LIPIcs, Volume 273
WABI 2023, September 4-6, 2023, Houston, TX, USA
Editors: Djamal Belazzougui and Aïda Ouangraoua
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 1-400, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@Proceedings{belazzougui_et_al:LIPIcs.WABI.2023, title = {{LIPIcs, Volume 273, WABI 2023, Complete Volume}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {1--400}, 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}, URN = {urn:nbn:de:0030-drops-186250}, doi = {10.4230/LIPIcs.WABI.2023}, annote = {Keywords: LIPIcs, Volume 273, WABI 2023, Complete Volume} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 0:i-0:xiv, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{belazzougui_et_al:LIPIcs.WABI.2023.0, author = {Belazzougui, Djamal and Ouangraoua, A\"{i}da}, title = {{Front Matter, Table of Contents, Preface, Conference Organization}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {0:i--0:xiv}, 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.2023.0}, URN = {urn:nbn:de:0030-drops-186267}, doi = {10.4230/LIPIcs.WABI.2023.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Teresa M. Przytycka. Algorithmic Approaches to Study Mutational Processes in Cancer (Invited Talk). In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 1:1-1:2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{przytycka:LIPIcs.WABI.2023.1, author = {Przytycka, Teresa M.}, title = {{Algorithmic Approaches to Study Mutational Processes in Cancer}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {1:1--1:2}, 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.2023.1}, URN = {urn:nbn:de:0030-drops-186278}, doi = {10.4230/LIPIcs.WABI.2023.1}, annote = {Keywords: Biological Networks, Cancer, Mutational Signatures, DNA Damage, DNA Repair} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Chengze Shen, Baqiao Liu, Kelly P. Williams, and Tandy Warnow. EMMA: Adding Sequences into a Constraint Alignment with High Accuracy and Scalability (Abstract). In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 2:1-2:2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{shen_et_al:LIPIcs.WABI.2023.2, author = {Shen, Chengze and Liu, Baqiao and Williams, Kelly P. and Warnow, Tandy}, title = {{EMMA: Adding Sequences into a Constraint Alignment with High Accuracy and Scalability}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {2:1--2:2}, 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.2023.2}, URN = {urn:nbn:de:0030-drops-186285}, doi = {10.4230/LIPIcs.WABI.2023.2}, annote = {Keywords: Multiple sequence alignment, constraint alignment, MAFFT} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Eleanor Wedell, Chengze Shen, and Tandy Warnow. BATCH-SCAMPP: Scaling Phylogenetic Placement Methods to Place Many Sequences (Abstract). In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 3:1-3:2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{wedell_et_al:LIPIcs.WABI.2023.3, author = {Wedell, Eleanor and Shen, Chengze and Warnow, Tandy}, title = {{BATCH-SCAMPP: Scaling Phylogenetic Placement Methods to Place Many Sequences}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {3:1--3:2}, 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.2023.3}, URN = {urn:nbn:de:0030-drops-186296}, doi = {10.4230/LIPIcs.WABI.2023.3}, annote = {Keywords: Phylogenetic Placement, EPA-ng, Phylogenetics} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Shayesteh Arasti and Siavash Mirarab. Optimal Subtree Prune and Regraft for Quartet Score in Sub-Quadratic Time. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 4:1-4:20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{arasti_et_al:LIPIcs.WABI.2023.4, author = {Arasti, Shayesteh and Mirarab, Siavash}, title = {{Optimal Subtree Prune and Regraft for Quartet Score in Sub-Quadratic Time}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {4:1--4:20}, 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.2023.4}, URN = {urn:nbn:de:0030-drops-186309}, doi = {10.4230/LIPIcs.WABI.2023.4}, annote = {Keywords: Phylogenetics, Gene tree discordance, Quartet score, Quartet distance, Subtree prune and regraft, Tree search, ASTRAL} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Junyan Dai, Tobias Rubel, Yunheng Han, and Erin K. Molloy. Leveraging Constraints Plus Dynamic Programming for the Large Dollo Parsimony Problem. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 5:1-5:23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{dai_et_al:LIPIcs.WABI.2023.5, author = {Dai, Junyan and Rubel, Tobias and Han, Yunheng and Molloy, Erin K.}, title = {{Leveraging Constraints Plus Dynamic Programming for the Large Dollo Parsimony Problem}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {5:1--5:23}, 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.2023.5}, URN = {urn:nbn:de:0030-drops-186312}, doi = {10.4230/LIPIcs.WABI.2023.5}, annote = {Keywords: phylogenetics, parsimony, Dollo, Camin-Sokal, dynamic programming, constraints} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Paweł Górecki, Natalia Rutecka, Agnieszka Mykowiecka, and Jarosław Paszek. Simultaneous Reconstruction of Duplication Episodes and Gene-Species Mappings. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 6:1-6:18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{gorecki_et_al:LIPIcs.WABI.2023.6, author = {G\'{o}recki, Pawe{\l} and Rutecka, Natalia and Mykowiecka, Agnieszka and Paszek, Jaros{\l}aw}, title = {{Simultaneous Reconstruction of Duplication Episodes and Gene-Species Mappings}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {6:1--6:18}, 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.2023.6}, URN = {urn:nbn:de:0030-drops-186329}, doi = {10.4230/LIPIcs.WABI.2023.6}, annote = {Keywords: Genomic Duplication, Gene-Species Mapping, Duplication Episode, Gene Tree, Species Tree} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Leo van Iersel, Mark Jones, Esther Julien, and Yukihiro Murakami. Making a Network Orchard by Adding Leaves. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 7:1-7:20, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{vaniersel_et_al:LIPIcs.WABI.2023.7, author = {van Iersel, Leo and Jones, Mark and Julien, Esther and Murakami, Yukihiro}, title = {{Making a Network Orchard by Adding Leaves}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {7:1--7:20}, 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.2023.7}, URN = {urn:nbn:de:0030-drops-186333}, doi = {10.4230/LIPIcs.WABI.2023.7}, annote = {Keywords: Phylogenetics, Network, Orchard Networks, Proximity Measures, NP-hardness} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Yunheng Han and Erin K. Molloy. Quartets Enable Statistically Consistent Estimation of Cell Lineage Trees Under an Unbiased Error and Missingness Model (Abstract). In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 8:1-8:2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{han_et_al:LIPIcs.WABI.2023.8, author = {Han, Yunheng and Molloy, Erin K.}, title = {{Quartets Enable Statistically Consistent Estimation of Cell Lineage Trees Under an Unbiased Error and Missingness Model}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {8:1--8:2}, 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.2023.8}, URN = {urn:nbn:de:0030-drops-186347}, doi = {10.4230/LIPIcs.WABI.2023.8}, annote = {Keywords: Tumor Phylogenetics, Cell Lineage Trees, Quartets, Supertrees, ASTRAL} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Mrinmoy Saha Roddur, Sagi Snir, and Mohammed El-Kebir. Inferring Temporally Consistent Migration Histories. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 9:1-9:22, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{roddur_et_al:LIPIcs.WABI.2023.9, author = {Roddur, Mrinmoy Saha and Snir, Sagi and El-Kebir, Mohammed}, title = {{Inferring Temporally Consistent Migration Histories}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {9:1--9:22}, 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.2023.9}, URN = {urn:nbn:de:0030-drops-186357}, doi = {10.4230/LIPIcs.WABI.2023.9}, annote = {Keywords: Metastasis, Migration, Integer Linear Programming, Maximum parsimony} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Nicola Rizzo, Manuel Cáceres, and Veli Mäkinen. Finding Maximal Exact Matches in Graphs. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 10:1-10:17, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{rizzo_et_al:LIPIcs.WABI.2023.10, author = {Rizzo, Nicola and C\'{a}ceres, Manuel and M\"{a}kinen, Veli}, title = {{Finding Maximal Exact Matches in Graphs}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {10:1--10:17}, 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.2023.10}, URN = {urn:nbn:de:0030-drops-186364}, doi = {10.4230/LIPIcs.WABI.2023.10}, annote = {Keywords: Sequence to graph alignment, bidirectional BWT, r-index, suffix tree, founder graphs} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Yutong Qiu, Yihang Shen, and Carl Kingsford. Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 11:1-11:22, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{qiu_et_al:LIPIcs.WABI.2023.11, author = {Qiu, Yutong and Shen, Yihang and Kingsford, Carl}, title = {{Revisiting the Complexity of and Algorithms for the Graph Traversal Edit Distance and Its Variants}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {11:1--11:22}, 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.2023.11}, URN = {urn:nbn:de:0030-drops-186374}, doi = {10.4230/LIPIcs.WABI.2023.11}, annote = {Keywords: Integer Linear Programming, Genome Graphs, Flow Network, Graph Comparison} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Jyotshna Rajput, Ghanshyam Chandra, and Chirag Jain. Co-Linear Chaining on Pangenome Graphs. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 12:1-12:18, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{rajput_et_al:LIPIcs.WABI.2023.12, author = {Rajput, Jyotshna and Chandra, Ghanshyam and Jain, Chirag}, title = {{Co-Linear Chaining on Pangenome Graphs}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {12:1--12:18}, 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.2023.12}, URN = {urn:nbn:de:0030-drops-186389}, doi = {10.4230/LIPIcs.WABI.2023.12}, annote = {Keywords: Sequence alignment, variation graph, genome sequencing, path cover} }
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