Identifying essential genes in a given organism is important for research on their fundamental roles in organism survival. Furthermore, if possible, uncovering the links between core functions or pathways with these essential genes will further help us obtain deep insight into the key roles of these genes. In this study, we investigated the essential and non-essential genes reported in a previo...

Idiopathic pulmonary fibrosis (IPF) is the most common interstitial pneumonia and the most aggressive interstitial lung disease. Usually, IPF is confirmed by the histopathological pattern of typical interstitial pneumonia and requires an integrated multidisciplinary approach from pulmonologists, radiologists and pathologists. However, these diagnoses are performed at an advanced stage of IPF. A...

Availability of a large number of complete genomes enables us to compare several genomes and to search common and different features between genomes in terms of protein sequence similarities, which we call comparative genomics. It produces information about proteins useful for the assignment of the function to genes and for the research on the evolution of the genome. The large number of genes ...

Metabolic pathway databases such as KEGG contain information on thousands of enzymatic reactions drawn from the biomedical literature. Ensuring consistency of such large metabolic pathways is essential to their proper use. In this paper, we develop an efficient method to determine consistency of an important class of enzymatic reactions, and test the method on the latest release of the KEGG LIG...

Wallerian degeneration is a critical biological process that occurs in distal nerve stumps after nerve injury. To systematically investigate molecular changes underlying Wallerian degeneration, we used a rat sciatic nerve transection model to examine microarray analysis outcomes and investigate significantly involved Kyoto Enrichment of Genes and Genomes (KEGG) pathways in injured distal nerve ...

Giant freshwater prawn (GFP; Macrobrachium rosenbergii) is an exotic species that was introduced into China in 1976 and thereafter it became a major species in freshwater aquaculture. However the gene discovery in this species has been limited to small-scale data collection in China. We used the next generation sequencing technology for the experiment; the transcriptome was sequenced of samples...