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Masaru Tomita Vis

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*2009
56EEKazuharu Arakawa, Satoshi Tamaki, Nobuaki Kono, Nobuhiro Kido, Keita Ikegami, Ryu Ogawa, Masaru Tomita: Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics 10: (2009)
55EEHaruo Suzuki, Rintaro Saito, Masaru Tomita: Measure of synonymous codon usage diversity among genes in bacteria. BMC Bioinformatics 10: (2009)
54EEKumar Selvarajoo, Masaru Tomita, Masa Tsuchiya: Can Complex Cellular Processes be Governed by Simple Linear Rules? J. Bioinformatics and Computational Biology 7(1): 243-268 (2009)
2008
53EEYukino 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)
52EEHiroshi 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)
51EEYoshiya Matsubara, Shinichi Kikuchi, Masahiro Sugimoto, Kotaro Oka, Masaru Tomita: Algebraic Method for the Analysis of Signaling Crosstalk. Artificial Life 14(1): 81-94 (2008)
50EEAnton Kratz, Masaru Tomita, Arun Krishnan: GeNESiS: gene network evolution simulation software. BMC Bioinformatics 9: (2008)
49EEKosaku 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
48EEYuri 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)
47EERichard Baran, Martin Robert, Makoto Suematsu, Tomoyoshi Soga, Masaru Tomita: Visualization of three-way comparisons of omics data. BMC Bioinformatics 8: (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, Autumn 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, Poul M. 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] [53] [56]
3Masanori Arita [29]
4Adam P. Arkin [30]
5Richard Baran [47]
6Gabor Bereczki [44]
7H. Bolouri [30]
8Benjamin J. Bornstein [30]
9D. Bray [30]
10Jaime G. Carbonell [5] [6] [8]
11Piero Carninci [39]
12Shi-Kuo Chang [17] [18]
13Gek Huey Chua [41]
14A. Cornish-Bowden [30]
15Gennaro Costagliola [17] [18]
16Autumn A. Cuellar [30]
17John Doyle (John C. Doyle) [30]
18Serge Dronov [30]
19Andrew Finney [30]
20Taro Fuchikawa [28]
21Kenji Fujimoto [28]
22Hiroyuki Fujita [45]
23Katsuya Fukuda [45]
24Ryuta Fukuda [22]
25Ernst Dieter Gilles [30]
26Martin Ginkel [30]
27Victoria Gor [30]
28Igor Goryanin [30]
29Junko Hara [22]
30Kenta Hashimoto [21] [23] [26]
31Alexander G. Hauptmann [6]
32Yoshihide Hayashizaki [39]
33Philip J. Hayes [6]
34W. J. Hedley [30]
35Kenji Higashi [39]
36Kenichi Higo [39]
37Izumi Hirabayashi [45]
38Charlie Hodgman (T. Charles Hodgman) [30]
39J. H. Hofmeyr [30]
40Bin Hu [35]
41Michael Hucka [30]
42Peter J. Hunter [30]
43C. A. Hutchison III [21]
44Katsuhiko Ikeda [31]
45Keita Ikegami [56]
46Masa Inakage [37]
47Yasushi Ishihama [49]
48N. Ishikawa [32]
49Daiki Ito [38]
50Hitomi Itoh [34]
51Nick S. Juty [30]
52Kazunari Kaizu [35] [53]
53Akio Kanai [33]
54J. L. Kasberger [30]
55Jun Kawai [39]
56Nobuhiro Kido [56]
57Takashi Kido [19]
58Shinichi Kikuchi [28] [29] [42] [48] [51]
59Shoshi Kikuchi [39]
60Noriyuki Kitagawa [28] [39]
61Sumie Kitamura-Abe [34]
62Hiroaki Kitano [30]
63Tomoya Kitayama [38] [40]
64Yasushi Kiyoki [37]
65Yusuke Kobayashi [31]
66Shigen Kojima [40]
67Nobuaki Kono [46] [56]
68Shunichi Kosugi [39]
69Anton Kratz [50]
70Andreas Kremling [30]
71Arun Krishnan [41] [50]
72Ursula Kummer [30]
73Kuo-Bin Li [41]
74Leslie M. Loew [30]
75D. Lucio [30]
76Kenichi Matsubara [39]
77Yoshiya Matsubara [42] [51]
78Ryo Matsushima [23]
79Tatekimi Matsuzaki [31]
80Yuri Matsuzaki [21] [23] [48]
81Pedro Mendes [30]
82E. Minch [30]
83Teruko Mitamura [9]
84Fumihiko Miyoshi [21] [23] [32] [53]
85Eric Mjolsness [30]
86Koya Mori [31]
87Kazuo Murakami [39]
88Masato Murakami [45]
89Yasuhiro Naito [32] [52]
90Hiromu Nakajima [52]
91Hisako Nakano [23]
92Yoichi Nakayama [23] [30] [32] [40] [43] [53]
93M. R. Nelson [30]
94Poul M. F. Nielsen [30]
95Nicolas Le Novère [30]
96Ryu Ogawa [56]
97Yukino Ogawa [53]
98Hiroshi Ohno [52]
99S. Ohta [32]
100Yasuhiro Ohtomo [39]
101Kotaro Oka [28] [51]
102Y. Osada [20]
103Christopher J. F. Pickett [26]
104Martin Robert [47]
105Y. Sadamoto [32]
106Hiroaki Saito (Hiroaki Saitoh) [12]
107K. Saito [21]
108Rintaro Saito [20] [33] [55]
109Yusuke Saito [23]
110Naomichi Sakai [45]
111T. Sakurada [30]
112H. Sasamoto [32]
113Misaki Sato [33]
114Koji Satoh [39]
115Masahiko Satoh [37]
116Herbert M. Sauro [30]
117Koichiro Sawa [45]
118James C. Schaff [30]
119Kumar Selvarajoo [54]
120William Rodman Shankle [22]
121Bruce E. Shapiro [30]
122S. Shimizu [23]
123Thomas Simon Shimizu [21] [30]
124Kosaku Shinoda [43] [49]
125A. Shiozawa [32]
126Tomoyoshi Soga [47]
127Hugh D. Spence [30]
128Jörg Stelling [30]
129Makoto Suematsu [47]
130Masahiro Sugimoto [38] [42] [51]
131Tomomi Sunako [39]
132Haruo Suzuki [55]
133Katsutoshi Takahashi [29]
134Koichi Takahashi [21] [23] [30] [32]
135Kouichi Takahashi [26] [35] [38]
136Kohtaro Takei [28]
137Satoshi Tamaki [46] [56]
138S. Tanida [21]
139Hideto Tomabechi [9] [11] [15]
140Daisuke Tominaga [29]
141Masa Tsuchiya [54]
142Akihiro Tsutsumi [34]
143Hitomi Umeki [33]
144J. C. Venter [21]
145J. Wagner [30]
146J. Wang [30]
147Takanori Washio [34] [39]
148Yohei Yamada [26] [43]
149Tomoya Yamashita [39]
150Hiroshi Yanagawa [39]
151Katsuyuki Yugi [21] [23] [26] [36] [40]

Colors in the list of coauthors

Copyright © Tue Nov 3 08:52:44 2009 by Michael Ley (ley@uni-trier.de)