Kiyoshi Asai / Professor / Department of Computational Biology
Department of Computational Biology and Medical Sciences / / Bioinformatics

Career Summary
1983: Graduated/B.Eng., Faculty of Engineering, University of Tokyo
1985: Graduated/M.Eng., Graduate School of Engineering, University of Tokyo
1985-2001: Researcher, Electrotechnical Laboratory (ETL), AIST
2000-2006: Visiting Professor, Nara Institute of Science and Technology (NAIST)
2001-2003: Deputy Director, Computational Biology Research Center (CBRC), AIST
2003-present: Professor, University of Tokyo
2007-present: Director, Computational Biology Research Center (CBRC), AIST (concurrent)
Educational Activities
Graduate school: Genome Sequence Analysis
Faculty of Science: Sequence Analysis
Research Activities
Mathematical theories, especially with stochastic frameworks, and their applications to life science.
The GeneDecoder, a stochastic gene-finding software, and its application to genome analysis of Aspergillus oryzae (Koji). International collaboration on comparative genomics of A. oryzae, A. nidulans, and A. fumigatus (Literatures 1-3).
Algorithms for the analysis of RNA sequences based on their secondary structures: secondary structure predictions, structural alignments (, Literature 4).
Collaborations with experimental biologists in "the functional RNA project" (Literatures 5-6).
Functional RNA database (, Literature 7).
1) Machida, M., Asai, K. et al.: "Genome sequencing and analysis of Aspergillus oryzae," Nature 438, 1157-1161 (2005).
2) Nierman, W.C. et al.:"Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus," Nature 438, 1151-1156 (2005).
3) Galagan, J.E. et al.:"Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae," Nature 438, 1105-1115 (2005).
4) Asai, K. et al.:" web servers for analyses of RNA sequences," Nucleic Acids Res. Epub 2008 Apr 25.
5) Kawamura, Y. et al.:"Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells," Nature 453, 793-797 (2008).
6) Azuma-Mukai, A. et al.:"Characterization of endogenous human Argonautes and their miRNA partners in RNA silencing," PNAS 105, 7964-7969 (2008).
7) Kin, T. et al.:"fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences," Nucleic Acids Res. 35, D145-D148 (2007).
Other Activities
Project sub-leader in "the functional RNA project" of NEDO.
Member of Grant-in-Aid for Scientific Research on Priority Areas "Comparative Genomics."
Board member of Japanese Society for Bioinformatics (JSBi).
Member of Information Processing Society of Japan (IPSJ).
Member of International Society for Computational Biology (ISCB).
Future Plan
More emphasis on understanding of biology from an information science viewpoint than on developing useful software tools.
Messages to Students
Computational biology is a research field for understanding and modeling living systems through information science.