@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}
}
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