Homepage of Veli Mäkinen

	Veli Mäkinen, PhD, Professor Department of Computer Science P. O. Box 68 (Gustaf Hällströmin katu 2b) FIN-00014 University of Helsinki Finland Room: A239b Phone: +358 9 191 51281 Mobile: +358 50 4009152 Email: First.Last(at)cs.helsinki.fi Also affiliated with: CoECG HIIT
Recent activities Organizer for CPM 2012 PC member, SPIRE 2012, BIOINFORMATICS 2012 Professor in charge of MBI Research Research group on Genome-scale algorithmics Publications Projects Software Teaching See here. Past activities Co-organizer, The Fourth Workshop on Compression, Text, and Algorithms 2009. PC member, CPM 2011, CPM 2008 PC member, SPIRE 2010, SPIRE 2009, SPIRE 2007, SPIRE 2006, SPIRE 2005 Organizer, ICML/UAI/COLT 2008 Organizer, Merkkijonopäivä 2008 (national seminar on string processing) Program Chair, Summer School on Algorithmic Data Analysis Local organizer, PMSB 2006 Workshop Recent trends in Stringology - study group, spring 2004 FDK Research Seminar, autumn 2003	Selected publications Efficient Path Kernels for Reaction Function Prediction. Accepted to 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

Veli Mäkinen, PhD,
Professor

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

Room: A239b
Phone: +358 9 191 51281
Mobile: +358 50 4009152
Email: First.Last(at)cs.helsinki.fi

Also affiliated with:

Recent activities

Organizer for CPM 2012

PC member, SPIRE 2012, BIOINFORMATICS 2012

Professor in charge of MBI

Research

Research group on Genome-scale algorithmics

Publications

Projects

Software

Teaching

See here.

Past activities

Co-organizer, The Fourth Workshop on Compression, Text, and Algorithms 2009.

PC member, CPM 2011, CPM 2008

PC member, SPIRE 2010, SPIRE 2009, SPIRE 2007, SPIRE 2006, SPIRE 2005

Organizer, ICML/UAI/COLT 2008

Organizer, Merkkijonopäivä 2008 (national seminar on string processing)

Program Chair, Summer School on Algorithmic Data Analysis

Local organizer, PMSB 2006 Workshop

Recent trends in Stringology - study group, spring 2004

FDK Research Seminar, autumn 2003

Selected publications

Efficient Path Kernels for Reaction Function Prediction. Accepted to 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

Visiting Israel

Department of Computer Science

Department information