vmakinen's picture

Veli Mäkinen

Professor

Contact Information

Veli.Makinen[at]cs.helsinki.fi
http://www.cs.helsinki.fi/u/vmakinen/
A239b
(09) 19151281

Principal Investigator of

Examiner for exams

(to registration)

Biological Sequence Analysis
Biologiska sekvensanalys
Biological Sequence Analysis

  • Register 19.04.2013 (Renewal exam)

Teaching

2013 spring
Project in Biological Sequence Analysis
Projekt i biologiska sekvensanalys
Biologisen sekvenssianalyysin harjoitustyö

  • Lecturer , in charge

2013 spring
Biological Sequence Analysis
Biologiska sekvensanalys
Biological Sequence Analysis

  • Assistant
  • Lecturer , in charge

2012 spring
Project in Data Compression Techniques
Project in Data Compression Techniques
Project in Data Compression Techniques

  • Lecturer , in charge

2012 spring
Project in String Processing Algorithms
Projekt i sträng bearbetning algoritmerna
Merkkijonomenetelmien harjoitustyö

  • Lecturer , in charge

2012 spring
MSc Thesis Seminar on Bioinformatics
MSc Thesis Seminar on Bioinformatics
MSc Thesis Seminar on Bioinformatics

  • In charge

2011 autumn
Seminar: Pattern Discovery in Bioinformatics
Seminar: Pattern Discovery in Bioinformatics
Seminaari: Hahmontunnistus bioinformatiikassa

  • In charge

2011 autumn
Algorithms for Bioinformatics
Algoritmer för bioinformatik
Algoritmit bioinformatiikassa

  • Lecturer , in charge

2011 summer
Intensive course on population genetics
Intensive course on population genetics
Intensive course on population genetics

  • Lecturer

2011 spring
Biological Sequence Analysis
Biologiska sekvensanalys
Biological Sequence Analysis

  • Assistant
  • Lecturer , in charge

2010 autumn
Elements of Bioinformatics
Elements of Bioinformatics
Elements of Bioinformatics

  • Lecturer , in charge

2010 autumn
Algorithms for Bioinformatics
Algoritmer för bioinformatik
Algoritmit bioinformatiikassa

  • Lecturer , in charge

2010 spring
Seminar: Sequence Assembly
r
Seminar: Sequence Assembly

  • In charge

2008 autumn
Data Compression Techniques
Datakompression tekniker
Tiedon tiivistämisen tekniikat

  • Lecturer , in charge

2007 spring
Advanced Data Structures
Avancerade datastrukturer
Advanced Data Structures

  • Assistant
  • Lecturer , in charge

2006 spring
Data Compression Techniques
Datakompression tekniker
Tiedon tiivistämisen tekniikat

  • Lecturer , in charge

2005 autumn
Elements of Bioinformatics -2005
Inslag av bioinformatik -2005
Bioinformatiikan perusteet -2005

  • Lecturer , in charge

2004 autumn
Pattern Analysis in Sequences
Pattern Analysis in Sequences
Pattern Analysis in Sequences

  • In charge

2004 spring
Scientific Writing
Att skriva vetenskaplig text
Tieteellisen kirjoittamisen kurssi

  • Instructor

2003 autumn
String Processing Algorithms
Metoder för behandling av teckensträngar
Merkkijonomenetelmät

  • Assistant
  • Lecturer , in charge

2001 spring
String Processing Algorithms
Metoder för behandling av teckensträngar
Merkkijonomenetelmät

  • Assistant

Publications

Publications gathered from the TUHAT database profile.

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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › A1 Refereed journal article

2011

Algoritmitutkimuksen rooli bioinformatiikassa

Mäkinen, V. 07.2011 In : Tietojenkäsittelytiede. 32, p. 10-15. 6 p.

Publication: Contribution to journal › 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 › A1 Refereed journal article

Indexing Finite Language Representation of Population Genotypes

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

Publication: Conference contribution › 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 › A1 Refereed journal article

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

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

Publication: Contribution to journal › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › A1 Refereed journal article

Space-efficient algorithms for document retrieval

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

Publication: Conference contribution › 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 › 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 › 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 › 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 › 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 › 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 › B1 Unrefereed journal article

Position-restricted substring searching

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

Publication: Conference contribution › 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 › 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 › 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 › 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 › A1 Refereed journal article

Practical Implementation of Rank and Select Queries

GonzÅ¡lez, R. , Grabowski, S. , Mäkinen, V. & Navarro, G. 2005

Publication: Conference contribution › 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 › A1 Refereed journal article

Succinct Suffix Arrays Based on Run-Length Encoding

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

Publication: Conference contribution › 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 › 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 › 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 › A4 Article in conference publication (refereed)

Compressed Compact Suffix Arrays

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

Publication: Conference contribution › A4 Article in conference publication (refereed)

Finding Missing Patterns

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

Publication: Conference contribution › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › 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 › A4 Article in conference publication (refereed)

2002

Local Similarity Based Point-Pattern Matching

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

Publication: Conference contribution › 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 › 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 › A4 Article in conference publication (refereed)

Using Edit Distance in Point-Pattern Matching

Mäkinen, V. 2001 p. 153-161.

Publication: Conference contribution › A4 Article in conference publication (refereed)

2000

Compact Suffix Array

Mäkinen, V. 2000 p. 305-319.

Publication: Conference contribution › A4 Article in conference publication (refereed)