24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 1-454, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@Proceedings{pissis_et_al:LIPIcs.WABI.2024, title = {{LIPIcs, Volume 312, WABI 2024, Complete Volume}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {1--454}, 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}, URN = {urn:nbn:de:0030-drops-206430}, doi = {10.4230/LIPIcs.WABI.2024}, annote = {Keywords: LIPIcs, Volume 312, WABI 2024, Complete Volume} }
24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 0:i-0:xii, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{pissis_et_al:LIPIcs.WABI.2024.0, author = {Pissis, Solon P. and Sung, Wing-Kin}, title = {{Front Matter, Table of Contents, Preface, Conference Organization}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {0:i--0:xii}, 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.2024.0}, URN = {urn:nbn:de:0030-drops-206447}, doi = {10.4230/LIPIcs.WABI.2024.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization} }
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} }
Luís Cunha, Ignasi Sau, and Uéverton Souza. On the Complexity of the Median and Closest Permutation Problems. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 2:1-2:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{cunha_et_al:LIPIcs.WABI.2024.2, author = {Cunha, Lu{\'\i}s and Sau, Ignasi and Souza, U\'{e}verton}, title = {{On the Complexity of the Median and Closest Permutation Problems}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {2:1--2:23}, 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.2024.2}, URN = {urn:nbn:de:0030-drops-206468}, doi = {10.4230/LIPIcs.WABI.2024.2}, annote = {Keywords: Median problem, Closest problem, Genome rearrangements, Parameterized complexity} }
Yao-ban Chan. An Efficient Algorithm for the Reconciliation of a Gene Network and Species Tree. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 3:1-3:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{chan:LIPIcs.WABI.2024.3, author = {Chan, Yao-ban}, title = {{An Efficient Algorithm for the Reconciliation of a Gene Network and Species Tree}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {3:1--3:17}, 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.2024.3}, URN = {urn:nbn:de:0030-drops-206472}, doi = {10.4230/LIPIcs.WABI.2024.3}, annote = {Keywords: Reconciliation, recombination, paralog exchange, phylogenetic network, gene duplication, gene loss} }
Stephen Hwang, Nathaniel K. Brown, Omar Y. Ahmed, Katharine M. Jenike, Sam Kovaka, Michael C. Schatz, and Ben Langmead. MEM-Based Pangenome Indexing for k-mer Queries. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 4:1-4:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{hwang_et_al:LIPIcs.WABI.2024.4, author = {Hwang, Stephen and Brown, Nathaniel K. and Ahmed, Omar Y. and Jenike, Katharine M. and Kovaka, Sam and Schatz, Michael C. and Langmead, Ben}, title = {{MEM-Based Pangenome Indexing for k-mer Queries}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {4:1--4:17}, 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.2024.4}, URN = {urn:nbn:de:0030-drops-206482}, doi = {10.4230/LIPIcs.WABI.2024.4}, annote = {Keywords: Pangenomics, Comparative genomics, Compressed indexing} }
Lukas Hübner and Alexandros Stamatakis. Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{hubner_et_al:LIPIcs.WABI.2024.5, author = {H\"{u}bner, Lukas and Stamatakis, Alexandros}, title = {{Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {5:1--5:22}, 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.2024.5}, URN = {urn:nbn:de:0030-drops-206499}, doi = {10.4230/LIPIcs.WABI.2024.5}, annote = {Keywords: bioinformatics, population genetics, algorithms} }
Mahmudur Rahman Hera and David Koslicki. Cosine Similarity Estimation Using FracMinHash: Theoretical Analysis, Safety Conditions, and Implementation. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 6:1-6:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{hera_et_al:LIPIcs.WABI.2024.6, author = {Hera, Mahmudur Rahman and Koslicki, David}, title = {{Cosine Similarity Estimation Using FracMinHash: Theoretical Analysis, Safety Conditions, and Implementation}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {6:1--6:16}, 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.2024.6}, URN = {urn:nbn:de:0030-drops-206502}, doi = {10.4230/LIPIcs.WABI.2024.6}, annote = {Keywords: Hashing, sketching, FracMinHash, Min-Hash, k-mer, similarity, theory} }
Yuanyuan Qi and Mohammed El-Kebir. Sapling: Inferring and Summarizing Tumor Phylogenies from Bulk Data Using Backbone Trees. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 7:1-7:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{qi_et_al:LIPIcs.WABI.2024.7, author = {Qi, Yuanyuan and El-Kebir, Mohammed}, title = {{Sapling: Inferring and Summarizing Tumor Phylogenies from Bulk Data Using Backbone Trees}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {7:1--7:19}, 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.2024.7}, URN = {urn:nbn:de:0030-drops-206518}, doi = {10.4230/LIPIcs.WABI.2024.7}, annote = {Keywords: Cancer, intra-tumor heterogeneity, consensus, maximum agreement} }
Sebastian Schmidt, Santeri Toivonen, Paul Medvedev, and Alexandru I. Tomescu. Applying the Safe-And-Complete Framework to Practical Genome Assembly. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 8:1-8:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{schmidt_et_al:LIPIcs.WABI.2024.8, author = {Schmidt, Sebastian and Toivonen, Santeri and Medvedev, Paul and Tomescu, Alexandru I.}, title = {{Applying the Safe-And-Complete Framework to Practical Genome Assembly}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {8:1--8:16}, 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.2024.8}, URN = {urn:nbn:de:0030-drops-206520}, doi = {10.4230/LIPIcs.WABI.2024.8}, annote = {Keywords: Genome assembly, Omnitigs, Safe-and-complete framework, graph algorithm, HiFi sequencing data, Assembly evaluation} }
Tsuyoshi Urata, Manato Yokoyama, and Momoko Hayamizu. Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 9:1-9:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{urata_et_al:LIPIcs.WABI.2024.9, author = {Urata, Tsuyoshi and Yokoyama, Manato and Hayamizu, Momoko}, title = {{Orientability of Undirected Phylogenetic Networks to a Desired Class: Practical Algorithms and Application to Tree-Child Orientation}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {9:1--9:17}, 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.2024.9}, URN = {urn:nbn:de:0030-drops-206531}, doi = {10.4230/LIPIcs.WABI.2024.9}, annote = {Keywords: Phylogenetic Networks, Tree-Child Networks, Graph Orientation Algorithms} }
Lore Depuydt, Luca Renders, Simon Van de Vyver, Lennart Veys, Travis Gagie, and Jan Fostier. b-move: Faster Bidirectional Character Extensions in a Run-Length Compressed Index. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 10:1-10:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{depuydt_et_al:LIPIcs.WABI.2024.10, author = {Depuydt, Lore and Renders, Luca and Van de Vyver, Simon and Veys, Lennart and Gagie, Travis and Fostier, Jan}, title = {{b-move: Faster Bidirectional Character Extensions in a Run-Length Compressed Index}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {10:1--10:18}, 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.2024.10}, URN = {urn:nbn:de:0030-drops-206546}, doi = {10.4230/LIPIcs.WABI.2024.10}, annote = {Keywords: Pan-genomics, FM-index, r-index, Move Structure, Bidirectional Search, Approximate Pattern Matching, Lossless Alignment, Cache Efficiency} }
Ragnar Groot Koerkamp and Giulio Ermanno Pibiri. The mod-minimizer: A Simple and Efficient Sampling Algorithm for Long k-mers. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 11:1-11:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{grootkoerkamp_et_al:LIPIcs.WABI.2024.11, author = {Groot Koerkamp, Ragnar and Pibiri, Giulio Ermanno}, title = {{The mod-minimizer: A Simple and Efficient Sampling Algorithm for Long k-mers}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {11:1--11:23}, 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.2024.11}, URN = {urn:nbn:de:0030-drops-206552}, doi = {10.4230/LIPIcs.WABI.2024.11}, annote = {Keywords: Minimizers, Randomized algorithms, Sketching, Hashing} }
Leonard Bohnenkämper, Jens Stoye, and Daniel Dörr. Reconstructing Rearrangement Phylogenies of Natural Genomes. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 12:1-12:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{bohnenkamper_et_al:LIPIcs.WABI.2024.12, author = {Bohnenk\"{a}mper, Leonard and Stoye, Jens and D\"{o}rr, Daniel}, title = {{Reconstructing Rearrangement Phylogenies of Natural Genomes}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {12:1--12:16}, 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.2024.12}, URN = {urn:nbn:de:0030-drops-206564}, doi = {10.4230/LIPIcs.WABI.2024.12}, annote = {Keywords: genome rearrangement, ancestral reconstruction, small parsimony, integer linear programming, double-cut-and-join} }
Md. Hasin Abrar and Paul Medvedev. PLA-index: A k-mer Index Exploiting Rank Curve Linearity. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 13:1-13:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{abrar_et_al:LIPIcs.WABI.2024.13, author = {Abrar, Md. Hasin and Medvedev, Paul}, title = {{PLA-index: A k-mer Index Exploiting Rank Curve Linearity}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {13:1--13:18}, 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.2024.13}, URN = {urn:nbn:de:0030-drops-206578}, doi = {10.4230/LIPIcs.WABI.2024.13}, annote = {Keywords: K-mer index, Piece-wise linear approximation, Learned index} }
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} }
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} }
Bertrand Marchand, Nadia Tahiri, Olivier Tremblay-Savard, and Manuel Lafond. Finding Maximum Common Contractions Between Phylogenetic Networks. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 16:1-16:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{marchand_et_al:LIPIcs.WABI.2024.16, author = {Marchand, Bertrand and Tahiri, Nadia and Tremblay-Savard, Olivier and Lafond, Manuel}, title = {{Finding Maximum Common Contractions Between Phylogenetic Networks}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {16:1--16:24}, 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.2024.16}, URN = {urn:nbn:de:0030-drops-206606}, doi = {10.4230/LIPIcs.WABI.2024.16}, annote = {Keywords: Phylogenetic networks, contractions, algorithms, weakly galled trees} }
Ragnar Groot Koerkamp. A*PA2: Up to 19× Faster Exact Global Alignment. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 17:1-17:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{grootkoerkamp:LIPIcs.WABI.2024.17, author = {Groot Koerkamp, Ragnar}, title = {{A*PA2: Up to 19× Faster Exact Global Alignment}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {17:1--17:25}, 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.2024.17}, URN = {urn:nbn:de:0030-drops-206610}, doi = {10.4230/LIPIcs.WABI.2024.17}, annote = {Keywords: Edit distance, Pairwise alignment, A*, Shortest path, Dynamic programming} }
Kimon Boehmer, Sarah J. Berkemer, Sebastian Will, and Yann Ponty. RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 18:1-18:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{boehmer_et_al:LIPIcs.WABI.2024.18, author = {Boehmer, Kimon and Berkemer, Sarah J. and Will, Sebastian and Ponty, Yann}, title = {{RNA Triplet Repeats: Improved Algorithms for Structure Prediction and Interactions}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {18:1--18:23}, 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.2024.18}, URN = {urn:nbn:de:0030-drops-206625}, doi = {10.4230/LIPIcs.WABI.2024.18}, annote = {Keywords: RNA folding, RNA interactions, triplet repeats, dynamic programming, NP-hardness} }
Théo Boury, Laurent Bulteau, and Yann Ponty. RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 19:1-19:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{boury_et_al:LIPIcs.WABI.2024.19, author = {Boury, Th\'{e}o and Bulteau, Laurent and Ponty, Yann}, title = {{RNA Inverse Folding Can Be Solved in Linear Time for Structures Without Isolated Stacks or Base Pairs}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {19:1--19:23}, 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.2024.19}, URN = {urn:nbn:de:0030-drops-206632}, doi = {10.4230/LIPIcs.WABI.2024.19}, annote = {Keywords: RNA structure, String Design, Parameterized Complexity, Uniform Sampling} }
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} }
Giovanni Buzzega, Alessio Conte, Roberto Grossi, and Giulia Punzi. McDag: Indexing Maximal Common Subsequences in Practice. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 21:1-21:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{buzzega_et_al:LIPIcs.WABI.2024.21, author = {Buzzega, Giovanni and Conte, Alessio and Grossi, Roberto and Punzi, Giulia}, title = {{McDag: Indexing Maximal Common Subsequences in Practice}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {21:1--21:18}, 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.2024.21}, URN = {urn:nbn:de:0030-drops-206650}, doi = {10.4230/LIPIcs.WABI.2024.21}, annote = {Keywords: Index data structure, DAG, Common subsequence, Inclusion-wise maximality, LCS} }
Xiaofei Carl Zang, Xiang Li, Kyle Metcalfe, Tuval Ben-Yehezkel, Ryan Kelley, and Mingfu Shao. Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 22:1-22:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{zang_et_al:LIPIcs.WABI.2024.22, author = {Zang, Xiaofei Carl and Li, Xiang and Metcalfe, Kyle and Ben-Yehezkel, Tuval and Kelley, Ryan and Shao, Mingfu}, title = {{Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {22:1--22:17}, 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.2024.22}, URN = {urn:nbn:de:0030-drops-206660}, doi = {10.4230/LIPIcs.WABI.2024.22}, annote = {Keywords: Genome assembly, de Bruijn graph, synthetic long reads, anchor-guided assembly, LoopSeq} }
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} }
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