• 2625 Citations
  • 17 h-Index
19962020

Research output per year

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Research Output

Conference contribution

Configuring area and performance: Empirical evaluation on an FPGA-based biochemical simulator

Ooya, T., Yamada, H., Ishimori, T., Shibata, Y., Osana, Y., Oguri, K., Yoshimi, M., Nishikawa, Y., Funahashi, A., Hiroi, N. & Amano, H., 2009 Nov 25, FPL 09: 19th International Conference on Field Programmable Logic and Applications. p. 679-682 4 p. 5272335. (FPL 09: 19th International Conference on Field Programmable Logic and Applications).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA

Iwanagra, N., Shibata, Y., Yoshimi, M., Osana, Y., Iwaoka, Y., Fukushima, T., Amano, H., Funahashi, A., Hiroi, N., Kitano, H. & Oguri, K., 2005 Dec 1, Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL. p. 666-669 4 p. 1515809. (Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL; vol. 2005).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

10 Citations (Scopus)

Fabrication method to a high resolution control in the space of cell culturing environment with microfluidic system

Hiraiwa, T., Kimura, T., Takenaka, Y., Tanamoto, R., Ota, H., Kimura, H., Taguchi, Y., Miki, N., Matsumoto, Y., Oka, K., Funahashi, A. & Hiroi, N., 2014 Jan 1, MEMS 2014 - 27th IEEE International Conference on Micro Electro Mechanical Systems. Institute of Electrical and Electronics Engineers Inc., p. 264-267 4 p. 6765626. (Proceedings of the IEEE International Conference on Micro Electro Mechanical Systems (MEMS)).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method

Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Osana, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Yamada, H., Kitano, H. & Amano, H., 2007 Dec 1, Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL. p. 254-259 6 p. 4380656. (Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

14 Citations (Scopus)

In vivo oriented modeling with consideration of intracellular crowding

Hiroi, N., Iba, K., Tabira, A., Okuhara, T., Kubojima, T., Hiraiwa, T., Kobayashi, T. J., Oka, K. & Funahashi, A., 2013 Oct 31, 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013. p. 2716-2719 4 p. 6610101. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Citation (Scopus)

L-turn routing: An adaptive routing in irregular networks

Koibuchi, M., Funahashi, A., Jouraku, A. & Amano, H., 2001, Proceedings of the International Conference on Parallel Processing. Institute of Electrical and Electronics Engineers Inc., Vol. 2001-January. p. 383-392 10 p. 952084

Research output: Chapter in Book/Report/Conference proceedingConference contribution

48 Citations (Scopus)

Performance evaluation of an FPGA-based biochemical simulator ReCSiP

Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Kitano, H., Amano, H., Shibata, Y. & Iwanaga, N., 2006 Dec 1, Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL. p. 845-850 6 p. 4101089. (Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

4 Citations (Scopus)

Practical implementation of a network-based Stochastic biochemical simulation system on an FPGA

Yoshimi, M., Nishikawa, Y., Osana, Y., Funahashi, A., Hiroi, N., Shibata, Y., Yamada, H., Kitano, H. & Amano, H., 2008 Nov 3, Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL. p. 663-666 4 p. 4630034. (Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

5 Citations (Scopus)

Requirement of spatiotemporal resolution for imaging intracellular temperature distribution

Hiroi, N., Tanimoto, R., Ii, K., Ozeki, M., Mashimo, K. & Funahashi, A., 2017, Biomedical Imaging and Sensing Conference. SPIE, Vol. 10251. 102510Q

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Routing algorithms based on 2D turn model for irregular networks

Jouraku, A., Koibuchi, M., Amano, H. & Funahashi, A., 2002 Jan 1, Proceedings - International Symposium on Parallel Architectures, Algorithms and Networks, I-SPAN 2002. Hsu, D. F., Saldana, R. P. & Ibarra, O. H. (eds.). IEEE Computer Society, p. 289-294 6 p. 1004296. (Proceedings of the International Symposium on Parallel Architectures, Algorithms and Networks, I-SPAN; vol. 2002-January).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

13 Citations (Scopus)

The design of scalable stochastic biochemical simulator on FPGA

Yoshimi, M., Osana, Y., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H. & Amano, H., 2005 Dec 1, Proceedings - 2005 IEEE International Conference on Field Programmable Technology. p. 339-340 2 p. 1568590. (Proceedings - 2005 IEEE International Conference on Field Programmable Technology; vol. 2005).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

6 Citations (Scopus)
Editorial

Editorial: Quantitative biology: Dynamics of living systems

Hiroi, N., Draviam, V. M. & Funahashi, A., 2016 Jun 2, In : Frontiers in Physiology. 7, JUN, 196.

Research output: Contribution to journalEditorial

1 Citation (Scopus)

Meeting report of the international workshop on quantitative biology 2012: Mesoscopic and microscopic worlds meet

Draviam, V. M., Funahashi, A., Hiroi, N., Kimura, A. & Kobayashi, T. J., 2013, In : Frontiers in Physiology. 3 JAN, Article 479.

Research output: Contribution to journalEditorial

Review article

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

Hucka, M., Finney, A., Bornstein, B. J., Keating, S. M., Shapiro, B. E., Matthews, J., Kovitz, B. L., Schilstra, M. J., Funahashi, A., Doyle, J. C. & Kitano, H., 2004 Jun, In : Systems biology. 1, 1, p. 41-53 13 p.

Research output: Contribution to journalReview article

156 Citations (Scopus)

The DBCLS BioHackathon: Standardization and interoperability for bioinformatics web services and workflows

Katayama, T., Arakawa, K., Nakao, M., Ono, K., Aoki-Kinoshita, K. F., Yamamoto, Y., Yamaguchi, A., Kawashima, S., Chun, H. W., Aerts, J., Aranda, B., Barboza, L. H., Bonnal, R. J. P., Bruskiewich, R., Bryne, J. C., Fernández, J. M., Funahashi, A., Gordon, P. M. K., Goto, N., Groscurth, A. & 37 others, Gutteridge, A., Holland, R., Kano, Y., Kawas, E. A., Kerhornou, A., Kibukawa, E., Kinjo, A. R., Kuhn, M., Lapp, H., Lehvaslaiho, H., Nakamura, H., Nakamura, Y., Nishizawa, T., Nobata, C., Noguchi, T., Oinn, T. M., Okamoto, S., Owen, S., Pafilis, E., Pocock, M., Prins, P., Ranzinger, R., Reisinger, F., Salwinski, L., Schreiber, M., Senger, M., Shigemoto, Y., Standley, D. M., Sugawara, H., Tashiro, T., Trelles, O., Vos, R. A., Wilkinson, M. D., York, W., Zmasek, C. M., Asai, K. & Takagi, T., 2010 Aug 21, In : Journal of Biomedical Semantics. 1, 8.

Research output: Contribution to journalReview article

22 Citations (Scopus)

The Systems Biology Graphical Notation

Novère, N. L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., Bergman, F. T., Gauges, R., Ghazal, P., Kawaji, H., Li, L., Matsuoka, Y., Villéger, A., Boyd, S. E., Calzone, L., Courtot, M. & 19 others, Dogrusoz, U., Freeman, T. C., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G., Goryanin, I., Kell, D. B., Sander, C., Sauro, H., Snoep, J. L., Kohn, K. & Kitano, H., 2009 Aug, In : Nature Biotechnology. 27, 8, p. 735-741 7 p.

Research output: Contribution to journalReview article

524 Citations (Scopus)

Using process diagrams for the graphical representation of biological networks

Kitano, H., Funahashi, A., Matsuoka, Y. & Oda, K., 2005 Aug 1, In : Nature Biotechnology. 23, 8, p. 961-966 6 p.

Research output: Contribution to journalReview article

322 Citations (Scopus)