Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Clément Agret, Bastien Cazaux, and Antoine Limasset. Toward Optimal Fingerprint Indexing for Large Scale Genomics. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 25:1-25:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{agret_et_al:LIPIcs.WABI.2022.25, author = {Agret, Cl\'{e}ment and Cazaux, Bastien and Limasset, Antoine}, title = {{Toward Optimal Fingerprint Indexing for Large Scale Genomics}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {25:1--25:15}, 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.2022.25}, URN = {urn:nbn:de:0030-drops-170598}, doi = {10.4230/LIPIcs.WABI.2022.25}, annote = {Keywords: Data Structure, Indexation, Local Sensitive Hashing, Genomes, Databases} }
Published in: LIPIcs, Volume 212, 32nd International Symposium on Algorithms and Computation (ISAAC 2021)
Massimo Equi, Tuukka Norri, Jarno Alanko, Bastien Cazaux, Alexandru I. Tomescu, and Veli Mäkinen. Algorithms and Complexity on Indexing Elastic Founder Graphs. In 32nd International Symposium on Algorithms and Computation (ISAAC 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 212, pp. 20:1-20:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{equi_et_al:LIPIcs.ISAAC.2021.20, author = {Equi, Massimo and Norri, Tuukka and Alanko, Jarno and Cazaux, Bastien and Tomescu, Alexandru I. and M\"{a}kinen, Veli}, title = {{Algorithms and Complexity on Indexing Elastic Founder Graphs}}, booktitle = {32nd International Symposium on Algorithms and Computation (ISAAC 2021)}, pages = {20:1--20:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-214-3}, ISSN = {1868-8969}, year = {2021}, volume = {212}, editor = {Ahn, Hee-Kap and Sadakane, Kunihiko}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2021.20}, URN = {urn:nbn:de:0030-drops-154532}, doi = {10.4230/LIPIcs.ISAAC.2021.20}, annote = {Keywords: orthogonal vectors hypothesis, multiple sequence alignment, segmentation} }
Published in: LIPIcs, Volume 198, 48th International Colloquium on Automata, Languages, and Programming (ICALP 2021)
Massimo Cairo, Romeo Rizzi, Alexandru I. Tomescu, and Elia C. Zirondelli. Genome Assembly, from Practice to Theory: Safe, Complete and Linear-Time. In 48th International Colloquium on Automata, Languages, and Programming (ICALP 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 198, pp. 43:1-43:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{cairo_et_al:LIPIcs.ICALP.2021.43, author = {Cairo, Massimo and Rizzi, Romeo and Tomescu, Alexandru I. and Zirondelli, Elia C.}, title = {{Genome Assembly, from Practice to Theory: Safe, Complete and Linear-Time}}, booktitle = {48th International Colloquium on Automata, Languages, and Programming (ICALP 2021)}, pages = {43:1--43:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-195-5}, ISSN = {1868-8969}, year = {2021}, volume = {198}, editor = {Bansal, Nikhil and Merelli, Emanuela and Worrell, James}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2021.43}, URN = {urn:nbn:de:0030-drops-141122}, doi = {10.4230/LIPIcs.ICALP.2021.43}, annote = {Keywords: Graph algorithm, strong connectivity, reachability under failures} }
Published in: LIPIcs, Volume 191, 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)
Sangsoo Park, Sung Gwan Park, Bastien Cazaux, Kunsoo Park, and Eric Rivals. A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs. In 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 191, pp. 22:1-22:9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{park_et_al:LIPIcs.CPM.2021.22, author = {Park, Sangsoo and Park, Sung Gwan and Cazaux, Bastien and Park, Kunsoo and Rivals, Eric}, title = {{A Linear Time Algorithm for Constructing Hierarchical Overlap Graphs}}, booktitle = {32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)}, pages = {22:1--22:9}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-186-3}, ISSN = {1868-8969}, year = {2021}, volume = {191}, editor = {Gawrychowski, Pawe{\l} and Starikovskaya, Tatiana}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2021.22}, URN = {urn:nbn:de:0030-drops-139736}, doi = {10.4230/LIPIcs.CPM.2021.22}, annote = {Keywords: overlap graph, hierarchical overlap graph, shortest superstring problem, border array} }
Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)
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-dev.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} }
Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)
Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, and Jens Stoye. Finding All Maximal Perfect Haplotype Blocks in Linear Time. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 8:1-8:9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{alanko_et_al:LIPIcs.WABI.2019.8, author = {Alanko, Jarno and Bannai, Hideo and Cazaux, Bastien and Peterlongo, Pierre and Stoye, Jens}, title = {{Finding All Maximal Perfect Haplotype Blocks in Linear Time}}, booktitle = {19th International Workshop on Algorithms in Bioinformatics (WABI 2019)}, pages = {8:1--8:9}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-123-8}, ISSN = {1868-8969}, year = {2019}, volume = {143}, editor = {Huber, Katharina T. and Gusfield, Dan}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.8}, URN = {urn:nbn:de:0030-drops-110388}, doi = {10.4230/LIPIcs.WABI.2019.8}, annote = {Keywords: Population genomics, selection coefficient, haplotype block, positional Burrows-Wheeler Transform} }
Published in: LIPIcs, Volume 128, 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)
Bastien Cazaux and Eric Rivals. Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding. In 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 128, pp. 24:1-24:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{cazaux_et_al:LIPIcs.CPM.2019.24, author = {Cazaux, Bastien and Rivals, Eric}, title = {{Linking BWT and XBW via Aho-Corasick Automaton: Applications to Run-Length Encoding}}, booktitle = {30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)}, pages = {24:1--24:20}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-103-0}, ISSN = {1868-8969}, year = {2019}, volume = {128}, editor = {Pisanti, Nadia and P. Pissis, Solon}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2019.24}, URN = {urn:nbn:de:0030-drops-104955}, doi = {10.4230/LIPIcs.CPM.2019.24}, annote = {Keywords: Data Structure, Algorithm, Aho-Corasick Tree, compression, RLE} }
Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
Tuukka Norri, Bastien Cazaux, Dmitry Kosolobov, and Veli Mäkinen. Minimum Segmentation for Pan-genomic Founder Reconstruction in Linear Time. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 15:1-15:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{norri_et_al:LIPIcs.WABI.2018.15, author = {Norri, Tuukka and Cazaux, Bastien and Kosolobov, Dmitry and M\"{a}kinen, Veli}, title = {{Minimum Segmentation for Pan-genomic Founder Reconstruction in Linear Time}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {15:1--15:15}, 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.2018.15}, URN = {urn:nbn:de:0030-drops-93175}, doi = {10.4230/LIPIcs.WABI.2018.15}, annote = {Keywords: Pan-genome indexing, founder reconstruction, dynamic programming, positional Burrows-Wheeler transform, range minimum query} }
Published in: LIPIcs, Volume 103, 17th International Symposium on Experimental Algorithms (SEA 2018)
Bastien Cazaux, Samuel Juhel, and Eric Rivals. Practical lower and upper bounds for the Shortest Linear Superstring. In 17th International Symposium on Experimental Algorithms (SEA 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 103, pp. 18:1-18:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{cazaux_et_al:LIPIcs.SEA.2018.18, author = {Cazaux, Bastien and Juhel, Samuel and Rivals, Eric}, title = {{Practical lower and upper bounds for the Shortest Linear Superstring}}, booktitle = {17th International Symposium on Experimental Algorithms (SEA 2018)}, pages = {18:1--18:14}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-070-5}, ISSN = {1868-8969}, year = {2018}, volume = {103}, editor = {D'Angelo, Gianlorenzo}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2018.18}, URN = {urn:nbn:de:0030-drops-89530}, doi = {10.4230/LIPIcs.SEA.2018.18}, annote = {Keywords: greedy, approximation, overlap, Concat-Cycles, cyclic cover, linear time, text compression} }
Published in: LIPIcs, Volume 105, 29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018)
Bastien Cazaux and Eric Rivals. Superstrings with multiplicities. In 29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 105, pp. 21:1-21:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{cazaux_et_al:LIPIcs.CPM.2018.21, author = {Cazaux, Bastien and Rivals, Eric}, title = {{Superstrings with multiplicities}}, booktitle = {29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018)}, pages = {21:1--21:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-074-3}, ISSN = {1868-8969}, year = {2018}, volume = {105}, editor = {Navarro, Gonzalo and Sankoff, David and Zhu, Binhai}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2018.21}, URN = {urn:nbn:de:0030-drops-86881}, doi = {10.4230/LIPIcs.CPM.2018.21}, annote = {Keywords: greedy algorithm, approximation, overlap, cyclic cover, APX, subset system} }
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