Ishida laboratory
  • Publications

Publication list

論文誌

    2014年
  1. Suzuki S, Kakuta M, Ishida T, Akiyama Y., "Faster sequence homology searches by clustering subsequences.", Bioinformatics, pii: btu780. [Epub ahead of print]
  2. Matsuoka, S., Sato, H., Tatebe, O., Koibuchi, M., Fujiwara, I., Suzuki, S., Kakuta, M., Ishida, T., Akiyama, Y., Suzumura, T., Ueno, K., Kanezashi, H. and Miyoshi, T. “Extreme Big Data (EBD): Next Generation Big Data Infrastructure Technologies Towards Yottabyte/Year”, Supercomputing frontiers and innovations, 1(2), 89-107, 2014
  3. Suzuki, S., Ishida, T. and Akiyama, Y. “GHOSTX: An improved sequence homology search　algorithm using a query suffix array and a database suffix array”, PLoS ONE, 6;9(8):e103833, 2014
  4. Ohue, M., Shimoda, T., Suzuki, S., Matsuzaki, Y., Ishida, T. and Akiyama, Y. “MEGADOCK 4.0: an ultra–high-performance protein–protein docking software for heterogeneous supercomputers”, Bioinformatics, 30(22):3281-3, 2014
  5. You, H., Kim, G.E., Na, C.H., Lee, S., Lee, C.J., Cho, K.H., Akiyama, Y., Ishida, T. and No, K.T. “An empirical model for gas phase acidity and basicity estimation”, SAR QSAR Environ Res., 25, 91-115, 2014
  6. Ohue, M., Matsuzaki, Y., Uchikoga, N., Ishida, T. and Akiyama, Y. “MEGADOCK: An all-to-all protein-protein interaction prediction system using tertiary structure data”, Protein and Peptide Letters, 21, 766-778, 2014

    7. 2013年
  7. Matsuzaki, Y., Uchikoga, N., Ohue, M., Shimoda, T., Sato, T., Ishida, T. and Akiyama, Y. “MEGADOCK 3.0: A high-performance protein-protein interaction prediction software using hybrid parallel computing for petascale supercomputing environments”, Source Code for Biology and Medicine, 8, 18, 2013
  8. Namiki, Y.*, Ishida, T.* and Akiyama, Y. “Acceleration of sequence clustering using longest common subsequence filtering”, BMC bioinformatics, 14, S7, 2013 (*These authors equally contributed to this work.)
  9. Ren, A., Ishida, T. and Akiyama, Y. “Assessing statistical reliability of phylogenetic trees via a speedy double bootstrap method”, Mol Phylogenet Evol, 67, 429–435, 2013
  10. Ohue, M., Matsuzaki, Y., Ishida, T. and Akiyama, Y. “Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods”, BMC Proceedings, 7, S6, 2013

    11. 2012年
  11. Oates, M.E., Romero, P., Ishida, T., Ghalwash, M., Mizianty, M., Dosztányi, Z., Uversky, V.N., Obradovic, Z., Kurgan, L., Dunker, A.K. and Gough, J. “D2P2: database of disordered protein predictions”, Nucleic Acids Res, 41, D508-D516, 2012
  12. Suzuki, S., Ishida, T., Kurokawa, K., and Akiyama, Y. “GHOSTM: A GPU-Accelerated Homology Search Tool for Metagenomics”, PLoS ONE, 7, e36060, 2012

    13. 2011年
  13. Fleishman, S., Whitehead, T., Strauch, E.M., Corn, J.E., Qin, S., Zhou, H.X., Mitchell, J.C., Demerdash, O.N.A., Takeda-Shitaka, M., Terashi, G., Moal, I.H., Li, X., Bates, P.A., Zacharias, M., Park, H., Ko, J.S., Lee, H., Seok, C., Bourquard, T., Bernauer, J., Poupon, A., Aze, J., Soner, S., Ovali, S. K., Ozbek, P., Tal, N. B., Haliloglu, T., Hwang, H., Vreven, T., Pierce, B.G., Weng, Z., Perez-Cano, L., Pons, C., Fernandez-Recio, J., Jiang, F., Yang, F., Gong, X., Cao, L., Xu, X., Liu, B., Wang, P., Li, C., Wang, C., Robert, C.H., Guharoy, M., Liu, S., Huang, Y., Li, L., Guo, D., Chen, Y., Xiao, Y., London, N., Itzhaki, Z., Schueler-Furman, O., Inbar, Y., Patapov, V., Cohen, M., Schreiber, G., Tsuchiya, Y., Kanamori, E., Standley, D.M., Nakamura, H., Kinoshita, K., Driggers, C.M., Hall, R.G., Morgan, J.L., Hsu, V.L., Zhan, J., Yang, Y., Zhou, Y., Kastritis, P.L., Bonvin, A.M.J.J., Zhang, W., Camacho, C.J., Kilambi, K.P., Sircar, A., Gray, J.J., Ohue, M., Uchikoga, N., Matsuzaki, Y., Ishida, T., Akiyama, A., Khashan, R., Bush, S., Fouches, D., Tropsha, A., Esquivel-Rodriguez, J., Kihara, D., Stranges, P.B., Jacak, R., Kuhlman, B., Huang, S.Y., Zou, X., Wodak, S.J., Janin, J. and Baker, D. “Community-wide assessment of protein-interface modeling suggests improvements to design methodology”, J Mol Biol, 414, 289-302, 2011
  14. Kusuma, W.A., Ishida, T. and Akiyama, Y., “Combined Approach for de novo DNA Sequence Assembly of Very Short Reads”, IPSJ Transactions on Bioinformatics (TBIO), 4, 21-33, 2011
  15. Shirota, M., Ishida, T. and Kinoshita, K., “Absolute quality evaluation of protein model structures using statistical potentials with respect to the native and reference states”, Proteins, 79, 1550-1563, 2011

    16. 2010年以前
  16. Shirota, M., Ishida, T. and Kinoshita, K., “Development of a new meta-score for protein structure prediction from seven all-atom distance dependent potentials using support vector regression”, Genome Inform, 23, 149-158, 2009
  17. Higurashi, M.*, Ishida, T.* and Kinoshita, K., “PiSite: a database of protein interaction sites using multiple binding states in the PDB”, Nucleic Acids Res, 37, D360-364, 2009. (*These authors equally contributed to this work.)
  18. Shirota, M., Ishida, T. and Kinoshita, K., “Analyses on hydrophobicity and attractiveness of all-atom distance-dependent potentials”, Protein Sci, 18, 1906-1915, 2009
  19. Shirota, M., Ishida, T. and Kinoshita, K., “Effects of surface-to-volume ratio of proteins on hydrophilic residues: decrease in occurrence and increase in buried fraction”, Protein Sci, 17, 1596-1602, 2008
  20. Ishida, T. and Kinoshita, K., “Prediction of disordered regions in proteins based on the meta approach”, Bioinformatics, 24, 1344-1348, 2008
  21. Higurashi, M., Ishida, T. and Kinoshita, K., “Identification of transient hub proteins and the possible structural basis for their multiple interactions”, Protein Sci, 17, 72-78, 2008
  22. Tsukamoto, K., Shimizu, H., Ishida, T., Akiyama, Y. and Nukina, N., “Evaluation for interaction energy between glutamine and various chemical compounds for developing the virtual screening system using DFT quantum chemical calculations”, WSEAS TRANSACTIONS ON COMPUTERS, 6, 636-641, 2007
  23. Ishida, T. and Kinoshita, K., “PrDOS: prediction of disordered protein regions from amino acid sequence”, Nucleic Acids Res, 35, W460-464, 2007
  24. 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, 85-95, 2006
  25. Ishida, T., Nakamura, S. and Shimizu, K., “Potential for assessing quality of protein structure based on contact number prediction”, Proteins, 64, 940-947, 2006
  26. Ishida, T., Nishimura, T., Nozaki, M., Inoue, T., Terada, T., Nakamura, S. and Shimizu, K., “Development of an ab initio protein structure prediction system ABLE”, Genome Inform, 14, 228-237, 2003


国際会議発表（査読付き）

    2014年
  1. Komatsu, Y., Ishida, T. and Akiyama, Y. “Metagenomic Phylogenetic Classification Using Improved Naïve Bayes”, Emerging Intelligent Computing Technology and Applications - 10th International Conference ICIC 2014, Aug. 2014
  2. Ban, T., Ishida, T. and Akiyama, Y. “Improvement of a conformational search on protein-ligand docking based on optimal arrangement of multiple small search grids”, The 2014 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'14), 176-181, Jul. 2014

    3. 2013年
  3. Shimoda, T., Ishida, T., Suzuki, S., Ohue, M. and Akiyama, Y. “MEGADOCK-GPU: Acceleration of Protein-Protein Docking Calculation on GPUs”, Proc. of 2nd International Workshop on Parallel and Cloud-based Bioinformatics and Biomedicine (ParBio2013), 884-890, Sep. 2013
  4. Obata, Y., Ishida, T., Natsume, T. and Akiyama, Y. “Acceleration of tandem mass spectrometry analysis software CoCoozo using multi-core CPUs and graphics processing units”, The 2013 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'13), 149-154, Jul. 2013
  5. Ren, A., Ishida, T. and Akiyama, Y. “SDBP: An easy-to-use R program package for assessing reliability of estimated phylogenetic trees based on the speedy double bootstrap method”, The 2013 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'13), 143-148, Jul. 2013
  6. Ohue, M., Matsuzaki, Y., Shimoda, T., Ishida, T. and Akiyama, Y. “Highly Precise Protein-Protein Interaction Prediction Based on Consensus Between Template-Based and de Novo Docking Methods”, The 8th Great Lakes Bioinformatics Conference (GLBIO 2013), 100-109, May 2013

    7. 2012年
  7. Ohue, M., Matsuzaki, Y., Ishida, T. and Akiyama, Y. “Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: an Application to Interaction Pathway Analysis”, The 7th IAPR International Conference on Pattern Recognition in Bioinformatics (PRIB 2012), Lecture Note in Bioinformatics 7632, 178-187, Nov. 2012
  8. Suzuki, S., Ishida, T. and Akiyama, Y. “An Ultra-Fast Computing Pipeline for Metagenome Analysis with Next-Generation DNA Sequencers”, Proceedings of the 2012 SC Companion: High Performance Computing, Networking, Storage and Analysis, 1549-1550, Nov. 2012
  9. Namiki, Y., Ishida, T. and Akiyama, Y. “Fast DNA Sequence Clustering Based on Longest Common Subsequence”, Emerging Intelligent Computing Technology and Applications - 8th International Conference ICIC 2012, Proceedings. Communications in Computer and Information Science 304, 453-460, Jul. 2012