Department of Computer Science

Old homepage of Veli Mäkinen - check new homepage

Official foto taken at HIIT

Veli Mäkinen, PhD, Professor

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

Room: A240, Phone: +358 50 41 51 706, Email: First.Last(at)

Also affiliated with:

Short bio

Selected publications

  • Using Minimum Path Cover to Boost Dynamic Programming on DAGs: Co-Linear Chaining Extended. Accepted to RECOMB 2018 (subject to revisions, with Kuosmanen et al.)
  • Computational Pan-Genomics: Status, Promises and Challenges. Briefings in Bioinformatics, 2016. (with Marschall et al.) [Article online]
  • Genome-Scale Algorithm Design: Biological Sequence Analysis in the Era of High-Throughput Sequencing. Cambridge University Press, 2015. (with Belazzougui, Cunial, Tomescu) [Book webpage]
  • Explaining a Weighted DAG with Few Paths for Solving Genome-Guided Multi-assembly. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2015. (with Tomescu et al.)
  • Fast In-Memory XPath Search using Compressed Indexes. Software Practice and Experience, 45(3):399-434, 2015. (with Arroyuelo et al.)
  • 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)
  • 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

Current activities



See here.

Some past activities