Space-Efficient Algorithms for Document Retrieval. - Niko Välimäki; Veli Mäkinen (CPM, 2007)

Compressed suffix tree - a basis for genome-scale sequence analysis. - Niko Välimäki; Wolfgang Gerlach; Kashyap Dixit; Veli Mäkinen (Bioinform., 2007)

Space Efficient String Mining under Frequency Constraints. - Johannes Fischer 001; Veli Mäkinen; Niko Välimäki (ICDM, 2008)

Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections. - Jouni Sirén; Niko Välimäki; Veli Mäkinen; Gonzalo Navarro 001 (SPIRE, 2008)

Storage and Retrieval of Individual Genomes. - Veli Mäkinen; Gonzalo Navarro 001; Jouni Sirén; Niko Välimäki (RECOMB, 2009)

Fast In-Memory XPath Search over Compressed Text and Tree Indexes - Diego Arroyuelo; Francisco Claude; Sebastian Maneth; Veli Mäkinen; Gonzalo Navarro 001; Kim Nguyen 001; Jouni Sirén; Niko Välimäki (CoRR, 2009)

Engineering a compressed suffix tree implementation. - Niko Välimäki; Veli Mäkinen; Wolfgang Gerlach; Kashyap Dixit (ACM J. Exp. Algorithmics, 2009)

Unified View of Backward Backtracking in Short Read Mapping. - Veli Mäkinen; Niko Välimäki; Antti Laaksonen; Riku Katainen (Algorithms and Applications, 2010)

Storage and Retrieval of Highly Repetitive Sequence Collections. - Veli Mäkinen; Gonzalo Navarro 001; Jouni Sirén; Niko Välimäki (J. Comput. Biol., 2010)

Indexing Finite Language Representation of Population Genotypes. - Jouni Sirén; Niko Välimäki; Veli Mäkinen (WABI, 2011)

Fast scaffolding with small independent mixed integer programs. - Leena Salmela; Veli Mäkinen; Niko Välimäki; Johannes Ylinen; Esko Ukkonen (Bioinform., 2011)

Efficient Path Kernels for Reaction Function Prediction. - Markus Heinonen; Niko Välimäki; Veli Mäkinen; Juho Rousu (BIOINFORMATICS, 2012)

Least Random Suffix/Prefix Matches in Output-Sensitive Time. - Niko Välimäki (CPM, 2012)

Forbidden Patterns. - Johannes Fischer 001; Travis Gagie; Tsvi Kopelowitz; Moshe Lewenstein; Veli Mäkinen; Leena Salmela; Niko Välimäki (LATIN, 2012)

Distributed String Mining for High-Throughput Sequencing Data. - Niko Välimäki; Simon J. Puglisi (WABI, 2012)

Approximate all-pairs suffix/prefix overlaps. - Niko Välimäki; Susana Ladra; Veli Mäkinen (Inf. Comput., 2012)

Applications of Compressed Data Structures on Sequences and Structured Data. - Niko Välimäki (2012)

Scalable and Versatile k-mer Indexing for High-Throughput Sequencing Data. - Niko Välimäki; Eric Rivals (ISBRA, 2013)

Random projection based clustering for population genomics. - Sotiris K. Tasoulis; Lu Cheng 004; Niko Välimäki; Nicholas J. Croucher; Simon R. Harris; William P. Hanage; Teemu Roos; Jukka Corander (IEEE BigData, 2014)

Exploration and retrieval of whole-metagenome sequencing samples. - Sohan Seth; Niko Välimäki; Samuel Kaski; Antti Honkela (Bioinform., 2014)

Multi-pattern matching with bidirectional indexes. - Simon Gog; Kalle Karhu; Juha Kärkkäinen; Veli Mäkinen; Niko Välimäki (J. Discrete Algorithms, 2014)

Indexing Graphs for Path Queries with Applications in Genome Research. - Veli Mäkinen; Niko Välimäki; Jouni Sirén (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Fast in-memory XPath search using compressed indexes. - Diego Arroyuelo; Francisco Claude; Sebastian Maneth; Veli Mäkinen; Gonzalo Navarro 001; Kim Nguyen 001; Jouni Sirén; Niko Välimäki (Softw. Pract. Exp., 2015)

Towards pan-genome read alignment to improve variation calling. - Daniel Valenzuela 001; Tuukka Norri; Niko Välimäki; Esa Pitkänen; Veli Mäkinen (BMC Genom., 2018)