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Masaru Tomita: [Publications] [Author Rank by year] [Co-authors] [Prefers] [Cites] [Cited by]

Publications of Author

  1. Hideto Tomabechi, Masaru Tomita
    The Integration of Unification-Based Syntax/Semantics and Memory-Based Pragmatics for Real-Time Understanding of Noisy Continuous Speech Input. [Citation Graph (0, 0)][DBLP]
    AAAI, 1988, pp:724-728 [Conf]
  2. Masaru Tomita
    Graph-Structured Stack and Natural Language Parsing. [Citation Graph (0, 0)][DBLP]
    ACL, 1988, pp:249-257 [Conf]
  3. Gennaro Costagliola, Shi-Kuo Chang, Masaru Tomita
    Parsing 2D Languages by a Pictorial GLR Parser. [Citation Graph (0, 0)][DBLP]
    Advanced Visual Interfaces, 1992, pp:319-333 [Conf]
  4. Philip J. Hayes, Alexander G. Hauptmann, Jaime G. Carbonell, Masaru Tomita
    Parsing Spoken Language: A Semantic Caseframe Approach. [Citation Graph (0, 0)][DBLP]
    COLING, 1986, pp:587-592 [Conf]
  5. Hiroaki Saito, Masaru Tomita
    Parsing noisy sentences. [Citation Graph (0, 0)][DBLP]
    COLING, 1988, pp:561-566 [Conf]
  6. Hideto Tomabechi, Masaru Tomita
    Application of the direct memory access paradigm to NL interfaces to knowledge-based systems. [Citation Graph (0, 0)][DBLP]
    COLING, 1988, pp:661-666 [Conf]
  7. Masaru Tomita
    LR Parsers For Natural Languages. [Citation Graph (0, 0)][DBLP]
    COLING, 1984, pp:354-357 [Conf]
  8. Masaru Tomita
    Disambiguating Grammatically Ambiguous Sentences By Asking. [Citation Graph (0, 0)][DBLP]
    COLING, 1984, pp:476-480 [Conf]
  9. Masaru Tomita
    "Linguistic" sentences and "real" sentences. [Citation Graph (0, 0)][DBLP]
    COLING, 1988, pp:453- [Conf]
  10. Masaru Tomita
    Combining lexicon-driven parsing and phrase-structure-based parsing. [Citation Graph (0, 0)][DBLP]
    COLING, 1988, pp:667-670 [Conf]
  11. Masaru Tomita
    The Generalized LR Parser/Compiler V8-4: A Software Package for Practical NL Projects. [Citation Graph (0, 0)][DBLP]
    COLING, 1990, pp:59-63 [Conf]
  12. Masaru Tomita, Jaime G. Carbonell
    Another Stride Towards Knowledge-Based Machine Translation. [Citation Graph (0, 0)][DBLP]
    COLING, 1986, pp:633-638 [Conf]
  13. Masaru Tomita
    Toward Computer Simulation of the Whole Cell. [Citation Graph (0, 0)][DBLP]
    Gene Regulations and Metabolism, 2002, pp:273-288 [Conf]
  14. Hideto Tomabechi, Teruko Mitamura, Masaru Tomita
    Direct Memory Access Translation for Speech Input. [Citation Graph (0, 0)][DBLP]
    FGCS, 1988, pp:1100-1107 [Conf]
  15. Masaru Tomita
    E-CELL Project: Towards Whole Cell Simulation. [Citation Graph (0, 0)][DBLP]
    German Conference on Bioinformatics, 2001, pp:1- [Conf]
  16. Masaru Tomita
    An Efficient Context-Free Parsing Algorithm for Natural Languages. [Citation Graph (0, 0)][DBLP]
    IJCAI, 1985, pp:756-764 [Conf]
  17. Masaru Tomita, Jaime G. Carbonell
    The Universal Parser Architecture for Knowledge-based Machine Translation. [Citation Graph (0, 0)][DBLP]
    IJCAI, 1987, pp:718-721 [Conf]
  18. Gabor Bereczki, Masaru Tomita
    An interaction knowledgebase for biomolecular modeling. [Citation Graph (0, 0)][DBLP]
    Industrial Conference on Data Mining - Workshops, 2006, pp:101-110 [Conf]
  19. Masahiro Sugimoto, Kouichi Takahashi, Tomoya Kitayama, Daiki Ito, Masaru Tomita
    Distributed Cell Biology Simulations with E-Cell System. [Citation Graph (0, 0)][DBLP]
    LSGRID, 2004, pp:20-31 [Conf]
  20. 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. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2000, pp:290-298 [Conf]
  21. Yasushi Kiyoki, Masa Inakage, Masahiko Satoh, Masaru Tomita
    Future Directions for Cyber Knowledge and Databases. [Citation Graph (0, 0)][DBLP]
    SAINT Workshops, 2004, pp:495-501 [Conf]
  22. Gennaro Costagliola, Masaru Tomita, Shi-Kuo Chang
    A Generalized Parser for 2-D Languages. [Citation Graph (0, 0)][DBLP]
    VL, 1991, pp:98-104 [Conf]
  23. Kazuharu Arakawa, Koya Mori, Katsuhiko Ikeda, Tatekimi Matsuzaki, Yusuke Kobayashi, Masaru Tomita
    G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2003, v:19, n:2, pp:305-306 [Journal]
  24. 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, S. Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, Igor Goryanin, W. J. Hedley, T. Charles Hodgman, J. H. Hofmeyr, P. 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. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2003, v:19, n:4, pp:524-531 [Journal]
  25. Shinichi Kikuchi, Daisuke Tominaga, Masanori Arita, Katsutoshi Takahashi, Masaru Tomita
    Dynamic modeling of genetic networks using genetic algorithm and S-system. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2003, v:19, n:5, pp:643-650 [Journal]
  26. 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). [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2005, v:21, n:9, pp:1758-1763 [Journal]
  27. Y. Osada, Rintaro Saito, Masaru Tomita
    Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 1999, v:15, n:7, pp:578-581 [Journal]
  28. Misaki Sato, Hitomi Umeki, Rintaro Saito, Akio Kanai, Masaru Tomita
    Computational Analysis of Stop Codon Readthrough in D.melanogaster. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2003, v:19, n:11, pp:1371-1380 [Journal]
  29. Koichi Takahashi, N. Ishikawa, Y. Sadamoto, H. Sasamoto, S. Ohta, A. Shiozawa, Fumihiko Miyoshi, Y. Naito, Yoichi Nakayama, Masaru Tomita
    E-Cell 2: Multi-platform E-Cell simulation system. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2003, v:19, n:13, pp:1727-1729 [Journal]
  30. Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita
    A multi-algorithm, multi-timescale method for cell simulation. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2004, v:20, n:4, pp:- [Journal]
  31. Masaru Tomita
    Towards Computer Aided Design (CAD) of Useful Microorganisms. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2001, v:17, n:12, pp:1091-1092 [Journal]
  32. 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. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 1999, v:15, n:1, pp:72-84 [Journal]
  33. Katsuyuki Yugi, Masaru Tomita
    A general computational model of mitochondrial metabolism in a whole organelle scale. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2004, v:20, n:11, pp:1795-1796 [Journal]
  34. Kazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita
    GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. [Citation Graph (0, 0)][DBLP]
    BMC Bioinformatics, 2006, v:7, n:, pp:168- [Journal]
  35. Yoshiya Matsubara, Shinichi Kikuchi, Masahiro Sugimoto, Masaru Tomita
    Parameter estimation for stiff equations of biosystems using radial basis function networks. [Citation Graph (0, 0)][DBLP]
    BMC Bioinformatics, 2006, v:7, n:, pp:230- [Journal]
  36. Katsuyuki Yugi, Yoichi Nakayama, Shigen Kojima, Tomoya Kitayama, Masaru Tomita
    A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks. [Citation Graph (0, 0)][DBLP]
    BMC Bioinformatics, 2005, v:6, n:, pp:299- [Journal]
  37. Masaru Tomita
    An Efficient Augmented-Context-Free Parsing Algorithm. [Citation Graph (0, 0)][DBLP]
    Computational Linguistics, 1987, v:13, n:1-2, pp:31-46 [Journal]
  38. Kouichi Takahashi, Katsuyuki Yugi, Kenta Hashimoto, Yohei Yamada, Christopher J. F. Pickett, Masaru Tomita
    Computational Challenges in Cell Simulation: A Software Engineering Approach. [Citation Graph (0, 0)][DBLP]
    IEEE Intelligent Systems, 2002, v:17, n:5, pp:64-71 [Journal]
  39. Ryuta Fukuda, Junko Hara, William Rodman Shankle, Masaru Tomita
    Proposition of cortical connectivity between 30 cytoarchitectural areas of human cerebral cortex. [Citation Graph (0, 0)][DBLP]
    Neurocomputing, 2000, v:32, n:, pp:749-755 [Journal]
  40. Masaru Tomita, Takashi Kido
    Sacrificial Acts in Single Round Prisoner`S Dilemma. [Citation Graph (0, 0)][DBLP]
    Informatica (Slovenia), 1994, v:18, n:4, pp:- [Journal]
  41. 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. [Citation Graph (0, 0)][DBLP]
    J. Bioinformatics and Computational Biology, 2004, v:2, n:2, pp:309-332 [Journal]
  42. Gek Huey Chua, Arun Krishnan, Kuo-Bin Li, Masaru Tomita
    Multiresolution Analysis Uncovers Hidden Conservation of Properties in Structurally and Functionally Similar Proteins. [Citation Graph (0, 0)][DBLP]
    J. Bioinformatics and Computational Biology, 2006, v:4, n:6, pp:1245-1268 [Journal]
  43. Masaru Tomita
    Sentence disambiguation by asking. [Citation Graph (0, 0)][DBLP]
    Machine Translation, 1986, v:1, n:1, pp:39-51 [Journal]
  44. 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. [Citation Graph (0, 0)][DBLP]
    Neural Networks, 2003, v:16, n:9, pp:1389-1398 [Journal]

  45. Algebraic Method for the Analysis of Signaling Crosstalk. [Citation Graph (, )][DBLP]


  46. Comparative Study of Circadian Oscillatory Network Models of Drosophila. [Citation Graph (, )][DBLP]


  47. Construction of a Biological Tissue Model Based on a Single-Cell Model: A Computer Simulation of Metabolic Heterogeneity in the Liver Lobule. [Citation Graph (, )][DBLP]


  48. Robust effects of Tsr-CheBp and CheA-CheYp affinity in bacterial chemotaxis. [Citation Graph (, )][DBLP]


  49. Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments. [Citation Graph (, )][DBLP]


  50. emPAI Calc - for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. [Citation Graph (, )][DBLP]


  51. Visualization of three-way comparisons of omics data. [Citation Graph (, )][DBLP]


  52. GeNESiS: gene network evolution simulation software. [Citation Graph (, )][DBLP]


  53. Measure of synonymous codon usage diversity among genes in bacteria. [Citation Graph (, )][DBLP]


  54. Genome Projector: zoomable genome map with multiple views. [Citation Graph (, )][DBLP]


  55. MathDAMP: a package for differential analysis of metabolite profiles. [Citation Graph (, )][DBLP]


  56. HybGFS: a hybrid method for genome-fingerprint scanning. [Citation Graph (, )][DBLP]


  57. Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. [Citation Graph (, )][DBLP]


  58. Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions. [Citation Graph (, )][DBLP]


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