Akihiko Konagaya

Publication Activity (10 Years)

Years Active: 1984-2023
Publications (10 Years): 11

Top Topics

Atomic Force Microscopy

Inverse Problems

Probabilistic Data Association

Top Venues

New Gener. Comput.

BMC Syst. Biol.

Publications

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)
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) (2022)
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) (2022)
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) (2019)
Gregory Gutmann, Akihiko Konagaya
Predictive Simulation: Using Regression and Artificial Neural Networks to Negate Latency in Networked Interactive Virtual Reality. CoRR (2019)
Yuhui Zhang, Greg Gutmann, Akihiko Konagaya
Irregular Convolutional Auto-Encoder on Point Clouds. CoRR (2019)
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) (2017)
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) (2017)
Gregory Gutmann, Daisuke Inoue, Akira Kakugo, Akihiko Konagaya
Real-time 3D microtubule gliding simulation accelerated by GPU computing. Int. J. Autom. Comput. 13 (2) (2016)
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)
Bulibuli Mahemuti, Daisuke Inoue, Akira Kakugo, Akihiko Konagaya
Investigation of the microtubule dynamics with probabilistic data association filter. NEMS (2016)
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 (2015)
Akihiko Konagaya
Molecular Robotics and Controlling. New Gener. Comput. 33 (3) (2015)
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) (2015)
Yuexing Han, Daisuke Inoue, Akira Kakugo, Akihiko Konagaya
Tracking single microtubules by using B-spline curves and Hausdorff distance. IPTA (2014)
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)
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)
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) (2013)
Satoshi Murata, Akihiko Konagaya, Satoshi Kobayashi, Hirohide Saito, Masami Hagiya
Molecular Robotics: A New Paradigm for Artifacts. New Gener. Comput. 31 (1) (2013)
Daniel P. Berrar, Akihiko Konagaya, Alfons Schuster
Turing Test Considered Mostly Harmless. New Gener. Comput. 31 (4) (2013)
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)
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) (2008)
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)
Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya
Multiple Sequence Alignment Based on Dynamic Programming Using FPGA. IEICE Trans. Inf. Syst. (12) (2007)
Takeshi Arikuma, Sumi Yoshikawa, Kentaro Watanabe, Akihiko Konagaya
Ontology-Driven Hypothetic Assertion (OHA) for Drug Interaction Prediction. IMSCCS (2007)
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)
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) (2007)
Akihiko Konagaya, Richard O. Sinnott, Peter W. Arzberger
Life Science Grid. New Gener. Comput. 25 (4) (2007)
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) (2007)
Hiroshi Kobayashi, Ryuzo Azuma, Akihiko Konagaya
Kinetic Analysis of Ligand-Receptor Complex Formation with the Aid of Computer Simulation. AINA Workshops (1) (2007)
Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya
An FPGA Implementation of Multiple Sequence Alignment Based on Carrillo-Lipman Method. FPL (2007)
Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya
Multidimensional Dynamic Programming for Homology Search on Distributed Systems. Euro-Par (2006)
Ryuzo Azuma, Tetsuji Kitagawa, Hiroshi Kobayashi, Akihiko Konagaya
Particle Simulation Approach for Sub-cellular Dynamics and Interactions of Biological Molecules. IMSCCS (1) (2006)
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)
Craig A. Stewart, Michael Schroeder, Concettina Guerra, Akihiko Konagaya
Topic 17: High-Performance Bioinformatics. Euro-Par (2006)
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)
Akihiko Konagaya
Trends in life science grid: from computing grid to knowledge grid. BMC Bioinform. 7 (S-5) (2006)
Shigeru Takasaki, Yoshihiro Kawamura, Akihiko Konagaya
Selecting effective siRNA sequences based on the self-organizing map and statistical techniques. Comput. Biol. Chem. 30 (3) (2006)
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)
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)
Akihiko Konagaya
OBIGrid: Towards the 'Ba' for Sharing Resources, Services and Knowledge for Bioinformatics. CCGRID (2006)
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) (2005)
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)
Eli Kaminuma, Naohiko Heida, Yuko Tsumoto, Miki Nakazawa, Nobuharu Goto, Akihiko Konagaya, Minami Matsui, Tetsuro Toyoda
Phenotypic Analysis. J. Bioinform. Comput. Biol. 3 (2) (2005)
Tetsuya Sakurai, Masakazu Satou, Kenji Akiyama, Kei Iida, Motoaki Seki, Takashi Kuromori, Takuya Ito, Akihiko Konagaya, Tetsuro Toyoda, Kazuo Shinozaki
resources ranging from transcriptome to phenome. Nucleic Acids Res. 33 (Database-Issue) (2005)
Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya
Multidimensional Dynamic Programming for Homology Search. FPL (2005)
Yoshiki Yamaguchi, Tsutomu Maruyama, Ryuzo Azuma, Akihiko Konagaya
Spatiotemporal Simulation of a Single Living Cell. FPT (2005)
Junko Hosaka, Igor Kurochkin, Akihiko Konagaya
PBIE: A Data Preparation Toolkit Toward Developing a Parsing-Based Information Extraction System. LREC (2004)
Sumi Yoshikawa, Kenji Satou, Akihiko Konagaya
Drug Interaction Ontology (DIO) for Inferences of Possible Drug-drug Interactions. MedInfo (2004)
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) (2004)
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)
Shouji Tatsumoto, Kenji Satou, Akihiko Konagaya
Prediction of Protein Secondary Structure from PDB Structure Information Based on Sequence Segments Homology Searching. METMBS (2004)
Akihiko Konagaya, Fumikazu Konishi, Mariko Hatakeyama, Kenji Satou
The Superstructure toward Open Bioinformatics Grid. New Gener. Comput. 22 (2) (2004)
Tetsuo Shibuya, Hisashi Kashima, Akihiko Konagaya
Efficient filtering methods for clustering cDNAs with spliced sequence alignment. Bioinform. 20 (1) (2004)
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) (2004)
Yoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya
Three-Dimensional Dynamic Programming for Homology Search. FPL (2004)
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)
Kenji Satou, Yasuhiko Nakashima, Shin'ichi Tsuji, Xavier Défago, Akihiko Konagaya
An Integrated System for Distributed Bioinformatics Environment on Grids. LSGRID (2004)
Fumikazu Konishi, Akihiko Konagaya
The Architectural Design of High-Throughput BLAST Services on OBIGrid. LSGRID (2004)
Kaoru Yamamoto, Taku Kudo, Akihiko Konagaya, Yuji Matsumoto
Use of morphological analysis in protein name recognition. J. Biomed. Informatics 37 (6) (2004)
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) (2004)
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)
Kaoru Yamamoto, Taku Kudo, Akihiko Konagaya, Yuji Matsumoto
Protein Name Tagging for Biomedical Annotation in Text. BioNLP@ACL (2003)
Tetsuro Toyoda, Akihiko Konagaya
KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data. Bioinform. 19 (3) (2003)
Sumi Yoshikawa, Akihiko Konagaya
DIO: Drug Interaction Ontology - Application to Inferences in Possible Drug-Drug Interactions. METMBS (2003)
Tetsuro Toyoda, Yoshiki Mochizuki, Akihiko Konagaya
GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs. Bioinform. 19 (3) (2003)
Shouji Tatsumoto, Kenji Satou, Akihiko Konagaya, Jun'ichi Kurita, Hideto Shimahara, Shin-ichi Tate
Development of Support Tool for NMR Spectrum Analysis. METMBS (2003)
Makoto Taiji, Tetsu Narumi, Yousuke Ohno, Akihiko Konagaya
MDGRAPE-3: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations. PARCO (2003)
Yohei Minakuchi, Kenji Satou, Akihiko Konagaya
Prediction of Protein-Protein Interaction Sites Using Support Vector Machines. METMBS (2003)
Junko Hosaka, Judice L. Y. Koh, Akihiko Konagaya
Effect of utilizing terminology on extraction of protein-protein interaction information from biomedical literature. EACL (2003)
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)
Shuhei Kimura, Akihiko Konagaya
High dimensional function optimization using a new genetic local search suitable for parallel computers. SMC (2003)
Yoshiki Yamaguchi, Yosuke Miyajima, Tsutomu Maruyama, Akihiko Konagaya
High Speed Homology Search Using Run-Time Reconfiguration. FPL (2002)
Yoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya
High Speed Homology Search with FPGAs. Pacific Symposium on Biocomputing (2002)
Akihiko Konagaya
OBIGrid: Towards a New Distributed Platform for Bioinformatics. SRDS (2002)
Xavier Défago, Akihiko Konagaya
Circle formation for oblivious anonymous mobile robots with no common sense of orientation. POMC (2002)
Masato Motomura, Toshiaki Inoue, Sunao Torii, Akihiko Konagaya
Ordered multithreading: a novel technique for exploiting thread-level parallelism. PACT (1995)
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) (1995)
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)
Yukiko Fujiwara, Minoru Asogawa, Akihiko Konagaya
Stochastic Motif Extraction Using Hidden Markov Model. ISMB (1994)
Tsutomu Maruyama, Tetsuya Hirose, Akihiko Konagaya
A Fine-Grained Parallel Genetic Algorithm for Distributed Parallel Systems. ICGA (1993)
Hidetoshi Tanaka, Masato Ishikawa, Kiyoshi Asai, Akihiko Konagaya
Hidden Markov Models and Iterative Aligners: Study of Their Equivalence and Possibilities. ISMB (1993)
Koichi Konishi, Tsutomu Maruyama, Akihiko Konagaya, Kaoru Yoshida, Takashi Chikayama
Implementing Streams on Parallel Machines with Distributed Memory. FGCS (1992)
Tsutomu Maruyama, Akihiko Konagaya, Koichi Konishi
An Asynchronous Fine-Grained Parallel Genetic Algorithm. PPSN (1992)
Akihiko Konagaya
A Stochastic Approach to Genetic Information Processing. ALT (1992)
Kenji Yamanishi, Akihiko Konagaya
Learning Stochastic Motifs from Genetic Sequences. ML (1991)
Atsushi Atarashi, Akihiko Konagaya, Shinichi Habata, Minoru Yokota
Implementation and Evaluation of Dynamic Predicates on the Sequential Inference Machine CHI. ICCL (1990)
Akihiko Konagaya, Shinichi Habata, Atsushi Atarashi, Minoru Yokota
Performance Evaluation of a Sequential Inference Machine CHI. NACLP (1989)
Hidenori Itoh, Hidetoshi Monoi, Shigeki Shibayama, Nobuyoshi Miyazaki, Haruo Yokota, Akihiko Konagaya
Knowledge Base System in Logic Programming Paradigm. FGCS (1988)
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)
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)
Akihiko Konagaya, Mamoru Umemura
Knowledge Information Processing Language: ShapeUp. New Gener. Comput. 2 (2) (1984)
Tetsuo Ida, Akihiko Konagaya
Comparison of Closure Reduction and Combinatory Reduction Schemes. RIMS Symposia on Software Science and Engineering (1984)