Jouni Sirén

Publication Activity (10 Years)

Years Active: 2008-2024
Publications (10 Years): 18

Top Topics

Subgraph Matching

Fukunaga Koontz

Document Retrieval

Top Venues

Publications

Andrej Baláz, Travis Gagie, Adrián Goga, Simon Heumos, Gonzalo Navarro, Alessia Petescia, Jouni Sirén
Wheeler Maps. LATIN (1) (2024)
Andrej Baláz, Travis Gagie, Adrián Goga, Simon Heumos, Gonzalo Navarro, Alessia Petescia, Jouni Sirén
Wheeler maps. CoRR (2023)
Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén
Computational graph pangenomics: a tutorial on data structures and their applications. Nat. Comput. 21 (1) (2022)
Jouni Sirén, Benedict Paten
GBZ file format for pangenome graphs. Bioinform. 38 (22) (2022)
Marco Oliva, Massimiliano Rossi, Jouni Sirén, Giovanni Manzini, Tamer Kahveci, Travis Gagie, Christina Boucher
Efficiently Merging r-indexes. DCC (2021)
Xian Chang, Jordan Eizenga, Adam M. Novak, Jouni Sirén, Benedict Paten
Distance indexing and seed clustering in sequence graphs. Bioinform. 36 (Supplement-1) (2020)
Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin
Haplotype-aware graph indexes. Bioinform. 36 (2) (2020)
Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin
Haplotype-aware graph indexes. WABI (2018)
Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin
Haplotype-aware graph indexes. CoRR (2018)
Andrea Farruggia, Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
Relative Suffix Trees. Comput. J. 61 (5) (2018)
Jouni Sirén
Indexing Variation Graphs. ALENEX (2017)
Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
Document retrieval on repetitive string collections. Inf. Retr. J. 20 (3) (2017)
Travis Gagie, Giovanni Manzini, Jouni Sirén
Wheeler graphs: A framework for BWT-based data structures. Theor. Comput. Sci. 698 (2017)
Jouni Sirén
Indexing Variation Graphs. CoRR (2016)
Anthony J. Cox, Andrea Farruggia, Travis Gagie, Simon J. Puglisi, Jouni Sirén
RLZAP: Relative Lempel-Ziv with Adaptive Pointers. SPIRE (2016)
Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
Document Retrieval on Repetitive String Collections. CoRR (2016)
Anthony J. Cox, Andrea Farruggia, Travis Gagie, Simon J. Puglisi, Jouni Sirén
RLZAP: Relative Lempel-Ziv with Adaptive Pointers. CoRR (2016)
Jouni Sirén
Burrows-Wheeler Transform for Terabases. DCC (2016)
Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
Relative Compressed Suffix Trees. CoRR (2015)
Christina Boucher, Alexander Bowe, Travis Gagie, Giovanni Manzini, Jouni Sirén
Relative Select. SPIRE (2015)
Jouni Sirén
Burrows-Wheeler transform for terabases. CoRR (2015)
Christina Boucher, Alexander Bowe, Travis Gagie, Giovanni Manzini, Jouni Sirén
Relative Select. CoRR (2015)
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)
Travis Gagie, Aleksi Hartikainen, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
Document Counting in Compressed Space. DCC (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)
Travis Gagie, Giovanni Manzini, Jouni Sirén
Reusing an FM-index. CoRR (2014)
Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
Document Retrieval on Repetitive Collections. ESA (2014)
Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
Document Retrieval on Repetitive Collections. CoRR (2014)
Travis Gagie, Aleksi Hartikainen, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
Document Counting in Practice. CoRR (2014)
Djamal Belazzougui, Travis Gagie, Simon Gog, Giovanni Manzini, Jouni Sirén
Relative FM-Indexes. SPIRE (2014)
Travis Gagie, Kalle Karhu, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
Document Listing on Repetitive Collections. CPM (2013)
Paolo Ferragina, Jouni Sirén, Rossano Venturini
Distribution-Aware Compressed Full-Text Indexes. Algorithmica 67 (4) (2013)
Paolo Ferragina, Jouni Sirén, Rossano Venturini
Distribution-Aware Compressed Full-Text Indexes. ESA (2011)
Jouni Sirén, Niko Välimäki, Veli Mäkinen
Indexing Finite Language Representation of Population Genotypes. WABI (2011)
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)
Jouni Sirén
Sampled Longest Common Prefix Array. CPM (2010)
Jouni Sirén
Sampled Longest Common Prefix Array CoRR (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)
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)
Jouni Sirén
Compressed Suffix Arrays for Massive Data. SPIRE (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)