Comparison of Closure Reduction and Combinatory Reduction Schemes. - Tetsuo Ida; Akihiko Konagaya (RIMS Symposia on Software Science and Engineering, 1984)

Knowledge Information Processing Language: ShapeUp. - Akihiko Konagaya; Mamoru Umemura (New Gener. Comput., 1984)

Design of a High-speed Prolog Machine (HPM). - Ryosei Nakazaki; Akihiko Konagaya; Shinichi Habata; Hideo Shimazu; Mamoru Umemura; Masahiro Yamamoto; Minoru Yokota; Takashi Chikayama (ISCA, 1985)

A Co-Operative Programming Environment for a Back-End Type Sequential Inference Machine CHI. - Akihiko Konagaya; Ryosei Nakazaki; Mamoru Umemura (Parallel Algorithms and Architectures, 1987)

Knowledge Base System in Logic Programming Paradigm. - Hidenori Itoh; Hidetoshi Monoi; Shigeki Shibayama; Nobuyoshi Miyazaki; Haruo Yokota; Akihiko Konagaya (FGCS, 1988)

Performance Evaluation of a Sequential Inference Machine CHI. - Akihiko Konagaya; Shinichi Habata; Atsushi Atarashi; Minoru Yokota (NACLP, 1989)

Implementation and Evaluation of Dynamic Predicates on the Sequential Inference Machine CHI. - Atsushi Atarashi; Akihiko Konagaya; Shinichi Habata; Minoru Yokota (ICCL, 1990)

Learning Stochastic Motifs from Genetic Sequences. - Kenji Yamanishi; Akihiko Konagaya (ML, 1991)

A Stochastic Approach to Genetic Information Processing. - Akihiko Konagaya (ALT, 1992)

Implementing Streams on Parallel Machines with Distributed Memory. - Koichi Konishi; Tsutomu Maruyama; Akihiko Konagaya; Kaoru Yoshida; Takashi Chikayama (FGCS, 1992)

An Asynchronous Fine-Grained Parallel Genetic Algorithm. - Tsutomu Maruyama; Akihiko Konagaya; Koichi Konishi (PPSN, 1992)

A Fine-Grained Parallel Genetic Algorithm for Distributed Parallel Systems. - Tsutomu Maruyama; Tetsuya Hirose; Akihiko Konagaya (ICGA, 1993)

Hidden Markov Models and Iterative Aligners: Study of Their Equivalence and Possibilities. - Hidetoshi Tanaka; Masato Ishikawa; Kiyoshi Asai; Akihiko Konagaya (ISMB, 1993)

Stochastic Motif Extraction Using Hidden Markov Model. - Yukiko Fujiwara; Minoru Asogawa; Akihiko Konagaya (ISMB, 1994)

Ordered multithreading: a novel technique for exploiting thread-level parallelism. - Masato Motomura; Toshiaki Inoue; Sunao Torii; Akihiko Konagaya (PACT, 1995)

A combination of a functional motif model and a structural motif model for a database validation. - Minoru Asogawa; Yukiko Fujiwara; Akihiko Konagaya (HICSS (5), 1995)

Cache-processor coupling: a fast and wide on-chip data cache design. - Masato Motomura; Toshiaki Inoue; Hachiro Yamada; Akihiko Konagaya (IEEE J. Solid State Circuits, 1995)

High Speed Homology Search Using Run-Time Reconfiguration. - Yoshiki Yamaguchi; Yosuke Miyajima; Tsutomu Maruyama; Akihiko Konagaya (FPL, 2002)

Circle formation for oblivious anonymous mobile robots with no common sense of orientation. - Xavier Défago; Akihiko Konagaya (POMC, 2002)

High Speed Homology Search with FPGAs. - Yoshiki Yamaguchi; Tsutomu Maruyama; Akihiko Konagaya (Pacific Symposium on Biocomputing, 2002)

OBIGrid: Towards a New Distributed Platform for Bioinformatics. - Akihiko Konagaya (SRDS, 2002)

Protein Name Tagging for Biomedical Annotation in Text. - Kaoru Yamamoto; Taku Kudo; Akihiko Konagaya; Yuji Matsumoto 001 (BioNLP@ACL, 2003)

Inference of S-system models of genetic networks using a genetic local search. - Shuhei Kimura; Mariko Hatakeyama; Akihiko Konagaya (IEEE Congress on Evolutionary Computation, 2003)

Effect of utilizing terminology on extraction of protein-protein interaction information from biomedical literature. - Junko Hosaka; Judice L. Y. Koh; Akihiko Konagaya (EACL, 2003)

Prediction of Protein-Protein Interaction Sites Using Support Vector Machines. - Yohei Minakuchi; Kenji Satou; Akihiko Konagaya (METMBS, 2003)

Development of Support Tool for NMR Spectrum Analysis. - Shouji Tatsumoto; Kenji Satou; Akihiko Konagaya; Jun'ichi Kurita; Hideto Shimahara; Shin-ichi Tate (METMBS, 2003)

DIO: Drug Interaction Ontology - Application to Inferences in Possible Drug-Drug Interactions. - Sumi Yoshikawa; Akihiko Konagaya (METMBS, 2003)

MDGRAPE-3: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations. - Makoto Taiji; Tetsu Narumi; Yousuke Ohno; Akihiko Konagaya (PARCO, 2003)

Protein Explorer: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations. - Makoto Taiji; Tetsu Narumi; Yousuke Ohno; Noriyuki Futatsugi; Atsushi Suenaga; Naoki Takada; Akihiko Konagaya (SC, 2003)

High dimensional function optimization using a new genetic local search suitable for parallel computers. - Shuhei Kimura; Akihiko Konagaya (SMC, 2003)

KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data. - Tetsuro Toyoda; Akihiko Konagaya (Bioinform., 2003)

GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs. - Tetsuro Toyoda; Yoshiki Mochizuki; Akihiko Konagaya (Bioinform., 2003)

Three-Dimensional Dynamic Programming for Homology Search. - Yoshiki Yamaguchi; Tsutomu Maruyama; Akihiko Konagaya (FPL, 2004)

TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks. - Naohiko Heida; Yoshikazu Hasegawa; Yoshiki Mochizuki; Katsura Hirosawa; Akihiko Konagaya; Tetsuro Toyoda (ISMB/ECCB (Supplement of Bioinformatics), 2004)

PBIE: A Data Preparation Toolkit Toward Developing a Parsing-Based Information Extraction System. - Junko Hosaka; Igor Kurochkin; Akihiko Konagaya (LREC, 2004)

Genome-Wide Functional Annotation Environment forin OBIGrid. - Akinobu Fukuzaki; Takeshi Nagashima; Kaori Ide; Fumikazu Konishi; Mariko Hatakeyama; Shigeyuki Yokoyama; Seiki Kuramitsu; Akihiko Konagaya (LSGRID, 2004)

The Architectural Design of High-Throughput BLAST Services on OBIGrid. - Fumikazu Konishi; Akihiko Konagaya (LSGRID, 2004)

An Integrated System for Distributed Bioinformatics Environment on Grids. - Kenji Satou; Yasuhiko Nakashima; Shin'ichi Tsuji; Xavier Défago; Akihiko Konagaya (LSGRID, 2004)

Drug Interaction Ontology (DIO) for Inferences of Possible Drug-drug Interactions. - Sumi Yoshikawa; Kenji Satou; Akihiko Konagaya (MedInfo, 2004)

Prediction of Protein Secondary Structure from PDB Structure Information Based on Sequence Segments Homology Searching. - Shouji Tatsumoto; Kenji Satou; Akihiko Konagaya (METMBS, 2004)

OBIYagns: a grid-based biochemical simulator with a parameter estimator. - Shuhei Kimura; Takuji Kawasaki; Mariko Hatakeyama; Takashi Naka; Fumikazu Konishi; Akihiko Konagaya (Bioinform., 2004)

Efficient filtering methods for clustering cDNAs with spliced sequence alignment. - Tetsuo Shibuya; Hisashi Kashima; Akihiko Konagaya (Bioinform., 2004)

Use of morphological analysis in protein name recognition. - Kaoru Yamamoto; Taku Kudo; Akihiko Konagaya; Yuji Matsumoto 001 (J. Biomed. Informatics, 2004)

FREP: a database of functional repeats in mouse cDNAs. - Takeshi Nagashima; Hideo Matsuda; Diego G. Silva; Nikolai Petrovsky; Akihiko Konagaya; Christian Schönbach (Nucleic Acids Res., 2004)

Life Sciences and Cyberinfrastructure: Dual and Interacting Revolutions that will Drive Future Science. - Peter W. Arzberger; Abbas Farazdel; Akihiko Konagaya; Larry Ang; Shinji Shimojo; Rick L. Stevens (New Gener. Comput., 2004)

The Superstructure toward Open Bioinformatics Grid. - Akihiko Konagaya; Fumikazu Konishi; Mariko Hatakeyama; Kenji Satou (New Gener. Comput., 2004)

Multidimensional Dynamic Programming for Homology Search. - Shingo Masuno; Tsutomu Maruyama; Yoshiki Yamaguchi; Akihiko Konagaya (FPL, 2005)

Spatiotemporal Simulation of a Single Living Cell. - Yoshiki Yamaguchi; Tsutomu Maruyama; Ryuzo Azuma; Akihiko Konagaya (FPT, 2005)

Software-Aided Mass Spectrometry Analysis for Identification of Protein-Protein Interaction in Signal Transduction Pathways. - Aki Hasegawa; Kazumi Kuriyama-Matsumura; Xiaomei Yu; Mariko Hatakeyama; Akihiko Konagaya (ICDE Workshops, 2005)

Inference of S-system models of genetic networks using a cooperative coevolutionary algorithm. - Shuhei Kimura; Kaori Ide; Aiko Kashihara; Makoto Kano; Mariko Hatakeyama; Ryoji Masui; Noriko Nakagawa; Shigeyuki Yokoyama; Seiki Kuramitsu; Akihiko Konagaya (Bioinform., 2005)

Three-dimensional Definition of Leaf Morphological Traits of arabidopsis in Silico Phenotypic Analysis. - Eli Kaminuma; Naohiko Heida; Yuko Tsumoto; Miki Nakazawa; Nobuharu Goto; Akihiko Konagaya; Minami Matsui; Tetsuro Toyoda (J. Bioinform. Comput. Biol., 2005)

RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome. - Tetsuya Sakurai; Masakazu Satou; Kenji Akiyama; Kei Iida; Motoaki Seki; Takashi Kuromori; Takuya Ito; Akihiko Konagaya; Tetsuro Toyoda; Kazuo Shinozaki (Nucleic Acids Res., 2005)

Drug Interaction Ontology (DIO) and the Resource-Sensitive Logical Inferences. - Mitsuhiro Okada; Yutaro Sugimoto; Sumi Yoshikawa; Akihiko Konagaya (Essays Dedicated to Joseph A. Goguen, 2006)

OBIGrid: Towards the 'Ba' for Sharing Resources, Services and Knowledge for Bioinformatics. - Akihiko Konagaya (CCGRID, 2006)

Improving the Research Environment of High Performance Computing for Non-cluster Experts Based on Knoppix Instant Computing Technology. - Fumikazu Konishi; Manabu Ishii; Shingo Ohki; Yusuke Hamano; Shuichi Fukuda; Akihiko Konagaya (Euro-Par, 2006)

Multidimensional Dynamic Programming for Homology Search on Distributed Systems. - Shingo Masuno; Tsutomu Maruyama; Yoshiki Yamaguchi; Akihiko Konagaya (Euro-Par, 2006)

Topic 17: High-Performance Bioinformatics. - Craig A. Stewart; Michael Schroeder 001; Concettina Guerra; Akihiko Konagaya (Euro-Par, 2006)

Particle Simulation Approach for Sub-cellular Dynamics and Interactions of Biological Molecules. - Ryuzo Azuma; Tetsuji Kitagawa; Hiroshi Kobayashi; Akihiko Konagaya (IMSCCS (1), 2006)

Particle simulation approach for subcellular dynamics and interactions of biological molecules. - Ryuzo Azuma; Tetsuji Kitagawa; Hiroshi Kobayashi; Akihiko Konagaya (BMC Bioinform., 2006)

Trends in life science grid: from computing grid to knowledge grid. - Akihiko Konagaya (BMC Bioinform., 2006)

Selecting effective siRNA sequences by using radial basis function network and decision tree learning. - Shigeru Takasaki; Yoshihiro Kawamura; Akihiko Konagaya (BMC Bioinform., 2006)

Selecting effective siRNA sequences based on the self-organizing map and statistical techniques. - Shigeru Takasaki; Yoshihiro Kawamura; Akihiko Konagaya (Comput. Biol. Chem., 2006)

Seeing Is Knowing: Visualization of Parameter-Parameter Dependencies in Biomedical Network Models. - Akihiko Konagaya; Ryuzo Azuma; Ryo Umetsu; Shingo Ohki; Fumikazu Konishi; Kazumi Matsumura; Sumi Yoshikawa (Grid Computing for Bioinformatics and Computational Biology, 2007)

Kinetic Analysis of Ligand-Receptor Complex Formation with the Aid of Computer Simulation. - Hiroshi Kobayashi; Ryuzo Azuma; Akihiko Konagaya (AINA Workshops (1), 2007)

RABC: A Conceptual Design of Pervasive Infrastructure for Browser Computing based on Ajax technologies. - Fumikazu Konishi; Manabu Ishii; Shingo Ohki; Ryo Umetsu; Akihiko Konagaya (CCGRID, 2007)

An FPGA Implementation of Multiple Sequence Alignment Based on Carrillo-Lipman Method. - Shingo Masuno; Tsutomu Maruyama; Yoshiki Yamaguchi; Akihiko Konagaya (FPL, 2007)

High speed tablation system using an FPGA designed for distribution tables of frequent DNA subsequences. - Yoshiki Yamaguchi; Tsutomu Maruyama; Fumikazu Konishi; Akihiko Konagaya (FPL, 2007)

Ontology-Driven Hypothetic Assertion (OHA) for Drug Interaction Prediction. - Takeshi Arikuma; Sumi Yoshikawa; Kentaro Watanabe; Akihiko Konagaya (IMSCCS, 2007)

Multiple Sequence Alignment Based on Dynamic Programming Using FPGA. - Shingo Masuno; Tsutomu Maruyama; Yoshiki Yamaguchi; Akihiko Konagaya (IEICE Trans. Inf. Syst., 2007)

Discovering Dynamic Characteristics of Biochemical Pathways using Geometric Patterns among Parameter-Parameter Dependencies in Differential Equations. - Ryuzo Azuma; Ryo Umetsu; Shingo Ohki; Fumikazu Konishi; Sumi Yoshikawa; Akihiko Konagaya; Kazumi Matsumura (New Gener. Comput., 2007)

Life Science Grid. - Akihiko Konagaya; Richard O. Sinnott; Peter W. Arzberger (New Gener. Comput., 2007)

Mesoscopic-level Simulation of Dynamics and Interactions of Biological Molecules Using Monte Carlo Simulation. - Yoshiki Yamaguchi; Tsutomu Maruyama; Ryuzo Azuma; Moritoshi Yasunaga; Akihiko Konagaya (J. VLSI Signal Process., 2007)

Drug interaction prediction using ontology-driven hypothetical assertion framework for pathway generation followed by numerical simulation. - Takeshi Arikuma; Sumi Yoshikawa; Ryuzo Azuma; Kentaro Watanabe; Kazumi Matsumura; Akihiko Konagaya (BMC Bioinform., 2008)

Guest Editorial Introduction to the Special Section on BioGrid: Biomedical Computations on the Grid. - Chun-Hsi Huang; Akihiko Konagaya; Vincenzo Lanza; Peter M. A. Sloot (IEEE Trans. Inf. Technol. Biomed., 2008)

Estimation of feasible solution space using Cluster Newton Method: application to pharmacokinetic analysis of irinotecan with physiologically-based pharmacokinetic models. - Kenta Yoshida; Kazuya Maeda; Hiroyuki Kusuhara; Akihiko Konagaya (BMC Syst. Biol., 2013)

Turing Test Considered Mostly Harmless. - Daniel P. Berrar; Akihiko Konagaya; Alfons Schuster (New Gener. Comput., 2013)

Molecular Robotics: A New Paradigm for Artifacts. - Satoshi Murata; Akihiko Konagaya; Satoshi Kobayashi; Hirohide Saito; Masami Hagiya (New Gener. Comput., 2013)

Tracking single microtubules by using B-spline curves and Hausdorff distance. - Yuexing Han; Daisuke Inoue; Akira Kakugo; Akihiko Konagaya (IPTA, 2014)

Implementing a modeling software for animated protein-complex interactions using a physics simulation library. - Yutaka Ueno; Shuntaro Ito; Akihiko Konagaya (J. Bioinform. Comput. Biol., 2014)

Cluster Newton Method for Sampling Multiple Solutions of Underdetermined Inverse Problems: Application to a Parameter Identification Problem in Pharmacokinetics. - Yasunori Aoki; Ken Hayami; Hans De Sterck; Akihiko Konagaya (SIAM J. Sci. Comput., 2014)

Improvements to the cluster Newton method for underdetermined inverse problems. - Philippe Gaudreau; Ken Hayami; Yasunori Aoki; Hassan Safouhi; Akihiko Konagaya (J. Comput. Appl. Math., 2015)

Automatic Recognition of DNA Pliers in Atomic Force Microscopy Images. - Yuexing Han; Akito Hara; Akinori Kuzuya; Ryosuke Watanabe; Yuichi Ohya; Akihiko Konagaya (New Gener. Comput., 2015)

Molecular Robotics and Controlling. - Akihiko Konagaya (New Gener. Comput., 2015)

Using a master and slave approach for GPGPU computing to achieve optimal scaling in a 3D real-time simulation. - Gregory Gutmann; Daisuke Inoue; Akira Kakugo; Akihiko Konagaya (NEMS, 2016)

Investigation of the microtubule dynamics with probabilistic data association filter. - Bulibuli Mahemuti; Daisuke Inoue; Akira Kakugo; Akihiko Konagaya (NEMS, 2016)

Real-time 3D microtubule gliding simulation accelerated by GPU computing. - Gregory Gutmann; Daisuke Inoue; Akira Kakugo; Akihiko Konagaya (Int. J. Autom. Comput., 2016)

Constraint-based perturbation analysis with cluster Newton method: a case study of personalized parameter estimations with irinotecan whole-body physiologically based pharmacokinetic model. - Shun Asami; Daisuke Kiga; Akihiko Konagaya (BMC Syst. Biol., 2017)

Parallel Interaction Detection Algorithms for a Particle-based Live Controlled Real-time Microtubule Gliding Simulation System Accelerated by GPGPU. - Gregory Gutmann; Daisuke Inoue; Akira Kakugo; Akihiko Konagaya (New Gener. Comput., 2017)

A high-performance haptic rendering system for virtual reality molecular modeling. - Arif Pramudwiatmoko; Satoru Tsutoh; Gregory Gutmann; Yutaka Ueno; Akihiko Konagaya (Artif. Life Robotics, 2019)

Irregular Convolutional Auto-Encoder on Point Clouds. - Yuhui Zhang; Greg Gutmann; Akihiko Konagaya (CoRR, 2019)

Predictive Simulation: Using Regression and Artificial Neural Networks to Negate Latency in Networked Interactive Virtual Reality. - Gregory Gutmann; Akihiko Konagaya (CoRR, 2019)

A novel transfer learning for recognition of overlapping nano object. - Yuexing Han; Yuhong Liu; Bing Wang; Qiaochuan Chen; Leilei Song; Lin Tong; Chuanbin Lai; Akihiko Konagaya (Neural Comput. Appl., 2022)

Utility of constraints reflecting system stability on analyses for biological models. - Yoshiaki Kariya; Masashi Honma; Keita Tokuda; Akihiko Konagaya; Hiroshi Suzuki (PLoS Comput. Biol., 2022)

Co-creation environment with cloud virtual reality and real-time artificial intelligence toward the design of molecular robots. - Akihiko Konagaya; Gregory Gutmann; Yuhui Zhang (J. Integr. Bioinform., 2023)