Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Leonard Bohnenkämper, Jens Stoye, and Daniel Dörr. Reconstructing Rearrangement Phylogenies of Natural Genomes. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 12:1-12:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{bohnenkamper_et_al:LIPIcs.WABI.2024.12, author = {Bohnenk\"{a}mper, Leonard and Stoye, Jens and D\"{o}rr, Daniel}, title = {{Reconstructing Rearrangement Phylogenies of Natural Genomes}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {12:1--12:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-340-9}, ISSN = {1868-8969}, year = {2024}, volume = {312}, editor = {Pissis, Solon P. and Sung, Wing-Kin}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.12}, URN = {urn:nbn:de:0030-drops-206564}, doi = {10.4230/LIPIcs.WABI.2024.12}, annote = {Keywords: genome rearrangement, ancestral reconstruction, small parsimony, integer linear programming, double-cut-and-join} }
Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Adam Cicherski, Anna Lisiecka, and Norbert Dojer. AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 23:1-23:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{cicherski_et_al:LIPIcs.WABI.2024.23, author = {Cicherski, Adam and Lisiecka, Anna and Dojer, Norbert}, title = {{AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {23:1--23:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-340-9}, ISSN = {1868-8969}, year = {2024}, volume = {312}, editor = {Pissis, Solon P. and Sung, Wing-Kin}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.23}, URN = {urn:nbn:de:0030-drops-206673}, doi = {10.4230/LIPIcs.WABI.2024.23}, annote = {Keywords: pangenome, variation graph, genome alignment, population genomics} }
Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)
Yuto Nakashima, Dominik Köppl, Mitsuru Funakoshi, Shunsuke Inenaga, and Hideo Bannai. Edit and Alphabet-Ordering Sensitivity of Lex-Parse. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 75:1-75:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{nakashima_et_al:LIPIcs.MFCS.2024.75, author = {Nakashima, Yuto and K\"{o}ppl, Dominik and Funakoshi, Mitsuru and Inenaga, Shunsuke and Bannai, Hideo}, title = {{Edit and Alphabet-Ordering Sensitivity of Lex-Parse}}, booktitle = {49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)}, pages = {75:1--75:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-335-5}, ISSN = {1868-8969}, year = {2024}, volume = {306}, editor = {Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.75}, URN = {urn:nbn:de:0030-drops-206314}, doi = {10.4230/LIPIcs.MFCS.2024.75}, annote = {Keywords: Compression sensitivity, Lex-parse, Fibonacci words} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
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} }
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.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)
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} }
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