jfr's Albrecht:M [4 articles]

Abstract

BACKGROUND: Cancer re-sequencing programs rely on DNA isolated from fresh snap frozen tissues, the preparation of which is combined with additional preservation efforts. Tissue samples at pathology departments are routinely stored as formalin-fixed and paraffin-embedded (FFPE) samples and their use would open up access to a variety of clinical trials. However, FFPE preparation is incompatible with many down-stream molecular biology techniques such as PCR based amplification methods and gene expression studies. METHODOLOGY/PRINCIPAL FINDINGS: Here we investigated the sample quality requirements of ...

Abstract

Summary: Recent studies have revealed that alternative splicing plays an important role in the observed protein and interaction diversity. Special microarrays allow for measuring gene expression at the exon level and thus for studying alternative transcripts and their corresponding protein domain architecture. We have developed the Cytoscape plugin DomainGraph that enables the visualization and detailed study of domain-domain interactions forming protein interaction networks. In addition, the integration of exon expression data supports the analysis of alternative splicing events and the characterization ...

Abstract

BACKGROUND:The Distributed Annotation System (DAS) is a widely adopted protocol for dynamically integrating a wide range of biological data from geographically diverse sources. DAS continues to expand its applicability and evolve in response to new challenges facing integrative bioinformatics.RESULTS:Here we describe the various infrastructure components of DAS and present a new extended version of the DAS specification. Version 1.53E incorporates several recent developments, including its extension to serve new data types and an ontology for protein features.CONCLUSION:Our extensions to the DAS ...

Abstract

Summary: Rapidly increasing amounts of molecular interaction data are being produced by various experimental techniques and computational prediction methods. In order to gain insight into the organization and structure of the resultant large complex networks formed by the interacting molecules, we have developed the versatile Cytoscape plugin NetworkAnalyzer. It computes and displays a comprehensive set of topological parameters, which includes the number of nodes, edges, and connected components, the network diameter, radius, density, centralization, heterogeneity, and clustering coefficient, the characteristic path ...