Publications

Books

  • Tan Tin Wee, Peter Arzberger, Akihiko Konagaya (Ed): Grid Computing in Life Sciences: Proceedings of the 2nd International Science Grid Workshop, Lsgrid 2005, World Scientific Publishing Co., Inc., (2006)
  • Akihiko Konagaya, Kenji Satou (Ed): Grid Computing in Life Science: First International Life Science Grid Workshop, LSGRID 2004, LNBI 3370, Springer, (2005)LSGRID2004.pdf

Research Papers

  • Go Yoshizawa, Rinie van Est, Daisuke Yoshinaga, Mikihito Tanaka, Ryuma Shineha, Akihiko Konagaya: Responsible innovation in molecular robotics in Japan, Chem-Bio Informatics Journal, 18, pp.164-172 (2018).
    DOI:10.1273/cbij.18.164
  • Ryuzo Azuma, Sae Kishi, Greg Gutmann, Akihiko Konagaya: “All-atom molecular dynamics of film supported flat-shaped DNA origami in water”, Chem-Bio Informatics Journal, 18, pp.96-118 (2018).
    DOI:10.1273/cbij.18.96
  • Kenta Yoshida, Kazuya Maeda, Akihiko Konagaya, Hiroyuki Kusuhara: “Accurate Estimation of In Vivo Inhibition Constants of Inhibitors and Fraction Metabolized of Substrates with Physiologically Based Pharmacokinetic Drug–Drug Interaction Models Incorporating Parent Drugs and Metabolites of Substrates with Cluster Newton Method, DRUG METABOLISM AND DISPOSITION, 46, pp.1805-1816 (2018)
    DOI:10.1124/dmd.118.081828
  • Shun Asami, Daisuke Kiga, Akihiko Konagaya: Constraint-based Perturvation Analysis with Cluster Newton Method : A Case Study of Personalized Parameter Estimations with Irinotecan Whole-Body Physiologically Based Pharmacokinetic Model, BMC Systems Biology, Vol.11 (Suppl 7): 129 (2017).
    DOI: 10.1186/s12918-017-0513-2
  • Atsuko Sato, Hitomi Yuki, Chiduru Watanabe, Jun-ichi Saito, Akihiko Konagaya, Teruki Honma: Prediction of the site of CYP3A4 metabolism of tolterodine by molecular dynamics simulation from multiple initial structures of the CYP3A4-tolterodine complex, Chem-Bio Informatics Journal, 17, 38-52 (2017).
    DOI: 10.1273/cbij.17.38
  • Greg Gutmann Daisuke Inoue, Akira Kakugo, Akihiko Konagaya: Parallel Interaction Detection Algorithms for a Particle-based Live Controlled Real-time Microtubule Gliding Simulation System Accelerated by GPGPUInter. J. of New Generation Computing (NGC), First Online 03 March  (2017).PDF
    DOI: 10.1007/s00354-017-0011-5
  • Daisuke Inoue, Takahiro Nitta, Rashedul Kabir, Kazuki Sada, Jian Ping Gong, Akihiko Konagaya, Akira Kakugo: Sensing surface mechanical deformation using active probes driven by motor proteins, Nature Communications, 7:12557, Oct. 3 (2016).
    DOI: 10.1038/ncomms12557
  • Greg Gutmann Daisuke Inoue, Akira Kakugo, Akihiko Konagaya: Real-Time 3D Microtubule Gliding Simulation Accelarated by GPU Computing, Inter. J. of Automation and Computing (IJAC), 19 Feb. 2 (2016), pp. 1-9.
    DOI: 10.1007/s11633-015-0947-1
  • Greg Gutmann Daisuke Inoue, Akira Kakugo, Akihiko Konagaya: Using a Master and Slave approach for GPGPU Computing to Achieve Optimal Scaling in a 3D
    Real-Time Simulation, in Proc. the IEEE Ann. Int. Conf. on Nano/Micro Engineerd and Molecular Systems (NEMS), Matsushima, Japan, 17-20 April, (2016), A3L-E-4
  • Bulibuli Mahemuti, Daisuke Inoue, Akira Kakugo, Akihiko Konagaya: Investigation of the Microtubule Dynamics with Probabilistic Data Association Filter, in Proc. the IEEE Ann. Int. Conf. on Nano/Micro Engineerd and Molecular Systems (NEMS), Matsushima, Japan, 17-20 April, (2016), A3L-E-5
  • Daisuke Inoue, Bulbul Mahemoti, Arif Md. Rashedul Kabir, Tamann Ishrat Farhana, Kiyotaka Tokuraku, Kazuki Sada, Akihiko Konagaya, Akira Kakugo: Depletion force induced collective motion of microtubules driven by knesin, Nanoscale,  (2015) online
  • Yuexing Han, Akito Hara, Akinori Kuzuya, Rousuke Watanabe, Yuichi Ohya, Akihiko Konagaya: Automatic Recognition of DNA Pliers in Atomic Force Microscopy Images, New Generation Computing, 33(3), 253-270 (2015) doi: 10.1007/s00354-015-0305-4
  • Philippe Gaudreau, Ken Hayami, Y. Aoki, Hassan Safouhi, Akihiko Konagaya:
    Improvements to the cluster Newton method for underdetermined inverse problems.J. Computational Applied Mathematics283:122-141(2015)
  • Yutaka Ueno, Shuntaro Ito, Akihiko Konagaya: Implementing a modeling software for animated protein-complex interactions using a physics simulation library.J. Bioinformatics and Computational Biology12(6)(2014)
  • Greg Gutmann, Daisuke Inoue, Akira Kakugo, Akihiko Konagaya: Real-Time 3D Microtubule Gliding Simulation, Life System Modeling and Simulation, Communications in Compuer and Information Science, vol. 461, pp.13-22 (2014) PDF
  • Yasunori Aoki, Ken Hayami, Hans De Sterck, Akihiko Konagaya: Cluster Newton Method for Sampling Multiple Solutions of Underdetermined Inverse Problems:Application to a Parameter Identification Problem in Pharmacokinetics, SIAM J. Scientific Computing, 36 (1), B14-B44 (2014) PDF
  • Daniel Berrar, Akihiko Konagaya, Alfons Schuster: Turing Test Considered Mostly Harmless, New Generation Computing, vol. 31, no.4, pp.241-263 (2013) PDF
  • Akihiko konagaya, Masami Hagiya, Satoshi Kobayashi, Hirohide Saito, Satoshi Murata: Molecular Robotics Project: Toward Artifacts with Sensors, Actuators and Intelligence, in Proc. of Int. Conf. on Applied and Theoretical Information Systems Research, Nov, 2013, Taipei PDF
  • Han Y, Hara A, Kuzuya A, Watanabe R, Ohya Y, Konagaya A: Automatic Recognition of DNA Nanostructures on Atomic Force Microscopy (AFM) Image: First Experience on DNA Pliers, in Proc. of Int. Conf. on Applied and Theoretical Information Systems Research, Nov, 2013, Taipei PDF
  • Yoshida K, Maeda K, Kusuhara H, Konagaya A: Estimation of feasible solution space using Cluster Newton Method: application to pharmacokinetic analysis of irinotecan with physiologically-based pharmacokinetic models, BMC Systems Biology 2013, 7 (Suppl 3): S3 (2013) PDF
  • Murata S, Konagaya A, Kobayashi S, Saito H, Hagiya M: Molecular Robotics: A New Paradigm for Artifacts,New Generation Computing, Ohmsha, Ltd. and Springer, vol.31, no.1, pp.27-45 (2013) PDF
  • Akihiko K: Towards an In Silico Approach to Personalized Pharmacokinetics, Molecular Interactions, Prof. Aurella Meghea (Ed), ISBN: 978-953-51-0079-9, In Tech (2012) PDF
  • Aoki Y, Hayami K, De Sterck Hans, Konagaya A: Cluster Newton Method for Sampling Multiple Solutions of an Underdetermined Inverse Problem: Parmeter Identificaiton for Pharmacokinetics, NII Technical Report, NII-2011-002E (2011) PDF
  • Arikuma T, Yoshikawa S, Azuma R, Watanabe K, Muramatsu K, Konagaya A.: Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical simulation, BMC Bioinformatics, vol. 9 (Suppl 6), S11 (2008) PDF
  • Azuma R., Umetsu R., Ohki S., Konishi F., Yoshikawa S., Konagaya A., and Matsumura K.: Discovering dynamic characteristics of biochemical pathways using geometric patterns among parameter-parameter dependencies in differential equations. New Generation Computing Vol.25, No.4, pp.425-441 (2007)
    PDF
  • Arikuma, T., Yoshikawa, S., Watanabe, K., Matsumura, K., and Konagaya, A., : Ontology-driven hypothetic assertion (OHA) for drug interaction prediction. International Multi-Symposiums on Computer and Computational Sciences 2007 (IMSCCS07), Iowa, USA, August (2007)
    PDF
  • Konagaya, A. :Trends in life science grid: from computing grid to knowledge grid, BMC Bioinformatics, Vol.7 5, ppS10-S10, (2006)
    PMID: 17254294
  • Takasaki, S., Kawamura, Y., and Konagaya, A. :Selecting effective siRNA sequences by using radial basis function network and decision tree learning, BMC Bioinformatics, Vol.7 S5, ppS22-S22, (2006)
    PMID: 17254307
  • Azuma, R., Kitagawa, T., Kobayashi, H., and Konagaya, A. :Particle simulation approach for sub-cellular dynamic and interactions of biological molecules, BMC Bioinformatics, Vol.7 Suppl.4, ppS20-1-S20-13, (2006)
    PMID: 17217513
  • Konagaya, A. :International Conference etc. OBIGrid: Towards the “Ba” for sharing resources, Services and knowledge for bioinformatics, 4th International Workshop on Biomedical Computations on the Grid (BioGrid’06), Singapore, Singapore, May (2006)
    PDF
  • Konagaya, A.: The Grid as a “Ba” for Biomedical Knowledge Creation. Grid Computing in Life Sciences (LSGRID2005), World Scientific, pp.1-10, 2006
    PDF
  • Umetsu, R., Ohki, S., Fukuzaki, A., Konagaya A., Shinbara, D., Saito, M., Watanabe, K., Kitagawa, T. and Hoshino, T.: An Architecture Design of Open Genome Services, Grid Computing in Life Sciences (LSGRID2005), World Scientific, pp.87-98, 2006
    PDF
  • Satou, K., Nakashima, Y., Tsuji, S, Defago, X., and Konagaya, A.: An Integrated System for Distributed Bioinformatics Environment on Grids, Grid Computing in Life Science (LSGRID2004), LNBI Springer, 8-19, Heidelberg, Germany (2005)
    PDF
  • Konishi, F. and Konagaya, A.: The Architectural Design of High-Throughput BLAST Services on OBIGrid, Grid Computing in Life Science (LSGRID2004), LNBI Springer, 32-42, Heidelberg, Germany (2005)
    PDF
  • Fukuzaki, A., Nagashima, T., Ide, K., Konishi, F., Hatakeyama, M., Yokoyama, S., Kuramitsu, S., and Konagaya, A.: Genome-wide functional annotation environment for Thermus thermophilus in OBIGrid, Grid Computing in Life Science (LSGRID2004), LNBI Springer, 82-91, Heidelberg, Germany (2005)
    PDF
  • P.W. Arzberger, A. Farazdel, A. Konagaya, L. Ang, S. Shimojo and R.L. Stevens: “Life Sciences and Cyberinfrastructure: Dual and Interacting Revolutions that will Drive Future Science”, New Generation Computing,
    vol.22, pp.970-110 , 2004.
    PDF
  • A. Konagaya, F. Konishi, M. Hatakeyama and K. Satou: “The Superstructure toward Open Bioinformatics Grid”, New Generation Computing, vol.22, pp.167-176 , 2004.
    PDF
  • Yoshikawa,S., Satou,K., Konagaya,A.: Drug Interaction Ontology (DIO) for Inferences of Possible Drug-Drug Interactions, Medinfo, vol. 11(Pt 1), pp.454-458 (2004) MID:15360854 PDF