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.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} }
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.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} }
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.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} }
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.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} }
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.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} }
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.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} }
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.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} }
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.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} }
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.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} }
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.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} }
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.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} }
Brandon Jew, Jiajin Li, Sriram Sankararaman, and Jae Hoon Sul. An Efficient Linear Mixed Model Framework for Meta-Analytic Association Studies Across Multiple Contexts. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 10:1-10:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{jew_et_al:LIPIcs.WABI.2021.10, author = {Jew, Brandon and Li, Jiajin and Sankararaman, Sriram and Sul, Jae Hoon}, title = {{An Efficient Linear Mixed Model Framework for Meta-Analytic Association Studies Across Multiple Contexts}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {10:1--10:17}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.10}, URN = {urn:nbn:de:0030-drops-143632}, doi = {10.4230/LIPIcs.WABI.2021.10}, annote = {Keywords: Meta-analysis, Linear mixed models, multiple-context genetic association} }
Anuradha Wickramarachchi and Yu Lin. LRBinner: Binning Long Reads in Metagenomics Datasets. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 11:1-11:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{wickramarachchi_et_al:LIPIcs.WABI.2021.11, author = {Wickramarachchi, Anuradha and Lin, Yu}, title = {{LRBinner: Binning Long Reads in Metagenomics Datasets}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {11:1--11:18}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.11}, URN = {urn:nbn:de:0030-drops-143644}, doi = {10.4230/LIPIcs.WABI.2021.11}, annote = {Keywords: Metagenomics binning, long reads, machine learning, clustering} }
Kazushi Kitaya and Tetsuo Shibuya. Compression of Multiple k-Mer Sets by Iterative SPSS Decomposition. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 12:1-12:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{kitaya_et_al:LIPIcs.WABI.2021.12, author = {Kitaya, Kazushi and Shibuya, Tetsuo}, title = {{Compression of Multiple k-Mer Sets by Iterative SPSS Decomposition}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {12:1--12:17}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.12}, URN = {urn:nbn:de:0030-drops-143659}, doi = {10.4230/LIPIcs.WABI.2021.12}, annote = {Keywords: sequencing data, k-mer, de Bruijn graph, compression, colored de Bruijn graph} }
Travis Gagie, Garance Gourdel, and Giovanni Manzini. Compressing and Indexing Aligned Readsets. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 13:1-13:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{gagie_et_al:LIPIcs.WABI.2021.13, author = {Gagie, Travis and Gourdel, Garance and Manzini, Giovanni}, title = {{Compressing and Indexing Aligned Readsets}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {13:1--13:21}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.13}, URN = {urn:nbn:de:0030-drops-143660}, doi = {10.4230/LIPIcs.WABI.2021.13}, annote = {Keywords: data compression, compact data structures, FM-index, Burrows-Wheeler Transform, EBWT, XBWT, DNA reads} }
Ali Ebrahimpour-Boroojeny, Sanjay Rajopadhye, and Hamidreza Chitsaz. BPPart: RNA-RNA Interaction Partition Function in the Absence of Entropy. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 14:1-14:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{ebrahimpourboroojeny_et_al:LIPIcs.WABI.2021.14, author = {Ebrahimpour-Boroojeny, Ali and Rajopadhye, Sanjay and Chitsaz, Hamidreza}, title = {{BPPart: RNA-RNA Interaction Partition Function in the Absence of Entropy}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {14:1--14:24}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.14}, URN = {urn:nbn:de:0030-drops-143673}, doi = {10.4230/LIPIcs.WABI.2021.14}, annote = {Keywords: RNA-RNA Interaction, Partition Function, RNA Secondary Structure} }
Hamza Išerić, Can Alkan, Faraz Hach, and Ibrahim Numanagić. BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 15:1-15:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{iseric_et_al:LIPIcs.WABI.2021.15, author = {I\v{s}eri\'{c}, Hamza and Alkan, Can and Hach, Faraz and Numanagi\'{c}, Ibrahim}, title = {{BISER: Fast Characterization of Segmental Duplication Structure in Multiple Genome Assemblies}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {15:1--15:18}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.15}, URN = {urn:nbn:de:0030-drops-143681}, doi = {10.4230/LIPIcs.WABI.2021.15}, annote = {Keywords: genome analysis, fast alignment, segmental duplications, core duplicons, sequence decomposition} }
Lucia Williams, Alexandru I. Tomescu, and Brendan Mumey. Flow Decomposition with Subpath Constraints. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 16:1-16:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{williams_et_al:LIPIcs.WABI.2021.16, author = {Williams, Lucia and Tomescu, Alexandru I. and Mumey, Brendan}, title = {{Flow Decomposition with Subpath Constraints}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {16:1--16:15}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.16}, URN = {urn:nbn:de:0030-drops-143695}, doi = {10.4230/LIPIcs.WABI.2021.16}, annote = {Keywords: Flow decomposition, subpath constraints, RNA-Seq} }
Marcin Wawerka, Dawid Dąbkowski, Natalia Rutecka, Agnieszka Mykowiecka, and Paweł Górecki. Conflict Resolution Algorithms for Deep Coalescence Phylogenetic Networks. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 17:1-17:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{wawerka_et_al:LIPIcs.WABI.2021.17, author = {Wawerka, Marcin and D\k{a}bkowski, Dawid and Rutecka, Natalia and Mykowiecka, Agnieszka and G\'{o}recki, Pawe{\l}}, title = {{Conflict Resolution Algorithms for Deep Coalescence Phylogenetic Networks}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {17:1--17:21}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.17}, URN = {urn:nbn:de:0030-drops-143708}, doi = {10.4230/LIPIcs.WABI.2021.17}, annote = {Keywords: Phylogenetic Network, Gene Tree, Species Tree, Deep Coalescence, Reticulation, Optimal Displayed Tree} }
Ron Zeira, Geoffrey Mon, and Benjamin J. Raphael. Genome Halving and Aliquoting Under the Copy Number Distance. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 18:1-18:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{zeira_et_al:LIPIcs.WABI.2021.18, author = {Zeira, Ron and Mon, Geoffrey and Raphael, Benjamin J.}, title = {{Genome Halving and Aliquoting Under the Copy Number Distance}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {18:1--18:25}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.18}, URN = {urn:nbn:de:0030-drops-143711}, doi = {10.4230/LIPIcs.WABI.2021.18}, annote = {Keywords: Genome rearrangements, Copy number distance, Whole genome duplication, polyploidization, genome halving distance, genome aliquoting distance} }
Ardalan Naseri, William Yue, Shaojie Zhang, and Degui Zhi. Efficient Haplotype Block Matching in Bi-Directional PBWT. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 19:1-19:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{naseri_et_al:LIPIcs.WABI.2021.19, author = {Naseri, Ardalan and Yue, William and Zhang, Shaojie and Zhi, Degui}, title = {{Efficient Haplotype Block Matching in Bi-Directional PBWT}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {19:1--19:13}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.19}, URN = {urn:nbn:de:0030-drops-143729}, doi = {10.4230/LIPIcs.WABI.2021.19}, annote = {Keywords: PBWT, Bi-directional, Haplotype Matching} }
Spencer Krieger and John Kececioglu. Fast Approximate Shortest Hyperpaths for Inferring Pathways in Cell Signaling Hypergraphs. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 20:1-20:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{krieger_et_al:LIPIcs.WABI.2021.20, author = {Krieger, Spencer and Kececioglu, John}, title = {{Fast Approximate Shortest Hyperpaths for Inferring Pathways in Cell Signaling Hypergraphs}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {20:1--20:20}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.20}, URN = {urn:nbn:de:0030-drops-143733}, doi = {10.4230/LIPIcs.WABI.2021.20}, annote = {Keywords: Systems biology, cell signaling networks, reaction pathways, directed hypergraphs, shortest hyperpaths, efficient heuristics, hyperpath enumeration} }
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