@Proceedings{schwartz_et_al:LIPIcs.WABI.2017,
  title =	{{LIPIcs, Volume 88, WABI'17, Complete Volume}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017},
  URN =		{urn:nbn:de:0030-drops-78120},
  doi =		{10.4230/LIPIcs.WABI.2017},
  annote =	{Keywords: Nonnumerical Algorithms and Problems, Pattern Matching, Algorithms, Life and Medical Sciences}
}
@InProceedings{schwartz_et_al:LIPIcs.WABI.2017.0,
  author =	{Schwartz, Russell and Reinert, Knut},
  title =	{{Front Matter, Table of Contents, Preface, List of Authors}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{0:i--0:xiv},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.0},
  URN =		{urn:nbn:de:0030-drops-76348},
  doi =		{10.4230/LIPIcs.WABI.2017.0},
  annote =	{Keywords: Front Matter, Table of Contents, Preface, List of Authors}
}
@InProceedings{alipanahi_et_al:LIPIcs.WABI.2017.1,
  author =	{Alipanahi, Bahar and Salmela, Leena and Puglisi, Simon J. and Muggli, Martin and Boucher, Christina},
  title =	{{Disentangled Long-Read De Bruijn Graphs via Optical Maps}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{1:1--1:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.1},
  URN =		{urn:nbn:de:0030-drops-76614},
  doi =		{10.4230/LIPIcs.WABI.2017.1},
  annote =	{Keywords: Positional de Bruijn graph, Genome Assembly, Long Read Data, Optical maps}
}
@InProceedings{bayzid_et_al:LIPIcs.WABI.2017.2,
  author =	{Bayzid, Md. Shamsuzzoha and Warnow, Tandy},
  title =	{{Gene Tree Parsimony for Incomplete Gene Trees}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{2:1--2:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.2},
  URN =		{urn:nbn:de:0030-drops-76495},
  doi =		{10.4230/LIPIcs.WABI.2017.2},
  annote =	{Keywords: Gene duplication and loss, gene tree parsimony, deep coalescence}
}
@InProceedings{brubach_et_al:LIPIcs.WABI.2017.3,
  author =	{Brubach, Brian and Ghurye, Jay and Pop, Mihai and Srinivasan, Aravind},
  title =	{{Better Greedy Sequence Clustering with Fast Banded Alignment}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{3:1--3:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.3},
  URN =		{urn:nbn:de:0030-drops-76425},
  doi =		{10.4230/LIPIcs.WABI.2017.3},
  annote =	{Keywords: Sequence Clustering, Metagenomics, String Algorithms}
}
@InProceedings{almirantis_et_al:LIPIcs.WABI.2017.4,
  author =	{Almirantis, Yannis and Charalampopoulos, Panagiotis and Gao, Jia and Iliopoulos, Costas S. and Mohamed, Manal and Pissis, Solon P. and Polychronopoulos, Dimitris},
  title =	{{Optimal Computation of Overabundant Words}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{4:1--4:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.4},
  URN =		{urn:nbn:de:0030-drops-76468},
  doi =		{10.4230/LIPIcs.WABI.2017.4},
  annote =	{Keywords: overabundant words, avoided words, suffix tree, DNA sequence analysis}
}
@InProceedings{ciach_et_al:LIPIcs.WABI.2017.5,
  author =	{Ciach, Michal Aleksander and Muszewska, Anna and G\'{o}recki, Pawel},
  title =	{{Detecting Locus Acquisition Events in Gene Trees}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{5:1--5:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.5},
  URN =		{urn:nbn:de:0030-drops-76545},
  doi =		{10.4230/LIPIcs.WABI.2017.5},
  annote =	{Keywords: rank, taxon, ranked species tree, speciation, gene duplication, gene loss, horizontal gene transfer}
}
@InProceedings{bayegan_et_al:LIPIcs.WABI.2017.6,
  author =	{Bayegan, Amir H. and Clote, Peter},
  title =	{{An IP Algorithm for RNA Folding Trajectories}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{6:1--6:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.6},
  URN =		{urn:nbn:de:0030-drops-76437},
  doi =		{10.4230/LIPIcs.WABI.2017.6},
  annote =	{Keywords: Integer programming, RNA secondary structure, folding trajectory, feedback vertex problem, conflict digraph}
}
@InProceedings{girotto_et_al:LIPIcs.WABI.2017.7,
  author =	{Girotto, Samuele and Comin, Matteo and Pizzi, Cinzia},
  title =	{{Fast Spaced Seed Hashing}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{7:1--7:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.7},
  URN =		{urn:nbn:de:0030-drops-76501},
  doi =		{10.4230/LIPIcs.WABI.2017.7},
  annote =	{Keywords: k-mers, spaced seeds, efficient hashing}
}
@InProceedings{elmabrouk_et_al:LIPIcs.WABI.2017.8,
  author =	{El-Mabrouk, Nadia and Ouangraoua, A\"{i}da},
  title =	{{A General Framework for Gene Tree Correction Based on Duplication-Loss Reconciliation}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{8:1--8:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.8},
  URN =		{urn:nbn:de:0030-drops-76565},
  doi =		{10.4230/LIPIcs.WABI.2017.8},
  annote =	{Keywords: Gene tree correction, Supertree, Polytomy, Reconciliation, Phylogeny}
}
@InProceedings{crochemore_et_al:LIPIcs.WABI.2017.9,
  author =	{Crochemore, Maxime and Francisco, Alexandre P. and Pissis, Solon P. and Vaz, C\'{a}tia},
  title =	{{Towards Distance-Based Phylogenetic Inference in Average-Case Linear-Time}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{9:1--9:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.9},
  URN =		{urn:nbn:de:0030-drops-76529},
  doi =		{10.4230/LIPIcs.WABI.2017.9},
  annote =	{Keywords: computational biology, phylogenetic inference, Hamming distance}
}
@InProceedings{gunady_et_al:LIPIcs.WABI.2017.10,
  author =	{Gunady, Mohamed K. and Cornwell, Steffen and Mount, Stephen M. and Bravo, H\'{e}ctor Corrada},
  title =	{{Yanagi: Transcript Segment Library Construction for RNA-Seq Quantification}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{10:1--10:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.10},
  URN =		{urn:nbn:de:0030-drops-76487},
  doi =		{10.4230/LIPIcs.WABI.2017.10},
  annote =	{Keywords: RNA-Seq, Genome Sequencing, Kmer-based alignment, Transcriptome Quantification, Differential Alternative Splicing}
}
@InProceedings{hu_et_al:LIPIcs.WABI.2017.11,
  author =	{Hu, Chenyue W. and Li, Hanyang and Qutub, Amina A.},
  title =	{{Shrinkage Clustering: A Fast and Size-Constrained Algorithm for Biomedical Applications}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{11:1--11:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.11},
  URN =		{urn:nbn:de:0030-drops-76556},
  doi =		{10.4230/LIPIcs.WABI.2017.11},
  annote =	{Keywords: Clustering, Matrix Factorization, Cancer Subtyping, Gene Expression}
}
@InProceedings{jabbari_et_al:LIPIcs.WABI.2017.12,
  author =	{Jabbari, Hosna and Wark, Ian and Montemagno, Carlo and Will, Sebastian},
  title =	{{Sparsification Enables Predicting Kissing Hairpin Pseudoknot Structures of Long RNAs in Practice}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{12:1--12:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.12},
  URN =		{urn:nbn:de:0030-drops-76408},
  doi =		{10.4230/LIPIcs.WABI.2017.12},
  annote =	{Keywords: RNA, secondary structure prediction, pseudoknots, space efficiency, sparsification}
}
@InProceedings{kim_et_al:LIPIcs.WABI.2017.13,
  author =	{Kim, Jongkyu and Reinert, Knut},
  title =	{{Vaquita: Fast and Accurate Identification of Structural Variation Using Combined Evidence}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{13:1--13:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.13},
  URN =		{urn:nbn:de:0030-drops-76352},
  doi =		{10.4230/LIPIcs.WABI.2017.13},
  annote =	{Keywords: Structural variation}
}
@InProceedings{abramova_et_al:LIPIcs.WABI.2017.14,
  author =	{Abramova, Anastasiia and Korobeynikov, Anton},
  title =	{{Assessing the Significance of Peptide Spectrum Match Scores}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{14:1--14:11},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.14},
  URN =		{urn:nbn:de:0030-drops-76411},
  doi =		{10.4230/LIPIcs.WABI.2017.14},
  annote =	{Keywords: mass spectrometry, natural products, peptide spectrum matches, statistical significance}
}
@InProceedings{mao_et_al:LIPIcs.WABI.2017.15,
  author =	{Mao, Shunfu and Mohajer, Soheil and Ramachandran, Kannan and Tse, David and Kannan, Sreeram},
  title =	{{abSNP: RNA-Seq SNP Calling in Repetitive Regions via Abundance Estimation}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{15:1--15:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.15},
  URN =		{urn:nbn:de:0030-drops-76582},
  doi =		{10.4230/LIPIcs.WABI.2017.15},
  annote =	{Keywords: RNA-Seq, SNP Calling, Repetitive Region, Multiply Mapped Reads, Abundance Estimation}
}
@InProceedings{nikumbh_et_al:LIPIcs.WABI.2017.16,
  author =	{Nikumbh, Sarvesh and Ebert, Peter and Pfeifer, Nico},
  title =	{{All Fingers Are Not the Same: Handling Variable-Length Sequences in a Discriminative Setting Using Conformal Multi-Instance Kernels}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{16:1--16:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.16},
  URN =		{urn:nbn:de:0030-drops-76459},
  doi =		{10.4230/LIPIcs.WABI.2017.16},
  annote =	{Keywords: Multiple instance learning, conformal MI kernels, 5C, Hi-C}
}
@InProceedings{nojgaard_et_al:LIPIcs.WABI.2017.17,
  author =	{Nojgaard, Nikolai and Gei{\ss}, Manuela and Merkle, Daniel and Stadler, Peter F. and Wieseke, Nicolas and Hellmuth, Marc},
  title =	{{Forbidden Time Travel: Characterization of Time-Consistent Tree Reconciliation Maps}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{17:1--17:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.17},
  URN =		{urn:nbn:de:0030-drops-76362},
  doi =		{10.4230/LIPIcs.WABI.2017.17},
  annote =	{Keywords: Tree Reconciliation, Horizontal Gene Transfer, Reconciliation Map, Time-Consistency, History of gene families}
}
@InProceedings{almodaresi_et_al:LIPIcs.WABI.2017.18,
  author =	{Almodaresi, Fatemeh and Pandey, Prashant and Patro, Rob},
  title =	{{Rainbowfish: A Succinct Colored de Bruijn Graph Representation}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{18:1--18:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.18},
  URN =		{urn:nbn:de:0030-drops-76576},
  doi =		{10.4230/LIPIcs.WABI.2017.18},
  annote =	{Keywords: de Bruijn graph, succinct data structures, rank and select operation, colored de Bruijn graph}
}
@InProceedings{polishko_et_al:LIPIcs.WABI.2017.19,
  author =	{Polishko, Anton and Hasan, Md. Abid and Pan, Weihua and Bunnik, Evelien M. and Le Roch, Karine and Lonardi, Stefano},
  title =	{{ThIEF: Finding Genome-wide Trajectories of Epigenetics Marks}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{19:1--19:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.19},
  URN =		{urn:nbn:de:0030-drops-76375},
  doi =		{10.4230/LIPIcs.WABI.2017.19},
  annote =	{Keywords: Nucleosomes, Histone Marks, Histone Tail Modifications, Epigenetics, Genomics}
}
@InProceedings{prochazka_et_al:LIPIcs.WABI.2017.20,
  author =	{Proch\'{a}zka, Petr and Holub, Jan},
  title =	{{Byte-Aligned Pattern Matching in Encoded Genomic Sequences}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{20:1--20:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.20},
  URN =		{urn:nbn:de:0030-drops-76538},
  doi =		{10.4230/LIPIcs.WABI.2017.20},
  annote =	{Keywords: genomic sequences, pattern matching, q-gram inverted index}
}
@InProceedings{quedenfeld_et_al:LIPIcs.WABI.2017.21,
  author =	{Quedenfeld, Jens and Rahmann, Sven},
  title =	{{Analysis of Min-Hashing for Variant Tolerant DNA Read Mapping}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{21:1--21:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.21},
  URN =		{urn:nbn:de:0030-drops-76598},
  doi =		{10.4230/LIPIcs.WABI.2017.21},
  annote =	{Keywords: read mapping, min-Hashing, variant, SNP, analysis of algorithms}
}
@InProceedings{roayaeiardakany_et_al:LIPIcs.WABI.2017.22,
  author =	{Roayaei Ardakany, Abbas and Lonardi, Stefano},
  title =	{{Efficient and Accurate Detection of Topologically Associating Domains from Contact Maps}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{22:1--22:11},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.22},
  URN =		{urn:nbn:de:0030-drops-76446},
  doi =		{10.4230/LIPIcs.WABI.2017.22},
  annote =	{Keywords: Chromatin, TADs, 3D genome, Hi-C, contact maps}
}
@InProceedings{shah_et_al:LIPIcs.WABI.2017.23,
  author =	{Shah, Nidhi and Altschul, Stephen F. and Pop, Mihai},
  title =	{{Outlier Detection in BLAST Hits}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{23:1--23:11},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.23},
  URN =		{urn:nbn:de:0030-drops-76512},
  doi =		{10.4230/LIPIcs.WABI.2017.23},
  annote =	{Keywords: Taxonomy classification, Metagenomics, Sequence alignment, Outlier detection}
}
@InProceedings{simonaitis_et_al:LIPIcs.WABI.2017.24,
  author =	{Simonaitis, Pijus and Swenson, Krister M.},
  title =	{{Finding Local Genome Rearrangements}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{24:1--24:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.24},
  URN =		{urn:nbn:de:0030-drops-76604},
  doi =		{10.4230/LIPIcs.WABI.2017.24},
  annote =	{Keywords: genome rearrangement, double cut and join, maximum edge-disjoint cycle packing, Hi-C, NP-complete, approximation algorithm}
}
@InProceedings{toivonen_et_al:LIPIcs.WABI.2017.25,
  author =	{Toivonen, Jarkko and Taipale, Jussi and Ukkonen, Esko},
  title =	{{Seed-driven Learning of Position Probability Matrices from Large Sequence Sets}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{25:1--25:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.25},
  URN =		{urn:nbn:de:0030-drops-76470},
  doi =		{10.4230/LIPIcs.WABI.2017.25},
  annote =	{Keywords: motif finding, transcription factor binding site, sequence analysis, Hamming distance, seed}
}
@InProceedings{frank_et_al:LIPIcs.WABI.2017.26,
  author =	{Frank, Yves and Hruz, Tomas and Tschager, Thomas and Venzin, Valentin},
  title =	{{Improved De Novo Peptide Sequencing using LC Retention Time Information}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{26:1--26:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.26},
  URN =		{urn:nbn:de:0030-drops-76383},
  doi =		{10.4230/LIPIcs.WABI.2017.26},
  annote =	{Keywords: Computational proteomics, Peptide identification, Mass spectrometry, De novo peptide sequencing, Retention time prediction}
}
@InProceedings{christensen_et_al:LIPIcs.WABI.2017.27,
  author =	{Christensen, Sarah and Molloy, Erin K. and Vachaspati, Pranjal and Warnow, Tandy},
  title =	{{Optimal Completion of Incomplete Gene Trees in Polynomial Time Using OCTAL}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{27:1--27:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.27},
  URN =		{urn:nbn:de:0030-drops-76392},
  doi =		{10.4230/LIPIcs.WABI.2017.27},
  annote =	{Keywords: phylogenomics, missing data, coalescent-based species tree estimation, gene trees}
}