5 Search Results for "Burkhard, Hans-Dieter"

Document
DOI: 10.4230/OASIcs.GCB.2013.56
Efficient Interpretation of Tandem Mass Tags in Top-Down Proteomics

Authors: Anna Katharina Hildebrandt, Ernst Althaus, Hans-Peter Lenhof, Chien-Wen Hung, Andreas Tholey, and Andreas Hildebrandt

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

Abstract
Mass spectrometry is the major analytical tool for the identification and quantification of proteins in biological samples. In so-called top-down proteomics, separation and mass spectrometric analysis is performed at the level of intact proteins, without preparatory digestion steps. It has been shown that the tandem mass tag (TMT) labeling technology, which is often used for quantification based on digested proteins (bottom-up studies), can be applied in top-down proteomics as well. This, however, leads to a complex interpretation problem, where we need to annotate measured peaks with their respective generating protein, the number of charges, and the a priori unknown number of TMT-groups attached to this protein. In this work, we give an algorithm for the efficient enumeration of all valid annotations that fulfill available experimental constraints. Applying the algorithm to real-world data, we show that the annotation problem can indeed be efficiently solved. However, our experiments also demonstrate that reliable annotation in complex mixtures requires at least partial sequence information and high mass accuracy and resolution to go beyond the proof-of-concept stage.
Cite as

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)

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@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}
}
Document
DOI: 10.4230/DFU.SciViz.2010.30
Generalized Swap Operation for Tetrahedrizations

Authors: Burkhard Lehner, Bernd Hamann, and Georg Umlauf

Published in: Dagstuhl Follow-Ups, Volume 1, Scientific Visualization: Advanced Concepts (2010)

Abstract
Mesh optimization of 2D and 3D triangulations is used in multiple applications extensively. For example, mesh optimization is crucial in the context of adaptively discretizing geometry, typically representing the geometrical boundary conditions of a numerical simulation, or adaptively discretizing the entire space over which various dependent variables of a numerical simulation must be approximated. Together with operations applied to the vertices the so-called edge or face swap operations are the building block of all optimization approaches. To speed up the optimization or to avoid local minima of the function measuring overall mesh quality these swaps are combined to generalized swap operations with a less local impact on the triangulation. Despite the fact that these swap operations change only the connectivity of a triangulation, it depends on the geometry of the triangulation whether the generalized swap will generate inconsistently oriented or degenerate simplices. Because these are undesirable for numerical reasons, this paper is concerned with geometric criteria that guarantee the generalized swaps for a 3D triangulation to yield only valid, non-degenerate triangulations.
Cite as

Burkhard Lehner, Bernd Hamann, and Georg Umlauf. Generalized Swap Operation for Tetrahedrizations. In Scientific Visualization: Advanced Concepts. Dagstuhl Follow-Ups, Volume 1, pp. 30-44, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InCollection{lehner_et_al:DFU.SciViz.2010.30,
  author =	{Lehner, Burkhard and Hamann, Bernd and Umlauf, Georg},
  title =	{{Generalized Swap Operation for Tetrahedrizations}},
  booktitle =	{Scientific Visualization: Advanced Concepts},
  pages =	{30--44},
  series =	{Dagstuhl Follow-Ups},
  ISBN =	{978-3-939897-19-4},
  ISSN =	{1868-8977},
  year =	{2010},
  volume =	{1},
  editor =	{Hagen, Hans},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DFU.SciViz.2010.30},
  URN =		{urn:nbn:de:0030-drops-26956},
  doi =		{10.4230/DFU.SciViz.2010.30},
  annote =	{Keywords: 3D Triangulation, Geometric Conditions, Swap Operations}
}
Document
DOI: 10.4230/DagSemProc.06251.1
06251 Abstracts Collection – Multi-Robot Systems: Perception, Behaviors, Learning, and Action

Authors: Hans-Dieter Burkhard, Martin Riedmiller, Uwe Schwiegelshohn, and Manuela Veloso

Published in: Dagstuhl Seminar Proceedings, Volume 6251, Multi-Robot Systems: Perception, Behaviors, Learning, and Action (2006)

Abstract
From 19.06.06 to 23.06.06, the Dagstuhl Seminar 06251 ``Multi-Robot Systems: Perception, Behaviors, Learning, and Action'' was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.
Cite as

Hans-Dieter Burkhard, Martin Riedmiller, Uwe Schwiegelshohn, and Manuela Veloso. 06251 Abstracts Collection – Multi-Robot Systems: Perception, Behaviors, Learning, and Action. In Multi-Robot Systems: Perception, Behaviors, Learning, and Action. Dagstuhl Seminar Proceedings, Volume 6251, pp. 1-9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{burkhard_et_al:DagSemProc.06251.1,
  author =	{Burkhard, Hans-Dieter and Riedmiller, Martin and Schwiegelshohn, Uwe and Veloso, Manuela},
  title =	{{06251 Abstracts Collection – Multi-Robot Systems: Perception, Behaviors, Learning, and Action}},
  booktitle =	{Multi-Robot Systems: Perception, Behaviors, Learning, and Action},
  pages =	{1--9},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{6251},
  editor =	{Hans-Dieter Burkhard and Martin Riedmiller and Uwe Schwiegelshohn and Manuela Veloso},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.06251.1},
  URN =		{urn:nbn:de:0030-drops-8444},
  doi =		{10.4230/DagSemProc.06251.1},
  annote =	{Keywords: Autonomous robots, multi-robot systems, object recognition, robot-human interaction, modeling, robot simulation}
}
Document
DOI: 10.4230/DagSemProc.06251.2
06251 Executive Summary – Multi-Robot Systems: Perception, Behaviors, Learning, and Action

Authors: Uwe Schwiegelshohn, Walter Nistico, and Matthias Hebbel

Published in: Dagstuhl Seminar Proceedings, Volume 6251, Multi-Robot Systems: Perception, Behaviors, Learning, and Action (2006)

Abstract
The Dagstuhl Seminar on Multi-Robot Systems (06251) was held in June 20-23, 2006. It had the goal to bring researchers together from different areas of robotics to discuss current research topics on autonomous and interacting robots. The technical focus was on perception, behaviors, learning, and action. The seminar took directly place after the RoboCup robot soccer competitions and the subsequent symposium in Bremen. Thus researchers from many different countries were able to join the seminar and address issues without taking into account upcoming competitions or events.
Cite as

Uwe Schwiegelshohn, Walter Nistico, and Matthias Hebbel. 06251 Executive Summary – Multi-Robot Systems: Perception, Behaviors, Learning, and Action. In Multi-Robot Systems: Perception, Behaviors, Learning, and Action. Dagstuhl Seminar Proceedings, Volume 6251, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

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@InProceedings{schwiegelshohn_et_al:DagSemProc.06251.2,
  author =	{Schwiegelshohn, Uwe and Nistico, Walter and Hebbel, Matthias},
  title =	{{06251 Executive Summary – Multi-Robot Systems: Perception, Behaviors, Learning, and Action}},
  booktitle =	{Multi-Robot Systems: Perception, Behaviors, Learning, and Action},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{6251},
  editor =	{Hans-Dieter Burkhard and Martin Riedmiller and Uwe Schwiegelshohn and Manuela Veloso},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.06251.2},
  URN =		{urn:nbn:de:0030-drops-8432},
  doi =		{10.4230/DagSemProc.06251.2},
  annote =	{Keywords: Summary}
}
Document
DOI: 10.4230/DagSemRep.111
Object-Orientation with Parallelism and Persistence (Dagstuhl Seminar 9514)

Authors: Burkhard Freitag, Clifford B. Jones, Christian Lengauer, and Hans-Jörg Schek

Published in: Dagstuhl Seminar Reports. Dagstuhl Seminar Reports, Volume 1 (2021)

Abstract
Cite as

Burkhard Freitag, Clifford B. Jones, Christian Lengauer, and Hans-Jörg Schek. Object-Orientation with Parallelism and Persistence (Dagstuhl Seminar 9514). Dagstuhl Seminar Report 111, pp. 1-22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (1995)

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@TechReport{freitag_et_al:DagSemRep.111,
  author =	{Freitag, Burkhard and Jones, Clifford B. and Lengauer, Christian and Schek, Hans-J\"{o}rg},
  title =	{{Object-Orientation with Parallelism and Persistence (Dagstuhl Seminar 9514)}},
  pages =	{1--22},
  ISSN =	{1619-0203},
  year =	{1995},
  type = 	{Dagstuhl Seminar Report},
  number =	{111},
  institution =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemRep.111},
  URN =		{urn:nbn:de:0030-drops-149997},
  doi =		{10.4230/DagSemRep.111},
}
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