Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)
25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 1-430, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@Proceedings{brejova_et_al:LIPIcs.WABI.2025, title = {{LIPIcs, Volume 344, WABI 2025, Complete Volume}}, booktitle = {25th International Conference on Algorithms for Bioinformatics (WABI 2025)}, pages = {1--430}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-386-7}, ISSN = {1868-8969}, year = {2025}, volume = {344}, editor = {Brejov\'{a}, Bro\v{n}a and Patro, Rob}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025}, URN = {urn:nbn:de:0030-drops-243498}, doi = {10.4230/LIPIcs.WABI.2025}, annote = {Keywords: LIPIcs, Volume 344, WABI 2025, Complete Volume} }
Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)
25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 0:i-0:xvi, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{brejova_et_al:LIPIcs.WABI.2025.0, author = {Brejov\'{a}, Bro\v{n}a and Patro, Rob}, title = {{Front Matter, Table of Contents, Preface, Conference Organization}}, booktitle = {25th International Conference on Algorithms for Bioinformatics (WABI 2025)}, pages = {0:i--0:xvi}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-386-7}, ISSN = {1868-8969}, year = {2025}, volume = {344}, editor = {Brejov\'{a}, Bro\v{n}a and Patro, Rob}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.0}, URN = {urn:nbn:de:0030-drops-243477}, doi = {10.4230/LIPIcs.WABI.2025.0}, annote = {Keywords: Front Matter, Table of Contents, Preface, Conference Organization} }
Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)
Alessio Campanelli, Giulio Ermanno Pibiri, and Rob Patro. Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 6:1-6:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{campanelli_et_al:LIPIcs.WABI.2025.6, author = {Campanelli, Alessio and Pibiri, Giulio Ermanno and Patro, Rob}, title = {{Fast Pseudoalignment Queries on Compressed Colored de Bruijn Graphs}}, booktitle = {25th International Conference on Algorithms for Bioinformatics (WABI 2025)}, pages = {6:1--6:21}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-386-7}, ISSN = {1868-8969}, year = {2025}, volume = {344}, editor = {Brejov\'{a}, Bro\v{n}a and Patro, Rob}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.6}, URN = {urn:nbn:de:0030-drops-239327}, doi = {10.4230/LIPIcs.WABI.2025.6}, annote = {Keywords: Colored de Bruijn graphs, Pseudoalignment, Repetition-aware compression} }
Published in: LIPIcs, Volume 338, 23rd International Symposium on Experimental Algorithms (SEA 2025)
Lorraine A. K. Ayad, Gabriele Fici, Ragnar Groot Koerkamp, Grigorios Loukides, Rob Patro, Giulio Ermanno Pibiri, and Solon P. Pissis. U-Index: A Universal Indexing Framework for Matching Long Patterns. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 4:1-4:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)
@InProceedings{ayad_et_al:LIPIcs.SEA.2025.4, author = {Ayad, Lorraine A. K. and Fici, Gabriele and Groot Koerkamp, Ragnar and Loukides, Grigorios and Patro, Rob and Pibiri, Giulio Ermanno and Pissis, Solon P.}, title = {{U-Index: A Universal Indexing Framework for Matching Long Patterns}}, booktitle = {23rd International Symposium on Experimental Algorithms (SEA 2025)}, pages = {4:1--4:18}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-375-1}, ISSN = {1868-8969}, year = {2025}, volume = {338}, editor = {Mutzel, Petra and Prezza, Nicola}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.4}, URN = {urn:nbn:de:0030-drops-232420}, doi = {10.4230/LIPIcs.SEA.2025.4}, annote = {Keywords: Text Indexing, Sketching, Minimizers, Hashing} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Jamshed Khan, Tobias Rubel, Laxman Dhulipala, Erin Molloy, and Rob Patro. Fast, Parallel, and Cache-Friendly Suffix Array Construction. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 16:1-16:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{khan_et_al:LIPIcs.WABI.2023.16, author = {Khan, Jamshed and Rubel, Tobias and Dhulipala, Laxman and Molloy, Erin and Patro, Rob}, title = {{Fast, Parallel, and Cache-Friendly Suffix Array Construction}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {16:1--16:21}, 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.2023.16}, URN = {urn:nbn:de:0030-drops-186424}, doi = {10.4230/LIPIcs.WABI.2023.16}, annote = {Keywords: Suffix Array, Longest Common Prefix, Data Structures, Indexing, Parallel Algorithms} }
Published in: LIPIcs, Volume 273, 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)
Jason Fan, Noor Pratap Singh, Jamshed Khan, Giulio Ermanno Pibiri, and Rob Patro. Fulgor: A Fast and Compact {k-mer} Index for Large-Scale Matching and Color Queries. In 23rd International Workshop on Algorithms in Bioinformatics (WABI 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 273, pp. 18:1-18:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)
@InProceedings{fan_et_al:LIPIcs.WABI.2023.18, author = {Fan, Jason and Singh, Noor Pratap and Khan, Jamshed and Pibiri, Giulio Ermanno and Patro, Rob}, title = {{Fulgor: A Fast and Compact \{k-mer\} Index for Large-Scale Matching and Color Queries}}, booktitle = {23rd International Workshop on Algorithms in Bioinformatics (WABI 2023)}, pages = {18:1--18:21}, 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.2023.18}, URN = {urn:nbn:de:0030-drops-186446}, doi = {10.4230/LIPIcs.WABI.2023.18}, annote = {Keywords: k-mers, Colored de Bruijn Graph, Compression, Read-mapping} }
Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)
Jason Fan, Skylar Chan, and Rob Patro. Perplexity: Evaluating Transcript Abundance Estimation in the Absence of Ground Truth. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 4:1-4:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)
@InProceedings{fan_et_al:LIPIcs.WABI.2021.4, author = {Fan, Jason and Chan, Skylar and Patro, Rob}, title = {{Perplexity: Evaluating Transcript Abundance Estimation in the Absence of Ground Truth}}, booktitle = {21st International Workshop on Algorithms in Bioinformatics (WABI 2021)}, pages = {4:1--4:22}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-200-6}, ISSN = {1868-8969}, year = {2021}, volume = {201}, editor = {Carbone, Alessandra and El-Kebir, Mohammed}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.4}, URN = {urn:nbn:de:0030-drops-143578}, doi = {10.4230/LIPIcs.WABI.2021.4}, annote = {Keywords: RNA-seq, transcript abundance estimation, model selection} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Fatemeh Almodaresi, Prashant Pandey, and Rob Patro. Rainbowfish: A Succinct Colored de Bruijn Graph Representation. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 18:1-18:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{almodaresi_et_al:LIPIcs.WABI.2017.18, author = {Almodaresi, Fatemeh and Pandey, Prashant and Patro, Rob}, title = {{Rainbowfish: A Succinct Colored de Bruijn Graph Representation}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {18:1--18:15}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.18}, URN = {urn:nbn:de:0030-drops-76576}, doi = {10.4230/LIPIcs.WABI.2017.18}, annote = {Keywords: de Bruijn graph, succinct data structures, rank and select operation, colored de Bruijn graph} }
Published in: Dagstuhl Follow-Ups, Volume 2, Scientific Visualization: Interactions, Features, Metaphors (2011)
Youngmin Kim, Robert Patro, Cheuk Yiu Ip, Dianne P. O’Leary, and Andriy Anishkin. Salient Frame Detection for Molecular Dynamics Simulations. In Scientific Visualization: Interactions, Features, Metaphors. Dagstuhl Follow-Ups, Volume 2, pp. 160-175, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2011)
@InCollection{kim_et_al:DFU.Vol2.SciViz.2011.160, author = {Kim, Youngmin and Patro, Robert and Yiu Ip, Cheuk and O’Leary, Dianne P. and Anishkin, Andriy}, title = {{Salient Frame Detection for Molecular Dynamics Simulations}}, booktitle = {Scientific Visualization: Interactions, Features, Metaphors}, pages = {160--175}, series = {Dagstuhl Follow-Ups}, ISBN = {978-3-939897-26-2}, ISSN = {1868-8977}, year = {2011}, volume = {2}, editor = {Hagen, Hans}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DFU.Vol2.SciViz.2011.160}, URN = {urn:nbn:de:0030-drops-32926}, doi = {10.4230/DFU.Vol2.SciViz.2011.160}, annote = {Keywords: Saliency based analysis, Molecular Dynamics, Simulation} }
Published in: Dagstuhl Follow-Ups, Volume 1, Scientific Visualization: Advanced Concepts (2010)
Robert Patro, Cheuk Yiu Ip, and Amitabh Varshney. Saliency Guided Summarization of Molecular Dynamics Simulations. In Scientific Visualization: Advanced Concepts. Dagstuhl Follow-Ups, Volume 1, pp. 321-335, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)
@InCollection{patro_et_al:DFU.SciViz.2010.321, author = {Patro, Robert and Ip, Cheuk Yiu and Varshney, Amitabh}, title = {{Saliency Guided Summarization of Molecular Dynamics Simulations}}, booktitle = {Scientific Visualization: Advanced Concepts}, pages = {321--335}, series = {Dagstuhl Follow-Ups}, ISBN = {978-3-939897-19-4}, ISSN = {1868-8977}, year = {2010}, volume = {1}, editor = {Hagen, Hans}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DFU.SciViz.2010.321}, URN = {urn:nbn:de:0030-drops-27134}, doi = {10.4230/DFU.SciViz.2010.321}, annote = {Keywords: Molecuar Dynamics, Saliency, Simulation} }
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