Niko Välimäki
firstname.lastname@cs.helsinki.fi
Personal
- Doctoral student
- Working in Succinct Data Structures group.
- Funded by Helsinki Graduate School in Computer Science and Engineering.
- Supervised by Veli Mäkinen.
Study & research interests
- Compressed data structures
- Succinct full-text indexes
- Design and analysis of algorithms
Teaching
- Data compression techniques, course assistant, spring 2012.
- Algorithms for Bioinformatics, course assistant, fall 2011.
- Algorithms for Bioinformatics, course assistant, fall 2010.
- Data compression techniques, course assistant, fall 2008.
- Teacher tutor, since January 2008.
Journal publications
- Leena Salmela, Veli Mäkinen, Niko Välimäki, Johannes Ylinen and Esko Ukkonen: Fast Scaffolding with Small Independent Mixed Integer Programs. Bioinformatics, Vol. 27, No. 23, pages 3259-3265, 2011.
- Niko Välimäki, Susana Ladra and Veli Mäkinen: Approximate All-Pairs Suffix/Prefix Overlaps. To appear in Information & Computation CPM 2010 Special Issue, 2011.
- Veli Mäkinen, Gonzalo Navarro, Jouni Siren and Niko Välimäki: Storage and Retrieval of Highly Repetitive Sequence Collections. Journal of Computational Biology, Vol. 17, No. 3, pages 281-308, 2010.
- Niko Välimäki, Veli Mäkinen, Wolfgang Gerlach and Kashyap Dixit: Engineering a Compressed Suffix Tree Implementation. ACM Journal of Experimental Algorithmics, Vol. 14, No. 4.2, August 2009.
- Niko Välimäki, Wolfgang Gerlach, Kashyap Dixit and Veli Mäkinen: Compressed Suffix Tree - A Basis for Genome-scale Sequence Analysis. Bioinformatics, 23(5), Application note, pages 629-630, 2007.
Refereed conference papers
- Johannes Fischer, Travis Gagie, Tsvi Kopelowitz, Veli Mäkinen, Leena Salmela and Niko Välimäki: Forbidden Patterns. Accepted to 10th Latin American Theoretical INformatics Symposium (LATIN 2012), Arequipa, Peru, 2012.
- Markus Heinonen, Veli Mäkinen, Juho Rousu and Niko Välimäki: Efficient Path Kernels for Reaction Function Prediction. Accepted to Bioinformatics 2012, Algarve, Portugal, February, 2012.
- Jouni Sirén, Niko Välimäki, and Veli Mäkinen: Indexing Finite Language Representation of Population Genotypes. In Proc. 11th Workshop on Algorithms for Bioinformatics (WABI'11), Springer-Verlag, LNCS 6833, pages 270-281, Saarbrücken, Germany, September 5-7, 2011.
- Niko Välimäki, Susana Ladra and Veli Mäkinen: Approximate All-Pairs Suffix/Prefix Overlaps. In Proc. 21st Annual Symposium on Combinatorial Pattern Matching (CPM'10), Springer-Verlag, LNCS 6129, pages 76-87, New York, USA, June 21-23, 2010.
- D. Arroyuelo, F. Claude, S. Maneth, V. Mäkinen, G. Navarro, K. Nguyen, J. Siren and N. Välimäki: Fast In-Memory XPath Search over Compressed Text and Tree Indexes. In Proc. 26th IEEE International Conference on Data Engineering (ICDE'10), pages 417-428, Long Beach, California, March 1-6, 2010.
- Veli Mäkinen, Gonzalo Navarro, Jouni Siren and Niko Välimäki: Storage and Retrieval of Individual Genomes. In Proc. 13th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2009), Springer-Verlag, LNCS 5541, pages 121-137, Tucson, Arizona, May 18-21, 2009.
- Johannes Fischer, Veli Mäkinen and Niko Välimäki: Space-Efficient String Mining under Frequency Constraints. In Proc. 8th IEEE International Conference on Data Mining (ICDM 2008), IEEE Computer Society, pages 193-202, Pisa, Italy, December 15-19, 2008.
- Jouni Siren, Niko Välimäki, Veli Mäkinen and Gonzalo Navarro: Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections. In Proc. 15th Symposium on String Processing and Information Retrieval (SPIRE 2008), Springer-Verlag, LNCS 5280, pages 164-175, Melbourne, Australia, November 10-12, 2008.
- Niko Välimäki and Veli Mäkinen: Space-Efficient Data Structures for Document Retrieval. In Proc. 18th Annual Symposium on Combinatorial Pattern Matching (CPM 2007), Springer-Verlag, LNCS 4580, pages 205-215, Canada, July 9-11, 2007.
- Niko Välimäki, Wolfgang Gerlach, Kashyap Dixit and Veli Mäkinen: Engineering a Compressed Suffix Tree Implementation. In Proc. 6th Workshop on Experimental Algorithms (WEA 2007), Springer-Verlag, LNCS 4525, pages 217-228, June 6-8, Italy, 2007.
Other
- Niko Välimäki (joint work with M. Heinonen, V. Mäkinen and J. Rousu): Efficient Path Kernels for Reaction Function Prediction. Presentation at the Get-Together for String Algorithms Researchers, October 27, University of Helsinki, 2011.
- V. Mäkinen, N. Välimäki, A. Laaksonen and R. Katainen: Unified View of Backward Backtracking in Short Read Mapping. In Algorithms and Applications: Essays Dedicated to Esko Ukkonen on the Occasion of His 60th Birthday (Eds. Tapio Elomaa, Pekka Orponen, Heikki Mannila), Springer-Verlag, LNCS 6060, pp. 182-195, 2010.
- Niko Välimäki (joint work with D. Arroyuelo, F. Claude, S. Maneth, V. Mäkinen, G. Navarro, K. Nguyen and J. Siren): Compact In-Memory XML Self-Index. Presentation at the 4th Workshop on Compression, Text, and Algorithms, August 28, Saariselkä, Finland, 2009.
- Niko Välimäki (joint work with V. Mäkinen, G. Navarro and J. Siren): Storage and Retrieval of Individual Genomes. Presentation at the 3rd Workshop on Compression, Text, and Algorithms, November 13, Melbourne, Australia, 2008.
- Niko Välimäki (joint work with J. Fischer and V. Mäkinen): Tilatehokas merkkijonojoukkojen louhinta. Presentation at Merkkijonopäivä 2008, Department of Computer Science, University of Helsinki, January 10, Finland, 2008.
- Veli Mäkinen, Jouni Sirén and Niko Välimäki: Storage and Retrieval of Individual Genomes and other Repetitive Sequence Collections. Technical report C-2008-1, Department of Computer Science, University of Helsinki, Finland, 2008.
- Niko Välimäki: Tiiviit loppuosaindeksit tiedonhaussa. Master's thesis, Report C-series, Department of Computer Science, University of Helsinki, Finland, 2007.
- Kashyap Dixit, Wolfgang Gerlach, Veli Mäkinen and Niko Välimäki: Engineering a Compressed Suffix Tree Implementation. Technical report C-2006-37, Department of Computer Science, University of Helsinki, Finland, September 2006.
Previous update: 30.01.2012

