Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Veronica Guerrini, Alessio Conte, Roberto Grossi, Gianni Liti, Giovanna Rosone, and Lorenzo Tattini. phyBWT: Alignment-Free Phylogeny via eBWT Positional Clustering. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 23:1-23:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{guerrini_et_al:LIPIcs.WABI.2022.23, author = {Guerrini, Veronica and Conte, Alessio and Grossi, Roberto and Liti, Gianni and Rosone, Giovanna and Tattini, Lorenzo}, title = {{phyBWT: Alignment-Free Phylogeny via eBWT Positional Clustering}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {23:1--23:19}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.23}, URN = {urn:nbn:de:0030-drops-170577}, doi = {10.4230/LIPIcs.WABI.2022.23}, annote = {Keywords: Phylogeny, partition tree, BWT, positional cluster, alignment-free, reference-free, assembly-free} }
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: LIPIcs, Volume 132, 46th International Colloquium on Automata, Languages, and Programming (ICALP 2019)
Giulia Bernardini, Paweł Gawrychowski, Nadia Pisanti, Solon P. Pissis, and Giovanna Rosone. Even Faster Elastic-Degenerate String Matching via Fast Matrix Multiplication. In 46th International Colloquium on Automata, Languages, and Programming (ICALP 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 132, pp. 21:1-21:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{bernardini_et_al:LIPIcs.ICALP.2019.21, author = {Bernardini, Giulia and Gawrychowski, Pawe{\l} and Pisanti, Nadia and Pissis, Solon P. and Rosone, Giovanna}, title = {{Even Faster Elastic-Degenerate String Matching via Fast Matrix Multiplication}}, booktitle = {46th International Colloquium on Automata, Languages, and Programming (ICALP 2019)}, pages = {21:1--21:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-109-2}, ISSN = {1868-8969}, year = {2019}, volume = {132}, editor = {Baier, Christel and Chatzigiannakis, Ioannis and Flocchini, Paola and Leonardi, Stefano}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2019.21}, URN = {urn:nbn:de:0030-drops-105973}, doi = {10.4230/LIPIcs.ICALP.2019.21}, annote = {Keywords: string algorithms, pattern matching, elastic-degenerate string, matrix multiplication, fast Fourier transform} }
Published in: LIPIcs, Volume 128, 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)
Nicola Prezza and Giovanna Rosone. Space-Efficient Computation of the LCP Array from the Burrows-Wheeler Transform. In 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 128, pp. 7:1-7:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{prezza_et_al:LIPIcs.CPM.2019.7, author = {Prezza, Nicola and Rosone, Giovanna}, title = {{Space-Efficient Computation of the LCP Array from the Burrows-Wheeler Transform}}, booktitle = {30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)}, pages = {7:1--7:18}, 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.2019.7}, URN = {urn:nbn:de:0030-drops-104782}, doi = {10.4230/LIPIcs.CPM.2019.7}, annote = {Keywords: Burrows-Wheeler Transform, LCP array, DNA reads} }
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)
Nicola Prezza, Nadia Pisanti, Marinella Sciortino, and Giovanna Rosone. Detecting Mutations by eBWT. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 3:1-3:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{prezza_et_al:LIPIcs.WABI.2018.3, author = {Prezza, Nicola and Pisanti, Nadia and Sciortino, Marinella and Rosone, Giovanna}, title = {{Detecting Mutations by eBWT}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {3:1--3:15}, 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.2018.3}, URN = {urn:nbn:de:0030-drops-93051}, doi = {10.4230/LIPIcs.WABI.2018.3}, annote = {Keywords: BWT, LCP Array, SNPs, Reference-free, Assembly-free} }
Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
Mai Alzamel, Lorraine A. K. Ayad, Giulia Bernardini, Roberto Grossi, Costas S. Iliopoulos, Nadia Pisanti, Solon P. Pissis, and Giovanna Rosone. Degenerate String Comparison and Applications. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 21:1-21:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{alzamel_et_al:LIPIcs.WABI.2018.21, author = {Alzamel, Mai and Ayad, Lorraine A. K. and Bernardini, Giulia and Grossi, Roberto and Iliopoulos, Costas S. and Pisanti, Nadia and Pissis, Solon P. and Rosone, Giovanna}, title = {{Degenerate String Comparison and Applications}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {21:1--21:14}, 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.2018.21}, URN = {urn:nbn:de:0030-drops-93236}, doi = {10.4230/LIPIcs.WABI.2018.21}, annote = {Keywords: degenerate strings, generalised degenerate strings, elastic-degenerate strings, string comparison, palindromes} }
Published in: LIPIcs, Volume 78, 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017)
Roberto Grossi, Costas S. Iliopoulos, Chang Liu, Nadia Pisanti, Solon P. Pissis, Ahmad Retha, Giovanna Rosone, Fatima Vayani, and Luca Versari. On-Line Pattern Matching on Similar Texts. In 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 78, pp. 9:1-9:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{grossi_et_al:LIPIcs.CPM.2017.9, author = {Grossi, Roberto and Iliopoulos, Costas S. and Liu, Chang and Pisanti, Nadia and Pissis, Solon P. and Retha, Ahmad and Rosone, Giovanna and Vayani, Fatima and Versari, Luca}, title = {{On-Line Pattern Matching on Similar Texts}}, booktitle = {28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017)}, pages = {9:1--9:14}, 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.2017.9}, URN = {urn:nbn:de:0030-drops-73379}, doi = {10.4230/LIPIcs.CPM.2017.9}, annote = {Keywords: string algorithms, pattern matching, degenerate strings, elastic-degenerate strings, on-line algorithms} }
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