Published in: LIPIcs, Volume 223, 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)
Sharma V. Thankachan. Compact Text Indexing for Advanced Pattern Matching Problems: Parameterized, Order-Isomorphic, 2D, etc. (Invited Talk). In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 3:1-3:3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{thankachan:LIPIcs.CPM.2022.3, author = {Thankachan, Sharma V.}, title = {{Compact Text Indexing for Advanced Pattern Matching Problems: Parameterized, Order-Isomorphic, 2D, etc.}}, booktitle = {33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)}, pages = {3:1--3:3}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-234-1}, ISSN = {1868-8969}, year = {2022}, volume = {223}, editor = {Bannai, Hideo and Holub, Jan}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.3}, URN = {urn:nbn:de:0030-drops-161300}, doi = {10.4230/LIPIcs.CPM.2022.3}, annote = {Keywords: Text Indexing, Suffix Trees, String Matching} }
Published in: LIPIcs, Volume 212, 32nd International Symposium on Algorithms and Computation (ISAAC 2021)
Dhrumil Patel and Rahul Shah. Inverse Suffix Array Queries for 2-Dimensional Pattern Matching in Near-Compact Space. In 32nd International Symposium on Algorithms and Computation (ISAAC 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 212, pp. 60:1-60:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{patel_et_al:LIPIcs.ISAAC.2021.60, author = {Patel, Dhrumil and Shah, Rahul}, title = {{Inverse Suffix Array Queries for 2-Dimensional Pattern Matching in Near-Compact Space}}, booktitle = {32nd International Symposium on Algorithms and Computation (ISAAC 2021)}, pages = {60:1--60:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-214-3}, ISSN = {1868-8969}, year = {2021}, volume = {212}, editor = {Ahn, Hee-Kap and Sadakane, Kunihiko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2021.60}, URN = {urn:nbn:de:0030-drops-154932}, doi = {10.4230/LIPIcs.ISAAC.2021.60}, annote = {Keywords: Pattern Matching, Succinct Data Structures} }
Published in: LIPIcs, Volume 212, 32nd International Symposium on Algorithms and Computation (ISAAC 2021)
Paolo Ferragina, Giovanni Manzini, and Giorgio Vinciguerra. Repetition- and Linearity-Aware Rank/Select Dictionaries. In 32nd International Symposium on Algorithms and Computation (ISAAC 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 212, pp. 64:1-64:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{ferragina_et_al:LIPIcs.ISAAC.2021.64, author = {Ferragina, Paolo and Manzini, Giovanni and Vinciguerra, Giorgio}, title = {{Repetition- and Linearity-Aware Rank/Select Dictionaries}}, booktitle = {32nd International Symposium on Algorithms and Computation (ISAAC 2021)}, pages = {64:1--64:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-214-3}, ISSN = {1868-8969}, year = {2021}, volume = {212}, editor = {Ahn, Hee-Kap and Sadakane, Kunihiko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2021.64}, URN = {urn:nbn:de:0030-drops-154974}, doi = {10.4230/LIPIcs.ISAAC.2021.64}, annote = {Keywords: Data compression, Compressed data structures, Entropy} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Travis Gagie, Garance Gourdel, and Giovanni Manzini. Compressing and Indexing Aligned Readsets. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 13:1-13:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{gagie_et_al:LIPIcs.WABI.2021.13, author = {Gagie, Travis and Gourdel, Garance and Manzini, Giovanni}, title = {{Compressing and Indexing Aligned Readsets}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {13:1--13:21}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.13}, URN = {urn:nbn:de:0030-drops-143660}, doi = {10.4230/LIPIcs.WABI.2021.13}, annote = {Keywords: data compression, compact data structures, FM-index, Burrows-Wheeler Transform, EBWT, XBWT, DNA reads} }
Published in: Dagstuhl Reports, Volume 9, Issue 6 (2020)
Travis Gagie, Giovanni Manzini, Gonzalo Navarro, and Jens Stoye. 25 Years of the Burrows-Wheeler Transform (Dagstuhl Seminar 19241). In Dagstuhl Reports, Volume 9, Issue 6, pp. 55-68, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@Article{gagie_et_al:DagRep.9.6.55, author = {Gagie, Travis and Manzini, Giovanni and Navarro, Gonzalo and Stoye, Jens}, title = {{25 Years of the Burrows-Wheeler Transform (Dagstuhl Seminar 19241)}}, pages = {55--68}, journal = {Dagstuhl Reports}, ISSN = {2192-5283}, year = {2019}, volume = {9}, number = {6}, editor = {Gagie, Travis and Manzini, Giovanni and Navarro, Gonzalo and Stoye, Jens}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagRep.9.6.55}, URN = {urn:nbn:de:0030-drops-114874}, doi = {10.4230/DagRep.9.6.55}, annote = {Keywords: Bioinformatics, Burrows-Wheeler Transform, Combinatorics on Words, Data Compression, Data Structures, Indexing, Sequence Alignment} }
Published in: LIPIcs, Volume 138, 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)
Alberto Dennunzio, Enrico Formenti, Darij Grinberg, and Luciano Margara. Additive Cellular Automata Over Finite Abelian Groups: Topological and Measure Theoretic Properties. In 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 138, pp. 68:1-68:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{dennunzio_et_al:LIPIcs.MFCS.2019.68, author = {Dennunzio, Alberto and Formenti, Enrico and Grinberg, Darij and Margara, Luciano}, title = {{Additive Cellular Automata Over Finite Abelian Groups: Topological and Measure Theoretic Properties}}, booktitle = {44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)}, pages = {68:1--68:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-117-7}, ISSN = {1868-8969}, year = {2019}, volume = {138}, editor = {Rossmanith, Peter and Heggernes, Pinar and Katoen, Joost-Pieter}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2019.68}, URN = {urn:nbn:de:0030-drops-110126}, doi = {10.4230/LIPIcs.MFCS.2019.68}, annote = {Keywords: Cellular Automata, Symbolic Dynamics, Complex Systems} }
Published in: LIPIcs, Volume 128, 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)
Raffaele Giancarlo, Giovanni Manzini, Giovanna Rosone, and Marinella Sciortino. A New Class of Searchable and Provably Highly Compressible String Transformations. In 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 128, pp. 12:1-12:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{giancarlo_et_al:LIPIcs.CPM.2019.12, author = {Giancarlo, Raffaele and Manzini, Giovanni and Rosone, Giovanna and Sciortino, Marinella}, title = {{A New Class of Searchable and Provably Highly Compressible String Transformations}}, booktitle = {30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)}, pages = {12:1--12:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-103-0}, ISSN = {1868-8969}, year = {2019}, volume = {128}, editor = {Pisanti, Nadia and P. Pissis, Solon}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2019.12}, URN = {urn:nbn:de:0030-drops-104833}, doi = {10.4230/LIPIcs.CPM.2019.12}, annote = {Keywords: Data Indexing and Compression, Burrows-Wheeler Transformation, Combinatorics on Words} }
Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
Christina Boucher, Travis Gagie, Alan Kuhnle, and Giovanni Manzini. Prefix-Free Parsing for Building Big BWTs. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 2:1-2:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{boucher_et_al:LIPIcs.WABI.2018.2, author = {Boucher, Christina and Gagie, Travis and Kuhnle, Alan and Manzini, Giovanni}, title = {{Prefix-Free Parsing for Building Big BWTs}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {2:1--2:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.2}, URN = {urn:nbn:de:0030-drops-93044}, doi = {10.4230/LIPIcs.WABI.2018.2}, annote = {Keywords: Burrows-Wheeler Transform, prefix-free parsing, compression-aware algorithms, genomic databases} }
Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
Lavinia Egidi, Felipe A. Louza, Giovanni Manzini, and Guilherme P. Telles. External memory BWT and LCP computation for sequence collections with applications. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 10:1-10:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{egidi_et_al:LIPIcs.WABI.2018.10, author = {Egidi, Lavinia and Louza, Felipe A. and Manzini, Giovanni and Telles, Guilherme P.}, title = {{External memory BWT and LCP computation for sequence collections with applications}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {10:1--10:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.10}, URN = {urn:nbn:de:0030-drops-93122}, doi = {10.4230/LIPIcs.WABI.2018.10}, annote = {Keywords: Burrows-Wheeler Transform, Longest Common Prefix Array, All pairs suffix-prefix overlaps, Succinct de Bruijn graph, Maximal repeats} }
Published in: LIPIcs, Volume 87, 25th Annual European Symposium on Algorithms (ESA 2017)
Travis Gagie, Giovanni Manzini, and Rossano Venturini. An Encoding for Order-Preserving Matching. In 25th Annual European Symposium on Algorithms (ESA 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 87, pp. 38:1-38:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{gagie_et_al:LIPIcs.ESA.2017.38, author = {Gagie, Travis and Manzini, Giovanni and Venturini, Rossano}, title = {{An Encoding for Order-Preserving Matching}}, booktitle = {25th Annual European Symposium on Algorithms (ESA 2017)}, pages = {38:1--38:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-049-1}, ISSN = {1868-8969}, year = {2017}, volume = {87}, editor = {Pruhs, Kirk and Sohler, Christian}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2017.38}, URN = {urn:nbn:de:0030-drops-78726}, doi = {10.4230/LIPIcs.ESA.2017.38}, annote = {Keywords: Compact data structures, encodings, order-preserving matching} }
Published in: LIPIcs, Volume 78, 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017)
Giovanni Manzini. Wheeler Graphs: Variations on a Theme by Burrows and Wheeler. In 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 78, p. 1:1, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{manzini:LIPIcs.CPM.2017.1, author = {Manzini, Giovanni}, title = {{Wheeler Graphs: Variations on a Theme by Burrows and Wheeler}}, booktitle = {28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017)}, pages = {1:1--1:1}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-039-2}, ISSN = {1868-8969}, year = {2017}, volume = {78}, editor = {K\"{a}rkk\"{a}inen, Juha and Radoszewski, Jakub and Rytter, Wojciech}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2017.1}, URN = {urn:nbn:de:0030-drops-73343}, doi = {10.4230/LIPIcs.CPM.2017.1}, annote = {Keywords: compressed data structures, pattern matching} }
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