Jouni Sirén

47 papers A* 1A 3B 6C 8Journal 25Unranked 3
YearRankTypeTitle / Venue / Authors
2025 — conf
Graph Indexing Beyond Wheeler Graphs.
The Expanding World of Compressed Data
Jarno N. Alanko, Elena Biagi, Massimo Equi, Veli Mäkinen, Simon J. Puglisi, Nicola Rizzo, Kunihiko Sadakane, Jouni Sirén
2025 C conf
Lossless Pangenome Indexing Using Tag Arrays.
WABI
Parsa Eskandar, Benedict Paten, Jouni Sirén
2024 — conf
Wheeler Maps.
LATIN (1)
Andrej Baláz, Travis Gagie, Adrián Goga, Simon Heumos, Gonzalo Navarro, Alessia Petescia, Jouni Sirén
2023 J jnl
Wheeler maps.
CoRR
Andrej Baláz, Travis Gagie, Adrián Goga, Simon Heumos, Gonzalo Navarro, Alessia Petescia, Jouni Sirén
2022 J jnl
Computational graph pangenomics: a tutorial on data structures and their applications.
Nat. Comput.
Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén
2022 J jnl
GBZ file format for pangenome graphs.
Bioinform.
Jouni Sirén, Benedict Paten
2021 B conf
Efficiently Merging r-indexes.
DCC
Marco Oliva, Massimiliano Rossi, Jouni Sirén, Giovanni Manzini, Tamer Kahveci, Travis Gagie, Christina Boucher
2020 J jnl
Distance indexing and seed clustering in sequence graphs.
Bioinform.
Xian Chang, Jordan Eizenga, Adam M. Novak, Jouni Sirén, Benedict Paten
2020 J jnl
Haplotype-aware graph indexes.
Bioinform.
Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin
2018 C conf
Haplotype-aware graph indexes.
WABI
Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin
2018 J jnl
Haplotype-aware graph indexes.
CoRR
Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin
2018 J jnl
Relative Suffix Trees.
Comput. J.
Andrea Farruggia, Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2017 J jnl
Document retrieval on repetitive string collections.
Inf. Retr. J.
Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2017 A conf
Indexing Variation Graphs.
ALENEX
Jouni Sirén
2017 J jnl
Wheeler graphs: A framework for BWT-based data structures.
Theor. Comput. Sci.
Travis Gagie, Giovanni Manzini, Jouni Sirén
2016 B conf
Burrows-Wheeler Transform for Terabases.
DCC
Jouni Sirén
2016 J jnl
Document Retrieval on Repetitive String Collections.
CoRR
Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2016 J jnl
Indexing Variation Graphs.
CoRR
Jouni Sirén
2016 C conf
RLZAP: Relative Lempel-Ziv with Adaptive Pointers.
SPIRE
Anthony J. Cox, Andrea Farruggia, Travis Gagie, Simon J. Puglisi, Jouni Sirén
2016 J jnl
RLZAP: Relative Lempel-Ziv with Adaptive Pointers.
CoRR
Anthony J. Cox, Andrea Farruggia, Travis Gagie, Simon J. Puglisi, Jouni Sirén
2015 J jnl
Burrows-Wheeler transform for terabases.
CoRR
Jouni Sirén
2015 B conf
Document Counting in Compressed Space.
DCC
Travis Gagie, Aleksi Hartikainen, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2015 J jnl
Fast in-memory XPath search using compressed indexes.
Softw. Pract. Exp.
Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki
2015 J jnl
Relative Compressed Suffix Trees.
CoRR
Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2015 C conf
Relative Select.
SPIRE
Christina Boucher, Alexander Bowe, Travis Gagie, Giovanni Manzini, Jouni Sirén
2015 J jnl
Relative Select.
CoRR
Christina Boucher, Alexander Bowe, Travis Gagie, Giovanni Manzini, Jouni Sirén
2014 J jnl
Document Counting in Practice.
CoRR
Travis Gagie, Aleksi Hartikainen, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2014 A conf
Document Retrieval on Repetitive Collections.
ESA
Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2014 J jnl
Document Retrieval on Repetitive Collections.
CoRR
Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2014 J jnl
Indexing Graphs for Path Queries with Applications in Genome Research.
IEEE ACM Trans. Comput. Biol. Bioinform.
Veli Mäkinen, Niko Välimäki, Jouni Sirén
2014 C conf
Relative FM-Indexes.
SPIRE
Djamal Belazzougui, Travis Gagie, Simon Gog, Giovanni Manzini, Jouni Sirén
2014 J jnl
Reusing an FM-index.
CoRR
Travis Gagie, Giovanni Manzini, Jouni Sirén
2013 J jnl
Distribution-Aware Compressed Full-Text Indexes.
Algorithmica
Paolo Ferragina, Jouni Sirén, Rossano Venturini
2013 B conf
Document Listing on Repetitive Collections.
CPM
Travis Gagie, Kalle Karhu, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2012 — —
Compressed Full-Text Indexes for Highly Repetitive Collections.
Jouni Sirén
2011 A conf
Distribution-Aware Compressed Full-Text Indexes.
ESA
Paolo Ferragina, Jouni Sirén, Rossano Venturini
2011 C conf
Indexing Finite Language Representation of Population Genotypes.
WABI
Jouni Sirén, Niko Välimäki, Veli Mäkinen
2010 A* conf
Fast in-memory XPath search using compressed indexes.
ICDE
Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki
2010 J jnl
Indexing Finite Language Representation of Population Genotypes
CoRR
Jouni Sirén, Niko Välimäki, Veli Mäkinen
2010 J jnl
Sampled Longest Common Prefix Array
CoRR
Jouni Sirén
2010 B conf
Sampled Longest Common Prefix Array.
CPM
Jouni Sirén
2010 J jnl
Storage and Retrieval of Highly Repetitive Sequence Collections.
J. Comput. Biol.
Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki
2009 C conf
Compressed Suffix Arrays for Massive Data.
SPIRE
Jouni Sirén
2009 J jnl
Fast In-Memory XPath Search over Compressed Text and Tree Indexes
CoRR
Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki
2009 B conf
Storage and Retrieval of Individual Genomes.
RECOMB
Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki
2008 C conf
Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections.
SPIRE
Jouni Sirén, Niko Välimäki, Veli Mäkinen, Gonzalo Navarro
2008 — conf
Storage and Retrieval of Individual Genomes.
Structure-Based Compression of Complex Massive Data
Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki