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)

Compressed Suffix Arrays for Massive Data. - Jouni Sirén (SPIRE, 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)

Sampled Longest Common Prefix Array. - Jouni Sirén (CPM, 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)

Compressed Full-Text Indexes for Highly Repetitive Collections. - Jouni Sirén (2012)

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

Distribution-Aware Compressed Full-Text Indexes. - Paolo Ferragina; Jouni Sirén; Rossano Venturini (Algorithmica, 2013)

Document Retrieval on Repetitive Collections. - Gonzalo Navarro 001; Simon J. Puglisi; Jouni Sirén (ESA, 2014)

Relative FM-Indexes. - Djamal Belazzougui; Travis Gagie; Simon Gog; Giovanni Manzini; Jouni Sirén (SPIRE, 2014)

Document Counting in Practice. - Travis Gagie; Aleksi Hartikainen; Juha Kärkkäinen; Gonzalo Navarro 001; Simon J. Puglisi; Jouni Sirén (CoRR, 2014)

Reusing an FM-index. - Travis Gagie; Giovanni Manzini; Jouni Sirén (CoRR, 2014)

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

Document Counting in Compressed Space. - Travis Gagie; Aleksi Hartikainen; Juha Kärkkäinen; Gonzalo Navarro 001; Simon J. Puglisi; Jouni Sirén (DCC, 2015)

Relative Select. - Christina Boucher 001; Alexander Bowe; Travis Gagie; Giovanni Manzini; Jouni Sirén (SPIRE, 2015)

Relative Compressed Suffix Trees. - Travis Gagie; Gonzalo Navarro 001; Simon J. Puglisi; Jouni Sirén (CoRR, 2015)

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)

Burrows-Wheeler Transform for Terabases. - Jouni Sirén (DCC, 2016)

RLZAP: Relative Lempel-Ziv with Adaptive Pointers. - Anthony J. Cox; Andrea Farruggia; Travis Gagie; Simon J. Puglisi; Jouni Sirén (SPIRE, 2016)

Indexing Variation Graphs. - Jouni Sirén (ALENEX, 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)

Wheeler graphs: A framework for BWT-based data structures. - Travis Gagie; Giovanni Manzini; Jouni Sirén (Theor. Comput. Sci., 2017)

Relative Suffix Trees. - Andrea Farruggia; Travis Gagie; Gonzalo Navarro 001; Simon J. Puglisi; Jouni Sirén (Comput. J., 2018)

Distance indexing and seed clustering in sequence graphs. - Xian Chang; Jordan Eizenga; Adam M. Novak; Jouni Sirén; Benedict Paten (Bioinform., 2020)

Haplotype-aware graph indexes. - Jouni Sirén; Erik Garrison; Adam M. Novak; Benedict Paten; Richard Durbin (Bioinform., 2020)

Efficiently Merging r-indexes. - Marco Oliva; Massimiliano Rossi 001; Jouni Sirén; Giovanni Manzini; Tamer Kahveci; Travis Gagie; Christina Boucher 001 (DCC, 2021)

Computational graph pangenomics: a tutorial on data structures and their applications. - Jasmijn A. Baaijens; Paola Bonizzoni; Christina Boucher 001; Gianluca Della Vedova; Yuri Pirola; Raffaella Rizzi; Jouni Sirén (Nat. Comput., 2022)

GBZ file format for pangenome graphs. - Jouni Sirén; Benedict Paten (Bioinform., 2022)

Wheeler Maps. - Andrej Baláz; Travis Gagie; Adrián Goga; Simon Heumos; Gonzalo Navarro 001; Alessia Petescia; Jouni Sirén (LATIN (1), 2024)

Graph Indexing Beyond Wheeler Graphs. - Jarno N. Alanko; Elena Biagi 002; Massimo Equi; Veli Mäkinen; Simon J. Puglisi; Nicola Rizzo 001; Kunihiko Sadakane; Jouni Sirén (The Expanding World of Compressed Data, 2025)

Lossless Pangenome Indexing Using Tag Arrays. - Parsa Eskandar; Benedict Paten; Jouni Sirén (WABI, 2025)