Jouni Sirén

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Benedict PatenProfessor; Associate Director, UC Santa Cruz Genomics Institute, University of CaliforniaCorreu electrònic verificat a ucsc.edu
Jordan M EizengaPostdoctoral Researcher, Genomics Institute, University of California Santa CruzCorreu electrònic verificat a ucsc.edu
Gonzalo NavarroUniversity of ChileCorreu electrònic verificat a dcc.uchile.cl
Erik GarrisonAssociate Professor, University of Tennessee Health Science CenterCorreu electrònic verificat a uthsc.edu
Veli MäkinenProfessor of Computer Science, University of HelsinkiCorreu electrònic verificat a helsinki.fi
Niko VälimäkiPostdoctoral researcher, University of HelsinkiCorreu electrònic verificat a cs.helsinki.fi
Glenn HickeyArenaria Inc.Correu electrònic verificat a arenaria.ca
Travis GagieAssociate Professor at Dalhousie UniversityCorreu electrònic verificat a dal.ca
Xian ChangUC Santa Cruz Genomics InstituteCorreu electrònic verificat a ucsc.edu
Eric T. DawsonNVIDIACorreu electrònic verificat a nvidia.com
Jean MonlongINSERM IRSD, Toulouse, FranceCorreu electrònic verificat a inserm.fr
Richard DurbinDept of Genetics, University of CambridgeCorreu electrònic verificat a cam.ac.uk
Simon J. PuglisiProfessor, Department of Computer Science, University of HelsinkiCorreu electrònic verificat a cs.helsinki.fi
Shilpa GargUniversity of ManchesterCorreu electrònic verificat a manchester.ac.uk
Andrew CarrollGoogleCorreu electrònic verificat a google.com
Pi-Chuan ChangGoogleCorreu electrònic verificat a google.com
Simon HeumosPhD Student @Quantitative Biology Center TübingenCorreu electrònic verificat a qbic.uni-tuebingen.de
Giovanni ManziniUniversity of PisaCorreu electrònic verificat a unipi.it
Michael F. Linindependent (mlin.net LLC)Correu electrònic verificat a mlin.net
David HausslerScientific Director, UC Santa Cruz Genomics Institute, University of California, Santa CruzCorreu electrònic verificat a soe.ucsc.edu

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Jouni Sirén

UC Santa Cruz Genomics Institute

Correu electrònic verificat a ucsc.edu - Pàgina d'inici

Algorithm engineering Bioinformatics Compressed data structures Data compression String algorithms


Títol Ordena per cites Ordena per any Ordena per títol	Citada per Citada per	Any
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	667	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	617	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	319	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	259	2010
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	257*	2021
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	250	2020
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	233	2020
Wheeler graphs: A framework for BWT-based data structures T Gagie, G Manzini, J Sirén Theoretical computer science 698, 67-78, 2017	116	2017
Indexing variation graphs J Sirén 2017 Proceedings of the ninteenth workshop on algorithm engineering and …, 2017	110	2017
Haplotype-aware graph indexes J Sirén, E Garrison, AM Novak, B Paten, R Durbin arXiv preprint arXiv:1805.03834, 2018	105	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	93	2008
Compressed suffix arrays for massive data J Sirén International Symposium on String Processing and Information Retrieval, 63-74, 2009	65	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	55	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	43	2023
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	30	2023
Burrows-Wheeler transform for terabases J Sirén 2016 Data Compression Conference (DCC), 211-220, 2016	26	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	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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