Department of Computer Science

Niko Välimäki

Genome-Scale Biology Program &
Department of Medical and Clinical Genetics
Biomedicum Helsinki
P.O. Box 63 (Haartmaninkatu 8)
FI-00014 University of Helsinki,
Finland

firstname.lastname@helsinki.fi

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Journal publications

  1. Sharon Peacock, Claire Chewapreecha, Matthew Holden, Minna Vehkala, Niko Välimäki, Zhirong Yang, Simon Harris, Alison Mather, Apichai Tuanyok, Birgit De Smet, Simon Le Hello, Chantal Bizet, Mark Mayo, Vanaporn Wuthiekanun, Direk Limmathurotsakul, Rattanaphone Phetsouvanh, Brian G. Spratt, Jukka Corander, Paul Keim, Gordon Dougan, David Dance, Bart Currie, and Julian Parkhill: Global and regional dissemination and evolution of Burkholderia pseudomallei. Nature Microbiology, Accepted, December 8, 2016.

  2. Ann-Katrin Llarena, Ji Zhang, Minna Vehkala, Niko Välimäki, Marjaana Hakkinen, Marja-Liisa Hänninen, Mati Roasto, Mihkel Mäesaar, Eduardo Taboada, Dillon Barker, Giuliano Garofolo, Cesare Cammà, Elisabetta Di Giannatale, Jukka Corander and Mirko Rossi: Monomorphic genotypes within a generalist lineage of Campylobacter jejuni show signs of global dispersion. Microbial Genomics, Accepted, September 12, 2016.

  3. Alan McNally, Yaara Oren, Darren Kelly, Ben Pascoe, Steven Dunn, Tristan Seecharan, Minna Vehkala, Niko Välimäki, Michael Prentice, Amgad Ashour, Oren Avram, Tal Pupko, Ulrich Dobrindt, Ivan Literak, Sebastian Guenther, Katharina Schauffler, Lothar Wieler, Zong Zhiyong, Samuel Sheppard, James McInerney and Jukka Corander: Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations. PLOS Genetics, Accepted, August 5, 2016.

  4. John Lees, Minna Vehkala, Niko Välimäki, Simon Harris, Claire Chewapreecha, Nick Croucher, Pekka Marttinen, Mark Davies, Andrew Steer, Steven Tong, Antti Honkela, Julian Parkhill, Stephen Bentley and Jukka Corander: Sequence element enrichment analysis to determine the genetic basis of bacterial phenotypes. Nature Communications, Accepted, July 28, 2016.

  5. Niko Välimäki, Hande Demir, Esa Pitkänen, Eevi Kaasinen, Atte Karppinen, Leena Kivipelto, Camilla Schalin-Jäntti, Lauri A. Aaltonen and Auli Karhu: Whole-Genome Sequencing of Growth Hormone (GH) - secreting Pituitary Adenomas. The Journal of Clinical Endocrinology & Metabolism, Vol. 100, No. 10, doi:10.1210/jc.2015-3129, August 17, 2015.

  6. Riku Katainen, Kashyap Dave, Esa Pitkänen, Kimmo Palin, Teemu Kivioja, Niko Välimäki, Alexandra E Gylfe, Heikki Ristolainen, Ulrika A Hänninen, Tatiana Cajuso, Johanna Kondelin, Tomas Tanskanen, Jukka-Pekka Mecklin, Heikki Järvinen, Laura Renkonen-Sinisalo, Anna Lepistö, Eevi Kaasinen, Outi Kilpivaara, Sari Tuupanen, Martin Enge, Jussi Taipale and Lauri A Aaltonen: CTCF/cohesin-binding sites are frequently mutated in cancer. Nature Genetics, Vol. 47, doi:10.1038/ng.3335, June 8, 2015.

  7. Lucy Weinert, Roy Chaudhuri, Jinhong Wang, Sarah Peters, Jukka Corander, Thibaut Jombart, Abiyad Baig, Kate Howell, Minna Vehkala, Niko Välimäki, David Harris, Bich Chieu Tran Thi, Chau Nguyen Van Vinh, James Campbell, Constance Schultsz, Julian Parkhill, Stephen Bentley, Paul Langford, Andrew Rycroft, Brendan Wren, Jeremy Farrar, Stephen Baker, Ngo Hoa, Matthew Holden, Alexander Tucker and Duncan Maskell: Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis. Nature Communications, Vol. 6, No. 6740, doi:10.1038/ncomms7740, March 31, 2015.

  8. Virpi Ahola, Rainer Lehtonen, Panu Somervuo, Leena Salmela, Patrik Koskinen, Pasi Rastas, Niko Välimäki, Lars Paulin, Jouni Kvist, Niklas Wahlberg, Jaakko Tanskanen, Emily Hornett, Laura Ferguson, Shiqi Luo, Zijuan Cao, Maaike de Jong, Anne Duplouy, Olli-Pekka Smolander, Heiko Vogel, Rajiv McCoy, Kui Qian, Swee Chong Wong, Qin Zhang, Freed Ahmad, Jani Haukka, Aruj Joshi, Jarkko Salojärvi, Christopher Wheat, Ewald Grosse-Wilde, Daniel Hughes, Riku Katainen, Esa Pitkänen, Johannes Ylinen, Robert Waterhouse, Mikko Turunen, Anna Vähärautio, Sami Ojanen, Alan Schulman, Minna Taipale, Daniel Lawson, Esko Ukkonen, Veli Mäkinen, Marian Goldsmith, Liisa Holm, Petri Auvinen, Mikko Frilander and Ilkka Hanski: The Glanville fritillary genome retains an ancient karyotype and reveals selective chromosomal fusions in Lepidoptera. Nature Communications, Vol. 5, No. 4737, doi:10.1038/ncomms5737, September 5, 2014.

  9. Sohan Seth, Niko Välimäki, Samuel Kaski and Antti Honkela: Exploration and retrieval of whole-metagenome sequencing samples. Bioinformatics, Vol. 30, No. 17, doi:10.1093/bioinformatics/btu340, May 19, 2014.

  10. Esa Pitkänen, Tatiana Cajuso, Riku Katainen, Eevi Kaasinen, Niko Välimäki, Kimmo Palin, Jussi Taipale, Lauri A. Aaltonen and Outi Kilpivaara: Frequent L1 retrotranspositions originating from TTC28 in colorectal cancer, OncoTarget, Vol. 5, No. 3, pages 853-859, 2014.

  11. Jouni Sirén, Niko Välimäki and Veli Mäkinen: Indexing Graphs for Path Queries with Applications in Genome Research. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 11, pages 375-388, 2014.

  12. Simon Gog, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen and Niko Välimäki: Multi-Pattern Matching with Bidirectional Indexes. Journal of Discrete Algorithms, Volume 24, pages 26-39, 2014.

  13. D. Arroyuelo, F. Claude, S. Maneth, V. Mäkinen, G. Navarro, K. Nguyen, J. Sirén and N. Välimäki: Fast In-Memory XPath Search using Compressed Indexes. Software: Practice and Experience, doi:10.1002/spe.2227, 2013.

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

  15. 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.

  16. Veli Mäkinen, Gonzalo Navarro, Jouni Sirén and Niko Välimäki: Storage and Retrieval of Highly Repetitive Sequence Collections. Journal of Computational Biology, Vol. 17, No. 3, pages 281-308, 2010.

  17. 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.

  18. 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. S. Tasoulis, L. Cheng, N. Välimäki, N. Croucher, S. Harris, W. Hanage, T. Roos, and J. Corander: Random projection based clustering for population genomics. In Proc. 2014 IEEE International Conference on Big Data (IEEE BigData-2014), pages 675-682, Washington DC, USA, October 27-30, 2014.

  2. Sohan Seth, Niko Välimäki, Samuel Kaski and Antti Honkela: Differential analysis of whole-genome shotgun sequences, In Proc. 8th International Workshop on Machine Learning in Systems Biology (MLSB'14), Extended abstract (online), pages 61-64, 2014.

  3. Niko Välimäki and Eric Rivals: Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data. In Proc. 9th International Symposium on Bioinformatics Research and Applications (ISBRA'13), Springer-Verlag, LNBI 7875, pages 237-248, Charlotte, North Carolina, May 20-22, 2013.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. D. Arroyuelo, F. Claude, S. Maneth, V. Mäkinen, G. Navarro, K. Nguyen, J. Sirén 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.

  12. Veli Mäkinen, Gonzalo Navarro, Jouni Sirén 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.

  13. 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.

  14. Jouni Sirén, 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.

  15. 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.

  16. 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 Wellcome Trust Sanger Institute, Computational Genomics & Durbin group (Dr Richard Durbin), Hinxton, Cambridge, UK, September 2015 - March 2016.

  2. Niko Välimäki: Insights from whole-genome sequencing of somatotropinomas. Presentation at the 4th European NeuroEndocrine Association Workshop: Acromegaly, Marseille, France, December 10-12, 2015.

  3. Niko Välimäki: Distributed String Mining. In Indexes and Computation over Compressed Structured Data (Dagstuhl Seminar 13232), Dagstuhl Reports, Vol. 27, No. 23, 10.4230/DagRep.3.6.22, pages 35-36, 2013.

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

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

  6. 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.

  7. 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.

  8. 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.

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

  10. Niko Välimäki (joint work with D. Arroyuelo, F. Claude, S. Maneth, V. Mäkinen, G. Navarro, K. Nguyen and J. Sirén): Compact In-Memory XML Self-Index. Presentation at the 4th Workshop on Compression, Text, and Algorithms, August 28, Saariselkä, Finland, 2009.

  11. Niko Välimäki (joint work with V. Mäkinen, G. Navarro and J. Sirén): Storage and Retrieval of Individual Genomes. Presentation at the 3rd Workshop on Compression, Text, and Algorithms, November 13, Melbourne, Australia, 2008.

  12. 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.

  13. 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.

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

  15. 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: 08.12.2016

firstname.lastname@helsinki.fi