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University of Helsinki Department of Computer Science
 

Department of Computer Science

Niko Välimäki

Niko

Personal

firstname.lastname@cs.helsinki.fi

Postdoctoral researcher in

I obtained my Ph.D. in Computer Science from the University of Helsinki in 2012. My Ph.D. supervisor was prof. Veli Mäkinen from the Genome-Scale Algorithmics group. I have received funding (mostly) from Hecse doctoral programme, ALGODAN and Academy of Finland.

Journal publications

  1. Simon Gog, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen and Niko Välimäki: Multi-Pattern Matching with Bidirectional Indexes. Accepted to the Journal of Discrete Algorithms, 2013.

  2. Niko Välimäki, Susana Ladra and Veli Mäkinen: Approximate All-Pairs Suffix/Prefix Overlaps. Information and Computation, 10.1016/j.ic.2012.02.002, Vol. 213, pages 49-58, 2012.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  1. Niko Välimäki and Eric Rivals: Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data. Accepted to the 9th International Symposium on Bioinformatics Research and Applications (ISBRA'13), Charlotte, North Carolina, May 20-22, 2013.

  2. Niko Välimäki and Simon J. Puglisi: Distributed String Mining for High-Throughput Sequencing Data. In Proc. 12th Workshop on Algorithms in Bioinformatics (WABI'12), Springer-Verlag, LNCS 7534, pages 441-452, Ljubljana, Slovenia, September 9-14, 2012.

  3. Simon Gog, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen and Niko Välimäki: Multi-Pattern Matching with Bidirectional Indexes. In Proc. 18th Annual International Computing and Combinatorics Conference (COCOON'12), Springer-Verlag, LNCS 7434, pages 384-395, Sydney, Australia, August 20-22, 2012.

  4. Niko Välimäki: Least Random Suffix/Prefix Matches in Output-Sensitive Time. In Proc. 23rd Annual Symposium on Combinatorial Pattern Matching (CPM'12), Springer-Verlag, LNCS 7354, pages 269-279, Helsinki, Finland, July 3-5, 2012.

  5. Johannes Fischer, Travis Gagie, Tsvi Kopelowitz, Moshe Lewenstein, Veli Mäkinen, Leena Salmela and Niko Välimäki: Forbidden Patterns. In Proc. 10th Latin American Theoretical INformatics Symposium (LATIN'12), Springer-Verlag, LNCS 7256, pages 327-337, Arequipa, Peru, 2012.

  6. Markus Heinonen, Niko Välimäki, Veli Mäkinen and Juho Rousu: Efficient Path Kernels for Reaction Function Prediction. In Proc. 3rd International Conference on Bioinformatics Models, Methods and Algorithms (Bioinformatics'12), SciTePress, pages 202-207, Algarve, Portugal, February, 2012.

  7. 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.

  8. 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.

  9. 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.

  10. 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'09), Springer-Verlag, LNCS 5541, pages 121-137, Tucson, Arizona, May 18-21, 2009.

  11. Johannes Fischer, Veli Mäkinen and Niko Välimäki: Space-Efficient String Mining under Frequency Constraints. In Proc. 8th IEEE International Conference on Data Mining (ICDM'08), IEEE Computer Society, pages 193-202, Pisa, Italy, December 15-19, 2008.

  12. 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'08), Springer-Verlag, LNCS 5280, pages 164-175, Melbourne, Australia, November 10-12, 2008.

  13. Niko Välimäki and Veli Mäkinen: Space-Efficient Data Structures for Document Retrieval. In Proc. 18th Annual Symposium on Combinatorial Pattern Matching (CPM'07), Springer-Verlag, LNCS 4580, pages 205-215, Canada, July 9-11, 2007.

  14. Niko Välimäki, Wolfgang Gerlach, Kashyap Dixit and Veli Mäkinen: Engineering a Compressed Suffix Tree Implementation. In Proc. 6th Workshop on Experimental Algorithms (WEA'07), Springer-Verlag, LNCS 4525, pages 217-228, June 6-8, Italy, 2007.

Other

  1. Research visit to the Institut de Biologie Computationelle, Methods and Algorithms for Bioinformatics (CNRS Research Director Eric Rivals), Montpellier, France, January 2013.

  2. Niko Välimäki: Applications of Compressed Data Structures on Sequences and Structured Data. Presentation at the Institut de Biologie Computationelle, Montpellier, France, January 11, 2013.

  3. Niko Välimäki: Applications of Compressed Data Structures on Sequences and Structured Data. Ph.D. thesis, Department of Computer Science, Series of Publications A, Report A-2012-7, University of Helsinki, August 2012.

  4. 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, University of Helsinki, October 27, 2011.

  5. 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.

  6. Junior researcher award ("Hyvä tutkija -palkinto") by the Department of Computer Science, University of Helsinki, 2009.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Niko Välimäki: Tiiviit loppuosaindeksit tiedonhaussa. Master's thesis, Report C-series, Department of Computer Science, University of Helsinki, Finland, 2007.

  12. 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.

Teaching

  • Algorithms for Bioinformatics, course assistant, fall 2012.
  • 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.

Previous update: 02.04.2013


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