@Proceedings{kingsford_et_al:LIPIcs.WABI.2020,
title = {{LIPIcs, Volume 172, WABI 2020, Complete Volume}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {1--360},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020},
URN = {urn:nbn:de:0030-drops-127881},
doi = {10.4230/LIPIcs.WABI.2020},
annote = {Keywords: LIPIcs, Volume 172, WABI 2020, Complete Volume}
}
@InProceedings{kingsford_et_al:LIPIcs.WABI.2020.0,
author = {Kingsford, Carl and Pisanti, Nadia},
title = {{Front Matter, Table of Contents, Preface, Conference Organization}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {0:i--0:x},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.0},
URN = {urn:nbn:de:0030-drops-127891},
doi = {10.4230/LIPIcs.WABI.2020.0},
annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization}
}
@InProceedings{zimerman_et_al:LIPIcs.WABI.2020.1,
author = {Zimerman, Galia R. and Svetlitsky, Dina and Zehavi, Meirav and Ziv-Ukelson, Michal},
title = {{Approximate Search for Known Gene Clusters in New Genomes Using PQ-Trees}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {1:1--1:24},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.1},
URN = {urn:nbn:de:0030-drops-127906},
doi = {10.4230/LIPIcs.WABI.2020.1},
annote = {Keywords: PQ-Tree, Gene Cluster, Efflux Pump}
}
@InProceedings{zabeti_et_al:LIPIcs.WABI.2020.2,
author = {Zabeti, Hooman and Dexter, Nick and Safari, Amir Hosein and Sedaghat, Nafiseh and Libbrecht, Maxwell and Chindelevitch, Leonid},
title = {{An Interpretable Classification Method for Predicting Drug Resistance in M. Tuberculosis}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {2:1--2:18},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.2},
URN = {urn:nbn:de:0030-drops-127911},
doi = {10.4230/LIPIcs.WABI.2020.2},
annote = {Keywords: Drug resistance, whole-genome sequencing, interpretable machine learning, integer linear programming, rule-based learning}
}
@InProceedings{rubert_et_al:LIPIcs.WABI.2020.3,
author = {Rubert, Diego P. and Martinez, F\'{a}bio V. and Braga, Mar{\'\i}lia D. V.},
title = {{Natural Family-Free Genomic Distance}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {3:1--3:23},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.3},
URN = {urn:nbn:de:0030-drops-127926},
doi = {10.4230/LIPIcs.WABI.2020.3},
annote = {Keywords: Comparative genomics, Genome rearrangement, DCJ-indel distance}
}
@InProceedings{zentgraf_et_al:LIPIcs.WABI.2020.4,
author = {Zentgraf, Jens and Rahmann, Sven},
title = {{Fast Lightweight Accurate Xenograft Sorting}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {4:1--4:16},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.4},
URN = {urn:nbn:de:0030-drops-127933},
doi = {10.4230/LIPIcs.WABI.2020.4},
annote = {Keywords: xenograft sorting, alignment-free method, Cuckoo hashing, k-mer}
}
@InProceedings{weber_et_al:LIPIcs.WABI.2020.5,
author = {Weber, Leah L. and El-Kebir, Mohammed},
title = {{Phyolin: Identifying a Linear Perfect Phylogeny in Single-Cell DNA Sequencing Data of Tumors}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {5:1--5:14},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.5},
URN = {urn:nbn:de:0030-drops-127946},
doi = {10.4230/LIPIcs.WABI.2020.5},
annote = {Keywords: Constraint programming, intra-tumor heterogeneity, combinatorial optimization}
}
@InProceedings{schrinner_et_al:LIPIcs.WABI.2020.6,
author = {Schrinner, Sven and Goel, Manish and Wulfert, Michael and Spohr, Philipp and Schneeberger, Korbinian and Klau, Gunnar W.},
title = {{The Longest Run Subsequence Problem}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {6:1--6:13},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.6},
URN = {urn:nbn:de:0030-drops-127951},
doi = {10.4230/LIPIcs.WABI.2020.6},
annote = {Keywords: alignments, assembly, string algorithm, longest subsequence}
}
@InProceedings{makinen_et_al:LIPIcs.WABI.2020.7,
author = {M\"{a}kinen, Veli and Cazaux, Bastien and Equi, Massimo and Norri, Tuukka and Tomescu, Alexandru I.},
title = {{Linear Time Construction of Indexable Founder Block Graphs}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {7:1--7:18},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.7},
URN = {urn:nbn:de:0030-drops-127961},
doi = {10.4230/LIPIcs.WABI.2020.7},
annote = {Keywords: Pangenome indexing, founder reconstruction, multiple sequence alignment, compressed data structures, string matching}
}
@InProceedings{mallawaarachchi_et_al:LIPIcs.WABI.2020.8,
author = {Mallawaarachchi, Vijini G. and Wickramarachchi, Anuradha S. and Lin, Yu},
title = {{GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {8:1--8:21},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.8},
URN = {urn:nbn:de:0030-drops-127974},
doi = {10.4230/LIPIcs.WABI.2020.8},
annote = {Keywords: Metagenomics binning, contigs, assembly graphs, overlapped binning}
}
@InProceedings{mukherjee_et_al:LIPIcs.WABI.2020.9,
author = {Mukherjee, Kingshuk and Rossi, Massimiliano and Salmela, Leena and Boucher, Christina},
title = {{Fast and Efficient Rmap Assembly Using the Bi-Labelled de Bruijn Graph}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {9:1--9:16},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.9},
URN = {urn:nbn:de:0030-drops-127982},
doi = {10.4230/LIPIcs.WABI.2020.9},
annote = {Keywords: optical maps, de Bruijn graph, assembly}
}
@InProceedings{gatter_et_al:LIPIcs.WABI.2020.10,
author = {Gatter, Thomas and von L\"{o}hneysen, Sarah and Drozdova, Polina and Hartmann, Tom and Stadler, Peter F.},
title = {{Economic Genome Assembly from Low Coverage Illumina and Nanopore Data}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {10:1--10:22},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.10},
URN = {urn:nbn:de:0030-drops-127991},
doi = {10.4230/LIPIcs.WABI.2020.10},
annote = {Keywords: Nanopore sequencing, Illumina sequencing, genome assembly, spanning tree, unitigs, anchors}
}
@InProceedings{dufresne_et_al:LIPIcs.WABI.2020.11,
author = {Dufresne, Yoann and Sun, Chen and Marijon, Pierre and Lavenier, Dominique and Chauve, Cedric and Chikhi, Rayan},
title = {{A Graph-Theoretic Barcode Ordering Model for Linked-Reads}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {11:1--11:17},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.11},
URN = {urn:nbn:de:0030-drops-128001},
doi = {10.4230/LIPIcs.WABI.2020.11},
annote = {Keywords: DNA sequencing, graph algorithms, linked-reads, interval graphs, cliques}
}
@InProceedings{ma_et_al:LIPIcs.WABI.2020.12,
author = {Ma, Cong and Zheng, Hongyu and Kingsford, Carl},
title = {{Exact Transcript Quantification Over Splice Graphs}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {12:1--12:18},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.12},
URN = {urn:nbn:de:0030-drops-128013},
doi = {10.4230/LIPIcs.WABI.2020.12},
annote = {Keywords: RNA-seq, alternative splicing, transcript quantification, splice graph, network flow}
}
@InProceedings{selbach_et_al:LIPIcs.WABI.2020.13,
author = {Selbach, Leonie and Kowalski, Tobias and Gerwert, Klaus and Buchin, Maike and Mosig, Axel},
title = {{Shape Decomposition Algorithms for Laser Capture Microdissection}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {13:1--13:17},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.13},
URN = {urn:nbn:de:0030-drops-128020},
doi = {10.4230/LIPIcs.WABI.2020.13},
annote = {Keywords: Laser capture microdissection, shape decomposition, skeletonization}
}
@InProceedings{jahn_et_al:LIPIcs.WABI.2020.14,
author = {Jahn, Katharina and Beerenwinkel, Niko and Zhang, Louxin},
title = {{The Bourque Distances for Mutation Trees of Cancers}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {14:1--14:22},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.14},
URN = {urn:nbn:de:0030-drops-128039},
doi = {10.4230/LIPIcs.WABI.2020.14},
annote = {Keywords: mutation trees, clonal trees, tree distance, phylogenetic trees, tree metric, Robinson - Foulds distance, Bourque distance}
}
@InProceedings{yu_et_al:LIPIcs.WABI.2020.15,
author = {Yu, Xilin and Le, Thien and Christensen, Sarah and Molloy, Erin K. and Warnow, Tandy},
title = {{Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {15:1--15:17},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.15},
URN = {urn:nbn:de:0030-drops-128048},
doi = {10.4230/LIPIcs.WABI.2020.15},
annote = {Keywords: supertrees, divide-and-conquer, phylogeny estimation}
}
@InProceedings{rahman_et_al:LIPIcs.WABI.2020.16,
author = {Rahman, Amatur and Chikhi, Rayan and Medvedev, Paul},
title = {{Disk Compression of k-mer Sets}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {16:1--16:18},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.16},
URN = {urn:nbn:de:0030-drops-128057},
doi = {10.4230/LIPIcs.WABI.2020.16},
annote = {Keywords: de Bruijn graphs, compression, k-mer sets, spectrum-preserving string sets}
}
@InProceedings{ganesh_et_al:LIPIcs.WABI.2020.17,
author = {Ganesh, Arun and Sy, Aaron},
title = {{Near-Linear Time Edit Distance for Indel Channels}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {17:1--17:18},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.17},
URN = {urn:nbn:de:0030-drops-128061},
doi = {10.4230/LIPIcs.WABI.2020.17},
annote = {Keywords: edit distance, average-case analysis, dynamic programming, sequence alignment}
}
@InProceedings{frisby_et_al:LIPIcs.WABI.2020.18,
author = {Frisby, Trevor S. and Langmead, Christopher J.},
title = {{Fold Family-Regularized Bayesian Optimization for Directed Protein Evolution}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {18:1--18:17},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.18},
URN = {urn:nbn:de:0030-drops-128077},
doi = {10.4230/LIPIcs.WABI.2020.18},
annote = {Keywords: Protein design, Bayesian Optimization, Gaussian Process Regression, Regularization}
}
@InProceedings{cantone_et_al:LIPIcs.WABI.2020.19,
author = {Cantone, Domenico and Faro, Simone and Pavone, Arianna},
title = {{Sequence Searching Allowing for Non-Overlapping Adjacent Unbalanced Translocations}},
booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)},
pages = {19:1--19:14},
series = {Leibniz International Proceedings in Informatics (LIPIcs)},
ISBN = {978-3-95977-161-0},
ISSN = {1868-8969},
year = {2020},
volume = {172},
editor = {Kingsford, Carl and Pisanti, Nadia},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2020.19},
URN = {urn:nbn:de:0030-drops-128086},
doi = {10.4230/LIPIcs.WABI.2020.19},
annote = {Keywords: Text processing, approximate matching, inversions, sequence matching}
}
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