LIPIcs, Volume 172
WABI 2020, September 7-9, 2020, Pisa, Italy (Virtual Conference)
Editors: Carl Kingsford and Nadia Pisanti
LIPIcs, Volume 128
CPM 2019, June 18-20, 2019, Pisa, Italy
Editors: Nadia Pisanti and Solon P. Pissis
Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)
Itai Boneh, Shay Golan, and Arseny Shur. String 2-Covers with No Length Restrictions. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 31:1-31:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{boneh_et_al:LIPIcs.ESA.2024.31, author = {Boneh, Itai and Golan, Shay and Shur, Arseny}, title = {{String 2-Covers with No Length Restrictions}}, booktitle = {32nd Annual European Symposium on Algorithms (ESA 2024)}, pages = {31:1--31:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-338-6}, ISSN = {1868-8969}, year = {2024}, volume = {308}, editor = {Chan, Timothy and Fischer, Johannes and Iacono, John and Herman, Grzegorz}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2024.31}, URN = {urn:nbn:de:0030-drops-211029}, doi = {10.4230/LIPIcs.ESA.2024.31}, annote = {Keywords: Quasi-periodicity, String cover, Range query, Range stabbing} }
Published in: LIPIcs, Volume 308, 32nd Annual European Symposium on Algorithms (ESA 2024)
Zsuzsanna Lipták, Francesco Masillo, and Gonzalo Navarro. A Textbook Solution for Dynamic Strings. In 32nd Annual European Symposium on Algorithms (ESA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 308, pp. 86:1-86:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{liptak_et_al:LIPIcs.ESA.2024.86, author = {Lipt\'{a}k, Zsuzsanna and Masillo, Francesco and Navarro, Gonzalo}, title = {{A Textbook Solution for Dynamic Strings}}, booktitle = {32nd Annual European Symposium on Algorithms (ESA 2024)}, pages = {86:1--86:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-338-6}, ISSN = {1868-8969}, year = {2024}, volume = {308}, editor = {Chan, Timothy and Fischer, Johannes and Iacono, John and Herman, Grzegorz}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2024.86}, URN = {urn:nbn:de:0030-drops-211576}, doi = {10.4230/LIPIcs.ESA.2024.86}, annote = {Keywords: dynamic strings, splay trees, dynamic data structures, LCP, circular strings} }
Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Rocco Ascone, Giulia Bernardini, Alessio Conte, Massimo Equi, Esteban Gabory, Roberto Grossi, and Nadia Pisanti. A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 14:1-14:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{ascone_et_al:LIPIcs.WABI.2024.14, author = {Ascone, Rocco and Bernardini, Giulia and Conte, Alessio and Equi, Massimo and Gabory, Esteban and Grossi, Roberto and Pisanti, Nadia}, title = {{A Unifying Taxonomy of Pattern Matching in Degenerate Strings and Founder Graphs}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {14:1--14:21}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-340-9}, ISSN = {1868-8969}, year = {2024}, volume = {312}, editor = {Pissis, Solon P. and Sung, Wing-Kin}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.14}, URN = {urn:nbn:de:0030-drops-206586}, doi = {10.4230/LIPIcs.WABI.2024.14}, annote = {Keywords: Pangenomics, pattern matching, degenerate string, founder graph, fine-grained complexity} }
Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Adam Cicherski, Anna Lisiecka, and Norbert Dojer. AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 23:1-23:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{cicherski_et_al:LIPIcs.WABI.2024.23, author = {Cicherski, Adam and Lisiecka, Anna and Dojer, Norbert}, title = {{AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {23:1--23:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-340-9}, ISSN = {1868-8969}, year = {2024}, volume = {312}, editor = {Pissis, Solon P. and Sung, Wing-Kin}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.23}, URN = {urn:nbn:de:0030-drops-206673}, doi = {10.4230/LIPIcs.WABI.2024.23}, annote = {Keywords: pangenome, variation graph, genome alignment, population genomics} }
Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)
Daniel Hambly, Rhyd Lewis, and Padraig Corcoran. Determining Fixed-Length Paths in Directed and Undirected Edge-Weighted Graphs. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 15:1-15:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{hambly_et_al:LIPIcs.SEA.2024.15, author = {Hambly, Daniel and Lewis, Rhyd and Corcoran, Padraig}, title = {{Determining Fixed-Length Paths in Directed and Undirected Edge-Weighted Graphs}}, booktitle = {22nd International Symposium on Experimental Algorithms (SEA 2024)}, pages = {15:1--15:11}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-325-6}, ISSN = {1868-8969}, year = {2024}, volume = {301}, editor = {Liberti, Leo}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.15}, URN = {urn:nbn:de:0030-drops-203805}, doi = {10.4230/LIPIcs.SEA.2024.15}, annote = {Keywords: Graphs, paths, backtracking, integer programming, Yen’s algorithm} }
Published in: LIPIcs, Volume 259, 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)
Esteban Gabory, Moses Njagi Mwaniki, Nadia Pisanti, Solon P. Pissis, Jakub Radoszewski, Michelle Sweering, and Wiktor Zuba. Comparing Elastic-Degenerate Strings: Algorithms, Lower Bounds, and Applications. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 11:1-11:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{gabory_et_al:LIPIcs.CPM.2023.11, author = {Gabory, Esteban and Mwaniki, Moses Njagi and Pisanti, Nadia and Pissis, Solon P. and Radoszewski, Jakub and Sweering, Michelle and Zuba, Wiktor}, title = {{Comparing Elastic-Degenerate Strings: Algorithms, Lower Bounds, and Applications}}, booktitle = {34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)}, pages = {11:1--11:20}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-276-1}, ISSN = {1868-8969}, year = {2023}, volume = {259}, editor = {Bulteau, Laurent and Lipt\'{a}k, Zsuzsanna}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2023.11}, URN = {urn:nbn:de:0030-drops-179650}, doi = {10.4230/LIPIcs.CPM.2023.11}, annote = {Keywords: elastic-degenerate string, sequence comparison, languages intersection, pangenome, acronym identification} }
Published in: LIPIcs, Volume 212, 32nd International Symposium on Algorithms and Computation (ISAAC 2021)
Panagiotis Charalampopoulos, Huiping Chen, Peter Christen, Grigorios Loukides, Nadia Pisanti, Solon P. Pissis, and Jakub Radoszewski. Pattern Masking for Dictionary Matching. In 32nd International Symposium on Algorithms and Computation (ISAAC 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 212, pp. 65:1-65:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{charalampopoulos_et_al:LIPIcs.ISAAC.2021.65, author = {Charalampopoulos, Panagiotis and Chen, Huiping and Christen, Peter and Loukides, Grigorios and Pisanti, Nadia and Pissis, Solon P. and Radoszewski, Jakub}, title = {{Pattern Masking for Dictionary Matching}}, booktitle = {32nd International Symposium on Algorithms and Computation (ISAAC 2021)}, pages = {65:1--65:19}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2021.65}, URN = {urn:nbn:de:0030-drops-154982}, doi = {10.4230/LIPIcs.ISAAC.2021.65}, annote = {Keywords: string algorithms, dictionary matching, wildcards, record linkage, query term dropping} }
Published in: LIPIcs, Volume 191, 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)
Nadia Pisanti. On-Line Pattern Matching on D-Texts (Invited Talk). In 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 191, pp. 3:1-3:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{pisanti:LIPIcs.CPM.2021.3, author = {Pisanti, Nadia}, title = {{On-Line Pattern Matching on D-Texts}}, booktitle = {32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)}, pages = {3:1--3:2}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-186-3}, ISSN = {1868-8969}, year = {2021}, volume = {191}, editor = {Gawrychowski, Pawe{\l} and Starikovskaya, Tatiana}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2021.3}, URN = {urn:nbn:de:0030-drops-139548}, doi = {10.4230/LIPIcs.CPM.2021.3}, annote = {Keywords: pattern matching, elastic-degenerate string, matrix multiplication} }
Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)
20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 1-360, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@Proceedings{kingsford_et_al:LIPIcs.WABI.2020, title = {{LIPIcs, Volume 172, WABI 2020, Complete Volume}}, booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)}, pages = {1--360}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-161-0}, ISSN = {1868-8969}, year = {2020}, volume = {172}, editor = {Kingsford, Carl and Pisanti, Nadia}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020}, URN = {urn:nbn:de:0030-drops-127881}, doi = {10.4230/LIPIcs.WABI.2020}, annote = {Keywords: LIPIcs, Volume 172, WABI 2020, Complete Volume} }
Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)
20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 0:i-0:x, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@InProceedings{kingsford_et_al:LIPIcs.WABI.2020.0, author = {Kingsford, Carl and Pisanti, Nadia}, title = {{Front Matter, Table of Contents, Preface, Conference Organization}}, booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)}, pages = {0:i--0:x}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-161-0}, ISSN = {1868-8969}, year = {2020}, volume = {172}, editor = {Kingsford, Carl and Pisanti, Nadia}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.0}, URN = {urn:nbn:de:0030-drops-127891}, doi = {10.4230/LIPIcs.WABI.2020.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization} }
Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)
Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi, and Michal Ziv-Ukelson. Approximate Search for Known Gene Clusters in New Genomes Using PQ-Trees. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 1:1-1:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@InProceedings{zimerman_et_al:LIPIcs.WABI.2020.1, author = {Zimerman, Galia R. and Svetlitsky, Dina and Zehavi, Meirav and Ziv-Ukelson, Michal}, title = {{Approximate Search for Known Gene Clusters in New Genomes Using PQ-Trees}}, booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)}, pages = {1:1--1:24}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-161-0}, ISSN = {1868-8969}, year = {2020}, volume = {172}, editor = {Kingsford, Carl and Pisanti, Nadia}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.1}, URN = {urn:nbn:de:0030-drops-127906}, doi = {10.4230/LIPIcs.WABI.2020.1}, annote = {Keywords: PQ-Tree, Gene Cluster, Efflux Pump} }
Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)
Hooman Zabeti, Nick Dexter, Amir Hosein Safari, Nafiseh Sedaghat, Maxwell Libbrecht, and Leonid Chindelevitch. An Interpretable Classification Method for Predicting Drug Resistance in M. Tuberculosis. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 2:1-2:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@InProceedings{zabeti_et_al:LIPIcs.WABI.2020.2, author = {Zabeti, Hooman and Dexter, Nick and Safari, Amir Hosein and Sedaghat, Nafiseh and Libbrecht, Maxwell and Chindelevitch, Leonid}, title = {{An Interpretable Classification Method for Predicting Drug Resistance in M. Tuberculosis}}, booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)}, pages = {2:1--2:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-161-0}, ISSN = {1868-8969}, year = {2020}, volume = {172}, editor = {Kingsford, Carl and Pisanti, Nadia}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.2}, URN = {urn:nbn:de:0030-drops-127911}, doi = {10.4230/LIPIcs.WABI.2020.2}, annote = {Keywords: Drug resistance, whole-genome sequencing, interpretable machine learning, integer linear programming, rule-based learning} }
Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)
Diego P. Rubert, Fábio V. Martinez, and Marília D. V. Braga. Natural Family-Free Genomic Distance. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 3:1-3:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@InProceedings{rubert_et_al:LIPIcs.WABI.2020.3, author = {Rubert, Diego P. and Martinez, F\'{a}bio V. and Braga, Mar{\'\i}lia D. V.}, title = {{Natural Family-Free Genomic Distance}}, booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)}, pages = {3:1--3:23}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-161-0}, ISSN = {1868-8969}, year = {2020}, volume = {172}, editor = {Kingsford, Carl and Pisanti, Nadia}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.3}, URN = {urn:nbn:de:0030-drops-127926}, doi = {10.4230/LIPIcs.WABI.2020.3}, annote = {Keywords: Comparative genomics, Genome rearrangement, DCJ-indel distance} }
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