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Masaru Tomita

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2008
51EEYukino Ogawa, Kazuharu Arakawa, Kazunari Kaizu, Fumihiko Miyoshi, Yoichi Nakayama, Masaru Tomita: Comparative Study of Circadian Oscillatory Network Models of Drosophila. Artificial Life 14(1): 29-48 (2008)
50EEHiroshi Ohno, Yasuhiro Naito, Hiromu Nakajima, Masaru Tomita: Construction of a Biological Tissue Model Based on a Single-Cell Model: A Computer Simulation of Metabolic Heterogeneity in the Liver Lobule. Artificial Life 14(1): 3-28 (2008)
49EEYoshiya Matsubara, Shinichi Kikuchi, Masahiro Sugimoto, Kotaro Oka, Masaru Tomita: Algebraic Method for the Analysis of Signaling Crosstalk. Artificial Life 14(1): 81-94 (2008)
48EEKosaku Shinoda, Masaru Tomita, Yasushi Ishihama: Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments. Bioinformatics 24(14): 1590-1595 (2008)
2007
47EEYuri Matsuzaki, Shinichi Kikuchi, Masaru Tomita: Robust effects of Tsr-CheBp and CheA-CheYp affinity in bacterial chemotaxis. Artificial Intelligence in Medicine 41(2): 145-150 (2007)
46EESatoshi Tamaki, Kazuharu Arakawa, Nobuaki Kono, Masaru Tomita: Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics. Genomics, Proteomics & Bioinformatics 5(1): 53-58 (2007)
45EEHiroyuki Fujita, Katsuya Fukuda, Koichiro Sawa, Masaru Tomita, Masato Murakami, Naomichi Sakai, Izumi Hirabayashi: Consideration on Contact Mechanism of YBaCuO Bulk Superconductor with Deposited Metal Layer. IEICE Transactions 90-C(7): 1421-1428 (2007)
2006
44 Gabor Bereczki, Masaru Tomita: An interaction knowledgebase for biomolecular modeling. Industrial Conference on Data Mining - Workshops 2006: 101-110
43EEKazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita: GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. BMC Bioinformatics 7: 168 (2006)
42EEYoshiya Matsubara, Shinichi Kikuchi, Masahiro Sugimoto, Masaru Tomita: Parameter estimation for stiff equations of biosystems using radial basis function networks. BMC Bioinformatics 7: 230 (2006)
41EEGek Huey Chua, Arun Krishnan, Kuo-Bin Li, Masaru Tomita: Multiresolution Analysis Uncovers Hidden Conservation of Properties in Structurally and Functionally Similar Proteins. J. Bioinformatics and Computational Biology 4(6): 1245-1268 (2006)
2005
40EEKatsuyuki Yugi, Yoichi Nakayama, Shigen Kojima, Tomoya Kitayama, Masaru Tomita: A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks. BMC Bioinformatics 6: 299 (2005)
39EENoriyuki Kitagawa, Takanori Washio, Shunichi Kosugi, Tomoya Yamashita, Kenji Higashi, Hiroshi Yanagawa, Kenichi Higo, Koji Satoh, Yasuhiro Ohtomo, Tomomi Sunako, Kazuo Murakami, Kenichi Matsubara, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki, Shoshi Kikuchi, Masaru Tomita: Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa). Bioinformatics 21(9): 1758-1763 (2005)
2004
38EEMasahiro Sugimoto, Kouichi Takahashi, Tomoya Kitayama, Daiki Ito, Masaru Tomita: Distributed Cell Biology Simulations with E-Cell System. LSGRID 2004: 20-31
37EEYasushi Kiyoki, Masa Inakage, Masahiko Satoh, Masaru Tomita: Future Directions for Cyber Knowledge and Databases. SAINT Workshops 2004: 495-501
36EEKatsuyuki Yugi, Masaru Tomita: A general computational model of mitochondrial metabolism in a whole organelle scale. Bioinformatics 20(11): 1795-1796 (2004)
35EEKouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita: A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics 20(4): (2004)
34EESumie Kitamura-Abe, Hitomi Itoh, Takanori Washio, Akihiro Tsutsumi, Masaru Tomita: Characterization of the Splice Sites in Gt-ag and Gc-ag Introns in Higher Eukaryotes Using Full-length Cdnas. J. Bioinformatics and Computational Biology 2(2): 309-332 (2004)
2003
33 Misaki Sato, Hitomi Umeki, Rintaro Saito, Akio Kanai, Masaru Tomita: Computational Analysis of Stop Codon Readthrough in D.melanogaster. Bioinformatics 19(11): 1371-1380 (2003)
32 Koichi Takahashi, N. Ishikawa, Y. Sadamoto, H. Sasamoto, S. Ohta, A. Shiozawa, Fumihiko Miyoshi, Yasuhiro Naito, Yoichi Nakayama, Masaru Tomita: E-Cell 2: Multi-platform E-Cell simulation system. Bioinformatics 19(13): 1727-1729 (2003)
31 Kazuharu Arakawa, Koya Mori, Katsuhiko Ikeda, Tatekimi Matsuzaki, Yusuke Kobayashi, Masaru Tomita: G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. Bioinformatics 19(2): 305-306 (2003)
30 Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, D. Bray, A. Cornish-Bowden, A. A. Cuellar, Serge Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, Igor Goryanin, W. J. Hedley, T. Charles Hodgman, J. H. Hofmeyr, Peter J. Hunter, Nick S. Juty, J. L. Kasberger, Andreas Kremling, Ursula Kummer, Nicolas Le Novère, Leslie M. Loew, D. Lucio, Pedro Mendes, E. Minch, Eric Mjolsness, Yoichi Nakayama, M. R. Nelson, P. F. Nielsen, T. Sakurada, James C. Schaff, Bruce E. Shapiro, Thomas Simon Shimizu, Hugh D. Spence, Jörg Stelling, Koichi Takahashi, Masaru Tomita, J. Wagner, J. Wang: The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19(4): 524-531 (2003)
29 Shinichi Kikuchi, Daisuke Tominaga, Masanori Arita, Katsutoshi Takahashi, Masaru Tomita: Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics 19(5): 643-650 (2003)
28EEShinichi Kikuchi, Kenji Fujimoto, Noriyuki Kitagawa, Taro Fuchikawa, Michiko Abe, Kotaro Oka, Kohtaro Takei, Masaru Tomita: Kinetic simulation of signal transduction system in hippocampal long-term potentiation with dynamic modeling of protein phosphatase 2A. Neural Networks 16(9): 1389-1398 (2003)
2002
27 Masaru Tomita: Toward Computer Simulation of the Whole Cell. Gene Regulations and Metabolism 2002: 273-288
26EEKouichi Takahashi, Katsuyuki Yugi, Kenta Hashimoto, Yohei Yamada, Christopher J. F. Pickett, Masaru Tomita: Computational Challenges in Cell Simulation: A Software Engineering Approach. IEEE Intelligent Systems 17(5): 64-71 (2002)
2001
25 Masaru Tomita: E-CELL Project: Towards Whole Cell Simulation. German Conference on Bioinformatics 2001: 1
24 Masaru Tomita: Towards Computer Aided Design (CAD) of Useful Microorganisms. Bioinformatics 17(12): 1091-1092 (2001)
2000
23EEMasaru Tomita, Kenta Hashimoto, Koichi Takahashi, Yuri Matsuzaki, Ryo Matsushima, Katsuyuki Yugi, Fumihiko Miyoshi, Hisako Nakano, Yusuke Saito, S. Shimizu, Yoichi Nakayama: The E-CELL project: towards integrative simulation of cellular processes. RECOMB 2000: 290-298
22EERyuta Fukuda, Junko Hara, William Rodman Shankle, Masaru Tomita: Proposition of cortical connectivity between 30 cytoarchitectural areas of human cerebral cortex. Neurocomputing 32-33: 749-755 (2000)
1999
21 Masaru Tomita, Kenta Hashimoto, Koichi Takahashi, Thomas Simon Shimizu, Yuri Matsuzaki, Fumihiko Miyoshi, K. Saito, S. Tanida, Katsuyuki Yugi, J. C. Venter, C. A. Hutchison III: E-CELL: software environment for whole-cell simulation. Bioinformatics 15(1): 72-84 (1999)
20 Y. Osada, Rintaro Saito, Masaru Tomita: Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes. Bioinformatics 15(7): 578-581 (1999)
1994
19 Masaru Tomita, Takashi Kido: Sacrificial Acts in Single Round Prisoner`S Dilemma. Informatica (Slovenia) 18(4): (1994)
1992
18 Gennaro Costagliola, Shi-Kuo Chang, Masaru Tomita: Parsing 2D Languages by a Pictorial GLR Parser. Advanced Visual Interfaces 1992: 319-333
1991
17 Gennaro Costagliola, Masaru Tomita, Shi-Kuo Chang: A Generalized Parser for 2-D Languages. VL 1991: 98-104
1990
16EEMasaru Tomita: The Generalized LR Parser/Compiler V8-4: A Software Package for Practical NL Projects. COLING 1990: 59-63
1988
15 Hideto Tomabechi, Masaru Tomita: The Integration of Unification-Based Syntax/Semantics and Memory-Based Pragmatics for Real-Time Understanding of Noisy Continuous Speech Input. AAAI 1988: 724-728
14 Masaru Tomita: Graph-Structured Stack and Natural Language Parsing. ACL 1988: 249-257
13 Masaru Tomita: "Linguistic" sentences and "real" sentences. COLING 1988: 453
12 Hiroaki Saito, Masaru Tomita: Parsing noisy sentences. COLING 1988: 561-566
11 Hideto Tomabechi, Masaru Tomita: Application of the direct memory access paradigm to NL interfaces to knowledge-based systems. COLING 1988: 661-666
10 Masaru Tomita: Combining lexicon-driven parsing and phrase-structure-based parsing. COLING 1988: 667-670
9 Hideto Tomabechi, Teruko Mitamura, Masaru Tomita: Direct Memory Access Translation for Speech Input. FGCS 1988: 1100-1107
1987
8 Masaru Tomita, Jaime G. Carbonell: The Universal Parser Architecture for Knowledge-based Machine Translation. IJCAI 1987: 718-721
7 Masaru Tomita: An Efficient Augmented-Context-Free Parsing Algorithm. Computational Linguistics 13(1-2): 31-46 (1987)
1986
6 Philip J. Hayes, Alexander G. Hauptmann, Jaime G. Carbonell, Masaru Tomita: Parsing Spoken Language: A Semantic Caseframe Approach. COLING 1986: 587-592
5 Masaru Tomita, Jaime G. Carbonell: Another Stride Towards Knowledge-Based Machine Translation. COLING 1986: 633-638
4EEMasaru Tomita: Sentence disambiguation by asking. Machine Translation 1(1): 39-51 (1986)
1985
3 Masaru Tomita: An Efficient Context-Free Parsing Algorithm for Natural Languages. IJCAI 1985: 756-764
1984
2EEMasaru Tomita: LR Parsers For Natural Languages. COLING 1984: 354-357
1EEMasaru Tomita: Disambiguating Grammatically Ambiguous Sentences By Asking. COLING 1984: 476-480

Coauthor Index

1Michiko Abe [28]
2Kazuharu Arakawa [31] [43] [46] [51]
3Masanori Arita [29]
4Adam P. Arkin [30]
5Gabor Bereczki [44]
6H. Bolouri [30]
7Benjamin J. Bornstein [30]
8D. Bray [30]
9Jaime G. Carbonell [5] [6] [8]
10Piero Carninci [39]
11Shi-Kuo Chang [17] [18]
12Gek Huey Chua [41]
13A. Cornish-Bowden [30]
14Gennaro Costagliola [17] [18]
15A. A. Cuellar [30]
16John Doyle (John C. Doyle) [30]
17Serge Dronov [30]
18Andrew Finney [30]
19Taro Fuchikawa [28]
20Kenji Fujimoto [28]
21Hiroyuki Fujita [45]
22Katsuya Fukuda [45]
23Ryuta Fukuda [22]
24Ernst Dieter Gilles [30]
25Martin Ginkel [30]
26Victoria Gor [30]
27Igor Goryanin [30]
28Junko Hara [22]
29Kenta Hashimoto [21] [23] [26]
30Alexander G. Hauptmann [6]
31Yoshihide Hayashizaki [39]
32Philip J. Hayes [6]
33W. J. Hedley [30]
34Kenji Higashi [39]
35Kenichi Higo [39]
36Izumi Hirabayashi [45]
37Charlie Hodgman (T. Charles Hodgman) [30]
38J. H. Hofmeyr [30]
39Bin Hu [35]
40Michael Hucka [30]
41Peter J. Hunter [30]
42C. A. Hutchison III [21]
43Katsuhiko Ikeda [31]
44Masa Inakage [37]
45Yasushi Ishihama [48]
46N. Ishikawa [32]
47Daiki Ito [38]
48Hitomi Itoh [34]
49Nick S. Juty [30]
50Kazunari Kaizu [35] [51]
51Akio Kanai [33]
52J. L. Kasberger [30]
53Jun Kawai [39]
54Takashi Kido [19]
55Shinichi Kikuchi [28] [29] [42] [47] [49]
56Shoshi Kikuchi [39]
57Noriyuki Kitagawa [28] [39]
58Sumie Kitamura-Abe [34]
59Hiroaki Kitano [30]
60Tomoya Kitayama [38] [40]
61Yasushi Kiyoki [37]
62Yusuke Kobayashi [31]
63Shigen Kojima [40]
64Nobuaki Kono [46]
65Shunichi Kosugi [39]
66Andreas Kremling [30]
67Arun Krishnan [41]
68Ursula Kummer [30]
69Kuo-Bin Li [41]
70Leslie M. Loew [30]
71D. Lucio [30]
72Kenichi Matsubara [39]
73Yoshiya Matsubara [42] [49]
74Ryo Matsushima [23]
75Tatekimi Matsuzaki [31]
76Yuri Matsuzaki [21] [23] [47]
77Pedro Mendes [30]
78E. Minch [30]
79Teruko Mitamura [9]
80Fumihiko Miyoshi [21] [23] [32] [51]
81Eric Mjolsness [30]
82Koya Mori [31]
83Kazuo Murakami [39]
84Masato Murakami [45]
85Yasuhiro Naito [32] [50]
86Hiromu Nakajima [50]
87Hisako Nakano [23]
88Yoichi Nakayama [23] [30] [32] [40] [43] [51]
89M. R. Nelson [30]
90P. F. Nielsen [30]
91Nicolas Le Novère [30]
92Yukino Ogawa [51]
93Hiroshi Ohno [50]
94S. Ohta [32]
95Yasuhiro Ohtomo [39]
96Kotaro Oka [28] [49]
97Y. Osada [20]
98Christopher J. F. Pickett [26]
99Y. Sadamoto [32]
100Hiroaki Saito (Hiroaki Saitoh) [12]
101K. Saito [21]
102Rintaro Saito [20] [33]
103Yusuke Saito [23]
104Naomichi Sakai [45]
105T. Sakurada [30]
106H. Sasamoto [32]
107Misaki Sato [33]
108Koji Satoh [39]
109Masahiko Satoh [37]
110Herbert M. Sauro [30]
111Koichiro Sawa [45]
112James C. Schaff [30]
113William Rodman Shankle [22]
114Bruce E. Shapiro [30]
115S. Shimizu [23]
116Thomas Simon Shimizu [21] [30]
117Kosaku Shinoda [43] [48]
118A. Shiozawa [32]
119Hugh D. Spence [30]
120Jörg Stelling [30]
121Masahiro Sugimoto [38] [42] [49]
122Tomomi Sunako [39]
123Katsutoshi Takahashi [29]
124Koichi Takahashi [21] [23] [30] [32]
125Kouichi Takahashi [26] [35] [38]
126Kohtaro Takei [28]
127Satoshi Tamaki [46]
128S. Tanida [21]
129Hideto Tomabechi [9] [11] [15]
130Daisuke Tominaga [29]
131Akihiro Tsutsumi [34]
132Hitomi Umeki [33]
133J. C. Venter [21]
134J. Wagner [30]
135J. Wang [30]
136Takanori Washio [34] [39]
137Yohei Yamada [26] [43]
138Tomoya Yamashita [39]
139Hiroshi Yanagawa [39]
140Katsuyuki Yugi [21] [23] [26] [36] [40]

Colors in the list of coauthors

Copyright © Sun May 17 03:24:02 2009 by Michael Ley (ley@uni-trier.de)