Published in: LIPIcs, Volume 259, 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)
Igor Tatarnikov, Ardavan Shahrabi Farahani, Sana Kashgouli, and Travis Gagie. MONI Can Find k-MEMs. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 26:1-26:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{tatarnikov_et_al:LIPIcs.CPM.2023.26, author = {Tatarnikov, Igor and Shahrabi Farahani, Ardavan and Kashgouli, Sana and Gagie, Travis}, title = {{MONI Can Find k-MEMs}}, booktitle = {34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)}, pages = {26:1--26:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-276-1}, ISSN = {1868-8969}, year = {2023}, volume = {259}, editor = {Bulteau, Laurent and Lipt\'{a}k, Zsuzsanna}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2023.26}, URN = {urn:nbn:de:0030-drops-179802}, doi = {10.4230/LIPIcs.CPM.2023.26}, annote = {Keywords: Compact data structures, Burrows-Wheeler Transform, run-length compression, maximal exact matches} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Taher Mun, Naga Sai Kavya Vaddadi, and Ben Langmead. Pangenomic Genotyping with the Marker Array. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 19:1-19:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{mun_et_al:LIPIcs.WABI.2022.19, author = {Mun, Taher and Vaddadi, Naga Sai Kavya and Langmead, Ben}, title = {{Pangenomic Genotyping with the Marker Array}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {19:1--19:17}, 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.2022.19}, URN = {urn:nbn:de:0030-drops-170530}, doi = {10.4230/LIPIcs.WABI.2022.19}, annote = {Keywords: Sequence alignment indexing genotyping} }
Published in: LIPIcs, Volume 233, 20th International Symposium on Experimental Algorithms (SEA 2022)
Nathaniel K. Brown, Travis Gagie, and Massimiliano Rossi. RLBWT Tricks. In 20th International Symposium on Experimental Algorithms (SEA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 233, pp. 16:1-16:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{brown_et_al:LIPIcs.SEA.2022.16, author = {Brown, Nathaniel K. and Gagie, Travis and Rossi, Massimiliano}, title = {{RLBWT Tricks}}, booktitle = {20th International Symposium on Experimental Algorithms (SEA 2022)}, pages = {16:1--16:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-251-8}, ISSN = {1868-8969}, year = {2022}, volume = {233}, editor = {Schulz, Christian and U\c{c}ar, Bora}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2022.16}, URN = {urn:nbn:de:0030-drops-165500}, doi = {10.4230/LIPIcs.SEA.2022.16}, annote = {Keywords: Compressed String Indexes, Repetitive Text Collections, Burrows-Wheeler Transform} }
Published in: LIPIcs, Volume 233, 20th International Symposium on Experimental Algorithms (SEA 2022)
Sara Giuliani, Giuseppe Romana, and Massimiliano Rossi. Computing Maximal Unique Matches with the r-Index. In 20th International Symposium on Experimental Algorithms (SEA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 233, pp. 22:1-22:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{giuliani_et_al:LIPIcs.SEA.2022.22, author = {Giuliani, Sara and Romana, Giuseppe and Rossi, Massimiliano}, title = {{Computing Maximal Unique Matches with the r-Index}}, booktitle = {20th International Symposium on Experimental Algorithms (SEA 2022)}, pages = {22:1--22:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-251-8}, ISSN = {1868-8969}, year = {2022}, volume = {233}, editor = {Schulz, Christian and U\c{c}ar, Bora}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2022.22}, URN = {urn:nbn:de:0030-drops-165568}, doi = {10.4230/LIPIcs.SEA.2022.22}, annote = {Keywords: Burrows-Wheeler Transform, r-index, maximal unique matches, bioinformatics, pangenomics} }
Published in: LIPIcs, Volume 223, 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)
Davide Cenzato and Zsuzsanna Lipták. A Theoretical and Experimental Analysis of BWT Variants for String Collections. In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 25:1-25:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{cenzato_et_al:LIPIcs.CPM.2022.25, author = {Cenzato, Davide and Lipt\'{a}k, Zsuzsanna}, title = {{A Theoretical and Experimental Analysis of BWT Variants for String Collections}}, booktitle = {33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)}, pages = {25:1--25:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-234-1}, ISSN = {1868-8969}, year = {2022}, volume = {223}, editor = {Bannai, Hideo and Holub, Jan}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.25}, URN = {urn:nbn:de:0030-drops-161529}, doi = {10.4230/LIPIcs.CPM.2022.25}, annote = {Keywords: Burrows-Wheeler-Transform, extended BWT, string collections, repetitiveness measures, r, compression} }
Published in: LIPIcs, Volume 190, 19th International Symposium on Experimental Algorithms (SEA 2021)
Simon J. Puglisi and Bella Zhukova. Document Retrieval Hacks. In 19th International Symposium on Experimental Algorithms (SEA 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 190, pp. 12:1-12:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{puglisi_et_al:LIPIcs.SEA.2021.12, author = {Puglisi, Simon J. and Zhukova, Bella}, title = {{Document Retrieval Hacks}}, booktitle = {19th International Symposium on Experimental Algorithms (SEA 2021)}, pages = {12:1--12:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-185-6}, ISSN = {1868-8969}, year = {2021}, volume = {190}, editor = {Coudert, David and Natale, Emanuele}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2021.12}, URN = {urn:nbn:de:0030-drops-137848}, doi = {10.4230/LIPIcs.SEA.2021.12}, annote = {Keywords: String Processing, Pattern matching, Document listing, Document retrieval, Succinct data structures, Repetitive text collections} }
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 160, 18th International Symposium on Experimental Algorithms (SEA 2020)
Zsuzsanna Lipták, Simon J. Puglisi, and Massimiliano Rossi. Pattern Discovery in Colored Strings. In 18th International Symposium on Experimental Algorithms (SEA 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 160, pp. 12:1-12:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@InProceedings{liptak_et_al:LIPIcs.SEA.2020.12, author = {Lipt\'{a}k, Zsuzsanna and Puglisi, Simon J. and Rossi, Massimiliano}, title = {{Pattern Discovery in Colored Strings}}, booktitle = {18th International Symposium on Experimental Algorithms (SEA 2020)}, pages = {12:1--12:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-148-1}, ISSN = {1868-8969}, year = {2020}, volume = {160}, editor = {Faro, Simone and Cantone, Domenico}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2020.12}, URN = {urn:nbn:de:0030-drops-120862}, doi = {10.4230/LIPIcs.SEA.2020.12}, annote = {Keywords: property testing, suffix tree, pattern mining} }
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