Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Tomáš Vinař. Bioinformatics of Pathogens (Invited Talk). In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 1:1-1:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{vinar:LIPIcs.WABI.2024.1, author = {Vina\v{r}, Tom\'{a}\v{s}}, title = {{Bioinformatics of Pathogens}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {1:1--1:2}, 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.2024.1}, URN = {urn:nbn:de:0030-drops-206455}, doi = {10.4230/LIPIcs.WABI.2024.1}, annote = {Keywords: sequence analysis, genome assembly, neural networks, probabilistic modeling} }
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)
Jens Zentgraf and Sven Rahmann. Swiftly Identifying Strongly Unique k-Mers. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 15:1-15:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{zentgraf_et_al:LIPIcs.WABI.2024.15, author = {Zentgraf, Jens and Rahmann, Sven}, title = {{Swiftly Identifying Strongly Unique k-Mers}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {15:1--15:15}, 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.2024.15}, URN = {urn:nbn:de:0030-drops-206593}, doi = {10.4230/LIPIcs.WABI.2024.15}, annote = {Keywords: k-mer, Hamming distance, strong uniqueness, parallelization, algorithm engineering} }
Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Alitzel López Sánchez, José Antonio Ramírez-Rafael, Alejandro Flores-Lamas, Maribel Hernández-Rosales, and Manuel Lafond. The Path-Label Reconciliation (PLR) Dissimilarity Measure for Gene Trees. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 20:1-20:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{lopezsanchez_et_al:LIPIcs.WABI.2024.20, author = {L\'{o}pez S\'{a}nchez, Alitzel and Ram{\'\i}rez-Rafael, Jos\'{e} Antonio and Flores-Lamas, Alejandro and Hern\'{a}ndez-Rosales, Maribel and Lafond, Manuel}, title = {{The Path-Label Reconciliation (PLR) Dissimilarity Measure for Gene Trees}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {20:1--20:21}, 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.2024.20}, URN = {urn:nbn:de:0030-drops-206645}, doi = {10.4230/LIPIcs.WABI.2024.20}, annote = {Keywords: Reconciliation, gene trees, species trees, evolutionary scenarios} }
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 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)
Paola Bonizzoni, Clelia De Felice, Brian Riccardi, Rocco Zaccagnino, and Rosalba Zizza. Unveiling the Connection Between the Lyndon Factorization and the Canonical Inverse Lyndon Factorization via a Border Property. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 31:1-31:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{bonizzoni_et_al:LIPIcs.MFCS.2024.31, author = {Bonizzoni, Paola and De Felice, Clelia and Riccardi, Brian and Zaccagnino, Rocco and Zizza, Rosalba}, title = {{Unveiling the Connection Between the Lyndon Factorization and the Canonical Inverse Lyndon Factorization via a Border Property}}, booktitle = {49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)}, pages = {31:1--31:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-335-5}, ISSN = {1868-8969}, year = {2024}, volume = {306}, editor = {Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.31}, URN = {urn:nbn:de:0030-drops-205879}, doi = {10.4230/LIPIcs.MFCS.2024.31}, annote = {Keywords: Lyndon words, Lyndon factorization, Combinatorial algorithms on words} }
Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)
Wiktor Zuba, Grigorios Loukides, Solon P. Pissis, and Sharma V. Thankachan. Approximate Suffix-Prefix Dictionary Queries. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 85:1-85:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{zuba_et_al:LIPIcs.MFCS.2024.85, author = {Zuba, Wiktor and Loukides, Grigorios and Pissis, Solon P. and Thankachan, Sharma V.}, title = {{Approximate Suffix-Prefix Dictionary Queries}}, booktitle = {49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)}, pages = {85:1--85:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-335-5}, ISSN = {1868-8969}, year = {2024}, volume = {306}, editor = {Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.85}, URN = {urn:nbn:de:0030-drops-206416}, doi = {10.4230/LIPIcs.MFCS.2024.85}, annote = {Keywords: all-pairs suffix-prefix, suffix-prefix queries, suffix tree, k-errata tree} }
Published in: LIPIcs, Volume 296, 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)
Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, and Yuri Pirola. Solving the Minimal Positional Substring Cover Problem in Sublinear Space. In 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 296, pp. 12:1-12:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{bonizzoni_et_al:LIPIcs.CPM.2024.12, author = {Bonizzoni, Paola and Boucher, Christina and Cozzi, Davide and Gagie, Travis and Pirola, Yuri}, title = {{Solving the Minimal Positional Substring Cover Problem in Sublinear Space}}, booktitle = {35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)}, pages = {12:1--12:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-326-3}, ISSN = {1868-8969}, year = {2024}, volume = {296}, editor = {Inenaga, Shunsuke and Puglisi, Simon J.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2024.12}, URN = {urn:nbn:de:0030-drops-201225}, doi = {10.4230/LIPIcs.CPM.2024.12}, annote = {Keywords: Positional Burrows-Wheeler Transform, r-index, minimal position substring cover, set-maximal exact matches} }
Published in: LIPIcs, Volume 161, 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)
Giulia Bernardini, Paola Bonizzoni, and Paweł Gawrychowski. On Two Measures of Distance Between Fully-Labelled Trees. In 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 161, pp. 6:1-6:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@InProceedings{bernardini_et_al:LIPIcs.CPM.2020.6, author = {Bernardini, Giulia and Bonizzoni, Paola and Gawrychowski, Pawe{\l}}, title = {{On Two Measures of Distance Between Fully-Labelled Trees}}, booktitle = {31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)}, pages = {6:1--6:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-149-8}, ISSN = {1868-8969}, year = {2020}, volume = {161}, editor = {G{\o}rtz, Inge Li and Weimann, Oren}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2020.6}, URN = {urn:nbn:de:0030-drops-121318}, doi = {10.4230/LIPIcs.CPM.2020.6}, annote = {Keywords: Tree distance, Cancer progression, Approximation algorithms, Fine-grained complexity} }
Published in: LIPIcs, Volume 128, 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)
Giulia Bernardini, Paola Bonizzoni, Gianluca Della Vedova, and Murray Patterson. A Rearrangement Distance for Fully-Labelled Trees. In 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 128, pp. 28:1-28:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{bernardini_et_al:LIPIcs.CPM.2019.28, author = {Bernardini, Giulia and Bonizzoni, Paola and Della Vedova, Gianluca and Patterson, Murray}, title = {{A Rearrangement Distance for Fully-Labelled Trees}}, booktitle = {30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)}, pages = {28:1--28:15}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2019.28}, URN = {urn:nbn:de:0030-drops-104998}, doi = {10.4230/LIPIcs.CPM.2019.28}, annote = {Keywords: Tree rearrangement distance, Cancer progression, Approximation algorithms, Computational complexity} }
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