Published in: LIPIcs, Volume 265, 21st International Symposium on Experimental Algorithms (SEA 2023)
Diego Díaz-Domínguez, Saska Dönges, Simon J. Puglisi, and Leena Salmela. Simple Runs-Bounded FM-Index Designs Are Fast. In 21st International Symposium on Experimental Algorithms (SEA 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 265, pp. 7:1-7:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2023)
@InProceedings{diazdominguez_et_al:LIPIcs.SEA.2023.7, author = {D{\'\i}az-Dom{\'\i}nguez, Diego and D\"{o}nges, Saska and Puglisi, Simon J. and Salmela, Leena}, title = {{Simple Runs-Bounded FM-Index Designs Are Fast}}, booktitle = {21st International Symposium on Experimental Algorithms (SEA 2023)}, pages = {7:1--7:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-279-2}, ISSN = {1868-8969}, year = {2023}, volume = {265}, editor = {Georgiadis, Loukas}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2023.7}, URN = {urn:nbn:de:0030-drops-183579}, doi = {10.4230/LIPIcs.SEA.2023.7}, annote = {Keywords: data structures, efficient algorithms} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Leena Salmela. Efficient Solutions to Biological Problems Using de Bruijn Graphs (Invited Talk). In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 1:1-1:2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2022)
@InProceedings{salmela:LIPIcs.WABI.2022.1, author = {Salmela, Leena}, title = {{Efficient Solutions to Biological Problems Using de Bruijn Graphs}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {1:1--1:2}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2022.1}, URN = {urn:nbn:de:0030-drops-170357}, doi = {10.4230/LIPIcs.WABI.2022.1}, annote = {Keywords: de Bruijn graph, variable order de Bruijn graph, genome assembly, sequencing error correction, k-mers} }
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.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 128, 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)
Niko Kiirala, Leena Salmela, and Alexandru I. Tomescu. Safe and Complete Algorithms for Dynamic Programming Problems, with an Application to RNA Folding. In 30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 128, pp. 8:1-8:16, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2019)
@InProceedings{kiirala_et_al:LIPIcs.CPM.2019.8, author = {Kiirala, Niko and Salmela, Leena and Tomescu, Alexandru I.}, title = {{Safe and Complete Algorithms for Dynamic Programming Problems, with an Application to RNA Folding}}, booktitle = {30th Annual Symposium on Combinatorial Pattern Matching (CPM 2019)}, pages = {8:1--8:16}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2019.8}, URN = {urn:nbn:de:0030-drops-104794}, doi = {10.4230/LIPIcs.CPM.2019.8}, annote = {Keywords: RNA secondary structure, RNA folding, Safe solution, Safe and complete algorithm, Counting problem} }
Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)
Riku Walve, Pasi Rastas, and Leena Salmela. Kermit: Guided Long Read Assembly using Coloured Overlap Graphs. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 11:1-11:11, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)
@InProceedings{walve_et_al:LIPIcs.WABI.2018.11, author = {Walve, Riku and Rastas, Pasi and Salmela, Leena}, title = {{Kermit: Guided Long Read Assembly using Coloured Overlap Graphs}}, booktitle = {18th International Workshop on Algorithms in Bioinformatics (WABI 2018)}, pages = {11:1--11:11}, 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.2018.11}, URN = {urn:nbn:de:0030-drops-93135}, doi = {10.4230/LIPIcs.WABI.2018.11}, annote = {Keywords: Genome assembly, Linkage maps, Coloured overlap graph} }
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.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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