Kyushu University Academic Staff Educational and Research Activities Database
List of Papers
Hiroto Saigo Last modified date:2018.08.01

Associate Professor / Department of Informatics / Faculty of Information Science and Electrical Engineering


Papers
1. Clarence White, Hamid D. Ismail, Hiroto Saigo, K. C. Dukka B., CNN-BLPred: a Convolutional neural network based predictor for β-Lactamases (BL) and their classes, BMC Bioinformatics 18(16): 221-232, 2017.12.
2. Ismail, H.D., Saigo, H., Bahadur, K.C.D., RF-NR: Random forest based approach for improved classification of Nuclear Receptors, IEEE Transactions on Computational Biology and Bioinformatics , 2017.11, The Nuclear Receptor (NR) superfamily plays an important role in key biological, developmental and physiological processes. Developing a method for the classification of NR proteins is an important step towards understanding the structure and functions of the newly discovered NR protein. The recent studies on NR classification are either unable to achieve optimum accuracy or are not designed for all the known NR subfamilies. In this study we developed RF-NR, which is a Random Forest based approach for improved classification of nuclear receptors. The RF-NR can predict whether a query protein sequence belongs to one of the eight NR subfamilies or it is a non-NR sequence. The RF-NR uses spectrum-like features namely: Amino Acid Composition, Di-peptide Composition and Tripeptide Composition. Benchmarking on two independent datasets with varying sequence redundancy reduction criteria, the RF-NR achieves better (or comparable) accuracy than other existing methods. The added advantage of our approach is that we can also obtain biological insights about the important features that are required to classify NR subfamilies..
3. Suryanto, C. H., Saigo, H., Fukui, K. , Protein Structure Comparison Based on 3D Molecular Visualization Images , 2017.01.
4. Saigo, H., Vert, J.-P., Ueda, N. and Akutsu, T., Protein homology detection using string alignment kernels, 20, 11, 1682-1689, 2004.01.
5. Ralaivola, L., Swamidass, J. S., Saigo, H. and Baldi, P., Graph Kernels for Chemical Informatics, 18, 8, 1093-1110, 2005.01.
6. Matsuda, S., Vert, J.-P., Saigo, H., Ueda, N., Toh, H. and Akutsu, T., A novel representation of protein sequences for prediction of subcellular location using support vector machines, 14, 2804-2813, 2005.01.
7. Cheng, J., Saigo, H. and Baldi, P., Large-scale prediction of disulphide bridges using kernel methods, two-dimensional recursive neural networks, and weighted graph matching,, 62, 3, 617-629, 2006.02.
8. Danziger, S. A., Swamidass, S. J., Zeng, J., Dearth, L. R., Lu, Q., Cheng, J. H., Cheng, J. L., Hoang, V. P., Saigo, H., Luo, R., Baldi, P., Brachmann, R. K. and Lathrop, R. H., Functional census of mutation sequence spaces: The example of p53 cancer rescue mutants, 3, 2, 114-125, 2006.04.
9. Saigo, H., Vert J.-P. and Akutsu, T., Optimizing amino acid substitution matrices with a local alignment kernel, 7, 246, 1-12, 2006.05.
10. Saigo, H., Uno, T. and Tsuda, K., Mining complex genotypic features for predicting HIV-1 drug resistance, 23, 18, 2455-2462, 2007.09.
11. Saigo, H., Nowozin, S., Kadowaki, T., Kudo, T., and Tsuda, K., gBoost: A mathematical programming approach to graph classification and regression, 75, 1, 69-89, 2009.04.
12. Saigo, H., Hattori, M., Kashima, H., and Tsuda, K., Reaction graph kernels that predict EC numbers of unknown enzymatic reactions in the secondary metabolism of plant, 11(supple 1), 1-7, 2010.10.
13. Saigo, H., Altmann, A., Bogojeska, J., Mueller, F., Nowozin, S., and Lengauer, T. , Learnig from past treatments and their outcome improves prediction of in vivo response t anti-HIV therapy , 10, 1, 2011.01.
14. Yamanishi, Y., Pauwels, E., Saigo, H., Stoven, V. , Extracting sets of chemical substructures and protein domains governing drug-target interactions , 51, 5, 1183-1194, 2011.05.
15. Kodama, K., Saigo, H., KDSNP: a Kernel-based approach to Detecting high-order genetic SNP interactions, 14, 5, 1644003, 2016.10.
16. Shao, Z., Hirayama, Y., Yamanishi, Y., Saigo, H., Mining discriminative patterns from graph data with multiple labels and its application to QSAR, 55, 12, 2519-2527, 2015.12.
17. Saigo, H., Kashima, H., Tsuda, K., Fast iterative mining using sparsity-inducing loss functions, 96-D, 8, 1766-1773, 2013.08.