31. Published

    Approximate string matching with reduced alphabet

    Salmela, L. & Tarhio, J., 2010, Algorithms and Applications.Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday.Lecture Notes in Computer Science, Volume 6060. Elomaa, T., Mannila, H. & Orponen, P. (eds.). Berlin - Heidelberg, p. 210220

    Research output: Chapter in Book/Report/Conference proceedingChapterScientificpeer-review

  32. Published

    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

  33. Published

    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, p. Article No. 30

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

  34. Published

    Improving practical exact string matching

    Durian, B., Holub, J., Peltola, H. & Tarhio, J., 2010, In : Information Processing Letters. 110, 4, p. 148-153

    Research output: Contribution to journalArticleScientificpeer-review

  35. Published

    Kaksikymmentä vuotta Tietojenkäsittelytiede-lehteä

    Tarhio, J., 2010, In : Tietojenkäsittelytiede. 31, p. 4

    Research output: Contribution to journalArticleScientific

  36. Published

    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

  37. 2009
  38. Published

    Linjauksia

    Tarhio, J., 2009, In : Tietojenkäsittelytiede. 29, p. 4-5

    Research output: Contribution to journalArticleProfessional

  39. Published

    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

  40. Published

    String Processing and Information Retrieval: 16th International Symposium, SPIRE 2009 Saariselkä, Finland, August 25-27, 2009 Proceedings

    Karlgren, J., Tarhio, J. & Hyyrö, H., 2009, Berlin, (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); no. 5721).

    Research output: Working paperProfessional

  41. Published

    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

  42. Published

    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

  43. Published

    Using reads to annotate the genome: influence of length, background distribution, and sequence errors on prediction capacity

    Philippe, N., Boureux, A., Bréhélin, L., Tarhio, J., Commes, T. & Rivals, E., 2009, In : Nucleic Acids Research. 37, 15, p. e104

    Research output: Contribution to journalArticleScientificpeer-review

  44. 2008
  45. Published

    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

  46. Published

    Fast parameterized matching with q-grams

    Salmela, L. & Tarhio, J., 2008, In : Journal of Discrete Algorithms. 6, 3, p. 408-419

    Research output: Contribution to journalArticleScientificpeer-review

  47. Published

    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

  48. Published

    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

  49. 2007
  50. Published

    A framework for research on technology-enhanced special education

    Jormanainen, I., Kärnä-Lin, E., Lahti, L., Pihlainen-Bednarik, K., Sutinen, E., Tarhio, J. & Virnes, M., 2007, p. 54-55, (7th IEEE International Conference on Advanced Learning Technologies, ICALT 2007, July 18-20 2007, Niigata, Japan).

    Research output: Working paperProfessional

  51. Published

    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

  52. Published

    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

  53. Published

    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

  54. Published

    Transcriptome annotation using tandem SAGE tags

    Rivals, E., Boureux, A., Lejeune, M., Ottones, F., Pérez, O., Tarhio, J., Pierrat, F., Ruffle, F., Commes, T. & Marti, J., 2007, In : Nucleic Acids Research. 35, 17, p. e108

    Research output: Contribution to journalArticleScientificpeer-review

  55. Published

    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

  56. 2006
  57. Published

    Ajatuksia konferenssiartikkeleista

    Tarhio, J., 2006, In : Tietojenkäsittelytiede. 25, p. 8-9

    Research output: Contribution to journalArticleProfessional

  58. Published

    Multi-Pattern String Matching with q-Grams

    Salmela, L., Tarhio, J. & Kytöjoki, J., 2006, In : ACM Journal of Experimental Algorithmics. 11, p. 1-19

    Research output: Contribution to journalArticleScientificpeer-review

  59. Published

    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

  60. 2005
  61. Published

    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

  62. Published

    Indexing text with approximate q-grams

    Navarro, G., Sutinen, E. & Tarhio, J., 2005, In : Journal of Discrete Algorithms. 3, 2-4, p. 157-175

    Research output: Contribution to journalArticleScientificpeer-review

  63. Published

    LZgrep: a Boyer-Moore string matching tool for Ziv-Lempel compressed text

    Navarro, G. & Tarhio, J., 2005, In : Software: Practice and Experience. 35, 12, p. 1107-1130

    Research output: Contribution to journalArticleScientificpeer-review

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