Simon J. Puglisi

ORCID

Publication Activity (10 Years)

Years Active: 2005-2023
Publications (10 Years): 104

Top Venues

Publications

Jarno N. Alanko, Elena Biagi, Simon J. Puglisi
Longest Common Prefix Arrays for Succinct k-Spectra. SPIRE (2023)
Philip Bille, Inge Li Gørtz, Simon J. Puglisi, Simon R. Tarnow
Hierarchical Relative Lempel-Ziv Compression. SEA (2023)
Jarno N. Alanko, Simon J. Puglisi, Jaakko Vuohtoniemi
-Spectra via Subset Rank Queries on the Spectral Burrows-Wheeler Transform. ACDA (2023)
Juha Kärkkäinen, Marcin Piatkowski, Simon J. Puglisi
String inference from longest-common-prefix array. Theor. Comput. Sci. 942 (2023)
Jarno N. Alanko, Elena Biagi, Simon J. Puglisi, Jaakko Vuohtoniemi
Subset Wavelet Trees. SEA (2023)
Jarno N. Alanko, Jaakko Vuohtoniemi, Tommi Mäklin, Simon J. Puglisi
-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes. Bioinform. 39 (Supplement-1) (2023)
Diego Díaz-Domínguez, Saska Dönges, Simon J. Puglisi, Leena Salmela
Simple Runs-Bounded FM-Index Designs Are Fast. SEA (2023)
Jarno N. Alanko, Elena Biagi, Simon J. Puglisi
Longest Common Prefix Arrays for Succinct k-Spectra. CoRR (2023)
Golnaz Badkobeh, Sara Giuliani, Zsuzsanna Lipták, Simon J. Puglisi
On Compressing Collections of Substring Samples. ICTCS (2022)
Golnaz Badkobeh, Alessandro De Luca, Gabriele Fici, Simon J. Puglisi
Maximal Closed Substrings. CoRR (2022)
Hideo Bannai, Tomohiro I, Tomasz Kociumaka, Dominik Köppl, Simon J. Puglisi
Computing Longest (Common) Lyndon Subsequences. CoRR (2022)
Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela
Computing all-vs-all MEMs in run-length encoded collections of HiFi reads. CoRR (2022)
Golnaz Badkobeh, Alessandro De Luca, Gabriele Fici, Simon J. Puglisi
Maximal Closed Substrings. SPIRE (2022)
Philip Bille, Inge Li Gørtz, Simon J. Puglisi, Simon R. Tarnow
Hierarchical Relative Lempel-Ziv Compression. CoRR (2022)
Zsuzsanna Lipták, Francesco Masillo, Simon J. Puglisi
Suffix Sorting via Matching Statistics. WABI (2022)
Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela
Computing All-vs-All MEMs in Run-Length-Encoded Collections of HiFi Reads. SPIRE (2022)
Zsuzsanna Lipták, Francesco Masillo, Simon J. Puglisi
Suffix sorting via matching statistics. CoRR (2022)
Saska Dönges, Simon J. Puglisi, Rajeev Raman
On Dynamic Bitvector Implementations. DCC (2022)
Riku Walve, Simon J. Puglisi, Leena Salmela
Space-Efficient Indexing of Spaced Seeds for Accurate Overlap Computation of Raw Optical Mapping Data. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (4) (2022)
Dominik Köppl, Simon J. Puglisi, Rajeev Raman
Fast and Simple Compact Hashing via Bucketing. Algorithmica 84 (9) (2022)
Hideo Bannai, Tomohiro I, Tomasz Kociumaka, Dominik Köppl, Simon J. Puglisi
Computing Longest (Common) Lyndon Subsequences. IWOCA (2022)
Djamal Belazzougui, Manuel Cáceres, Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Gonzalo Navarro, Alberto Ordóñez Pereira, Simon J. Puglisi, Yasuo Tabei
Block trees. J. Comput. Syst. Sci. 117 (2021)
Simon J. Puglisi, Bella Zhukova
Document Retrieval Hacks. SEA (2021)
Bahar Alipanahi, Alan Kuhnle, Simon J. Puglisi, Leena Salmela, Christina Boucher
Succinct dynamic de Bruijn graphs. Bioinform. 37 (14) (2021)
Golnaz Badkobeh, Pawel Gawrychowski, Juha Kärkkäinen, Simon J. Puglisi, Bella Zhukova
Tight upper and lower bounds on suffix tree breadth. Theor. Comput. Sci. 854 (2021)
Djamal Belazzougui, Dmitry Kosolobov, Simon J. Puglisi, Rajeev Raman
Weighted Ancestors in Suffix Trees Revisited. CoRR (2021)
Zsuzsanna Lipták, Simon J. Puglisi, Massimiliano Rossi
Pattern Discovery in Colored Strings. ACM J. Exp. Algorithmics 26 (2021)
Simon J. Puglisi, Bella Zhukova
Smaller RLZ-Compressed Suffix Arrays. DCC (2021)
Danyang Ma, Simon J. Puglisi, Rajeev Raman, Bella Zhukova
On Elias-Fano for Rank Queries in FM-Indexes. DCC (2021)
Djamal Belazzougui, Dmitry Kosolobov, Simon J. Puglisi, Rajeev Raman
Weighted Ancestors in Suffix Trees Revisited. CPM (2021)
Simon J. Puglisi, Bella Zhukova
Relative Lempel-Ziv Compression of Suffix Arrays. SPIRE (2020)
Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher
Fast and accurate correction of optical mapping data via spaced seeds. Bioinform. 36 (9) (2020)
Manuel Cáceres, Simon J. Puglisi, Bella Zhukova
Fast Indexes for Gapped Pattern Matching. CoRR (2020)
Dmitry Kosolobov, Daniel Valenzuela, Gonzalo Navarro, Simon J. Puglisi
Lempel-Ziv-Like Parsing in Small Space. Algorithmica 82 (11) (2020)
Hideo Bannai, Travis Gagie, Gary Hoppenworth, Simon J. Puglisi, Luís M. S. Russo
More Time-Space Tradeoffs for Finding a Shortest Unique Substring. Algorithms 13 (9) (2020)
Leena Salmela, Kingshuk Mukherjee, Simon J. Puglisi, Martin D. Muggli, Christina Boucher
Fast and accurate correction of optical mapping data via spaced seeds. Bioinform. 36 (3) (2020)
Zsuzsanna Lipták, Simon J. Puglisi, Massimiliano Rossi
Pattern Discovery in Colored Strings. CoRR (2020)
Manuel Cáceres, Simon J. Puglisi, Bella Zhukova
Fast Indexes for Gapped Pattern Matching. SOFSEM (2020)
Zsuzsanna Lipták, Simon J. Puglisi, Massimiliano Rossi
Pattern Discovery in Colored Strings. SEA (2020)
Dominik Köppl, Simon J. Puglisi, Rajeev Raman
Fast and Simple Compact Hashing via Bucketing. SEA (2020)
Hayam Alamro, Golnaz Badkobeh, Djamal Belazzougui, Costas S. Iliopoulos, Simon J. Puglisi
Computing the Antiperiod(s) of a String. CPM (2019)
Martin D. Muggli, Simon J. Puglisi, Christina Boucher
Kohdista: an efficient method to index and query possible Rmap alignments. Algorithms Mol. Biol. 14 (1) (2019)
Rafael Ktistakis, Philippe Fournier-Viger, Simon J. Puglisi, Rajeev Raman
Succinct BWT-Based Sequence Prediction. DEXA (2) (2019)
Daniel Valenzuela, Dmitry Kosolobov, Gonzalo Navarro, Simon J. Puglisi
Lempel-Ziv-like Parsing in Small Space. CoRR (2019)
Simon Gog, Juha Kärkkäinen, Dominik Kempa, Matthias Petri, Simon J. Puglisi
Fixed Block Compression Boosting in FM-Indexes: Theory and Practice. Algorithmica 81 (4) (2019)
Simon J. Puglisi, Massimiliano Rossi
On Lempel-Ziv Decompression in Small Space. DCC (2019)
Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali, Simon J. Puglisi
Bidirectional Variable-Order de Bruijn Graphs. Int. J. Found. Comput. Sci. 29 (8) (2018)
Veli Mäkinen, Simon J. Puglisi
Editorial: Special Issue on "Combinatorial Algorithms" (IWOCA 2016). Theory Comput. Syst. 62 (6) (2018)
Diego Díaz-Domínguez, Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Gonzalo Navarro, Simon J. Puglisi
Assembling Omnitigs using Hidden-Order de Bruijn Graphs. CoRR (2018)
Andreas Poyias, Simon J. Puglisi, Rajeev Raman
m-Bonsai: A Practical Compact Dynamic Trie. Int. J. Found. Comput. Sci. 29 (8) (2018)
Martin D. Muggli, Simon J. Puglisi, Christina Boucher
A Succinct Solution to Rmap Alignment. WABI (2018)
Héctor Ferrada, Dominik Kempa, Simon J. Puglisi
Hybrid Indexing Revisited. ALENEX (2018)
Golnaz Badkobeh, Gabriele Fici, Simon J. Puglisi
Algorithms for Anti-Powers in Strings. CoRR (2018)
Golnaz Badkobeh, Gabriele Fici, Simon J. Puglisi
Algorithms for anti-powers in strings. Inf. Process. Lett. 137 (2018)
José Fuentes-Sepúlveda, Juha Kärkkäinen, Dmitry Kosolobov, Simon J. Puglisi
Run Compressed Rank/Select for Large Alphabets. DCC (2018)
Andrea Farruggia, Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
Relative Suffix Trees. Comput. J. 61 (5) (2018)
Juha Kärkkäinen, Dominik Kempa, Yuto Nakashima, Simon J. Puglisi, Arseny M. Shur
On the Size of Lempel-Ziv and Lyndon Factorizations. STACS (2017)
José Fuentes-Sepúlveda, Juha Kärkkäinen, Dmitry Kosolobov, Simon J. Puglisi
Run Compressed Rank/Select for Large Alphabets. CoRR (2017)
Andreas Poyias, Simon J. Puglisi, Rajeev Raman
Compact Dynamic Rewritable (CDRW) Arrays. ALENEX (2017)
Alice Héliou, Solon P. Pissis, Simon J. Puglisi
emMAW: computing minimal absent words in external memory. Bioinform. 33 (17) (2017)
Juha Kärkkäinen, Marcin Piatkowski, Simon J. Puglisi
String Inference from Longest-Common-Prefix Array. ICALP (2017)
Golnaz Badkobeh, Travis Gagie, Shunsuke Inenaga, Dmitry Kosolobov, Simon J. Puglisi
On Two LZ78-style Grammars: Compression Bounds and Compressed-Space Computation. CoRR (2017)
Bahar Alipanahi, Leena Salmela, Simon J. Puglisi, Martin D. Muggli, Christina Boucher
Disentangled Long-Read De Bruijn Graphs via Optical Maps. WABI (2017)
Simon J. Puglisi
Dynamic Succinct Data Structures and Compressed Random Access Memory. Stringology (2017)
Martin D. Muggli, Alexander Bowe, Noelle R. Noyes, Paul S. Morley, Keith E. Belk, Robert Raymond, Travis Gagie, Simon J. Puglisi, Christina Boucher
Succinct colored de Bruijn graphs. Bioinform. 33 (20) (2017)
Yasuo Tabei, Simon J. Puglisi
Scalable Similarity Search for Molecular Descriptors. SISAP (2017)
Golnaz Badkobeh, Juha Kärkkäinen, Simon J. Puglisi, Bella Zhukova
On Suffix Tree Breadth. SPIRE (2017)
Golnaz Badkobeh, Travis Gagie, Shunsuke Inenaga, Tomasz Kociumaka, Dmitry Kosolobov, Simon J. Puglisi
On Two LZ78-style Grammars: Compression Bounds and Compressed-Space Computation. SPIRE (2017)
Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi, Bella Zhukova
Engineering External Memory Induced Suffix Sorting. ALENEX (2017)
Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
Document retrieval on repetitive string collections. Inf. Retr. J. 20 (3) (2017)
Andreas Poyias, Simon J. Puglisi, Rajeev Raman
m-Bonsai: a Practical Compact Dynamic Trie. CoRR (2017)
Travis Gagie, Christopher Hoobin, Simon J. Puglisi
Block Graphs in Practice. Math. Comput. Sci. 11 (2) (2017)
Anthony J. Cox, Andrea Farruggia, Travis Gagie, Simon J. Puglisi, Jouni Sirén
RLZAP: Relative Lempel-Ziv with Adaptive Pointers. SPIRE (2016)
Yasuo Tabei, Hiroto Saigo, Yoshihiro Yamanishi, Simon J. Puglisi
Scalable Partial Least Squares Regression on Grammar-Compressed Data Matrices. CoRR (2016)
Djamal Belazzougui, Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
Lempel-Ziv Decoding in External Memory. SEA (2016)
Yasuo Tabei, Simon J. Puglisi
Scalable Similarity Search for Molecular Descriptors. CoRR (2016)
Golnaz Badkobeh, Hideo Bannai, Keisuke Goto, Tomohiro I, Costas S. Iliopoulos, Shunsuke Inenaga, Simon J. Puglisi, Shiho Sugimoto
Closed factorization. Discret. Appl. Math. 212 (2016)
Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
Document Retrieval on Repetitive String Collections. CoRR (2016)
Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
Lazy Lempel-Ziv Factorization Algorithms. ACM J. Exp. Algorithmics 21 (1) (2016)
Djamal Belazzougui, Simon J. Puglisi
Range Predecessor and Lempel-Ziv Parsing. SODA (2016)
Travis Gagie, Simon J. Puglisi, Daniel Valenzuela
Analyzing Relative Lempel-Ziv Reference Construction. SPIRE (2016)
Anthony J. Cox, Andrea Farruggia, Travis Gagie, Simon J. Puglisi, Jouni Sirén
RLZAP: Relative Lempel-Ziv with Adaptive Pointers. CoRR (2016)
Yuka Tanimura, Tomohiro I, Hideo Bannai, Shunsuke Inenaga, Simon J. Puglisi, Masayuki Takeda
Deterministic sub-linear space LCE data structures with efficient construction. CoRR (2016)
Juha Kärkkäinen, Dominik Kempa, Yuto Nakashima, Simon J. Puglisi, Arseny M. Shur
On the Size of Lempel-Ziv and Lyndon Factorizations. CoRR (2016)
Yasuo Tabei, Hiroto Saigo, Yoshihiro Yamanishi, Simon J. Puglisi
Scalable Partial Least Squares Regression on Grammar-Compressed Data Matrices. KDD (2016)
Yuka Tanimura, Tomohiro I, Hideo Bannai, Shunsuke Inenaga, Simon J. Puglisi, Masayuki Takeda
Deterministic Sub-Linear Space LCE Data Structures With Efficient Construction. CPM (2016)
Juha Kärkkäinen, Marcin Piatkowski, Simon J. Puglisi
String Inference from the LCP Array. CoRR (2016)
Djamal Belazzougui, Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
Lempel-Ziv Decoding in External Memory. CoRR (2016)
Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali, Simon J. Puglisi
Bidirectional Variable-Order de Bruijn Graphs. LATIN (2016)
Simon Gog, Juha Kärkkäinen, Dominik Kempa, Matthias Petri, Simon J. Puglisi
Faster, Minuter. DCC (2016)
Costas S. Iliopoulos, Simon J. Puglisi
Foreword. Theor. Comput. Sci. 656 (2016)
Golnaz Badkobeh, Travis Gagie, Szymon Grabowski, Yuto Nakashima, Simon J. Puglisi, Shiho Sugimoto
Longest Common Abelian Factors and Large Alphabets. SPIRE (2016)
Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén
Relative Compressed Suffix Trees. CoRR (2015)
Djamal Belazzougui, Simon J. Puglisi
Range Predecessor and Lempel-Ziv Parsing. CoRR (2015)
Martin D. Muggli, Simon J. Puglisi, Roy Ronen, Christina Boucher
Misassembly detection using paired-end sequence reads and optical mapping data. Bioinform. 31 (12) (2015)
Djamal Belazzougui, Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Alberto Ordóñez Pereira, Simon J. Puglisi, Yasuo Tabei
Queries on LZ-Bounded Encodings. DCC (2015)
Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi
Parallel External Memory Suffix Sorting. CPM (2015)
Djamal Belazzougui, Patrick Hagge Cording, Simon J. Puglisi, Yasuo Tabei
Access, Rank, and Select in Grammar-compressed Strings. ESA (2015)
Hideo Bannai, Travis Gagie, Shunsuke Inenaga, Juha Kärkkäinen, Dominik Kempa, Marcin Piatkowski, Simon J. Puglisi, Shiho Sugimoto
Diverse Palindromic Factorization Is NP-complete. DLT (2015)
Travis Gagie, Shunsuke Inenaga, Juha Kärkkäinen, Dominik Kempa, Marcin Piatkowski, Simon J. Puglisi, Shiho Sugimoto
Diverse Palindromic Factorization is NP-Complete. CoRR (2015)

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Publication Activity (10 Years)

Top Topics

Top Venues

Simon J. Puglisi