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Documents authored by Middendorf, Martin

Document
DOI: 10.4230/OASIcs.GCB.2013.14
On Weighting Schemes for Gene Order Analysis

Authors: Matthias Bernt, Nicolas Wieseke, and Martin Middendorf

Published in: OASIcs, Volume 34, German Conference on Bioinformatics 2013

Abstract
Gene order analysis aims at extracting phylogenetic information from the comparison of the order and orientation of the genes on the genomes of different species. This can be achieved by computing parsimonious rearrangement scenarios, i.e. to determine a sequence of rearrangements events that transforms one given gene order into another such that the sum of weights of the included rearrangement events is minimal. In this sequence only certain types of rearrangements, given by the rearrangement model, are admissible and weights are assigned with respect to the rearrangement type. The choice of a suitable rearrangement model and corresponding weights for the included rearrangement types is important for the meaningful reconstruction. So far the analysis of weighting schemes for gene order analysis has not been considered sufficiently. In this paper weighting schemes for gene order analysis are considered for two rearrangement models: 1) inversions, transpositions, and inverse transpositions; 2) inversions, block interchanges, and inverse transpositions. For both rearrangement models we determined properties of the weighting functions that exclude certain types of rearrangements from parsimonious rearrangement scenarios.
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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)

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@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.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}
}
Document
DOI: 10.4230/DagSemProc.09041.5
09041 Working Group on EMO for Robust Multiobjective Optimization (1st Round)

Authors: Joerg Fliege, Nicola Beume, Juergen Branke, Heinrich Braun, Nirupam Chakraborti, Kalyanmoy Deb, Sabine Helwig, Joshua Knowles, Martin Middendorf, Sanaz Mostaghim, Silvia Poles, Salazar Daniel, Shukla Pradymn, and El-Ghazli Talbi

Published in: Dagstuhl Seminar Proceedings, Volume 9041, Hybrid and Robust Approaches to Multiobjective Optimization (2009)

Abstract
This group explored various robust methodologies for multiobjective optimization.
Cite as

Joerg Fliege, Nicola Beume, Juergen Branke, Heinrich Braun, Nirupam Chakraborti, Kalyanmoy Deb, Sabine Helwig, Joshua Knowles, Martin Middendorf, Sanaz Mostaghim, Silvia Poles, Salazar Daniel, Shukla Pradymn, and El-Ghazli Talbi. 09041 Working Group on EMO for Robust Multiobjective Optimization (1st Round). In Hybrid and Robust Approaches to Multiobjective Optimization. Dagstuhl Seminar Proceedings, Volume 9041, pp. 1-5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{fliege_et_al:DagSemProc.09041.5,
  author =	{Fliege, Joerg and Beume, Nicola and Branke, Juergen and Braun, Heinrich and Chakraborti, Nirupam and Deb, Kalyanmoy and Helwig, Sabine and Knowles, Joshua and Middendorf, Martin and Mostaghim, Sanaz and Poles, Silvia and Salazar Daniel and Shukla Pradymn and Talbi, El-Ghazli},
  title =	{{09041 Working Group on EMO for Robust Multiobjective Optimization (1st Round)}},
  booktitle =	{Hybrid and Robust Approaches to Multiobjective Optimization},
  pages =	{1--5},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9041},
  editor =	{Kalyanmoy Deb and Salvatore Greco and Kaisa Miettinen and Eckart Zitzler},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09041.5},
  URN =		{urn:nbn:de:0030-drops-20030},
  doi =		{10.4230/DagSemProc.09041.5},
  annote =	{Keywords: Robust multiobjective optimization}
}
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