Masaru Tomita

Masaru Tomita, Tomoyoshi Soga, Rainer Machné, 2013, 2013 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC).

E-CELL2: E-CELL Simulation System for Windows

Masaru Tomita, Kouichi Takahashi, Yoichi Nakayama, 2002 .

On Automatic Composition of Stereotypic Documents in Foreign Languages

Masaru Tomita, Hiroaki Saito, M. Tomita, 1986 .

Massively parallel spoken language processing using a parallel associative processor IXM2

Hiroaki Kitano, Masaru Tomita, Tetsuya Higuchi, 1990, ICSLP.

Kinetic simulation of signal transduction system in hippocampal long-term potentiation with dynamic modeling of protein phosphatase 2A

Masaru Tomita, Kenji Fujimoto, Shinichi Kikuchi, 2003, Neural Networks.

Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes

Masaru Tomita, Koichi Takahashi, Makoto Suematsu, 2015, PLoS Comput. Biol..

S PEECH T RANS : An Experimental Real-Time Speech-to-Speech Translation System

Hideto Tomabechi, Masaru Tomita, Hiroaki Saito, 1990 .

Sacrificial Acts in Single Round Prisoner's Dilemma

Takashi Kido, Masaru Tomita, 1994, Informatica.

The Genome-Based E-CELL Modeling (GEM) System

Masaru Tomita, Kazuharu Arakawa, Yoichi Nakayama, 2005 .

Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes

Masaru Tomita, Rintaro Saito, Y. Osada, 1999, Bioinform..

A multi-algorithm, multi-timescale method for cell simulation

Masaru Tomita, Bin Hu, Kouichi Takahashi, 2004, Bioinform..

Parsing 2-Dimensional Language

Masaru Tomita, 1989, IWPT.

The Generalized LR Parser/Compiler V8-4: A Software Package for Practical NL Projects

Masaru Tomita, M. Tomita, 1990, COLING.

GLR Parsing for Noisy Input

Masaru Tomita, Hiroaki Saito, 1991 .

Characteristic Analysis of DC Electric Railway Systems with Superconducting Power Cables Connecting Power Substations

Masaru Tomita, Hiroyuki Ohsaki, T. Koseki, 2014 .

Integrative modeling of gene expression and metabolism with E-CELL System

Masaru Tomita, Kenta Hashimoto, Pawan Kumar Dhar, 2006, Artificial Life and Robotics.

Development of the Bacteria Analysis System on G-Language Genome Analysis Environment

Masaru Tomita, Kazuharu Arakawa, Koya Mori, 2001 .

A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks

Masaru Tomita, Yoichi Nakayama, Tomoya Kitayama, 2005, BMC Bioinformatics.

Direct Memory Access Translation for Speech Input

Hideto Tomabechi, Masaru Tomita, Teruko Mitamura, 1988, FGCS.

Parsing Spoken Language: a Semantic Caseframe Approach

Jaime G. Carbonell, Masaru Tomita, Alexander G. Hauptmann, 1986, COLING.

Result of Magnetic Shielding Experiment about Flow of Flux

Masaru Tomita, Takashi Sasakawa, Naoto Tagawa, 1998 .

E-Cell System Version 3: A Software Platform for Integrative Computational Biology

Masaru Tomita, Takeshi Sakurada, Masahiro Sugimoto, 2003 .

Comparative Study of Circadian Oscillatory Network Models of Drosophila

Masaru Tomita, Kazuharu Arakawa, Yoichi Nakayama, 2008, Artificial Life.

Computational Analysis of Stop Codon Readthrough in D.melanogaster

Masaru Tomita, Rintaro Saito, Akio Kanai, 2003, Bioinform..

Interactive/Personal Machine Translation

Masaru Tomita, 1986 .

"Linguistic" sentences and "real" sentences

Masaru Tomita, 1988, COLING.

Measure of synonymous codon usage diversity among genes in bacteria

Masaru Tomita, Rintaro Saito, Haruo Suzuki, 2009, BMC Bioinformatics.

Computational Challenges in Cell Simulation: A Software Engineering Approach

Masaru Tomita, Christopher J. F. Pickett, Kouichi Takahashi, 2002, IEEE Intell. Syst..

Differential metabolomics software for capillary electrophoresis-mass spectrometry data analysis

Masaru Tomita, Richard Baran, Martin Robert, 2010, Metabolomics.

GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes

Masaru Tomita, Kazuharu Arakawa, Yoichi Nakayama, 2006, BMC Bioinformatics.

New Approaches to Machine Translation

Jaime G. Carbonell, Masaru Tomita, J. Carbonell, 1985, TMI.

Design and Development of Software Environment for Whole-Cell Simulation

Yuki Fujita, Masaru Tomita, Takeshi Sakurada, 2001 .

Proposition of cortical connectivity between 30 cytoarchitectural areas of human cerebral cortex

Masaru Tomita, Ryuta Fukuda, Junko Hara, 2000, Neurocomputing.

Characterization of the Splice Sites in Gt-ag and Gc-ag Introns in Higher Eukaryotes Using Full-length Cdnas

Masaru Tomita, Takanori Washio, Sumie Kitamura-Abe, 2004, J. Bioinform. Comput. Biol..

Genome Projector: zoomable genome map with multiple views

Masaru Tomita, Nobuaki Kono, Kazuharu Arakawa, 2009, BMC Bioinformatics.

E-CELL Simulation Environment Version 3: System Architecture of Simulation Engine

Masaru Tomita, Masaaki Kawata, Takeshi Sakurada, 2001 .

A web server for interactive and zoomable Chaos Game Representation images

Masaru Tomita, Kazuharu Arakawa, Kazuki Oshita, 2009, Source Code for Biology and Medicine.

Time-resolved metabolomics reveals metabolic modulation in rice foliage

Masaru Tomita, Shigeru Sato, Masanori Arita, 2008, BMC Systems Biology.

Knowledge-Based Machine Translation, The CMU Approach

Jaime G. Carbonell, Masaru Tomita, J. Carbonell, 1987 .

Building Working Cells in Computer : -Computer Simulation of the Cell Based on Genome Information-

Masaru Tomita, M. Tomita, 2000 .

Application of the direct memory access paradigm to NL interfaces to knowledge-based systems

Hideto Tomabechi, Masaru Tomita, 1988, COLING.

Can Complex Cellular Processes be Governed by Simple Linear Rules?

Masa Tsuchiya, Masaru Tomita, Kumar Selvarajoo, 2009, J. Bioinform. Comput. Biol..

E-CELL: software environment for whole-cell simulation

Masaru Tomita, Koichi Takahashi, Yuri Matsuzaki, 1999, Bioinform..

Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data

Masaru Tomita, Yasushi Ishihama, Nozomu Yachie, 2010, BMC Bioinformatics.

GLR* – An Efficient Noise-skipping Parsing Algorithm For Context Free Grammars

Alon Lavie, Masaru Tomita, A. Lavie, 1993, IWPT.

Microarray Visualization System on the G-Language GAE

Masaru Tomita, Hirotada Mori, Yohei Yamada, 2003 .

The E-CELL project: towards integrative simulation of cellular processes

Masaru Tomita, Koichi Takahashi, Yuri Matsuzaki, 2000, RECOMB '00.

E-CELL Project Overview:Towards Integrative Simulation of Cellular Processes

Thomas S. Shimizu, Masaru Tomita, Yuri Matsuzaki, 1998 .

Inferring rules of Escherichia coli translational efficiency using an artificial neural network

Masaru Tomita, Shinichi Kikuchi, Koya Mori, 2007, Biosyst..

Feasibility study of personal interactive machine translation systems

Masaru Tomita, 1985 .

Book Reviews: Machine Translation: A Knowledge-Based Approach

Sergei Nirenburg, Jaime G. Carbonell, Masaru Tomita, 1993, CL.

An interaction knowledgebase for biomolecular modeling

Masaru Tomita, Gabor Bereczki, 2006, Industrial Conference on Data Mining - Workshops.

Next-generation Integrated Simulation Technique : Development of a Modeling and Simulation Environment for Systems Biology

Masaru Tomita, Yuri Matsuzaki, Takeshi Sakurada, 2007 .

MMMDB: Mouse Multiple Tissue Metabolome Database

Masaru Tomita, Tomoyoshi Soga, Masahiro Sugimoto, 2011, Nucleic Acids Res..

HybGFS: a hybrid method for genome-fingerprint scanning

Masaru Tomita, Tomoyoshi Soga, Takeshi Masuda, 2006, BMC Bioinformatics.

Multiresolution Analysis Uncovers Hidden Conservation of Properties in Structurally and Functionally Similar Proteins

Masaru Tomita, Arun Krishnan, Kuo-Bin Li, 2006, J. Bioinform. Comput. Biol..

A generalized parser for 2-D languages

Masaru Tomita, Gennaro Costagliola, Shi-Kuo Chang, 1991, Proceedings 1991 IEEE Workshop on Visual Languages.

Combination of quantitative changes in ionic components to enhance the contractile force during T-tubule development

Masaru Tomita, Hitomi Sano, Yasuhiro Naito, 2016, 2016 Computing in Cardiology Conference (CinC).

Pathway Finding from Given Time-Courses Using Genetic Algorithm

Masaru Tomita, Shinichi Kikuchi, Masanori Arita, 2001 .

Generalized L.R. Parsing

Masaru Tomita, 1991 .

Consideration on Contact Mechanism of YBaCuO Bulk Superconductor with Deposited Metal Layer

Hiroyuki Fujita, Masaru Tomita, Koichiro Sawa, 2007, IEICE Trans. Electron..

Distributed Cell Biology Simulations with E-Cell System

Masaru Tomita, Masahiro Sugimoto, Kouichi Takahashi, 2004, LSGRID.

Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics

Masaru Tomita, Nobuaki Kono, Kazuharu Arakawa, 2007, Genom. Proteom. Bioinform..

Simulation study on the balance of glycolytic ATP production and oxidative phosphorylation in embryonic and adult ventricular cells

Masaru Tomita, Hitomi Sano, Yasuhiro Naito, 2016, 2016 Computing in Cardiology Conference (CinC).

A Generic Software Platform for Brain-inspired Cognitive Computing

Masaru Tomita, Koichi Takahashi, Hiroshi Yamakawa, 2015, BICA.

Efficient Parsing for Natural Language: A Fast Algorithm for Practical Systems

Masaru Tomita, M. Tomita, 1985 .

The Generalized LR Parsing Algorithm

Masaru Tomita, See-Kiong Ng, 1991 .

E-Cell 2: Multi-platform E-Cell simulation system

Masaru Tomita, Koichi Takahashi, S. Ohta, 2003, Bioinform..

Formal Specification of the Algorithm

Masaru Tomita, 1986 .

A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation

Masaru Tomita, Satya Nanda Vel Arjunan, M. Tomita, 2009, Systems and Synthetic Biology.

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

Hiroaki Kitano, Masaru Tomita, Peter J. Hunter, 2003, Bioinform..

Toward Computer Simulation of the Whole Cell

Masaru Tomita, 2002, Gene Regulations and Metabolism.

eXpanda: An Integrated Platform for Network Analysis and Visualization

Masaru Tomita, Hiroyuki Nakamura, Nozomu Yachie, 2007, Silico Biol..

MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data

Masaru Tomita, Masahiro Sugimoto, Hitoshi Iuchi, 2018, BMC Bioinformatics.

LR Parsers For Natural Languages

Masaru Tomita, Masaru Tomita, M. Tomita, 1984, Annual Meeting of the Association for Computational Linguistics.

Informal Description of the Algorithm

Masaru Tomita, 1986 .

Differences of Translation Termination Sites Among the Three Stop Codons

Masaru Tomita, Rintaro Saito, Yosuke Ozawa, 1999 .

Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments

Masaru Tomita, Yasushi Ishihama, Kosaku Shinoda, 2008, Bioinform..

Application of the Direct Memory Access paradigm to natural language interfaces to knowledge-based systems

Hideto Tomabechi, Masaru Tomita, 1988, COLING 1988.

G-Language Genome Analysis Environment

Masaru Tomita, Kazuharu Arakawa, Koya Mori, 2001 .

Sensitivity analysis of ectopic electrical activity in the pulmonary vein myocardium

Masaru Tomita, Yuichiro Tanaka, Hitomi Sano, 2015, 2015 Computing in Cardiology Conference (CinC).

Left-to-Right On-Line Parsing

Masaru Tomita, 1986 .

In Silico Models for Metabolic Systems Engineering

Masaru Tomita, Kumar Selvarajoo, Vel Arjunan, 2010 .

An Efficient Context-Free Parsing Algorithm for Natural Languages

Masaru Tomita, M. Tomita, 1985, IJCAI.

SPLITS: A New Program for Predicting Split and Intron-Containing tRNA Genes at the Genome Level

Masaru Tomita, Nozomu Yachie, Motomu Matsui, 2006, Silico Biol..

MathDAMP: a package for differential analysis of metabolite profiles

Masaru Tomita, Richard Baran, Martin Robert, 2006, BMC Bioinformatics.

Development of Comparative Genome Analysis System (COMGA) on the G-Language Genome Analysis Environment

Masaru Tomita, Kazuharu Arakawa, Seira Nakamura, 2002 .

Future directions for cyber knowledge and databases

Yasushi Kiyoki, Masaru Tomita, Masa Inakage, 2004, 2004 International Symposium on Applications and the Internet Workshops. 2004 Workshops..

The design philosophy of personal machine translation system

Masaru Tomita, M. Tomita, 1984 .

Time-structure of the yeast metabolism in vivo.

Masaru Tomita, David Lloyd, Kalesh Sasidharan, 2012, Advances in experimental medicine and biology.

Development of Bottom-Fermenting Saccharomyces Strains That Produce High SO2 Levels, Using Integrated Metabolome and Transcriptome Analysis

Masaru Tomita, Tomoyoshi Soga, Satoru Mizutani, 2008, Applied and Environmental Microbiology.

Toward large-scale modeling of the microbial cell for computer simulation.

Masaru Tomita, Martin Robert, Yoichi Nakayama, 2004, Journal of biotechnology.

Large-scale prediction of cationic metabolite identity and migration time in capillary electrophoresis mass spectrometry using artificial neural networks.

Masaru Tomita, Shinichi Kikuchi, Tomoyoshi Soga, 2005, Analytical chemistry.

Transcriptome-wide Variability in Single Embryonic Development Cells

Vincent Piras, Masaru Tomita, Kumar Selvarajoo, 2014, Scientific Reports.

Metabolomic profiling of anionic metabolites by capillary electrophoresis mass spectrometry.

Masaru Tomita, Tomoyoshi Soga, M. Tomita, 2009, Analytical chemistry.

Contribution of quantitative changes in individual ionic current systems to the embryonic development of ventricular myocytes: a simulation study

Masaru Tomita, Yasuhiro Naito, M. Tomita, 2013, The Journal of Physiological Sciences.

Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol

Masaru Tomita, Martin Robert, Tomoyoshi Soga, 2014, Nature Communications.

Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System

Masaru Tomita, Satya Nanda Vel Arjunan, 2009 .

Inhibitory effect of phosphoenolpyruvate on glycolytic enzymes in Escherichia coli.

Masaru Tomita, Masataka Yoshino, Hirotada Mori, 2007, Research in microbiology.

Unveiling cellular biochemical reactions via metabolomics-driven approaches.

Masaru Tomita, Tomoyoshi Soga, Yoshiaki Ohashi, 2010, Current opinion in microbiology.

Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis.

Masaru Tomita, Yasushi Ishihama, M. Tomita, 2008, Journal of proteome research.

[E-Cell simulation system and its application to the modeling of circadian rhythm].

Masaru Tomita, Yoichi Nakayama, Fumihiko Miyoshi, 2003, Seikagaku. The Journal of Japanese Biochemical Society.

On dynamics of overlapping genes in bacterial genomes.

Masaru Tomita, Yoichi Nakayama, Yoko Fukuda, 2003, Gene.

Urinary Polyamine Biomarker Panels with Machine-Learning Differentiated Colorectal Cancers, Benign Disease, and Healthy Controls

Masaru Tomita, Tomoyoshi Soga, Masahiro Sugimoto, 2018, International journal of molecular sciences.

Precise mapping and dynamics of tRNA-derived fragments (tRFs) in the development of Triops cancriformis (tadpole shrimp)

Masaru Tomita, Yuka Hirose, M. Tomita, 2015, BMC Genetics.

Depiction of metabolome changes in histidine-starved Escherichia coli by CE-TOFMS.

Masaru Tomita, Tomoyoshi Soga, Seira Nakamura, 2008, Molecular bioSystems.

Systems Biology, Metabolomics, and Cancer Metabolism

Masaru Tomita, Kenjiro Kami, M. Tomita, 2012, Science.

Simulation of developmental changes in action potentials with ventricular cell models

Masaru Tomita, Yasuhiro Naito, Hitomi Itoh, 2006, Systems and Synthetic Biology.

Roles of Hemoglobin Allostery in Hypoxia-induced Metabolic Alterations in Erythrocytes

Masaru Tomita, Tomoyoshi Soga, Yoichi Nakayama, 2007, Journal of Biological Chemistry.

Indeterminacy of Reverse Engineering of Gene Regulatory Networks: The Curse of Gene Elasticity

Masaru Tomita, Alessandro Giuliani, Arun Krishnan, 2007, PloS one.

Global microRNA elevation by inducible Exportin 5 regulates cell cycle entry.

Masaru Tomita, Toshifumi Inada, Taro Fukao, 2013, RNA.

Unbiased Quantitation of Escherichia coli Membrane Proteome Using Phase Transfer Surfactants*

Masaru Tomita, Natsumi Saito, Yasushi Ishihama, 2009, Molecular & Cellular Proteomics.

Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns

Masaru Tomita, Jun Kawai, Piero Carninci, 2010, BMC Genomics.

A Mathematical Model for the Kai-Protein–Based Chemical Oscillator and Clock Gene Expression Rhythms in Cyanobacteria

Masaru Tomita, Yoichi Nakayama, Fumihiko Miyoshi, 2007, Journal of biological rhythms.

Evolution of Overlapping Genes: Comparative Genomics of Mycoplasma genitalium and Mycoplasma pneumoniae

Masaru Tomita, Yoko Fukuda, Takanori Washio, 1998 .

Predictive value of CD24 and CD44 for neoadjuvant chemotherapy response and prognosis in primary breast cancer patients.

Masaru Tomita, Masahiro Sugimoto, Takayuki Ueno, 2010, Journal of medical and dental sciences.

Physical laws shape biology.

Masaru Tomita, Kumar Selvarajoo, M. Tomita, 2013, Science.

Computer Simulation of Human Erythrocyte Using the E-CELL System

Masaru Tomita, Yoichi Nakayama, Y. Nakayama, 1999 .

Parameter Estimation Mechanism of E-CELL Simulation Environment

Tomoharu Iwata, Masaru Tomita, Yusuke Saito, 1999 .

Metabolomic anatomy of an animal model revealing homeostatic imbalances in dyslipidaemia.

Masaru Tomita, Tomoyoshi Soga, Yoshiaki Ohashi, 2011, Molecular bioSystems.

Gene expression waves

Alfredo Colosimo, Masaru Tomita, Alessandro Giuliani, 2007, The FEBS journal.

Modeling of Human Red Blood Cell Using the E-CELL Simulation System

Masaru Tomita, Hisako Nakano, M. Tomita, 1998 .

Computational methods for microRNA target prediction.

Masaru Tomita, M. Tomita, A. Kanai, 2007, Methods in enzymology.

In silico modeling and metabolome analysis of long-stored erythrocytes to improve blood storage methods.

Masaru Tomita, Tomoyoshi Soga, Makoto Suematsu, 2009, Journal of biotechnology.

A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity

Masaru Tomita, Jillian F. Banfield, Kosuke Fujishima, 2011, Nucleic acids research.

One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale.

Masaru Tomita, Nobuo Tanaka, Mio Iwasaki, 2010, Analytical chemistry.

Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions

Masa Tsuchiya, Vincent Piras, Masaru Tomita, 1997, PloS one.

Dynamic responses of the intracellular metabolite concentrations of the wild type and pykA mutant Escherichia coli against pulse addition of glucose or NH3 under those limiting continuous cultures

Masaru Tomita, Kazuyuki Shimizu, Md. Aminul Hoque, 2005 .

Positive Autoregulation Delays the Expression Phase of Mammalian Clock Gene Per2

Masaru Tomita, Tomoyoshi Soga, Nobuya Koike, 2011, PloS one.

A Yeast Metabolite Extraction Protocol Optimised for Time-Series Analyses

Masaru Tomita, Tomoyoshi Soga, Kalesh Sasidharan, 2012, PloS one.

Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program

Masaru Tomita, Tomoyoshi Soga, Rainer Machné, 2014, Microbial cell.

Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis

Masaru Tomita, Martin Robert, Tomoyoshi Soga, 2012, Current bioinformatics.

E‐Cell: Computer Simulation of the Cell

Masaru Tomita, Yoichi Nakayama, Pawan K. Dhar, 2012 .

Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea

Masaru Tomita, Kosuke Fujishima, Junichi Sugahara, 2009, Proceedings of the National Academy of Sciences.

Fast and global detection of periodic sequence repeats in large genomic resources

Masaru Tomita, Nozomu Yachie, Hideto Mori, 2018, bioRxiv.

ApA Dinucleotide Periodicity in Prokaryote, Eukaryote, and Organelle Genomes

Masaru Tomita, Masahiko Wada, Yukihiro Kawashima, 1999, Journal of Molecular Evolution.

Metabolic and morphological changes of an oil accumulating trebouxiophycean alga in nitrogen-deficient conditions

Masaru Tomita, Tomoyoshi Soga, Takuro Ito, 2012, Metabolomics.

Tracking global gene expression responses in T cell differentiation.

Vincent Piras, Masaru Tomita, Kumar Selvarajoo, 2015, Gene.

Qualitative and quantitative analysis of amino acids by capillary electrophoresis‐electrospray ionization‐tandem mass spectrometry

Masaru Tomita, Martin Robert, Tomoyoshi Soga, 2004, Electrophoresis.

Effects of processing and storage conditions on charged metabolomic profiles in blood

Masaru Tomita, Tomoyoshi Soga, Masahiro Sugimoto, 2015, Electrophoresis.

Quantitative Modeling of Mitochondrial Energy Metabolism Using E-CELL Simulation Environment

Masaru Tomita, Katsuyuki Yugi, 2000 .

Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue

Masaru Tomita, Nobuaki Kono, Kazuharu Arakawa, 2019, Scientific Reports.

Computer Simulation of Human Erythrocyte using the E-CELL system

Masaru Tomita, Yoichi Nakayama, Ayako Kinoshita, 2001 .

Reconsidering plasmid maintenance factors for computational plasmid design

Masaru Tomita, Masaki Shintani, Taku Oshima, 2018, Computational and structural biotechnology journal.

Analysis of nucleotides by pressure-assisted capillary electrophoresis-mass spectrometry using silanol mask technique.

Masaru Tomita, Tomoyoshi Soga, Kaori Sugawara, 2007, Journal of chromatography. A.

Serial assembly of Thermus megaplasmid DNA in the genome of Bacillus subtilis 168: a BAC-based domino method applied to DNA with a high GC content.

Masaru Tomita, Shinya Kaneko, Mitsuru Sato, 2012, Biotechnology journal.

Prediction of metabolite identity from accurate mass, migration time prediction and isotopic pattern information in CE‐TOFMS data

Masaru Tomita, Martin Robert, Tomoyoshi Soga, 2010, Electrophoresis.

Rapid DNA, RNA and protein extraction protocols optimized for slow continuously growing yeast cultures

Masaru Tomita, Cornelia Amariei, Kalesh Sasidharan, 2012, Yeast.

Quantifying periodicity in omics data

Masaru Tomita, Cornelia Amariei, Douglas B. Murray, 2014, Front. Cell Dev. Biol..

Simultaneous determination of the main metabolites in rice leaves using capillary electrophoresis mass spectrometry and capillary electrophoresis diode array detection.

Masaru Tomita, Tomoyoshi Soga, Shigeru Sato, 2004, The Plant journal : for cell and molecular biology.

Changes in the charged metabolite and sugar profiles of pasteurized and unpasteurized Japanese sake with storage.

Masaru Tomita, Tomoyoshi Soga, Masahiro Sugimoto, 2012, Journal of agricultural and food chemistry.

Alteration of metabolomic profiles by titanium dioxide nanoparticles in human gingivitis model.

Masaru Tomita, Tomoyoshi Soga, Masahiro Sugimoto, 2015, Biomaterials.

G-language System as a platform for large-scale analysis of high-throughput omics data

Masaru Tomita, Kazuharu Arakawa, M. Tomita, 2006 .

Onco-proteogenomics: a novel approach to identify cancer-specific mutations combining proteomics and transcriptome deep sequencing

Masaru Tomita, Naoyuki Sugiyama, Mohamed Helmy, 2010, Genome Biology.

Update on the Keio collection of Escherichia coli single-gene deletion mutants

Masaru Tomita, Hirotada Mori, Natsuko Yamamoto, 2009, Molecular systems biology.

Model-based definition of population heterogeneity and its effects on metabolism in sporulating Bacillus subtilis.

Masaru Tomita, Tomoyoshi Soga, Mineo Morohashi, 2007, Journal of biochemistry.

Construction of a Simulation Model of Diabetes for Pathophysiological Analysis Using E-Cell System

Masaru Tomita, Yasuhiro Naito, Hiromu Nakajima, 2002 .

Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes

Masaru Tomita, Nobuaki Kono, Kazuharu Arakawa, 2011, BMC Genomics.

A new role for expressed pseudogenes as ncRNA: regulation of mRNA stability of its homologous coding gene

Masaru Tomita, Atsushi Yoshiki, Rintaro Saito, 2004, Journal of Molecular Medicine.

Is central dogma a global property of cellular information flow?

Vincent Piras, Masaru Tomita, Kumar Selvarajoo, 2012, Front. Physio..

Computational prediction of nucleosome positioning by calculating the relative fragment frequency index of nucleosomal sequences

Masaru Tomita, Rintaro Saito, Noriyuki Kitagawa, 2010, FEBS letters.

Direct measurement of isotopomer of intracellular metabolites using capillary electrophoresis time-of-flight mass spectrometry for efficient metabolic flux analysis.

Masaru Tomita, Tomoyoshi Soga, Takashi Hirasawa, 2007, Journal of chromatography. A.

Computational analysis of microRNA‐mediated antiviral defense in humans

Masaru Tomita, Nozomu Yachie, M. Tomita, 2007, FEBS letters.

Predicting the Kinetic Properties Associated with Redox Imbalance after Oxidative Crisis in G6PD-Deficient Erythrocytes: A Simulation Study

Masaru Tomita, Hanae Shimo, Taiko Nishino, 2011, Advances in hematology.

Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data.

Masaru Tomita, Piero Carninci, Yoshihide Hayashizaki, 2002, Genome research.

Disrupted tRNA Gene Diversity and Possible Evolutionary Scenarios

Masaru Tomita, Kosuke Fujishima, Junichi Sugahara, 2009, Journal of Molecular Evolution.

Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA.

Masaru Tomita, Nozomu Yachie, Rintaro Saito, 2011, Gene.

Microscale phosphoproteome analysis of 10,000 cells from human cancer cell lines.

Masaru Tomita, Naoyuki Sugiyama, Yasushi Ishihama, 2011, Analytical chemistry.

Theoretical Biology and Medical Modelling

Masaru Tomita, Yoichi Nakayama, Ayako Kinoshita, 2022 .

Metabolomic study of Chilean biomining bacteria Acidithiobacillus ferrooxidans strain Wenelen and Acidithiobacillus thiooxidans strain Licanantay

Masaru Tomita, Tomoyoshi Soga, Patricio Martínez, 2012, Metabolomics.

On Negative Selection Against ATG Triplets Near Start Codons in Eukaryotic and Prokaryotic Genomes

Masaru Tomita, Rintaro Saito, M. Tomita, 1999, Journal of Molecular Evolution.

Dynamic Simulation and Metabolome Analysis of Long-Term Erythrocyte Storage in Adenine–Guanosine Solution

Masaru Tomita, Tomoyoshi Soga, Makoto Suematsu, 2013, PloS one.

Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification

Masaru Tomita, Nozomu Yachie, Rintaro Saito, 2011, BMC Genomics.

A problem in multivariate analysis of codon usage data and a possible solution

Masaru Tomita, Rintaro Saito, M. Tomita, 2005, FEBS letters.

Comparative analysis of base correlations in 5' untranslated regions of various species.

Masaru Tomita, Rintaro Saito, M. Tomita, 2006, Gene.

Proteome-Wide Prediction of Novel DNA/RNA-Binding Proteins Using Amino Acid Composition and Periodicity in the Hyperthermophilic Archaeon Pyrococcus furiosus

Masaru Tomita, Kosuke Fujishima, M. Tomita, 2007, DNA research : an international journal for rapid publication of reports on genes and genomes.

Emergent Genome-Wide Control in Wildtype and Genetically Mutated Lipopolysaccarides-Stimulated Macrophages

Masa Tsuchiya, Vincent Piras, Masaru Tomita, 2009, PloS one.

The 'weighted sum of relative entropy': a new index for synonymous codon usage bias.

Masaru Tomita, Rintaro Saito, M. Tomita, 2004, Gene.

Space in systems biology of signaling pathways – towards intracellular molecular crowding in silico

Masaru Tomita, Satya Nanda Vel Arjunan, M. Tomita, 2005, FEBS letters.

On the interplay of gene positioning and the role of rho‐independent terminators in Escherichia coli

Masaru Tomita, Kazuharu Arakawa, Nozomu Yachie, 2006, FEBS letters.

Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli

Masaru Tomita, Hirotada Mori, Kenji Nakahigashi, 2011, BMC Genomics.

A Comprehensive Resource of Interacting Protein Regions for Refining Human Transcription Factor Networks

Masaru Tomita, Rintaro Saito, Shigeo Fujimori, 2010, PloS one.

Identification and expression analysis of putative mRNA‐like non‐coding RNA in Drosophila

Masaru Tomita, M. Tomita, K. Yasuda, 2005, Genes to cells : devoted to molecular & cellular mechanisms.

Comprehensive Computational Analysis of Bacterial CRP/FNR Superfamily and Its Target Motifs Reveals Stepwise Evolution of Transcriptional Networks

Masaru Tomita, Motomu Matsui, M. Tomita, 2013, Genome biology and evolution.

Computational assessment of insulin secretion and insulin sensitivity from 2-h oral glucose tolerance tests for clinical use for type 2 diabetes

Masaru Tomita, Yasuhiro Naito, Masato Kasuga, 2011, The Journal of Physiological Sciences.

Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data.

Masaru Tomita, Kazuyuki Shimizu, Kenji Nakahigashi, 2012, Molecular bioSystems.

Dynamic simulation of an in vitro multi‐enzyme system

Masaru Tomita, Masataka Yoshino, Hirotada Mori, 2007, FEBS letters.

Large-scale tRNA intron transposition in the archaeal order Thermoproteales represents a novel mechanism of intron gain.

Masaru Tomita, Kosuke Fujishima, Junichi Sugahara, 2010, Molecular biology and evolution.

Implications from a Network-Based Topological Analysis of Ubiquitin Unfolding Simulations

Masaru Tomita, Alessandro Giuliani, Arun Krishnan, 2008, PloS one.

Redox regulation in respiring Saccharomyces cerevisiae.

Masaru Tomita, Ken Haynes, Douglas B. Murray, 2011, Biochimica et biophysica acta.

Prediction of liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome using artificial neural networks.

Masaru Tomita, Martin Robert, Tomoyoshi Soga, 2006, Journal of proteome research.

Capillary electrophoresis‐mass spectrometry‐based metabolome analysis of serum and saliva from neurodegenerative dementia patients

Masaru Tomita, Tomoyoshi Soga, Masahiro Sugimoto, 2013, Electrophoresis.

Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.

Masaru Tomita, Yutaka Kyono, Naoyuki Sugiyama, 2008, Journal of proteome research.

Multi-faceted integrated omics analysis revealed parsley (Petroselinum crispum) as a novel dietary intervention in dextran sodium sulphate induced colitic mice

Hiroshi Tanaka, Masaru Tomita, Hisanori Kato, 2014 .

Automatic Transformation of Kinetic Equations into S-System and GMA Forms

Masaru Tomita, Yoichi Nakayama, Ayako Kinoshita, 2002 .

Modeling of Signal Transduction for Bacterial Chemotaxis Using the E-CELL Simulation System

Masaru Tomita, Yuri Matsuzaki, Tom Shimizu, 1998 .

Comparative expression analysis uncovers novel features of endogenous antisense transcription.

Masaru Tomita, Hajime Nakaoka, Rintaro Saito, 2008, Human molecular genetics.

In Silico Analysis of Phosphoproteome Data Suggests a Rich-get-richer Process of Phosphosite Accumulation over Evolution*S

Masaru Tomita, Nozomu Yachie, Rintaro Saito, 2009, Molecular & Cellular Proteomics.

Predicting Novel Features of Toll-Like Receptor 3 Signaling in Macrophages

Masa Tsuchiya, Masaru Tomita, Kumar Selvarajoo, 2009, PloS one.

Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli.

Masaru Tomita, Kazuharu Arakawa, Reina Uno, 2007, Gene.

Sustained MAPK activation is dependent on continual NGF receptor regeneration

Masaru Tomita, Shinichi Kikuchi, Likai Mao, 2004, Development, growth & differentiation.

GC-compositional strand bias around transcription start sites in plants and fungi

Masaru Tomita, Shigeo Fujimori, Takanori Washio, 2005, BMC Genomics.

Computational analysis of microRNA targets in Caenorhabditis elegans.

Masaru Tomita, Nozomu Yachie, Rintaro Saito, 2006, Gene.

A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription

Masaru Tomita, Kenichi Higo, Shoshi Kikuchi, 2003, FEBS letters.

Signaling Flux Redistribution at Toll-Like Receptor Pathway Junctions

Masa Tsuchiya, Masaru Tomita, Kumar Selvarajoo, 2008, PloS one.

Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry.

Masaru Tomita, Tomoyoshi Soga, Yoshiaki Ohashi, 2002, Analytical chemistry.

Modeling of Transcription and DNA Replication Using the E-CELL Simulation System

Thomas S. Shimizu, Masaru Tomita, Fumihiko Miyoshi, 1998 .