Veli Mäkinen

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  1. 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.

    Publication: Contribution to journalA1 Refereed journal article

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

    Kuosmanen, A. E., Norri, T. S. & Mäkinen, V. A. T. 9 Jan 2017 In : Briefings in Bioinformatics. 11 p.

    Publication: Contribution to journalA1 Refereed journal article

  3. 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

    Publication: Contribution to journalA1 Refereed journal article

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

    The Computational Pan-Genomics Consortium, Mäkinen, V. A. T. & Valenzuela, S. D. A. 20 Oct 2016 In : Briefings in Bioinformatics. p. 1-18 18 p.

    Publication: Contribution to journalA1 Refereed journal article

  5. 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)

    Publication: Book/anthologyC2 Edited book, compilation, conference proceeding or special issue of journal

  6. Fully Dynamic de Bruijn Graphs

    Belazzougui, D., Gagie, T., Mäkinen, V. & Previtali, M. 2016 In : Lecture Notes in Computer Science. 9954, p. 145-152 8 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  7. Identification of Variant Compositions in Related Strains Without Reference

    Rautiainen, M., Salmela, L. & Mäkinen, V. 2016 In : Lecture Notes in Computer Science. 9702, p. 158-170 13 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  8. Bidirectional Variable-Order de Bruijn Graphs

    Belazzougui, D., Gagie, T., Mäkinen, V. A. T., Previtali, M. & Puglisi, S. J. 2016 p. 164-178 9 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  9. 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 p. 272-277 6 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  10. 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 p. 111-121 11 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  11. 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.

    Publication: Contribution to journalA1 Refereed journal article

  12. 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.

    Publication: Contribution to journalA1 Refereed journal article

  13. SNV-PPILP

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

    Publication: Sound and image mediaI2 ICT programs or applications

  14. 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.

    Publication: Contribution to journalA1 Refereed journal article

  15. 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.

    Publication: Contribution to book/anthologyA3 Contribution to book/other compilations (refereed)

  16. 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.

    Publication: Book/anthologyC1 Published scientific monograph

  17. Diploid Alignments and Haplotyping

    Mäkinen, V. & Valenzuela, D. 2015 p. 235-246 12 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  18. 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.

    Publication: Contribution to journalA1 Refereed journal article

  19. Gap2Seq

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

    Publication: Sound and image mediaI2 ICT programs or applications

  20. 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.

    Publication: Contribution to journalA1 Refereed journal article

  21. Gap filling as exact path length problem

    Salmela, L., Sahlin, K., Mäkinen, V. & Tomescu, A. I. 2015 p. 281-292 12 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

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

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

    Publication: Contribution to journalB1 Unrefereed journal article

  23. 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.

    Publication: Contribution to journalA1 Refereed journal article

  24. Recombination-aware alignment of diploid individuals

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

    Publication: Contribution to journalA1 Refereed journal article

  25. 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

    Publication: Contribution to journalA1 Refereed journal article

  26. 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., Qian, 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

    Publication: Contribution to journalA1 Refereed journal article

  27. 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.

    Publication: Contribution to journalA1 Refereed journal article

  28. 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.

    Publication: Contribution to journalA1 Refereed journal article

  29. 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 p. 85-98

    Publication: Conference contributionA4 Article in conference publication (refereed)

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

    Belazzougui, D., Cunial, F., Kärkkäinen, J. & Mäkinen, V. 2013 p. 133-144

    Publication: Conference contributionA4 Article in conference publication (refereed)

  31. Haploid to diploid alignment for variation calling assessment

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

    Publication: Contribution to journalA1 Refereed journal article

  32. 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.

    Publication: Contribution to journalA1 Refereed journal article

  33. Efficient Path Kernels for Reaction Function Prediction

    Heinonen, M., Välimäki, N., Mäkinen, V. & Rousu, J. 2012 6 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  34. 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.

    Publication: Contribution to journalA1 Refereed journal article

  35. 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.

    Publication: Contribution to journalA1 Refereed journal article

  36. Approximate all-pairs suffix/prefix overlaps

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

    Publication: Contribution to journalA1 Refereed journal article

  37. Multi-Pattern Matching with Bidirectional Indexes

    Gog, S., Karhu, K., Kärkkäinen, J., Mäkinen, V. & Välimäki, N. 2012 p. 384-395

    Publication: Conference contributionA4 Article in conference publication (refereed)

  38. Forbidden Patterns

    Fischer, J., Gagie, T., Kopelowitz, T., Lewenstein, M., Mäkinen, V., Salmela, L. & Välimäki, N. 2012 p. 327-337

    Publication: Conference contributionA4 Article in conference publication (refereed)

  39. Indexed Multi-Pattern Matching

    Gagie, T., Karhu, K., Kärkkäinen, J., Mäkinen, V., Salmela, L. & Tarhio, J. 2012 p. 399-407 10 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  40. Algoritmitutkimuksen rooli bioinformatiikassa

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

    Publication: Contribution to journalB1 Unrefereed journal article

  41. 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.

    Publication: Contribution to journalA1 Refereed journal article

  42. 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.

    Publication: Contribution to journalA1 Refereed journal article

  43. Missing pattern discovery

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

    Publication: Contribution to journalA1 Refereed journal article

  44. Engineering a Compressed Suffix Tree Implementation

    Välimäki, N., Gerlach, W., Dixit, K. & Mäkinen, V. 2007 p. 217-228 12 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  45. Compact Suffix Array

    Mäkinen, V. 2000 p. 305-319

    Publication: Conference contributionA4 Article in conference publication (refereed)

  46. Using Edit Distance in Point-Pattern Matching

    Mäkinen, V. 2001 p. 153-161

    Publication: Conference contributionA4 Article in conference publication (refereed)

  47. Approximate Matching of Run-Length Compressed Strings

    Mäkinen, V., Navarro, G. & Ukkonen, E. 2001 p. 31-49

    Publication: Conference contributionA4 Article in conference publication (refereed)

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

    Mäkinen, V. 2001 p. 189-201

    Publication: Conference contributionA4 Article in conference publication (refereed)

  49. Local Similarity Based Point-Pattern Matching

    Mäkinen, V. & Ukkonen, E. 2002 p. 115-132

    Publication: Conference contributionA4 Article in conference publication (refereed)

  50. 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)

    Publication: Contribution to book/anthologyB2 Contribution to book/other compilations (non-refereed)

  51. Algorithms for Transposition Invariant String Matching

    Mäkinen, V., Navarro, G. & Ukkonen, E. 2003 p. 191-202

    Publication: Conference contributionA4 Article in conference publication (refereed)

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

    Lemström, K. & Mäkinen, V. 2003 p. 237-253

    Publication: Conference contributionA4 Article in conference publication (refereed)

  53. A simple alphabet-independent FM-index

    Grabowski, S., Mäkinen, V., Navarro, G. & Salinger, A. 2005 p. 231-245

    Publication: Conference contributionA4 Article in conference publication (refereed)

  54. Flexible music retrieval in sublinear time

    Fredriksson, K., Mäkinen, V. & Navarro, G. 2005 p. 174-189

    Publication: Conference contributionA4 Article in conference publication (refereed)

  55. Succinct Suffix Arrays Based on Run-Length Encoding

    Mäkinen, V. & Navarro, G. 2005 p. 45-56

    Publication: Conference contributionA4 Article in conference publication (refereed)

  56. Finding Missing Patterns

    Inenaga, S., Kivioja, T. & Mäkinen, V. 2004 p. 463-474

    Publication: Conference contributionA4 Article in conference publication (refereed)

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

    Grabowski, S., Mäkinen, V. & Navarro, G. 2004 p. 210-211

    Publication: Conference contributionA4 Article in conference publication (refereed)

  58. An Alphabet-Friendly FM-Index

    Ferragina, P., Manzini, G., Mäkinen, V. & Navarro, G. 2004 p. 150-160

    Publication: Conference contributionA4 Article in conference publication (refereed)

  59. Rotation and Lighting Invariant Template Matching

    Fredriksson, K., Mäkinen, V. & Navarro, G. 2004 p. 39-48

    Publication: Conference contributionA4 Article in conference publication (refereed)

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

    Mäkinen, V., Navarro, G. & Sadakane, K. 2004 p. 681-692

    Publication: Conference contributionA4 Article in conference publication (refereed)

  61. Compressed Compact Suffix Arrays

    Mäkinen, V. & Navarro, G. 2004 p. 420-433

    Publication: Conference contributionA4 Article in conference publication (refereed)

  62. Indexing Finite Language Representation of Population Genotypes

    Sirén, J., Välimäki, N. & Mäkinen, V. 2011 p. 270-281

    Publication: Conference contributionA4 Article in conference publication (refereed)

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

    Ukkonen, E., Lemström, K. & Mäkinen, V. 2003 p. 193-199

    Publication: Conference contributionA4 Article in conference publication (refereed)

  64. The C-BRAHMS Project

    Lemström, K., Mäkinen, V., Pienimäki, A., Turkia, M. & Ukkonen, E. 2003 p. 237-238

    Publication: Conference contributionA4 Article in conference publication (refereed)

  65. Implicit compression boosting with applications to self-indexing

    Mäkinen, V. & Navarro, G. 2007 p. 229-241 13 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  66. Approximate Matching of Run-length Compressed Strings

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

    Publication: Contribution to journalA1 Refereed journal article

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

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

    Publication: Contribution to journalA1 Refereed journal article

  68. 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.

    Publication: Contribution to journalA1 Refereed journal article

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

    Sirén, J., Välimäki, N., Mäkinen, V. & Navarro, G. 2008 p. 164-175 12 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  70. Storage and retrieval of individual genomes

    Mäkinen, V., Navarro, G., Sirén, J. & Välimäki, N. 2009 5541, p. 121-137 17 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  71. Approximate All-Pairs Suffix/Prefix Overlaps

    Välimäki, N., Ladra, S. & Mäkinen, V. 2010 In : Lecture Notes in Computer Science. 6129, p. 76-87

    Publication: Conference contributionA4 Article in conference publication (refereed)

  72. 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.

    Publication: Contribution to journalA1 Refereed journal article

  73. Maximum Line-Pair Stabbing Problem and its Variations

    Böcker, S. & Mäkinen, V. 2005 p. 183–186 4 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  74. Practical Implementation of Rank and Select Queries

    González, R., Grabowski, S., Mäkinen, V. & Navarro, G. 2005

    Publication: Conference contributionB3 Unrefereed article in conference proceedings

  75. 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.

    Publication: Contribution to journalA1 Refereed journal article

  76. 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)

    Publication: Contribution to book/anthologyA3 Contribution to book/other compilations (refereed)

  77. 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 p. 417-428 12 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  78. 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.

    Publication: Contribution to journalA1 Refereed journal article

  79. Faster entropy-bounded compressed suffix trees

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

    Publication: Contribution to journalA1 Refereed journal article

  80. 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)

    Publication: Book/anthologyC1 Published scientific monograph

  81. 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)

    Publication: Book/anthologyC1 Published scientific monograph

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

    Mäkinen, V., Navarro, G., Siren, J. & Välimäki, N. 2008 14 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  83. 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 17 p.

    Publication: Conference contributionB3 Unrefereed article in conference proceedings

  84. 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)

    Publication: Book/anthologyC2 Edited book, compilation, conference proceeding or special issue of journal

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

    Mäkinen, V. & Navarro, G. 2008 p. 422-431 10 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  86. Space-efficient string mining under frequency constraints

    Fischer, J., Mäkinen, V. & Välimäki, N. 2008 p. 193-202 10 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

  87. Point pattern matching

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

    Publication: Contribution to book/anthologyA3 Contribution to book/other compilations (refereed)

  88. Compressed text indexing

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

    Publication: Contribution to book/anthologyA3 Contribution to book/other compilations (refereed)

  89. Compressed suffix array

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

    Publication: Contribution to book/anthologyA3 Contribution to book/other compilations (refereed)

  90. Kauniita algoritmeja vääriin ongelmiin

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

    Publication: Contribution to journalE1 Popular article, newspaper article

  91. 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.

    Publication: Contribution to journalA1 Refereed journal article

  92. 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.

    Publication: Contribution to journalA1 Refereed journal article

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

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

    Publication: Conference contributionA4 Article in conference publication (refereed)

  94. Fast index based filters for music retrieval

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

    Publication: Conference contributionA4 Article in conference publication (refereed)

  95. Space-efficient algorithms for document retrieval

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

    Publication: Conference contributionA4 Article in conference publication (refereed)

  96. 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.

    Publication: Contribution to journalA1 Refereed journal article

  97. Compressed full-text indexes

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

    Publication: Contribution to journalA1 Refereed journal article

  98. Rotation and lighting invariant template matching

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

    Publication: Contribution to journalA1 Refereed journal article

  99. 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

    Publication: Contribution to journalA1 Refereed journal article

  100. Peak alignment using restricted edit distances

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

    Publication: Contribution to journalA1 Refereed journal article

  101. Rank and select revisited and extended

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

    Publication: Contribution to journalA1 Refereed journal article

  102. 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)

    Publication: Book/anthologyC2 Edited book, compilation, conference proceeding or special issue of journal

  103. Compressed full-text indexes

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

    Publication: Book/anthologyC1 Published scientific monograph

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

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

    Publication: Contribution to journalB1 Unrefereed journal article

  105. Position-restricted substring searching

    Mäkinen, V. & Navarro, G. 2006 p. 703-714 12 p.

    Publication: Conference contributionA4 Article in conference publication (refereed)

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

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

    Publication: Conference contributionA4 Article in conference publication (refereed)

  107. 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.

    Publication: Contribution to journalA1 Refereed journal article

  108. 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.

    Publication: Contribution to journalA1 Refereed journal article

  109. 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.

    Publication: Contribution to journalA1 Refereed journal article

  110. Transposition invariant string matching

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

    Publication: Contribution to journalA1 Refereed journal article

  111. 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.

    Publication: Contribution to journalA1 Refereed journal article