Katsuhisa Horimoto HP

(April 2011)

 

 

Katsuhisa Horimoto, Ph.D.

Leader of Biological Network Team,

Computational Biology Research Center (CBRC),

National Institute of Advanced Industrial Science and Technology (AIST)

address: 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan

e-mail: k.horimoto@aist.go.jp

phone: +81 3 3599 8711 (direct)

fax: +81 3 3599 8081

 

堀本　勝久　（ほりもと　かつひさ）、理学博士

研究チーム長、生体ネットワークチーム、

生命情報工学研究センター(CBRC)、

産業技術総合研究所 (AIST)

住所：〒135-0064 東京都江東区青海 2-4-7

メール：k.horimoto@aist.go.jp

電話：03-3599-8711 （直通）

ファックス：03-3599-8081

 

 

 

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 Division 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.)–present   : a leader, of Biological Network Team, Computational Biology Research Center (CBRC), 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

 

 

 

Motto (sorry, only in Japanese)

 

Ÿ 「魂によって感覚を癒し、感覚によって魂を癒す」-オスカー・ワイルド（福田恒存訳）「ドリアングレイの肖像」

-      健全な精神の下で研究生活を継続するために。

Ÿ 「世界は単純な記号と決まりからできている」-三島由紀夫「午後の曳航」

-      複雑な現象を前にして悩むことに淫することなく、明快な決断を下すために。

Ÿ 「紅旗征戎非吾事」-藤原定家「明月記」

-      研究以外の活動を怠惰の言い訳にしないために。

Ÿ 「才能に勝る努力なし」-つかこうへい

-      「作業」だけの「努力賞」を期待することなく、「アイディア」を絞り出す努力を怠らないために。

 

 

Research Interests

 

[Research field]

Computational Systems Biology

-      Estimation and modeling of molecular relationships, which are responsible for biological phenomena and are narrowed down so as to be experimentally verified, from system viewpoint

 

[Present research themes]

ü   [Methodology] “Network Screening”: Detection of activated networks under particular conditions in known networks, by estimating the consistency of the graph with the measured data – network structure analysis

ü   [Methodology] Accuracy enhancement in the parameter optimization, by using symbolic computation techniques – network dynamics

ü   [Methodology] Clinical-outcome oriented identification of molecular functions in diseases – computational clinical analysis

ü   [Application] Trace the changes of regulatory networks in biological phenomena, especially disease progressions

ü   [Application] Define master regulators in diseases

ü   [Application] Clarify molecular mechanisms of pluripotency in stem cells

 

 

 

Achievements

 

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

(2) Papers in proceedings (refereed and in English, only)

(3) Books (in English, only)

(4) Academic activities (international, only)

(5) Prizes (international, only)

(6) Funding (in Japanese, only)

 

 

(1) Papers in journals

 

[2011]

1.   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. in press.

2.   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. in press.

3.   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., in press.

4.   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.

[2010]

5.   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.

6.   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.

7.   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.

8.   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.

[2009]

9.   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.

10. 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.

11. 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

[2008]

12. 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.

13. 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.

14. 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.

15. 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.

[2007]

16. 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.

17. Yoshida, H., Anai, H. and Horimoto, K., Derivation of rigorous conditions for high cell–type diversity by algebraic approach. BioSystems, 90, 486–495, 2007.

[2006]

18. 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

19. 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.

20. 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.

21. 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]

22. 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.

23. 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.

24. 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.

25. 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.

[2004]

26. 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.

27. 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.

28. 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.

[2003]

29. 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]

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

31. 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]

32. 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

33. Horimoto, K. and Toh, H. Statistical Estimation of Cluster Boundaries in Gene Expression Profile Data. Bioinformatics, 17, 1143-1151, 2001.

34. Horimoto, K., Fukuchi, S. and Mori, K. Comprehensive Comparison between Locations of Orthologous Genes on Archaeal and Bacterial Genomes. Bioinformatics, 17, 791-802, 2001.

35. 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]

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

[1999]

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

[1998]

38. 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.

39. 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.

40. 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]

41. 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.

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

[1995]

43. 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]

44. 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.

[1993]

45. 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]

46. 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]

47. 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]

48. 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.

[1989]

49. 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]

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

 

 

(2) Papers in proceedings

 

[2011]

1.   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, in press.

[2010]

2.   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, in press.

3.   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.

4.   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.

5.   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.

6.   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.

7.   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]

8.   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.

9.   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.

10. 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.

11. Akutsu, T., Tamura, T. and Horimoto, K.: Complementing Networks Using Observed Data. Lecture Notes in Artificial Intelligence 5809, pp. 126-140, 2009.

[2008]

12. 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.

13. 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.

14. 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.

15. 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.

16. 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]

17. 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.

18. 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.

19. 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

20. 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.

[2005]

21. 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.

22. 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.

23. 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.

24. 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.

25. 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.

26. 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]

27. 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.

28. 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.

29. 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.

30. 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.

31. 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.

32. 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.

33. 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.

[2000]

34. 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.

35. 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.

[1997]

36. 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]

37. 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

38. 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.

[1994]

39. 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.

[1990]

40. 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.

 

 

(3) Books

 

1.   Horimoto, K., Nakatsui, M and Popov, N. (eds): Algebraic and Numeric Biology, Lecture Notes in Computer Science, Springer, Heidelberg, in press.

2.   Saito, S. and Horimoto, K.: Network Screening: Detection of Active Regulatory Networks. In Emmert-Streib, F., Dehmer, M., Salvador, A. and Graber, A. (eds): Applied statistics for Network Biology: Methods in Systems Biology, Wiley, in press.

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

 

 

(4) Academic activities

 

Ÿ  Associate Editor of BMC Systems Biology

Ÿ  Member of Technical Committee on Systems Biology in IEEE

Ÿ  Initiate and Organize “International Conference on Algebraic Biology”, with Profs. Hirokazu Anai, Bruno Buchberger, Reihard Laubenbaher, Bad Mishra (2005, 2007, 2008, 2010)

Ÿ  Initiate and Organize “Symposium on Systems and Synthetic Biology (TriSys)”, with Profs. Luonan Chen, Sunghoon Kim (2009, 2010)

 

 

(5) Prizes

 

Ÿ   Oxford University Press Bioinformatics Prize (2001), with Dr. Hiroyuki Toh, in The Twelfth International Conference on Genome Informatics (GIW2001)

Ÿ   The Best Poster Award (2005), with Drs. Shigeru Orii, Hirokazu Anai, in BIOINFO 2005: 2005 International Joint Conference of AASBi, InCoB and KSBI

Ÿ   The Best Poster Award of GIW2010 (2010), with Drs. Yong Wang, Luonan Chen, in The 21th International Conference on Genome Informatics (GIW2010)

 

 

(6) Funding

 

Ÿ  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

Ÿ  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

Ÿ  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

Ÿ  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

Ÿ  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

Ÿ  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

Ÿ  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

Ÿ  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

Ÿ  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

Ÿ  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

Ÿ  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

Ÿ  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

Ÿ  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

Ÿ  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

Ÿ  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

Ÿ  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