[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] |
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.
|