Simon J. Puglisi

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Travis GagieAssociate Professor at Dalhousie UniversityVerified email at dal.ca
Juha KärkkäinenDepartment of Computer scienceVerified email at cs.helsinki.fi
Andrew TurpinLions Eye Institute and Curtin UniversityVerified email at curtin.edu.au
Gonzalo NavarroUniversity of ChileVerified email at dcc.uchile.cl
Dominik KempaAssistant Professor, Stony Brook UniversityVerified email at cs.stonybrook.edu
W F SmythProfessor Emeritus, Computer Science, McMaster UniversityVerified email at mcmaster.ca
Christina BoucherUniversity of FloridaVerified email at ufl.edu
Paweł GawrychowskiUniversity of WrocławVerified email at cs.uni.wroc.pl
Justin ZobelComputing and Information Systems, University of MelbourneVerified email at unimelb.edu.au
Ranjan Sinha, Ph.D.IBM Fellow, VP & CTO at IBMVerified email at us.ibm.com
Jouni SirénUC Santa Cruz Genomics InstituteVerified email at ucsc.edu
Golnaz BadkobehGoldsmiths, University of LondonVerified email at gold.ac.uk
Yasuo TabeiUnit leader at RIKEN-AIPVerified email at riken.go.jp
Yakov NekrichAssociate Professor, Michigan Technological UniveristyVerified email at uwaterloo.ca
Daniel ValenzuelaResearch Scientist, Varian Medical SystemsVerified email at varian.com
Hideo BannaiProfessor, M&D Data Science Center, Tokyo Medical and Dental University, JapanVerified email at tmd.ac.jp
Bertil SchmidtProfessor of Computer Science, University of MainzVerified email at uni-mainz.de
Héctor FerradaUniversidad de ChileVerified email at dcc.uchile.cl
Veli MäkinenProfessor of Computer Science, University of HelsinkiVerified email at helsinki.fi
J. Shane CulpepperRMIT University, School of Computing TechnologiesVerified email at rmit.edu.au

Simon J. Puglisi

Professor, Department of Computer Science, University of Helsinki

Verified email at cs.helsinki.fi - Homepage

Algorithms Data Structures Pattern Matching Data Compression #UnivHelsinkiCS


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A taxonomy of suffix array construction algorithms SJ Puglisi, WF Smyth, AH Turpin acm Computing Surveys (CSUR) 39 (2), 4-es, 2007	405	2007
SHREC: a short-read error correction method J Schröder, H Schröder, SJ Puglisi, R Sinha, B Schmidt Bioinformatics 25 (17), 2157-2163, 2009	210	2009
Relative Lempel-Ziv compression of genomes for large-scale storage and retrieval S Kuruppu, SJ Puglisi, J Zobel String Processing and Information Retrieval: 17th International Symposium …, 2010	180	2010
Permuted longest-common-prefix array J Kärkkäinen, G Manzini, SJ Puglisi Combinatorial Pattern Matching: 20th Annual Symposium, CPM 2009 Lille …, 2009	142	2009
Order-preserving matching J Kim, P Eades, R Fleischer, SH Hong, CS Iliopoulos, K Park, SJ Puglisi, ... Theoretical Computer Science 525, 68-79, 2014	140	2014
New algorithms on wavelet trees and applications to information retrieval T Gagie, G Navarro, SJ Puglisi Theoretical Computer Science 426, 25-41, 2012	125	2012
Succinct colored de Bruijn graphs MD Muggli, A Bowe, NR Noyes, PS Morley, KE Belk, R Raymond, T Gagie, ... Bioinformatics 33 (20), 3181-3187, 2017	113	2017
A faster grammar-based self-index T Gagie, P Gawrychowski, J Kärkkäinen, Y Nekrich, SJ Puglisi Language and Automata Theory and Applications: 6th International Conference …, 2012	108	2012
Optimized relative Lempel-Ziv compression of genomes S Kuruppu, SJ Puglisi, J Zobel Proceedings of the Thirty-Fourth Australasian Computer Science Conference …, 2011	106	2011
Range quantile queries: Another virtue of wavelet trees T Gagie, SJ Puglisi, A Turpin String Processing and Information Retrieval: 16th International Symposium …, 2009	95	2009
LZ77-Based Self-indexing with Faster Pattern Matching. T Gagie, P Gawrychowski, J Kärkkäinen, Y Nekrich, SJ Puglisi LATIN 8392, 731-742, 2014	88	2014
Top-k Ranked Document Search in General Text Databases JS Culpepper, G Navarro, SJ Puglisi, A Turpin Algorithms–ESA 2010: 18th Annual European Symposium, Liverpool, UK …, 2010	81	2010
Colored range queries and document retrieval T Gagie, J Kärkkäinen, G Navarro, SJ Puglisi Theoretical Computer Science 483, 36-50, 2013	78	2013
Linear time Lempel-Ziv factorization: Simple, fast, small J Kärkkäinen, D Kempa, SJ Puglisi Combinatorial Pattern Matching: 24th Annual Symposium, CPM 2013, Bad …, 2013	77	2013
How many runs can a string contain? SJ Puglisi, J Simpson, WF Smyth Theoretical Computer Science 401 (1-3), 165-171, 2008	75	2008
Variable-order de Bruijn graphs C Boucher, A Bowe, T Gagie, SJ Puglisi, K Sadakane 2015 data compression conference, 383-392, 2015	74	2015
A fast hybrid short read fragment assembly algorithm B Schmidt, R Sinha, B Beresford-Smith, SJ Puglisi Bioinformatics 25 (17), 2279-2280, 2009	71	2009
Space-time tradeoffs for longest-common-prefix array computation SJ Puglisi, A Turpin Algorithms and Computation: 19th International Symposium, ISAAC 2008, Gold …, 2008	61	2008
Relative Lempel-Ziv factorization for efficient storage and retrieval of web collections C Hoobin, SJ Puglisi, J Zobel arXiv preprint arXiv:1106.2587, 2011	59	2011
Data structures based on k-mers for querying large collections of sequencing data sets C Marchet, C Boucher, SJ Puglisi, P Medvedev, M Salson, R Chikhi Genome Research 31 (1), 1-12, 2021	58	2021

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