Katsuhisa Horimoto HP
(Jan. 2016)

 

 

堀本 勝久

 

Katsuhisa Horimoto, Ph.D.
  Deputy Director   Molecular Profiling Research Center for Drug Discovery (molprof)
  National Institute of Advanced Industrial Science and Technology (AIST)

  address: 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, JAPAN
 メールアドレス
  phone: +81 3 3599 8618(direct)
  fax: +81 3 3599 2064

 

堀本 勝久 (ほりもと かつひさ)、理学博士
  産業技術総合研究所(AIST)
  創薬分子プロファイル研究センター(molprof)副センター長

  住所: 〒135-0064 東京都江東区青海2-4-7
 メールアドレス
  電話: 03-3599-8618 (直通)
  ファックス: 03-3599-2068

 

c.v.

 First name: Katsuhisa
 Family name: Horimoto
 Born: Nov. 20, 1958
 Sex: Male

 

Education:

  1982–1986: Department of Applied Biological Science, Faculty of Science and Technology, Science University of Tokyo
  1986–1988: Master course in Graduate School of Science and Technology, Science University of Tokyo
  1988: M.Sc. degree in Biophysics in 1986, from Science University of Tokyo
  1988–1991: Doctor course in Graduate School of Science and Technology, Science University of Tokyo
  1991: Dr.Sc. degree in Biophysics in 1991, from Science University of Tokyo

 



Profession:

  1991(Apr.)–1997(Mar.): a research associate, of Research Institute for Life Sciences, Science University of Tokyo
  1997(Apr.)–2001(Sep.): an associate professor, of General Education (Mathematics), Saga Medical School
  2002(Oct.)–2006(Mar.): a professor, of Laboratory of Biostatistics, Institute of Medical Science, University of Tokyo
  2006(Apr.)–2013(Mar.): a leader, of Biological Network Team, Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST)
  2013(Apr.)–present : a deputy director, of Molecular Profiling Research Center for Drug Discovery (molprof), National Institute of Advanced Industrial Science and Technology (AIST)

  2008(Apr.)–2009(Mar.): a visiting professor, of Institute for Chemical Research, Kyoto University
  2008(Oct.)–2013(Sep.): an adjunct professor, of Institute for Systems Biology, Shanghai University
  2011(Aug,)-2015(Sep.): an adjunct professor, of Center of Systems Biology, Soochow University

 



Motto (sorry, only in Japanese)

 

Research Interests

[Research field] Computational Systems Pharmacology

 

Achievements

 (1) Papers (refereed and in English, only)
 (2) Books (in English, only)
 (3) Academic activities (international, only)
 (4) Prizes (international, only)
 (5) Funding (in Japanese, only)

 

(1) Papers (refereed and in English, only)

[2015]

  1. 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.
  2. 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.

[2014]

  1. 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

[2013]

  1. 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.
  2. 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.
  3. 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.
  4. 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
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.

[2012]

  1. 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.
  2. 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.
  3. 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.
  4. 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
  5. 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.
  6. 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.
  7. 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.
  8. 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.

[2011]

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.

[2010]

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.

[2009]

  1. 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.
  2. 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.
  3. 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
  4. 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.
  5. 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.
  6. 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.
  7. Akutsu, T., Tamura, T. and Horimoto, K.: Complementing Networks Using Observed Data. Lecture Notes in Artificial Intelligence 5809, pp. 126-140, 2009.

[2008]

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.

[2007]

  1. 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.
  2. Yoshida, H., Anai, H. and Horimoto, K., Derivation of rigorous conditions for high cell–type diversity by algebraic approach. BioSystems, 90, 486–495, 2007.
  3. 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.
  4. 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.
  5. 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
  6. 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.

[2006]

  1. 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
  2. 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.
  3. 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.
  4. 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.

[2005]

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.

[2004]

  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.

[2003]

  1. 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.

[2002]

  1. Toh, H. and Horimoto, K. System for Automatically Inferring a Genetic Network from Expression Profiles. J. Biol. Phys., 28, 449-464, 2002.
  2. 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.

[2001]

  1. 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
  2. Horimoto, K. and Toh, H. Statistical Estimation of Cluster Boundaries in Gene Expression Profile Data. Bioinformatics, 17, 1143-1151, 2001.
  3. Horimoto, K., Fukuchi, S. and Mori, K. Comprehensive Comparison between Locations of Orthologous Genes on Archaeal and Bacterial Genomes. Bioinformatics, 17, 791-802, 2001.
  4. 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.

[2000]

  1. Horimoto, K. and Fukuchi, S. Feasibility of Gene-Location Distance in Microbial Genome Analysis. INFORMATION, 3, 263-269, 2000.
  2. 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.
  3. 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.

[1999]

  1. Horimoto, K., Mori, K. and Fukuchi, S. Measures for Circular Genome Comparison. INFORMATION, 2, 83-90, 1999.

[1998]

  1. 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.
  2. 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.
  3. 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.

[1997]

  1. 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.
  2. Oshima, K., Hofuku, I. and Horimoto, K. New Interpolating Functions for Non-Decreasing Time Series Data. Nonlinear Analysis, 30, 995-1006, 1997.
  3. 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.

[1996]

  1. 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
  2. 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.

[1995]

  1. 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.

[1994]

  1. 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.
  2. 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.

[1993]

  1. 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.

[1992]

  1. 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.

[1991]

  1. 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.

[1990]

  1. 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.
  2. 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.

[1989]

  1. 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.

[1987]

  1. Kunisawa, K., Horimoto, K. and Otsuka, J. Accumulation Pattern of Amino Acid Substitutions in Protein Evolution. J. Mol. Evol. 24, 357-365, 1987.

 

(2) Books (in English, only)

  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. 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) Academic activities (international, only)

 

(4) Prizes (international, only)

 

(5) Funding (in Japanese, only)