LIPIcs, Volume 242
WABI 2022, September 5-7, 2022, Potsdam, Germany
Editors: Christina Boucher and Sven Rahmann
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-dev.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-dev.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-dev.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-dev.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-dev.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-dev.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-dev.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-dev.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} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Bertrand Marchand, Sebastian Will, Sarah J. Berkemer, Laurent Bulteau, and Yann Ponty. Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 7:1-7:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{marchand_et_al:LIPIcs.WABI.2022.7, author = {Marchand, Bertrand and Will, Sebastian and Berkemer, Sarah J. and Bulteau, Laurent and Ponty, Yann}, title = {{Automated Design of Dynamic Programming Schemes for RNA Folding with Pseudoknots}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {7:1--7:24}, 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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.7}, URN = {urn:nbn:de:0030-drops-170414}, doi = {10.4230/LIPIcs.WABI.2022.7}, annote = {Keywords: RNA folding, treewidth, dynamic programming} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Baqiao Liu and Tandy Warnow. Fast and Accurate Species Trees from Weighted Internode Distances. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 8:1-8:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{liu_et_al:LIPIcs.WABI.2022.8, author = {Liu, Baqiao and Warnow, Tandy}, title = {{Fast and Accurate Species Trees from Weighted Internode Distances}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {8:1--8:24}, 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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.8}, URN = {urn:nbn:de:0030-drops-170424}, doi = {10.4230/LIPIcs.WABI.2022.8}, annote = {Keywords: Species tree estimation, ASTRID, ASTRAL, multi-species coalescent, incomplete lineage sorting} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Giulio Ermanno Pibiri. On Weighted k-mer Dictionaries. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 9:1-9:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{pibiri:LIPIcs.WABI.2022.9, author = {Pibiri, Giulio Ermanno}, title = {{On Weighted k-mer Dictionaries}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {9:1--9:20}, 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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.9}, URN = {urn:nbn:de:0030-drops-170439}, doi = {10.4230/LIPIcs.WABI.2022.9}, annote = {Keywords: K-Mers, Weights, Compression, Hashing} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Yoshihiko Suzuki and Gene Myers. Accurate k-mer Classification Using Read Profiles. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 10:1-10:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{suzuki_et_al:LIPIcs.WABI.2022.10, author = {Suzuki, Yoshihiko and Myers, Gene}, title = {{Accurate k-mer Classification Using Read Profiles}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {10:1--10:20}, 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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.10}, URN = {urn:nbn:de:0030-drops-170446}, doi = {10.4230/LIPIcs.WABI.2022.10}, annote = {Keywords: K-mer, K-mer count, K-mer classification, HiFi sequencing} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Eden Ozery, Meirav Zehavi, and Michal Ziv-Ukelson. New Algorithms for Structure Informed Genome Rearrangement. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 11:1-11:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{ozery_et_al:LIPIcs.WABI.2022.11, author = {Ozery, Eden and Zehavi, Meirav and Ziv-Ukelson, Michal}, title = {{New Algorithms for Structure Informed Genome Rearrangement}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {11:1--11:19}, 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.2022.11}, URN = {urn:nbn:de:0030-drops-170454}, doi = {10.4230/LIPIcs.WABI.2022.11}, annote = {Keywords: PQ-tree, Gene Cluster, Breakpoint Distance} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Jens Zentgraf and Sven Rahmann. Fast Gapped k-mer Counting with Subdivided Multi-Way Bucketed Cuckoo Hash Tables. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 12:1-12:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{zentgraf_et_al:LIPIcs.WABI.2022.12, author = {Zentgraf, Jens and Rahmann, Sven}, title = {{Fast Gapped k-mer Counting with Subdivided Multi-Way Bucketed Cuckoo Hash Tables}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {12:1--12:20}, 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-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.12}, URN = {urn:nbn:de:0030-drops-170467}, doi = {10.4230/LIPIcs.WABI.2022.12}, annote = {Keywords: gapped k-mer, k-mer, counting, Cuckoo hashing, parallelization} }
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