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2020 – today
- 2023
[j38]Akihiko Konagaya
, Gregory Gutmann, Yuhui Zhang:
Co-creation environment with cloud virtual reality and real-time artificial intelligence toward the design of molecular robots. J. Integr. Bioinform. 20(1) (2023)- 2022
- [j37]Yuexing Han, Yuhong Liu, Bing Wang, Qiaochuan Chen, Leilei Song, Lin Tong, Chuanbin Lai, Akihiko Konagaya:
A novel transfer learning for recognition of overlapping nano object. Neural Comput. Appl. 34(7): 5729-5741 (2022) - [j36]Yoshiaki Kariya, Masashi Honma, Keita Tokuda, Akihiko Konagaya, Hiroshi Suzuki:
Utility of constraints reflecting system stability on analyses for biological models. PLoS Comput. Biol. 18(9): 1010441 (2022)
2010 – 2019
- 2019
- [j35]Arif Pramudwiatmoko, Satoru Tsutoh, Gregory Gutmann, Yutaka Ueno, Akihiko Konagaya:
A high-performance haptic rendering system for virtual reality molecular modeling. Artif. Life Robotics 24(4): 542-549 (2019) - [i2]Yuhui Zhang, Greg Gutmann, Akihiko Konagaya:
Irregular Convolutional Auto-Encoder on Point Clouds. CoRR abs/1910.02686 (2019) - [i1]Gregory Gutmann, Akihiko Konagaya:
Predictive Simulation: Using Regression and Artificial Neural Networks to Negate Latency in Networked Interactive Virtual Reality. CoRR abs/1910.04703 (2019) - 2017
- [j34]Shun Asami, Daisuke Kiga, Akihiko Konagaya:
Constraint-based perturbation analysis with cluster Newton method: a case study of personalized parameter estimations with irinotecan whole-body physiologically based pharmacokinetic model. BMC Syst. Biol. 11(S-7): 151-162 (2017) - [j33]Gregory 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 GPGPU. New Gener. Comput. 35(2): 157-180 (2017) - 2016
- [j32]Gregory Gutmann, Daisuke Inoue, Akira Kakugo, Akihiko Konagaya:
Real-time 3D microtubule gliding simulation accelerated by GPU computing. Int. J. Autom. Comput. 13(2): 108-116 (2016) - [c53]Gregory 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. NEMS 2016: 95-100 - [c52]Bulibuli Mahemuti, Daisuke Inoue, Akira Kakugo, Akihiko Konagaya:
Investigation of the microtubule dynamics with probabilistic data association filter. NEMS 2016: 101-106 - 2015
- [j31]Philippe Gaudreau, Ken Hayami, Yasunori Aoki, Hassan Safouhi, Akihiko Konagaya:
Improvements to the cluster Newton method for underdetermined inverse problems. J. Comput. Appl. Math. 283: 122-141 (2015) - [j30]Akihiko Konagaya:
Molecular Robotics and Controlling. New Gener. Comput. 33(3): 211-212 (2015) - [j29]Yuexing Han, Akito Hara, Akinori Kuzuya, Ryosuke Watanabe, Yuichi Ohya, Akihiko Konagaya:
Automatic Recognition of DNA Pliers in Atomic Force Microscopy Images. New Gener. Comput. 33(3): 253-270 (2015) - 2014
- [j28]Yutaka Ueno, Shuntaro Ito, Akihiko Konagaya:
Implementing a modeling software for animated protein-complex interactions using a physics simulation library. J. Bioinform. Comput. Biol. 12(6) (2014) - [j27]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. Sci. Comput. 36(1) (2014) - [c51]Yuexing Han, Daisuke Inoue, Akira Kakugo, Akihiko Konagaya:
Tracking single microtubules by using B-spline curves and Hausdorff distance. IPTA 2014: 193-198 - 2013
- [j26]Kenta Yoshida, Kazuya Maeda, Hiroyuki Kusuhara, Akihiko Konagaya:
Estimation of feasible solution space using Cluster Newton Method: application to pharmacokinetic analysis of irinotecan with physiologically-based pharmacokinetic models. BMC Syst. Biol. 7(S-3): S3 (2013) - [j25]Satoshi Murata, Akihiko Konagaya, Satoshi Kobayashi, Hirohide Saito, Masami Hagiya:
Molecular Robotics: A New Paradigm for Artifacts. New Gener. Comput. 31(1): 27-45 (2013) - [j24]Daniel P. Berrar, Akihiko Konagaya, Alfons Schuster:
Turing Test Considered Mostly Harmless. New Gener. Comput. 31(4): 241-263 (2013)
2000 – 2009
- 2008
- [j23]Takeshi Arikuma, Sumi Yoshikawa, Ryuzo Azuma, Kentaro Watanabe, Kazumi Matsumura, Akihiko Konagaya:
Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical simulation. BMC Bioinform. 9(S-6) (2008) - [j22]Chun-Hsi Huang, Akihiko Konagaya, Vincenzo Lanza, Peter M. A. Sloot:
Guest Editorial Introduction to the Special Section on BioGrid: Biomedical Computations on the Grid. IEEE Trans. Inf. Technol. Biomed. 12(2): 133-137 (2008) - 2007
- [j21]Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya:
Multiple Sequence Alignment Based on Dynamic Programming Using FPGA. IEICE Trans. Inf. Syst. 90-D(12): 1939-1946 (2007) - [j20]Akihiko Konagaya, Richard O. Sinnott, Peter W. Arzberger:
Life Science Grid. New Gener. Comput. 25(4): 337-338 (2007) - [j19]Ryuzo Azuma, Ryo Umetsu, Shingo Ohki, Fumikazu Konishi, Sumi Yoshikawa, Akihiko Konagaya, Kazumi Matsumura:
Discovering Dynamic Characteristics of Biochemical Pathways using Geometric Patterns among Parameter-Parameter Dependencies in Differential Equations. New Gener. Comput. 25(4): 425-441 (2007) - [j18]Yoshiki Yamaguchi, Tsutomu Maruyama, Ryuzo Azuma, Moritoshi Yasunaga, Akihiko Konagaya:
Mesoscopic-level Simulation of Dynamics and Interactions of Biological Molecules Using Monte Carlo Simulation. J. VLSI Signal Process. 48(3): 287-299 (2007) - [c50]Hiroshi Kobayashi, Ryuzo Azuma, Akihiko Konagaya:
Kinetic Analysis of Ligand-Receptor Complex Formation with the Aid of Computer Simulation. AINA Workshops (1) 2007: 727-732 - [c49]Fumikazu Konishi, Manabu Ishii, Shingo Ohki, Ryo Umetsu, Akihiko Konagaya:
RABC: A Conceptual Design of Pervasive Infrastructure for Browser Computing based on Ajax technologies. CCGRID 2007: 661-672 - [c48]Yoshiki Yamaguchi, Tsutomu Maruyama, Fumikazu Konishi, Akihiko Konagaya:
High speed tablation system using an FPGA designed for distribution tables of frequent DNA subsequences. FPL 2007: 145-150 - [c47]Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya:
An FPGA Implementation of Multiple Sequence Alignment Based on Carrillo-Lipman Method. FPL 2007: 489-492 - [c46]Takeshi Arikuma, Sumi Yoshikawa, Kentaro Watanabe, Akihiko Konagaya:
Ontology-Driven Hypothetic Assertion (OHA) for Drug Interaction Prediction. IMSCCS 2007: 1-8 - [p1]Akihiko Konagaya, Ryuzo Azuma, Ryo Umetsu, Shingo Ohki, Fumikazu Konishi, Kazumi Matsumura, Sumi Yoshikawa:
Seeing Is Knowing: Visualization of Parameter-Parameter Dependencies in Biomedical Network Models. Grid Computing for Bioinformatics and Computational Biology 2007: 375-387 - 2006
- [j17]Ryuzo Azuma, Tetsuji Kitagawa, Hiroshi Kobayashi, Akihiko Konagaya:
Particle simulation approach for subcellular dynamics and interactions of biological molecules. BMC Bioinform. 7(S-4) (2006) - [j16]Akihiko Konagaya:
Trends in life science grid: from computing grid to knowledge grid. BMC Bioinform. 7(S-5) (2006) - [j15]Shigeru Takasaki, Yoshihiro Kawamura, Akihiko Konagaya:
Selecting effective siRNA sequences by using radial basis function network and decision tree learning. BMC Bioinform. 7(S-5) (2006) - [j14]Shigeru Takasaki, Yoshihiro Kawamura, Akihiko Konagaya:
Selecting effective siRNA sequences based on the self-organizing map and statistical techniques. Comput. Biol. Chem. 30(3): 169-178 (2006) - [c45]Mitsuhiro Okada, Yutaro Sugimoto, Sumi Yoshikawa, Akihiko Konagaya:
Drug Interaction Ontology (DIO) and the Resource-Sensitive Logical Inferences. Essays Dedicated to Joseph A. Goguen 2006: 616-642 - [c44]Akihiko Konagaya:
OBIGrid: Towards the 'Ba' for Sharing Resources, Services and Knowledge for Bioinformatics. CCGRID 2006: 37 - [c43]Craig A. Stewart, Michael Schroeder, Concettina Guerra, Akihiko Konagaya:
Topic 17: High-Performance Bioinformatics. Euro-Par 2006: 1125-1126 - [c42]Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya:
Multidimensional Dynamic Programming for Homology Search on Distributed Systems. Euro-Par 2006: 1127-1137 - [c41]Fumikazu Konishi, Manabu Ishii, Shingo Ohki, Yusuke Hamano, Shuichi Fukuda, Akihiko Konagaya:
Improving the Research Environment of High Performance Computing for Non-cluster Experts Based on Knoppix Instant Computing Technology. Euro-Par 2006: 1169-1178 - [c40]Ryuzo Azuma, Tetsuji Kitagawa, Hiroshi Kobayashi, Akihiko Konagaya:
Particle Simulation Approach for Sub-cellular Dynamics and Interactions of Biological Molecules. IMSCCS (1) 2006: 150-157 - 2005
- [j13]Shuhei Kimura, Kaori Ide, Aiko Kashihara, Makoto Kano, Mariko Hatakeyama, Ryoji Masui, Noriko Nakagawa, Shigeyuki Yokoyama, Seiki Kuramitsu, Akihiko Konagaya:
Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. Bioinform. 21(7): 1154-1163 (2005) - [j12]Eli Kaminuma, Naohiko Heida, Yuko Tsumoto, Miki Nakazawa, Nobuharu Goto, Akihiko Konagaya, Minami Matsui, Tetsuro Toyoda:
Three-dimensional Definition of Leaf Morphological Traits of arabidopsis in Silico Phenotypic Analysis. J. Bioinform. Comput. Biol. 3(2): 401-414 (2005) - [j11]Tetsuya Sakurai, Masakazu Satou, Kenji Akiyama, Kei Iida, Motoaki Seki, Takashi Kuromori, Takuya Ito, Akihiko Konagaya, Tetsuro Toyoda, Kazuo Shinozaki:
RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome. Nucleic Acids Res. 33(Database-Issue): 647-650 (2005) - [c39]Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya:
Multidimensional Dynamic Programming for Homology Search. FPL 2005: 173-178 - [c38]Yoshiki Yamaguchi, Tsutomu Maruyama, Ryuzo Azuma, Akihiko Konagaya:
Spatiotemporal Simulation of a Single Living Cell. FPT 2005: 267-274 - [c37]Aki Hasegawa, Kazumi Kuriyama-Matsumura, Xiaomei Yu, Mariko Hatakeyama, Akihiko Konagaya:
Software-Aided Mass Spectrometry Analysis for Identification of Protein-Protein Interaction in Signal Transduction Pathways. ICDE Workshops 2005: 1157 - [e1]Akihiko Konagaya, Kenji Satou:
Grid Computing in Life Science, First International Workshop on Life Science Grid, LSGRID 2004, Kanazawa, Japan, May 31 - June 1, 2004, Revised Selected andInvited Papers. Lecture Notes in Computer Science 3370, Springer 2005, ISBN 3-540-25208-8 [contents] - 2004
- [j10]Tetsuo Shibuya, Hisashi Kashima, Akihiko Konagaya:
Efficient filtering methods for clustering cDNAs with spliced sequence alignment. Bioinform. 20(1): 29-39 (2004) - [j9]Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, Akihiko Konagaya:
OBIYagns: a grid-based biochemical simulator with a parameter estimator. Bioinform. 20(10): 1646-1648 (2004) - [j8]Kaoru Yamamoto, Taku Kudo, Akihiko Konagaya, Yuji Matsumoto:
Use of morphological analysis in protein name recognition. J. Biomed. Informatics 37(6): 471-482 (2004) - [j7]Takeshi Nagashima, Hideo Matsuda, Diego G. Silva, Nikolai Petrovsky, Akihiko Konagaya, Christian Schönbach:
FREP: a database of functional repeats in mouse cDNAs. Nucleic Acids Res. 32(Database-Issue): 471-475 (2004) - [j6]Peter W. Arzberger, Abbas Farazdel, Akihiko Konagaya, Larry Ang, Shinji Shimojo, Rick L. Stevens:
Life Sciences and Cyberinfrastructure: Dual and Interacting Revolutions that will Drive Future Science. New Gener. Comput. 22(2): 97-110 (2004) - [j5]Akihiko Konagaya, Fumikazu Konishi, Mariko Hatakeyama, Kenji Satou:
The Superstructure toward Open Bioinformatics Grid. New Gener. Comput. 22(2): 167-176 (2004) - [c36]Yoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya:
Three-Dimensional Dynamic Programming for Homology Search. FPL 2004: 505-515 - [c35]Naohiko Heida, Yoshikazu Hasegawa, Yoshiki Mochizuki, Katsura Hirosawa, Akihiko Konagaya, Tetsuro Toyoda:
TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks. ISMB/ECCB (Supplement of Bioinformatics) 2004: 152-160 - [c34]Junko Hosaka, Igor Kurochkin, Akihiko Konagaya:
PBIE: A Data Preparation Toolkit Toward Developing a Parsing-Based Information Extraction System. LREC 2004 - [c33]Kenji Satou, Yasuhiko Nakashima, Shin'ichi Tsuji, Xavier Défago, Akihiko Konagaya:
An Integrated System for Distributed Bioinformatics Environment on Grids. LSGRID 2004: 8-19 - [c32]Fumikazu Konishi, Akihiko Konagaya:
The Architectural Design of High-Throughput BLAST Services on OBIGrid. LSGRID 2004: 32-42 - [c31]Akinobu Fukuzaki, Takeshi Nagashima, Kaori Ide, Fumikazu Konishi, Mariko Hatakeyama, Shigeyuki Yokoyama, Seiki Kuramitsu, Akihiko Konagaya:
Genome-Wide Functional Annotation Environment forin OBIGrid. LSGRID 2004: 82-91 - [c30]Sumi Yoshikawa, Kenji Satou, Akihiko Konagaya:
Drug Interaction Ontology (DIO) for Inferences of Possible Drug-drug Interactions. MedInfo 2004: 454-458 - [c29]Shouji Tatsumoto, Kenji Satou, Akihiko Konagaya:
Prediction of Protein Secondary Structure from PDB Structure Information Based on Sequence Segments Homology Searching. METMBS 2004: 250-255 - 2003
- [j4]Tetsuro Toyoda, Akihiko Konagaya:
KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data. Bioinform. 19(3): 433-434 (2003) - [j3]Tetsuro Toyoda, Yoshiki Mochizuki, Akihiko Konagaya:
GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs. Bioinform. 19(3): 437-438 (2003) - [c28]Kaoru Yamamoto, Taku Kudo, Akihiko Konagaya, Yuji Matsumoto:
Protein Name Tagging for Biomedical Annotation in Text. BioNLP@ACL 2003: 65-72 - [c27]Shuhei Kimura, Mariko Hatakeyama, Akihiko Konagaya:
Inference of S-system models of genetic networks using a genetic local search. IEEE Congress on Evolutionary Computation 2003: 631-638 - [c26]Junko Hosaka, Judice L. Y. Koh, Akihiko Konagaya:
Effect of utilizing terminology on extraction of protein-protein interaction information from biomedical literature. EACL 2003: 107-110 - [c25]Yohei Minakuchi, Kenji Satou, Akihiko Konagaya:
Prediction of Protein-Protein Interaction Sites Using Support Vector Machines. METMBS 2003: 22-28 - [c24]Shouji Tatsumoto, Kenji Satou, Akihiko Konagaya, Jun'ichi Kurita, Hideto Shimahara, Shin-ichi Tate:
Development of Support Tool for NMR Spectrum Analysis. METMBS 2003: 159-164 - [c23]Sumi Yoshikawa, Akihiko Konagaya:
DIO: Drug Interaction Ontology - Application to Inferences in Possible Drug-Drug Interactions. METMBS 2003: 231-236 - [c22]Makoto Taiji, Tetsu Narumi, Yousuke Ohno, Akihiko Konagaya:
MDGRAPE-3: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations. PARCO 2003: 669-676 - [c21]Makoto Taiji, Tetsu Narumi, Yousuke Ohno, Noriyuki Futatsugi, Atsushi Suenaga, Naoki Takada, Akihiko Konagaya:
Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations. SC 2003: 15 - [c20]Shuhei Kimura, Akihiko Konagaya:
High dimensional function optimization using a new genetic local search suitable for parallel computers. SMC 2003: 335-342 - 2002
- [c19]Yoshiki Yamaguchi, Yosuke Miyajima, Tsutomu Maruyama, Akihiko Konagaya:
High Speed Homology Search Using Run-Time Reconfiguration. FPL 2002: 281-291 - [c18]Xavier Défago, Akihiko Konagaya:
Circle formation for oblivious anonymous mobile robots with no common sense of orientation. POMC 2002: 97-104 - [c17]Yoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya:
High Speed Homology Search with FPGAs. Pacific Symposium on Biocomputing 2002: 271-282 - [c16]Akihiko Konagaya:
OBIGrid: Towards a New Distributed Platform for Bioinformatics. SRDS 2002: 380-
1990 – 1999
- 1995
- [j2]Masato Motomura, Toshiaki Inoue, Hachiro Yamada, Akihiko Konagaya:
Cache-processor coupling: a fast and wide on-chip data cache design. IEEE J. Solid State Circuits 30(4): 375-382 (1995) - [c15]Masato Motomura, Toshiaki Inoue, Sunao Torii, Akihiko Konagaya:
Ordered multithreading: a novel technique for exploiting thread-level parallelism. PACT 1995: 37-48 - [c14]Minoru Asogawa, Yukiko Fujiwara, Akihiko Konagaya:
A combination of a functional motif model and a structural motif model for a database validation. HICSS (5) 1995: 174-183 - 1994
- [c13]Yukiko Fujiwara, Minoru Asogawa, Akihiko Konagaya:
Stochastic Motif Extraction Using Hidden Markov Model. ISMB 1994: 121-129 - 1993
- [c12]Tsutomu Maruyama, Tetsuya Hirose, Akihiko Konagaya:
A Fine-Grained Parallel Genetic Algorithm for Distributed Parallel Systems. ICGA 1993: 184-190 - [c11]Hidetoshi Tanaka, Masato Ishikawa, Kiyoshi Asai, Akihiko Konagaya:
Hidden Markov Models and Iterative Aligners: Study of Their Equivalence and Possibilities. ISMB 1993: 395-401 - 1992
- [c10]Akihiko Konagaya:
A Stochastic Approach to Genetic Information Processing. ALT 1992: 25-36 - [c9]Koichi Konishi, Tsutomu Maruyama, Akihiko Konagaya, Kaoru Yoshida, Takashi Chikayama:
Implementing Streams on Parallel Machines with Distributed Memory. FGCS 1992: 791-798 - [c8]Tsutomu Maruyama, Akihiko Konagaya, Koichi Konishi:
An Asynchronous Fine-Grained Parallel Genetic Algorithm. PPSN 1992: 569-578 - 1991
- [c7]Kenji Yamanishi, Akihiko Konagaya:
Learning Stochastic Motifs from Genetic Sequences. ML 1991: 467-471 - 1990
- [c6]Atsushi Atarashi, Akihiko Konagaya, Shinichi Habata, Minoru Yokota:
Implementation and Evaluation of Dynamic Predicates on the Sequential Inference Machine CHI. ICCL 1990: 236-244
1980 – 1989
- 1989
- [c5]Akihiko Konagaya, Shinichi Habata, Atsushi Atarashi, Minoru Yokota:
Performance Evaluation of a Sequential Inference Machine CHI. NACLP 1989: 1165-1179 - 1988
- [c4]Hidenori Itoh, Hidetoshi Monoi, Shigeki Shibayama, Nobuyoshi Miyazaki, Haruo Yokota, Akihiko Konagaya:
Knowledge Base System in Logic Programming Paradigm. FGCS 1988: 37-53 - 1987
- [c3]Akihiko Konagaya, Ryosei Nakazaki, Mamoru Umemura:
A Co-Operative Programming Environment for a Back-End Type Sequential Inference Machine CHI. Parallel Algorithms and Architectures 1987: 196-205 - 1985
- [c2]Ryosei Nakazaki, Akihiko Konagaya, Shinichi Habata, Hideo Shimazu, Mamoru Umemura, Masahiro Yamamoto, Minoru Yokota, Takashi Chikayama:
Design of a High-speed Prolog Machine (HPM). ISCA 1985: 191-197 - 1984
- [j1]Akihiko Konagaya, Mamoru Umemura:
Knowledge Information Processing Language: ShapeUp. New Gener. Comput. 2(2): 195-201 (1984) - [c1]Tetsuo Ida, Akihiko Konagaya:
Comparison of Closure Reduction and Combinatory Reduction Schemes. RIMS Symposia on Software Science and Engineering 1984: 261-291
Coauthor Index
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