Ryo YOSHIDA
Associate Professor, Spatial and Time Series Modeling Group, Department of Statistical Modeling; Data Assimilation Research Group, Prediction and Knowledge Research Center
Phone: +81-(0)50-5533-8500
E-mail: yoshidar
Personal
Homepage:		 http://daweb.ism.ac.jp/~yoshidar/
Date of Birth: October 1975
Education: Bachelor of Economics, Dept. of Economics, Kyoto Sangyo Univ, 1999.
Master of Economics, Dept. of Economics, Kyoto Sangyo Univ, 2001.
Doctor of Philosophy in Statistical Science, Dept. of Statistical Science, The Graduate University for Advanced Studies, 2004.
Degree: Doctor of Philosophy in Statistical Science, The Graduate University for Advanced Studies, 2003, Title of doctoral thesis: Mixture Models in Bayesian Computation and Mixed Factors Analysis.
Employment: October 2004 - March 2005 Research Fellow, Research Organization of Information and Systems, The Institute of Statistical Mathematics
April 2005 - July 2005 Research Fellow, Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo
August 2005 - March 2007 Assistant Professor, Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo
April 2007 Assistant Professor, Department of Statistical Modeling; Prediction and Knowledge Research Center, The Institute of Statistical Mathematics
Research
Fields:		 Bioinformatics, Systems biology, Statistical science
Research
Themes:		 Graphical modelling and statistical inferences of biochemical reaction regulatory circuits, Statistical analysis of genome-wide gene expression profiles and proteome data

Selected Papers
(1)R.Yoshida, T.Higuchi, S.Imoto (2004) A mixed factors model for dimension reduction and extraction of a group structure in gene expression data, Proc. IEEE 3rd Computational Systems Bioinformatics, 161-172.
(2)R.Yoshida, S.Imoto, T.Higuchi (2005) A penalized likelihood estimation on transcriptional module-based clustering, Lecture Note in Computer Science, 3482, Springer-Verlag, 389-401.
(3)R.Yoshida, T.Higuchi, S.Imoto (2005) Estimating time-dependent gene networks from time series DNA microarray data by dynamic linear model with Markov switching, Proc. IEEE 4th Computational Systems Bioinformatics, 289-298.
(4)R.Yoshida, T.Higuchi, S.Imoto, S.Miyano (2006) ArrayCluster: an analytic tool for clustering, data visualization and module finder on gene expression profiles, Bioinformatics, 22, 1538-1539.
(5)M.Nagasaki, R.Yamaguchi, R.Yoshida, S.Imoto, A.Doi, Y.Tamada, H.Matsuno, S.Miyano, T.Higuchi (2006) Genomic data assimilation for estimating Hybrid Functional Petri Net from time-course gene expression data, Genome Informatics, 17(1), 46-61.
(6)R.Yoshida, K. Numata, S.Imoto, M.Nagasaki, A.Doi, K.Ueno, S.Miyano (2006) A statistical framework for genome-wide discovery of biomarker splice variations with GeneChip Human Exon 1.0 ST arrays, Genome Informatics, 17(1), 88-99.
(7)S.Tasaki, M.Nagasaki, M.Oyama, H.Hata, K.Ueno, R.Yoshida, T.Higuchi, S.Sugano, S.Miyano (2006) Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data, Genome Informatics, 17(2), 226-238.
(8)R.Yamaguchi, R.Yoshida, S.Imoto, T.Higuchi, S.Miyano (2007) Finding module-based gene networks in time-course gene expression data with state space models, IEEE Signal Processing Magazine, 24(1), 37-46.
(9)P.K.Gupta, R.Yoshida, S.Imoto, R.Yamaguchi, S.Miyano (2007) Statistical absolute evaluation of gene ontology terms with gene expression data, Lecture Note in Bioinformatics, Springer-Verlag, 4463, 146-157.
(10)M.Henmi, R.Yoshida, S.Eguchi (2007) Importance sampling with the estimated sampler, Biometrika, 94(4), 985-991.
(11)R.Yamaguchi, M.Yamamoto, S.Imoto, M.Nagasaki, R.Yoshida, K.Tsuji, A.Ishige, H.Asou, K.Watanabe, S.Miyano (2007) Identification of activated transcription factors from microarray gene expression data of Kampo-medicine treated mice, Genome Informatics, 18, 119-129.
(12)O.Hirose, R.Yoshida, R.Yamaguchi, S.Imoto, T.Higuchi, S.Miyano (2007) Clustering with time course gene expression profiles and the mixture of state space models, Genome Informatics, 18, 258-266.
(13)R.Yoshida, K.Numata, S.Imoto, M.Nagasaki, A.Doi, K.Ueno, S.Miyano (2007) Computational genome-wide discovery of aberrant splice variations with exon expression profiles, Proc. IEEE 7th International Symposium on Bioinformatics & Bioengineering, 715-722.
(14)O.Hirose*, R.Yoshida*, S.Imoto, R.Yamaguchi, T.Higuchi, D.Stephen Charnock-Jones, C.Print, S.Miyano (2008) Statistical inference of transcriptional module-based gene networks from time course gene expression profiles by using state space models, Bioinformatics, 23, 932-942.
(15)O.Hirose, R.Yoshida, R.Yamaguchi, S.Imoto, T.Higuchi, S.Miyano (2008) Analyzing time course gene expression data with biological and technical replicates to estimate gene networks by state space models, Proc. 2nd Asia International Conference on Modelling & Simulation, 940-946.
(16)R.Yamaguchi, S.Imoto, M.Yamauchi, M.Nagasaki, R.Yoshida, T.Shimamura, Y.Hatanaka, K.Ueno, T.Higuchi, N.Gotoh, S.Miyano (2008) Predicting differences in gene regulatory systems by state space models, Genome Informatics, 21, 101-113.
(17)K.Numata, R.Yoshida, M.Nagasaki, A.Saito, S.Imoto, S.Miyano (2008) ExonMiner: Web service for analysis of GeneChip exon array data, BMC bioinformatics, 9, 494.
(18)R.Yoshida, M.Nagasaki, R.Yamaguchi, S.Imoto, S.Miyano, T.Higuchi (2008) Bayesian learning of biological pathways on genomic data assimilation, Bioinformatics, 24(22), 2592-2601.
(19)R.Yoshida, T.Higuchi (2009) Graphical modeling of intercellular biochemical pathways and statistical inference, Journal of the Japan Statistical Society (Japanese issue) 38(2), 213-236.
(20)K.Nakamura, R.Yoshida, M.Nagasaki, S.Miyano, T.Higuchi (2009) Parameter estimation of in silico biological pathways with particle filtering towards a petascale computing, Pacific Symposium on Biocomputing, 227-238.
(21)K.Kojima, R.Yamaguchi, S.Imoto, M.Yamauchi, M.Nagasaki, R.Yoshida, T.Shimamura, K.Ueno, T.Higuchi, N.Gotoh, S.Miyano (2009) A state space representation of VAR models with sparse learning for dynamic gene networks, Genome Informatics, 22, 56-68.

Membership of Academic Societies
Japan Statistical Society, Japanese Society for Bioinformatics

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