1. 研究課題
    • 分子進化(東京理科大学・助手)
    • データベース(東京理科大学・助手)
    • タンパク質構造予測 (東京理科大学・助手)
    • ゲノム比較 (佐賀医科大学・助教授)
    • 計算システム生物学 (東京大学・特任教授)
    • 代数生物学 (産総研生命情報科学研究センター・チーム長)
    • 計算システム薬理学 (産総研創薬分子プロファイリング研究センター・副センター長)
    • 計算創薬 (ソシウム株式会社・CTO/産総研人工知能研究センター・招聘研究員/埼玉医科大学国際医療センター・客員教授)
  2. 研究論文(英文、査読有のみ)
  3. 著書 (英文のみ)
  4. 学術活動(国際活動のみ)
  5. 学術賞罰(国際賞罰のみ)
  6. 競争的研究資金(国内のみ)
  1. 研究論文(英文、査読有のみ)
    1. [2020]
    2. T. Tomonari, Y. Sato, H. Tanaka, T. Tanaka, Y. Fujino, Y. Mitsui, A. Hirao, K. Okamoto, H. Miyamoto, N. Muguruma, H. Kagiwada, M. Kitazawa, K. Fukui, K. Horimoto, T. Takayama: Potential use of lenvatinib for patients with unresectable hepatocellular carcinoma including after treatment with sorafenib: Real-world evidence and in vitro assessment via protein phosphorylation array. Oncotarget, 11(26): 2531–2542、2020.
    3. Manabe, T., Yasuda, H., Terai, H., Kagiwada, H., Hamamoto, J., Ebisudani, T., Kobayashi, K., Masuzawa, K., Ikemura, S., Kawada, I., Hayashi, Y., Fukui, K., Horimoto, K., Fukunaga, K., Soejima, K.: IGF2 autocrine-mediated IGF1R activation is a clinically relevant mechanism of osimertinib resistance in lung cancer. MOL CANCER RES, 549-559, 18, 2020.
    4. M. Li, Z. Liu, B. Qian, W. Liu, K. Horimoto, H. Zhou, L. Chen: “Dysfunctions” induced by Roux-en-Y gastric bypass surgery are concomitant with metabolic improvement independent of weight loss. Cell Discovery, 6:4,2020.
    5. M. Kitazawa, T. Hatta, Y. Sasaki, K. Fukui, K. Ogawa, E. Fukuda, N. Goshima, N. Okita, Y. Yamada, H. Nakagama, T. Natsume, K. Horimoto: Promotion of the Warburg effect is associated with poor benefit from adjuvant chemotherapy in colorectal cancer. Cancer Sci. 111(2): 658–666, 2020
    6. H. Kagamu, S. Kitano, O. Yamaguchi, K. Yoshimura, K. Horimoto, M. Kitazawa, K. Fukui, A. Shiono, A. Mouri, F. Nishihara, Y. Miura, K. Hashimoto, Y. Murayama, K.i Kaira and K. Kobayashi: CD4+ T-cell immunity in the peripheral blood correlates with anti-PD-1 antibody therapy response. Cancer Immunology Research, 334-344, 8(3), 2020
    7. [2019]
    8. T. Amemiya, M. M. Gromiha, K. Horimoto, and K. Fukui: Drug repositioning for dengue haemorrhagic fevers by integrating multiple omics analyses. Scientific Reports, 9: 523, 2019.
    9. S. Yamasaki,T. Amemiya1, Y. Yabuki, K. Horimoto, K. Fukui: ToGo-WF: prediction of RNA tertiary structures and RNA–RNA/protein interactions using the KNIME workflow. Journal of Computer-Aided Molecular Design, 33:497–507, 2019
    10. [2018]
    11. Y. Okuma, K. Morikawa, H. Tanaka, T. Yokoyama, H. Itani, K. Horiuchi, H. Nakagawa, N. Takahashi, A. Bessho, K. Soejima, K. Kishi, A. Togashi, Y. Kanai, K. Ueda, K. Horimoto, N. Matsutani & N. Seki: Prospective exosome-focused translational research for afatinib study of non-small cell lung cancer patients expressing EGFR (EXTRA study). Thorac Cancer 10(2): 395-400, 2018.
    12. [2017]
    13. Yamakado, M, Tanaka, T., Nagao, K., Imaizumi, A., Komatsu, M., Daimon, T., Miyano, H., Tani, M., Toda, A., Yamamoto, H., Horimoto, K., Ishizaka, Y.: Plasma amino acid profile associated with fatty liver disease and co-occurrence of metabolic risk factors. Sci. Rep. 7: 14485, 2017.
    14. Inoue M., Horimoto K.: Relationship between regulatory pattern of gene expression level and gene function. PLoS ONE 12(5): e0177430, 2017.
    15. Matsumoto, M., Matsuzaki, F., Oshikawa, K., Goshima, N., Mori, M., Kawamura, Y., Ogawa, K., Fukuda, E., Nakatsumi, H., Natsume, T., Fukui, K., Horimoto, K., Nagashima, T., Funayama, R., Nakayama, K., Nakayama, K. I.: A large-scale targeted proteomics assay resource based on an in vitro human proteome. Nature Methods, 14(3): 251-258, 2017.
    16. [2015]
    17. Yamakado, M., Nagao, K., Imaizumi, A., Tani, M., Toda, A., Tanaka, T., Jinzu, H., Miyano, H., Yamamoto, H., Daimon, T., Horimoto, K., Ishizaka, Y.: Plasma Free Amino Acid Profiles Predict Four-Year Risk of Developing Diabetes, Metabolic Syndrome, Dyslipidemia, and Hypertension in Japanese Population. Sci. Rep. 5, 11918, 2015.
    18. Tanaka, H., Goto, H., Inoko, A., Makihara, H., Enomoto, A., Horimoto, K., Matsuyama, M., Kurita, K., Izawa, I., Inagaki, M.: Cytokinetic failure-induced tetraploidy develops into aneuploidy, triggering skin aging in phospho-vimentin deficient mice. J. Biol. Chem. 290: 12984-12998, 2015.
    19. [2014]
    20. Kinoshita, T. Nagamatsu, G., Saito, S., Takubo, K., Horimoto, K., Suda, T.: Telomerase Reverse Transcriptase has an Extratelomeric Function in Somatic Cell Reprogramming. J. Biol. Chem., 289: 15776-15787,2014
    21. [2013]
    22. Umemura, M., Koike, H., Nagano, N., Ishii, T., Kawano, J., Yamane, N., Kozone, I., Horimoto, K., Shin-ya, S., Asai, K., Yu,J., Bennett, J.W., Machida, M.: MIDDAS-M: Motif-Independent De Novo Detection of Secondary Metabolite Gene Clusters through the Integration of Genome Sequencing and Transcriptome Data. PLoS ONE, 8(12): e84028, 2013.
    23. Bae, T., Rho, K., Choi, J.W., Horimoto, K., Kim, W., Kim, S.: Identification of upstream regulators for prognostic expression signature genes in colorectal cancer. BMC Systems Biology, 7:86, 2013.
    24. Liu, Z.P., Zhang, W., Horimoto, K., Chen, L.: Gaussian graphical model for identifying significantly responsive regulatory networks from time course high-throughput data. IET Syst. Biol., 7: 143–152, 2013.
    25. Ueda, T., Honda, M., Horimoto, K., Aburatani, S., Saito, S., Yamashita, T., Sakai, Y., Nakamura, M., Takatori, H., Sunagozaka, H., Kaneko, S.: Gene expression profiling of hepatitis B- and hepatitis C-related hepatocellular carcinoma using graphical Gaussian modeling. Genomics, 101: 238-248, 2013
    26. Kosaka, T., Nagamatsu, G., Saito, S., Oya, M., Suda, T., Horimoto, K.: Identification of drug candidate against prostate cancer from the aspect of somatic cell reprogramming. Cancer Sci. 104: 1017–1026, 2013.
    27. Zhang, R., Yan, C., Zhou, X., Qian, B., Li, F., Sun, Y., Shi, C., Li, B., Saito, S., Horimoto, K., Zhou, H.: Association of Rev-erbα in Adipose Tissues with Type 2 Diabetes Mellitus Amelioration after Gastric Bypass Surgery in Goto-Kakizaki Rats. American Journal of Physiology – Regulatory, Integrative and Comparative Physiology, 305: R134-46, 2013.
    28. Nagamatsu, G., Kosaka, T., Saito, S., Takubo, K., Horimoto, K., Oya, M., Suda, T.: Induction of pluripotent stem cells from primordial germ cells by single reprogramming factors. Stem Cells, 31:479–487, 2013.
    29. Sun, Y., Han, X., Saito, S., Horimoto, K., Zhou, H.: Functional Networks in Diabetes-Progression by Comparison of Gene Expressions from Three Issues of Goto-Kakizaki Rats. Current Bioinformatics, 8: 63-71, 2013.
    30. Yu, T., Toshimori, A., Jinrong, X., Saito, S., Zhou, X., Horimoto, K., Fan, Z., Shimizu, K., Zhou, H.: Cellular relationships of testicular germ cell tumors by partial canonical correlation analysis for gene expression signatures. Current Bioinformatics, 8: 72-79, 2013.
    31. Saito, S., Zhou, X., Bae, T., Kim, S., Horimoto, K.: Identification of master regulator candidates in conjunction with network screening and inference. Int. J. of Data Mining and Bioinformatics, 8(3): 366-380, 2013.
    32. [2012]
    33. Nagamatsu, G., Kosaka, T., Saito, S., Takubo, K., Akiyama, H., Sudo, T., Horimoto, K., Oya, M., Suda, T.: Tracing the conversion process for primordial germ cells to pluripotent stem cells. Biology of Reproduction, 86, 1–11, 2012.
    34. Nagamatsu, G., Saito, S., Kosaka, T., Takubo, K., Oya, M., Horimoto, K., Suda, T.: Optimal ratio of transcription factors for somatic cell reprogramming. J. Biol. Chem., 287: 36273-82, 2012.
    35. Nakajima, N., Tamura, T., Yamanishi, Y., Horimoto, K., Akutsu, T.: Network Completion Using Dynamic Programming and Least-Squares Fitting. The Scientific World Journal, 2012: 957620, 2012.
    36. Piao, G., Saito, S., Sun, Y., Liu, Z., Wang, Y., Han, X., Wu, J., Zhou, H., Chen, L. and Horimoto, K.: A computational procedure for identifying master regulator candidates for diabetes progression in Goto-Kakizaki rat, BMC Sys. Biol., 6(Suppl1), S2, 2012
    37. Liu, Z.P., Zhang, W., Horimoto, K., Chen, L.: A Gaussian Graphical Model for Identifying Significantly Responsive Regulatory Networks from Time Series Gene Expression Data. Proceedings of The 6th IEEE International Conference on Systems Biology (ISB 2012), pp. 142-147.
    38. Zhou, X., Saito, S., Horimoto, K., Chen, L. and Zhou, H.: Network Clustering along Diabetes Progression in Three Tissues of Goto-Kakizaki Rats. Proceedings of 6th IEEE International Conference on Systems Biology (ISB 2012), pp. 86-91.
    39. Toshimori, A., Shimizu, K., Yu,T., Fan, Z., Zhou, X., Saito, S., Horimoto, K., Jinrong, X. and Zhou, H.: Exploration of cellular relationships from characteristically expressed genes. Proceedings of 5th International Conference on Intelligent Informatics in Biology and Medicine, pp. 567- 572, 2012.
    40. Nakatsui, M., Sedoglavic, A., Lemaire, F., Boulier, F., Urguplu, A. and Horimoto, K. : A General Procedure for the Accurate Parameter Estimation in Dynamic Systems Using New Estimation Errors. Algebraic and Numeric Biology, Springer, Heidelberg, pp. 149-166, 2012.
    41. [2011]
    42. Miyagi, Y., Higashiyama, M., Gochi, A., Akaike, M., Ishikawa, T., Miura, T., Saruki, N., Bando, E., Kimura, H., Imamura, F., Moriyama, M., Ikeda, I., Chiba, A., Oshita, F., Imaizumi, A., Yamamoto, H., Miyano, H., Horimoto, K., Tochikubo, O., Mitsushima, T., Yamakado, M., and Okamoto, N.: Plasma free amino acid profiling of five types of cancer patients and its application for early detection. PLoS One, 6(9), e24143, 2011.
    43. Zhou, H., Saito, S., Hu, R., Piao, G., Wang, J., Liu, Z., Horimoto, K. and Chen, L.: Network Screening of Goto-Kakizaki Rat Liver Microarray Data during Diabetic Progression. BMC Sys. Biol. 5(Suppl 1), S16, 2011.
    44. Saito, S., Onuma, Y., Ito, Y., Tateno, H., Toyoda, M., Akutsu, H., Nishino, K., Chikazawa, E., Fukawatase, Y., Miyagawa, Y., Okita, H., Kiyokawa, N., Shimma, Y, Umezawa, A., Hirabayashi, J., Horimoto, K. and Asashima, M.: Potential linkages between the inner and outer cellular states of human induced pluripotent stem cells. BMC Sys. Biol. 5(Suppl 1), S17, 2011.
    45. Nakatsu, M., Horimoto, K., Lemaire, F., Ürgüplü, A., Sedoglavic, A. and Boulier, F.: Brute force meets Bruno force in parameter optimization: Introduction of novel constraints for parameter estimation by symbolic computation. IET Sys. Biol., 5, 281–292, 2011.
    46. Tateno, H., Toyota, M., Saito, S., Onuma, Y., Ito, Y., Hiemori, K., Fukumura, M., Matsushima, A., Nakanishi, M., Ohnuma, K., Akutsu, H., Umezawa, A., Horimoto, K., Hirabayashi, J. and Asashima, M.: Glycome Diagnosis of Human Induced Pluripotent Stem Cells Using Lectin Microarray. J. Biol. Chem., 286, 20345–20353, 2011.
    47. Saito, S., Hirokawa, T. and Horimoto, K.: Discovery of Chemical Compound Groups with Common Structures by a Network Analysis Approach. J. Chem. Inf. Model. 51, 61-68, 2011.
    48. Wang, Y., Horimoto, K., and Chen, L.: An integrated gene regulatory network inference pipeline. Proceedings of the 30th Chinese Control Conference, pp. 6593 – 6598, 2011.
    49. Horimoto, K.: On Two Issues of Molecular Network Models in Systems Biology – A Review. Proceedings of Tenth International Symposium on Operations Research and Its Applications (ISORA 2011), pp. 22–27, 2011.
    50. Piao, G., Qian, B., Saito, S., Liu, Z., Zeng, T., Wang, Y., Wu, J., Zhou, H., Chen, L. and Horimoto, K.: Phenotype-Difference Oriented Identification of Molecular Functions for Diabetes Progression in Goto-Kakizaki Rat. Proceedings of 5th IEEE International Conference on Systems Biology (ISB 2011), pp. 111-116, 2011.
    51. Saito, S., Sun, Y., Liu, Z., Wang, Y., Han, X., Zhou, H., Chen, L. and Horimoto, K.: Identification of Master Regulator Candidates for Diabetes Progression in Goto-Kakizaki Rat by a Computational Procedure. Proceedings of 5th IEEE International Conference on Systems Biology (ISB 2011), pp. 169-174, 2011.
    52. [2010]
    53. Oda, Y., Yoshimura, Y., Ohnishi1, H., Tadokoro, M., Katsube, Y., Sasao, M., Kubo, Y., Hattori, K., Saito, S., Horimoto, K., Yuba, S., and Ohgushi, H. : Induction of pluripotent stem cells from human third molar mesenchymal stromal cells. J. Biol. Chem., 285, 29270-29278, 2010.
    54. Honda, M., Sakai, A., Yamashita, T., Nakamoto, Y., Mizukoshi, E., Sakai, Y., Yamashita, T., Nakamura, M., Shirasaki, T., Horimoto, K., Tanaka, Y., Tokunaga, K., Mizokami, M., Kaneko, S. and Hokuriku Liver Study Group: Hepatic ISGs is associated with genetic variation in IL28B and outcome of IFN therapy for chronic hepatitis C. Gastroenterology, 139, 499-509, 2010.
    55. Nakatsui, M., Horimoto, K., Okamoto, M., Tokumoto, Y. and Miyake, J.: Parameter Optimization by Using Differential Elimination: a General Approach for Introducing Constraints into Objective Function. BMC Sys. Biol., 4(Suppl 2), 59, 2010.
    56. Ootsuji, H., Honda, M., Takamura, M., Usui, S., Okajima, M., D, Okada, H., Sakai, Y., Takamura, T., Horimoto, K. and Kaneko, S.: Altered Hepatic Gene Expression Profiles Associated with Myocardial Ischemia. Circ Cardiovasc Genet, 3, 68 – 77, 2010.
    57. Saito, S., Zhou, X., Bae, T., Kim, S. and Horimoto, K.: A Procedure for Identifying Master Regulators in Conjunction with Network Screening and Inference. Proceedings of IEEE International Conference on Bioinformatics & Biomedicine, pp. 296-301, 2010.
    58. Wang, Y., Zhang, X.-Z., Horimoto, K., and Chen, L.: System Identification Models for Gene Regulation System. Proceedings of The 29th Chinese Control Conference (CCC), Beijing, pp. 6239-6244, 2010.
    59. Tamura, T., Yamanishi, Y., Tanabe, M., Goto, S., Kanehisa, M., Horimoto, K. and Akutsu, T.: Integer Programming-based Method for Completing Signal Pathways and its Application to Analysis of Colorectal Cancer. Proceedings of The Tenth Annual International Workshop on Bioinformatics and Systems Biology, pp. 193-203, 2010.
    60. Nakatsui, M. and Horimoto, K.: Improvement of Estimation Accuracy in Parameter Optimization by Symbolic Computation. Proceedings of IEEE Multi-conference on Systems and Control, pp. 1720 – 1724, 2010.
    61. Zhou, H., Saito, S., Hu, R., Piao, G., Wang, J., Liu, Z., Horimoto, K. and Chen, L. : Significant Regulatory Networks from Goto-Kakizaki Rat Liver Microarray Data during Diabetic Progression. Proceedings of the 4th International Conference on Computational Systems Biology (ISB 2010), pp. 196–203, 2010.
    62. Saito, S., Onuma, Y., Ito, Y., Tateno, H., Toyoda, M., Akutsu, H., Nishino, K., Chikazawa, E., Fukawatase, Y., Miyagawa, Y., Okita, H., Kiyokawa, N., Shimma, Y, Umezawa, A., Hirabayashi, J., Horimoto, K. and Asashima, M.: Potential Linkages Between the Inner and Outer Cellular States of Human Induced Pluripotent Stem Cells. Proceedings of the 4th International Conference on Computational Systems Biology (ISB 2010), pp. 381–388, 2010.
    63. [2009]
    64. Morioka, R., Arita, M., Sakamoto, K., Kawaguchi, S., Tei, H. and Horimoto, K.: Period-Phase Map: Two-diemsional Selection of Circadian Rhythm-Related Genes. IET Sys. Biol., 3, 487-495, 2009.
    65. Tokumoto, Y., Horimoto, K. and Miyake, J.: TRAIL inhibited the cyclic AMP responsible element mediated gene expression. Biochem. Biophys. Res. Commun., 381, 533- 536, 2009.
    66. Ura, S., Honda, M., Yamashita, T., Ueda, T., Takatori, H., Nishino, R., Sunagozaka, H., Sakai, Y., Horimoto, K. and Kaneko, S.: Differential miRNA expression between hepatitis B and hepatitis C leading disease progression to HCC. Hepatology, 49, 1098-1112, 2009
    67. Saito, S., Honda, M., Kaneko, S., and Horimoto, K.: Detection of network structure changes by graphical chain modeling: a case study of hepatitis C virus-related hepatocellular carcinoma. Proceedings of 48th IEEE Conference on Decision and Control, pp. 5624-5630, 2009.
    68. Saito, S. and Horimoto, K.: Co-Expressed Gene Assessment Based on the Path Consistency Algorithm: Operon Detention in Escherichia coli. Proceedings of IEEE International Conference on Systems, Man and Cybernetics, pp. 4280-4286, 2009.
    69. Nakatsui, M. and Horimoto, K.: Parameter Optimization in the network dynamics including unmeasured variables by the symbolic-numeric approach. Proceedings of the Third International Symposium on Optimization and Systems Biology (OSB’09), pp. 245–253, 2009.
    70. Akutsu, T., Tamura, T. and Horimoto, K.: Complementing Networks Using Observed Data. Lecture Notes in Artificial Intelligence 5809, pp. 126-140, 2009.
    71. [2008]
    72. Yoshida, H., Horimoto, K. and Anai, H.: Inference of Probabilities over a Stochastic IL-System by Quantifier Elimination. Math.Comput.Sci., 1, 473–485, 2008.
    73. Nishino, R., Honda, M., Yamashita, T., Takatori, H., Minato, H., Zen, Y., Sasaki, M., Takamura, H., Horimoto, K., Ohta, T., Nakanuma and Y., Kaneko, S.: Identification of novel candidate tumour marker genes for intrahepatic cholangiocarcinoma. J. Hepatol., 49, 207–216, 2008.
    74. Hayashida, M., Sun, F., Aburatani, S., Horimoto, K. and Akutsu, T.: Integer Programming-based Approach to Allocation of Reporter Genes for Cell Array Analysis. Int. J. Bioinformatics Research and Applications, 4, 385-399, 2008.
    75. Saito, S., Aburatani, S. and Horimoto, K.: Network evaluation from the consistency of the graph structure with the measured data. BMC Sys. Biol. 2, 84, 2008.
    76. Tominaga, D., Tokumoto, Y., Nakatsui, M., Sun, F., Miyake, J. and Horimoto, K.: Analysis of network dynamics including hidden variables by symbolic-numeric approach. Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB’08), pp. 242–248, 2008.
    77. Morioka, R., Arita, M., Sakamoto, K., Kawaguchi, S., Tei, H. and Horimoto, K.: Phase Shifts of Circadian Transcripts in Rat Suprachiasmatic Nucleus. Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB’08), pp. 109–114, 2008.
    78. Nakatsui, M., Yoshida, H. and Horimoto, K.: An Algebraic-Numeric Algorithm for the Model Selection in Network Motifs in Escherichia coli. Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB’08), pp. 257–264, 2008.
    79. Zhang, Z.Y., Horimoto, K. and Liu, Z.: Time Series Segmentation for Gene Regulatory Process with Time-Window-Extension Technique. Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB’08), pp. 198–203, 2008.
    80. Wu, Z.K., Zhang, Z.Y., Zhang, L.W. and Horimoto, K.: Revealing Disease Related Interactions by Correlation Analysis. Proceedings of the Second International Symposium on Optimization and Systems Biology (OSB’08), pp. 341–349, 2008.
    81. [2007]
    82. Aburatani, S., Sun, F., Saito, S., Honda, M., Kaneko, S. and Horimoto, K., Gene systems network inferred from expression profiles in hepatocellular carcinogenesis by graphical Gaussian model. EURASIP J. Bioinfo. Systems Biol., 47214, 2007.
    83. Yoshida, H., Anai, H. and Horimoto, K., Derivation of rigorous conditions for high cell–type diversity by algebraic approach. BioSystems, 90, 486–495, 2007.
    84. Sato, T., Yamanishi, Y., Horimoto, K., Kanehisa, M. and Toh, H., Inference of Protein-Protein Interactions by Using Co-evolutionary Information. In Anai, H., Horimoto, K. and Kutsia, T. (eds), Algebraic Biology 2007, Lecture Notes in Computer Science 4545, p.322-333, Springer, Heidelberg, 2007.
    85. Yoshida, H., Nakagawa, K., Anai, H. and Horimoto, K. Exact parameter determination for Parkinson’s disease diagnosis with PET using an algebraic approach. In Anai, H., Horimoto, K. and Kutsia, T. (eds), Algebraic Biology 2007, Lecture Notes in Computer Science 4545, p.110-124, Springer, Heidelberg, 2007.
    86. Yoshida, H., Nakagawa, K., Anai, H. and Horimoto, K., An Algebraic-Numeric Algorithm for the Model Selection in Kinetic Networks. Proceedings of 10th CASC, LNCS 4770, p.433-447, Springer, Heidelberg, 2007
    87. Hayashida, M., Sun, F., Aburatani, S., Horimoto, K. and Akutsu, T., Integer Programming-based Approach to Allocation of Reporter Genes for Cell Array Analysis. Proceedings of 10th OSB, Lecture Notes in Operation Research, p.288-301, World Publishing Corporation, Beijing, 2007.
    88. [2006]
    89. Aburatani, S., Saito, S., Toh, H. and Horimoto, K.: A Graphical Chain Model for Inferring Regulatory System Networks from Gene Expression Profiles. Statistical Methodology, 3, 17-28, 2006
    90. Anai, H., Orii, S. and Horimoto, K.: Symbolic-Numeric Estimation of Parameters in Biochemical Models by Quantifier Elimination. J. Bioinfo. Comput. Biol. 4, 1097-1117, 2006.
    91. Sato, T., Yamanishi, Y., Horimoto, K., Kanehisa, M. and Toh, H.: Partial Correlation Coefficient between Distance Matrices as a New Indicator of Protein-Protein Interactions. Bioinformatics 22, 2488-2492, 2006.
    92. Dukka Bahadur, K.C., Tomita, E., Suzuki, J., Horimoto, K. and Akutsu, T. Protein threading with profiles and distance constraints using clique based algorithms. J. Bioinfo. Comput. Biol., 4, 19-42, 2006.
    93. [2005]
    94. Aburatani, S., Goto, K., Saito, S., Toh, H. and Horimoto, K. ASIAN: A Web Server for Inferring a Regulatory Network Framework from Gene Expression Profiles. Nucleic Acids Res, 33, W659-W664, 2005.
    95. Kinjyo, A., Horimoto, K. and Nishikawa, K. Predicting Absolute Contact Numbers of Native Protein Structure from Amino Acid Sequence. PROTEINS – Structure, Function and Bioinformatics, 58, 158-165, 2005.
    96. Aburatani, S., Sakai, H., Murakami, H. and Horimoto, K. Elucidation of the Relationships among the LexA-Regulated Genes in SOS Response. Genome Informatics, 16, 95-105, 2005.
    97. Murakami, H., Sakai, H., Aburatani, S. and Horimoto, K. Relationship between Segmental Duplications and Repeat Sequences in Human Chromosome 7. Genome Informatics, 16, 13-21, 2005.
    98. Orii, S. Anai, H. and Horimoto, K. Symbolic-Numeric Optimization by Quantifier Elimination: an Application to Biological Kinetic Model. Proceedings of the 9th World Multi-Conference on Systemics, Cybernetics and Informatics. 8, 15-20, 2005.
    99. Saito, S., Aburatani, S. and Horimoto, K. Network Inference Tool on Personal Computer. Proceedings of the 9th World Multi-Conference on Systemics, Cybernetics and Informatics. 8, 21-24, 2005.
    100. Murakami, H., Sakai, H., Aburatani, S. and Horimoto, K. Relationship between Segmental Duplications and Repeat Sequences in Human Chromosome 7. Proceedings of the 9th World Multi-Conference on Systemics, Cybernetics and Informatics. 8, 10-14, 2005.
    101. Sakai, H., Murakami, H., Aburatani, S., Horimoto, K. and Kanehisa, M. Bayesian Approach for Sequence Pattern Search in Tissue Specifc Alternative Splicing. Proceedings of the 9th World Multi-Conference on Systemics, Cybernetics and Informatics. 8, 25-30, 2005.
    102. Aburatani, S., Sakai, H., Murakami, H. and Horimoto, K. Application of Statistical Methods to Elucidate the Network of LexA-Regulated Genes. Proceedings of the 9th World Multi-Conference on Systemics, Cybernetics and Informatics. 8, 1-5, 2005.
    103. Sato, K and Horimoto, K. Comparison between Profile-Profile Methods based on Hidden Markov Models and Multiple Alignments. Proceedings of the 9th World Multi-Conference on Systemics, Cybernetics and Informatics. 8, 31-37, 2005.
    104. [2004]
    105. Aburatani, S., Goto, K., Saito, S., Fumoto, M., Imaizumi, A., Sugaya, N., Murakami, H., Sato, M., Toh, H. and Horimoto, K. ASIAN: A Web Site for Network Inference. Bioinformatics, 20, 2853-2856, 2004.
    106. Murakami, H., Sugaya, N., Sato, M., Imaizumi, A., Aburatani, S. and Horimoto, K. Detection of Inter-Spread Repeat Sequence in Genomic DNA Sequence. Genome Informatics, 15, 170-179, 2004.
    107. Sugaya, N., Sato, M., Murakami, H., Imaizumi, A., Aburatani, S. and Horimoto, K. Causes for the Large Genome Size in a Cyanobacterium Anabaena sp. PCC7120. Genome Informatics, 15, 229-238, 2004.
    108. Murakami, H., Sugaya, N., Sato, M., Imaizumi, A., Aburatani, S. and Horimoto, K. STEPSTONE: A Program to Detect Inter-Spread Repeats in DNA Sequences. Proceedings of the 8th World Multi-Conference on Systemics, Cybernetics and Informatics. 7, 12-18, 2004.
    109. Sugaya, N., Sato, M., Murakami, H., Imaizumi, A., Aburatani, S. and Horimoto, K. Genome-Size Increase in Anabaena sp. PCC7120. Proceedings of the 8th World Multi-Conference on Systemics, Cybernetics and Informatics. 7, 35-40, 2004.
    110. Sato, M., Sugaya, N., Murakami, H., Imaizumi, A., Aburatani, S., Akutsu, T. and Horimoto, K. Remote Homolog Detection by Match-Node profile in Hidden Markov Model. Proceedings of the 8th World Multi-Conference on Systemics, Cybernetics and Informatics. 7, 27-34, 2004.
    111. Imaizumi, A., Sugaya, N., Murakami, H., Sato, M., Aburatani, S. and Horimoto, K. Network Reconstruction of Genetic Relationship in Tryptophan Metabolism from Gene Expression Profiles. Proceedings of the 8th World Multi-Conference on Systemics, Cybernetics and Informatics. 7, 4-11, 2004.
    112. Aburatani, S., Sugaya, N., Murakami, H., Sato, M., Imaizumi, A. and Horimoto, K. Internet Tool for Network Inference: ASIAN (Automatic System for Inferring A Network). Proceedings of the 8th World Multi-Conference on Systemics, Cybernetics and Informatics. 7, 1-3, 2004.
    113. Sakai, H., Maruyama, O., Murakami, H., Sugaya, N., Sato, M., Imaizumi, A., Aburatani, S., Horimoto, K. and Kanehisa, M. Finding Characteristic Sequence Patterns of Alternative Splicing in Human Genomic DNA. Proceedings of the 8th World Multi-Conference on Systemics, Cybernetics and Informatics. 7, 19-26, 2004.
    114. Akutsu, T., Hayashida, M., Tomita, E., Suzuki, J. and Horimoto, K. Protein Threading with Profiles and Constraints. Fourth IEEE Symposium on Bioinformatics and Bioengineering (BIBE2004), 537-544, 2004.
    115. [2003]
    116. Aburatani, S., Kuhara, S., Toh, H. and Horimoto, K. Deduction of a Gene Regulatory Relationship Framework from Gene Expression Data by the Application of Graphical Gaussian Modeling. Signal Processing, 83, 777-788, 2003.
    117. [2002]
    118. Toh, H. and Horimoto, K. System for Automatically Inferring a Genetic Network from Expression Profiles. J. Biol. Phys., 28, 449-464, 2002.
    119. Toh, H. and Horimoto, K. Inference of a Genetic Network by a Combined Approach of Cluster Analysis and Graphical Gaussian Modeling. Bioinformatics, 18, 287-297, 2002.
    120. [2001]
    121. Horimoto, K., Aburatani, S., Kuhara, S. and Toh, H. ASIAN – Automatic System for Inferring a Network from Gene Expression Profiles. Res. Commun. Biochem. Cell Mol. Biol., 5, 192-207, 2001
    122. Horimoto, K. and Toh, H. Statistical Estimation of Cluster Boundaries in Gene Expression Profile Data. Bioinformatics, 17, 1143-1151, 2001.
    123. Horimoto, K., Fukuchi, S. and Mori, K. Comprehensive Comparison between Locations of Orthologous Genes on Archaeal and Bacterial Genomes. Bioinformatics, 17, 791-802, 2001.
    124. Akutsu, T. and Horimoto, K. Local Multiple Alignment of Real Numerical Sequences: Detection of Subtle Motifs from Protein Sequences and Structure. Genome Informatics, 12, 83-92, 2001.
    125. [2000]
    126. Horimoto, K. and Fukuchi, S. Feasibility of Gene-Location Distance in Microbial Genome Analysis. INFORMATION, 3, 263-269, 2000.
    127. Fukuchi, S. and Horimoto, K. Classification of Linear Chromosomes. In: Begehr,H.G.W., Gilbert,R.P. and Kajiwara,J. (eds) Proceedings of Second International Congress ISAAC vol.2, Kluwer Academic Publisher, New York, p.1265-1274, 2000.
    128. Suzuki, H., Fukuchi, S. and Horimoto, K. A Procedure for Detecting Similarity between Distantly Related Protein Families. In: Begehr,H.G.W., Gilbert,R.P. and Kajiwara,J. (eds) Proceedings of Second International Congress ISAAC vol.2, Kluwer Academic Publisher. New York. p.1275-1283, 2000.
    129. [1999]
    130. Horimoto, K., Mori, K. and Fukuchi, S. Measures for Circular Genome Comparison. Information, 2, 83-90, 1999.
    131. [1998]
    132. Horimoto, K., Mori, K. and Otsuka, J. Quantitative Estimation of Gene Mobility on Circular Genomes: Mode of Gene Transpositions on Metazoan Mitochondria. Res. Commun. Biochem. Cell Mol. Biol. 2, 359-369, 1998.
    133. Horimoto, K., Mori, K. and Otsuka, J. Effect of Duplications, Inversions, and Insertions or Deletions on Dissimilarity between Mitochondrial Genomes. Res. Commun. Biochem. Cell Mol. Biol. 2, 347-357, 1998.
    134. Horimoto, K., Suyama, M., Toh, H., Mori, K. and Otsuka, J. A Method for Comparing Circular Genomes from Gene Locations: Application to Mitochondrial Genomes. Bioinformatics, 14, 789-802, 1998.
    135. [1997]
    136. Horimoto, K., Hofuku, I. and Oshima, K. Population Dynamics of HIV Positive by Application of a Locally Modified Gompertz Curve: A Case Study for Japan. Nonlinear Analysis, 30, 985-993, 1997.
    137. Oshima, K., Hofuku, I. and Horimoto, K. New Interpolating Functions for Non-Decreasing Time Series Data. Nonlinear Analysis, 30, 995-1006, 1997.
    138. Oshima, K., Hofuku, I. and Horimoto, K. Application of weighted ranking methods for tie-break simulations. In: Bainov, D. (ed) Proceedings of the Seventh International Colloquium on Differential Equations. p.313-320, VSP, The Netherlands, 1997.
    139. [1996]
    140. Oshima, K., Nomura, S. and Horimoto, K. An experimental algorithm for finding eigenvalues. In: Bainov, D (ed.) Proceedings of the Sixth International Colloquium on Differential Equations. p.189-196, VSP, Netherlands, 1996
    141. Horimoto, K., Oshima, K., Tsugita, A. and Otsuka, J. Protein Superfamily Database (PROSUP). In: Dabois, D. E. and Gershon, N. (eds.) Information Revolution: Impact on Science and Technology. p.256-262, Springer, Berlin, 1996.
    142. [1995]
    143. Lu-Ping Chow, Fukaya, N., Miyatake, N., Horimoto, K., Sugiura, Y., Tabuchi, K., Ueno, Y. and Tsugita, A. Resolution of Fusarium sporotrichioides Proteins by Two Dimensional Polyacrylamide Gel Electrophoresis and Identification by Sequence Homology Comparison in Protein Data Base. J. Biomedi.Sci. 2, 343-352, 1995.
    144. [1994]
    145. Horimoto, K., Yamamoto, H., Yanagi, K., Oshima, K. and Otsuka, J. A Simple Procedure for Assigning a Sequence Motif with an Obscure Pattern: Application to Basic/Helix-Loop-Helix Motif. Protein Engineering, 7, 1433-1440, 1994.
    146. Otsuka, J., Fukuchi, S. and Horimoto, K. Approaches to Biological Problems from Sequence Analyses. In Glaeser, P. S. and Millward, M. T. L. (eds.) New Data Challenges in Our Information Age. CODATA Proceedings Series vol. 2, p.155-164, CODATA, Paris, 1994.
    147. [1993]
    148. Otsuka, J., Miyazaki, K. and Horimoto, K. Divergence Pattern and Selective Mode in Protein Evolution: the Example of Vertebrate Myoglobins and Hemoglobin Chains. J. Mol. Evol. 36, 153-181, 1993.
    149. [1992]
    150. Otsuka, J., Miyachi, H. and Horimoto, K. Structure Model of Core Proteins in Photosystem I Inferred from the Comparison with those in Photosystem II and Bacteria; an Application of Principal Component Analysis to Detect the Similar Regions between Distantly Related Families of Proteins. Biochim. Biophys. Acta 1118, 194-210, 1992.
    151. [1991]
    152. Horimoto, K., Suzuki, H. and Otsuka, J. Principal Component Analysis to Detect the Similarity of Distantly Related Proteins; its Application to Cytochromes c, c1 and f. Protein Seq. Data Anal. 4, 33-42, 1991.
    153. [1990]
    154. Horimoto, K., Suzuki, H. and Otsuka, J. Discrimination between Adaptive and Neutral Amino Acid Substitutions in Vertebrate Hemoglobins. J. Mol. Evol. 31, 302-324, 1990.
    155. Horimoto, K., Suzuki, H., Miyatake, N., Fukuchi, S. and Otsuka, J., Research of Biological Evolution with Use of Protein Database, Proc. of Informatics Symposium 1990、p.79-88, 1990.
    156. [1989]
    157. Horimoto, K., Otsuka, J. and Kunisawa, K. Rapid Evolutionary Repair of Base Mispairings in Stem Regions of Eukaryotic 5S rRNA. Protein Seq. Data Anal. 2, 93-99, 1989.
    158. [1987]
    159. Kunisawa, K., Horimoto, K. and Otsuka, J. Accumulation Pattern of Amino Acid Substitutions in Protein Evolution. J. Mol. Evol. 24, 357-365, 1987.
  2. 著書 (英文のみ)
    1. Horimoto, K., Nakatsui, M and Popov, N. (eds): Algebraic and Numeric Biology, Lecture Notes in Computer Science, Vol. 6479, Springer, Heidelberg, 2012.
    2. Saito, S. and Horimoto, K.: Network Screening: A New Method to Identify Active Networks from an Ensemble of Known Networks. in Applied Statistics for Network Biology: Methods in Systems Biology (eds M. Dehmer, F. Emmert-Streib, A. Graber and A. Salvador), Chapter 13, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, 2011.
    3. Aburatani, S., Saito, S., and Horimoto, K.: ASIAN: Automatic System for Inferring A Network. In Krawetz, S. (ed): Bioinformatics for Systems Biology: Second Edition, Introduction to Informatics, p.563-577, Humana Press, New Jersey, 2009.
    4. Anai, H. and Horimoto, K. (eds): Symbolic Computation in Biology, Math. Comput. Sci., 2, 399-556, 2009.
    5. Horimoto, K., Regensburger, G., Rosenkranz, M. and Yoshida, H. (eds): Algebraic Biology, Lecture Notes in Computer Science 5147, Springer, Heidelberg, 2008.
    6. 6. Anai, H., Horimoto, K. and Kutsia, T. (eds) Algebraic Biology, Lecture Notes in Computer Science 4545, Springer, Heidelberg, 2007.
    7. Anai, H. and Horimoto, K. (eds): Algebraic Biology – Computer Algebra in Biology, Universal Academy Press, Tokyo, 2005
  3. 学術活動(国際活動のみ)
    • Associate Editor of BMC Systems Biology
    • Member of Technical Committee on Systems Biology in IEEE
    • Initiate and Organize “International Conference on Algebraic Biology”, with Profs. Hirokazu Anai, Bruno Buchberger, Reihard Laubenbaher, Bad Mishra (2005, 2007, 2008, 2010)
    • Initiate and Organize “Symposium on Systems and Synthetic Biology (TriSys)”, with Profs. Luonan Chen, Sunghoon Kim (2009, 2010,2011,2013,2015)
  4. 学術賞(国際賞のみ)
    • Oxford University Press Bioinformatics Prize (2001), with Dr. Hiroyuki Toh, in The Twelfth International Conference on Genome Informatics (GIW2001)
    • The Best Poster Award (2005), with Drs. Shigeru Orii, Hirokazu Anai, in BIOINFO 2005: 2005 International Joint Conference of AASBi, InCoB and KSBI
    • The Best Poster Award of GIW2010 (2010), with Drs. Yong Wang, Luonan Chen, in The 21th International Conference on Genome Informatics (GIW2010)
  5. 研究資金(国内のみ)
    • 国立研究開発法人日本医療研究開発機構:「次世代治療・診断実現のための創薬基盤技術開発事業(患者層別化マーカー探索技術の開発)」分担、2平成30年度~令和4年度
    • 文部科学省科学研究費補助金、基盤研究(B) (一般):「NAFLD/NASH肝細胞リン酸化活性プロファイリングと新規治療標的分子の同定」分担、平成30年度~令和2年度
    • 文部科学省科学研究費補助金、基盤研究(B) (一般):「Connectivity Map解析に基づいた新しい大腸癌予防薬の開発」分担、平成29年度~令和元年度
    • 国立研究開発法人日本医療研究開発機構:「創薬支援推進事業(創薬支援インフォマティクスシステム構築)」分担、平成27~31年度
    • 文部科学省科学研究費補助金、基盤研究(B) (一般): 「肝炎ウイルス治療後の肝発癌機序とバイオマーカーの同定に関する研究」、分担、平成27~29年度
    • 国立研究開発法人日本医療研究開発機構:「先駆的医薬品・医療機器研究発掘支援事業(数理情報解析技術を活用した創薬標的候補探索)」(代表)平成26年度
    • 文部科学省科学研究費補助金、基盤研究(B) (一般): 「C型慢性肝炎治療成績の向上と肝発癌阻止を目指した分子基盤の確立」、分担、平成24~26年度
    • 日本学術振興会: 「二国間交流事業・セミナー」、代表、平成23年度
    • 新エネルギー・産業技術総合開発機構研究委託: 「エピゲノム修飾のメカニズムを活用した創薬基盤技術の開発」、分担、平成22~26年度
    • 厚生労働省科学研究費補助金、肝炎等克服緊急対策研究事業: 「ウイルス性肝疾患に対する分子標的治療創薬に関する研究」、分担、平成22~24年度
    • 日本学術振興会: 「外国人招へい研究者(短期)」、代表、平成21年度
    • 新エネルギー・産業技術総合開発機構研究委託: 「iPS細胞等幹細胞産業応用促進基盤技術開発」、分担、平成21~22年度
    • 文部科学省科学研究費補助金、基盤研究(B) (一般): 「C型慢性肝炎インターフェロン療法の応答・不応答に関わる宿主遺伝子の探索」、分担、平成21~23年度
    • 文部科学省科学研究費補助金、特定領域研究生命システム情報: 「グラフィカル・モデルに基づく生命情報からの因果・関連性解析」、公募研究(代表)、平成20~21年度
    • 文部科学省科学研究費補助金、基盤研究(A) (一般): 「細胞内ネットワークモデルと分子計測データとの整合性評価法の開発」、代表、平成19~21年度
    • 新エネルギー・産業技術総合開発機構研究委託: 「モデル細胞を用いた遺伝子機能等解析技術開発/細胞アレイ等による遺伝子機能の解析技術開発」、分担、平成17~21年度
    • 文部科学省科学研究費補助金、基盤研究(A) (一般): 「計算代数統計学の展開」、分担、平成19~21年度
    • 厚生労働省科学研究費補助金、肝炎等克服緊急対策研究事業: 「ジェノミクス技術を用いたウイルス性肝炎に対する新規診断・治療法の開発」、分担、平成19~21年度
    • 戦略的創造研究推進事業CREST: 「シミュレーション技術の革新と実用化基盤の構築/数値/数式ハイブリッド計算に基づくロバスト最適化プラットフォームの構築」、分担、平成15~20年度
    • 文部科学省科学研究費補助金、特定領域研究生命システム情報: 「グラフィカル・ガウシアン・モデルによる相互作用推定法の拡張とその適用」公募研究(代表)、平成17~19年度
    • 文部科学省科学研究費補助金、特定領域研究ゲノム情報科学: 「グラフィカル・モデリングに基づく相互作用推定法の理論的研究と適用」公募研究(代表)、平成15~16年度
    • 文部科学省科学研究費補助金、基盤研究(B)(一般): 「遺伝子配置に基づく巨視的なゲノム構造比較」公募研究(代表)平成15~16年度
    • 文部科学省科学研究費補助金、特定領域研究(C)ゲノム情報科学: 「遺伝子配置情報に基づくゲノム構造比較法の開発」公募研究(代表)、平成12~14年度