Department of Biosciences and Informatics

Research Output 1987 2019

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Conference contribution
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 proceedingConference contribution

Brain-Computer Interfaces
Brain computer interface
Patient rehabilitation
Computer Systems
Rehabilitation
2017
4 Citations (Scopus)

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 proceedingConference contribution

Display devices

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 proceedingConference contribution

Thermal Diffusion
Thermal diffusion
thermal diffusion
Temperature Distribution
Temperature distribution
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 proceedingConference contribution

Screening
Throughput
Microfluidics
Biological fuel cells
Sorting
2014
4 Citations (Scopus)

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Brain computer interface
Patient rehabilitation
Muscle
Electroencephalography
Brain

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, Proceedings of the IEEE International Conference on Micro Electro Mechanical Systems (MEMS). Institute of Electrical and Electronics Engineers Inc., p. 264-267 4 p. 6765626

Research output: Chapter in Book/Report/Conference proceedingConference contribution

cell culturing
Microfluidics
Chemical activation
Fabrication
fabrication

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 proceedingConference contribution

Liposomes
Centrifuges
Microfluidics
2013
8 Citations (Scopus)

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, Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS. p. 265-268 4 p. 6609488

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Brain-Computer Interfaces
Brain computer interface
Upper Extremity
Electric Stimulation
Survivors
1 Citation (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, Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS. p. 2716-2719 4 p. 6610101

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Space Simulation
Cytoskeleton
Organelles
Reaction rates
Molecules
7 Citations (Scopus)

Is event-related desynchronization a biomarker representing corticospinal excitability?

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Imagery (Psychotherapy)
Biomarkers
Brain-Computer Interfaces
Motor Neurons
Motor Evoked Potentials

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, Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBS. p. 273-276 4 p. 6609490

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Brain-Computer Interfaces
Brain computer interface
Brain
Dystonia
Electroencephalography
2012

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

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Microarrays
Profiling
Microarray
Chemical analysis
High Accuracy
2011
1 Citation (Scopus)

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, IEEE International Conference on Rehabilitation Robotics. 5975489

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Sensory feedback
Sensory Feedback
Electric Stimulation
Stroke
Skin
13 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, 2011 ACM Conference on Bioinformatics, Computational Biology and Biomedicine, BCB 2011. p. 116-124 9 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Metagenome
Genes
Genome
Scaffolds
Metagenomics
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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Particle accelerators
Field programmable gate arrays (FPGA)
Information use
Simulators
Degradation

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

Sakakibara, Y., 2010, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 6158 LNCS. 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 proceedingConference contribution

Finite Automata
Finite automata
Bacteria
Finite State Automata
Escherichia Coli
3 Citations (Scopus)

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.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Untranslated RNA
Conservation
RNA
Genome
Support vector machines
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, Echinoderms: Durham - Proceedings of the 12th International Echinoderm Conference. p. 457-462 6 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Asterina pectinifera
Asteroidea
morphogenesis
metalloproteinases
membrane
2009
1 Citation (Scopus)

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, ReConFig'09 - 2009 International Conference on ReConFigurable Computing and FPGAs. p. 125-130 6 p. 5382039

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Field programmable gate arrays (FPGA)
Chemical reactions
Pipelines
Kinetics
Networks (circuits)
1 Citation (Scopus)

A non-parametric bayesian approach for predicting RNA secondary structures

Sato, K., Hamada, M., Mituyama, T., Asai, K. & Sakakibara, Y., 2009, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 5724 LNBI. 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 proceedingConference contribution

RNA Secondary Structure
RNA
Bayesian Approach
Dirichlet Process
Structure Prediction
2 Citations (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, FPL 09: 19th International Conference on Field Programmable Logic and Applications. p. 679-682 4 p. 5272335

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Field programmable gate arrays (FPGA)
Simulators
Hardware
Data transfer
Computer hardware

Evaluation of mixed reality sickness by changing the time lag between real images and virtual images in an advanced driver assistance system

Nakajima, S., Ino, S., Yamashita, K., Sato, M. & Kimura, A., 2009, IFMBE Proceedings. 12 ed. Vol. 25. p. 426-429 4 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Advanced driver assistance systems
Time delay
Neurology
Medicine
Image processing

Operon structure optimization by random self-assembly

Nakagawa, Y., Yugi, K., Tsuge, K., Itaya, M., Yanagawa, H. & Sakakibara, Y., 2009, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 5347 LNCS. 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 proceedingConference contribution

Structure Optimization
Self-assembly
Self assembly
Genes
Gene
2008
4 Citations (Scopus)

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

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Field programmable gate arrays (FPGA)
Scalability
Simulators
Throughput
Hardware
2007
2 Citations (Scopus)

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Simulators
Hardware
Field programmable gate arrays (FPGA)
Costs
Pipelines
1 Citation (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, ICFPT 2007 - International Conference on Field Programmable Technology. p. 193-200 8 p. 4439249

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Field programmable gate arrays (FPGA)
Simulators
Throughput
1 Citation (Scopus)

Stem kernels for RNA sequence analyses

Sakakibara, Y., Asai, K. & Sato, K., 2007, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 4414 LNBI. p. 278-291 14 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

RNA Sequence Analysis
RNA
kernel
Secondary Structure
Genome
2006

Characterization and cell transfection of pDNA/chitosan nanoparticles coated with hyaluronic acid

Yang, Z. H., Koyama, Y. & Sato, T., 2006, Polymer Preprints, Japan. 1 ed. Vol. 55. p. 1860 1 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Hyaluronic acid
Chitosan
Nanoparticles
Cytotoxicity
Gene expression
11 Citations (Scopus)

Development of an in vivo computer based on Escherichia coli

Nakagawa, H., Sakamoto, K. & Sakakibara, Y., 2006, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 3892 LNCS. 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 proceedingConference contribution

Escherichia coli
Escherichia Coli
Finite automata
Finite State Automata
Protein Synthesis
1 Citation (Scopus)

Discriminative detection of cis-acting regulatory variation from location data

Kawada, Y. & Sakakibara, Y., 2006, Series on Advances in Bioinformatics and Computational Biology. Vol. 3. p. 89-98 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Genes
Transcription factors
Transcription Factors
Binding sites
Yeast

Inhibition of influenza virus infection by minimized peptides which bind to hemagglutinin

Saito, T., Matsubara, T. & Sato, T., 2006, Polymer Preprints, Japan. 1 ed. Vol. 55. p. 1823 1 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Viruses
Peptides
Bacteriophages
Sugars
Amino acids
5 Citations (Scopus)

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

Kuramochi, J. & Sakakibara, Y., 2006, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 3892 LNCS. 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 proceedingConference contribution

Finite Automata
Finite automata
Tube
Encoding
Experiment

Selection of sugar-binding peptides from a scaffold-containing library

Matsubara, T. & Sato, T., 2006, Polymer Preprints, Japan. 1 ed. Vol. 55. p. 1824 1 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Scaffolds (biology)
Bacteriophages
Sugars
Peptides
DNA

Structure and function of oligosaccharide-binding peptides that selected from random libraries

Matsubara, T., Iijima, K., Sumi, M. & Sato, T., 2006, Polymer Preprints, Japan. 2 ed. Vol. 55. p. 5221-5222 2 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Oligosaccharides
Peptides
Bacteriophages
Lipid bilayers
Viruses

Structures and intracellular delivery of pDNA/sugar-modified chitosan complexes

Sato, T., Hashimoto, M., Morimoto, M., Saimoto, H., Shigemasa, Y. & Yanagie, H., 2006, Polymer Preprints, Japan. 2 ed. Vol. 55. p. 5371-5372 2 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Chitosan
Sugars
DNA
Macrophages
Microscopes
2005

Directed evolution of hemagglutinin-binding peptides by in silico screening

Matsubara, T., Onishi, A. & Sato, T., 2005, Polymer Preprints, Japan. 1 ed. Vol. 54. p. 2083 1 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Peptides
Screening
Bacteriophages
Molecular modeling
Viruses
1 Citation (Scopus)

Discriminative discovery of transcription factor binding sites from location data

Kawada, Y. & Sakakibara, Y., 2005, Proceedings - 2005 IEEE Computational Systems Bioinformatics Conference, CSB 2005. Vol. 2005. p. 86-92 7 p. 1498010

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Transcription factors
Binding sites
Transcription Factors
Genes
Chromatin Immunoprecipitation

Encapsulation of proteins in chitosan particles using various cross-linking agents and their characterization

Niwa, M. & Sato, T., 2005, Polymer Preprints, Japan. 1 ed. Vol. 54. p. 2178 1 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Chitosan
Encapsulation
Proteins
Salts
Biodegradability

Gene transfer and analysis of the gene expression mechanism using pDNA/chitosan complexes coated with lactose-modified PEG derivatives

Okan, R., Koya, K., Koyama, Y. & Sato, T., 2005, Polymer Preprints, Japan. 1 ed. Vol. 54. p. 2145 1 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Gene transfer
Chitosan
Gene expression
Polyethylene glycols
Derivatives

Gene transfer into macrophage using chitosan nanoparticle modified with mannose

Hashimoto, M., Morimoto, M., Saimoto, H., Shigemasa, Y., Yanagie, H. & Sato, T., 2005, Polymer Preprints, Japan. 1 ed. Vol. 54. p. 2144 1 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Gene transfer
Macrophages
Chitosan
Nanoparticles
Assays

Molecular evolution of GM3-binding peptides using a phage display method

Kubota, H., Matsubara, T. & Sato, T., 2005, Polymer Preprints, Japan. 1 ed. Vol. 54. p. 2082 1 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Bacteriophages
Peptides
Display devices
Viruses
Ceramides

Peptides bound to stereoregular PMMAs

Sawada, T., Matsuno, H., Matsubara, T., Sato, T., Kitayama, T. & Serizawa, T., 2005, Polymer Preprints, Japan. 2 ed. Vol. 54. p. 4867-4868 2 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Bacteriophages
Polymethyl methacrylates
Peptides
Assays
DNA

Selection of peptides with the recognition of stereoregular PMMA from phage library

Sawada, T., Matsuno, H., Matsubara, T., Sato, T., Kitayama, T. & Serizawa, T., 2005, Polymer Preprints, Japan. 1 ed. Vol. 54. p. 2081 1 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Bacteriophages
Polymethyl methacrylates
Peptides
Assays
DNA
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 proceedingConference contribution

Grammatical Inference
Greece
5 Citations (Scopus)

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

Matsui, H., Sato, K. & Sakakibara, Y., 2004, Proceedings - 2004 IEEE Computational Systems Bioinformatics Conference, CSB 2004. p. 290-299 10 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

RNA
Context sensitive grammars
Binary codes
Dynamic programming
Websites
2001

Spatial and temporal variation of secondary flow during intermittent oscillatory flow in model human central airways

Tanaka, G., Oka, K. & Tanishita, K., 2001, American Society of Mechanical Engineers, Bioengineering Division (Publication) BED. Kamm, R. D., Schmid-Schoenbein, G. W., Atesian, G. A. & Hefzy, M. S. (eds.). Vol. 50. p. 399-400 2 p.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Secondary flow
Flow velocity
1997
1 Citation (Scopus)

Adaptive routing on the recursive diagonal torus

Funahashi, A., Hanawa, T., Kudoh, T. & Amano, H., 1997, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Springer Verlag, Vol. 1336. p. 171-182 12 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 1336).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Adaptive Routing
Torus
Interconnection Networks
Routing algorithms
Routing Algorithm