| 2008 | ||
|---|---|---|
| 68 | 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 Bioinformatics 9(S-6): (2008) | |
| 67 | 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 Transactions on Information Technology in Biomedicine 12(2): 133-137 (2008) | |
| 2007 | ||
| 66 | 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 | |
| 65 | 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 | |
| 64 | 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 | |
| 63 | Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya: An FPGA Implementation of Multiple Sequence Alignment Based on Carrillo-Lipman Method. FPL 2007: 489-492 | |
| 62 | Takeshi Arikuma, Sumi Yoshikawa, Kentaro Watanabe, Akihiko Konagaya: Ontology-Driven Hypothetic Assertion (OHA) for Drug Interaction Prediction. IMSCCS 2007: 1-8 | |
| 61 | Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya: Multiple Sequence Alignment Based on Dynamic Programming Using FPGA. IEICE Transactions 90-D(12): 1939-1946 (2007) | |
| 60 | Akihiko Konagaya, Richard O. Sinnott, Peter W. Arzberger: Life Science Grid. New Generation Comput. 25(4): 337-338 (2007) | |
| 59 | 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 Generation Comput. 25(4): 425-441 (2007) | |
| 58 | Yoshiki Yamaguchi, Tsutomu Maruyama, Ryuzo Azuma, Moritoshi Yasunaga, Akihiko Konagaya: Mesoscopic-level Simulation of Dynamics and Interactions of Biological Molecules Using Monte Carlo Simulation. VLSI Signal Processing 48(3): 287-299 (2007) | |
| 2006 | ||
| 57 | Akihiko Konagaya: OBIGrid: Towards the 'Ba' for Sharing Resources, Services and Knowledge for Bioinformatics. CCGRID 2006: 37 | |
| 56 | 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 | |
| 55 | Craig A. Stewart, Michael Schroeder, Concettina Guerra, Akihiko Konagaya: Topic 17: High-Performance Bioinformatics. Euro-Par 2006: 1125-1126 | |
| 54 | Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya: Multidimensional Dynamic Programming for Homology Search on Distributed Systems. Euro-Par 2006: 1127-1137 | |
| 53 | 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 | |
| 52 | 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 | |
| 51 | Ryuzo Azuma, Tetsuji Kitagawa, Hiroshi Kobayashi, Akihiko Konagaya: Particle simulation approach for subcellular dynamics and interactions of biological molecules. BMC Bioinformatics 7(S-4): (2006) | |
| 50 | Shigeru Takasaki, Yoshihiro Kawamura, Akihiko Konagaya: Selecting effective siRNA sequences by using radial basis function network and decision tree learning. BMC Bioinformatics 7(S-5): (2006) | |
| 49 | Akihiko Konagaya: Trends in life science grid: from computing grid to knowledge grid. BMC Bioinformatics 7(S-5): (2006) | |
| 48 | Shigeru Takasaki, Yoshihiro Kawamura, Akihiko Konagaya: Selecting effective siRNA sequences based on the self-organizing map and statistical techniques. Computational Biology and Chemistry 30(3): 169-178 (2006) | |
| 2005 | ||
| 47 | 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 Springer 2005 | |
| 46 | Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya: Multidimensional Dynamic Programming for Homology Search. FPL 2005: 173-178 | |
| 45 | Yoshiki Yamaguchi, Tsutomu Maruyama, Ryuzo Azuma, Akihiko Konagaya: Spatiotemporal Simulation of a Single Living Cell. FPT 2005: 267-274 | |
| 44 | 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 | |
| 43 | 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. Bioinformatics 21(7): 1154-1163 (2005) | |
| 42 | 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. Bioinformatics and Computational Biology 3(2): 401-414 (2005) | |
| 41 | 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 Research 33(Database-Issue): 647-650 (2005) | |
| 2004 | ||
| 40 | Yoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya: Three-Dimensional Dynamic Programming for Homology Search. FPL 2004: 505-515 | |
| 39 | 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 | |
| 38 | Fumikazu Konishi, Akihiko Konagaya: The Architectural Design of High-Throughput BLAST Services on OBIGrid. LSGRID 2004: 32-42 | |
| 37 | Kenji Satou, Yasuhiko Nakashima, Shin'ichi Tsuji, Xavier Défago, Akihiko Konagaya: An Integrated System for Distributed Bioinformatics Environment on Grids. LSGRID 2004: 8-19 | |
| 36 | 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 | |
| 35 | 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 | |
| 34 | Tetsuo Shibuya, Hisashi Kashima, Akihiko Konagaya: Efficient filtering methods for clustering cDNAs with spliced sequence alignment. Bioinformatics 20(1): 29-39 (2004) | |
| 33 | Shuhei Kimura, Takuji Kawasaki, Mariko Hatakeyama, Takashi Naka, Fumikazu Konishi, Akihiko Konagaya: OBIYagns: a grid-based biochemical simulator with a parameter estimator. Bioinformatics 20(10): 1646-1648 (2004) | |
| 32 | Kaoru Yamamoto, Taku Kudo, Akihiko Konagaya, Yuji Matsumoto: Use of morphological analysis in protein name recognition. Journal of Biomedical Informatics 37(6): 471-482 (2004) | |
| 31 | 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 Generation Comput. 22(2): (2004) | |
| 30 | Akihiko Konagaya, Fumikazu Konishi, Mariko Hatakeyama, Kenji Satou: The Superstructure toward Open Bioinformatics Grid. New Generation Comput. 22(2): (2004) | |
| 29 | Takeshi Nagashima, Hideo Matsuda, Diego G. Silva, Nikolai Petrovsky, Akihiko Konagaya, Christian Schönbach: FREP: a database of functional repeats in mouse cDNAs. Nucleic Acids Research 32(Database-Issue): 471-475 (2004) | |
| 2003 | ||
| 28 | 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 | |
| 27 | Shuhei Kimura, Mariko Hatakeyama, Akihiko Konagaya: Inference of S-system models of genetic networks using a genetic local search. IEEE Congress on Evolutionary Computation (1) 2003: 631-638 | |
| 26 | 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 | |
| 25 | Yohei Minakuchi, Kenji Satou, Akihiko Konagaya: Prediction of Protein-Protein Interaction Sites Using Support Vector Machines. METMBS 2003: 22-28 | |
| 24 | Sumi Yoshikawa, Akihiko Konagaya: DIO: Drug Interaction Ontology - Application to Inferences in Possible Drug-Drug Interactions. METMBS 2003: 231-236 | |
| 23 | Makoto Taiji, Tetsu Narumi, Yousuke Ohno, Akihiko Konagaya: MDGRAPE-3: A Petaflops Special-Purpose Computer System for Molecular Dynamics Simulations. PARCO 2003: 669-676 | |
| 22 | 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 | |
| 21 | Tetsuro Toyoda, Akihiko Konagaya: KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data. Bioinformatics 19(3): 433-434 (2003) | |
| 20 | Tetsuro Toyoda, Yoshiki Mochizuki, Akihiko Konagaya: GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs. Bioinformatics 19(3): 437-438 (2003) | |
| 2002 | ||
| 19 | Yoshiki Yamaguchi, Yosuke Miyajima, Tsutomu Maruyama, Akihiko Konagaya: High Speed Homology Search Using Run-Time Reconfiguration. FPL 2002: 281-291 | |
| 18 | Xavier Défago, Akihiko Konagaya: Circle formation for oblivious anonymous mobile robots with no common sense of orientation. POMC 2002: 97-104 | |
| 17 | Yoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya: High Speed Homology Search with FPGAs. Pacific Symposium on Biocomputing 2002: 271-282 | |
| 16 | Akihiko Konagaya: OBIGrid: Towards a New Distributed Platform for Bioinformatics. SRDS 2002: 380- | |
| 1995 | ||
| 15 | 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 | ||
| 14 | Yukiko Fujiwara, Minoru Asogawa, Akihiko Konagaya: Stochastic Motif Extraction Using Hidden Markov Model. ISMB 1994: 121-129 | |
| 1993 | ||
| 13 | Tsutomu Maruyama, Tetsuya Hirose, Akihiko Konagaya: A Fine-Grained Parallel Genetic Algorithm for Distributed Parallel Systems. ICGA 1993: 184-190 | |
| 12 | 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 | ||
| 11 | Akihiko Konagaya: A Stochastic Approach to Genetic Information Processing. ALT 1992: 25-36 | |
| 10 | Koichi Konishi, Tsutomu Maruyama, Akihiko Konagaya, Kaoru Yoshida, Takashi Chikayama: Implementing Streams on Parallel Machines with Distributed Memory. FGCS 1992: 791-798 | |
| 9 | Tsutomu Maruyama, Akihiko Konagaya, Koichi Konishi: An Asynchronous Fine-Grained Parallel Genetic Algorithm. PPSN 1992: 569-578 | |
| 1991 | ||
| 8 | Kenji Yamanishi, Akihiko Konagaya: Learning Stochastic Motifs from Genetic Sequences. ML 1991: 467-471 | |
| 1990 | ||
| 7 | Atsushi Atarashi, Akihiko Konagaya, Shinichi Habata, Minoru Yokota: Implementation and Evaluation of Dynamic Predicates on the Sequential Inference Machine CHI. ICCL 1990: 236-244 | |
| 1989 | ||
| 6 | Akihiko Konagaya, Shinichi Habata, Atsushi Atarashi, Minoru Yokota: Performance Evaluation of a Sequential Inference Machine CHI. NACLP 1989: 1165-1179 | |
| 1988 | ||
| 5 | Hidenori Itoh, Hidetoshi Monoi, Shigeki Shibayama, Nobuyoshi Miyazaki, Haruo Yokota, Akihiko Konagaya: Knowledge Base System in Logic Programming Paradigm. FGCS 1988: 37-53 | |
| 1987 | ||
| 4 | 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 | ||
| 3 | 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 | ||
| 2 | Tetsuo Ida, Akihiko Konagaya: Comparison of Closure Reduction and Combinatory Reduction Schemes. RIMS Symposia on Software Science and Engineering 1984: 261-291 | |
| 1 | Akihiko Konagaya, Mamoru Umemura: Knowledge Information Processing Language: ShapeUp. New Generation Comput. 2(2): 195-201 (1984) | |