Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)
Sebastian Schmidt, Santeri Toivonen, Paul Medvedev, and Alexandru I. Tomescu. Applying the Safe-And-Complete Framework to Practical Genome Assembly. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 8:1-8:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{schmidt_et_al:LIPIcs.WABI.2024.8, author = {Schmidt, Sebastian and Toivonen, Santeri and Medvedev, Paul and Tomescu, Alexandru I.}, title = {{Applying the Safe-And-Complete Framework to Practical Genome Assembly}}, booktitle = {24th International Workshop on Algorithms in Bioinformatics (WABI 2024)}, pages = {8:1--8:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-340-9}, ISSN = {1868-8969}, year = {2024}, volume = {312}, editor = {Pissis, Solon P. and Sung, Wing-Kin}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.8}, URN = {urn:nbn:de:0030-drops-206520}, doi = {10.4230/LIPIcs.WABI.2024.8}, annote = {Keywords: Genome assembly, Omnitigs, Safe-and-complete framework, graph algorithm, HiFi sequencing data, Assembly evaluation} }
Published in: LIPIcs, Volume 296, 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)
Paola Bonizzoni, Christina Boucher, Davide Cozzi, Travis Gagie, and Yuri Pirola. Solving the Minimal Positional Substring Cover Problem in Sublinear Space. In 35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 296, pp. 12:1-12:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)
@InProceedings{bonizzoni_et_al:LIPIcs.CPM.2024.12, author = {Bonizzoni, Paola and Boucher, Christina and Cozzi, Davide and Gagie, Travis and Pirola, Yuri}, title = {{Solving the Minimal Positional Substring Cover Problem in Sublinear Space}}, booktitle = {35th Annual Symposium on Combinatorial Pattern Matching (CPM 2024)}, pages = {12:1--12:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-326-3}, ISSN = {1868-8969}, year = {2024}, volume = {296}, editor = {Inenaga, Shunsuke and Puglisi, Simon J.}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2024.12}, URN = {urn:nbn:de:0030-drops-201225}, doi = {10.4230/LIPIcs.CPM.2024.12}, annote = {Keywords: Positional Burrows-Wheeler Transform, r-index, minimal position substring cover, set-maximal exact matches} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Nicola Rizzo, Manuel Cáceres, and Veli Mäkinen. Finding Maximal Exact Matches in Graphs. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 10:1-10:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{rizzo_et_al:LIPIcs.WABI.2023.10, author = {Rizzo, Nicola and C\'{a}ceres, Manuel and M\"{a}kinen, Veli}, title = {{Finding Maximal Exact Matches in Graphs}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {10:1--10:17}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2023.10}, URN = {urn:nbn:de:0030-drops-186364}, doi = {10.4230/LIPIcs.WABI.2023.10}, annote = {Keywords: Sequence to graph alignment, bidirectional BWT, r-index, suffix tree, founder graphs} }
Published in: LIPIcs, Volume 259, 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)
Manuel Cáceres. Parameterized Algorithms for String Matching to DAGs: Funnels and Beyond. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 7:1-7:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{caceres:LIPIcs.CPM.2023.7, author = {C\'{a}ceres, Manuel}, title = {{Parameterized Algorithms for String Matching to DAGs: Funnels and Beyond}}, booktitle = {34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)}, pages = {7:1--7:19}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2023.7}, URN = {urn:nbn:de:0030-drops-179619}, doi = {10.4230/LIPIcs.CPM.2023.7}, annote = {Keywords: string matching, parameterized algorithms, FPT inside P, string algorithms, graph algorithms, directed acyclic graphs, labeled graphs, funnels} }
Published in: LIPIcs, Volume 259, 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)
Massimo Equi, Arianne Meijer-van de Griend, and Veli Mäkinen. From Bit-Parallelism to Quantum String Matching for Labelled Graphs. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 9:1-9:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{equi_et_al:LIPIcs.CPM.2023.9, author = {Equi, Massimo and Meijer-van de Griend, Arianne and M\"{a}kinen, Veli}, title = {{From Bit-Parallelism to Quantum String Matching for Labelled Graphs}}, booktitle = {34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)}, pages = {9:1--9:20}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2023.9}, URN = {urn:nbn:de:0030-drops-179637}, doi = {10.4230/LIPIcs.CPM.2023.9}, annote = {Keywords: Bit-parallelism, quantum computation, string matching, level DAGs} }
Published in: LIPIcs, Volume 223, 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)
Nicola Rizzo and Veli Mäkinen. Indexable Elastic Founder Graphs of Minimum Height. In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 19:1-19:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{rizzo_et_al:LIPIcs.CPM.2022.19, author = {Rizzo, Nicola and M\"{a}kinen, Veli}, title = {{Indexable Elastic Founder Graphs of Minimum Height}}, booktitle = {33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)}, pages = {19:1--19:19}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.19}, URN = {urn:nbn:de:0030-drops-161467}, doi = {10.4230/LIPIcs.CPM.2022.19}, annote = {Keywords: multiple sequence alignment, pattern matching, data structures, segmentation algorithms, dynamic programming, suffix tree} }
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.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 212, 32nd International Symposium on Algorithms and Computation (ISAAC 2021)
Dhrumil Patel and Rahul Shah. Inverse Suffix Array Queries for 2-Dimensional Pattern Matching in Near-Compact Space. In 32nd International Symposium on Algorithms and Computation (ISAAC 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 212, pp. 60:1-60:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{patel_et_al:LIPIcs.ISAAC.2021.60, author = {Patel, Dhrumil and Shah, Rahul}, title = {{Inverse Suffix Array Queries for 2-Dimensional Pattern Matching in Near-Compact Space}}, booktitle = {32nd International Symposium on Algorithms and Computation (ISAAC 2021)}, pages = {60:1--60:14}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2021.60}, URN = {urn:nbn:de:0030-drops-154932}, doi = {10.4230/LIPIcs.ISAAC.2021.60}, annote = {Keywords: Pattern Matching, Succinct Data Structures} }
Published in: LIPIcs, Volume 191, 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)
Shahbaz Khan. Optimal Construction of Hierarchical Overlap Graphs. In 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 191, pp. 17:1-17:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{khan:LIPIcs.CPM.2021.17, author = {Khan, Shahbaz}, title = {{Optimal Construction of Hierarchical Overlap Graphs}}, booktitle = {32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)}, pages = {17:1--17:11}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2021.17}, URN = {urn:nbn:de:0030-drops-139683}, doi = {10.4230/LIPIcs.CPM.2021.17}, annote = {Keywords: Hierarchical Overlap Graphs, String algorithms, Genome assembly} }
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.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 161, 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)
Veli Mäkinen and Kristoffer Sahlin. Chaining with Overlaps Revisited. In 31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 161, pp. 25:1-25:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@InProceedings{makinen_et_al:LIPIcs.CPM.2020.25, author = {M\"{a}kinen, Veli and Sahlin, Kristoffer}, title = {{Chaining with Overlaps Revisited}}, booktitle = {31st Annual Symposium on Combinatorial Pattern Matching (CPM 2020)}, pages = {25:1--25:12}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-149-8}, ISSN = {1868-8969}, year = {2020}, volume = {161}, editor = {G{\o}rtz, Inge Li and Weimann, Oren}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2020.25}, URN = {urn:nbn:de:0030-drops-121500}, doi = {10.4230/LIPIcs.CPM.2020.25}, annote = {Keywords: Sparse Dynamic Programming, Chaining, Maximal Exact Matches, Longest Common Subsequence} }
Published in: LIPIcs, Volume 132, 46th International Colloquium on Automata, Languages, and Programming (ICALP 2019)
Massimo Equi, Roberto Grossi, Veli Mäkinen, and Alexandru I. Tomescu. On the Complexity of String Matching for Graphs. In 46th International Colloquium on Automata, Languages, and Programming (ICALP 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 132, pp. 55:1-55:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{equi_et_al:LIPIcs.ICALP.2019.55, author = {Equi, Massimo and Grossi, Roberto and M\"{a}kinen, Veli and Tomescu, Alexandru I.}, title = {{On the Complexity of String Matching for Graphs}}, booktitle = {46th International Colloquium on Automata, Languages, and Programming (ICALP 2019)}, pages = {55:1--55:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-109-2}, ISSN = {1868-8969}, year = {2019}, volume = {132}, editor = {Baier, Christel and Chatzigiannakis, Ioannis and Flocchini, Paola and Leonardi, Stefano}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2019.55}, URN = {urn:nbn:de:0030-drops-106314}, doi = {10.4230/LIPIcs.ICALP.2019.55}, annote = {Keywords: exact pattern matching, graph query, graph search, labeled graphs, string matching, string search, strong exponential time hypothesis, heterogeneous networks, variation graphs} }
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.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: Dagstuhl Seminar Proceedings, Volume 8261, Structure-Based Compression of Complex Massive Data (2008)
Angela Bonifati, Gregory Leighton, Veli Mäkinen, Sebastian Maneth, Gonzalo Navarro, and Andrea Pugliese. An In-Memory XQuery/XPath Engine over a Compressed Structured Text Representation. In Structure-Based Compression of Complex Massive Data. Dagstuhl Seminar Proceedings, Volume 8261, pp. 1-17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)
@InProceedings{bonifati_et_al:DagSemProc.08261.6, author = {Bonifati, Angela and Leighton, Gregory and M\"{a}kinen, Veli and Maneth, Sebastian and Navarro, Gonzalo and Pugliese, Andrea}, title = {{An In-Memory XQuery/XPath Engine over a Compressed Structured Text Representation}}, booktitle = {Structure-Based Compression of Complex Massive Data}, pages = {1--17}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2008}, volume = {8261}, editor = {Stefan B\"{o}ttcher and Markus Lohrey and Sebastian Maneth and Wojcieh Rytter}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08261.6}, URN = {urn:nbn:de:0030-drops-16776}, doi = {10.4230/DagSemProc.08261.6}, annote = {Keywords: Compressed self-index, compressed XML representation, XPath, XQuery} }
Published in: Dagstuhl Seminar Proceedings, Volume 8261, Structure-Based Compression of Complex Massive Data (2008)
Veli Mäkinen, Gonzalo Navarro, Jouni Sirén, and Niko Välimäki. Storage and Retrieval of Individual Genomes. In Structure-Based Compression of Complex Massive Data. Dagstuhl Seminar Proceedings, Volume 8261, pp. 1-14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)
@InProceedings{makinen_et_al:DagSemProc.08261.10, author = {M\"{a}kinen, Veli and Navarro, Gonzalo and Sir\'{e}n, Jouni and V\"{a}lim\"{a}ki, Niko}, title = {{Storage and Retrieval of Individual Genomes}}, booktitle = {Structure-Based Compression of Complex Massive Data}, pages = {1--14}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2008}, volume = {8261}, editor = {Stefan B\"{o}ttcher and Markus Lohrey and Sebastian Maneth and Wojcieh Rytter}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08261.10}, URN = {urn:nbn:de:0030-drops-16743}, doi = {10.4230/DagSemProc.08261.10}, annote = {Keywords: Pattern matching, text indexing, compressed data structures, comparative genomics} }
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