Veli Mäkinen

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  1. Sparse Dynamic Programming on DAGs with Small Width

    Mäkinen, V., Tomescu, A. I., Kuosmanen, A., Paavilainen, T., Gagie, T. & Chikhi, R., Feb 2019, In : ACM transactions on algorithms.. 15, 2, p. Article No. 29 21 p.

    Research output: Contribution to journalArticleScientificpeer-review

  2. Applying the Positional Burrows–Wheeler Transform to All-Pairs Hamming distance

    Mäkinen, V. & Norri, T., Jun 2019, In : Information Processing Letters. 146, p. 17-19 3 p.

    Research output: Contribution to journalArticleScientificpeer-review

  3. Hardness of Covering Alignment: Phase Transition in Post-Sequence Genomics

    Rizzi, R., Cairo, M., Mäkinen, V., Tomescu, A. I. & Valenzuela, D., Feb 2019, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 16, 1, p. 23-30 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  4. Bidirectional Variable-Order de Bruijn Graphs

    Belazzougui, D., Gagie, T., Mäkinen, V., Previtali, M. & Puglisi, S. J., Dec 2018, In : International Journal of Foundations of Computer Science. 29, 8, p. 1279-1295 17 p.

    Research output: Contribution to journalArticleScientificpeer-review

  5. Minimum Segmentation for Pan-genomic Founder Reconstruction in Linear Time

    Norri, T., Cazaux, B., Kosolobov, D. & Mäkinen, V., 2018, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Parida, L. & Ukkonen, E. (eds.). Dagstuhl: Schloss Dagstuhl Leibniz Center for Informatics, p. 15:1-15:15 15 p. (Leibniz International Proceedings in Informatics (LIPIcs); vol. 113).

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

  6. Discovery of potential causative mutations in human coding and noncoding genome with the interactive software BasePlayer

    Katainen, R., Donner, I., Cajuso, T., Kaasinen, E., Palin, K., Mäkinen, V., Aaltonen, L. A. & Pitkänen, E., Nov 2018, In : Nature Protocols. 13, 11, p. 2580-2600 21 p.

    Research output: Contribution to journalArticleScientificpeer-review

  7. Editorial: Special Issue on "Combinatorial Algorithms" (IWOCA 2016)

    Makinen, V. & Puglisi, S. J., Aug 2018, In : Theory of Computing Systems. 62, 6, p. 1349-1350 2 p.

    Research output: Contribution to journalEditorialScientific

  8. A safe and complete algorithm for metagenomic assembly

    Acosta, N. O., Mäkinen, V. & Tomescu, A. I., 7 Feb 2018, In : Algorithms for Molecular Biology. 13, 12 p., 3.

    Research output: Contribution to journalArticleScientificpeer-review

  9. Towards pan-genome read alignment to improve variation calling

    Valenzuela, D., Norri, T., Välimäki, N., Pitkänen, E. & Mäkinen, V., 9 May 2018, In : BMC Genomics. 19, 8 p., 87.

    Research output: Contribution to journalArticleScientificpeer-review

  10. Variant genotyping with gap filling

    Walve, R., Salmela, L. & Mäkinen, V., 8 Sep 2017, In : PLoS One. 12, 9, 12 p., e0184608.

    Research output: Contribution to journalArticleScientificpeer-review

  11. Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-linear Chaining Extended

    Kuosmanen, A., Paavilainen, T., Gagie, T., Chikhi, R., Tomescu, A. & Mäkinen, V., Apr 2018, Research in Computational Molecular Biology : 22nd Annual International Conference, RECOMB 2018, Paris, France, April 21-24, 2018, Proceedings. Raphael, B. J. (ed.). Cham: Springer International Publishing AG, p. 105-121 17 p. (Lecture Notes in Bioinformatics; vol. 10812).

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

  12. Interval scheduling maximizing minimum coverage

    Mäkinen, V., Staneva, V., Tomescu, A. I., Valenzuela, D. & Wilzbach, S., 10 Jul 2017, In : Discrete Applied Mathematics. 225, p. 130-135 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  13. Evaluating approaches to find exon chains based on long reads

    Kuosmanen, A., Norri, T. & Mäkinen, V., May 2018, In : Briefings in Bioinformatics. 19, 3, p. 404-414 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  14. A framework for space-efficient read clustering in metagenomic samples

    Alanko, J., Cunial, F., Belazzougui, D. & Mäkinen, V., 14 Mar 2017, In : BMC Bioinformatics. 18, Suppl 3, 12 p., 59.

    Research output: Contribution to journalArticleScientificpeer-review

  15. Computational pan-genomics: status, promises and challenges

    The Computational Pan-Genomics Consortium, Mäkinen, V. A. T. & Valenzuela, S. D. A., Jan 2018, In : Briefings in Bioinformatics. 19, 1, p. 118-135 18 p.

    Research output: Contribution to journalArticleScientificpeer-review

  16. Combinatorial Algorithms: 27th International Workshop, IWOCA 2016, Helsinki, Finland, August 17-19, 2016, Proceedings

    Mäkinen, V. (ed.), Puglisi, S. J. (ed.) & Salmela, L. (ed.), 2016, Cham: Springer International Publishing . 434 p. (Theoretical Computer Science and General Issues; vol. 9843)

    Research output: Book/ReportAnthology or special issueScientificpeer-review

  17. Fully Dynamic de Bruijn Graphs

    Belazzougui, D., Gagie, T., Mäkinen, V. & Previtali, M., 2016, String Processing and Information Retrieval: 23rd International Symposium, SPIRE 2016, Beppu, Japan, October 18-20, 2016, Proceedings. Springer, p. 145-152 8 p. (Lecture Notes in Computer Science; vol. 9954).

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

  18. Identification of Variant Compositions in Related Strains Without Reference

    Rautiainen, M., Salmela, L. & Mäkinen, V., 2016, Algorithms for Computational Biology: Third International Conference, AlCoB 2016, Trujillo, Spain, June 21-22, 2016, Proceedings. Botón-Fernández, M., Martín-Vide, C., Santander-Jiménez, S. & Vega-Rodríguez, M. A. (eds.). Springer International Publishing , p. 158-170 13 p. (Lecture Notes in Computer Science; vol. 9702).

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

  19. Bidirectional Variable-Order de Bruijn Graphs

    Belazzougui, D., Gagie, T., Mäkinen, V. A. T., Previtali, M. & Puglisi, S. J., 2016, Theoretical informatics: LATIN 2016: 12th Latin American Symposium, Ensenada, Mexico, April 11-15, 2016 : proceedings. Kranakis, E., Navarro, G. & Chávez, E. (eds.). Berlin: Springer, p. 164-178 9 p. (Lecture Notes in Computer Science; vol. 9644).

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

  20. On using Longer RNA-seq Reads to Improve Transcript Prediction Accuracy

    Kuosmanen, A. E., Sobih, A. A. M., Rizzi, R., Mäkinen, V. A. T. & Tomescu, A. I., 2016, Proceedings of the 9th International Joint Conference on Biomedical Engineering Systems and Technologies. Gilbert, J., Azhari, H., Ali, H., Quintão, C., Sliwa, J., Ruiz, C., Fred, A. & Gamboa, H. (eds.). SCITEPRESS Science And Technology Publications , p. 272-277 6 p.

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

  21. MetaFlow: Metagenomic Profiling Based on Whole-Genome Coverage Analysis with Min-Cost Flows

    Sobih, A. A. M., Tomescu, A. I. & Mäkinen, V. A. T., 8 Apr 2016, Research in Computational Molecular Biology: 20th Annual Conference, RECOMB 2016, Santa Monica, CA, USA, April 17-21, 2016, Proceedings. Singh, M. (ed.). Cham: Springer International Publishing AG, p. 111-121 11 p. (Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science); vol. 9649).

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

  22. Gap Filling as Exact Path Length Problem

    Salmela, L., Sahlin, K., Mäkinen, V. & Tomescu, A. I., 9 May 2016, In : Journal of Computational Biology. 23, 5, p. 347-361 15 p.

    Research output: Contribution to journalArticleScientificpeer-review

  23. Explaining a Weighted DAG with Few Paths for Solving Genome-Guided Multi-Assembly

    Tomescu, A. I., Gagie, T., Popa, A., Rizzi, R., Kuosmanen, A. E. & Mäkinen, V. A. T., Dec 2015, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 12, 6, p. 1345-1354 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  24. SNV-PPILP

    van Rens, K., Mäkinen, V. A. T. & Tomescu, A. I., 2015

    Research output: Non-textual formSoftwareScientific

  25. Repeat- and error-aware comparison of deletions

    Wittler, R., Marschall, T., Schönhuth, A. & Mäkinen, V., Sep 2015, In : Bioinformatics. 31, 18, p. 2947-2954 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  26. Compressed Suffix Array

    Belazzougui, D., Mäkinen, V. A. T. & Valenzuela, S. D. A., 2015, Encyclopedia of Algorithms. Kao, M-Y. (ed.). New York: Springer, 6 p.

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

  27. Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing

    Mäkinen, V. A. T., Belazzougui, D., Cunial, F. & Tomescu, A. I., May 2015, Cambrigde University Press. 391 p.

    Research output: Book/ReportBookScientificpeer-review

  28. Diploid Alignments and Haplotyping

    Mäkinen, V. & Valenzuela, D., 2015, Bioinformatics Research and Applications: 11th International Symposium, ISBRA 2015, Norfolk, USA, June 6-9, 2015, Proceedings . Harrison, R., Li, Y. & Măndoiu, I. (eds.). Cham: Springer International Publishing AG, p. 235-246 12 p. (Lecture notes in computer science; vol. 9096)(LNCS sublibrary. SL 8, Bioinformatics).

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

  29. Fast in-memory XPath search using compressed indexes

    Arroyuelo, D., Claude, F., Maneth, S., Mäkinen, V., Navarro, G., Nguyen, K., Sirén, J. & Välimäki, N., Mar 2015, In : Software: Practice & Experience. 45, 3, p. 399-434 36 p.

    Research output: Contribution to journalArticleScientificpeer-review

  30. Gap2Seq

    Salmela, L. M., Sahlin, K., Mäkinen, V. A. T. & Tomescu, A. I., 2015

    Research output: Non-textual formSoftwareScientific

  31. SNV-PPILP: refined SNV calling for tumor data using perfect phylogenies and ILP

    van Rens, K. E., Mäkinen, V. & Tomescu, A. I., 1 Apr 2015, In : Bioinformatics. 31, 7, p. 1133-1135 3 p.

    Research output: Contribution to journalArticleScientificpeer-review

  32. Gap filling as exact path length problem

    Salmela, L., Sahlin, K., Mäkinen, V. & Tomescu, A. I., 2015, Research in Computational Molecular Biology : 19th Annual International Conference, RECOMB 2015, Warsaw, Poland, April 12-15, 2015, Proceedings . Przytycka, T. M. (ed.). Cham: Springer International Publishing AG, p. 281-292 12 p. (Lecture Notes in Bioinformatics; vol. 9029).

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

  33. Editorial: Special Issue on Algorithms for Sequence Analysis and Storage

    Mäkinen, V., 2014, In : Algorithms. 7, 1, p. 186-187

    Research output: Contribution to journalArticleScientific

  34. Indexing Graphs for Path Queries with Applications in Genome Research

    Sirén, J., Välimäki, N. & Mäkinen, V., 2014, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 11, 2, p. 375-388 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  35. Recombination-aware alignment of diploid individuals

    Mäkinen, V. & Valenzuela, D., 2014, In : BMC Genomics. 15, Suppl 6, p. S15 9 p.

    Research output: Contribution to journalArticleScientificpeer-review

  36. On the complexity of Minimum Path Cover with Subpath Constraints for multi-assembly

    Rizzi, R., Tomescu, A. I. & Mäkinen, V., 10 Sep 2014, In : BMC Bioinformatics. 15, S9, p. S5

    Research output: Contribution to journalArticleScientificpeer-review

  37. The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera

    Ahola, V., Lehtonen, R., Somervuo, P., Salmela, L., Koskinen, P., Rastas, P., Valimaki, N., Paulin, L., Kvist, J., Wahlberg, N., Tanskanen, J., Hornett, E. A., Ferguson, L. C., Luo, S., Cao, Z., de Jong, M. A., Duplouy, A., Smolander, O-P., Vogel, H., McCoy, R. C. & 27 othersQian, K., Wong, S. C., Zhang, Q., Ahmad, F., Haukka, J. K., Joshi, A., Salojarvi, J., Wheat, C. W., Grosse-Wilde, E., Hughes, D., Katainen, R., Pitkanen, E., Ylinen, J., Waterhouse, R. M., Turunen, M., Vaharautio, A., Ojanen, S. P., Schulman, A. H., Taipale, M., Lawson, D., Ukkonen, E., Makinen, V., Goldsmith, M. R., Holm, L., Auvinen, P., Frilander, M. J. & Hanski, I., Sep 2014, In : Nature Communications. 5, 9 p., 4737.

    Research output: Contribution to journalArticleScientificpeer-review

  38. Dynamic entropy-compressed sequences and full-text indexes

    Mäkinen, V. & Navarro, G., 2006, In : Lecture Notes in Computer Science. 4009, p. 306-317 12 p.

    Research output: Contribution to journalArticleScientificpeer-review

  39. Multi-pattern matching with bidirectional indexes

    Gog, S., Karhu, K., Kärkkäinen, J., Mäkinen, V. & Välimäki, N., 2014, In : Journal of Discrete Algorithms. 24, p. 26-39 14 p.

    Research output: Contribution to journalArticleScientificpeer-review

  40. A Novel Combinatorial Method for Estimating Transcript Expression with RNA-Seq: Bounding the Number of Paths

    Tomescu, A. I., Kuosmanen, A., Rizzi, R. & Mäkinen, V., 2013, Algorithms in Bioinformatics: 13th International Workshop, WABI 2013, Sophia Antipolis, France, September 2-4, 2013. Proceedings. Darling, A. & Stoye, J. (eds.). Springer-Verlag, p. 85-98 (Lecture Notes in Computer Science; no. 8126).

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

  41. Versatile succinct representations of the bidirectional Burrows-Wheeler transform

    Belazzougui, D., Cunial, F., Kärkkäinen, J. & Mäkinen, V., 2013, Algorithms – ESA 2013: 21st Annual European Symposium, Sophia Antipolis, France, September 2-4, 2013. Proceedings. Bodlaender, H. L. & Italiano, G. F. (eds.). Springer-Verlag, p. 133-144 (Lecture Notes in Computer Science; vol. 8125).

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

  42. Haploid to diploid alignment for variation calling assessment

    Mäkinen, V. & Rahkola, J., Oct 2013, In : BMC Bioinformatics. 14, (Suppl 15):S13, 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  43. A novel min-cost flow method for estimating transcript expression with RNA-Seq

    Tomescu, A. I., Kuosmanen, A., Rizzi, R. & Mäkinen, V., 10 Apr 2013, In : BMC Bioinformatics. 14, (Suppl 5):S15, 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  44. Efficient Path Kernels for Reaction Function Prediction

    Heinonen, M., Välimäki, N., Mäkinen, V. & Rousu, J., 2012, 3rd International Conference on Bioinformatics Models, Methods and Algorithms, 1-4 Feb 2012, Algarve, Portugal.: Proceedings. 6 p.

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

  45. Detection of Viruses in Sweetpotato from Honduras and Guatemala Augmented by Deep-Sequencing of Small-RNAs

    Kashif, M., Pietila, S., Artola, K., Jones, R. A. C., Tugume, A. K., Makinen, V. & Valkonen, J. P. T., Oct 2012, In : Plant Disease. 96, 10, p. 1430-1437 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  46. Normalized N50 Assembly Metric using Gap-Restricted Co-Linear Chaining

    Mäkinen, V., Salmela, L. & Ylinen, J., 3 Oct 2012, In : BMC Bioinformatics. 13, p. 255 5 p.

    Research output: Contribution to journalArticleScientificpeer-review

  47. Approximate all-pairs suffix/prefix overlaps

    Välimäki, N., Ladra, S. & Mäkinen, V., 2012, In : Information and Computation. 213, p. 49-58 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  48. Multi-Pattern Matching with Bidirectional Indexes

    Gog, S., Karhu, K., Kärkkäinen, J., Mäkinen, V. & Välimäki, N., 2012, Computing and Combinatorics: 18th Annual International Conference, COCOON 2012, Sydney, Australia, August 20-22, 2012. Proceedings. Gudmundsson, J., Mestre, J. & Viglas, T. (eds.). Springer-Verlag, p. 384-395 (Lecture Notes in Computer Science; vol. 7434).

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

  49. Forbidden Patterns

    Fischer, J., Gagie, T., Kopelowitz, T., Lewenstein, M., Mäkinen, V., Salmela, L. & Välimäki, N., 2012, LATIN 2012: Theoretical Informatics: 10th Latin American Symposium, Arequipa, Peru, April 16-20, 2012. Proceedings. Fernández-Baca, D. (ed.). Springer-Verlag, p. 327-337 (Lecture Notes in Computer Science; vol. 7256).

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

  50. Indexed Multi-Pattern Matching

    Gagie, T., Karhu, K., Kärkkäinen, J., Mäkinen, V., Salmela, L. & Tarhio, J., 2012, LATIN 2012: Theoretical Informatics: 10th Latin American Symposium, Arequipa, Peru, April 16-20, 2012. Proceedings. Springer-Verlag, p. 399-407 10 p. (Lecture Notes in Computer Science; vol. 7256).

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

  51. Algoritmitutkimuksen rooli bioinformatiikassa

    Mäkinen, V., Jul 2011, In : Tietojenkäsittelytiede. 32, p. 10-15 6 p.

    Research output: Contribution to journalArticleScientific

  52. Fast scaffolding with small independent mixed integer programs

    Salmela, L., Mäkinen, V., Välimäki, N., Ylinen, J. & Ukkonen, E., 2011, In : Bioinformatics. 27, 23, p. 3259-3265 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  53. The Cycle Switching Graph of the Steiner Triple Systems of Order 19 is Connected

    Kaski, P., Mäkinen, V. & Östergård, P. R. J., 2011, In : Graphs and Combinatorics. 27, 4, p. 539-546 8 p.

    Research output: Contribution to journalArticleScientificpeer-review

  54. Missing pattern discovery

    Angelov, S., Inenaga, S., Kivioja, T. & Mäkinen, V., 2011, In : Journal of Discrete Algorithms. 9, 2, p. 153-165 13 p.

    Research output: Contribution to journalArticleScientificpeer-review

  55. Engineering a Compressed Suffix Tree Implementation

    Välimäki, N., Gerlach, W., Dixit, K. & Mäkinen, V., 2007, Experimental Algorithms. Springer-Verlag, p. 217-228 12 p. (LNCS; vol. 4525).

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

  56. Compact Suffix Array

    Mäkinen, V., 2000, Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching (CPM 2000). Springer-Verlag, p. 305-319 (LNCS; vol. 1848).

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

  57. Using Edit Distance in Point-Pattern Matching

    Mäkinen, V., 2001, Proceedings of the 8th International Symposium on String Processing and Information Retrieval (SPIRE 2001). IEEE Computer Society, p. 153-161

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

  58. Approximate Matching of Run-Length Compressed Strings

    Mäkinen, V., Navarro, G. & Ukkonen, E., 2001, Proceedings of the 12th Annual Symposium on Combinatorial Pattern Matching (CPM 2001). Springer-Verlag, p. 31-49 (LNCS; vol. 2089).

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

  59. Trade Off Between Compression and Search Times in Compact Suffix Array

    Mäkinen, V., 2001, Proceedings of the Third International Workshop on Algorithm Engineering and Experimentation (ALENEX 2001). Springer-Verlag, p. 189-201 (LNCS; vol. 2153).

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

  60. Local Similarity Based Point-Pattern Matching

    Mäkinen, V. & Ukkonen, E., 2002, Proceedings of the 13th Annual Symposium on Combinatorial Pattern Matching (CPM 2002). Springer-Verlag, p. 115-132 (LNCS; vol. 2373).

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

  61. Sweepline the Music!

    Ukkonen, E., Lemström, K. & Mäkinen, V., 2003, Computer Science in Perspective, Essays Dedicated to Thomas Ottmann. Springer-Verlag, p. 330-342 13 p. (LNCS; vol. 2598).

    Research output: Chapter in Book/Report/Conference proceedingChapterScientific

  62. Algorithms for Transposition Invariant String Matching

    Mäkinen, V., Navarro, G. & Ukkonen, E., 2003, Proceedings of the 20th Annual Symposium on Theoretical Aspects of Computer Science (STACS 2003): Proceedings of the 20th Annual Symposium on Theoretical Aspects of Computer Science (STACS 2003). Springer-Verlag, p. 191-202 (LNCS; vol. 2607).

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

  63. On Minimizing Pattern Splitting in Multi-track String Matching

    Lemström, K. & Mäkinen, V., 2003, Unknown host publication. Springer-Verlag, p. 237-253 (LNCS; vol. 2676).

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

  64. A simple alphabet-independent FM-index

    Grabowski, S., Mäkinen, V., Navarro, G. & Salinger, A., 2005, Proceedings of the Prague Stringology Conference (PSC 2005). Department of Computer Science and Engineering, Faculty of Electrical Engineering, Czech Technical University, p. 231-245

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

  65. Flexible music retrieval in sublinear time

    Fredriksson, K., Mäkinen, V. & Navarro, G., 2005, Proceedings of the Prague Stringology Conference (PSC 2005). Department of Computer Science and Engineering, Faculty of Electrical Engineering, Czech Technical University, p. 174-189

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

  66. Succinct Suffix Arrays Based on Run-Length Encoding

    Mäkinen, V. & Navarro, G., 2005, Proceedings of the 16th Annual Symposium on Combinatorial Pattern Matching (CPM 2005). Springer-Verlag, p. 45-56 (LNCS; vol. 3537).

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

  67. Finding Missing Patterns

    Inenaga, S., Kivioja, T. & Mäkinen, V., 2004, Proceedings of the 4th International Workshop on Algorithms in Bioinformatics (WABI 2004). Springer-Verlag, p. 463-474 (LNCS; vol. 3240).

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

  68. First Huffman, Then Burrows-Wheeler: A Simple Alphabet-Independent FM-index

    Grabowski, S., Mäkinen, V. & Navarro, G., 2004, Proceedings of the 11th International Conference on String Processing and Information Retrieval (SPIRE 2004). Springer-Verlag, p. 210-211 (LNCS; vol. 3246).

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

  69. An Alphabet-Friendly FM-Index

    Ferragina, P., Manzini, G., Mäkinen, V. & Navarro, G., 2004, Proceedings of the 11th International Conference on String Processing and Information Retrieval (SPIRE 2004). Springer-Verlag, p. 150-160 (LNCS; vol. 3246).

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

  70. Rotation and Lighting Invariant Template Matching

    Fredriksson, K., Mäkinen, V. & Navarro, G., 2004, Proceedings of the 6th Latin American Symposium on Theoretical Informatics (LATIN 2004). Springer-Verlag, p. 39-48 (LNCS; vol. 2976).

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

  71. Advantages of Backward Searching: Efficient Secondary Memory and Distributed Implementation of Compressed Suffix Arrays

    Mäkinen, V., Navarro, G. & Sadakane, K., 2004, Proceedings of the 15th International Symposium on Algorithms and Computation (ISAAC 2004). Springer-Verlag, p. 681-692 (LNCS; vol. 3341).

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

  72. Compressed Compact Suffix Arrays

    Mäkinen, V. & Navarro, G., 2004, Proceedings of the 15th Annual Symposium on Combinatorial Pattern Matching (CPM 2004). Springer-Verlag, p. 420-433 (LNCS; vol. 3109).

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

  73. Indexing Finite Language Representation of Population Genotypes

    Sirén, J., Välimäki, N. & Mäkinen, V., 2011, Algorithms in Bioinformatics: 11th International Workshop, WABI 2011. Przytycka, T. M. & Sagot, M-F. (eds.). Springer, p. 270-281 (Lecture Notes in Bioinformatics; vol. 6833).

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

  74. Geometric algorithms for transposition invariant content-based music retrieval

    Ukkonen, E., Lemström, K. & Mäkinen, V., 2003, Proc. 4th International Conference on Music Information Retrieval. Hoos, H. & Bainbridge, D. (eds.). p. 193-199

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

  75. The C-BRAHMS Project

    Lemström, K., Mäkinen, V., Pienimäki, A., Turkia, M. & Ukkonen, E., 2003, Proc. 4th International Conference on Music Information Retrieval. Hoos, H. & Bainbridge, D. (eds.). p. 237-238

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

  76. Implicit compression boosting with applications to self-indexing

    Mäkinen, V. & Navarro, G., 2007, String Processing and Information Retrieval. Springer, p. 229-241 13 p. (Lecture notes in computer science; vol. 4726).

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

  77. Approximate Matching of Run-length Compressed Strings

    Mäkinen, V., Navarro, G. & Ukkonen, E., 2003, In : Algorithmica. 35, 4, p. 347–369

    Research output: Contribution to journalArticleScientificpeer-review

  78. Compact Suffix Array — A Space-efficient Full-text Index

    Mäkinen, V., 2003, In : Fundamenta Informaticae. 56, 1-2, p. 191–210

    Research output: Contribution to journalArticleScientificpeer-review

  79. Engineering a Compressed Suffix Tree Implementation

    Välimäki, N., Mäkinen, V., Gerlach, W. & Dixit, K., 2009, In : ACM Journal of Experimental Algorithmics. 14, 4.2, p. 4.2:1-4.2:23 23 p.

    Research output: Contribution to journalArticleScientificpeer-review

  80. Run-length compressed indexes are superior for highly repetitive sequence collections

    Sirén, J., Välimäki, N., Mäkinen, V. & Navarro, G., 2008, String Processing and Information Retrieval: 15th International Symposium, SPIRE 2008. Amir, A., Turpin, A. & Moffat, A. (eds.). Springer, p. 164-175 12 p. (Lecture Notes in Computer Science; no. 5280).

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

  81. Storage and retrieval of individual genomes

    Mäkinen, V., Navarro, G., Sirén, J. & Välimäki, N., 2009, Research in Computational Molecular Biology: 13th Annual International Conference, RECOMB 2009. Batzoglou, S. (ed.). Springer, p. 121-137 17 p. (Lecture Notes in Computer Science; no. 5541).

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

  82. Approximate All-Pairs Suffix/Prefix Overlaps

    Välimäki, N., Ladra, S. & Mäkinen, V., 2010, CPM 2010: Proceedings of the 21st Annual Symposium on Combinatorial Pattern Matching . Germany: Springer-Verlag, Vol. 21. p. 76-87 (Lecture Notes in Computer Science; vol. 6129).

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

  83. Storage and Retrieval of Highly Repetitive Sequence Collections

    Mäkinen, V., Navarro, G., Sirén, J. & Välimäki, N., 2010, In : Journal of Computational Biology. 17, 3, p. 281-308 28 p.

    Research output: Contribution to journalArticleScientificpeer-review

  84. Maximum Line-Pair Stabbing Problem and its Variations

    Böcker, S. & Mäkinen, V., 2005, Proceedings of the 21st European Workshop on Computational Geometry. p. 183–186 4 p.

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

  85. Practical Implementation of Rank and Select Queries

    González, R., Grabowski, S., Mäkinen, V. & Navarro, G., 2005, Poster Proceedings of 4th International Workshop on Efficient and Experimental Algorithms .

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  86. Filtering methods for content-based retrieval on indexed symbolic music databases

    Lemstrom, K., Mikkila, N. & Makinen, V., 2010, In : Information Retrieval Journal. 13, p. 1-21 21 p.

    Research output: Contribution to journalArticleScientificpeer-review

  87. Unified view of backward backtracking in short read mapping

    Mäkinen, V., Välimäki, N., Laaksonen, A. & Katainen, R., 2010, Algorithms and applications: Essays dedicated to Esko Ukkonen on the occasion of his 60th birthday. Elomaa, T., Mannila, H. & Orponen, P. (eds.). Springer-Verlag, 14 p. (Lecture Notes in Computer Science; vol. 2010, no. 6060).

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

  88. Fast in-memory XPath search using compressed indexes

    Arroyuelo, D., Claude, F., Maneth, S., Mäkinen, V., Navarro, G., Nguyen, K., Sirén, J. & Välimäki, N., 2010, ICDE 2010: 26th IEEE International Conference on Data Engineering. IEEE Computer Society, p. 417-428 12 p.

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

  89. Efficient construction of maximal and minimal representations of motifs of a string

    Nicolas, F., Mäkinen, V. & Ukkonen, E., 2009, In : Theoretical Computer Science. 410 (2009), p. 2999-3005 7 p.

    Research output: Contribution to journalArticleScientificpeer-review

  90. Faster entropy-bounded compressed suffix trees

    Fischer, J., Mäkinen, V. & Navarro, G., 2009, In : Theoretical Computer Science. 410 (2009), p. 5354-5364 11 p.

    Research output: Contribution to journalArticleScientificpeer-review

  91. Storage and retrieval of individual genomes and other repetitive sequence collections

    Mäkinen, V., Siren, J. & Välimäki, N., 2008, Helsinki: Helsingin yliopisto, tietojenkäsittelytieteen laitos. 18 p. (Department of Computer Science Series of Publications C)

    Research output: Book/ReportBookScientificpeer-review

  92. Run-length compressed indexes for repetitive sequence collections

    Mäkinen, V., Navarro, G., Siren, J. & Välimäki, N., 2008, Helsinki: Helsingin yliopisto, tietojenkäsittelytieteen laitos. 39 p. (Department of Computer Science Series of Publications C)

    Research output: Book/ReportBookScientificpeer-review

  93. Storage and retrieval of individual genomes (extended abstract)

    Mäkinen, V., Navarro, G., Siren, J. & Välimäki, N., 2008, Dagstuhl seminar proceedings. 14 p. (Dagstuhl seminar proceedings; no. 08261).

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

  94. An in-memory XQuery/XPath engine over a compressed structured text representation

    Bonifati, A., Leighton, G., Mäkinen, V., Maneth, S., Navarro, G. & Pugliese, A., 2008, Dagstuhl seminar proceedings. Böttcher, S., Lohrey, M., Maneth, S. & Rytter, W. (eds.). 17 p. (Dagstuhl Seminar Proceedings; no. 08261).

    Research output: Chapter in Book/Report/Conference proceedingConference contributionScientific

  95. From data to knowledge: final report 2002-2007

    Mäkinen, V. (ed.), Lindén, G. (ed.) & Kujala, I. (ed.), 2008, Helsinki: University of Helsinki. 144 p. (Julkaisusarja / Helsingin yliopisto, tietojenkäsittelytieteen laitosB; no. 2008-1)

    Research output: Book/ReportAnthology or special issueScientificpeer-review

  96. On self-indexing images: image compression with added value

    Mäkinen, V. & Navarro, G., 2008, Data Compression Conference: DCC 2008. p. 422-431 10 p.

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

  97. Space-efficient string mining under frequency constraints

    Fischer, J., Mäkinen, V. & Välimäki, N., 2008, Eighth IEEE International Conference on Data Mining, ICDM 2008, 15-19 December, 2008, Pisa, Italy: IEEE Computer Society 2008. p. 193-202 10 p.

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

  98. Point pattern matching

    Mäkinen, V. & Ukkonen, E., 2008, Encyclopedia of Algorithms. Boston, MA: Springer-Verlag, p. 657-660 4 p.

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

  99. Compressed text indexing

    Mäkinen, V. & Navarro, G., 2008, Encyclopedia of Algorithms. Boston, MA: Springer-Verlag, p. 176-178 3 p.

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

  100. Compressed suffix array

    Mäkinen, V., 2008, Encyclopedia of Algorithms. Boston, MA: Springer-Verlag, p. 174-176 3 p.

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

  101. Kauniita algoritmeja vääriin ongelmiin

    Mäkinen, V., 14 Dec 2008, In : Luova : tiedettä & teknologiaa.

    Research output: Contribution to journalArticleGeneral public

  102. Combinatorial approaches for mass spectra recalibration

    Böcker, S. & Mäkinen, V., 2008, In : IEEE/ACM Transactions on Computational Biology and Bioinformatics. 5, 1, p. 91-100 10 p.

    Research output: Contribution to journalArticleScientificpeer-review

  103. Dynamic entropy-compressed sequences and full-text indexes

    Mäkinen, V. & Navarro, G., 2008, In : ACM transactions on algorithms.. 4, 3, p. art. 32 38 p.

    Research output: Contribution to journalArticleScientificpeer-review

  104. An(other) entropy-bounded compressed suffix tree

    Fischer, J., Mäkinen, V. & Navarro, G., 2008, Combinatorial pattern matching. p. 152-165 14 p.

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

  105. Fast index based filters for music retrieval

    Lemström, K., Mikkilä, N. & Mäkinen, V., 2008, ISMIR 2008. p. 677-682 6 p.

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

  106. Space-efficient algorithms for document retrieval

    Välimäki, N. & Mäkinen, V., 2007, Combinatorial pattern matching. p. 205-215 11 p.

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

  107. Compressed suffix tree: a basis for genome-scale sequence analysis

    Välimäki, N., Gerlach, W., Dixit, K. & Mäkinen, V., 2007, In : Bioinformatics. 23, 5, p. 629-630 2 p.

    Research output: Contribution to journalArticleScientificpeer-review

  108. Compressed full-text indexes

    Navarro, G. & Mäkinen, V., 2007, In : ACM Computing Surveys. 39, 1, p. Article No. 2

    Research output: Contribution to journalArticleScientificpeer-review

  109. Rotation and lighting invariant template matching

    Fredriksson, K., Mäkinen, V. & Navarro, G., 2007, In : Information and Computation. 205, 7, p. 1096-1113 18 p.

    Research output: Contribution to journalArticleScientificpeer-review

  110. Compressed representations of sequences and full-text indexes

    Ferragina, P., Manzini, G., Mäkinen, V. & Navarro, G., 2007, In : ACM transactions on algorithms.. 3, 2, p. Art. 20

    Research output: Contribution to journalArticleScientificpeer-review

  111. Peak alignment using restricted edit distances

    Mäkinen, V., 2007, In : Biomolecular engineering. 24, 3, p. 337-342 6 p.

    Research output: Contribution to journalArticleScientificpeer-review

  112. Rank and select revisited and extended

    Mäkinen, V. & Navarro, G., 2007, In : Theoretical Computer Science. 387, 3, p. 332-347 16 p.

    Research output: Contribution to journalArticleScientificpeer-review

  113. Summer School on Algorithmic Data Analysis (SADA 2007) and Annual Hecse Poster Session

    Mäkinen, V. (ed.), Linden, G. (ed.) & Toivonen, H. (ed.), 2007, Helsinki: Helsingin yliopisto, tietojenkäsittelytieteen laitos. 110 p. (Series of publications / Department of Computer ScienceB; no. 2007-4)

    Research output: Book/ReportAnthology or special issueScientificpeer-review

  114. Compressed full-text indexes

    Navarro, G. & Mäkinen, V., 2006, Santiago: University of Chile, Department of Computer Science. 66 p.

    Research output: Book/ReportBookScientificpeer-review

  115. Itseindeksit: kun tiivistetty teksti ja sen indeksi ovatkin sama asia

    Mäkinen, V., 2006, In : Tietojenkäsittelytiede. 2006, 25, p. 28-37 10 p.

    Research output: Contribution to journalArticleScientific

  116. Position-restricted substring searching

    Mäkinen, V. & Navarro, G., 2006, LATIN 2006: THEORETICAL INFORMATICS. p. 703-714 12 p. (Lecture Notes in Computer Science; vol. 3887).

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

  117. Dynamic entrocopy-compressed sequences and full-text indexes

    Mäkinen, V. & Navarro, G., 2006, Combinatorial pattern matching. p. 306-317 12 p.

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

  118. A simple alphabet-independent FM-index

    Grabowski, S., Navarro, G., Przywarski, R., Salinger, A. & Mäkinen, V., 2006, In : International Journal of Foundations of Computer Science. 17, 6, p. 1365-1384 20 p.

    Research output: Contribution to journalArticleScientificpeer-review

  119. Flexible music retrieval in sublinear time

    Fredriksson, K., Mäkinen, V. & Navarro, G., 2006, In : International Journal of Foundations of Computer Science. 17, 6, p. 1345-1364 20 p.

    Research output: Contribution to journalArticleScientificpeer-review

  120. On minimizing pattern splitting in multi-track string matching

    Lemström, K. & Mäkinen, V., 2005, In : Journal of Discrete Algorithms. 3, 2-4, p. 248-266 19 p.

    Research output: Contribution to journalArticleScientificpeer-review

  121. Transposition invariant string matching

    Mäkinen, V., Navarro, G. & Ukkonen, E., 2005, In : Journal of Algorithms. 56, p. 124-153 30 p.

    Research output: Contribution to journalArticleScientificpeer-review

  122. Succinct suffix arrays based on run-length encoding

    Mäkinen, V. & Navarro, G., 2005, In : Nordic Journal of Computing. 12, 1, p. 44-66 23 p.

    Research output: Contribution to journalArticleScientificpeer-review