The accumulation of biological data has recently been accelerated by various high-throughput “omics” technologies such as genomics, transcriptomics, proteomics, and so on. The field of genome informatics is aimed at utilizing this data, or finding some principles behind the data, for understanding complex living systems by integrating the data with current biological knowledge using various computational techniques. In this laboratory we focus on developing computational methods and tools for comparative genome analysis, which is a useful approach for finding functional or evolutionary clues to interpreting the genomic information of various species. The current focus of our research is on the comparative analysis of microbial genomes, the number of which has been increasing rapidly. Extracting useful information from such a growing number of genomes is a major challenge in genomics research. Interestingly, many of the completed genomic sequences are closely related to each other. We are now trying to develop methods and tools to conduct comparative analyses not only of distantly related genomes but also of closely related genomes, since we can extract different types of information about biological functions and evolutionary processes from comparisons of genomes at different evolutionary distances.
Uchiyama, I. (2008). Multiple genome alignment for identifying the core structure among moderately related microbial genomes. BMC Genomics, 9, 515
Uchiyama, I., Higuchi, T., and Kobayashi, I. (2006). CGAT: a comparative genome analysis tool for visualizing alignments in the analysis of complex evolutionary changes between closely related genomes. BMC Bioinformatics 7, 472.
Uchiyama, I. (2006). Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes. Nucleic Acids Res. 34, 647-658.
Takami, H., Takaki, Y., Chee, G-J., Nishi, S., Shimamura, S., Suzuki, H., Matsui, S., and Uchiyama, I. (2004). Thermoadaptation trait revealed by the genome sequence of thermophilic Geobacilllus kaustophilus. Nucleic Acids Res. 32, 6292-6303.
Uchiyama, I. (2003). MBGD: Microbial genome database for comparative analysis. Nucleic Acids Res. 31, 58-62.