Department of Biosciences and Informatics

Research output

Research output per year 1985 2005 2006 2007 2008 2010 2011 2012 2013 2014 2015 2016 2017 2018 2019 2020 2021 2022 2023

• 791 Article
• 58 Conference contribution
• 35 Review article
• 16 Chapter
• 45 More
  • 12 Paper
  • 12 Comment/debate
  • 12 Editorial
  • 3 Conference article
  • 3 Letter
  • 3 Short survey

Research output per year

Research output per year

Search results

• 2021

  Control and measurement of nano/micro-space temperature that changes cellular behavior

  Nakamura, T., Saito, T., Tanimoto, R., Yamada, T., Funahashi, A., Taniguchi, A., Nonaka, S., Sakamoto, J., Kamei, Y., Tominaga, M., Okabe, K., Yanase, Y., Kishi, H. & Hiroi, N. F., 2021, JSAP-OSA Joint Symposia, JSAP 2021. Optica Publishing Group (formerly OSA), 10p-N404-14. (Optics InfoBase Conference Papers).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Electrical Field Chamber with Dinamically Adaptable Stimuli for Myocyte Orientation during Cultivation

  Ramirez, S. R. M., Yamada, T., Funahashi, A. & Onoe, H., 2021 Jan 25, 34th IEEE International Conference on Micro Electro Mechanical Systems, MEMS 2021. Institute of Electrical and Electronics Engineers Inc., p. 498-501 4 p. 9375303. (Proceedings of the IEEE International Conference on Micro Electro Mechanical Systems (MEMS); vol. 2021-January).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • muscle cells 100%
  • stimuli 68%
  • Electric Field 66%
  • Regenerative Medicine 58%
  • chambers 58%

• Human Augmentation for Skill Acquisition and Skill Transfer

  Koike, H., Rekimoto, J., Ushiba, J., Furuya, S. & Ito, A., 2021 May 8, Extended Abstracts of the 2021 CHI Conference on Human Factors in Computing Systems, CHI EA 2021. Association for Computing Machinery, (Conference on Human Factors in Computing Systems - Proceedings).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  Open Access

  • Robotics 100%
  • Augmented reality 68%
  • Sports 66%
  • Virtual reality 58%
  • Artificial intelligence 57%
  2 Citations (Scopus)
• 2020

  Dielectrophoretic sorting system for screening of NAD(P)-dependent oxidoreductases.

  Kanai, Y., Shimokihara, S., Shitara, S., Oyobiki, R., Watanabe, T., Einaga, Y., Wakamatsu, K., Matsumoto, Y., Fujiwara, K. & Doi, N., 2020, 21st International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2017. Chemical and Biological Microsystems Society, p. 1383-1384 2 p. (21st International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2017).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Oxidoreductases 100%
  • Dielectrophoresis 88%
  • Enzymes 75%
  • Flow Injection Analysis 73%
  • Sorting 64%
• 2019

  Development of Rehabilitation System with Brain-Computer Interface for Subacute Stroke Patients

  Hashimoto, Y., Kakui, T., Ushiba, J., Liu, M., Kamada, K. & Ota, T., 2019 Jan 16, Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018. Institute of Electrical and Electronics Engineers Inc., p. 51-56 6 p. 8616013. (Proceedings - 2018 IEEE International Conference on Systems, Man, and Cybernetics, SMC 2018).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Brain-Computer Interfaces 100%
  • Brain computer interface 84%
  • Rehabilitation 70%
  • Patient rehabilitation 69%
  • Computer Systems 68%
  3 Citations (Scopus)
• 2018

  Improvement of microtas for directed evolution of NAD(P)-dependent oxidoreductases

  Goto, H., Kanai, Y., Yotsui, A., Shimokihara, S., Shitara, S., Einaga, Y., Matsumoto, Y., Miki, N., Fujiwara, K. & Doi, N., 2018, 22nd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2018. Chemical and Biological Microsystems Society, p. 2247-2249 3 p. (22nd International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2018; vol. 4).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Microbeads 100%
  • Oxidoreductases 97%
  • Diamond 60%
  • Enzymes 49%
  • Sorting 41%
• 2017

  Malleable embodiment: Changing sense of embodiment by spatial-temporal deformation of virtual human body

  Kasahara, S., Konno, K., Owaki, R., Nishi, T., Takeshita, A., Ito, T., Kasuga, S. & Ushiba, J., 2017 May 2, CHI 2017 - Proceedings of the 2017 ACM SIGCHI Conference on Human Factors in Computing Systems: Explore, Innovate, Inspire. Association for Computing Machinery, Vol. 2017-May. p. 6438-6448 11 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Display devices 100%
  33 Citations (Scopus)

• Requirement of spatiotemporal resolution for imaging intracellular temperature distribution

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

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Thermal Diffusion 100%
  • Thermal diffusion 90%
  • Temperature Distribution 83%
  • thermal diffusion 74%
  • Imaging 73%
• 2015

  Development of μtas for high-throughput screening of nad(p)-dependent oxidoreductases

  Shimokihara, S., Shitara, S., Oyobiki, R., Watanabe, T., Einaga, Y., Matsumoto, Y., Fujiwara, K., Horisawa, K. & Doi, N., 2015, MicroTAS 2015 - 19th International Conference on Miniaturized Systems for Chemistry and Life Sciences. Chemical and Biological Microsystems Society, p. 1302-1304 3 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Oxidoreductases 100%
  • Screening 61%
  • Throughput 45%
  • Microfluidics 23%
  • Biological fuel cells 18%
  2 Citations (Scopus)
• 2014

  A task-oriented brain-computer interface rehabilitation system for patients with stroke hemiplegia

  Ushiba, J., Morishita, A. & Maeda, T., 2014 Oct 22, 2014 4th International Conference on Wireless Communications, Vehicular Technology, Information Theory and Aerospace and Electronic Systems, VITAE 2014 - Co-located with Global Wireless Summit. Institute of Electrical and Electronics Engineers Inc., 6934416. (2014 4th International Conference on Wireless Communications, Vehicular Technology, Information Theory and Aerospace and Electronic Systems, VITAE 2014 - Co-located with Global Wireless Summit).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Brain computer interface 100%
  • Patient rehabilitation 82%
  • Muscle 81%
  • Electroencephalography 42%
  • Occupational therapy 36%
  6 Citations (Scopus)

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

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

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • cell culturing 100%
  • Microfluidics 62%
  • Displacement 48%
  • Vacuum 47%
  • Fabrication 43%

• The rapid synthesis of cell-sized liposomes by centrifuge-based microfluidic device

  Morita, M., Onoe, H., Yanagisawa, M., Fujiwara, K., Saito, H. & Takinoue, M., 2014, 18th International Conference on Miniaturized Systems for Chemistry and Life Sciences, MicroTAS 2014. Chemical and Biological Microsystems Society, p. 336-338 3 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Liposomes 100%
  • Centrifuges 73%
  • Microfluidics 64%
• 2013

  Functional recovery in upper limb function in stroke survivors by using brain-computer interface A single case A-B-A-B design

  Ono, T., Mukaino, M. & Ushiba, J., 2013 Oct 31, 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013. p. 265-268 4 p. 6609488. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Brain-Computer Interfaces 100%
  • Brain computer interface 84%
  • Electric Stimulation 67%
  • Upper Extremity 67%
  • Survivors 64%
  17 Citations (Scopus)

• In vivo oriented modeling with consideration of intracellular crowding

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

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Space Simulation 100%
  • Reaction rates 73%
  • Cytoskeleton 65%
  • Molecules 63%
  • Organelles 62%
  1 Citation (Scopus)

• Is event-related desynchronization a biomarker representing corticospinal excitability?

  Takemi, M., Masakado, Y., Liu, M. & Ushiba, J., 2013 Oct 31, 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013. p. 281-284 4 p. 6609492. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Brain-Computer Interfaces 100%
  • Biomarkers 91%
  • Motor Neurons 71%
  • Motor Evoked Potentials 46%
  • Sensorimotor Cortex 45%
  13 Citations (Scopus)

• Treatment effectiveness of brain-computer interface training for patients with focal hand dystonia: A double-case study

  Hashimoto, Y., Ota, T., Mukaino, M. & Ushiba, J., 2013 Oct 31, 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2013. p. 273-276 4 p. 6609490. (Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Focal Task-Specific Dystonia 100%
  • Brain-Computer Interfaces 82%
  • Brain computer interface 69%
  • Brain 50%
  • Dystonia 35%
  2 Citations (Scopus)
• 2012

  Poster: In silico microarray algorithm: Accurate and fast taxonomic profiling from short read sequences

  Tagami, T., Hachiya, T. & Sakakibara, Y., 2012 May 8, 2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012. 6182660. (2012 IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, ICCABS 2012).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Profiling 100%
  • Microarray 90%
  • Microarrays 80%
  • Chemical analysis 45%
  • High Accuracy 24%
• 2011

  A sensory feedback system utilizing cutaneous electrical stimulation for stroke patients with sensory loss

  Kita, K., Takeda, K., Osu, R., Sakata, S., Otaka, Y. & Ushiba, J., 2011, 2011 IEEE International Conference on Rehabilitation Robotics, ICORR 2011 - Rehab Week Zurich 2011. 5975489. (IEEE International Conference on Rehabilitation Robotics).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Sensory feedback 100%
  • Sensory Feedback 88%
  • Electric Stimulation 65%
  • Stroke 48%
  • Skin 39%
  2 Citations (Scopus)

• MetaVelvet: AAAn extension of Velvet assembler to de novo metagenome assembly from short sequence reads

  Namiki, T., Hachiya, T., Tanaka, H. & Sakakibara, Y., 2011 Dec 1, 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. p. 116-124 9 p. (2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Metagenome 100%
  • Genomics 72%
  • Scaffolds 72%
  • Genome 47%
  • Genes 16%
  15 Citations (Scopus)
• 2010

  A datapath classification method for FPGA-based scientific application accelerator systems

  Ogawa, Y., Ooya, T., Osana, Y., Yoshimi, M., Nishikawa, Y., Funahashi, A., Hiroi, N., Amano, H., Shibata, Y. & Oguri, K., 2010, Proceedings - 2010 International Conference on Field-Programmable Technology, FPT'10. p. 441-444 4 p. 5681455. (Proceedings - 2010 International Conference on Field-Programmable Technology, FPT'10).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Field Programmable Gate Array 100%
  • Accelerator 87%
  • Particle accelerators 64%
  • Resources 59%
  • Field programmable gate arrays (FPGA) 51%

• Development of a bacteria computer: From in silico finite automata to in vitro and in vivo

  Sakakibara, Y., 2010 Jul 29, Programs, Proofs, Processes - 6th Conference on Computability in Europe, CiE 2010, Proceedings. p. 362-371 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6158 LNCS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Bacteria 100%
  • Finite automata 87%
  • Finite Automata 82%
  • Escherichia Coli 56%
  • Finite State Automata 52%

• Improvement of structure conservation index with centroid estimators

  Okada, Y., Sato, K. & Sakakibara, Y., 2010, Pacific Symposium on Biocomputing 2010, PSB 2010. p. 88-97 10 p. (Pacific Symposium on Biocomputing 2010, PSB 2010).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Centroid 100%
  • Untranslated RNA 95%
  • Conservation 84%
  • Alignment 73%
  • Support Vector Machine 51%
  3 Citations (Scopus)

• Studies on function of MC5 molecule that is a novel membrane-type metalloproteinase of astacin family during morphogenesis of the starfish, Asterina pectinifera

  Hamanaka, G., Matsumoto, M., Hoshi, M. & Kaneko, H., 2010 Dec 1, Echinoderms: Durham - Proceedings of the 12th International Echinoderm Conference. p. 457-462 6 p. (Echinoderms: Durham - Proceedings of the 12th International Echinoderm Conference).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • astacin 100%
  • Asterina pectinifera 95%
  • Asteroidea 73%
  • morphogenesis 71%
  • metalloproteinases 67%
  3 Citations (Scopus)
• 2009

  A modular approach to heterogeneous biochemical model simulation on an FPGA

  Yamada, H., Osana, Y., Ishimori, T., Ooya, T., Yoshimi, M., Nishikawa, Y., Funahashi, A., Hiroi, N., Amano, H., Shibata, Y. & Oguri, K., 2009 Dec 1, ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs. p. 125-130 6 p. 5382039. (ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Field programmable gate arrays (FPGA) 100%
  • Chemical reactions 60%
  • Pipelines 46%
  • Networks (circuits) 33%
  1 Citation (Scopus)

• A non-parametric bayesian approach for predicting RNA secondary structures

  Sato, K., Hamada, M., Mituyama, T., Asai, K. & Sakakibara, Y., 2009, Algorithms in Bioinformatics - 9th International Workshop, WABI 2009, Proceedings. p. 286-297 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5724 LNBI).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • RNA Secondary Structure 100%
  • RNA 79%
  • Structure Prediction 70%
  • Bayesian Approach 65%
  • Dirichlet Process 54%
  1 Citation (Scopus)

• Configuring area and performance: Empirical evaluation on an FPGA-based biochemical simulator

  Ooya, T., Yamada, H., Ishimori, T., Shibata, Y., Osana, Y., Oguri, K., Yoshimi, M., Nishikawa, Y., Funahashi, A., Hiroi, N. & Amano, H., 2009 Nov 25, FPL 09: 19th International Conference on Field Programmable Logic and Applications. p. 679-682 4 p. 5272335. (FPL 09: 19th International Conference on Field Programmable Logic and Applications).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Field Programmable Gate Array 100%
  • Simulator 81%
  • Hardware 77%
  • Field programmable gate arrays (FPGA) 51%
  • Trade-offs 48%
  2 Citations (Scopus)

• Operon structure optimization by random self-assembly

  Nakagawa, Y., Yugi, K., Tsuge, K., Itaya, M., Yanagawa, H. & Sakakibara, Y., 2009 Nov 27, DNA Computing - 14th International Meeting on DNA Computing, DNA14, Revised Selected Papers. p. 33-40 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5347 LNCS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Structure Optimization 100%
  • Self-assembly 81%
  • Self assembly 76%
  • Gene 57%
  • Genes 55%
• 2008

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

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

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Field programmable gate arrays (FPGA) 100%
  • Scalability 32%
  • Simulators 29%
  • Throughput 28%
  • Computer hardware 23%
  5 Citations (Scopus)
• 2007

  A combining technique of rate law functions for a cost-effective reconfigurable biological simulator

  Yamada, H., Iwanaga, N., Shibata, Y., Osana, Y., Yoshimi, M., Iwaoka, Y., Nishikawa, Y., Kojima, T., Amano, H., Funahashi, A., Hiroi, N., Hiroaki Kitano, K. & Kiyoshi Oguri, O., 2007, Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL. p. 808-811 4 p. 4380774. (Proceedings - 2007 International Conference on Field Programmable Logic and Applications, FPL).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Simulators 100%
  • Computer hardware 80%
  • Field programmable gate arrays (FPGA) 56%
  • Costs 52%
  • Pipelines 52%
  2 Citations (Scopus)

• A framework for implementing a network-based stochastic biochemical simulator on an FPGA

  Yoshimi, M., Nishikawa, Y., Kojima, T., Osana, Y., Funahashi, A., Hiroi, N., Shibata, Y., Yamada, H., Kitano, H. & Amano, H., 2007 Dec 1, ICFPT 2007 - International Conference on Field Programmable Technology. p. 193-200 8 p. 4439249. (ICFPT 2007 - International Conference on Field Programmable Technology).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Field programmable gate arrays (FPGA) 100%
  • Simulators 89%
  • Throughput 85%
  1 Citation (Scopus)

• Stem kernels for RNA sequence analyses

  Sakakibara, Y., Asai, K. & Sato, K., 2007, Bioinformatics Research and Development - First International Conference, BIRD 2007 Proceedings. Springer Verlag, p. 278-291 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4414 LNBI).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • RNA 100%
  • kernel 56%
  • Secondary Structure 32%
  • Support Vector Machine 18%
  • Genome 16%
  1 Citation (Scopus)
• 2006

  An FPGA implementation of high throughput stochastic simulator for large-scale biochemical systems

  Yoshimi, M., Osana, Y., Iwaoka, Y., Nishikawa, Y., Kojima, T., Shibata, Y., Iwanaga, N., Funahashi, A., Hiroi, N., Kitano, H. & Amano, H., 2006 Dec 1, Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL. p. 227-232 6 p. 4100980. (Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • FPGA Implementation 100%
  • High Throughput 75%
  • Simulator 69%
  • Field Programmable Gate Array 56%
  • Stochastic Simulation 46%
  6 Citations (Scopus)

• Development of an in vivo computer based on Escherichia coli

  Nakagawa, H., Sakamoto, K. & Sakakibara, Y., 2006 Jul 13, DNA Computing - 11th International Workshop on DNA Computing, DNA11, Revised Selected Papers. p. 203-212 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3892 LNCS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Escherichia Coli 100%
  • Escherichia coli 90%
  • Finite automata 55%
  • Protein Synthesis 51%
  • Finite State Automata 39%
  13 Citations (Scopus)

• Discriminative detection of cis-acting regulatory variation from location data

  Kawada, Y. & Sakakibara, Y., 2006 Dec 1, Proceedings of the 4th Asia-Pacific Bioinformatics Conference, APBC 2006. p. 89-98 10 p. (Series on Advances in Bioinformatics and Computational Biology; vol. 3).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Transcription factors 100%
  • Genes 88%
  • Binding Site 65%
  • Binding sites 64%
  • Yeast 55%
  1 Citation (Scopus)

• Intensive in vitro experiments of implementing and executing finite automata in test tube

  Kuramochi, J. & Sakakibara, Y., 2006 Jul 13, DNA Computing - 11th International Workshop on DNA Computing, DNA11, Revised Selected Papers. p. 193-202 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3892 LNCS).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Finite automata 100%
  • Finite Automata 94%
  • Tube 94%
  • Experiment 69%
  • Encoding 55%
  5 Citations (Scopus)

• Performance evaluation of an FPGA-based biochemical simulator ReCSiP

  Osana, Y., Yoshimi, M., Iwaoka, Y., Kojima, T., Nishikawa, Y., Funahashi, A., Hiroi, N., Kitano, H., Amano, H., Shibata, Y. & Iwanaga, N., 2006 Dec 1, Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL. p. 845-850 6 p. 4101089. (Proceedings - 2006 International Conference on Field Programmable Logic and Applications, FPL).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Field Programmable Gate Array 100%
  • Performance Evaluation 84%
  • Simulator 81%
  • Field programmable gate arrays (FPGA) 51%
  • Reaction Mechanism 49%
  4 Citations (Scopus)
• 2005

  A framework for ODE-based multimodel biochemical simulations on an FPGA

  Osana, Y., Fukushima, T., Yoshimi, M., Iwaoka, Y., Funahashi, A., Hiroi, N., Shibata, Y., Iwanaga, N., Kitano, H. & Amano, H., 2005 Dec 1, Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL. p. 574-577 4 p. 1515788. (Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL; vol. 2005).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Field programmable gate arrays (FPGA) 100%
  • Simulators 59%
  • Simulation platform 45%
  • Chemical reactions 40%
  • Microprocessor chips 36%
  3 Citations (Scopus)

• Discriminative discovery of transcription factor binding sites from location data

  Kawada, Y. & Sakakibara, Y., 2005 Dec 1, Proceedings - 2005 IEEE Computational SystemsBioinformatics Conference, CSB 2005. p. 86-92 7 p. 1498010. (Proceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005; vol. 2005).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Transcription factors 100%
  • Binding sites 97%
  • Genomics 72%
  • Binding Sites 53%
  • Transcription Factors 52%
  1 Citation (Scopus)

• Efficient scheduling of rate law functions for ODE-based multimodel biochemical simulation on an FPGA

  Iwanagra, N., Shibata, Y., Yoshimi, M., Osana, Y., Iwaoka, Y., Fukushima, T., Amano, H., Funahashi, A., Hiroi, N., Kitano, H. & Oguri, K., 2005 Dec 1, Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL. p. 666-669 4 p. 1515809. (Proceedings - 2005 International Conference on Field Programmable Logic and Applications, FPL; vol. 2005).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Field programmable gate arrays (FPGA) 100%
  • Scheduling 84%
  • Throughput 56%
  • Reconfigurable hardware 54%
  • Computer hardware 47%
  10 Citations (Scopus)
• 2004

  Grammatical inference: Algorithms and applications: 7th international colloquium, ICGI 2004 Athens, Greece, october 11-13, 2004 proceedings

  Paliouras, G. & Sakakibara, Y., 2004, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer Verlag, Vol. 3264. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 3264).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

• Pair stochastic tree adjoining grammars for aligning and predicting pseudoknot RNA structures

  Matsui, H., Sato, K. & Sakakibara, Y., 2004 Jan 1, Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. IEEE Computer Society, p. 290-299 10 p. (Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • RNA 100%
  • Genomics 17%
  • Context sensitive grammars 14%
  • Binary codes 10%
  • Dynamic programming 8%
  7 Citations (Scopus)
• 2000

  Albumin uptake into endothelial cells in separated flow

  Kudo, S., Yamaguchi, R., Sato, M., Oka, K. & Tanishita, K., 2000, Advances in Bioengineering. American Society of Mechanical Engineers (ASME), p. 83-84 2 p. (ASME International Mechanical Engineering Congress and Exposition, Proceedings (IMECE); vol. 2000-D).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Endothelial cells 100%
  • Shear stress 61%
  • Channel flow 15%
  • Microscopes 12%
  • Scanning 10%

• Distribution of oxygen tension in neocortical areas in the ratsomatosensory cortex

  Masamoto, K., Oka, K., Kobayashi, H., Sannohe, Y., Takizawa, N. & Tanishita, K., 2000, Advances in Bioengineering. American Society of Mechanical Engineers (ASME), p. 295-296 2 p. (ASME International Mechanical Engineering Congress and Exposition, Proceedings (IMECE); vol. 2000-D).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Oxygen 100%
  • Rats 73%
  • Spatial distribution 68%
  • Needles 65%
  • Brain 51%
• 1999

  Albumin transport across the endothelial cells under the shear stress applied

  Tsuzaka, M., Takenouchi, M., Ikeda, M., Oka, K. & Tanishita, K., 1999 Dec 1, American Society of Mechanical Engineers, Bioengineering Division (Publication) BED. ASME, Vol. 42. p. 293-294 2 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Inulin 100%
  • Endothelial cells 79%
  • Monolayers 69%
  • Shear stress 48%
  • Membranes 44%
  1 Citation (Scopus)

• Using encapsulation to improve the viability of cryopreserved cells

  Matsumoto, Y., Morinaga, Y., Ujihira, M., Oka, K. & Tanishita, K., 1999 Dec 1, American Society of Mechanical Engineers, Bioengineering Division (Publication) BED. ASME, Vol. 44. p. 57-58 2 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Alginate 100%
  • Encapsulation 77%
  • Latent heat 77%
  • Freezing 74%
  • Cells 66%
  1 Citation (Scopus)

• USING ENCAPSULATION TO IMPROVE THE VIABILITY OF CRYOPRESERVED CELLS

  Matsumoto, Y., Morinaga, Y., Ujihira, M., Oka, K. & Tanishita, K., 1999, Advances in Heat and Mass Transfer in Biotechnology. American Society of Mechanical Engineers (ASME), p. 57-58 2 p. (ASME International Mechanical Engineering Congress and Exposition, Proceedings (IMECE); vol. 1999-E).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Alginate 100%
  • Encapsulation 77%
  • Latent heat 77%
  • Freezing 74%
  • Dopamine 52%

• Variation of wall shear stress direction in aortic arch model

  Fujioka, H., Shuto, Y., Oka, K. & Tanishita, K., 1999 Dec 1, American Society of Mechanical Engineers, Bioengineering Division (Publication) BED. ASME, Vol. 42. p. 591-592 2 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Arches 100%
  • Shear stress 83%

• Wall shear stress distribution on the surface of realistic endothelial cell model

  Fukushima, S., Nagatsu, A., Kaibara, M., Oka, K. & Tanishita, K., 1999 Dec 1, American Society of Mechanical Engineers, Bioengineering Division (Publication) BED. ASME, Vol. 43. p. 39-40 2 p.

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

  • Endothelial cells 100%
  • Velocity measurement 69%
  • Shear stress 61%
  • Stress concentration 57%

• WALL SHEAR STRESS DISTRIBUTION ON THE SURFACE OF REALISTIC ENDOTHELIAL CELL MODEL

  Fukushima, S., Nagatsu, A., Kaibara, M., Oka, K. & Tanishita, K., 1999, Advances in Bioengineering. American Society of Mechanical Engineers (ASME), p. 39-40 2 p. (ASME International Mechanical Engineering Congress and Exposition, Proceedings (IMECE); vol. 1999-D).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution
• 1998

  DETERMINATION OF MICROSCOPIC WALL SHEAR STRESS DISTRIBUTION ON ENDOTHELIAL CELL MODEL

  Fukushima, S., Deguchi, T., Nishida, M., Kaibara, M., Oka, K. & Tanishita, K., 1998, Advances in Bioengineering. American Society of Mechanical Engineers (ASME), p. 109-110 2 p. (ASME International Mechanical Engineering Congress and Exposition, Proceedings (IMECE); vol. 1998-D).

  Research output: Chapter in Book/Report/Conference proceeding › Conference contribution