Books Software Infrastructure for Effective Communication and Reuse of Computational Models. “System Modeling in Cellular Biology:
From Concepts to Nuts and Bolts” Joint 2006/03 MIT Press Zoltan Szallasi, Jörg Stelling and Vipul Periwal Finney, A., Hucka, M., Bornstein, B., Keating, S., Shapiro, B., Matthews, J., Kovitz, B., Schilstra, M., FUNAHASHI Akira, Doyle, J., and Kitano, H.
Books SBML Models and MathSBML “Introduction to Systems Biology” Joint 2007/07 Humana Press Sangdun Choi Shapiro, B., Finney, A., Hucka, M., Bornstein, B., Funahashi, A., Jouraku, A., Keating, S., Novere, N., Matthews, J., and Schilstra, M. pp.395-421
Books CellDesigner software: a graphical biological network editor and workbench interfacing simulator “Introduction to Systems Biology” Individual 2007/07 Humana Press Sangdun Choi FUNAHASHI Akira pp.422-434
Books Kinetics of Dimension Restricted Condition “Introduction to Systems Biology” Joint 2007/07 Humana Press Sangdun Choi Hiroi, N. and Funahashi, A. pp.261-281
Academic Papers Fault tolerance of the TBSF (Tandem Banyan Switching Fabrics) and PBSF (Piled Banyan Switching Fabrics). Joint 1996/08 IEICE Transactions on Information and Systems VolE79-D,No8 Funahashi, A., Hanawa, T., and Amano, H. pp.1180-1189
Academic Papers Adaptive routing for Recursive Diagonal Torus. Joint 2000/11 IEICE Transactions on Information and Systems J89-D-I巻11号 Funahashi, A., Jouraku, A., and Amano, H. pp.1143-1153
Academic Papers The Impact of Output Selection Function on Adaptive Routing. Joint 2001/04 IPSJ Journal 42巻4号 Koibuchi, M., Funahashi, A., Jouraku, A., and Amano, H. pp.704-713
Academic Papers Recursive Diagonal Torus: an interconnection network for massively parallel computers. Joint 2001/07 IEEE Trans. on Parallel and Distributed Systems Vol12,No7 Yang, Y., Funahashi, A., Jouraku, A., Nishi, H., Amano, H., and Sueyoshi, T. pp.701-715
Academic Papers L-turn routing: An Adaptive Routing in Irregular Networks Joint 2001/08 IPSJ Journal of High Performance Computing System 42巻SIG9号 Koibuchi, M., Funahashi, A., Jouraku, A., and Amano, H. pp.119-134
Academic Papers The Impact of Output Selection Function on Adaptive Routing. Joint 2001/11 ISCA Information: An International Journal Vol4,No4 Funahashi, A., Koibuchi, M., Jouraku, A., and Amano, H. pp.541-550
Academic Papers Z-routing: Adaptive routing on irregular networks Joint 2002/03 IPSJ Journal 43巻3号 Igawa, Y. and Funahashi, A. pp.754-763
Academic Papers An Output Selection Function based on the characteristic of virtual channel Joint 2002/03 IPSJ Journal 43巻3号 Sugiyama, S. and Funahashi, A. pp.764-775
Academic Papers CellDesigner: a process diagram editor for gene-regulatory and biochemical networks. Joint 2003/11 BioSilico Vol1,No5 Funahashi, A., Tanimura, N., Morohashi, M., and Kitano, H. pp.159-162
Academic Papers Molecular Interaction Map of Macrophage. Joint 2004/08 AfCS Report Vol2,No14 Oda, K., Kimura, T, Matsuoka, Y., Funahashi, A., Muramatsu, M., and Kitano, H. pp.1-12
Academic Papers Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. Joint 2004/09 IEE Systems Biology Vol1,No1 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., and Kitano, H. pp.41-53
Academic Papers A comprehensive pathway map of epidermal growth factor receptor signaling. Joint 2005/05 Nature Molecular Systems Biology Vol1,No1 Oda, K., Matsuoka, Y., Funahashi, A., and Kitano, H. pp.1-17
Academic Papers Using process diagrams for the graphical representation of biological networks. Joint 2005/08 Nature Biotechnology Vol23,No8 Kitano, H., Funahashi, A., Matsuoka, Y., and Oda, K. pp.961-966
Academic Papers Analysis for Dimension-Restricted Kinetics with Bacterial Endonuclease Movement. Joint 2006/01 WSEAS Transactions on Biology and Biomedicine Vol3,No1 Hiroi, N., Funahashi, A., and Kitano, H. pp.1-6
Academic Papers Comparative studies of suppression of malignant cancer cell phenotype by antisense oligo DNA and small interfering RNA. Individual 2006/01 Cancer Gene Therapy Vol13,No1 Hiroi, N., Funahashi, A., and Kitano, H. pp.7-12
Academic Papers ReCSiP: an FPGA-Based General Purpose Biochemical Simulator Joint 2006/06 IEICE Transactions on Information and Systems J89-D巻6号 Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H. pp.1163-1172
Academic Papers FPGA-Based Stochastic Biochemical Simulator Joint 2007/02 IPSJ Transactions on Advanced Computing System 48巻SIG 3 (ACS 17)号 Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H., and Amano, H. pp.45-58
Academic Papers An integration of CellDesigner and SABIO-RK Joint 2007/03 In Silico Biology Vol7,No2 FUNAHASHI Akira, JOURAKU Akiya, MATSUOKA Yukiko, KITANO Hiroaki pp.S81-S90.
Academic Papers ReCSiP: An FPGA-Based Biochemical Simulator Joint 2007/07 Electronics and Communications in Japan (Part II: Electronics) Vol90,No7 Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H pp.1-10
Academic Papers Deduction of intracellular sub-systems from a topological description of the network. Joint 2007/08 Molecular Biosystems Vol3,No8 NORDLING Torbjorn, HIROI, Noriko, FUNAHASHI Akira and KITANO Hiroaki pp.523-529