LIPIcs, Volume 242
WABI 2022, September 5-7, 2022, Potsdam, Germany
Editors: Christina Boucher and Sven Rahmann
Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)
Nico Bertram, Johannes Fischer, and Lukas Nalbach. Move-r: Optimizing the r-index. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 1:1-1:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{bertram_et_al:LIPIcs.SEA.2024.1, author = {Bertram, Nico and Fischer, Johannes and Nalbach, Lukas}, title = {{Move-r: Optimizing the r-index}}, booktitle = {22nd International Symposium on Experimental Algorithms (SEA 2024)}, pages = {1:1--1:19}, 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.2024.1}, URN = {urn:nbn:de:0030-drops-203662}, doi = {10.4230/LIPIcs.SEA.2024.1}, annote = {Keywords: Compressed Text Index, Burrows-Wheeler Transform} }
Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)
Patrick Dinklage, Johnnes Fischer, and Nicola Prezza. Top- k Frequent Patterns in Streams and Parameterized-Space LZ Compression. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 9:1-9:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{dinklage_et_al:LIPIcs.SEA.2024.9, author = {Dinklage, Patrick and Fischer, Johnnes and Prezza, Nicola}, title = {{Top- k Frequent Patterns in Streams and Parameterized-Space LZ Compression}}, booktitle = {22nd International Symposium on Experimental Algorithms (SEA 2024)}, pages = {9:1--9:20}, 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.2024.9}, URN = {urn:nbn:de:0030-drops-203748}, doi = {10.4230/LIPIcs.SEA.2024.9}, annote = {Keywords: compression, streaming, heavy hitters, algorithm engineering} }
Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)
Dominika Draesslerová, Omar Ahmed, Travis Gagie, Jan Holub, Ben Langmead, Giovanni Manzini, and Gonzalo Navarro. Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 10:1-10:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{draesslerova_et_al:LIPIcs.SEA.2024.10, author = {Draesslerov\'{a}, Dominika and Ahmed, Omar and Gagie, Travis and Holub, Jan and Langmead, Ben and Manzini, Giovanni and Navarro, Gonzalo}, title = {{Taxonomic Classification with Maximal Exact Matches in KATKA Kernels and Minimizer Digests}}, booktitle = {22nd International Symposium on Experimental Algorithms (SEA 2024)}, pages = {10:1--10:13}, 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.2024.10}, URN = {urn:nbn:de:0030-drops-203756}, doi = {10.4230/LIPIcs.SEA.2024.10}, annote = {Keywords: Taxonomic classification, metagenomics, KATKA, maximal exact matches, string kernels, minimizer digests} }
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 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, and Travis Gagie. Acceleration of FM-Index Queries Through Prefix-Free Parsing. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 13:1-13:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{hong_et_al:LIPIcs.WABI.2023.13, author = {Hong, Aaron and Oliva, Marco and K\"{o}ppl, Dominik and Bannai, Hideo and Boucher, Christina and Gagie, Travis}, title = {{Acceleration of FM-Index Queries Through Prefix-Free Parsing}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {13:1--13:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-294-5}, ISSN = {1868-8969}, year = {2023}, volume = {273}, editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.13}, URN = {urn:nbn:de:0030-drops-186390}, doi = {10.4230/LIPIcs.WABI.2023.13}, annote = {Keywords: FM-index, pangenomics, scalability, word-based indexing, random access} }
Published in: LIPIcs, Volume 259, 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)
Igor Tatarnikov, Ardavan Shahrabi Farahani, Sana Kashgouli, and Travis Gagie. MONI Can Find k-MEMs. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 26:1-26:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{tatarnikov_et_al:LIPIcs.CPM.2023.26, author = {Tatarnikov, Igor and Shahrabi Farahani, Ardavan and Kashgouli, Sana and Gagie, Travis}, title = {{MONI Can Find k-MEMs}}, booktitle = {34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)}, pages = {26:1--26:14}, 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.2023.26}, URN = {urn:nbn:de:0030-drops-179802}, doi = {10.4230/LIPIcs.CPM.2023.26}, annote = {Keywords: Compact data structures, Burrows-Wheeler Transform, run-length compression, maximal exact matches} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 1-474, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@Proceedings{boucher_et_al:LIPIcs.WABI.2022, title = {{LIPIcs, Volume 242, WABI 2022, Complete Volume}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {1--474}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022}, URN = {urn:nbn:de:0030-drops-170338}, doi = {10.4230/LIPIcs.WABI.2022}, annote = {Keywords: LIPIcs, Volume 242, WABI 2022, Complete Volume} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 0:i-0:xii, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{boucher_et_al:LIPIcs.WABI.2022.0, author = {Boucher, Christina and Rahmann, Sven}, title = {{Front Matter, Table of Contents, Preface, Conference Organization}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {0:i--0:xii}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.0}, URN = {urn:nbn:de:0030-drops-170347}, doi = {10.4230/LIPIcs.WABI.2022.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Leena Salmela. Efficient Solutions to Biological Problems Using de Bruijn Graphs (Invited Talk). In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 1:1-1:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{salmela:LIPIcs.WABI.2022.1, author = {Salmela, Leena}, title = {{Efficient Solutions to Biological Problems Using de Bruijn Graphs}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {1:1--1:2}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.1}, URN = {urn:nbn:de:0030-drops-170357}, doi = {10.4230/LIPIcs.WABI.2022.1}, annote = {Keywords: de Bruijn graph, variable order de Bruijn graph, genome assembly, sequencing error correction, k-mers} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Sebastian Schmidt and Jarno N. Alanko. Eulertigs: Minimum Plain Text Representation of k-mer Sets Without Repetitions in Linear Time. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 2:1-2:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{schmidt_et_al:LIPIcs.WABI.2022.2, author = {Schmidt, Sebastian and Alanko, Jarno N.}, title = {{Eulertigs: Minimum Plain Text Representation of k-mer Sets Without Repetitions in Linear Time}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {2:1--2:21}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.2}, URN = {urn:nbn:de:0030-drops-170361}, doi = {10.4230/LIPIcs.WABI.2022.2}, annote = {Keywords: Spectrum preserving string sets, Eulerian cycle, Suffix tree, Bidirected arc-centric de Bruijn graph, k-mer based methods} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Alitzel López Sánchez and Manuel Lafond. Predicting Horizontal Gene Transfers with Perfect Transfer Networks. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 3:1-3:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{lopezsanchez_et_al:LIPIcs.WABI.2022.3, author = {L\'{o}pez S\'{a}nchez, Alitzel and Lafond, Manuel}, title = {{Predicting Horizontal Gene Transfers with Perfect Transfer Networks}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {3:1--3:22}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.3}, URN = {urn:nbn:de:0030-drops-170376}, doi = {10.4230/LIPIcs.WABI.2022.3}, annote = {Keywords: Horizontal gene transfer, tree-based networks, perfect phylogenies, character-based, gene-expression, indirect phylogenetic methods} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Ahsan Sanaullah, Degui Zhi, and Shaoije Zhang. Haplotype Threading Using the Positional Burrows-Wheeler Transform. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 4:1-4:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{sanaullah_et_al:LIPIcs.WABI.2022.4, author = {Sanaullah, Ahsan and Zhi, Degui and Zhang, Shaoije}, title = {{Haplotype Threading Using the Positional Burrows-Wheeler Transform}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {4:1--4:14}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.4}, URN = {urn:nbn:de:0030-drops-170386}, doi = {10.4230/LIPIcs.WABI.2022.4}, annote = {Keywords: Substring Cover, PBWT, Haplotype Threading, Haplotype Matching} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Mathieu Gascon and Nadia El-Mabrouk. Non-Binary Tree Reconciliation with Endosymbiotic Gene Transfer. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 5:1-5:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{gascon_et_al:LIPIcs.WABI.2022.5, author = {Gascon, Mathieu and El-Mabrouk, Nadia}, title = {{Non-Binary Tree Reconciliation with Endosymbiotic Gene Transfer}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {5:1--5:20}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.5}, URN = {urn:nbn:de:0030-drops-170390}, doi = {10.4230/LIPIcs.WABI.2022.5}, annote = {Keywords: Reconciliation, Duplication, Endosymbiotic gene transfer, Multifurcated gene tree, Polytomy} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Konstantinn Bonnet, Tobias Marschall, and Daniel Doerr¹. Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 6:1-6:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{bonnet_et_al:LIPIcs.WABI.2022.6, author = {Bonnet, Konstantinn and Marschall, Tobias and Doerr¹, Daniel}, title = {{Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {6:1--6:23}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.6}, URN = {urn:nbn:de:0030-drops-170403}, doi = {10.4230/LIPIcs.WABI.2022.6}, annote = {Keywords: founder set reconstruction, variation graph, pangenomics, NAHR, homologous recombination} }