: : Publications : : : :

Publications

Book chapters etc. | Presentations or other articles

Peer Reviewed Papers

[61] Sugiyama, K., Nomura, O., Irie, J., Ishizawa, Y., Takauji, S., Hayakawa, M., Tamada, Y., Hanada, H. Effects of rewarming therapies on outcomes in accidental hypothermia: A secondary analysis of a multicenter prospective study, The American Journal of Emergency Medicine, 79, 91-96, 2024. (Full text)

[60] Kasai, S., Watanabe, K., Ide, S., Ishimoto, Y., Sasaki, M., Umemura Y., Tatsuo, S., Kakeda, S., Mikami, T., Tamada, Y., Miki, Y., Wakabayashi, K., Tomiyama, M., Kakeda, S. FLAIR Hyperintensities in the Anterior Part of the Callosal Splenium in the Elderly Population: A Large Cohort Study, Academic Radiology, 2024. In Press. (Full text)

[59] Tomoto, M., Mineharu, Y., Sato, N., Tamada, Y., Nogami-Itoh, M., Kuroda, M., Adachi, J., Takeda, Y., Mizuguchi, K., Kumanogoh, A., Natsume-Kitatani, Y., Okuno, Y. Idiopathic pulmonary fibrosis-specific Bayesian network integrating extracellular vesicle proteome and clinical information, Scientific Reports, 14, 1315, 2024. (Full text)

[58] Umemura, Y., Watanabe, K., Kasai, S., Ide, S., Ishimoto, Y., Sasaki, M., Nagaya, H., Tatsuo, S., Mikami, T., Tamada, Y., Tomiyama, M., Kakeda, S. Choroid plexus enlargement in mild cognitive impairment on MRI: a large cohort study, European Radiology, 2024. (Full text)

[57] Kasai, S., Watanabe, K., Umemura, Y., Ishimoto, Y., Sasaki, M., Nagaya, H., Tatsuo, S., Mikami, T., Tamada, Y., Ide, S., Tomiyama, M., Matsuzaka, M., Kakeda, S., Altered structural hippocampal intra-networks in a general elderly Japanese population with mild cognitive impairment, Scientific Reports, 13, 13330, 2023. (Full text)

[56] Nakamura, K., Uchino, E., Sato, N., Araki, A., Terayama, K., Kojima, R., Murashita, K., Itoh, K., Mikami, T., Tamada, Y., Okuno, Y. Individual health-disease phase diagrams for disease prevention based on machine learning, Journal of Biomedical Informatics, 104448, 2023. (Full text)

[55] Shimizu, S., Kondo, J., Onuma, K., Coppo, R., Ota, K., Kamada, M., Harada, Y., Tanaka, Y., Nakazawa, M.A, Tamada, Y., Okuno, Y., Kawada, K., Obama, K., Coffey, R.J., Fujiwara, Y., Inoue, M. Inhibition of the bone morphogenetic protein pathway suppresses tumor growth through downregulation of epidermal growth factor receptor in MEK/ERK-dependent colorectal cancer, Cancer Science, 114, 3636–3648, 2023. (Full text)

[54] Yamauchi, T., Koyama N., Hirai, A., Suganuma, H., Suzuki, S., Murashita, K., Mikami, T., Tamada, Y., Sato, N., Imoto, S., Itoh, K., Nakaji, S. Definition of a dietary pattern expressing the intake of vegetables and fruits and its association with intestinal microbiota, Nutrients, 15(9), 2104, 2023. (Full text)

[53] Tatara, Y., Yamazaki, H., Katsuoka, F., Chiba, M., Saigusa, D., Kasai, S., Nakamura, T., Inoue, J., Aoki, Y., Shoji, M., Motoike, I., Tamada, Y., Hashizume, K., Shoji, M., Kinoshita, K., Murashita, M., Nakaji, S., Yamamoto, M., Itoh, K.. Multiomics and artificial intelligence enabled peripheral blood-based prediction of amnestic mild cognitive impairment, Current Research in Translational Medicine, 71 (1), 103367, 2023. (Full text)

[52] Yamaguchi, T., Nomura, A., Matsubara, A., Hisada, T., Tamada, Y., Mikami, T., Ishida, M., Effect of gut microbial composition and diversity on major inhaled allergen sensitization and onset of allergic rhinitis, Allergology International, 72(1), 135–142, 2023. (Full text)

[51] Tsubokawa, M., Nishimura, M., Mikami, T., Ishida, M., Hisada, T., Tamada, Y. Association of gut microbial genera with heart rate variability in the general Japanese population: the Iwaki cross-sectional research study, Metabolites, 12(8), 730, 2022. (Full text)

[50] Tsubokawa, M., Nishimura, M., Murashita, K., Iwane, T., Tamada, Y. Correlation between glycation-related biomarkers and quality of life in the general Japanese population: the Iwaki cross-sectional research study, International Journal of Environmental Research and Public Health, 19(15), 9391, 2022. (Full text)

[49] Tsubokawa, M., Nishimura, M., Tamada, Y., Nakaji, S. Factors associated with reduced heart rate variability in the general Japanese population: the Iwaki cross-sectional research study, Healthcare, 10(5), 793, 2022. (Full text).

[48] Sato, N., Tamada, Y., Yu, G., Okuno, Y. CBNplot: Bayesian network plots for enrichment analysis, Bioinformatics, 38(10), 2959–2960, 2022 (Full text).

[47] Ozato, N., Yamaguchi, T., Mori, K., Katashima, M., Kumagai, M., Murashita, K., Tamada, Y., Katsuragi, Y., Kakuta, M., Imoto, S., Ihara, K., Nakaji, S. Two Blautia Species Associated with Visceral Fat Accumulation: A One-Year Longitudinal Study, Biology, 11(2), 318, 2022. (Full text)

[46] Nakazawa, M.A., Tamada, Y., Tanaka, Y., Ikeguchi, M., Higashihara, K., Okuno, Y., Novel cancer subtyping method based on patient-specific gene regulatory network, Scientific Reports, 11, 23653, 2021. (Full text)

[45] Tanaka, Y., Higashihara, K., Nakazawa, M.A., Yamashita, F., Tamada, Y., Okuno, Y., Dynamic changes in gene-to-gene regulatory networks in response to SARS-CoV-2 infection, Scientific Reports, 11, 11241, 2021. (Full text)

[44] Uchino, E., Suzuki, K., Sato, N., Kojima, R., Tamada, Y., Hiragi, S., Yokoi, H., Yugami, N., Minamiguchi, S., Haga, S., Yanagita, M., Okuno, Y. Classification of glomerular pathological findings using deep learning and nephrologist–AI collective intelligence approach, International Journal of Medical Informatics, 141, 104231, 2020. (Abstract)

[43] Tanaka, Y., Tamada, Y., Ikeguchi, M., Yamashita, F., Okuno, Y., System-based differential gene network analysis for characterizing a sample-specific subnetwork, Biomolecules, 10(2), 306, 2020. (Full text)

[42] Kasajima, R., Yamaguchi, R., Shimizu, E., Tamada, Y., Niida, A., Tremmel, G., Kishida, T., Aoki, I., Imoto, S., Miyano, S., Uemura, H., Miyagi, Y. Variant analysis of prostate cancer in Japanese patients and a new attempt to predict related biological pathways, Oncology Reports, 43 (3), 943-952, 2020. (Abstract).

[41] Tamada, Y., Memory Efficient Parallel Algorithm for Optimal DAG Structure Search using Direct Communication, Journal of Parallel and Distributed Computing, 119, 27-35, 2018. (Full text, Supplement)

[40] Honda, H.^*, Tamada, Y.^*, Suda, R., Efficient Parallel Algorithm for Optimal DAG Structure Search on Parallel Computer with Torus Network, In Proceedings of the 16th International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP 2016), Lecture Notes in Computer Science 10048, 483-502, 2016. (* These authors contributed equally to this work.) (Publisher site, Conference web site)

[39] Okazawa, H., Mao, Y., Tamura, T., Yuki, Y., Abe, D., Tamada, Y., Imoto, S., Tanaka, H., Homma, H., and Miyano, S., The hnRNP-Htt axis regulates necrotic cell death induced by transcriptional repression through impaired RNA splicing, Cell Death & Diseases, 7, e2207, 2016. (Full Text)

[38] Kato, T., Inoue, H., Imoto, S., Tamada, Y., Miyamoto, T., Matsuo, Y., Nakamura, Y., and Park, J.H., Oncogenic roles of TOPK and MELK, and effective growth suppression by small molecular inhibitors in kidney cancer cells, Oncotarget, 7(4), 17652-17664, 2016. (Full Text)

[37] Nakata, A., Yoshida, R., Yamaguchi, R., Yamauchi, M., Tamada, Y., Fujita, A., Shimamura, T., Imoto, S., Higuchi, T., Nomura, M., Kimura, T., Nokihara, H., Higashiyama, M., Kondoh, K., Nishihara, H., Tojo, A., Yano, S., Miyano, S., and Gotoh, N., Elevated β-catenin pathway as a novel target for patients with resistance to EGF receptor targeting drugs, Scientific Reports, 5, 13076, 2015. (Full Text)

[36] Arima, C.^*, Kajino, T.^*, Tamada, Y.^*, Imoto, S., Shimada, Y., Nakatochi, M., Suzuki, M., Isomura, H., Yatabe, Y., Yamaguchi, T., Yanagisawa, K., Miyano, S., Takahashi, T., Lung adenocarcinoma subtypes definable by lung development-related miRNA expression profiles in association with clinicopathologic features, Carcinogenesis, 35 (10), 2224-2231, 2014. (* These authors contributed equally to this work.) (Publisher site, Pubmed)

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

[34] Ogami, K., Yamaguchi, R., Imoto, S., Tamada, Y., Araki, H., Print C., and Miyano, S., Computational gene network analysis reveals TNF-induced angiogenesis, BMC Systems Biology, 6(Suppl 2), S12, 2012. (Full Text & PDF, Selected paper for Special Issue of GIW2012.)

[33] Wang, L., Hurley, D., Watkins, W., Araki, H., Tamada, Y., Muthukaruppan, A., Ranjard, L., Derkac, E., Imoto, S., Miyano, S., Crampin, E., and Print, C.G., Cell cycle gene networks are associated with melanoma prognosis, PLoS ONE, 7(4), e34247, 2012. (Full Text & PDF)

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

[31] Tamada, Y., Shimamura, T., Yamaguchi, R., Imoto, S., Nagasaki, M., and Miyano, S., SiGN: Large-scale gene network estimation environment for high performance computing, Genome Informatics, 25 (1), 40-52, 2011. (Abstract & PDF)

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

[29] Tamada, Y., Imoto, S., and Miyano, S., Parallel algorithm for learning optimal Bayesian network structure, Journal of Machine Learning Research, 12, 2437−2459, 2011. (Abstract & PDF)

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

[27] Tamada, Y., Imoto, S., Araki, H., Nagasaki, M., Print, C., Charnock-Jones, D.S., and Miyano, S., 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, 2011. (Abstract & PDF, Online Supplement)

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

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

[24] Miyano, S., Yamaguchi, R., Tamada, Y., Nagasaki, M., and Imoto, S., Gene Networks Viewed through Two Models, Proceedings of the 1st International Conference on Bioinformatics and Computational Biology (BICoB 2009), LNBI 4652, 54-66, 2009.

[23] Tamada, Y.^*, Araki, H.^*, Imoto, S.^*, Nagasaki, M., Doi, A., Nakinishi, Y., Tomiyasu, Y., Yasuda, K., Dunmore, B., Sanders, D., Humphreys, S., Print, C., Charnock-Jones, D.S., Tashiro, K., Kuhara, S., and Miyano, S., Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks, Pacific Symposium on Biocomputing (PSB2009), 14, 251-263, 2009. (Online Supplement, * These authors equally contributed to this work.)

[22] Hatanaka, Y., Nagasaki, M., Yamaguchi, R., Obayashi, T., Numata, K., Fujita, A., Shimamura, T., Tamada, Y., Imoto, S., Kinoshita, K., Nakai, K., and Miyano, S., A novel strategy to search conserved transcription factor binding sites among coepressing genes in human, Proc. Eighth International Workshop on Bioinformatics and Systems Biology, 20, 212-221, 2008.

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

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

[19] Nagasaki, M., Yamaguchi, R., Yoshida, R., Imoto, S., Doi, A., Tamada, Y., Matsuno, H., Miyano, S., Higuchi, T. Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data, Genome informatics. (Proceedings of the International Conference on Genome Informatics), 17 (1), 46-61, 2006. (Full Text)

[18] Washio, T., Higuchi, T., Imoto, S., Tamada, Y., Sato, K., and Motoda, H. Graph mining and its application to statistical modeling, Proceedings of the Institute of Statistical Mathematics, 54 (2), 315-332, 2006. (in Japanese with English abstract)

[17] Tamada, Y., Imoto, S., and Miyano, S., Utilizing heterogeneous genomic data to estimate gene networks, Proceedings of the Institute of Statistical Mathematics, 54 (2), 333-356, 2006. (in Japanese with English abstract)

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

[15] Imoto, S., Tamada, Y., Araki, H., Yasuda, K., Print, C.G., Charnock-Jones, S.D., Sanders, D., Savoie, C.J., Tashiro, K., Kuhara, S., and Miyano, S., Computational strategy for discovering druggable gene networks from genome-wide DNA expression profiles, Pacific Symposium on Biocomputing (PSB 2006), 11, 559-571, 2006.

[14] Tamada, Y., Bannai, H., Imoto, S., Katayama, T., Kanehisa, M., and Miyano, S., Utilizing evolutionary information and gene expression data for estimating gene networks with Bayesian network models, Journal of Bioinformatics and Computational Biology, 3 (6), 1295–1313, 2005. (abstract, supplementary information)

[13] Nariai, N., Tamada, Y., Imoto, S., and Miyano, S., Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data, Bioinformatics, 21 Suppl. 2, ii206–ii212, 2005.

[12] Tamada, Y., Imoto, S., Tashiro, K., Kuhara, S., and Miyano, S., Identifying drug active pathways from gene networks estimated by gene expression data, Genome Informatics, 16 (1), 182–191, 2005.

[11] Hirose, O., Nariai, N., Tamada, Y., Bannai, H., Imoto, S. and Miyano, S., Estimating gene networks from expression data and binding location data via Boolean networks, In Proceedings of the First International Workshop on Data Mining and Bioinformatics (DMBIO), Lecture Notes in Computer Science, 3482, 349–356, Springer-varlag, 2005.

[10] Tamada, Y., Kim, S., Bannai, H., Imoto, S., Tashiro, K., Kuhara, S., and Miyano, S., Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection, Bioinformatics, 19 Suppl.2, ii227-ii236, 2003.

[9] Ott, S., Tamada, Y., Bannai, H., Nakai, K., and Miyano, S., Intrasplicing - Analysis of Long Intron Sequences, Proceedings of the eighth Pacific Symposium on Biocomputing (PSB 2003), 8, 339-350, 2003. (The electric version is available on the conference site.)

[8] Tamada, Y., Bannai, H., Maruyama, O., and Miyano, S., Foundations of Designing Knowledge Discovery Processes, Progress in Discovery Science 2001(Lecture Notes in Artificial Intelligence 2281), Springer-Verlag, 459–470, 2002.

[7] Bannai, H., Tamada, Y., Maruyama, O., Nakai, K., and Miyano, S., Extensive Feature Detection of N-Terminal Protein Sorting Signals, Bioinformatics, 18 (2), 298–305, 2002. (abstract, PubMed)

[6] Maruyama, O., Bannai, H., Tamada, Y., Kuhara, S., and Miyano, S., Fast algorithm for extracting multiple unordered short motifs using bit operations, Information Sciences, 146 (1-4), 115–126, 2002. (Abstract)

[5] Maruyama, O., Kuhara, S., Bannai, H., Miyano, S. and Tamada, Y., Fast algorithm for extracting multiple unordered short motifs using bit operations, In Proceedings of the 6th Joint Conference on Information Science (JCIS 2002), 1180–1185, 2002. (Conference proceedings version of the above paper)

[4] Bannai, H., Tamada, Y., Maruyama, O., and Miyano, S., HypothesisCreator: Concepts for Accelerating the Computational Knowledge Discovery Process, Electronic Transactions on Artificial Intelligence, 5, Section B, 73–83, 2001. (Extended version of [2]. Full text)

[3] Bannai, H., Tamada, Y., Maruyama, O., and Miyano, S., VML: A View Modeling Language for Computational Knowledge Discovery, In Proceedings of the 4th International Conference on Discovery Science, 30–44, 2001.

[2] Bannai, H., Tamada, Y., Maruyama, O., and Miyano, S., HypothesisCreator: Concepts for Accelerating the Computational Knowledge Discovery Process, Linköping Electronic Articles in Computer and Information Science, 6, 19, 2001. (Full text)

[1] Bannai, H., Tamada, Y., Maruyama, O., and Miyano, S., Views: Fundamental Building Blocks in the Process of Knowledge Discovery. In Proceedings of the 14th International FLAIRS Conference, 233-238, AAAI Press, 2001.

Book Chapters etc.

[B9]	Tanaka, Y., Kojima, R., Tamada, Y., Kamada, M., and Okuno, Y. Development of artificial intelligence for drug discovery using graph structure Jikken Igaku, 37 (16), 2702-2707, 2019. (Article without review on Japanese medical journal)
[B8]	Iwata, H., Kojima, R., Tamada, Y.． *Drug target discovery, drug repositioning and omics mechanism analysis for in cilico* drug development**. THE CELL, 51 (7), 318-321 (4-7), 2019. (Article without review on Japanese local journal)
[B2]	Imoto, S., Tamada, Y., Araki, H., and Miyano, S., 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, 501-532, 2011.
[B1]	Imoto, S., Tamada, Y., Savoie, C.J., and Miyano, S., 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, 2006.

Other papers, Oral & Poster Presentations, etc

FY2021

(April 2021 - March 2012)

[P78]	Nakazawa, M.A., Tamada, Y., Tanaka Y., Ikeguchi, M., Higashihara, K., Okuno, Y., Novel cancer subtyping method based on patient-specific gene regulatory network, BioRxiv, 2021.03.24.436731, 2021. (Link) (preprint of the paper accepted in Scientific Reports.)
[P77]	Tanaka, Y., Higashihara, K., Nakazawa, M.A., Yamashita, F., Tamada, Y., Okuno, Y., Dynamic change of gene-to-gene regulatory networks in response to SARS-CoV-2 infection, arXiv, 2008.09261, 2020. (Link, Supplementary Information) preprint of the paper accepted in Scientific Reports.

FY2012

(April 2012 - March 2013)

[P55]	Tamada, T., Shimamura, T., Yamaguchi, R., Niida, A., Saito, A., Nagasaki, M., Imoto, S., Miyano, S., (Japanese title. English translation: SiGN-BN: Large scale gene network estimation software using Bayesian network), MEXT Next-generation integrated simulation of living matter Symposium @ Tokyo (Mar. 11, 2013). Poster presentation. (Japanese local symposium)
[P54]	Tamada, T., (Japanese title. English translation: Large scale gene network estimation from gene expression data, Quantitative omics workshop @ Osaka University (Jan. 22, 2013). Oral presentation. (Japanese local workshop)
[P53]	Tamada, Y., Shimamura, T., Yamaguchi, R., Niida, A., Saito, A., Nagasaki, M., Imoto, S., Miyano, S., (Japanese title. English translation: SiGN-BN: Large scale gene network estimation program using Bayesian network, ISLiM workshop @ Tokyo University (Jan. 10-11, 2013). Poster presentation. (Japanese local workshop)
[P52]	Tamada, Y., SiGN: Large-scale Gene Network Estimation Software for K Computer and HGC Supercomputer System, IIBMP: Informatics In Biology, Medicine and Pharmacology @ Tokyo (Oct. 14-17, 2012). Poster presentation.
[P51]	Tamada, Y., Large-scale Gene Network Estimation with K Computer, The 50-th annual meeting of the Biophysical Society of Japan @ Nagoya University (Sep. 23, 2012). Oral presentation．
[P50]	Tamada, Y., Shimamura, T., Yamaguchi, R., Niida, A., Saito A., Imoto S., Nagasaki, M., Miyano, S., (Japanese title. English translation: Cancer prognosis prediction and drug response pathway prediction using gene network estimation with supercomptuer), The 12 th The University of Tokyo Life science symposium @ The University of Tokyo (Jun. 30, 2012). Poster presentation. (Japanese local symposium)

FY2011

(April 2011 - March 2012)

[P49]	Tamada, Y., (Japanese title. English translation: Large scale gene network estimation with supercomputer, 情報処理学会第74回全国大会 @ Nagoya Institute of Technology (Mar. 8, 2012). Oral presentation. (Japanese local workshop)
[P48]	Tamada, Y., Shimamura, T., Yamaguchi, R., Niida, A., Saito, A., Nagasaki, M., Imoto, S., Miyano, S., (Japanese title. English translation: SiGN-BN: Large scale gene network estimation software using Bayesian network, 文部科学省「革新的ハイパフォーマンス・コンピューティング・インフラ（HPCI）の構築」・次世代ナノ統合シミュレーションソフトウェアの研究開発（ナノ）・次世代生命体統合シミュレーションソフトウェアの研究開発（ライフ）公開シンポジウム @ ニチイ学館　神戸ポートアイランドセンター（兵庫県神戸市） (Mar. 5-6, 2012). Poster presentation.
[P47]	Tamada, Y., Shimamura, T., Yamaguchi, R., Niida, A., Saito, A., Nagasaki, M., Imoto, S., Miyano, S., SiGN-BN: ベイジアンネットワークによる大規模遺伝子ネットワーク推定プログラム, ISLiM 成果報告会 2011 @ Takeda Hall, The University of Tokyo (Dec. 21-22, 2011). Poster Presentation.
[P46]	Tamada, Y., 大規模遺伝子ネットワーク推定ソフトウェア SiGN, HGC スパコン Web サービス利用法講習会 @ 東京大学医科学研究所ヒトゲノム解析センター（東京都港区） (Oct. 25, 2011). 講習会講師.
[P45]	Tamada, Y., Shimamura, T., Yamaguchi, R., Nagasaki, M., Imoto, S., Miyano, S., 大規模遺伝子ネットワーク推定ソフトウェア SiGN, Biosupercomuting Summer School 2011 @ Awaji Yumebutai International Conference Center (Sep. 26 - 27, 2011). Poster display (no presentation).

FY 2010

(April 2010 - March 2011)

[P44]	Tamada, Y., Large-scale gene network estimation algorithms with high performance computing, IPR Seminer: New Era of Biosimulations with Supercomputers @ Institute for Protein Research (IPR), Osaka University (Mar. 4, 2011). Oral Presentation.
[P43]	Tamada, Y, (Title in Japanese), The 1st Workshop for Applied Systems Biology (Domestic workshop) @ Tokyo, Japan (Feb. 28, 2011). Oral Presentation.
[P42]	Tamada, Y, Shimamura, T., Yamaguchi, R., Nagasaki, M., Imoto, S., and Miyano, S., (Title in Japanese), The 3rd Biosupercomputing Symposium @ Kobe, Japan (Feb. 21-22, 2011). Poster Presentation. Selected as the Best Poster Award.
[P41]	Tamada, Y, (Title in Japanese), The 3rd Biosupercomputing Symposium @ Kobe, Japan (Feb. 21-22, 2011). Oral Presentation.
[P40]	Tamada, Y, (Title in Japanese), Seminar at Suda Laboratory at Department of Computer Science, Graduate School of Information Science and Technology, The University of tokyo. @ Tokyo, Japan (Jan. 28, 2011). Seminar Presentation.
[P39]	Tamada, Y, Shimamura, T., Yamaguchi, R., Imoto, S., and Miyano, S., SiGN: Large-scale gene network estimation environment for high performance computing, The 2010 Annual Conference of The Japanese Society for Bioinformatics (JSBi2010) @ Fukuoka, Japan (Dec. 13-15, 2010). Poster Presentation. Selected Poster for an Oral Presentation.
[P38]	Tamada, Y, (Title in Japanese), Domestic workshop held at Shonan village center @ Kanagawa, Japan (July 5, 2010). Oral & Poster Presentation.

FY 2009

(April 2009 - March 2010)

[P37]	Tamada, Y., Imoto, S., Nagasaki, M., and Miyano, S., Parallel algorithms for estimating multi-scale gene networks using nonparametric Bayesian Networks, The 2nd Biosupercomputing Symposium (BSCS2010) @ Tokyo, Japan (Mar. 18-19, 2010). Poster Presentation. Selected as the Poster Award.
[P36]	Tamada, Y., Supercomputing on Gene Network Estimation with Bayesian Networks, The 2nd NUS-UT Workshop on Computational Systems Biology @ Tokyo, Japan (Feb. 22-23, 2010). Oral Preseantation.
[P35]	Tamada, Y., Imoto, S., Araki, H., Nagasaki, M., and Miyano S., A Parallel Algorithm for Estimating Genome-Wide Gene Networks using Nonparametric Bayesian Networks. The 20th International Conference on Genome Informatics (GIW2009) @ Yokohama, Japan (Dec 14-16, 2009). Poster Presentation. Selected Poster for an Oral Presetantion.
[P34]	Tamada, Y., Imoto, S., Nagasaki, M., and Miyano S., Large Scale Gene Network Estimation using Nonparamtric Bayesian Networks and Its Application to the Signal Transduction Pathway Analysis, The 2nd Joint Workshop on Computational Science (JWCS2009) @ RIKEN Yokohama, Japan (Jul. 9-10, 2009). Poster Presentation.
[P33]	Tamada, Y., Shimamura, T., Fujita, A., Niida, A., Kojima, K., Perrier, E., Numata, K., Nagasaki, M., Saito, A., Imoto, S., and Miyano, S., (Title in Japanese), Domestic workshop held at Institute of Medical Science, The University of Tokyo @ Tokyo, Japan (May 28-19, 2009). Poster Presentation.

FY 2008

(April 2008 - March 2009)

[P32]	Tamada, Y., Araki, H., Imoto, S., Nagasaki, M., Doi, A., Nakanishi, Y., Tomiyasu, Y., Yasuda, K., Dunmore, B., Sanders, D., Humphreys, S., Print, C., Charnock-Jones, D.S., Tashiro, K., Kuhara, S., and Miyano, S., Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks, The Pasific Symposium on Biocomputing (PSB) 2009 @ Hawaii, USA (Jan. 5-9, 2009). Oral Presentation.
[P31]	Tamada, Y., Imoto, S., Nagasaki, M., and Miyano, S., (Title in Japanese), Biosupercomputing Symposium (BSCS) 2008 @ Tokyo, Japan. (Dec. 25-26, 2008). Poster Presentation.
[P30]	Tamada, Y., Shimamura, T., Yamaguchi, R., Imoto, S., Nagasaki, M., Saito, A., Ueno, K., Hatanaka, Y., Fujita, A., Numata, K., Perrier, E., Kojima, K., Yoshida, R., Higuchi, T., Yamauchi, M., Gotoh, N., and Miyano, S., Computational Strategies for Reconstructing Large-Scale Gene Networks, The 1st Joint Workshop on Computational Science @ RIKEN Wako, Japan (Jul. 7-8, 2008). Poster Presentation.
[P29]	Tamada, Y., Imoto, S., Araki, H., Nagasaki, M., Yamaguchi, R., Tomiyasu, Y., Yasuda, K., Print, C.G., Charnock-Jones, S., Tashiro, K., Kuhara, S., and Miyano, S., Strategic Method for Finding Signaling Pathways that Control Drug-related Gene Networks, The 16th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2008) @ Toronto, Canada (Jul. 20-23, 2008). Poster Presentation.
[P28]	Tamada, Y., Computational Drug Target Gene Discovery, The 1st NUS-UT Joint Workshop on Computational Systems Biology @ Singapore (Sep. 29-30, 2008). Oral Presentation.

FY 2006

(April 2006 - March 2007)

[P27]

Tamada, Y., Bannai, H., Imoto, S., Katayama, T., Kanehisa, M., Tashiro, K., Kuhara, S., and Miyano, S., (Title in Japanese), Domestic seminor on statistical mathematics @ The Insitute of Statistical Mathematics, Tokyo, Japan (May 10, 2006). Oral Presentation.

FY 2005

(April 2005 - March 2006)

[P26]	Tamada, Y., (Title in Japanese), Domestic annual workshop at the Institute of Statistical Mathematics, Tokyo, Japan (Mar. 17, 2006). Oral Presentation.
[P25]	Tamada, Y., Bannai, H., Imoto, S., Katayama, T., Kanehisa, M., Tashiro, K., Kuhara, S., and Miyano, S. (Title in Japanese), Domestic workshop on bioinformatics and statistical science held at the Institute of Statistical Mathematics @ Tokyo, Japan (Jan. 16 2006). Oral Presentation
[P24]	Tamada, Y., Imoto, S., Higuchi, T., Tashiro, K., Kuhara, S., and Miyano S., Identification of Drug Active Pathways Based on Gene Networks and Drug Response Gene Expression Data, Pacific Symposium on Biocomputing (PSB) 2006 @ Hawaii, USA (Jan. 3-7, 2006). Poster Presentation.
[P23]	Tamada, Y., Imoto, S., Tashiro K., Kuhara S., and Miyano S., Identification of Drug Active Pathways Based on Gene Networks Estimated by Bayesian Networks and Gene Expression Data, The 16th International Conference on Genome Informatics (GIW2005) @ Yokohama, Japan (Dec. 19-21, 2005). Poster Presentation.
[P22]	Tamada, Y., (Title in Japanese), Domestic workshop on data assimilation @ Okinawa, Japan (Nov. 21-22, 2005). Poster Presentation.
[P21]	Tamada, Y., (Title Forgotten), European Conference on Computational Biology (ECCB05). @ Madrid, Spain (Sep. 28 - Oct. 1, 2005). Poster Presentation.
[P20]	Tamada, Y., Imoto, S., Tashiro, K., Kuhara, S., and Miyano, S., Identifying Drug Active Pathways from Gene Networks Estimated by Gene Expression Data, The fifth Annual International Workshop on Bioinformatics and Systems Biology (ISBS2005) @ Berlin, Germany (Aug. 22-25, 2005). Oral Presentation.

FY 2004

(April 2004 - March 2005)

[P19]	Tamada, Y., Bannai, B., Imoto, S., Katayama, T., Kanehisa, M. and Miyano, S., Estimating gene networks from gene expression data and evolutionary information using Bayesian network models, The 3rd Asia Pacific Bioinformatics Conference (APBC2005) @ Singapore (Jan. 17-21, 2005). Poster Presentation.
[P18]	Tamada, Y., Bannai, B., Imoto, S., Katayama, T., Kanehisa, M. and Miyano, S., Estimating gene networks utilizing evolutionary information and gene expression data with Bayesian network models, Pacific Symposium on Biocomputing (PSB) 2005 @ Hawaii, USA (Jan. 4-8, 2005). Poster Presentation.
[P17]	Nariai, N., Tamada, Y., Imoto, S., and Miyano, S., Estimating Regulatory Networks from DNA Microarrays and Protein-Protein Interactions, December, 2004 (GIW 2004 Poster).
[P16]	Tamada, Y., Bannai, B., Imoto, S., Katayama, T., Kanehisa, M., and Miyano, S., Modeling gene networks utilizing evolutionary information using Bayesian network models, December, 2004 (GIW 2004 Poster).
[P15]	Tamada, Y., Bannai, H., Imoto, S., Katayama, K., and Miyano, S., (Title in Japanese), Domestic conference on statistics @ Hanamaki, Iwate, Japan (Sep. 4, 2004). Oral Presentation.

FY 2003

(April 2003 - March 2004)

[P14]	Tamada, Y., Kim, S.Y., Bannai, B., Imoto, S., Tashiro, L., Kuhara, S., and Miyano, S., Combining Gene Expression Data with DNA Sequence Information for Estimating Gene Networks Using Bayesian Network Model, Genome Informatics, 14, 352-353, 2003. Poster Presentation at The 14th International Conference on Genome Informatics (GIW2003) @ Yokohama, Japan (Dec. 14-17, 2003).
[P13]	Tamada, Y., Kim, S.Y., Bannai, H., Imoto, S., Tashiro, K., Kuhara, S., and Miyano S., Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection, European Conference on Computational Biology (ECCB) 2003 @ Paris, France (Sep. 27-30, 2003). Poster & Oral Presentation.
[P12]	Tamada, Y., Kim, S.Y., Bannai, H., Imoto, S., Tashiro, K., Kuhara, S., and Miyano, S., (Title in Japanese), Domestic conference on statistics @ Nagoya, Japan (Aug. 3, 2003). Oral Presentation.
[P11]	Tamada, Y., Kim, S.Y., Bannai, H., Imoto, S., Tashiro, K., Kuhara, S., and Miyano, S., Combining Bayesian Network Model with Promoter Element Detection for Estimating Gene Networks from Gene Expression Data, The 11th International Conference on Intelligent Systems for Molecular Biology (ISMB2003) @ Brisbane, Australia (Jun. 29 - Jul. 3, 2003). Poster Presentation.

FY 2002

(April 2002 - March 2003)

[P10]	Ott, S. ^, Tamada, Y.^, Bannai, H., Nakai, K., and Miyano, S., Intrasplicing - Analysis of Long Intron Sequences, Eighth Pacific Symposium on Biocomputing (PSB 2003) @ Hawaii, USA (Jan. 3-7, 2003). Poster Presentation. (*) Equally contributed to this work.
[P9]	Tamada, Y., Ott, S., Bannai, B., Kim, S.Y., Nakai, K., and Miyano, S., Analysis of Aberrant Splicing Data, Genome Informatics 13, 424-425, 2002. Poster Presentation at The 13th International Conference on Genome Informatics (GIW2002) @ Tokyo, Japan (Dec. 16-18, 2002).
[P8]	Bannai, B., Nakai, K., Ott, S., and Tamada, Y., Search for Structure in Long Introns, The 10th International Conference on Intelligent Systems for Molecular Biology (ISMB2002) @ Edmonton, Canada (Aug. 3-7, 2002). Co-author's Poster Presentation.
[P7]	Bannai, B., Tamada, Y., Ott, S., Kim, S.Y., Nakai, K., and Miyano, S., Correlation between Intron Length and Its Base Composition, The 10th International Conference on Intelligent Systems for Molecular Biology (ISMB2002) @ Edmonton, Canada (Aug. 3-7, 2002). Co-author's Poster Presentation.

FY 2001

(April 2001 - March 2002)

[P6]

Bannai, B., Tamada, Y., Maruyama, O., Nakai, K., and Miyano, S., iPSORT: Simple rules for predicting N-terminal protein sorting signals, The 9th International Conference on Intelligent Systems for Molecular Biology (ISMB2001) @ Copenhagen, Denmark (Jul. 21-25, 2001). Co-author's Poster Presentation.

FY 2000

(April 2000 - March 2001)

[P5]	Tamada, Y., Bannai, B., Maruyama, O., and Miyano, S., HypothesisCreator: A Framework for Knowledge Discovery Application Development. Genome Informatics 11, 360-361, 2000. Poster Presentation at The 11th Workshop on Genome Informatics (GIW2000) @ Tokyo, Japan (Dec. 18-19, 2000).
[P4]	Bannai, B., Tamada, Y., Maruyama, O., Nakai, K., and Miyano, S., Charaterization of Subcellular Localization Signals Using HypothesisCreator. Genome Informatics, 11, 362-363, 2000. Co-author's Poster Presentation at The 11th Workshop on Genome Informatics (GIW2000) @ Tokyo, Japan (Dec. 18-19, 2000).
[P3]	Bannai, B., Tamada, Y., Maruyama, O., and Miyano, S., HypothesisCreator : An environment that assists the design and implementation of computational experiments for knowledge discovery from genomic databases, The 8th International Conference on Intelligent Systems for Molecular Biology (ISMB2000) @ San Diego, California, USA (Aug. 19-23, 2000).
[P2]	Maruyama, O., Tamada, Y., Matsumoto, S., Miyano, S., ViewDesigner: A Tool of Designing Views on Data in Discovery System HypothesisCreator. Currents in Computational Molecular Biology (Frontiers Science Series), 30, 22-23, 2000. Co-author's Poster Presentation at The 4th Annual International Conference on Computational Molecular Biology (RECOMB2000) @ Tokyo, Japan (Apr. 8-11, 2000).

FY 1999

(April 1999 - March 2000)

[P1]	Tamada, Y., Matsumoto, S., Maruyama, O., and Miyano, S., ViewDesigner: A Tool for Designing Viewscopes in Discovery System HypothesisCreator. Genome Informatics, 10, 215-216, 1999. Software Demonstration at The 10th Workshop on Genome Informatics (GIW99) @ Tokyo Japan (Dec. 14-15, 1999).

[61]	Sugiyama, K., Nomura, O., Irie, J., Ishizawa, Y., Takauji, S., Hayakawa, M., Tamada, Y., Hanada, H. Effects of rewarming therapies on outcomes in accidental hypothermia: A secondary analysis of a multicenter prospective study, The American Journal of Emergency Medicine, 79, 91-96, 2024. (Full text)
[60]	Kasai, S., Watanabe, K., Ide, S., Ishimoto, Y., Sasaki, M., Umemura Y., Tatsuo, S., Kakeda, S., Mikami, T., Tamada, Y., Miki, Y., Wakabayashi, K., Tomiyama, M., Kakeda, S. FLAIR Hyperintensities in the Anterior Part of the Callosal Splenium in the Elderly Population: A Large Cohort Study, Academic Radiology, 2024. In Press. (Full text)
[59]	Tomoto, M., Mineharu, Y., Sato, N., Tamada, Y., Nogami-Itoh, M., Kuroda, M., Adachi, J., Takeda, Y., Mizuguchi, K., Kumanogoh, A., Natsume-Kitatani, Y., Okuno, Y. Idiopathic pulmonary fibrosis-specific Bayesian network integrating extracellular vesicle proteome and clinical information, Scientific Reports, 14, 1315, 2024. (Full text)
[58]	Umemura, Y., Watanabe, K., Kasai, S., Ide, S., Ishimoto, Y., Sasaki, M., Nagaya, H., Tatsuo, S., Mikami, T., Tamada, Y., Tomiyama, M., Kakeda, S. Choroid plexus enlargement in mild cognitive impairment on MRI: a large cohort study, European Radiology, 2024. (Full text)
[57]	Kasai, S., Watanabe, K., Umemura, Y., Ishimoto, Y., Sasaki, M., Nagaya, H., Tatsuo, S., Mikami, T., Tamada, Y., Ide, S., Tomiyama, M., Matsuzaka, M., Kakeda, S., Altered structural hippocampal intra-networks in a general elderly Japanese population with mild cognitive impairment, Scientific Reports, 13, 13330, 2023. (Full text)
[56]	Nakamura, K., Uchino, E., Sato, N., Araki, A., Terayama, K., Kojima, R., Murashita, K., Itoh, K., Mikami, T., Tamada, Y., Okuno, Y. Individual health-disease phase diagrams for disease prevention based on machine learning, Journal of Biomedical Informatics, 104448, 2023. (Full text)
[55]	Shimizu, S., Kondo, J., Onuma, K., Coppo, R., Ota, K., Kamada, M., Harada, Y., Tanaka, Y., Nakazawa, M.A, Tamada, Y., Okuno, Y., Kawada, K., Obama, K., Coffey, R.J., Fujiwara, Y., Inoue, M. Inhibition of the bone morphogenetic protein pathway suppresses tumor growth through downregulation of epidermal growth factor receptor in MEK/ERK-dependent colorectal cancer, Cancer Science, 114, 3636–3648, 2023. (Full text)
[54]	Yamauchi, T., Koyama N., Hirai, A., Suganuma, H., Suzuki, S., Murashita, K., Mikami, T., Tamada, Y., Sato, N., Imoto, S., Itoh, K., Nakaji, S. Definition of a dietary pattern expressing the intake of vegetables and fruits and its association with intestinal microbiota, Nutrients, 15(9), 2104, 2023. (Full text)
[53]	Tatara, Y., Yamazaki, H., Katsuoka, F., Chiba, M., Saigusa, D., Kasai, S., Nakamura, T., Inoue, J., Aoki, Y., Shoji, M., Motoike, I., Tamada, Y., Hashizume, K., Shoji, M., Kinoshita, K., Murashita, M., Nakaji, S., Yamamoto, M., Itoh, K.. Multiomics and artificial intelligence enabled peripheral blood-based prediction of amnestic mild cognitive impairment, Current Research in Translational Medicine, 71 (1), 103367, 2023. (Full text)
[52]	Yamaguchi, T., Nomura, A., Matsubara, A., Hisada, T., Tamada, Y., Mikami, T., Ishida, M., Effect of gut microbial composition and diversity on major inhaled allergen sensitization and onset of allergic rhinitis, Allergology International, 72(1), 135–142, 2023. (Full text)
[51]	Tsubokawa, M., Nishimura, M., Mikami, T., Ishida, M., Hisada, T., Tamada, Y. Association of gut microbial genera with heart rate variability in the general Japanese population: the Iwaki cross-sectional research study, Metabolites, 12(8), 730, 2022. (Full text)
[50]	Tsubokawa, M., Nishimura, M., Murashita, K., Iwane, T., Tamada, Y. Correlation between glycation-related biomarkers and quality of life in the general Japanese population: the Iwaki cross-sectional research study, International Journal of Environmental Research and Public Health, 19(15), 9391, 2022. (Full text)
[49]	Tsubokawa, M., Nishimura, M., Tamada, Y., Nakaji, S. Factors associated with reduced heart rate variability in the general Japanese population: the Iwaki cross-sectional research study, Healthcare, 10(5), 793, 2022. (Full text).
[48]	Sato, N., Tamada, Y., Yu, G., Okuno, Y. CBNplot: Bayesian network plots for enrichment analysis, Bioinformatics, 38(10), 2959–2960, 2022 (Full text).
[47]	Ozato, N., Yamaguchi, T., Mori, K., Katashima, M., Kumagai, M., Murashita, K., Tamada, Y., Katsuragi, Y., Kakuta, M., Imoto, S., Ihara, K., Nakaji, S. Two Blautia Species Associated with Visceral Fat Accumulation: A One-Year Longitudinal Study, Biology, 11(2), 318, 2022. (Full text)
[46]	Nakazawa, M.A., Tamada, Y., Tanaka, Y., Ikeguchi, M., Higashihara, K., Okuno, Y., Novel cancer subtyping method based on patient-specific gene regulatory network, Scientific Reports, 11, 23653, 2021. (Full text)
[45]	Tanaka, Y., Higashihara, K., Nakazawa, M.A., Yamashita, F., Tamada, Y., Okuno, Y., Dynamic changes in gene-to-gene regulatory networks in response to SARS-CoV-2 infection, Scientific Reports, 11, 11241, 2021. (Full text)
[44]	Uchino, E., Suzuki, K., Sato, N., Kojima, R., Tamada, Y., Hiragi, S., Yokoi, H., Yugami, N., Minamiguchi, S., Haga, S., Yanagita, M., Okuno, Y. Classification of glomerular pathological findings using deep learning and nephrologist–AI collective intelligence approach, International Journal of Medical Informatics, 141, 104231, 2020. (Abstract)
[43]	Tanaka, Y., Tamada, Y., Ikeguchi, M., Yamashita, F., Okuno, Y., System-based differential gene network analysis for characterizing a sample-specific subnetwork, Biomolecules, 10(2), 306, 2020. (Full text)
[42]	Kasajima, R., Yamaguchi, R., Shimizu, E., Tamada, Y., Niida, A., Tremmel, G., Kishida, T., Aoki, I., Imoto, S., Miyano, S., Uemura, H., Miyagi, Y. Variant analysis of prostate cancer in Japanese patients and a new attempt to predict related biological pathways, Oncology Reports, 43 (3), 943-952, 2020. (Abstract).
[41]	Tamada, Y., Memory Efficient Parallel Algorithm for Optimal DAG Structure Search using Direct Communication, Journal of Parallel and Distributed Computing, 119, 27-35, 2018. (Full text, Supplement)
[40]	Honda, H.^, Tamada, Y.^, Suda, R., Efficient Parallel Algorithm for Optimal DAG Structure Search on Parallel Computer with Torus Network, In Proceedings of the 16th International Conference on Algorithms and Architectures for Parallel Processing (ICA3PP 2016), Lecture Notes in Computer Science 10048, 483-502, 2016. (* These authors contributed equally to this work.) (Publisher site, Conference web site)
[39]	Okazawa, H., Mao, Y., Tamura, T., Yuki, Y., Abe, D., Tamada, Y., Imoto, S., Tanaka, H., Homma, H., and Miyano, S., The hnRNP-Htt axis regulates necrotic cell death induced by transcriptional repression through impaired RNA splicing, Cell Death & Diseases, 7, e2207, 2016. (Full Text)
[38]	Kato, T., Inoue, H., Imoto, S., Tamada, Y., Miyamoto, T., Matsuo, Y., Nakamura, Y., and Park, J.H., Oncogenic roles of TOPK and MELK, and effective growth suppression by small molecular inhibitors in kidney cancer cells, Oncotarget, 7(4), 17652-17664, 2016. (Full Text)
[37]	Nakata, A., Yoshida, R., Yamaguchi, R., Yamauchi, M., Tamada, Y., Fujita, A., Shimamura, T., Imoto, S., Higuchi, T., Nomura, M., Kimura, T., Nokihara, H., Higashiyama, M., Kondoh, K., Nishihara, H., Tojo, A., Yano, S., Miyano, S., and Gotoh, N., Elevated β-catenin pathway as a novel target for patients with resistance to EGF receptor targeting drugs, Scientific Reports, 5, 13076, 2015. (Full Text)
[36]	Arima, C.^, Kajino, T.^, Tamada, Y.^, Imoto, S., Shimada, Y., Nakatochi, M., Suzuki, M., Isomura, H., Yatabe, Y., Yamaguchi, T., Yanagisawa, K., Miyano, S., Takahashi, T., Lung adenocarcinoma subtypes definable by lung development-related miRNA expression profiles in association with clinicopathologic features, Carcinogenesis, 35 (10), 2224-2231, 2014. ( These authors contributed equally to this work.) (Publisher site, Pubmed)
[35]	Affara, M., Sanders, D., Araki, A., Tamada, Y., Dunmore, B.J., Humphreys, S., Imoto, S., Savoie, C., Miyano, S., Kuhara, S., Jeffries, D., Print, C., and Charnock-Jones, D.S., Vasohibin-1 is identified as a master-regulator of endothelial cell apoptosis using gene network analysis, BMC Genomics, 14, 23, 2013.
[34]	Ogami, K., Yamaguchi, R., Imoto, S., Tamada, Y., Araki, H., Print C., and Miyano, S., Computational gene network analysis reveals TNF-induced angiogenesis, BMC Systems Biology, 6(Suppl 2), S12, 2012. (Full Text & PDF, Selected paper for Special Issue of GIW2012.)
[33]	Wang, L., Hurley, D., Watkins, W., Araki, H., Tamada, Y., Muthukaruppan, A., Ranjard, L., Derkac, E., Imoto, S., Miyano, S., Crampin, E., and Print, C.G., Cell cycle gene networks are associated with melanoma prognosis, PLoS ONE, 7(4), e34247, 2012. (Full Text & PDF)
[32]	Hurley, D., Araki, H., Tamada, Y., Dunmore, B., Sanders, D., Humphreys, S., Affara, M., Imoto, S., Yasuda, K., Tomiyasu, Y., Tashiro, K., Savoie, C., Cho, V., Smith, S., Kuhara, S., Miyano, S., Charnock-Jones, D.S., J. Crampin, E.J., and Print, C.G., Gene network inference and visualization tools for biologists: application to new human transcriptome datasets, Nucleic Acids Research 40(6), 2377-2398, 2012. (Abstract & PDF)
[31]	Tamada, Y., Shimamura, T., Yamaguchi, R., Imoto, S., Nagasaki, M., and Miyano, S., SiGN: Large-scale gene network estimation environment for high performance computing, Genome Informatics, 25 (1), 40-52, 2011. (Abstract & PDF)
[30]	Imoto, S., Kojima, K., Perrier, E., Tamada, Y., and Miyano S., Searching optimal Bayesian network structure on constraint search space: super-structure approach, Lecture Notes in Computer Science, Sprigner-Verlag, 6797, 210-218, 2011.
[29]	Tamada, Y., Imoto, S., and Miyano, S., Parallel algorithm for learning optimal Bayesian network structure, Journal of Machine Learning Research, 12, 2437−2459, 2011. (Abstract & PDF)
[28]	Tamada, Y., Yamaguchi, R., Imoto, S., Hirose, O., Yoshida, R., Nagasaki, M., and Miyano, S., SiGN-SSM: open source parallel software for estimating gene networks with state space models, Bioinformatics, 27 (8), 1172-1173, 2011. (Abstract, SiGN-SSM Web Site)
[27]	Tamada, Y., Imoto, S., Araki, H., Nagasaki, M., Print, C., Charnock-Jones, D.S., and Miyano, S., 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, 2011. (Abstract & PDF, Online Supplement)
[26]	Shimamura, T., Imoto, S., Nagasaki, M., Yamauchi, M., Yamaguchi, R., Fujita, A., Tamada, Y., Gotoh, N., and Miyano, S., Collocation-based sparse estimation for inferring continuous-time dynamic gene networks, Genome Informatics, 24, 164-178, 2010.
[25]	Araki, H.^, Tamada, Y.^, Imoto, S.^, Dunmore, B., Sanders, D., Humphrey, S., Nagasaki, M., Doi, A., Nakanishi, Y., Yasuda, K., Tomiyasu, Y., Tashiro, K., Print, C., Charnock-Jones, D.S, Kuhara, S., and Miyano, S., Analysis of PPARα-dependent and PPARα-independent transcript regulation following fenofibrate treatment of human endothelial cells, Angiogenesis, 12 (3), 221-229, 2009. ( These authors equally contributed to this work.)
[24]	Miyano, S., Yamaguchi, R., Tamada, Y., Nagasaki, M., and Imoto, S., Gene Networks Viewed through Two Models, Proceedings of the 1st International Conference on Bioinformatics and Computational Biology (BICoB 2009), LNBI 4652, 54-66, 2009.
[23]	Tamada, Y.^, Araki, H.^, Imoto, S.^, Nagasaki, M., Doi, A., Nakinishi, Y., Tomiyasu, Y., Yasuda, K., Dunmore, B., Sanders, D., Humphreys, S., Print, C., Charnock-Jones, D.S., Tashiro, K., Kuhara, S., and Miyano, S., Unraveling dynamic activities of autocrine pathways that control drug-response transcriptome networks, Pacific Symposium on Biocomputing (PSB2009), 14, 251-263, 2009. (Online Supplement, These authors equally contributed to this work.)
[22]	Hatanaka, Y., Nagasaki, M., Yamaguchi, R., Obayashi, T., Numata, K., Fujita, A., Shimamura, T., Tamada, Y., Imoto, S., Kinoshita, K., Nakai, K., and Miyano, S., A novel strategy to search conserved transcription factor binding sites among coepressing genes in human, Proc. Eighth International Workshop on Bioinformatics and Systems Biology, 20, 212-221, 2008.
[21]	Affara, M., Dunmore, B., Savoie, C.J., Imoto, S., Tamada, Y., Araki, H., Charnock-Jones, S., Miyano, S., and Print, C.G., Understanding endothelial cell apoptosis: What can the transcriptome glycome and proteome reveal?, Philosophical Transactions of Royal Society, 62 (1484), 1469-1487, 2007.
[20]	Termier, A., Tamada, Y., Numata, K., Imoto, S., Washio, T., and Higuchi, T., DIGDAG, a first algorithm to mine closed frequent embedded sub-DAGs, Proc. 5th International Workshop on Mining and Learning with Graphs, 2007. (MLG2007, Refereed conference).
[19]	Nagasaki, M., Yamaguchi, R., Yoshida, R., Imoto, S., Doi, A., Tamada, Y., Matsuno, H., Miyano, S., Higuchi, T. Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data, Genome informatics. (Proceedings of the International Conference on Genome Informatics), 17 (1), 46-61, 2006. (Full Text)
[18]	Washio, T., Higuchi, T., Imoto, S., Tamada, Y., Sato, K., and Motoda, H. Graph mining and its application to statistical modeling, Proceedings of the Institute of Statistical Mathematics, 54 (2), 315-332, 2006. (in Japanese with English abstract)
[17]	Tamada, Y., Imoto, S., and Miyano, S., Utilizing heterogeneous genomic data to estimate gene networks, Proceedings of the Institute of Statistical Mathematics, 54 (2), 333-356, 2006. (in Japanese with English abstract)
[16]	Termier, A., Tamada, Y., Imoto, S., Washio, T., and Higuchi, T., From closed tree mining towards closed DAG mining, Proc. International Workshop on Data Mining and Statistical Science, 1-7, 2006.
[15]	Imoto, S., Tamada, Y., Araki, H., Yasuda, K., Print, C.G., Charnock-Jones, S.D., Sanders, D., Savoie, C.J., Tashiro, K., Kuhara, S., and Miyano, S., Computational strategy for discovering druggable gene networks from genome-wide DNA expression profiles, Pacific Symposium on Biocomputing (PSB 2006), 11, 559-571, 2006.
[14]	Tamada, Y., Bannai, H., Imoto, S., Katayama, T., Kanehisa, M., and Miyano, S., Utilizing evolutionary information and gene expression data for estimating gene networks with Bayesian network models, Journal of Bioinformatics and Computational Biology, 3 (6), 1295–1313, 2005. (abstract, supplementary information)
[13]	Nariai, N., Tamada, Y., Imoto, S., and Miyano, S., Estimating gene regulatory networks and protein-protein interactions of Saccharomyces cerevisiae from multiple genome-wide data, Bioinformatics, 21 Suppl. 2, ii206–ii212, 2005.
[12]	Tamada, Y., Imoto, S., Tashiro, K., Kuhara, S., and Miyano, S., Identifying drug active pathways from gene networks estimated by gene expression data, Genome Informatics, 16 (1), 182–191, 2005.
[11]	Hirose, O., Nariai, N., Tamada, Y., Bannai, H., Imoto, S. and Miyano, S., Estimating gene networks from expression data and binding location data via Boolean networks, In Proceedings of the First International Workshop on Data Mining and Bioinformatics (DMBIO), Lecture Notes in Computer Science, 3482, 349–356, Springer-varlag, 2005.
[10]	Tamada, Y., Kim, S., Bannai, H., Imoto, S., Tashiro, K., Kuhara, S., and Miyano, S., Estimating gene networks from gene expression data by combining Bayesian network model with promoter element detection, Bioinformatics, 19 Suppl.2, ii227-ii236, 2003.
[9]	Ott, S., Tamada, Y., Bannai, H., Nakai, K., and Miyano, S., Intrasplicing - Analysis of Long Intron Sequences, Proceedings of the eighth Pacific Symposium on Biocomputing (PSB 2003), 8, 339-350, 2003. (The electric version is available on the conference site.)
[8]	Tamada, Y., Bannai, H., Maruyama, O., and Miyano, S., Foundations of Designing Knowledge Discovery Processes, Progress in Discovery Science 2001(Lecture Notes in Artificial Intelligence 2281), Springer-Verlag, 459–470, 2002.
[7]	Bannai, H., Tamada, Y., Maruyama, O., Nakai, K., and Miyano, S., Extensive Feature Detection of N-Terminal Protein Sorting Signals, Bioinformatics, 18 (2), 298–305, 2002. (abstract, PubMed)
[6]	Maruyama, O., Bannai, H., Tamada, Y., Kuhara, S., and Miyano, S., Fast algorithm for extracting multiple unordered short motifs using bit operations, Information Sciences, 146 (1-4), 115–126, 2002. (Abstract)
[5]	Maruyama, O., Kuhara, S., Bannai, H., Miyano, S. and Tamada, Y., Fast algorithm for extracting multiple unordered short motifs using bit operations, In Proceedings of the 6th Joint Conference on Information Science (JCIS 2002), 1180–1185, 2002. (Conference proceedings version of the above paper)
[4]	Bannai, H., Tamada, Y., Maruyama, O., and Miyano, S., HypothesisCreator: Concepts for Accelerating the Computational Knowledge Discovery Process, Electronic Transactions on Artificial Intelligence, 5, Section B, 73–83, 2001. (Extended version of [2]. Full text)
[3]	Bannai, H., Tamada, Y., Maruyama, O., and Miyano, S., VML: A View Modeling Language for Computational Knowledge Discovery, In Proceedings of the 4th International Conference on Discovery Science, 30–44, 2001.
[2]	Bannai, H., Tamada, Y., Maruyama, O., and Miyano, S., HypothesisCreator: Concepts for Accelerating the Computational Knowledge Discovery Process, Linköping Electronic Articles in Computer and Information Science, 6, 19, 2001. (Full text)
[1]	Bannai, H., Tamada, Y., Maruyama, O., and Miyano, S., Views: Fundamental Building Blocks in the Process of Knowledge Discovery. In Proceedings of the 14th International FLAIRS Conference, 233-238, AAAI Press, 2001.