Shu-Bo Zhang

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Quantifying the semantic similarities between pairs of terms in the Gene Ontology (GO) structure can help to explore the functional relationships between biological entities. A common approach to this problem is to measure the information they have in common based on the information content of their common ancestors. However, many studies have their(More)
Measuring the semantic similarity between pairs of terms in Gene Ontology (GO) can help to compare genes that can not be compared by other computational methods. In this study, we proposed a hybrid method to calculate the semantic similarity between two GO terms by taking into account multiple common ancestors of they have in common, and aggregating the(More)
Measuring the similarity between pairs of biological entities is important in molecular biology. The introduction of Gene Ontology (GO) provides us with a promising approach to quantifying the semantic similarity between two genes or gene products. This kind of similarity measure is closely associated with the GO terms annotated to biological entities under(More)
Phylogeny inference is an importance issue in computational biology. Some early approaches based on characteristics such as the maximum parsimony algorithm and the maximum likelihood algorithm will become intractable when the number of taxonomic units is large. Recent algorithms based on distance data which adopt an agglomerative scheme are widely used for(More)
Query expansion methods based on search logs could improve the quality of search results to some extends. But when the search logs are sparse, this kind of query expansion methods will have poor quality of search results and are unable to meet the user's search request, etc. This paper presents the search log sparseness oriented query extension method. By(More)
Predicting the location where a protein resides within a cell is important in cell biology. Computational approaches to this issue have attracted more and more attentions from the community of biomedicine. Among the protein features used to predict the subcellular localization of proteins, the feature derived from Gene Ontology (GO) has been shown to be(More)
Identifying protein-protein interactions is important in molecular biology. Experimental methods to this issue have their limitations, and computational approaches have attracted more and more attentions from the biological community. The semantic similarity derived from the Gene Ontology (GO) annotation has been regarded as one of the most powerful(More)
The estimation of the frequency of a complex exponential sinusoid that is corrupted by random noise is fundamental in the domain of signal processing, as it has a variety of application in many areas. In this study, we presented a frequency estimator in the frequency domain of a complex signal. The estimator is composed of two steps: a standard maximum bin(More)
Protein subcellular localization prediction is important to functional annotation of protein. In this study, a hybrid system based on the sorting mechanism of protein was proposed to predict protein subcellular localization. At first, an unknown protein sequence was divided into two sub-sequences at certain position, then features were extracted from them(More)
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