• 2584 引用
  • 17 h指数
19962020

年単位の研究成果

Pureに変更を加えた場合、すぐここに表示されます。

研究成果

Article

Acceleration of discrete stochastic biochemical simulation using GPGPU

Sumiyoshi, K., Hirata, K., Hiroi, N. & Funahashi, A., 2015 1 1, : : Frontiers in Physiology. 6, FEB, 42.

研究成果: Article

7 引用 (Scopus)

A comprehensive pathway map of epidermal growth factor receptor signaling.

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

研究成果: Article

686 引用 (Scopus)

A proteomic study of mitotic phase-Specific interactors of EB1 reveals a role for SXIP-Mediated protein interactions in anaphase onset

Tamura, N., Simon, J. E., Nayak, A., Shenoy, R., Hiroi, N., Boilot, V., Funahashi, A. & Draviam, V. M., 2015 2 15, : : Biology Open. 4, 2, p. 155-169 15 p.

研究成果: Article

17 引用 (Scopus)
1 引用 (Scopus)

Automated tracking of mitotic spindle pole positions shows that LGN is required for spindle rotation but not orientation maintenance

Corrigan, A. M., Shrestha, R. L., Zulkipli, I., Hiroi, N., Liu, Y., Tamura, N., Yang, B., Patel, J., Funahashi, A., Donald, A. & Draviam, V. M., 2013 8 15, : : Cell Cycle. 12, 16, p. 2643-2655 13 p.

研究成果: Article

16 引用 (Scopus)

Automatic pipeline construction focused on similarity of rate law functions for an FPGA-based biochemical simulator

Yamada, H., Ogawa, Y., Ooya, T., Ishimori, T., Osana, Y., Yoshimi, M., Nishikawa, Y., Funahashi, A., Hiroi, N., Amano, H., Shibata, Y. & Oguri, K., 2010 12 1, : : IPSJ Transactions on System LSI Design Methodology. 3, p. 244-256 13 p.

研究成果: Article

2 引用 (Scopus)

BioPAX support in CellDesigner

Mi, H., Muruganujan, A., Demir, E., Matsuoka, Y., Funahashi, A., Kitano, H. & Thomas, P. D., 2011 12 1, : : Bioinformatics. 27, 24, p. 3437-3438 2 p., btr586.

研究成果: Article

13 引用 (Scopus)

CellDesigner 3.5: A versatile modeling tool for biochemical networks

Funahashi, A., Matsuoka, Y., Jouraku, A., Morohashi, M., Kikuchi, N. & Kitano, H., 2008 8, : : Proceedings of the IEEE. 96, 8, p. 1254-1265 12 p., 4567412.

研究成果: Article

295 引用 (Scopus)
16 引用 (Scopus)

Deduction of intracellular sub-systems from a topological description of the network

Nordling, T. E. M., Hiroi, N., Funahashi, A. & Kitano, H., 2007 1 1, : : Molecular BioSystems. 3, 8, p. 523-529 7 p.

研究成果: Article

7 引用 (Scopus)
公開

Detection of Temperature Difference in Neuronal Cells

Tanimoto, R., Hiraiwa, T., Nakai, Y., Shindo, Y., Oka, K., Hiroi, N. & Funahashi, A., 2016 3 1, : : Scientific Reports. 6, 22071.

研究成果: Article

47 引用 (Scopus)

From microscopy data to in silico environments for in vivo-oriented simulations

Hiroi, N., Klann, M., Iba, K., Heras Ciechomski, P. D., Yamashita, S., Tabira, A., Okuhara, T., Kubojima, T., Okada, Y., Oka, K., Mange, R., Unger, M., Funahashi, A. & Koeppl, H., 2012, : : Eurasip Journal on Bioinformatics and Systems Biology. 2012, 1, 7.

研究成果: Article

5 引用 (Scopus)

High-speed microscopy with an electrically tunable lens to image the dynamics of in vivo molecular complexes

Nakai, Y., Ozeki, M., Hiraiwa, T., Tanimoto, R., Funahashi, A., Hiroi, N., Taniguchi, A., Nonaka, S., Boilot, V., Shrestha, R., Clark, J., Tamura, N., Draviam, V. M. & Oku, H., 2015 1 1, : : Review of Scientific Instruments. 86, 1, 013707.

研究成果: Article

32 引用 (Scopus)

Identification of a master transcription factor and a regulatory mechanism for desiccation tolerance in the anhydrobiotic cell line Pv11

Yamada, T. G., Hiki, Y., Hiroi, N. F., Shagimardanova, E., Gusev, O., Cornette, R., Kikawada, T. & Funahashi, A., 2020 1 1, : : PloS one. 15, 3, e0230218.

研究成果: Article

公開

Integration of cell designer and SABIO-RK

Funahashi, A., Jouraku, A., Matsuoka, Y. & Kitano, H., 2007 6 11, : : In Silico Biology. 7, SUPPL. 2, p. 81-90 10 p.

研究成果: Article

47 引用 (Scopus)

LibSBMLSim: A reference implementation of fully functional SBML simulator

Takizawa, H., Nakamura, K., Tabira, A., Chikahara, Y., Matsui, T., Hiroi, N. & Funahashi, A., 2013 6 1, : : Bioinformatics. 29, 11, p. 1474-1476 3 p.

研究成果: Article

10 引用 (Scopus)
7 引用 (Scopus)

Modeling and simulation using cellDesigner

Matsuoka, Y., Funahashi, A., Ghosh, S. & Kitano, H., 2014 1 1, : : Methods in Molecular Biology. 1164, p. 121-145 25 p.

研究成果: Article

33 引用 (Scopus)

Neural differentiation dynamics controlled by multiple feedback loops in a comprehensive molecular interaction network

Iwasaki, T., Takiguchi, R., Hiraiwa, T., Yamada, T. G., Yamazaki, K., Hiroi, N. F. & Funahashi, A., 2020 2 1, : : Processes. 8, 2, 166.

研究成果: Article

公開

Physiological environment induces quick response - slow exhaustion reactions

Hiroi, N., Lu, J., Iba, K., Tabira, A., Yamashita, S., Okada, Y., Flamm, C., Oka, K., Köhler, G. & Funahashi, A., 2011, : : Frontiers in Physiology. 2 SEP, Article 50.

研究成果: Article

8 引用 (Scopus)

Physiological intracellular crowdedness is defined by the perimeter-to-area ratio of sub-cellular compartments

Hiroi, N., Okuhara, T., Kubojima, T., Iba, K., Tabira, A., Yamashita, S., Okada, Y., Kobayashi, T. J. & Funahashi, A., 2012 9 25, : : Frontiers in Physiology. 3 JUL, Article 293.

研究成果: Article

1 引用 (Scopus)

Predicting the future direction of cell movement with convolutional neural networks

Nishimoto, S., Tokuoka, Y., Yamada, T. G., Hiroi, N. F. & Funahashi, A., 2019, : : PloS one. 14, 9, e0221245.

研究成果: Article

公開
1 引用 (Scopus)

ReCSiP: An FPGA-based general-purpose biochemical simulator

Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H. & Amano, H., 2007 7 1, : : Electronics and Communications in Japan, Part II: Electronics (English translation of Denshi Tsushin Gakkai Ronbunshi). 90, 7, p. 1-10 10 p.

研究成果: Article

10 引用 (Scopus)
55 引用 (Scopus)

Simulation technology and its application in systems biology

Funahashi, A. & Hiroi, N., 2016, : : Folia Pharmacologica Japonica. 147, 2, p. 101-106 6 p.

研究成果: Article

Software support for SBGN maps: SBGN-ML and LibSBGN

Van Iersel, M. P., Villéger, A. C., Czauderna, T., Boyd, S. E., Bergmann, F. T., Luna, A., Demir, E., Sorokin, A., Dogrusoz, U., Matsuoka, Y., Funahashi, A., Aladjem, M. I., Mi, H., Moodie, S. L., Kitano, H., Le novère, N. & Schreiber, F., 2012 8, : : Bioinformatics. 28, 15, p. 2016-2021 6 p., bts270.

研究成果: Article

46 引用 (Scopus)

The principles of whole-cell modeling

Karr, J. R., Takahashi, K. & Funahashi, A., 2015 10 1, : : Current Opinion in Microbiology. 27, p. 18-24 7 p.

研究成果: Article

28 引用 (Scopus)

The systems biology simulation core algorithm

Keller, R., Dörr, A., Tabira, A., Funahashi, A., Ziller, M. J., Adams, R., Rodriguez, N., Novère, N. L., Hiroi, N., Planatscher, H., Zell, A. & Dräger, A., 2013 7 5, : : BMC Systems Biology. 7, 55.

研究成果: Article

20 引用 (Scopus)

Transcriptome analysis of the anhydrobiotic cell line Pv11 infers the mechanism of desiccation tolerance and recovery

Yamada, T., Suetsugu, Y., Deviatiiarov, R., Gusev, O., Cornette, R., Nesmelov, A., Hiroi, N., Kikawada, T. & Funahashi, A., 2018 12 1, : : Scientific Reports. 8, 1, 17941.

研究成果: Article

2 引用 (Scopus)
公開
Chapter

CellDesigner: A graphical biological network editor and workbench interfacing simulator

Funahashi, A., Morohashi, M., Matsuoka, Y., Jouraku, A. & Kitano, H., 2007 12 1, Introduction to Systems Biology. Humana Press, p. 422-434 13 p.

研究成果: Chapter

1 引用 (Scopus)

Kinetics of dimension-restricted conditions

Hiroi, N. & Funahashi, A., 2007 12 1, Introduction to Systems Biology. Humana Press, p. 261-281 21 p.

研究成果: Chapter

2 引用 (Scopus)

SBML models and MathSBML

Shapiro, B. E., Finney, A., Hucka, M., Bornstein, B., Funahashi, A., Jouraku, A., Keating, S. M., Le Novère, N., Matthews, J. & Schilstra, M. J., 2007 12 1, Introduction to Systems Biology. Humana Press, p. 395-421 27 p.

研究成果: Chapter

2 引用 (Scopus)
Comment/debate

Erratum: The systems biology graphical notation (Nature Biotechnology (2009) 27 (735-741))

Le Novère, N., 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. および19人, 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 9 1, : : Nature Biotechnology. 27, 9, 1 p.

研究成果: Comment/debate

2 引用 (Scopus)
Conference article

Pipeline scheduling with input port constraints for an FPGA-based biochemical simulator

Ishimori, T., Yamada, H., Shibata, Y., Osana, Y., Yoshimi, M., Nishikawa, Y., Amano, H., Funahashi, A., Hiroi, N. & Oguri, K., 2009 6 22, : : Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5453, p. 368-373 6 p.

研究成果: Conference article

3 引用 (Scopus)
Conference contribution

A combining technique of rate law functions for a cost-effective reconfigurable biological simulator

Yamada, H., Iwanaga, N., Shibata, Y., Osana, Y., Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Amano, H., Funahashi, A., Hiroi, N., Hiroaki Kitano, K. & Kiyoshi Oguri, O., 2007 12 1, Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL. p. 808-811 4 p. 4380774. (Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL).

研究成果: Conference contribution

2 引用 (Scopus)

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, 巻 1336. p. 171-182 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); 巻数 1336).

研究成果: Conference contribution

1 引用 (Scopus)

A datapath classification method for FPGA-based scientific application accelerator systems

Ogawa, Y., Ooya, T., Osana, Y., Yoshimi, M., Nishikawa, Y., Funahashi, A., Hiroi, N., Amano, H., Shibata, Y. & Oguri, K., 2010 12 1, Proceedings - 2010 International Conference on Field-Programmable Technology, FPT'10. p. 441-444 4 p. 5681455. (Proceedings - 2010 International Conference on Field-Programmable Technology, FPT'10).

研究成果: Conference contribution

A framework for implementing a network-based stochastic biochemical simulator on an FPGA

Yoshimi, M., Nishikawa, Y., Kojima, T., Osana, Y., Funahashi, A., Hiroi, N., Shibata, Y., Yamada, H., Kitano, H. & Amano, H., 2007 12 1, ICFPT 2007 - International Conference on Field Programmable Technology. p. 193-200 8 p. 4439249. (ICFPT 2007 - International Conference on Field Programmable Technology).

研究成果: Conference contribution

1 引用 (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 12 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; 巻数 2005).

研究成果: Conference contribution

3 引用 (Scopus)

A modular approach to heterogeneous biochemical model simulation on an FPGA

Yamada, H., Osana, Y., Ishimori, T., Ooya, T., Yoshimi, M., Nishikawa, Y., Funahashi, A., Hiroi, N., Amano, H., Shibata, Y. & Oguri, K., 2009 12 1, ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs. p. 125-130 6 p. 5382039. (ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs).

研究成果: Conference contribution

1 引用 (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 12 1, Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005. 1420035. (Proceedings - 19th IEEE International Parallel and Distributed Processing Symposium, IPDPS 2005; 巻数 2005).

研究成果: Conference contribution

4 引用 (Scopus)

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 12 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).

研究成果: Conference contribution

6 引用 (Scopus)

Celldesigner: A modeling tool for biochemical networks

Funahashi, A., Matsuoka, Y., Jouraku, A., Kitano, H. & Kikuchi, N., 2006 12 1, Proceedings of the 2006 Winter Simulation Conference, WSC. p. 1707-1712 6 p. 4117804. (Proceedings - Winter Simulation Conference).

研究成果: Conference contribution

19 引用 (Scopus)

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 11 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).

研究成果: Conference contribution

2 引用 (Scopus)