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\n  \n article\n \n \n (82)\n \n \n
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\n \n\n \n \n \n \n \n A comprehensive pathway map of epidermal growth factor receptor signaling.\n \n \n \n\n\n \n Oda, K.; Matsuoka, Y.; Funahashi, A.; and Kitano, H.\n\n\n \n\n\n\n Molecular systems biology, 1(1): 2005–0010. 2005.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{oda2005comprehensive,\n  title={A comprehensive pathway map of epidermal growth factor receptor signaling},\n  author={Oda, Kanae and Matsuoka, Yukiko and Funahashi, Akira and Kitano, Hiroaki},\n  journal={Molecular systems biology},\n  volume={1},\n  number={1},\n  pages={2005--0010},\n  year={2005},\n  publisher={John Wiley \\& Sons, Ltd Chichester, UK}\n}\n\n
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\n \n\n \n \n \n \n \n Using process diagrams for the graphical representation of biological networks.\n \n \n \n\n\n \n Kitano, H.; Funahashi, A.; Matsuoka, Y.; and Oda, K.\n\n\n \n\n\n\n Nature biotechnology, 23(8): 961–966. 2005.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{kitano2005using,\n  title={Using process diagrams for the graphical representation of biological networks},\n  author={Kitano, Hiroaki and Funahashi, Akira and Matsuoka, Yukiko and Oda, Kanae},\n  journal={Nature biotechnology},\n  volume={23},\n  number={8},\n  pages={961--966},\n  year={2005},\n  publisher={Nature Publishing Group}\n}\n\n
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\n\n\n
\n \n\n \n \n \n \n \n CellDesigner: a process diagram editor for gene-regulatory and biochemical networks.\n \n \n \n\n\n \n Funahashi, A.; Morohashi, M.; Kitano, H.; and Tanimura, N.\n\n\n \n\n\n\n Biosilico, 1(5): 159–162. 2003.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{funahashi2003celldesigner,\n  title={CellDesigner: a process diagram editor for gene-regulatory and biochemical networks},\n  author={Funahashi, Akira and Morohashi, Mineo and Kitano, Hiroaki and Tanimura, Naoki},\n  journal={Biosilico},\n  volume={1},\n  number={5},\n  pages={159--162},\n  year={2003},\n  publisher={Elsevier}\n}\n\n
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\n \n\n \n \n \n \n \n Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.\n \n \n \n\n\n \n 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 others\n\n\n \n\n\n\n Systems biology, 1(1): 41–53. 2004.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{hucka2004evolving,\n  title={Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project},\n  author={Hucka, Michael and Finney, ABBJ and Bornstein, Benjamin J and Keating, Sarah M and Shapiro, Bruce E and Matthews, Joanne and Kovitz, Ben L and Schilstra, Maria J and Funahashi, Akira and Doyle, John C and others},\n  journal={Systems biology},\n  volume={1},\n  number={1},\n  pages={41--53},\n  year={2004},\n  publisher={IET Digital Library}\n}\n\n
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\n \n\n \n \n \n \n \n Recursive diagonal torus: an interconnection network for massively parallel computers.\n \n \n \n\n\n \n Yang, Y.; Funahashi, A.; Jouraku, A.; Nishi, H.; Amano, H.; and Sueyoshi, T.\n\n\n \n\n\n\n IEEE Transactions on Parallel and Distributed Systems, 12(7): 701–715. 2001.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{yang2001recursive,\n  title={Recursive diagonal torus: an interconnection network for massively parallel computers},\n  author={Yang, Yulu and Funahashi, Akira and Jouraku, Akiya and Nishi, Hiroaki and Amano, Hideharu and Sueyoshi, Toshinori},\n  journal={IEEE Transactions on Parallel and Distributed Systems},\n  volume={12},\n  number={7},\n  pages={701--715},\n  year={2001},\n  publisher={IEEE}\n}\n\n
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\n\n\n
\n \n\n \n \n \n \n \n CellDesigner 3.5: a versatile modeling tool for biochemical networks.\n \n \n \n\n\n \n Funahashi, A.; Matsuoka, Y.; Jouraku, A.; Morohashi, M.; Kikuchi, N.; and Kitano, H.\n\n\n \n\n\n\n Proceedings of the IEEE, 96(8): 1254–1265. 2008.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{funahashi2008celldesigner,\n  title={CellDesigner 3.5: a versatile modeling tool for biochemical networks},\n  author={Funahashi, Akira and Matsuoka, Yukiko and Jouraku, Akiya and Morohashi, Mineo and Kikuchi, Norihiro and Kitano, Hiroaki},\n  journal={Proceedings of the IEEE},\n  volume={96},\n  number={8},\n  pages={1254--1265},\n  year={2008},\n  publisher={IEEE}\n}\n\n
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\n \n\n \n \n \n \n \n Molecular interaction map of a macrophage.\n \n \n \n\n\n \n Oda, K.; Kimura, T.; Matsuoka, Y.; Funahashi, A.; Muramatsu, M.; and Kitano, H.\n\n\n \n\n\n\n AfCS Research Reports, 2(14): 1–12. 2004.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{oda2004molecular,\n  title={Molecular interaction map of a macrophage},\n  author={Oda, Kanae and Kimura, Tomomi and Matsuoka, Yukiko and Funahashi, Akira and Muramatsu, Masaaki and Kitano, Hiroaki},\n  journal={AfCS Research Reports},\n  volume={2},\n  number={14},\n  pages={1--12},\n  year={2004}\n}\n\n
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\n\n\n
\n \n\n \n \n \n \n \n Integration of CellDesigner and SABIO-RK.\n \n \n \n\n\n \n Funahashi, A.; Jouraku, A.; Matsuoka, Y.; and Kitano, H.\n\n\n \n\n\n\n In silico biology, 7(2 Supplement): 81–90. 2007.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{funahashi2007integration,\n  title={Integration of CellDesigner and SABIO-RK},\n  author={Funahashi, Akira and Jouraku, Akiya and Matsuoka, Yukiko and Kitano, Hiroaki},\n  journal={In silico biology},\n  volume={7},\n  number={2 Supplement},\n  pages={81--90},\n  year={2007},\n  publisher={IOS Press}\n}\n\n
\n
\n\n\n\n
\n\n\n
\n \n\n \n \n \n \n \n Software infrastructure for effective communication and reuse of computational models.\n \n \n \n\n\n \n Finney, A.; Hucka, M.; Bornstein, B. J; Keating, S. M; Shapiro, B. E; Matthews, J.; Kovitz, B. L; Schilstra, M. J; Funahashi, A.; Doyle, J.; and others\n\n\n \n\n\n\n . 2006.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{finney2006software,\n  title={Software infrastructure for effective communication and reuse of computational models},\n  author={Finney, Andrew and Hucka, Michael and Bornstein, Benjamin J and Keating, Sarah M and Shapiro, Bruce E and Matthews, Joanne and Kovitz, Ben L and Schilstra, Maria J and Funahashi, Akira and Doyle, John and others},\n  year={2006},\n  publisher={MIT Press}\n}\n\n
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\n \n\n \n \n \n \n \n Deduction of intracellular sub-systems from a topological description of the network.\n \n \n \n\n\n \n Nordling, T. E.; Hiroi, N.; Funahashi, A.; and Kitano, H.\n\n\n \n\n\n\n Molecular BioSystems, 3(8): 523–529. 2007.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{nordling2007deduction,\n  title={Deduction of intracellular sub-systems from a topological description of the network},\n  author={Nordling, Torbj{\\"o}rn EM and Hiroi, Noriko and Funahashi, Akira and Kitano, Hiroaki},\n  journal={Molecular BioSystems},\n  volume={3},\n  number={8},\n  pages={523--529},\n  year={2007},\n  publisher={Royal Society of Chemistry}\n}\n\n
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\n \n\n \n \n \n \n \n Comparative studies of suppression of malignant cancer cell phenotype by antisense oligo DNA and small interfering RNA.\n \n \n \n\n\n \n Hiroi, N; Funahashi, A.; and Kitano, H\n\n\n \n\n\n\n Cancer gene therapy, 13(1): 7–12. 2006.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{hiroi2006comparative,\n  title={Comparative studies of suppression of malignant cancer cell phenotype by antisense oligo DNA and small interfering RNA},\n  author={Hiroi, N and Funahashi, Akira and Kitano, H},\n  journal={Cancer gene therapy},\n  volume={13},\n  number={1},\n  pages={7--12},\n  year={2006},\n  publisher={Nature Publishing Group}\n}\n\n
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\n \n\n \n \n \n \n \n ReCSiP: An FPGA-based general-purpose biochemical simulator.\n \n \n \n\n\n \n Osana, Y.; Yoshimi, M.; Iwaoka, Y.; Kojima, T.; Nishikawa, Y.; Funahashi, A.; Hiroi, N.; Shibata, Y.; Iwanaga, N.; Kitano, H.; and others\n\n\n \n\n\n\n Electronics and Communications in Japan (Part II: Electronics), 90(7): 1–10. 2007.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{osana2007recsip,\n  title={ReCSiP: An FPGA-based general-purpose biochemical simulator},\n  author={Osana, Yasunori and Yoshimi, Masato and Iwaoka, Yow and Kojima, Toshinori and Nishikawa, Yuri and Funahashi, Akira and Hiroi, Noriko and Shibata, Yuichiro and Iwanaga, Naoki and Kitano, Hiroaki and others},\n  journal={Electronics and Communications in Japan (Part II: Electronics)},\n  volume={90},\n  number={7},\n  pages={1--10},\n  year={2007},\n  publisher={Wiley Subscription Services, Inc., A Wiley Company Hoboken}\n}\n\n
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\n \n\n \n \n \n \n \n The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.\n \n \n \n\n\n \n Katayama, T.; Arakawa, K.; Nakao, M.; Ono, K.; Aoki-Kinoshita, K. F; Yamamoto, Y.; Yamaguchi, A.; Kawashima, S.; Chun, H.; Aerts, J.; and others\n\n\n \n\n\n\n Journal of biomedical semantics, 1(1): 8. 2010.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{katayama2010dbcls,\n  title={The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows},\n  author={Katayama, Toshiaki and Arakawa, Kazuharu and Nakao, Mitsuteru and Ono, Keiichiro and Aoki-Kinoshita, Kiyoko F and Yamamoto, Yasunori and Yamaguchi, Atsuko and Kawashima, Shuichi and Chun, Hong-Woo and Aerts, Jan and others},\n  journal={Journal of biomedical semantics},\n  volume={1},\n  number={1},\n  pages={8},\n  year={2010},\n  publisher={BioMed Central}\n}\n\n
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\n \n\n \n \n \n \n \n Converting KEGG DB to SBML.\n \n \n \n\n\n \n Funahashi, A.; and Kitano, H.\n\n\n \n\n\n\n Bioinformatics, 6. 2003.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{funahashi2003converting,\n  title={Converting KEGG DB to SBML},\n  author={Funahashi, Akira and Kitano, Hiroaki},\n  journal={Bioinformatics},\n  volume={6},\n  year={2003}\n}\n\n
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\n \n\n \n \n \n \n \n Fault Tolerance of the TBSF (Tandem Banyan Switching Fabrics) and PBSF (Piled Banyan Switching Fabrics).\n \n \n \n\n\n \n Funahashi, A.; Hanawa, T.; and Amano, H.\n\n\n \n\n\n\n IEICE TRANSACTIONS on Information and Systems, 79(8): 1180–1189. 1996.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{funahashi1996fault,\n  title={Fault Tolerance of the TBSF (Tandem Banyan Switching Fabrics) and PBSF (Piled Banyan Switching Fabrics)},\n  author={Funahashi, Akira and Hanawa, Toshihiro and Amano, Hideharu},\n  journal={IEICE TRANSACTIONS on Information and Systems},\n  volume={79},\n  number={8},\n  pages={1180--1189},\n  year={1996},\n  publisher={The Institute of Electronics, Information and Communication Engineers}\n}\n\n
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\n \n\n \n \n \n \n \n The ERATO Systems Biology Workbench and Systems Biology Markup Language: an integrated environment and standardization for systems biology.\n \n \n \n\n\n \n Funahashi, A.\n\n\n \n\n\n\n Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme, 48(7): 810. 2003.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{funahashi2003erato,\n  title={The ERATO Systems Biology Workbench and Systems Biology Markup Language: an integrated environment and standardization for systems biology},\n  author={Funahashi, Akira},\n  journal={Tanpakushitsu kakusan koso. Protein, nucleic acid, enzyme},\n  volume={48},\n  number={7},\n  pages={810},\n  year={2003}\n}\n\n
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\n \n\n \n \n \n \n \n The Process Diagram: Rationale and Definition.\n \n \n \n\n\n \n Kitano, H.; Matsuoka, Y.; Oda, K.; and Funahashi, A.\n\n\n \n\n\n\n Available via the World Wide Web at http://www. systemsbiology. org/cd/documents/ProcessDiagram. html,104. 2004.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{kitano2004process,\n  title={The Process Diagram: Rationale and Definition},\n  author={Kitano, Hiroaki and Matsuoka, Yukiko and Oda, Kanane and Funahashi, Akira},\n  journal={Available via the World Wide Web at http://www. systemsbiology. org/cd/documents/ProcessDiagram. html},\n  pages={104},\n  year={2004}\n}\n\n
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\n \n\n \n \n \n \n \n BioPAX support in CellDesigner.\n \n \n \n\n\n \n Mi, H.; Muruganujan, A.; Demir, E.; Matsuoka, Y.; Funahashi, A.; Kitano, H.; and Thomas, P. D\n\n\n \n\n\n\n Bioinformatics, 27(24): 3437–3438. 2011.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{mi2011biopax,\n  title={BioPAX support in CellDesigner},\n  author={Mi, Huaiyu and Muruganujan, Anushya and Demir, Emek and Matsuoka, Yukiko and Funahashi, Akira and Kitano, Hiroaki and Thomas, Paul D},\n  journal={Bioinformatics},\n  volume={27},\n  number={24},\n  pages={3437--3438},\n  year={2011},\n  publisher={Oxford University Press}\n}\n\n
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\n \n\n \n \n \n \n \n Automatic pipeline construction focused on similarity of rate law functions for an FPGA-based biochemical simulator.\n \n \n \n\n\n \n Yamada, H.; Ogawa, Y.; Ooya, T.; Ishimori, T.; Osana, Y.; Yoshimi, M.; Nishikawa, Y.; Funahashi, A.; Hiroi, N.; Amano, H.; and others\n\n\n \n\n\n\n IPSJ Transactions on System LSI Design Methodology, 3: 244–256. 2010.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
\n 
@article{yamada2010automatic,\n  title={Automatic pipeline construction focused on similarity of rate law functions for an FPGA-based biochemical simulator},\n  author={Yamada, Hideki and Ogawa, Yui and Ooya, Tomonori and Ishimori, Tomoya and Osana, Yasunori and Yoshimi, Masato and Nishikawa, Yuri and Funahashi, Akira and Hiroi, Noriko and Amano, Hideharu and others},\n  journal={IPSJ Transactions on System LSI Design Methodology},\n  volume={3},\n  pages={244--256},\n  year={2010},\n  publisher={Information Processing Society of Japan}\n}\n\n
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\n \n\n \n \n \n \n \n A Hardware Accelerator for Biochemical Simulations.\n \n \n \n\n\n \n Osana, Y.; Yoshimi, M.; Iwaoka, Y.; Kojima, T.; Nishikawa, Y.; Shibata, Y.; Iwanaga, N.; Funahashi, A.; Hiroi, N.; Kitano, H.; and others\n\n\n \n\n\n\n . .\n \n\n\n\n
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@article{osanahardware,\n  title={A Hardware Accelerator for Biochemical Simulations},\n  author={Osana, Yasunori and Yoshimi, Masato and Iwaoka, Yow and Kojima, Toshinori and Nishikawa, Yuri and Shibata, Yuichiro and Iwanaga, Naoki and Funahashi, Akira and Hiroi, Noriko and Kitano, Hiroaki and others}\n}\n\n
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\n \n\n \n \n \n \n \n COMPUTATIONAL SYSTEMS BIOLOGY.\n \n \n \n\n\n \n Funahashi, A; Matsuoka, Y; Jouraku, A; Morohashi, M; Kikuchi, N; Kitano, H; Schmidt, J.; Delp, S.; Sherman, M.; Taylor, C.; and others\n\n\n \n\n\n\n Proceedings of the IEEE, 96(8). 2008.\n \n\n\n\n
\n\n\n\n \n\n \n\n \n link\n  \n \n\n bibtex\n \n\n \n\n \n\n \n \n \n \n \n \n \n\n  \n \n \n\n\n\n
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@article{funahashi2008computational,\n  title={COMPUTATIONAL SYSTEMS BIOLOGY},\n  author={Funahashi, A and Matsuoka, Y and Jouraku, A and Morohashi, M and Kikuchi, N and Kitano, H and Schmidt, JP and Delp, SL and Sherman, MA and Taylor, CA and others},\n  journal={Proceedings of the IEEE},\n  volume={96},\n  number={8},\n  year={2008}\n}\n\n
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\n \n\n \n \n \n \n \n Hardware-resource Utilization Analysis on an FPGA-Based Biochemical Simulator ReCSiP.\n \n \n \n\n\n \n Osana, Y; and others\n\n\n \n\n\n\n The Institute of Electronics Information and Communication Technical Report CPSY2005-63, 105(516). 2006.\n \n\n\n\n
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@article{osana2006hardware,\n  title={Hardware-resource Utilization Analysis on an FPGA-Based Biochemical Simulator ReCSiP},\n  author={Osana, Y and others},\n  journal={The Institute of Electronics Information and Communication Technical Report CPSY2005-63},\n  volume={105},\n  number={516},\n  year={2006}\n}\n\n
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\n \n\n \n \n \n \n \n Analysis for dimension-restricted reaction kinetics with a bacterial endonuclease movement.\n \n \n \n\n\n \n HIROI, N.; FUNAHASHI, A.; and KITANO, H.\n\n\n \n\n\n\n . .\n \n\n\n\n
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@article{hiroianalysis,\n  title={Analysis for dimension-restricted reaction kinetics with a bacterial endonuclease movement},\n  author={HIROI, NORIKO and FUNAHASHI, AKIRA and KITANO, HIROAKI}\n}\n\n
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\n \n\n \n \n \n \n \n 3P-239 分子クラウディング効果が細胞内化学反応に及ぼす影響 (数理生物学, 第 47 回日本生物物理学会年会).\n \n \n \n\n\n \n Yashima, K.; Hiroi, N.; Funahashi, A.; and Oka, K.\n\n\n \n\n\n\n 生物物理, 49: S191. 2009.\n \n\n\n\n
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@article{yashima20093p,\n  title={3P-239 分子クラウディング効果が細胞内化学反応に及ぼす影響 (数理生物学, 第 47 回日本生物物理学会年会)},\n  author={Yashima, Kenta and Hiroi, Noriko and Funahashi, Akira and Oka, Kotaro},\n  journal={生物物理},\n  volume={49},\n  pages={S191},\n  year={2009},\n  publisher={一般社団法人 日本生物物理学会}\n}\n\n
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\n \n\n \n \n \n \n \n LibSBGN: Electronic Processing of SBGN maps.\n \n \n \n\n\n \n van Iersel, M. P; Boyd, S. E; Bergmann, F.; Moodie, S.; Schreiber, F.; Czauderna, T.; Demir, E.; Le Novère, N.; Sorokin, A.; Mi, H.; and others\n\n\n \n\n\n\n . 2011.\n \n\n\n\n
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@article{van2011libsbgn,\n  title={LibSBGN: Electronic Processing of SBGN maps},\n  author={van Iersel, Martijn P and Boyd, Sarah E and Bergmann, Frank and Moodie, Stuart and Schreiber, Falk and Czauderna, Tobias and Demir, Emek and Le Nov{\\`e}re, Nicolas and Sorokin, Anatoly and Mi, Huaiyu and others},\n  year={2011},\n  publisher={Nature Publishing Group}\n}\n\n
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\n \n\n \n \n \n \n \n Physiological environment induces quick response–slow exhaustion reactions.\n \n \n \n\n\n \n Hiroi, N.; Lu, J.; Iba, K.; Tabira, A.; Yamashita, S.; Okada, Y.; Christoph, F.; Oka, K.; Köhler, G.; and Funahashi, A.\n\n\n \n\n\n\n Frontiers in Physiology, 2: 50. 2011.\n \n\n\n\n
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@article{hiroi2011physiological,\n  title={Physiological environment induces quick response--slow exhaustion reactions},\n  author={Hiroi, Noriko and Lu, James and Iba, Keisuke and Tabira, Akito and Yamashita, Shuji and Okada, Yasunori and Christoph, Flamm and Oka, Kotaro and K{\\"o}hler, Gottfried and Funahashi, Akira},\n  journal={Frontiers in Physiology},\n  volume={2},\n  pages={50},\n  year={2011},\n  publisher={Frontiers}\n}\n\n
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\n \n\n \n \n \n \n \n The CellDesigner Layout Proposal.\n \n \n \n\n\n \n TANIMURA, N.; NAKAYAMA, M.; INAGAKI, Y.; SAITO, T.; FUNAHASHI, A.; and KITANO, H.\n\n\n \n\n\n\n . .\n \n\n\n\n
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@article{tanimuracelldesigner,\n  title={The CellDesigner Layout Proposal},\n  author={TANIMURA, Naoki and NAKAYAMA, Maki and INAGAKI, Yuichiro and SAITO, Takayuki and FUNAHASHI, Akira and KITANO, Hiroaki}\n}\n\n
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\n \n\n \n \n \n \n \n The systems biology graphical notation.\n \n \n \n\n\n \n Le Novere, N.; Hucka, M.; Mi, H.; Moodie, S.; Schreiber, F.; Sorokin, A.; Demir, E.; Wegner, K.; Aladjem, M. I; Wimalaratne, S. M; and others\n\n\n \n\n\n\n Nature biotechnology, 27(8): 735–741. 2009.\n \n\n\n\n
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@article{le2009systems,\n  title={The systems biology graphical notation},\n  author={Le Novere, Nicolas and Hucka, Michael and Mi, Huaiyu and Moodie, Stuart and Schreiber, Falk and Sorokin, Anatoly and Demir, Emek and Wegner, Katja and Aladjem, Mirit I and Wimalaratne, Sarala M and others},\n  journal={Nature biotechnology},\n  volume={27},\n  number={8},\n  pages={735--741},\n  year={2009},\n  publisher={Nature Publishing Group}\n}\n\n
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\n \n\n \n \n \n \n \n Software support for SBGN maps: SBGN-ML and LibSBGN.\n \n \n \n\n\n \n 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.; and others\n\n\n \n\n\n\n Bioinformatics, 28(15): 2016–2021. 2012.\n \n\n\n\n
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@article{van2012software,\n  title={Software support for SBGN maps: SBGN-ML and LibSBGN},\n  author={Van Iersel, Martijn P and Vill{\\'e}ger, Alice C and Czauderna, Tobias and Boyd, Sarah E and Bergmann, Frank T and Luna, Augustin and Demir, Emek and Sorokin, Anatoly and Dogrusoz, Ugur and Matsuoka, Yukiko and others},\n  journal={Bioinformatics},\n  volume={28},\n  number={15},\n  pages={2016--2021},\n  year={2012},\n  publisher={Oxford University Press}\n}\n\n
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\n \n\n \n \n \n \n \n From microscopy data to in silico environments for in vivo-oriented simulations.\n \n \n \n\n\n \n Hiroi, N.; Klann, M.; Iba, K.; de Heras Ciechomski, P.; Yamashita, S.; Tabira, A.; Okuhara, T.; Kubojima, T.; Okada, Y.; Oka, K.; and others\n\n\n \n\n\n\n EURASIP Journal on Bioinformatics and Systems Biology, 2012(1): 7. 2012.\n \n\n\n\n
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@article{hiroi2012microscopy,\n  title={From microscopy data to in silico environments for in vivo-oriented simulations},\n  author={Hiroi, Noriko and Klann, Michael and Iba, Keisuke and de Heras Ciechomski, Pablo and Yamashita, Shuji and Tabira, Akito and Okuhara, Takahiro and Kubojima, Takeshi and Okada, Yasunori and Oka, Kotaro and others},\n  journal={EURASIP Journal on Bioinformatics and Systems Biology},\n  volume={2012},\n  number={1},\n  pages={7},\n  year={2012},\n  publisher={Springer International Publishing}\n}\n\n
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\n \n\n \n \n \n \n \n Physiological intracellular crowdedness is defined by the perimeter-to-area ratio of sub-cellular compartments.\n \n \n \n\n\n \n Hiroi, N.; Okuhara, T.; Kubojima, T.; Iba, K.; Tabira, A.; Yamashita, S.; Okada, Y.; Kobayashi, T. J; and Funahashi, A.\n\n\n \n\n\n\n Frontiers in physiology, 3: 293. 2012.\n \n\n\n\n
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@article{hiroi2012physiological,\n  title={Physiological intracellular crowdedness is defined by the perimeter-to-area ratio of sub-cellular compartments},\n  author={Hiroi, Noriko and Okuhara, Takahiro and Kubojima, Takeshi and Iba, Keisuke and Tabira, Akito and Yamashita, Shuji and Okada, Yasunori and Kobayashi, Tetsuya J and Funahashi, Akira},\n  journal={Frontiers in physiology},\n  volume={3},\n  pages={293},\n  year={2012},\n  publisher={Frontiers}\n}\n\n
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\n \n\n \n \n \n \n \n Mathematical modeling of sustainable synaptogenesis by repetitive stimuli suggests signaling mechanisms in vivo.\n \n \n \n\n\n \n Takizawa, H.; Hiroi, N.; and Funahashi, A.\n\n\n \n\n\n\n PLoS One, 7(12): e51000. 2012.\n \n\n\n\n
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@article{takizawa2012mathematical,\n  title={Mathematical modeling of sustainable synaptogenesis by repetitive stimuli suggests signaling mechanisms in vivo},\n  author={Takizawa, Hiromu and Hiroi, Noriko and Funahashi, Akira},\n  journal={PLoS One},\n  volume={7},\n  number={12},\n  pages={e51000},\n  year={2012},\n  publisher={Public Library of Science}\n}\n\n
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\n \n\n \n \n \n \n \n Meeting report of the International Workshop on Quantitative Biology 2012: mesoscopic and microscopic worlds meet.\n \n \n \n\n\n \n Draviam, V. M\n\n\n \n\n\n\n Frontiers in Physiology, 3: 479. 2013.\n \n\n\n\n
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@article{draviam2013meeting,\n  title={Meeting report of the International Workshop on Quantitative Biology 2012: mesoscopic and microscopic worlds meet},\n  author={Draviam, Viji M},\n  journal={Frontiers in Physiology},\n  volume={3},\n  pages={479},\n  year={2013},\n  publisher={Frontiers}\n}\n\n
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\n \n\n \n \n \n \n \n LibSBMLSim: a reference implementation of fully functional SBML simulator.\n \n \n \n\n\n \n Takizawa, H.; Nakamura, K.; Tabira, A.; Chikahara, Y.; Matsui, T.; Hiroi, N.; and Funahashi, A.\n\n\n \n\n\n\n Bioinformatics, 29(11): 1474–1476. 2013.\n \n\n\n\n
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@article{takizawa2013libsbmlsim,\n  title={LibSBMLSim: a reference implementation of fully functional SBML simulator},\n  author={Takizawa, Hiromu and Nakamura, Kazushige and Tabira, Akito and Chikahara, Yoichi and Matsui, Tatsuhiro and Hiroi, Noriko and Funahashi, Akira},\n  journal={Bioinformatics},\n  volume={29},\n  number={11},\n  pages={1474--1476},\n  year={2013},\n  publisher={Oxford University Press}\n}\n\n
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\n \n\n \n \n \n \n \n Perspectives of nanodiamond formation from the organic matter at low PT parameters.\n \n \n \n\n\n \n Simakov, S.\n\n\n \n\n\n\n Nature Precedings,1–1. 2010.\n \n\n\n\n
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@article{simakov2010perspectives,\n  title={Perspectives of nanodiamond formation from the organic matter at low PT parameters},\n  author={Simakov, Sergei},\n  journal={Nature Precedings},\n  pages={1--1},\n  year={2010},\n  publisher={Nature Publishing Group}\n}\n\n
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\n \n\n \n \n \n \n \n The systems biology simulation core algorithm.\n \n \n \n\n\n \n Keller, R.; Dörr, A.; Tabira, A.; Funahashi, A.; Ziller, M. J; Adams, R.; Rodriguez, N.; Le Novère, N.; Hiroi, N.; Planatscher, H.; and others\n\n\n \n\n\n\n BMC systems biology, 7(1): 55. 2013.\n \n\n\n\n
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@article{keller2013systems,\n  title={The systems biology simulation core algorithm},\n  author={Keller, Roland and D{\\"o}rr, Alexander and Tabira, Akito and Funahashi, Akira and Ziller, Michael J and Adams, Richard and Rodriguez, Nicolas and Le Nov{\\`e}re, Nicolas and Hiroi, Noriko and Planatscher, Hannes and others},\n  journal={BMC systems biology},\n  volume={7},\n  number={1},\n  pages={55},\n  year={2013},\n  publisher={BioMed Central}\n}\n\n
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\n \n\n \n \n \n \n \n Automated tracking of mitotic spindle pole positions shows that LGN is required for spindle rotation but not orientation maintenance.\n \n \n \n\n\n \n Corrigan, A. M; Shrestha, R. L; Zulkipli, I.; Hiroi, N.; Liu, Y.; Tamura, N.; Yang, B.; Patel, J.; Funahashi, A.; Donald, A.; and others\n\n\n \n\n\n\n Cell Cycle, 12(16): 2643–2655. 2013.\n \n\n\n\n
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@article{corrigan2013automated,\n  title={Automated tracking of mitotic spindle pole positions shows that LGN is required for spindle rotation but not orientation maintenance},\n  author={Corrigan, Adam M and Shrestha, Roshan L and Zulkipli, Ihsan and Hiroi, Noriko and Liu, Yingjun and Tamura, Naoka and Yang, Bing and Patel, Jessica and Funahashi, Akira and Donald, Athene and others},\n  journal={Cell Cycle},\n  volume={12},\n  number={16},\n  pages={2643--2655},\n  year={2013},\n  publisher={Taylor \\& Francis}\n}\n\n
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\n \n\n \n \n \n \n \n Assessing uncertainty in model parameters based on sparse and noisy experimental data.\n \n \n \n\n\n \n Hiroi, N.; Swat, M.; and Funahashi, A.\n\n\n \n\n\n\n Frontiers in physiology, 5: 128. 2014.\n \n\n\n\n
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@article{hiroi2014assessing,\n  title={Assessing uncertainty in model parameters based on sparse and noisy experimental data},\n  author={Hiroi, Noriko and Swat, Maciej and Funahashi, Akira},\n  journal={Frontiers in physiology},\n  volume={5},\n  pages={128},\n  year={2014},\n  publisher={Frontiers}\n}\n\n
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\n \n\n \n \n \n \n \n A proteomic study of mitotic phase-specific interactors of EB1 reveals a role for SXIP-mediated protein interactions in anaphase onset.\n \n \n \n\n\n \n Tamura, N.; Simon, J. E; Nayak, A.; Shenoy, R.; Hiroi, N.; Boilot, V.; Funahashi, A.; and Draviam, V. M\n\n\n \n\n\n\n Biology open, 4(2): 155–169. 2015.\n \n\n\n\n
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@article{tamura2015proteomic,\n  title={A proteomic study of mitotic phase-specific interactors of EB1 reveals a role for SXIP-mediated protein interactions in anaphase onset},\n  author={Tamura, Naoka and Simon, Judith E and Nayak, Arnab and Shenoy, Rajesh and Hiroi, Noriko and Boilot, Viviane and Funahashi, Akira and Draviam, Viji M},\n  journal={Biology open},\n  volume={4},\n  number={2},\n  pages={155--169},\n  year={2015},\n  publisher={The Company of Biologists Ltd}\n}\n\n
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\n \n\n \n \n \n \n \n High-speed microscopy with an electrically tunable lens to image the dynamics of in vivo molecular complexes.\n \n \n \n\n\n \n Nakai, Y.; Ozeki, M.; Hiraiwa, T.; Tanimoto, R.; Funahashi, A.; Hiroi, N.; Taniguchi, A.; Nonaka, S.; Boilot, V.; Shrestha, R.; and others\n\n\n \n\n\n\n Review of Scientific Instruments, 86(1): 013707. 2015.\n \n\n\n\n
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@article{nakai2015high,\n  title={High-speed microscopy with an electrically tunable lens to image the dynamics of in vivo molecular complexes},\n  author={Nakai, Yuichiro and Ozeki, Mitsunori and Hiraiwa, Takumi and Tanimoto, Ryuichi and Funahashi, Akira and Hiroi, Noriko and Taniguchi, Atsushi and Nonaka, Shigenori and Boilot, Viviane and Shrestha, Roshan and others},\n  journal={Review of Scientific Instruments},\n  volume={86},\n  number={1},\n  pages={013707},\n  year={2015},\n  publisher={AIP Publishing LLC}\n}\n\n
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\n \n\n \n \n \n \n \n Acceleration of discrete stochastic biochemical simulation using GPGPU.\n \n \n \n\n\n \n Sumiyoshi, K.; Hirata, K.; Hiroi, N.; and Funahashi, A.\n\n\n \n\n\n\n Frontiers in Physiology, 6: 42. 2015.\n \n\n\n\n
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@article{sumiyoshi2015acceleration,\n  title={Acceleration of discrete stochastic biochemical simulation using GPGPU},\n  author={Sumiyoshi, Kei and Hirata, Kazuki and Hiroi, Noriko and Funahashi, Akira},\n  journal={Frontiers in Physiology},\n  volume={6},\n  pages={42},\n  year={2015},\n  publisher={Frontiers}\n}\n\n
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\n \n\n \n \n \n \n \n 4.3 DNA Structural Dynamics (Team 5).\n \n \n \n\n\n \n Erban, R.; Funahashi, A.; Herajy, M.; Kobayashi, T. J; Takahashi, K.; and Togashi, Y.\n\n\n \n\n\n\n Multiscale Spatial Computational Systems Biology,191. .\n \n\n\n\n
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@article{erban4,\n  title={4.3 DNA Structural Dynamics (Team 5)},\n  author={Erban, Radek and Funahashi, Akira and Herajy, Mostafa and Kobayashi, Tetsuya J and Takahashi, Koichi and Togashi, Yuichi},\n  journal={Multiscale Spatial Computational Systems Biology},\n  pages={191}\n}\n\n
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\n \n\n \n \n \n \n \n 4.5 Towards a standard exchange format for spatial, multilevel multicellular models (Team 7).\n \n \n \n\n\n \n de Back, W.; Deutsch, A.; Drasdo, D.; Funahashi, A.; and Uhrmacher, A. M\n\n\n \n\n\n\n Multiscale Spatial Computational Systems Biology,214. .\n \n\n\n\n
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@article{citation-72,\n  title={4.5 Towards a standard exchange format for spatial, multilevel multicellular models (Team 7)},\n  author={de Back, Walter and Deutsch, Andreas and Drasdo, Dirk and Funahashi, Akira and Uhrmacher, Adelinde M},\n  journal={Multiscale Spatial Computational Systems Biology},\n  pages={214}\n}\n\n
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\n \n\n \n \n \n \n \n The principles of whole-cell modeling.\n \n \n \n\n\n \n Karr, J. R; Takahashi, K.; and Funahashi, A.\n\n\n \n\n\n\n Current opinion in microbiology, 27: 18–24. 2015.\n \n\n\n\n
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@article{karr2015principles,\n  title={The principles of whole-cell modeling},\n  author={Karr, Jonathan R and Takahashi, Koichi and Funahashi, Akira},\n  journal={Current opinion in microbiology},\n  volume={27},\n  pages={18--24},\n  year={2015},\n  publisher={Elsevier Current Trends}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Simulation technology and its application in systems biology.\n  \n  \n  \n\n\n  \n  Funahashi, A.;  and Hiroi, N.\n\n\n  \n\n\n\n  Folia Pharmacologica Japonica, 147(2): 101–106.  2016.\n  \n\n\n\n
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@article{funahashi2016simulation,\n  title={Simulation technology and its application in systems biology},\n  author={Funahashi, Akira and Hiroi, Noriko},\n  journal={Folia Pharmacologica Japonica},\n  volume={147},\n  number={2},\n  pages={101--106},\n  year={2016},\n  publisher={Japanese Pharmacological Society}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Detection of temperature difference in neuronal cells.\n  \n  \n  \n\n\n  \n  Tanimoto, R.; Hiraiwa, T.; Nakai, Y.; Shindo, Y.; Oka, K.; Hiroi, N.;  and Funahashi, A.\n\n\n  \n\n\n\n  Scientific reports, 6: 22071.  2016.\n  \n\n\n\n
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@article{tanimoto2016detection,\n  title={Detection of temperature difference in neuronal cells},\n  author={Tanimoto, Ryuichi and Hiraiwa, Takumi and Nakai, Yuichiro and Shindo, Yutaka and Oka, Kotaro and Hiroi, Noriko and Funahashi, Akira},\n  journal={Scientific reports},\n  volume={6},\n  pages={22071},\n  year={2016},\n  publisher={Nature Publishing Group}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Quantitative biology: Dynamics of living systems.\n  \n  \n  \n\n\n  \n  Hiroi, N.; Draviam, V. M;  and Funahashi, A.\n\n\n  \n\n\n\n  Frontiers in physiology, 7: 196.  2016.\n  \n\n\n\n
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@article{hiroi2016quantitative,\n  title={Quantitative biology: Dynamics of living systems},\n  author={Hiroi, Noriko and Draviam, Viji M and Funahashi, Akira},\n  journal={Frontiers in physiology},\n  volume={7},\n  pages={196},\n  year={2016},\n  publisher={Frontiers}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  3.15 Computational Platform for Systems Biology.\n  \n  \n  \n\n\n  \n  Funahashi, A.\n\n\n  \n\n\n\n  Multiscale Spatial Computational Systems Biology,152.  .\n  \n\n\n\n
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@article{funahashi3,\n  title={3.15 Computational Platform for Systems Biology},\n  author={Funahashi, Akira},\n  journal={Multiscale Spatial Computational Systems Biology},\n  pages={152}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  3P-239 Effect of molecular crowding on in vivo macromolecular reactions (Mathematical biology, The 47th Annual Meeting of the Biophysical Society of Japan).\n  \n  \n  \n\n\n  \n  Yashima, K.; Hiroi, N.; Funahashi, A.;  and Oka, K.\n\n\n  \n\n\n\n  Seibutsu Butsuri, 49(supplement): S191.  2009.\n  \n\n\n\n
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@article{yashima20093p,\n  title={3P-239 Effect of molecular crowding on in vivo macromolecular reactions (Mathematical biology, The 47th Annual Meeting of the Biophysical Society of Japan)},\n  author={Yashima, Kenta and Hiroi, Noriko and Funahashi, Akira and Oka, Kotaro},\n  journal={Seibutsu Butsuri},\n  volume={49},\n  number={supplement},\n  pages={S191},\n  year={2009},\n  publisher={The Biophysical Society of Japan General Incorporated Association}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  CellDesigner.\n  \n  \n  \n\n\n  \n  Funahashi, A.; Tanimura, N; Morohashi, M;  and Kitano, H\n\n\n  \n\n\n\n  Systems Biology Institute http://www. systems-biology. org/002.  2007.\n  \n\n\n\n
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@article{funahashi2007celldesigner,\n  title={CellDesigner},\n  author={Funahashi, Akira and Tanimura, N and Morohashi, M and Kitano, H},\n  journal={Systems Biology Institute http://www. systems-biology. org/002},\n  year={2007}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Effects of Limbering Up Exercises to Prevent Falls on Physical Performance and Fall Risks in Elderly Workers.\n  \n  \n  \n\n\n  \n  Kawagoe, T; Nagata, H; Shobuda, Y; Ueda, M; Tominaga, R; Kuga, H; Funahashi, A; Hosomoto, K;  and Kobayashi, T\n\n\n  \n\n\n\n  Research and Practice for Fall Injury Control in the Workplace, 57: 69.  2010.\n  \n\n\n\n
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@article{kawagoe2010effects,\n  title={Effects of Limbering Up Exercises to Prevent Falls on Physical Performance and Fall Risks in Elderly Workers},\n  author={Kawagoe, T and Nagata, H and Shobuda, Y and Ueda, M and Tominaga, R and Kuga, H and Funahashi, A and Hosomoto, K and Kobayashi, T},\n  journal={Research and Practice for Fall Injury Control in the Workplace},\n  volume={57},\n  pages={69},\n  year={2010}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Configuration and evaluation of self routing switches Configuration and evaluation of self routing switches 8, 1988.\n  \n  \n  \n\n\n  \n  FUNAHASHI, A.; HANAWA, T.;  and AMANO, H.\n\n\n  \n\n\n\n  IEICE transactions on information and systems, 79(8): 1180–1189.  1996.\n  \n\n\n\n
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@article{funahashi1996configuration,\n  title={Configuration and evaluation of self routing switches Configuration and evaluation of self routing switches 8, 1988},\n  author={FUNAHASHI, Akira and HANAWA, Toshihiro and AMANO, Hideharu},\n  journal={IEICE transactions on information and systems},\n  volume={79},\n  number={8},\n  pages={1180--1189},\n  year={1996}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Supplemental figures.\n  \n  \n  \n\n\n  \n  Takizawa, H.; Nakamura, K.; Tabira, A.; Chikahara, Y.; Matsui, T.; Hiroi, N.;  and Funahashi, A.\n\n\n  \n\n\n\n  .  .\n  \n\n\n\n
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@article{takizawasupplemental,\n  title={Supplemental figures},\n  author={Takizawa, Hiromu and Nakamura, Kazushige and Tabira, Akito and Chikahara, Yoichi and Matsui, Tatsuhiro and Hiroi, Noriko and Funahashi, Akira}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Convolutional neural network-based instance segmentation algorithm to acquire quantitative criteria of early mouse development.\n  \n  \n  \n\n\n  \n  Tokuoka, Y.; Yamada, T. G; Hiroi, N. F; Kobayashi, T. J; Yamagata, K.;  and Funahashi, A.\n\n\n  \n\n\n\n  BioRxiv,324186.  2018.\n  \n\n\n\n
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@article{tokuoka2018convolutional,\n  title={Convolutional neural network-based instance segmentation algorithm to acquire quantitative criteria of early mouse development},\n  author={Tokuoka, Yuta and Yamada, Takahiro G and Hiroi, Noriko F and Kobayashi, Tetsuya J and Yamagata, Kazuo and Funahashi, Akira},\n  journal={BioRxiv},\n  pages={324186},\n  year={2018},\n  publisher={Cold Spring Harbor Laboratory}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Transcriptome analysis of the anhydrobiotic cell line Pv11 infers the mechanism of desiccation tolerance and recovery.\n  \n  \n  \n\n\n  \n  Yamada, T. G; Suetsugu, Y.; Deviatiiarov, R.; Gusev, O.; Cornette, R.; Nesmelov, A.; Hiroi, N.; Kikawada, T.;  and Funahashi, A.\n\n\n  \n\n\n\n  Scientific reports, 8(1): 1–11.  2018.\n  \n\n\n\n
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@article{yamada2018transcriptome,\n  title={Transcriptome analysis of the anhydrobiotic cell line Pv11 infers the mechanism of desiccation tolerance and recovery},\n  author={Yamada, Takahiro G and Suetsugu, Yoshitaka and Deviatiiarov, Ruslan and Gusev, Oleg and Cornette, Richard and Nesmelov, Alexander and Hiroi, Noriko and Kikawada, Takahiro and Funahashi, Akira},\n  journal={Scientific reports},\n  volume={8},\n  number={1},\n  pages={1--11},\n  year={2018},\n  publisher={Nature Publishing Group}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Predicting the future direction of cell movement with convolutional neural networks.\n  \n  \n  \n\n\n  \n  Nishimoto, S.; Tokuoka, Y.; Yamada, T. G; Hiroi, N. F;  and Funahashi, A.\n\n\n  \n\n\n\n  PloS one, 14(9): e0221245.  2019.\n  \n\n\n\n
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@article{nishimoto2019predicting,\n  title={Predicting the future direction of cell movement with convolutional neural networks},\n  author={Nishimoto, Shori and Tokuoka, Yuta and Yamada, Takahiro G and Hiroi, Noriko F and Funahashi, Akira},\n  journal={PloS one},\n  volume={14},\n  number={9},\n  pages={e0221245},\n  year={2019},\n  publisher={Public Library of Science San Francisco, CA USA}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Quantitative analysis of sensitivity to a Wnt3a gradient in determination of the pole-to-pole axis of mitotic cells by using a microfluidic device.\n  \n  \n  \n\n\n  \n  Hiraiwa, T.; Nakai, Y.; Yamada, T. G; Tanimoto, R.; Kimura, H.; Matsumoto, Y.; Miki, N.; Hiroi, N.;  and Funahashi, A.\n\n\n  \n\n\n\n  FEBS open bio, 8(12): 1920–1935.  2018.\n  \n\n\n\n
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@article{hiraiwa2018quantitative,\n  title={Quantitative analysis of sensitivity to a Wnt3a gradient in determination of the pole-to-pole axis of mitotic cells by using a microfluidic device},\n  author={Hiraiwa, Takumi and Nakai, Yuichiro and Yamada, Takahiro G and Tanimoto, Ryuichi and Kimura, Hiroshi and Matsumoto, Yoshinori and Miki, Norihisa and Hiroi, Noriko and Funahashi, Akira},\n  journal={FEBS open bio},\n  volume={8},\n  number={12},\n  pages={1920--1935},\n  year={2018}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Dollars and sense.\n  \n  \n  \n\n\n  \n  Le Novère, N.; Hucka, M.; Mi, H.; Moodie, S.; Schreiber, F.; Sorokin, A.; Demir, E.; Wegner, K.; Aladjem, M. I; Wimalaratne, S. M;  and others\n\n\n  \n\n\n\n  .  2005.\n  \n\n\n\n
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@article{le2005dollars,\n  title={Dollars and sense},\n  author={Le Nov{\\`e}re, Nicolas and Hucka, Michael and Mi, Huaiyu and Moodie, Stuart and Schreiber, Falk and Sorokin, Anatoly and Demir, Emek and Wegner, Katja and Aladjem, Mirit I and Wimalaratne, Sarala M and others},\n  year={2005}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Transcriptome analysis of the anhydrobiotic cell line Pv11 infers the mechanism of desiccation tolerance and recovery.\n  \n  \n  \n\n\n  \n  Nesmelov, A; Funahashi, A; Deviatiiarov, R; Suetsugu, Y; Gusev, O; Kikawada, T; Hiroi, N; Yamada, T;  and Cornette, R\n\n\n  \n\n\n\n  .  .\n  \n\n\n\n
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@article{nesmelovtranscriptome,\n  title={Transcriptome analysis of the anhydrobiotic cell line Pv11 infers the mechanism of desiccation tolerance and recovery},\n  author={Nesmelov, A and Funahashi, A and Deviatiiarov, R and Suetsugu, Y and Gusev, O and Kikawada, T and Hiroi, N and Yamada, T and Cornette, R}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Erratum: The systems biology graphical notation (Nature Biotechnology (2009) 27 (735-741)).\n  \n  \n  \n\n\n  \n  Le Novère, N.; Hucka, M.; Mi, H.; Moodie, S.; Schreiber, F.; Sorokin, A.; Demir, E.; Wegner, K.; Aladjem, M. I; Wimalaratne, S. M;  and others\n\n\n  \n\n\n\n  Nature Biotechnology, 27(9): 864.  2009.\n  \n\n\n\n
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@article{le2009erratum,\n  title={Erratum: The systems biology graphical notation (Nature Biotechnology (2009) 27 (735-741))},\n  author={Le Nov{\\`e}re, Nicolas and Hucka, Michael and Mi, Huaiyu and Moodie, Stuart and Schreiber, Falk and Sorokin, Anatoly and Demir, Emek and Wegner, Katja and Aladjem, Mirit I and Wimalaratne, Sarala M and others},\n  journal={Nature Biotechnology},\n  volume={27},\n  number={9},\n  pages={864},\n  year={2009},\n  publisher={Nature Publishing Group}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Software support for SBGN maps: SBGN-ML and LibSBGN.\n  \n  \n  \n\n\n  \n  Van, M.; Villeger, A.; Czauderna, T; Boyd, S.; Bergmann, F.; Luna, A; Demir, E; Sorokin, A; Dogrusoz, U; Matsuoka, Y;  and others\n\n\n  \n\n\n\n  .  2012.\n  \n\n\n\n
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@article{van2012software,\n  title={Software support for SBGN maps: SBGN-ML and LibSBGN},\n  author={Van, MP and Villeger, AC and Czauderna, T and Boyd, SE and Bergmann, FT and Luna, A and Demir, E and Sorokin, A and Dogrusoz, U and Matsuoka, Y and others},\n  year={2012},\n  publisher={Oxford University Press}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Activation of cell migration via morphological changes in focal adhesions depends on shear stress in MYCN-amplified neuroblastoma cells.\n  \n  \n  \n\n\n  \n  Hiraiwa, T.; Yamada, T. G; Miki, N.; Funahashi, A.;  and Hiroi, N.\n\n\n  \n\n\n\n  Journal of the Royal Society Interface, 16(152): 20180934.  2019.\n  \n\n\n\n
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@article{hiraiwa2019activation,\n  title={Activation of cell migration via morphological changes in focal adhesions depends on shear stress in MYCN-amplified neuroblastoma cells},\n  author={Hiraiwa, Takumi and Yamada, Takahiro G and Miki, Norihisa and Funahashi, Akira and Hiroi, Noriko},\n  journal={Journal of the Royal Society Interface},\n  volume={16},\n  number={152},\n  pages={20180934},\n  year={2019},\n  publisher={The Royal Society}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  The JSBML project: a fully featured Java API for working with systems biology models.\n  \n  \n  \n\n\n  \n  Rodriguez, N.; Hamm, T. M; Schulte, R.; Watanabe, L.; Vazirabad, I. Y; Kofia, V.; Myers, C. J; Funahashi, A.; Le Novère, N.; Hucka, M.;  and others\n\n\n  \n\n\n\n  F1000Research, 6.  2017.\n  \n\n\n\n
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@article{rodriguez2017jsbml,\n  title={The JSBML project: a fully featured Java API for working with systems biology models},\n  author={Rodriguez, Nicolas and Hamm, Thomas M and Schulte, Roman and Watanabe, Leandro and Vazirabad, Ibrahim Y and Kofia, Victor and Myers, Chris J and Funahashi, Akira and Le Nov{\\`e}re, Nicolas and Hucka, Michael and others},\n  journal={F1000Research},\n  volume={6},\n  year={2017}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Transcriptome analysis of Pv11 cells infers the mechanism of desiccation tolerance and recovery.\n  \n  \n  \n\n\n  \n  Yamada, T. G; Suetsugu, Y.; Deviatiiarov, R.; Gusev, O.; Cornette, R.; Nesmelov, A.; Hiroi, N.; Kikawada, T.;  and Funahashi, A.\n\n\n  \n\n\n\n  BioRxiv,368175.  2018.\n  \n\n\n\n
\n\n\n\n  \n\n  \n\n  \n  link\n   \n  \n\n  bibtex\n    \n\n  \n\n  \n\n  \n  \n  \n  \n  \n  \n  \n\n   \n  \n  \n\n\n\n
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@article{yamada2018transcriptome,\n  title={Transcriptome analysis of Pv11 cells infers the mechanism of desiccation tolerance and recovery},\n  author={Yamada, Takahiro G and Suetsugu, Yoshitaka and Deviatiiarov, Ruslan and Gusev, Oleg and Cornette, Richard and Nesmelov, Alexander and Hiroi, Noriko and Kikawada, Takahiro and Funahashi, Akira},\n  journal={BioRxiv},\n  pages={368175},\n  year={2018},\n  publisher={Cold Spring Harbor Laboratory}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  LibSBGN: Electronic Processing of SBGN maps.\n  \n  \n  \n\n\n  \n  Demir, E.; Dogrusoz, U.; Le Novère, N.; Matsuoka, Y.; Sorokin, A.; Funahashi, A.; Mi, H.; Kitano, H.; Aladjem, M.; van Iersel, M.;  and others\n\n\n  \n\n\n\n  Nature Precedings,1–1.  2011.\n  \n\n\n\n
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@article{demir2011libsbgn,\n  title={LibSBGN: Electronic Processing of SBGN maps},\n  author={Demir, Emek and Dogrusoz, Ugur and Le Nov{\\`e}re, Nicolas and Matsuoka, Yukiko and Sorokin, Anatoly and Funahashi, Akira and Mi, Huaiyu and Kitano, Hiroaki and Aladjem, Mirit and van Iersel, Martijn and others},\n  journal={Nature Precedings},\n  pages={1--1},\n  year={2011},\n  publisher={Nature Publishing Group}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  LibSBGN: Electronic Processing of SBGN maps.\n  \n  \n  \n\n\n  \n  Demir, E.; Dogrusoz, U.; Le Novère, N.; Matsuoka, Y.; Sorokin, A.; Funahashi, A.; Mi, H.; Kitano, H.; Aladjem, M.; van Iersel, M.;  and others\n\n\n  \n\n\n\n  Nature Precedings,1–1.  2010.\n  \n\n\n\n
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@article{demir2010libsbgn,\n  title={LibSBGN: Electronic Processing of SBGN maps},\n  author={Demir, Emek and Dogrusoz, Ugur and Le Nov{\\`e}re, Nicolas and Matsuoka, Yukiko and Sorokin, Anatoly and Funahashi, Akira and Mi, Huaiyu and Kitano, Hiroaki and Aladjem, Mirit and van Iersel, Martijn and others},\n  journal={Nature Precedings},\n  pages={1--1},\n  year={2010},\n  publisher={Nature Publishing Group}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  XitoSBML: a modeling tool for creating spatial SBML models from microscopic images.\n  \n  \n  \n\n\n  \n  Ii, K.; Mashimo, K.; Ozeki, M.; Yamada, T. G; Hiroi, N. F;  and Funahashi, A.\n\n\n  \n\n\n\n  Frontiers in Genetics, 10: 1027.  2019.\n  \n\n\n\n
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@article{ii2019xitosbml,\n  title={XitoSBML: a modeling tool for creating spatial SBML models from microscopic images},\n  author={Ii, Kaito and Mashimo, Kota and Ozeki, Mitsunori and Yamada, Takahiro G and Hiroi, Noriko F and Funahashi, Akira},\n  journal={Frontiers in Genetics},\n  volume={10},\n  pages={1027},\n  year={2019},\n  publisher={Frontiers}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Interconversion Between BioPAX and SBML Project Documentation.\n  \n  \n  \n\n\n  \n  Nguyen, T.; Hucka, M.; Rodriquez, N.; Dräger, A.; Myers, C.;  and Funahashi, A.\n\n\n  \n\n\n\n  .  2016.\n  \n\n\n\n
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@article{nguyen2016interconversion,\n  title={Interconversion Between BioPAX and SBML Project Documentation},\n  author={Nguyen, Tramy and Hucka, Michael and Rodriquez, Nicolas and Dr{\\"a}ger, Andreas and Myers, Chris and Funahashi, Akira},\n  year={2016}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Deep learning for non-invasive determination of the differentiation status of human neuronal cells by using phase-contrast photomicrographs.\n  \n  \n  \n\n\n  \n  Ooka, M.; Tokuoka, Y.; Nishimoto, S.; Hiroi, N. F; Yamada, T. G;  and Funahashi, A.\n\n\n  \n\n\n\n  Applied Sciences, 9(24): 5503.  2019.\n  \n\n\n\n
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@article{ooka2019deep,\n  title={Deep learning for non-invasive determination of the differentiation status of human neuronal cells by using phase-contrast photomicrographs},\n  author={Ooka, Maya and Tokuoka, Yuta and Nishimoto, Shori and Hiroi, Noriko F and Yamada, Takahiro G and Funahashi, Akira},\n  journal={Applied Sciences},\n  volume={9},\n  number={24},\n  pages={5503},\n  year={2019},\n  publisher={Multidisciplinary Digital Publishing Institute}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Neural differentiation dynamics controlled by multiple feedback loop motifs in a comprehensive molecular interaction network.\n  \n  \n  \n\n\n  \n  Iwasaki, T.; Takiguchi, R.; Hiraiwa, T.; Yamada, T. G; Yamazaki, K.; Hiroi, N.;  and Funahashi, A.\n\n\n  \n\n\n\n  .  2019.\n  \n\n\n\n
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@article{iwasaki2019neural,\n  title={Neural differentiation dynamics controlled by multiple feedback loop motifs in a comprehensive molecular interaction network},\n  author={Iwasaki, Tsuyoshi and Takiguchi, Ryo and Hiraiwa, Takumi and Yamada, Takahiro G and Yamazaki, Kazuto and Hiroi, Noriko and Funahashi, Akira},\n  year={2019},\n  publisher={Preprints}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Neural differentiation dynamics controlled by multiple feedback loops in a comprehensive molecular interaction network.\n  \n  \n  \n\n\n  \n  Iwasaki, T.; Takiguchi, R.; Hiraiwa, T.; Yamada, T. G; Yamazaki, K.; Hiroi, N. F;  and Funahashi, A.\n\n\n  \n\n\n\n  Processes, 8(2): 166.  2020.\n  \n\n\n\n
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@article{iwasaki2020neural,\n  title={Neural differentiation dynamics controlled by multiple feedback loops in a comprehensive molecular interaction network},\n  author={Iwasaki, Tsuyoshi and Takiguchi, Ryo and Hiraiwa, Takumi and Yamada, Takahiro G and Yamazaki, Kazuto and Hiroi, Noriko F and Funahashi, Akira},\n  journal={Processes},\n  volume={8},\n  number={2},\n  pages={166},\n  year={2020},\n  publisher={Multidisciplinary Digital Publishing Institute}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Identification of a master transcription factor and a regulatory mechanism for desiccation tolerance in the anhydrobiotic cell line Pv11.\n  \n  \n  \n\n\n  \n  Yamada, T. G; Hiki, Y.; Hiroi, N. F; Shagimardanova, E.; Gusev, O.; Cornette, R.; Kikawada, T.;  and Funahashi, A.\n\n\n  \n\n\n\n  PloS one, 15(3): e0230218.  2020.\n  \n\n\n\n
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@article{yamada2020identification,\n  title={Identification of a master transcription factor and a regulatory mechanism for desiccation tolerance in the anhydrobiotic cell line Pv11},\n  author={Yamada, Takahiro G and Hiki, Yusuke and Hiroi, Noriko F and Shagimardanova, Elena and Gusev, Oleg and Cornette, Richard and Kikawada, Takahiro and Funahashi, Akira},\n  journal={PloS one},\n  volume={15},\n  number={3},\n  pages={e0230218},\n  year={2020},\n  publisher={Public Library of Science San Francisco, CA USA}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Neural differentiation dynamics controlled by multiple feedback loop motifs in a comprehensive molecular interaction network.\n  \n  \n  \n\n\n  \n  Hiroi, N.; Iwasaki, T; Takiguchi, R; Hiraiwa, T; Yamada, T.; Yamazaki, K;  and Funahashi, A\n\n\n  \n\n\n\n  .  2019.\n  \n\n\n\n
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@article{hiroi2019neural,\n  title={Neural differentiation dynamics controlled by multiple feedback loop motifs in a comprehensive molecular interaction network},\n  author={Hiroi, NF and Iwasaki, T and Takiguchi, R and Hiraiwa, T and Yamada, TG and Yamazaki, K and Funahashi, A},\n  year={2019}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.\n  \n  \n  \n\n\n  \n  Ostaszewski, M.; Mazein, A.; Gillespie, M. E; Kuperstein, I.; Niarakis, A.; Hermjakob, H.; Pico, A. R; Willighagen, E. L; Evelo, C. T; Hasenauer, J.;  and others\n\n\n  \n\n\n\n  Scientific data, 7(1): 1–4.  2020.\n  \n\n\n\n
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@article{ostaszewski2020covid,\n  title={COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms},\n  author={Ostaszewski, Marek and Mazein, Alexander and Gillespie, Marc E and Kuperstein, Inna and Niarakis, Anna and Hermjakob, Henning and Pico, Alexander R and Willighagen, Egon L and Evelo, Chris T and Hasenauer, Jan and others},\n  journal={Scientific data},\n  volume={7},\n  number={1},\n  pages={1--4},\n  year={2020},\n  publisher={Nature Publishing Group}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Coarse grain parallelization and acceleration of biochemical ODE simulation using GPGPU.\n  \n  \n  \n\n\n  \n  Nakamura, K.; Sumiyoshi, K.; Hiroi, N.;  and Funahashi, A.\n\n\n  \n\n\n\n  IEICE Proceedings Series, 1(29).  2012.\n  \n\n\n\n
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@article{nakamura2012coarse,\n  title={Coarse grain parallelization and acceleration of biochemical ODE simulation using GPGPU},\n  author={Nakamura, Kazushige and Sumiyoshi, Kei and Hiroi, Noriko and Funahashi, Akira},\n  journal={IEICE Proceedings Series},\n  volume={1},\n  number={29},\n  year={2012},\n  publisher={The Institute of Electronics, Information and Communication Engineers}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms.\n  \n  \n  \n\n\n  \n  Ostaszewski, M.; Mazein, A.; Gillespie, M. E; Kuperstein, I.; Niarakis, A.; Hermjakob, H.; Pico, A. R; Willighagen, E. L; Evelo, C. T; Hasenauer, J.;  and others\n\n\n  \n\n\n\n  Scientific data, 7(1): 1–1.  2020.\n  \n\n\n\n
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@article{ostaszewski2020author,\n  title={Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms},\n  author={Ostaszewski, Marek and Mazein, Alexander and Gillespie, Marc E and Kuperstein, Inna and Niarakis, Anna and Hermjakob, Henning and Pico, Alexander R and Willighagen, Egon L and Evelo, Chris T and Hasenauer, Jan and others},\n  journal={Scientific data},\n  volume={7},\n  number={1},\n  pages={1--1},\n  year={2020},\n  publisher={Nature Publishing Group}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  SBML Level 3: an extensible format for the exchange and reuse of biological models.\n  \n  \n  \n\n\n  \n  Keating, S. M; Waltemath, D.; König, M.; Zhang, F.; Dräger, A.; Chaouiya, C.; Bergmann, F. T; Finney, A.; Gillespie, C. S; Helikar, T.;  and others\n\n\n  \n\n\n\n  Molecular Systems Biology, 16(8): e9110.  2020.\n  \n\n\n\n
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@article{keating2020sbml,\n  title={SBML Level 3: an extensible format for the exchange and reuse of biological models},\n  author={Keating, Sarah M and Waltemath, Dagmar and K{\\"o}nig, Matthias and Zhang, Fengkai and Dr{\\"a}ger, Andreas and Chaouiya, Claudine and Bergmann, Frank T and Finney, Andrew and Gillespie, Colin S and Helikar, Tom{\\'a}{\\v{s}} and others},\n  journal={Molecular Systems Biology},\n  volume={16},\n  number={8},\n  pages={e9110},\n  year={2020}\n}\n
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\n       \n      incollection\n      \n        \n        (4)\n        \n      \n    
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\n  \n\n  \n  \n  \n  \n  \n  Kinetics of dimension-restricted conditions.\n  \n  \n  \n\n\n  \n  Hiroi, N.;  and Funahashi, A.\n\n\n  \n\n\n\n  In Introduction to Systems Biology, pages 261–281. Humana Press,  2007.\n  \n\n\n\n
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@incollection{hiroi2007kinetics,\n  title={Kinetics of dimension-restricted conditions},\n  author={Hiroi, Noriko and Funahashi, Akira},\n  booktitle={Introduction to Systems Biology},\n  pages={261--281},\n  year={2007},\n  publisher={Humana Press}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  CellDesigner: a graphical biological network editor and workbench interfacing simulator.\n  \n  \n  \n\n\n  \n  Funahashi, A.; Morohashi, M.; Matsuoka, Y.; Jouraku, A.;  and Kitano, H.\n\n\n  \n\n\n\n  In Introduction to Systems Biology, pages 422–434. Humana Press,  2007.\n  \n\n\n\n
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@incollection{funahashi2007celldesigner,\n  title={CellDesigner: a graphical biological network editor and workbench interfacing simulator},\n  author={Funahashi, Akira and Morohashi, Mineo and Matsuoka, Yukiko and Jouraku, Akiya and Kitano, Hiroaki},\n  booktitle={Introduction to Systems Biology},\n  pages={422--434},\n  year={2007},\n  publisher={Humana Press}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  SBML models and MathSBML.\n  \n  \n  \n\n\n  \n  Shapiro, B. E; Finney, A.; Hucka, M.; Bornstein, B.; Funahashi, A.; Jouraku, A.; Keating, S. M; Le Novère, N.; Matthews, J.;  and Schilstra, M. J\n\n\n  \n\n\n\n  In Introduction to Systems Biology, pages 395–421. Humana Press,  2007.\n  \n\n\n\n
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@incollection{shapiro2007sbml,\n  title={SBML models and MathSBML},\n  author={Shapiro, Bruce E and Finney, Andrew and Hucka, Michael and Bornstein, Benjamin and Funahashi, Akira and Jouraku, Akiya and Keating, Sarah M and Le Nov{\\`e}re, Nicolas and Matthews, Joanne and Schilstra, Maria J},\n  booktitle={Introduction to Systems Biology},\n  pages={395--421},\n  year={2007},\n  publisher={Humana Press}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Modeling and simulation using CellDesigner.\n  \n  \n  \n\n\n  \n  Matsuoka, Y.; Funahashi, A.; Ghosh, S.;  and Kitano, H.\n\n\n  \n\n\n\n  In Transcription Factor Regulatory Networks, pages 121–145. Humana Press, New York, NY,  2014.\n  \n\n\n\n
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@incollection{matsuoka2014modeling,\n  title={Modeling and simulation using CellDesigner},\n  author={Matsuoka, Yukiko and Funahashi, Akira and Ghosh, Samik and Kitano, Hiroaki},\n  booktitle={Transcription Factor Regulatory Networks},\n  pages={121--145},\n  year={2014},\n  publisher={Humana Press, New York, NY}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  L-turn routing: An adaptive routing in irregular networks.\n  \n  \n  \n\n\n  \n  Koibuchi, M.; Funahashi, A.; Jouraku, A.;  and Amano, H.\n\n\n  \n\n\n\n  In International Conference on Parallel Processing, 2001., pages 383–392,  2001. IEEE\n  \n\n\n\n
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@inproceedings{koibuchi2001turn,\n  title={L-turn routing: An adaptive routing in irregular networks},\n  author={Koibuchi, Michihiro and Funahashi, Akira and Jouraku, Akiya and Amano, Hideharu},\n  booktitle={International Conference on Parallel Processing, 2001.},\n  pages={383--392},\n  year={2001},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Routing algorithms based on 2D turn model for irregular networks.\n  \n  \n  \n\n\n  \n  Jouraku, A.; Koibuchi, M.; Amano, H.;  and Funahashi, A.\n\n\n  \n\n\n\n  In Proceedings International Symposium on Parallel Architectures, Algorithms and Networks. I-SPAN'02, pages 289–294,  2002. IEEE\n  \n\n\n\n
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@inproceedings{jouraku2002routing,\n  title={Routing algorithms based on 2D turn model for irregular networks},\n  author={Jouraku, Akiya and Koibuchi, Michihiro and Amano, Hideharu and Funahashi, Akira},\n  booktitle={Proceedings International Symposium on Parallel Architectures, Algorithms and Networks. I-SPAN'02},\n  pages={289--294},\n  year={2002},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method.\n  \n  \n  \n\n\n  \n  Yoshimi, M.; Iwaoka, Y.; Nishikawa, Y.; Kojima, T.; Osana, Y.; Funahashi, A.; Hiroi, N.; Shibata, Y.; Iwanaga, N.; Yamada, H.;  and others\n\n\n  \n\n\n\n  In 2007 International Conference on Field Programmable Logic and Applications, pages 254–259,  2007. IEEE\n  \n\n\n\n
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@inproceedings{yoshimi2007fpga,\n  title={FPGA implementation of a data-driven stochastic biochemical simulator with the next reaction method},\n  author={Yoshimi, Masato and Iwaoka, Yow and Nishikawa, Yuri and Kojima, Toshinori and Osana, Yasunori and Funahashi, Akira and Hiroi, Noriko and Shibata, Yuichiro and Iwanaga, Naoki and Yamada, Hideki and others},\n  booktitle={2007 International Conference on Field Programmable Logic and Applications},\n  pages={254--259},\n  year={2007},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Converting KEGG pathway database to SBML.\n  \n  \n  \n\n\n  \n  Funahashi, A.; Jouraku, A.;  and Kitano, H.\n\n\n  \n\n\n\n  In 8th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004),  2004. \n  \n\n\n\n
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@inproceedings{funahashi2004converting,\n  title={Converting KEGG pathway database to SBML},\n  author={Funahashi, Akira and Jouraku, Akiya and Kitano, Hiroaki},\n  booktitle={8th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2004)},\n  year={2004}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  The impact of output selection function on adaptive routing.\n  \n  \n  \n\n\n  \n  Funahashi, A.\n\n\n  \n\n\n\n  In Proc. International Conference on Computers And Their Applications, March 2001,  2001. \n  \n\n\n\n
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@inproceedings{funahashi2001impact,\n  title={The impact of output selection function on adaptive routing},\n  author={Funahashi, Akira},\n  booktitle={Proc. International Conference on Computers And Their Applications, March 2001},\n  year={2001}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  CellDesigner: a modeling tool for biochemical networks.\n  \n  \n  \n\n\n  \n  Funahashi, A.; Matsuoka, Y.; Jouraku, A.; Kitano, H.;  and Kikuchi, N.\n\n\n  \n\n\n\n  In Proceedings of the 2006 Winter Simulation Conference, pages 1707–1712,  2006. IEEE\n  \n\n\n\n
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@inproceedings{funahashi2006celldesigner,\n  title={CellDesigner: a modeling tool for biochemical networks},\n  author={Funahashi, Akira and Matsuoka, Yukiko and Jouraku, Akiya and Kitano, Hiroaki and Kikuchi, Norihiro},\n  booktitle={Proceedings of the 2006 Winter Simulation Conference},\n  pages={1707--1712},\n  year={2006},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Performance evaluation of an FPGA-based biochemical simulator ReCSiP.\n  \n  \n  \n\n\n  \n  Amano, H; Kitano, N; Iwanaga, N; Shibata, Y; Hiroi, N; Funahashi, A.; Nishikawa, Y; Kojima, T; Iwaoka, Y; Yoshimi, M;  and others\n\n\n  \n\n\n\n  In 2006 International Conference on Field Programmable Logic and Applications, pages 1–6,  2006. IEEE\n  \n\n\n\n
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@inproceedings{amano2006performance,\n  title={Performance evaluation of an FPGA-based biochemical simulator ReCSiP},\n  author={Amano, H and Kitano, N and Iwanaga, N and Shibata, Y and Hiroi, N and Funahashi, Akira and Nishikawa, Y and Kojima, T and Iwaoka, Y and Yoshimi, M and others},\n  booktitle={2006 International Conference on Field Programmable Logic and Applications},\n  pages={1--6},\n  year={2006},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  The design of scalable stochastic biochemical simulator on FPGA.\n  \n  \n  \n\n\n  \n  Yoshimi, M.; Osana, Y.; Iwaoka, Y.; Funahashi, A.; Hiroi, N.; Shibata, Y.; Iwanaga, N.; Kitano, H.;  and Amano, H.\n\n\n  \n\n\n\n  In Proceedings. 2005 IEEE International Conference on Field-Programmable Technology, 2005., pages 339–340,  2005. IEEE\n  \n\n\n\n
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@inproceedings{yoshimi2005design,\n  title={The design of scalable stochastic biochemical simulator on FPGA},\n  author={Yoshimi, Masato and Osana, Yasunori and Iwaoka, Yow and Funahashi, Akira and Hiroi, Noriko and Shibata, Yuichiro and Iwanaga, Naoki and Kitano, Hiroaki and Amano, Hideharu},\n  booktitle={Proceedings. 2005 IEEE International Conference on Field-Programmable Technology, 2005.},\n  pages={339--340},\n  year={2005},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA.\n  \n  \n  \n\n\n  \n  Iwanaga, N.; Shibata, Y.; Yoshimi, M.; Osana, Y.; Iwaoka, Y.; Fukushima, T.; Amano, H.; Funahashi, A.; Hiroi, N.; Kitano, H.;  and others\n\n\n  \n\n\n\n  In International Conference on Field Programmable Logic and Applications, 2005., pages 666–669,  2005. IEEE\n  \n\n\n\n
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@inproceedings{iwanaga2005efficient,\n  title={Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA},\n  author={Iwanaga, Naoki and Shibata, Yuichiro and Yoshimi, Masato and Osana, Yasunori and Iwaoka, Yow and Fukushima, Tomonori and Amano, Hideharu and Funahashi, Akira and Hiroi, Noriko and Kitano, Hiroaki and others},\n  booktitle={International Conference on Field Programmable Logic and Applications, 2005.},\n  pages={666--669},\n  year={2005},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  An FPGA-based, multi-model simulation method for biochemical systems.\n  \n  \n  \n\n\n  \n  Osana, Y.; Fukushima, T.; Yoshimi, M.; Iwaoka, Y.; Funahashi, A.; Hiroi, N.; Shibata, Y.; Kitano, H.;  and Amano, H.\n\n\n  \n\n\n\n  In 19th IEEE International Parallel and Distributed Processing Symposium, pages 4–pp,  2005. IEEE\n  \n\n\n\n
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@inproceedings{osana2005fpga,\n  title={An FPGA-based, multi-model simulation method for biochemical systems},\n  author={Osana, Yasunori and Fukushima, Tomonori and Yoshimi, Masato and Iwaoka, Yow and Funahashi, Akira and Hiroi, Noriko and Shibata, Yuichiro and Kitano, Hiroaki and Amano, Hideharu},\n  booktitle={19th IEEE International Parallel and Distributed Processing Symposium},\n  pages={4--pp},\n  year={2005},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  A torus assignment for an interconnection network recursive diagonal torus.\n  \n  \n  \n\n\n  \n  Fan, Q.; Yang, Y.; Funahashi, A.;  and Amano, H.\n\n\n  \n\n\n\n  In Proceedings Fourth International Symposium on Parallel Architectures, Algorithms, and Networks (I-SPAN'99), pages 74–79,  1999. IEEE\n  \n\n\n\n
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@inproceedings{fan1999torus,\n  title={A torus assignment for an interconnection network recursive diagonal torus},\n  author={Fan, Qin and Yang, Yulu and Funahashi, Akira and Amano, Hideharu},\n  booktitle={Proceedings Fourth International Symposium on Parallel Architectures, Algorithms, and Networks (I-SPAN'99)},\n  pages={74--79},\n  year={1999},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  An FPGA implementation of high throughput stochastic simulator for large-scale biochemical systems.\n  \n  \n  \n\n\n  \n  Yoshimi, M.; Osana, Y.; Iwaoka, Y.; Nishikawa, Y.; Kojima, T.; Funahashi, A.; Hiroi, N.; Shibata, Y.; Iwanaga, N.; Kitano, H.;  and others\n\n\n  \n\n\n\n  In 2006 International Conference on Field Programmable Logic and Applications, pages 1–6,  2006. IEEE\n  \n\n\n\n
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@inproceedings{yoshimi2006fpga,\n  title={An FPGA implementation of high throughput stochastic simulator for large-scale biochemical systems},\n  author={Yoshimi, Masato and Osana, Yasunori and Iwaoka, Yow and Nishikawa, Yuri and Kojima, Toshinori and Funahashi, Akira and Hiroi, Noriko and Shibata, Yuichiro and Iwanaga, Naoki and Kitano, Hiroaki and others},\n  booktitle={2006 International Conference on Field Programmable Logic and Applications},\n  pages={1--6},\n  year={2006},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  A combining technique of rate law functions for a cost-effective reconfigurable biological simulator.\n  \n  \n  \n\n\n  \n  Yamada, H.; Iwanaga, N.; Shibata, Y.; Osana, Y.; Yoshimi, M.; Iwaoka, Y.; Nishikawa, Y.; Kojima, T.; Amano, H.; Funahashi, A.;  and others\n\n\n  \n\n\n\n  In 2007 International Conference on Field Programmable Logic and Applications, pages 808–811,  2007. IEEE\n  \n\n\n\n
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@inproceedings{yamada2007combining,\n  title={A combining technique of rate law functions for a cost-effective reconfigurable biological simulator},\n  author={Yamada, Hideki and Iwanaga, Naoki and Shibata, Yuichiro and Osana, Yasunori and Yoshimi, Masato and Iwaoka, Yow and Nishikawa, Yuri and Kojima, Toshinori and Amano, Hideharu and Funahashi, Akira and others},\n  booktitle={2007 International Conference on Field Programmable Logic and Applications},\n  pages={808--811},\n  year={2007},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Practical implementation of a network-based stochastic biochemical simulation system on an FPGA.\n  \n  \n  \n\n\n  \n  Yoshimi, M.; Nishikawa, Y.; Osana, Y.; Funahashi, A.; Shibata, Y.; Yamada, H.; Hiroi, N.; Kitano, H.;  and Amano, H.\n\n\n  \n\n\n\n  In 2008 International Conference on Field Programmable Logic and Applications, pages 663–666,  2008. IEEE\n  \n\n\n\n
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@inproceedings{yoshimi2008practical,\n  title={Practical implementation of a network-based stochastic biochemical simulation system on an FPGA},\n  author={Yoshimi, Masato and Nishikawa, Yuri and Osana, Yasunori and Funahashi, Akira and Shibata, Yuichiro and Yamada, Hideki and Hiroi, Noriko and Kitano, Hiroaki and Amano, Hideharu},\n  booktitle={2008 International Conference on Field Programmable Logic and Applications},\n  pages={663--666},\n  year={2008},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Adaptive routing on the recursive Diagonal torus.\n  \n  \n  \n\n\n  \n  Funahashi, A.; Hanawa, T.; Kudoh, T;  and Amano, H.\n\n\n  \n\n\n\n  In International Symposium on High Performance Computing, pages 171–182,  1997. Springer, Berlin, Heidelberg\n  \n\n\n\n
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@inproceedings{funahashi1997adaptive,\n  title={Adaptive routing on the recursive Diagonal torus},\n  author={Funahashi, Akira and Hanawa, Toshihiro and Kudoh, T and Amano, Hideharu},\n  booktitle={International Symposium on High Performance Computing},\n  pages={171--182},\n  year={1997},\n  organization={Springer, Berlin, Heidelberg}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Pipeline scheduling with input port constraints for an FPGA-Based biochemical simulator.\n  \n  \n  \n\n\n  \n  Ishimori, T.; Yamada, H.; Shibata, Y.; Osana, Y.; Yoshimi, M.; Nishikawa, Y.; Amano, H.; Funahashi, A.; Hiroi, N.;  and Oguri, K.\n\n\n  \n\n\n\n  In International Workshop on Applied Reconfigurable Computing, pages 368–373,  2009. Springer, Berlin, Heidelberg\n  \n\n\n\n
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@inproceedings{ishimori2009pipeline,\n  title={Pipeline scheduling with input port constraints for an FPGA-Based biochemical simulator},\n  author={Ishimori, Tomoya and Yamada, Hideki and Shibata, Yuichiro and Osana, Yasunori and Yoshimi, Masato and Nishikawa, Yuri and Amano, Hideharu and Funahashi, Akira and Hiroi, Noriko and Oguri, Kiyoshi},\n  booktitle={International Workshop on Applied Reconfigurable Computing},\n  pages={368--373},\n  year={2009},\n  organization={Springer, Berlin, Heidelberg}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  MMLRU selection function: An output selection function on adaptive routing.\n  \n  \n  \n\n\n  \n  Koibuchi, M.\n\n\n  \n\n\n\n  In Proc. ISCA 14th International Conference on Parallel and Distributed Computing Systems, Aug. 2001,  2001. \n  \n\n\n\n
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@inproceedings{koibuchi2001mmlru,\n  title={MMLRU selection function: An output selection function on adaptive routing},\n  author={Koibuchi, Michihiro},\n  booktitle={Proc. ISCA 14th International Conference on Parallel and Distributed Computing Systems, Aug. 2001},\n  year={2001}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  A framework for ODE-based multimodel biochemical simulations on an FPGAs.\n  \n  \n  \n\n\n  \n  Osana, Y.; Fukushima, T.; Yoshimi, M.; Iwaoka, Y.; Amano, H; Funahashi, A; Hiroi, N; Kitano, H; Shibata, Y;  and Iwanaga, N\n\n\n  \n\n\n\n  In International Conference on Field Programmable Logic and Applications, 2005., pages 574–577,  2005. IEEE\n  \n\n\n\n
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@inproceedings{osana2005framework,\n  title={A framework for ODE-based multimodel biochemical simulations on an FPGAs},\n  author={Osana, Yasunori and Fukushima, Tomonori and Yoshimi, Masato and Iwaoka, Yow and Amano, H and Funahashi, A and Hiroi, N and Kitano, H and Shibata, Y and Iwanaga, N},\n  booktitle={International Conference on Field Programmable Logic and Applications, 2005.},\n  pages={574--577},\n  year={2005},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  A framework for implementing a network-based stochastic biochemical simulator on an fpga.\n  \n  \n  \n\n\n  \n  Yoshimi, M.; Nishikawa, Y.; Kojima, T.; Osana, Y.; Funahashi, A.; Hiroi, N.; Shibata, Y.; Yamada, H.; Kitano, H.;  and Amano, H.\n\n\n  \n\n\n\n  In 2007 International Conference on Field-Programmable Technology, pages 193–200,  2007. IEEE\n  \n\n\n\n
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@inproceedings{yoshimi2007framework,\n  title={A framework for implementing a network-based stochastic biochemical simulator on an fpga},\n  author={Yoshimi, Masato and Nishikawa, Yuri and Kojima, Toshinori and Osana, Yasunori and Funahashi, Akira and Hiroi, Noriko and Shibata, Yuichiro and Yamada, Hideki and Kitano, Hiroaki and Amano, Hideharu},\n  booktitle={2007 International Conference on Field-Programmable Technology},\n  pages={193--200},\n  year={2007},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  A modular approach to heterogeneous biochemical model simulation on an FPGA.\n  \n  \n  \n\n\n  \n  Yamada, H.; Osana, Y.; Ishimori, T.; Ooya, T.; Yoshimi, M.; Nishikawa, Y.; Funahashi, A.; Hiroi, N.; Amano, H.; Shibata, Y.;  and others\n\n\n  \n\n\n\n  In 2009 International Conference on Reconfigurable Computing and FPGAs, pages 125–130,  2009. IEEE\n  \n\n\n\n
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@inproceedings{yamada2009modular,\n  title={A modular approach to heterogeneous biochemical model simulation on an FPGA},\n  author={Yamada, Hideki and Osana, Yasunori and Ishimori, Tomoya and Ooya, Tomonori and Yoshimi, Masato and Nishikawa, Yuri and Funahashi, Akira and Hiroi, Noriko and Amano, Hideharu and Shibata, Yuichiro and others},\n  booktitle={2009 International Conference on Reconfigurable Computing and FPGAs},\n  pages={125--130},\n  year={2009},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Configuring area and performance: Empirical evaluation on an FPGA-based biochemical simulator.\n  \n  \n  \n\n\n  \n  Ooya, T.; Yamada, H.; Ishimori, T.; Shibata, Y.; Osana, Y.; Oguri, K.; Yoshimi, M.; Nishikawa, Y.; Funahashi, A.; Hiroi, N.;  and others\n\n\n  \n\n\n\n  In 2009 International Conference on Field Programmable Logic and Applications, pages 679–682,  2009. IEEE\n  \n\n\n\n
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@inproceedings{ooya2009configuring,\n  title={Configuring area and performance: Empirical evaluation on an FPGA-based biochemical simulator},\n  author={Ooya, Tomonori and Yamada, Hideki and Ishimori, Tomoya and Shibata, Yuichiro and Osana, Yasunori and Oguri, Kiyoshi and Yoshimi, Masato and Nishikawa, Yuri and Funahashi, Akira and Hiroi, Noriko and others},\n  booktitle={2009 International Conference on Field Programmable Logic and Applications},\n  pages={679--682},\n  year={2009},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Dynamic modes in biological systems: Why should a biologist care?.\n  \n  \n  \n\n\n  \n  Nordling, T. E.; Hiroi, N.;  and Funahashi, A.\n\n\n  \n\n\n\n  In The 8th International Conference on Systems Biology (ICSB-2007), Long Beach (USA),  2007. \n  \n\n\n\n
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@inproceedings{nordling2007dynamic,\n  title={Dynamic modes in biological systems: Why should a biologist care?},\n  author={Nordling, Torbj{\\"o}rn EM and Hiroi, Noriko and Funahashi, Akira},\n  booktitle={The 8th International Conference on Systems Biology (ICSB-2007), Long Beach (USA)},\n  year={2007}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  A datapath classification method for FPGA-based scientific application accelerator systems.\n  \n  \n  \n\n\n  \n  Ogawa, Y.; Ooya, T.; Osana, Y.; Yoshimi, M.; Nishikawa, Y.; Funahashi, A.; Hiroi, N.; Amano, H.; Shibata, Y.;  and Oguri, K.\n\n\n  \n\n\n\n  In 2010 International Conference on Field-Programmable Technology, pages 441–444,  2010. IEEE\n  \n\n\n\n
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@inproceedings{ogawa2010datapath,\n  title={A datapath classification method for FPGA-based scientific application accelerator systems},\n  author={Ogawa, Yui and Ooya, Tomonori and Osana, Yasunori and Yoshimi, Masato and Nishikawa, Yuri and Funahashi, Akira and Hiroi, Noriko and Amano, Hideharu and Shibata, Yuichiro and Oguri, Kiyoshi},\n  booktitle={2010 International Conference on Field-Programmable Technology},\n  pages={441--444},\n  year={2010},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  In vivo oriented modeling with consideration of intracellular crowding.\n  \n  \n  \n\n\n  \n  Hiroi, N.; Iba, K.; Tabira, A.; Okuhara, T.; Kubojima, T.; Hiraiwa, T.; Kobayashi, T. J; Oka, K.;  and Funahashi, A.\n\n\n  \n\n\n\n  In 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), pages 2716–2719,  2013. IEEE\n  \n\n\n\n
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@inproceedings{hiroi2013vivo,\n  title={In vivo oriented modeling with consideration of intracellular crowding},\n  author={Hiroi, Noriko and Iba, Keisuke and Tabira, Akito and Okuhara, Takahiro and Kubojima, Takeshi and Hiraiwa, Takumi and Kobayashi, Tetsuya J and Oka, Kotaro and Funahashi, Akira},\n  booktitle={2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)},\n  pages={2716--2719},\n  year={2013},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Fabrication method to a high resolution control in the space of cell culturing environment with microfluidic system.\n  \n  \n  \n\n\n  \n  Hiraiwa, T.; Kimura, T.; Takenaka, Y.; Tanamoto, R.; Ota, H.; Kimura, H.; Taguchi, Y.; Miki, N.; Matsumoto, Y.; Oka, K.;  and others\n\n\n  \n\n\n\n  In 2014 IEEE 27th International Conference on Micro Electro Mechanical Systems (MEMS), pages 264–267,  2014. IEEE\n  \n\n\n\n
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@inproceedings{hiraiwa2014fabrication,\n  title={Fabrication method to a high resolution control in the space of cell culturing environment with microfluidic system},\n  author={Hiraiwa, Takumi and Kimura, Tadamasa and Takenaka, Yuma and Tanamoto, Ryo and Ota, Hiroki and Kimura, Hiroshi and Taguchi, Yoshihiro and Miki, Norihisa and Matsumoto, Yoshinori and Oka, Kotaro and others},\n  booktitle={2014 IEEE 27th International Conference on Micro Electro Mechanical Systems (MEMS)},\n  pages={264--267},\n  year={2014},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Power reduction techniques for dynamically reconfigurable processor arrays.\n  \n  \n  \n\n\n  \n  Nishimura, T.; Hirai, K.; Saito, Y.; Nakamura, T.; Hasegawa, Y.; Tsutsusmi, S.; Tunbunheng, V.;  and Amano, H.\n\n\n  \n\n\n\n  In 2008 International Conference on Field Programmable Logic and Applications, pages 305–310,  2008. IEEE\n  \n\n\n\n
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@inproceedings{nishimura2008power,\n  title={Power reduction techniques for dynamically reconfigurable processor arrays},\n  author={Nishimura, Takashi and Hirai, Keiichiro and Saito, Yoshiki and Nakamura, Takuro and Hasegawa, Yohei and Tsutsusmi, Shinichi and Tunbunheng, Vasutan and Amano, Hideharu},\n  booktitle={2008 International Conference on Field Programmable Logic and Applications},\n  pages={305--310},\n  year={2008},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  An I/O mechanism on a dynamically reconfigurable processor-which should be moved: data or configuration?.\n  \n  \n  \n\n\n  \n  Amano, H.; Abe, S.; Deguchi, K.;  and Hasegawa, Y.\n\n\n  \n\n\n\n  In International Conference on Field Programmable Logic and Applications, 2005., pages 347–352,  2005. IEEE\n  \n\n\n\n
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@inproceedings{amano2005mechanism,\n  title={An I/O mechanism on a dynamically reconfigurable processor-which should be moved: data or configuration?},\n  author={Amano, Hideharu and Abe, Shohei and Deguchi, Katsuaki and Hasegawa, Yohei},\n  booktitle={International Conference on Field Programmable Logic and Applications, 2005.},\n  pages={347--352},\n  year={2005},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Requirement of spatiotemporal resolution for imaging intracellular temperature distribution.\n  \n  \n  \n\n\n  \n  Hiroi, N.; Tanimoto, R.; Ii, K.; Ozeki, M.; Mashimo, K.;  and Funahashi, A.\n\n\n  \n\n\n\n  In Biomedical Imaging and Sensing Conference, volume 10251, pages 102510Q,  2017. International Society for Optics and Photonics\n  \n\n\n\n
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@inproceedings{hiroi2017requirement,\n  title={Requirement of spatiotemporal resolution for imaging intracellular temperature distribution},\n  author={Hiroi, Noriko and Tanimoto, Ryuichi and Ii, Kaito and Ozeki, Mitsunori and Mashimo, Kota and Funahashi, Akira},\n  booktitle={Biomedical Imaging and Sensing Conference},\n  volume={10251},\n  pages={102510Q},\n  year={2017},\n  organization={International Society for Optics and Photonics}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Routing Algorithms Based on 2D Turn Model for Irregular Networks.\n  \n  \n  \n\n\n  \n  Amano, A. J. M. K. H.;  and Funahashi, A.\n\n\n  \n\n\n\n  In 2002 International Symposium on Parallel Architectures, Algorithms, and Networks, pages 289,  2002. IEEE\n  \n\n\n\n
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@inproceedings{amano2002routing,\n  title={Routing Algorithms Based on 2D Turn Model for Irregular Networks},\n  author={Amano, Akiya Jouraku Michihiro Koibuchi Hideharu and Funahashi, Akira},\n  booktitle={2002 International Symposium on Parallel Architectures, Algorithms, and Networks},\n  pages={289},\n  year={2002},\n  organization={IEEE}\n}\n\n
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\n  \n\n  \n  \n  \n  \n  \n  Introduction to systems biology.\n  \n  \n  \n\n\n  \n  Choi, S.\n\n\n  \n\n\n\n   2007.\n  \n\n\n\n
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@misc{choi2007introduction,\n  title={Introduction to systems biology},\n  author={Choi, Sangdun},\n  year={2007},\n  publisher={Humana press New Jersey:}\n}\n\n
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