21 Search Results for "Huber, Christian"

Document
DOI: 10.4230/LIPIcs.TYPES.2019.5
From Cubes to Twisted Cubes via Graph Morphisms in Type Theory

Authors: Gun Pinyo and Nicolai Kraus

Published in: LIPIcs, Volume 175, 25th International Conference on Types for Proofs and Programs (TYPES 2019)

Abstract
Cube categories are used to encode higher-dimensional categorical structures. They have recently gained significant attention in the community of homotopy type theory and univalent foundations, where types carry the structure of higher groupoids. Bezem, Coquand, and Huber [Bezem et al., 2014] have presented a constructive model of univalence using a specific cube category, which we call the BCH cube category. The higher categories encoded with the BCH cube category have the property that all morphisms are invertible, mirroring the fact that equality is symmetric. This might not always be desirable: the field of directed type theory considers a notion of equality that is not necessarily invertible. This motivates us to suggest a category of twisted cubes which avoids built-in invertibility. Our strategy is to first develop several alternative (but equivalent) presentations of the BCH cube category using morphisms between suitably defined graphs. Starting from there, a minor modification allows us to define our category of twisted cubes. We prove several first results about this category, and our work suggests that twisted cubes combine properties of cubes with properties of globes and simplices (tetrahedra).
Cite as

Gun Pinyo and Nicolai Kraus. From Cubes to Twisted Cubes via Graph Morphisms in Type Theory. In 25th International Conference on Types for Proofs and Programs (TYPES 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 175, pp. 5:1-5:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

Copy BibTex To Clipboard

@InProceedings{pinyo_et_al:LIPIcs.TYPES.2019.5,
  author =	{Pinyo, Gun and Kraus, Nicolai},
  title =	{{From Cubes to Twisted Cubes via Graph Morphisms in Type Theory}},
  booktitle =	{25th International Conference on Types for Proofs and Programs (TYPES 2019)},
  pages =	{5:1--5:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-158-0},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{175},
  editor =	{Bezem, Marc and Mahboubi, Assia},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TYPES.2019.5},
  URN =		{urn:nbn:de:0030-drops-130694},
  doi =		{10.4230/LIPIcs.TYPES.2019.5},
  annote =	{Keywords: homotopy type theory, cubical sets, directed equality, graph morphisms}
}
Document
DOI: 10.4230/OASIcs.WCET.2019.4
Worst-Case Energy-Consumption Analysis by Microarchitecture-Aware Timing Analysis for Device-Driven Cyber-Physical Systems

Authors: Phillip Raffeck, Christian Eichler, Peter Wägemann, and Wolfgang Schröder-Preikschat

Published in: OASIcs, Volume 72, 19th International Workshop on Worst-Case Execution Time Analysis (WCET 2019)

Abstract
Many energy-constrained cyber-physical systems require both timeliness and the execution of tasks within given energy budgets. That is, besides knowledge on worst-case execution time (WCET), the worst-case energy consumption (WCEC) of operations is essential. Unfortunately, WCET analysis approaches are not directly applicable for deriving WCEC bounds in device-driven cyber-physical systems: For example, a single memory operation can lead to a significant power-consumption increase when thereby switching on a device (e.g. transceiver, actuator) in the embedded system. However, as we demonstrate in this paper, existing approaches from microarchitecture-aware timing analysis (i.e. considering cache and pipeline effects) are beneficial for determining WCEC bounds: We extended our framework on whole-system analysis with microarchitecture-aware timing modeling to precisely account for the execution time that devices are kept (in)active. Our evaluations based on a benchmark generator, which is able to output benchmarks with known baselines (i.e. actual WCET and actual WCEC), and an ARM Cortex-M4 platform validate that the approach significantly reduces analysis pessimism in whole-system WCEC analyses.
Cite as

Phillip Raffeck, Christian Eichler, Peter Wägemann, and Wolfgang Schröder-Preikschat. Worst-Case Energy-Consumption Analysis by Microarchitecture-Aware Timing Analysis for Device-Driven Cyber-Physical Systems. In 19th International Workshop on Worst-Case Execution Time Analysis (WCET 2019). Open Access Series in Informatics (OASIcs), Volume 72, pp. 4:1-4:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

Copy BibTex To Clipboard

@InProceedings{raffeck_et_al:OASIcs.WCET.2019.4,
  author =	{Raffeck, Phillip and Eichler, Christian and W\"{a}gemann, Peter and Schr\"{o}der-Preikschat, Wolfgang},
  title =	{{Worst-Case Energy-Consumption Analysis by Microarchitecture-Aware Timing Analysis for Device-Driven Cyber-Physical Systems}},
  booktitle =	{19th International Workshop on Worst-Case Execution Time Analysis (WCET 2019)},
  pages =	{4:1--4:12},
  series =	{Open Access Series in Informatics (OASIcs)},
  ISBN =	{978-3-95977-118-4},
  ISSN =	{2190-6807},
  year =	{2019},
  volume =	{72},
  editor =	{Altmeyer, Sebastian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/OASIcs.WCET.2019.4},
  URN =		{urn:nbn:de:0030-drops-107699},
  doi =		{10.4230/OASIcs.WCET.2019.4},
  annote =	{Keywords: WCEC, WCRE, WCET, michroarchitecture analysis, whole-system analysis}
}
Document
DOI: 10.4230/LIPIcs.FSCD.2019.11
Homotopy Canonicity for Cubical Type Theory

Authors: Thierry Coquand, Simon Huber, and Christian Sattler

Published in: LIPIcs, Volume 131, 4th International Conference on Formal Structures for Computation and Deduction (FSCD 2019)

Abstract
Cubical type theory provides a constructive justification of homotopy type theory and satisfies canonicity: every natural number is convertible to a numeral. A crucial ingredient of cubical type theory is a path lifting operation which is explained computationally by induction on the type involving several non-canonical choices. In this paper we show by a sconing argument that if we remove these equations for the path lifting operation from the system, we still retain homotopy canonicity: every natural number is path equal to a numeral.
Cite as

Thierry Coquand, Simon Huber, and Christian Sattler. Homotopy Canonicity for Cubical Type Theory. In 4th International Conference on Formal Structures for Computation and Deduction (FSCD 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 131, pp. 11:1-11:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

Copy BibTex To Clipboard

@InProceedings{coquand_et_al:LIPIcs.FSCD.2019.11,
  author =	{Coquand, Thierry and Huber, Simon and Sattler, Christian},
  title =	{{Homotopy Canonicity for Cubical Type Theory}},
  booktitle =	{4th International Conference on Formal Structures for Computation and Deduction (FSCD 2019)},
  pages =	{11:1--11:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-107-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{131},
  editor =	{Geuvers, Herman},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2019.11},
  URN =		{urn:nbn:de:0030-drops-105188},
  doi =		{10.4230/LIPIcs.FSCD.2019.11},
  annote =	{Keywords: cubical type theory, univalence, canonicity, sconing, Artin glueing}
}
Document
DOI: 10.4230/LIPIcs.FSCD.2019.25
Gluing for Type Theory

Authors: Ambrus Kaposi, Simon Huber, and Christian Sattler

Published in: LIPIcs, Volume 131, 4th International Conference on Formal Structures for Computation and Deduction (FSCD 2019)

Abstract
The relationship between categorical gluing and proofs using the logical relation technique is folklore. In this paper we work out this relationship for Martin-Löf type theory and show that parametricity and canonicity arise as special cases of gluing. The input of gluing is two models of type theory and a pseudomorphism between them and the output is a displayed model over the first model. A pseudomorphism preserves the categorical structure strictly, the empty context and context extension up to isomorphism, and there are no conditions on preservation of type formers. We look at three examples of pseudomorphisms: the identity on the syntax, the interpretation into the set model and the global section functor. Gluing along these result in syntactic parametricity, semantic parametricity and canonicity, respectively.
Cite as

Ambrus Kaposi, Simon Huber, and Christian Sattler. Gluing for Type Theory. In 4th International Conference on Formal Structures for Computation and Deduction (FSCD 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 131, pp. 25:1-25:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

Copy BibTex To Clipboard

@InProceedings{kaposi_et_al:LIPIcs.FSCD.2019.25,
  author =	{Kaposi, Ambrus and Huber, Simon and Sattler, Christian},
  title =	{{Gluing for Type Theory}},
  booktitle =	{4th International Conference on Formal Structures for Computation and Deduction (FSCD 2019)},
  pages =	{25:1--25:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-107-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{131},
  editor =	{Geuvers, Herman},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.FSCD.2019.25},
  URN =		{urn:nbn:de:0030-drops-105323},
  doi =		{10.4230/LIPIcs.FSCD.2019.25},
  annote =	{Keywords: Martin-L\"{o}f type theory, logical relations, parametricity, canonicity, quotient inductive types}
}
Document
DOI: 10.4230/DagSemProc.08101.1
08101 Abstracts Collection – Computational Proteomics

Authors: Knut Reinert, Christian Huber, Kathrin Marcus, Michal Linial, and Oliver Kohlbacher

Published in: Dagstuhl Seminar Proceedings, Volume 8101, Computational Proteomics (2008)

Abstract
The second Dagstuhl Seminar on emph{Computational Proteomics} took place from March 3rd to 7th, 2008 in Schloss Dagstuhl--Leibniz Center for Informatics. This highly international meeting brought together researchers from computer science and from proteomics to discuss the state of the art and future developments at the interface between experiment and theory. This interdisciplinary exchange covered a wide range of topics, from new experimental methods resulting in more complex data we will have to expect in the future to purely theoretical studies of what level of experimental accuracy is required in order to solve certain problems. A particular focus was also on the application side, where the participants discussed more complex experimental methodologies that are enabled by more sophisticated computational techniques. Quantitative aspects of protein expression analysis as well as posttranslational modifications in the context of disease development and diagnosis were discussed. The seminar sparked a number of new ideas and collaborations and has resulted in several joint grant applications and paper submissions. This paper describes the seminar topics, its goals and results. The executive summary is followed by the abstracts of the presentations given. Links to extended abstracts or full papers are provided, if available.
Cite as

Knut Reinert, Christian Huber, Kathrin Marcus, Michal Linial, and Oliver Kohlbacher. 08101 Abstracts Collection – Computational Proteomics. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 8101, pp. 1-34, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

Copy BibTex To Clipboard

@InProceedings{reinert_et_al:DagSemProc.08101.1,
  author =	{Reinert, Knut and Huber, Christian and Marcus, Kathrin and Linial, Michal and Kohlbacher, Oliver},
  title =	{{08101 Abstracts  Collection – Computational Proteomics}},
  booktitle =	{Computational Proteomics},
  pages =	{1--34},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8101},
  editor =	{Christian Huber and Oliver Kohlbacher and Michal Linial and Katrin Marcus and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.08101.1},
  URN =		{urn:nbn:de:0030-drops-17840},
  doi =		{10.4230/DagSemProc.08101.1},
  annote =	{Keywords: Bioinformatics, biomedicine, proteomics, analytical chemistry}
}
Document
DOI: 10.4230/DagSemProc.08101.2
Towards de novo identification of metabolites by analyzing tandem mass spectra

Authors: Sebastian Böcker and Florian Rasche

Published in: Dagstuhl Seminar Proceedings, Volume 8101, Computational Proteomics (2008)

Abstract
Mass spectrometry is among the most widely used technologies in proteomics and metabolomics. For metabolites, de novo interpretation of spectra is even more important than for protein data, because metabolite spectra databases cover only a small fraction of naturally occurring metabolites. In this work, we analyze a method for fully automated de novo identification of metabolites from tandem mass spectra. Mass spectrometry data is usually assumed to be insufficient for identification of molecular structures, so we want to estimate the molecular formula of the unknown metabolite, a crucial step for its identification. This is achieved by calculating the possible formulas of the fragment peaks and then reconstructing the most likely fragmentation tree from this information. We present tests on real mass spectra showing that our algorithms solve the reconstruction problem suitably fast and provide excellent results: For all 32 test compounds the correct solution was among the top five suggestions, for 26 compounds the first suggestion of the exact algorithm was correct.
Cite as

Sebastian Böcker and Florian Rasche. Towards de novo identification of metabolites by analyzing tandem mass spectra. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 8101, pp. 1-5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

Copy BibTex To Clipboard

@InProceedings{bocker_et_al:DagSemProc.08101.2,
  author =	{B\"{o}cker, Sebastian and Rasche, Florian},
  title =	{{Towards de novo identification of metabolites by analyzing tandem mass spectra}},
  booktitle =	{Computational Proteomics},
  pages =	{1--5},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8101},
  editor =	{Christian Huber and Oliver Kohlbacher and Michal Linial and Katrin Marcus and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.08101.2},
  URN =		{urn:nbn:de:0030-drops-17839},
  doi =		{10.4230/DagSemProc.08101.2},
  annote =	{Keywords: Tandem mass spectrometry, metabolomics, de novo interpretation}
}
Document
DOI: 10.4230/DagSemProc.05471.3
A machine learning approach for prediction of DNA and peptide HPLC retention times

Authors: Marc Sturm, Sascha Quinten, Christian G. Huber, and Oliver Kohlbacher

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
High performance liquid chromatography (HPLC) has become one of the most efficient methods for the separation of biomolecules. It is an important tool in DNA purification after synthesis as well as DNA quantification. In both cases the separability of different oligonucleotides is essential. The prediction of oligonucleotide retention times prior to the experiment may detect superimposed nucleotides and thereby help to avoid futile experiments. In 2002 Gilar et al. proposed a simple mathematical model for the prediction of DNA retention times, that reliably works at high temperatures only (at least 70°C). To cover a wider temperature rang we incorporated DNA secondary structure information in addition to base composition and length. We used support vector regression (SVR) for the model generation and retention time prediction. A similar problem arises in shotgun proteomics. Here HPLC coupled to a mass spectrometer (MS) is used to analyze complex peptide mixtures (thousands of peptides). Predicting peptide retention times can be used to validate tandem-MS peptide identifications made by search engines like SEQUEST. Recently several methods including multiple linear regression and artificial neural networks were proposed, but SVR has not been used so far.
Cite as

Marc Sturm, Sascha Quinten, Christian G. Huber, and Oliver Kohlbacher. A machine learning approach for prediction of DNA and peptide HPLC retention times. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

Copy BibTex To Clipboard

@InProceedings{sturm_et_al:DagSemProc.05471.3,
  author =	{Sturm, Marc and Quinten, Sascha and Huber, Christian G. and Kohlbacher, Oliver},
  title =	{{A machine learning approach for prediction of DNA and peptide HPLC retention times}},
  booktitle =	{Computational Proteomics},
  pages =	{1--5},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.3},
  URN =		{urn:nbn:de:0030-drops-5484},
  doi =		{10.4230/DagSemProc.05471.3},
  annote =	{Keywords: High performance liquid chromatography, mass spectrometry, retention time, prediction, peptide, DNA, support vector regression}
}
Document
DOI: 10.4230/DagSemProc.05471.13
OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics

Authors: Knut Reinert, Oliver Kohlbacher, Clemens Gröpl, Eva Lange, Ole Schulz-Trieglaff, Marc Sturm, and Nico Pfeifer

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
In the talk we describe the freely available software library OpenMS which is currently under development at the Freie Universität Berlin and the Eberhardt-Karls Universität Tübingen. We give an overview of the goals and problems in differential proteomics with HPLC and then describe in detail the implemented approaches for signal processing, peak detection and data reduction currently employed in OpenMS. After this we describe methods to identify the differential expression of peptides and propose strategies to avoid MS/MS identification of peptides of interest. We give an overview of the capabilities and design principles of OpenMS and demonstrate its ease of use. Finally we describe projects in which OpenMS will be or was already deployed and thereby demonstrate its versatility.
Cite as

Knut Reinert, Oliver Kohlbacher, Clemens Gröpl, Eva Lange, Ole Schulz-Trieglaff, Marc Sturm, and Nico Pfeifer. OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-7, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

Copy BibTex To Clipboard

@InProceedings{reinert_et_al:DagSemProc.05471.13,
  author =	{Reinert, Knut and Kohlbacher, Oliver and Gr\"{o}pl, Clemens and Lange, Eva and Schulz-Trieglaff, Ole and Sturm, Marc and Pfeifer, Nico},
  title =	{{OpenMS - A Framework for Quantitative HPLC/MS-Based Proteomics}},
  booktitle =	{Computational Proteomics},
  pages =	{1--7},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.13},
  URN =		{urn:nbn:de:0030-drops-5463},
  doi =		{10.4230/DagSemProc.05471.13},
  annote =	{Keywords: Proteomics, C++, Differential expression}
}
Document
DOI: 10.4230/DagSemProc.05471.1
05471 Abstract Collection – Computational Proteomics

Authors: Christian G. Huber, Oliver Kohlbacher, and Knut Reinert

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
From 20.11.05 to 25.11.05, the Dagstuhl Seminar 05471 ``Computational Proteomics'' 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

Christian G. Huber, Oliver Kohlbacher, and Knut Reinert. 05471 Abstract Collection – Computational Proteomics. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

Copy BibTex To Clipboard

@InProceedings{huber_et_al:DagSemProc.05471.1,
  author =	{Huber, Christian G. and Kohlbacher, Oliver and Reinert, Knut},
  title =	{{05471 Abstract Collection – Computational Proteomics}},
  booktitle =	{Computational Proteomics},
  pages =	{1--15},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.1},
  URN =		{urn:nbn:de:0030-drops-5569},
  doi =		{10.4230/DagSemProc.05471.1},
  annote =	{Keywords: Proteomics, mass spectrometry, MALDI, HPLC-MS, differential expression, clinical proteomics, quantitation, identification}
}
Document
DOI: 10.4230/DagSemProc.05471.2
05471 Executive Summary – Computational Proteomics

Authors: Christian G. Huber, Oliver Kohlbacher, and Knut Reinert

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
The Dagstuhl Seminar on Computational Proteomics brought together researchers from computer science and from proteomics to discuss the state of the art and future developments at the interface between experiment and theory. This interdisciplinary exchange covered a wide range of topics, from new experimental methods resulting in more complex data we will have to expect in the future to purely theoretical studies of what level of experimental accuracy is required in order to solve certain problems. A particular focus was also on the application side, where the participants discussed more complex experimental methodologies that are enabled by more sophisticated computational techniques. Quantitative aspects of protein expression analysis as well as posttranslational modifications in the context of disease development and diagnosis were discussed. The seminar sparked a number of new ideas and collaborations and resulted in joint grant applications and publications.
Cite as

Christian G. Huber, Oliver Kohlbacher, and Knut Reinert. 05471 Executive Summary – Computational Proteomics. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

Copy BibTex To Clipboard

@InProceedings{huber_et_al:DagSemProc.05471.2,
  author =	{Huber, Christian G. and Kohlbacher, Oliver and Reinert, Knut},
  title =	{{05471 Executive Summary – Computational Proteomics}},
  booktitle =	{Computational Proteomics},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.2},
  URN =		{urn:nbn:de:0030-drops-5406},
  doi =		{10.4230/DagSemProc.05471.2},
  annote =	{Keywords: Proteomics, mass spectrometry, MALDI, HPLC-MS, differential expression, clinical proteomics, quantitation, identification}
}
Document
DOI: 10.4230/DagSemProc.05471.4
An Algorithm for Feature Finding in LC/MS Raw Data

Authors: Clemens Gröpl

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
Liquid chromatography coupled with mass spectrometry is an established method in shotgun proteomics. A key step in the data processing pipeline is to transform the raw data acquired by the mass spectrometer into a list of features. In this context, a emph{feature} is defined as the two-dimensional integration with respect to retention time (RT) and mass-over-charge (m/z) of the eluting signal belonging to a single charge variant of a measurand (e.g., a peptide). Features are characterized by attributes like average mass-to-charge ratio, centroid retention time, intensity, and quality. We present a new algorithm for feature finding which has been developed as a part of a combined experimental and algorithmic approach to absolutely quantify proteins from complex samples with unprecedented precision. The method was applied to the analysis of myoglobin in human blood serum, which is an important diagnostic marker for myocardial infarction. Our approach was able to determine the absolute amount of myoglobin in a serum sample through a series of standard addition experiments with a relative error of 2.5\%. It compares favorably to a manual analysis of the same data set since we could improve the precision and conduct the whole analysis pipeline in a small fraction of the time. We anticipate that our automatic quantitation method will facilitate further absolute or relative quantitation of even more complex peptide samples. The algorithm was implemented in the publicly available software framework OpenMS (www.OpenMS.de)
Cite as

Clemens Gröpl. An Algorithm for Feature Finding in LC/MS Raw Data. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-9, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

Copy BibTex To Clipboard

@InProceedings{gropl:DagSemProc.05471.4,
  author =	{Gr\"{o}pl, Clemens},
  title =	{{An Algorithm for Feature Finding in LC/MS Raw Data}},
  booktitle =	{Computational Proteomics},
  pages =	{1--9},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.4},
  URN =		{urn:nbn:de:0030-drops-5341},
  doi =		{10.4230/DagSemProc.05471.4},
  annote =	{Keywords: Computational Proteomics, Quantitative Analysis, Liquid Chromatography, Mass Spectrometry, Algorithm, Software}
}
Document
DOI: 10.4230/DagSemProc.05471.5
Combinatorial Approaches for Mass Spectra Recalibration

Authors: Sebastian Böcker and Veli Mäkinen

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
Mass spectrometry has become one of the most popular analysis techniques in Proteomics and Systems Biology. With the creation of larger datasets, the automated recalibration of mass spectra becomes important to ensure that every peak in the sample spectrum is correctly assigned to some peptide and protein. Algorithms for recalibrating mass spectra have to be robust with respect to wrongly assigned peaks, as well as efficient due to the amount of mass spectrometry data. The recalibration of mass spectra leads us to the problem of finding an optimal matching between mass spectra under measurement errors. We have developed two deterministic methods that allow robust computation of such a matching: The first approach uses a computational geometry interpretation of the problem, and tries to find two parallel lines with constant distance that stab a maximal number of points in the plane. The second approach is based on finding a maximal common approximate subsequence, and improves existing algorithms by one order of magnitude exploiting the sequential nature of the matching problem. We compare our results to a computational geometry algorithm using a topological line-sweep.
Cite as

Sebastian Böcker and Veli Mäkinen. Combinatorial Approaches for Mass Spectra Recalibration. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

Copy BibTex To Clipboard

@InProceedings{bocker_et_al:DagSemProc.05471.5,
  author =	{B\"{o}cker, Sebastian and M\"{a}kinen, Veli},
  title =	{{Combinatorial Approaches for Mass Spectra Recalibration}},
  booktitle =	{Computational Proteomics},
  pages =	{1--6},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.5},
  URN =		{urn:nbn:de:0030-drops-5455},
  doi =		{10.4230/DagSemProc.05471.5},
  annote =	{Keywords: Mass spectrometry recalibration computational geometry}
}
Document
DOI: 10.4230/DagSemProc.05471.6
Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins

Authors: Nathanaël Delmotte, Bettina Mayr, Andreas Leinenbach, Knut Reinert, Oliver Kohlbacher, Christoph Klein, and Christian G. Huber

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
The serum complexity makes the absolute quantitative analysis of medium to low-abundant proteins very challenging. Tens of thousands proteins are present in human serum and dispersed over an extremely wide dynamic range. The reliable identification and quantitation of proteins, which are potential biomarkers of disease, in serum or plasma as matrix still represents one of the most difficult analytical challenges. The difficulties arise from the presence of a few, but highly abundant proteins in serum and from the non-availability of isotope-labeled proteins, which serve to calibrate the method and to account for losses during sample preparation. For the absolute quantitation of serum proteins, we have developed an analytical scheme based on first-dimension separation of the intact proteins by anion-exchange high-performance liquid chromatography (HPLC), followed by proteolytic digestion and second-dimension separation of the tryptic peptides by reversed-phase HPLC in combination with electrospray ionization mass spectrometry (ESI-MS). The potential of mass spectrometric peptide identification in complex mixtures by means of peptide mass fingerprinting (PMF) and peptide fragment fingerprinting (PFF) was evaluated and compared utilizing synthetic mixtures of commercially available proteins and electrospray-ion trap- or electrospray time-of-flight mass spectrometers. While identification of peptides by PFF is fully supported by automated spectrum interpretation and database search routines, reliable identification by PMF still requires substantial efforts of manual calibration and careful data evaluation in order to avoid false positives. Quantitation of the identified peptides, however, is preferentially performed utilizing full-scan mass spectral data typical of PMF. Algorithmic solutions for PMF that incorporate both recalibration and automated feature finding on the basis of peak elution profiles and isotopic patterns are therefore highly desirable in order to speed up the process of data evaluation and calculation of quantitative results. Calibration for quantitative analysis of serum proteins was performed upon addition of known amounts of authentic protein to the serum sample. This was essential for the analysis of human serum samples, for which isotope-labeled protein standards are usually not available. We present the application of multidimensional HPLC-ESI-MS to the absolute quantitative analysis of myoglobin in human serum, a very sensitive biomarker for myocardial infarction. It was possible to determine myoglobin concentrations in human serum down to 100-500 ng/mL. Calibration graphs were linear over at least one order of magnitude and the relative standard deviation of the method ranged from 7-15%.
Cite as

Nathanaël Delmotte, Bettina Mayr, Andreas Leinenbach, Knut Reinert, Oliver Kohlbacher, Christoph Klein, and Christian G. Huber. Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

Copy BibTex To Clipboard

@InProceedings{delmotte_et_al:DagSemProc.05471.6,
  author =	{Delmotte, Nathana\"{e}l and Mayr, Bettina and Leinenbach, Andreas and Reinert, Knut and Kohlbacher, Oliver and Klein, Christoph and Huber, Christian G.},
  title =	{{Evaluation of LC-MS data for the absolute quantitative analysis of marker proteins}},
  booktitle =	{Computational Proteomics},
  pages =	{1--5},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.6},
  URN =		{urn:nbn:de:0030-drops-5397},
  doi =		{10.4230/DagSemProc.05471.6},
  annote =	{Keywords: RP-HPLC, monolith, Mascot, Myoglobin, Absolute quantitation, Serum}
}
Document
DOI: 10.4230/DagSemProc.05471.7
Future Challenges in Proteomics

Authors: Hartmut Schlüter

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
The benefits of the present proteomic approaches for the life science community are limited by 3 major problems. 1. The identification of proteins, regardless whether the peptide mass fingerprint or the shot-gun approach is used, usually is based on an incomplete set of peptides leaving large parts of the full amino acid sequence and other structural details of the original protein species in the dark; 2. Missing validation of many of the identified proteins by orthogonal biological experiments thus risking false positive results; 3. Missing standardization in nomenclature. In sum these problems may hinder progress in life science projects employing proteomic strategies and may be especially risky for system biology approaches since the ambiguities resulting from the above mentioned problems may cause wrong models. It is recommended to guide future proteome analytical investigations by a hypothesis and to focus to a smaller number of proteins which should ideally be analyzed in detail covering 100 % sequence coverage as well as all posttranslational modifications and will allow validation by additional biological experiments.
Cite as

Hartmut Schlüter. Future Challenges in Proteomics. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-5, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

Copy BibTex To Clipboard

@InProceedings{schluter:DagSemProc.05471.7,
  author =	{Schl\"{u}ter, Hartmut},
  title =	{{Future Challenges in Proteomics}},
  booktitle =	{Computational Proteomics},
  pages =	{1--5},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.7},
  URN =		{urn:nbn:de:0030-drops-5449},
  doi =		{10.4230/DagSemProc.05471.7},
  annote =	{Keywords: Protein species, proteome, identification}
}
Document
DOI: 10.4230/DagSemProc.05471.8
Glycosylation Patterns of Proteins Studied by Liquid Chromatography-Mass Spectrometry and Bioinformatic Tools

Authors: Hansjörg Toll, Peter Berger, Andreas Hofmann, Andreas Hildebrandt, Herbert Oberacher, Hans Peter Lenhof, and Christian G. Huber

Published in: Dagstuhl Seminar Proceedings, Volume 5471, Computational Proteomics (2006)

Abstract
Due to their extensive structural heterogeneity, the elucidation of glycosylation patterns in glycoproteins such as the subunits of chorionic gonadotropin (CG), CG-alpha and CG-beta remains one of the most challenging problems in the proteomic analysis of posttranslational modifications. In consequence, glycosylation is usually studied after decomposition of the intact proteins to the proteolytic peptide level. However, by this approach all information about the combination of the different glycopeptides in the intact protein is lost. In this study we have, therefore, attempted to combine the results of glycan identification after tryptic digestion with molecular mass measurements on the intact glycoproteins. Despite the extremely high number of possible combinations of the glycans identified in the tryptic peptides by high-performance liquid chromatography-mass spectrometry (> 1000 for CG-alpha and > 10.000 for CG-beta), the mass spectra of intact CG-alpha and CG-beta revealed only a limited number of glycoforms present in CG preparations from pools of pregnancy urines. Peak annotations for CG-alpha were performed with the help of an algorithm that generates a database containing all possible modifications of the proteins (inclusive possible artificial modifications such as oxidation or truncation) and subsequent searches for combinations fitting the mass difference between the polypeptide backbone and the measured molecular masses. Fourteen different glycoforms of CG-alpha, including methionine-oxidized and N-terminally truncated forms, were readily identified. For CG-beta, however, the relatively high mass accuracy of ± 2 Da was still insufficient to unambiguously assign the possible combinations of posttranslational modifications. Finally, the mass spectrometric fingerprints of the intact molecules were shown to be very useful for the characterization of glycosylation patterns in different CG preparations.
Cite as

Hansjörg Toll, Peter Berger, Andreas Hofmann, Andreas Hildebrandt, Herbert Oberacher, Hans Peter Lenhof, and Christian G. Huber. Glycosylation Patterns of Proteins Studied by Liquid Chromatography-Mass Spectrometry and Bioinformatic Tools. In Computational Proteomics. Dagstuhl Seminar Proceedings, Volume 5471, pp. 1-6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2006)

Copy BibTex To Clipboard

@InProceedings{toll_et_al:DagSemProc.05471.8,
  author =	{Toll, Hansj\"{o}rg and Berger, Peter and Hofmann, Andreas and Hildebrandt, Andreas and Oberacher, Herbert and Lenhof, Hans Peter and Huber, Christian G.},
  title =	{{Glycosylation Patterns of Proteins Studied by Liquid Chromatography-Mass Spectrometry and Bioinformatic Tools}},
  booktitle =	{Computational Proteomics},
  pages =	{1--6},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2006},
  volume =	{5471},
  editor =	{Christian G. Huber and Oliver Kohlbacher and Knut Reinert},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/DagSemProc.05471.8},
  URN =		{urn:nbn:de:0030-drops-5431},
  doi =		{10.4230/DagSemProc.05471.8},
  annote =	{Keywords: Liquid chromatography, mass spectrometry, glycoproteins, glycosylation, peak annotation}
}
  • Refine by Author
  • 7 Kohlbacher, Oliver
  • 6 Huber, Christian G.
  • 5 Reinert, Knut
  • 3 Gröpl, Clemens
  • 2 Böcker, Sebastian
  • Show More...

  • Refine by Classification
  • 3 Theory of computation → Type theory
  • 1 Computer systems organization → Embedded and cyber-physical systems
  • 1 Hardware → Power and energy
  • 1 Hardware → Static timing analysis
  • 1 Theory of computation → Computability
  • Show More...

  • Refine by Keyword
  • 5 Proteomics
  • 5 mass spectrometry
  • 3 MALDI
  • 3 identification
  • 2 HPLC-MS
  • Show More...

  • Refine by Type
  • 21 document

  • Refine by Publication Year
  • 15 2006
  • 3 2019
  • 2 2008
  • 1 2020

Questions / Remarks / Feedback
X

Feedback for Dagstuhl Publishing


Thanks for your feedback!

Feedback submitted

Could not send message

Please try again later or send an E-mail
© 2023-2024 Schloss Dagstuhl – LZI GmbH Imprint Privacy Contact