Jouni Sirén

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Gonzalo NavarroUniversity of ChileVerified email at dcc.uchile.cl
Veli MäkinenProfessor of Computer Science, University of HelsinkiVerified email at helsinki.fi
Niko VälimäkiPostdoctoral researcher, University of HelsinkiVerified email at cs.helsinki.fi
Travis GagieAssociate Professor at Dalhousie UniversityVerified email at dal.ca
Benedict PatenAssociate Professor; Associate Director, UC Santa Cruz Genomics Institute, University of CaliforniaVerified email at ucsc.edu
Jordan M EizengaPhD Student in Bioinformatics, University of California Santa Cruz Genomics InstituteVerified email at ucsc.edu
Erik GarrisonUniversity of Tennessee Health Science CenterVerified email at uthsc.edu
Glenn HickeyArenaria Inc.Verified email at arenaria.ca
Simon J. PuglisiAssociate Professor, Department of Computer Science, University of HelsinkiVerified email at cs.helsinki.fi
Eric T. DawsonNVIDIAVerified email at nvidia.com
Richard DurbinDept of Genetics, University of CambridgeVerified email at cam.ac.uk
William JonesUniversity of South DakotaVerified email at usd.edu
Giovanni ManziniUniversity of PisaVerified email at unipi.it
Shilpa GargUniversity of CopenhagenVerified email at bio.ku.dk
Michael F. Linindependent (mlin.net LLC)Verified email at mlin.net
Sebastian ManethProfessor für Informatik, Universität BremenVerified email at uni-bremen.de
Diego ArroyueloDepartamento de Informática, Universidad Técnica Federico Santa MaríaVerified email at inf.utfsm.cl
Kim NguyenAssistant Professor of Computer Science, Université Paris-Sud, FranceVerified email at lri.fr
Francisco ClaudeLinkedInVerified email at recoded.cl
Juha KärkkäinenDepartment of Computer scienceVerified email at cs.helsinki.fi

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	211	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	187	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	144	2014
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	84	2008
Indexing variation graphs J Sirén 2017 Proceedings of the ninteenth workshop on algorithm engineering and …, 2017	65	2017
Storage and retrieval of individual genomes V Mäkinen, G Navarro, J Sirén, N Välimäki Annual International Conference on Research in Computational Molecular …, 2009	59	2009
Compressed suffix arrays for massive data J Sirén International Symposium on String Processing and Information Retrieval, 63-74, 2009	55	2009
Wheeler graphs: A framework for BWT-based data structures T Gagie, G Manzini, J Sirén Theoretical computer science 698, 67-78, 2017	52	2017
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	34	2020
Haplotype-aware graph indexes J Sirén, E Garrison, AM Novak, B Paten, R Durbin arXiv preprint arXiv:1805.03834, 2018	34	2018
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	34	2010
Indexing finite language representation of population genotypes J Sirén, N Välimäki, V Mäkinen Algorithms in Bioinformatics, 270-281, 2011	24	2011
Document listing on repetitive collections T Gagie, K Karhu, G Navarro, SJ Puglisi, J Sirén Annual Symposium on Combinatorial Pattern Matching, 107-119, 2013	22	2013
Sampled longest common prefix array J Sirén Annual Symposium on Combinatorial Pattern Matching, 227-237, 2010	22	2010
Burrows-Wheeler transform for terabases J Sirén 2016 Data Compression Conference (DCC), 211-220, 2016	21	2016
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	20	2015
Compressed full-text indexes for highly repetitive collections J Sirén Helsingin yliopisto, 2012	19	2012
Relative FM-indexes D Belazzougui, T Gagie, S Gog, G Manzini, J Sirén International Symposium on String Processing and Information Retrieval, 52-64, 2014	18	2014
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	16	2017
Distribution-aware compressed full-text indexes P Ferragina, J Sirén, R Venturini Algorithmica 67 (4), 529-546, 2013	16	2013

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