Jouni Sirén

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Benedict PatenProfessor; Associate Director, UC Santa Cruz Genomics Institute, University of California確認したメールアドレス: ucsc.edu
Jordan M EizengaPostdoctoral Researcher, Genomics Institute, University of California Santa Cruz確認したメールアドレス: ucsc.edu
Gonzalo NavarroUniversity of Chile確認したメールアドレス: dcc.uchile.cl
Erik GarrisonAssociate Professor, University of Tennessee Health Science Center確認したメールアドレス: uthsc.edu
Veli MäkinenProfessor of Computer Science, University of Helsinki確認したメールアドレス: helsinki.fi
Niko VälimäkiPostdoctoral researcher, University of Helsinki確認したメールアドレス: cs.helsinki.fi
Glenn HickeyArenaria Inc.確認したメールアドレス: arenaria.ca
Travis GagieAssociate Professor at Dalhousie University確認したメールアドレス: dal.ca
Xian ChangUC Santa Cruz Genomics Institute確認したメールアドレス: ucsc.edu
Eric T. DawsonNVIDIA確認したメールアドレス: nvidia.com
Jean MonlongINSERM IRSD, Toulouse, France確認したメールアドレス: inserm.fr
Richard DurbinDept of Genetics, University of Cambridge確認したメールアドレス: cam.ac.uk
Shilpa GargUniversity of Manchester確認したメールアドレス: manchester.ac.uk
Simon J. PuglisiProfessor, Department of Computer Science, University of Helsinki確認したメールアドレス: cs.helsinki.fi
Andrew CarrollGoogle確認したメールアドレス: google.com
Pi-Chuan ChangGoogle確認したメールアドレス: google.com
Simon HeumosPhD Student @Quantitative Biology Center Tübingen確認したメールアドレス: qbic.uni-tuebingen.de
Giovanni ManziniUniversity of Pisa確認したメールアドレス: unipi.it
Michael F. Linindependent (mlin.net LLC)確認したメールアドレス: mlin.net
David HausslerScientific Director, UC Santa Cruz Genomics Institute, University of California, Santa Cruz確認したメールアドレス: soe.ucsc.edu

フォロー

Jouni Sirén

UC Santa Cruz Genomics Institute

確認したメールアドレス: ucsc.edu - ホームページ

Algorithm engineering Bioinformatics Compressed data structures Data compression String algorithms


タイトル引用回数順公開年順タイトル順	引用先引用先	年
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	665	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	613	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	256*	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	232	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	54	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	42	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	29	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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