Pattern Kits - Travis Gagie; Kalle Karhu; Juha Kärkkäinen; Veli Mäkinen; Leena Salmela (CoRR, 2010)

GAST, a Genomic Alignment Search Tool. - Kalle Karhu; Juho Mäkinen; Jussi Rautio; Jorma Tarhio; Hugh Salamon (BIOINFORMATICS, 2011)

Improving Exact Search of Multiple Patterns From a Compressed Suffix Array. - Kalle Karhu (Stringology, 2011)

Indexed Multi-pattern Matching. - Travis Gagie; Kalle Karhu; Juha Kärkkäinen; Veli Mäkinen; Leena Salmela; Jorma Tarhio (LATIN, 2012)

Document Listing on Repetitive Collections. - Travis Gagie; Kalle Karhu; Gonzalo Navarro 001; Simon J. Puglisi; Jouni Sirén (CPM, 2013)

String Searching Methods for Bioinformatics ; Merkkijonohaun Menetelmät Bioinformatiikassa. - Kalle Karhu (2013)

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

The impact of manual threshold selection in medical additive manufacturing. - Maureen van Eijnatten; Juha Koivisto; Kalle Karhu; Tymour Forouzanfar; Jan Wolff (Int. J. Comput. Assist. Radiol. Surg., 2017)

Document retrieval on repetitive string collections. - Travis Gagie; Aleksi Hartikainen; Kalle Karhu; Juha Kärkkäinen; Gonzalo Navarro 001; Simon J. Puglisi; Jouni Sirén (Inf. Retr. J., 2017)

A Graph-Theoretical Approach for Motif Discovery in Protein Sequences. - Elena Czeizler; Tommi Hirvola; Kalle Karhu (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)