Akihiko Konagaya

2008
64	EE	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
63	EE	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
62	EE	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
61	EE	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
60	EE	Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya: An FPGA Implementation of Multiple Sequence Alignment Based on Carrillo-Lipman Method. FPL 2007: 489-492
59	EE	Takeshi Arikuma, Sumi Yoshikawa, Kentaro Watanabe, Akihiko Konagaya: Ontology-Driven Hypothetic Assertion (OHA) for Drug Interaction Prediction. IMSCCS 2007: 1-8
58	EE	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)
57	EE	Akihiko Konagaya, Richard O. Sinnott, Peter W. Arzberger: Life Science Grid. New Generation Comput. 25(4): 337-338 (2007)
56	EE	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)
55	EE	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
54	EE	Akihiko Konagaya: OBIGrid: Towards the 'Ba' for Sharing Resources, Services and Knowledge for Bioinformatics. CCGRID 2006: 37
53	EE	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
52	EE	Craig A. Stewart, Michael Schroeder, Concettina Guerra, Akihiko Konagaya: Topic 17: High-Performance Bioinformatics. Euro-Par 2006: 1125-1126
51	EE	Shingo Masuno, Tsutomu Maruyama, Yoshiki Yamaguchi, Akihiko Konagaya: Multidimensional Dynamic Programming for Homology Search on Distributed Systems. Euro-Par 2006: 1127-1137
50	EE	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
49	EE	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
48	EE	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	EE	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	EE	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	EE	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	EE	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	EE	Yoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya: Three-Dimensional Dynamic Programming for Homology Search. FPL 2004: 505-515
39	EE	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	EE	Fumikazu Konishi, Akihiko Konagaya: The Architectural Design of High-Throughput BLAST Services on OBIGrid. LSGRID 2004: 32-42
37	EE	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	EE	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	EE	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	EE	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	EE	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	EE	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	EE	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	EE	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	EE	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	EE	Yoshiki Yamaguchi, Yosuke Miyajima, Tsutomu Maruyama, Akihiko Konagaya: High Speed Homology Search Using Run-Time Reconfiguration. FPL 2002: 281-291
18	EE	Xavier Défago, Akihiko Konagaya: Circle formation for oblivious anonymous mobile robots with no common sense of orientation. POMC 2002: 97-104
17	EE	Yoshiki Yamaguchi, Tsutomu Maruyama, Akihiko Konagaya: High Speed Homology Search with FPGAs. Pacific Symposium on Biocomputing 2002: 271-282
16	EE	Akihiko Konagaya: OBIGrid: Towards a New Distributed Platform for Bioinformatics. SRDS 2002: 380-
1995
15	EE	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)

Coauthor Index

1	Kenji Akiyama	[41]
2	Larry Ang	[31]
3	Takeshi Arikuma	[59]
4	Peter W. Arzberger	[31] [57]
5	Kiyoshi Asai	[12]
6	Minoru Asogawa	[14] [15]
7	Atsushi Atarashi	[6] [7]
8	Ryuzo Azuma	[45] [49] [55] [56] [63]
9	Takashi Chikayama	[3] [10]
10	Xavier Défago	[18] [37]
11	Abbas Farazdel	[31]
12	Yukiko Fujiwara	[14] [15]
13	Shuichi Fukuda	[50]
14	Akinobu Fukuzaki	[36]
15	Noriyuki Futatsugi	[22]
16	Nobuharu Goto	[42]
17	Concettina Guerra	[52]
18	Shinichi Habata	[3] [6] [7]
19	Yusuke Hamano	[50]
20	Aki Hasegawa	[44]
21	Yoshikazu Hasegawa	[39]
22	Mariko Hatakeyama	[27] [30] [33] [36] [43] [44]
23	Naohiko Heida	[39] [42]
24	Katsura Hirosawa	[39]
25	Tetsuya Hirose	[13]
26	Junko Hosaka	[28]
27	Chun-Hsi Huang	[64]
28	Tetsuo Ida	[2]
29	Kaori Ide	[36] [43]
30	Kei Iida	[41]
31	Manabu Ishii	[50] [62]
32	Masato Ishikawa	[12]
33	Takuya Ito	[41]
34	Hidenori Itoh	[5]
35	Eli Kaminuma	[42]
36	Makoto Kano	[43]
37	Aiko Kashihara	[43]
38	Hisashi Kashima	[34]
39	Yoshihiro Kawamura	[48]
40	Takuji Kawasaki	[33]
41	Shuhei Kimura	[27] [33] [43]
42	Tetsuji Kitagawa	[49]
43	Hiroshi Kobayashi	[49] [63]
44	Judice L. Y. Koh	[28]
45	Fumikazu Konishi	[30] [33] [36] [38] [50] [56] [61] [62]
46	Koichi Konishi	[9] [10]
47	Taku Kudo	[32]
48	Seiki Kuramitsu	[36] [43]
49	Jun'ichi Kurita	[26]
50	Kazumi Kuriyama-Matsumura	[44]
51	Takashi Kuromori	[41]
52	Vincenzo Lanza	[64]
53	Tsutomu Maruyama	[9] [10] [13] [17] [19] [40] [45] [46] [51] [55] [58] [60] [61]
54	Ryoji Masui	[43]
55	Shingo Masuno	[46] [51] [58] [60]
56	Hideo Matsuda	[29]
57	Minami Matsui	[42]
58	Yuji Matsumoto	[32]
59	Kazumi Matsumura	[56]
60	Yohei Minakuchi	[25]
61	Yosuke Miyajima	[19]
62	Nobuyoshi Miyazaki	[5]
63	Yoshiki Mochizuki	[20] [39]
64	Hidetoshi Monoi	[5]
65	Takeshi Nagashima	[29] [36]
66	Takashi Naka	[33]
67	Noriko Nakagawa	[43]
68	Yasuhiko Nakashima	[37]
69	Ryosei Nakazaki	[3] [4]
70	Miki Nakazawa	[42]
71	Tetsu Narumi	[22] [23]
72	Shingo Ohki	[50] [56] [62]
73	Yousuke Ohno	[22] [23]
74	Mitsuhiro Okada	[53]
75	Nikolai Petrovsky	[29]
76	Tetsuya Sakurai	[41]
77	Kenji Satou	[25] [26] [30] [35] [37] [47]
78	Masakazu Satou	[41]
79	Christian Schönbach	[29]
80	Michael Schroeder	[52]
81	Motoaki Seki	[41]
82	Shigeki Shibayama	[5]
83	Tetsuo Shibuya	[34]
84	Hideto Shimahara	[26]
85	Hideo Shimazu	[3]
86	Shinji Shimojo	[31]
87	Kazuo Shinozaki	[41]
88	Diego G. Silva	[29]
89	Richard O. Sinnott	[57]
90	Peter M. A. Sloot	[64]
91	Rick L. Stevens (Rick Stevens)	[31]
92	Craig A. Stewart	[52]
93	Atsushi Suenaga	[22]
94	Yutaro Sugimoto	[53]
95	Makoto Taiji	[22] [23]
96	Naoki Takada	[22]
97	Shigeru Takasaki	[48]
98	Hidetoshi Tanaka	[12]
99	Shin-ichi Tate	[26]
100	Shouji Tatsumoto	[26] [35]
101	Tetsuro Toyoda	[20] [21] [39] [41] [42]
102	Shin'ichi Tsuji	[37]
103	Yuko Tsumoto	[42]
104	Mamoru Umemura	[1] [3] [4]
105	Ryo Umetsu	[56] [62]
106	Kentaro Watanabe	[59]
107	Yoshiki Yamaguchi	[17] [19] [40] [45] [46] [51] [55] [58] [60] [61]
108	Kaoru Yamamoto	[32]
109	Masahiro Yamamoto	[3]
110	Kenji Yamanishi	[8]
111	Moritoshi Yasunaga	[55]
112	Haruo Yokota	[5]
113	Minoru Yokota	[3] [6] [7]
114	Shigeyuki Yokoyama	[36] [43]
115	Kaoru Yoshida	[10]
116	Sumi Yoshikawa	[24] [53] [56] [59]
117	Xiaomei Yu	[44]

Colors in the list of coauthors