Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Aaron Hong, Marco Oliva, Dominik Köppl, Hideo Bannai, Christina Boucher, and Travis Gagie. Acceleration of FM-Index Queries Through Prefix-Free Parsing. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 13:1-13:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{hong_et_al:LIPIcs.WABI.2023.13, author = {Hong, Aaron and Oliva, Marco and K\"{o}ppl, Dominik and Bannai, Hideo and Boucher, Christina and Gagie, Travis}, title = {{Acceleration of FM-Index Queries Through Prefix-Free Parsing}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {13:1--13:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-294-5}, ISSN = {1868-8969}, year = {2023}, volume = {273}, editor = {Belazzougui, Djamal and Ouangraoua, A\"{i}da}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.13}, URN = {urn:nbn:de:0030-drops-186390}, doi = {10.4230/LIPIcs.WABI.2023.13}, annote = {Keywords: FM-index, pangenomics, scalability, word-based indexing, random access} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 1-474, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@Proceedings{boucher_et_al:LIPIcs.WABI.2022, title = {{LIPIcs, Volume 242, WABI 2022, Complete Volume}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {1--474}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022}, URN = {urn:nbn:de:0030-drops-170338}, doi = {10.4230/LIPIcs.WABI.2022}, annote = {Keywords: LIPIcs, Volume 242, WABI 2022, Complete Volume} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 0:i-0:xii, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{boucher_et_al:LIPIcs.WABI.2022.0, author = {Boucher, Christina and Rahmann, Sven}, title = {{Front Matter, Table of Contents, Preface, Conference Organization}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {0:i--0:xii}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-243-3}, ISSN = {1868-8969}, year = {2022}, volume = {242}, editor = {Boucher, Christina and Rahmann, Sven}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.0}, URN = {urn:nbn:de:0030-drops-170347}, doi = {10.4230/LIPIcs.WABI.2022.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization} }
Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)
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-dev.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} }
Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
Christina Boucher, Travis Gagie, Alan Kuhnle, and Giovanni Manzini. Prefix-Free Parsing for Building Big BWTs. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 2:1-2:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{boucher_et_al:LIPIcs.WABI.2018.2, author = {Boucher, Christina and Gagie, Travis and Kuhnle, Alan and Manzini, Giovanni}, title = {{Prefix-Free Parsing for Building Big BWTs}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {2:1--2:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.2}, URN = {urn:nbn:de:0030-drops-93044}, doi = {10.4230/LIPIcs.WABI.2018.2}, annote = {Keywords: Burrows-Wheeler Transform, prefix-free parsing, compression-aware algorithms, genomic databases} }
Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
Martin D. Muggli, Simon J. Puglisi, and Christina Boucher. A Succinct Solution to Rmap Alignment. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 12:1-12:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{muggli_et_al:LIPIcs.WABI.2018.12, author = {Muggli, Martin D. and Puglisi, Simon J. and Boucher, Christina}, title = {{A Succinct Solution to Rmap Alignment}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {12:1--12:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-082-8}, ISSN = {1868-8969}, year = {2018}, volume = {113}, editor = {Parida, Laxmi and Ukkonen, Esko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.12}, URN = {urn:nbn:de:0030-drops-93143}, doi = {10.4230/LIPIcs.WABI.2018.12}, annote = {Keywords: Optical mapping, index based data structures, FM-index, graph algorithms} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Bahar Alipanahi, Leena Salmela, Simon J. Puglisi, Martin Muggli, and Christina Boucher. Disentangled Long-Read De Bruijn Graphs via Optical Maps. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 1:1-1:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@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-dev.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} }
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