Simon J. Puglisi

218 papers A* 4A 12B 44C 29Misc 10Journal 100Unranked 18

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Finding maximal closed substrings. Theor. Comput. Sci. Golnaz Badkobeh, Alessandro De Luca, Gabriele Fici, Simon J. Puglisi
2026	J	`jnl`	Matching statistics - a survey. Theor. Comput. Sci. Zsuzsanna Lipták, Francesco Masillo, Simon J. Puglisi
2026	A	`ed.`	Proceedings of the 28th Symposium on Algorithm Engineering and Experiments, ALENEX 2026, Vancouver, BC, Canada, January 11-12, 2026 ALENEX Rezaul Chowdhury, Simon J. Puglisi, Bin Ren, Nate Veldt
2026	J	`jnl`	Sensitivity of Repetitiveness Measures to String Reversal. CoRR Hideo Bannai, Yuto Fujie, Peaker Guo, Shunsuke Inenaga, Yuto Nakashima, Simon J. Puglisi, Cristian Urbina
2025	A	`conf`	Batched k-Mer Lookup on the Spectral Burrows-Wheeler Transform. ALENEX Jarno N. Alanko, Elena Biagi, Joel Mackenzie, Simon J. Puglisi
2025	—	`conf`	Compact Data Structures for Collections of Sets. From Strings to Graphs, and Back Again Jarno N. Alanko, Philip Bille, Inge Li Gørtz, Gonzalo Navarro, Simon J. Puglisi
2025	B	`conf`	Compressed Dictionary Matching on Run-Length Encoded Strings. CPM Philip Bille, Inge Li Gørtz, Simon J. Puglisi, Simon R. Tarnow
2025	J	`jnl`	Compressed Dictionary Matching on Run-Length Encoded Strings. CoRR Philip Bille, Inge Li Gørtz, Simon J. Puglisi, Simon R. Tarnow
2025	J	`jnl`	Finimizers: Variable-Length Bounded-Frequency Minimizers for $k$-mer Sets. IEEE Trans. Comput. Biol. Bioinform. Jarno N. Alanko, Elena Biagi, Simon J. Puglisi
2025	—	`conf`	Graph Indexing Beyond Wheeler Graphs. The Expanding World of Compressed Data Jarno N. Alanko, Elena Biagi, Massimo Equi, Veli Mäkinen, Simon J. Puglisi, Nicola Rizzo, Kunihiko Sadakane, Jouni Sirén
2025	C	`conf`	Massively Parallel Computation of Matching Statistics. SPIRE Anastasia C. Diseth, Keijo Heljanko, Simon J. Puglisi
2025	B	`conf`	Succinct Rank Dictionaries Revisited. SEA Saska Dönges, Simon J. Puglisi
2024	B	`ed.`	35th Annual Symposium on Combinatorial Pattern Matching, CPM 2024, Fukuoka, Japan, June 25-27, 2024 CPM Shunsuke Inenaga, Simon J. Puglisi
2024	J	`jnl`	Computing Longest Lyndon Subsequences and Longest Common Lyndon Subsequences. Algorithmica Hideo Bannai, Tomohiro I, Tomasz Kociumaka, Dominik Köppl, Simon J. Puglisi
2024	Misc	`conf`	Fast Matching Statistics for Sets of Long Similar Strings. PSC Zsuzsanna Lipták, Martina Luca, Francesco Masillo, Simon J. Puglisi
2024	A	`conf`	Height-Bounded Lempel-Ziv Encodings. ESA Hideo Bannai, Mitsuru Funakoshi, Diptarama Hendrian, Myuji Matsuda, Simon J. Puglisi
2024	J	`jnl`	Height-bounded Lempel-Ziv encodings. CoRR Hideo Bannai, Mitsuru Funakoshi, Diptarama Hendrian, Myuji Matsuda, Simon J. Puglisi
2024	Misc	`conf`	On Practical Data Structures for Sorted Range Reporting. PSC Golnaz Badkobeh, Sehar Naveed, Simon J. Puglisi
2024	J	`jnl`	Suffix sorting via matching statistics. Algorithms Mol. Biol. Zsuzsanna Lipták, Francesco Masillo, Simon J. Puglisi
2023	A	`ed.`	31st Annual European Symposium on Algorithms, ESA 2023, Amsterdam, The Netherlands, September 4-6, 2023 ESA Inge Li Gørtz, Martin Farach-Colton, Simon J. Puglisi, Grzegorz Herman
2023	B	`conf`	Hierarchical Relative Lempel-Ziv Compression. SEA Philip Bille, Inge Li Gørtz, Simon J. Puglisi, Simon R. Tarnow
2023	C	`conf`	Longest Common Prefix Arrays for Succinct k-Spectra. SPIRE Jarno N. Alanko, Elena Biagi, Simon J. Puglisi
2023	J	`jnl`	Longest Common Prefix Arrays for Succinct k-Spectra. CoRR Jarno N. Alanko, Elena Biagi, Simon J. Puglisi
2023	B	`conf`	Simple Runs-Bounded FM-Index Designs Are Fast. SEA Diego Díaz-Domínguez, Saska Dönges, Simon J. Puglisi, Leena Salmela
2023	—	`conf`	Small Searchable ACDA Jarno N. Alanko, Simon J. Puglisi, Jaakko Vuohtoniemi
2023	J	`jnl`	String inference from longest-common-prefix array. Theor. Comput. Sci. Juha Kärkkäinen, Marcin Piatkowski, Simon J. Puglisi
2023	B	`conf`	Subset Wavelet Trees. SEA Jarno N. Alanko, Elena Biagi, Simon J. Puglisi, Jaakko Vuohtoniemi
2023	J	`jnl`	Themisto: a scalable colored Bioinform. Jarno N. Alanko, Jaakko Vuohtoniemi, Tommi Mäklin, Simon J. Puglisi
2022	C	`conf`	Computing All-vs-All MEMs in Run-Length-Encoded Collections of HiFi Reads. SPIRE Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela
2022	C	`conf`	Computing Longest (Common) Lyndon Subsequences. IWOCA Hideo Bannai, Tomohiro I, Tomasz Kociumaka, Dominik Köppl, Simon J. Puglisi
2022	J	`jnl`	Computing Longest (Common) Lyndon Subsequences. CoRR Hideo Bannai, Tomohiro I, Tomasz Kociumaka, Dominik Köppl, Simon J. Puglisi
2022	J	`jnl`	Computing all-vs-all MEMs in run-length encoded collections of HiFi reads. CoRR Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela
2022	J	`jnl`	Fast and Simple Compact Hashing via Bucketing. Algorithmica Dominik Köppl, Simon J. Puglisi, Rajeev Raman
2022	J	`jnl`	Hierarchical Relative Lempel-Ziv Compression. CoRR Philip Bille, Inge Li Gørtz, Simon J. Puglisi, Simon R. Tarnow
2022	C	`conf`	Maximal Closed Substrings. SPIRE Golnaz Badkobeh, Alessandro De Luca, Gabriele Fici, Simon J. Puglisi
2022	J	`jnl`	Maximal Closed Substrings. CoRR Golnaz Badkobeh, Alessandro De Luca, Gabriele Fici, Simon J. Puglisi
2022	—	`conf`	On Compressing Collections of Substring Samples. ICTCS Golnaz Badkobeh, Sara Giuliani, Zsuzsanna Lipták, Simon J. Puglisi
2022	B	`conf`	On Dynamic Bitvector Implementations. DCC Saska Dönges, Simon J. Puglisi, Rajeev Raman
2022	J	`jnl`	Space-Efficient Indexing of Spaced Seeds for Accurate Overlap Computation of Raw Optical Mapping Data. IEEE ACM Trans. Comput. Biol. Bioinform. Riku Walve, Simon J. Puglisi, Leena Salmela
2022	C	`conf`	Suffix Sorting via Matching Statistics. WABI Zsuzsanna Lipták, Francesco Masillo, Simon J. Puglisi
2022	J	`jnl`	Suffix sorting via matching statistics. CoRR Zsuzsanna Lipták, Francesco Masillo, Simon J. Puglisi
2021	B	`ed.`	46th International Symposium on Mathematical Foundations of Computer Science, MFCS 2021, Tallinn, Estonia, August 23-27, 2021 MFCS Filippo Bonchi, Simon J. Puglisi
2021	J	`jnl`	Block trees. J. Comput. Syst. Sci. Djamal Belazzougui, Manuel Cáceres, Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Gonzalo Navarro, Alberto Ordóñez Pereira, Simon J. Puglisi, Yasuo Tabei
2021	B	`conf`	Document Retrieval Hacks. SEA Simon J. Puglisi, Bella Zhukova
2021	B	`conf`	On Elias-Fano for Rank Queries in FM-Indexes. DCC Danyang Ma, Simon J. Puglisi, Rajeev Raman, Bella Zhukova
2021	J	`jnl`	Pattern Discovery in Colored Strings. ACM J. Exp. Algorithmics Zsuzsanna Lipták, Simon J. Puglisi, Massimiliano Rossi
2021	B	`conf`	Smaller RLZ-Compressed Suffix Arrays. DCC Simon J. Puglisi, Bella Zhukova
2021	J	`jnl`	Succinct dynamic de Bruijn graphs. Bioinform. Bahar Alipanahi, Alan Kuhnle, Simon J. Puglisi, Leena Salmela, Christina Boucher
2021	J	`jnl`	Tight upper and lower bounds on suffix tree breadth. Theor. Comput. Sci. Golnaz Badkobeh, Pawel Gawrychowski, Juha Kärkkäinen, Simon J. Puglisi, Bella Zhukova
2021	B	`conf`	Weighted Ancestors in Suffix Trees Revisited. CPM Djamal Belazzougui, Dmitry Kosolobov, Simon J. Puglisi, Rajeev Raman
2021	J	`jnl`	Weighted Ancestors in Suffix Trees Revisited. CoRR Djamal Belazzougui, Dmitry Kosolobov, Simon J. Puglisi, Rajeev Raman
2020	B	`conf`	Fast Indexes for Gapped Pattern Matching. SOFSEM Manuel Cáceres, Simon J. Puglisi, Bella Zhukova
2020	J	`jnl`	Fast Indexes for Gapped Pattern Matching. CoRR Manuel Cáceres, Simon J. Puglisi, Bella Zhukova
2020	B	`conf`	Fast and Simple Compact Hashing via Bucketing. SEA Dominik Köppl, Simon J. Puglisi, Rajeev Raman
2020	J	`jnl`	Fast and accurate correction of optical mapping data via spaced seeds. Bioinform. Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher
2020	J	`jnl`	Fast and accurate correction of optical mapping data via spaced seeds. Bioinform. Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher
2020	J	`jnl`	Lempel-Ziv-Like Parsing in Small Space. Algorithmica Dmitry Kosolobov, Daniel Valenzuela, Gonzalo Navarro, Simon J. Puglisi
2020	J	`jnl`	More Time-Space Tradeoffs for Finding a Shortest Unique Substring. Algorithms Hideo Bannai, Travis Gagie, Gary Hoppenworth, Simon J. Puglisi, Luís M. S. Russo
2020	B	`conf`	Pattern Discovery in Colored Strings. SEA Zsuzsanna Lipták, Simon J. Puglisi, Massimiliano Rossi
2020	J	`jnl`	Pattern Discovery in Colored Strings. CoRR Zsuzsanna Lipták, Simon J. Puglisi, Massimiliano Rossi
2020	C	`conf`	Relative Lempel-Ziv Compression of Suffix Arrays. SPIRE Simon J. Puglisi, Bella Zhukova
2019	B	`conf`	Computing the Antiperiod(s) of a String. CPM Hayam Alamro, Golnaz Badkobeh, Djamal Belazzougui, Costas S. Iliopoulos, Simon J. Puglisi
2019	J	`jnl`	Fixed Block Compression Boosting in FM-Indexes: Theory and Practice. Algorithmica Simon Gog, Juha Kärkkäinen, Dominik Kempa, Matthias Petri, Simon J. Puglisi
2019	J	`jnl`	Kohdista: an efficient method to index and query possible Rmap alignments. Algorithms Mol. Biol. Martin D. Muggli, Simon J. Puglisi, Christina Boucher
2019	J	`jnl`	Lempel-Ziv-like Parsing in Small Space. CoRR Daniel Valenzuela, Dmitry Kosolobov, Gonzalo Navarro, Simon J. Puglisi
2019	B	`conf`	On Lempel-Ziv Decompression in Small Space. DCC Simon J. Puglisi, Massimiliano Rossi
2019	C	`ed.`	String Processing and Information Retrieval - 26th International Symposium, SPIRE 2019, Segovia, Spain, October 7-9, 2019, Proceedings SPIRE Nieves R. Brisaboa, Simon J. Puglisi
2019	—	`conf`	Succinct BWT-Based Sequence Prediction. DEXA (2) Rafael Ktistakis, Philippe Fournier-Viger, Simon J. Puglisi, Rajeev Raman
2018	C	`conf`	A Succinct Solution to Rmap Alignment. WABI Martin D. Muggli, Simon J. Puglisi, Christina Boucher
2018	J	`jnl`	Algorithms for Anti-Powers in Strings. CoRR Golnaz Badkobeh, Gabriele Fici, Simon J. Puglisi
2018	J	`jnl`	Algorithms for anti-powers in strings. Inf. Process. Lett. Golnaz Badkobeh, Gabriele Fici, Simon J. Puglisi
2018	J	`jnl`	Assembling Omnitigs using Hidden-Order de Bruijn Graphs. CoRR Diego Díaz-Domínguez, Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Gonzalo Navarro, Simon J. Puglisi
2018	J	`jnl`	Bidirectional Variable-Order de Bruijn Graphs. Int. J. Found. Comput. Sci. Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali, Simon J. Puglisi
2018	J	`jnl`	Editorial: Special Issue on "Combinatorial Algorithms" (IWOCA 2016). Theory Comput. Syst. Veli Mäkinen, Simon J. Puglisi
2018	A	`conf`	Hybrid Indexing Revisited. ALENEX Héctor Ferrada, Dominik Kempa, Simon J. Puglisi
2018	J	`jnl`	Relative Suffix Trees. Comput. J. Andrea Farruggia, Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2018	B	`conf`	Run Compressed Rank/Select for Large Alphabets. DCC José Fuentes-Sepúlveda, Juha Kärkkäinen, Dmitry Kosolobov, Simon J. Puglisi
2018	J	`jnl`	m-Bonsai: A Practical Compact Dynamic Trie. Int. J. Found. Comput. Sci. Andreas Poyias, Simon J. Puglisi, Rajeev Raman
2017	B	`ed.`	16th International Symposium on Experimental Algorithms, SEA 2017, London, UK, June 21-23, 2017 SEA Costas S. Iliopoulos, Solon P. Pissis, Simon J. Puglisi, Rajeev Raman
2017	J	`jnl`	Block Graphs in Practice. Math. Comput. Sci. Travis Gagie, Christopher Hoobin, Simon J. Puglisi
2017	A	`conf`	Compact Dynamic Rewritable (CDRW) Arrays. ALENEX Andreas Poyias, Simon J. Puglisi, Rajeev Raman
2017	C	`conf`	Disentangled Long-Read De Bruijn Graphs via Optical Maps. WABI Bahar Alipanahi, Leena Salmela, Simon J. Puglisi, Martin D. Muggli, Christina Boucher
2017	J	`jnl`	Document retrieval on repetitive string collections. Inf. Retr. J. Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2017	Misc	`conf`	Dynamic Succinct Data Structures and Compressed Random Access Memory. PSC Simon J. Puglisi
2017	A	`conf`	Engineering External Memory Induced Suffix Sorting. ALENEX Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi, Bella Zhukova
2017	C	`conf`	On Suffix Tree Breadth. SPIRE Golnaz Badkobeh, Juha Kärkkäinen, Simon J. Puglisi, Bella Zhukova
2017	C	`conf`	On Two LZ78-style Grammars: Compression Bounds and Compressed-Space Computation. SPIRE Golnaz Badkobeh, Travis Gagie, Shunsuke Inenaga, Tomasz Kociumaka, Dmitry Kosolobov, Simon J. Puglisi
2017	J	`jnl`	On Two LZ78-style Grammars: Compression Bounds and Compressed-Space Computation. CoRR Golnaz Badkobeh, Travis Gagie, Shunsuke Inenaga, Tomasz Kociumaka, Dmitry Kosolobov, Simon J. Puglisi
2017	A	`conf`	On the Size of Lempel-Ziv and Lyndon Factorizations. STACS Juha Kärkkäinen, Dominik Kempa, Yuto Nakashima, Simon J. Puglisi, Arseny M. Shur
2017	J	`jnl`	Run Compressed Rank/Select for Large Alphabets. CoRR José Fuentes-Sepúlveda, Juha Kärkkäinen, Dmitry Kosolobov, Simon J. Puglisi
2017	B	`conf`	Scalable Similarity Search for Molecular Descriptors. SISAP Yasuo Tabei, Simon J. Puglisi
2017	A*	`conf`	String Inference from Longest-Common-Prefix Array. ICALP Juha Kärkkäinen, Marcin Piatkowski, Simon J. Puglisi
2017	J	`jnl`	Succinct colored de Bruijn graphs. Bioinform. Martin D. Muggli, Alexander Bowe, Noelle R. Noyes, Paul S. Morley, Keith E. Belk, Robert Raymond, Travis Gagie, Simon J. Puglisi, Christina Boucher
2017	J	`jnl`	emMAW: computing minimal absent words in external memory. Bioinform. Alice Héliou, Solon P. Pissis, Simon J. Puglisi
2017	J	`jnl`	m-Bonsai: a Practical Compact Dynamic Trie. CoRR Andreas Poyias, Simon J. Puglisi, Rajeev Raman
2016	C	`conf`	Analyzing Relative Lempel-Ziv Reference Construction. SPIRE Travis Gagie, Simon J. Puglisi, Daniel Valenzuela
2016	B	`conf`	Bidirectional Variable-Order de Bruijn Graphs. LATIN Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali, Simon J. Puglisi
2016	J	`jnl`	Closed factorization. Discret. Appl. Math. Golnaz Badkobeh, Hideo Bannai, Keisuke Goto, Tomohiro I, Costas S. Iliopoulos, Shunsuke Inenaga, Simon J. Puglisi, Shiho Sugimoto
2016	C	`ed.`	Combinatorial Algorithms - 27th International Workshop, IWOCA 2016, Helsinki, Finland, August 17-19, 2016, Proceedings IWOCA Veli Mäkinen, Simon J. Puglisi, Leena Salmela
2016	B	`conf`	Deterministic Sub-Linear Space LCE Data Structures With Efficient Construction. CPM Yuka Tanimura, Tomohiro I, Hideo Bannai, Shunsuke Inenaga, Simon J. Puglisi, Masayuki Takeda
2016	J	`jnl`	Deterministic sub-linear space LCE data structures with efficient construction. CoRR Yuka Tanimura, Tomohiro I, Hideo Bannai, Shunsuke Inenaga, Simon J. Puglisi, Masayuki Takeda
2016	J	`jnl`	Document Retrieval on Repetitive String Collections. CoRR Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2016	B	`conf`	Faster, Minuter. DCC Simon Gog, Juha Kärkkäinen, Dominik Kempa, Matthias Petri, Simon J. Puglisi
2016	J	`jnl`	Foreword. Theor. Comput. Sci. Costas S. Iliopoulos, Simon J. Puglisi
2016	J	`jnl`	Lazy Lempel-Ziv Factorization Algorithms. ACM J. Exp. Algorithmics Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
2016	—	`ch.`	Lempel-Ziv Compression. Encyclopedia of Algorithms Simon J. Puglisi
2016	B	`conf`	Lempel-Ziv Decoding in External Memory. SEA Djamal Belazzougui, Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
2016	J	`jnl`	Lempel-Ziv Decoding in External Memory. CoRR Djamal Belazzougui, Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
2016	C	`conf`	Longest Common Abelian Factors and Large Alphabets. SPIRE Golnaz Badkobeh, Travis Gagie, Szymon Grabowski, Yuto Nakashima, Simon J. Puglisi, Shiho Sugimoto
2016	J	`jnl`	On the Size of Lempel-Ziv and Lyndon Factorizations. CoRR Juha Kärkkäinen, Dominik Kempa, Yuto Nakashima, Simon J. Puglisi, Arseny M. Shur
2016	C	`conf`	RLZAP: Relative Lempel-Ziv with Adaptive Pointers. SPIRE Anthony J. Cox, Andrea Farruggia, Travis Gagie, Simon J. Puglisi, Jouni Sirén
2016	J	`jnl`	RLZAP: Relative Lempel-Ziv with Adaptive Pointers. CoRR Anthony J. Cox, Andrea Farruggia, Travis Gagie, Simon J. Puglisi, Jouni Sirén
2016	A*	`conf`	Range Predecessor and Lempel-Ziv Parsing. SODA Djamal Belazzougui, Simon J. Puglisi
2016	A*	`conf`	Scalable Partial Least Squares Regression on Grammar-Compressed Data Matrices. KDD Yasuo Tabei, Hiroto Saigo, Yoshihiro Yamanishi, Simon J. Puglisi
2016	J	`jnl`	Scalable Partial Least Squares Regression on Grammar-Compressed Data Matrices. CoRR Yasuo Tabei, Hiroto Saigo, Yoshihiro Yamanishi, Simon J. Puglisi
2016	J	`jnl`	Scalable Similarity Search for Molecular Descriptors. CoRR Yasuo Tabei, Simon J. Puglisi
2016	J	`jnl`	String Inference from the LCP Array. CoRR Juha Kärkkäinen, Marcin Piatkowski, Simon J. Puglisi
2015	A	`conf`	Access, Rank, and Select in Grammar-compressed Strings. ESA Djamal Belazzougui, Patrick Hagge Cording, Simon J. Puglisi, Yasuo Tabei
2015	J	`jnl`	Approximate pattern matching in LZ77-compressed texts. J. Discrete Algorithms Travis Gagie, Pawel Gawrychowski, Simon J. Puglisi
2015	C	`conf`	Diverse Palindromic Factorization Is NP-complete. DLT Hideo Bannai, Travis Gagie, Shunsuke Inenaga, Juha Kärkkäinen, Dominik Kempa, Marcin Piatkowski, Simon J. Puglisi, Shiho Sugimoto
2015	J	`jnl`	Diverse Palindromic Factorization is NP-Complete. CoRR Travis Gagie, Shunsuke Inenaga, Juha Kärkkäinen, Dominik Kempa, Marcin Piatkowski, Simon J. Puglisi, Shiho Sugimoto
2015	B	`conf`	Document Counting in Compressed Space. DCC Travis Gagie, Aleksi Hartikainen, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2015	—	`conf`	Fast and efficient compression of high-throughput sequencing reads. BCB Christopher Hoobin, Trey Kind, Christina Boucher, Simon J. Puglisi
2015	J	`jnl`	Misassembly detection using paired-end sequence reads and optical mapping data. Bioinform. Martin D. Muggli, Simon J. Puglisi, Roy Ronen, Christina Boucher
2015	B	`conf`	Parallel External Memory Suffix Sorting. CPM Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
2015	B	`conf`	Queries on LZ-Bounded Encodings. DCC Djamal Belazzougui, Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Alberto Ordóñez Pereira, Simon J. Puglisi, Yasuo Tabei
2015	J	`jnl`	Range Predecessor and Lempel-Ziv Parsing. CoRR Djamal Belazzougui, Simon J. Puglisi
2015	J	`jnl`	Relative Compressed Suffix Trees. CoRR Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2015	C	`ed.`	String Processing and Information Retrieval - 22nd International Symposium, SPIRE 2015, London, UK, September 1-4, 2015, Proceedings SPIRE Costas S. Iliopoulos, Simon J. Puglisi, Emine Yilmaz
2015	B	`conf`	Variable-Order de Bruijn Graphs. DCC Christina Boucher, Alexander Bowe, Travis Gagie, Simon J. Puglisi, Kunihiko Sadakane
2014	—	`conf`	Block Graphs in Practice. ICABD Travis Gagie, Christopher Hoobin, Simon J. Puglisi
2014	Misc	`conf`	Closed Factorization. PSC Golnaz Badkobeh, Hideo Bannai, Keisuke Goto, Tomohiro I, Costas S. Iliopoulos, Shunsuke Inenaga, Simon J. Puglisi, Shiho Sugimoto
2014	J	`jnl`	Document Counting in Practice. CoRR Travis Gagie, Aleksi Hartikainen, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2014	A	`conf`	Document Retrieval on Repetitive Collections. ESA Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2014	J	`jnl`	Document Retrieval on Repetitive Collections. CoRR Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2014	C	`conf`	Efficient Indexed Alignment of Contigs to Optical Maps. WABI Martin D. Muggli, Simon J. Puglisi, Christina Boucher
2014	J	`jnl`	General Document Retrieval in Compact Space. ACM J. Exp. Algorithmics Gonzalo Navarro, Simon J. Puglisi, Daniel Valenzuela
2014	B	`conf`	Hybrid Compression of Bitvectors for the FM-Index. DCC Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
2014	B	`conf`	LZ77-Based Self-indexing with Faster Pattern Matching. LATIN Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Yakov Nekrich, Simon J. Puglisi
2014	B	`conf`	Lempel-Ziv Parsing in External Memory. DCC Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
2014	J	`jnl`	Misassembly Detection using Paired-End Sequence Reads and Optical Mapping Data. CoRR Martin D. Muggli, Simon J. Puglisi, Roy Ronen, Christina Boucher
2014	J	`jnl`	Order-preserving matching. Theor. Comput. Sci. Jinil Kim, Peter Eades, Rudolf Fleischer, Seok-Hee Hong, Costas S. Iliopoulos, Kunsoo Park, Simon J. Puglisi, Takeshi Tokuyama
2014	J	`jnl`	Queries on LZ-Bounded Encodings. CoRR Djamal Belazzougui, Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Alberto Ordóñez Pereira, Simon J. Puglisi, Yasuo Tabei
2014	J	`jnl`	Rank, select and access in grammar-compressed strings. CoRR Djamal Belazzougui, Simon J. Puglisi, Yasuo Tabei
2014	B	`conf`	Relative Lempel-Ziv with Constant-Time Random Access. DCC Travis Gagie, Simon J. Puglisi
2014	C	`conf`	Relative Lempel-Ziv with Constant-Time Random Access. SPIRE Héctor Ferrada, Travis Gagie, Simon Gog, Simon J. Puglisi
2014	J	`jnl`	Searching and Indexing Genomic Databases via Kernelization. CoRR Travis Gagie, Simon J. Puglisi
2014	B	`conf`	String Range Matching. CPM Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
2014	J	`jnl`	Variable-Order de Bruijn Graphs. CoRR Christina Boucher, Alexander Bowe, Travis Gagie, Simon J. Puglisi, Kunihiko Sadakane
2013	J	`jnl`	AliBI: An Alignment-Based Index for Genomic Datasets. CoRR Héctor Ferrada, Travis Gagie, Tommi Hirvola, Simon J. Puglisi
2013	J	`jnl`	Colored range queries and document retrieval. Theor. Comput. Sci. Travis Gagie, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi
2013	Misc	`conf`	Crochemore's String Matching Algorithm: Simplification, Extensions, Applications. PSC Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
2013	B	`conf`	Document Listing on Repetitive Collections. CPM Travis Gagie, Kalle Karhu, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
2013	J	`jnl`	Enhanced string covering. Theor. Comput. Sci. Tomás Flouri, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Simon J. Puglisi, W. F. Smyth, Wojciech Tyczynski
2013	J	`jnl`	Hybrid Indexes for Repetitive Datasets. CoRR Héctor Ferrada, Travis Gagie, Tommi Hirvola, Simon J. Puglisi
2013	J	`jnl`	Lempel-Ziv Parsing in External Memory. CoRR Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
2013	A	`conf`	Lempel-Ziv factorization: Simple, fast, practical. ALENEX Dominik Kempa, Simon J. Puglisi
2013	J	`jnl`	Lightweight Lempel-Ziv Parsing CoRR Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
2013	B	`conf`	Lightweight Lempel-Ziv Parsing. SEA Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
2013	B	`conf`	Linear Time Lempel-Ziv Factorization: Simple, Fast, Small. CPM Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
2013	J	`jnl`	Order Preserving Matching CoRR Jinil Kim, Peter Eades, Rudolf Fleischer, Seok-Hee Hong, Costas S. Iliopoulos, Kunsoo Park, Simon J. Puglisi, Takeshi Tokuyama
2012	C	`conf`	A Faster Grammar-Based Self-index. LATA Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Yakov Nekrich, Simon J. Puglisi
2012	C	`conf`	Distributed String Mining for High-Throughput Sequencing Data. WABI Niko Välimäki, Simon J. Puglisi
2012	J	`jnl`	Editorial. J. Discrete Algorithms Laurent Mouchard, Simon J. Puglisi
2012	J	`jnl`	Linear Time Lempel-Ziv Factorization: Simple, Fast, Small CoRR Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
2012	J	`jnl`	New algorithms on wavelet trees and applications to information retrieval. Theor. Comput. Sci. Travis Gagie, Gonzalo Navarro, Simon J. Puglisi
2012	Misc	`conf`	New and Efficient Approaches to the Quasiperiodic Characterisation of a String. PSC Tomás Flouri, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Simon J. Puglisi, William F. Smyth, Wojciech Tyczynski
2012	J	`jnl`	Practical Efficient String Mining. IEEE Trans. Knowl. Data Eng. Jasbir Dhaliwal, Simon J. Puglisi, Andrew Turpin
2012	J	`jnl`	Revisiting bounded context block-sorting transformations. Softw. Pract. Exp. J. Shane Culpepper, Matthias Petri, Simon J. Puglisi
2012	B	`conf`	Slashing the Time for BWT Inversion. DCC Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
2012	—	`conf`	Trends in Suffix Sorting: A Survey of Low Memory Algorithms. ACSC Jasbir Dhaliwal, Simon J. Puglisi, Andrew Turpin
2011	J	`jnl`	A Compressed Self-Index for Genomic Databases CoRR Travis Gagie, Juha Kärkkäinen, Yakov Nekrich, Simon J. Puglisi
2011	—	`conf`	Backwards Search in Context Bound Text Transformations. CCP Matthias Petri, Gonzalo Navarro, J. Shane Culpepper, Simon J. Puglisi
2011	—	`conf`	Cache Friendly Burrows-Wheeler Inversion. CCP Juha Kärkkäinen, Simon J. Puglisi
2011	J	`jnl`	Faster Approximate Pattern Matching in Compressed Repetitive Texts CoRR Travis Gagie, Pawel Gawrychowski, Simon J. Puglisi
2011	B	`conf`	Faster Approximate Pattern Matching in Compressed Repetitive Texts. ISAAC Travis Gagie, Pawel Gawrychowski, Simon J. Puglisi
2011	J	`jnl`	Fixed Block Compression Boosting in FM-Indexes CoRR Juha Kärkkäinen, Simon J. Puglisi
2011	C	`conf`	Fixed Block Compression Boosting in FM-Indexes. SPIRE Juha Kärkkäinen, Simon J. Puglisi
2011	—	`conf`	Optimized Relative Lempel-Ziv Compression of Genomes. ACSC Shanika Kuruppu, Simon J. Puglisi, Justin Zobel
2011	B	`conf`	Practical Compressed Document Retrieval. SEA Gonzalo Navarro, Simon J. Puglisi, Daniel Valenzuela
2011	J	`jnl`	Reference Sequence Construction for Relative Compression of Genomes CoRR Shanika Kuruppu, Simon J. Puglisi, Justin Zobel
2011	C	`conf`	Reference Sequence Construction for Relative Compression of Genomes. SPIRE Shanika Kuruppu, Simon J. Puglisi, Justin Zobel
2011	J	`jnl`	Relative Lempel-Ziv Factorization for Efficient Storage and Retrieval of Web Collections CoRR Christopher Hoobin, Simon J. Puglisi, Justin Zobel
2011	J	`jnl`	Relative Lempel-Ziv Factorization for Efficient Storage and Retrieval of Web Collections. Proc. VLDB Endow. Christopher Hoobin, Simon J. Puglisi, Justin Zobel
2011	A*	`conf`	Sample selection for dictionary-based corpus compression. SIGIR Christopher Hoobin, Simon J. Puglisi, Justin Zobel
2010	C	`conf`	Colored Range Queries and Document Retrieval. SPIRE Travis Gagie, Gonzalo Navarro, Simon J. Puglisi
2010	C	`conf`	Dual-Sorted Inverted Lists. SPIRE Gonzalo Navarro, Simon J. Puglisi
2010	J	`jnl`	Fast, Practical Algorithms for Computing All the Repeats in a String. Math. Comput. Sci. Simon J. Puglisi, William F. Smyth, Munina Yusufu
2010	—	`conf`	Medium-Space Algorithms for Inverse BWT. ESA (1) Juha Kärkkäinen, Simon J. Puglisi
2010	J	`jnl`	New Algorithms on Wavelet Trees and Applications to Information Retrieval CoRR Travis Gagie, Gonzalo Navarro, Simon J. Puglisi
2010	—	`conf`	Presenting Query Aspects to Support Exploratory Search. AUIC Mingfang Wu, Andrew Turpin, Simon J. Puglisi, Falk Scholer, James A. Thom
2010	C	`conf`	Relative Lempel-Ziv Compression of Genomes for Large-Scale Storage and Retrieval. SPIRE Shanika Kuruppu, Simon J. Puglisi, Justin Zobel
2010	—	`conf`	Top- ESA (2) J. Shane Culpepper, Gonzalo Navarro, Simon J. Puglisi, Andrew Turpin
2009	J	`jnl`	A fast hybrid short read fragment assembly algorithm. Bioinform. Bertil Schmidt, Ranjan Sinha, Bryan Beresford-Smith, Simon J. Puglisi
2009	A	`conf`	Document Compaction for Efficient Query Biased Snippet Generation. ECIR Yohannes Tsegay, Simon J. Puglisi, Andrew Turpin, Justin Zobel
2009	B	`conf`	Permuted Longest-Common-Prefix Array. CPM Juha Kärkkäinen, Giovanni Manzini, Simon J. Puglisi
2009	C	`conf`	Range Quantile Queries: Another Virtue of Wavelet Trees. SPIRE Travis Gagie, Simon J. Puglisi, Andrew Turpin
2009	B	`conf`	Reducing Space Requirements for Disk Resident Suffix Arrays. DASFAA Alistair Moffat, Simon J. Puglisi, Ranjan Sinha
2009	J	`jnl`	SHREC: a short-read error correction method. Bioinform. Jan Schröder, Heiko Schröder, Simon J. Puglisi, Ranjan Sinha, Bertil Schmidt
2009	Misc	`conf`	Testing Stream Ciphers by Finding the Longest Substring of a Given Density. ACISP Serdar Boztas, Simon J. Puglisi, Andrew Turpin
2008	Misc	`conf`	Fast Optimal Algorithms for Computing All the Repeats in a String. PSC Simon J. Puglisi, William F. Smyth, Munina Yusufu
2008	J	`jnl`	How many runs can a string contain? Theor. Comput. Sci. Simon J. Puglisi, Jamie Simpson, William F. Smyth
2008	—	`conf`	Improving suffix array locality for fast pattern matching on disk. SIGMOD Conference Ranjan Sinha, Simon J. Puglisi, Alistair Moffat, Andrew Turpin
2008	J	`jnl`	Lempel-Ziv Factorization Using Less Time & Space. Math. Comput. Sci. Gang Chen, Simon J. Puglisi, William F. Smyth
2008	—	`conf`	RMIT University at TREC 2008: Relevance Feedback Track. TREC Yohannes Tsegay, Falk Scholer, Simon J. Puglisi
2008	B	`conf`	Space-Time Tradeoffs for Longest-Common-Prefix Array Computation. ISAAC Simon J. Puglisi, Andrew Turpin
2008	J	`jnl`	The expected number of runs in a word. Australas. J Comb. Simon J. Puglisi, Jamie Simpson
2008	J	`jnl`	Words with Simple Burrows-Wheeler Transforms. Electron. J. Comb. Jamie Simpson, Simon J. Puglisi
2007	J	`jnl`	A taxonomy of suffix array construction algorithms. ACM Comput. Surv. Simon J. Puglisi, William F. Smyth, Andrew Turpin
2007	J	`jnl`	An efficient, versatile approach to suffix sorting. ACM J. Exp. Algorithmics Michael A. Maniscalco, Simon J. Puglisi
2007	—	`conf`	Efficient token based clone detection with flexible tokenization. ESEC/SIGSOFT FSE Hamid Abdul Basit, Simon J. Puglisi, William F. Smyth, Andrew Turpin, Stan Jarzabek
2007	B	`conf`	Fast and Practical Algorithms for Computing All the Runs in a String. CPM Gang Chen, Simon J. Puglisi, William F. Smyth
2007	—	`conf`	RMIT University at the TREC 2007 Enterprise Track. TREC Mingfang Wu, Falk Scholer, Milad Shokouhi, Simon J. Puglisi, Halil Ali
2006	J	`jnl`	A New Periodicity Lemma. SIAM J. Discret. Math. Kangmin Fan, Simon J. Puglisi, William F. Smyth, Andrew Turpin
2006	C	`conf`	Inverted Files Versus Suffix Arrays for Locating Patterns in Primary Memory. SPIRE Simon J. Puglisi, William F. Smyth, Andrew Turpin
2006	Misc	`conf`	Suffix arrays: what are they good for? ADC Simon J. Puglisi, William F. Smyth, Andrew Turpin
2005	Misc	`conf`	A taxonomy of suffix array construction algorithms. PSC Simon J. Puglisi, William F. Smyth, Andrew Turpin
2005	B	`conf`	The Performance of Linear Time Suffix Sorting Algorithms. DCC Simon J. Puglisi, William F. Smyth, Andrew Turpin