22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 1-474, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@Proceedings{boucher_et_al:LIPIcs.WABI.2022, title = {{LIPIcs, Volume 242, WABI 2022, Complete Volume}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {1--474}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022}, URN = {urn:nbn:de:0030-drops-170338}, doi = {10.4230/LIPIcs.WABI.2022}, annote = {Keywords: LIPIcs, Volume 242, WABI 2022, Complete Volume} }
22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 0:i-0:xii, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{boucher_et_al:LIPIcs.WABI.2022.0, author = {Boucher, Christina and Rahmann, Sven}, title = {{Front Matter, Table of Contents, Preface, Conference Organization}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {0:i--0:xii}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.0}, URN = {urn:nbn:de:0030-drops-170347}, doi = {10.4230/LIPIcs.WABI.2022.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization} }
Leena Salmela. Efficient Solutions to Biological Problems Using de Bruijn Graphs (Invited Talk). In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 1:1-1:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{salmela:LIPIcs.WABI.2022.1, author = {Salmela, Leena}, title = {{Efficient Solutions to Biological Problems Using de Bruijn Graphs}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {1:1--1:2}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.1}, URN = {urn:nbn:de:0030-drops-170357}, doi = {10.4230/LIPIcs.WABI.2022.1}, annote = {Keywords: de Bruijn graph, variable order de Bruijn graph, genome assembly, sequencing error correction, k-mers} }
Sebastian Schmidt and Jarno N. Alanko. Eulertigs: Minimum Plain Text Representation of k-mer Sets Without Repetitions in Linear Time. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 2:1-2:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{schmidt_et_al:LIPIcs.WABI.2022.2, author = {Schmidt, Sebastian and Alanko, Jarno N.}, title = {{Eulertigs: Minimum Plain Text Representation of k-mer Sets Without Repetitions in Linear Time}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {2:1--2:21}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.2}, URN = {urn:nbn:de:0030-drops-170361}, doi = {10.4230/LIPIcs.WABI.2022.2}, annote = {Keywords: Spectrum preserving string sets, Eulerian cycle, Suffix tree, Bidirected arc-centric de Bruijn graph, k-mer based methods} }
Alitzel López Sánchez and Manuel Lafond. Predicting Horizontal Gene Transfers with Perfect Transfer Networks. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 3:1-3:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{lopezsanchez_et_al:LIPIcs.WABI.2022.3, author = {L\'{o}pez S\'{a}nchez, Alitzel and Lafond, Manuel}, title = {{Predicting Horizontal Gene Transfers with Perfect Transfer Networks}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {3:1--3:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.3}, URN = {urn:nbn:de:0030-drops-170376}, doi = {10.4230/LIPIcs.WABI.2022.3}, annote = {Keywords: Horizontal gene transfer, tree-based networks, perfect phylogenies, character-based, gene-expression, indirect phylogenetic methods} }
Ahsan Sanaullah, Degui Zhi, and Shaoije Zhang. Haplotype Threading Using the Positional Burrows-Wheeler Transform. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 4:1-4:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{sanaullah_et_al:LIPIcs.WABI.2022.4, author = {Sanaullah, Ahsan and Zhi, Degui and Zhang, Shaoije}, title = {{Haplotype Threading Using the Positional Burrows-Wheeler Transform}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {4:1--4:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.4}, URN = {urn:nbn:de:0030-drops-170386}, doi = {10.4230/LIPIcs.WABI.2022.4}, annote = {Keywords: Substring Cover, PBWT, Haplotype Threading, Haplotype Matching} }
Mathieu Gascon and Nadia El-Mabrouk. Non-Binary Tree Reconciliation with Endosymbiotic Gene Transfer. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 5:1-5:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{gascon_et_al:LIPIcs.WABI.2022.5, author = {Gascon, Mathieu and El-Mabrouk, Nadia}, title = {{Non-Binary Tree Reconciliation with Endosymbiotic Gene Transfer}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {5:1--5:20}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.5}, URN = {urn:nbn:de:0030-drops-170390}, doi = {10.4230/LIPIcs.WABI.2022.5}, annote = {Keywords: Reconciliation, Duplication, Endosymbiotic gene transfer, Multifurcated gene tree, Polytomy} }
Konstantinn Bonnet, Tobias Marschall, and Daniel Doerr¹. Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 6:1-6:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{bonnet_et_al:LIPIcs.WABI.2022.6, author = {Bonnet, Konstantinn and Marschall, Tobias and Doerr¹, Daniel}, title = {{Constructing Founder Sets Under Allelic and Non-Allelic Homologous Recombination}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {6:1--6:23}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.6}, URN = {urn:nbn:de:0030-drops-170403}, doi = {10.4230/LIPIcs.WABI.2022.6}, annote = {Keywords: founder set reconstruction, variation graph, pangenomics, NAHR, homologous recombination} }
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.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} }
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.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} }
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.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} }
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.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} }
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} }
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.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} }
Marília D. V. Braga, Leonie R. Brockmann, Katharina Klerx, and Jens Stoye. A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 13:1-13:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{braga_et_al:LIPIcs.WABI.2022.13, author = {Braga, Mar{\'\i}lia D. V. and Brockmann, Leonie R. and Klerx, Katharina and Stoye, Jens}, title = {{A Linear Time Algorithm for an Extended Version of the Breakpoint Double Distance}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {13:1--13:16}, 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.2022.13}, URN = {urn:nbn:de:0030-drops-170472}, doi = {10.4230/LIPIcs.WABI.2022.13}, annote = {Keywords: Comparative genomics, genome rearrangement, breakpoint distance, double-cut-and-join (DCJ) distance, double distance} }
Yoshihiro Shibuya, Djamal Belazzougui, and Gregory Kucherov. Efficient Reconciliation of Genomic Datasets of High Similarity. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 14:1-14:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{shibuya_et_al:LIPIcs.WABI.2022.14, author = {Shibuya, Yoshihiro and Belazzougui, Djamal and Kucherov, Gregory}, title = {{Efficient Reconciliation of Genomic Datasets of High Similarity}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {14:1--14:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.14}, URN = {urn:nbn:de:0030-drops-170481}, doi = {10.4230/LIPIcs.WABI.2022.14}, annote = {Keywords: k-mers, sketching, Invertible Bloom Lookup Tables, IBLT, MinHash, syncmers, minimizers} }
Wei Wei and David Koslicki. WGSUniFrac: Applying UniFrac Metric to Whole Genome Shotgun Data. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 15:1-15:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{wei_et_al:LIPIcs.WABI.2022.15, author = {Wei, Wei and Koslicki, David}, title = {{WGSUniFrac: Applying UniFrac Metric to Whole Genome Shotgun Data}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {15:1--15:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.15}, URN = {urn:nbn:de:0030-drops-170494}, doi = {10.4230/LIPIcs.WABI.2022.15}, annote = {Keywords: UniFrac, beta-diversity, Whole Genome Shotgun, microbial community similarity} }
Giulia Bernardini, Leo van Iersel, Esther Julien, and Leen Stougie. Reconstructing Phylogenetic Networks via Cherry Picking and Machine Learning. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 16:1-16:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{bernardini_et_al:LIPIcs.WABI.2022.16, author = {Bernardini, Giulia and van Iersel, Leo and Julien, Esther and Stougie, Leen}, title = {{Reconstructing Phylogenetic Networks via Cherry Picking and Machine Learning}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {16:1--16:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.16}, URN = {urn:nbn:de:0030-drops-170507}, doi = {10.4230/LIPIcs.WABI.2022.16}, annote = {Keywords: Phylogenetics, Hybridization, Cherry Picking, Machine Learning, Heuristic} }
Daniel Gibney, Sharma V. Thankachan, and Srinivas Aluru. Feasibility of Flow Decomposition with Subpath Constraints in Linear Time. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 17:1-17:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{gibney_et_al:LIPIcs.WABI.2022.17, author = {Gibney, Daniel and Thankachan, Sharma V. and Aluru, Srinivas}, title = {{Feasibility of Flow Decomposition with Subpath Constraints in Linear Time}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {17:1--17:16}, 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.2022.17}, URN = {urn:nbn:de:0030-drops-170516}, doi = {10.4230/LIPIcs.WABI.2022.17}, annote = {Keywords: Flow networks, flow decomposition, subpath constraints} }
Adrián Goga and Andrej Baláž. Prefix-Free Parsing for Building Large Tunnelled Wheeler Graphs. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 18:1-18:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{goga_et_al:LIPIcs.WABI.2022.18, author = {Goga, Adri\'{a}n and Bal\'{a}\v{z}, Andrej}, title = {{Prefix-Free Parsing for Building Large Tunnelled Wheeler Graphs}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {18:1--18:12}, 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.2022.18}, URN = {urn:nbn:de:0030-drops-170529}, doi = {10.4230/LIPIcs.WABI.2022.18}, annote = {Keywords: Wheeler graphs, BWT tunnelling, prefix-free parsing, pangenomic graphs} }
Taher Mun, Naga Sai Kavya Vaddadi, and Ben Langmead. Pangenomic Genotyping with the Marker Array. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 19:1-19:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{mun_et_al:LIPIcs.WABI.2022.19, author = {Mun, Taher and Vaddadi, Naga Sai Kavya and Langmead, Ben}, title = {{Pangenomic Genotyping with the Marker Array}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {19:1--19:17}, 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.2022.19}, URN = {urn:nbn:de:0030-drops-170530}, doi = {10.4230/LIPIcs.WABI.2022.19}, annote = {Keywords: Sequence alignment indexing genotyping} }
Zsuzsanna Lipták, Francesco Masillo, and Simon J. Puglisi. Suffix Sorting via Matching Statistics. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 20:1-20:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{liptak_et_al:LIPIcs.WABI.2022.20, author = {Lipt\'{a}k, Zsuzsanna and Masillo, Francesco and Puglisi, Simon J.}, title = {{Suffix Sorting via Matching Statistics}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {20:1--20:15}, 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.2022.20}, URN = {urn:nbn:de:0030-drops-170545}, doi = {10.4230/LIPIcs.WABI.2022.20}, annote = {Keywords: Generalized suffix array, matching statistics, string collections, compressed representation, data structures, efficient algorithms} }
Pijus Simonaitis and Benjamin J. Raphael. A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 21:1-21:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{simonaitis_et_al:LIPIcs.WABI.2022.21, author = {Simonaitis, Pijus and Raphael, Benjamin J.}, title = {{A Maximum Parsimony Principle for Multichromosomal Complex Genome Rearrangements}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {21:1--21:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.21}, URN = {urn:nbn:de:0030-drops-170552}, doi = {10.4230/LIPIcs.WABI.2022.21}, annote = {Keywords: Genome rearrangements, maximum parsimony, cancer evolution, chromothripsis, structural variation, affected chromosomes} }
Ke Chen and Mingfu Shao. Locality-Sensitive Bucketing Functions for the Edit Distance. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 22:1-22:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{chen_et_al:LIPIcs.WABI.2022.22, author = {Chen, Ke and Shao, Mingfu}, title = {{Locality-Sensitive Bucketing Functions for the Edit Distance}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {22:1--22:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.22}, URN = {urn:nbn:de:0030-drops-170563}, doi = {10.4230/LIPIcs.WABI.2022.22}, annote = {Keywords: Locality-sensitive hashing, locality-sensitive bucketing, long reads, embedding} }
Veronica Guerrini, Alessio Conte, Roberto Grossi, Gianni Liti, Giovanna Rosone, and Lorenzo Tattini. phyBWT: Alignment-Free Phylogeny via eBWT Positional Clustering. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 23:1-23:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{guerrini_et_al:LIPIcs.WABI.2022.23, author = {Guerrini, Veronica and Conte, Alessio and Grossi, Roberto and Liti, Gianni and Rosone, Giovanna and Tattini, Lorenzo}, title = {{phyBWT: Alignment-Free Phylogeny via eBWT Positional Clustering}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {23:1--23:19}, 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.2022.23}, URN = {urn:nbn:de:0030-drops-170577}, doi = {10.4230/LIPIcs.WABI.2022.23}, annote = {Keywords: Phylogeny, partition tree, BWT, positional cluster, alignment-free, reference-free, assembly-free} }
Diego P. Rubert and Marília D. V. Braga. Gene Orthology Inference via Large-Scale Rearrangements for Partially Assembled Genomes. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 24:1-24:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{rubert_et_al:LIPIcs.WABI.2022.24, author = {Rubert, Diego P. and Braga, Mar{\'\i}lia D. V.}, title = {{Gene Orthology Inference via Large-Scale Rearrangements for Partially Assembled Genomes}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {24:1--24:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.24}, URN = {urn:nbn:de:0030-drops-170586}, doi = {10.4230/LIPIcs.WABI.2022.24}, annote = {Keywords: Comparative genomics, double-cut-and-join, indels, gene orthology} }
Clément Agret, Bastien Cazaux, and Antoine Limasset. Toward Optimal Fingerprint Indexing for Large Scale Genomics. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 25:1-25:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{agret_et_al:LIPIcs.WABI.2022.25, author = {Agret, Cl\'{e}ment and Cazaux, Bastien and Limasset, Antoine}, title = {{Toward Optimal Fingerprint Indexing for Large Scale Genomics}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {25:1--25:15}, 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.2022.25}, URN = {urn:nbn:de:0030-drops-170598}, doi = {10.4230/LIPIcs.WABI.2022.25}, annote = {Keywords: Data Structure, Indexation, Local Sensitive Hashing, Genomes, Databases} }