Jouni Sirén

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Benedict PatenProfessor; Associate Director, UC Santa Cruz Genomics Institute, University of California在 ucsc.edu 的電子郵件地址已通過驗證
Gonzalo NavarroUniversity of Chile在 dcc.uchile.cl 的電子郵件地址已通過驗證
Jordan M EizengaPostdoctoral Researcher, Genomics Institute, University of California Santa Cruz在 ucsc.edu 的電子郵件地址已通過驗證
Erik GarrisonAssociate Professor, University of Tennessee Health Science Center在 uthsc.edu 的電子郵件地址已通過驗證
Veli MäkinenProfessor of Computer Science, University of Helsinki在 helsinki.fi 的電子郵件地址已通過驗證
Niko VälimäkiPostdoctoral researcher, University of Helsinki在 cs.helsinki.fi 的電子郵件地址已通過驗證
Glenn HickeyArenaria Inc.在 arenaria.ca 的電子郵件地址已通過驗證
Travis GagieAssociate Professor at Dalhousie University在 dal.ca 的電子郵件地址已通過驗證
Xian ChangUC Santa Cruz Genomics Institute在 ucsc.edu 的電子郵件地址已通過驗證
Eric T. DawsonNVIDIA在 nvidia.com 的電子郵件地址已通過驗證
Richard DurbinDept of Genetics, University of Cambridge在 cam.ac.uk 的電子郵件地址已通過驗證
Jean MonlongINSERM IRSD, Toulouse, France在 inserm.fr 的電子郵件地址已通過驗證
Simon J. PuglisiProfessor, Department of Computer Science, University of Helsinki在 cs.helsinki.fi 的電子郵件地址已通過驗證
Shilpa GargTechnical University of Denmark在 biosustain.dtu.dk 的電子郵件地址已通過驗證
Andrew CarrollGoogle在 google.com 的電子郵件地址已通過驗證
Pi-Chuan ChangGoogle在 google.com 的電子郵件地址已通過驗證
Simon HeumosPhD Student @Quantitative Biology Center Tübingen在 qbic.uni-tuebingen.de 的電子郵件地址已通過驗證
Giovanni ManziniUniversity of Pisa在 unipi.it 的電子郵件地址已通過驗證
Michael F. Linindependent (mlin.net LLC)在 mlin.net 的電子郵件地址已通過驗證
David HausslerScientific Director, UC Santa Cruz Genomics Institute, University of California, Santa Cruz在 soe.ucsc.edu 的電子郵件地址已通過驗證

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Jouni Sirén

UC Santa Cruz Genomics Institute

在 ucsc.edu 的電子郵件地址已通過驗證 - 首頁

Algorithm engineering Bioinformatics Compressed data structures Data compression String algorithms


標題按引用次數排序按年份排序按標題排序	引用次數引用次數	年份
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	628	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	526	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	308	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	252	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	227*	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	224	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	218	2020
Wheeler graphs: A framework for BWT-based data structures T Gagie, G Manzini, J Sirén Theoretical computer science 698, 67-78, 2017	113	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	96	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	45	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	35	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	27	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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