Publications

publications

Most updated information could be found in Google Scholar page.

Publication

Publication

Papers

  1. 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., Bruskiewich, R., Bryne, J. C., Fern ndez, J. M., Funahashi, A., Gordon, P. M, Goto, N., Groscurth, A., Gutteridge, A., Holland, R., Kano, Y., Kawas, E., 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., Wilkinson, M. D., York, W., Zmasek, C. M., Asai, K., and Takagi, T..
    "The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.." Journal of biomedical semantics. 1 (1). January 2010. pp. 8. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=2939597&tool=pmcentrez&rendertype=abstract
  2. Yamada, H., Ogawa, Y., Ooya, T., Ishimori, T., Osana, Y., Yoshimi, M., Nishikawa, Y., Funahashi, A., Hiroi, N., Amano, H., Shibata, Y., and Oguri, K..
    "Automatic Pipeline Construction Focused on Similarity of Rate Law Functions for an FPGA-based Biochemical Simulator." IPSJ Transactions on System LSI Design Methodology. vol. 3. 2010. pp. 244--256.
  3. Funahashi, A., Matsuoka, Y., Jouraku, A., Takizawa, H., Hiroi, N., Ghosh, S., Kikuchi, N., and Kitano, H..
    "Design and Implementation of CellDesigner." Journal of the Society of Instrument and Control Engineers. 49 (8). Aug 2010. pp. 531--536.
  4. Novere, 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., Villeger, A., Boyd, S. E., Calzone, L., Courtot, M., 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., and Kitano, H..
    "The Systems Biology Graphical Notation." Nature Biotechnology. 27 (8). 2009. pp. 735--741. http://dx.doi.org/10.1038/nbt.1558
  5. Iwaoka, Y., Osana, Y., Yoshimi, M., Nishikawa, Y., Kojima, T., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "A Biochemical Model Compiler for Simulations on an FPGA (In Japanese)." IEICE Transactions on Information and Systems. J91-D (9). September 2008. pp. 2205--2216.
  6. Funahashi, A., Matsuoka, Y., Jouraku, A., Morohashi, M., Kikuchi, N., and Kitano, H..
    "CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks." Proceedings of the IEEE, Special Issue: Computational Systems Biology. 96 (8). August 2008. pp. 1254-1265.
  7. Yoshimi, M., Nishikawa, Y., Osana, Y. Funahashi, A., Hiroi, N., Shibata, Y., Yamada, H., Kitano, H., and Amano, H..
    "Design and Evaluation of an FPGA-Based Stochasitc Biochemical Simulator for High-Throughput Execution (In Japanese)." IPSJ Transactions on Advanced Computing System. 1 (3). Dec 2008. pp. 120-135.
  8. Nordling, T., Hiroi, N., Funahashi, A., and Kitano, H..
    "Deduction of intracellular sub-systems from a topological description of the network." Molecular Biosystems. 3 (8). August 2007. pp. 523-529.
  9. Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "ReCSiP: An FPGA-Based Biochemical Simulator (English translation of Osana et.al, on Trans. IEICE J89-D)." Electronics and Communications in Japan (Part II: Electronics). 90 (7). July 2007. pp. 1--10.
  10. Funahashi, A., Jouraku, A., Matsuoka, Y., and Kitano, H..
    "An integration of CellDesigner and SABIO-RK." In Silico Biology. 7 (2). March 2007. pp. S81--S90.
  11. Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H., and Amano, H..
    "FPGA-Based Stochastic Biochemical Simulator (In Japanese)." IPSJ Transactions on Advanced Computing System (In Japanese). 48 (SIG 3 (ACS 17)). February 2007. pp. 45--58.
  12. Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "ReCSiP: an FPGA-Based General Purpose Biochemical Simulator (In Japanese)." IEICE Transactions on Information and Systems. J89-D (6). June 2006. pp. 1163--1172.
  13. Hiroi, N., Funahashi, A., and Kitano, H..
    "Analysis for Dimension-Restricted Kinetics with Bacterial Endonuclease Movement." WSEAS Transactions on Biology and Biomedicine. 3 (1). January 2006. pp. 1--6.
  14. Hiroi, N., Funahashi, A., and Kitano, H..
    "Comparative studies of suppression of malignant cancer cell phenotype by antisense oligo DNA and small interfering RNA." Cancer Gene Therapy. 13 (1). January 2006. pp. 7--12. http://www.nature.com/cgt/journal/v13/n1/abs/7700869a.html
  15. Kitano, H., Funahashi, A., Matsuoka, Y., and Oda, K..
    "Using process diagrams for the graphical representation of biological networks." Nature Biotechnology. 23 (8). August 2005. pp. 961--966. http://www.nature.com/nbt/journal/v23/n8/abs/nbt1111.html
  16. Oda, K., Matsuoka, Y., Funahashi, A., and Kitano, H..
    "A comprehensive pathway map of epidermal growth factor receptor signaling." Nature Molecular Systems Biology. 1 (1). May 2005. pp. 1--17. http://www.nature.com/msb/journal/v1/n1/full/msb4100014.html
  17. 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..
    "Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project." IEE Systems Biology. 1 (1). September 2004. pp. 41-53. http://sbml.org/documents/papers/iee-paper-printed.pdf
  18. Oda, K., Kimura, T, Matsuoka, Y., Funahashi, A., Muramatsu, M., and Kitano, H..
    "Molecular Interaction Map of Macrophage." AfCS Report. 2 (14). August 2004. pp. 1--12. http://afcs.lbl.gov/reports/v2/DA0014/DA0014.htm
  19. Funahashi, A., Tanimura, N., Morohashi, M., and Kitano, H..
    "CellDesigner: a process diagram editor for gene-regulatory and biochemical networks." BioSilico. 1 (5). November 2003. pp. 159--162. http://www.symbio.jst.go.jp/symbio/paper/BioSilicoNov2003Funahashi.pdf
  20. Sugiyama, S. and Funahashi, A..
    "An Output Selection Function based on the characteristic of virtual channel (In Japanese)." IPSJ Journal. 43 (3). March 2002. pp. 764--775.
  21. Igawa, Y. and Funahashi, A..
    "Z-routing: Adaptive routing on irregular networks (In Japanese)." IPSJ Journal. 43 (3). March 2002. pp. 754--763.
  22. Funahashi, A., Koibuchi, M., Jouraku, A., and Amano, H..
    "The Impact of Output Selection Function on Adaptive Routing." ISCA Information: An International Journal. 4 (4). November 2001. pp. 541--550. http://www.symbio.jst.go.jp/~funa/papers/info2001.pdf
  23. Koibuchi, M., Funahashi, A., Jouraku, A., and Amano, H..
    "L-turn routing: An Adaptive Routing in Irregular Networks (In Japanese)." IPSJ Journal of High Performance Computing System. 42 (SIG 9). August 2001. pp. 119--134.
  24. Yang, Y., Funahashi, A., Jouraku, A., Nishi, H., Amano, H., and Sueyoshi, T..
    "Recursive Diagonal Torus: an interconnection network for massively parallel computers." IEEE Trans. on Parallel and Distributed Systems. 12 (7). July 2001. pp. 701--715. http://www.symbio.jst.go.jp/~funa/papers/ieee2001.pdf
  25. Koibuchi, M., Funahashi, A., Jouraku, A., and Amano, H..
    "The Impact of Output Selection Function on Adaptive Routing." IPSJ Journal. 42 (4). April 2001. pp. 704--713.
  26. Funahashi, A., Jouraku, A., and Amano, H..
    "Adaptive routing for Recursive Diagonal Torus (In Japanese)." IEICE Transactions on Information and Systems. J83-D-I (11). November 2000. pp. 1143--1153. http://www.symbio.jst.go.jp/~funa/papers/ieice2000.pdf
  27. Funahashi, A., Hanawa, T., and Amano, H..
    "Fault tolerance of the TBSF (Tandem Banyan Switching Fabrics) and PBSF (Piled Banyan Switching Fabrics)." IEICE Transactions on Information and Systems. E79-D (8). August 1996. pp. 1180--1189. http://www.symbio.jst.go.jp/~funa/papers/ieice96.pdf

Conference Papers

  1. Yoshimi, M., Nishikawa, Y., Osana, Y., Funahashi, A., Hiroi, N., Shibata, Y., Yamada, H., Kitano, H., and Amano, H..
    "Practical Implementation of a Network-based Stochastic Biochemical Simulation System on an FPGA." The 18th International Conference on Field Programmable Logic and Applications(FPL'08). Heidelberg, Germany. September 2008.
  2. Yamada, H., Iwanaga, N., Shibata, Y., Osana, Y., Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Amano, H., Funahashi, A., Hiroi, N., Kitano, H., and Oguri, K..
    "A Combining Technique of Rate Law Functions for a Cost-effective Reconfigurable Biological Simulator." The 17th International Conference on Field Programmable Logic and Applications(FPL'07). Amsterdam, Netherlands. August 2007. pp. 808--811.
  3. Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Osana, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Yamada, H., Kitano, H., and Amano, H..
    "FPGA Implementation of a data-driven stochastic biochemical simulator with the next reaction method." The 17th International Conference on Field Programmable Logic and Applications(FPL'07). Amsterdam, Netherlands. August 2007. pp. 254--259.
  4. Funahashi, A., Jouraku, A., Matsuoka, Y., Kikuchi, N., and Kitano, H..
    "An integration of CellDesigner and SABIO-RK." Storage and Annotation of Reaction Kinetics Data. Heidelberg, Germany. May 2007.
  5. Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H., and Amano, H..
    "A Hardware Accelerator for Biochemical Simulations." Winter Simulation Conference 2006. Monterey, USA. December 2006.
  6. Funahashi, A., Matsuoka, Y., Jouraku, A., Kikuchi, N., and Kitano, H..
    "CellDesigner: A Modeling Tool for Biochemical Networks." Winter Simulation Conference 2006. Monterey, USA. December 2006. pp. 1707--1712.
  7. Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "An FPGA Implementation of High Throughput Stochastic Simulator for Large-Scale Biochemical Systems." Proceedings of 2006 International Conference on Field Programmable Logic and Applications. Madrid, Spain. August 2006. pp. 227-232.
  8. Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "Performance Evaluation of an FPGA-based Biochemical Simulator ReCSiP." Proceedings of 2006 International Conference on Field Programmable Logic and Applications. Madrid, Spain. August 2006. pp. 845--850.
  9. Hiroi, N., Funahashi, A., and Kitano, H..
    "Kinetics for in vivo molecular diffusion." Conference on Systems Biology of Mammalian Cells (SBMC 2006). Heidelberg, Germany. July 2006. pp. 11--12. http://sbmc06.de/
  10. Nishikawa, Y., Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "An Evaluation and Investigation of Dual-Thread Numerical Integration Mechanism for FPGA-based Biochemical Simulator ReCSiP." Coolchips IX. Yokohama, Japan. April 2006. pp. 195-197.
  11. Hiroi, N., Funahashi, A., and Kitano, H..
    "Two numerical model analysis for the movement of a restriction enzyme." Foundations of Systems Biology in Engineering (FOSBE 2005). Santa Barbara, USA. August 2005. pp. 263--266. http://www.fosbe.org/
  12. Hiroi, N., Funahashi, A., and Kitano, H..
    "Analysis for dimension restriction kinetics with bacterial endonuclease movement." The 2005 WSEAS International Conference on Cellular and Molecular Biology -- Biophysics and Bioengineering. Athens, Greece. July 2005. pp. 1--6. http://www.worldses.org/conferences/2005/greece/bio/index.html
  13. Hucka, M., Finney, A., Bornstein, B., Shapiro, B., Kovitz, B., Keating, S., Matthews, J., Funahashi, A., Sauro, H., Doyle, J., and Kitano, H..
    "Software Infrastructure for Enabling Greater Collaboration in Computational Modeling: The Systems Biology Markup Language (SBML) Project." International Conference on Molecular Systems Biology (ICMSB'04). Tahoe City, USA. August 2004.
  14. Funahashi, A..
    "Software platform for systems biology." Kitano Symbiotic Systems Project Symposium. MeSci, Tokyo. September 2003. http://www.symbio.jst.go.jp/symbio/sympo/index_e.htm
  15. Hucka, M., Finney, A., Sauro, H., Bornstein, B., Shapiro, B., Schilstra, M., Kovitz, B., Matthews, J., Keating, S., Funahashi, A., Doyle, J., and Kitano, H..
    "Systems Biology Markup Language (SBML): Recent Progress and Current Directions." First IECA Conference on Systems Biology of E. coli. Tsuruoka, Japan. June 2003.
  16. Hucka, M., Finney, A., Sauro, H., Bornstein, B., Shapiro, B., Schilstra, M., Kovitz, B., Matthews, J., Keating, S., Funahashi, A., Doyle, J., and Kitano, H..
    "The Systems Biology Markup Language (SBML) Level 2." Beyond Genome 2003 Systems Biology: Pathways to Drug Development. San Diego, USA. June 2003.
  17. Jouraku, A., Koibuchi, M., Amano, H., and Funahashi, A..
    "Routing Algorithms on 2D Turn Model for Irregular Networks." Proc. of the IEEE International Symposium on Parallel Architectures, Algorithms, and Networks (ISPAN 2002). Rockwell Center, Philippines. May 2002. pp. 289--294. http://www.am.ics.keio.ac.jp/proj/anlys/papers/cluster2003.pdf
  18. Koibuchi, M., Funahashi, A., Jouraku, A., and Amano, H..
    "L-turn routing: An Adaptive Routing in Irregular Networks." Proc. of the IEEE International Conference on Parallel Processing (ICPP 2001). Valencia, Spain. September 2001. pp. 374--383. http://www.symbio.jst.go.jp/~funa/papers/icpp2001.pdf
  19. Koibuchi, M., Jouraku, A., Funahashi, A., and Amano, H..
    "MMLRU selection function: An Output Selection Function on Adaptive Routing." Proc. of the ISCA 14th International Conference on Parallel and Distributed Computing Systems (PDCS 2001). Texas, USA. August 2001. pp. 1--6. http://www.symbio.jst.go.jp/~funa/papers/pdcs2001.pdf
  20. Funahashi, A., Koibuchi, M., Jouraku, A., and Amano, H..
    "Adaptive routing on irregular networks. (In Japanese)." Proc. of the 13th Joint Symposium on Parallel Processing (JSPP 2001). Kyoto, Japan. June 2001. pp. 247--254. http://www.symbio.jst.go.jp/~funa/papers/jspp2001.pdf
  21. Koibuchi, M., Funahashi, A., Jouraku, A., and Amano, H..
    "An Output Selection Function on Adaptive Routing. (In Japanese)." Proc. of the 13th Joint Symposium on Parallel Processing (JSPP 2001). Kyoto, Japan. June 2001. pp. 255--262. http://www.symbio.jst.go.jp/~funa/papers/jspp2001mmlru.pdf
  22. Funahashi, A., Koibuchi, M., Jouraku, A., and Amano, H..
    "The Impact of Output Selection Function on Adaptive Routing." Proc. of the ISCA International Conference on Computers And Their Applications (CATA 2001). March 2001. pp. 241--246. http://www.symbio.jst.go.jp/~funa/papers/cata2001.pdf
  23. Koibuchi, M., Funahashi, A., Jouraku, A., and Amano, H..
    "An impact of output selection function on adaptive routing. (In Japanese)." Proc. of the 12th Joint Symposium on Parallel Processing (JSPP 2000). Tokyo, Japan. May 2000. pp. 181--188. http://www.symbio.jst.go.jp/~funa/papers/jspp2000.pdf
  24. Funahashi, A., Jouraku, A., and Amano, H..
    "Adaptive routing on the Recursive Diagonal Torus." Proc. of the ISCA 12th International Conference on Parallel and Distributed Computing Systems (PDCS'99). Florida, USA. August 1999. pp. 171--177. http://www.symbio.jst.go.jp/~funa/papers/pdcs1999.pdf
  25. Fan, Q., Yang, Y., Funahashi, A., and Amano, H..
    "A Torus Assignment for an Interconnection Network Recursive Diagonal Torus." Proc. of the IEEE International Symposium on Parallel Architectures, Algorithms and Networks (ISPAN'99). Fremantle, Australia. June 1999. pp. 74--79. http://www.symbio.jst.go.jp/~funa/papers/ispan1999.pdf
  26. Funahashi, A., Hanawa, T., Kudoh, T., and Amano, H..
    "Adaptive routing on the Recursive Diagonal Torus." Proc. of the International Symposium on High Performance Computing (ISHPC'97). Fukuoka, Japan. November 1997. pp. 171--182. http://www.symbio.jst.go.jp/~funa/papers/ishpc1999.pdf
  27. Yasukawa, H., Funahashi, A., Nishimura, K., Hanawa, T., and Amano, H..
    "Multistage Interconnection Network with Cache control mechanism : MINC. (In Japanese)." Proc. of the 8th Joint Symposium on Parallel Processing (JSPP'96). Tokyo, Japan. June 1996. pp. 129--136. http://www.symbio.jst.go.jp/~funa/papers/jspp1996.pdf
  28. Funahashi, A., Hanawa, T., and Amano, H..
    "Fault tolerance of the MIN with multiple outlets." Proc. of the 1995 IEEE Pacific Rim International Symposium on Fault-Tolerant Systems (PRFTS'95). , USA. December 1995. pp. 204--209. http://www.symbio.jst.go.jp/~funa/papers/prfts1996.pdf

Books

  1. Funahashi, A..
    "CellDesigner software: a graphical biological network editor and workbench interfacing simulator (Chapter 21 of Introduction to Systems Biology)." Sangdun Choi. Humana Press, NJ USA. ISBN: 1-58829-706-3. July 2007.
  2. Hiroi, N. and Funahashi, A..
    "Kinetics of Dimension Restricted Condition (Chapter 14 of Introduction to Systems Biology)." Sangdun Choi. Humana Press, NJ USA. ISBN: 1-58829-706-3. July 2007.
  3. Shapiro, B., Finney, A., Hucka, M., Bornstein, B., Funahashi, A., Jouraku, A., Keating, S., Novere, N., Matthews, J., and Schilstra, M..
    "SBML Models and MathSBML (Chapter 20 of Introduction to Systems Biology)." Sangdun Choi. Humana Press, NJ USA. ISBN: 1-58829-706-3. July 2007.
  4. Finney, A., Hucka, M., Bornstein, B., Keating, S., Shapiro, B., Matthews, J., Kovitz, B., Schilstra, M., Funahashi, A., Doyle, J., and Kitano, H..
    "Software Infrastructure for Effective Communication and Reuse of Computational Models (Chapter 17 of System Modeling in Cellular Biology)." Zallasi, Z. and Stelling, J. and Perial, V.. MIT Press, NJ USA. ISBN: 0-262-19548-8. March 2006. http://mitpress.mit.edu/catalog/item/default.asp?ttype=2&tid=10923
  5. Funahashi, A. and Nishimoto, R..
    "An introduction to FreeBSD." SHUWA SYSTEM co., LTD. ISBN: 4-87966-816-8. August 1998.

Reviews

  1. Funahashi, A..
    "Software Standardization for Systems Biology (In Japanese)." BioTechnology Journal. 5 (1). January 2005. pp. 39--46. http://www.yodosha.co.jp/btjournal/bookdata/489706161X/sedit1.html
  2. Funahashi, A..
    "SBML and SBW: A Software platform for Systems Biology (In Japanese)." PNE. 48 (7). July 2003. pp. 810--816. http://www.kyoritsu-pub.co.jp/pne/libs/2003/usual06.html
  3. Funahashi, A., Morohashi, M., Hucka, M., Finney, A., Sauro, H., Bolouri, H., Doyle, J., and Kitano, H..
    "Software platform for Systems Biology (In Japanese)." Nature Insight. 423 (6940). June 2003. pp. 48--57. http://www.natureasia.com/campaign/computationalbiology/index.php
  4. Funahashi, A..
    "Mastering Zsh: 13 Completions (In Japanese)." UNIX USER. no. 5, . May 2003. pp. 105--118. http://www.unixuser.jp/magazine/2003/200305.html
  5. Funahashi, A..
    "Mastering Zsh: 12 Modules (In Japanese)." UNIX USER. no. 4, . April 2003. pp. 103--112. http://www.unixuser.jp/magazine/2003/200304.html
  6. Funahashi, A..
    "Mastering Zsh: 11 History, hash and compiled functions (In Japanese)." UNIX USER. no. 3, . March 2003. pp. 97--104. http://www.unixuser.jp/magazine/2003/200303.html
  7. Funahashi, A..
    "Mastering Zsh: 10 Builtin functions (In Japanese)." UNIX USER. no. 2, . February 2003. pp. 99--104. http://www.unixuser.jp/magazine/2003/200302.html
  8. Funahashi, A..
    "Mastering Zsh: 09 Shell functions (In Japanese)." UNIX USER. no. 1, . January 2003. pp. 79--88. http://www.unixuser.jp/magazine/2003/200301.html
  9. Funahashi, A..
    "Mastering Zsh: 08 Redirection, pipe and expansion of variables (In Japanese)." UNIX USER. no. 12, . December 2002. pp. 105--112. http://www.unixuser.jp/magazine/2002/200212.html
  10. Funahashi, A..
    "Mastering Zsh: 07 Using expansion of filenames and variables (In Japanese)." UNIX USER. no. 11, . November 2002. pp. 95--100. http://www.unixuser.jp/magazine/2002/200211.html
  11. Funahashi, A..
    "Mastering Zsh: 06 Job control and history (In Japanese)." UNIX USER. no. 10, . October 2002. pp. 97--104. http://www.unixuser.jp/magazine/2002/200210.html
  12. Funahashi, A..
    "Mastering Zsh: 05 Using setopt, login and logout (In Japanese)." UNIX USER. no. 9, . September 2002. pp. 93--100. http://www.unixuser.jp/magazine/2002/200209.html
  13. Funahashi, A..
    "Mastering Zsh: 04 Key bindings and mail check (In Japanese)." UNIX USER. no. 8, . August 2002. pp. 101--108. http://www.unixuser.jp/magazine/2002/200208.html
  14. Funahashi, A..
    "Mastering Zsh: 03 Using setopt (In Japanese)." UNIX USER. no. 7, . July 2002. pp. 95--100. http://www.unixuser.jp/magazine/2002/200207.html
  15. Funahashi, A..
    "Mastering Zsh: 02 Configuration and completion (In Japanese)." UNIX USER. no. 6, . June 2002. pp. 73--80. http://www.unixuser.jp/magazine/2002/200206.html
  16. Funahashi, A..
    "Mastering Zsh: 01 Introduction (In Japanese)." UNIX USER. no. 5, . May 2002. pp. 79--86. http://www.unixuser.jp/magazine/2002/200205.html
  17. Funahashi, A..
    "Installation of qmail." UNIX USER. no. 4, . April 2001. pp. 48--55. http://www.unixuser.jp/magazine/2001/200104.html

Talks, Classes

  1. Tetsuya J. Kobayashi and Funahashi, A..
    "Systems Biology: from Quantitative Biology to Computational Biology." to be announced. Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo. October 2008.
  2. Funahashi, A..
    "CellDesigner 4.0: A Process Diagram Editor for Gene-Regulatory and Biochemical Networks." Tutorials at ICSB 2008. Goteborg, Sweden. August 2008.
  3. Le Novere, N., Hucka, M., Kitano, H., and Funahashi, A..
    "The Process Diagrams of the Systems Biology Graphical Notation." Tutorials at ICSB 2008. Goteborg, Sweden. August 2008.
  4. Funahashi, A..
    "CellDesigner 4.0: A Process Diagram Editor for Gene-Regulatory and Biochemical Networks." Tutorials at ICSB 2007. California, USA. October 2007.
  5. Funahashi, A..
    "CellDesigner tutorial." Tutorials at ICSB 2006. Yokohama, Japan. October 2006.
  6. Funahashi, A..
    "Software platform for Systems Biology (In Japanese)." Systems Biology course. Dept. of Biosciences and Informatics, Keio University, Yokohama. October 2006.
  7. Funahashi, A..
    "Software platform for Systems Biology (In Japanese)." Systems Biology course. Dept. of Biosciences and Informatics, Keio University, Yokohama. November 2005.
  8. Funahashi, A..
    "Programming (In Japanese)." UNIX course. Tohoku University of Community Service and Science, Yamagata. February 2005.
  9. Funahashi, A..
    "Software platform for Systems Biology (In Japanese)." Systems Biology course. Dept. of Biosciences and Informatics, Keio University, Yokohama. December 2004.
  10. Funahashi, A..
    "Software platform for Systems Biology (In Japanese)." Systems Biology course. Graduate School of Science and Engineering, Waseda University, Tokyo. July 2004. http://www2.sci.waseda.ac.jp/midas/SYLLABUS/ref_frame?2004360120T27001+index
  11. Funahashi, A..
    "Principle of text-based data format (In Japanese)." UNIX course. Tohoku University of Community Service and Science, Yamagata. February 2004. http://www.koeki-u.ac.jp/extension16.html
  12. Funahashi, A..
    "SBML and SBW: A Software platform for Systems Biology (In Japanese)." Bioinformatics seminar. Fuji Research Institute Corporation, Tokyo. December 2003. http://www.jbic.or.jp/bio_info/2003/03110702.pdf
  13. Funahashi, A..
    "Introduction of SBML, SBW compliant software." Systems Biology Workshop and Tutorial, SBML/SBW Tutorial. MeSci, Tokyo. September 2003. http://www.symbio.jst.go.jp/symbio/sympo/index_we.htm
  14. Funahashi, A..
    "Science of community service and computers (In Japanese)." UNIX course. Tohoku University of Community Service and Science, Yamagata. February 2003. http://www.koeki-u.ac.jp/news28.html

Workshops

  1. Ishimori, T., Yamada, H., Shibata, Y., Osana, Y., Yoshimi, M., Nishikawa, Y., Kojima, T., Amano, H., Funahashi, A., Hiroi, N., Kitano, H., and Oguri, K..
    "Pipeline Scheduling with Input Port Constraints for an FPGA-based Biochemical Simulator." Technical Committee on Reconfigurable Systems (RECONF). May 2008. pp. 113--118.
  2. Funahashi, A..
    "CellDesigner 4.0beta." Super-hackathon: Standards and Ontologies for Systems Biology. Okinawa, Japan. January 2008.
  3. Yamada, H., Iwanaga, N., Shibata, Y., Osana, Y., Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Amano, H., Funahashi, A., Hiroi, N., Kitano, H., and Oguri, K..
    "Automatic combining of rate law functions for an FPGA-based biochemical simulator ReCSiP." Technical Committee on Reconfigurable Systems (RECONF). May 2007. pp. 13--18.
  4. Funahashi, A..
    "CellDesigner 4, towards CellDesigner 5." Second BioModels.net training camp. Manchester, UK. January 2007.
  5. Kojima, T., Osana, Y., Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "Implementation and Evaluation of General-Purpose Host Interface on ReCSiP Board." FPGA/PLD Design Conference. January 2007. pp. 33--40.
  6. Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Osana, Y., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H., and Amano, H..
    "Empirical Analysis on Implementation of High-Speed Stochastic Biochemical Simulator on an FPGA." The 29th PARTHENON Workshop. December 2006. pp. 29--36.
  7. Funahashi, A..
    "CellDesigner update." The 11th Forum on Software Platforms for Systems Biology. Yokohama, Japan. October 2006. http://www.sbml.org/workshops/eleventh/
  8. Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H., and Amano, H..
    "FPGA-based Stochastic Biochemical Simulator." Symposium on Advanced Computing Systems and Infrastructures(SACSIS2006). May 2006. pp. 151--158.
  9. Kojima, T., Osana, Y., Yoshimi, M., Nishikawa, Y., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "Implementation and Evaluation of General-Purpose Host Interface on ReCSiP Board." Technical Committee on Reconfigurable Systems (RECONF). May 2006. pp. 55--60.
  10. Nishikawa, Y., Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "A Performance Improvement Strategy for Numerical Integration on an FPGA-Based Biochemical Simulator ReCSiP." Technical Committee on Reconfigurable Systems (RECONF). Keio Univ, Yokohama. January 2006. pp. 53--58. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
  11. Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "Hardware-resource Utilization Analysis on an FPGA-Based Biochemical Simulator ReCSiP." Technical Committee on Reconfigurable Systems (RECONF). Keio Univ, Yokohama. January 2006. pp. 59--64. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
  12. Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "Stochastic Biochemical Simulator with a Data-transfer Network on an FPGA." Technical Committee on Reconfigurable Systems (RECONF). Keio Univ, Yokohama. January 2006. pp. 47--52. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
  13. Iwaoka, Y., Osana, Y., Yoshimi, M., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "A System Design of Accelerating Biochemical Simulations on Programmable Hardware." The 10th Forum on Software Platforms for Systems Biology. Boston, Massachusetts. October 2005. http://www.sbml.org/workshops/tenth/index.html
  14. Funahashi, A..
    "CellDesigner 3.0." The 10th Forum on Software Platforms for Systems Biology. Boston, Massachusetts. October 2005. http://www.sbml.org/workshops/tenth/index.html
  15. Iwaoka, Y., Osana, Y., Yoshimi, M., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "Building of the SBML System for an FPGA-based Biochemical Simulator (In Japanese)." Technical Committee on Reconfigurable Systems (RECONF). Hiroshima. September 2005. pp. 61--66. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
  16. Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "The Control Mechanism of an FPGA-Based Biochemical Simulator ReCSiP (In Japanese)." Technical Committee on Reconfigurable Systems (RECONF). Hiroshima. September 2005. pp. 55--60. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
  17. Yoshimi, M., Osana, Y., Iwaoka, Y., Fukushima, T., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "Design of a Heap-tree Based Scalable Stochastic Biochemical Simulator on an FPGA (In Japanese)." Technical Committee on Reconfigurable Systems (RECONF). Kyoto Univ, Kyoto. May 2005. pp. 37--42. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
  18. Osana, Y., Iwaoka, Y., Fukushima, T., Yoshimi, M., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H., and Amano, H..
    "Implementation and Evaluation of Numerical Integrators on ReCSiP (In Japanese)." Technical Committee on Reconfigurable Systems (RECONF). Kyoto Univ, Kyoto. May 2005. pp. 49--54. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
  19. Iwanaga, N., Shibata, Y., Yoshimi, M., Osana, Y., Iwaoka, Y., Fukushima, T., Amano, H., Funahashi, A., Hiroi, N., Kitano, H., and Oguri, K..
    "Scheduling of Rate Law Functions for an FPGA-based Biochemical Simulator (In Japanese)." Technical Committee on Reconfigurable Systems (RECONF). Kyoto Univ, Kyoto. May 2005. pp. 43--48. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
  20. Iwaoka, Y., Osana, Y., Fukushima, T., Yoshimi, M., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "Design of cellular simulation platform for SBML model (In Japanese)." IEICE Technical Report [CPSY/RECONF]. Yokohama, Japan. January 2005. pp. 63--68. http://www.ieice.org/ken/program/index.php?mode=program&tgs_regid=3c536169dc1a42e123983394bef1dda8c941d2af527b4dcfa59b3886ad81b6b3&tgid=CPSY&layout=html1&lang=eng
  21. Osana, Y., Fukushima, T., Yoshimi, M., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "Design of the SBML Processor for an FPGA-based Biochemical Simulator (In Japanese)." IPSJ Technical Report [SHINING 2005]. Naha, Japan. January 2005. pp. 13--18. http://www.hpcc.jp/sigarc/Program/arc153.txt
  22. Funahashi, A..
    "CellDesigner and Hardware Accelerated Simulator." The Ninth Workshop on Software Platforms for Systems Biology. Heidelberg, Germany. October 2004. http://www.sbml.org/workshops/ninth/index.html
  23. Hucka, M., Finney, A., Bornstein, B., Shapiro, B., Kovitz, B., Keating, S., Matthews, J., Funahashi, A., Sauro, H., Doyle, J., and Kitano, H..
    "Software Infrastructure for Enabling Greater Collaboration in Computational Modeling: The Systems Biology Markup Language (SBML) Project." EMBS Minisymposium "The Global Physiome Project and Standards for Model Representation". San Francisco, USA. September 2004.
  24. Hucka, M., Finney, A., Bornstein, B., Shapiro, B., Kovitz, B., Keating, S., Matthews, J., and Funahashi, A..
    "A Roundup of Software Tools for SBML from SBML.org." BioPathways meeting (ISMB 2004). Glasgow, Scotland. August 2004.
  25. Hucka, M., Finney, A., Bornstein, B., Shapiro, B., Kovitz, B., Keating, S., Matthews, J., Funahashi, A., Sauro, H., Doyle, J., and Kitano, H..
    "Efforts Towards Spatial Representations for the Systems Biology Markup Language (SBML) Level 3." Computational Methods for Spatially Realistic Cellular Simulations. Pittsburgh, USA. August 2004.
  26. Funahashi, A..
    "CellDesigner." The Seventh Workshop on Software Platforms for Systems Biology. Florida, USA. May 2004. http://www.sbml.org/workshops/seventh/index.html
  27. Funahashi, A. and Kitano, H..
    "Current implementation of CellDesigner and KEGG to SBML converter." First SBML Hackathon. Virginia, USA. July 2003. http://calvin.bioinformatics.vt.edu/sbml-hackathon/
  28. Hucka, M., Finney, A., Sauro, H., Bornstein, B., Shapiro, B., Schilstra, M., Kovitz, B., Matthews, J., Keating, S., Funahashi, A., Doyle, J., and Kitano, H..
    "Systems Biology Markup Language (SBML): Recent Progress and Current Directions." BioPathways meeting (ISMB 2003). Brisbane, Australia. July 2003.
  29. Funahashi, A. and Kitano, H..
    "Converting KEGG DB to SBML." The Sixth Workshop on Software Platforms for Systems Biology. Stockholm, Sweden. December 2002. http://www.sbml.org/workshops/sixth/sbmlsbwstockholm.htm
  30. Funahashi, A., Tanimura, N., and Kitano, H..
    "Diagram proposal - Proposal for SBEdit's extension of SBML - Level 1." The Fifth Workshop on Software Platforms for Systems Biology. Hertfordshire, UK. July 2002. http://www.sbml.org/workshops/fifth/sbmlsbwhatfieldforumtemplate.htm
  31. Igawa, Y. and Funahashi, A..
    "Adaptive routing on irregular networks." IEICE Technical Report [Computer System]. 1--8. April 2001. http://www.symbio.jst.go.jp/ funa/papers/cpsy2001.pdf
  32. Jouraku, A., Koibuchi, M., Funahashi, A., and Amano, H..
    "L-turn routing: An Adaprive Routing in Irregular Networks (In Japanese)." IEICE Technical Report [Computer System]. April 2001. pp. 89--96. http://www.symbio.jst.go.jp/ funa/papers/cpsy2001-lturn.pdf
  33. Koibuchi, M., Jouraku, A., Funahashi, A., and Amano, H..
    "MMLRU selection function: An output selection function on Adaptive Routing." IEICE Technical Report [Computer System]. April 2001. pp. 97--104. http://www.symbio.jst.go.jp/ funa/papers/cpsy2001-mmlru.pdf
  34. Koibuchi, M., Funahashi, A., Jouraku, A., Wakabayashi, M., and Amano, H..
    "An Adaptive Routing in Irregular Networks (In Japanese)." IEICE Technical Report [Computer System] (SWoPP 2000). August 2000. pp. 33--40. http://www.symbio.jst.go.jp/ funa/papers/swopp2000.pdf
  35. Jouraku, A., Funahashi, A., Koibuchi, M., Wakabayashi, M., and Amano, H..
    "An Evaluation System of Interconnection Networks." IEICE Technical Report [Computer System] (HOKKE 2000). March 2000. pp. 47--52. http://www.symbio.jst.go.jp/ funa/papers/hokke2000.pdf
  36. Jouraku, A., Funahashi, A., Nishimura, K., and Amano, H..
    "Adaptive routing on the Recursive Diagonal Torus (In Japanese)." IEICE Technical Report [Computer System]. January 1998. pp. 67--74. http://www.symbio.jst.go.jp/ funa/papers/cpsy1998.pdf
  37. Funahashi, A., Hanawa, T., Kudoh, T., and Amano, H..
    "Adaptive routing for Recursive Diagonal Torus (In Japanese)." IEICE Technical Report [Computer System]. October 1996. pp. 47--54. http://www.symbio.jst.go.jp/ funa/papers/cpsy1996.pdf
  38. Yasukawa, H., Amano, H., Funahashi, A., and Hanawa, T..
    "Multistage Interconnection Network with Cache control mechanism: MINC." IEICE Technical Report [Computer System]. October 1995. pp. 7--12. http://www.symbio.jst.go.jp/ funa/papers/cpsy1995title.pdf
  39. Funahashi, A., Hanawa, T., and Amano, H..
    "Fault tolerance of the MIN with multiple outlets (In Japanese)." IEICE Technical Report [Fault Tolerant System]. August 1995. pp. 63--70. http://www.symbio.jst.go.jp/ funa/papers/swopp1995.pdf
  40. Funahashi, A., Hanawa, T., and Amano, H..
    "Analysis of fault tolerance of the MIN with multiple outlets (In Japanese)." Proceedings 50th. Information Processing Society of Japan. March 1995. pp. 6-21--6-22. http://www.symbio.jst.go.jp/ funa/papers/zenkoku1995.pdf

Posters

  1. Cedersund, G., Funahashi, A., Kitano, H., and Krantz, M..
    "A contingency-based approach to mapping and modelling of cellular networks." The 9th International Conference on Systems Biology (ICSB2008). Goteborg, Sweden. August 2008.
  2. Funahashi, A., Jouraku, A., Matsuoka, Y., Kikuchi, N., and Kitano, H..
    "CellDesigner4.0: A Process Diagram Editor for Gene-regulatory and Biochemical Networks." The 9th International Conference on Systems Biology (ICSB2008). Goteborg, Sweden. August 2008.
  3. Jouraku, A., Ohta, N., Funahashi, A., and Kitano, H..
    "KEGG2SBML: A tool for converting KEGG metabolic pathway database to SBML." The 9th International Conference on Systems Biology (ICSB2008). Goteborg, Sweden. August 2008.
  4. Mi, H., Muruganujan, A., Matsuoka, Y., Funahashi, A., Kitano, H., and Thomas, P..
    "PANTHER Pathway Applet - An SBGN compatible pathway visualizing tool based on CellDesigner 4.0." The 9th International Conference on Systems Biology (ICSB2008). Goteborg, Sweden. August 2008.
  5. Funahashi, A., Matsuoka, Y., Jouraku, A., Sugimura, H., Oikawa, Y., Kikuchi, N., and Kitano, H..
    "CellDesigner4.0beta: A Modeling Tool for Biochemical Networks." The 8th International Conference on Systems Biology (ICSB2007). Long Beach, USA. October 2007.
  6. Hiroi, N., Schuster, E., Ward, J., Piper, M., Jouraku, A., Funahashi, A., Gemes, D., Partridge, L., Novere, N. L., and Thornton, J..
    "Comparison of Insulin signaling pathways among 4 species and 3 tissues of mouse." The 8th International Conference on Systems Biology (ICSB2007). Long Beach, USA. October 2007.
  7. Nordling, T. E. M., Hiroi, N., and Funahashi, A..
    "Dynamic modes in biological systems: Why should a biologist care?." The 8th International Conference on Systems Biology (ICSB2007). Long Beach, USA. October 2007.
  8. Kitano, H., Funahashi, A., Hucka, M., and Novere, N. L..
    "Systems Biology Graphical Notation." The 8th International Conference on Systems Biology (ICSB2007). Long Beach, USA. October 2007.
  9. Hiroi, N., Nordling, T., Funahashi, A., and Kitano, H..
    "Detection of functional modules in graphs depend on a linearisation of the biochemical network." 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), 6th European Conference on Computational Biology (ECCB). Vienna, Austria. July 2007.
  10. Funahashi, A., Jouraku, A., Matsuoka, Y., Kikuchi, N., and Kitano, H..
    "CellDesigner3.5: A Process Diagram Editor for Gene-regulatory and Biochemical Networks." Computational Cell Biology 2007. New York, USA. March 2007.
  11. Hiroi, N., Funahashi, A., and Kitano, H..
    "The Impact of Spatial Restriction on Biological Systems." Computational Cell Biology 2007. New York, USA. March 2007.
  12. Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "Hardware Design of a Stochastic Biochemical Simulator." Winter Simulation Conference 2006. Monterey, USA. December 2006.
  13. Hiroi, N., Funahashi, A., and Kitano, H..
    "Kinetic modeling method for spatially restricted reactions." Winter Simulation Conference 2006. Monterey, USA. December 2006.
  14. Iwaoka, Y., Osana, Y., Yoshimi, M., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "An Acceleration of a Biochemical Simulator on Programmable Hardware." The 7th International Conference on Systems Biology (ICSB2006). Yokohama, Japan. October 2006.
  15. Funahashi, A., Matsuoka, Y., Jouraku, A., Kikuchi, N., and Kitano, H..
    "CellDesigner3.1: A Process Diagram Editor for Gene-regulatory and Biochemical Networks." The 7th International Conference on Systems Biology (ICSB2006). Yokohama, Japan. October 2006.
  16. Kitano, H., Hucka, M., Novere, N. L., and Funahashi, A..
    "Systems Biology Graphical Notation (SBGN) Project." The 7th International Conference on Systems Biology (ICSB2006). Yokohama, Japan. October 2006.
  17. Hiroi, N., Funahashi, A., Suzuki, H., Yamamoto, T., and Murray, D..
    "Systems Energetics" - a new approach for cellular systems dynamics -." The 7th International Conference on Systems Biology (ICSB2006). Yokohama, Japan. October 2006.
  18. Hiroi, N., Funahashi, A., and Kitano, H..
    "in vivo reaction modeling by DRRK." The 7th International Conference on Systems Biology (ICSB2006). Yokohama, Japan. October 2006.
  19. Funahashi, A., Matsuoka, Y., Jouraku, A., Kikuchi, N., and Kitano, H..
    "CellDesigner: A modeling tool for biochemical networks." Conference on Systems Biology of Mammalian Cells (SBMC 2006). Heidelberg, Germany. July 2006. http://sbmc06.de/
  20. Yoshimi, M., Osana, Y., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "The Design of Scalable Stochastic Biochemical Simulator on FPGA." 2005 IEEE International Conference on Field Programmable Technology. December 2005.
  21. Hiroi, N., Funahashi, A., Jouraku, A., and Kitano, H..
    "Dimension-restriction affects the reaction rate and accuracy." 6th International Conference on Systems Biology (ICSB 2005). Boston, Massachusetts. October 2005.
  22. Hucka, M., Finney, A., Bornstein, B., Shapiro, B., Keating, S., Schilstra, M., Funahashi, A., Jouraku, A., Matthews, J., and Kovitz, B..
    "Software from The SBML Team: LibSBML, MathSBML, SBMLToolbox, CellML2SBML, KEGG2SBML, SBML Test Suite, and the Online Tools." 6th International Conference on Systems Biology (ICSB 2005). Boston, Massachusetts. October 2005.
  23. Osana, Y., Iwaoka, Y., Fukushima, T., Yoshimi, M., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "A Framework for ODE-based Multimodel Biochemical Simulations on an FPGA." The 15th Field Programmable Logic and its applications(FPL 2005). Tampere, Finland. August 2005.
  24. Iwanaga, N., Shibata, Y., Yoshimi, M., Osana, Y., Iwaoka, Y., Fukushima, T., Amano, H., Funahashi, A., Hiroi, N., Kitano, H., and Oguri, K..
    "Efficient Scheculing of Rate Law Functions for ODE-based Multimodel Biochemical Simulation on an FPGA." The 15th Field Programmable Logic and its applications(FPL 2005). Tampere, Finland. August 2005.
  25. Hiroi, N., Funahashi, A., and Kitano, H..
    "Analysis for the movement of a enzyme." 13th Annual International conference on Intelligent Systems for Molecular Biology (ISMB 2005). Detroit, USA. June 2005.
  26. Osana, Y., Fukushima, T., Yoshimi, M., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
    "An FPGA-Based, Multi-model Simulation Method for Biochemical Systems." 12th Reconfigurable Architecture Workshop (RAW 2005). Denver, USA. April 2005.
  27. Funahashi, A., Tanimura, N., Matsuoka, Y., Yoshinaga, N., and Kitano, H..
    "CellDesigner2.0: A Process Diagram Editor for Gene-regulatory and Biochemical Networks." 1st FEBS Advanced Lecture Course Systems Biology. Gosau, Austria. March 2005.
  28. Hiroi, N., Funahashi, A., and Kitano, H..
    "Two Numerical Model Analyses for the Movement of a Restriction Enzyme." 1st FEBS Advanced Lecture Course Systems Biology. Gosau, Austria. March 2005.
  29. Funahashi, A., Tanimura, N., Matsuoka, Y., Yoshinaga, N., and Kitano, H..
    "CellDesigner2.0: A Process Diagram Editor for Gene-regulatory and Biochemical Networks." 15th International Conference on Genome Informatics (GIW 2004). Yokohama, Japan. December 2004.
  30. Jouraku, A., Funahashi, A., and Kitano, H..
    "Converting the KEGG Pathway Database to SBML." 5th International Conference on Systems Biology (ICSB 2004). Heidelberg, Germany. October 2004. http://www.sbml.org/documents/posters/kegg2sbmlICSB2004.pdf
  31. Hiroi, N., Funahashi, A., and Kitano, H..
    "Dimension restricted model analysis reveals the restriction enzyme diffusion along DNA is linear but not sliding." 2nd International Conference on Pathways, Networks, and Systems: Theory and Experiments. Crete, Greece. October 2004.
  32. Hiroi, N., Funahashi, A., and Kitano, H..
    "Analysis of the restriction enzyme diffusion manner to reach the specific DNA site." 5th New England Biolabs Meeting on Restriction/Modification. Bristol, UK. September 2004.
  33. Hucka, M., Finney, A., Bornstein, B., Shapiro, B., Keating, S., Funahashi, A., Schilstra, M., Kovitz, B., and Matthews, J..
    "SBML Software and Services." 12th International Conference on Intelligent Systems for Molecular Biology (ISMB 2004). Glasgow, Scotland. July 2004. http://sbml.org/documents/posters/ismb-2004-software-poster.pdf
  34. Funahashi, A., Jouraku, A., and Kitano, H..
    "Converting KEGG pathway database to SBML." 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB2004). San Diego, USA. March 2004.
  35. Funahashi, A., Tanimura, N., and Kitano, H..
    "CellDesigner: A Process Diagram Editor for Gene-regulatory and Biochemical Networks.." 4th International Conference on Systems Biology (ICSB 2003). St Louis, USA. November 2003.
  36. Hiroi, N., Funahashi, A., Nordling, T., and Kitano, H..
    "In silico analysis for anchorage independent cell cycle start mechanisms." 4th International Conference on Systems Biology (ICSB 2003). St Louis, USA. November 2003.
  37. Finney, A., Hucka, M., Sauro, H., Bolouri, H., Bornstein, B., Shapiro, B., Kovitz, B., Matthews, J., Keating, S., Funahashi, A., Doyle, J., and Kitano, H..
    "Systems Biology Markup Language Levels 2 and 3." 4th International Conference on Systems Biology (ICSB 2003). St Louis, USA. November 2003.
  38. Hucka, M., Finney, A., Sauro, H., Bolouri, H., Bornstein, B., Shapiro, B., Schilstra, M., Kovitz, B., Matthews, J., Keating, S., Funahashi, A., Doyle, J., and Kitano, H..
    "The Systems Biology Markup Language (SBML)." 11th International Conference on Intelligent Systems for Molecular Biology (ISMB 2003). Brisbane, Australia. July 2003. http://www.sbml.org/documents/posters/sbml-poster-ismb-2003-screen.pdf
  39. Funahashi, A., Tanimura, N., and Kitano, H..
    "CellDesigner: A Process Diagram Editor for Gene-regulatory and Biochemical Networks." First IECA Conference on Systems Biology of E.coli. Tsuruoka, Japan. June 2003.
  40. Hucka, M., Finney, A., Sauro, H., Bolouri, H., Bornstein, B., Shapiro, B., Schilstra, M., Kovitz, B., Matthews, J., Keating, S., Funahashi, A., Doyle, J., and Kitano, H..
    "The Systems Biology Markup Language (SBML)." First IECA Conference on Systems Biology of E.coli. Tsuruoka, Japan. June 2003. http://www.sbml.org/documents/posters/sbml-poster-ieca-2003-screen.pdf
  41. Finney, A., Hucka, M., Sauro, H., Bolouri, H., Bornstein, B., Shapiro, B., Schilstra, M., Kovitz, B., Matthews, J., Keating, S., Funahashi, A., Doyle, J., and Kitano, H..
    "The Systems Biology Markup Language (SBML)." Beyond Genome 2003 Systems Biology: Pathways to Drug Development. San Diego, Japan. June 2003. http://www.sbml.org/documents/posters/sbml-poster-byg-2003.pdf
  42. Bolouri, H., Hucka, M., Finney, A., Sauro, H., Funahashi, A., Bornstein, B., Kovitz, B., Keating, S., Matthews, J., Shapiro, B., Doyle, J., and Kitano, H..
    "The Systems Biology Workbench(SBW) Version 1.0: Framework and Modules.." Pacific Symposium on Biocomputing(PSB) 2003. Hawaii, USA. January 2003.
  43. Funahashi, A. and Kitano, H..
    "Converting KEGG DB to SBML." 3rd International Conference on Systems Biology (ICSB 2002). Stockholm, Sweden. December 2002.

Akira Funahashi <funa @ bio.keio.ac.jp>
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Last modified: Tue Sep 28 22:44:02 JST 2010


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Funahashi Lab.
Room 516 and 417, Bld 14,
Department of Biosciences and Informatics, Keio University,
3-14-1 Hiyoshi Kouhoku-ku, Yokohama 223-8522 JAPAN

Phone: +81-45-566-1797
Email: info _at_ fun.bio.keio.ac.jp