Masaru Tomita

Masahiro Takada, Masahiro Sugimoto, Yasuhiro Naito, Hyeong-Gon Moon, Wonshik Han, Dong-Young Noh, Masahide Kondo, Katsumasa Kuroi, Hironobu Sasano, Takashi Inamoto, Masaru Tomita, Masakazu Toi: Prediction of axillary lymph node metastasis in primary breast cancer patients using a decision tree-based model. BMC Med. Inf. & Decision Making 12: 54 (2012)

Masahiro Sugimoto, Satsuki Ikeda, Kanako Niigata, Masaru Tomita, Hideyo Sato, Tomoyoshi Soga: MMMDB: Mouse Multiple Tissue Metabolome Database. Nucleic Acids Research 40(Database-Issue): 809-814 (2012)

Nozomu Yachie, Rintaro Saito, Naoyuki Sugiyama, Masaru Tomita, Yasushi Ishihama: Integrative Features of the Yeast Phosphoproteome and Protein-Protein Interaction Map. PLoS Computational Biology 7(1) (2011)

Kazuki Oshita, Kazuharu Arakawa, Masaru Tomita: KBWS: an EMBOSS associated package for accessing bioinformatics web services. Source Code for Biology and Medicine 6: 8 (2011)

Kosaku Shinoda, Masaru Tomita, Yasushi Ishihama: emPAI Calc - for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. Bioinformatics 26(4): 576-577 (2010)

Haruna Imamura, Nozomu Yachie, Rintaro Saito, Yasushi Ishihama, Masaru Tomita: Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. BMC Bioinformatics 11: 232 (2010)

Yosuke Ozawa, Rintaro Saito, Shigeo Fujimori, Hisashi Kashima, Masamichi Ishizaka, Hiroshi Yanagawa, Etsuko Miyamoto-Sato, Masaru Tomita: Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions. BMC Bioinformatics 11: 350 (2010)

Kazuharu Arakawa, Nobuhiro Kido, Kazuki Oshita, Masaru Tomita: G-language genome analysis environment with REST and SOAP web service interfaces. Nucleic Acids Research 38(Web-Server-Issue): 700-705 (2010)

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)

Haruo Suzuki, Rintaro Saito, Masaru Tomita: Measure of synonymous codon usage diversity among genes in bacteria. BMC Bioinformatics 10 (2009)

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)

Kazuharu Arakawa, Kazuki Oshita, Masaru Tomita: A web server for interactive and zoomable Chaos Game Representation images. Source Code for Biology and Medicine 4: 6 (2009)

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)

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)

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)

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)

Kyota Ishii, Seira Nakamura, Mineo Morohashi, Masahiro Sugimoto, Yoshiaki Ohashi, Shinichi Kikuchi, Masaru Tomita: Comparison of metabolite production capability indices generated by network analysis methods. Biosystems 91(1): 166-170 (2008)

Anton Kratz, Masaru Tomita, Arun Krishnan: GeNESiS: gene network evolution simulation software. BMC Bioinformatics 9 (2008)

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)

Koya Mori, Rintaro Saito, Shinichi Kikuchi, Masaru Tomita: Inferring rules of Escherichia coli translational efficiency using an artificial neural network. Biosystems 90(2): 414-420 (2007)

Richard Baran, Martin Robert, Makoto Suematsu, Tomoyoshi Soga, Masaru Tomita: Visualization of three-way comparisons of omics data. BMC Bioinformatics 8 (2007)

Haruo Suzuki, Rintaro Saito, Masaru Tomita: Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria. EURASIP J. Bioinformatics and Systems Biology 2007 (2007)

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)

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)

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)

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)

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)

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)

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)

Gabor Bereczki, Masaru Tomita: An interaction knowledgebase for biomolecular modeling. Industrial Conference on Data Mining - Workshops 2006: 101-110

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)

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)

Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita: A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics 20(4): 538-546 (2004)

Katsuyuki Yugi, Masaru Tomita: A general computational model of mitochondrial metabolism in a whole organelle scale. Bioinformatics 20(11): 1795-1796 (2004)

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)

Masahiro Sugimoto, Kouichi Takahashi, Tomoya Kitayama, Daiki Ito, Masaru Tomita: Distributed Cell Biology Simulations with E-Cell System. LSGRID 2004: 20-31

Yasushi Kiyoki, Masa Inakage, Masahiko Satoh, Masaru Tomita: Future Directions for Cyber Knowledge and Databases. SAINT Workshops 2004: 495-501

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)

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)

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)

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)

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)

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)

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)

Masaru Tomita: Toward Computer Simulation of the Whole Cell. Gene Regulations and Metabolism 2002: 273-288

Masaru Tomita: Towards Computer Aided Design (CAD) of Useful Microorganisms. Bioinformatics 17(12): 1091-1092 (2001)

Masaru Tomita: E-CELL Project: Towards Whole Cell Simulation. German Conference on Bioinformatics 2001: 1

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)

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

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)

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)

Masaru Tomita, Takashi Kido: Sacrificial Acts in Single Round Prisoner`S Dilemma. Informatica (Slovenia) 18(4) (1994)

Sergei Nirenburg, Jaime G. Carbonell, Masaru Tomita, Kenneth Goodman: Machine translation - a knowledge-based approach. Morgan Kaufmann 1992, isbn 978-1-55860-128-4, pp. I-XIV, 1-258

Gennaro Costagliola, Shi-Kuo Chang, Masaru Tomita: Parsing 2D Languages by a Pictorial GLR Parser. Advanced Visual Interfaces 1992: 319-333

Gennaro Costagliola, Masaru Tomita, Shi-Kuo Chang: A Generalized Parser for 2-D Languages. VL 1991: 98-104

Masaru Tomita: The Generalized LR Parser/Compiler V8-4: A Software Package for Practical NL Projects. COLING 1990: 59-63

Hiroaki Kitano, Tetsuya Higuchi, Masaru Tomita: Massively parallel spoken language processing using a parallel associative processor IXM2. ICSLP 1990

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

Masaru Tomita: Graph-Structured Stack and Natural Language Parsing. ACL 1988: 249-257

Masaru Tomita: "Linguistic" sentences and "real" sentences. COLING 1988: 453

Hiroaki Saito, Masaru Tomita: Parsing noisy sentences. COLING 1988: 561-566

Hideto Tomabechi, Masaru Tomita: Application of the direct memory access paradigm to NL interfaces to knowledge-based systems. COLING 1988: 661-666

Masaru Tomita: Combining lexicon-driven parsing and phrase-structure-based parsing. COLING 1988: 667-670

Hideto Tomabechi, Teruko Mitamura, Masaru Tomita: Direct Memory Access Translation for Speech Input. FGCS 1988: 1100-1107

Masaru Tomita: An Efficient Augmented-Context-Free Parsing Algorithm. Computational Linguistics 13(1-2): 31-46 (1987)

Masaru Tomita, Jaime G. Carbonell: The Universal Parser Architecture for Knowledge-based Machine Translation. IJCAI 1987: 718-721

Masaru Tomita: Sentence disambiguation by asking. Machine Translation 1(1): 39-51 (1986)

Philip J. Hayes, Alexander G. Hauptmann, Jaime G. Carbonell, Masaru Tomita: Parsing Spoken Language: A Semantic Caseframe Approach. COLING 1986: 587-592

Masaru Tomita, Jaime G. Carbonell: Another Stride Towards Knowledge-Based Machine Translation. COLING 1986: 633-638

Masaru Tomita: An Efficient Context-Free Parsing Algorithm for Natural Languages. IJCAI 1985: 756-764

Masaru Tomita: LR Parsers For Natural Languages. COLING 1984: 354-357

Masaru Tomita: Disambiguating Grammatically Ambiguous Sentences By Asking. COLING 1984: 476-480