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Publications 2012 2019

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2019

On Lempel-Ziv Decompression in Small Space

Puglisi, S. J. & Rossi, M., 2019, 2019 DATA COMPRESSION CONFERENCE (DCC). New York: IEEE, p. 221-230 10 p. (IEEE Data Compression Conference).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2018

Run compressed rank/select for large alphabets

Fuentes-Sepulveda, J., Karkkainen, J., Kosolobov, D. & Puglisi, S., 2018, 2018 Data Compression Conference 27–30 March 2018 Snowbird, Utah, USA. Bilgin, A., Marcellin, M. W., Serra-Sagrista, J. & Storer, J. A. (eds.). IEEE, p. 315-324 10 p. (DCC).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2017

Disentangled long-read de Bruijn graphs via optical maps

Alipahani, B., Salmela, L., Puglisi, S. J., Muggli, M. & Boucher, C., 2017, 17th International Workshop on Algorithms in Bioinformatics, WABI 2017. Schwartz, R. & Reinert, K. (eds.). Dagstuhl: Schloss Dagstuhl - Leibniz-Zentrum für Informatik, p. 1:1-1:14 14 p. (Leibniz International Proceedings in Informatics; vol. 88).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Open Access
File

Engineering External Memory Induced Suffix Sorting

Kärkkäinen, J., Kempa, D., Puglisi, S. J. & Zhukova, B., 2017, 2017 Proceedings of the Ninteenth Workshop on Algorithm Engineering and Experiments (ALENEX). Fekete, S. & Ramachandran, V. (eds.). Society for Industrial and Applied Mathematics, p. 98-108 11 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

On Suffix Tree Breadth

Badkobeh, G., Kärkkäinen, J., Puglisi, S. J. & Zhukova, B., Sep 2017, String Processing and Information Retrieval: 24th International Symposium, SPIRE 2017. Palermo, Italy, September 26-29, 2017. Proceedings. Fici, G., Sciortino, M. & Venturini, R. (eds.). Cham: Springer, p. 68-73 6 p. (Lecture Notes in Computer Science; vol. 10508).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

On the Size of Lempel-Ziv and Lyndon Factorizations

Kärkkäinen, J., Kempa, D., Nakashima, Y., Puglisi, S. J. & Shur, A. M., 2017, 34th Symposium on Theoretical Aspects of Computer Science (STACS 2017). Vollmer, H. & Vallée, B. (eds.). Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 13 p. 45. (Leibniz International Proceedings in Informatics (LIPIcs); vol. 66).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Open Access
File

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

Kosolobov, D., Puglisi, S. J., Kociumaka, T., Gagie, T., Badkobeh, G. & Inenaga, S., 2017, String Processing and Information Retrieval: 24th International Symposium, SPIRE 2017 Palermo, Italy, September 26–29, 2017 Proceedings 123. Fici, G., Sciortino, M. & Venturini, R. (eds.). Cham: Springer, p. 51-67 17 p. (Lecture Notes in Computer Science (LNCS); no. 10508).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Open Access

String Inference from Longest-Common-Prefix Array

Kärkkäinen, J., Piątkowski, M. & Puglisi, S. J., 2017, 44th International Colloquium on Automata, Languages, and Programming (ICALP 2017). Chatzigiannakis, I., Indyk, P., Kuhn, F. & Muscholl, A. (eds.). Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 14 p. 62. (Leibniz International Proceedings in Informatics (LIPIcs); vol. 80).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Open Access
File
2016

Analyzing Relative Lempel-Ziv Reference Construction

Gagie, T., Puglisi, S. J. & Valenzuela, D., 18 Oct 2016, String Processing and Information Retrieval: 23rd International Symposium, SPIRE 2016, Beppu, Japan, October 18-20, 2016, Proceedings. Springer, p. 160-165 6 p. (Lecture Notes in Computer Science; vol. 9954).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Bidirectional Variable-Order de Bruijn Graphs

Belazzougui, D., Gagie, T., Mäkinen, V. A. T., Previtali, M. & Puglisi, S. J., 2016, Theoretical informatics: LATIN 2016: 12th Latin American Symposium, Ensenada, Mexico, April 11-15, 2016 : proceedings. Kranakis, E., Navarro, G. & Chávez, E. (eds.). Berlin: Springer, p. 164-178 9 p. (Lecture Notes in Computer Science; vol. 9644).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Faster, Minuter

Gog, S., Kärkkäinen, J., Kempa, D., Petri, M. & Puglisi, S. J., 2016, DCC 2016: 2016 Data Compression Conference, 29 March-1 April 2016, Snowbird, Utah, USA. Bilgin, A., Marcellin, M. W., Serra-Sagrista, J. & Storer, J. A. (eds.). New York, NY: IEEE, p. 53-62 10 p. ( IEEE Data Compression Conference).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Lempel-Ziv Decoding in External Memory

Belazzougui, D., Kärkkäinen, J., Kempa, D. & Puglisi, S. J., 2016, Experimental Algorithms: 15th International Symposium, SEA 2016, St. Petersburg, Russia, June 5-8, 2016, Proceedings. Goldberg, A. V. & Kulikov, A. S. (eds.). Cham: Springer International Publishing , p. 63-74 12 p. (Lecture Notes in Computer Science; vol. 9685).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Longest Common Abelian Factors and Large Alphabets

Badkobeh, G., Gagie, T., Grabowski, S., Nakashima, Y., Puglisi, S. J. & Sugimoto, S., 2016, String Processing and Information Retrieval: 23rd International Symposium, SPIRE 2016, Beppu, Japan, October 18-20, 2016, Proceedings. Inenaga, S., Sadakane, K. & Sakai, T. (eds.). Springer International Publishing AG, p. 254-259 6 p. (Lecture Notes in Computer Science; vol. 9954).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2015

Access, Rank, and Select in Grammar-compressed Strings

Belazzougui, D., Cording, P. H., Puglisi, S. J. & Tabei, Y., 2015, Algorithms – ESA 2015: 23rd Annual European Symposium Patras, Greece, September 14–16, 2015, Proceedings. Bansal, N. & Finocchi, I. (eds.). Heidelberg: Springer, p. 142-154 13 p. (Lecture Notes in Computer Science; vol. 9294).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Diverse Palindromic Factorization is NP-Complete

Bannai, H., Gagie, T., Inenaga, S., Kärkkäinen, J. T., Kempa, D., Piątkowski, M., Puglisi, S. J. & Sugimoto, S., 2015, Developments in Language Theory: 19th International Conference, DLT 2015, Liverpool, UK, July 27-30, 2015, Proceedings. Potapov, I. (ed.). Cham: Springer International Publishing AG, p. 85-96 12 p. (Lecture Notes in Computer Science; vol. 9168).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Document Counting in Compressed Space

Gagie, T., Hartikainen, A., Kärkkäinen, J., Navarro, G., Puglisi, S. J. & Sirén, J., 2015, DCC 2015: 2015 Data Compression Conference, 7-9 April 2015, Snowbird, Utah, USA. Bilgin, A., Marcellin, M. W., Serra-Sagrista, J. & Storer, J. A. (eds.). Los Alamitos, CA: IEEE, p. 103-112 10 p. (Data Compression Conference. Proceedings ).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Fast and efficient compression of high-throughput sequencing reads

Hoobin, C., Kind, T., Boucher, C. & Puglisi, S. J., 2015, Proceedings of the 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics . New York: ACM , p. 325-334 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Parallel External Memory Suffix Sorting

Kärkkäinen, J., Kempa, D. & Puglisi, S. J., 16 Jun 2015, Combinatorial Pattern Matching: 26th Annual Symposium, CPM 2015, Ischia Island, Italy, June 29 -- July 1, 2015, Proceedings. Cicalese, F., Porat, E. & Vaccaro, U. (eds.). Springer International Publishing AG, p. 329-342 14 p. (Lecture Notes in Computer Science; vol. 9133).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Queries on LZ-Bounded Encodings

Belazzougui, D., Gagie, T., Gawrychowski, P., Kärkkäinen, J., Pereira, A. O., Puglisi, S. J. & Tabei, Y., 2015, Proceedings DCC 2015 Data Compression Conference: 7-9 April 2015, Snowbird, Utah, USA. Bilgin, A., Marcellin, M. W., Serra-Sagrista, J. & Storer, J. A. (eds.). Los Alamitos, CA: IEEE Computer Society Conference Publishing Services, p. 83-92 10 p. (IEEE Data Compression Conference).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Variable-Order de Bruijn Graphs

Boucher, C., Bowe, A., Gagie, T., Puglisi, S. J. & Sadakane, K., 2015, DCC 2015 : 2015 Data Compression Conference, 7-9 April 2015, Snowbird, Utah, USA. Bilgin, A., Marcellin, M. W., Serra-Sagrista, J. & Storer, J. A. (eds.). Los Alamitos, CA: IEEE, p. 383-392 10 p. (Data Compression Conference. Proceedings ).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2014

Block Graphs in Practice

Gagie, T., Hoobin, C. & Puglisi, S. J., 2014, Unknown host publication. Iliopoulos, C. S. & Langiu, A. (eds.). CEUR-WS.org, p. 30-36 7 p. (CEUR Workshop Proceedings; vol. 1146).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Document Retrieval on Repetitive Collections

Navarro, G., Puglisi, S. J. & Sirén, J., 2014, Proceedings of the 22th Annual European Symposium on Algorithms (ESA 2014): 22th Annual European Symposium, Wroclaw, Poland, September 8-10, 2014. Proceedings. Schulz, A. S. & Wagner, D. (eds.). Berlin: Springer, p. 725-736 12 p. (Lecture Notes in Computer Science; vol. 8737).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Hybrid Compression of Bitvectors for the FM-Index

Kärkkäinen, J., Kempa, D. & Puglisi, S., 2014, Proceedings [of] Data Compression Conference 26-28 March 2014, Snowbird, Utah, USA. Bilgin, A., Marcellin, M. W., Serra-Sagristà, J. & Storer, J. A. (eds.). Los Alamitos, CA: IEEE, p. 302-311 10 p. (Data Compression Conference).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Lempel-Ziv Parsing in External Memory

Kärkkäinen, J., Kempa, D. & Puglisi, S. J., 2014, Proceedings [of] Data Compression Conference 26-28 March 2014, Snowbird, Utah, USA. Bilgin, A., Marcellin, M. W., Serra-Sagristà, J. & Storer, J. A. (eds.). Los Alamitos, CA: IEEE, p. 153-162 10 p. (Data Compression Conference).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Relative Lempel-Ziv with Constant-Time Random Access

Ferrada, H., Gagie, T., Gog, S. & Puglisi, S. J., 2014, String Processing and Information Retrieval : 21st International Symposium, SPIRE 2014, Ouro Preto, Brazil, October 20-22, 2014. Proceedings. Moura, E. S. D. & Crochemore, M. (eds.). Cham: Springer, p. 13-17 5 p. (Lecture Notes in Computer Science; vol. 8799).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Relative Lempel-Ziv with Constant-Time Random Access.

Ferrada Escobar, H. R., Puglisi, S. J., Gagie, T. & Navarro, G., 2014, Unknown host publication.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

String Range Matching

Kärkkäinen, J., Kempa, D. & Puglisi, S. J., 2014, Combinatorial Pattern Matching: 25th Annual Symposium, CPM 2014, Moscow, Russia, June 16-18, 2014. Proceedings. Kulikov, A. S., Kuznetsov, S. O. & Pevzner, P. (eds.). Springer International Publishing AG, p. 232-241 10 p. (Lecture Notes in Computer Science; vol. 8486).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2013

Crochemore’s String Matching Algorithm: Simplification, Extensions, Applications

Kärkkäinen, J., Kempa, D. & Puglisi, S., 2013, Proceedings of the Prague Stringology Conference 2013. Holub, J. & Žďárek, J. (eds.). Czech Technical University in Prague, Department of Theoretical Computer Science, Faculty of Information Technology, p. 168-175 8 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Document Listing on Repetitive Collections

Gagie, T., Karhu, K., Navarro, G., Puglisi, S. & Siren, J., 2013, Combinatorial Pattern Matching: 24th Annual Symposium, CPM 2013, Bad Herrenalb, Germany, June 17-19, 2013. Proceedings. Fischer, J. & Sanders, P. (eds.). Springer-Verlag, p. 107-119 (Lecture Notes in Computer Science; vol. 7922).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Lempel-Ziv factorization: Simple, fast, practical

Kempa, D. & Puglisi, S., Jan 2013, Proceedings of the Meeting on Algorithm Engineering and Experiments (ALENEX). Sanders, P. & Zeh, N. (eds.). Philadelphia: Society for Industrial and Applied Mathematics, p. 103-112 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

Lightweight Lempel-Ziv Parsing

Kärkkäinen, J., Kempa, D. & Puglisi, S., 2013, Experimental Algorithms: 12th International Symposium, SEA 2013, Rome, Italy, June 5-7, 2013. Proceedings. Bonifaci, V., Demetrescu, C. & Marchetti-Spaccamela, A. (eds.). Springer-Verlag, p. 139-150 12 p. (Lecture Notes in Computer Science; vol. 7933).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

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

Kärkkäinen, J., Kempa, D. & Puglisi, S., 2013, Combinatorial Pattern Matching: 24th Annual Symposium, CPM 2013, Bad Herrenalb, Germany, June 17-19, 2013. Proceedings. Fischer, J. & Sanders, P. (eds.). Springer-Verlag, p. 189-200 12 p. (Lecture Notes in Computer Science; vol. 7922).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review

2012

Distributed String Mining for High-Throughput Sequencing Data

Välimäki, N. & Puglisi, S. J., 2012, Algorithms in Bioinformatics: 12th International Workshop, WABI 2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings. Raphael, B. & Tang, J. (eds.). Springer-Verlag, p. 441-452 (Lecture Notes in Computer Science; vol. 7534).

Research output: Chapter in Book/Report/Conference proceedingConference contributionScientificpeer-review