Jouni Sirén
Jouni Sirén
UC Santa Cruz Genomics Institute
Verified email at - Homepage
Cited by
Cited by
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
A draft human pangenome reference
WW Liao, M Asri, J Ebler, D Doerr, M Haukness, G Hickey, S Lu, JK Lucas, ...
Nature 617 (7960), 312-324, 2023
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
Pangenome graphs
JM Eizenga, AM Novak, JA Sibbesen, S Heumos, A Ghaffaari, G Hickey, ...
Annual review of genomics and human genetics 21, 139-162, 2020
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
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, 1-17, 2020
Wheeler graphs: A framework for BWT-based data structures
T Gagie, G Manzini, J Sirén
Theoretical computer science 698, 67-78, 2017
Indexing variation graphs
J Sirén
2017 Proceedings of the ninteenth workshop on algorithm engineering and …, 2017
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
Haplotype-aware graph indexes
J Sirén, E Garrison, AM Novak, B Paten, R Durbin
arXiv preprint arXiv:1805.03834, 2018
Compressed suffix arrays for massive data
J Sirén
International Symposium on String Processing and Information Retrieval, 63-74, 2009
Storage and retrieval of individual genomes
V Mäkinen, G Navarro, J Sirén, N Välimäki
Research in Computational Molecular Biology: 13th Annual International …, 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
Computational graph pangenomics: a tutorial on data structures and their applications
JA Baaijens, P Bonizzoni, C Boucher, G Della Vedova, Y Pirola, R Rizzi, ...
Natural Computing 21 (1), 81-108, 2022
Sampled longest common prefix array
J Sirén
Annual Symposium on Combinatorial Pattern Matching, 227-237, 2010
Haplotype-aware pantranscriptome analyses using spliced pangenome graphs
JA Sibbesen, JM Eizenga, AM Novak, J Sirén, X Chang, E Garrison, ...
Nature Methods 20 (2), 239-247, 2023
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
Combinatorial Pattern Matching: 24th Annual Symposium, CPM 2013, Bad …, 2013
Indexing finite language representation of population genotypes
J Sirén, N Välimäki, V Mäkinen
Algorithms in Bioinformatics, 270-281, 2011
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