20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 1-360, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 0:i-0:x, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Galia R. Zimerman, Dina Svetlitsky, Meirav Zehavi, and Michal Ziv-Ukelson. Approximate Search for Known Gene Clusters in New Genomes Using PQ-Trees. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 1:1-1:24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Hooman Zabeti, Nick Dexter, Amir Hosein Safari, Nafiseh Sedaghat, Maxwell Libbrecht, and Leonid Chindelevitch. An Interpretable Classification Method for Predicting Drug Resistance in M. Tuberculosis. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 2:1-2:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Diego P. Rubert, Fábio V. Martinez, and Marília D. V. Braga. Natural Family-Free Genomic Distance. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 3:1-3:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Jens Zentgraf and Sven Rahmann. Fast Lightweight Accurate Xenograft Sorting. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 4:1-4:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Leah L. Weber and Mohammed El-Kebir. Phyolin: Identifying a Linear Perfect Phylogeny in Single-Cell DNA Sequencing Data of Tumors. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 5:1-5:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Sven Schrinner, Manish Goel, Michael Wulfert, Philipp Spohr, Korbinian Schneeberger, and Gunnar W. Klau. The Longest Run Subsequence Problem. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 6:1-6:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Veli Mäkinen, Bastien Cazaux, Massimo Equi, Tuukka Norri, and Alexandru I. Tomescu. Linear Time Construction of Indexable Founder Block Graphs. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 7:1-7:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Vijini G. Mallawaarachchi, Anuradha S. Wickramarachchi, and Yu Lin. GraphBin2: Refined and Overlapped Binning of Metagenomic Contigs Using Assembly Graphs. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 8:1-8:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Kingshuk Mukherjee, Massimiliano Rossi, Leena Salmela, and Christina Boucher. Fast and Efficient Rmap Assembly Using the Bi-Labelled de Bruijn Graph. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 9:1-9:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Thomas Gatter, Sarah von Löhneysen, Polina Drozdova, Tom Hartmann, and Peter F. Stadler. Economic Genome Assembly from Low Coverage Illumina and Nanopore Data. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 10:1-10:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Yoann Dufresne, Chen Sun, Pierre Marijon, Dominique Lavenier, Cedric Chauve, and Rayan Chikhi. A Graph-Theoretic Barcode Ordering Model for Linked-Reads. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 11:1-11:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Cong Ma, Hongyu Zheng, and Carl Kingsford. Exact Transcript Quantification Over Splice Graphs. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 12:1-12:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Leonie Selbach, Tobias Kowalski, Klaus Gerwert, Maike Buchin, and Axel Mosig. Shape Decomposition Algorithms for Laser Capture Microdissection. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 13:1-13:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Katharina Jahn, Niko Beerenwinkel, and Louxin Zhang. The Bourque Distances for Mutation Trees of Cancers. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 14:1-14:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Xilin Yu, Thien Le, Sarah Christensen, Erin K. Molloy, and Tandy Warnow. Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 15:1-15:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Amatur Rahman, Rayan Chikhi, and Paul Medvedev. Disk Compression of k-mer Sets. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 16:1-16:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Arun Ganesh and Aaron Sy. Near-Linear Time Edit Distance for Indel Channels. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 17:1-17:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Trevor S. Frisby and Christopher J. Langmead. Fold Family-Regularized Bayesian Optimization for Directed Protein Evolution. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 18:1-18:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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} }
Domenico Cantone, Simone Faro, and Arianna Pavone. Sequence Searching Allowing for Non-Overlapping Adjacent Unbalanced Translocations. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 19:1-19:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@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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