@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}
}