Masaru Tomita

	2009
58		Kazuharu 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)
57		Haruo Suzuki, Rintaro Saito, Masaru Tomita: Measure of synonymous codon usage diversity among genes in bacteria. BMC Bioinformatics 10: (2009)
56		Kumar 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
55		Yukino 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)
54		Hiroshi 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)
53		Yoshiya Matsubara, Shinichi Kikuchi, Masahiro Sugimoto, Kotaro Oka, Masaru Tomita: Algebraic Method for the Analysis of Signaling Crosstalk. Artificial Life 14(1): 81-94 (2008)
52		Anton Kratz, Masaru Tomita, Arun Krishnan: GeNESiS: gene network evolution simulation software. BMC Bioinformatics 9: (2008)
51		Kosaku 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
50		Yuri 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)
49		Richard Baran, Martin Robert, Makoto Suematsu, Tomoyoshi Soga, Masaru Tomita: Visualization of three-way comparisons of omics data. BMC Bioinformatics 8: (2007)
48		Satoshi 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)
47		Hiroyuki 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
46		Gabor Bereczki, Masaru Tomita: An interaction knowledgebase for biomolecular modeling. Industrial Conference on Data Mining - Workshops 2006: 101-110
45		Kazuharu 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)
44		Yoshiya Matsubara, Shinichi Kikuchi, Masahiro Sugimoto, Masaru Tomita: Parameter estimation for stiff equations of biosystems using radial basis function networks. BMC Bioinformatics 7: 230 (2006)
43		Kosaku Shinoda, Nozomu Yachie, Takeshi Masuda, Naoyuki Sugiyama, Masahiro Sugimoto, Tomoyoshi Soga, Masaru Tomita: HybGFS: a hybrid method for genome-fingerprint scanning. BMC Bioinformatics 7: 479 (2006)
42		Richard Baran, Hayataro Kochi, Natsumi Saito, Makoto Suematsu, Tomoyoshi Soga, Takaaki Nishioka, Martin Robert, Masaru Tomita: MathDAMP: a package for differential analysis of metabolite profiles. BMC Bioinformatics 7: 530 (2006)
41		Gek 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
40		Katsuyuki 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)
39		Noriyuki 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
38		Masahiro Sugimoto, Kouichi Takahashi, Tomoya Kitayama, Daiki Ito, Masaru Tomita: Distributed Cell Biology Simulations with E-Cell System. LSGRID 2004: 20-31
37		Yasushi Kiyoki, Masa Inakage, Masahiko Satoh, Masaru Tomita: Future Directions for Cyber Knowledge and Databases. SAINT Workshops 2004: 495-501
36		Katsuyuki Yugi, Masaru Tomita: A general computational model of mitochondrial metabolism in a whole organelle scale. Bioinformatics 20(11): 1795-1796 (2004)
35		Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita: A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics 20(4): (2004)
34		Sumie 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)
28		Shinichi 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
26		Kouichi 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
23		Masaru 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
22		Ryuta 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
16		Masaru 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
4		Masaru 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
2		Masaru Tomita: LR Parsers For Natural Languages. COLING 1984: 354-357
1		Masaru Tomita: Disambiguating Grammatically Ambiguous Sentences By Asking. COLING 1984: 476-480

Coauthor Index

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

Colors in the list of coauthors