Shigeyuki OBA

Profile

Senior Lecturer Integrated Systems Biology Laboratory (Ishii lab.), Department of Systems Science, Graduate School of Informatics, Kyoto University, Japan. Researcher PRESTO, Japan Science and Technology Agency.

Biography

• Oct. 2008 - Mar. 2014
  Researcher, PRESTO, JST.
• Apr. 2008 -
  Senior Lecturer, at Kyoto University
• Apr. 2003- Mar. 2008
  Assistant Professor, at NAIST
• Oct. 2002- Mar. 2003
  Research Associate, 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

• High-dimensional Infromation Processing
  • Bioinformatics
    • Integrated modeling of heterogeneous datasets comming from multiple origins
    • Development of prognosis system of cancer malignancy
  • Statistical Data Mining
    • Multiple Simultaneous Hypothesis Testing on complex high-dimensional problems
    • Bayes inference of hierarchical models
    • Intrinsic factor extraction from high dimensional data

Softwares

Publications

Journal Papers

1. Nakae, K., Ikegaya, Y., Ishikawa, T., Oba, S., and Ishii, S.
   A predictive approach for identifying interactions in neuron-glia systems based on functional multicellular calcium imaging.
   Submitted.
2. Oba, S., Nakae, K., Ikegaya, Y., Aki, S., Yoshimoto, J., and Ishii, S.
   Empirical Bayesian significance measure of neuronal spike response.
   Submitted.
3. Kukita, Y., Uchida, J., Oba, S., Nishino, K., Kumagai, T., Taniguchi, K., Okuyama, T., Imamura, F., and Kato K.
   Quantitative identification of mutant alleles derived from lung cancer in plasma cell-free DNA via anomaly detection using deep sequencing data.
   PLoS ONE 8(11): e81468. doi:10.1371/journal.pone.0081468.
4. Kouno, M., Nakae, K., Oba, S., & Ishii, S. (2012)
   Microscopic image restoration based on tensor factorization of rotated patches.
   Artificial Life and Robotics, 17, 417-425.
5. Kim, W., Matsui, T., Yamao, M., Ishibashi, M., Tamada, K., Takumi, T., Kohno, K., Oba, S., Ishii, S., Sakumura, Y., and Bessho, Y. (2011)
   The period of the somite segmentation clock is sensitive to Notch activity.
   Molecular Biology of Cell, 22(18), 3541-3549.
6. Takahashi, N., Oba, S., Yukinawa, N., Ujita, S., Mizunuma, M., Matsuki, N., Ishii, S., and Ikegaya, Y. (2011)
   High-speed multineuron calcium imaging using Nipkow-type confocal microscopy.
   Current Protocols in Neuroscience, 2:Unit2.14.
7. Hotta, S., Oba, S., and Ishii, S. (2010)
   Visual attention model involving feature-based inhibition of return.
   Artificial Life and Robotics, 15(2), 129-132.
8. Oba, S. and Ishii, S. (2010)
   Differential gene detection incorporating common expression pattern.
   Journal of Physics, Conference Series, 197(012007), doi:10.1088/1742-6596/197/1/012007.
9. Oba, S. and Ishii, S. (2009)
   Optimal Sufficient Statistics for Parametric and Non-Parametric Multiple Simultaneous Hypothesis Testing.
   The International Journal of Biostatistics, 5, 1, Article 20.
   DOI: 10.2202/1557-4679.1163
10. Suzuki, I., Takenouchi, T., Ohira, M., Oba, S., and Ishii, S. (2009)
    Robust Model Selection for Classification of Microarrays.
    Cancer Informatics, 7, pp. 141-157.
11. M. Yu, M. Ohira, Y. Li, H. Niizuma, M. Oo, Y. Zhu, T. Ozaki, E. Isogai, Y. Nakamura, T. Koda, S. Oba, B. Yu, and A. Nakagawara. (2009)
    High expression of ncRAN, a novel non-coding RNA mapped to chromosome 17q25.1, is associated with poor prognosis in neuroblastoma.
    International Journal of Oncology, 34, pp. 931-938.
    DOI: 10.3892/ijo_00000219.
12. Shirahata, M., Oba, S., Iwao-Koizumi, K., Saito, S., Ueno, N., Oda, M., Hashimoto, M., Ishii, S, Takahashi, J. A. and Kato, K. (2009)
    Using gene expression profiling to identify a prognostic molecular spectrum in gliomas.
    Cancer Science, 100(1), 165-172.
    DOI 10.1111/j.1349-7006.2008.01002.x
13. 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, pp. 441-449.
    (published online 16 July 2007) (* equally contributed).
14. Yukinawa, N., Oba, S., Kato, K., and Ishii, S. (2009)
    Optimal aggregation of binary classifiers for multi-class cancer diagnosis using gene expression profiles.
    IEEE/ACM Transactions of Computational Biology and Bioinformatics, 6(2), pp. 333-343.
15. Yukinawa, N., Takenouchi, T., Oba, S. and Ishii, S (2007)
    Combining multiple decisions: applications to bioinformatics.
    Journal of Physics: Conference Series 95 012018 (13pp).
16. Tanabe, A., Fukumizu, K., Oba, S., Takenouchi, T., and Ishii, S. (2007)
    Parameter Estimation for von Mises-Fisher Distributions.
    Computational Statistics, 22, 145--157.
17. 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.
18. Oba, S. & Ishii, S. (2006)
    Semi-supervised discovery of differential genes.
    BMC Bioinformatics, 7:414.
19. 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.
20. Yukinawa, N., Yoshimoto, J., Oba, S.,and Ishii, S. (2005)
    System identification of gene expression time-series based on a linear dynamical system model with variational Bayesian estimation. IPSJ Transactions on Mathematical Modeling and Its Applications. 46(10), 57-65.
    
21. 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.
22. 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.
23. 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.
24. 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)
25. 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.
26. 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.
27. 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.
28. 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]
29. 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)
30. Oba, S., Sato, M. and Ishii, S. (2003)
    On-line Learning Methods for Gaussian Prosesses.
    IEICE transactions, E86-D(3), pp. 650-654.
31. 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

1. Kouno, M., Nakae, K., Oba, S., and Ishii, S. (2012)
   Microscopic image restoration based on tensor factorization of rotated patches. International Symosium on Artificial Life and Robotics, 902-905.
2. Aki, S., Oba, S., Nakae, K., and Ishii, S. (2012)
   A sparse random method to estimate neuronal structure from spike sequence. International Symosium on Artificial Life and Robotics, 718-721.
3. Kambara,S. and Oba, S. (2012)
   Density map of attentional capacity allocation. International Symposium on Artificial Life and Robotics, 710-713.
4. Harima, H., Oba, S., and Ishii, S. (2011)
   Multiple granger causality tests for network structure estimation from time-series data. International Symposium on Artificial Life and Robotics, GS14-4.
5. Hotta, S., Oba, S., and Ishii, S. (2010)
   Visual attention model involving feature based inhibition of return. International Symposium on Artificial Life and Robotics, 533-536.
6. Maeda, C., Oba, S., Yukinawa, N. and Ishii, S.(2008)
   Detection of multiple overlapping string-shaped objects using special clustering.
   International Symposium on Artificial Life and Robotics (AROB 13th '08), GS18-5.
7. Sodebayashi, K., Oba, S., and Ishii, S. (2008)
   Two-Way Factor Analysis for Missing Value Estimation of Matrix Data.
   International Symposium on Artificial Life and Robotics (AROB 13th '08), GS5-6.
8. Nomura, H., Oba, S., and Ishii, S. (2008)
   Re-weighted ODP for differential gene expression analysis.
   International Symposium on Artificial Life and Robotics (AROB 13th '08), GS5-2.
9. Furuya, M., Oba, S., and Ishii, S. (2008)
   Collaborative filtering based on a Weighted Maximum Margin Matrix Factorization.
   International Symposium on Artificial Life and Robotics (AROB 13th '08), GS14-5.
10. Oba, S., Kawanabe, M., Mueller, K-R., and Ishii, S.(2007)
    Heterogeneous Component Analysis.
    In proceedings of 21st annual conference on Neural Information Processing Systems (NIPS 2007)
11. 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.
12. Oba, S. and Ishii, S. (2006)
    Hierarchical Bayes Approach to Array CGH Data Normalization.
    Genome Informatics Workshop (GIW2006), p. 94.
13. 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.
14. 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.
15. Suzuki, I., Oba, S., and Ishii, S. (2005)
    A selection criterion for robust classifiers: cancer prognosis with microarray gene expression.
    Genome Informatics Workshop (GIW2005)
16. 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.
17. 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.
18. 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.
19. 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.
20. 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.
21. 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
22. 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
23. 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
24. 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
25. Kawase, N., Oba, S., Ishii, S. (2003)
    Significant test of clusters in gene expression profile data
    Genome Informatics Workshop (GIW2003), pp.332-333
26. 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.
27. 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.
28. 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
29. 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.
30. 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.
31. 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.