Jouni Sirén

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Benedict PatenProfessor; Associate Director, UC Santa Cruz Genomics Institute, University of CaliforniaVerified email at ucsc.edu
Gonzalo NavarroUniversity of ChileVerified email at dcc.uchile.cl
Jordan M EizengaPostdoctoral Researcher, Genomics Institute, University of California Santa CruzVerified email at ucsc.edu
Erik GarrisonAssociate Professor, University of Tennessee Health Science CenterVerified email at uthsc.edu
Veli MäkinenProfessor of Computer Science, University of HelsinkiVerified email at helsinki.fi
Niko VälimäkiPostdoctoral researcher, University of HelsinkiVerified email at cs.helsinki.fi
Glenn HickeyArenaria Inc.Verified email at arenaria.ca
Travis GagieAssociate Professor at Dalhousie UniversityVerified email at dal.ca
Xian ChangUC Santa Cruz Genomics InstituteVerified email at ucsc.edu
Eric T. DawsonNVIDIAVerified email at nvidia.com
Richard DurbinDept of Genetics, University of CambridgeVerified email at cam.ac.uk
Jean MonlongINSERM IRSD, Toulouse, FranceVerified email at inserm.fr
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
Giovanni ManziniUniversity of PisaVerified email at unipi.it
Simon HeumosPhD Student @Quantitative Biology Center TübingenVerified email at qbic.uni-tuebingen.de
Andrew CarrollGoogleVerified email at google.com
Pi-Chuan ChangGoogleVerified email at google.com
Michael F. Linindependent (mlin.net LLC)Verified email at mlin.net
David HausslerScientific Director, UC Santa Cruz Genomics Institute, University of California, Santa CruzVerified email at soe.ucsc.edu

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	603	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	463	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	307	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	248	2010
Pangenome graphs JM Eizenga, AM Novak, JA Sibbesen, S Heumos, A Ghaffaari, G Hickey, ... Annual review of genomics and human genetics 21 (1), 139-162, 2020	209	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	206*	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	200	2020
Wheeler graphs: A framework for BWT-based data structures T Gagie, G Manzini, J Sirén Theoretical computer science 698, 67-78, 2017	110	2017
Indexing variation graphs J Sirén 2017 Proceedings of the ninteenth workshop on algorithm engineering and …, 2017	106	2017
Haplotype-aware graph indexes J Sirén, E Garrison, AM Novak, B Paten, R Durbin arXiv preprint arXiv:1805.03834, 2018	94	2018
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	91	2008
Compressed suffix arrays for massive data J Sirén International Symposium on String Processing and Information Retrieval, 63-74, 2009	66	2009
Storage and retrieval of individual genomes V Mäkinen, G Navarro, J Sirén, N Välimäki Research in Computational Molecular Biology: 13th Annual International …, 2009	63	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	56	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	37	2022
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	33	2023
Burrows-Wheeler transform for terabases J Sirén 2016 Data Compression Conference (DCC), 211-220, 2016	26	2016
Gaps and complex structurally variant loci in phased genome assemblies D Porubsky, MR Vollger, WT Harvey, AN Rozanski, P Ebert, G Hickey, ... Genome research 33 (4), 496-510, 2023	25	2023
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	25	2013
Indexing finite language representation of population genotypes J Sirén, N Välimäki, V Mäkinen Algorithms in Bioinformatics, 270-281, 2011	25	2011

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