Simon J. Puglisi

According to our database, Simon J. Puglisi authored at least 153 papers between 2005 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Suffix sorting via matching statistics.

Zsuzsanna Lipták, Francesco Masillo, Simon J. Puglisi

Algorithms Mol. Biol., December, 2024

Computing Longest Lyndon Subsequences and Longest Common Lyndon Subsequences.

Hideo Bannai, Tomohiro I, Tomasz Kociumaka, Dominik Köppl, Simon J. Puglisi

Algorithmica, March, 2024

Height-bounded Lempel-Ziv encodings.

Hideo Bannai, Mitsuru Funakoshi, Diptarama Hendrian, Myuji Matsuda, Simon J. Puglisi

CoRR, 2024

2023

String inference from longest-common-prefix array.

Juha Kärkkäinen, Marcin Piatkowski, Simon J. Puglisi

Theor. Comput. Sci., 2023

Themisto: a scalable colored <i>k</i>-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes.

Jarno N. Alanko, Jaakko Vuohtoniemi, Tommi Mäklin, Simon J. Puglisi

Bioinform., 2023

Simple Runs-Bounded FM-Index Designs Are Fast.

Diego Díaz-Domínguez, Saska Dönges, Simon J. Puglisi, Leena Salmela

Proceedings of the 21st International Symposium on Experimental Algorithms, 2023

Hierarchical Relative Lempel-Ziv Compression.

Philip Bille, Inge Li Gørtz, Simon J. Puglisi, Simon R. Tarnow

Proceedings of the 21st International Symposium on Experimental Algorithms, 2023

Subset Wavelet Trees.

Jarno N. Alanko, Elena Biagi, Simon J. Puglisi, Jaakko Vuohtoniemi

Proceedings of the 21st International Symposium on Experimental Algorithms, 2023

Longest Common Prefix Arrays for Succinct k-Spectra.

Jarno N. Alanko, Elena Biagi, Simon J. Puglisi

Proceedings of the String Processing and Information Retrieval, 2023

Small Searchable <i>κ</i>-Spectra via Subset Rank Queries on the Spectral Burrows-Wheeler Transform.

Jarno N. Alanko, Simon J. Puglisi, Jaakko Vuohtoniemi

Proceedings of the SIAM Conference on Applied and Computational Discrete Algorithms, 2023

2022

Space-Efficient Indexing of Spaced Seeds for Accurate Overlap Computation of Raw Optical Mapping Data.

Riku Walve, Simon J. Puglisi, Leena Salmela

IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Fast and Simple Compact Hashing via Bucketing.

Dominik Köppl, Simon J. Puglisi, Rajeev Raman

Algorithmica, 2022

Computing All-vs-All MEMs in Run-Length-Encoded Collections of HiFi Reads.

Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela

Proceedings of the String Processing and Information Retrieval, 2022

Maximal Closed Substrings.

Golnaz Badkobeh, Alessandro De Luca, Gabriele Fici, Simon J. Puglisi

Proceedings of the String Processing and Information Retrieval, 2022

Computing Longest (Common) Lyndon Subsequences.

Hideo Bannai, Tomohiro I, Tomasz Kociumaka, Dominik Köppl, Simon J. Puglisi

Proceedings of the Combinatorial Algorithms - 33rd International Workshop, 2022

On Compressing Collections of Substring Samples.

Golnaz Badkobeh, Sara Giuliani, Zsuzsanna Lipták, Simon J. Puglisi

Proceedings of the 23rd Italian Conference on Theoretical Computer Science, 2022

On Dynamic Bitvector Implementations.

Saska Dönges, Simon J. Puglisi, Rajeev Raman

Proceedings of the Data Compression Conference, 2022

2021

Succinct dynamic de Bruijn graphs.

Bahar Alipanahi, Alan Kuhnle, Simon J. Puglisi, Leena Salmela, Christina Boucher

Bioinform., August, 2021

Tight upper and lower bounds on suffix tree breadth.

Golnaz Badkobeh, Pawel Gawrychowski, Juha Kärkkäinen, Simon J. Puglisi, Bella Zhukova

Theor. Comput. Sci., 2021

Pattern Discovery in Colored Strings.

Zsuzsanna Lipták, Simon J. Puglisi, Massimiliano Rossi

ACM J. Exp. Algorithmics, 2021

Block trees.

Djamal Belazzougui, Manuel Cáceres, Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Gonzalo Navarro, Alberto Ordóñez Pereira, Simon J. Puglisi, Yasuo Tabei

J. Comput. Syst. Sci., 2021

Document Retrieval Hacks.

Simon J. Puglisi, Bella Zhukova

Proceedings of the 19th International Symposium on Experimental Algorithms, 2021

Smaller RLZ-Compressed Suffix Arrays.

Simon J. Puglisi, Bella Zhukova

Proceedings of the 31st Data Compression Conference, 2021

On Elias-Fano for Rank Queries in FM-Indexes.

Danyang Ma, Simon J. Puglisi, Rajeev Raman, Bella Zhukova

Proceedings of the 31st Data Compression Conference, 2021

Weighted Ancestors in Suffix Trees Revisited.

Djamal Belazzougui, Dmitry Kosolobov, Simon J. Puglisi, Rajeev Raman

Proceedings of the 32nd Annual Symposium on Combinatorial Pattern Matching, 2021

2020

Fast and accurate correction of optical mapping data via spaced seeds.

Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher

Bioinform., 2020

More Time-Space Tradeoffs for Finding a Shortest Unique Substring.

Hideo Bannai, Travis Gagie, Gary Hoppenworth, Simon J. Puglisi, Luís M. S. Russo

Algorithms, 2020

Lempel-Ziv-Like Parsing in Small Space.

Dmitry Kosolobov, Daniel Valenzuela, Gonzalo Navarro, Simon J. Puglisi

Algorithmica, 2020

Relative Lempel-Ziv Compression of Suffix Arrays.

Simon J. Puglisi, Bella Zhukova

Proceedings of the String Processing and Information Retrieval, 2020

Fast Indexes for Gapped Pattern Matching.

Manuel Cáceres, Simon J. Puglisi, Bella Zhukova

Proceedings of the SOFSEM 2020: Theory and Practice of Computer Science, 2020

2019

Kohdista: an efficient method to index and query possible Rmap alignments.

Martin D. Muggli, Simon J. Puglisi, Christina Boucher

Algorithms Mol. Biol., 2019

Fixed Block Compression Boosting in FM-Indexes: Theory and Practice.

Simon Gog, Juha Kärkkäinen, Dominik Kempa, Matthias Petri, Simon J. Puglisi

Algorithmica, 2019

Succinct BWT-Based Sequence Prediction.

Rafael Ktistakis, Philippe Fournier-Viger, Simon J. Puglisi, Rajeev Raman

Proceedings of the Database and Expert Systems Applications, 2019

On Lempel-Ziv Decompression in Small Space.

Simon J. Puglisi, Massimiliano Rossi

Proceedings of the Data Compression Conference, 2019

Computing the Antiperiod(s) of a String.

Hayam Alamro, Golnaz Badkobeh, Djamal Belazzougui, Costas S. Iliopoulos, Simon J. Puglisi

Proceedings of the 30th Annual Symposium on Combinatorial Pattern Matching, 2019

2018

Editorial: Special Issue on "Combinatorial Algorithms" (IWOCA 2016).

Veli Mäkinen, Simon J. Puglisi

Theory Comput. Syst., 2018

Algorithms for anti-powers in strings.

Golnaz Badkobeh, Gabriele Fici, Simon J. Puglisi

Inf. Process. Lett., 2018

m-Bonsai: A Practical Compact Dynamic Trie.

Andreas Poyias, Simon J. Puglisi, Rajeev Raman

Int. J. Found. Comput. Sci., 2018

Bidirectional Variable-Order de Bruijn Graphs.

Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali, Simon J. Puglisi

Int. J. Found. Comput. Sci., 2018

Assembling Omnitigs using Hidden-Order de Bruijn Graphs.

Diego Díaz-Domínguez, Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Gonzalo Navarro, Simon J. Puglisi

CoRR, 2018

Relative Suffix Trees.

Andrea Farruggia, Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén

Comput. J., 2018

A Succinct Solution to Rmap Alignment.

Martin D. Muggli, Simon J. Puglisi, Christina Boucher

Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

Run Compressed Rank/Select for Large Alphabets.

José Fuentes-Sepúlveda, Juha Kärkkäinen, Dmitry Kosolobov, Simon J. Puglisi

Proceedings of the 2018 Data Compression Conference, 2018

Hybrid Indexing Revisited.

Héctor Ferrada, Dominik Kempa, Simon J. Puglisi

Proceedings of the Twentieth Workshop on Algorithm Engineering and Experiments, 2018

2017

Block Graphs in Practice.

Travis Gagie, Christopher Hoobin, Simon J. Puglisi

Math. Comput. Sci., 2017

Document retrieval on repetitive string collections.

Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén

Inf. Retr. J., 2017

On Two LZ78-style Grammars: Compression Bounds and Compressed-Space Computation.

Golnaz Badkobeh, Travis Gagie, Shunsuke Inenaga, Dmitry Kosolobov, Simon J. Puglisi

CoRR, 2017

Succinct colored de Bruijn graphs.

Martin D. Muggli, Alexander Bowe, Noelle R. Noyes, Paul S. Morley, Keith E. Belk, Robert Raymond, Travis Gagie, Simon J. Puglisi, Christina Boucher

Bioinform., 2017

emMAW: computing minimal absent words in external memory.

Alice Héliou, Solon P. Pissis, Simon J. Puglisi

Bioinform., 2017

Disentangled Long-Read De Bruijn Graphs via Optical Maps.

Bahar Alipanahi, Leena Salmela, Simon J. Puglisi, Martin D. Muggli, Christina Boucher

Proceedings of the 17th International Workshop on Algorithms in Bioinformatics, 2017

Dynamic Succinct Data Structures and Compressed Random Access Memory.

Simon J. Puglisi

Proceedings of the Prague Stringology Conference 2017, 2017

On the Size of Lempel-Ziv and Lyndon Factorizations.

Juha Kärkkäinen, Dominik Kempa, Yuto Nakashima, Simon J. Puglisi, Arseny M. Shur

Proceedings of the 34th Symposium on Theoretical Aspects of Computer Science, 2017

On Suffix Tree Breadth.

Golnaz Badkobeh, Juha Kärkkäinen, Simon J. Puglisi, Bella Zhukova

Proceedings of the String Processing and Information Retrieval, 2017

On Two LZ78-style Grammars: Compression Bounds and Compressed-Space Computation.

Golnaz Badkobeh, Travis Gagie, Shunsuke Inenaga, Tomasz Kociumaka, Dmitry Kosolobov, Simon J. Puglisi

Proceedings of the String Processing and Information Retrieval, 2017

Scalable Similarity Search for Molecular Descriptors.

Yasuo Tabei, Simon J. Puglisi

Proceedings of the Similarity Search and Applications - 10th International Conference, 2017

Compact Dynamic Rewritable (CDRW) Arrays.

Andreas Poyias, Simon J. Puglisi, Rajeev Raman

Proceedings of the Ninteenth Workshop on Algorithm Engineering and Experiments, 2017

Engineering External Memory Induced Suffix Sorting.

Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi, Bella Zhukova

Proceedings of the Ninteenth Workshop on Algorithm Engineering and Experiments, 2017

2016

Lempel-Ziv Compression.

Simon J. Puglisi

Encyclopedia of Algorithms, 2016

Foreword.

Costas S. Iliopoulos, Simon J. Puglisi

Theor. Comput. Sci., 2016

Lazy Lempel-Ziv Factorization Algorithms.

Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi

ACM J. Exp. Algorithmics, 2016

Closed factorization.

Golnaz Badkobeh, Hideo Bannai, Keisuke Goto, Tomohiro I, Costas S. Iliopoulos, Shunsuke Inenaga, Simon J. Puglisi, Shiho Sugimoto

Discret. Appl. Math., 2016

String Inference from the LCP Array.

Juha Kärkkäinen, Marcin Piatkowski, Simon J. Puglisi

CoRR, 2016

Lempel-Ziv Decoding in External Memory.

Djamal Belazzougui, Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi

Proceedings of the Experimental Algorithms - 15th International Symposium, 2016

Analyzing Relative Lempel-Ziv Reference Construction.

Travis Gagie, Simon J. Puglisi, Daniel Valenzuela

Proceedings of the String Processing and Information Retrieval, 2016

RLZAP: Relative Lempel-Ziv with Adaptive Pointers.

Anthony J. Cox, Andrea Farruggia, Travis Gagie, Simon J. Puglisi, Jouni Sirén

Proceedings of the String Processing and Information Retrieval, 2016

Longest Common Abelian Factors and Large Alphabets.

Golnaz Badkobeh, Travis Gagie, Szymon Grabowski, Yuto Nakashima, Simon J. Puglisi, Shiho Sugimoto

Proceedings of the String Processing and Information Retrieval, 2016

Range Predecessor and Lempel-Ziv Parsing.

Djamal Belazzougui, Simon J. Puglisi

Proceedings of the Twenty-Seventh Annual ACM-SIAM Symposium on Discrete Algorithms, 2016

Scalable Partial Least Squares Regression on Grammar-Compressed Data Matrices.

Yasuo Tabei, Hiroto Saigo, Yoshihiro Yamanishi, Simon J. Puglisi

Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2016

Faster, Minuter.

Simon Gog, Juha Kärkkäinen, Dominik Kempa, Matthias Petri, Simon J. Puglisi

Proceedings of the 2016 Data Compression Conference, 2016

Deterministic Sub-Linear Space LCE Data Structures With Efficient Construction.

Yuka Tanimura, Tomohiro I, Hideo Bannai, Shunsuke Inenaga, Simon J. Puglisi, Masayuki Takeda

Proceedings of the 27th Annual Symposium on Combinatorial Pattern Matching, 2016

2015

Approximate pattern matching in LZ77-compressed texts.

Travis Gagie, Pawel Gawrychowski, Simon J. Puglisi

J. Discrete Algorithms, 2015

Relative Compressed Suffix Trees.

Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén

CoRR, 2015

Diverse Palindromic Factorization is NP-Complete.

Travis Gagie, Shunsuke Inenaga, Juha Kärkkäinen, Dominik Kempa, Marcin Piatkowski, Simon J. Puglisi, Shiho Sugimoto

CoRR, 2015

Misassembly detection using paired-end sequence reads and optical mapping data.

Martin D. Muggli, Simon J. Puglisi, Roy Ronen, Christina Boucher

Bioinform., 2015

Access, Rank, and Select in Grammar-compressed Strings.

Djamal Belazzougui, Patrick Hagge Cording, Simon J. Puglisi, Yasuo Tabei

Proceedings of the Algorithms - ESA 2015, 2015

Diverse Palindromic Factorization Is NP-complete.

Hideo Bannai, Travis Gagie, Shunsuke Inenaga, Juha Kärkkäinen, Dominik Kempa, Marcin Piatkowski, Simon J. Puglisi, Shiho Sugimoto

Proceedings of the Developments in Language Theory - 19th International Conference, 2015

Document Counting in Compressed Space.

Travis Gagie, Aleksi Hartikainen, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén

Proceedings of the 2015 Data Compression Conference, 2015

Variable-Order de Bruijn Graphs.

Christina Boucher, Alexander Bowe, Travis Gagie, Simon J. Puglisi, Kunihiko Sadakane

Proceedings of the 2015 Data Compression Conference, 2015

Queries on LZ-Bounded Encodings.

Djamal Belazzougui, Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Alberto Ordóñez Pereira, Simon J. Puglisi, Yasuo Tabei

Proceedings of the 2015 Data Compression Conference, 2015

Parallel External Memory Suffix Sorting.

Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi

Proceedings of the Combinatorial Pattern Matching - 26th Annual Symposium, 2015

Fast and efficient compression of high-throughput sequencing reads.

Christopher Hoobin, Trey Kind, Christina Boucher, Simon J. Puglisi

Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014

Order-preserving matching.

Jinil Kim, Peter Eades, Rudolf Fleischer, Seok-Hee Hong, Costas S. Iliopoulos, Kunsoo Park, Simon J. Puglisi, Takeshi Tokuyama

Theor. Comput. Sci., 2014

General Document Retrieval in Compact Space.

Gonzalo Navarro, Simon J. Puglisi, Daniel Valenzuela

ACM J. Exp. Algorithmics, 2014

Searching and Indexing Genomic Databases via Kernelization.

Travis Gagie, Simon J. Puglisi

CoRR, 2014

Document Counting in Practice.

Travis Gagie, Aleksi Hartikainen, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén

CoRR, 2014

Rank, select and access in grammar-compressed strings.

Djamal Belazzougui, Simon J. Puglisi, Yasuo Tabei

CoRR, 2014

Efficient Indexed Alignment of Contigs to Optical Maps.

Martin D. Muggli, Simon J. Puglisi, Christina Boucher

Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

Relative Lempel-Ziv with Constant-Time Random Access.

Héctor Ferrada, Travis Gagie, Simon Gog, Simon J. Puglisi

Proceedings of the String Processing and Information Retrieval, 2014

LZ77-Based Self-indexing with Faster Pattern Matching.

Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Yakov Nekrich, Simon J. Puglisi

Proceedings of the LATIN 2014: Theoretical Informatics - 11th Latin American Symposium, Montevideo, Uruguay, March 31, 2014

Document Retrieval on Repetitive Collections.

Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén

Proceedings of the Algorithms - ESA 2014, 2014

Hybrid Compression of Bitvectors for the FM-Index.

Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi

Proceedings of the Data Compression Conference, 2014

Lempel-Ziv Parsing in External Memory.

Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi

Proceedings of the Data Compression Conference, 2014

Relative Lempel-Ziv with Constant-Time Random Access.

Travis Gagie, Simon J. Puglisi

Proceedings of the Data Compression Conference, 2014

String Range Matching.

Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi

Proceedings of the Combinatorial Pattern Matching - 25th Annual Symposium, 2014

2013

Colored range queries and document retrieval.

Travis Gagie, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi

Theor. Comput. Sci., 2013

Enhanced string covering.

Tomás Flouri, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Simon J. Puglisi, W. F. Smyth, Wojciech Tyczynski

Theor. Comput. Sci., 2013

AliBI: An Alignment-Based Index for Genomic Datasets.

Héctor Ferrada, Travis Gagie, Tommi Hirvola, Simon J. Puglisi

CoRR, 2013

Hybrid Indexes for Repetitive Datasets.

Héctor Ferrada, Travis Gagie, Tommi Hirvola, Simon J. Puglisi

CoRR, 2013

Lightweight Lempel-Ziv Parsing.

Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi

Proceedings of the Experimental Algorithms, 12th International Symposium, 2013

Crochemore's String Matching Algorithm: Simplification, Extensions, Applications.

Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi

Proceedings of the Prague Stringology Conference 2013, Prague, Czech Republic, 2013

Linear Time Lempel-Ziv Factorization: Simple, Fast, Small.

Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi

Proceedings of the Combinatorial Pattern Matching, 24th Annual Symposium, 2013

Document Listing on Repetitive Collections.

Travis Gagie, Kalle Karhu, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén

Proceedings of the Combinatorial Pattern Matching, 24th Annual Symposium, 2013

Lempel-Ziv factorization: Simple, fast, practical.

Dominik Kempa, Simon J. Puglisi

Proceedings of the 15th Meeting on Algorithm Engineering and Experiments, 2013

2012

Practical Efficient String Mining.

Jasbir Dhaliwal, Simon J. Puglisi, Andrew Turpin

IEEE Trans. Knowl. Data Eng., 2012

New algorithms on wavelet trees and applications to information retrieval.

Travis Gagie, Gonzalo Navarro, Simon J. Puglisi

Theor. Comput. Sci., 2012

Revisiting bounded context block-sorting transformations.

J. Shane Culpepper, Matthias Petri, Simon J. Puglisi

Softw. Pract. Exp., 2012

Editorial.

Laurent Mouchard, Simon J. Puglisi

J. Discrete Algorithms, 2012

Distributed String Mining for High-Throughput Sequencing Data.

Niko Välimäki, Simon J. Puglisi

Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

New and Efficient Approaches to the Quasiperiodic Characterisation of a String.

Tomás Flouri, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Simon J. Puglisi, William F. Smyth, Wojciech Tyczynski

Proceedings of the Prague Stringology Conference 2012, 2012

A Faster Grammar-Based Self-index.

Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Yakov Nekrich, Simon J. Puglisi

Proceedings of the Language and Automata Theory and Applications, 2012

Slashing the Time for BWT Inversion.

Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi

Proceedings of the 2012 Data Compression Conference, Snowbird, UT, USA, April 10-12, 2012, 2012

Trends in Su x Sorting: A Survey of Low Memory Algorithms.

Jasbir Dhaliwal, Simon J. Puglisi, Andrew Turpin

Proceedings of the Thirty-Fifth Australasian Computer Science Conference, 2012

2011

Relative Lempel-Ziv Factorization for Efficient Storage and Retrieval of Web Collections.

Christopher Hoobin, Simon J. Puglisi, Justin Zobel

Proc. VLDB Endow., 2011

A Compressed Self-Index for Genomic Databases

Travis Gagie, Juha Kärkkäinen, Yakov Nekrich, Simon J. Puglisi

CoRR, 2011

Practical Compressed Document Retrieval.

Gonzalo Navarro, Simon J. Puglisi, Daniel Valenzuela

Proceedings of the Experimental Algorithms - 10th International Symposium, 2011

Reference Sequence Construction for Relative Compression of Genomes.

Shanika Kuruppu, Simon J. Puglisi, Justin Zobel

Proceedings of the String Processing and Information Retrieval, 2011

Fixed Block Compression Boosting in FM-Indexes.

Juha Kärkkäinen, Simon J. Puglisi

Proceedings of the String Processing and Information Retrieval, 2011

Sample selection for dictionary-based corpus compression.

Christopher Hoobin, Simon J. Puglisi, Justin Zobel

Proceedings of the Proceeding of the 34th International ACM SIGIR Conference on Research and Development in Information Retrieval, 2011

Faster Approximate Pattern Matching in Compressed Repetitive Texts.

Travis Gagie, Pawel Gawrychowski, Simon J. Puglisi

Proceedings of the Algorithms and Computation - 22nd International Symposium, 2011

Backwards Search in Context Bound Text Transformations.

Matthias Petri, Gonzalo Navarro, J. Shane Culpepper, Simon J. Puglisi

Proceedings of the First International Conference on Data Compression, 2011

Cache Friendly Burrows-Wheeler Inversion.

Juha Kärkkäinen, Simon J. Puglisi

Proceedings of the First International Conference on Data Compression, 2011

Optimized Relative Lempel-Ziv Compression of Genomes.

Shanika Kuruppu, Simon J. Puglisi, Justin Zobel

Proceedings of the Thirty-Fourth Australasian Computer Science Conference, 2011

2010

Fast, Practical Algorithms for Computing All the Repeats in a String.

Simon J. Puglisi, William F. Smyth, Munina Yusufu

Math. Comput. Sci., 2010

Dual-Sorted Inverted Lists.

Gonzalo Navarro, Simon J. Puglisi

Proceedings of the String Processing and Information Retrieval, 2010

Relative Lempel-Ziv Compression of Genomes for Large-Scale Storage and Retrieval.

Shanika Kuruppu, Simon J. Puglisi, Justin Zobel

Proceedings of the String Processing and Information Retrieval, 2010

Colored Range Queries and Document Retrieval.

Travis Gagie, Gonzalo Navarro, Simon J. Puglisi

Proceedings of the String Processing and Information Retrieval, 2010

Medium-Space Algorithms for Inverse BWT.

Juha Kärkkäinen, Simon J. Puglisi

Proceedings of the Algorithms, 2010

Top-<i>k</i> Ranked Document Search in General Text Databases.

J. Shane Culpepper, Gonzalo Navarro, Simon J. Puglisi, Andrew Turpin

Proceedings of the Algorithms, 2010

Presenting Query Aspects to Support Exploratory Search.

Mingfang Wu, Andrew Turpin, Simon J. Puglisi, Falk Scholer, James A. Thom

Proceedings of the User Interfaces 2010, 2010

2009

SHREC: a short-read error correction method.

Jan Schröder, Heiko Schröder, Simon J. Puglisi, Ranjan Sinha, Bertil Schmidt

Bioinform., 2009

A fast hybrid short read fragment assembly algorithm.

Bertil Schmidt, Ranjan Sinha, Bryan Beresford-Smith, Simon J. Puglisi

Bioinform., 2009

Range Quantile Queries: Another Virtue of Wavelet Trees.

Travis Gagie, Simon J. Puglisi, Andrew Turpin

Proceedings of the String Processing and Information Retrieval, 2009

Document Compaction for Efficient Query Biased Snippet Generation.

Yohannes Tsegay, Simon J. Puglisi, Andrew Turpin, Justin Zobel

Proceedings of the Advances in Information Retrieval, 2009

Reducing Space Requirements for Disk Resident Suffix Arrays.

Alistair Moffat, Simon J. Puglisi, Ranjan Sinha

Proceedings of the Database Systems for Advanced Applications, 2009

Permuted Longest-Common-Prefix Array.

Juha Kärkkäinen, Giovanni Manzini, Simon J. Puglisi

Proceedings of the Combinatorial Pattern Matching, 20th Annual Symposium, 2009

Testing Stream Ciphers by Finding the Longest Substring of a Given Density.

Serdar Boztas, Simon J. Puglisi, Andrew Turpin

Proceedings of the Information Security and Privacy, 14th Australasian Conference, 2009

2008

How many runs can a string contain?

Simon J. Puglisi, Jamie Simpson, William F. Smyth

Theor. Comput. Sci., 2008

Lempel-Ziv Factorization Using Less Time & Space.

Gang Chen, Simon J. Puglisi, William F. Smyth

Math. Comput. Sci., 2008

Words with Simple Burrows-Wheeler Transforms.

Jamie Simpson, Simon J. Puglisi

Electron. J. Comb., 2008

The expected number of runs in a word.

Simon J. Puglisi, Jamie Simpson

Australas. J Comb., 2008

RMIT University at TREC 2008: Relevance Feedback Track.

Yohannes Tsegay, Falk Scholer, Simon J. Puglisi

Proceedings of The Seventeenth Text REtrieval Conference, 2008

Fast Optimal Algorithms for Computing All the Repeats in a String.

Simon J. Puglisi, William F. Smyth, Munina Yusufu

Proceedings of the Prague Stringology Conference 2008, Prague, Czech Republic, 2008

Improving suffix array locality for fast pattern matching on disk.

Ranjan Sinha, Simon J. Puglisi, Alistair Moffat, Andrew Turpin

Proceedings of the ACM SIGMOD International Conference on Management of Data, 2008

Space-Time Tradeoffs for Longest-Common-Prefix Array Computation.

Simon J. Puglisi, Andrew Turpin

Proceedings of the Algorithms and Computation, 19th International Symposium, 2008

2007

An efficient, versatile approach to suffix sorting.

Michael A. Maniscalco, Simon J. Puglisi

ACM J. Exp. Algorithmics, 2007

A taxonomy of suffix array construction algorithms.

Simon J. Puglisi, William F. Smyth, Andrew Turpin

ACM Comput. Surv., 2007

RMIT University at the TREC 2007 Enterprise Track.

Mingfang Wu, Falk Scholer, Milad Shokouhi, Simon J. Puglisi, Halil Ali

Proceedings of The Sixteenth Text REtrieval Conference, 2007

Efficient token based clone detection with flexible tokenization.

Hamid Abdul Basit, Simon J. Puglisi, William F. Smyth, Andrew Turpin, Stan Jarzabek

Proceedings of the 6th joint meeting of the European Software Engineering Conference and the ACM SIGSOFT International Symposium on Foundations of Software Engineering, 2007

Fast and Practical Algorithms for Computing All the Runs in a String.

Gang Chen, Simon J. Puglisi, William F. Smyth

Proceedings of the Combinatorial Pattern Matching, 18th Annual Symposium, 2007

2006

A New Periodicity Lemma.

Kangmin Fan, Simon J. Puglisi, William F. Smyth, Andrew Turpin

SIAM J. Discret. Math., 2006

Inverted Files Versus Suffix Arrays for Locating Patterns in Primary Memory.

Simon J. Puglisi, William F. Smyth, Andrew Turpin

Proceedings of the String Processing and Information Retrieval, 2006

Suffix arrays: what are they good for?

Simon J. Puglisi, William F. Smyth, Andrew Turpin

Proceedings of the Database Technologies 2006, 2006

2005

The Performance of Linear Time Suffix Sorting Algorithms.

Simon J. Puglisi, William F. Smyth, Andrew Turpin

Proceedings of the 2005 Data Compression Conference (DCC 2005), 2005