Masaru Tomita

103 papers A* 4B 12Misc 2Journal 62Unranked 21
YearRankTypeTitle / Venue / Authors
2022 J jnl
iDMET: network-based approach for integrating differential analysis of cancer metabolomics.
BMC Bioinform.
Rira Matsuta, Hiroyuki Yamamoto, Masaru Tomita, Rintaro Saito
2019 J jnl
Automatic Fault Detection and Isolation Method for Roller Bearing Using Hybrid-GA and Sequential Fuzzy Inference.
Sensors
Yusuke Kobayashi, Liuyang Song, Masaru Tomita, Peng Chen
2018 J jnl
MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data.
BMC Bioinform.
Hitoshi Iuchi, Masahiro Sugimoto, Masaru Tomita
2016 — conf
BriCA: A Modular Software Platform for Whole Brain Architecture.
ICONIP (1)
Kotone Itaya, Koichi Takahashi, Masayoshi Nakamura, Moriyoshi Koizumi, Naoya Arakawa, Masaru Tomita, Hiroshi Yamakawa
2016 — conf
Combination of Quantitative Changes in Ionic Components to Enhance the Contractile Force during T-tubule Development.
CinC
Maiko Wakita, Hitomi Sano, Yasuhiro Naito, Masaru Tomita
2016 — conf
Simulation Study on the Balance of Glycolytic ATP Production and Oxidative Phosphorylation in Embryonic and Adult Ventricular Cells.
CinC
Hitomi Sano, Yasuhiro Naito, Masaru Tomita
2015 — conf
A Generic Software Platform for Brain-inspired Cognitive Computing.
BICA
Koichi Takahashi, Kotone Itaya, Masayoshi Nakamura, Moriyoshi Koizumi, Naoya Arakawa, Masaru Tomita, Hiroshi Yamakawa
2015 — conf
Modeling and Simulation of Developmental Changes in Contractile Apparatus of Ventricular Cells.
CinC
Mao Takiguchi, Tamami Toki, Hitomi Sano, Yasuhiro Naito, Masaru Tomita
2015 J jnl
Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes.
PLoS Comput. Biol.
Hanae Shimo, Satya Nanda Vel Arjunan, Hiroaki Machiyama, Taiko Nishino, Makoto Suematsu, Hideaki Fujita, Masaru Tomita, Koichi Takahashi
2015 — conf
Sensitivity Analysis of Ectopic Electrical Activity in Pulmonary Vein Myocardium.
CinC
Hitomi Sano, Yuichiro Tanaka, Yasuhiro Naito, Masaru Tomita
2014 — conf
Contribution of Developmental Changes in Energy Metabolism to Excitation-Contraction Coupling of a Ventricular Cell: A Simulation Study.
CinC
Hitomi Sano, Tamami Toki, Yasuhiro Naito, Masaru Tomita
2014 J jnl
G-Links: a gene-centric link acquisition service.
F1000Research
Kazuki Oshita, Masaru Tomita, Kazuharu Arakawa
2013 J jnl
GEMBASSY: an EMBOSS associated software package for comprehensive genome analyses.
Source Code Biol. Medicine
Hidetoshi Itaya, Kazuki Oshita, Kazuharu Arakawa, Masaru Tomita
2013 — conf
The dynamics of cellular energetics during continuous yeast culture.
EMBC
Cornelia Amariei, Rainer Machné, Kalesh Sasidharan, Willi Gottstein, Masaru Tomita, Tomoyoshi Soga, David Lloyd, Douglas B. Murray
2012 J jnl
MMMDB: Mouse Multiple Tissue Metabolome Database.
Nucleic Acids Res.
Masahiro Sugimoto, Satsuki Ikeda, Kanako Niigata, Masaru Tomita, Hideyo Sato, Tomoyoshi Soga
2012 J jnl
Prediction of axillary lymph node metastasis in primary breast cancer patients using a decision tree-based model.
BMC Medical Informatics Decis. Mak.
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
2011 J jnl
Integrative Features of the Yeast Phosphoproteome and Protein-Protein Interaction Map.
PLoS Comput. Biol.
Nozomu Yachie, Rintaro Saito, Naoyuki Sugiyama, Masaru Tomita, Yasushi Ishihama
2011 J jnl
KBWS: an EMBOSS associated package for accessing bioinformatics web services.
Source Code Biol. Medicine
Kazuki Oshita, Kazuharu Arakawa, Masaru Tomita
2010 J jnl
G-language genome analysis environment with REST and SOAP web service interfaces.
Nucleic Acids Res.
Kazuharu Arakawa, Nobuhiro Kido, Kazuki Oshita, Masaru Tomita
2010 J jnl
Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions.
BMC Bioinform.
Yosuke Ozawa, Rintaro Saito, Shigeo Fujimori, Hisashi Kashima, Masamichi Ishizaka, Hiroshi Yanagawa, Etsuko Miyamoto-Sato, Masaru Tomita
2010 J jnl
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data.
BMC Bioinform.
Haruna Imamura, Nozomu Yachie, Rintaro Saito, Yasushi Ishihama, Masaru Tomita
2010 J jnl
emPAI Calc - for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry.
Bioinform.
Kosaku Shinoda, Masaru Tomita, Yasushi Ishihama
2009 J jnl
A web server for interactive and zoomable Chaos Game Representation images.
Source Code Biol. Medicine
Kazuharu Arakawa, Kazuki Oshita, Masaru Tomita
2009 J jnl
Can Complex Cellular Processes be Governed by Simple Linear Rules?
J. Bioinform. Comput. Biol.
Kumar Selvarajoo, Masaru Tomita, Masa Tsuchiya
2009 J jnl
Genome Projector: zoomable genome map with multiple views.
BMC Bioinform.
Kazuharu Arakawa, Satoshi Tamaki, Nobuaki Kono, Nobuhiro Kido, Keita Ikegami, Ryu Ogawa, Masaru Tomita
2009 J jnl
Measure of synonymous codon usage diversity among genes in bacteria.
BMC Bioinform.
Haruo Suzuki, Rintaro Saito, Masaru Tomita
2009 J jnl
Network features and pathway analyses of a signal transduction cascade.
Frontiers Neuroinformatics
Ryoji Yanashima, Noriyuki Kitagawa, Yoshiya Matsubara, Robert Weatheritt, Kotaro Oka, Shinichi Kikuchi, Masaru Tomita, Shun Ishizaki
2008 J jnl
Algebraic Method for the Analysis of Signaling Crosstalk.
Artif. Life
Yoshiya Matsubara, Shinichi Kikuchi, Masahiro Sugimoto, Kotaro Oka, Masaru Tomita
2008 J jnl
Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments.
Bioinform.
Kosaku Shinoda, Masaru Tomita, Yasushi Ishihama
2008 J jnl
Comparative Study of Circadian Oscillatory Network Models of
Artif. Life
Yukino Ogawa, Kazuharu Arakawa, Kazunari Kaizu, Fumihiko Miyoshi, Yoichi Nakayama, Masaru Tomita
2008 J jnl
Comparison of metabolite production capability indices generated by network analysis methods.
Biosyst.
Kyota Ishii, Seira Nakamura, Mineo Morohashi, Masahiro Sugimoto, Yoshiaki Ohashi, Shinichi Kikuchi, Masaru Tomita
2008 J jnl
Construction of a Biological Tissue Model Based on a Single-Cell Model: A Computer Simulation of Metabolic Heterogeneity in the Liver Lobule.
Artif. Life
Hiroshi Ohno, Yasuhiro Naito, Hiromu Nakajima, Masaru Tomita
2008 J jnl
GeNESiS: gene network evolution simulation software.
BMC Bioinform.
Anton Kratz, Masaru Tomita, Arun Krishnan
2008 J jnl
Time-resolved metabolomics reveals metabolic modulation in rice foliage.
BMC Syst. Biol.
Shigeru Sato, Masanori Arita, Tomoyoshi Soga, Takaaki Nishioka, Masaru Tomita
2007 J jnl
Consideration on Contact Mechanism of YBaCuO Bulk Superconductor with Deposited Metal Layer.
IEICE Trans. Electron.
Hiroyuki Fujita, Katsuya Fukuda, Koichiro Sawa, Masaru Tomita, Masato Murakami, Naomichi Sakai, Izumi Hirabayashi
2007 J jnl
Inferring rules of Escherichia coli translational efficiency using an artificial neural network.
Biosyst.
Koya Mori, Rintaro Saito, Shinichi Kikuchi, Masaru Tomita
2007 J jnl
Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics.
Genom. Proteom. Bioinform.
Satoshi Tamaki, Kazuharu Arakawa, Nobuaki Kono, Masaru Tomita
2007 J jnl
Robust effects of Tsr-CheBp and CheA-CheYp affinity in bacterial chemotaxis.
Artif. Intell. Medicine
Yuri Matsuzaki, Shinichi Kikuchi, Masaru Tomita
2007 J jnl
Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria.
EURASIP J. Bioinform. Syst. Biol.
Haruo Suzuki, Rintaro Saito, Masaru Tomita
2007 J jnl
Visualization of three-way comparisons of omics data.
BMC Bioinform.
Richard Baran, Martin Robert, Makoto Suematsu, Tomoyoshi Soga, Masaru Tomita
2007 J jnl
eXpanda: An Integrated Platform for Network Analysis and Visualization.
Silico Biol.
Yoshiteru Negishi, Hiroyuki Nakamura, Nozomu Yachie, Rintaro Saito, Masaru Tomita
2006 — conf
An interaction knowledgebase for biomolecular modeling.
ICDM (Workshops)
Gabor Bereczki, Masaru Tomita
2006 J jnl
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes.
BMC Bioinform.
Kazuharu Arakawa, Yohei Yamada, Kosaku Shinoda, Yoichi Nakayama, Masaru Tomita
2006 J jnl
GPAC: Benchmarking the Sensitivity of Genome Informatics Analysis to Genome Annotation Completeness.
Silico Biol.
Kazuharu Arakawa, Yoichi Nakayama, Masaru Tomita
2006 J jnl
HybGFS: a hybrid method for genome-fingerprint scanning.
BMC Bioinform.
Kosaku Shinoda, Nozomu Yachie, Takeshi Masuda, Naoyuki Sugiyama, Masahiro Sugimoto, Tomoyoshi Soga, Masaru Tomita
2006 J jnl
MEGU: Pathway Mapping Web-Service Based on KEGG and SVG.
Silico Biol.
Nobuaki Kono, Kazuharu Arakawa, Masaru Tomita
2006 J jnl
MathDAMP: a package for differential analysis of metabolite profiles.
BMC Bioinform.
Richard Baran, Hayataro Kochi, Natsumi Saito, Makoto Suematsu, Tomoyoshi Soga, Takaaki Nishioka, Martin Robert, Masaru Tomita
2006 J jnl
Multiresolution Analysis Uncovers Hidden Conservation of Properties in Structurally and Functionally Similar Proteins.
J. Bioinform. Comput. Biol.
Gek Huey Chua, Arun Krishnan, Kuo-Bin Li, Masaru Tomita
2006 J jnl
Parameter estimation for stiff equations of biosystems using radial basis function networks.
BMC Bioinform.
Yoshiya Matsubara, Shinichi Kikuchi, Masahiro Sugimoto, Masaru Tomita
2006 J jnl
SPLITS: A New Program for Predicting Split and Intron-Containing tRNA Genes at the Genome Level.
Silico Biol.
Junichi Sugahara, Nozomu Yachie, Yasuhiko Sekine, Akiko Soma, Motomu Matsui, Masaru Tomita, Akio Kanai
2005 J jnl
A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks.
BMC Bioinform.
Katsuyuki Yugi, Yoichi Nakayama, Shigen Kojima, Tomoya Kitayama, Masaru Tomita
2005 J jnl
Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa).
Bioinform.
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
2005 J jnl
KEGG-Based Pathway Visualization Tool for Complex Omics Data.
Silico Biol.
Kazuharu Arakawa, Nobuaki Kono, Yohei Yamada, Hirotada Mori, Masaru Tomita
2004 J jnl
A general computational model of mitochondrial metabolism in a whole organelle scale.
Bioinform.
Katsuyuki Yugi, Masaru Tomita
2004 J jnl
A multi-algorithm, multi-timescale method for cell simulation.
Bioinform.
Kouichi Takahashi, Kazunari Kaizu, Bin Hu, Masaru Tomita
2004 J jnl
Characterization of the Splice Sites in Gt-ag and Gc-ag Introns in Higher Eukaryotes Using Full-length Cdnas.
J. Bioinform. Comput. Biol.
Sumie Kitamura-Abe, Hitomi Itoh, Takanori Washio, Akihiro Tsutsumi, Masaru Tomita
2004 — conf
Distributed Cell Biology Simulations with E-Cell System.
LSGRID
Masahiro Sugimoto, Kouichi Takahashi, Tomoya Kitayama, Daiki Ito, Masaru Tomita
2004 — conf
Future Directions for Cyber Knowledge and Databases.
SAINT Workshops
Yasushi Kiyoki, Masa Inakage, Masahiko Satoh, Masaru Tomita
2003 J jnl
Computational Analysis of Stop Codon Readthrough in D.melanogaster.
Bioinform.
Misaki Sato, Hitomi Umeki, Rintaro Saito, Akio Kanai, Masaru Tomita
2003 J jnl
Dynamic modeling of genetic networks using genetic algorithm and S-system.
Bioinform.
Shinichi Kikuchi, Daisuke Tominaga, Masanori Arita, Katsutoshi Takahashi, Masaru Tomita
2003 J jnl
E-Cell 2: Multi-platform E-Cell simulation system.
Bioinform.
Koichi Takahashi, Naota Ishikawa, Yasuhiro Sadamoto, Hiroyuki Sasamoto, Seiji Ohta, Akira Shiozawa, Fumihiko Miyoshi, Yasuhiro Naito, Yoichi Nakayama, Masaru Tomita
2003 J jnl
G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining.
Bioinform.
Kazuharu Arakawa, Koya Mori, Katsuhiko Ikeda, Tatekimi Matsuzaki, Yusuke Kobayashi, Masaru Tomita
2003 J jnl
Kinetic simulation of signal transduction system in hippocampal long-term potentiation with dynamic modeling of protein phosphatase 2A.
Neural Networks
Shinichi Kikuchi, Kenji Fujimoto, Noriyuki Kitagawa, Taro Fuchikawa, Michiko Abe, Kotaro Oka, Kohtaro Takei, Masaru Tomita
2003 J jnl
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Bioinform.
Michael Hucka, Andrew Finney, Herbert M. Sauro, H. Bolouri, John C. Doyle, Hiroaki Kitano, Adam P. Arkin, Benjamin J. Bornstein, Dennis Bray, Athel Cornish-Bowden, Autumn A. Cuellar, Serge Dronov, Ernst Dieter Gilles, Martin Ginkel, Victoria Gor, Igor Goryanin, W. J. Hedley, T. Charles Hodgman, Jan-Hendrik S. 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
2002 J jnl
Computational Challenges in Cell Simulation: A Software Engineering Approach.
IEEE Intell. Syst.
Kouichi Takahashi, Katsuyuki Yugi, Kenta Hashimoto, Yohei Yamada, Christopher J. F. Pickett, Masaru Tomita
2002 J jnl
Integrative modeling of gene expression and metabolism with E-CELL System.
Artif. Life Robotics
Kenta Hashimoto, Sae Seno, Pawan Kumar Dhar, Masaru Tomita
2002 — conf
Toward Computer Simulation of the Whole Cell.
Gene Regulations and Metabolism
Masaru Tomita
2001 — conf
E-CELL Project: Towards Whole Cell Simulation.
German Conference on Bioinformatics
Masaru Tomita
2001 J jnl
Towards Computer Aided Design (CAD) of Useful Microorganisms.
Bioinform.
Masaru Tomita
2000 J jnl
Proposition of cortical connectivity between 30 cytoarchitectural areas of human cerebral cortex.
Neurocomputing
Ryuta Fukuda, Junko Hara, William Rodman Shankle, Masaru Tomita
2000 B conf
The E-CELL project: towards integrative simulation of cellular processes.
RECOMB
Masaru Tomita, Kenta Hashimoto, Koichi Takahashi, Yuri Matsuzaki, Ryo Matsushima, Katsuyuki Yugi, Fumihiko Miyoshi, Hisako Nakano, Yusuke Saito, Tom Shimizu, Yoichi Nakayama
1999 J jnl
Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes.
Bioinform.
Y. Osada, Rintaro Saito, Masaru Tomita
1999 J jnl
E-CELL: software environment for whole-cell simulation.
Bioinform.
Masaru Tomita, Kenta Hashimoto, Koichi Takahashi, Thomas Simon Shimizu, Yuri Matsuzaki, Fumihiko Miyoshi, Kanako Saito, Sakura Tanida, Katsuyuki Yugi, J. Craig Venter, Clyde A. Hutchison III
1999 B conf
Predicting human cortical connectivity for language areas using the Conel database.
IJCNN
Ryuta Fukuda, Junko Hara, William Rodman Shankle, Toshio Inui, Masaru Tomita
1994 — conf
JANUS 93: towards spontaneous speech translation.
ICASSP (1)
Monika Woszczyna, Naomi Aoki-Waibel, Finn Dag Buø, Noah Coccaro, Keiko Horiguchi, Thomas Kemp, Alon Lavie, Arthur E. McNair, Thomas Polzin, Ivica Rogina, Carolyn P. Rosé, Tanja Schultz, Bernhard Suhm, Masaru Tomita, Alex Waibel
1994 J jnl
Sacrificial Acts in Single Round Prisoner's Dilemma.
Informatica (Slovenia)
Masaru Tomita, Takashi Kido
1993 — conf
Recent advances in JANUS: a speech translation system.
EUROSPEECH
Monika Woszczyna, Noah Coccaro, Andreas Eisele, Alon Lavie, Arthur E. McNair, Thomas Polzin, Ivica Rogina, Carolyn P. Rosé, Tilo Sloboda, Masaru Tomita, J. Tsutsumi, Naomi Aoki-Waibel, Alex Waibel, Wayne H. Ward
1993 — conf
Recent advances in JANUS: a speech translation system.
HLT
Monika Woszczyna, Noah Coccaro, Andreas Eisele, Alon Lavie, Arthur E. McNair, Thomas Polzin, Ivica Rogina, Carolyn P. Rosé, Tilo Sloboda, Masaru Tomita, J. Tsutsumi, Naomi Aoki-Waibel, Alex Waibel, Wayne H. Ward
1992 — book
Machine translation - a knowledge-based approach.
Sergei Nirenburg, Jaime G. Carbonell, Masaru Tomita, Kenneth Goodman
1992 B conf
Parsing 2D Languages by a Pictorial GLR Parser.
Advanced Visual Interfaces
Gennaro Costagliola, Shi-Kuo Chang, Masaru Tomita
1991 — conf
A Generalized Parser for 2-D Languages.
VL
Gennaro Costagliola, Masaru Tomita, Shi-Kuo Chang
1990 — conf
Massively parallel spoken language processing using a parallel associative processor IXM2.
ICSLP
Hiroaki Kitano, Tetsuya Higuchi, Masaru Tomita
1990 B conf
The Generalized LR Parser/Compiler V8-4: A Software Package for Practical NL Projects.
COLING
Masaru Tomita
1989 — conf
Massively Parallel Parsing in ΦDmDialog: Integrated Architecture for Parsing Speech Inputs.
IWPT
Hiroaki Kitano, Teruko Mitamura, Masaru Tomita
1989 — conf
Parsing 2-Dimensional Language.
IWPT
Masaru Tomita
1989 — ed.
Proceedings of the First International Workshop on Parsing Technologies, IWPT 1989, Pittsburgh, Pennsylvania, USA, August 1989
IWPT
Masaru Tomita
1988 B conf
"Linguistic" sentences and "real" sentences.
COLING
Masaru Tomita
1988 B conf
Application of the direct memory access paradigm to NL interfaces to knowledge-based systems.
COLING
Hideto Tomabechi, Masaru Tomita
1988 B conf
Combining lexicon-driven parsing and phrase-structure-based parsing.
COLING
Masaru Tomita
1988 — conf
Direct Memory Access Translation for Speech Input.
FGCS
Hideto Tomabechi, Teruko Mitamura, Masaru Tomita
1988 A* conf
Graph-Structured Stack and Natural Language Parsing.
ACL
Masaru Tomita
1988 B conf
Parsing noisy sentences.
COLING
Hiroaki Saito, Masaru Tomita
1988 A* conf
The Integration of Unification-Based Syntax/Semantics and Memory-Based Pragmatics for Real-Time Understanding of Noisy Continuous Speech Input.
AAAI
Hideto Tomabechi, Masaru Tomita
1987 J jnl
An Efficient Augmented-Context-Free Parsing Algorithm.
Comput. Linguistics
Masaru Tomita
1987 A* conf
The Universal Parser Architecture for Knowledge-based Machine Translation.
IJCAI
Masaru Tomita, Jaime G. Carbonell
1986 Misc conf
An efficient word lattice parsing algorithm for continuous speech recognition.
ICASSP
Masaru Tomita
1986 B conf
Another Stride Towards Knowledge-Based Machine Translation.
COLING
Masaru Tomita, Jaime G. Carbonell
1986 Misc conf
On quick word spotting techniques.
ICASSP
Sei-ichi Nakagawa, Alexander G. Hauptmann, Masaru Tomita
1986 B conf
Parsing Spoken Language: A Semantic Caseframe Approach.
COLING
Philip J. Hayes, Alexander G. Hauptmann, Jaime G. Carbonell, Masaru Tomita
1986 J jnl
Sentence disambiguation by asking.
Mach. Transl.
Masaru Tomita
1985 A* conf
An Efficient Context-Free Parsing Algorithm for Natural Languages.
IJCAI
Masaru Tomita
1984 B conf
Disambiguating Grammatically Ambiguous Sentences By Asking.
COLING
Masaru Tomita
1984 B conf
LR Parsers For Natural Languages.
COLING
Masaru Tomita