BACKGROUND: High-throughput sequencing has made it theoretically possible to obtain high-quality de novo assembled genome sequences but in practice DNA extracts are often contaminated with sequences from other organisms. Currently, there are few exis...
IEEE/ACM transactions on computational biology and bioinformatics
Nov 22, 2017
MicroRNAs (miRNAs) play critical roles in regulating gene expression at post-transcriptional levels. Numerous experimental studies indicate that alterations and dysregulations in miRNAs are associated with important complex diseases, especially cance...
IEEE/ACM transactions on computational biology and bioinformatics
Nov 9, 2017
Gene Regulatory Network (GRN) is a virtual network in a cellular context of an organism, comprising a set of genes and their internal relationships to regulate protein production rate (gene expression level) of each other through coded proteins. Comp...
Next generation sequencing technologies used in metagenomics yield numerous sequencing fragments which come from thousands of different species. Accurately identifying genes from metagenomics fragments is one of the most fundamental issues in metagen...
IEEE/ACM transactions on computational biology and bioinformatics
Nov 7, 2017
Disease gene prediction is a challenging task that has a variety of applications such as early diagnosis and drug development. The existing machine learning methods suffer from the imbalanced sample issue because the number of known disease genes (po...
IEEE/ACM transactions on computational biology and bioinformatics
Nov 3, 2017
Pathway similarity search plays a vital role in the post-genomics era. Unfortunately, pathway similarity search involves the graph isomorphism problem which is NP-complete. Therefore, efficient search algorithms are desirable. In this work, we propos...
IEEE/ACM transactions on computational biology and bioinformatics
Oct 30, 2017
In gene expression data analysis, the problems of cancer classification and gene selection are closely related. Successfully selecting informative genes will significantly improve the classification performance. To identify informative genes from a l...
It has been acknowledged that source databases recording experimentally supported human protein-protein interactions (PPIs) exhibit limited overlap. Thus, the reconstruction of a comprehensive PPI network requires appropriate integration of multiple ...
Concurrent exposure to a wide variety of xenobiotics and their combined toxic effects can play a pivotal role in health and disease, yet are largely unexplored. Investigating the totality of these exposures, i.e., the "exposome", and their specific b...
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...
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