Published in: LIPIcs, Volume 105, 29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018)
Brian Brubach. Fast Matching-based Approximations for Maximum Duo-Preservation String Mapping and its Weighted Variant. In 29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 105, pp. 5:1-5:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{brubach:LIPIcs.CPM.2018.5, author = {Brubach, Brian}, title = {{Fast Matching-based Approximations for Maximum Duo-Preservation String Mapping and its Weighted Variant}}, booktitle = {29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018)}, pages = {5:1--5:14}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2018.5}, URN = {urn:nbn:de:0030-drops-87066}, doi = {10.4230/LIPIcs.CPM.2018.5}, annote = {Keywords: approximation algorithm, maximum duo-preservation string mapping, minimum common string partition, string comparison, streaming algorithm, comparative genomics} }
Published in: LIPIcs, Volume 105, 29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018)
Brian Brubach and Jay Ghurye. A Succinct Four Russians Speedup for Edit Distance Computation and One-against-many Banded Alignment. In 29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 105, pp. 13:1-13:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)
@InProceedings{brubach_et_al:LIPIcs.CPM.2018.13, author = {Brubach, Brian and Ghurye, Jay}, title = {{A Succinct Four Russians Speedup for Edit Distance Computation and One-against-many Banded Alignment}}, booktitle = {29th Annual Symposium on Combinatorial Pattern Matching (CPM 2018)}, pages = {13:1--13:12}, 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.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2018.13}, URN = {urn:nbn:de:0030-drops-86965}, doi = {10.4230/LIPIcs.CPM.2018.13}, annote = {Keywords: edit distance, banded alignment, one-against-many alignment, genomics, method of the Four Russians} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Brian Brubach, Jay Ghurye, Mihai Pop, and Aravind Srinivasan. Better Greedy Sequence Clustering with Fast Banded Alignment. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 3:1-3:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{brubach_et_al:LIPIcs.WABI.2017.3, author = {Brubach, Brian and Ghurye, Jay and Pop, Mihai and Srinivasan, Aravind}, title = {{Better Greedy Sequence Clustering with Fast Banded Alignment}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {3:1--3:13}, 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.2017.3}, URN = {urn:nbn:de:0030-drops-76425}, doi = {10.4230/LIPIcs.WABI.2017.3}, annote = {Keywords: Sequence Clustering, Metagenomics, String Algorithms} }
Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)
Nidhi Shah, Stephen F. Altschul, and Mihai Pop. Outlier Detection in BLAST Hits. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 23:1-23:11, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@InProceedings{shah_et_al:LIPIcs.WABI.2017.23, author = {Shah, Nidhi and Altschul, Stephen F. and Pop, Mihai}, title = {{Outlier Detection in BLAST Hits}}, booktitle = {17th International Workshop on Algorithms in Bioinformatics (WABI 2017)}, pages = {23:1--23:11}, 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.2017.23}, URN = {urn:nbn:de:0030-drops-76512}, doi = {10.4230/LIPIcs.WABI.2017.23}, annote = {Keywords: Taxonomy classification, Metagenomics, Sequence alignment, Outlier detection} }
Published in: Dagstuhl Reports, Volume 6, Issue 8 (2017)
Gene Myers, Mihai Pop, Knut Reinert, and Tandy Warnow. Next Generation Sequencing (Dagstuhl Seminar 16351). In Dagstuhl Reports, Volume 6, Issue 8, pp. 91-130, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)
@Article{myers_et_al:DagRep.6.8.91, author = {Myers, Gene and Pop, Mihai and Reinert, Knut and Warnow, Tandy}, title = {{Next Generation Sequencing (Dagstuhl Seminar 16351)}}, pages = {91--130}, journal = {Dagstuhl Reports}, ISSN = {2192-5283}, year = {2017}, volume = {6}, number = {8}, editor = {Myers, Gene and Pop, Mihai and Reinert, Knut and Warnow, Tandy}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagRep.6.8.91}, URN = {urn:nbn:de:0030-drops-68395}, doi = {10.4230/DagRep.6.8.91}, annote = {Keywords: Cancer, DNA Sequence Assembly, Expression Profiles, Next Generation Sequencing, Sequence analysis, Software Engineering (Tools \& Libraries)} }
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