RNA Informatics Team

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Research Topics

The aim of RNA Informatics Team is to build a data analysis infrastructure for transcriptome and epigenome.

Modern bio-industry has long been seeing the age of mass data analysis. Thusly, we have to meet the requirement of the industry to develop data analysis infrastructure for efficient knowledge discovery from the mass data. Such the infrastructure includes a sequence mapping tool, a RNA secondary structure prediction tool, a database that integrates raw data and their derived results, a genome browser and a bioinformatics workbench that help searching, browsing, and reusing data from a database. In order to realize the aim, we are currently committing the following research themes: Development of RNA data analysis tools[1, 2, 3], Development of fast sequence data analysis tools[4], Development of the Functional RNA database [5], and Development of an epigenome database.


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Team Member

Toutai Mituyama
Leader E-mail
Toutai Mituyama
Key Words

database, microarray, noncoding, microRNA, giga sequencer


Kazutaka Katoh
Invited Senior
Research Scientist
E-mail
Key Words

Sequence alignment, Molecular evolution, Molecular phylogenetic analysis

Kana Shimizu
Senior Research Scientist
E-mail
Key Words

sequence analysis, algorithm, giga-sequencer, protein intrinsic disorder

Yutaka Saito
AIST
Research Staff
E-mail
Key Words

Epigenetics, Functional RNA, Noncoding RNA, Sequence analysis, Kernel methods


Papers List

  • Hamada, M., Yamada, K., Sato, K., Frith, M., Asai, K., "CentroidHomfold-LAST: accurate prediction of RNA secondary structure using automatically collected homologous sequences", Nucleic Acids Res. Vol. 39 Web Server issue, W100-W106, (2011).
  • Terai, G., Mituyama, T., Asai, K., "Prediction of conserved miRNA precursors and their mature forms by integrating positionspecific structural features, Aural presentation", The 16th Annual Meeting of The RNA Society and The RNA Society of Japan 13th, (2011).
  • "Searching for Structural RNA Motifs by Using the Energy Model of Secondary Structures", Aural presentation, The 16th Annual Meeting of The RNA Society and The RNA Society of Japan 13th, (2011).
  • Shimizu, K., "Fast and exact algorithm for Next Generation Sequencing data analysis", Aural presentation, ISMB/ECCB, (2011).
  • Mituyama, T., "An identification of secondary structure conserved elements in mammalian syntenic regions", Aural presentation, IEEE International Conference on Systems Biology, (2011).
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