Kaname Kojima

Kaname Kojima Ph. D.

Assistant Professor

Division of Biomedical Information Analysis,Department of Integrative Genomics,
Tohoku Medical Megabank Organization, Tohoku University

Address: 8F #West, IDAC Research Building, Tohoku University,
4-1 Seiryo-machi, Aoba-ku, Sendai-shi, Miyagi 980-8575, JAPAN
Phone & Fax: +81-22-273-6051
E-mail: kojima [at] megabank [dot] tohoku [dot] ac [dot] jp

Research Interests

Machine Learning, Artificial Intelligence, Genome Data Analysis

Educational Background

2011 Doctor of Information Science and Technology (Computer Science), University of Tokyo
2008 Master of Information Science and Technology (Computer Science), University of Tokyo
2005 Bachelor of Engineering (Computer Science), Tokyo Institute of Technology


Journal papers and refereed proceedings (peer reviewed)

15. Kojima, K., Nariai, N., Mimori, T., Takahashi, M., Yamaguchi-Kabata, Y., Sato, Y. Nagasaki, M.:
A statistical variant calling approach from pedigree information and local haplotyping with phase informative reads,
Bioinformatics, 29 (22), 2835-2843

14. Fujita, A., Severino, P., Kojima, K., Sato, J.R., Patriota, A.G., Miyano, S.: Functional clustering of time series gene expression data by Granger causality, BMC Systems Biology, 6:137, 2012.

13. Kojima, K., Imoto, S., Yamaguchi, R., Fujita, A., Yamauchi, M., Gotoh, N., Miyano, S.: Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing, BMC Genomics, 13(Suppl 1):S6, 2012. (Special Issue of The 10th Asia-Pacific Bioinformatics Conference)

12. Imoto, S., Kojima, K., Perrier, E., Tamada, Y., Miyano, S.: Searching optimal Bayesian network structure on constraint search space: super-structure approach, Lecture Notes in Computer Science, Sprigner-Verlag, 6797, 210-218, 2010. (Special Issue of International Workshop on Advanced Methodologies for Bayesian Networks)

11. Higashigaki, T.*, Kojima, K.*, Yamaguchi, R., Inoue, M., Imoto, S, Miyano, S.: Identifying Hidden Confounders in Gene Networks by Bayesian Networks, Proceedings of 10th International Conference on Bioinformatics and Bioengineering, 168-173, 2010 (*equal contributors).

10. Kojima, K., Perrier, E., Imoto, S., Miyano, S.: Optimal search on clustered structural constraint for learning Bayesian network structure, Journal of Machine Learning Research, 11:285-310, 2010.

9. Fujita, A., Sato, J.R., Kojima, K., Gomes, L.R., Nagasaki, M., Sogayar, M.C., Miyano, S.: Identification of Granger causality between gene sets, Journal of Bioinformatics and Computational Biology, 8(4): 679-701, 2010.

8. Kojima, K., Nagasaki, M., Miyano, S.: An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information, BMC Bioinformatics, 11:335, 2010.

7. Kojima, K., Imoto, S., Nagasaki, M., Miyano, S.: Gene network clustering for graph layout based on microarray gene expression data, Genome Informatics, 24: 84-95, 2010. (Special Issue of The 10th Annual International Workshop on Bioinformatics and Systems Biology)

6. Kojima, K., Yamaguchi, R., Imoto, S., Yamauchi, M., Nagasaki, M., Yoshida, R., Shimamura, T., Ueno, K., Higuchi, T., Gotoh, N., Miyano, S.: A state space representation of VAR models with sparse learning for dynamic gene networks, Genome Informatics, 22: 56-68, 2009. (Special Issue of The 9th Annual International Workshop on Bioinformatics and Systems Biology)

5. Hashimoto, T.B., Nagasaki, M., Kojima, K., Miyano, S.: BFL: a node and edge betweenness based fast layout algorithm for large scale networks, BMC Bioinformatics, 10:19, 2009.

4. Kojima, K., Fujita, A., Shimamura, T., Imoto, S., Miyano, S.: Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data, Genome Informatics, 20: 37-51, 2008. (Special Issue of The 8th Annual International Workshop on Bioinformatics and Systems Biology)

3. Kojima, K., Nagasaki, M., Miyano, S.: Fast grid layout algorithm for biological networks with sweep calculation, Bioinformatics, 24(12): 1426-1432, 2008.

2. Kojima, K., Nagasaki, M., Jeong, E., Kato, M., Miyano, S.: An efficient grid layout algorithm for biological networks utilizing various biological attributes, BMC Bioinformatics, 8:76, 2007.

1. Iwano,K., Kojima, K., Furui, S.: A weight estimation method using LDA for multi-band speech recognition, INTERSPEECH(ICSLP), 2534-2537, 2006.