Homepage of Veli Mäkinen

Selected publications

• A Novel Min-Cost Flow Method for Estimating Transcript Expression with RNA-Seq. Accepted to RECOMB-Seq 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)
• Indexing Finite Language Representation of Population Genotypes. In Proc. WABI 2011. (with Sirén & Välimäki)
• Fast In-Memory XPath Search using Compressed Indexes. In Proc. ICDE 2010. (with Arroyuelo et al.)
• Storage and Retrieval of Highly Repetitive Sequence Collections. Journal of Computational Biology 17(3):281-308, 2010 (with Navarro, Sirén, Välimäki) Earlier in RECOMB 2009.
• 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)
• Filtering methods for content-based retrieval on indexed symbolic music databases. Information Retrieval, 13(1):1-21, 2010. (with Lemström & Mikkilä)
• Complete list here... and with citation information in google citations