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Contents


Advertizement

    ADVERTIZEMENT 1


    2nd Biothermology Workshop will be held on December 25th and 26, 2017, at Pharmacology Department, the University of Tokyo, Japan.
    Venue
    The details will be announced soon.


    ADVERTIZEMENT 2


    The eBook "Quantitative Biology: Dynamics of living systems", edited by Viji M Draviam, Tetsuya J. Kobayashi, Akira Funahashi, Chun-Biu Li, Douglas B Murray, Hiroaki Takagi, Ziya Kalay, Rinshi S Kasai, Jason Edward Shoemaker, Akatsuki Kimura, Naoki A Irie, and Noriko Hiroi has been compiled and is now available online.

    pdf format
    epub(for iBook) format


    Acknowledgement

    ACKNOWLEDGEMENT



    1. Thank you to all the speakers and the participants of International Workshop on Quantitative Biology 2017 on April 14th, Fri., and 15th Sat. 2017, at Keio University, Yokohama, Japan.

    The 4th International workshop on Quantitative Biology (IWQB-2017) had been held to discuss about the following topics;
    Cellular decisions are frequently made in a dynamic manner. This temporal complexity added to spatial intricacies makes it difficult to interpret cell biology data alone. Systematic advances in technologies for high-throughput imaging, image organisation and analysis are enabling new quantitative studies of dynamic cellular processes.
    This s workshop is organized on conceptual and technological advances in Quantitative Cell Biology: (i) emerging technologies of image acquisition and analysis and (ii) Dynamic decisions at the sub-cellular level.

    Topics included:
    - Cell division mechanisms
    - Cytoskeletal regulation
    - Emerging microscopy tools
    - Advances in Image analysis methods
    - Novel fluorescent probes
    - Automation of big-data-experiments

    The talks of the conference were in English to help the international audience that would be attending the conference.

    We also had poster sessions as well and so we encourage students and young researchers to participate at the conference.

    2. Thank you for the organizers who
    Invited me for giving a talk titled "Requirement of spatiotemporal resolution for imaging intracellular temperature distribution."
    (doi:10.1117/12.2275012) at
    SPIE Technologies and Applications of Structured Light
    Dates: 18 - 21 April 2017
    Location: Yokohama, Japan
    Authors: Noriko Hiroi, Ryuichi Tanimoto, Kaito Ii, Mitsunori Ozeki, Kota Mashimo, and Akira Funahashi.

    Special thanks to Dr. Tatsuki Tahara, Prof. Osamu Matoba for the kind invitation to the conference.

    3. Thank you for the organizers who
    Invited me for giving a talk titled "The foundation of Biothermology from the point of view of nano/microscale thermophysical properties of biopolymers" at
    EMN Europe Meetings, on Quantum
    Dates: June 18-22, 2017
    Location: Vienna, Austria
    Authors: Noriko Hiroi, Takayuki Nakamura, Takaya Saito, and Akira Funahashi.

    Special thanks to Ms. Julia Schindelar(Natural History Musium, Austria) and Dr. Martin Loose(IST, Austria) for kind hosting and had a time for discussion for our common scientific interest.


    4. Thank you to all the speakers and the participants of "EMERGING RESEARCH CHALLENGES IN BIOLOGY"
    Dates: Jun 23rd, 2017
    Location: Queen Mary University of London, Graduate Center.
    Speakers
    Yutaka Matsubayashi (King's College London) "A moving source of matrix components is essential for de novo basement membrane formation."
    Tetsuya J. Kobayashi (the University of Tokyo) "Quantitative characterization of mammalian early embryogenesis: Progress report."
    Noriko Hiroi (Keio University) "Asymmetric division, cell migration, and differentiation control in microfluidic devices."
    David Dang (Queen Mary University of London) "Automated analysis of 3-Dimensional movements of the mitotic spindle in human epithelial cells."

    Special thanks to Dr. Viji M. Draviam (Queen Mary University of London, UK) for the kind invitation and hospitality.


    Biothermology Workshop
      Many thanks to Presenters, attendees and organisers for your big effort and contribution to the workshop!

      Biothermology Workshop held at Okazaki Confernce Center, on December 10th sat. and 11th sun., 2016.


      Registration form is here workshop poster (pdf)

      The list of the organisers
      Toshio Usui(Kyoto University)
      Koki Okabe(University of Tokyo)
      Yasuhiro Kamei(National Insutitute of Basic Biology)
      Takeshi Kitano(Kumamoto University)
      Hiroyuki Kimura(Shizuoka University)
      Shigeki Kiyonaka(Kyoto University)
      Reiko Sakaguchi(Kyoto University)
      Yoshikatsu Sato(Nagoya University)
      Yuichi Togashi(Hiroshima University)
      Masahiro Nakano(Osaka University)
      Takahiro Hamada(University of Tokyo)
      Noriko Hiroi(Keio University)
      Tsuyoshi Furumoto(Ryukoku University)

      The list of the speakers
      Makoto Tominaga(Okazaki Institute for Integrative Bioscience) *The leader of "Integrated understanding of biological phenomena with temperature as a key theme (Thermal Biology)" research project.
      Masato Umeda(Kyoto University)
      Yasuko Inaba(Miyazaki University)
      Koki Okabe(University of Toyko)
      Kotaro Oyama(Tokyo Jikei University)
      Atsushi Kuhara(Konan University)
      Miwa Onishi(Kobe University)
      Atsushi Nagano(Ryukoku University)
      Soya Shinkai(Hiroshima University)
      Shoichi Toyabe(Tohoku University)
      Takahiro Sagawa(University of Tokyo)
      Noriko Hiroi(Keio University)
      Akihiko Ishijima(Osaka University)
      Masahiro Nakano(Osaka University)
      Reiko Sakaguchi(Kyoto University)
      Yasuhiro Kamei(National Insutitute of Basic Biology)
      Tatsuki Tahara(Kansai University)
      Yoshihiro Taguchi(Keio University)
      Takahiro Hamada(University of Tokyo)
      Tsuyoshi Hurumoto(Ryukoku University)
      Hiroyuki Kimura(Shizuoka University)
      Haruyuki Atomi(Kyoto University)
      Yoshifumi Yamaguchi(University of Tokyo)
      Tadashi Nomura(Kyoto Prefectural University of Medicine)

      Biothermology International Meeting
        Thanks to Presenters for their big contribution to this meeting!

        1st Biothermology International Meeting


        was held on Jun 21st, 2016, at Parc 55 SanFrancisco Hotel's meeting room (Fillmore, at 4th Floor), from 19:00 to 22:00.
        This event is acceppted as an ancillary meeting by ISSCR2016 CEO, Nancy Witty on May 10th.

        epub or pdf program file is here.

        Target Audience

        Biophysics people who are interested in differentiation process of stem cells, especially who explore new indexes to investigate, including temperature of cells/tissues or intracellular spaces and organelles are expected. Engineering people who develop sensors/detectors of temperature and so on may find collaborating opportunities at the meeting. Medical/pharmaceutical researchers may have interest the quantitative indexes for their applications.

        Aim of this Meeting

        This meeting focuses mainly about Biothermology, which has just launched in Japan by researchers of Biophysics and Cell/Molecular Biology.
        Our plan is to bring together the interesting target and new technology at one place and try to find solutions for biological problems, for example, how to analyse the intracellular dynamics of temperature to estimate the impact of it on neural differentiation etc.

        Presenter and Moderator
        Noriko Hiroi (Keio Univ. Japan)
        "Environment gives forces, cells produce energy; how their combinations affect the fate of a cell?"
        Abstract: Analysing intracellular temperature is a nowadays topic under the development of detection technologies. The heterogeneity of temperature at each subdomain of a cell shocked researchers because the discovered difference of temperature between subdomains was unexpectedly large to explain based on the assumption that a cell is a water vacuole. I will start this talk by sharing basic knowledge about Biothermology and will show how far this knowledge may bring us to the exit of 105 gap issue. The discussion among the presenters should be expanded to the effect of the temperature at cellular differentiation and its combination with forces, including shear stress and tension between a cell and its environment. My talk will close by presenting the probable effect of the combination of force and temperature distribution on cellular differentiation.

        Presenters

        1.Hiroki Ota (UC Berkeley, USA)
        "Highly deformable devices and systems using liquid metal for healthcare and medical application"
        Abstract: Mechanically deformable devices and sensors enable conformal coverage of electronic systems on curved and soft surfaces. Sensors utilizing liquids confined in soft templates as the sensing component present the ideal platform for such applications, as liquids are inherently more deformable than solids. However, to date, liquid-based devices have been limited to metal lines based on a single liquid component given the difficulty in the fabrication and system integration. Here we demonstrate a platform for the fabrication of liquid- devices and 3-D liquid-state system, presenting an important advancement for expanding liquid electronics. The device architecture and fabrication scheme we present are generic for different sensing liquids, enabling demonstration of sensors responsive to different stimuli. As a proof of concept, we demonstrate temperature, humidity and oxygen sensors by using different ionic liquids, exhibiting high sensitivity with excellent mechanical deformability arising from the inherent property of the liquid phase and 3-D liquid system having active and passive liquid devices by 3-D printer.

        2.Hirohide Saito (CiRA, Japan)
        "MicroRNA switches that identify and isolate target cells in high-resolution"

        3.Shinji Masui (CiRA, Japan)
        "Regulation of cellular identity by a transcriptional mechanism responding to physical force."
        Abstract: Multicellular organisms are maintained by homeostasis of cellular differentiation states. However, many are still unclear about the mechanisms how these states are maintained. Previously we have shown that transcription factors maintaining expression of cell type-specific genes inhibit reprogramming to pluripotency. Taking advantage of this mechanism, in this study we performed screening for genes maintaining cell states using reprogramming system in neural progenitor cells. As a result, we found that β-actin, specifically its monomer, maintained cell type-specific gene expression through suppressing the activity of a transcription factor Srf. We further show that suppressing the β-actin-Srf pathway contributes to the maintenance of cell states in multiple cell types of diverse lineages. We discuss a possible mechanism how Srf regulates cell type-specific genes through their regulatory elements.

        4.Alex Dann (Stanford Univ, USA)
        "Fluorescent molecular tension sensors measure force transmission by single integrins in living cells."
        Abstract: Integrins mediate cell adhesion to the extracellular matrix and enable the construction of complex, multicellular organisms, yet fundamental aspects of integrin-based adhesion remain poorly understood. Notably, recent estimates of the load experienced by integrins span two orders of magnitude, a discrepancy arising from limitations inherent to existing techniques. Here we use FRET-based molecular tension sensors (MTSs) to directly measure the distribution of forces experienced by individual integrins in living cells. We find that a large fraction of integrins bear modest loads of 1-3 pN, while subpopulations bearing higher loads are enriched within adhesions. Further, our data indicate that the synergy site, a secondary binding site thought to reinforce the fibronectinα5β1-integrin bond, affects biochemical recognition but not overall force generation in our system. We suggest that a substantial population of integrins exerting forces well below their load-bearing capacities can provide cells and tissues with physical resiliency.

        References

        [1]Tanimoto R, Hiraiwa T, Nakai Y, Shindo Y, Oka K, Hiroi N, and Funahashi A.
        "Detection of Temperature Difference in Neuronal Cells" Scientific Reports(2016)Vol.6, Article number 22071, doi: 10.1038/srep22071
        [2]Hiroki Ota,Kevin Chen,Yongjing Lin,Daisuke Kiriya,Hiroshi Shiraki,Zhibin Yu,Tae-Jun Ha & Ali Javey
        "Highly deformable liquid-state heterojunction sensors" Nature Communications(2014)Vol. 5, Article number 5032, doi:10.1038/ncomms6032
        [3]Liliana Wroblewska, Tasuku Kitada, Kei Endo, Velia Siciliano, Breanna Stillo, Hirohide Saito, and Ron Weiss.
        "Mammalian synthetic circuits with RNA binding proteins for RNA-only delivery" Nature Biotechnology(2015)Vol.33(8):839-41. doi: 10.1038/nbt.3301.
        [4]Kitazawa K, Hikichi T, Nakamura T, Mitsunaga K, Tanaka A, Nakamura M, Yamakawa T, Furukawa S, Takasaka M, Goshima N, Watanabe A, Okita K, Kawasaki S, Ueno M, Kinoshita S, Masui S. "OVOL2 Maintains the Transcriptional Program of Human Corneal Epithelium by Suppressing Epithelial-to-Mesenchymal Transition" Cell Rep.(2016)Vol.15(6),pp1359-68. Link
        [5]Nakayama KH, Surya VN, Gole M, Walker TW, Yang W, Lai ES, Ostrowski MA, Fuller GG, Dunn AR, Huang NF. "Nanoscale Patterning of Extracellular Matrix Alters Endothelial Function under Shear Stress" Nano Letters. (2016) 16 (1), pp 410-419. doi: 10.1021/acs.nanolett.5b040280 Link

        This meeting is sponsored by IKEDA SCIENTIFIC Co., Ltd, and Keio University. We deeply thank to Dr. Jason Shoemaker (Univ. Pittsburgh, USA) for his kind helps to organize this meeting.


        PUBLICATION
          Publication

          Publication

          Papers

          1. Tanimoto R, Hiraiwa T, Nakai Y, Shindo Y, Oka K, Hiroi N, and Funahashi A.
            "Detection of Temperature Difference in Neuronal Cells" Scientific Reports(2016)Vol.6, Article number 22071, doi: 10.1038/srep22071
          2. Tamura N, Simon JEL, Nayak A, Shenoy R, Hiroi N, Boilot V, Funahashi A, and Draviam VM.
            "A proteomic study of mitotic phase-specific interactors of EB1 reveals a role for SXIP-mediated protein interactions in anaphase onset" Biology Open(2015)Vol.4, pp. 155 - 169.
          3. Sumiyoshi K, Hirata K, Hiroi N, and Funahashi A.
            "Acceleration of discrete stochastic biochemical simulation using GPGPU" Front. Physiol.(2015) Vol.6, doi: 10.3389/fphys.2015.00042.
          4. 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 VM, Oku H.
            "High-speed microscopy with an electrical tunable lens to image the dynamics of in vivo molecular complexes" AIP Rev. Sci. Instrum.(2015) Vol.86, doi: 10.1063/1.4905330.
          5. Hiroi N, Swat M, and Funahashi A.
            "Assessing uncertainty in model parameters based on sparse and noisy experimental data" Front. Physiol.(2014) Vol.5, doi: 10.3389/fphys.2014.00128.
          6. Corrigan AM, Shrestha RL, Zulkipli I, Hiroi N, Liu Y, Tamura N, Yang B, Patel J, Funahashi A, Donald, A and Draviam VM.
            "Automated tracking of mitotic spindle pole positions show that LGN is required for spindle rotation but not orientation maintenance" Cell Cycle July, 2013 accepted.
          7. Keller R, Dörr A, Tabira A, Funahashi A, Ziller MJ, Adams R, Rodriguez N, Le Novère N, Hiroi N, Planatscher H, Zell A, and Drager A.
            "The systems biology simulation core algorithm" BMC Systems Biology Jun, 2013 accepted.
          8. Hiromu Takizawa, Kazushige Nakamura, Akito Tabira, Yoichi Chikahara, Tatsuhiro Matsui, Noriko Hiroi, and Akira Funahashi.
            "LibSBMLSim: A reference inplementation of fully functional SBML simulator" Bioinformatics First published online April 5, 2013. doi: 10.1093/bioinformatics/btt157
          9. Hiromu Takizawa, Noriko Hiroi, and Akira Funahashi.
            "Mathematical Modeling of Sustainable Synaptogenesis by Repetitive Stimuli Suggests Signaling Mechanisms" PLoS One Dec 20th 2012 published on line http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0051000.
          10. Noriko Hiroi, Takahiro Okuhara, Takeshi Kubojima, Keisuke Iba, Akito Tabira, Shuji Yamashita, Yasunori Okada, Tetsuya J. Kobayashi, and Akira Funahashi.
            "Physiological inracellular crowdedness is defined by perimeter to area ratio of subcellular compartments" Frontiers in Fractal Physiology July 2012 accepted. http://www.frontiersin.org/Fractal_Physiology/10.3389/fphys.2012.00293/abstract
          11. Noriko Hiroi, Michael Klann, Keisuke Iba, Pablo deHeras Ciechomski, Shuji Yamashita, Akito Tabira, Takahiro Okuhara, Takeshi Kubojima, Yasunori Okada, Kotaro Oka, Robin Mange, Michael Unger, Akira Funahashi, and Heinz Koeppl.
            "From Microscopy Data to in silico Environments for in vivo Oriented Simulations" EURASIP Journal on Bioinformatics and Systems Biology May. 2012. http://bsb.eurasipjournals.com/content/2012/1/7/abstract
          12. Noriko Hiroi, James Lu, Keisuke Iba, Akito Tabira, Shuji Yamashita, Yasunori Okada, Flamm Christoph, Kotaro Oka, Gottfried Koehler, Akira Funahashi.
            "Physiological environment induce quick response - slow exhaustion reactions" Frontiers in Systems Physiology August. 2011. http://www.frontiersin.org/systems_physiology/10.3389/fphys.2011.00050/abstract
          13. Funahashi, A., Matsuoka, Y., Jouraku, A., Takizawa, H., Hiroi, N., Ghosh, S., Kikuchi, N., and Kitano, H.
            "CellDesigner, Amodeling tool of biochemical networks: the design and implementation" SICE Journal. 49(8). August. 2010.
          14. Yamada, H., Ogawa, Y., Ooya, T., Ishimori, T., Osana, Y., Yoshimi, M., Nishikawa, Y., Funahashi, A., Hiroi, N., Amano, H., Shibata, Y., and Oguri, K.
            "Automatic Pipeline Construction Focused on Similarity of Rate Law Functions for an FPGA-based Biochemical Simulator" IPSJ Journal (accepted). 2010.
          15. Iwaoka, Y., Osana, Y., Yoshimi, M., Nishikawa, Y., Kojima, T., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "A Biochemical Model Compiler for Simulations on an FPGA (In Japanese)." IEICE Transactions on Information and Systems. 2008.
          16. Yoshimi, M., Nishikawa, Y., Osana, Y. Funahashi, A., Hiroi, N., Shibata, Y., Yamada, H., Kitano, H., and Amano, H..
            "Design and Evaluation of an FPGA-Based Stochasitc Biochemical Simulator for High-Throughput Execution (In Japanese)." IPSJ Transactions on Advanced Computing System. 2008.
          17. Nordling, T., Hiroi, N., Funahashi, A., and Kitano, H..
            "Deduction of intracellular sub-systems from a topological description of the network." Molecular Biosystems. 3 (8). August2007. pp.523-529.http://pubs.rsc.org/en/Content/ArticleLanding/2007/MB/b702142a
          18. Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "ReCSiP: An FPGA-Based Biochemical Simulator (English translation of Osana et.al, on Trans. IEICE J89-D)." Electronics and Communications in Japan (Part II: Electronics). 90 (7). July2007. pp.1--10.
          19. Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H., and Amano, H..
            "FPGA-Based Stochastic Biochemical Simulator (In Japanese)." IPSJ Transactions on Advanced Computing System (In Japanese). 48 (SIG 3 (ACS 17)). February2007. pp.45--58.
          20. Hiroi, N., Funahashi, A., and Kitano, H..
            "Analysis for Dimension-Restricted Kinetics with Bacterial Endonuclease Movement." WSEAS Transactions on Biology and Biomedicine. 3 (1). January2006. pp.1--6. http://www.wseas.us/e-library/conferences/2005athens/bio/papers
          21. Hiroi, N., Funahashi, A., and Kitano, H..
            "Comparative studies of suppression of malignant cancer cell phenotype by antisense oligo DNA and small interfering RNA." Cancer Gene Therapy. 13 (1). January2006. pp.7--12. http://www.nature.com/cgt/journal/v13/n1/abs/7700869a.html
          22. Hiroi, N., Ito, T., Yamamoto, H. Ochiya, T., Jinno, S., and Okayama, H.
            "Mammalian Rcd1 is a novel transcriptional cofactor that mediates retinoic acid-induced cell differentiation." EMBO J. 21 (19). 2002. pp.5235--5244. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC129043/?tool=pubmed
          23. Hiroi, N., Maruta, H., and Tanuma, S.
            "Fas-mediated apoptosis in Jurkat cells is suppressed in the pre-G2/M phase." Apoptosis. 4 (4). August1999. pp.255--261. http://www.springerlink.com/content/w954385w03668743/

          Books

          1. Ishimori, T., Yamada, H., Shibata, Y., Osana, Y., Yoshimi, M., Nishikawa, Y., Amano, H., Funahashi, A., Hiroi, N., and Oguri, K..
            "Pipeline Scheduling with Input Port Constraints for an FPGA-Based Biochemical Simulator (Chapter 43 of Reconfigurable Computing: Architectures, Tools and Applications, Lecture Notes in Computer Science)." Jurgen Becker, Roger Woods, Peter Athanas, and Fearghal Morgan. Springer Berlin / Heidelberg. ISBN: 978-3-642-00640-1. March2009.
          2. Hiroi, N. and Funahashi, A..
            "Kinetics of Dimension Restricted Condition (Chapter 14 of Introduction to Systems Biology)." Sangdun Choi. Humana Press, NJ USA. ISBN: 1-58829-706-3. July2007.
          3. Hiroi, N. and Maruta, H.
            "Apoptosis experimental protocol 2/2." (C)Shujunsha Co.Ltd.. ISBN: 4-87962-191-9. March1999.

          Talks, Classes

          1. Hiroi, N.
            "The foundation of Biothermology from the point of view of nano/microscale thermophysical properties of biopolymers." EMN Meeting on Quantum . Vienna, Austria. Jun, 2017
          2. Hiroi, N. Tanimoto, R., Ii, K., Ozeki, M., Mashimo, K., Funahashi, A.
            "Requirement of spatiotemporal resolution for imaging intracellular temperature distribution." SPIE Technologies and Applications of Structured Light . Yokohama, Japan. April, 2017
          3. Hiroi, N.
            "Anisotropy shaped by and for the Dynamic Distributoin of Heat." Japan q-bio week, Tokyo Symposium. Tokyo, Japan. Jan., 2016
          4. Hiroi, N.
            "How Temperature Distribution may change biological State." the 9th NIBB Bioimaging Forum. Okazaki, Japan. Jan., 2015
          5. Okuhara T, Kubojima T, Tanimoto R, Nakai Y, Hiroi N. , Funahashi A.
            "Spatial Entropy Extraction from Transmission Electron Microscopy Images for the Analyses of in vivo Environment." Quantitative Bioimaging. Paris, France. Jan., 2015
          6. Nakai Y, Hiroi N, Funahashi A
            "Development of high-speed 3D imaging system with electrically tunable lens." Quantitative Bioimaging. Paris, France. Jan., 2015
          7. Tanimoto R, Hiraiwa T, Shindo Y, Oka K, Funahashi A, Hiroi N.
            "Detection and functional Analyses of Temperature Distribution in neuronal Cells." Quantitative Bioimaging. Paris, France. Jan., 2015
          8. Nakai Y, Hiroi N, Funahashi A
            "Development of high-speed 3D imaging system with electrically tunable lens." EuBIAS 2015. Paris, France. Jan., 2015
          9. Hiroi, N.
            "Bioimage Informatics, the edge to open Quantitative view of Biology." International Workshop on Quantitative Biology 2014. Melbourne, Australia. Sep., 2014
          10. Hiroi, N.
            "Hurdles and solutions in automatic 3D tracking of comets." UK-JAPAN NETWORK for High Speed Microscopy in Cells. Cambridge, UK. May., 2014
          11. Tanimoto R, Hiroi N, Funahashi A, N.
            "Detection and Analyses of intracellular Distribution of Temperature." Winter q-bio. Hawai, USA. Feb., 2014
          12. Hiroi, N.
            "Robust Inhomogeneity to Time and Space in a Living System." Complex Dynamics and Networks. Tsuruoka, Japan. Nov., 2013
          13. Hiroi, N..
            "in vivo oriented modeling with consideration of intracellular crowding." IEEE Engineering in Medicine and Biology Society (EMBC'13). Osaka, Japan. July, 2013.
            *the acceptted conference paper is in the list with the same title.
          14. Hiroi, N..
            "Visualize the Thermo-Dynamicity during Neuronal Cell Differentiation." FluoroFest Workshop. Kyoto, Japan. Nov, 2012.
          15. Hiroi, N..
            "in vivo oriented modeling for basic biochemical reaction systems." FOSBE2012 Redox Systems Biology Workshop. Tsuruoka, Japan. Oct, 2012.
          16. Hiroi, N..
            "A collaborative project on human stress response." Janet Thornton 60th birthday symposium. Cambridge, UK. June2009.
          17. Hiroi, N.and Funahashi, A..
            "Deduction of elements for enzyme behaviors on DNA (In Japanese)." 8th conference of Nuclear Dynamics. Shizuoka, JPN. June2009.
          18. Hiroi, N., Funahashi, A., and Kitano, H..
            "Analysis for dimension restriction kinetics with bacterial endonuclease movement." the 2005 WSEAS International Conference on Cellular and Molecular Biology -- Biophysics and Bioengineering. Athens, Greece. July2006.
          19. Hiroi, N., Funahashi, A., and Kitano, H..
            "Kinetics for in vivo molecular diffusion." Systems Biology for Mammalian Cell 2006. Heidelberg, Germany. July2006.
          20. Hiroi, N.
            "Methods of Biological Experiments" September - January of 2014 - 2015, Keio University JPN
          21. Funahashi A, Hiroi, N.
            "Systems Biology" September - January of 2012 and 2015, Keio University JPN
          22. Ushiba J, Doi N, Funahashi A, Matsumoto M, Miyamoto K, Tashiro E, Hotta K, Matsubara T, Sato K, Hiroi, N, Horisawa K.
            "Topics in Biosciences and Informatics 2" April - July of 2012 and 2015, Keio University JPN
          23. Imoto M, Oka K, Sakakibara Y, Sato T, Ushiba J, Doi N, Funahashi A, Matsumoto M, Miyamoto K, Tashiro E, Hotta K, Matsubara T, Sato K, Hiroi, N.
            "Seminar in Biosciences and Informatics" April - March of 2012 and 2015, Keio University JPN
          24. Oka K, Sato T, Ushiba J, Funahashi A, Miyamoto K, Hotta K, Matsubara T, Yoshida, S, Hiroi, N.
            "Advanced Laboratory Course in Biosciences and Informatics" September - January of 2009-2015, Keio University JPN
          25. Imoto M, Oka K, Kasuga S, Sakakibara Y, Sato T, Ushiba J, Doi N, Funahashi A, Matsumoto M, Miyamoto K, Tashiro E, Hotta K, Matsubara T, Hiroi, N, Horisawa K.
            "Basic Laboratory Course in Biosciences" September - January of 2009-2015, Keio University JPN
          26. Imoto M, Oka K, Sakakibara Y, Sato T, Ushiba J, Doi N, Funahashi A, Matsumoto M, Miyamoto K, Tashiro E, Hotta K, Matsubara T, Hiroi, N.
            "Introduction to Biology Today" April - March of 2015, Keio University JPN
          27. Hiroi, N..
            "Introduction to Biology." April-August, 2013-2015, Keio University JPN
          28. Hiroi, N..
            "Biology, make-up lectures for students from abroad." Biology. April-March, 2009-2012, Keio University JPN
          29. Sakakibara, Y., Sato, K., Ushiba, J., Hiroi, N..
            "Bioprogramming 1" April-July of 2010-2011, Keio University JPN
          30. Saikawa Y, Chiba A, Nishikawa S, Hasegawa T, Hayase J, Hiroi N.
            "Laboratory in Science" September - January of 2009-2010, 2014, Keio Unversity JPN
          31. Hiroi, N..
            "Biochemistry" Basic science for Nursing. September-March of 1999-2001, Tokyo metropolitan public health nursing school JPN

          Conference Papers

          1. Hiroi, N.Tanamoto R, Ii K, Ozeki M, Mashimo K, and Funahashi A.
            "Requirement of Spatiotemporal resolution for imaging intracellular temperature distribution." SPIE Technologies and Applications of Structured Light , Yokohama, Japan. April, 2017.
          2. Hiraiwa, T., Kimura T, Takeneka Y, Tanamoto R, Ota H, Kimura H, Funahashi A, Taguchi Y, Miki N, Matsumoto Y, Oka K, Hiroi, N.
            "Fabrication method to grant high resolution control ion the space of cell culturing environment with microfluidic system." The 27th IEEE International Conference on Micro Eloctro Mechanical Systems(MEMS), San Francisco, USA. Jan, 2014.
          3. Hiroi, N., Iba, K., Tabira, A., Okuhara, T., Kubojima, T., Hiraiwa, T., Kobayashi, T.J., Oka, K. and Funahashi A.
            "in vivo oriented modeling with consideration of intracellular crowding." IEEE Engineering and Medicine and Biology Society (EMBC'13), Osaka, Japan. July, 2013 accepted.
          4. Nakamura, K., Sumiyoshi, K., Hiroi, N., Funahashi A.
            "Coarse grain parallelization and acceleration of biochemical ODE simulation using GPGPU." 2012 International Symposium on Nonlinear Theory and its Applications, Palma, Majorca, Spain. Oct 22nd to 26th, 2012
          5. Hiroi, N., Lu J, Iba K, Tabira A, Yamashita S, Okada Y, Flamm C, Funahashi A, and Koehler G.
            "A Study into the Crowdedness of Intracellular Environment: Estimation of Fractal Dimensionality and Anomalous Diffusion." Eighth International Workshop on Computational Systems Biology, Jun 6-8, 2011, Zurich, Switzerland, ISBN 978-952-15-2591-9
          6. Yui Ogawa, Tomonori Ooya, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano, Yuichiro Shibata and Kiyoshi Oguri.
            "A datapath classification method for FPGA-based scientific application accelerator systems" Field-Programmable Technology (FPT), 2010 International Conference on, Beijing, China, Dec. 2010(http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5681455). IEEE/IET Electronic Library (IEL), IBM Journal of Research and Development, VDE VERLAG Conference Proceedings 441 - 444
          7. Yamada H, Osana Y, Ishimori T, Ooya T, Yoshimi M, Nishikawa Y, Funahashi A, Hiroi, N., Amano H, Shibata Y and Oguri K..
            "A Modular Approach to Heterogeneous Biochemical Model Simulation on an FPGA." 2009 International Conference on ReConFigurable Computing and FPGAs December 9-11, 2009, Cancun, Mexico
          8. Tomonori OOYA, Hideki YAMADA, Tomoya ISHIMORI, Yuichiro SHIBATA, Yasunori OSANA, Masato YOSHIMI, Yuri NISHIKAWA, Hideharu AMANO, Akira FUNAHASHI, Hiroi, N., and Oguri, K..
            "Performance evaluation of an auto-generation algorithm of hardware modules for an FPGA-based general-purpose biochemical simulator." 2009 International Conference on ReConFigurable Computing and FPGAs. December 9-11, 2009, Cancun, Mexico
          9. T. Ooya, H. Yamada, T. Ishimori, Y. Shibata, Y. Osana, K. Oguri M. Yoshimi, Y. Nishikawa, A. Funahashi, Hiroi, N., H. Amano..
            "CONFIGURING AREA AND PERFORMANCE: EMPIRICAL EVALUATION ON AN FPGA-BASED BIOCHEMICAL SIMULATOR." 19th International Conference on Field Programmable Logic and Applications. Czech Republic, August 31-September 2, 2009.
          10. Yamada, H., Ishimori, T., Ooya, T. Shibata, Y., Osana, Y., Yoshimi, M., Nishikawa, Y., Amano, H., Funahashi, A., Hiroi, N., and Oguri, K..
            "Automatic Pipeline Construction Focused on Similarity of Rate Law Functions for an FPGA-based Biochemical Simulatior (In Japanese)." September2009.
          11. Yoshimi, M., Nishikawa, Y., Osana, Y., Funahashi, A., Hiroi, N., Shibata, Y., Yamada, H., Kitano, H., and Amano, H..
            "Practical Implementation of a Network-based Stochastic Biochemical Simulation System on an FPGA." The 18th International Conference on Field Programmable Logic and Applications(FPL'08). Heidelberg, Germany. September2008.
          12. Yamada, H., Iwanaga, N., Shibata, Y., Osana, Y., Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Amano, H., Funahashi, A., Hiroi, N., Kitano, H., and Oguri, K..
            "A Combining Tequnique of Rate Law Functions for a Cost-effective Reconfigurable Biological Simulator." The 17th International Conference on Field Programmable Logic and Applications(FPL'07). Amsterdam, Netherlands. August2007. pp.808--811.
          13. Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Osana, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Yamada, H., Kitano, H., and Amano, H..
            "FPGA Implementation of a data-driven stochastic biochemical simulator with the next reaction method." The 17th International Conference on Field Programmable Logic and Applications(FPL'07). Amsterdam, Netherlands. August2007. pp.254--259.
          14. Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H., and Amano, H..
            "A Hardware Accelerator for Biochemical Simulations." Winter Simulation Conference 2006. Monterey, USA. December2006.
          15. Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "An FPGA Implementation of High Throughput Stochastic Simulator for Large-Scale Biochemical Systems." Proceedings of 2006 International Conference on Field Programmable Logic and Applications. Madrid, Spain. August2006. pp.227-232.
          16. Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "Performance Evaluation of an FPGA-based Biochemical Simulator ReCSiP." Proceedings of 2006 International Conference on Field Programmable Logic and Applications. Madrid, Spain. August2006. pp.845--850.
          17. Hiroi, N., Funahashi, A., and Kitano, H..
            "Kinetics for in vivo molecular diffusion." Conference on Systems Biology of Mammalian Cells (SBMC 2006). Heidelberg, Germany. July2006. pp.11--12. http://sbmc06.de/
          18. Nishikawa, Y., Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "An Evaluation and Investigation of Dual-Thread Numerical Integration Mechanism for FPGA-based Biochemical Simulator ReCSiP." Coolchips IX. Yokohama, Japan. April2006. pp.195-197.
          19. Hiroi, N., Funahashi, A., and Kitano, H..
            "Two numerical model analysis for the movement of a restriction enzyme." Foundations of Systems Biology in Engineering (FOSBE 2005). Santa Barbara, USA. August2005. pp.263--266. http://www.fosbe.org/
          20. Hiroi, N., Funahashi, A., and Kitano, H..
            "Analysis for dimension restriction kinetics with bacterial endonuclease movement." The 2005 WSEAS International Conference on Cellular and Molecular Biology -- Biophysics and Bioengineering. Athens, Greece. July2005. pp.1--6. http://www.worldses.org/conferences/2005/greece/bio/index.html

          Reviews

          1. Noriko Hiroi, Viji Draviam, and Akira Funahashi.
            "Quantitative Biology: Dynamics of living systems." Frontiers in Systems Biology, 7, 196.
          2. Akira Funahashi and Noriko Hiroi.
            "Simulation technology and its application in systems biology." Folia Pharmacological Japonica, 147 (2), pp.101-106.

          Workshops

          1. Viji Draviam, and Akira Funahashi, and Noriko Hiroi, and Akatsuki Kimura and Tetsuya Kobayashi.
            "Meeting Report of the International Workshop on Quantitative Biology 2012: Mesoscopic and microscopic worlds meet." Frontiers in Systems Biology, http://www.frontiersin.org/Systems_Biology/10.3389/fphys.2012.00479/full International Workshop on Quantitative Biology 2012 was hold on Nov 22, 2012 Tokyo, Japan.
          2. Akira Funahashi, and Noriko Hiroi..
            "High-Speed & High Efficient automated experimental systems(In Japanese)." KLL Techno-mall. Dec 11, 2009 Tokyo, Japan.
          3. Funahashi, A. and Hiroi, N..
            "Quantitative analysis of nuclear crowdedness(In Japanese)." 8th conference of Nuclear Dynamics. June, 2009 Shizuoka, Japan.
          4. Ishimori, T., Yamada, H., Shibata, Y., Osana, Y., Yoshimi, M., Nishikawa, Y., Kojima, T., Amano, H., Funahashi, A., Hiroi, N., Kitano, H., and Oguri, K..
            "Pipeline Scheduling with Input Port Constraints for an FPGA-based Biochemical Simulator." Technical Committee on Reconfigurable Systems (RECONF). May2008. pp.113--118.
          5. Yamada, H., Iwanaga, N., Shibata, Y., Osana, Y., Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Amano, H., Funahashi, A., Hiroi, N., Kitano, H., and Oguri, K..
            "Automatic combining of rate law functions for an FPGA-based biochemical simulator ReCSiP." Technical Committee on Reconfigurable Systems (RECONF). May2007. pp.13--18.
          6. Kojima, T., Osana, Y., Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "Implementation and Evaluation of General-Purpose Host Interface on ReCSiP Board." FPGA/PLD Design Conference. January2007. pp.33--40.
          7. Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Osana, Y., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H., and Amano, H..
            "Empirical Analysis on Implementation of High-Speed Stochastic Biochemical Simulator on an FPGA." The 29th PARTHENON Workshop. December2006. pp.29--36.
          8. Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H., and Amano, H..
            "FPGA-based Stochastic Biochemical Simulator." Symposium on Advanced Computing Systems and Infrastructures(SACSIS2006). May2006. pp.151--158.
          9. Kojima, T., Osana, Y., Yoshimi, M., Nishikawa, Y., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "Implementation and Evaluation of General-Purpose Host Interface on ReCSiP Board." Technical Committee on Reconfigurable Systems (RECONF). May2006. pp.55--60.
          10. Nishikawa, Y., Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "A Performance Improvement Strategy for Numerical Integration on an FPGA-Based Biochemical Simulator ReCSiP." Technical Committee on Reconfigurable Systems (RECONF). Keio Univ, Yokohama. January2006. pp.53--58. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
          11. Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "Hardware-resource Utilization Analysis on an FPGA-Based Biochemical Simulator ReCSiP." Technical Committee on Reconfigurable Systems (RECONF). Keio Univ, Yokohama. January2006. pp.59--64. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
          12. Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "Stochastic Biochemical Simulator with a Data-transfer Network on an FPGA." Technical Committee on Reconfigurable Systems (RECONF). Keio Univ, Yokohama. January2006. pp.47--52. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
          13. Iwaoka, Y., Osana, Y., Yoshimi, M., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "A System Design of Accelerating Biochemical Simulations on Programmable Hardware." The 10th Forum on Software Platforms for Systems Biology. Boston, Massachusetts. October2005. http://www.sbml.org/workshops/tenth/index.html
          14. Iwaoka, Y., Osana, Y., Yoshimi, M., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "Building of the SBML System for an FPGA-based Biochemical Simulator (In Japanese)." Technical Committee on Reconfigurable Systems (RECONF). Hiroshima. September2005. pp.61--66. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
          15. Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "The Control Mechanism of an FPGA-Based Biochemical Simulator ReCSiP (In Japanese)." Technical Committee on Reconfigurable Systems (RECONF). Hiroshima. September2005. pp.55--60. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
          16. Yoshimi, M., Osana, Y., Iwaoka, Y., Fukushima, T., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "Design of a Heap-tree Based Scalable Stochastic Biochemical Simulator on an FPGA (In Japanese)." Technical Committee on Reconfigurable Systems (RECONF). Kyoto Univ, Kyoto. May2005. pp.37--42. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
          17. Osana, Y., Iwaoka, Y., Fukushima, T., Yoshimi, M., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H., and Amano, H..
            "Implementation and Evaluation of Numerical Integrators on ReCSiP (In Japanese)." Technical Committee on Reconfigurable Systems (RECONF). Kyoto Univ, Kyoto. May2005. pp.49--54. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
          18. Iwanaga, N., Shibata, Y., Yoshimi, M., Osana, Y., Iwaoka, Y., Fukushima, T., Amano, H., Funahashi, A., Hiroi, N., Kitano, H., and Oguri, K..
            "Scheduling of Rate Law Functions for an FPGA-based Biochemical Simulator (In Japanese)." Technical Committee on Reconfigurable Systems (RECONF). Kyoto Univ, Kyoto. May2005. pp.43--48. http://www.ieice.org/ken/program/index.php?instsoc=IEICE-D&tgid=RECONF&year=&region=&schkey=&sch1=1&pskey=&ps1=1&ps2=1&ps3=1&ps4=1&ps5=1&search_mode=&pnum=0&psize=2&layout=&lang=eng
          19. Iwaoka, Y., Osana, Y., Fukushima, T., Yoshimi, M., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "Design of cellular simulation platform for SBML model (In Japanese)." IEICE Technical Report [CPSY/RECONF]. Yokohama, Japan. January2005. pp.63--68. http://www.ieice.org/ken/program/index.php?mode=program&tgs_regid=3c536169dc1a42e123983394bef1dda8c941d2af527b4dcfa59b3886ad81b6b3&tgid=CPSY&layout=html1&lang=eng
          20. Osana, Y., Fukushima, T., Yoshimi, M., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "Design of the SBML Processor for an FPGA-based Biochemical Simulator (In Japanese)." IPSJ Technical Report [SHINING 2005]. Naha, Japan. January2005. pp.13--18. http://www.hpcc.jp/sigarc/Program/arc153.txt
          21. Hiroi, N., Odaira, N., Inoue, T., Shiokawa, D., Maruta, H., and Tanuma, S..
            "Suppression mechanism of Fas-mediated apoptosis in M phase Jurkat cells (In Japanese)." 70th. Conference of The Japanese Biochemical Society. Kanazawa, JPN. October1997.
          22. Hiroi, N., Maruta, H., and Tanuma, S..
            "Apoptosis suppression of Jurkat cells during M phase (In Japanese)." Tokyo, JPN. July1997.
          23. Hiroi, N., Maruta, H., and Tanuma, S..
            "The sensitivity for Fas-mediated apoptosis of Jurkat cells during M phase (In Japanese)." 117th. Conference of The Parmaceutical Society of Japan. Tokyo, JPN. March1997.
          24. Maruta, H., Harada, Y., Hiroi, N., Tanimoto, Y., and Tanuma, S..
            "Apoptosis suppression depending on the cell cycle mechanism (In Japanese)." 68th. Conference of The Japanese Biochemical Society. Sendai, JPN. July1995.
          25. Maruta, H., Harada, Y., Hiroi, N., Tanimoto, Y., and Tanuma, S..
            "Apoptosis suppression of HL-60 cells depending on the cell cycle mechanism (In Japanese)." 4th. Apoptosis Meeting. July1995.

          Posters

          1. Kei Sumiyoshi, Noriko Hiroi, and Akira Funahashi.
            "Acceleration of Stochastic Biochemical Simulation by GPU." International Workshop on Quantitative Biology 2012 , p27, Tokyo, Japan, Nov. 2012
          2. Kazushige Nakamura, Kazuki Hirata, Noriko Hiroi, and Akira Funahashi.
            "Design and Implementation of GPU accelerated biochemical ODE simulator." International Workshop on Quantitative Biology 2012 , p28, Tokyo, Japan, Nov. 2012
          3. Tatsuhiro Matsui, Noriko Hiroi, and Akira Funahashi.
            "Implementation of spatial model simulatior and its SBML support." International Workshop on Quantitative Biology 2012 , p29, Tokyo, Japan, Nov. 2012
          4. Takaaki Chishiki, Noriko Hiroi, and Akira Funahashi.
            "Bio-Flow layout algorithm: an auto-layout algorithm of biochemical networks." International Workshop on Quantitative Biology 2012, p30, Tokyo, Japan, Nov. 2012
          5. Takahiro Okuhara, Akito Tabira, Noriko Hiroi, and Akira Funahashi.
            "Understanding the characteristics of intracellular reaction space from the point of view of bio-molecular organization." International Workshop on Quantitative Biology 2012, p31, Tokyo, Japan, Nov. 2012
          6. Takumi Hiraiwa, Noriko Hiroi, and Akira Funahashi.
            "Fabrication of a microfluidic device for long term cell culturing with spatiotemporal fluid-control system." International Workshop on Quantitative Biology 2012 , p32, Tokyo, Japan, Nov. 2012
          7. Tadamasa Kimura, Noriko Hiroi, and Akira Funahashi.
            "Development of microfluidics systems for Flexible and Automated Biological Experiments." International Workshop on Quantitative Biology 2012 , p33, Tokyo, Japan, Nov. 2012
          8. Mitsunari Kobayashi, Noriko Hiroi, and Akira Funahashi.
            "Establishment of Compression Algorithm aimed for efficient analysis on Biological sequences." International Workshop on Quantitative Biology 2012, p34, Tokyo, Japan, Nov. 2012
          9. Takeshi Kubojima, Takumi Hiraiwa, Mitsunori Ozeki, Noriko Hiroi, and Akira Funahashi.
            "Thermo-Dynamicity affects neuronal cellular function." International Workshop on Quantitative Biology 2012, p50, Tokyo, Japan, Nov. 2012
          10. Noriko Hiroi, Takahiro Okuhara, Takeshi Kubojima, Keisuke Iba, Akito Tabira, Shuji Yamashita, Yasunori Okada, James Lu, Michael Klann, Heinz Koeppl, Christoph Flamm, Gotfried Koehler, Kotaro Oka, Tetsuya J. Kobayashi and Akira Funahashi.
            "in vivo oriented modeling with consideration of the effect of inracellular crowding." International Workshop on Quantitative Biology 2012, p53, Tokyo, Japan, Nov. 2012
          11. Kazushige Nakamura, Kazuki Hirata, Noriko Hiroi, and Akira Funahashi.
            "Design and Implementation of GPU accelerated biochemical ODE simulator." 5th Annual meeting of Japanese Society for Quantitative Biology, Japan, Nov. 2012
          12. Ryo Takiguchi, Takumi Hiraiwa, Tadamasa Kimura, Noriko Hiroi, Akira Funahashi, Tsuyoshi Iwasaki, and Kazuto Yamazaki.
            "Mathematical modeling of the molecular mechanism of neuronal stem cell to neuron.(in Japanese)" 5th Annual meeting of Japanese Society for Quantitative Biology, Tokyo, Japan, Nov. 2012
          13. Tsuyoshi Iwasaki, Kazuto Yamazaki, Ryo Takiguchi, Takumi Hiraiwa, Tadamasa Kimura, Noriko Hiroi, and Akira Funahashi.
            "Building application platform of mathematical models of neuronal differentiation from pluripotent stem cells." 5th Annual meeting of Japanese Society for Quantitative Biology, Tokyo, Japan, Nov. 2012
          14. Takumi Hiraiwa, Noriko Hiroi, and Akira Funahashi.
            "Fabrication of a microfluidic device for long term cell culturing with spatiotemporal fluid-control system.(in Japanese)" 5th Annual meeting of Japanese Society for Quantitative Biology, Tokyo, Japan, Nov. 2012
          15. Takeshi Kubojima, Takumi Hiraiwa, Mitsunori Ozeki, Noriko Hiroi, and Akira Funahashi.
            "Impact of Thermo-Dynamicity at the Functions of Neuronal networks." 5th Annual meeting of Japanese Society for Quantitative Biology, Tokyo, Japan, Nov. 2012
          16. Takeshi Kubojima, Keisuke Iba, Noriko Hiroi, Tetsuya Kobayashi and Akira Funahashi.
            "Numerical analyses for the general representation of molecular behaviors in vivo (in Japanese)." 5th Annual meeting of Japanese Society for Quantitative Biology, Tokyo, Japan, Nov. 2012
          17. Takahiro Okuhara, Noriko Hiroi, and Akira Funahashi.
            "Analyses of construction mechanisms of in vivo reaction space with macromolecules (in Japanese)." 5th Annual meeting of Japanese Society for Quantitative Biology, Tokyo, Japan, Nov. 2012
          18. Takaaki Chishiki, Noriko Hiroi, and Akira Funahashi.
            "Bio-Flow layout algorithm: an auto-layout algorithm of biochemical networks (in Japanese)." 5th Annual meeting of Japanese Society for Quantitative Biology, Tokyo, Japan, Nov. 2012
          19. Akira Funahashi, Yukiko Matsuoka, Noriko Hiroi, Samik Ghosh, Norihiro Kikuchi, and Hiroaki Kitano.
            "CellDesigner: the design and the development of a biochemical network editor." The 5th Annual meeting of Japanese Society for Quantitative Biology, Tokyo, Japan, Nov. 2012
          20. Yoichi Tikahara, Kazushige Nakamura, Noriko Hiroi, and Akira Funahashi.
            "Acceleration of biochemical network simulator with variable step-size numerical integration(in Japanese)." The 5th Annual meeting of Japanese Society for Quantitative Biology, Tokyo, Japan, Nov. 2012
          21. Tadamasa Kimura, Noriko Hiroi, and Akira Funahashi.
            "Development of microfluidics systems for Flexible and Automated Biological Experiments." The 5th Annual meeting of Japanese Society for Quantitative Biology, Tokyo, Japan, Nov. 2012
          22. Noriko Hiroi, Hiromu Takizawa, and Akira Funahashi.
            "Repetitive stimuli bring about Sustainable Synaptogenesis." International Conference on Systems Biology 2012, Toronto, Canada, Aug. 2012
          23. Yui Ogawa, Tomonori Ooya, Yasunori Osana, Masato Yoshimi, Yuri Nishikawa, Akira Funahashi, Noriko Hiroi, Hideharu Amano, Yuichiro Shibata and Kiyoshi Oguri.
            "A datapath classification method for FPGA-based scientific application accelerator systems" FPT 2010, Beijing, China, Dec. 2010(http://tiger.cs.tsinghua.edu.cn/fpt2010/).
          24. Kazuki Hirata, Nobuyuki Ohta, Akiya Jouraku, Noriko Hiroi, Akira Funahashi, and Yoshitaka Suetsugu..
            "Design and Implementation of high-performance sequence analysis environment using MULTI-GPUs." The 33rd Annual Meeting of the Molecular Biology Society of Japan. Dec 2010 Kobe, Japan.
          25. Akira Funahashi, Yukiko Matsuoka, Hiromu Takizawa, Noriko Hiroi, Samik Ghosh, Norihiro Kikuchi, and Hiroaki Kitano.
            "CellDesigner: the design and the development of a biochemical network editor." The 3rd annual mtg of q-bio.jp,Tokyo, Japan, Nov. 2010
          26. Takumi Hiraiwa, Noriko Hiroi, Yoshinori Matsumoto, Norihisa Miki, Kotaro Oka and Akira Funahashi.
            "Generic design for long-span cell culture devices."The 3rd annual mtg of q-bio.jp, Tokyo, Japan,Nov. 2010
          27. Noriko Hiroi, Keisuke Iba, Akito Tabira, and Akira Funahashi.
            "Effector Values Estimation of Intracellular Constrained Level."The 3rd annual mtg of q-bio.jp, Tokyo, Japan, Nov. 2010
          28. Kazushige Nakamura, Tetsuya J Kobayashi, Noriko Hiroi, and Akira Funahashi.
            "Development of a biochemical network simulator by GPGPU." The 3rd annual mtg of q-bio.jp,Tokyo, Japan, Nov. 2010
          29. Sakuma Suguru, Ryousuke Yamazaki, Yusuke Niino, Noriko Hiroi, Akira Funahashi and Kotaro Oka.
            "Mathematical analysis of movement mechanism of nerve growth cone"The 3rd annual mtg of q-bio.jp,Tokyo, Japan, Nov. 2010
          30. Hiromu Takizawa, Noriko Hiroi, and Akira Funahashi.
            "Insulin Network Analysis with CellDesigner Plugin." ICSB 2010, Oct. Edinburgh, UK.
          31. Sakuma Suguru, Ryousuke Yamazaki, Yusuke Niino, Noriko Hiroi, Akira Funahashi and Kotaro Oka.
            "Mathematical analysis of movement mechanism of nerve growth cone" ICSB 2010, Oct. Edinburgh, UK.
          32. Takumi Hiraiwa, Keisuke Iba, Suguru Sakuma, Hiromu Takizawa, Noriko Hiroi, and Akira Funahashi.
            "The Development of an Automated Experimental Systems using MicrofluidicDevices for Use of Molecular and Cellular Biological Experimnents." ICSB 2010, Oct. Edinburgh, UK.
          33. Keisuke Iba, Akito Tabira, Noriko Hiroi, and Akira Funahashi.
            "Spatial constrained level of a mammalian cell estimated by Diffusion Coefficient and Static structure". ICSB 2010, Oct. Edinburgh, UK.
          34. Akito Tabira, Noriko Hiroi, and Akira Funahashi..
            "Analysis of intracellular crowdedness by FRAP." The 19th annual meeting of Japanese Bioimaging Society. Sep 9 - 11, 2010 Kanagawa, Japan.
          35. Nobuyuki Ohta, Tetsuya Kobayashi Noriko Hiroi, and Akira Funahashi..
            "Design and Implementation of Software infrastructure towards Bioimage Informatics." The 19th annual meeting of Japanese Bioimaging Society. Sep 9 - 11, 2010 Kanagawa, Japan.
          36. Akito Tabira, Keisuke Iba, Noriko Hiroi, and Akira Funahashi..
            "Indexes of spatial constrained level provide a perspective of intra-nuclear environment of eukaryotic cells." The 9th conference of Nuclear Dynamics. May 27 - 29, 2010 Shizuoka, Japan.
          37. Akito Tabira, Noriko Hiroi, and Akira Funahashi..
            "Analysis of intracellular crowdedness by FRAP." The 2nd Annual Meeting of the Japanese Society for Quantitative Biology. Jan 9 - 11, 2010 Osaka, Japan.
          38. Keisuke Iba, Noriko Hiroi, and Akira Funahashi..
            "Stochastic model simulation of intracellular molecular behaviors under spatial restriction." The 2nd Annual Meeting of the Japanese Society for Quantitative Biology. Jan 9 - 11, 2010 Osaka, Japan.
          39. Akira Funahashi, Akiya Jouraku, Yukiko Matsuoka, Hiromu Takizawa, Noriko Hiroi, Norihiro Kikuchi, and Hiroaki Kitano..
            "Design and development of CellDesigner: a modeling tool of biochemical network." The 2nd Annual Meeting of the Japanese Society for Quantitative Biology. Jan 9 - 11, 2010 Osaka, Japan.
          40. Noriko Hiroi, and Akira Funahashi..
            "An automated controlling system for microfluidic devises." The 2nd Annual Meeting of the Japanese Society for Quantitative Biology. Jan 9 - 11, 2010 Osaka, Japan.
          41. Kazuki Hirata, Nobuyuki Ohta, Noriko Hiroi, Akira Funahashi, and Yoshitaka Suetsugu..
            "Design and Implementation of high-performance sequence analysis environment using GPGPU." The 32nd Annual Meeting of the Molecular Biology Society of Japan. Dec 9 - 12, 2009 Yokohama, Japan.
          42. Noriko Hiroi, and Akira Funahashi..
            "High-Speed & High Efficient automated experimental systems." KLL Techno-mall. Dec 11, 2009 Tokyo, Japan.
          43. Kenta Yashima, Noriko Hiroi, Akira Funahashi, and Kotaro Oka..
            "Effect of molecular crowding on in vivo macromolecular reactions." The 47th Annual Meeting of the Biophysical Society of Japan. Dec 9 - 12, Yokohama, Japan. Oct 30 - Nov 1 2009, Tokushima, Japan.
          44. Hiroi, N., Schuster, E., Ward, J., Piper, M., Jouraku, A., Funahashi, A., Gemes, D., Partridge, L., Novere, N. L., and Thornton, J..
            "Comparison of Insulin signaling pathways among 4 species and 3 tissues of mouse." The 8th International Conference on Systems Biology (ICSB2007). Long Beach, USA. October2007.
          45. Nordling, T. E. M., Hiroi, N., and Funahashi, A..
            "Dynamic modes in biological systems: Why should a biologist care?." The 8th International Conference on Systems Biology (ICSB2007). Long Beach, USA. October2007.
          46. Hiroi, N., Nordling, T., Funahashi, A., and Kitano, H..
            "Detection of functional modules in graphs depend on a linearisation of the biochemical network." 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), 6th European Conference on Computational Biology (ECCB). Vienna, Austria. July2007.
          47. Hiroi, N., Funahashi, A., and Kitano, H..
            "The Impact of Spatial Restriction on Biological Systems." Computational Cell Biology 2007. New York, USA. March2007.
          48. Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "Hardware Design of a Stochastic Biochemical Simulator." Winter Simulation Conference 2006. Monterey, USA. December2006.
          49. Hiroi, N., Funahashi, A., and Kitano, H..
            "Kinetic modeling method for spatially restricted reactions." Winter Simulation Conference 2006. Monterey, USA. December2006.
          50. Iwaoka, Y., Osana, Y., Yoshimi, M., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "An Acceleration of a Biochemical Simulator on Programmable Hardware." The 7th International Conference on Systems Biology (ICSB2006). Yokohama, Japan. October2006.
          51. Hiroi, N., Funahashi, A., Suzuki, H., Yamamoto, T., and Murray, D..
            "Systems Energetics" - a new approach for cellular systems dynamics -." The 7th International Conference on Systems Biology (ICSB2006). Yokohama, Japan. October2006.
          52. Hiroi, N., Funahashi, A., and Kitano, H..
            "in vivo reaction modeling by DRRK." The 7th International Conference on Systems Biology (ICSB2006). Yokohama, Japan. October2006.
          53. Yoshimi, M., Osana, Y., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "The Design of Scalable Stochastic Biochemical Simulator on FPGA." 2005 IEEE International Conference on Field Programmable Technology. December2005.
          54. Hiroi, N., Funahashi, A., Jouraku, A., and Kitano, H..
            "Dimension-restriction affects the reaction rate and accuracy." 6th International Conference on Systems Biology (ICSB 2005).Link Boston, Massachusetts. October2005.
          55. Osana, Y., Iwaoka, Y., Fukushima, T., Yoshimi, M., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "A Framework for ODE-based Multimodel Biochemical Simulations on an FPGA." The 15th Field Programmable Logic and its applications(FPL 2005). Tampere, Finland. August2005.
          56. Iwanaga, N., Shibata, Y., Yoshimi, M., Osana, Y., Iwaoka, Y., Fukushima, T., Amano, H., Funahashi, A., Hiroi, N., Kitano, H., and Oguri, K..
            "Efficient Scheculing of Rate Law Functions for ODE-based Multimodel Biochemical Simulation on an FPGA." The 15th Field Programmable Logic and its applications(FPL 2005). Tampere, Finland. August2005.
          57. Hiroi, N., Funahashi, A., and Kitano, H..
            "Analysis for the movement of a enzyme." 13th Annual International conference on Intelligent Systems for Molecular Biology (ISMB 2005). Detroit, USA. June2005.
          58. Osana, Y., Fukushima, T., Yoshimi, M., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H., and Amano, H..
            "An FPGA-Based, Multi-model Simulation Method for Biochemical Systems." 12th Reconfigurable Architecture Workshop (RAW 2005). Denver, USA. April2005.
          59. Hiroi, N., Funahashi, A., and Kitano, H..
            "Two Numerical Model Analyses for the Movement of a Restriction Enzyme." 1st FEBS Advanced Lecture Course Systems Biology. Gosau, Austria. March2005.
          60. Hiroi, N., Funahashi, A., and Kitano, H..
            "Dimension restricted model analysis reveals the restriction enzyme diffusion along DNA is linear but not sliding." 2nd International Conference on Pathways, Networks, and Systems: Theory and Experiments. Crete, Greece. October2004.
          61. Hiroi, N., Funahashi, A., and Kitano, H..
            "Analysis of the restriction enzyme diffusion manner to reach the specific DNA site." 5th New England Biolabs Meeting on Restriction/Modification. Bristol, UK. September2004.
          62. Hiroi, N., Funahashi, A., Nordling, T., and Kitano, H..
            "In silico analysis for anchorage independent cell cycle start mechanisms." 4th International Conference on Systems Biology (ICSB 2003). St Louis, USA. November2003.
          63. Hiroi, N., Jinno, S., and Okayama, H..
            "Mammalian Rcd1 is a novel transcription cofactor essential for retinoic acid-induced F9 differentiation." Mechanisms of eukaryotic transcription. NY, USA. August2001.
          64. Hiroi, N., Jinno, S., and Okayama, H..
            "A conserved role for mammalian Rcd1 in cell differentiation (In Japanese)." 73th. Conference of The Japanese Biochemical Society. Yokohhama, JPN. October2000.
          65. Hiroi, N., Jinno, S., and Okayama, H..
            "Molecular Analysis of Mammalian Rcd1 (In Japanese)." 22th. Conference of The Molecular Biology Society of Japan. Hakata, JPN. December1999.
          66. Hiroi, N., Inoue, T., Shiokawa, D., Maruta, H., and Tanuma, S..
            "DNase gamma suppression mechanisms during M phase (In Japanese)." 118th. Conference of The Parmaceutical Society of Japan. Kyoto, JPN. March1998.
          67. Hiroi, N., Morito, A., Maruta, H. Yasuda, H., and Tanuma, S..
            "Apoptosis suppression mechanisms during M phase (In Japanese)." 69th. Conference of The Japanese Biochemical Society & 20th. Conference of The Molecular Biology Society of Japan. Sapporo, JPN. August1997.


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