• 2607 Citations
  • 17 h-Index
19962020

Research output per year

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Research Output

Article

Acceleration of discrete stochastic biochemical simulation using GPGPU

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

Research output: Contribution to journalArticle

7 Citations (Scopus)

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 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 Feb 15, In : Biology Open. 4, 2, p. 155-169 15 p.

Research output: Contribution to journalArticle

17 Citations (Scopus)

Assessing uncertainty in model parameters based on sparse and noisy experimental data

Hiroi, N., Swat, M. & Funahashi, A., 2014, In : Frontiers in Physiology. 5 APR, Article 128.

Research output: Contribution to journalArticle

1 Citation (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 Aug 15, In : Cell Cycle. 12, 16, p. 2643-2655 13 p.

Research output: Contribution to journalArticle

16 Citations (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 Dec 1, In : IPSJ Transactions on System LSI Design Methodology. 3, p. 244-256 13 p.

Research output: Contribution to journalArticle

2 Citations (Scopus)

BioPAX support in CellDesigner

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

Research output: Contribution to journalArticle

13 Citations (Scopus)

CellDesigner 3.5: A versatile modeling tool for biochemical networks

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

Research output: Contribution to journalArticle

295 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)

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

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

Research output: Contribution to journalArticle

7 Citations (Scopus)

Deep learning for non-invasive determination of the differentiation status of human neuronal cells by using phase-contrast photomicrographs

Ooka, M., Tokuoka, Y., Nishimoto, S., Hiroi, N., Yamada, T. G. & Funahashi, A., 2019 Dec 1, In : Applied Sciences (Switzerland). 9, 24, 5503.

Research output: Contribution to journalArticle

Open Access

Detection of Temperature Difference in Neuronal Cells

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

Research output: Contribution to journalArticle

48 Citations (Scopus)

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

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, In : Eurasip Journal on Bioinformatics and Systems Biology. 2012, 1, 7.

Research output: Contribution to journalArticle

5 Citations (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 Jan 1, In : Review of Scientific Instruments. 86, 1, 013707.

Research output: Contribution to journalArticle

32 Citations (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, In : PloS one. 15, 3, e0230218.

Research output: Contribution to journalArticle

Open Access

Integration of cell designer and SABIO-RK

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

Research output: Contribution to journalArticle

47 Citations (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 Jun 1, In : Bioinformatics. 29, 11, p. 1474-1476 3 p.

Research output: Contribution to journalArticle

10 Citations (Scopus)

Mathematical Modeling of Sustainable Synaptogenesis by Repetitive Stimuli Suggests Signaling Mechanisms In Vivo

Takizawa, H., Hiroi, N. & Funahashi, A., 2012 Dec 20, In : PloS one. 7, 12, e51000.

Research output: Contribution to journalArticle

7 Citations (Scopus)

Modeling and simulation using cellDesigner

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

Research output: Contribution to journalArticle

33 Citations (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. & Funahashi, A., 2020 Feb 1, In : Processes. 8, 2, 166.

Research output: Contribution to journalArticle

Open Access

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, In : Frontiers in Physiology. 2 SEP, Article 50.

Research output: Contribution to journalArticle

9 Citations (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, In : Frontiers in Physiology. 3 JUL, Article 293.

Research output: Contribution to journalArticle

1 Citation (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 Sep 1, In : PloS one. 14, 9, e0221245.

Research output: Contribution to journalArticle

Open Access
1 Citation (Scopus)

Quantitative analysis of sensitivity to a Wnt3a gradient in determination of the pole-to-pole axis of mitotic cells by using a microfluidic device

Hiraiwa, T., Nakai, Y., Yamada, T. G., Tanimoto, R., Kimura, H., Matsumoto, Y., Miki, N., Hiroi, N. & Funahashi, A., 2018 Dec, In : FEBS Open Bio. 8, 12, p. 1920-1935 16 p.

Research output: Contribution to journalArticle

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 Jul 1, In : Electronics and Communications in Japan, Part II: Electronics (English translation of Denshi Tsushin Gakkai Ronbunshi). 90, 7, p. 1-10 10 p.

Research output: Contribution to journalArticle

10 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)

Simulation technology and its application in systems biology

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

Research output: Contribution to journalArticle

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 Aug, In : Bioinformatics. 28, 15, p. 2016-2021 6 p., bts270.

Research output: Contribution to journalArticle

47 Citations (Scopus)

The principles of whole-cell modeling

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

Research output: Contribution to journalArticle

30 Citations (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 Jul 5, In : BMC Systems Biology. 7, 55.

Research output: Contribution to journalArticle

20 Citations (Scopus)

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

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

Research output: Contribution to journalArticle

2 Citations (Scopus)

XitoSBML: A Modeling Tool for Creating Spatial Systems Biology Markup Language Models From Microscopic Images

Ii, K., Mashimo, K., Ozeki, M., Yamada, T. G., Hiroi, N. & Funahashi, A., 2019 Oct 22, In : Frontiers in Genetics. 10, 1027.

Research output: Contribution to journalArticle

Open Access
Chapter

CellDesigner: A graphical biological network editor and workbench interfacing simulator

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

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Kinetics of dimension-restricted conditions

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

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (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 Dec 1, Introduction to Systems Biology. Humana Press, p. 395-421 27 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)
Comment/debate

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

Ostaszewski, M., Mazein, A., Gillespie, M. E., Kuperstein, I., Niarakis, A., Hermjakob, H., Pico, A. R., Willighagen, E. L., Evelo, C. T., Hasenauer, J., Schreiber, F., Dräger, A., Demir, E., Wolkenhauer, O., Furlong, L. I., Barillot, E., Dopazo, J., Orta-Resendiz, A., Messina, F., Valencia, A. & 5 others, Funahashi, A., Kitano, H., Auffray, C., Balling, R. & Schneider, R., 2020 Dec 1, In : Scientific Data. 7, 1, 136.

Research output: Contribution to journalComment/debate

Open Access
5 Citations (Scopus)

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. & 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 Sep 1, In : Nature Biotechnology. 27, 9, 1 p.

Research output: Contribution to journalComment/debate

2 Citations (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 Jun 22, In : Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 5453, p. 368-373 6 p.

Research output: Contribution to journalConference article

3 Citations (Scopus)
6 Citations (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 Dec 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).

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

2 Citations (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, 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)

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 Dec 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).

Research output: Chapter in Book/Report/Conference proceedingConference 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 Dec 1, ICFPT 2007 - International Conference on Field Programmable Technology. p. 193-200 8 p. 4439249. (ICFPT 2007 - International Conference on Field Programmable Technology).

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

1 Citation (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)

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 Dec 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).

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

1 Citation (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)

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)