The Performance of Linear Time Suffix Sorting Algorithms. - Simon J. Puglisi; William F. Smyth; Andrew Turpin (DCC, 2005)

Suffix arrays: what are they good for? - Simon J. Puglisi; William F. Smyth; Andrew Turpin (ADC, 2006)

Inverted Files Versus Suffix Arrays for Locating Patterns in Primary Memory. - Simon J. Puglisi; William F. Smyth; Andrew Turpin (SPIRE, 2006)

A New Periodicity Lemma. - Kangmin Fan; Simon J. Puglisi; William F. Smyth; Andrew Turpin (SIAM J. Discret. Math., 2006)

Fast and Practical Algorithms for Computing All the Runs in a String. - Gang Chen; Simon J. Puglisi; William F. Smyth (CPM, 2007)

Efficient token based clone detection with flexible tokenization. - Hamid Abdul Basit; Simon J. Puglisi; William F. Smyth; Andrew Turpin; Stan Jarzabek (ESEC/SIGSOFT FSE, 2007)

RMIT University at the TREC 2007 Enterprise Track. - Mingfang Wu; Falk Scholer; Milad Shokouhi; Simon J. Puglisi; Halil Ali (TREC, 2007)

A taxonomy of suffix array construction algorithms. - Simon J. Puglisi; William F. Smyth; Andrew Turpin (ACM Comput. Surv., 2007)

An efficient, versatile approach to suffix sorting. - Michael A. Maniscalco; Simon J. Puglisi (ACM J. Exp. Algorithmics, 2007)

Space-Time Tradeoffs for Longest-Common-Prefix Array Computation. - Simon J. Puglisi; Andrew Turpin (ISAAC, 2008)

Improving suffix array locality for fast pattern matching on disk. - Ranjan Sinha; Simon J. Puglisi; Alistair Moffat; Andrew Turpin (SIGMOD Conference, 2008)

Fast Optimal Algorithms for Computing All the Repeats in a String. - Simon J. Puglisi; William F. Smyth; Munina Yusufu (Stringology, 2008)

RMIT University at TREC 2008: Relevance Feedback Track. - Yohannes Tsegay; Falk Scholer; Simon J. Puglisi (TREC, 2008)

The expected number of runs in a word. - Simon J. Puglisi; Jamie Simpson (Australas. J Comb., 2008)

Words with Simple Burrows-Wheeler Transforms. - Jamie Simpson; Simon J. Puglisi (Electron. J. Comb., 2008)

Lempel-Ziv Factorization Using Less Time & Space. - Gang Chen; Simon J. Puglisi; William F. Smyth (Math. Comput. Sci., 2008)

How many runs can a string contain? - Simon J. Puglisi; Jamie Simpson; William F. Smyth (Theor. Comput. Sci., 2008)

Testing Stream Ciphers by Finding the Longest Substring of a Given Density. - Serdar Boztas; Simon J. Puglisi; Andrew Turpin (ACISP, 2009)

Permuted Longest-Common-Prefix Array. - Juha Kärkkäinen; Giovanni Manzini; Simon J. Puglisi (CPM, 2009)

Reducing Space Requirements for Disk Resident Suffix Arrays. - Alistair Moffat; Simon J. Puglisi; Ranjan Sinha (DASFAA, 2009)

Document Compaction for Efficient Query Biased Snippet Generation. - Yohannes Tsegay; Simon J. Puglisi; Andrew Turpin; Justin Zobel (ECIR, 2009)

Range Quantile Queries: Another Virtue of Wavelet Trees. - Travis Gagie; Simon J. Puglisi; Andrew Turpin (SPIRE, 2009)

A fast hybrid short read fragment assembly algorithm. - Bertil Schmidt; Ranjan Sinha; Bryan Beresford-Smith; Simon J. Puglisi (Bioinform., 2009)

SHREC: a short-read error correction method. - Jan Schröder; Heiko Schröder 001; Simon J. Puglisi; Ranjan Sinha; Bertil Schmidt (Bioinform., 2009)

Presenting Query Aspects to Support Exploratory Search. - Mingfang Wu; Andrew Turpin; Simon J. Puglisi; Falk Scholer; James A. Thom (AUIC, 2010)

Top-k Ranked Document Search in General Text Databases. - J. Shane Culpepper; Gonzalo Navarro 001; Simon J. Puglisi; Andrew Turpin (ESA (2), 2010)

Medium-Space Algorithms for Inverse BWT. - Juha Kärkkäinen; Simon J. Puglisi (ESA (1), 2010)

Colored Range Queries and Document Retrieval. - Travis Gagie; Gonzalo Navarro 001; Simon J. Puglisi (SPIRE, 2010)

Relative Lempel-Ziv Compression of Genomes for Large-Scale Storage and Retrieval. - Shanika Kuruppu; Simon J. Puglisi; Justin Zobel (SPIRE, 2010)

Dual-Sorted Inverted Lists. - Gonzalo Navarro 001; Simon J. Puglisi (SPIRE, 2010)

Fast, Practical Algorithms for Computing All the Repeats in a String. - Simon J. Puglisi; William F. Smyth; Munina Yusufu (Math. Comput. Sci., 2010)

Optimized Relative Lempel-Ziv Compression of Genomes. - Shanika Kuruppu; Simon J. Puglisi; Justin Zobel (ACSC, 2011)

Cache Friendly Burrows-Wheeler Inversion. - Juha Kärkkäinen; Simon J. Puglisi (CCP, 2011)

Backwards Search in Context Bound Text Transformations. - Matthias Petri; Gonzalo Navarro 001; J. Shane Culpepper; Simon J. Puglisi (CCP, 2011)

Faster Approximate Pattern Matching in Compressed Repetitive Texts. - Travis Gagie; Pawel Gawrychowski; Simon J. Puglisi (ISAAC, 2011)

Sample selection for dictionary-based corpus compression. - Christopher Hoobin; Simon J. Puglisi; Justin Zobel (SIGIR, 2011)

Fixed Block Compression Boosting in FM-Indexes. - Juha Kärkkäinen; Simon J. Puglisi (SPIRE, 2011)

Reference Sequence Construction for Relative Compression of Genomes. - Shanika Kuruppu; Simon J. Puglisi; Justin Zobel (SPIRE, 2011)

Practical Compressed Document Retrieval. - Gonzalo Navarro 001; Simon J. Puglisi; Daniel Valenzuela 001 (SEA, 2011)

A Compressed Self-Index for Genomic Databases - Travis Gagie; Juha Kärkkäinen; Yakov Nekrich; Simon J. Puglisi (CoRR, 2011)

Relative Lempel-Ziv Factorization for Efficient Storage and Retrieval of Web Collections. - Christopher Hoobin; Simon J. Puglisi; Justin Zobel (Proc. VLDB Endow., 2011)

Trends in Suffix Sorting: A Survey of Low Memory Algorithms. - Jasbir Dhaliwal; Simon J. Puglisi; Andrew Turpin (ACSC, 2012)

Slashing the Time for BWT Inversion. - Juha Kärkkäinen; Dominik Kempa; Simon J. Puglisi (DCC, 2012)

A Faster Grammar-Based Self-index. - Travis Gagie; Pawel Gawrychowski; Juha Kärkkäinen; Yakov Nekrich; Simon J. Puglisi (LATA, 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 (Stringology, 2012)

Distributed String Mining for High-Throughput Sequencing Data. - Niko Välimäki; Simon J. Puglisi (WABI, 2012)

Editorial. - Laurent Mouchard; Simon J. Puglisi (J. Discrete Algorithms, 2012)

Revisiting bounded context block-sorting transformations. - J. Shane Culpepper; Matthias Petri; Simon J. Puglisi (Softw. Pract. Exp., 2012)

New algorithms on wavelet trees and applications to information retrieval. - Travis Gagie; Gonzalo Navarro 001; Simon J. Puglisi (Theor. Comput. Sci., 2012)

Practical Efficient String Mining. - Jasbir Dhaliwal; Simon J. Puglisi; Andrew Turpin (IEEE Trans. Knowl. Data Eng., 2012)

Lempel-Ziv factorization: Simple, fast, practical. - Dominik Kempa; Simon J. Puglisi (ALENEX, 2013)

Document Listing on Repetitive Collections. - Travis Gagie; Kalle Karhu; Gonzalo Navarro 001; Simon J. Puglisi; Jouni Sirén (CPM, 2013)

Linear Time Lempel-Ziv Factorization: Simple, Fast, Small. - Juha Kärkkäinen; Dominik Kempa; Simon J. Puglisi (CPM, 2013)

Crochemore's String Matching Algorithm: Simplification, Extensions, Applications. - Juha Kärkkäinen; Dominik Kempa; Simon J. Puglisi (Stringology, 2013)

Lightweight Lempel-Ziv Parsing. - Juha Kärkkäinen; Dominik Kempa; Simon J. Puglisi (SEA, 2013)

Hybrid Indexes for Repetitive Datasets. - Héctor Ferrada; Travis Gagie; Tommi Hirvola; Simon J. Puglisi (CoRR, 2013)

AliBI: An Alignment-Based Index for Genomic Datasets. - Héctor Ferrada; Travis Gagie; Tommi Hirvola; Simon J. Puglisi (CoRR, 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)

Colored range queries and document retrieval. - Travis Gagie; Juha Kärkkäinen; Gonzalo Navarro 001; Simon J. Puglisi (Theor. Comput. Sci., 2013)

String Range Matching. - Juha Kärkkäinen; Dominik Kempa; Simon J. Puglisi (CPM, 2014)

Relative Lempel-Ziv with Constant-Time Random Access. - Travis Gagie; Simon J. Puglisi (DCC, 2014)

Lempel-Ziv Parsing in External Memory. - Juha Kärkkäinen; Dominik Kempa; Simon J. Puglisi (DCC, 2014)

Hybrid Compression of Bitvectors for the FM-Index. - Juha Kärkkäinen; Dominik Kempa; Simon J. Puglisi (DCC, 2014)

Document Retrieval on Repetitive Collections. - Gonzalo Navarro 001; Simon J. Puglisi; Jouni Sirén (ESA, 2014)

LZ77-Based Self-indexing with Faster Pattern Matching. - Travis Gagie; Pawel Gawrychowski; Juha Kärkkäinen; Yakov Nekrich; Simon J. Puglisi (LATIN, 2014)

Relative Lempel-Ziv with Constant-Time Random Access. - Héctor Ferrada; Travis Gagie; Simon Gog; Simon J. Puglisi (SPIRE, 2014)

Efficient Indexed Alignment of Contigs to Optical Maps. - Martin D. Muggli; Simon J. Puglisi; Christina Boucher 001 (WABI, 2014)

Rank, select and access in grammar-compressed strings. - Djamal Belazzougui; Simon J. Puglisi; Yasuo Tabei (CoRR, 2014)

Document Counting in Practice. - Travis Gagie; Aleksi Hartikainen; Juha Kärkkäinen; Gonzalo Navarro 001; Simon J. Puglisi; Jouni Sirén (CoRR, 2014)

Searching and Indexing Genomic Databases via Kernelization. - Travis Gagie; Simon J. Puglisi (CoRR, 2014)

General Document Retrieval in Compact Space. - Gonzalo Navarro 001; Simon J. Puglisi; Daniel Valenzuela 001 (ACM J. Exp. Algorithmics, 2014)

Order-preserving matching. - Jinil Kim; Peter Eades; Rudolf Fleischer; Seok-Hee Hong 001; Costas S. Iliopoulos; Kunsoo Park; Simon J. Puglisi; Takeshi Tokuyama (Theor. Comput. Sci., 2014)

Fast and efficient compression of high-throughput sequencing reads. - Christopher Hoobin; Trey Kind; Christina Boucher 001; Simon J. Puglisi (BCB, 2015)

Parallel External Memory Suffix Sorting. - Juha Kärkkäinen; Dominik Kempa; Simon J. Puglisi (CPM, 2015)

Queries on LZ-Bounded Encodings. - Djamal Belazzougui; Travis Gagie; Pawel Gawrychowski; Juha Kärkkäinen; Alberto Ordóñez Pereira; Simon J. Puglisi; Yasuo Tabei (DCC, 2015)

Variable-Order de Bruijn Graphs. - Christina Boucher 001; Alexander Bowe; Travis Gagie; Simon J. Puglisi; Kunihiko Sadakane (DCC, 2015)

Document Counting in Compressed Space. - Travis Gagie; Aleksi Hartikainen; Juha Kärkkäinen; Gonzalo Navarro 001; Simon J. Puglisi; Jouni Sirén (DCC, 2015)

Diverse Palindromic Factorization Is NP-complete. - Hideo Bannai; Travis Gagie; Shunsuke Inenaga; Juha Kärkkäinen; Dominik Kempa; Marcin Piatkowski; Simon J. Puglisi; Shiho Sugimoto (DLT, 2015)

Access, Rank, and Select in Grammar-compressed Strings. - Djamal Belazzougui; Patrick Hagge Cording; Simon J. Puglisi; Yasuo Tabei (ESA, 2015)

Misassembly detection using paired-end sequence reads and optical mapping data. - Martin D. Muggli; Simon J. Puglisi; Roy Ronen; Christina Boucher 001 (Bioinform., 2015)

Diverse Palindromic Factorization is NP-Complete. - Travis Gagie; Shunsuke Inenaga; Juha Kärkkäinen; Dominik Kempa; Marcin Piatkowski; Simon J. Puglisi; Shiho Sugimoto (CoRR, 2015)

Relative Compressed Suffix Trees. - Travis Gagie; Gonzalo Navarro 001; Simon J. Puglisi; Jouni Sirén (CoRR, 2015)

Approximate pattern matching in LZ77-compressed texts. - Travis Gagie; Pawel Gawrychowski; Simon J. Puglisi (J. Discrete Algorithms, 2015)

Deterministic Sub-Linear Space LCE Data Structures With Efficient Construction. - Yuka Tanimura; Tomohiro I; Hideo Bannai; Shunsuke Inenaga; Simon J. Puglisi; Masayuki Takeda (CPM, 2016)

Faster, Minuter. - Simon Gog; Juha Kärkkäinen; Dominik Kempa; Matthias Petri; Simon J. Puglisi (DCC, 2016)

Scalable Partial Least Squares Regression on Grammar-Compressed Data Matrices. - Yasuo Tabei; Hiroto Saigo; Yoshihiro Yamanishi; Simon J. Puglisi (KDD, 2016)

Range Predecessor and Lempel-Ziv Parsing. - Djamal Belazzougui; Simon J. Puglisi (SODA, 2016)

Longest Common Abelian Factors and Large Alphabets. - Golnaz Badkobeh; Travis Gagie; Szymon Grabowski; Yuto Nakashima 001; Simon J. Puglisi; Shiho Sugimoto (SPIRE, 2016)

RLZAP: Relative Lempel-Ziv with Adaptive Pointers. - Anthony J. Cox; Andrea Farruggia; Travis Gagie; Simon J. Puglisi; Jouni Sirén (SPIRE, 2016)

Analyzing Relative Lempel-Ziv Reference Construction. - Travis Gagie; Simon J. Puglisi; Daniel Valenzuela 001 (SPIRE, 2016)

Lempel-Ziv Decoding in External Memory. - Djamal Belazzougui; Juha Kärkkäinen; Dominik Kempa; Simon J. Puglisi (SEA, 2016)

String Inference from the LCP Array. - Juha Kärkkäinen; Marcin Piatkowski; Simon J. Puglisi (CoRR, 2016)

Closed factorization. - Golnaz Badkobeh; Hideo Bannai; Keisuke Goto 001; Tomohiro I; Costas S. Iliopoulos; Shunsuke Inenaga; Simon J. Puglisi; Shiho Sugimoto (Discret. Appl. Math., 2016)

Lazy Lempel-Ziv Factorization Algorithms. - Juha Kärkkäinen; Dominik Kempa; Simon J. Puglisi (ACM J. Exp. Algorithmics, 2016)

Foreword. - Costas S. Iliopoulos; Simon J. Puglisi (Theor. Comput. Sci., 2016)

Lempel-Ziv Compression. - Simon J. Puglisi (Encyclopedia of Algorithms, 2016)

Engineering External Memory Induced Suffix Sorting. - Juha Kärkkäinen; Dominik Kempa; Simon J. Puglisi; Bella Zhukova (ALENEX, 2017)

Compact Dynamic Rewritable (CDRW) Arrays. - Andreas Poyias; Simon J. Puglisi; Rajeev Raman (ALENEX, 2017)

Scalable Similarity Search for Molecular Descriptors. - Yasuo Tabei; Simon J. Puglisi (SISAP, 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 (SPIRE, 2017)

On Suffix Tree Breadth. - Golnaz Badkobeh; Juha Kärkkäinen; Simon J. Puglisi; Bella Zhukova (SPIRE, 2017)

On the Size of Lempel-Ziv and Lyndon Factorizations. - Juha Kärkkäinen; Dominik Kempa; Yuto Nakashima 001; Simon J. Puglisi; Arseny M. Shur (STACS, 2017)

Dynamic Succinct Data Structures and Compressed Random Access Memory. - Simon J. Puglisi (Stringology, 2017)

Disentangled Long-Read De Bruijn Graphs via Optical Maps. - Bahar Alipanahi; Leena Salmela; Simon J. Puglisi; Martin D. Muggli; Christina Boucher 001 (WABI, 2017)

emMAW: computing minimal absent words in external memory. - Alice Héliou; Solon P. Pissis; Simon J. Puglisi (Bioinform., 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 001 (Bioinform., 2017)

Document retrieval on repetitive string collections. - Travis Gagie; Aleksi Hartikainen; Kalle Karhu; Juha Kärkkäinen; Gonzalo Navarro 001; Simon J. Puglisi; Jouni Sirén (Inf. Retr. J., 2017)

Block Graphs in Practice. - Travis Gagie; Christopher Hoobin; Simon J. Puglisi (Math. Comput. Sci., 2017)

Hybrid Indexing Revisited. - Héctor Ferrada; Dominik Kempa; Simon J. Puglisi (ALENEX, 2018)

Run Compressed Rank/Select for Large Alphabets. - José Fuentes-Sepúlveda; Juha Kärkkäinen; Dmitry Kosolobov; Simon J. Puglisi (DCC, 2018)

A Succinct Solution to Rmap Alignment. - Martin D. Muggli; Simon J. Puglisi; Christina Boucher 001 (WABI, 2018)

Relative Suffix Trees. - Andrea Farruggia; Travis Gagie; Gonzalo Navarro 001; Simon J. Puglisi; Jouni Sirén (Comput. J., 2018)

Assembling Omnitigs using Hidden-Order de Bruijn Graphs. - Diego Díaz-Domínguez; Djamal Belazzougui; Travis Gagie; Veli Mäkinen; Gonzalo Navarro 001; Simon J. Puglisi (CoRR, 2018)

Bidirectional Variable-Order de Bruijn Graphs. - Djamal Belazzougui; Travis Gagie; Veli Mäkinen; Marco Previtali; Simon J. Puglisi (Int. J. Found. Comput. Sci., 2018)

m-Bonsai: A Practical Compact Dynamic Trie. - Andreas Poyias; Simon J. Puglisi; Rajeev Raman (Int. J. Found. Comput. Sci., 2018)

Algorithms for anti-powers in strings. - Golnaz Badkobeh; Gabriele Fici; Simon J. Puglisi (Inf. Process. Lett., 2018)

Editorial: Special Issue on "Combinatorial Algorithms" (IWOCA 2016). - Veli Mäkinen; Simon J. Puglisi (Theory Comput. Syst., 2018)

Computing the Antiperiod(s) of a String. - Hayam Alamro; Golnaz Badkobeh; Djamal Belazzougui; Costas S. Iliopoulos; Simon J. Puglisi (CPM, 2019)

On Lempel-Ziv Decompression in Small Space. - Simon J. Puglisi; Massimiliano Rossi 001 (DCC, 2019)

Succinct BWT-Based Sequence Prediction. - Rafael Ktistakis; Philippe Fournier-Viger; Simon J. Puglisi; Rajeev Raman (DEXA (2), 2019)

Fixed Block Compression Boosting in FM-Indexes: Theory and Practice. - Simon Gog; Juha Kärkkäinen; Dominik Kempa; Matthias Petri; Simon J. Puglisi (Algorithmica, 2019)

Kohdista: an efficient method to index and query possible Rmap alignments. - Martin D. Muggli; Simon J. Puglisi; Christina Boucher 001 (Algorithms Mol. Biol., 2019)

Fast Indexes for Gapped Pattern Matching. - Manuel Cáceres; Simon J. Puglisi; Bella Zhukova (SOFSEM, 2020)

Relative Lempel-Ziv Compression of Suffix Arrays. - Simon J. Puglisi; Bella Zhukova (SPIRE, 2020)

Lempel-Ziv-Like Parsing in Small Space. - Dmitry Kosolobov; Daniel Valenzuela 001; Gonzalo Navarro 001; Simon J. Puglisi (Algorithmica, 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)

Fast and accurate correction of optical mapping data via spaced seeds. - Leena Salmela; Kingshuk Mukherjee; Simon J. Puglisi; Martin D. Muggli; Christina Boucher 001 (Bioinform., 2020)

Weighted Ancestors in Suffix Trees Revisited. - Djamal Belazzougui; Dmitry Kosolobov; Simon J. Puglisi; Rajeev Raman (CPM, 2021)

On Elias-Fano for Rank Queries in FM-Indexes. - Danyang Ma; Simon J. Puglisi; Rajeev Raman; Bella Zhukova (DCC, 2021)

Smaller RLZ-Compressed Suffix Arrays. - Simon J. Puglisi; Bella Zhukova (DCC, 2021)

Document Retrieval Hacks. - Simon J. Puglisi; Bella Zhukova (SEA, 2021)

Block trees. - Djamal Belazzougui; Manuel Cáceres; Travis Gagie; Pawel Gawrychowski; Juha Kärkkäinen; Gonzalo Navarro 001; Alberto Ordóñez Pereira; Simon J. Puglisi; Yasuo Tabei (J. Comput. Syst. Sci., 2021)

Pattern Discovery in Colored Strings. - Zsuzsanna Lipták; Simon J. Puglisi; Massimiliano Rossi 001 (ACM J. Exp. Algorithmics, 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)

Succinct dynamic de Bruijn graphs. - Bahar Alipanahi; Alan Kuhnle; Simon J. Puglisi; Leena Salmela; Christina Boucher 001 (Bioinform., 2021)

On Dynamic Bitvector Implementations. - Saska Dönges; Simon J. Puglisi; Rajeev Raman (DCC, 2022)

On Compressing Collections of Substring Samples. - Golnaz Badkobeh; Sara Giuliani; Zsuzsanna Lipták; Simon J. Puglisi (ICTCS, 2022)

Computing Longest (Common) Lyndon Subsequences. - Hideo Bannai; Tomohiro I; Tomasz Kociumaka; Dominik Köppl; Simon J. Puglisi (IWOCA, 2022)

Maximal Closed Substrings. - Golnaz Badkobeh; Alessandro De Luca 002; Gabriele Fici; Simon J. Puglisi (SPIRE, 2022)

Computing All-vs-All MEMs in Run-Length-Encoded Collections of HiFi Reads. - Diego Díaz-Domínguez; Simon J. Puglisi; Leena Salmela (SPIRE, 2022)

Fast and Simple Compact Hashing via Bucketing. - Dominik Köppl; Simon J. Puglisi; Rajeev Raman (Algorithmica, 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)

Small Searchable κ-Spectra via Subset Rank Queries on the Spectral Burrows-Wheeler Transform. - Jarno N. Alanko; Simon J. Puglisi; Jaakko Vuohtoniemi (ACDA, 2023)

Longest Common Prefix Arrays for Succinct k-Spectra. - Jarno N. Alanko; Elena Biagi 002; Simon J. Puglisi (SPIRE, 2023)

Subset Wavelet Trees. - Jarno N. Alanko; Elena Biagi 002; Simon J. Puglisi; Jaakko Vuohtoniemi (SEA, 2023)

Hierarchical Relative Lempel-Ziv Compression. - Philip Bille; Inge Li Gørtz; Simon J. Puglisi; Simon R. Tarnow (SEA, 2023)

Simple Runs-Bounded FM-Index Designs Are Fast. - Diego Díaz-Domínguez; Saska Dönges; Simon J. Puglisi; Leena Salmela (SEA, 2023)

Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes. - Jarno N. Alanko; Jaakko Vuohtoniemi; Tommi Mäklin; Simon J. Puglisi (Bioinform., 2023)

String inference from longest-common-prefix array. - Juha Kärkkäinen; Marcin Piatkowski; Simon J. Puglisi (Theor. Comput. Sci., 2023)

Height-Bounded Lempel-Ziv Encodings. - Hideo Bannai; Mitsuru Funakoshi; Diptarama Hendrian; Myuji Matsuda; Simon J. Puglisi (ESA, 2024)

On Practical Data Structures for Sorted Range Reporting. - Golnaz Badkobeh; Sehar Naveed; Simon J. Puglisi (PSC, 2024)

Fast Matching Statistics for Sets of Long Similar Strings. - Zsuzsanna Lipták; Martina Luca; Francesco Masillo; Simon J. Puglisi (PSC, 2024)

Computing Longest Lyndon Subsequences and Longest Common Lyndon Subsequences. - Hideo Bannai; Tomohiro I; Tomasz Kociumaka; Dominik Köppl; Simon J. Puglisi (Algorithmica, 2024)

Suffix sorting via matching statistics. - Zsuzsanna Lipták; Francesco Masillo; Simon J. Puglisi (Algorithms Mol. Biol., 2024)

Graph Indexing Beyond Wheeler Graphs. - Jarno N. Alanko; Elena Biagi 002; Massimo Equi; Veli Mäkinen; Simon J. Puglisi; Nicola Rizzo 001; Kunihiko Sadakane; Jouni Sirén (The Expanding World of Compressed Data, 2025)

Compact Data Structures for Collections of Sets. - Jarno N. Alanko; Philip Bille; Inge Li Gørtz; Gonzalo Navarro 001; Simon J. Puglisi (From Strings to Graphs, and Back Again, 2025)

Compressed Dictionary Matching on Run-Length Encoded Strings. - Philip Bille; Inge Li Gørtz; Simon J. Puglisi; Simon R. Tarnow (CPM, 2025)

Succinct Rank Dictionaries Revisited. - Saska Dönges; Simon J. Puglisi (SEA, 2025)