Veli Mäkinen
Yhteystiedot
Vastuullinen tutkija ryhmässä
Julkaisut
2012
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 journal ⺠A1 Refereed journal article
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. 10.2012 In : Plant Disease. 96, 10, p. 1430-1437. 8 p.Publication: Contribution to journal ⺠A1 Refereed journal article
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. 10.2012 In : Plant Disease. 96, 10, p. 1430-1437. 8 p.Publication: Contribution to journal ⺠A1 Refereed journal article
Efficient Path Kernels for Reaction Function Prediction
Heinonen, M. , Välimäki, N. , Mäkinen, V. & Rousu, J. 2012 6 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Forbidden Patterns
Fischer, J. , Gagie, T. , Kopelowitz, T. , Lewenstein, M. , Mäkinen, V. , Salmela, L. & Välimäki, N. 2012 p. 327-337.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Indexed Multi-Pattern Matching
Gagie, T. , Karhu, K. , Kärkkäinen, J. , Mäkinen, V. , Salmela, L. & Tarhio, J. 2012 p. 399-407. 10 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Multi-Pattern Matching with Bidirectional Indexes
Gog, S. , Karhu, K. , Kärkkäinen, J. , Mäkinen, V. & Välimäki, N. 2012 p. 384-395.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Normalized N50 Assembly Metric using Gap-Restricted Co-Linear Chaining
Mäkinen, V. , Salmela, L. & Ylinen, J. 03.10.2012 In : BMC Bioinformatics. 13, p. 255. 5 p.Publication: Contribution to journal ⺠A1 Refereed journal article
2011
Algoritmitutkimuksen rooli bioinformatiikassa
Mäkinen, V. 07.2011 In : Tietojenkäsittelytiede. 32, p. 10-15. 6 p.Publication: Contribution to journal ⺠B1 Unrefereed journal article
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 journal ⺠A1 Refereed journal article
Indexing Finite Language Representation of Population Genotypes
Sirén, J. , Välimäki, N. & Mäkinen, V. 2011 p. 270-281.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
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 journal ⺠A1 Refereed journal article
The Cycle Switching Graph of the Steiner Triple Systems of Order 19 is Connected
Kaski, P. , Mäkinen, V. & Åstergård, P. R. J. 2011 In : Graphs and Combinatorics. 27, 4, p. 539-546. 8 p.Publication: Contribution to journal ⺠A1 Refereed journal article
2010
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 contribution ⺠A4 Article in conference publication (refereed)
Fast in-memory XPath search using compressed indexes
Arroyuelo, D. , Claude, F. , Maneth, S. , Mäkinen, V. , Navarro, G. , Nguyen, K. , Siren, J. L. T. & Välimäki, N. 2010 p. 417-428. 12 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Filtering methods for content-based retrieval on indexed symbolic music databases
Lemstrom, K. , Mikkila, N. & Makinen, V. 2010 In : Information retrieval.13, p. 1-21. 21 p.Publication: Contribution to journal ⺠A1 Refereed journal article
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 journal ⺠A1 Refereed journal article
Unified view of backward backtracking in short read mapping
Mäkinen, V. , Välimäki, N. , Laaksonen , A. & Katainen , R. 2010 In: 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; 6060).Publication: Contribution to book/anthology ⺠A3 Contribution to book/other compilations (refereed)
2009
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 journal ⺠A1 Refereed journal article
Engineering a Compressed Suffix Tree Implementation
Välimäki, N. , Mäkinen, V. , Gerlach, W. & Dixit, K. 2009 In : Journal of Experimental Algorithmics. 14, 4.2, p. 4.2:1-4.2:23. 23 p.Publication: Contribution to journal ⺠A1 Refereed journal article
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 journal ⺠A1 Refereed journal article
Storage and retrieval of individual genomes
Mäkinen, V. , Navarro, G. , Sirén, J. & Välimäki, N. 2009 5541, p. 121-137. 17 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
2008
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 contribution ⺠B3 Unrefereed article in conference proceedings
An(other) entropy-bounded compressed suffix tree
Fischer, J. , Mäkinen, V. & Navarro, G. 2008 p. 152-165. 14 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
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 journal ⺠A1 Refereed journal article
Compressed suffix array
Mäkinen, V. 2008 In: Encyclopedia of Algorithms. Boston, MA: Springer-Verlag, p. 174-176. 3 p.Publication: Contribution to book/anthology ⺠A3 Contribution to book/other compilations (refereed)
Compressed text indexing
Mäkinen, V. & Navarro, G. 2008 In: Encyclopedia of Algorithms. Boston, MA: Springer-Verlag, p. 176-178. 3 p.Publication: Contribution to book/anthology ⺠A3 Contribution to book/other compilations (refereed)
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 journal ⺠A1 Refereed journal article
Fast index based filters for music retrieval
Lemström, K. , Mikkilä, N. & Mäkinen, V. 2008 p. 677-682. 6 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
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; 2008-1).Publication: Book/anthology ⺠C2 Edited book, compilation, conference proceeding or special issue of journal
Kauniita algoritmeja vääriin ongelmiin
Mäkinen, V. 14.12.2008 In : Luova : tiedettä & teknologiaa.Publication: Contribution to journal ⺠E1 Popular article, newspaper article
On self-indexing images: image compression with added value
Mäkinen, V. & Navarro, G. 2008 p. 422-431. 10 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Point pattern matching
Mäkinen, V. & Ukkonen, E. 2008 In: Encyclopedia of Algorithms. Boston, MA: Springer-Verlag, p. 657-660. 4 p.Publication: Contribution to book/anthology ⺠A3 Contribution to book/other compilations (refereed)
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 contribution ⺠A4 Article in conference publication (refereed)
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/anthology ⺠C1 Published scientific monograph
Space-efficient string mining under frequency constraints
Fischer, J. , Mäkinen, V. & Välimäki, N. 2008 p. 193-202. 10 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Storage and retrieval of individual genomes (extended abstract)
Mäkinen, V. , Navarro, G. , Siren, J. & Välimäki, N. 2008 14 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
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/anthology ⺠C1 Published scientific monograph
2007
Compressed full-text indexes
Navarro, G. & Mäkinen, V. 2007 In : ACM Computing Surveys. 39, 1, p. Article No. 2.Publication: Contribution to journal ⺠A1 Refereed journal article
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 journal ⺠A1 Refereed journal article
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 journal ⺠A1 Refereed journal article
Engineering a Compressed Suffix Tree Implementation
Välimäki, N. , Gerlach, W. , Dixit, K. & Mäkinen, V. 2007 p. 217-228. 12 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Implicit compression boosting with applications to self-indexing
Mäkinen, V. & Navarro, G. 2007 p. 229-241. 13 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Peak alignment using restricted edit distances
Mäkinen, V. 2007 In : Biomolecular engineering. 24, 3, p. 337-342. 6 p.Publication: Contribution to journal ⺠A1 Refereed journal article
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 journal ⺠A1 Refereed journal article
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 journal ⺠A1 Refereed journal article
Space-efficient algorithms for document retrieval
Välimäki, N. & Mäkinen, V. 2007 p. 205-215. 11 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
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; 2007-4).Publication: Book/anthology ⺠C2 Edited book, compilation, conference proceeding or special issue of journal
2006
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 journal ⺠A1 Refereed journal article
Compressed full-text indexes
Navarro, G. & Mäkinen, V. 2006 Santiago: University of Chile, Department of Computer Science. 66 p.Publication: Book/anthology ⺠C1 Published scientific monograph
Dynamic entrocopy-compressed sequences and full-text indexes
Mäkinen, V. & Navarro, G. 2006 p. 306-317. 12 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
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 journal ⺠A1 Refereed journal article
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 journal ⺠B1 Unrefereed journal article
Position-restricted substring searching
Mäkinen, V. & Navarro, G. 2006 p. 703-714. 12 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
2005
A simple alphabet-independent FM-index
Grabowski, S. , Mäkinen, V. , Navarro, G. & Salinger, A. 2005 p. 231-245.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Flexible music retrieval in sublinear time
Fredriksson, K. , Mäkinen, V. & Navarro, G. 2005 p. 174-189.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Maximum Line-Pair Stabbing Problem and its Variations
Böcker, S. & Mäkinen, V. 2005 p. 183–186. 4 p.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
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 journal ⺠A1 Refereed journal article
Practical Implementation of Rank and Select Queries
GonzÅ¡lez, R. , Grabowski, S. , Mäkinen, V. & Navarro, G. 2005Publication: Conference contribution ⺠B3 Unrefereed article in conference proceedings
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 journal ⺠A1 Refereed journal article
Succinct Suffix Arrays Based on Run-Length Encoding
Mäkinen, V. & Navarro, G. 2005 p. 45-56.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Transposition invariant string matching
Mäkinen, V. , Navarro, G. & Ukkonen, E. 2005 In : Journal of Algorithms. 56, p. 124-153. 30 p.Publication: Contribution to journal ⺠A1 Refereed journal article
2004
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 contribution ⺠A4 Article in conference publication (refereed)
An Alphabet-Friendly FM-Index
Ferragina, P. , Manzini, G. , Mäkinen, V. & Navarro, G. 2004 p. 150-160.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Compressed Compact Suffix Arrays
Mäkinen, V. & Navarro, G. 2004 p. 420-433.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Finding Missing Patterns
Inenaga, S. , Kivioja, T. & Mäkinen, V. 2004 p. 463-474.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
First Huffman, Then Burrows-Wheeler: A Simple Alphabet-Independent FM-index
Grabowski, S. , Mäkinen, V. & Navarro, G. 2004 p. 210-211.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Rotation and Lighting Invariant Template Matching
Fredriksson, K. , Mäkinen, V. & Navarro, G. 2004 p. 39-48.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
2003
Algorithms for Transposition Invariant String Matching
Mäkinen, V. , Navarro, G. & Ukkonen, E. 2003 p. 191-202.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Approximate Matching of Run-length Compressed Strings
Mäkinen, V. , Navarro, G. & Ukkonen, E. 2003 In : Algorithmica. 35, 4, p. 347–369.Publication: Contribution to journal ⺠A1 Refereed journal article
Compact Suffix Array — A Space-efficient Full-text Index
Mäkinen, V. 2003 In : Fundamenta Informaticae. 56, 1-2, p. 191–210.Publication: Contribution to journal ⺠A1 Refereed journal article
Geometric algorithms for transposition invariant content-based music retrieval
Ukkonen, E. , Lemström, K. & Mäkinen, V. 2003 p. 193-199.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
On Minimizing Pattern Splitting in Multi-track String Matching
Lemström, K. & Mäkinen, V. 2003 p. 237-253.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Sweepline the Music!
Ukkonen, E. , Lemström, K. & Mäkinen, V. 2003 In: Computer Science in Perspective, Essays Dedicated to Thomas Ottmann. Springer-Verlag, p. 330-342. 13 p. (LNCS).Publication: Contribution to book/anthology ⺠B2 Contribution to book/other compilations (non-refereed)
The C-BRAHMS Project
Lemström, K. , Mäkinen, V. , Pienimäki, A. , Turkia, M. & Ukkonen, E. 2003 p. 237-238.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
2002
Local Similarity Based Point-Pattern Matching
Mäkinen, V. & Ukkonen, E. 2002 p. 115-132.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
2001
Approximate Matching of Run-Length Compressed Strings
Mäkinen, V. , Navarro, G. & Ukkonen, E. 2001 p. 31-49.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Trade Off Between Compression and Search Times in Compact Suffix Array
Mäkinen, V. 2001 p. 189-201.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Using Edit Distance in Point-Pattern Matching
Mäkinen, V. 2001 p. 153-161.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
2000
Compact Suffix Array
Mäkinen, V. 2000 p. 305-319.Publication: Conference contribution ⺠A4 Article in conference publication (refereed)
Osoite: Tietojenkäsittelytieteen laitos, PL 68 (Gustaf Hällströmin katu 2b), 00014 Helsingin yliopisto
Aukioloajat: Normaalisti syys- ja kevätlukukausien aikana ma - pe klo 7.45-19.45.
Puhelin: (09) 1911 (yliopiston vaihde)
Sähköposti: Palveluosoitteet
Faksi: (09) 1915 1120