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