相关论文: Identifying Essential Hub Genes and Protein Comple…
Network alignment aims to uncover topologically similar regions in the protein-protein interaction (PPI) networks of two or more species under the assumption that topologically similar regions tend to perform similar functions. Although…
The Gene Ontology (GO) provides a knowledge base to effectively describe proteins. However, measuring similarity between proteins based on GO remains a challenge. In this paper, we propose a new similarity measure, information coefficient…
Topological analysis of large scale protein-protein interaction networks (PINs) is important for understanding the organisational and functional principles of individual proteins. The number of interactions that a protein has in a PIN has…
Gene Ontology (GO) terms are frequently used to score alignments between protein-protein interaction (PPI) networks. Methods exist to measure the GO similarity between two proteins in isolation, but pairs of proteins in a network alignment…
Accurate prediction of protein function is essential for elucidating molecular mechanisms and advancing biological and therapeutic discovery. Yet experimental annotation lags far behind the rapid growth of protein sequence data.…
Effective biomedical data integration depends on automated term normalization, the mapping of natural language biomedical terms to standardized identifiers. This linking of terms to identifiers is essential for semantic interoperability.…
The study of biological processes can greatly benefit from tools that automatically predict gene functions or directly cluster genes based on shared functionality. Existing data mining methods predict protein functionality by exploiting…
The last decade has seen the advent and consolidation of ontology based tools for the identification and biological interpretation of classes of genes, such as the Gene Ontology. The information accumulated time-by-time and included in the…
Essential protein plays a crucial role in the process of cell life. The identification of essential proteins can not only promote the development of drug target technology, but also contribute to the mechanism of biological evolution. There…
In this work, we propose a novel centrality metric, referred to as star centrality, which incorporates information from the closed neighborhood of a node, rather than solely from the node itself, when calculating its topological importance.…
Semantic similarity measures (SSMs) refer to a set of algorithms used to quantify the similarity of two or more terms belonging to the same ontology. Ontology terms may be associated to concepts, for instance in computational biology gene…
In computational biology, biological entities such as genes or proteins are usually annotated with terms extracted from Gene Ontology (GO). The functional similarity among terms of an ontology is evaluated by using Semantic Similarity…
A large number of protein sequences are becoming available through the application of novel high-throughput sequencing technologies. Experimental functional characterization of these proteins is time-consuming and expensive, and is often…
The increasing availability of high throughput data arising from gene expression studies leads to the necessity of methods for summarizing the available information. As annotation quality improves it is becoming common to rely on the Gene…
The Gene Ontology (GO) is a major bioinformatics ontology that provides structured controlled vocabularies to classify gene and proteins function and role. The GO and its annotations to gene products are now an integral part of functional…
The organization and mining of malaria genomic and post-genomic data is highly motivated by the necessity to predict and characterize new biological targets and new drugs. Biological targets are sought in a biological space designed from…
In several domains such as linguistics, molecular biology or social sciences, holistic effects are hardly well-defined by modeling with single units, but more and more studies tend to understand macro structures with the help of meaningful…
Protein-protein interaction (PPI) networks provide valuable insights into the function of biological systems, and aligning multiple PPI networks can reveal important functional relationships between different species. However, assessing the…
Topological network alignment aims to align two networks node-wise in order to maximize the observed common connection (edge) topology between them. The topological alignment of two Protein-Protein Interaction (PPI) networks should thus…
Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…