BACKGROUND: Gene Ontology (GO) is one of the most popular bioinformatics resources. In the past decade, Gene Ontology-based gene semantic similarity has been effectively used to model gene-to-gene interactions in multiple research areas. However, mos...
BACKGROUND: Rheumatism represents any disease condition marked with inflammation and pain in the joints, muscles, or connective tissues. Many traditional Chinese drugs have been used for a long time to treat rheumatism. However, a comprehensive infor...
BACKGROUND: Breast cancer is one of the leading causes of deaths for women. It is of great necessity to develop effective methods for breast cancer detection and diagnosis. Recent studies have focused on gene-based signatures for outcome predictions....
BACKGROUND: Positive semi-definiteness is a critical property in kernel methods for Support Vector Machine (SVM) by which efficient solutions can be guaranteed through convex quadratic programming. However, a lot of similarity functions in applicatio...
BACKGROUND: Translating in vitro results to clinical tests is a major challenge in systems biology. Here we present a new Multi-Task learning framework which integrates thousands of cell line expression experiments to reconstruct drug specific respon...
BACKGROUND: The human phenome has been widely used with a variety of genomic data sources in the inference of disease genes. However, most existing methods thus far derive phenotype similarity based on the analysis of biomedical databases by using th...
BACKGROUND: High-throughput experimental techniques have been dramatically improved and widely applied in the past decades. However, biological interpretation of the high-throughput experimental results, such as differential expression gene sets deri...
BACKGROUND: Active module, defined as an area in biological network that shows striking changes in molecular activity or phenotypic signatures, is important to reveal dynamic and process-specific information that is correlated with cellular or diseas...
BACKGROUND: Measures of gene functional similarity are essential tools for gene clustering, gene function prediction, evaluation of protein-protein interaction, disease gene prioritization and other applications. In recent years, many gene functional...
BACKGROUND: Protein-protein interactions (PPIs) are essential to most biological processes. Since bioscience has entered into the era of genome and proteome, there is a growing demand for the knowledge about PPI network. High-throughput biological te...