• 2625 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

2020

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. および5人, Funahashi, A., Kitano, H., Auffray, C., Balling, R. & Schneider, R., 2020 12 1, : : Scientific Data. 7, 1, 136.

研究成果: Comment/debate

公開
5 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, : : PloS one. 15, 3, e0230218.

研究成果: Article

公開

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 2 1, : : Processes. 8, 2, 166.

研究成果: Article

公開
2019
公開

Predicting the future direction of cell movement with convolutional neural networks

Nishimoto, S., Tokuoka, Y., Yamada, T. G., Hiroi, N. F. & Funahashi, A., 2019 9 1, : : PloS one. 14, 9, e0221245.

研究成果: Article

公開
2 引用 (Scopus)
公開
2018

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 12 1, : : Scientific reports. 8, 1, 17941.

研究成果: Article

2 引用 (Scopus)
2017

Requirement of spatiotemporal resolution for imaging intracellular temperature distribution

Hiroi, N., Tanimoto, R., Ii, K., Ozeki, M., Mashimo, K. & Funahashi, A., 2017, Biomedical Imaging and Sensing Conference. SPIE, 巻 10251. 102510Q

研究成果: Conference contribution

2016

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

50 引用 (Scopus)

Editorial: Quantitative biology: Dynamics of living systems

Hiroi, N., Draviam, V. M. & Funahashi, A., 2016 6 2, : : Frontiers in Physiology. 7, JUN, 196.

研究成果: Editorial

1 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

2015

Acceleration of discrete stochastic biochemical simulation using GPGPU

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

研究成果: Article

7 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

18 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)

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

30 引用 (Scopus)
2014
1 引用 (Scopus)

Fabrication method to a high resolution control in the space of cell culturing environment with microfluidic system

Hiraiwa, T., Kimura, T., Takenaka, Y., Tanamoto, R., Ota, H., Kimura, H., Taguchi, Y., Miki, N., Matsumoto, Y., Oka, K., Funahashi, A. & Hiroi, N., 2014 1 1, MEMS 2014 - 27th IEEE International Conference on Micro Electro Mechanical Systems. Institute of Electrical and Electronics Engineers Inc., p. 264-267 4 p. 6765626. (Proceedings of the IEEE International Conference on Micro Electro Mechanical Systems (MEMS)).

研究成果: Conference contribution

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

35 引用 (Scopus)
2013

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)

In vivo oriented modeling with consideration of intracellular crowding

Hiroi, N., Iba, K., Tabira, A., Okuhara, T., Kubojima, T., Hiraiwa, T., Kobayashi, T. J., Oka, K. & Funahashi, A., 2013 10 31, 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013. p. 2716-2719 4 p. 6610101. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

研究成果: Conference contribution

1 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)

Meeting report of the international workshop on quantitative biology 2012: Mesoscopic and microscopic worlds meet

Draviam, V. M., Funahashi, A., Hiroi, N., Kimura, A. & Kobayashi, T. J., 2013, : : Frontiers in Physiology. 3 JAN, Article 479.

研究成果: Editorial

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

21 引用 (Scopus)
2012

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)
7 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, : : Frontiers in Physiology. 3 JUL, Article 293.

研究成果: Article

1 引用 (Scopus)

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

48 引用 (Scopus)
2011

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)

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

9 引用 (Scopus)
2010

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, 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

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, : : IPSJ Transactions on System LSI Design Methodology. 3, p. 244-256 13 p.

研究成果: Article

2 引用 (Scopus)

The DBCLS BioHackathon: Standardization and interoperability for bioinformatics web services and workflows

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. P., Bruskiewich, R., Bryne, J. C., Fernández, J. M., Funahashi, A., Gordon, P. M. K., Goto, N., Groscurth, A. および37人, Gutteridge, A., Holland, R., Kano, Y., Kawas, E. A., 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. A., Wilkinson, M. D., York, W., Zmasek, C. M., Asai, K. & Takagi, T., 2010 8 21, : : Journal of Biomedical Semantics. 1, 8.

研究成果: Review article

22 引用 (Scopus)
2009

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)

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)

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)

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)

The Systems Biology Graphical Notation

Novère, 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., 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 8, : : Nature Biotechnology. 27, 8, p. 735-741 7 p.

研究成果: Review article

524 引用 (Scopus)
2008

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

296 引用 (Scopus)

Practical implementation of a network-based Stochastic biochemical simulation system on an FPGA

Yoshimi, M., Nishikawa, Y., Osana, Y., Funahashi, A., Hiroi, N., Shibata, Y., Yamada, H., Kitano, H. & Amano, H., 2008 11 3, Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL. p. 663-666 4 p. 4630034. (Proceedings - 2008 International Conference on Field Programmable Logic and Applications, FPL).

研究成果: Conference contribution

5 引用 (Scopus)
2007

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)

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)

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)

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

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

研究成果: Article

7 引用 (Scopus)

FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method

Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Osana, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Yamada, H., Kitano, H. & Amano, H., 2007 12 1, Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL. p. 254-259 6 p. 4380656. (Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL).

研究成果: Conference contribution

14 引用 (Scopus)

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)

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)

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)

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)