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Successful applications of the gene ontology to infer functional relationships between gene products in recent years have raised the need for computational methods to automatically calculate semantic similarity between gene products based on the gene ontology. To meet this challenge, several methods have been proposed to derive semantic similarity between gene products based on semantic similarity...
The emergence of high-throughput technologies leads to abundant protein-protein interaction (PPI) data and microarray gene expression profiles, and provides a great opportunity for the identification of novel protein complexes using computational methods. By combining these two types of data, we propose a novel Graph Fragmentation Algorithm (GFA) for protein complex identification. Adapted from a...
With the accelerating advancement of biomedical research, it has been widely accepted that genetic variation plays a critical role in the pathogenesis of human inherited diseases. As an important type of genetic variation, nonsynonymous single nucleotide polymorphisms (nsSNPs) that occur in protein coding regions lead to amino acid substitutions in proteins, affecting structures and functions of proteins,...
The combined use of gene expression profiles and protein-protein interaction (PPI) networks has recently shed light on breast cancer research by selecting a small number of subnetworks as disease markers and then using them for the classification of metastasis. Based on previously identified subnetwork markers, we compare three ensemble learning approaches (AdaBoost, LogitBoost and random forest)...
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