Niko Välimäki

According to our database, Niko Välimäki authored at least 24 papers between 2007 and 2018.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2018

Towards pan-genome read alignment to improve variation calling.

Daniel Valenzuela, Tuukka Norri, Niko Välimäki, Esa Pitkänen, Veli Mäkinen

BMC Genom., 2018

2015

Fast in-memory XPath search using compressed indexes.

Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki

Softw. Pract. Exp., 2015

2014

Indexing Graphs for Path Queries with Applications in Genome Research.

Veli Mäkinen, Niko Välimäki, Jouni Sirén

IEEE ACM Trans. Comput. Biol. Bioinform., 2014

Multi-pattern matching with bidirectional indexes.

Simon Gog, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Niko Välimäki

J. Discrete Algorithms, 2014

Exploration and retrieval of whole-metagenome sequencing samples.

Sohan Seth, Niko Välimäki, Samuel Kaski, Antti Honkela

Bioinform., 2014

Random projection based clustering for population genomics.

Sotiris K. Tasoulis, Lu Cheng, Niko Välimäki, Nicholas J. Croucher, Simon R. Harris, William P. Hanage, Teemu Roos, Jukka Corander

Proceedings of the 2014 IEEE International Conference on Big Data (IEEE BigData 2014), 2014

2013

Scalable and Versatile <i>k</i>-mer Indexing for High-Throughput Sequencing Data.

Niko Välimäki, Eric Rivals

Proceedings of the Bioinformatics Research and Applications, 9th International Symposium, 2013

2012

Applications of Compressed Data Structures on Sequences and Structured Data.

Niko Välimäki

PhD thesis, 2012

Approximate all-pairs suffix/prefix overlaps.

Niko Välimäki, Susana Ladra, Veli Mäkinen

Inf. Comput., 2012

Distributed String Mining for High-Throughput Sequencing Data.

Niko Välimäki, Simon J. Puglisi

Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

Forbidden Patterns.

Johannes Fischer, Travis Gagie, Tsvi Kopelowitz, Moshe Lewenstein, Veli Mäkinen, Leena Salmela, Niko Välimäki

Proceedings of the LATIN 2012: Theoretical Informatics, 2012

Least Random Suffix/Prefix Matches in Output-Sensitive Time.

Niko Välimäki

Proceedings of the Combinatorial Pattern Matching - 23rd Annual Symposium, 2012

Efficient Path Kernels for Reaction Function Prediction.

Markus Heinonen, Niko Välimäki, Veli Mäkinen, Juho Rousu

Proceedings of the BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Vilamoura, Algarve, Portugal, 1, 2012

2011

Fast scaffolding with small independent mixed integer programs.

Leena Salmela, Veli Mäkinen, Niko Välimäki, Johannes Ylinen, Esko Ukkonen

Bioinform., 2011

Indexing Finite Language Representation of Population Genotypes.

Jouni Sirén, Niko Välimäki, Veli Mäkinen

Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

2010

Storage and Retrieval of Highly Repetitive Sequence Collections.

Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki

J. Comput. Biol., 2010

Unified View of Backward Backtracking in Short Read Mapping.

Veli Mäkinen, Niko Välimäki, Antti Laaksonen, Riku Katainen

Proceedings of the Algorithms and Applications, 2010

2009

Engineering a compressed suffix tree implementation.

Niko Välimäki, Veli Mäkinen, Wolfgang Gerlach, Kashyap Dixit

ACM J. Exp. Algorithmics, 2009

Fast In-Memory XPath Search over Compressed Text and Tree Indexes

Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki

CoRR, 2009

Storage and Retrieval of Individual Genomes.

Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki

Proceedings of the Research in Computational Molecular Biology, 2009

2008

Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections.

Jouni Sirén, Niko Välimäki, Veli Mäkinen, Gonzalo Navarro

Proceedings of the String Processing and Information Retrieval, 2008

Space Efficient String Mining under Frequency Constraints.

Johannes Fischer, Veli Mäkinen, Niko Välimäki

Proceedings of the 8th IEEE International Conference on Data Mining (ICDM 2008), 2008

2007

Compressed suffix tree - a basis for genome-scale sequence analysis.

Niko Välimäki, Wolfgang Gerlach, Kashyap Dixit, Veli Mäkinen

Bioinform., 2007

Space-Efficient Algorithms for Document Retrieval.

Niko Välimäki, Veli Mäkinen

Proceedings of the Combinatorial Pattern Matching, 18th Annual Symposium, 2007