Computational Biology Research Center[CBRC]

Research Topics

■ Network inference by Structural Equation Modeling
■ Revealing the mechanism of specified odor substance from enzyme activity
■ Pathway analysis for bio-fuel biosynthesis in microalgae
■ Development of distance metric learning algorithms for ranking gene expression data.
■ Machine learning approaches to the study of drug-induced liver injuries.

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Team Member

Kentaro Tomii

Leader E-mail

website

Key Words

protein structure prediction, profile-profile alignment, FORTE, sequence alignment

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Sachiyo Aburatani

Senior Research Scientist

website

E-mail

Key Words

Gene Expression Analysis, Covariance Structure Analysis, Network Inference

Kazunori Yamada

AIST
Research Staff

website

E-mail

Key Words

Protein structure prediction, In silico drug discovery, Interactome analysis

Papers List

• ■ Nishino, T., Rago, F., Hori, T., Tomii, K., Cheeseman, I.M., Fukagawa, T. : "CENP-T provides a structural platform for outer kinetochore assembly", EMBO J., advance online publication 18 January 2013.
• ■ Kimura, M., Kose, S., Okumura, N., Imai, K., Furuta, M., Sakiyama, N., Tomii, K., Horton, P., Takao, T., Imamoto N. : " Identification of cargo proteins specific for the nucleocytoplasmic transport carrier transportin by combination of an in vitro transport system and SILAC-based quantitative proteomics", Mol. Cell Proteomics, 12, (1), 145-157 (2013).
• ■ Tsuji, J., Frith, M., Tomii, K., Horton, P. : "Mammalian NUMT insertion is non-random", Nucleic Acid Res. 40,(18), 9073-9088 (2012).
• ■Tomii, K., Sawada, Y., Honda, S.: "Convergent evolution in structural elements of proteins investigated using cross profile analysis", BMC Bioinformatics, 13,11 (2012).
• ■Itsuki, A., Aburatani, S., Kanazawa: "Numbers and Biomass of Bacteria and Fungi Obtained by the Dilution Plate Count and Direct Microscopic Count Methods", S. J. Agric. Sci. and Tech. (accepted).
• ■ Ito, J., Tabei, Y., Shimizu, K., Tsuda, K., Tomii, K. : "PoSSuM: a database of similar protein-ligand binding and putative pockets", Nucleic Acid Res., 40, D541-D548 (2012).
• ■Ito, J., Tabei, Y., Shimizu, K., Tomii,K., Tsuda, K.: "PDB-scale analysis of known and putative ligand-binding sites with structural sketches.", Proteins, 80, pp.747-763 (2012).
• ■Aburatani, S.: "Application of Structure Equation Modeling for inferring a serial transcriptional regulation in yeast", Gene Regulation and Systems Biology., 2011-5. pp.75-88 (2011).
• ■ Hatano, A., Chiba, H., Moesa, H.A., Taniguchi, T., Nagaie, S., Yamanegi, K., Takai-Igarashi, T., Tanaka, H., Fujibuchi, W.: "CELLPEDIA: a repository for human cell information for cell studies and differentiation analyses", Database (Oxford)., 2011 Oct 29;2011:bar046 (2011).
• ■ Aburatani, S.: "Development of network inference among LexA/RecA-dependent manner genes in SOS response", Journal of Nucleic Acids Investigation., 1(1), pp.71-75 (2010).