Publications by authors named "Daniel Wiegreffe"
Article Synopsis
- Sequence alignments are crucial for genomic data analysis, but often rely on dividing long sequences into shorter intervals, which can lose the original context.
- To address this issue, the paper introduces a graph structure to retain the order of genomic sequences during alignment, enhancing the visualization of structural variations.
- The authors propose a new graph drawing framework that offers a hierarchical layout for comparative genome analysis, along with algorithms and a prototype example for practical application.
Article Synopsis
- The MutationExplorer webserver helps scientists understand how changes in a protein's sequence can affect its structure and function by showing 3D models.
- Users can enter specific mutations and see how the protein's energy changes and how it might behave.
- The tool allows for easy uploads of large data, making it quick for researchers to see how different variations in proteins influence their properties.
The possible effects of mutations on stability and function of a protein can only be understood in the context of protein 3D structure. The MutationExplorer webserver maps sequence changes onto protein structures and allows users to study variation by inputting sequence changes. As the user enters variants, the 3D model evolves, and estimated changes in energy are highlighted.
View Article and Find Full Text PDFMolecular dynamics simulation is a proven technique for computing and visualizing the time-resolved motion of macromolecules at atomic resolution. The MDsrv is a tool that streams MD trajectories and displays them interactively in web browsers without requiring advanced skills, facilitating interactive exploration and collaborative visual analysis. We have now enhanced the MDsrv to further simplify the upload and sharing of MD trajectories and improve their online viewing and analysis.
View Article and Find Full Text PDFExperts face the task of deciding where and how land reuse-transforming previously used areas into landscape and utility areas-can be performed. This decision is based on which area should be used, which restrictions exist, and which conditions have to be fulfilled for reusing this area. Information about the restrictions and the conditions is available as mostly textual, nonspatial data associated to areas overlapping the target areas.
View Article and Find Full Text PDFBackground: In epigenetics, the change of the combination of histone modifications at the same genomic location during cell differentiation is of great interest for understanding the function of these modifications and their combinations. Besides analyzing them locally for individual genomic locations or globally using correlations between different cells types, intermediate level analyses of these changes are of interest. More specifically, the different distributions of these combinations for different cell types, respectively, are compared to gain new insights.
View Article and Find Full Text PDFMotivation: RNA secondary structure is a useful representation for studying the function of RNA, which captures most of the free energy of RNA folding. Using empirically determined energy parameters, secondary structures of nucleic acids can be efficiently computed by recursive algorithms. Several software packages supporting this task are readily available.
View Article and Find Full Text PDFObjective: Sierra Platinum is a fast and robust peak-caller for replicated ChIP-seq experiments with visual quality-control and -steering. The required computing resources are optimized but still may exceed the resources available to researchers at biological research institutes.
Results: Sierra Platinum Service provides the full functionality of Sierra Platinum: using a web interface, a new instance of the service can be generated.