Published in: Dagstuhl Reports, Volume 2, Issue 7 (2013)
Alberto Apostolico, Andreas Dress, and Laxmi Parida. Structure Discovery in Biology: Motifs, Networks & Phylogenies (Dagstuhl Seminar 12291). In Dagstuhl Reports, Volume 2, Issue 7, pp. 92-117, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)
@Article{apostolico_et_al:DagRep.2.7.92, author = {Apostolico, Alberto and Dress, Andreas and Parida, Laxmi}, title = {{Structure Discovery in Biology: Motifs, Networks \& Phylogenies (Dagstuhl Seminar 12291)}}, pages = {92--117}, journal = {Dagstuhl Reports}, ISSN = {2192-5283}, year = {2012}, volume = {2}, number = {7}, editor = {Apostolico, Alberto and Dress, Andreas and Parida, Laxmi}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagRep.2.7.92}, URN = {urn:nbn:de:0030-drops-37509}, doi = {10.4230/DagRep.2.7.92}, annote = {Keywords: mathematical biology, computational biology, algorithmic bioinformatics, pattern discovery, networks, phylogenetics, stringology} }
Published in: Dagstuhl Seminar Proceedings, Volume 10231, Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010)
Matteo Comin and Davide Verzotto. Remote Homology Detection of Protein Sequences. In Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings, Volume 10231, pp. 1-20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)
@InProceedings{comin_et_al:DagSemProc.10231.7, author = {Comin, Matteo and Verzotto, Davide}, title = {{Remote Homology Detection of Protein Sequences}}, booktitle = {Structure Discovery in Biology: Motifs, Networks \& Phylogenies}, pages = {1--20}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2010}, volume = {10231}, editor = {Alberto Apostolico and Andreas Dress and Laxmi Parida}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.10231.7}, URN = {urn:nbn:de:0030-drops-27419}, doi = {10.4230/DagSemProc.10231.7}, annote = {Keywords: Classification of protein sequences, irredundant patterns} }
Published in: Dagstuhl Seminar Proceedings, Volume 10231, Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010)
Alberto Apostolico, Andreas Dress, and Laxmi Parida. 10231 Abstracts Collection – Structure Discovery in Biology: Motifs, Networks & Phylogenies. In Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings, Volume 10231, pp. 1-20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)
@InProceedings{apostolico_et_al:DagSemProc.10231.1, author = {Apostolico, Alberto and Dress, Andreas and Parida, Laxmi}, title = {{10231 Abstracts Collection – Structure Discovery in Biology: Motifs, Networks \& Phylogenies}}, booktitle = {Structure Discovery in Biology: Motifs, Networks \& Phylogenies}, pages = {1--20}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2010}, volume = {10231}, editor = {Alberto Apostolico and Andreas Dress and Laxmi Parida}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.10231.1}, URN = {urn:nbn:de:0030-drops-26910}, doi = {10.4230/DagSemProc.10231.1}, annote = {Keywords: Mathematical biology, computational biology, algorithmic bioinformatics, pattern discovery, phylogenetics, networks} }
Published in: Dagstuhl Seminar Proceedings, Volume 10231, Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010)
Anne Bergeron, Julia Mixtacki, and Jens Stoye. A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance. In Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings, Volume 10231, pp. 1-25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)
@InProceedings{bergeron_et_al:DagSemProc.10231.2, author = {Bergeron, Anne and Mixtacki, Julia and Stoye, Jens}, title = {{A New Linear Time Algorithm to Compute the Genomic Distance Via the Double Cut and Join Distance}}, booktitle = {Structure Discovery in Biology: Motifs, Networks \& Phylogenies}, pages = {1--25}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2010}, volume = {10231}, editor = {Alberto Apostolico and Andreas Dress and Laxmi Parida}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.10231.2}, URN = {urn:nbn:de:0030-drops-26892}, doi = {10.4230/DagSemProc.10231.2}, annote = {Keywords: Comparative genomics, genomic distance computation, HP theory} }
Published in: Dagstuhl Seminar Proceedings, Volume 10231, Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010)
Matthias Gallé. A New Tree Distance Metric for Structural Comparison of Sequences. In Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings, Volume 10231, pp. 1-9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)
@InProceedings{galle:DagSemProc.10231.3, author = {Gall\'{e}, Matthias}, title = {{A New Tree Distance Metric for Structural Comparison of Sequences}}, booktitle = {Structure Discovery in Biology: Motifs, Networks \& Phylogenies}, pages = {1--9}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2010}, volume = {10231}, editor = {Alberto Apostolico and Andreas Dress and Laxmi Parida}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.10231.3}, URN = {urn:nbn:de:0030-drops-27375}, doi = {10.4230/DagSemProc.10231.3}, annote = {Keywords: Tree distance, structure discovery, Parseval metric, Tanimoto distance} }
Published in: Dagstuhl Seminar Proceedings, Volume 10231, Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010)
Cinzia Pizzi. Efficient computation of statistics for words with mismatches. In Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings, Volume 10231, pp. 1-22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)
@InProceedings{pizzi:DagSemProc.10231.4, author = {Pizzi, Cinzia}, title = {{Efficient computation of statistics for words with mismatches}}, booktitle = {Structure Discovery in Biology: Motifs, Networks \& Phylogenies}, pages = {1--22}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2010}, volume = {10231}, editor = {Alberto Apostolico and Andreas Dress and Laxmi Parida}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.10231.4}, URN = {urn:nbn:de:0030-drops-27384}, doi = {10.4230/DagSemProc.10231.4}, annote = {Keywords: Statistics on words, mismatches, dynamic programming, biological sequences.} }
Published in: Dagstuhl Seminar Proceedings, Volume 10231, Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010)
Raffaele Giancarlo, Davide Corona, Valeria Di Benedetto, Alessandra Gabriele, and Filippo Utro. Functional Information, Biomolecular Messages and Complexity of BioSequences and Structures. In Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings, Volume 10231, pp. 1-13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)
@InProceedings{giancarlo_et_al:DagSemProc.10231.6, author = {Giancarlo, Raffaele and Corona, Davide and Di Benedetto, Valeria and Gabriele, Alessandra and Utro, Filippo}, title = {{Functional Information, Biomolecular Messages and Complexity of BioSequences and Structures}}, booktitle = {Structure Discovery in Biology: Motifs, Networks \& Phylogenies}, pages = {1--13}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2010}, volume = {10231}, editor = {Alberto Apostolico and Andreas Dress and Laxmi Parida}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.10231.6}, URN = {urn:nbn:de:0030-drops-26884}, doi = {10.4230/DagSemProc.10231.6}, annote = {Keywords: Functional activity, sequence complexity, combinatorics on words, protein-DNA interaction.} }
Published in: Dagstuhl Seminar Proceedings, Volume 10231, Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010)
Andreas Dress, Wim Hordijk, Lin Wei, and Peter Serocka. The Ideal Storage Cellular Automaton Model. In Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings, Volume 10231, pp. 1-8, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)
@InProceedings{dress_et_al:DagSemProc.10231.8, author = {Dress, Andreas and Hordijk, Wim and Wei, Lin and Serocka, Peter}, title = {{The Ideal Storage Cellular Automaton Model}}, booktitle = {Structure Discovery in Biology: Motifs, Networks \& Phylogenies}, pages = {1--8}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2010}, volume = {10231}, editor = {Alberto Apostolico and Andreas Dress and Laxmi Parida}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.10231.8}, URN = {urn:nbn:de:0030-drops-27280}, doi = {10.4230/DagSemProc.10231.8}, annote = {Keywords: } }
Published in: Dagstuhl Seminar Proceedings, Volume 10231, Structure Discovery in Biology: Motifs, Networks & Phylogenies (2010)
Marius Nicolae, Serghei Mangul, Ion Mandoiu, and Alex Zelikovsky. Estimation of alternative splicing isoform frequencies from RNA-Seq data. In Structure Discovery in Biology: Motifs, Networks & Phylogenies. Dagstuhl Seminar Proceedings, Volume 10231, pp. 1-3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)
@InProceedings{nicolae_et_al:DagSemProc.10231.5, author = {Nicolae, Marius and Mangul, Serghei and Mandoiu, Ion and Zelikovsky, Alex}, title = {{Estimation of alternative splicing isoform frequencies from RNA-Seq data}}, booktitle = {Structure Discovery in Biology: Motifs, Networks \& Phylogenies}, pages = {1--3}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2010}, volume = {10231}, editor = {Alberto Apostolico and Andreas Dress and Laxmi Parida}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.10231.5}, URN = {urn:nbn:de:0030-drops-26876}, doi = {10.4230/DagSemProc.10231.5}, annote = {Keywords: RNA-Seq, alternative splicing isoforms, expectation maximization} }
Published in: Dagstuhl Seminar Proceedings, Volume 6201, Combinatorial and Algorithmic Foundations of Pattern and Association Discovery (2006)
Lee Jones and Konstantin Rybnikov. Local Minimax Learning of Approximately Polynomial Functions. In Combinatorial and Algorithmic Foundations of Pattern and Association Discovery. Dagstuhl Seminar Proceedings, Volume 6201, pp. 1-12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2007)
@InProceedings{jones_et_al:DagSemProc.06201.3, author = {Jones, Lee and Rybnikov, Konstantin}, title = {{Local Minimax Learning of Approximately Polynomial Functions}}, booktitle = {Combinatorial and Algorithmic Foundations of Pattern and Association Discovery}, pages = {1--12}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2007}, volume = {6201}, editor = {Rudolf Ahlswede and Alberto Apostolico and Vladimir I. Levenshtein}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.06201.3}, URN = {urn:nbn:de:0030-drops-8912}, doi = {10.4230/DagSemProc.06201.3}, annote = {Keywords: Local learning, statistical learning, estimator, minimax, convex optimization, quantifier elimination, semialgebraic, ridge regression, polynomial} }
Published in: Dagstuhl Seminar Proceedings, Volume 6201, Combinatorial and Algorithmic Foundations of Pattern and Association Discovery (2006)
Yury Lifshits. Solving Classical String Problems an Compressed Texts. In Combinatorial and Algorithmic Foundations of Pattern and Association Discovery. Dagstuhl Seminar Proceedings, Volume 6201, pp. 1-10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)
@InProceedings{lifshits:DagSemProc.06201.7, author = {Lifshits, Yury}, title = {{Solving Classical String Problems an Compressed Texts}}, booktitle = {Combinatorial and Algorithmic Foundations of Pattern and Association Discovery}, pages = {1--10}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2006}, volume = {6201}, editor = {Rudolf Ahlswede and Alberto Apostolico and Vladimir I. Levenshtein}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.06201.7}, URN = {urn:nbn:de:0030-drops-7984}, doi = {10.4230/DagSemProc.06201.7}, annote = {Keywords: Pattern matching, Compressed text} }
Published in: Dagstuhl Seminar Proceedings, Volume 6201, Combinatorial and Algorithmic Foundations of Pattern and Association Discovery (2006)
Rudolf Ahlswede, Alberto Apostolico, and Vladimir I. Levenshtein. 06201 Abstracts Collection – Combinatorial and Algorithmic Foundations of Pattern and Association Discovery. In Combinatorial and Algorithmic Foundations of Pattern and Association Discovery. Dagstuhl Seminar Proceedings, Volume 6201, pp. 1-15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)
@InProceedings{ahlswede_et_al:DagSemProc.06201.1, author = {Ahlswede, Rudolf and Apostolico, Alberto and Levenshtein, Vladimir I.}, title = {{06201 Abstracts Collection – Combinatorial and Algorithmic Foundations of Pattern and Association Discovery}}, booktitle = {Combinatorial and Algorithmic Foundations of Pattern and Association Discovery}, pages = {1--15}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2006}, volume = {6201}, editor = {Rudolf Ahlswede and Alberto Apostolico and Vladimir I. Levenshtein}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.06201.1}, URN = {urn:nbn:de:0030-drops-7873}, doi = {10.4230/DagSemProc.06201.1}, annote = {Keywords: Data compression, pattern matching, pattern discovery, search, sorting, molecular biology, reconstruction, genome rearrangements} }
Published in: Dagstuhl Seminar Proceedings, Volume 6201, Combinatorial and Algorithmic Foundations of Pattern and Association Discovery (2006)
Rudolf Ahlswede, Alberto Apostolico, and Vladimir I. Levenshtein. 06201 Executive Summary – Combinatorial and Algorithmic Foundations of Pattern and Association Discovery. In Combinatorial and Algorithmic Foundations of Pattern and Association Discovery. Dagstuhl Seminar Proceedings, Volume 6201, pp. 1-2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)
@InProceedings{ahlswede_et_al:DagSemProc.06201.2, author = {Ahlswede, Rudolf and Apostolico, Alberto and Levenshtein, Vladimir I.}, title = {{06201 Executive Summary – Combinatorial and Algorithmic Foundations of Pattern and Association Discovery}}, booktitle = {Combinatorial and Algorithmic Foundations of Pattern and Association Discovery}, pages = {1--2}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2006}, volume = {6201}, editor = {Rudolf Ahlswede and Alberto Apostolico and Vladimir I. Levenshtein}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.06201.2}, URN = {urn:nbn:de:0030-drops-7926}, doi = {10.4230/DagSemProc.06201.2}, annote = {Keywords: Data compression, pattern matching, pattern discovery, search, sorting, molecular biology, reconstruction, genome rearrangements} }
Published in: Dagstuhl Seminar Proceedings, Volume 6201, Combinatorial and Algorithmic Foundations of Pattern and Association Discovery (2006)
Rudolf Ahlswede, Christian Deppe, and Vladimir Lebedev. Non--binary error correcting codes with noiseless feedback, localized errors, or both. In Combinatorial and Algorithmic Foundations of Pattern and Association Discovery. Dagstuhl Seminar Proceedings, Volume 6201, pp. 1-4, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)
@InProceedings{ahlswede_et_al:DagSemProc.06201.4, author = {Ahlswede, Rudolf and Deppe, Christian and Lebedev, Vladimir}, title = {{Non--binary error correcting codes with noiseless feedback, localized errors, or both}}, booktitle = {Combinatorial and Algorithmic Foundations of Pattern and Association Discovery}, pages = {1--4}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2006}, volume = {6201}, editor = {Rudolf Ahlswede and Alberto Apostolico and Vladimir I. Levenshtein}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.06201.4}, URN = {urn:nbn:de:0030-drops-7849}, doi = {10.4230/DagSemProc.06201.4}, annote = {Keywords: Error-correcting codes, localized errors, feedback, variable length codes} }
Published in: Dagstuhl Seminar Proceedings, Volume 6201, Combinatorial and Algorithmic Foundations of Pattern and Association Discovery (2006)
Alberto Apostolico and Cinzia Pizzi. On the Monotonicity of the String Correction Factor for Words with Mismatches. In Combinatorial and Algorithmic Foundations of Pattern and Association Discovery. Dagstuhl Seminar Proceedings, Volume 6201, pp. 1-9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)
@InProceedings{apostolico_et_al:DagSemProc.06201.5, author = {Apostolico, Alberto and Pizzi, Cinzia}, title = {{On the Monotonicity of the String Correction Factor for Words with Mismatches}}, booktitle = {Combinatorial and Algorithmic Foundations of Pattern and Association Discovery}, pages = {1--9}, series = {Dagstuhl Seminar Proceedings (DagSemProc)}, ISSN = {1862-4405}, year = {2006}, volume = {6201}, editor = {Rudolf Ahlswede and Alberto Apostolico and Vladimir I. Levenshtein}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.06201.5}, URN = {urn:nbn:de:0030-drops-7899}, doi = {10.4230/DagSemProc.06201.5}, annote = {Keywords: Pattern discovery, Motif, Over-represented word, Monotone score, Correction Factor} }
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