Cellular Systems Analysis Team

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
Kentaro Tomii
Key Words

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

Sachiyo Aburatani
Senior Research Scientist
Key Words

Gene Expression Analysis, Covariance Structure Analysis, Network Inference

Kazunori Yamada
Research Staff
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).
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