: : Publications : : : :

研究業績 (Publications)

査読付き論文 | 書籍やその一部 (Books & Book chapters) | ポスター・口頭発表・その他論文

査読付き論文 (Peer Reviewed Papers)

[65] Miyazaki, T., Ozato, N., Yamaguchi, T., Sugiura, Y., Kawada, H., Katsuragi, Y., Osaki, N., Mikami, T., Ito, K., Murashita, K., Nakaji, S. & Tamada, Y.. Association of visceral fat area with early-stage locomotive syndrome across various age groups: a cross-sectional study, Scientific Reports, 14, 25498, 2024. (Full text)

[64] Mera, M., Michida, N., Honda, M., Sakamoto, K., Tamada, Y., Mikami, T., Nakaji, S. A Study of the Relationship between Driving and Health based on Large-scale Data Analysis using PLSA and t-SNE, IEEE Access, 12, 99614–99659, 2024. (Full text)

[63] Nakano, A., Ueno, H.M., Kawata, D., Tatara, Y., Tamada, Y., Mikami, T., Murashita, K., Nakaji, S., Itoh, K. Dairy consumption, bone turnover biomarkers, and osteo sono assessment index in Japanese adults: A cross-sectional analysis of data from the Iwaki Health Promotion Project, Bone Reports, 21, June 2024, 101770, 2024. (Full text)

[62] Sugimura, Y., Yang, Y., Kanda, A., Mawatari, A., Tamada, Y., Mikami, T., Nakaji, S., Ihara, K. Association between Gut Microbiota and Muscle Strength in Japanese General Population of the Iwaki Health Promotion Project, Microorganisms, 12 (3), 622, 2024. (Full text)

[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, 31 (7), 2922–2929, 2024. (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, 34 (8), 5297–5304. 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] 鷲尾隆, 樋口知之, 井元清哉, 玉田嘉紀, 佐藤健, 元田浩, グラフマイニングとその統計的モデリングへの応用, 統計数理, 54 (2), 315-332, 2006. (要旨)

[17] 玉田嘉紀, 井元清哉, 宮野悟, 異種ゲノムデータの統合による遺伝子ネットワーク推定手法, 統計数理, 54 (2), 333-356, 2006. (要旨)

[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.

書籍やその一部 (Books & Book Chapters)

[B13]	守　真太郎, 玉田嘉紀，徐睨哲. 弘前大学の数理・データサイエンス・AI教育プログラム～グループワークとデータサイエンスを融合した課題解決学習と岩木健康増進プロジェクトでのデータの利活用～．大学教育と情報 (JUCE Journal), 私立大学情報教育協会, Vol. 182 No.1, 35–40, 2023. (PDF)
[B12]	中路重之，井元清哉，玉田嘉紀，岡本哲平，大里直樹，飯野勢，佐藤憲明，小林恒，松原篤，久田貴義．岩木健康増進プロジェクトという単一フィールドでの多領域にわたる口腔内・腸内細菌研究． Microbiome Science，1 (1), 34–42, 2022.
[B11]	内野詠一郎，佐藤憲明，小島諒介，玉田嘉紀，柳田素子，奥野恭史．臨床データを用いた医療ビッグデータの解析と創薬への応用．日本腎臓学会誌，62 (2), 64–68, 2020.
[B10]	奥野恭史，小清水宏，鎌田真由美，玉田嘉紀，小島諒介，内野詠一郎．データ主導型個別化医療と予測医療．医学情報誌あいみっく, Vol. 41 No. 1 (2020年2月), 2–5, 2020．(PDF)
[B9]	田中良尚，小島諒介，玉田嘉紀，鎌田真由美，奥野恭史．分子レベルにおけるAIの創薬応用．実験医学．2019年10月号 Vol.37 No.16, 2702-2707, 2019. (出版社の案内)
[B8]	岩田浩明、小島諒介、玉田嘉紀．標的分子探索，ドラッグリポジショニング，オミクスメカニズム解明. 細胞．Vol. 51, No. 7, 318-321 (4-7), 2019. (出版社の案内)
[B7]	玉田嘉紀、佐藤憲明、奥野恭史．医療×AI - AI の基礎と医療への応用. 整形災害外科．Vol. 62, No. 3, 215-221, 2019. (出版社の案内)
[B6]	演習で学ぶ生命科学　第２版. 東京大学生命科学教科書編集委員会（編）, 羊土社, 2017.（出版社の案内）
[B5]	確率的グラフィカルモデル. 鈴木譲・植野真臣（編）, 共立出版, 2016. （出版社の案内）
[B4]	演習で学ぶ生命科学. 東京大学生命科学教科書編集委員会（編）, 羊土社, 2016.（出版社の案内）
[B3]	宮野悟, 伊東聰, Heewon Park, 白石友一, 島村徹平, 玉田嘉紀, 井元清哉, 「京」を使った大規模データ解析によるがんのシステム異常の網羅的解析. 永井良三, 宮野悟, 大江和彦（編）, 実験医学増刊号「ビッグデータ変革する生命科学・医療」(Vol. 34, No. 5), 羊土社, 89-94 (733-738), 2016.（出版社の案内）
[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.

ポスター・口頭発表・その他の論文など

FY2023

(April 2023 - March 2024)

[P94]	玉田嘉紀, 生命・医療・健康ビッグデータネットワーク解析, Symposium on Computational Disease Systems Biology （計算疾患システム生物学シンポジウム）@ 東京医科歯科大学 M&D タワー 21 階大学院講義室1 （東京都文京区）(Jan. 14, 2024). 招待講演
[P93]	玉田嘉紀, 大田雅照, 「富岳」を基軸とした創薬DXプラットホームの構築～富岳の仮想空間で薬をつくる～, 第3回スーパーコンピュータ「富岳」シンポジウム「富岳百景」－成果創出加速プログラム・政策対応利用課題・Society 5.0 推進利用課題－（オンライン）(Dec. 1, 2023) ．招待講演．
[P92]	玉田嘉紀, 弘前大学COI-NEXTにおける健康ビッグデータ超多項目解析, 第6回多階層システム医学シンポジウム @ 山口大学医学部医修館（山口県宇部市）(Dec. 2, 2023) ．招待講演．
[P91]	中澤麻衣, 玉田嘉紀, 奥野恭史, A novel method for gene knockdown simulation using Markov chain Monte Carlo methods (MCMC), 第12回生命医薬情報学連合大会 (IIBMP 2023) @ 柏の葉カンファレンスセンター（千葉県柏市）(Sep. 7-9, 2023) ．ポスター発表 (P-144)．
[P90]	太田可純, 原田陽平, 中澤麻衣, 玉田嘉紀, 奥野恭史, マルチオミクスネットワーク解析によるがん患者の薬剤感受性メカニズムの解明� (Multi-omics network analysis for Elucidating Drug Sensitivity Mechanisms of Individual Cancer Patients), 第12回生命医薬情報学連合大会 (IIBMP 2023) @ 柏の葉カンファレンスセンター（千葉県柏市）(Sep. 7-9, 2023) ．ポスター発表 (P-142)．
[P89]	玉田嘉紀, 中澤麻衣, 太田可純, 原田陽平, 藤本健二, 鎌田真由美, 奥野恭史, INGOR / SiGN-BN - Gene Network Estimation Software, 第12回生命医薬情報学連合大会 (IIBMP 2023) @ 柏の葉カンファレンスセンター（千葉県柏市）(Sep. 7-9, 2023) ．ポスター発表 (P-120)．
[P88]	藤本健二, 瀬尾茂人, 繁田浩功, 内田穣, 石井優, 玉田嘉紀, 松田秀雄, Cell tracking through video frame interpolation for live cell imaging, 第12回生命医薬情報学連合大会 (IIBMP 2023) @ 柏の葉カンファレンスセンター（千葉県柏市）(Sep. 7-9, 2023) ．ポスター発表 (P-14)．

FY2022

(April 2022 - March 2023)

[P87]	玉田嘉紀, スーパーコンピュータによる生命科学・健康医療超多項目データ解析, 神戸大学計算生命科学の基礎９ (Jan. 25, 2023)．オンライン講義．
[P86]	Ota, K., Harada, Y., Nakazawa, M.A., Tamada, Y., Kamada, M., Okuno, Y., ベイジアンネットワークを用いた薬剤感受性関連遺伝子ネットワークの抽出, 第11回生命医薬情報学連合大会 (IIBMP 2022) @ 千里ライフサイエンスセンター（大阪府豊中市）(Sep. 14, 2022) ．ポスター発表 (P-42)．
[P85]	Tomoto, M., Mineharu, Y., Sato, N., Nakazawa, M.A., Tamada, Y., Kamada, M., Okuno, Y., マルチオミクスデータを用いた特発性肺線維症のメカニズム解明, 第11回生命医薬情報学連合大会 (IIBMP 2022) @ 千里ライフサイエンスセンター（大阪府豊中市）(Sep. 13, 2022) ．ポスター発表 (P-79)．
[P84]	Nakazawa, M.A., Tamada, Y., Okuno, Y., 患者特異的な遺伝子制御ネットワークに基づくがん層別化手法の開発, 第11回生命医薬情報学連合大会 (IIBMP 2022) @ 千里ライフサイエンスセンター（大阪府豊中市）(Sep. 13, 2022) ．ポスター発表 (P-53)．
[P83]	Tamada, Y., Nakazawa, M.A., Ota, K., Tomoto, M., Ashine, R., Harada, Y., Kamada, M., Okuno, Y., シングル・サンプル遺伝子ネットワーク推定＆解析技術, 第11回生命医薬情報学連合大会 (IIBMP 2022) @ 千里ライフサイエンスセンター（大阪府豊中市）(Sep. 13, 2022) ．ポスター発表 (P-31)．
[P82]	玉田嘉紀, グラフニューラルネットワークを用いた超多項目・超大量ネットワーク解析, 統計数理研究所共同研究集会「諸科学における統計思考」 (Aug. 19, 2022)．オンライン招待講演．

FY2021

(April 2021 - March 2022)

[P81]	玉田嘉紀, 弘前大学COIを中心とした医療ビッグデータ解析, 令和３年度日医生涯教育講座、青森市医師会（オンライン）(Mar. 7, 2022)．招待講演．
[P80]	玉田嘉紀, 弘前大学での展開されるデータサイエンス I：弘前大学COIにおける健診ビッグデータ解析事例紹介「弘前大学COIビッグデータの紹介」, 弘前大学講演会「データサイエンスへの招待」第３回（オンライン）(Dec. 15, 2021)．招待講演．
[P79]	玉田嘉紀, 弘前大COIの進めるビッグデータ解析を通じたデータ利活用と拠点関連携, COI V1 共催シンポジウム（オンライン）(Sep. 29, 2021)．招待講演．
[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.

FY2020

(April 2020 - March 2021)

[P76]	玉田嘉紀, AIによる医療ビッグデータ解析, 第４４回弘前大学医師会教育講演会 @ 弘前市医師会館（青森県弘前市）(Mar. 22, 2021)．招待講演．
[P75]	玉田嘉紀, 多項目データの因果関係を説明可能な人工知能データ解析技術, 統計数理研究所共同研究集会「諸科学における大規模データと統計数理モデリング」（冬のオンライン会合シリーズ） (Dec. 17, 2020)．オンライン招待講演．
[P74]	玉田嘉紀, AIによる細胞内遺伝子ネットワーク解析, 患者由来ガンモデル講演会2020 (Oct. 30, 2020). オンライン招待講演.
[P73]	Tamada, T., Personalized gene network analysis with large scale Bayesian network estimation, 2nd ASHBi Mathematical Biology Workshop (Sep. 4, 2020). Oral invited talk (international online workshop)
[P72]	玉田嘉紀, 多項目データの因果関係を説明可能な人工知能データ解析技術, 科学技術振興機構 (JST) 主催京都大学新技術説明会 (Jul. 21, 2020). 資料発表のみ．

FY2019

(April 2019 - March 2020)

[P71]	早川龍雄, 内野詠一郎, 玉田嘉紀, 奥野恭史, 機械学習を利用した医療現場の退院時サマリ作成業務軽減に向けた試み，言語処理学会第26回年次大会 (NLP2020) (Mar. 18, 2020) オンライン口頭発表．
[P70]	内野詠一郎, 玉田嘉紀, 奥野恭史、電子カルテデータを用いた腎疾患AI, 第 93 回日本薬理学会年会 (Mar. 17, 2020)（紙上開催・要旨）
[P69]	Uchino, E., Kume, K., Iwamoto, K., Hayakawa, T., Sato, N., Tamada, Y., Yanagita, M., and Okuno, Y., Development of Machine Learning Models for Predicting Acute Kidney Injury Onset Using Electronic Medical Records, American Society of Nephrology (ASN) Kidney Week (Nov., 2019). Oral Presentation.

FY2018

(April 2018 - March 2019)

[P68]

早川龍雄, 井上和仁, 玉田嘉紀, 内野詠一郎, 奥野恭史, 電子カルテ診療録に対する機械学習を用いた重要キーワード抽出機能の開発と今後の診療支援機能への展望, 第 38 回医療情報学連合大会（第 19 回医療情報学会学術大会） @ 福岡国際会議場（福岡県福岡市） (Nov. 25, 2018). 一般演題（査読あり）．

[P67]

玉田嘉紀, ベイジアンネットワークの構造推定アルゴリズムの研究と医療データ解析への応用, 人工知能学会合同研究会2018 人工知能基本問題研究会合同研究会企画シンポジウム (SIG-FPAI)（第104回行動計量シンポジウム共催）@ 慶應義塾大学矢上キャンパス（神奈川県横浜市） (Nov. 23, 2018). 招待講演．

FY2017

(April 2017 - March 2018)

[P66]

玉田嘉紀, AI/Big Dataによる医療のイノベーション, 日本薬学会第138年会併催展示会日本薬科機器協会ワークショップ @ 石川県音楽堂・交流ホール（石川県金沢市） (Mar. 27, 2018). 富士通（株）によるワークショップでの招待講演・パネルディスカッション．

FY2015

(April 2015 - March 2016)

[P65]	Tamada, Y. Cancer Genome Research with Gene Network Analysis using Bayesian Networks, The second Workshop on Advanced Methodologies for Bayesian Networks (AMBN 2015) @ 慶応大学日吉キャンパス（神奈川県横浜市） (Nov. 18, 2015). 口頭発表．
[P64]	Tamada, Y., Tremmel, G., Niida, A., Yamaguchi, R., Imoto, S., and Miyano, S., The Cancer Network Galaxy: A Database of Cancer Gene Networks Estimated by SiGN-BN with K, Supercomputational Life Science 2015 @ 東京大学武田ホール（東京都文京区） (Oct. 20-21, 2015). ポスター発表．

FY2014

(April 2014 - March 2015)

[P63]	玉田嘉紀, ベイジアンネットワークとスーパーコンピュータを用いた遺伝子ネットワーク解析, 数学協働プログラム「確率的グラフィカルモデル」 @ 電気通信大学（東京都調布市） (Mar. 19, 2015). 招待講演.
[P62]	玉田嘉紀, 京による全ゲノム遺伝子ネットワーク推定ソフトウェアSiGN-BN NNSRの改良, 平成２６年度 HPCI 戦略プログラム分野１全体ワークショップ @ 理化学研究所計算科学研究機構（兵庫県神戸市） (Jan. 20, 2015). ポスター発表.
[P61]	玉田嘉紀, Gene Network Estimation and Analysis with SiGN, 第 14 回東京大学生命科学シンポジウム @ 東京大学伊藤国際学術研究センター（東京都文京区） (Apri. 26, 2014). ポスター発表.

FY2013

(April 2013 - March 2014)

[P60]	玉田嘉紀, バイオインフォマティクスにおけるスーパーコンピューティングの過去・現在・未来（と言う名の自分史と将来への希望）, バイオスーパーコンピューティング研究会ウィンタースクール 2014 @ 伊豆熱川温泉熱川ハイツ（静岡県賀茂郡東伊豆町）(Jan. 24, 2014)．口頭発表．
[P59]	玉田嘉紀, 京を用いた超並列アルゴリズムによる大規模遺伝子ネットワーク推定手法の研究開発とその応用, BiWO2013 HPCI Workshop @ 産業技術総合研究所生命情報工学研究センター (CBRC) 臨海副都心センター別館（東京都江東区） (Sep. 11, 2013). 口頭発表.
[P58]	玉田嘉紀, 観測データからその背後に潜むシステムを予測する遺伝子ネットワーク推定, NGS 現場の会第三回研究会 @ 神戸国際会議場（兵庫県神戸市） (Sep. 5, 2013). 口頭発表.
[P57]	玉田嘉紀, ゲノム解析・遺伝子ネットワーク解析におけるビッグデータ解析, 第10回戦略的高性能計算システム開発に関する国際ワークショップ (SDHPC) @ 北九州国際会議場（福岡県北九州市） (Jul. 30, 2013). 口頭発表.
[P56]	玉田嘉紀, Georg Tremmel, 新井田厚司, 斉藤あゆむ, 島村徹平, 山口類, 井元清哉, 宮野悟, The Cancer Network Galaxy: a database of cancer gene networks, 第 13 回東京大学生命科学シンポジウム @ 東京大学伊藤国際学術研究センター（東京都文京区） (Jun. 8, 2013). ポスター発表.

FY2012

(April 2012 - March 2013)

[P55]	玉田嘉紀, 島村徹平, 山口類, 新井田厚司, 斉藤あゆむ, 長﨑正朗, 井元清哉, 宮野悟, 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, 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」「グランドチャレンジ・アプリケーションの研究開発」公開シンポジウム @ 東京大学山上会館（東京都文京区） (Mar. 11, 2013). ポスター発表.
[P54]	玉田嘉紀, 遺伝子発現データからの大規模遺伝子ネットワーク推定, 定量オミックスワークショップ @ 大阪大学バイオ関連多目的研究施設（大阪府吹田市） (Jan. 22, 2013). 口頭発表．
[P53]	玉田嘉紀, 島村徹平, 山口類, 新井田厚司, 斉藤あゆむ, 長﨑正朗, 井元清哉, 宮野悟, 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 ソフトウェア研究開発報告会 @ 東京大学武田ホール（東京都文京区） (Jan. 10-11, 2013). ポスター発表.
[P52]	Tamada, Y., SiGN: Large-scale Gene Network Estimation Software for K Computer and HGC Supercomputer System, 生命医薬情報学連合大会 @ タワーホール船堀（東京都江戸川区） (Oct. 14-17, 2012). ポスター発表.
[P51]	Tamada, Y., Large-scale Gene Network Estimation with K Computer, 第 50 回日本生物物理学会年会 @ 名古屋大学東山キャンパス（愛知県名古屋市） (Sep. 23, 2012). 口頭発表．
[P50]	玉田嘉紀, 島村徹平, 山口類, 新井田厚司, 斉藤あゆむ, 井元清哉, 長﨑正朗, 宮野悟, スーパーコンピュータを用いた遺伝子ネットワーク推定による癌予後予測および薬剤応答パスウェイ予測, 第 12 回東京大学生命科学シンポジウム @ 東京大学山上会館（東京都文京区） (Jun. 30, 2012). ポスター発表.

FY2011

(April 2011 - March 2012)

[P49]	玉田嘉紀, スーパーコンピュータによる大規模遺伝子ネットワーク推定, 情報処理学会第74回全国大会 @ 名古屋工業大学御器所キャンパス（愛知県名古屋市） (Mar. 8, 2012). 口頭発表.
[P48]	玉田嘉紀, 島村徹平, 山口類, 新井田厚司, 斉藤あゆむ, 長崎正朗, 井元清哉, 宮野悟, 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, 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). ポスター発表.
[P47]	玉田嘉紀, 島村徹平, 山口類, 新井田厚司, 斉藤あゆむ, 長崎正朗, 井元清哉, 宮野悟, 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 @ 東京大学武田ホール（東京都文京区） (Dec. 21-22, 2011). ポスター発表.
[P46]	玉田嘉紀, 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]	玉田嘉紀, 島村徹平, 山口類, 長崎正朗, 井元清哉, 宮野悟, 大規模遺伝子ネットワーク推定ソフトウェア SiGN, バイオスーパーコンピューティングサマースクール2011 @ 淡路夢舞台国際会議場（兵庫県淡路市）(Sep. 26 - 27, 2011). ポスター掲示のみ．

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]	玉田嘉紀, ハイパフォーマンスコンピューティングによる大規模遺伝子ネットワークの推定とその応用, 日本バイオインフォマティクス学会第１回応用システムバイオロジー研究会 @ 東京医科歯科大学（東京都文京区） (Feb. 28, 2011). 口頭発表．
[P42]	玉田嘉紀, 島村徹平, 山口類, 長崎正朗, 井元清哉, 宮野悟, スーパーコンピューティングによる大規模遺伝子ネットワーク推定ソフトウェア SiGN, 第３回バイオスーパーコンピューティングシンポジウム @ 理化学研究所計算科学研究機構および甲南大学ポートアイランドキャンパス（兵庫県神戸市） (Feb. 21-22, 2011). ポスター発表. Selected as the Best Poster Award.
[P41]	玉田嘉紀, 遺伝子制御システムを解き明かす大規模遺伝子ネットワーク推定ソフトウェアの研究開発, 第３回バイオスーパーコンピューティングシンポジウム @ 理化学研究所計算科学研究機構および甲南大学ポートアイランドキャンパス（兵庫県神戸市） (Feb. 21-22, 2011). 口頭発表.
[P40]	玉田嘉紀, 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のための並列アルゴリズム, 東京大学大学院情報理工学系研究科コンピュータ科学専攻須田研究室第８回特別セミナー @ 東京大学理学部７号館２階２０２会議室（東京都文京区） (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, 2010 年日本バイオインフォマティクス学会年会) @ 九州大学医学部百年講堂（福岡県福岡市） (Dec. 13-15, 2010). Poster Presentation. Selected Poster for an Oral Presentation.
[P38]	玉田嘉紀, 非線形回帰によるベイジアンネットワークを用いた遺伝子発現データからの遺伝子ネットワーク推定とその並列アルゴリズム, 生命体統合シミュレーションサマースクール 2010 @ 湘南国際村センター（神奈川県三浦郡葉山町） (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, 第 2 回バイオスーパーコンピューティングシンポジウム (BSCS2010) @ MY PLAZA ホール（東京都千代田区）(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]	玉田嘉紀, 島村徹平, 藤田アンドレ, 新井田厚司, 小島要, Perrier, E., 沼田和幸, 長崎正朗, 斉藤あゆむ, 井元清哉, 宮野悟, 計測データから薬剤応答の動的ネットワークを抽出する統計解析法の開発, 東京大学医科学研究所研究成果発表会 @ 東京大学医科学研究所（東京都港区）(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]	玉田嘉紀, 井元清哉, 長崎正朗, 宮野悟, 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ソフトウェアの研究開発とその応用事例, バイオスーパーコンピューティング・シンポジウム（BSCS）2008 @ MY PLAZA ホール（東京都千代田区）(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]

玉田嘉紀, 坂内英夫, 井元清哉, 片山俊明, 金久實, 田代康介, 久原哲, 宮野悟, 異種ゲノムデータの統合による遺伝子ネットワーク推定, 統計数理研究所統計数理セミナー @ 統計数理研究所（東京都港区）(May 10, 2006). Oral Presentation.

FY 2005

(April 2005 - March 2006)

[P26]	玉田嘉紀, システムズバイオロジーにおける遺伝子ネットワークの推定とデータ同化手法の応用, 統計数理研究所平成１７年度研究報告会 @ 統計数理研究所（東京都港区）(Mar. 17, 2006). Oral Presentation.
[P25]	玉田嘉紀, 坂内英夫, 井元清哉, 片山俊明, 金久實, 田代康介, 久原哲, 宮野悟, 遺伝子ネットワーク推定における異種ゲノムデータの統合手法, バイオインフォマティクスと統計科学 @ 統計数理研究所（東京都港区） (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).

[65]	Miyazaki, T., Ozato, N., Yamaguchi, T., Sugiura, Y., Kawada, H., Katsuragi, Y., Osaki, N., Mikami, T., Ito, K., Murashita, K., Nakaji, S. & Tamada, Y.. Association of visceral fat area with early-stage locomotive syndrome across various age groups: a cross-sectional study, Scientific Reports, 14, 25498, 2024. (Full text)
[64]	Mera, M., Michida, N., Honda, M., Sakamoto, K., Tamada, Y., Mikami, T., Nakaji, S. A Study of the Relationship between Driving and Health based on Large-scale Data Analysis using PLSA and t-SNE, IEEE Access, 12, 99614–99659, 2024. (Full text)
[63]	Nakano, A., Ueno, H.M., Kawata, D., Tatara, Y., Tamada, Y., Mikami, T., Murashita, K., Nakaji, S., Itoh, K. Dairy consumption, bone turnover biomarkers, and osteo sono assessment index in Japanese adults: A cross-sectional analysis of data from the Iwaki Health Promotion Project, Bone Reports, 21, June 2024, 101770, 2024. (Full text)
[62]	Sugimura, Y., Yang, Y., Kanda, A., Mawatari, A., Tamada, Y., Mikami, T., Nakaji, S., Ihara, K. Association between Gut Microbiota and Muscle Strength in Japanese General Population of the Iwaki Health Promotion Project, Microorganisms, 12 (3), 622, 2024. (Full text)
[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, 31 (7), 2922–2929, 2024. (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, 34 (8), 5297–5304. 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]	鷲尾隆, 樋口知之, 井元清哉, 玉田嘉紀, 佐藤健, 元田浩, グラフマイニングとその統計的モデリングへの応用, 統計数理, 54 (2), 315-332, 2006. (要旨)
[17]	玉田嘉紀, 井元清哉, 宮野悟, 異種ゲノムデータの統合による遺伝子ネットワーク推定手法, 統計数理, 54 (2), 333-356, 2006. (要旨)
[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.