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Computing topological parameters of biological networks
UNLABELLED Rapidly increasing amounts of molecular interaction data are being produced by various experimental techniques and computational prediction methods. In order to gain insight into theExpand
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Topological analysis and interactive visualization of biological networks and protein structures
Computational analysis and interactive visualization of biological networks and protein structures are common tasks for gaining insight into biological processes. This protocol describes threeExpand
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AltAnalyze and DomainGraph: analyzing and visualizing exon expression data
TLDR
We present an end-to-end solution for the analysis and visualization of alternative splicing data from Affymetrix Exon and Gene Arrays at the level of proteins, domains, microRNA binding sites, molecular interactions and pathways. Expand
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PSICQUIC and PSISCORE: accessing and scoring molecular interactions
To study proteins in the context of a cellular system, it is essential that the molecules with which a protein interacts are identified and the functional consequence of each interaction isExpand
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Analyzing and visualizing residue networks of protein structures.
The study of individual amino acid residues and their molecular interactions in protein structures is crucial for understanding structure-function relationships. Recent work has indicated thatExpand
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Partitioning biological data with transitivity clustering
TLDR
We propose a bead-based registration framework for real-time multiview registration of time-lapse SPIM recordings of early Drosophila melanogaster embryos, which are very challenging samples to reconstruction owing to scattering of yolk. Expand
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FunSimMat: a comprehensive functional similarity database
TLDR
Functional similarity based on Gene Ontology (GO) annotation is used in diverse applications like gene clustering, gene expression data analysis, protein interaction prediction and evaluation. Expand
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Integrating biological data – the Distributed Annotation System
TLDR
We present a new extended version of the Distributed Annotation System (DAS) protocol that incorporates several recent developments, including its extension to serve new data types and an ontology for protein features. Expand
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Mining GO Annotations for Improving Annotation Consistency
Despite the structure and objectivity provided by the Gene Ontology (GO), the annotation of proteins is a complex task that is subject to errors and inconsistencies. Electronically inferredExpand
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Recent approaches to the prioritization of candidate disease genes
TLDR
We highlight recent methodological advances in this research field of candidate gene prioritization, which make use of phenotypic information and comprehensive knowledge integration. Expand
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