157 results on '"Schwämmle, Veit"'
Search Results
152. A Tutorial for Variance-Sensitive Clustering and the Quantitative Analysis of Protein Complexes.
- Author
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Schwämmle V and Hagensen CE
- Subjects
- Cluster Analysis, Data Interpretation, Statistical, Databases, Protein, Female, Humans, Multiprotein Complexes, Protein Binding, Research Design, Software, Breast Neoplasms metabolism, Neoplasm Proteins analysis, Proteome, Proteomics statistics & numerical data
- Abstract
Data clustering facilitates the identification of biologically relevant molecular features in quantitative proteomics experiments with thousands of measurements over multiple conditions. It finds groups of proteins or peptides with similar quantitative behavior across multiple experimental conditions. This co-regulatory behavior suggests that the proteins of such a group share their functional behavior and thus often can be mapped to the same biological processes and molecular subnetworks.While usual clustering approaches dismiss the variance of the measured proteins, VSClust combines statistical testing with pattern recognition into a common algorithm. Here, we show how to use the VSClust web service on a large proteomics data set and present further tools to assess the quantitative behavior of protein complexes.
- Published
- 2021
- Full Text
- View/download PDF
153. Community curation of bioinformatics software and data resources.
- Author
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Ison J, Ménager H, Brancotte B, Jaaniso E, Salumets A, Raček T, Lamprecht AL, Palmblad M, Kalaš M, Chmura P, Hancock JM, Schwämmle V, and Ienasescu HI
- Subjects
- Computational Biology standards, Database Management Systems, Europe, Humans, Community Participation, Computational Biology methods, Software
- Abstract
The corpus of bioinformatics resources is huge and expanding rapidly, presenting life scientists with a growing challenge in selecting tools that fit the desired purpose. To address this, the European Infrastructure for Biological Information is supporting a systematic approach towards a comprehensive registry of tools and databases for all domains of bioinformatics, provided under a single portal (https://bio.tools). We describe here the practical means by which scientific communities, including individual developers and projects, through major service providers and research infrastructures, can describe their own bioinformatics resources and share these via bio.tools., (© The Author(s) 2019. Published by Oxford University Press.)
- Published
- 2020
- Full Text
- View/download PDF
154. Automated workflow composition in mass spectrometry-based proteomics.
- Author
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Palmblad M, Lamprecht AL, Ison J, and Schwämmle V
- Subjects
- Computational Biology, Software, Mass Spectrometry, Proteomics, Workflow
- Abstract
Motivation: Numerous software utilities operating on mass spectrometry (MS) data are described in the literature and provide specific operations as building blocks for the assembly of on-purpose workflows. Working out which tools and combinations are applicable or optimal in practice is often hard. Thus researchers face difficulties in selecting practical and effective data analysis pipelines for a specific experimental design., Results: We provide a toolkit to support researchers in identifying, comparing and benchmarking multiple workflows from individual bioinformatics tools. Automated workflow composition is enabled by the tools' semantic annotation in terms of the EDAM ontology. To demonstrate the practical use of our framework, we created and evaluated a number of logically and semantically equivalent workflows for four use cases representing frequent tasks in MS-based proteomics. Indeed we found that the results computed by the workflows could vary considerably, emphasizing the benefits of a framework that facilitates their systematic exploration., Availability and Implementation: The project files and workflows are available from https://github.com/bio-tools/biotoolsCompose/tree/master/Automatic-Workflow-Composition., Supplementary Information: Supplementary data are available at Bioinformatics online., (© The Author(s) 2018. Published by Oxford University Press.)
- Published
- 2019
- Full Text
- View/download PDF
155. Computational and Statistical Methods for High-Throughput Mass Spectrometry-Based PTM Analysis.
- Author
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Schwämmle V and Vaudel M
- Subjects
- Databases, Protein, Search Engine, Software, User-Computer Interface, Web Browser, Computational Biology methods, Data Interpretation, Statistical, Data Mining methods, Mass Spectrometry, Protein Processing, Post-Translational, Proteins chemistry, Proteins metabolism, Proteomics methods
- Abstract
Cell signaling and functions heavily rely on post-translational modifications (PTMs) of proteins. Their high-throughput characterization is thus of utmost interest for multiple biological and medical investigations. In combination with efficient enrichment methods, peptide mass spectrometry analysis allows the quantitative comparison of thousands of modified peptides over different conditions. However, the large and complex datasets produced pose multiple data interpretation challenges, ranging from spectral interpretation to statistical and multivariate analyses. Here, we present a typical workflow to interpret such data.
- Published
- 2017
- Full Text
- View/download PDF
156. Tools and data services registry: a community effort to document bioinformatics resources.
- Author
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Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, and Brunak S
- Subjects
- Data Curation, Software, Computational Biology, Registries
- Abstract
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)
- Published
- 2016
- Full Text
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157. Consequences of the H theorem from nonlinear Fokker-Planck equations.
- Author
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Schwämmle V, Nobre FD, and Curado EM
- Abstract
A general type of nonlinear Fokker-Planck equation is derived directly from a master equation, by introducing generalized transition rates. The H theorem is demonstrated for systems that follow those classes of nonlinear Fokker-Planck equations, in the presence of an external potential. For that, a relation involving terms of Fokker-Planck equations and general entropic forms is proposed. It is shown that, at equilibrium, this relation is equivalent to the maximum-entropy principle. Families of Fokker-Planck equations may be related to a single type of entropy, and so, the correspondence between well-known entropic forms and their associated Fokker-Planck equations is explored. It is shown that the Boltzmann-Gibbs entropy, apart from its connection with the standard--linear Fokker-Planck equation--may be also related to a family of nonlinear Fokker-Planck equations.
- Published
- 2007
- Full Text
- View/download PDF
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