18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@Proceedings{parida_et_al:LIPIcs.WABI.2018, title = {{LIPIcs, Volume 113, WABI'18, Complete Volume}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018}, URN = {urn:nbn:de:0030-drops-97246}, doi = {10.4230/LIPIcs.WABI.2018}, annote = {Keywords: Applied computing, Bioinformatics, Theory of computation, Design and analysis of algorithms, Mathematics of computing, Probabilistic inference problem} }
18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 0:i-0:xvi, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{parida_et_al:LIPIcs.WABI.2018.0, author = {Parida, Laxmi and Ukkonen, Esko}, title = {{Front Matter, Table of Contents, Preface, Conference Organization}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {0:i--0:xvi}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.0}, URN = {urn:nbn:de:0030-drops-93028}, doi = {10.4230/LIPIcs.WABI.2018.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization} }
Hooman Zabeti, Tamon Stephen, Bonnie Berger, and Leonid Chindelevitch. A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 1:1-1:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{zabeti_et_al:LIPIcs.WABI.2018.1, author = {Zabeti, Hooman and Stephen, Tamon and Berger, Bonnie and Chindelevitch, Leonid}, title = {{A Duality-Based Method for Identifying Elemental Balance Violations in Metabolic Network Models}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {1:1--1:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.1}, URN = {urn:nbn:de:0030-drops-93034}, doi = {10.4230/LIPIcs.WABI.2018.1}, annote = {Keywords: Metabolic network analysis, elemental imbalance, linear programming, model verification} }
Christina Boucher, Travis Gagie, Alan Kuhnle, and Giovanni Manzini. Prefix-Free Parsing for Building Big BWTs. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 2:1-2:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{boucher_et_al:LIPIcs.WABI.2018.2, author = {Boucher, Christina and Gagie, Travis and Kuhnle, Alan and Manzini, Giovanni}, title = {{Prefix-Free Parsing for Building Big BWTs}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {2:1--2:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.2}, URN = {urn:nbn:de:0030-drops-93044}, doi = {10.4230/LIPIcs.WABI.2018.2}, annote = {Keywords: Burrows-Wheeler Transform, prefix-free parsing, compression-aware algorithms, genomic databases} }
Nicola Prezza, Nadia Pisanti, Marinella Sciortino, and Giovanna Rosone. Detecting Mutations by eBWT. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 3:1-3:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{prezza_et_al:LIPIcs.WABI.2018.3, author = {Prezza, Nicola and Pisanti, Nadia and Sciortino, Marinella and Rosone, Giovanna}, title = {{Detecting Mutations by eBWT}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {3:1--3:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.3}, URN = {urn:nbn:de:0030-drops-93051}, doi = {10.4230/LIPIcs.WABI.2018.3}, annote = {Keywords: BWT, LCP Array, SNPs, Reference-free, Assembly-free} }
Jouni Sirén, Erik Garrison, Adam M. Novak, Benedict J. Paten, and Richard Durbin. Haplotype-aware graph indexes. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 4:1-4:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{siren_et_al:LIPIcs.WABI.2018.4, author = {Sir\'{e}n, Jouni and Garrison, Erik and Novak, Adam M. and Paten, Benedict J. and Durbin, Richard}, title = {{Haplotype-aware graph indexes}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {4:1--4:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.4}, URN = {urn:nbn:de:0030-drops-93060}, doi = {10.4230/LIPIcs.WABI.2018.4}, annote = {Keywords: FM-indexes, variation graphs, haplotypes} }
Riccardo Dondi, Manuel Lafond, and Celine Scornavacca. Reconciling Multiple Genes Trees via Segmental Duplications and Losses. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 5:1-5:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{dondi_et_al:LIPIcs.WABI.2018.5, author = {Dondi, Riccardo and Lafond, Manuel and Scornavacca, Celine}, title = {{Reconciling Multiple Genes Trees via Segmental Duplications and Losses}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {5:1--5:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.5}, URN = {urn:nbn:de:0030-drops-93079}, doi = {10.4230/LIPIcs.WABI.2018.5}, annote = {Keywords: Gene trees/species tree reconciliation, phylogenetics, computational complexity, fixed-parameter algorithms} }
Tamal K. Dey and Sayan Mandal. Protein Classification with Improved Topological Data Analysis. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 6:1-6:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{dey_et_al:LIPIcs.WABI.2018.6, author = {Dey, Tamal K. and Mandal, Sayan}, title = {{Protein Classification with Improved Topological Data Analysis}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {6:1--6:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.6}, URN = {urn:nbn:de:0030-drops-93082}, doi = {10.4230/LIPIcs.WABI.2018.6}, annote = {Keywords: topological data analysis, persistent homology, simplicial collapse, supervised learning, topology based protein feature vector, protein classification} }
Barak Sternberg and Roded Sharan. A Dynamic Algorithm for Network Propagation. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 7:1-7:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{sternberg_et_al:LIPIcs.WABI.2018.7, author = {Sternberg, Barak and Sharan, Roded}, title = {{A Dynamic Algorithm for Network Propagation}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {7:1--7:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.7}, URN = {urn:nbn:de:0030-drops-93095}, doi = {10.4230/LIPIcs.WABI.2018.7}, annote = {Keywords: Network propagation, Dynamic graph algorithm, protein-protein interaction network} }
Qiuyi (Richard) Zhang, Satish Rao, and Tandy Warnow. New Absolute Fast Converging Phylogeny Estimation Methods with Improved Scalability and Accuracy. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 8:1-8:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{zhang_et_al:LIPIcs.WABI.2018.8, author = {Zhang, Qiuyi (Richard) and Rao, Satish and Warnow, Tandy}, title = {{New Absolute Fast Converging Phylogeny Estimation Methods with Improved Scalability and Accuracy}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {8:1--8:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.8}, URN = {urn:nbn:de:0030-drops-93108}, doi = {10.4230/LIPIcs.WABI.2018.8}, annote = {Keywords: phylogeny estimation, short quartets, sample complexity, absolute fast converging methods, neighbor joining, maximum likelihood} }
Yohei M. Rosen and Benedict J. Paten. An Average-Case Sublinear Exact Li and Stephens Forward Algorithm. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 9:1-9:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{rosen_et_al:LIPIcs.WABI.2018.9, author = {Rosen, Yohei M. and Paten, Benedict J.}, title = {{An Average-Case Sublinear Exact Li and Stephens Forward Algorithm}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {9:1--9:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.9}, URN = {urn:nbn:de:0030-drops-93116}, doi = {10.4230/LIPIcs.WABI.2018.9}, annote = {Keywords: Haplotype, Hidden Markov Model, Forward Algorithm, Lazy Evaluation} }
Lavinia Egidi, Felipe A. Louza, Giovanni Manzini, and Guilherme P. Telles. External memory BWT and LCP computation for sequence collections with applications. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 10:1-10:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{egidi_et_al:LIPIcs.WABI.2018.10, author = {Egidi, Lavinia and Louza, Felipe A. and Manzini, Giovanni and Telles, Guilherme P.}, title = {{External memory BWT and LCP computation for sequence collections with applications}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {10:1--10:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.10}, URN = {urn:nbn:de:0030-drops-93122}, doi = {10.4230/LIPIcs.WABI.2018.10}, annote = {Keywords: Burrows-Wheeler Transform, Longest Common Prefix Array, All pairs suffix-prefix overlaps, Succinct de Bruijn graph, Maximal repeats} }
Riku Walve, Pasi Rastas, and Leena Salmela. Kermit: Guided Long Read Assembly using Coloured Overlap Graphs. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 11:1-11:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{walve_et_al:LIPIcs.WABI.2018.11, author = {Walve, Riku and Rastas, Pasi and Salmela, Leena}, title = {{Kermit: Guided Long Read Assembly using Coloured Overlap Graphs}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {11:1--11:11}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.11}, URN = {urn:nbn:de:0030-drops-93135}, doi = {10.4230/LIPIcs.WABI.2018.11}, annote = {Keywords: Genome assembly, Linkage maps, Coloured overlap graph} }
Martin D. Muggli, Simon J. Puglisi, and Christina Boucher. A Succinct Solution to Rmap Alignment. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 12:1-12:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{muggli_et_al:LIPIcs.WABI.2018.12, author = {Muggli, Martin D. and Puglisi, Simon J. and Boucher, Christina}, title = {{A Succinct Solution to Rmap Alignment}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {12:1--12:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.12}, URN = {urn:nbn:de:0030-drops-93143}, doi = {10.4230/LIPIcs.WABI.2018.12}, annote = {Keywords: Optical mapping, index based data structures, FM-index, graph algorithms} }
Till Hartmann and Sven Rahmann. Spalter: A Meta Machine Learning Approach to Distinguish True DNA Variants from Sequencing Artefacts. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 13:1-13:8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{hartmann_et_al:LIPIcs.WABI.2018.13, author = {Hartmann, Till and Rahmann, Sven}, title = {{Spalter: A Meta Machine Learning Approach to Distinguish True DNA Variants from Sequencing Artefacts}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {13:1--13:8}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.13}, URN = {urn:nbn:de:0030-drops-93158}, doi = {10.4230/LIPIcs.WABI.2018.13}, annote = {Keywords: variant calling, sequencing error, technical artefact, meta machine learning, classification} }
Saugata Basu, Filippo Utro, and Laxmi Parida. Essential Simplices in Persistent Homology and Subtle Admixture Detection. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 14:1-14:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{basu_et_al:LIPIcs.WABI.2018.14, author = {Basu, Saugata and Utro, Filippo and Parida, Laxmi}, title = {{Essential Simplices in Persistent Homology and Subtle Admixture Detection}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {14:1--14:10}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.14}, URN = {urn:nbn:de:0030-drops-93166}, doi = {10.4230/LIPIcs.WABI.2018.14}, annote = {Keywords: population admixture, topological data analysis, persistent homology, population evolution} }
Tuukka Norri, Bastien Cazaux, Dmitry Kosolobov, and Veli Mäkinen. Minimum Segmentation for Pan-genomic Founder Reconstruction in Linear Time. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 15:1-15:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{norri_et_al:LIPIcs.WABI.2018.15, author = {Norri, Tuukka and Cazaux, Bastien and Kosolobov, Dmitry and M\"{a}kinen, Veli}, title = {{Minimum Segmentation for Pan-genomic Founder Reconstruction in Linear Time}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {15:1--15:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.15}, URN = {urn:nbn:de:0030-drops-93175}, doi = {10.4230/LIPIcs.WABI.2018.15}, annote = {Keywords: Pan-genome indexing, founder reconstruction, dynamic programming, positional Burrows-Wheeler transform, range minimum query} }
Martin S. Engler, Bertrand Caron, Lourens Veen, Daan P. Geerke, Alan E. Mark, and Gunnar W. Klau. Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 16:1-16:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{engler_et_al:LIPIcs.WABI.2018.16, author = {Engler, Martin S. and Caron, Bertrand and Veen, Lourens and Geerke, Daan P. and Mark, Alan E. and Klau, Gunnar W.}, title = {{Multiple-Choice Knapsack for Assigning Partial Atomic Charges in Drug-Like Molecules}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {16:1--16:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.16}, URN = {urn:nbn:de:0030-drops-93187}, doi = {10.4230/LIPIcs.WABI.2018.16}, annote = {Keywords: Multiple-choice knapsack, integer linear programming, pseudo-polynomial dynamic programming, partial charge assignment, molecular dynamics simulations} }
Stéphane Chrétien, Christophe Guyeux, and Serge Moulin. l1-Penalised Ordinal Polytomous Regression Estimators with Application to Gene Expression Studies. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 17:1-17:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{chretien_et_al:LIPIcs.WABI.2018.17, author = {Chr\'{e}tien, St\'{e}phane and Guyeux, Christophe and Moulin, Serge}, title = {{l1-Penalised Ordinal Polytomous Regression Estimators with Application to Gene Expression Studies}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {17:1--17:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.17}, URN = {urn:nbn:de:0030-drops-93199}, doi = {10.4230/LIPIcs.WABI.2018.17}, annote = {Keywords: LASSO, ordinal polytomous regression, Quantile Universal Threshold, Frank-Wolfe algorithm, Nesterov algorithm} }
Morteza Chalabi Hajkarim, Eli Upfal, and Fabio Vandin. Differentially Mutated Subnetworks Discovery. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 18:1-18:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{hajkarim_et_al:LIPIcs.WABI.2018.18, author = {Hajkarim, Morteza Chalabi and Upfal, Eli and Vandin, Fabio}, title = {{Differentially Mutated Subnetworks Discovery}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {18:1--18:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.18}, URN = {urn:nbn:de:0030-drops-93202}, doi = {10.4230/LIPIcs.WABI.2018.18}, annote = {Keywords: Cancer genomics, network analysis, combinatorial algorithm} }
Ryan A. Leo Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth, and Luay Nakhleh. DGEN: A Test Statistic for Detection of General Introgression Scenarios. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 19:1-19:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{elworth_et_al:LIPIcs.WABI.2018.19, author = {Elworth, Ryan A. Leo and Allen, Chabrielle and Benedict, Travis and Dulworth, Peter and Nakhleh, Luay}, title = {{DGEN: A Test Statistic for Detection of General Introgression Scenarios}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {19:1--19:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.19}, URN = {urn:nbn:de:0030-drops-93218}, doi = {10.4230/LIPIcs.WABI.2018.19}, annote = {Keywords: Introgression, genealogies, phylogenetic networks} }
Mehrdad Mansouri, Julian Booth, Margaryta Vityaz, Cedric Chauve, and Leonid Chindelevitch. PRINCE: Accurate Approximation of the Copy Number of Tandem Repeats. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 20:1-20:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{mansouri_et_al:LIPIcs.WABI.2018.20, author = {Mansouri, Mehrdad and Booth, Julian and Vityaz, Margaryta and Chauve, Cedric and Chindelevitch, Leonid}, title = {{PRINCE: Accurate Approximation of the Copy Number of Tandem Repeats}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {20:1--20:13}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.20}, URN = {urn:nbn:de:0030-drops-93227}, doi = {10.4230/LIPIcs.WABI.2018.20}, annote = {Keywords: Variable-Number Tandem Repeats, Copy number, Bacterial genomics} }
Mai Alzamel, Lorraine A. K. Ayad, Giulia Bernardini, Roberto Grossi, Costas S. Iliopoulos, Nadia Pisanti, Solon P. Pissis, and Giovanna Rosone. Degenerate String Comparison and Applications. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 21:1-21:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{alzamel_et_al:LIPIcs.WABI.2018.21, author = {Alzamel, Mai and Ayad, Lorraine A. K. and Bernardini, Giulia and Grossi, Roberto and Iliopoulos, Costas S. and Pisanti, Nadia and Pissis, Solon P. and Rosone, Giovanna}, title = {{Degenerate String Comparison and Applications}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {21:1--21:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.21}, URN = {urn:nbn:de:0030-drops-93236}, doi = {10.4230/LIPIcs.WABI.2018.21}, annote = {Keywords: degenerate strings, generalised degenerate strings, elastic-degenerate strings, string comparison, palindromes} }
Nikolai Karpov, Salem Malikic, Md. Khaledur Rahman, and S. Cenk Sahinalp. A Multi-labeled Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 22:1-22:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{karpov_et_al:LIPIcs.WABI.2018.22, author = {Karpov, Nikolai and Malikic, Salem and Rahman, Md. Khaledur and Sahinalp, S. Cenk}, title = {{A Multi-labeled Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {22:1--22:19}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.22}, URN = {urn:nbn:de:0030-drops-93242}, doi = {10.4230/LIPIcs.WABI.2018.22}, annote = {Keywords: Intra-tumor heterogeneity, tumor evolution, multi-labeled tree, tree edit distance, dynamic programming} }
Kai Dührkop, Marie A. Lataretu, W. Timothy J. White, and Sebastian Böcker. Heuristic Algorithms for the Maximum Colorful Subtree Problem. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 23:1-23:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{duhrkop_et_al:LIPIcs.WABI.2018.23, author = {D\"{u}hrkop, Kai and Lataretu, Marie A. and White, W. Timothy J. and B\"{o}cker, Sebastian}, title = {{Heuristic Algorithms for the Maximum Colorful Subtree Problem}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {23:1--23:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.23}, URN = {urn:nbn:de:0030-drops-93256}, doi = {10.4230/LIPIcs.WABI.2018.23}, annote = {Keywords: Fragmentation trees, Computational mass spectrometry} }
Mohammed El-Kebir. Parsimonious Migration History Problem: Complexity and Algorithms. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 24:1-24:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{elkebir:LIPIcs.WABI.2018.24, author = {El-Kebir, Mohammed}, title = {{Parsimonious Migration History Problem: Complexity and Algorithms}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {24:1--24:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.24}, URN = {urn:nbn:de:0030-drops-93263}, doi = {10.4230/LIPIcs.WABI.2018.24}, annote = {Keywords: Reconciliation, maximum parsimony, metastasis, infection, phylogenetics, phylogeography, fixed parameter tractability} }
Szymon Majewski, Michal Aleksander Ciach, Michal Startek, Wanda Niemyska, Blazej Miasojedow, and Anna Gambin. The Wasserstein Distance as a Dissimilarity Measure for Mass Spectra with Application to Spectral Deconvolution. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 25:1-25:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{majewski_et_al:LIPIcs.WABI.2018.25, author = {Majewski, Szymon and Ciach, Michal Aleksander and Startek, Michal and Niemyska, Wanda and Miasojedow, Blazej and Gambin, Anna}, title = {{The Wasserstein Distance as a Dissimilarity Measure for Mass Spectra with Application to Spectral Deconvolution}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {25:1--25:21}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.25}, URN = {urn:nbn:de:0030-drops-93270}, doi = {10.4230/LIPIcs.WABI.2018.25}, annote = {Keywords: Mass spectrometry, Tandem mass spectrometry, Wasserstein distance, Earth mover's distance, Similarity measure, Jaccard score, Tanimoto similarity} }
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