Jouni Sirén

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Benedict PatenAssociate Professor; Associate Director, UC Santa Cruz Genomics Institute, University of CaliforniaVerified email at ucsc.edu
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
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
Glenn HickeyArenaria Inc.Verified email at arenaria.ca
Travis GagieAssociate Professor at Dalhousie UniversityVerified email at dal.ca
Eric T. DawsonNVIDIAVerified email at nvidia.com
Xian ChangUC Santa Cruz Genomics InstituteVerified email at ucsc.edu
Richard DurbinDept of Genetics, University of CambridgeVerified email at cam.ac.uk
Simon J. PuglisiProfessor, Department of Computer Science, University of HelsinkiVerified email at cs.helsinki.fi
Shilpa GargTechnical University of DenmarkVerified email at biosustain.dtu.dk
Jean MonlongUC Santa Cruz Genomics Institute, University of California, Santa CruzVerified email at mail.mcgill.ca
Giovanni ManziniUniversity of PisaVerified email at unipi.it
Michael F. Linindependent (mlin.net LLC)Verified email at mlin.net
Andrew CarrollGoogleVerified email at google.com
Pi-Chuan ChangGoogleVerified email at google.com
David HausslerScientific Director, UC Santa Cruz Genomics Institute, University of California, Santa CruzVerified email at soe.ucsc.edu
David HellerPhD Student, Max Planck Institute for Molecular GeneticsVerified email at molgen.mpg.de

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	437	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	250	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	228	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, 1-17, 2020	134	2020
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	114	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	94*	2021
Wheeler graphs: A framework for BWT-based data structures T Gagie, G Manzini, J Sirén Theoretical computer science 698, 67-78, 2017	90	2017
Indexing variation graphs J Sirén 2017 Proceedings of the ninteenth workshop on algorithm engineering and …, 2017	89	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	89	2008
Haplotype-aware graph indexes J Sirén, E Garrison, AM Novak, B Paten, R Durbin arXiv preprint arXiv:1805.03834, 2018	69	2018
Storage and retrieval of individual genomes V Mäkinen, G Navarro, J Sirén, N Välimäki Research in Computational Molecular Biology: 13th Annual International …, 2009	62	2009
Compressed suffix arrays for massive data J Sirén String Processing and Information Retrieval: 16th International Symposium …, 2009	61	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	55	2015
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	36	2023
Sampled longest common prefix array J Sirén Combinatorial Pattern Matching: 21st Annual Symposium, CPM 2010, New York …, 2010	29	2010
Indexing finite language representation of population genotypes J Sirén, N Välimäki, V Mäkinen Algorithms in Bioinformatics, 270-281, 2011	26	2011
Burrows-Wheeler transform for terabases J Sirén 2016 Data Compression Conference (DCC), 211-220, 2016	24	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	24	2013
Document retrieval on repetitive string collections T Gagie, A Hartikainen, K Karhu, J Kärkkäinen, G Navarro, SJ Puglisi, ... Information Retrieval Journal 20, 253-291, 2017	20	2017
Relative FM-indexes D Belazzougui, T Gagie, S Gog, G Manzini, J Sirén String Processing and Information Retrieval: 21st International Symposium …, 2014	20	2014

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