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Book chapters

[B1] S. Imoto, H. Matsuno, S. Miyano (2005) Gene Networks: Estimation, Modeling and Simulation. in R. Eils and A. Kriete (Eds.), Computational Systems Biology, Academic Press, 205-228.

[B2] S. Imoto, Y. Tamada, C.J. Savoie, S. Miyano (2006) Analysis of Gene Networks for Drug Target Discovery and Validation. in J. Walker and M. Sioud (Eds.), Target Discovery and Validation, Volume 1, pp.33-56 (a volume of "Methods in Molecular Biology" series), Humana Press, USA.

[B3] S. Imoto and S. Miyano (2007) Bayesian Network Approach to Estimate Gene Networks. in A. Mittal, A. Kassim and T. Tan (Eds.), Bayesian Network Technologies: Applications and Graphical Models, Idea Group Publishers, USA. pp.269-299. (Refereed book chapter)

[B4] S. Imoto, Y. Tamada, H. Araki, S. Miyano (2010) Computational Drug Target Pathway Discovery: A Bayesian Network Approach. in H. Lu, B. Schokop, H. Zhao (Eds.), Handbook of Computational Statistics: Statistical Bioinformatics, Springer-Varlag. in press.

[B5] S. Imoto, H. Matsuno, S. Miyano (2013) Gene Networks: Estimation, Modeling and Simulation. in R. Eils and A. Kriete (Eds.), Computational Systems Biology, 2nd Edition, Academic Press, in press.

Journal papers and refereed proceedings (peer reviewed)

[J1] S. Imoto and S. Konishi (1999) Nonlinear regression models using B-spline and information criteria (in Japanese with English abstract), Proc. Inst. Statist. Math., 47, 359-373. PDF(878KB)

[J2] S. Imoto and S. Konishi (1999) Estimation of B-spline nonlinear regression models using information criteria (in Japanese), Jap. J. Appl. Statist., 28, 137-150.

[J3] T. Ando, S. Imoto, S. Konishi (2001) Estimating nonlinear regression models based on radial basis function networks (in Japanese with English abstract), Jap. J. Appl. Statist., 30, 19-35.

[J4] S. Imoto, T. Goto, S. Miyano (2002) Estimation of genetic networks and functional structures between genes by using Bayesian network and nonparametric regression, Pacific Symposium on Biocomputing, 7, 175-186. (PSB2002: Refereed conference) PDF(403KB)

[J5] S. Imoto, S. Kim, T. Goto, S. Aburatani, K. Tashiro, S. Kuhara and S. Miyano (2002) Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network, Proc. 1st IEEE Computer Society Bioinformatics Conference, 219-227. (CSB2002: Refereed conference. The number of accepted papers is 19 out of 103 submissions, This paper was selected as one of the best 10 papers) PDF(244KB)

[J6] M.J.L. de Hoon, S. Imoto, S. Miyano (2002) Statistical analysis of a small set of time-ordered gene expression data using linear splines, Bioinformatics, 18, 1477-1485. PDF(138KB)

[J7] M.J.L. de Hoon, S. Imoto, S. Miyano (2002) Inferring gene regulatory networks from time-ordered gene expression data using differential equations, Proc. 5th International Conference on Discovery Science, Lecture Note in Artificial Intelligence, 2534, 267-274, Springer-Verlag. (DS2002: Refereed conference) PDF(128KB)

[J8] M.J.L. de Hoon, S. Imoto, K. Kobayashi, N. Ogasawara, S. Miyano (2003) Inferring gene regulatory networks from time-ordered gene expression data of Bacillus subtilis using differential equations, Pacific Symposium on Biocomputing, 8, 17-28. (PSB2003: Refereed conference) PDF(166KB)

[J9] S. Kim, S. Imoto and S. Miyano (2003) Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data, Proc. 1st Computational Methods in Systems Biology, Lecture Note in Computer Science, 2602, 104-113, Springer-Verlag. (CMSB2003: Refereed conference. The number of accepted papers is 11 out of 39 submissions) PDF(179KB)

[J10] S. Imoto, S. Kim, T. Goto, S. Aburatani, K. Tashiro, S. Kuhara, S. Miyano (2003) Bayesian network and nonparametric heteroscedastic regression for nonlinear modeling of genetic network, Journal of Bioinformatics and Computational Biology, 1(2), 231-252. (This paper is an extended version of CSB2002 paper [J5]) PDF(751KB)

[J11] C.J. Savoie, S. Aburatani, S. Watanabe, Y. Eguchi, S. Muta, S. Imoto, S. Miyano, S. Kuhara, K. Tashiro (2003) Use of gene networks from full genome microarray libraries to identify functionally relevant drug-affected genes and gene regulation cascades, DNA Research, 10, 19-25. PDF(656KB)

[J12] S. Imoto and S. Konishi (2003) Selection of smoothing parameters in B-spline nonparametric regression models using information criteria, Annals of the Institute of Statistical Mathematics, 55(4), 671-687.

[J13] Y. Tamada, S. Kim, H. Bannai, S. Imoto, K. Tashiro, S. Kuhara, S. Miyano (2003) Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection, Bioinformatics, 19 Suppl.2, ii227-ii236. (ECCB2003: Refereed conference. The number of accepted paper with oral presentation is 27 out of 124 submissions) PDF(172KB)

[J14] M.J.L. de Hoon, S. Ott, S. Imoto, S. Miyano (2003) Validation of noisy dynamical system models of gene regulation inferred from time-course gene expression data at arbitrary time intervals, Proc. 2nd European Conference on Computational Biology, 26-28. (ECCB2003: Refereed conference. The number of accepted short papers with oral presentation is 15 out of 117 submissions) PDF(105KB)

[J15] S. Imoto, T. Higuchi, T. Goto, K. Tashiro, S. Kuhara, S. Miyano (2003) Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks, Proc. 2nd Computational Systems Bioinformatics, 104-113. (CSB2003: Refereed conference. The number of accepted papers with oral presentation is 28 out of 151 submissions. This paper was selected as one of the best 10 papers) PDF(232KB)

[J16] S. Imoto*, C.J. Savoie*, S. Aburatani*, S. Kim, K. Tashiro, S. Kuhara, S. Miyano (2003) Use of gene networks for identifying and validating drug targets, Journal of Bioinformatics and Computational Biology, 1(3), 459-474. PDF(1640KB) (*These authors equally contributed to this work)

[J17] S. Kim, S. Imoto, S. Miyano (2003) Inferring gene networks from time series microarray data using dynamic Bayesian networks, Briefings in Bioinformatics, 4(3), 228-235.

[J18] S. Konishi, T. Ando, S. Imoto (2004) Bayesian information criteria and smoothing parameter selection in radial basis function networks, Biometrika, 91(1), 27-43.

[J19] M.J.L. de Hoon, S. Imoto, J. Nolan, S. Miyano (2004) Open source clustering software, Bioinformatics, 20(9), 1453-1454. PDF(53KB)

[J20] M.J.L. de Hoon, S. Imoto, K. Kobayashi, N. Ogasawara, S. Miyano (2004) Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information, Pacific Symposium on Biocomputing, 9, 276-287. (PSB2004: Refereed conference) PDF(229KB)

[J21] N. Nariai, S. Kim, S. Imoto, S. Miyano (2004) Using protein-protein interactions for refining gene networks estimated from microarray data by Bayesian networks, Pacific Symposium on Biocomputing, 9, 336-347. (PSB2004: Refereed conference) PDF(242KB)

[J22] S. Ott, S. Imoto, S. Miyano (2004) Finding optimal models for small gene networks, Pacific Symposium on Biocomputing, 9, 557-567. (PSB2004: Refereed conference) PDF(113KB)

[J23] S. Kim, S. Imoto, S. Miyano (2004) Dynamic Bayesian network and nonparametric regression for nonlinear modeling of gene networks from time series gene expression data, Biosystems, 75(1-3), 57-65. (This paper is an extended version of CMSB2003 paper [J9]) PDF(311KB)

[J24] S. Imoto, T. Higuchi, T. Goto, K. Tashiro, S. Kuhara, S. Miyano (2004) Combining microarrays and biological knowledge for estimating gene networks via Bayesian networks, Journal of Bioinformatics and Computational Biology, 2(1), 77-98. (This paper is an extended version of CSB2003 paper [J15]) PDF(336KB)

[J25] R. Nakamichi, S. Imoto, S. Miyano (2004) Case-control study of binary trait considering interactions between SNPs and environmental effects using logistic regression, Proc. 4th IEEE Bioinformatics and Bioengineering, 73-78. (BIBE2004: Refereed conference)

[J26] M.J.L. de Hoon, Y. Makita, S. Imoto, K. Kobayashi, N. Ogasawara, K. Nakai, S. Miyano (2004) Predicting gene regulation by sigma factors in Bacillus subtilis from genome-wide data, Bioinformatics, 20 Suppl.1, i101-i108. (ISMB/ECCB2004: Refereed conference. The number of accepted papers with oral presentation is 50 out of 492 submissions)PDF(89KB)

[J27] Y. Araki, S. Konishi, S. Imoto (2004) Functional discriminant analysis for time-seriese gene expression data via radial basis function expansion, Proc. COMPSTAT 2004, 613-620, Physica-Verlag/Springer. (COMPSTAT2004: Refereed conference) PDF(147KB)

[J28] S. Imoto*, T. Higuchi*, S. Kim, E. Jeong, S. Miyano (2004) Residual bootstrapping and median filtering for robust estimation of gene networks from microarray data, Proc. 2nd Computational Methods in Systems Biology, Lecture Note in Bioinformatics, 3082, 149-160, Springer-Verlag. (CMSB2004: Refereed conference) (*These authors equally contributed to this work) PDF(291KB)

[J29] 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. 3rd Computational Systems Bioinformatics, 161-172. (CSB2004: Refereed conference) (The number of accepted papers is 30 out of 202 submissions) PDF(498KB)

[J30] T. Ando, S. Imoto, S. Miyano (2004) Functional data analysis of the dynamics of gene regulatory networks, Proc. Knowledge Exploration in Life Science Informatics, Lecture Note in Computer Science, 3303, 69-83, Springer-Verlag. (KELSI2004: Refereed conference)

[J31] T. Ando, S. Imoto, S. Miyano (2004) Kernel mixture survival models for identifying cancer subtypes, predicting patient's cancer types and survival probabilities, Genome Informatics, 15(2), 201-210. (GIW2004: Refereed conference)

[J32] T. Ando, S. Imoto, S. Konishi (2004) Adaptive learning machines for nonlinear classification and Bayesian information criterion, Bulletin of Informatics and Cybernetics, 36, 147-162.

[J33] R. Yoshida, S. Imoto, T. Higuchi (2005) A penalized likelihood estimation on transcriptional module-based clustering, Proc. 1st International Workshop on Data Mining and Bioinformatics, Lecture Note in Comupter Science, 3482, 389-401, Springer-Verlag. (DMBio2005: Refereed conference)

[J34] O. Hirose, N. Nariai, Y. Tamada, H. Bannai, S. Imoto, S. Miyano (2005) Estimating gene networks from expression data and binding location data via boolean networks, Proc. 1st International Workshop on Data Mining and Bioinformatics, Lecture Note in Computer Science, 3482, 349-356, Springer-Verlag. (DMBio2005: Refereed conference)

[J35] Y. Tamada, H. Bannai, S. Imoto, T. Katayama, M. Kanehisa, S. Miyano (2005) Utilizing evolutionary information and gene expression data for estimating gene regulations with Bayesian network models, Journal of Bioinformatics and Computational Biology, 3(6), 1295-1313. PDF(624KB)

[J36] R. Yoshida, S. Imoto and T. Higuchi. (2005) Estimating time-dependent gene networks from time series microarray data by dynamic linear models with Markov switching, Proc. 4th Computational Systems Bioinformatics, 289-298. (CSB2005: Refereed conference. The number of accepted papers is 30 out of 246 submissions) PDF(988KB)

[J37] Y. Tamada, S. Imoto, K. Tashiro, S. Kuhara, S. Miyano (2005) Identifying drug active pathways from gene networks estimated by gene expression data, Genome Informatics, 16(1), 182-191. (IBSB2005: Refereed conference)

[J38] N. Nariai, Y. Tamada, S. Imoto, S. Miyano (2005) Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data, Bioinformatics, 21, Suppl.2, ii206-ii212. (ECCB2005: Refereed conference. Selected as a full paper with oral presentation out of 209 submitted papers) PDF(354KB)

[J39] S. Imoto*, T. Higuchi*, T. Goto, S. Miyano (2006) Error tolerant model for incorporating biological knowledge with expression data in estimating gene networks, Statistical Methodology, 3(1), 1-16. (*These authors equally contributed to this work) PDF(1911KB)

[J40] S. Imoto*, Y. Tamada*, H. Araki*, K. Yasuda, C.G. Print, S.D. Charnock-Jones, D. Sanders, C.J. Savoie, K. Tashiro, S. Kuhara, S. Miyano (2006) Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles, Pacific Symposium on Biocomputing, 11, 559-571. (PSB2006: Refereed conference. Selected as a full paper with oral presentation. *These authors equally contributed to this work) PDF(487KB)

[J41] R. Nakamichi, S. Imoto, S. Miyano (2006) Statistical model selection method to analyze combinatorial effects of SNPs and environmental factors for binary disease, International Journal on Artificial Intelligence Tools, 15(5), 711-724.

[J42] 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.

[J43] 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.

[J44] 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.

[J45] A. Termier, Y. Tamada, S. Imoto, T. Washio, T. Higuchi (2006) From closed tree mining towards closed DAG mining, Proc. International Workshop on Data Mining and Statistical Science, 1-7.

[J46] Y. Tamada, S. Imoto, S. Miyano (2006) Estimating gene networks from gene expression data utilizing biological information (in Japanese with English abstract), Proc. Inst. Statist. Math., 54(2), 333-356.

[J47] T. Washio, T. Higuchi, S. Imoto, Y. Tamada, K. Sato, H. Motoda (2006) Graph mining and its application to statistical modeling (in Japanese with English abstract), Proc. Inst. Statist. Math., 54(2), 315-332.

[J48] M. Affara, B. Dunmore, C. Savoie, S. Imoto, Y. Tamada, H. Araki, D.S. Charnock-Jones, S. Miyano, C. Print (2007) Understanding endothelial cell apoptosis: what can the transcriptome glycome and proteome reveal? Philosophical Transactions of Royal Society, 62(1484), 1469-1487.

[J49] R. Yamaguchi, R. Yoshida, S. Imoto, T. Higuchi, S. Miyano (2007) Finding module-based gene networks with state-space models - Mining high-dimensional and short time-course gene expression data, IEEE Signal Processing Magazine, 24(1), 37-46.

[J50] P.K. Gupta, R. Yoshida, S. Imoto, R. Yamaguchi, S. Miyano (2007) Statistical absolute evaluation of gene ontology terms with gene expression data, Proc. 3rd International Symposium on Bioinformatics Research and Applications, Lecture Note in Bioinformatics, Springer-Verlag. 4463, 146-157. (ISBRA2007: Refereed conference)

[J51] A. Termier, Y. Tamada, K. Numata, S. Imoto, T. Washio, T. Higuchi (2007) DIGDAG, a first algorithm to mine closed frequent embedded sub-DAGs, Proc. 5th International Workshop on Mining and Learning with Graphs, CR-ROM. (MLG2007: Refereed conference)

[J52] R. Yamaguchi, M. Yamamoto, S. Imoto, M. Nagasaki, R. Yoshida, K. Tsuiji, 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. (IBSB2007: Refereed conference)

[J53] 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. (IBSB2007: Refereed conference)

[J54] K. Numata, S. Imoto, S. Miyano (2007) A structure learning algorithm for inference of gene networks from microarray gene expression data using Bayesian networks, Proc. IEEE 7th International Symposium on Bioinformatics & Bioengineering, 1280-1284. (IEEE BIBE2007: Refereed conference)

[J55] R. Yoshida, K. Numata, S. Imoto, M. Nagasaki, A. Doi, K. Ueno, S. Miyano, (2007) Computational discovery of aberrant splice variations with genome-wide exon expression profiles, Proc. IEEE 7th International Symposium on Bioinformatics & Bioengineering, 715-722. (IEEE BIBE2007: Refereed conference)

[J56] S. Imoto (2007) Knowledge discovery of causal relations among genes from microarray gene expression data (in Japanese with English abstract), Journal of Japan Statistical Sciety, 37(1), 55-70.

[J57] T. Shimamura, R. Yamaguchi, S. Imoto, S. Miyano (2007) Weighted lasso in graphical Gaussian modeling for large gene network estimation based on microarray data, Genome Informatics, 19, 142-153. (GIW2007: Refereed conference. The number of accepted papers is 16 out of 55 submissions)

[J58] T. Ando, S. Konishi, S. Imoto. (2008) Nonlinear regression modeling via regularized radial basis function networks, Journal of Statistical Planning and Inference, 138(11), 3616-3633.

[J59] O. Hirose, R. Yoshida, S. Imoto, R. Yamaguchi, T. Higuchi, Stephen D. 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, 24(7), 932-942.

[J60] 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. (AMS2008: Refereed conference)

[J61] Y. Hatanaka, M. Nagasaki, R. Yamaguchi, T. Obayashi, K. Numata, A. Fujita, T. Shimamura, T. Tamada, S. Imoto, K. Kinoshita, K. Nakai, S. Miyano (2008) A novel strategy to search conserved transcription factor binding sites among coexpressing genes, Genome Informatics, 20, 212-221.

[J62] K. Kojima, A. Fujita, T. Shimamura, S. Imoto, S. Miyano (2008) Estimation of nonlinear gene regulatory networks via L1 regularized NVAR from time series gene expression data, Genome Informatics, 20, 37-51.

[J63] 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. (GIW2008: Refereed conference. The number of accepted papers was 18 out of 55 submissions. This paper was selected as the top three papers in the conference)

[J64] A. Niida, A.D. Smith, S. Imoto, S. Tsutsumi, H. Aburatani, M.Q. Zhang, T. Akiyama (2008) Integrative bioinformatics analysis of transcriptional regulatory programs in breast cancer cells, BMC Bioinformatics, 9:404.

[J65] K. Numata, S. Imoto, S. Miyano (2008) Partial order-based Bayesian network learning algorithm for estimating gene networks, Proc. IEEE Bioinformatics and Biomedicine, 357-360. (BIBM2008: Refereed conference)

[J66] 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.

[J67] E. Perrier, S. Imoto, S. Miyano (2008) Finding optimal Bayesian network given a super-structure, Journal of Machine Learning Research, 9, 2251-2286.

[J68] 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.

[J69] Y. Watanabe, M. Yamamoto, N. Miura, M. Fukutake, A. Ishige, R. Yamaguchi, M. Nagasaki, S. Imoto, S. Miyano, J. Takeda, K. Watanabe (2008) Orengedokuto and berberine improve indomethacin-induced small intestinal injury via adenosine, Journal of Gastroenterology, 44, 380-389.

[J70] Y. Tamada*, H. Araki*, S. Imoto*, M. Nagasaki, A. Doi, Y. Nakinishi, Y. Tomiyasu, K. Yasuda, B. Dunmore, D. Sanders, S. Humphries, C. Print, D.S. Charnock-Jones, K. Tashiro, S. Kuhara, S. Miyano (2009) Unraveling dynamic activities of autoacine pathways that control drug-response transcriptome networks, Pacific Symposium on Biocomputing, 14, 251-263. (PSB2009: Refereed conference. Selected as a full paper with oral presentation. *These authors equally contributed to this work)

[J71] A. Niida, A.D. Smith, S. Imoto, S. Tsutsumi, H. Aburatani, M.Q. Zhang, T. Akiyama (2009) Gene set-based module discovery in the breast cancer transcriptome, BMC Bioinformatics, 10:71.

[J72] H. Araki*, Y. Tamada*, S. Imoto*, B. Dunmore, D. Sanders, S. Humphrey, M. Nagasaki, A. Doi, Y. Nakanishi, K. Yasuda, Y. Tomiyasu, K. Tashiro, C. Print, D.S. Charnock-Jones, S. Kuhara, S. Miyano (2009) Analysis of PPAR alpha-dependent and PPAR alpha-independent transcript regulation following fenofibrate treatment of human endothelial cells, Angiogenesis, 12(3), 221-229. (*These authors equally contributed to this work)

[J73] S. Miyano, R. Yamaguchi, Y. Tamada, M. Nagasaki, S. Imoto (2009) Gene networks viewed through two models, Proc. the 1st International Conference on Bioinformatics and Computational Biology (BICoB 2009), Lecture Note in Bioinformatics, 4652, 54-66.

[J74] T. Shimamura, S. Imoto, R. Yamaguchi, A. Fujita, M. Nagasaki, S. Miyano, (2009) Recursive regularization for inferring gene networks from time-course gene expression profiles, BMC Systems Biology, 3, 41.

[J75] A. Niida, S. Imoto, M. Nagasaki, R. Yamaguchi, S. Miyano (2009) A novel meta-analysis approach of cancer transcriptomes reveals prevailing transcriptional networks in cancer cells, Genome Informatics, 22, 121-131.

[J76] 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.

[J77] N. Yoshikawa, M. Nagasaki, M. Sano, S. Tokudome, K. Ueno, N. Shimizu, S. Imoto, S. Miyano, M. Suematsu, K. Fukuda, C. Morimoto, H. Tanaka (2009) Ligand-based gene expression profiling reveals novel roles of glucocorticoid receptor in cardiac metabolism, American Journal of Physiology, Endocrinology and Metabolism, 296, E1363-E1373.

[J78] R. Yamaguchi, S. Imoto, S. Miyano, (2010) Network-based predictions and simulations by biological state space models: search for drug mode of action, Journal of Computer Science and Technology, 25(1), 131-153.

[J79] K. Kojima, E. Perrier, S. Imoto, S. Miyano (2010) Optimal search on clustered structural constraint for learning Bayesian network structure, Journal of Machine Learning Research, 11, 285-310.

[J80] H. Sato*, H. Nakada*, R. Yamaguchi*, S. Imoto*, S. Miyano and M. Kami (2010) When should we intervene to control the 2009 influenza A(H1N1) pandemic?, Euro Surveillance, 15(1):pii=19455. Available online: http://www.eurosurveillance.org/ViewArticle.aspx?ArticleId=19455 (*These authors equally contributed to this work)

[J81] T. Shimamura, S. Imoto, R. Yamaguchi, M. Nagasaki, S. Miyano (2010) Inferring dynamic gene networks under varying conditions for transcriptomic network comparison, Bioinformatics, 26(8), 1064-1072.

[J82] T. Higashigaki, K. Kojima, R. Yamaguchi, M. Inoue, S. Imoto, S. Miyano (2010) Identifying hidden confounders in gene networks by Bayesian networks, Proc. 10th IEEE Bioinformatics and Bioengineering, 168-173. (BIBE2010: Refereed conference. Selected as a full paper with oral presentation)

[J83] A. Fujita, M. Nagasaki, S. Imoto, A. Saito, E. Ikeda, T. Shimamura, R. Yamaguchi, H. Suzuki, Y. Hayashizaki, S. Miyano (2010) Comparison of gene expression profiles produced by CAGE, illumina microarray and Real Time RT-PCR, Genome Informatics, 24, 56-68.

[J84] T. Shimamura, S. Imoto, M. Nagasaki, M. Yamauchim R. Yamaguchi, A. Fujita, Y. Tamada, N. Gotoh, S. Miyano (2010) Collocation-based sparse estimation for inferring continuous-time dynamic gene networks, Genome Informatics, 24, 164-178.

[J85] K. Kojima, S. Imoto, M. Nagasaki, S. Miyano (2010) Gene regulatory network clustering for graph layout based on microarray gene expression data, Genome Informatics, 24, 84-95.

[J86] A. Niida, S. Imoto, R. Yamaguchi, M. Nagasaki, S. Miyano (2010) Gene set-based module discovery decodes cis-regulatory codes governing diverse gene expression across human multiple tissues, PLoS ONE, 5(6), e10910.

[J87] Y. Sogawa, S. Shimizu1, A. Hyvarinen, T. Washio, T. Shimamura, S. Imoto (2010) Discovery of exogenous variables in data with more variables than observations, Proc. 20th International Conference on Artificial Neural Networks, 67-76.

[J88] S. Kawano, T. Shimamura, A. Niida, S. Imoto, R. Yamaguchi, M. Nagasaki, R. Yoshida, C. Print, and S. Miyano (2010) Discovering functional gene pathways associated with cancer heterogeneity via sparse supervised learning, Proc. IEEE Bioinformatics and Biomedicine, 253-258. (BIBM2010: Refereed conference. 61 papers are accepted as regular papers from 355 submissions (acceptance rate 17.2%))

[J89] A. Niida, S. Imoto, R. Yamaguchi, M. Nagasaki, A. Fujita, T. Shimamura, S. Miyano (2010) Model-free unsupervised gene set screening based on information enrichment in expression profiles, Bioinformatics, 26, 3090-3097.

[J90] Y. Tamada, S. Imoto, H. Araki, M. Nagasaki, C. Print, S. Charnock-Jones, S. Miyano (2011) Estimating genome-wide gene networks using nonparametric Bayesian network models on massively parallel computers, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 8 (3), 683-697.

[J91] Y. Tamada, R. Yamaguchi, S. Imoto, O. Hirose, R. Yoshida, M. Nagasaki, S. Miyano (2011) SiGN-SSM: open source parallel software for estimating gene networks with state space models, Bioinformatics, 27(8), 1172-1173.

[J92] M. Furu, Y. Kajita, S. Nagayama, T. Ishibe, Y. Shima, D. Uejima, T. Aoyama, T. Nakayama, T. Nakamura, Y. Nakashima, M. Ikegawa, S. Imoto, T. Katagiri, Y. Nakamura, J. Toguchida (2011) Identification of AFAP1L1 as a prognostic marker for spindle cell sarcomas, Oncogene, 30, 4015-4025.

[J93] M.M. Saito, S. Imoto, R. Yamaguchi, S. Miyano, T. Higuchi (2012) Parallel agent-based simulator for inuenza pandemic, Proc. DOCMAS, Lecture Note in Computer Science, Springer-Verlag, 7068, 361-370 (DOCMAS: Refereed conference)

[J94] T. Hasegawa, R. Yamaguchi, M. Nagasaki, S. Imoto, S. Miyano (2011) Comprehensive pharmacogenomic pathway screening by data assimilation, Proc. 7th International Symposium on Bioinformatics Research and Applications (ISBRA2011), Springer-Verlag Berlin, Heidelberg, LNCS, 6674, 160-171. (ISBRA2011: Refereed conference. 37 papers were accepted out of 92 submissions)

[J95] A. Sharma, C. Hock Koh, S. Imoto, S. Miyano (2011) A strategy of finding the optimal number of features on gene expression data, Electronics Letters, 47(8), 480-482.

[J96] Y. Tamada, T. Shimamura, R. Yamaguchi, S. Imoto, M. Nagasaki, S. Miyano (2011) SiGN: large-scale gene network estimation environment for high performance computing, Genome Informatics, 25, 40-52.

[J97] K. Katayama, R. Yamaguchi, S. Imoto, H. Tokunaga, Y. Imazu, K. Matuura, K. Watanabe, S. Miyano (2011) Symbolic hierarchical clustering for visual analogue scale data, KES-Springer Smart Innovations, Systems and Technologies Series, Springer-Verlag, 10, 799-805.

[J98] S. Imoto, K. Kojima, E. Perrier, Y. Tamada, S. Miyano (2011) Searching optimal Bayesian network structure on constraint search space: super-structure approach, Lecture Notes in Computer Science, Sprigner-Verlag, 6797, 210-218.

[J99] Y. Sogawa, S. Shimizu, T. Shimamura, A. Hyvarinen, T. Washio, S. Imoto (2011) Estimating exogenous variables in data with more variables than observations, Neural Networks, 24(8), 875-880.

[J100] T. Shimamura, S. Imoto, Y. Shimada, Y. Hosono, A. Niida, M. Nagasaki, R. Yamaguchi, T. Takahashi, S. Miyano (2011) A novel network profiling analysis reveals system changes in epithelial-mesenchymal transition, PLoS ONE, 6(6), e20804.

[J101] M. Saito, S. Imoto, R. Yamaguchi, S. Miyano, T. Higuchi (2011) Estimation of macroscopic parameter in agent-based pandemic simulation, Proc. 13th International Conference on Information Fusion, 1-6. (Fusion2011: Refereed conference)

[J102] Y. Tamada, S. Imoto, S. Miyano (2011) Parallel algorithm for learning optimal Bayesian network structure, Journal of Machine Learning Reseach, 12, 2437-2459.

[J103] M. Yamauchi, I. Yoshino, R. Yamaguchi, T. Shimamura, M. Nagasaki, S. Imoto, A. Niida, F. Koizumi, T. Kohno, J. Yokota, S. Miyano, N. Gotoh (2011) N-cadherin expression is a potential survival mechanism of gefitinib-resistant lung cancer cells, American Journal of Cancer Research, 1, 823-833.

[J104] R. Kogo, T. Shimamura, K. Mimori, K. Kawahara, S. Imoto, T. Sudo, F. Tanaka, K. Shibata, A. Suzuki, S. Komune, S. Miyano, M. Mori (2011) Long non-coding RNA HOTAIR regulates Polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers, Cancer Research, 71(20): 6320-6326. (Pub: 2011 Oct 15, Epub: 2011 Aug 23)

[J105] K. Kojima, S. Imoto, R. Yamaguchi, A. Fujita, M. Yamauchi, N. Gotoh, S. Miyano (2012) Identifying regulational alterations in gene regulatory networks by state space representation of vector autoregressive models and variational annealing, BMC Genomics, 13(Suppl 1):S6. (Special Issue of APBC2012, a refereed conference; 42 out of 129 submissions were accepted as oral presentation)

[J106] K. Katayama, R. Yamaguchi, S. Imoto, K. Matsuura, K. Watanabe, S. Miyano (2011) Clustering for visual analogue scale data in symbolic data analysis, Procedia Computer Science, 6, 370-374.

[J107] D. Hurley, H. Araki, T. Tamadaz, B. Dunmore, D. Sanders, S. Humphreys, M. Affara, S. Imoto, K. Yasuda, Y. Tomiyasu, K. Tashiro, C. Savoie, V. Cho, S. Smith, S. Kuhara, S., Miyano, D.S. Charnock-Jones, E.J. Crampin, C.G. Print (2012) Gene network inference and visualization tools for biologists: application to new human transcriptome datasets, Nucleic Acids Research, 40(6): 2377-2398. (Pub: 2012 Mar, Epub: 2011 Nov 24)

[J108] A. Sharma, S. Imoto, S. Miyano (2012) A top-r feature selection algorithm for microarray gene expression data, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(3): 754-64. (Pub: 2012 May-Jun)

[J109] K. Katayama, R. Yamaguchi, S. Imoto, K. Matsuura, K. Watanabe, S. Miyano (2011) Transform of visual analogue scale data and their clustering, International Journal of Knowledge Engineering and Soft Data Paradigms, 3(2), 143-151. (Pub: 2011 Mar)

[J110] A. Sharma, S. Imoto, S. Miyano, V. Sharma (2012) Null space based feature selection method for gene expression data, International Journal of Machine Learning and Cybernetics, 3(4): 269-276. (Pub: 2012 Dec 1, Epub: 2011 Nov 29)

[J111] L. Wang, D. Hurley, W. Watkins, H. Araki, Y. Tamada, A. Muthukaruppan, L. Ranjard, E. Derkac, S. Imoto, S. Miyano, E. Crampin, C. Print (2012) Cell cycle gene networks are associated with melanoma prognosis, PLoS ONE, 7(4): e34247. (Pub: 2012 Apr 20)

[J112] A. Sharma, S. Imoto, S. Miyano (2012) A filter based feature selection algorithm using null space of covariance matrix for DNA microarray gene expression data, Current Bioinformatics, 7(3): 289-294. (Pub: 2012 Sep 1)

[J113] S. Kawano, T. Shimamura, A. Niida, S. Imoto, R. Yamaguchi, M. Nagasaki, R. Yoshida, C. Print, S. Miyano (2012) Identifying gene pathways associated with cancer characteristics via sparse statistical methods, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(4):966-972. (Pub: 2012 Jul-Aug)

[J114] S. Ishimaru, K. Mimori, K. Yamamoto, H. Inoue, S. Imoto, S. Kawano, R. Yamaguchi, T. Sato, H. Toh, H. Iinuma, T. Maeda, H. Ishii, S. Suzuki, S. Tokudome, M. Watanabe, J. Tanaka, S. Kudo, K. Sugihara, . Hase, H. Mochizuki, M. Kusunoki, K. Yamada, Y. Shimada, Y. Moriya, G.F. Barnard, S. Miyano, M. Mori (2012) Increased risk for CRC in diabetic patients with the nonrisk allele of SNPs at 8q24, Annals of Surgical Oncology, 19(9):2853-2858. (Pub: 2012 Sep, Epub: 2012 Mar 21)

[J115] A. Sharma, S. Imoto, S. Miyano (2012) A between-class overlapping filter-based method for transcriptome data analysis. Journal of Bioinformatics and Computational Biology, 10(5):1250010. (Pub: 2012 Oct, Epub: 2012 Jun 22)

[J116] M. Saito, S. Imoto, R. Yamaguchi, S. Miyano, T. Higuchi (2012) Identifiability of local transmissibility parameters in agent-based pandemic simulation, Proc. 14th International Conference on Information FUSION, 2466-2471. (FUSION2012: Refereed conference) (Pub: 2012 Jul 9)

[J117] A. Niida, S. Imoto, T. Shimamura, S. Miyano (2012) Statistical model-based testing to evaluate the recurrence of genomic aberrations, Bioinformatics, 28, i115-i120. (ISMB2012: Refereed conference. Acceptance rate = 13%) (Pub: 2012 June 9)

[J118] M. Yamamoto, R. Yamaguchi, K. Muanakata, K. Takashima, M. Nishiyama, K. Hioki, Y. Ohnishi, M. Nagasaki, S. Imoto, S. Miyano, A. Ishige, K. Watanabe (2012) A microarray analysis of gnotobiotic mice indicating that microbial exposure during the neonatal period plays an essential role in immune system development. BMC Genomics, 13: 335. (Pub: 2012 Jul 23)

[J119] T. Tamura, M. Sone, Y. Nakamura, T. Shimamura, S. Imoto, S. Miyano, H. Okazawa (2013) A restricted level of PQBP1 is needed for the best longevity of Drosophila. Neurobiology of Aging, 34(1): 356.e11-20. (Pub: 2013 Jan, Epub: 2012 Aug 15)

[J120] M. Yamauchi, R. Yamaguchi, A. Nakata, T. Kohno, M. Nagasaki, T. Shimamura, S. Imoto, A. Saito, K. Ueno, Y. Hatanaka, R. Yoshida, T. Higuchi, M. Nomura, D. G. Beer, J. Yokota, S. Miyano, N. Gotoh (2012) Epidermal growth factor receptor tyrosine kinase defines critical prognostic genes of stage I lung adenocarcinoma. PLoS ONE, 7(9): e43923. (Pub: 2012 Sep 19)

[J121] A. Sharma, K.K. Paliwal, S. Imoto, S. Miyano (2012) Principal component analysis using QR decomposition. International Journal of Machine Learning and Cybernetics, online (10.1007/s13042-012-0131-7). (Pub online: 2012 Sep 12)

[J122] K. Ogami, R. Yamaguchi, S. Imoto, Y. Tamada, H. Araki, C. Print, S. Miyano (2012) Computational gene network analysis reveals TNF-induced angiogenesis. BMC Systems Biology, 6(Suppl 2): S12. (Selected as a full paper of Special Issue of GIW2012. Competition rate is 10/120) (Pub: 2012 Dec 12).

[J123] Y. Takatsuno, K. Mimori, K. Yamamoto T. Sato, A. Niida, H. Inoue, S. Imoto, S. Kawano, R. Yamaguchi, H. Toh, H. Iinuma, S. Ishimaru, H. Ishii, S. Suzuki, S. Tokudome, M. Watanabe, J. Tanaka, S. Kudo, H. Mochizuki, M. Kusunoki, K. Yamada, Y. Shimada, Y. Moriya, S. Miyano, K. Sugihara, M. Mori (2013) The rs6983267 SNP Is associated with MYC transcription efficiency, which promotes progression and worsens prognosis of colorectal cancer, Annals of Surgical Oncology, 20(4): 1395-1402. (Pub: 2013 Apr, Epub 2012 Sep 14)

[J124] K. Katayama, R. Yamaguchi, S. Imoto, K. Matsuura, K. Watanabe, S. Miyano (2012) Analysis of questionnaire for Traditional Medical and develop decision support system. Proc. International Workshop on Biomedical and Health Informatics, 762-763. (Pub: 2012 Oct 4)

[J125] K. Yuji*, S. Imoto*, R. Yamaguchi, T. Matsumura, N. Murashige, Y. Kodama, S. Miyano, K. Imai, M. Kami (2012) Forecasting Japan's physician shortage in 2035 as the first full-fledged aged society. PLoS ONE, 7(11): e50410. (*These authors equally contributed to this work) (Pub: 2012 Nov 30)

[J126] T. Yokobori, H. Iinuma, T. Shimamura, S. Imoto, H. Ishii, K. Sugimachi, M. Iwatsuki, D. Ota, M. Ohkuma, T. Iwaya, N. Nishida, R. Kogo, T. Sudo, F. Tanaka, K. Shibata, H. Toh, T. Sato, G.F. Barnard, T. Fukagawa, S. Yamamoto, H. Nakanishi, S. Sasaki, S. Miyano, T. Watanabe, H. Kuwano, K. Mimori, K. Pantel, M. Mori (2013) Plastin3 is a novel marker for circulating tumor cells undergoing the epitheial-mesenchymal transition and is associated with colorectal cancer prognosis. Cancer Research, 73(7): 2059-2069. (Pub: 2013 Apr, Epub: 2013 Feb 1)

[J127] M. Komatsu, T. Yoshimaru, T. Matsuo, K. Kiyotani, Y. Miyoshi, T. Tanahashi, K. Rokutan, R. Yamaguchi, A. Saito, S. Imoto, S. Miyano, Y. Nakamura, M. Sasa, M. Shimada, T. Katagiri (2013) Molecular features of triple negative breast cancer cells by genome-wide gene expression profiling analysis. Internal Journal of Oncology, 42(2), 478-506. (Epub 2012 Dec 18)

[J128] R. Yamaguchi, S. Imoto, M. Kami, K. Watanabe, S. Miyano, K. Yuji (2013) Does Twitter trigger bursts in signature collections? PLoS ONE, 8(3): e58252. (Pub: 2013 Mar 6)

[J129] M. Affara, D. Sanders, H. Araki, Y. Tamada, B.J. Dunmore, S. Humphreys, S. Imoto, C. Savoie, S. Miyano, S. Kuhara, D. Jeffries, C. Print, D.S. Charnock-Jones (2013) Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis. BMC Genomics, 14(1): 23. (Pub: 2013 Jan 16)

[J130] M. Kayano, S. Imoto, R. Yamaguchi, S. Miyano (2013) Multi-omics approach for estimating metabolic networks using low-order partial correlations, Journal of Computational Biology, 20(8), 571-582. (Published 30 July 2013)

[J131] A. Sharma, K.K. Paliwal, S. Imoto, S. Miyano, V. Sharma, R. Ananthanarayanan (2013) A Feature Selection Method using Fixed-Point Algorithm for DNA microarray gene expression data, International Journal of Knowledge-Based and Intelligent Engineering Systems, accepted on 2 March 2013.

[J132] A. Sharma, K.K. Paliwal, A. Dehzangi, J. Lyons, S. Imoto, S. Miyano (2013) A Strategy to select suitable physicochemical attributes of amino acids for protein fold recognition, BMC Bioinformatics, 14, 233. (Pub: 24 July 2013)

[J133] A. Niida, G. Tremmel, S. Imoto, S. Miyano (2013) Multilayer cluster heat map visualizing biological tensor data, Proc. Brazilian Symposium on Bioinformatics, Lecture Note on Bioinformatics, Springer, accepted on 10 July 2013.

[J134] M.M. Saito, S. Imoto, R. Yamaguchi, M. Tsubokura, M. Kami, H. Nakada, H. Sato, S. Miyano, T. Higuchi (2013) Enhancement of collective immunity by selective vaccination against emerging influenza pandemic, PLoS ONE, 8(9), e72866. (accepted on 23 July 2013, published 18 Sep 2013)

[J135] T. Yoshimaru, M. Komatsu, T. Matsuo, Y-A. Chen, Y. Murakami, K. Mizuguchi, E. Mizohata, T. Inoue, M. Akiyama, R. Yamaguchi, S. Imoto, S. Miyano, Y. Miyoshi, M. Sasah, Y. Nakamura, T. Katagiri (2013) Targeting the BIG3-PHB2 interaction to overcome tamoxifen resistance in breast cancer cells, Nature Communications, 4, 2443. (accepted 15 Aug 2013, Published 20 September 2013).

[J136] M.M. Saito, S. Imoto, R. Yamaguchi, H. Sato, H. Nakada, M. Kami, S. Miyano, T. Higuchi (2013) Extension and verification of the SEIR model on the 2009 influenza A (H1N1) pandemic in Japan, Mathematical Biosciences, accepted 23 Aug 2013.

[J137] K. Katayama, T. Yoshino, K. Munakata, R. Yamaguchi, S. Imoto, S. Miyano, K. Watanabe (2013) Prescription of Kampo drugs in the Japanese Health Care Insurance Program, Evidence-Based Complementary and Alternative Medicine, (Accepted: 9 October 2013)

[J138] S.S. Barclay, T. Tamura, H. Ito K. Fujita, K. Tagawa, T. Shimamura, A. Katsuta, H. Shiwaku, M. Sone, S. Imoto, S. Miyano, H. Okazawa (2013) Systems biology analysis of Drosophila in vivo screen data elucidates core networks for DNA damage repair in SCA1, Human Molecular Genetics, in press. (Accepted in Oct 17, 2013)

[J139] A. Sharma, K.K. Paliwal, S. Imoto, S. Miyano (2013) A feature selection method using improved regularized linear discriminant analysis, Machine Vision and Applications, (Accepted: 24 October 2013, Published online: 9 November 2013)

[J140] T. Yoshino, K. Katayama, K. Munakata, Y. Horiba, R. Yamaguchi, S. Imoto, S. Miyano, K. Watanabe (2013) Statistical Analysis of Hie (cold sensation) and Hiesho (cold disorder) in Kampo Clinic, Evidence-Based Complementary and Alternative Medicine, (Accepted: 13 November 2013)

[J141] K. Katayama, R. Yamaguchi, S. Imoto, K. Watanabe, S. Miyano (2013) Analysis of questionnaire for traditional medicine and development of decision support system, Evidence-Based Complementary and Alternative Medicine, (Accepted: 26 November 2013)

[J142] K. Yamaguchi, R. Yamaguchi, N. Takahashi, T. Ikenoue, T. Fujii, M. Shinozaki, G. Tsurita, K. Hata, A. Niida, S. Imoto, S. Miyano, Y. Nakamura, Y. Furukawa (2013) Overexpression of cohesion establishment factor DSCC1 through E2F in colorectal cancer, PLOS ONE, (Accepted: 2 December 2013)

[J143] H. Tokunaga, K. Munakata, K. Katayama, R. Yamaguchi, S. Imoto, S. Miyano, K. Watanabe (2014) Clinical data mining related to the Japanese Kampo concept "Hie" (oversensivity to coldness) in men and pre- and postmenopausal women, Evidence-Based Complementary and Alternative Medicine, (Accepted: 30 December 2013)

[J144] H. Nishiura, K. Ejima, K. Mizumoto, S. Nakaoka, H. Inaba, S. Imoto, R. Yamaguchi, M.M. Saito (2014) Cost-effective length and timing of school closure during an influenza pandemic depend on the severity, Theoretical Biology and Medical Modelling, 11:5. (Accepted: 20 January 2014, Published: 21 January 2014)

[J145] A. Sharma, A. Dehzangi, J. Lyons, S. Imoto, S. Miyano, K. Nakai, A. Patil (2014) Evaluation of sequence features from intrinsically disordered regions for the estimation of protein function, PLoS ONE, (Accepted: 30 January 2014)

[J146] T. Hasegawa, M. Nagasaki, R. Yamaguchi, S. Imoto, S. Miyano (2014) An efficient method of exploring simulation models by assimilating literature and biological observational data, BioSystems, 121, 54-66.

[J147] C. Arima, T. Kajino, Y. Tamada, S. Imoto, Y. Shimada, M. Nakatochi, M. Suzuki, H. Isomura, Y. Yatabe, T. Yamaguchi, K. Yanagisawa, S. Miyano, T. Takahashi (2014) Lung adenocarcinoma subtypes definable by lung development-related miRNA expression profiles in association with clinicopathologic features, Carcinogenesis, Online first. (Published: 5 June 2014)

[J148] T. Hasegawa, T. Mori, R. Yamaguchi, S. Imoto, S. Miyano, T. Akutsu (2014) An efficient data assimilation schema for restoration and extension of gene regulatory networks using time-course observation data, Journal of Computational Biology, in press.

[J149] H. Ito, H. Shiwaku, C. Yoshida, H. Homma, H. Luo, X. Chen, K. Fujita, L. Musante, U. Fischer, S.G.M. Frints, C. Romano, Y. Ikeuchi, T. Shimamura, S. Imoto, S. Miyano, S. Muramatsu, T. Kawauchi, M. Hoshino, M. Sudol, A. Arumughan, E.E. Wanker, T. Rich, C. Schwartz, F. Matsuzaki, A. Bonni, V.M. Kalscheuer, H. Okazawa (2014) In utero gene therapy rescues microcephaly caused by Pqbp1-hypofunction in neural stem progenitor cells, Molecular Psychiatry, Online first. (Accepted: 12 May 2014, Published: 29 July 2014)

[J150] T. Hasegawa, R. Yamaguchi, M. Nagasaki, S. Miyano, S. Imoto (2014) Inference of gene regulatory networks incorporating multi-Source biological knowledge via a state space model with L1 regularization, PLoS ONE, in press.

[J151] N. Usuyama, Y. Shiraishi, Y. Sato, H. Kume, Y. Homma, S. Ogawa, S. Miyano, S. Imoto (2014) HapMuC: somatic mutation calling using heterozygous germline variants near candidate mutations, Bioinformatics, in press.