Jouni Sirén
TitleCited byYear
Storage and retrieval of highly repetitive sequence collections
V Mäkinen, G Navarro, J Sirén, N Välimäki
Journal of Computational Biology 17 (3), 281-308, 2010
1672010
Indexing graphs for path queries with applications in genome research
J Sirén, N Välimäki, V Mäkinen
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) 11 …, 2014
1022014
Variation graph toolkit improves read mapping by representing genetic variation in the reference
E Garrison, J Sirén, AM Novak, G Hickey, JM Eizenga, ET Dawson, ...
Nature biotechnology, 2018
97*2018
Run-length compressed indexes are superior for highly repetitive sequence collections
J Sirén, N Välimäki, V Mäkinen, G Navarro
String Processing and Information Retrieval, 164-175, 2008
812008
Storage and retrieval of individual genomes
V Mäkinen, G Navarro, J Sirén, N Välimäki
Annual International Conference on Research in Computational Molecular …, 2009
592009
Compressed suffix arrays for massive data
J Sirén
International Symposium on String Processing and Information Retrieval, 63-74, 2009
512009
Indexing variation graphs
J Sirén
2017 Proceedings of the ninteenth workshop on algorithm engineering and …, 2017
482017
Fast in-memory XPath search using compressed indexes
D Arroyuelo, F Claude, S Maneth, V Mäkinen, G Navarro, K Nguyên, ...
2010 IEEE 26th International Conference on Data Engineering (ICDE 2010), 417-428, 2010
322010
Wheeler graphs: A framework for BWT-based data structures
T Gagie, G Manzini, J Sirén
Theoretical computer science 698, 67-78, 2017
272017
Document listing on repetitive collections
T Gagie, K Karhu, G Navarro, SJ Puglisi, J Sirén
Annual Symposium on Combinatorial Pattern Matching, 107-119, 2013
212013
Sampled longest common prefix array
J Sirén
Annual Symposium on Combinatorial Pattern Matching, 227-237, 2010
212010
Compressed full-text indexes for highly repetitive collections
J Sirén
Helsingin yliopisto, 2012
192012
Burrows-Wheeler transform for terabases
J Sirén
2016 Data Compression Conference (DCC), 211-220, 2016
182016
Indexing finite language representation of population genotypes
J Sirén, N Välimäki, V Mäkinen
Algorithms in Bioinformatics, 270-281, 2011
182011
Fast in‐memory XPath search using compressed indexes
D Arroyuelo, F Claude, S Maneth, V Mäkinen, G Navarro, K Nguyễn, ...
Software: Practice and Experience 45 (3), 399-434, 2015
162015
Relative FM-indexes
D Belazzougui, T Gagie, S Gog, G Manzini, J Sirén
International Symposium on String Processing and Information Retrieval, 52-64, 2014
152014
Distribution-aware compressed full-text indexes
P Ferragina, J Sirén, R Venturini
Algorithmica 67 (4), 529-546, 2013
122013
Document retrieval on repetitive collections
G Navarro, SJ Puglisi, J Sirén
European Symposium on Algorithms, 725-736, 2014
112014
Relative suffix trees
A Farruggia, T Gagie, G Navarro, SJ Puglisi, J Sirén
The computer journal 61 (5), 773-788, 2017
10*2017
Haplotype-aware graph indexes
J Sirén, E Garrison, AM Novak, B Paten, R Durbin
arXiv preprint arXiv:1805.03834, 2018
82018
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Articles 1–20