• 2607 Citations
  • 17 h-Index
19962020

Research output per year

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Research Output

2006

An FPGA implementation of high throughput stochastic simulator for large-scale biochemical systems

Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H. & Amano, H., 2006 Dec 1, Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL. p. 227-232 6 p. 4100980. (Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL).

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

6 Citations (Scopus)

Celldesigner: A modeling tool for biochemical networks

Funahashi, A., Matsuoka, Y., Jouraku, A., Kitano, H. & Kikuchi, N., 2006 Dec 1, Proceedings of the 2006 Winter Simulation Conference, WSC. p. 1707-1712 6 p. 4117804. (Proceedings - Winter Simulation Conference).

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

19 Citations (Scopus)

Comparative studies of suppression of malignant cancer cell phenotype by antisense oligo DNA and small interfering RNA

Hiroi, N., Funahashi, A. & Kitano, H., 2006 Jan 1, In : Cancer Gene Therapy. 13, 1, p. 7-12 6 p.

Research output: Contribution to journalArticle

16 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)
2005

A comprehensive pathway map of epidermal growth factor receptor signaling.

Oda, K., Matsuoka, Y., Funahashi, A. & Kitano, H., 2005, In : Molecular systems biology. 1, p. 2005.0010

Research output: Contribution to journalArticle

692 Citations (Scopus)

A framework for ODE-based multimodel biochemical simulations on an FPGA

Osana, Y., Fukushima, T., Yoshimi, M., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H. & Amano, H., 2005 Dec 1, Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL. p. 574-577 4 p. 1515788. (Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL; vol. 2005).

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

3 Citations (Scopus)

An FPGA-based, multi-model simulation method for biochemical systems

Osana, Y., Fukushima, T., Yoshimi, M., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., Kitano, H. & Amano, H., 2005 Dec 1, Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005. 1420035. (Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005; vol. 2005).

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

4 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)

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)

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

321 Citations (Scopus)
2004

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)
2002

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)
2001

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)

Recursive diagonal torus: An interconnection network for massively parallel computers

Yang, Y., Funahashi, A., Jouraku, A., Nishi, H., Amano, H. & Sueyoshi, T., 2001 Jul 1, In : IEEE Transactions on Parallel and Distributed Systems. 12, 7, p. 701-715 15 p.

Research output: Contribution to journalArticle

55 Citations (Scopus)
1999
6 Citations (Scopus)
1997

Adaptive routing on the recursive diagonal torus

Funahashi, A., Hanawa, T., Kudoh, T. & Amano, H., 1997, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer Verlag, Vol. 1336. p. 171-182 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 1336).

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

1 Citation (Scopus)
1996

Fault tolerance of the TBSF (Tandem Banyan Switching Fabrics) and PBSF (Piled Banyan Switching Fabrics)

Funahashi, A., Hanawa, T. & Amano, H., 1996 Jan 1, In : IEICE Transactions on Information and Systems. E79-D, 8, p. 1180-1189 10 p.

Research output: Contribution to journalArticle