@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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}
}
@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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