LIPIcs, Volume 201
WABI 2021, August 2-4, 2021, Virtual Conference
Editors: Alessandra Carbone and Mohammed El-Kebir
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
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-dev.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} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
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-dev.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} }
Published in: OASIcs, Volume 109, Eelco Visser Commemorative Symposium (EVCS 2023)
Houda Boukham, Guido Wachsmuth, Toine Hartman, Hamza Boucherit, Oskar van Rest, Hassan Chafi, Sungpack Hong, Martijn Dwars, Arnaud Delamare, and Dalila Chiadmi. Spoofax at Oracle: Domain-Specific Language Engineering for Large-Scale Graph Analytics. In Eelco Visser Commemorative Symposium (EVCS 2023). Open Access Series in Informatics (OASIcs), Volume 109, pp. 5:1-5:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{boukham_et_al:OASIcs.EVCS.2023.5, author = {Boukham, Houda and Wachsmuth, Guido and Hartman, Toine and Boucherit, Hamza and van Rest, Oskar and Chafi, Hassan and Hong, Sungpack and Dwars, Martijn and Delamare, Arnaud and Chiadmi, Dalila}, title = {{Spoofax at Oracle: Domain-Specific Language Engineering for Large-Scale Graph Analytics}}, booktitle = {Eelco Visser Commemorative Symposium (EVCS 2023)}, pages = {5:1--5:8}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-95977-267-9}, ISSN = {2190-6807}, year = {2023}, volume = {109}, editor = {L\"{a}mmel, Ralf and Mosses, Peter D. and Steimann, Friedrich}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.EVCS.2023.5}, URN = {urn:nbn:de:0030-drops-177756}, doi = {10.4230/OASIcs.EVCS.2023.5}, annote = {Keywords: language workbench, domain-specific language} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 1-400, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@Proceedings{carbone_et_al:LIPIcs.WABI.2021, title = {{LIPIcs, Volume 201, WABI 2021, Complete Volume}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {1--400}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021}, URN = {urn:nbn:de:0030-drops-143520}, doi = {10.4230/LIPIcs.WABI.2021}, annote = {Keywords: LIPIcs, Volume 201, WABI 2021, Complete Volume} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 0:i-0:x, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{carbone_et_al:LIPIcs.WABI.2021.0, author = {Carbone, Alessandra and El-Kebir, Mohammed}, title = {{Front Matter, Table of Contents, Preface, Conference Organization}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {0:i--0:x}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.0}, URN = {urn:nbn:de:0030-drops-143531}, doi = {10.4230/LIPIcs.WABI.2021.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Matthew LeMay, Yi-Chieh Wu, and Ran Libeskind-Hadas. The Most Parsimonious Reconciliation Problem in the Presence of Incomplete Lineage Sorting and Hybridization Is NP-Hard. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 1:1-1:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{lemay_et_al:LIPIcs.WABI.2021.1, author = {LeMay, Matthew and Wu, Yi-Chieh and Libeskind-Hadas, Ran}, title = {{The Most Parsimonious Reconciliation Problem in the Presence of Incomplete Lineage Sorting and Hybridization Is NP-Hard}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {1:1--1:10}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.1}, URN = {urn:nbn:de:0030-drops-143546}, doi = {10.4230/LIPIcs.WABI.2021.1}, annote = {Keywords: phylogenetics, reconciliation, deep coalescence, hybridization, NP-hardness} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Yoshiki Nakagawa, Satsuya Ohata, and Kana Shimizu. Efficient Privacy-Preserving Variable-Length Substring Match for Genome Sequence. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 2:1-2:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{nakagawa_et_al:LIPIcs.WABI.2021.2, author = {Nakagawa, Yoshiki and Ohata, Satsuya and Shimizu, Kana}, title = {{Efficient Privacy-Preserving Variable-Length Substring Match for Genome Sequence}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {2:1--2:23}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.2}, URN = {urn:nbn:de:0030-drops-143552}, doi = {10.4230/LIPIcs.WABI.2021.2}, annote = {Keywords: Private Genome Sequence Search, Secure Multiparty Computation, Secret Sharing, FM-index, Suffix Tree, Maximal Exact Match} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Yishu Wang, Arnaud Mary, Marie-France Sagot, and Blerina Sinaimeri. Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 3:1-3:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{wang_et_al:LIPIcs.WABI.2021.3, author = {Wang, Yishu and Mary, Arnaud and Sagot, Marie-France and Sinaimeri, Blerina}, title = {{Making Sense of a Cophylogeny Output: Efficient Listing of Representative Reconciliations}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {3:1--3:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.3}, URN = {urn:nbn:de:0030-drops-143564}, doi = {10.4230/LIPIcs.WABI.2021.3}, annote = {Keywords: Cophylogeny, Enumeration, Equivalence relation, Dynamic programming} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Jason Fan, Skylar Chan, and Rob Patro. Perplexity: Evaluating Transcript Abundance Estimation in the Absence of Ground Truth. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 4:1-4:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{fan_et_al:LIPIcs.WABI.2021.4, author = {Fan, Jason and Chan, Skylar and Patro, Rob}, title = {{Perplexity: Evaluating Transcript Abundance Estimation in the Absence of Ground Truth}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {4:1--4:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.4}, URN = {urn:nbn:de:0030-drops-143578}, doi = {10.4230/LIPIcs.WABI.2021.4}, annote = {Keywords: RNA-seq, transcript abundance estimation, model selection} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Nicolas Boria, Laurent Gourvès, Vangelis Th. Paschos, and Jérôme Monnot. The Maximum Duo-Preservation String Mapping Problem with Bounded Alphabet. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 5:1-5:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{boria_et_al:LIPIcs.WABI.2021.5, author = {Boria, Nicolas and Gourv\`{e}s, Laurent and Paschos, Vangelis Th. and Monnot, J\'{e}r\^{o}me}, title = {{The Maximum Duo-Preservation String Mapping Problem with Bounded Alphabet}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {5:1--5:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.5}, URN = {urn:nbn:de:0030-drops-143586}, doi = {10.4230/LIPIcs.WABI.2021.5}, annote = {Keywords: Maximum-Duo Preservation String Mapping, Bounded alphabet, Polynomial Time Approximation Scheme} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Celine Scornavacca and Mathias Weller. Treewidth-Based Algorithms for the Small Parsimony Problem on Networks. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 6:1-6:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{scornavacca_et_al:LIPIcs.WABI.2021.6, author = {Scornavacca, Celine and Weller, Mathias}, title = {{Treewidth-Based Algorithms for the Small Parsimony Problem on Networks}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {6:1--6:21}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.6}, URN = {urn:nbn:de:0030-drops-143591}, doi = {10.4230/LIPIcs.WABI.2021.6}, annote = {Keywords: Phylogenetics, parsimony, phylogenetic networks, parameterized complexity, dynamic programming, treewidth} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Bertrand Marchand, Yann Ponty, and Laurent Bulteau. Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 7:1-7:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{marchand_et_al:LIPIcs.WABI.2021.7, author = {Marchand, Bertrand and Ponty, Yann and Bulteau, Laurent}, title = {{Tree Diet: Reducing the Treewidth to Unlock FPT Algorithms in RNA Bioinformatics}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {7:1--7:23}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.7}, URN = {urn:nbn:de:0030-drops-143604}, doi = {10.4230/LIPIcs.WABI.2021.7}, annote = {Keywords: RNA, treewidth, FPT algorithms, RNA design, structure-sequence alignment} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Yoshihiro Shibuya, Djamal Belazzougui, and Gregory Kucherov. Space-Efficient Representation of Genomic k-Mer Count Tables. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 8:1-8:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{shibuya_et_al:LIPIcs.WABI.2021.8, author = {Shibuya, Yoshihiro and Belazzougui, Djamal and Kucherov, Gregory}, title = {{Space-Efficient Representation of Genomic k-Mer Count Tables}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {8:1--8:19}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.8}, URN = {urn:nbn:de:0030-drops-143619}, doi = {10.4230/LIPIcs.WABI.2021.8}, annote = {Keywords: k-mer counting, data structures, compression, minimizers, compressed static function, Bloom filter, empirical entropy} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Palash Sashittal, Simone Zaccaria, and Mohammed El-Kebir. Parsimonious Clone Tree Reconciliation in Cancer. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 9:1-9:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{sashittal_et_al:LIPIcs.WABI.2021.9, author = {Sashittal, Palash and Zaccaria, Simone and El-Kebir, Mohammed}, title = {{Parsimonious Clone Tree Reconciliation in Cancer}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {9:1--9:21}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.9}, URN = {urn:nbn:de:0030-drops-143624}, doi = {10.4230/LIPIcs.WABI.2021.9}, annote = {Keywords: Intra-tumor heterogeneity, phylogenetics, mixed integer linear programming} }
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