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ORCIDSimon J. Puglisi
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- affiliation: University of Helsinki, Finland
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2020 – today
- 2024
[j49]Hideo Bannai
, Tomohiro I, Tomasz Kociumaka, Dominik Köppl, Simon J. Puglisi:
Computing Longest Lyndon Subsequences and Longest Common Lyndon Subsequences. Algorithmica 86(3): 735-756 (2024)- [j48]Zsuzsanna Lipták, Francesco Masillo, Simon J. Puglisi:
Suffix sorting via matching statistics. Algorithms Mol. Biol. 19(1): 11 (2024) - [c103]Hideo Bannai, Mitsuru Funakoshi, Diptarama Hendrian, Myuji Matsuda, Simon J. Puglisi:
Height-Bounded Lempel-Ziv Encodings. ESA 2024: 18:1-18:18 - [c102]Zsuzsanna Lipták, Martina Luca, Francesco Masillo, Simon J. Puglisi:
Fast Matching Statistics for Sets of Long Similar Strings. PSC 2024: 3-15 - [c101]Golnaz Badkobeh, Sehar Naveed, Simon J. Puglisi:
On Practical Data Structures for Sorted Range Reporting. PSC 2024: 42-49 - [e7]Shunsuke Inenaga, Simon J. Puglisi:
35th Annual Symposium on Combinatorial Pattern Matching, CPM 2024, June 25-27, 2024, Fukuoka, Japan. LIPIcs 296, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2024, ISBN 978-3-95977-326-3 [contents] - [i46]Hideo Bannai, Mitsuru Funakoshi, Diptarama Hendrian, Myuji Matsuda, Simon J. Puglisi:
Height-bounded Lempel-Ziv encodings. CoRR abs/2403.08209 (2024) - 2023
- [j47]Jarno N. Alanko, Jaakko Vuohtoniemi, Tommi Mäklin, Simon J. Puglisi:
Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes. Bioinform. 39(Supplement-1): 260-269 (2023) - [j46]Juha Kärkkäinen, Marcin Piatkowski, Simon J. Puglisi:
String inference from longest-common-prefix array. Theor. Comput. Sci. 942: 180-199 (2023) - [c100]Jarno N. Alanko, Simon J. Puglisi, Jaakko Vuohtoniemi:
Small Searchable κ-Spectra via Subset Rank Queries on the Spectral Burrows-Wheeler Transform. ACDA 2023: 225-236 - [c99]Jarno N. Alanko, Elena Biagi, Simon J. Puglisi:
Longest Common Prefix Arrays for Succinct k-Spectra. SPIRE 2023: 1-13 - [c98]Jarno N. Alanko, Elena Biagi, Simon J. Puglisi, Jaakko Vuohtoniemi:
Subset Wavelet Trees. SEA 2023: 4:1-4:14 - [c97]Diego Díaz-Domínguez, Saska Dönges, Simon J. Puglisi, Leena Salmela:
Simple Runs-Bounded FM-Index Designs Are Fast. SEA 2023: 7:1-7:16 - [c96]Philip Bille, Inge Li Gørtz, Simon J. Puglisi, Simon R. Tarnow:
Hierarchical Relative Lempel-Ziv Compression. SEA 2023: 18:1-18:16 - [e6]Inge Li Gørtz, Martin Farach-Colton, Simon J. Puglisi, Grzegorz Herman:
31st Annual European Symposium on Algorithms, ESA 2023, September 4-6, 2023, Amsterdam, The Netherlands. LIPIcs 274, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2023, ISBN 978-3-95977-295-2 [contents] - [i45]Jarno N. Alanko, Elena Biagi, Simon J. Puglisi:
Longest Common Prefix Arrays for Succinct k-Spectra. CoRR abs/2306.04850 (2023) - 2022
- [j45]Dominik Köppl, Simon J. Puglisi, Rajeev Raman:
Fast and Simple Compact Hashing via Bucketing. Algorithmica 84(9): 2735-2766 (2022) - [j44]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): 2454-2462 (2022) - [c95]Saska Dönges, Simon J. Puglisi, Rajeev Raman:
On Dynamic Bitvector Implementations. DCC 2022: 252-261 - [c94]Golnaz Badkobeh, Sara Giuliani, Zsuzsanna Lipták, Simon J. Puglisi:
On Compressing Collections of Substring Samples. ICTCS 2022: 136-147 - [c93]Hideo Bannai, Tomohiro I, Tomasz Kociumaka, Dominik Köppl, Simon J. Puglisi:
Computing Longest (Common) Lyndon Subsequences. IWOCA 2022: 128-142 - [c92]Golnaz Badkobeh, Alessandro De Luca, Gabriele Fici, Simon J. Puglisi:
Maximal Closed Substrings. SPIRE 2022: 16-23 - [c91]Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela:
Computing All-vs-All MEMs in Run-Length-Encoded Collections of HiFi Reads. SPIRE 2022: 198-213 - [c90]Zsuzsanna Lipták, Francesco Masillo, Simon J. Puglisi:
Suffix Sorting via Matching Statistics. WABI 2022: 20:1-20:15 - [i44]Hideo Bannai, Tomohiro I, Tomasz Kociumaka, Dominik Köppl, Simon J. Puglisi:
Computing Longest (Common) Lyndon Subsequences. CoRR abs/2201.06773 (2022) - [i43]Zsuzsanna Lipták, Francesco Masillo, Simon J. Puglisi:
Suffix sorting via matching statistics. CoRR abs/2207.00972 (2022) - [i42]Philip Bille, Inge Li Gørtz, Simon J. Puglisi, Simon R. Tarnow:
Hierarchical Relative Lempel-Ziv Compression. CoRR abs/2208.11371 (2022) - [i41]Diego Díaz-Domínguez, Simon J. Puglisi, Leena Salmela:
Computing all-vs-all MEMs in run-length encoded collections of HiFi reads. CoRR abs/2208.14787 (2022) - [i40]Golnaz Badkobeh, Alessandro De Luca, Gabriele Fici, Simon J. Puglisi:
Maximal Closed Substrings. CoRR abs/2209.00271 (2022) - 2021
- [j43]Bahar Alipanahi, Alan Kuhnle, Simon J. Puglisi, Leena Salmela, Christina Boucher:
Succinct dynamic de Bruijn graphs. Bioinform. 37(14): 1946-1952 (2021) - [j42]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: 1-22 (2021) - [j41]Zsuzsanna Lipták, Simon J. Puglisi, Massimiliano Rossi:
Pattern Discovery in Colored Strings. ACM J. Exp. Algorithmics 26: 1.1:1-1.1:26 (2021) - [j40]Golnaz Badkobeh, Pawel Gawrychowski, Juha Kärkkäinen, Simon J. Puglisi, Bella Zhukova:
Tight upper and lower bounds on suffix tree breadth. Theor. Comput. Sci. 854: 63-67 (2021) - [c89]Djamal Belazzougui, Dmitry Kosolobov, Simon J. Puglisi, Rajeev Raman:
Weighted Ancestors in Suffix Trees Revisited. CPM 2021: 8:1-8:15 - [c88]Simon J. Puglisi, Bella Zhukova:
Smaller RLZ-Compressed Suffix Arrays. DCC 2021: 213-222 - [c87]Danyang Ma, Simon J. Puglisi, Rajeev Raman, Bella Zhukova:
On Elias-Fano for Rank Queries in FM-Indexes. DCC 2021: 223-232 - [c86]Simon J. Puglisi, Bella Zhukova:
Document Retrieval Hacks. SEA 2021: 12:1-12:12 - [e5]Filippo Bonchi, Simon J. Puglisi:
46th International Symposium on Mathematical Foundations of Computer Science, MFCS 2021, August 23-27, 2021, Tallinn, Estonia. LIPIcs 202, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2021, ISBN 978-3-95977-201-3 [contents] - [i39]Djamal Belazzougui, Dmitry Kosolobov, Simon J. Puglisi, Rajeev Raman:
Weighted Ancestors in Suffix Trees Revisited. CoRR abs/2103.00462 (2021) - 2020
- [j39]Dmitry Kosolobov, Daniel Valenzuela, Gonzalo Navarro, Simon J. Puglisi:
Lempel-Ziv-Like Parsing in Small Space. Algorithmica 82(11): 3195-3215 (2020) - [j38]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): 234 (2020) - [j37]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): 682-689 (2020) - [j36]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): 2974 (2020) - [c85]Manuel Cáceres, Simon J. Puglisi, Bella Zhukova:
Fast Indexes for Gapped Pattern Matching. SOFSEM 2020: 493-504 - [c84]Simon J. Puglisi, Bella Zhukova:
Relative Lempel-Ziv Compression of Suffix Arrays. SPIRE 2020: 89-96 - [c83]Dominik Köppl, Simon J. Puglisi, Rajeev Raman:
Fast and Simple Compact Hashing via Bucketing. SEA 2020: 7:1-7:14 - [c82]Zsuzsanna Lipták, Simon J. Puglisi, Massimiliano Rossi:
Pattern Discovery in Colored Strings. SEA 2020: 12:1-12:14 - [i38]Manuel Cáceres, Simon J. Puglisi, Bella Zhukova:
Fast Indexes for Gapped Pattern Matching. CoRR abs/2002.12662 (2020) - [i37]Zsuzsanna Lipták, Simon J. Puglisi, Massimiliano Rossi:
Pattern Discovery in Colored Strings. CoRR abs/2004.04858 (2020)
2010 – 2019
- 2019
- [j35]Simon Gog, Juha Kärkkäinen, Dominik Kempa, Matthias Petri, Simon J. Puglisi:
Fixed Block Compression Boosting in FM-Indexes: Theory and Practice. Algorithmica 81(4): 1370-1391 (2019) - [j34]Martin D. Muggli, Simon J. Puglisi, Christina Boucher:
Kohdista: an efficient method to index and query possible Rmap alignments. Algorithms Mol. Biol. 14(1): 25 (2019) - [c81]Hayam Alamro, Golnaz Badkobeh, Djamal Belazzougui, Costas S. Iliopoulos, Simon J. Puglisi:
Computing the Antiperiod(s) of a String. CPM 2019: 32:1-32:11 - [c80]Simon J. Puglisi, Massimiliano Rossi:
On Lempel-Ziv Decompression in Small Space. DCC 2019: 221-230 - [c79]Rafael Ktistakis, Philippe Fournier-Viger, Simon J. Puglisi, Rajeev Raman:
Succinct BWT-Based Sequence Prediction. DEXA (2) 2019: 91-101 - [e4]Nieves R. Brisaboa, Simon J. Puglisi:
String Processing and Information Retrieval - 26th International Symposium, SPIRE 2019, Segovia, Spain, October 7-9, 2019, Proceedings. Lecture Notes in Computer Science 11811, Springer 2019, ISBN 978-3-030-32685-2 [contents] - [i36]Daniel Valenzuela, Dmitry Kosolobov, Gonzalo Navarro, Simon J. Puglisi:
Lempel-Ziv-like Parsing in Small Space. CoRR abs/1903.01909 (2019) - 2018
- [j33]Andrea Farruggia, Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén:
Relative Suffix Trees. Comput. J. 61(5): 773-788 (2018) - [j32]Andreas Poyias, Simon J. Puglisi, Rajeev Raman:
m-Bonsai: A Practical Compact Dynamic Trie. Int. J. Found. Comput. Sci. 29(8): 1257-1278 (2018) - [j31]Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali, Simon J. Puglisi:
Bidirectional Variable-Order de Bruijn Graphs. Int. J. Found. Comput. Sci. 29(8): 1279-1295 (2018) - [j30]Golnaz Badkobeh, Gabriele Fici, Simon J. Puglisi:
Algorithms for anti-powers in strings. Inf. Process. Lett. 137: 57-60 (2018) - [j29]Veli Mäkinen, Simon J. Puglisi:
Editorial: Special Issue on "Combinatorial Algorithms" (IWOCA 2016). Theory Comput. Syst. 62(6): 1349-1350 (2018) - [c78]Héctor Ferrada, Dominik Kempa, Simon J. Puglisi:
Hybrid Indexing Revisited. ALENEX 2018: 1-8 - [c77]José Fuentes-Sepúlveda, Juha Kärkkäinen, Dmitry Kosolobov, Simon J. Puglisi:
Run Compressed Rank/Select for Large Alphabets. DCC 2018: 315-324 - [c76]Martin D. Muggli, Simon J. Puglisi, Christina Boucher:
A Succinct Solution to Rmap Alignment. WABI 2018: 12:1-12:16 - [i35]Diego Díaz-Domínguez, Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Gonzalo Navarro, Simon J. Puglisi:
Assembling Omnitigs using Hidden-Order de Bruijn Graphs. CoRR abs/1805.05228 (2018) - [i34]Golnaz Badkobeh, Gabriele Fici, Simon J. Puglisi:
Algorithms for Anti-Powers in Strings. CoRR abs/1805.10042 (2018) - 2017
- [j28]Alice Héliou, Solon P. Pissis, Simon J. Puglisi:
emMAW: computing minimal absent words in external memory. Bioinform. 33(17): 2746-2749 (2017) - [j27]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): 3181-3187 (2017) - [j26]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): 253-291 (2017) - [j25]Travis Gagie, Christopher Hoobin, Simon J. Puglisi:
Block Graphs in Practice. Math. Comput. Sci. 11(2): 191-196 (2017) - [c75]Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi, Bella Zhukova:
Engineering External Memory Induced Suffix Sorting. ALENEX 2017: 98-108 - [c74]Andreas Poyias, Simon J. Puglisi, Rajeev Raman:
Compact Dynamic Rewritable (CDRW) Arrays. ALENEX 2017: 109-119 - [c73]Juha Kärkkäinen, Marcin Piatkowski, Simon J. Puglisi:
String Inference from Longest-Common-Prefix Array. ICALP 2017: 62:1-62:14 - [c72]Yasuo Tabei, Simon J. Puglisi:
Scalable Similarity Search for Molecular Descriptors. SISAP 2017: 207-219 - [c71]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: 51-67 - [c70]Golnaz Badkobeh, Juha Kärkkäinen, Simon J. Puglisi, Bella Zhukova:
On Suffix Tree Breadth. SPIRE 2017: 68-73 - [c69]Juha Kärkkäinen, Dominik Kempa, Yuto Nakashima, Simon J. Puglisi, Arseny M. Shur:
On the Size of Lempel-Ziv and Lyndon Factorizations. STACS 2017: 45:1-45:13 - [c68]Simon J. Puglisi:
Dynamic Succinct Data Structures and Compressed Random Access Memory. Stringology 2017: 1-1 - [c67]Bahar Alipanahi, Leena Salmela, Simon J. Puglisi, Martin D. Muggli, Christina Boucher:
Disentangled Long-Read De Bruijn Graphs via Optical Maps. WABI 2017: 1:1-1:14 - [e3]Costas S. Iliopoulos, Solon P. Pissis, Simon J. Puglisi, Rajeev Raman:
16th International Symposium on Experimental Algorithms, SEA 2017, June 21-23, 2017, London, UK. LIPIcs 75, Schloss Dagstuhl - Leibniz-Zentrum für Informatik 2017, ISBN 978-3-95977-036-1 [contents] - [i33]Andreas Poyias, Simon J. Puglisi, Rajeev Raman:
m-Bonsai: a Practical Compact Dynamic Trie. CoRR abs/1704.05682 (2017) - [i32]Golnaz Badkobeh, Travis Gagie, Shunsuke Inenaga, Dmitry Kosolobov, Simon J. Puglisi:
On Two LZ78-style Grammars: Compression Bounds and Compressed-Space Computation. CoRR abs/1705.09538 (2017) - [i31]José Fuentes-Sepúlveda, Juha Kärkkäinen, Dmitry Kosolobov, Simon J. Puglisi:
Run Compressed Rank/Select for Large Alphabets. CoRR abs/1711.02910 (2017) - 2016
- [j24]Golnaz Badkobeh, Hideo Bannai, Keisuke Goto, Tomohiro I, Costas S. Iliopoulos, Shunsuke Inenaga, Simon J. Puglisi, Shiho Sugimoto:
Closed factorization. Discret. Appl. Math. 212: 23-29 (2016) - [j23]Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi:
Lazy Lempel-Ziv Factorization Algorithms. ACM J. Exp. Algorithmics 21(1): 2.4:1-2.4:19 (2016) - [j22]Costas S. Iliopoulos, Simon J. Puglisi:
Foreword. Theor. Comput. Sci. 656: 107 (2016) - [c66]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: 1:1-1:10 - [c65]Simon Gog, Juha Kärkkäinen, Dominik Kempa, Matthias Petri, Simon J. Puglisi:
Faster, Minuter. DCC 2016: 53-62 - [c64]Yasuo Tabei, Hiroto Saigo, Yoshihiro Yamanishi, Simon J. Puglisi:
Scalable Partial Least Squares Regression on Grammar-Compressed Data Matrices. KDD 2016: 1875-1884 - [c63]Djamal Belazzougui, Travis Gagie, Veli Mäkinen, Marco Previtali, Simon J. Puglisi:
Bidirectional Variable-Order de Bruijn Graphs. LATIN 2016: 164-178 - [c62]Djamal Belazzougui, Simon J. Puglisi:
Range Predecessor and Lempel-Ziv Parsing. SODA 2016: 2053-2071 - [c61]Anthony J. Cox, Andrea Farruggia, Travis Gagie, Simon J. Puglisi, Jouni Sirén:
RLZAP: Relative Lempel-Ziv with Adaptive Pointers. SPIRE 2016: 1-14 - [c60]Travis Gagie, Simon J. Puglisi, Daniel Valenzuela:
Analyzing Relative Lempel-Ziv Reference Construction. SPIRE 2016: 160-165 - [c59]Golnaz Badkobeh, Travis Gagie, Szymon Grabowski, Yuto Nakashima, Simon J. Puglisi, Shiho Sugimoto:
Longest Common Abelian Factors and Large Alphabets. SPIRE 2016: 254-259 - [c58]Djamal Belazzougui, Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi:
Lempel-Ziv Decoding in External Memory. SEA 2016: 63-74 - [e2]Veli Mäkinen, Simon J. Puglisi, Leena Salmela:
Combinatorial Algorithms - 27th International Workshop, IWOCA 2016, Helsinki, Finland, August 17-19, 2016, Proceedings. Lecture Notes in Computer Science 9843, Springer 2016, ISBN 978-3-319-44542-7 [contents] - [r1]Simon J. Puglisi:
Lempel-Ziv Compression. Encyclopedia of Algorithms 2016: 1095-1100 - [i30]Yuka Tanimura, Tomohiro I, Hideo Bannai, Shunsuke Inenaga, Simon J. Puglisi, Masayuki Takeda:
Deterministic sub-linear space LCE data structures with efficient construction. CoRR abs/1601.07670 (2016) - [i29]Djamal Belazzougui, Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi:
Lempel-Ziv Decoding in External Memory. CoRR abs/1602.00329 (2016) - [i28]Anthony J. Cox, Andrea Farruggia, Travis Gagie, Simon J. Puglisi, Jouni Sirén:
RLZAP: Relative Lempel-Ziv with Adaptive Pointers. CoRR abs/1605.04421 (2016) - [i27]Travis Gagie, Aleksi Hartikainen, Kalle Karhu, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén:
Document Retrieval on Repetitive String Collections. CoRR abs/1605.09362 (2016) - [i26]Juha Kärkkäinen, Marcin Piatkowski, Simon J. Puglisi:
String Inference from the LCP Array. CoRR abs/1606.04573 (2016) - [i25]Yasuo Tabei, Hiroto Saigo, Yoshihiro Yamanishi, Simon J. Puglisi:
Scalable Partial Least Squares Regression on Grammar-Compressed Data Matrices. CoRR abs/1606.05031 (2016) - [i24]Juha Kärkkäinen, Dominik Kempa, Yuto Nakashima, Simon J. Puglisi, Arseny M. Shur:
On the Size of Lempel-Ziv and Lyndon Factorizations. CoRR abs/1611.08898 (2016) - [i23]Yasuo Tabei, Simon J. Puglisi:
Scalable Similarity Search for Molecular Descriptors. CoRR abs/1611.10045 (2016) - 2015
- [j21]Martin D. Muggli, Simon J. Puglisi, Roy Ronen, Christina Boucher:
Misassembly detection using paired-end sequence reads and optical mapping data. Bioinform. 31(12): 80-88 (2015) - [j20]Travis Gagie, Pawel Gawrychowski, Simon J. Puglisi:
Approximate pattern matching in LZ77-compressed texts. J. Discrete Algorithms 32: 64-68 (2015) - [c57]Christopher Hoobin, Trey Kind, Christina Boucher, Simon J. Puglisi:
Fast and efficient compression of high-throughput sequencing reads. BCB 2015: 325-334 - [c56]Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi:
Parallel External Memory Suffix Sorting. CPM 2015: 329-342 - [c55]Djamal Belazzougui, Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Alberto Ordóñez Pereira, Simon J. Puglisi, Yasuo Tabei:
Queries on LZ-Bounded Encodings. DCC 2015: 83-92 - [c54]Travis Gagie, Aleksi Hartikainen, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén:
Document Counting in Compressed Space. DCC 2015: 103-112 - [c53]Christina Boucher, Alexander Bowe, Travis Gagie, Simon J. Puglisi, Kunihiko Sadakane:
Variable-Order de Bruijn Graphs. DCC 2015: 383-392 - [c52]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: 85-96 - [c51]Djamal Belazzougui, Patrick Hagge Cording, Simon J. Puglisi, Yasuo Tabei:
Access, Rank, and Select in Grammar-compressed Strings. ESA 2015: 142-154 - [e1]Costas S. Iliopoulos, Simon J. Puglisi, Emine Yilmaz:
String Processing and Information Retrieval - 22nd International Symposium, SPIRE 2015, London, UK, September 1-4, 2015, Proceedings. Lecture Notes in Computer Science 9309, Springer 2015, ISBN 978-3-319-23825-8 [contents] - [i22]Travis Gagie, Shunsuke Inenaga, Juha Kärkkäinen, Dominik Kempa, Marcin Piatkowski, Simon J. Puglisi, Shiho Sugimoto:
Diverse Palindromic Factorization is NP-Complete. CoRR abs/1503.04045 (2015) - [i21]Djamal Belazzougui, Simon J. Puglisi:
Range Predecessor and Lempel-Ziv Parsing. CoRR abs/1507.07080 (2015) - [i20]Travis Gagie, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén:
Relative Compressed Suffix Trees. CoRR abs/1508.02550 (2015) - 2014
- [j19]Gonzalo Navarro, Simon J. Puglisi, Daniel Valenzuela:
General Document Retrieval in Compact Space. ACM J. Exp. Algorithmics 19(1) (2014) - [j18]Jinil Kim, Peter Eades, Rudolf Fleischer, Seok-Hee Hong, Costas S. Iliopoulos, Kunsoo Park, Simon J. Puglisi, Takeshi Tokuyama:
Order-preserving matching. Theor. Comput. Sci. 525: 68-79 (2014) - [c50]Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi:
String Range Matching. CPM 2014: 232-241 - [c49]Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi:
Lempel-Ziv Parsing in External Memory. DCC 2014: 153-162 - [c48]Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi:
Hybrid Compression of Bitvectors for the FM-Index. DCC 2014: 302-311 - [c47]Travis Gagie, Simon J. Puglisi:
Relative Lempel-Ziv with Constant-Time Random Access. DCC 2014: 405 - [c46]Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén:
Document Retrieval on Repetitive Collections. ESA 2014: 725-736 - [c45]Travis Gagie, Christopher Hoobin, Simon J. Puglisi:
Block Graphs in Practice. ICABD 2014: 30-36 - [c44]Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Yakov Nekrich, Simon J. Puglisi:
LZ77-Based Self-indexing with Faster Pattern Matching. LATIN 2014: 731-742 - [c43]Héctor Ferrada, Travis Gagie, Simon Gog, Simon J. Puglisi:
Relative Lempel-Ziv with Constant-Time Random Access. SPIRE 2014: 13-17 - [c42]Golnaz Badkobeh, Hideo Bannai, Keisuke Goto, Tomohiro I, Costas S. Iliopoulos, Shunsuke Inenaga, Simon J. Puglisi, Shiho Sugimoto:
Closed Factorization. Stringology 2014: 162-168 - [c41]Martin D. Muggli, Simon J. Puglisi, Christina Boucher:
Efficient Indexed Alignment of Contigs to Optical Maps. WABI 2014: 68-81 - [i19]Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén:
Document Retrieval on Repetitive Collections. CoRR abs/1404.4909 (2014) - [i18]Djamal Belazzougui, Simon J. Puglisi, Yasuo Tabei:
Rank, select and access in grammar-compressed strings. CoRR abs/1408.3093 (2014) - [i17]Travis Gagie, Aleksi Hartikainen, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén:
Document Counting in Practice. CoRR abs/1409.6780 (2014) - [i16]Christina Boucher, Alexander Bowe, Travis Gagie, Simon J. Puglisi, Kunihiko Sadakane:
Variable-Order de Bruijn Graphs. CoRR abs/1411.2718 (2014) - [i15]Martin D. Muggli, Simon J. Puglisi, Roy Ronen, Christina Boucher:
Misassembly Detection using Paired-End Sequence Reads and Optical Mapping Data. CoRR abs/1411.5890 (2014) - [i14]Djamal Belazzougui, Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Alberto Ordóñez Pereira, Simon J. Puglisi, Yasuo Tabei:
Queries on LZ-Bounded Encodings. CoRR abs/1412.0967 (2014) - [i13]Travis Gagie, Simon J. Puglisi:
Searching and Indexing Genomic Databases via Kernelization. CoRR abs/1412.1591 (2014) - 2013
- [j17]Travis Gagie, Juha Kärkkäinen, Gonzalo Navarro, Simon J. Puglisi:
Colored range queries and document retrieval. Theor. Comput. Sci. 483: 36-50 (2013) - [j16]Tomás Flouri, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Simon J. Puglisi, W. F. Smyth, Wojciech Tyczynski:
Enhanced string covering. Theor. Comput. Sci. 506: 102-114 (2013) - [c40]Dominik Kempa, Simon J. Puglisi:
Lempel-Ziv factorization: Simple, fast, practical. ALENEX 2013: 103-112 - [c39]Travis Gagie, Kalle Karhu, Gonzalo Navarro, Simon J. Puglisi, Jouni Sirén:
Document Listing on Repetitive Collections. CPM 2013: 107-119 - [c38]Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi:
Linear Time Lempel-Ziv Factorization: Simple, Fast, Small. CPM 2013: 189-200 - [c37]Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi:
Crochemore's String Matching Algorithm: Simplification, Extensions, Applications. Stringology 2013: 168-175 - [c36]Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi:
Lightweight Lempel-Ziv Parsing. SEA 2013: 139-150 - [i12]Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi:
Lightweight Lempel-Ziv Parsing. CoRR abs/1302.1064 (2013) - [i11]Jinil Kim, Peter Eades, Rudolf Fleischer, Seok-Hee Hong, Costas S. Iliopoulos, Kunsoo Park, Simon J. Puglisi, Takeshi Tokuyama:
Order Preserving Matching. CoRR abs/1302.4064 (2013) - [i10]Héctor Ferrada, Travis Gagie, Tommi Hirvola, Simon J. Puglisi:
Hybrid Indexes for Repetitive Datasets. CoRR abs/1306.4037 (2013) - [i9]Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi:
Lempel-Ziv Parsing in External Memory. CoRR abs/1307.1428 (2013) - [i8]Héctor Ferrada, Travis Gagie, Tommi Hirvola, Simon J. Puglisi:
AliBI: An Alignment-Based Index for Genomic Datasets. CoRR abs/1307.6462 (2013) - 2012
- [j15]Laurent Mouchard, Simon J. Puglisi:
Editorial. J. Discrete Algorithms 17: 1 (2012) - [j14]J. Shane Culpepper, Matthias Petri, Simon J. Puglisi:
Revisiting bounded context block-sorting transformations. Softw. Pract. Exp. 42(8): 1037-1054 (2012) - [j13]Travis Gagie, Gonzalo Navarro, Simon J. Puglisi:
New algorithms on wavelet trees and applications to information retrieval. Theor. Comput. Sci. 426: 25-41 (2012) - [j12]Jasbir Dhaliwal, Simon J. Puglisi, Andrew Turpin:
Practical Efficient String Mining. IEEE Trans. Knowl. Data Eng. 24(4): 735-744 (2012) - [c35]Jasbir Dhaliwal, Simon J. Puglisi, Andrew Turpin:
Trends in Suffix Sorting: A Survey of Low Memory Algorithms. ACSC 2012: 91-98 - [c34]Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi:
Slashing the Time for BWT Inversion. DCC 2012: 99-108 - [c33]Travis Gagie, Pawel Gawrychowski, Juha Kärkkäinen, Yakov Nekrich, Simon J. Puglisi:
A Faster Grammar-Based Self-index. LATA 2012: 240-251 - [c32]Tomás Flouri, Costas S. Iliopoulos, Tomasz Kociumaka, Solon P. Pissis, Simon J. Puglisi, William F. Smyth, Wojciech Tyczynski:
New and Efficient Approaches to the Quasiperiodic Characterisation of a String. Stringology 2012: 75-88 - [c31]Niko Välimäki, Simon J. Puglisi:
Distributed String Mining for High-Throughput Sequencing Data. WABI 2012: 441-452 - [i7]Juha Kärkkäinen, Dominik Kempa, Simon J. Puglisi:
Linear Time Lempel-Ziv Factorization: Simple, Fast, Small. CoRR abs/1212.2952 (2012) - 2011
- [j11]Christopher Hoobin, Simon J. Puglisi, Justin Zobel:
Relative Lempel-Ziv Factorization for Efficient Storage and Retrieval of Web Collections. Proc. VLDB Endow. 5(3): 265-273 (2011) - [c30]Shanika Kuruppu, Simon J. Puglisi, Justin Zobel:
Optimized Relative Lempel-Ziv Compression of Genomes. ACSC 2011: 91-98 - [c29]Juha Kärkkäinen, Simon J. Puglisi:
Cache Friendly Burrows-Wheeler Inversion. CCP 2011: 38-42 - [c28]Matthias Petri, Gonzalo Navarro, J. Shane Culpepper, Simon J. Puglisi:
Backwards Search in Context Bound Text Transformations. CCP 2011: 82-91 - [c27]Travis Gagie, Pawel Gawrychowski, Simon J. Puglisi:
Faster Approximate Pattern Matching in Compressed Repetitive Texts. ISAAC 2011: 653-662 - [c26]Christopher Hoobin, Simon J. Puglisi, Justin Zobel:
Sample selection for dictionary-based corpus compression. SIGIR 2011: 1137-1138 - [c25]Juha Kärkkäinen, Simon J. Puglisi:
Fixed Block Compression Boosting in FM-Indexes. SPIRE 2011: 174-184 - [c24]Shanika Kuruppu, Simon J. Puglisi, Justin Zobel:
Reference Sequence Construction for Relative Compression of Genomes. SPIRE 2011: 420-425 - [c23]Gonzalo Navarro, Simon J. Puglisi, Daniel Valenzuela:
Practical Compressed Document Retrieval. SEA 2011: 193-205 - [i6]Juha Kärkkäinen, Simon J. Puglisi:
Fixed Block Compression Boosting in FM-Indexes. CoRR abs/1104.3810 (2011) - [i5]Christopher Hoobin, Simon J. Puglisi, Justin Zobel:
Relative Lempel-Ziv Factorization for Efficient Storage and Retrieval of Web Collections. CoRR abs/1106.2587 (2011) - [i4]Shanika Kuruppu, Simon J. Puglisi, Justin Zobel:
Reference Sequence Construction for Relative Compression of Genomes. CoRR abs/1106.3791 (2011) - [i3]Travis Gagie, Pawel Gawrychowski, Simon J. Puglisi:
Faster Approximate Pattern Matching in Compressed Repetitive Texts. CoRR abs/1109.2930 (2011) - [i2]Travis Gagie, Juha Kärkkäinen, Yakov Nekrich, Simon J. Puglisi:
A Compressed Self-Index for Genomic Databases. CoRR abs/1111.1355 (2011) - 2010
- [j10]Simon J. Puglisi, William F. Smyth, Munina Yusufu:
Fast, Practical Algorithms for Computing All the Repeats in a String. Math. Comput. Sci. 3(4): 373-389 (2010) - [c22]Mingfang Wu, Andrew Turpin, Simon J. Puglisi, Falk Scholer, James A. Thom:
Presenting Query Aspects to Support Exploratory Search. AUIC 2010: 23-32 - [c21]J. Shane Culpepper, Gonzalo Navarro, Simon J. Puglisi, Andrew Turpin:
Top-k Ranked Document Search in General Text Databases. ESA (2) 2010: 194-205 - [c20]Juha Kärkkäinen, Simon J. Puglisi:
Medium-Space Algorithms for Inverse BWT. ESA (1) 2010: 451-462 - [c19]Travis Gagie, Gonzalo Navarro, Simon J. Puglisi:
Colored Range Queries and Document Retrieval. SPIRE 2010: 67-81 - [c18]Shanika Kuruppu, Simon J. Puglisi, Justin Zobel:
Relative Lempel-Ziv Compression of Genomes for Large-Scale Storage and Retrieval. SPIRE 2010: 201-206 - [c17]Gonzalo Navarro, Simon J. Puglisi:
Dual-Sorted Inverted Lists. SPIRE 2010: 309-321 - [i1]Travis Gagie, Gonzalo Navarro, Simon J. Puglisi:
New Algorithms on Wavelet Trees and Applications to Information Retrieval. CoRR abs/1011.4532 (2010)
2000 – 2009
- 2009
- [j9]Jan Schröder, Heiko Schröder, Simon J. Puglisi, Ranjan Sinha, Bertil Schmidt:
SHREC: a short-read error correction method. Bioinform. 25(17): 2157-2163 (2009) - [j8]Bertil Schmidt, Ranjan Sinha, Bryan Beresford-Smith, Simon J. Puglisi:
A fast hybrid short read fragment assembly algorithm. Bioinform. 25(17): 2279-2280 (2009) - [c16]Serdar Boztas, Simon J. Puglisi, Andrew Turpin:
Testing Stream Ciphers by Finding the Longest Substring of a Given Density. ACISP 2009: 122-133 - [c15]Juha Kärkkäinen, Giovanni Manzini, Simon J. Puglisi:
Permuted Longest-Common-Prefix Array. CPM 2009: 181-192 - [c14]Alistair Moffat, Simon J. Puglisi, Ranjan Sinha:
Reducing Space Requirements for Disk Resident Suffix Arrays. DASFAA 2009: 730-744 - [c13]Yohannes Tsegay, Simon J. Puglisi, Andrew Turpin, Justin Zobel:
Document Compaction for Efficient Query Biased Snippet Generation. ECIR 2009: 509-520 - [c12]Travis Gagie, Simon J. Puglisi, Andrew Turpin:
Range Quantile Queries: Another Virtue of Wavelet Trees. SPIRE 2009: 1-6 - 2008
- [j7]Simon J. Puglisi, Jamie Simpson:
The expected number of runs in a word. Australas. J Comb. 42: 45-54 (2008) - [j6]Jamie Simpson, Simon J. Puglisi:
Words with Simple Burrows-Wheeler Transforms. Electron. J. Comb. 15(1) (2008) - [j5]Gang Chen, Simon J. Puglisi, William F. Smyth:
Lempel-Ziv Factorization Using Less Time & Space. Math. Comput. Sci. 1(4): 605-623 (2008) - [j4]Simon J. Puglisi, Jamie Simpson, William F. Smyth:
How many runs can a string contain? Theor. Comput. Sci. 401(1-3): 165-171 (2008) - [c11]Simon J. Puglisi, Andrew Turpin:
Space-Time Tradeoffs for Longest-Common-Prefix Array Computation. ISAAC 2008: 124-135 - [c10]Ranjan Sinha, Simon J. Puglisi, Alistair Moffat, Andrew Turpin:
Improving suffix array locality for fast pattern matching on disk. SIGMOD Conference 2008: 661-672 - [c9]Simon J. Puglisi, William F. Smyth, Munina Yusufu:
Fast Optimal Algorithms for Computing All the Repeats in a String. Stringology 2008: 161-169 - [c8]Yohannes Tsegay, Falk Scholer, Simon J. Puglisi:
RMIT University at TREC 2008: Relevance Feedback Track. TREC 2008 - 2007
- [j3]Simon J. Puglisi, William F. Smyth, Andrew Turpin:
A taxonomy of suffix array construction algorithms. ACM Comput. Surv. 39(2): 4 (2007) - [j2]Michael A. Maniscalco, Simon J. Puglisi:
An efficient, versatile approach to suffix sorting. ACM J. Exp. Algorithmics 12: 1.2:1-1.2:23 (2007) - [c7]Gang Chen, Simon J. Puglisi, William F. Smyth:
Fast and Practical Algorithms for Computing All the Runs in a String. CPM 2007: 307-315 - [c6]Hamid Abdul Basit, Simon J. Puglisi, William F. Smyth, Andrew Turpin, Stan Jarzabek:
Efficient token based clone detection with flexible tokenization. ESEC/SIGSOFT FSE 2007: 513-516 - [c5]Mingfang Wu, Falk Scholer, Milad Shokouhi, Simon J. Puglisi, Halil Ali:
RMIT University at the TREC 2007 Enterprise Track. TREC 2007 - 2006
- [j1]Kangmin Fan, Simon J. Puglisi, William F. Smyth, Andrew Turpin:
A New Periodicity Lemma. SIAM J. Discret. Math. 20(3): 656-668 (2006) - [c4]Simon J. Puglisi, William F. Smyth, Andrew Turpin:
Suffix arrays: what are they good for? ADC 2006: 17-18 - [c3]Simon J. Puglisi, William F. Smyth, Andrew Turpin:
Inverted Files Versus Suffix Arrays for Locating Patterns in Primary Memory. SPIRE 2006: 122-133 - 2005
- [c2]Simon J. Puglisi, William F. Smyth, Andrew Turpin:
The Performance of Linear Time Suffix Sorting Algorithms. DCC 2005: 358-367 - [c1]Simon J. Puglisi, William F. Smyth, Andrew Turpin:
A taxonomy of suffix array construction algorithms. Stringology 2005: 1-30
Coauthor Index
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