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We are developing a vendor-independent archive and on top of that a data warehouse for mass spectrometry metabolomics data. The archive schema resembles the communitydeveloped object model, the Java implementation of the model classes, and an editor (for both mzData XML files and the database) have been generated using the Eclipse Modeling Framework. Persistence is handled by the JDO2 -compliant framework JPOX. The main content of the Data Warehouse are the results of the signal processing and peak-picking tasks, carried out using the XCMS package from Bioconductor, putative identification and mass decomposition are added to the warehouse afterwards.We present the system architecture, current content, performance observations and describe the analysis tools on top of the warehouse.Availability: http://msbi.ipb-halle.de/
Publications
Arabidopsis thaliana and Cuscuta spec. represent a compatible host–parasite combination. Cuscuta produces a haustorium that penetrates the host tissue. In early stages of development the searching hyphae on the tip of the haustorial cone are connected to the host tissue by interspecific plasmodesmata. Ten days after infection, translocation of the fluorescent dyes, Texas Red (TR) and 5,6-carboxyfluorescein (CF), demonstrates the existence of a continuous connection between xylem and phloem of the host and parasite. Cuscuta becomes the dominant sink in this host–parasite system. Transgenic Arabidopsis plants expressing genes encoding the green fluorescent protein (GFP; 27 kDa) or a GFP–ubiquitin fusion (36 kDa), respectively, under the companion cell (CC)-specific AtSUC2 promoter were used to monitor the transfer of these proteins from the host sieve elements to those of Cuscuta. Although GFP is transferred unimpedly to the parasite, the GFP–ubiquitin fusion could not be detected in Cuscuta. A translocation of the GFP–ubiquitin fusion protein was found to be restricted to the phloem of the host, although a functional symplastic pathway exists between the host and parasite, as demonstrated by the transport of CF. These results indicate a peripheral size exclusion limit (SEL) between 27 and 36 kDa for the symplastic connections between host and Cuscuta sieve elements. Forty-six accessions of A.thaliana covering the entire range of its genetic diversity, as well as Arabidopsishalleri, were found to be susceptible towards Cuscutareflexa.
Books and chapters
Mass spectrometry is the work-horse technology of the emerging field of metabolomics. The identification of mass signals remains the largest bottleneck for a non-targeted approach: due to the analytical method, each metabolite in a complex mixture will give rise to a number of mass signals. In contrast to GC/MS measurements, for soft ionisation methods such as ESI-MS there are no extensive libraries of reference spectra or established deconvolution methods. We present a set of annotation methods which aim to group together mass signals measured from a single metabolite, based on rules for mass differences and peak shape comparison.Availability: The software and documentation is available as an R package on http://msbi.ipb-halle.de/
Books and chapters
Software engeneering today provides tools which minimize the need for manual coding of the typical components of an application, such as database, frontend and web application. Visual modelling brings together users and developers, and allows quick and direct communication about the topic. In the metabolomics community data models and XML formats for data interchange such as mzData are currently emerging. Using these standards as a show case, we present an infrastructure to support the use of these data standards and the process of getting there.
Books and chapters
2D-Nuclear magnetic resonance (NMR) spectroscopy is a powerful analytical method to elucidate the chemical structure of molecules. In contrast to 1D-NMR spectra, 2D-NMR spectra correlate the chemical shifts of 1H and 13C simultaneously. To curate or merge large spectra libraries a robust (and fast) duplicate detection is needed. We propose a definition of duplicates with the desired robustness properties mandatory for 2D-NMR experiments. A major gain in runtime performance wrt. previously proposed heuristics is achieved by mapping the spectra to simple discrete objects. We propose several appropriate data transformations for this task. In order to compensate for slight variations of the mapped spectra, we use appropriate hashing functions according to the locality sensitive hashing scheme, and identify duplicates by hash-collisions.