Jouni Sirén

According to our database, Jouni Sirén authored at least 31 papers between 2008 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2024

Wheeler Maps.

Andrej Baláz, Travis Gagie, Adrián Goga, Simon Heumos, Gonzalo Navarro, Alessia Petescia, Jouni Sirén

Proceedings of the LATIN 2024: Theoretical Informatics, 2024

2022

GBZ file format for pangenome graphs.

Jouni Sirén, Benedict Paten

Bioinform., November, 2022

Computational graph pangenomics: a tutorial on data structures and their applications.

Jasmijn A. Baaijens, Paola Bonizzoni, Christina Boucher, Gianluca Della Vedova, Yuri Pirola, Raffaella Rizzi, Jouni Sirén

Nat. Comput., 2022

2021

Efficiently Merging r-indexes.

Marco Oliva, Massimiliano Rossi, Jouni Sirén, Giovanni Manzini, Tamer Kahveci, Travis Gagie, Christina Boucher

Proceedings of the 31st Data Compression Conference, 2021

2020

Haplotype-aware graph indexes.

Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict Paten, Richard Durbin

Bioinform., 2020

Distance indexing and seed clustering in sequence graphs.

Xian Chang, Jordan Eizenga, Adam M. Novak, Jouni Sirén, Benedict Paten

Bioinform., 2020

2018

Relative Suffix Trees.

Andrea Farruggia, Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén

Comput. J., 2018

2017

Wheeler graphs: A framework for BWT-based data structures.

Travis Gagie, Giovanni Manzini, Jouni Sirén

Theor. Comput. Sci., 2017

Document retrieval on repetitive string collections.

Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén

Inf. Retr. J., 2017

Indexing Variation Graphs.

Jouni Sirén

Proceedings of the Ninteenth Workshop on Algorithm Engineering and Experiments, 2017

2016

RLZAP: Relative Lempel-Ziv with Adaptive Pointers.

Anthony J. Cox, Andrea Farruggia, Travis Gagie, Simon J. Puglisi, Jouni Sirén

Proceedings of the String Processing and Information Retrieval, 2016

Burrows-Wheeler Transform for Terabases.

Jouni Sirén

Proceedings of the 2016 Data Compression Conference, 2016

2015

Fast in-memory XPath search using compressed indexes.

Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki

Softw. Pract. Exp., 2015

Relative Compressed Suffix Trees.

Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén

CoRR, 2015

Relative Select.

Christina Boucher, Alexander Bowe, Travis Gagie, Giovanni Manzini, Jouni Sirén

Proceedings of the String Processing and Information Retrieval, 2015

Document Counting in Compressed Space.

Travis Gagie, Aleksi Hartikainen, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén

Proceedings of the 2015 Data Compression Conference, 2015

2014

Indexing Graphs for Path Queries with Applications in Genome Research.

Veli Mäkinen, Niko Välimäki, Jouni Sirén

IEEE ACM Trans. Comput. Biol. Bioinform., 2014

Reusing an FM-index.

Travis Gagie, Giovanni Manzini, Jouni Sirén

CoRR, 2014

Document Counting in Practice.

Travis Gagie, Aleksi Hartikainen, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén

CoRR, 2014

Relative FM-Indexes.

Djamal Belazzougui, Travis Gagie, Simon Gog, Giovanni Manzini, Jouni Sirén

Proceedings of the String Processing and Information Retrieval, 2014

Document Retrieval on Repetitive Collections.

Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén

Proceedings of the Algorithms - ESA 2014, 2014

2013

Distribution-Aware Compressed Full-Text Indexes.

Paolo Ferragina, Jouni Sirén, Rossano Venturini

Algorithmica, 2013

Document Listing on Repetitive Collections.

Travis Gagie, Kalle Karhu, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén

Proceedings of the Combinatorial Pattern Matching, 24th Annual Symposium, 2013

2012

Compressed Full-Text Indexes for Highly Repetitive Collections.

Jouni Sirén

PhD thesis, 2012

2011

Indexing Finite Language Representation of Population Genotypes.

Jouni Sirén, Niko Välimäki, Veli Mäkinen

Proceedings of the Algorithms in Bioinformatics - 11th International Workshop, 2011

2010

Storage and Retrieval of Highly Repetitive Sequence Collections.

Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki

J. Comput. Biol., 2010

Sampled Longest Common Prefix Array.

Jouni Sirén

Proceedings of the Combinatorial Pattern Matching, 21st Annual Symposium, 2010

2009

Fast In-Memory XPath Search over Compressed Text and Tree Indexes

Diego Arroyuelo, Francisco Claude, Sebastian Maneth, Veli Mäkinen, Gonzalo Navarro, Kim Nguyen, Jouni Sirén, Niko Välimäki

CoRR, 2009

Compressed Suffix Arrays for Massive Data.

Jouni Sirén

Proceedings of the String Processing and Information Retrieval, 2009

Storage and Retrieval of Individual Genomes.

Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, Niko Välimäki

Proceedings of the Research in Computational Molecular Biology, 2009

2008

Run-Length Compressed Indexes Are Superior for Highly Repetitive Sequence Collections.

Jouni Sirén, Niko Välimäki, Veli Mäkinen, Gonzalo Navarro

Proceedings of the String Processing and Information Retrieval, 2008