LIPIcs, Volume 143
WABI 2019, September 8-10, 2019, Niagara Falls, NY, USA
Editors: Katharina T. Huber and Dan Gusfield
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
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-dev.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} }
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
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-dev.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} }
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
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-dev.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} }
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
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-dev.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} }
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
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-dev.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} }
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
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-dev.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} }
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
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-dev.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} }
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
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-dev.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} }
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
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-dev.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} }
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
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-dev.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} }
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
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-dev.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} }
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
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-dev.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} }
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
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-dev.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} }
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
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-dev.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} }
Feedback for Dagstuhl Publishing