Niko Välimäki

Publication Activity (10 Years)

Years Active: 2007-2018
Publications (10 Years): 1

Top Topics

Compressed Text

Pattern Matching

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

Daniel Valenzuela, Tuukka Norri, Niko Välimäki, Esa Pitkänen, Veli Mäkinen
Towards pan-genome read alignment to improve variation calling. BMC Genom. 19 (S2) (2018)
Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki
Fast in-memory XPath search using compressed indexes. Softw. Pract. Exp. 45 (3) (2015)
Veli Mäkinen, Niko Välimäki, Jouni Sirén
Indexing Graphs for Path Queries with Applications in Genome Research. IEEE ACM Trans. Comput. Biol. Bioinform. 11 (2) (2014)
Sohan Seth, Niko Välimäki, Samuel Kaski, Antti Honkela
Exploration and retrieval of whole-metagenome sequencing samples. Bioinform. 30 (17) (2014)
Simon Gog, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Niko Välimäki
Multi-pattern matching with bidirectional indexes. J. Discrete Algorithms 24 (2014)
Sotiris K. Tasoulis, Lu Cheng, Niko Välimäki, Nicholas J. Croucher, Simon R. Harris, William P. Hanage, Teemu Roos, Jukka Corander
Random projection based clustering for population genomics. IEEE BigData (2014)
Niko Välimäki, Eric Rivals
-mer Indexing for High-Throughput Sequencing Data. ISBRA (2013)
Sohan Seth, Niko Välimäki, Samuel Kaski, Antti Honkela
Exploration and retrieval of whole-metagenome sequencing samples. CoRR (2013)
Markus Heinonen, Niko Välimäki, Veli Mäkinen, Juho Rousu
Efficient Path Kernels for Reaction Function Prediction. BIOINFORMATICS (2012)
Johannes Fischer, Travis Gagie, Tsvi Kopelowitz, Moshe Lewenstein, Veli Mäkinen, Leena Salmela, Niko Välimäki
Forbidden Patterns. LATIN (2012)
Niko Välimäki, Susana Ladra, Veli Mäkinen
Approximate all-pairs suffix/prefix overlaps. Inf. Comput. 213 (2012)
Niko Välimäki
Least Random Suffix/Prefix Matches in Output-Sensitive Time. CPM (2012)
Simon Gog, Kalle Karhu, Juha Kärkkäinen, Veli Mäkinen, Niko Välimäki
Multi-pattern Matching with Bidirectional Indexes. COCOON (2012)
Niko Välimäki, Simon J. Puglisi
Distributed String Mining for High-Throughput Sequencing Data. WABI (2012)
Leena Salmela, Veli Mäkinen, Niko Välimäki, Johannes Ylinen, Esko Ukkonen
Fast scaffolding with small independent mixed integer programs. Bioinform. 27 (23) (2011)
Jouni Sirén, Niko Välimäki, Veli Mäkinen
Indexing Finite Language Representation of Population Genotypes. WABI (2011)
Niko Välimäki, Susana Ladra, Veli Mäkinen
Approximate All-Pairs Suffix/Prefix Overlaps. CPM (2010)
Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki
Fast in-memory XPath search using compressed indexes. ICDE (2010)
Veli Mäkinen, Niko Välimäki, Antti Laaksonen, Riku Katainen
Unified View of Backward Backtracking in Short Read Mapping. Algorithms and Applications (2010)
Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki
Storage and Retrieval of Highly Repetitive Sequence Collections. J. Comput. Biol. 17 (3) (2010)
Jouni Sirén, Niko Välimäki, Veli Mäkinen
Indexing Finite Language Representation of Population Genotypes CoRR (2010)
Niko Välimäki, Veli Mäkinen, Wolfgang Gerlach, Kashyap Dixit
Engineering a compressed suffix tree implementation. ACM J. Exp. Algorithmics 14 (2009)
Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki
Fast In-Memory XPath Search over Compressed Text and Tree Indexes CoRR (2009)
Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki
Storage and Retrieval of Individual Genomes. RECOMB (2009)
Jouni Sirén, Niko Välimäki, Veli Mäkinen, Gonzalo Navarro
Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections. SPIRE (2008)
Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki
Storage and Retrieval of Individual Genomes. Structure-Based Compression of Complex Massive Data (2008)
Johannes Fischer, Veli Mäkinen, Niko Välimäki
Space Efficient String Mining under Frequency Constraints. ICDM (2008)
Niko Välimäki, Veli Mäkinen
Space-Efficient Algorithms for Document Retrieval. CPM (2007)
Niko Välimäki, Wolfgang Gerlach, Kashyap Dixit, Veli Mäkinen
Engineering a Compressed Suffix Tree Implementation. WEA (2007)
Niko Välimäki, Wolfgang Gerlach, Kashyap Dixit, Veli Mäkinen
Compressed suffix tree - a basis for genome-scale sequence analysis. Bioinform. 23 (5) (2007)