Jouni Sirén
Jouni Sirén
UC Santa Cruz Genomics Institute
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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 36 (9), 875-879, 2018
Indexing graphs for path queries with applications in genome research
J Sirén, N Välimäki, V Mäkinen
IEEE/ACM Transactions on Computational Biology and Bioinformatics 11 (2 …, 2014
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
Genotyping structural variants in pangenome graphs using the vg toolkit
G Hickey, D Heller, J Monlong, JA Sibbesen, J Sirén, J Eizenga, ...
Genome biology 21 (1), 1-17, 2020
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
Pangenome graphs
JM Eizenga, AM Novak, JA Sibbesen, S Heumos, A Ghaffaari, G Hickey, ...
Annual review of genomics and human genetics 21, 139, 2020
Indexing variation graphs
J Sirén
2017 Proceedings of the ninteenth workshop on algorithm engineering and …, 2017
Wheeler graphs: A framework for BWT-based data structures
T Gagie, G Manzini, J Sirén
Theoretical computer science 698, 67-78, 2017
Storage and retrieval of individual genomes
V Mäkinen, G Navarro, J Sirén, N Välimäki
Annual International Conference on Research in Computational Molecular …, 2009
Haplotype-aware graph indexes
J Sirén, E Garrison, AM Novak, B Paten, R Durbin
arXiv preprint arXiv:1805.03834, 2018
Pangenomics enables genotyping of known structural variants in 5202 diverse genomes
J Sirén, J Monlong, X Chang, AM Novak, JM Eizenga, C Markello, ...
Science 374 (6574), abg8871, 2021
Compressed suffix arrays for massive data
J Sirén
International Symposium on String Processing and Information Retrieval, 63-74, 2009
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
Sampled longest common prefix array
J Sirén
Annual Symposium on Combinatorial Pattern Matching, 227-237, 2010
Indexing finite language representation of population genotypes
J Sirén, N Välimäki, V Mäkinen
Algorithms in Bioinformatics, 270-281, 2011
Burrows-Wheeler transform for terabases
J Sirén
2016 Data Compression Conference (DCC), 211-220, 2016
Document listing on repetitive collections
T Gagie, K Karhu, G Navarro, SJ Puglisi, J Sirén
Annual Symposium on Combinatorial Pattern Matching, 107-119, 2013
Document retrieval on repetitive string collections
T Gagie, A Hartikainen, K Karhu, J Kärkkäinen, G Navarro, SJ Puglisi, ...
Information Retrieval Journal 20 (3), 253-291, 2017
Relative FM-indexes
D Belazzougui, T Gagie, S Gog, G Manzini, J Sirén
International Symposium on String Processing and Information Retrieval, 52-64, 2014
Compressed full-text indexes for highly repetitive collections
J Sirén
Helsingin yliopisto, 2012
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Artículos 1–20