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-dev.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 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Sebastian Schmidt and Jarno N. Alanko. Eulertigs: Minimum Plain Text Representation of k-mer Sets Without Repetitions in Linear Time. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 2:1-2:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{schmidt_et_al:LIPIcs.WABI.2022.2, author = {Schmidt, Sebastian and Alanko, Jarno N.}, title = {{Eulertigs: Minimum Plain Text Representation of k-mer Sets Without Repetitions in Linear Time}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {2:1--2:21}, 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.2022.2}, URN = {urn:nbn:de:0030-drops-170361}, doi = {10.4230/LIPIcs.WABI.2022.2}, annote = {Keywords: Spectrum preserving string sets, Eulerian cycle, Suffix tree, Bidirected arc-centric de Bruijn graph, k-mer based methods} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Giulio Ermanno Pibiri. On Weighted k-mer Dictionaries. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 9:1-9:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{pibiri:LIPIcs.WABI.2022.9, author = {Pibiri, Giulio Ermanno}, title = {{On Weighted k-mer Dictionaries}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {9:1--9:20}, 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.2022.9}, URN = {urn:nbn:de:0030-drops-170439}, doi = {10.4230/LIPIcs.WABI.2022.9}, annote = {Keywords: K-Mers, Weights, Compression, Hashing} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Yoshihiko Suzuki and Gene Myers. Accurate k-mer Classification Using Read Profiles. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 10:1-10:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{suzuki_et_al:LIPIcs.WABI.2022.10, author = {Suzuki, Yoshihiko and Myers, Gene}, title = {{Accurate k-mer Classification Using Read Profiles}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {10:1--10:20}, 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.2022.10}, URN = {urn:nbn:de:0030-drops-170446}, doi = {10.4230/LIPIcs.WABI.2022.10}, annote = {Keywords: K-mer, K-mer count, K-mer classification, HiFi sequencing} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Jens Zentgraf and Sven Rahmann. Fast Gapped k-mer Counting with Subdivided Multi-Way Bucketed Cuckoo Hash Tables. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 12:1-12:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{zentgraf_et_al:LIPIcs.WABI.2022.12, author = {Zentgraf, Jens and Rahmann, Sven}, title = {{Fast Gapped k-mer Counting with Subdivided Multi-Way Bucketed Cuckoo Hash Tables}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {12:1--12:20}, 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.2022.12}, URN = {urn:nbn:de:0030-drops-170467}, doi = {10.4230/LIPIcs.WABI.2022.12}, annote = {Keywords: gapped k-mer, k-mer, counting, Cuckoo hashing, parallelization} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Yoshihiro Shibuya, Djamal Belazzougui, and Gregory Kucherov. Efficient Reconciliation of Genomic Datasets of High Similarity. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 14:1-14:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{shibuya_et_al:LIPIcs.WABI.2022.14, author = {Shibuya, Yoshihiro and Belazzougui, Djamal and Kucherov, Gregory}, title = {{Efficient Reconciliation of Genomic Datasets of High Similarity}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {14:1--14:14}, 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.2022.14}, URN = {urn:nbn:de:0030-drops-170481}, doi = {10.4230/LIPIcs.WABI.2022.14}, annote = {Keywords: k-mers, sketching, Invertible Bloom Lookup Tables, IBLT, MinHash, syncmers, minimizers} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Zsuzsanna Lipták, Francesco Masillo, and Simon J. Puglisi. Suffix Sorting via Matching Statistics. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 20:1-20:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{liptak_et_al:LIPIcs.WABI.2022.20, author = {Lipt\'{a}k, Zsuzsanna and Masillo, Francesco and Puglisi, Simon J.}, title = {{Suffix Sorting via Matching Statistics}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {20:1--20:15}, 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.2022.20}, URN = {urn:nbn:de:0030-drops-170545}, doi = {10.4230/LIPIcs.WABI.2022.20}, annote = {Keywords: Generalized suffix array, matching statistics, string collections, compressed representation, data structures, efficient algorithms} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Ke Chen and Mingfu Shao. Locality-Sensitive Bucketing Functions for the Edit Distance. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 22:1-22:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{chen_et_al:LIPIcs.WABI.2022.22, author = {Chen, Ke and Shao, Mingfu}, title = {{Locality-Sensitive Bucketing Functions for the Edit Distance}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {22:1--22:14}, 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.2022.22}, URN = {urn:nbn:de:0030-drops-170563}, doi = {10.4230/LIPIcs.WABI.2022.22}, annote = {Keywords: Locality-sensitive hashing, locality-sensitive bucketing, long reads, embedding} }
Published in: LIPIcs, Volume 242, 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)
Veronica Guerrini, Alessio Conte, Roberto Grossi, Gianni Liti, Giovanna Rosone, and Lorenzo Tattini. phyBWT: Alignment-Free Phylogeny via eBWT Positional Clustering. In 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 242, pp. 23:1-23:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)
@InProceedings{guerrini_et_al:LIPIcs.WABI.2022.23, author = {Guerrini, Veronica and Conte, Alessio and Grossi, Roberto and Liti, Gianni and Rosone, Giovanna and Tattini, Lorenzo}, title = {{phyBWT: Alignment-Free Phylogeny via eBWT Positional Clustering}}, booktitle = {22nd International Workshop on Algorithms in Bioinformatics (WABI 2022)}, pages = {23:1--23:19}, 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.2022.23}, URN = {urn:nbn:de:0030-drops-170577}, doi = {10.4230/LIPIcs.WABI.2022.23}, annote = {Keywords: Phylogeny, partition tree, BWT, positional cluster, alignment-free, reference-free, assembly-free} }
Published in: LIPIcs, Volume 172, 20th International Workshop on Algorithms in Bioinformatics (WABI 2020)
Jens Zentgraf and Sven Rahmann. Fast Lightweight Accurate Xenograft Sorting. In 20th International Workshop on Algorithms in Bioinformatics (WABI 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 172, pp. 4:1-4:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)
@InProceedings{zentgraf_et_al:LIPIcs.WABI.2020.4, author = {Zentgraf, Jens and Rahmann, Sven}, title = {{Fast Lightweight Accurate Xenograft Sorting}}, booktitle = {20th International Workshop on Algorithms in Bioinformatics (WABI 2020)}, pages = {4:1--4:16}, 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.2020.4}, URN = {urn:nbn:de:0030-drops-127933}, doi = {10.4230/LIPIcs.WABI.2020.4}, annote = {Keywords: xenograft sorting, alignment-free method, Cuckoo hashing, k-mer} }
Published in: LIPIcs, Volume 149, 30th International Symposium on Algorithms and Computation (ISAAC 2019)
Ruben Brokkelkamp, Sven Polak, Guido Schäfer, and Yllka Velaj. Approximate Pricing in Networks: How to Boost the Betweenness and Revenue of a Node. In 30th International Symposium on Algorithms and Computation (ISAAC 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 149, pp. 13:1-13:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)
@InProceedings{brokkelkamp_et_al:LIPIcs.ISAAC.2019.13, author = {Brokkelkamp, Ruben and Polak, Sven and Sch\"{a}fer, Guido and Velaj, Yllka}, title = {{Approximate Pricing in Networks: How to Boost the Betweenness and Revenue of a Node}}, booktitle = {30th International Symposium on Algorithms and Computation (ISAAC 2019)}, pages = {13:1--13:15}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-130-6}, ISSN = {1868-8969}, year = {2019}, volume = {149}, editor = {Lu, Pinyan and Zhang, Guochuan}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2019.13}, URN = {urn:nbn:de:0030-drops-115091}, doi = {10.4230/LIPIcs.ISAAC.2019.13}, annote = {Keywords: Network pricing, Stackelberg network pricing, betweenness centrality, revenue maximization} }
Published in: LIPIcs, Volume 118, 29th International Conference on Concurrency Theory (CONCUR 2018)
Krishnendu Chatterjee, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Yaron Velner. Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies. In 29th International Conference on Concurrency Theory (CONCUR 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 118, pp. 11:1-11:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{chatterjee_et_al:LIPIcs.CONCUR.2018.11, author = {Chatterjee, Krishnendu and Kafshdar Goharshady, Amir and Ibsen-Jensen, Rasmus and Velner, Yaron}, title = {{Ergodic Mean-Payoff Games for the Analysis of Attacks in Crypto-Currencies}}, booktitle = {29th International Conference on Concurrency Theory (CONCUR 2018)}, pages = {11:1--11:17}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-087-3}, ISSN = {1868-8969}, year = {2018}, volume = {118}, editor = {Schewe, Sven and Zhang, Lijun}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2018.11}, URN = {urn:nbn:de:0030-drops-95497}, doi = {10.4230/LIPIcs.CONCUR.2018.11}, annote = {Keywords: Crypto-currency, Quantitative Verification, Mean-payoff Games} }
Published in: LIPIcs, Volume 118, 29th International Conference on Concurrency Theory (CONCUR 2018)
Mohamed Faouzi Atig, Ahmed Bouajjani, K. Narayan Kumar, and Prakash Saivasan. Verifying Quantitative Temporal Properties of Procedural Programs. In 29th International Conference on Concurrency Theory (CONCUR 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 118, pp. 15:1-15:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{atig_et_al:LIPIcs.CONCUR.2018.15, author = {Atig, Mohamed Faouzi and Bouajjani, Ahmed and Narayan Kumar, K. and Saivasan, Prakash}, title = {{Verifying Quantitative Temporal Properties of Procedural Programs}}, booktitle = {29th International Conference on Concurrency Theory (CONCUR 2018)}, pages = {15:1--15:17}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-087-3}, ISSN = {1868-8969}, year = {2018}, volume = {118}, editor = {Schewe, Sven and Zhang, Lijun}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2018.15}, URN = {urn:nbn:de:0030-drops-95531}, doi = {10.4230/LIPIcs.CONCUR.2018.15}, annote = {Keywords: Verification, Formal Methods, Pushdown systems, Visibly pushdown, Quantitative Temporal Properties} }
Published in: LIPIcs, Volume 118, 29th International Conference on Concurrency Theory (CONCUR 2018)
Filippo Bonchi, Barbara König, and Daniela Petrisan. Up-To Techniques for Behavioural Metrics via Fibrations. In 29th International Conference on Concurrency Theory (CONCUR 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 118, pp. 17:1-17:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{bonchi_et_al:LIPIcs.CONCUR.2018.17, author = {Bonchi, Filippo and K\"{o}nig, Barbara and Petrisan, Daniela}, title = {{Up-To Techniques for Behavioural Metrics via Fibrations}}, booktitle = {29th International Conference on Concurrency Theory (CONCUR 2018)}, pages = {17:1--17:17}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-087-3}, ISSN = {1868-8969}, year = {2018}, volume = {118}, editor = {Schewe, Sven and Zhang, Lijun}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2018.17}, URN = {urn:nbn:de:0030-drops-95552}, doi = {10.4230/LIPIcs.CONCUR.2018.17}, annote = {Keywords: behavioural metrics, bisimilarity, up-to techniques, coalgebras, fibrations} }
Published in: LIPIcs, Volume 118, 29th International Conference on Concurrency Theory (CONCUR 2018)
Nima Roohi, Pavithra Prabhakar, and Mahesh Viswanathan. Relating Syntactic and Semantic Perturbations of Hybrid Automata. In 29th International Conference on Concurrency Theory (CONCUR 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 118, pp. 26:1-26:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{roohi_et_al:LIPIcs.CONCUR.2018.26, author = {Roohi, Nima and Prabhakar, Pavithra and Viswanathan, Mahesh}, title = {{Relating Syntactic and Semantic Perturbations of Hybrid Automata}}, booktitle = {29th International Conference on Concurrency Theory (CONCUR 2018)}, pages = {26:1--26:16}, series = {Leibniz International Proceedings in Informatics (LIPIcs)}, ISBN = {978-3-95977-087-3}, ISSN = {1868-8969}, year = {2018}, volume = {118}, editor = {Schewe, Sven and Zhang, Lijun}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.CONCUR.2018.26}, URN = {urn:nbn:de:0030-drops-95644}, doi = {10.4230/LIPIcs.CONCUR.2018.26}, annote = {Keywords: Model Checking, Hybrid Automata, Approximation, Perturbation} }
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