BACKGROUND: NCBI's Gene Expression Omnibus (GEO) is a rich community resource containing millions of gene expression experiments from human, mouse, rat, and other model organisms. However, information about each experiment (metadata) is in the format...
BACKGROUND: In recent years, a rapidly increasing number of RNA transcripts has been generated by thousands of sequencing projects around the world, creating enormous volumes of transcript data to be analyzed. An important problem to be addressed whe...
BACKGROUND: One of the major challenges in the analysis of gene expression data is to identify local patterns composed of genes showing coherent expression across subsets of experimental conditions. Such patterns may provide an understanding of under...
BACKGROUND: The prediction of human gene-abnormal phenotype associations is a fundamental step toward the discovery of novel genes associated with human disorders, especially when no genes are known to be associated with a specific disease. In this c...
BACKGROUND: Although disease diagnosis has greatly benefited from next generation sequencing technologies, it is still difficult to make the right diagnosis purely based on sequencing technologies for many diseases with complex phenotypes and high ge...
BACKGROUND: Gene Ontology (GO) is a community effort to represent functional features of gene products. GO annotations (GOA) provide functional associations between GO terms and gene products. Due to resources limitation, only a small portion of anno...
IEEE/ACM transactions on computational biology and bioinformatics
Jun 15, 2017
A remaining key challenge of modern biology is annotating the functional roles of proteins. Various computational models have been proposed for this challenge. Most of them assume the annotations of annotated proteins are complete. But in fact, many ...
BACKGROUND: Complex diseases involve many genes, and these genes are often associated with several different illnesses. Disease similarity measurement can be based on shared genotype or phenotype. Quantifying relationships between genes can reveal pr...
Whereas genomes can be rapidly sequenced, the functions of many genes are incompletely or erroneously annotated because of a lack of experimental evidence or prior functional knowledge in sequence databases. To address this weakness, we describe here...
IEEE/ACM transactions on computational biology and bioinformatics
Apr 18, 2017
Sequence similarity is a commonly used measure to compare proteins. With the increasing use of ontologies, semantic (function) similarity is getting importance. The correlation between these measures has been applied in the evaluation of new semantic...