Shigeyuki OBA

Profile

Lecturer
at Integrated Systems Biology Laboratory (Ishii lab.) ,
Department of Systems Science,
Graduate School of Informatics,
Kyoto University, Japan.

e-mail: oba@sys.i.kyoto-u.ac.jp

Biography

Apr. 2008
Lecturer, at Kyoto University
Apr. 2003
Assistant Professor, at NAIST
Oct. 2002
Postdoctoral researcher, at NAIST
Sep. 2002
Ph. D(Engineering) in Information Science, Nara Institute of Science and Technology
Mar. 2001
Mastership of Science in Information Science, Nara Institute of Science and Technology
Mar. 1998
Mastership of Science in geophysics, Kyoto University
Mar. 1996
Bachelorship of Science in geophysics, Kyoto University

Research Interest

Machine Learning
- Multiple Simultaneous Hypothesis Testing
- Bayes inferences
  - Hierarchical models, Variational methods, Monte-Carlo methods
- Extracting hierarchical structures in data
High dimensional data analysis (feature extraction, clustering, regression and classification)
- Factor models (PCA, ICA, CCA, ...)
- kernel methods
Bioinformatics
- Gene expression data analysis
  - Gene selection within multiplicity of testing
  - Missing value estimation
  - Clustering, Feature extraction, Classification
  - Survival analysis
- Array comparative genomic analysis
  - Causality estimation

Original Software Page

Original softwares developed by Oba.

Publications

[Click here for complete list of publications including domestic papers]

Journal Papers

Yukinawa, N., Oba, S., Kato, K., and Ishii, S. (2007)
Optimal aggregation of binary classifiers for multi-class cancer prognosis.
IEEE Transactions of Computational Biology and Bioinformatics, (to appear).
Tomioka, N.*, Oba, S.*, Ohira, M.*, Misra, A., Fridlyland, J., Ishii, S., Nakamura, Y., Isogai, E., Hirata, T., Yoshida, Y., Todo, S., Kaneko, Y., Albertson, D. G., Pinkel, D., Feurstein, B. G., and Nakagawara, A.(2008)
Novel Risk Stratification of Patients with Neuroblastoma by Genomic Signature which is Independent of Molecular Signature.
Oncogene, 27, 441--449.
(published online 16 July 2007) (* equally contributed).
Tanabe, A., Fukumizu, K., Oba, S., Takenouchi, T., and Ishii, S. (2007)
Parameter Estimation for von Mises-Fisher Distributions.
Computational Statistics, 22, 145--157.
Oba, S., Tomioka, N., Ohira, M., & Ishii, S. (2006)
Combfit: A Normalization Method for Array CGH Data.
IPSJ Transactions on Bioinformatics, 47(17) (TBIO 1), 73--82.
Oba, S. & Ishii, S. (2006)
Semi-supervised discovery of differential genes.
BMC Bioinformatics, 7:414.
Yukinawa, N., Oba, S., Kato, K., Taniguchi, K., Iwao-Koizumi, K., Tamaki, Y., Noguchi, S., and Ishii, S. (2006)
A multi-class predictor based on a probabilistic model: Application to gene expression profiling-based diagnosis of thyroid tumors.
BMC Genomics, 7:190.
Motoori, M., Takemasa, I., Doki, Y., Saito, S., Miyata, H., Takiguchi, S., Fujiwara, Y., Yasuda, T., Yano, M., Kurokawa, Y., Komori, T., Yamasaki, M., Ueno, N., Oba, S., Ishii, S., Monden, M. and Kato, K.
Prediction of peritoneal metastasis in advanced gastric cancer by gene expression profiling of the primary site.
Eur. J. Cancer, 42(12), pp.1897-1903.
Motoori, M., Takemasa, I., Yano, M., Saito, S., Miyata, H., Takiguchi, S., Fujiwara, Y., Yasuda, T., Doki, Y., Kurokawa, Y., Ueno, N., Oba, S., Ishii, S., Monden, M., and Kato, K. (2005)
Prediction of recurrence in advanced gastric cancer patients after curative resection by gene expression profiling.
International Journal of Cancer. 114(6), pp.963-968.
Ohira, M., Oba, S., Nakamura, Y., Hirata, T., Ishii, S., and Nakagawara, A. (2005)
A review of DNA microarray analysis of human neuroblastomas.
Cancer Letters, 228 (1-2), pp. 5-11.
Ohira, M.*, Oba, S.*, Nakamura, Y., Isogai, E., Kaneko, S., Hirata, T., Kubo, H., Goto, T., Yamada, S., Yoshida, Y., Ishii, S.,and Nakagawara, A. (2005)
Expression profiling using a tumor-specific cDNA microarray predicts the prognosis of intermediate-risk neuroblastomas.
Cancer Cell, 7(4), pp.337-350. , (* equally contributed)
Kita-Matsuo, H., Yukinawa, N., Matoba, R., Saito, S., Oba, S., Ishii, S., and Kato, K. (2005)
Adaptor-tagged competitive polymerase chain reaction: amplification bias and quantified gene expression levels, Analytical Biochemistry, 339, pp.15-28.
Kurokawa, Y., Matoba, R., Takemasa, I., Nagano, H., Dono, K., Nakamori, S., Umeshita, K., Sakon, M., Ueno, N., Oba, S., Ishii, S., Kato, K., and Monden, M. (2004)
Molecular-based prediction of early recurrence in hepatocellular carcinoma.
Journal of Hepatology, 41,2, pp. 284-291.
Kurokawa, Y., Matoba, R., Takemasa, I., Nakamori, S., Tsujie, M., Nagano, H., Dono, K., Umeshita, K., Sakon, M., Ueno, N., Kita, H., Oba, S., Ishii, S., Kato, K., and Monden, M.(2003)
Molecular feature of non-B, non-C hepatocellular carcinoma: a PCR-array gene expression profiling study.
Journal of Hepatology, 39,6, pp.1004-1012.
Oba, S., Sato, M., Takemasa, I., Monden, M. Matsubara, K., and Ishii, S. (2003)
A Bayesian Missing value estimation method.
Bioinformatics, 19, pp.2088-2096. [application softwares for Java and for Matlab]
Muro, S.*, Takemasa, I.*, Oba, S.*, Matoba, R., Ueno, N., Maruyama, C., Yamashita, R., Sekimoto, M., Yamamoto, H., Nakamori, S., Monden, M., Ishii, S. and Kato, K. (2003)
Identification of expressed genes linked to malignancy of human colorectal carcinoma by parameteric clustering of quantitative expression data.
Genome Biology, 4, R21. (* equally contributed)
Oba, S., Sato, M. and Ishii, S. (2003)
On-line Learning Methods for Gaussian Prosesses.
IEICE transactions, E86-D(3), pp. 650-654.
Oba, S., Sato, M., Ishii, S. (2003)
Variational Bayes method for mixture of principal component analyzers.
Systems and Computers in Japan, 34(11), pp. 55-66.

Refereed Conference Proceedings

Oba, S., Kawanabe, M., Mueller, K-R., and Ishii, S.
Heterogeneous Component Analysis.
In proceedings of 21st annual conference on Neural Information Processing Systems (NIPS 2007)
Ishii, S., Yukinawa, N., Takenouchi, T., and Oba, S. (2007)
Combining multiple decisions: applications to bioinformatics.
In proceedings of the International Workshop on Statistical-Mechanical Informatics, pp. 151-161.
Oba, S. and Ishii, S. (2006)
Hierarchical Bayes Approach to Array CGH Data Normalization.
Genome Informatics Workshop (GIW2006), p. 94.
Yamamoto, K., Oba, S., & Ishii, S. (2006)
Considering False Negatives in Mixture Oncogenetic Trees Model for Chromosomal Alteration Data.
Genome Informatics Workshop (GIW2006), p. 134.
Oba, S., and Ishii, S. (2006)
Semi-supervised significance score of differential gene expressions.
In proceedings of International Conference on Artificial Neural Networks (ICANN '06), Lecture Notes in Computer Science, 4132, pp. 820-829.
Suzuki, I., Oba, S., and Ishii, S. (2005)
A selection criterion for robust classifiers: cancer prognosis with microarray gene expression.
Genome Informatics Workshop (GIW2005)
Oba, S., Yukinawa, N., Kato, K., and Ishii, S. (2005).
Multi-class pattern classification based on a probabilistic model combining binary classifiers,
International symposium on the art of statistical metaware at ISM.
Yukinawa, N., Oba, S., Kato, K., and Ishii, S.(2005)
Multi-class pattern classification based on a probabilistic model of combining binary classifiers.
In proceedings of International Conference on Artificial Neural Networks (ICANN 2005), Lecture Notes in Computer Science, 3697, pp.337-342.
Oba, S., Kato, K., & Ishii, S. (2005)
Multi-scale clustering for gene expression profiling data.
In proceedings of IEEE 5th Symposium on Bioinformatics and Bioengineering, pp.210-217.
Ogura, T., Oba, S., Hasegawa, F., Miyazawa, T.and Ishii, S. (2004).
Character string extraction from color documents using supervised learning., In proceedings of International Symposium on Nonlinear Theory and its Applications (NOLTA), pp. 701-704.
Yukinawa, N., Yoshimoto, J., Oba, S. and Ishii, S. (2004)
Modeling gene expression dynamics based on a linear dynamical system model.
International Symposium on Nonlinear Theory and its Applications (NOLTA), pp. 577-580.
Ohira M., Oba S., Nakamura Y., Isogai E., Kaneko S., Hirata T., Kubo H., Goto T., Yamada S., Yoshida Y., Ishii S. and Nakagawara A., (2004)
Molecular signature to predict the prognosis of neuroblastoma and its application to a diagnostic microarray of clinical use.
Advances in Neuroblastoma Research 2004, Luca Rotti award
Tomioka, N., Ohira, M., Oba, S., Misra, A., Nigro, J., Smirnov, I., Fridlyand, J., Todo, S., Pinkel, D., Albertson, D., Kaneko, Y., Goto, T., Ishii, S., Feuerstein, B.~G., Nakagawara, A. (2004)
Array comparative genomic hybridization (aCGH) defines genomic subgroups with a set of distinct aberrations which are strongly associated with the prognosis of patients with neuroblastoma,
Advances in Neuroblastoma Research 2004
Yukinawa, N., Yoshimoto, J., Oba, S. and Ishii, S. (2004)
System Identification of Cell-cycle-regulated Genes Based on a Linear Dynamical System Model,
Pacific Symposium on Biocomputing (PSB) 2004
Shimizu, H., Oba, S., Ishii, S. (2003)
Operon prediction by DNA microarray: an approach with a Bayesian network model.
Genome Informatics Workshop (GIW2003) , pp.310-311
Kawase, N., Oba, S., Ishii, S. (2003)
Significant test of clusters in gene expression profile data
Genome Informatics Workshop (GIW2003), pp.332-333
Oba, S., Ishii, S. and Sato, M. (2003)
Prior hyperparameters in Bayesian PCA.
In proceedings of Joint 13th International Conference on Artificial Neural Networks and 10th International Conference on Neural Information Processing (ICANN/ICONIP 2003), Lecture Notes in Computer Science, 2714, pp.271-279.
Oba, S., Sato, M., Takemasa, I., Monden, M., Matsubara, K., and Ishii, S. (2002)
Missing value estimation using mixture of PCAs.
In proceedings of International Conference on Artificial Neural Networks (ICANN2002), Lecture Notes in Computer Science, 2415, pp.492-497.
Sato, M., and Oba, S. (2002)
Incremental Sparse Kernel Machine.
In proceedings of International Conference on Artificial Neural Networks (ICANN2002), Lecture Notes in Computer Science, 2415, pp.700--706
Yoshioka, T., Morioka, R., Kobayashi, K., Oba, S., Ogasawara, N., and Ishii, S. (2002)
Clustering of gene expression data by mixture of PCA models.
In proceedings of International Conference on Artificial Neural Networks (ICANN 2002), Lecture Notes in Computer Science, 2415, pp.522-527.
Oba, S., Sato, M. and Ishii S.(2001)
On-line Learning Methods for Gaussian Prosesses.
In proceedings of International Conference on Artificial Neural Networks (ICANN2001), Lecture Notes in Computer Science, 2130, pp.292-299.
Oba, S., Sato M. and Ishii S. (2000)
Variational Bayes method for Mixture of Principal Component Analyzers.
In proceeding of 7th International Conference on Neural Information Processing (ICONIP2000), 2, pp.1416-1421.