Akihiko Konagaya

95 papers A* 1A 5B 13Misc 1Journal 40Unranked 33

Year	Rank	Type	Title / Venue / Authors
2023	J	`jnl`	Co-creation environment with cloud virtual reality and real-time artificial intelligence toward the design of molecular robots. J. Integr. Bioinform. Akihiko Konagaya, Gregory Gutmann, Yuhui Zhang
2022	J	`jnl`	A novel transfer learning for recognition of overlapping nano object. Neural Comput. Appl. Yuexing Han, Yuhong Liu, Bing Wang, Qiaochuan Chen, Leilei Song, Lin Tong, Chuanbin Lai, Akihiko Konagaya
2022	J	`jnl`	Utility of constraints reflecting system stability on analyses for biological models. PLoS Comput. Biol. Yoshiaki Kariya, Masashi Honma, Keita Tokuda, Akihiko Konagaya, Hiroshi Suzuki
2019	J	`jnl`	A high-performance haptic rendering system for virtual reality molecular modeling. Artif. Life Robotics Arif Pramudwiatmoko, Satoru Tsutoh, Gregory Gutmann, Yutaka Ueno, Akihiko Konagaya
2019	J	`jnl`	Irregular Convolutional Auto-Encoder on Point Clouds. CoRR Yuhui Zhang, Greg Gutmann, Akihiko Konagaya
2019	J	`jnl`	Predictive Simulation: Using Regression and Artificial Neural Networks to Negate Latency in Networked Interactive Virtual Reality. CoRR Gregory Gutmann, Akihiko Konagaya
2017	J	`jnl`	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. Shun Asami, Daisuke Kiga, Akihiko Konagaya
2017	J	`jnl`	Parallel Interaction Detection Algorithms for a Particle-based Live Controlled Real-time Microtubule Gliding Simulation System Accelerated by GPGPU. New Gener. Comput. Gregory Gutmann, Daisuke Inoue, Akira Kakugo, Akihiko Konagaya
2016	—	`conf`	Investigation of the microtubule dynamics with probabilistic data association filter. NEMS Bulibuli Mahemuti, Daisuke Inoue, Akira Kakugo, Akihiko Konagaya
2016	J	`jnl`	Real-time 3D microtubule gliding simulation accelerated by GPU computing. Int. J. Autom. Comput. Gregory Gutmann, Daisuke Inoue, Akira Kakugo, Akihiko Konagaya
2016	—	`conf`	Using a master and slave approach for GPGPU computing to achieve optimal scaling in a 3D real-time simulation. NEMS Gregory Gutmann, Daisuke Inoue, Akira Kakugo, Akihiko Konagaya
2015	J	`jnl`	Automatic Recognition of DNA Pliers in Atomic Force Microscopy Images. New Gener. Comput. Yuexing Han, Akito Hara, Akinori Kuzuya, Ryosuke Watanabe, Yuichi Ohya, Akihiko Konagaya
2015	J	`jnl`	Improvements to the cluster Newton method for underdetermined inverse problems. J. Comput. Appl. Math. Philippe Gaudreau, Ken Hayami, Yasunori Aoki, Hassan Safouhi, Akihiko Konagaya
2015	J	`jnl`	Molecular Robotics and Controlling. New Gener. Comput. Akihiko Konagaya
2014	J	`jnl`	Cluster Newton Method for Sampling Multiple Solutions of Underdetermined Inverse Problems: Application to a Parameter Identification Problem in Pharmacokinetics. SIAM J. Sci. Comput. Yasunori Aoki, Ken Hayami, Hans De Sterck, Akihiko Konagaya
2014	J	`jnl`	Implementing a modeling software for animated protein-complex interactions using a physics simulation library. J. Bioinform. Comput. Biol. Yutaka Ueno, Shuntaro Ito, Akihiko Konagaya
2014	—	`conf`	Tracking single microtubules by using B-spline curves and Hausdorff distance. IPTA Yuexing Han, Daisuke Inoue, Akira Kakugo, Akihiko Konagaya
2013	J	`jnl`	Estimation of feasible solution space using Cluster Newton Method: application to pharmacokinetic analysis of irinotecan with physiologically-based pharmacokinetic models. BMC Syst. Biol. Kenta Yoshida, Kazuya Maeda, Hiroyuki Kusuhara, Akihiko Konagaya
2013	J	`jnl`	Molecular Robotics: A New Paradigm for Artifacts. New Gener. Comput. Satoshi Murata, Akihiko Konagaya, Satoshi Kobayashi, Hirohide Saito, Masami Hagiya
2013	J	`jnl`	Turing Test Considered Mostly Harmless. New Gener. Comput. Daniel P. Berrar, Akihiko Konagaya, Alfons Schuster
2008	J	`jnl`	Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical simulation. BMC Bioinform. Takeshi Arikuma, Sumi Yoshikawa, Ryuzo Azuma, Kentaro Watanabe, Kazumi Matsumura, Akihiko Konagaya
2008	J	`jnl`	Guest Editorial Introduction to the Special Section on BioGrid: Biomedical Computations on the Grid. IEEE Trans. Inf. Technol. Biomed. Chun-Hsi Huang, Akihiko Konagaya, Vincenzo Lanza, Peter M. A. Sloot
2007	B	`conf`	An FPGA Implementation of Multiple Sequence Alignment Based on Carrillo-Lipman Method. FPL Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya
2007	J	`jnl`	Discovering Dynamic Characteristics of Biochemical Pathways using Geometric Patterns among Parameter-Parameter Dependencies in Differential Equations. New Gener. Comput. Ryuzo Azuma, Ryo Umetsu, Shingo Ohki, Fumikazu Konishi, Sumi Yoshikawa, Akihiko Konagaya, Kazumi Matsumura
2007	B	`conf`	High speed tablation system using an FPGA designed for distribution tables of frequent DNA subsequences. FPL Yoshiki Yamaguchi, Tsutomu Maruyama, Fumikazu Konishi, Akihiko Konagaya
2007	—	`conf`	Kinetic Analysis of Ligand-Receptor Complex Formation with the Aid of Computer Simulation. AINA Workshops (1) Hiroshi Kobayashi, Ryuzo Azuma, Akihiko Konagaya
2007	J	`jnl`	Life Science Grid. New Gener. Comput. Akihiko Konagaya, Richard O. Sinnott, Peter W. Arzberger
2007	J	`jnl`	Mesoscopic-level Simulation of Dynamics and Interactions of Biological Molecules Using Monte Carlo Simulation. J. VLSI Signal Process. Yoshiki Yamaguchi, Tsutomu Maruyama, Ryuzo Azuma, Moritoshi Yasunaga, Akihiko Konagaya
2007	J	`jnl`	Multiple Sequence Alignment Based on Dynamic Programming Using FPGA. IEICE Trans. Inf. Syst. Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya
2007	—	`conf`	Ontology-Driven Hypothetic Assertion (OHA) for Drug Interaction Prediction. IMSCCS Takeshi Arikuma, Sumi Yoshikawa, Kentaro Watanabe, Akihiko Konagaya
2007	B	`conf`	RABC: A Conceptual Design of Pervasive Infrastructure for Browser Computing based on Ajax technologies. CCGRID Fumikazu Konishi, Manabu Ishii, Shingo Ohki, Ryo Umetsu, Akihiko Konagaya
2007	—	`ch.`	Seeing Is Knowing: Visualization of Parameter-Parameter Dependencies in Biomedical Network Models. Grid Computing for Bioinformatics and Computational Biology Akihiko Konagaya, Ryuzo Azuma, Ryo Umetsu, Shingo Ohki, Fumikazu Konishi, Kazumi Matsumura, Sumi Yoshikawa
2006	—	`conf`	Drug Interaction Ontology (DIO) and the Resource-Sensitive Logical Inferences. Essays Dedicated to Joseph A. Goguen Mitsuhiro Okada, Yutaro Sugimoto, Sumi Yoshikawa, Akihiko Konagaya
2006	—	`conf`	Improving the Research Environment of High Performance Computing for Non-cluster Experts Based on Knoppix Instant Computing Technology. Euro-Par Fumikazu Konishi, Manabu Ishii, Shingo Ohki, Yusuke Hamano, Shuichi Fukuda, Akihiko Konagaya
2006	—	`conf`	Multidimensional Dynamic Programming for Homology Search on Distributed Systems. Euro-Par Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya
2006	B	`conf`	OBIGrid: Towards the 'Ba' for Sharing Resources, Services and Knowledge for Bioinformatics. CCGRID Akihiko Konagaya
2006	—	`conf`	Particle Simulation Approach for Sub-cellular Dynamics and Interactions of Biological Molecules. IMSCCS (1) Ryuzo Azuma, Tetsuji Kitagawa, Hiroshi Kobayashi, Akihiko Konagaya
2006	J	`jnl`	Particle simulation approach for subcellular dynamics and interactions of biological molecules. BMC Bioinform. Ryuzo Azuma, Tetsuji Kitagawa, Hiroshi Kobayashi, Akihiko Konagaya
2006	J	`jnl`	Selecting effective siRNA sequences based on the self-organizing map and statistical techniques. Comput. Biol. Chem. Shigeru Takasaki, Yoshihiro Kawamura, Akihiko Konagaya
2006	J	`jnl`	Selecting effective siRNA sequences by using radial basis function network and decision tree learning. BMC Bioinform. Shigeru Takasaki, Yoshihiro Kawamura, Akihiko Konagaya
2006	—	`conf`	Topic 17: High-Performance Bioinformatics. Euro-Par Craig A. Stewart, Michael Schroeder, Concettina Guerra, Akihiko Konagaya
2006	J	`jnl`	Trends in life science grid: from computing grid to knowledge grid. BMC Bioinform. Akihiko Konagaya
2005	—	`ed.`	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 LSGRID Akihiko Konagaya, Kenji Satou
2005	J	`jnl`	Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. Bioinform. Shuhei Kimura, Kaori Ide, Aiko Kashihara, Makoto Kano, Mariko Hatakeyama, Ryoji Masui, Noriko Nakagawa, Shigeyuki Yokoyama, Seiki Kuramitsu, Akihiko Konagaya
2005	B	`conf`	Multidimensional Dynamic Programming for Homology Search. FPL Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya
2005	J	`jnl`	RARGE: a large-scale database of RIKEN Nucleic Acids Res. Tetsuya Sakurai, Masakazu Satou, Kenji Akiyama, Kei Iida, Motoaki Seki, Takashi Kuromori, Takuya Ito, Akihiko Konagaya, Tetsuro Toyoda, Kazuo Shinozaki
2005	—	`conf`	Software-Aided Mass Spectrometry Analysis for Identification of Protein-Protein Interaction in Signal Transduction Pathways. ICDE Workshops Aki Hasegawa, Kazumi Kuriyama-Matsumura, Xiaomei Yu, Mariko Hatakeyama, Akihiko Konagaya
2005	—	`conf`	Spatiotemporal Simulation of a Single Living Cell. FPT Yoshiki Yamaguchi, Tsutomu Maruyama, Ryuzo Azuma, Akihiko Konagaya
2005	J	`jnl`	Three-dimensional Definition of Leaf Morphological Traits of J. Bioinform. Comput. Biol. Eli Kaminuma, Naohiko Heida, Yuko Tsumoto, Miki Nakazawa, Nobuharu Goto, Akihiko Konagaya, Minami Matsui, Tetsuro Toyoda
2004	—	`conf`	An Integrated System for Distributed Bioinformatics Environment on Grids. LSGRID Kenji Satou, Yasuhiko Nakashima, Shin'ichi Tsuji, Xavier Défago, Akihiko Konagaya
2004	—	`conf`	Drug Interaction Ontology (DIO) for Inferences of Possible Drug-drug Interactions. MedInfo Sumi Yoshikawa, Kenji Satou, Akihiko Konagaya
2004	J	`jnl`	Efficient filtering methods for clustering cDNAs with spliced sequence alignment. Bioinform. Tetsuo Shibuya, Hisashi Kashima, Akihiko Konagaya
2004	J	`jnl`	FREP: a database of functional repeats in mouse cDNAs. Nucleic Acids Res. Takeshi Nagashima, Hideo Matsuda, Diego G. Silva, Nikolai Petrovsky, Akihiko Konagaya, Christian Schönbach
2004	—	`conf`	Genome-Wide Functional Annotation Environment forin OBIGrid. LSGRID Akinobu Fukuzaki, Takeshi Nagashima, Kaori Ide, Fumikazu Konishi, Mariko Hatakeyama, Shigeyuki Yokoyama, Seiki Kuramitsu, Akihiko Konagaya
2004	J	`jnl`	Life Sciences and Cyberinfrastructure: Dual and Interacting Revolutions that will Drive Future Science. New Gener. Comput. Peter W. Arzberger, Abbas Farazdel, Akihiko Konagaya, Larry Ang, Shinji Shimojo, Rick L. Stevens
2004	J	`jnl`	OBIYagns: a grid-based biochemical simulator with a parameter estimator. Bioinform. Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, Akihiko Konagaya
2004	B	`conf`	PBIE: A Data Preparation Toolkit Toward Developing a Parsing-Based Information Extraction System. LREC Junko Hosaka, Igor Kurochkin, Akihiko Konagaya
2004	—	`conf`	Prediction of Protein Secondary Structure from PDB Structure Information Based on Sequence Segments Homology Searching. METMBS Shouji Tatsumoto, Kenji Satou, Akihiko Konagaya
2004	—	`conf`	The Architectural Design of High-Throughput BLAST Services on OBIGrid. LSGRID Fumikazu Konishi, Akihiko Konagaya
2004	J	`jnl`	The Superstructure toward Open Bioinformatics Grid. New Gener. Comput. Akihiko Konagaya, Fumikazu Konishi, Mariko Hatakeyama, Kenji Satou
2004	B	`conf`	Three-Dimensional Dynamic Programming for Homology Search. FPL Yoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya
2004	—	`conf`	TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks. ISMB/ECCB (Supplement of Bioinformatics) Naohiko Heida, Yoshikazu Hasegawa, Yoshiki Mochizuki, Katsura Hirosawa, Akihiko Konagaya, Tetsuro Toyoda
2004	J	`jnl`	Use of morphological analysis in protein name recognition. J. Biomed. Informatics Kaoru Yamamoto, Taku Kudo, Akihiko Konagaya, Yuji Matsumoto
2003	—	`conf`	DIO: Drug Interaction Ontology - Application to Inferences in Possible Drug-Drug Interactions. METMBS Sumi Yoshikawa, Akihiko Konagaya
2003	—	`conf`	Development of Support Tool for NMR Spectrum Analysis. METMBS Shouji Tatsumoto, Kenji Satou, Akihiko Konagaya, Jun'ichi Kurita, Hideto Shimahara, Shin-ichi Tate
2003	A	`conf`	Effect of utilizing terminology on extraction of protein-protein interaction information from biomedical literature. EACL Junko Hosaka, Judice L. Y. Koh, Akihiko Konagaya
2003	J	`jnl`	GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs. Bioinform. Tetsuro Toyoda, Yoshiki Mochizuki, Akihiko Konagaya
2003	B	`conf`	High dimensional function optimization using a new genetic local search suitable for parallel computers. SMC Shuhei Kimura, Akihiko Konagaya
2003	B	`conf`	Inference of S-system models of genetic networks using a genetic local search. IEEE Congress on Evolutionary Computation Shuhei Kimura, Mariko Hatakeyama, Akihiko Konagaya
2003	J	`jnl`	KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data. Bioinform. Tetsuro Toyoda, Akihiko Konagaya
2003	—	`conf`	MDGRAPE-3: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations. PARCO Makoto Taiji, Tetsu Narumi, Yousuke Ohno, Akihiko Konagaya
2003	—	`conf`	Prediction of Protein-Protein Interaction Sites Using Support Vector Machines. METMBS Yohei Minakuchi, Kenji Satou, Akihiko Konagaya
2003	A	`conf`	Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations. SC Makoto Taiji, Tetsu Narumi, Yousuke Ohno, Noriyuki Futatsugi, Atsushi Suenaga, Naoki Takada, Akihiko Konagaya
2003	—	`conf`	Protein Name Tagging for Biomedical Annotation in Text. BioNLP@ACL Kaoru Yamamoto, Taku Kudo, Akihiko Konagaya, Yuji Matsumoto
2002	—	`conf`	Circle formation for oblivious anonymous mobile robots with no common sense of orientation. POMC Xavier Défago, Akihiko Konagaya
2002	B	`conf`	High Speed Homology Search Using Run-Time Reconfiguration. FPL Yoshiki Yamaguchi, Yosuke Miyajima, Tsutomu Maruyama, Akihiko Konagaya
2002	Misc	`conf`	High Speed Homology Search with FPGAs. Pacific Symposium on Biocomputing Yoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya
2002	B	`conf`	OBIGrid: Towards a New Distributed Platform for Bioinformatics. SRDS Akihiko Konagaya
1995	—	`conf`	A combination of a functional motif model and a structural motif model for a database validation. HICSS (5) Minoru Asogawa, Yukiko Fujiwara, Akihiko Konagaya
1995	J	`jnl`	Cache-processor coupling: a fast and wide on-chip data cache design. IEEE J. Solid State Circuits Masato Motomura, Toshiaki Inoue, Hachiro Yamada, Akihiko Konagaya
1995	B	`conf`	Ordered multithreading: a novel technique for exploiting thread-level parallelism. PACT Masato Motomura, Toshiaki Inoue, Sunao Torii, Akihiko Konagaya
1994	A	`conf`	Stochastic Motif Extraction Using Hidden Markov Model. ISMB Yukiko Fujiwara, Minoru Asogawa, Akihiko Konagaya
1993	—	`conf`	A Fine-Grained Parallel Genetic Algorithm for Distributed Parallel Systems. ICGA Tsutomu Maruyama, Tetsuya Hirose, Akihiko Konagaya
1993	A	`conf`	Hidden Markov Models and Iterative Aligners: Study of Their Equivalence and Possibilities. ISMB Hidetoshi Tanaka, Masato Ishikawa, Kiyoshi Asai, Akihiko Konagaya
1992	B	`conf`	A Stochastic Approach to Genetic Information Processing. ALT Akihiko Konagaya
1992	A	`conf`	An Asynchronous Fine-Grained Parallel Genetic Algorithm. PPSN Tsutomu Maruyama, Akihiko Konagaya, Koichi Konishi
1992	—	`conf`	Implementing Streams on Parallel Machines with Distributed Memory. FGCS Koichi Konishi, Tsutomu Maruyama, Akihiko Konagaya, Kaoru Yoshida, Takashi Chikayama
1991	—	`conf`	Learning Stochastic Motifs from Genetic Sequences. ML Kenji Yamanishi, Akihiko Konagaya
1990	—	`conf`	Implementation and Evaluation of Dynamic Predicates on the Sequential Inference Machine CHI. ICCL Atsushi Atarashi, Akihiko Konagaya, Shinichi Habata, Minoru Yokota
1989	—	`conf`	Performance Evaluation of a Sequential Inference Machine CHI. NACLP Akihiko Konagaya, Shinichi Habata, Atsushi Atarashi, Minoru Yokota
1988	—	`conf`	Knowledge Base System in Logic Programming Paradigm. FGCS Hidenori Itoh, Hidetoshi Monoi, Shigeki Shibayama, Nobuyoshi Miyazaki, Haruo Yokota, Akihiko Konagaya
1987	—	`conf`	A Co-Operative Programming Environment for a Back-End Type Sequential Inference Machine CHI. Parallel Algorithms and Architectures Akihiko Konagaya, Ryosei Nakazaki, Mamoru Umemura
1985	A*	`conf`	Design of a High-speed Prolog Machine (HPM). ISCA Ryosei Nakazaki, Akihiko Konagaya, Shinichi Habata, Hideo Shimazu, Mamoru Umemura, Masahiro Yamamoto, Minoru Yokota, Takashi Chikayama
1984	—	`conf`	Comparison of Closure Reduction and Combinatory Reduction Schemes. RIMS Symposia on Software Science and Engineering Tetsuo Ida, Akihiko Konagaya
1984	J	`jnl`	Knowledge Information Processing Language: ShapeUp. New Gener. Comput. Akihiko Konagaya, Mamoru Umemura