Publications

Tamura, Y., Harada, Y., Nishikawa, S., Yamano, K., Kamiya, M., Shiota, T., Kuroda, T., Kuge, O., Sesaki, H., Imai, K., Tomii, K., & Endo, T. Tam41 is a CDP-diacylglycerol synthase required for cardiolipin biosynthesis in mitochondria. Cell Metabolism 25 April (2013). [PubMed]

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. 32(3), 424-436 (2013). [PubMed]

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). [PubMed]

Tsuji, J., Frith, M.C., Tomii, K., & Horton, P. Mammalian NUMT insertion is non-random. Nucleic Acids Res. 40(18), 9073-9088 (2012). [PubMed]

Tomii, K., Sawada, Y., & Honda, S. Convergent evolution in structural elements of proteins investigated using cross profile analysis. BMC Bioinformatics 13, 11 (2012). [PubMed]

Ito, J., Tabei, Y., Shimizu, K., Tsuda, K., & Tomii, K. PoSSuM: a database of similar protein-ligand binding and putative pockets. Nucleic Acids Res. 40 Database issue, D541-D548 (2012). [PubMed]

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(3), 747-763 (2012). [PubMed]

Mukai, Y., Yoshizawa, M., Sasaki, T., Ikeda, M., Tomii, K., Hirokawa, T., & Suwa, M. Discrimination of Golgi type II membrane proteins based on their hydropathy profiles and the amino acid propensities of their transmembrane regions. Biosci. Biotechnol. Biochem. 75(1), 82-88 (2011). [PubMed]

Motono, C., Nakata, J., Koike, R., Shimizu, K., Shirota, M., Amemiya, T., Tomii, K., Nagano, N., Sakaya, N., Misoo, K., Sato, M., Kidera, A., Hiroaki, H., Shirai, T., Kinoshita, K., Noguchi, T., & Ota, M. SAHG, a comprehensive database of predicted structures of all human proteins. Nucleic Acids Res. 39 Database issue, D487-D493 (2011). [PubMed]

Ito, J., Sonobe, Y., Ikeda, K., Tomii, K., & Higo, J. Universal partitioning of the hierarchical fold network of 50-residue segments in proteins. BMC Structural Biology 9, 34 (2009). [PubMed]

Ikeda, K., Hirokawa, T., Higo, J., & Tomii, K. Protein-segement universe exhibiting transitions at intermediate segment length in conformational subspaces. BMC Structural Biology 8, 37 (2008). [PubMed]

Shimizu, K., Muraoka, Y., Hirose, S., Tomii, K., & Noguchi, T. Predicting mostly disordered proteins by using structure-unknown protein data. BMC Bioinformatics 8, 78 (2007). [PubMed]

Iwaya, N., Goda, N., Fujiwara, K., Tanaka, T., Tomii, K., Tochio, H., Shirakawa, M., & Hiroaki, H. Fine-tuning of protein domain boundary by minimizing potential coiled coil regions. J. Biomol. NMR 37(1), 53-63 (2007). [PubMed]

Mukai, Y., Hirokawa, T., Tomii, K., Asai, K., Akiyama, Y., & Suwa, M. Identification of glycosyltransferases focusing on golgi transmembrane region. Trends in Glycoscience and Glycotechnology 19(105), 41-47 (2007). [J-STAGE]

Tomii, K., Hirokawa, T., & Motono, C. Protein structure prediction using a variety of profile libraries and 3D verification. Proteins 61 Suppl. 7, 114-121 (2005). [PubMed]

Ikeda, K., Tomii, K., Yokomizo, T., Mitomo, D., Maruyama, K., Suzuki, S., & Higo, J. Visualization of conformational distribution of short to medium size segments in globular proteins and identification of local structural motifs. Protein Sci. 14, 1253-1265 (2005). [PubMed]

Suenaga, A., Takada, N., Hatakeyama, M., Ichikawa, M., Yu, X., Tomii, K., Okimoto, N., Futatsugi, N., Narumi, T., Shirouzu, M., Yokoyama, S., Konagaya, A., & Taiji, M. Novel mechanism of interaction of p85 subunit of phosphatidylinositol 3-kinase and ErbB3 receptor-derived phosphotyrosyl peptides. J. Biol. Chem. 280, 1321-1326 (2005). [PubMed]

Shiozawa, K., Maita, N., Tomii, K., Seto, A., Goda, N., Akiyama, Y., Shimizu, T., Shirakawa, M., & Hiroaki, H. Crystallographic characterization of the N-terminal domain of PEX1. Acta Crystallogr. D Biol. Crystallogr. 60, 2098-2099 (2004). [PubMed]

Shiozawa, K., Maita, N., Tomii, K., Seto, A., Goda, N., Akiyama, Y., Shimizu, T., Shirakawa, M., & Hiroaki, H. Structure of the N-terminal domain of PEX1 AAA-ATPase. Characterization of a putative adaptor-binding domain. J Biol. Chem. 279, 50060-50068 (2004). [PubMed]

Tomii, K., & Akiyama, Y. FORTE: a profile-profile comparison tool for protein fold recognition. Bioinformatics. 20, 594-595 (2004). [PubMed]

Tomii, K., & Kanehisa, M. A comparative analysis of ABC transporters in complete microbial genomes. Genome Res. 8, 1048-1059 (1998). [PubMed]

Tomii, K., & Kanehisa, M. Analysis of amino acid indices and mutation matrices for sequence comparison and structure prediction of proteins. Protein Eng. 9, 27-36 (1996). [PubMed]

Book Chapters

Imai, K., Hayat, S., Sakiyama, N., Fujita, N., Tomii, K., Elofsson, A., & Horton, P. Localization prediction and structure-based in silico analysis of bacterial proteins: with emphasis on outer membrane proteins. Methods in Molecular Biology 939, 115-140 (2013). [PubMed]

Kato, T., Tsuda, K., Tomii, K., & Asai, K. A New Variational Framework for Rigid-Body Alignment. In Fred, A., Caelli, T., Duin, R. P. W., Campilho, A., & Ridder, D. (eds), Structural, Syntactic and Statistical Pattern Recognition, Springer, pp. 171-179 (2004). [Springer]

Tomii, K. & Kanehisa, M. Systematic Detection of Protein Structural Motifs. In Wang, J. T. L., Shapiro, B. A., & Shasha, D. (eds), Pattern Discovery in Biomolecular Data: Tools, Techniques, and Applications, Oxford University Press, Chapter 6, pp. 97-110 (1999). [Bioinformatics Organization]

Tomii, K. & Kanehisa, M. Current status of pathway analysis. Tanpakushitsu Kakusan Koso. 42, 3026-3032 (1997). [Article in Japanese] [PubMed]

Invitations, Presentations

SocBiN – Bioinformatics 2012, Stockholm, Sweden, June 13, 2012. [SocBiN]

Asian Workshop for Protein Structure Prediction Methodology, Seoul, Korea, September 19, 2009. [workshop site]

International Symposium on Multi-Scale Dynamics of Protein Complex Formation and Function, Tokyo, Japan, July 14, 2009. [symposium site]

CASP6 – 6^th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction, Gaeta, Italy, December 4-8, 2004. [CASP6]

ISCBB – International Symposium on Computational Biology and Bioinformatics, Gyeongju, Korea, November 26, 2004. [ISCBB]