Jouni Sirén

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Gonzalo NavarroUniversity of ChileVerified email at dcc.uchile.cl
Benedict PatenAssociate Professor; Associate Director, UC Santa Cruz Genomics Institute, University of CaliforniaVerified email at ucsc.edu
Veli MäkinenProfessor of Computer Science, University of HelsinkiVerified email at helsinki.fi
Niko VälimäkiPostdoctoral researcher, University of HelsinkiVerified email at cs.helsinki.fi
Erik GarrisonUniversity of Tennessee Health Science CenterVerified email at uthsc.edu
Jordan M EizengaPostdoctoral Researcher, Genomics Institute, University of California Santa CruzVerified email at ucsc.edu
Travis GagieAssociate Professor at Dalhousie UniversityVerified email at dal.ca
Glenn HickeyArenaria Inc.Verified email at arenaria.ca
Jonas Andreas SibbesenCenter for Health Data Science, University of CopenhagenVerified email at sund.ku.dk
Eric T. DawsonNVIDIAVerified email at nvidia.com
Simon J. PuglisiAssociate Professor, Department of Computer Science, University of HelsinkiVerified email at cs.helsinki.fi
Richard DurbinDept of Genetics, University of CambridgeVerified email at cam.ac.uk
Xian ChangUC Santa Cruz Genomics InstituteVerified email at ucsc.edu
Shilpa GargUniversity of CopenhagenVerified email at bio.ku.dk
William JonesUniversity of South DakotaVerified email at usd.edu
Giovanni ManziniUniversity of PisaVerified email at unipi.it
Jean MonlongUC Santa Cruz Genomics Institute, University of California, Santa CruzVerified email at mail.mcgill.ca
Michael F. Linindependent (mlin.net LLC)Verified email at mlin.net
Juha KärkkäinenDepartment of Computer scienceVerified email at cs.helsinki.fi
Andrew CarrollGoogleVerified email at google.com

Jouni Sirén

UC Santa Cruz Genomics Institute

Verified email at ucsc.edu - Homepage

Algorithm engineering Bioinformatics Compressed data structures Data compression String algorithms


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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	358	2018
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	216	2010
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	211	2014
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	100	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	90	2008
Indexing variation graphs J Sirén 2017 Proceedings of the ninteenth workshop on algorithm engineering and …, 2017	82	2017
Wheeler graphs: A framework for BWT-based data structures T Gagie, G Manzini, J Sirén Theoretical computer science 698, 67-78, 2017	79	2017
Pangenome graphs JM Eizenga, AM Novak, JA Sibbesen, S Heumos, A Ghaffaari, G Hickey, ... Annual review of genomics and human genetics 21, 139, 2020	67	2020
Storage and retrieval of individual genomes V Mäkinen, G Navarro, J Sirén, N Välimäki Annual International Conference on Research in Computational Molecular …, 2009	63	2009
Compressed suffix arrays for massive data J Sirén International Symposium on String Processing and Information Retrieval, 63-74, 2009	57	2009
Haplotype-aware graph indexes J Sirén, E Garrison, AM Novak, B Paten, R Durbin arXiv preprint arXiv:1805.03834, 2018	56	2018
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	55	2015
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	41*	2021
Sampled longest common prefix array J Sirén Annual Symposium on Combinatorial Pattern Matching, 227-237, 2010	29	2010
Indexing finite language representation of population genotypes J Sirén, N Välimäki, V Mäkinen Algorithms in Bioinformatics, 270-281, 2011	27	2011
Burrows-Wheeler transform for terabases J Sirén 2016 Data Compression Conference (DCC), 211-220, 2016	23	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	23	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	20	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	19	2014
Compressed full-text indexes for highly repetitive collections J Sirén Helsingin yliopisto, 2012	19	2012

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