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)
Xiaofei Carl Zang, Xiang Li, Kyle Metcalfe, Tuval Ben-Yehezkel, Ryan Kelley, and Mingfu Shao. Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 22:1-22:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{zang_et_al:LIPIcs.WABI.2024.22, author = {Zang, Xiaofei Carl and Li, Xiang and Metcalfe, Kyle and Ben-Yehezkel, Tuval and Kelley, Ryan and Shao, Mingfu}, title = {{Anchorage Accurately Assembles Anchor-Flanked Synthetic Long Reads}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {22:1--22:17}, 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.2024.22}, URN = {urn:nbn:de:0030-drops-206660}, doi = {10.4230/LIPIcs.WABI.2024.22}, annote = {Keywords: Genome assembly, de Bruijn graph, synthetic long reads, anchor-guided assembly, LoopSeq} }
Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)
Andreas Grigorjew, Fernando H. C. Dias, Andrea Cracco, Romeo Rizzi, and Alexandru I. Tomescu. Accelerating ILP Solvers for Minimum Flow Decompositions Through Search Space and Dimensionality Reductions. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 14:1-14:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{grigorjew_et_al:LIPIcs.SEA.2024.14, author = {Grigorjew, Andreas and Dias, Fernando H. C. and Cracco, Andrea and Rizzi, Romeo and Tomescu, Alexandru I.}, title = {{Accelerating ILP Solvers for Minimum Flow Decompositions Through Search Space and Dimensionality Reductions}}, booktitle = {22nd International Symposium on Experimental Algorithms (SEA 2024)}, pages = {14:1--14:19}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-325-6}, ISSN = {1868-8969}, year = {2024}, volume = {301}, editor = {Liberti, Leo}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.14}, URN = {urn:nbn:de:0030-drops-203792}, doi = {10.4230/LIPIcs.SEA.2024.14}, annote = {Keywords: Flow decomposition, Integer Linear Programming, Safety, RNA-seq, RNA transcript assembly, isoform} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
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} }
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
Hongyi Xin, Mingfu Shao, and Carl Kingsford. Context-Aware Seeds for Read Mapping. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 15:1-15:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{xin_et_al:LIPIcs.WABI.2019.15, author = {Xin, Hongyi and Shao, Mingfu and Kingsford, Carl}, title = {{Context-Aware Seeds for Read Mapping}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {15:1--15:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-123-8}, ISSN = {1868-8969}, year = {2019}, volume = {143}, editor = {Huber, Katharina T. and Gusfield, Dan}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.15}, URN = {urn:nbn:de:0030-drops-110452}, doi = {10.4230/LIPIcs.WABI.2019.15}, annote = {Keywords: Read Mapping, Seed and Extend, Edit Distance, Suffix Trie} }
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