Yutaka Akiyama

Brief CV:

Yutaka Akiyama, Dr. Eng. Professor, Department of Computer Science, Graduate School of Information Science and Technology, Tokyo Institute of Technology (also Head, Department of Computer Science, School of Engineering, Tokyo Institute of Technology, 2008-2010) Address: W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8552, Japan Phone: +81-3-5734-3645 Fax: +81-3-5734-3646 E-mail: Date of Birth: 30 May 1961 (Tokyo, Japan) Nationality: Japanese

Concurrent positions

1) Visiting Professor, Tokyo Medical and Dental University
2) Visiting Researcher, IT-Bio Institute, Waseda University

Yutaka Akiyama is a professor at the Department of Computer Science, Graduate School of Information Science and Engineering, Tokyo Institute of Technology. From April 2008, he also serves as Head of Department of Computer Science, School of Engineering.
He is also a visiting professor at Tokyo Medical and Dental University, and visiting researcher at IT-Bio institute at Waseda University.
His research interest covers wide range of bioinformatics and computational biology, including DNA sequence mapping/assembly, gene regulatory network estimation, protein tertiary structure prediction, protein molecular dynamics, protein-protein docking, protein mass-spectrometry analysis, and clearance pathway prediction for drug compounds.
He received B.S.(1984), M.S.(1988), and Ph.D(1990) in Electrical Engineering from Keio University. His Ph.D thesis was about theoretical studies and VLSI implementation of a novel neural network model called “Gaussian Machines”. On that study, he received Best Paper Award for Young Researcher of IPSJ National Convention (1988). After his enthusiastic activity to initiate world’s earliest bioinformatics WWW services (1995) on GenomeNet Japan operated at Kyoto University, he started his own computational biology research group (1996) as a part of Real World Computing national project with using massively parallel computers and large-scale PC clusters. In 2001, he created CBRC (www.cbrc.jp), the biggest bioinformatics research center in Japan and became its first director. In CBRC, he leaded several research projects, as well as two kinds of 5-year bioinformatics training project supported by MEXT, Japan. He intended to promote “supercomputing-based bioinformatics” by introducing large-scale “Magi” PC cluster (2001), and Asian first IBM Blue Gene (2005).
On April 2007, he moved to Tokyo Institute of Technology, when he finished first 6-year period of CBRC.
He is the president of the non-profit-organization called Initiative for Parallel Bioinformatics (www.ipab.org), and a secretary of Japanese Society for Bioinformatics (JSBi). He has been serving as an advisory member of more than 25 national scientific projects.

Work Experience:

Education:

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Selected publications:

	Akira Nukada, Yuichiro Hourai, Akira Nishida, Yutaka Akiyama: “High Performance 3D Convolution for Protein Docking on IBM Blue Gene”, Proc. ISPA 2007, 958-969 (2007).
	Daisuke Tominaga, Fukumi Iguchi, Yutaka Akiyama, Katsuhisa Horimoto: “Development of automated image processing procedure for cell-arrays”, The 11th World Multi-Conference on Systemics, Cybernetics and Informatics Proceedings, Vol. 4, pp. 19-24, 2007.7.
	Nagano, N., Noguchi, T., and Akiyama, Y.: "Systematic Comparison of Catalytic Mechanisms of Hydrolysis and Transfer Reactions Classified in the EzCatDB Database", PROTEINS: Structure, Function, and Bioinformatics, 66, pp.147-159, (2007).
	Tsukamoto, K., Shimizu, H., Ishida, T., Akiyama, Y., and Nukina, N.: “Aggregation mechanism of polyglutamine diseases revealed using quantum chemical calculations, fragment molecular orbital calculations, molecular dynamics simulations, and binding free energy calculations”, Journal of Molecular Structure: THEOCHEM, 778 (1-3), 85-95 (2006).
	Tomii, K. and Akiyama, Y.; FORTE: a profile-profile comparison tool for protein fold recognition, Bioinformatics, 2004, 20, 594-595.
	Hourai, Y., Akutsu T., and Akiyama Y.: “Optimizing Substitution Matrices by Separating Score Distributions”, Bioinformatics,2004, 20, 863-873.
	Sekijima, M., Motono, C., Yamasaki, S., Kaneko, K., and Akiyama, Y.: “Molecular dynamics simulation of dimeric and monomeric forms of human prion protein: Insight into dynamics and properties”, Biophysical Journal, 2003, 85, 1176-1185.
	Noguchi, T., and Akiyama, Y.: “PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB)”, Nucleic Acids Research, 2003, 31, 1.
	Nakano, T., Kaminuma, T., Sato, T., Fukuzawa, K., Akiyama, Y., Uebayashi, M., and Kitaura, K.: “Fragment Molecular Orbital Method: use of approximate electrostatic potential”, Chemical Physics Letters, 2002, 351, 475-480