19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@Proceedings{huber_et_al:LIPIcs.WABI.2019, title = {{LIPIcs, Volume 143, WABI'19, Complete Volume}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, 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}, URN = {urn:nbn:de:0030-drops-112994}, doi = {10.4230/LIPIcs.WABI.2019}, annote = {Keywords: Applied computing, Bioinformatics; Theory of computation, Design and analysis of algorithms; Mathematics of computing, Probabilistic inference problem} }
19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 0:i-0:xii, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{huber_et_al:LIPIcs.WABI.2019.0, author = {Huber, Katharina T. and Gusfield, Dan}, title = {{Front Matter, Table of Contents, Preface, Conference Organization}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {0:i--0:xii}, 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.2019.0}, URN = {urn:nbn:de:0030-drops-110307}, doi = {10.4230/LIPIcs.WABI.2019.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization} }
Jesper Jansson, Konstantinos Mampentzidis, and Sandhya T. P.. Building a Small and Informative Phylogenetic Supertree. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 1:1-1:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{jansson_et_al:LIPIcs.WABI.2019.1, author = {Jansson, Jesper and Mampentzidis, Konstantinos and T. P., Sandhya}, title = {{Building a Small and Informative Phylogenetic Supertree}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {1:1--1:14}, 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.2019.1}, URN = {urn:nbn:de:0030-drops-110316}, doi = {10.4230/LIPIcs.WABI.2019.1}, annote = {Keywords: phylogenetic tree, supertree, rooted triplet, approximation algorithm} }
Roland Wittler. Alignment- and Reference-Free Phylogenomics with Colored de Bruijn Graphs. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 2:1-2:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{wittler:LIPIcs.WABI.2019.2, author = {Wittler, Roland}, title = {{Alignment- and Reference-Free Phylogenomics with Colored de Bruijn Graphs}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {2:1--2:14}, 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.2019.2}, URN = {urn:nbn:de:0030-drops-110325}, doi = {10.4230/LIPIcs.WABI.2019.2}, annote = {Keywords: Phylogenomics, phylogenetics, phylogenetic splits, colored de Bruijn graphs} }
Nathan L. Clement. Quantified Uncertainty of Flexible Protein-Protein Docking Algorithms. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 3:1-3:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{clement:LIPIcs.WABI.2019.3, author = {Clement, Nathan L.}, title = {{Quantified Uncertainty of Flexible Protein-Protein Docking Algorithms}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {3:1--3:12}, 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.2019.3}, URN = {urn:nbn:de:0030-drops-110335}, doi = {10.4230/LIPIcs.WABI.2019.3}, annote = {Keywords: protein-protein docking, uncertainty quantification, protein flexibility, low-discrepancy sampling, high-dimensional sampling} }
Sarah Christensen, Erin K. Molloy, Pranjal Vachaspati, and Tandy Warnow. TRACTION: Fast Non-Parametric Improvement of Estimated Gene Trees. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 4:1-4:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{christensen_et_al:LIPIcs.WABI.2019.4, author = {Christensen, Sarah and Molloy, Erin K. and Vachaspati, Pranjal and Warnow, Tandy}, title = {{TRACTION: Fast Non-Parametric Improvement of Estimated Gene Trees}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {4:1--4:16}, 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.2019.4}, URN = {urn:nbn:de:0030-drops-110347}, doi = {10.4230/LIPIcs.WABI.2019.4}, annote = {Keywords: Gene tree correction, horizontal gene transfer, incomplete lineage sorting} }
Kohei Yamada, Zhi-Zhong Chen, and Lusheng Wang. Better Practical Algorithms for rSPR Distance and Hybridization Number. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 5:1-5:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{yamada_et_al:LIPIcs.WABI.2019.5, author = {Yamada, Kohei and Chen, Zhi-Zhong and Wang, Lusheng}, title = {{Better Practical Algorithms for rSPR Distance and Hybridization Number}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {5:1--5:12}, 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.2019.5}, URN = {urn:nbn:de:0030-drops-110355}, doi = {10.4230/LIPIcs.WABI.2019.5}, annote = {Keywords: phylogenetic tree, fixed-parameter algorithms, approximation algorithms, Monte Carlo tree search} }
Georgi D. Georgiev, Kevin F. Dodd, and Brian Y. Chen. pClay: A Precise Parallel Algorithm for Comparing Molecular Surfaces. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 6:1-6:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{georgiev_et_al:LIPIcs.WABI.2019.6, author = {Georgiev, Georgi D. and Dodd, Kevin F. and Chen, Brian Y.}, title = {{pClay: A Precise Parallel Algorithm for Comparing Molecular Surfaces}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {6:1--6:13}, 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.2019.6}, URN = {urn:nbn:de:0030-drops-110365}, doi = {10.4230/LIPIcs.WABI.2019.6}, annote = {Keywords: Specificity Annotation, Structure Comparison, Cavity Analysis} }
Kavya Vaddadi, Rajgopal Srinivasan, and Naveen Sivadasan. Read Mapping on Genome Variation Graphs. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 7:1-7:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{vaddadi_et_al:LIPIcs.WABI.2019.7, author = {Vaddadi, Kavya and Srinivasan, Rajgopal and Sivadasan, Naveen}, title = {{Read Mapping on Genome Variation Graphs}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {7:1--7:17}, 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.2019.7}, URN = {urn:nbn:de:0030-drops-110375}, doi = {10.4230/LIPIcs.WABI.2019.7}, annote = {Keywords: read mapping, pangenome, genome variation graphs, locality sensitive hashing} }
Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, and Jens Stoye. Finding All Maximal Perfect Haplotype Blocks in Linear Time. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 8:1-8:9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{alanko_et_al:LIPIcs.WABI.2019.8, author = {Alanko, Jarno and Bannai, Hideo and Cazaux, Bastien and Peterlongo, Pierre and Stoye, Jens}, title = {{Finding All Maximal Perfect Haplotype Blocks in Linear Time}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {8:1--8:9}, 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.2019.8}, URN = {urn:nbn:de:0030-drops-110388}, doi = {10.4230/LIPIcs.WABI.2019.8}, annote = {Keywords: Population genomics, selection coefficient, haplotype block, positional Burrows-Wheeler Transform} }
Roni Zoller, Meirav Zehavi, and Michal Ziv-Ukelson. A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 9:1-9:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{zoller_et_al:LIPIcs.WABI.2019.9, author = {Zoller, Roni and Zehavi, Meirav and Ziv-Ukelson, Michal}, title = {{A New Paradigm for Identifying Reconciliation-Scenario Altering Mutations Conferring Environmental Adaptation}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {9:1--9:13}, 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.2019.9}, URN = {urn:nbn:de:0030-drops-110398}, doi = {10.4230/LIPIcs.WABI.2019.9}, annote = {Keywords: Gene tree, Species tree, Reconciliation} }
Jie Liu, Yuanhao Huang, Ritambhara Singh, Jean-Philippe Vert, and William Stafford Noble. Jointly Embedding Multiple Single-Cell Omics Measurements. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 10:1-10:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{liu_et_al:LIPIcs.WABI.2019.10, author = {Liu, Jie and Huang, Yuanhao and Singh, Ritambhara and Vert, Jean-Philippe and Noble, William Stafford}, title = {{Jointly Embedding Multiple Single-Cell Omics Measurements}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {10:1--10:13}, 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.2019.10}, URN = {urn:nbn:de:0030-drops-110401}, doi = {10.4230/LIPIcs.WABI.2019.10}, annote = {Keywords: Manifold alignment, single-cell sequencing} }
Alexandra Gesine Cauer, Gürkan Yardımcı, Jean-Philippe Vert, Nelle Varoquaux, and William Stafford Noble. Inferring Diploid 3D Chromatin Structures from Hi-C Data. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 11:1-11:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{cauer_et_al:LIPIcs.WABI.2019.11, author = {Cauer, Alexandra Gesine and Yard{\i}mc{\i}, G\"{u}rkan and Vert, Jean-Philippe and Varoquaux, Nelle and Noble, William Stafford}, title = {{Inferring Diploid 3D Chromatin Structures from Hi-C Data}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {11:1--11:13}, 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.2019.11}, URN = {urn:nbn:de:0030-drops-110418}, doi = {10.4230/LIPIcs.WABI.2019.11}, annote = {Keywords: Genome 3D architecture, chromatin structure, Hi-C, 3D modeling} }
Alexey Markin and Oliver Eulenstein. Consensus Clusters in Robinson-Foulds Reticulation Networks. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 12:1-12:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{markin_et_al:LIPIcs.WABI.2019.12, author = {Markin, Alexey and Eulenstein, Oliver}, title = {{Consensus Clusters in Robinson-Foulds Reticulation Networks}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {12:1--12:12}, 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.2019.12}, URN = {urn:nbn:de:0030-drops-110420}, doi = {10.4230/LIPIcs.WABI.2019.12}, annote = {Keywords: Phylogenetics, phylogenetic tree, phylogenetic network, reticulation network, Robinson-Foulds, Pareto, RF-Net} }
Pijus Simonaitis, Annie Chateau, and Krister M. Swenson. Weighted Minimum-Length Rearrangement Scenarios. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 13:1-13:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{simonaitis_et_al:LIPIcs.WABI.2019.13, author = {Simonaitis, Pijus and Chateau, Annie and Swenson, Krister M.}, title = {{Weighted Minimum-Length Rearrangement Scenarios}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {13:1--13:17}, 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.2019.13}, URN = {urn:nbn:de:0030-drops-110436}, doi = {10.4230/LIPIcs.WABI.2019.13}, annote = {Keywords: Weighted genome rearrangement, Double cut and join (DCJ), Edge switch, Minimum-weight quadrangulation} }
Milad Miladi, Martin Raden, Sebastian Will, and Rolf Backofen. Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 14:1-14:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{miladi_et_al:LIPIcs.WABI.2019.14, author = {Miladi, Milad and Raden, Martin and Will, Sebastian and Backofen, Rolf}, title = {{Fast and Accurate Structure Probability Estimation for Simultaneous Alignment and Folding of RNAs}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {14:1--14:13}, 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.2019.14}, URN = {urn:nbn:de:0030-drops-110446}, doi = {10.4230/LIPIcs.WABI.2019.14}, annote = {Keywords: RNA secondary structure, Structural bioinformatics, Alignment, Algorithms} }
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} }
Alexander Tiskin. Bounded-Length Smith-Waterman Alignment. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 16:1-16:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{tiskin:LIPIcs.WABI.2019.16, author = {Tiskin, Alexander}, title = {{Bounded-Length Smith-Waterman Alignment}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {16:1--16:12}, 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.2019.16}, URN = {urn:nbn:de:0030-drops-110461}, doi = {10.4230/LIPIcs.WABI.2019.16}, annote = {Keywords: sequence alignment, local alignment, Smith, Waterman alignment, matrix searching} }
Chirag Jain, Haowen Zhang, Alexander Dilthey, and Srinivas Aluru. Validating Paired-End Read Alignments in Sequence Graphs. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 17:1-17:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{jain_et_al:LIPIcs.WABI.2019.17, author = {Jain, Chirag and Zhang, Haowen and Dilthey, Alexander and Aluru, Srinivas}, title = {{Validating Paired-End Read Alignments in Sequence Graphs}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {17:1--17:13}, 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.2019.17}, URN = {urn:nbn:de:0030-drops-110470}, doi = {10.4230/LIPIcs.WABI.2019.17}, annote = {Keywords: Sequence graphs, read mapping, index, sparse matrix-matrix multiplication} }
Yutong Qiu, Cong Ma, Han Xie, and Carl Kingsford. Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 18:1-18:5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{qiu_et_al:LIPIcs.WABI.2019.18, author = {Qiu, Yutong and Ma, Cong and Xie, Han and Kingsford, Carl}, title = {{Detecting Transcriptomic Structural Variants in Heterogeneous Contexts via the Multiple Compatible Arrangements Problem}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {18:1--18:5}, 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.2019.18}, URN = {urn:nbn:de:0030-drops-110483}, doi = {10.4230/LIPIcs.WABI.2019.18}, annote = {Keywords: transcriptomic structural variation, integer linear programming, heterogeneity} }
Qi Wang, R. A. Leo Elworth, Tian Rui Liu, and Todd J. Treangen. Faster Pan-Genome Construction for Efficient Differentiation of Naturally Occurring and Engineered Plasmids with Plaster. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 19:1-19:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{wang_et_al:LIPIcs.WABI.2019.19, author = {Wang, Qi and Elworth, R. A. Leo and Liu, Tian Rui and Treangen, Todd J.}, title = {{Faster Pan-Genome Construction for Efficient Differentiation of Naturally Occurring and Engineered Plasmids with Plaster}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {19:1--19:12}, 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.2019.19}, URN = {urn:nbn:de:0030-drops-110492}, doi = {10.4230/LIPIcs.WABI.2019.19}, annote = {Keywords: comparative genomics, sequence alignment, pan-genome, engineered plasmids} }
Jakub Truszkowski, Olivier Gascuel, and Krister M. Swenson. Rapidly Computing the Phylogenetic Transfer Index. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 20:1-20:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{truszkowski_et_al:LIPIcs.WABI.2019.20, author = {Truszkowski, Jakub and Gascuel, Olivier and Swenson, Krister M.}, title = {{Rapidly Computing the Phylogenetic Transfer Index}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {20:1--20:12}, 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.2019.20}, URN = {urn:nbn:de:0030-drops-110505}, doi = {10.4230/LIPIcs.WABI.2019.20}, annote = {Keywords: large phylogenies, bootstrap analysis, tree comparison, data structures on trees} }
Zhen Cao, Jiafan Zhu, and Luay Nakhleh. Empirical Performance of Tree-Based Inference of Phylogenetic Networks. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 21:1-21:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{cao_et_al:LIPIcs.WABI.2019.21, author = {Cao, Zhen and Zhu, Jiafan and Nakhleh, Luay}, title = {{Empirical Performance of Tree-Based Inference of Phylogenetic Networks}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {21:1--21:13}, 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.2019.21}, URN = {urn:nbn:de:0030-drops-110510}, doi = {10.4230/LIPIcs.WABI.2019.21}, annote = {Keywords: Phylogenetic networks, species tree, tree-based networks, multi-locus phylogeny} }
Mohammadamin Edrisi, Hamim Zafar, and Luay Nakhleh. A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 22:1-22:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{edrisi_et_al:LIPIcs.WABI.2019.22, author = {Edrisi, Mohammadamin and Zafar, Hamim and Nakhleh, Luay}, title = {{A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {22:1--22:13}, 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.2019.22}, URN = {urn:nbn:de:0030-drops-110525}, doi = {10.4230/LIPIcs.WABI.2019.22}, annote = {Keywords: Mutation calling, Single-cell sequencing, Integer linear programming, Perfect phylogeny} }
Natalie Sauerwald, Yihang Shen, and Carl Kingsford. Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 23:1-23:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{sauerwald_et_al:LIPIcs.WABI.2019.23, author = {Sauerwald, Natalie and Shen, Yihang and Kingsford, Carl}, title = {{Topological Data Analysis Reveals Principles of Chromosome Structure in Cellular Differentiation}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {23:1--23:16}, 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.2019.23}, URN = {urn:nbn:de:0030-drops-110537}, doi = {10.4230/LIPIcs.WABI.2019.23}, annote = {Keywords: topological data analysis, chromosome structure, Hi-C, topologically associating domains} }
Evgeny Polevikov and Mikhail Kolmogorov. Synteny Paths for Assembly Graphs Comparison. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 24:1-24:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{polevikov_et_al:LIPIcs.WABI.2019.24, author = {Polevikov, Evgeny and Kolmogorov, Mikhail}, title = {{Synteny Paths for Assembly Graphs Comparison}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {24:1--24:14}, 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.2019.24}, URN = {urn:nbn:de:0030-drops-110545}, doi = {10.4230/LIPIcs.WABI.2019.24}, annote = {Keywords: Assembly graphs, Genome assembly, Synteny blocks, Comparative Genomics} }
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