OASIcs, Volume 34
GCB 2013, September 10-13, 2013, Göttingen, Germany
Editors: Tim Beißbarth, Martin Kollmar, Andreas Leha, Burkhard Morgenstern, Anne-Kathrin Schultz, Stephan Waack, and Edgar Wingender
Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013
German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)
@Proceedings{beibarth_et_al:OASIcs.GCB.2013, title = {{OASIcs, Volume 34, GCB'13, Complete Volume}}, booktitle = {German Conference on Bioinformatics 2013}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-939897-59-0}, ISSN = {2190-6807}, year = {2013}, volume = {34}, editor = {Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013}, URN = {urn:nbn:de:0030-drops-42563}, doi = {10.4230/OASIcs.GCB.2013}, annote = {Keywords: Life and Medical Sciences} }
Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013
German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. i-xiii, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)
@InProceedings{beibarth_et_al:OASIcs.GCB.2013.i, author = {Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar}, title = {{Frontmatter, Table of Contents, Preface, Conference Organization}}, booktitle = {German Conference on Bioinformatics 2013}, pages = {i--xiii}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-939897-59-0}, ISSN = {2190-6807}, year = {2013}, volume = {34}, editor = {Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.i}, URN = {urn:nbn:de:0030-drops-42265}, doi = {10.4230/OASIcs.GCB.2013.i}, annote = {Keywords: Frontmatter, Table of Contents, Preface, Conference Organization} }
Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013
Kathrin Petra Aßhauer and Peter Meinicke. On the estimation of metabolic profiles in metagenomics. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 1-13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)
@InProceedings{ahauer_et_al:OASIcs.GCB.2013.1, author = {A{\ss}hauer, Kathrin Petra and Meinicke, Peter}, title = {{On the estimation of metabolic profiles in metagenomics}}, booktitle = {German Conference on Bioinformatics 2013}, pages = {1--13}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-939897-59-0}, ISSN = {2190-6807}, year = {2013}, volume = {34}, editor = {Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.1}, URN = {urn:nbn:de:0030-drops-42380}, doi = {10.4230/OASIcs.GCB.2013.1}, annote = {Keywords: metagenomics, metabolic profiling, taxonomic profiling, abundance estimation, mixture modeling} }
Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013
Matthias Bernt, Nicolas Wieseke, and Martin Middendorf. On Weighting Schemes for Gene Order Analysis. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 14-23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)
@InProceedings{bernt_et_al:OASIcs.GCB.2013.14, author = {Bernt, Matthias and Wieseke, Nicolas and Middendorf, Martin}, title = {{On Weighting Schemes for Gene Order Analysis}}, booktitle = {German Conference on Bioinformatics 2013}, pages = {14--23}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-939897-59-0}, ISSN = {2190-6807}, year = {2013}, volume = {34}, editor = {Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.14}, URN = {urn:nbn:de:0030-drops-42354}, doi = {10.4230/OASIcs.GCB.2013.14}, annote = {Keywords: Gene order analysis, maximum parsimony, weighting} }
Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013
Marcus Boden, Martin Schöneich, Sebastian Horwege, Sebastian Lindner, Chris Leimeister, and Burkhard Morgenstern. Alignment-free sequence comparison with spaced k-mers. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 24-34, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)
@InProceedings{boden_et_al:OASIcs.GCB.2013.24, author = {Boden, Marcus and Sch\"{o}neich, Martin and Horwege, Sebastian and Lindner, Sebastian and Leimeister, Chris and Morgenstern, Burkhard}, title = {{Alignment-free sequence comparison with spaced k-mers}}, booktitle = {German Conference on Bioinformatics 2013}, pages = {24--34}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-939897-59-0}, ISSN = {2190-6807}, year = {2013}, volume = {34}, editor = {Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.24}, URN = {urn:nbn:de:0030-drops-42334}, doi = {10.4230/OASIcs.GCB.2013.24}, annote = {Keywords: Alignment-free sequence comparison, phylogeny reconstruction} }
Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013
Corinna Ernst and Sven Rahmann. PanCake: A Data Structure for Pangenomes. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 35-45, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)
@InProceedings{ernst_et_al:OASIcs.GCB.2013.35, author = {Ernst, Corinna and Rahmann, Sven}, title = {{PanCake: A Data Structure for Pangenomes}}, booktitle = {German Conference on Bioinformatics 2013}, pages = {35--45}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-939897-59-0}, ISSN = {2190-6807}, year = {2013}, volume = {34}, editor = {Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.35}, URN = {urn:nbn:de:0030-drops-42314}, doi = {10.4230/OASIcs.GCB.2013.35}, annote = {Keywords: pangenome, data structure, core genome, comparative genomics} }
Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013
Holger Fröhlich and Gunnar W. Klau. Reconstructing Consensus Bayesian Network Structures with Application to Learning Molecular Interaction Networks. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 46-55, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)
@InProceedings{frohlich_et_al:OASIcs.GCB.2013.46, author = {Fr\"{o}hlich, Holger and Klau, Gunnar W.}, title = {{Reconstructing Consensus Bayesian Network Structures with Application to Learning Molecular Interaction Networks}}, booktitle = {German Conference on Bioinformatics 2013}, pages = {46--55}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-939897-59-0}, ISSN = {2190-6807}, year = {2013}, volume = {34}, editor = {Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.46}, URN = {urn:nbn:de:0030-drops-42273}, doi = {10.4230/OASIcs.GCB.2013.46}, annote = {Keywords: Bayesian Networks, Network Reverse Engineering, Minimum Feedback Arc Set, Maximum Acyclic Subgraph, Molecular Interaction Networks} }
Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013
Anna Katharina Hildebrandt, Ernst Althaus, Hans-Peter Lenhof, Chien-Wen Hung, Andreas Tholey, and Andreas Hildebrandt. Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 56-67, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)
@InProceedings{hildebrandt_et_al:OASIcs.GCB.2013.56, author = {Hildebrandt, Anna Katharina and Althaus, Ernst and Lenhof, Hans-Peter and Hung, Chien-Wen and Tholey, Andreas and Hildebrandt, Andreas}, title = {{Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics}}, booktitle = {German Conference on Bioinformatics 2013}, pages = {56--67}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-939897-59-0}, ISSN = {2190-6807}, year = {2013}, volume = {34}, editor = {Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.56}, URN = {urn:nbn:de:0030-drops-42304}, doi = {10.4230/OASIcs.GCB.2013.56}, annote = {Keywords: Mass spectrometry, TMT labeling, Top-down Proteomics} }
Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013
Rashid Ibragimov, Maximilian Malek, Jiong Guo, and Jan Baumbach. GEDEVO: An Evolutionary Graph Edit Distance Algorithm for Biological Network Alignment. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 68-79, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)
@InProceedings{ibragimov_et_al:OASIcs.GCB.2013.68, author = {Ibragimov, Rashid and Malek, Maximilian and Guo, Jiong and Baumbach, Jan}, title = {{GEDEVO: An Evolutionary Graph Edit Distance Algorithm for Biological Network Alignment}}, booktitle = {German Conference on Bioinformatics 2013}, pages = {68--79}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-939897-59-0}, ISSN = {2190-6807}, year = {2013}, volume = {34}, editor = {Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.68}, URN = {urn:nbn:de:0030-drops-42298}, doi = {10.4230/OASIcs.GCB.2013.68}, annote = {Keywords: Network Alignment, Graph Edit Distance, Evolutionary Algorithm, Protein-Protein Interactions} }
Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013
Heiner Klingenberg, Robin Martinjak, Frank Oliver Glöckner, Rolf Daniel, Thomas Lingner, and Peter Meinicke. Dinucleotide distance histograms for fast detection of rRNA in metatranscriptomic sequences. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 80-89, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)
@InProceedings{klingenberg_et_al:OASIcs.GCB.2013.80, author = {Klingenberg, Heiner and Martinjak, Robin and Gl\"{o}ckner, Frank Oliver and Daniel, Rolf and Lingner, Thomas and Meinicke, Peter}, title = {{Dinucleotide distance histograms for fast detection of rRNA in metatranscriptomic sequences}}, booktitle = {German Conference on Bioinformatics 2013}, pages = {80--89}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-939897-59-0}, ISSN = {2190-6807}, year = {2013}, volume = {34}, editor = {Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.80}, URN = {urn:nbn:de:0030-drops-42324}, doi = {10.4230/OASIcs.GCB.2013.80}, annote = {Keywords: Metatranscriptomics, metagenomics, rRNA detection, distance histograms} }
Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013
Andreas Leha, Klaus Jung, and Tim Beißbarth. Utilization of ordinal response structures in classification with high-dimensional expression data. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 90-100, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)
@InProceedings{leha_et_al:OASIcs.GCB.2013.90, author = {Leha, Andreas and Jung, Klaus and Bei{\ss}barth, Tim}, title = {{Utilization of ordinal response structures in classification with high-dimensional expression data}}, booktitle = {German Conference on Bioinformatics 2013}, pages = {90--100}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-939897-59-0}, ISSN = {2190-6807}, year = {2013}, volume = {34}, editor = {Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.90}, URN = {urn:nbn:de:0030-drops-42340}, doi = {10.4230/OASIcs.GCB.2013.90}, annote = {Keywords: Classification, High-Dimensional Data, Ordinal Response, Expression Data} }
Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013
Ioana M. Lemnian, Ralf Eggeling, and Ivo Grosse. Extended Sunflower Hidden Markov Models for the recognition of homotypic cis-regulatory modules}. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 101-109, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)
@InProceedings{lemnian_et_al:OASIcs.GCB.2013.101, author = {Lemnian, Ioana M. and Eggeling, Ralf and Grosse, Ivo}, title = {{Extended Sunflower Hidden Markov Models for the recognition of homotypic cis-regulatory modules\}}}, booktitle = {German Conference on Bioinformatics 2013}, pages = {101--109}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-939897-59-0}, ISSN = {2190-6807}, year = {2013}, volume = {34}, editor = {Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.101}, URN = {urn:nbn:de:0030-drops-42361}, doi = {10.4230/OASIcs.GCB.2013.101}, annote = {Keywords: Hidden Markov Models, cis-regulatory modules, de-novo motif discovery} }
Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013
Benedikt Löwes and Robert Giegerich. Avoiding Ambiguity and Assessing Uniqueness in Minisatellite Alignment. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 110-124, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)
@InProceedings{lowes_et_al:OASIcs.GCB.2013.110, author = {L\"{o}wes, Benedikt and Giegerich, Robert}, title = {{Avoiding Ambiguity and Assessing Uniqueness in Minisatellite Alignment}}, booktitle = {German Conference on Bioinformatics 2013}, pages = {110--124}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-939897-59-0}, ISSN = {2190-6807}, year = {2013}, volume = {34}, editor = {Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.110}, URN = {urn:nbn:de:0030-drops-42285}, doi = {10.4230/OASIcs.GCB.2013.110}, annote = {Keywords: minisatellite alignment, dynamic programming, ambiguity} }
Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013
Marcel Martin and Sven Rahmann. Aligning Flowgrams to DNA Sequences. In German Conference on Bioinformatics 2013. Open Access Series in Informatics (OASIcs), Volume 34, pp. 125-135, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)
@InProceedings{martin_et_al:OASIcs.GCB.2013.125, author = {Martin, Marcel and Rahmann, Sven}, title = {{Aligning Flowgrams to DNA Sequences}}, booktitle = {German Conference on Bioinformatics 2013}, pages = {125--135}, series = {Open Access Series in Informatics (OASIcs)}, ISBN = {978-3-939897-59-0}, ISSN = {2190-6807}, year = {2013}, volume = {34}, editor = {Bei{\ss}barth, Tim and Kollmar, Martin and Leha, Andreas and Morgenstern, Burkhard and Schultz, Anne-Kathrin and Waack, Stephan and Wingender, Edgar}, publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik}, address = {Dagstuhl, Germany}, URL = {https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.GCB.2013.125}, URN = {urn:nbn:de:0030-drops-42379}, doi = {10.4230/OASIcs.GCB.2013.125}, annote = {Keywords: flowgram, sequencing, alignment algorithm, scoring scheme} }
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