Accumulating evidences suggest that long non-coding RNAs (lncRNAs) perform important functions. Genome-wide chromatin-states area rich source of information about cellular state, yielding insights beyond what is typically obtained by transcriptome pr...
MOTIVATION: Systematically predicting gene (or protein) function based on molecular interaction networks has become an important tool in refining and enhancing the existing annotation catalogs, such as the Gene Ontology (GO) database. However, functi...
International journal of data mining and bioinformatics
Jan 1, 2015
The Gene Ontology (GO) has been used in estimating the semantic similarity of proteins since it has the largest and reliable vocabulary of gene products and characteristics. We developed a new method which can assess Protein-Protein Interactions (PPI...
International journal of data mining and bioinformatics
Jan 1, 2015
In order to analyse the similarity among microbial communities on functional state after assigning 16S rRNA sequences from all microbial communities to species. It's an important addition to the species-level relationship between two compared communi...
International journal of data mining and bioinformatics
Jan 1, 2015
Gene function prediction is an important problem in bioinformatics. Due to the inherent noise existing in the gene expression data, the attempt to improve the prediction accuracy resorting to new classification techniques is limited. With the emergen...
IEEE/ACM transactions on computational biology and bioinformatics
Jan 1, 2015
Identifying functionally similar or closely related genes and gene products has significant impacts on biological and clinical studies as well as drug discovery. In this paper, we propose an effective and practically useful method measuring both gene...
IEEE/ACM transactions on computational biology and bioinformatics
Jan 1, 2015
Because most complex genetic diseases are caused by defects of cell signaling, illuminating a signaling cascade is essential for understanding their mechanisms. We present three novel computational algorithms to reconstruct signaling networks between...
International journal of data mining and bioinformatics
Jan 1, 2015
The issue of ontology evolution and change management is inadequately addressed by available tools and algorithms, mostly due to the lack of suitable knowledge representation formalisms to deal with temporal abstract notations and the overreliance on...
Studies in health technology and informatics
Jan 1, 2015
Significant efforts have been undertaken for providing the Gene Ontology (GO) in a computable format as well as for enriching it with logical definitions. Automated approaches can thus be applied to GO for assisting its maintenance and for checking i...
Journal of computational biology : a journal of computational molecular cell biology
Jan 1, 2015
Liver cancer is one of the leading causes of cancer mortality worldwide. Hepatocellular carcinoma (HCC) is the main type of liver cancer. We applied a machine learning approach with maximum-relevance-minimum-redundancy (mRMR) algorithm followed by in...