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} }
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} }
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} }
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} }
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} }
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} }
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} }
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} }
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} }
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} }
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} }
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} }
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} }
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} }
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} }
Tizian Schulz and Paul Medvedev. Exact Sketch-Based Read Mapping. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 14:1-14:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{schulz_et_al:LIPIcs.WABI.2023.14, author = {Schulz, Tizian and Medvedev, Paul}, title = {{Exact Sketch-Based Read Mapping}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {14:1--14:19}, 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.2023.14}, URN = {urn:nbn:de:0030-drops-186403}, doi = {10.4230/LIPIcs.WABI.2023.14}, annote = {Keywords: Sequence Sketching, Long-read Mapping, Exact Algorithm, Dynamic Programming} }
Timothé Rouzé, Igor Martayan, Camille Marchet, and Antoine Limasset. Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 15:1-15:27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{rouze_et_al:LIPIcs.WABI.2023.15, author = {Rouz\'{e}, Timoth\'{e} and Martayan, Igor and Marchet, Camille and Limasset, Antoine}, title = {{Fractional Hitting Sets for Efficient and Lightweight Genomic Data Sketching}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {15:1--15:27}, 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.2023.15}, URN = {urn:nbn:de:0030-drops-186414}, doi = {10.4230/LIPIcs.WABI.2023.15}, annote = {Keywords: k-mer, subsampling, sketching, Jaccard, containment, metagenomics} }
Jamshed Khan, Tobias Rubel, Laxman Dhulipala, Erin Molloy, and Rob Patro. Fast, Parallel, and Cache-Friendly Suffix Array Construction. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 16:1-16:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{khan_et_al:LIPIcs.WABI.2023.16, author = {Khan, Jamshed and Rubel, Tobias and Dhulipala, Laxman and Molloy, Erin and Patro, Rob}, title = {{Fast, Parallel, and Cache-Friendly Suffix Array Construction}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {16:1--16:21}, 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.2023.16}, URN = {urn:nbn:de:0030-drops-186424}, doi = {10.4230/LIPIcs.WABI.2023.16}, annote = {Keywords: Suffix Array, Longest Common Prefix, Data Structures, Indexing, Parallel Algorithms} }
Amatur Rahman, Yoann Dufresne, and Paul Medvedev. Compression Algorithm for Colored de Bruijn Graphs. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 17:1-17:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{rahman_et_al:LIPIcs.WABI.2023.17, author = {Rahman, Amatur and Dufresne, Yoann and Medvedev, Paul}, title = {{Compression Algorithm for Colored de Bruijn Graphs}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {17:1--17:14}, 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.2023.17}, URN = {urn:nbn:de:0030-drops-186434}, doi = {10.4230/LIPIcs.WABI.2023.17}, annote = {Keywords: colored de Bruijn graphs, disk compression, k-mer sets, simplitigs, spectrum-preserving string sets} }
Jason Fan, Noor Pratap Singh, Jamshed Khan, Giulio Ermanno Pibiri, and Rob Patro. Fulgor: A Fast and Compact {k-mer} Index for Large-Scale Matching and Color Queries. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 18:1-18:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{fan_et_al:LIPIcs.WABI.2023.18, author = {Fan, Jason and Singh, Noor Pratap and Khan, Jamshed and Pibiri, Giulio Ermanno and Patro, Rob}, title = {{Fulgor: A Fast and Compact \{k-mer\} Index for Large-Scale Matching and Color Queries}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {18:1--18:21}, 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.2023.18}, URN = {urn:nbn:de:0030-drops-186446}, doi = {10.4230/LIPIcs.WABI.2023.18}, annote = {Keywords: k-mers, Colored de Bruijn Graph, Compression, Read-mapping} }
Mateo Gray, Sebastian Will, and Hosna Jabbari. SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 19:1-19:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{gray_et_al:LIPIcs.WABI.2023.19, author = {Gray, Mateo and Will, Sebastian and Jabbari, Hosna}, title = {{SparseRNAFolD: Sparse RNA Pseudoknot-Free Folding Including Dangles}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {19:1--19:18}, 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.2023.19}, URN = {urn:nbn:de:0030-drops-186454}, doi = {10.4230/LIPIcs.WABI.2023.19}, annote = {Keywords: RNA, MFE, Secondary Structure Prediction, Dangle, Sparsification, Space Complexity, Time Complexity} }
Théo Boury, Yann Ponty, and Vladimir Reinharz. Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 20:1-20:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{boury_et_al:LIPIcs.WABI.2023.20, author = {Boury, Th\'{e}o and Ponty, Yann and Reinharz, Vladimir}, title = {{Automatic Exploration of the Natural Variability of RNA Non-Canonical Geometric Patterns with a Parameterized Sampling Technique}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {20:1--20:22}, 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.2023.20}, URN = {urn:nbn:de:0030-drops-186460}, doi = {10.4230/LIPIcs.WABI.2023.20}, annote = {Keywords: Subgraph Isomorphism, 3D RNA, Parameterized Complexity, Tree Decomposition, Boltzmann sampling, Neighborhood metrics, Kink-Turn family} }
Xinyu Gu, Yuanyuan Qi, and Mohammed El-Kebir. Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 21:1-21:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{gu_et_al:LIPIcs.WABI.2023.21, author = {Gu, Xinyu and Qi, Yuanyuan and El-Kebir, Mohammed}, title = {{Balancing Minimum Free Energy and Codon Adaptation Index for Pareto Optimal RNA Design}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {21:1--21:20}, 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.2023.21}, URN = {urn:nbn:de:0030-drops-186479}, doi = {10.4230/LIPIcs.WABI.2023.21}, annote = {Keywords: Multi-objective optimization, dynamic programming, RNA sequence design, reverse translation, mRNA vaccine design} }
Leonard Bohnenkämper. Bridging Disparate Views on the DCJ-Indel Model for a Capping-Free Solution to the Natural Distance Problem. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 22:1-22:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{bohnenkamper:LIPIcs.WABI.2023.22, author = {Bohnenk\"{a}mper, Leonard}, title = {{Bridging Disparate Views on the DCJ-Indel Model for a Capping-Free Solution to the Natural Distance Problem}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {22:1--22:18}, 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.2023.22}, URN = {urn:nbn:de:0030-drops-186484}, doi = {10.4230/LIPIcs.WABI.2023.22}, annote = {Keywords: Comparative Genomics, Genome Rearrangement, Double-Cut-And-Join, Indels, Integer Linear Programming, Capping} }
Mohsen Ferdosi, Yuejun Ge, and Carl Kingsford. Reinforcement Learning for Robotic Liquid Handler Planning. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 23:1-23:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{ferdosi_et_al:LIPIcs.WABI.2023.23, author = {Ferdosi, Mohsen and Ge, Yuejun and Kingsford, Carl}, title = {{Reinforcement Learning for Robotic Liquid Handler Planning}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {23:1--23:16}, 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.2023.23}, URN = {urn:nbn:de:0030-drops-186494}, doi = {10.4230/LIPIcs.WABI.2023.23}, annote = {Keywords: Liquid Handler, Reinforcement Learning, Planning} }
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