Department of Computer Science

Homepage of Veli Mäkinen

Official foto taken at the department

Veli Mäkinen, PhD, Professor

Department of Computer Science, P. O. Box 68, (Gustaf Hällströmin katu 2b), FI-00014 University of Helsinki, Finland

Room: A239b, Phone: +358 50 41 51 706, Email: First.Last(at)

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Short bio

Selected publications

  • Indexing Graphs for Path Queries with Applications in Genome Research. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11(2):375-388, 2014. (with Sirén & Välimäki)
  • Fast In-Memory XPath Search using Compressed Indexes. To appear in Software Practice and Experience. (with Arroyuelo et al.)
  • Versatile succinct representations of the bidirectional Burrows-Wheeler transform. In Proc. ESA 2013. (with Belazzougui, Cunial, and Kärkkäinen)
  • A Novel Min-Cost Flow Method for Estimating Transcript Expression with RNA-Seq. BMC Bioinformatics, 14(Suppl 5):S15 (10 April 2013). (with Tomescu, Kuosmanen, and Rizzi)
  • Efficient Path Kernels for Reaction Function Prediction. In Proc. BIOINFORMATICS 2012. (with Heinonen, Välimäki, Rousu)
  • Fast Scaffolding with Small Independent Mixed Integer Programs. Bioinformatics 27(23):3259-3265, 2011 (with Salmela, Välimäki, Ylinen, Ukkonen)
  • Storage and Retrieval of Highly Repetitive Sequence Collections. Journal of Computational Biology 17(3):281-308, 2010 (with Navarro, Sirén, Välimäki)
  • Filtering methods for content-based retrieval on indexed symbolic music databases. Information Retrieval, 13(1):1-21, 2010. (with Lemström & Mikkilä)
  • Compressed Full-Text Indexes. ACM Computing Surveys, Vol. 39, No. 1, Article 2, 2007. (with Navarro)
  • Compressed Representations of Sequences and Full-Text Indexes. ACM Transactions on Algorithms, Vol. 3, Issue 2, Article 20, May 2007. (with Ferragina & Manzini & Navarro)
  • Combinatorial Approaches for Mass Spectra Recalibration. IEEE/ACM Transactions on Computational Biology and Bioinformatics,5(1):91-100, 2008. (with Böcker)
  • Transposition Invariant String Matching, Journal of Algorithms, 56(2):124-153, 2005. (with Navarro & Ukkonen)
  • Complete list here... and with citation information in google citations

Recent activities



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Past activities