Major research fields
Bioinformatics, Computer, Tree-thinking
Recent molecular biology is characterized by the rapid accumulation of enormous amount of heterogeneous data associated with the development of experimental technologies. In other words, the era of “big data” has arrived for molecular biology, which has changed the style of investigation from hypothesis testing to hypothesis construction. Mining such massive and heterogeneous data to construct new hypotheses is regarded as an important step to carry investigations forward. Without computers, however, it is impossible to process such data. The field to apply computer sciences to molecular biology is called “bioinformatics” or “computational biology”.
We have investigated computational biology with two different approaches. One of our approaches is the extraction of novel biological knowledge from the data such as nucleotide sequences, amino acid sequences, protein tertiary structures, expression profiles and genome sequences. We have revealed evolutionary relationship and evolutionary mechanisms of various organisms such as retroelements and type A influenza viruses. We also predicted functions and/or functional sites of various biological materials such as cryptochromes and the enzymes involved in arachidonic acid cascades. The other approach is the development of new methods or computational software to extract biological knowledge from the data. We have developed tools for structural alignment, protein-protein interaction interaction prediction, and functional site prediction.
The students who are interested in bioinformatics or computational biology are welcome to join us.
Major relevant publications
- Toh, H., Hayashida, H., Miyata, T. Sequence homology between retroviral reverse transcriptase and putative polymerase of hepatitis B virus and cauliflower mosaic virus. Nature 305, 827-829 (1983)
- Toh, H., Kikuno, R., Hayashida, H., Miyata, T., Kugimiya, W., Inouye, S., Yuki, S., Saigo, K. Close structural resemblance between putative polymerase of a Drosophila transposable genetic element 17.6 and pol gene product of Moloney murine leukaemia virus. EMBO J. 4, 1267-1272 (1985)
- Toh, H. Introduction of a distance cut-off approximation into structural alignment by the double dynamic programming algorithm. CABIOS 13, 387-396 (1997)
- rudler, R. Hitomi, K. Daiyasu, H., Toh, H., Kucho, K., Ishiura, M., Kanehisa, M., Roberts, V.A., Todo, T., Tainer, J.A., Getzoff, E. G. Identification of a New Cryptochrome Class: Structure, Function, and Evolution. Molecular Cell 11, 59-67 (2003)
- Sato, T., Yamanishi, Y., Kanehisa, M., Toh, H. The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships. Bioinformatics 21, 3482-3489 (2005)