Masaru Tomita | Academic Influence

Masaru Tomita's AcademicInfluence.com Rankings

Masaru Tomita

Computer Science

#1004

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#1040

Historical Rank

Artificial Intelligence

#1076

World Rank

#1095

Historical Rank

Database

#1710

World Rank

#1793

Historical Rank

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Computer Science

Masaru Tomita's Degrees

PhD Computer Science University of Tokyo

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Best Online PhD of Computer Science (Doctorates) 2025

Why Is Masaru Tomita Influential?

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According to Wikipedia, Masaru Tomita is a Japanese scientist in the fields of systems biology and computer science, best known as the founder of the E-Cell simulation system and/or the inventor of GLR parser algorithm. He served a professor of Keio University, Director of the Institute for Advanced Biosciences, and the founder and board member of various spinout companies, including Human Metabolome Technologies, Inc. and Spiber Inc. He is also the co-founder and on the board of directors of The Metabolomics Society. His father was the renowned composer and synthesiser pioneer Isao Tomita.

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Masaru Tomita's Published Works

Number of citations in a given year to any of this author's works

Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author

Published Works

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection (2006) (7032)
Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells (2013) (3424)
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models (2003) (3236)
Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs (2009) (1003)
Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. (2003) (865)
E-CELL: software environment for whole-cell simulation (1999) (848)
Quantitative metabolome profiling of colon and stomach cancer microenvironment by capillary electrophoresis time-of-flight mass spectrometry. (2009) (821)
Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles (2009) (761)
Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations (2007) (660)
Differential Metabolomics Reveals Ophthalmic Acid as an Oxidative Stress Biomarker Indicating Hepatic Glutathione Consumption* (2006) (613)
Six Classes of Nuclear Localization Signals Specific to Different Binding Grooves of Importin α* (2009) (514)
Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis. (2008) (467)
Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry. (2002) (447)
Dynamic modeling of genetic networks using genetic algorithm and S-system (2003) (433)
Phosphopeptide Enrichment by Aliphatic Hydroxy Acid-modified Metal Oxide Chromatography for Nano-LC-MS/MS in Proteomics Applications*S (2007) (405)
Large-scale identification of protein-protein interaction of Escherichia coli K-12. (2006) (393)
Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis (2008) (383)
Large-Scale Comparative Phosphoproteomics Identifies Conserved Phosphorylation Sites in Plants1[W][OA] (2010) (361)
Whole-cell simulation: a grand challenge of the 21st century. (2001) (330)
Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging. (2017) (290)
Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis (2012) (275)
Metabolomic profiling of anionic metabolites by capillary electrophoresis mass spectrometry. (2009) (274)
Space in systems biology of signaling pathways – towards intracellular molecular crowding in silico (2005) (263)
Simultaneous determination of the main metabolites in rice leaves using capillary electrophoresis mass spectrometry and capillary electrophoresis diode array detection. (2004) (251)
Update on the Keio collection of Escherichia coli single-gene deletion mutants (2009) (232)
Global metabolic reprogramming of colorectal cancer occurs at adenoma stage and is induced by MYC (2017) (225)
Depiction of metabolome changes in histidine-starved Escherichia coli by CE-TOFMS. (2008) (213)
Serum metabolomics reveals γ-glutamyl dipeptides as biomarkers for discrimination among different forms of liver disease. (2011) (201)
A multi-algorithm, multi-timescale method for cell simulation (2004) (191)
Design of peptide inhibitors for the importin alpha/beta nuclear import pathway by activity-based profiling. (2008) (182)
Gene Knockout and Metabolome Analysis of Carnitine/Organic Cation Transporter OCTN1 (2010) (162)
Metabolic profiling reveals new serum biomarkers for differentiating diabetic nephropathy (2012) (156)
E-Cell 2: Multi-platform E-Cell simulation system (2003) (156)
Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism (2009) (151)
Metabolomic anatomy of an animal model revealing homeostatic imbalances in dyslipidaemia. (2011) (148)
Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. (2003) (148)
MathDAMP: a package for differential analysis of metabolite profiles (2006) (148)
Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus (2017) (144)
Nuclear Export Signal Consensus Sequences Defined Using a Localization‐Based Yeast Selection System (2008) (143)
Identification of salivary metabolomic biomarkers for oral cancer screening (2016) (134)
emPAI Calc - for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry (2010) (134)
Metabolomic profiling of lung and prostate tumor tissues by capillary electrophoresis time-of-flight mass spectrometry (2012) (132)
Unbiased Quantitation of Escherichia coli Membrane Proteome Using Phase Transfer Surfactants* (2009) (132)
Pressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anions. (2002) (122)
One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale. (2010) (120)
Qualitative and quantitative analysis of amino acids by capillary electrophoresis‐electrospray ionization‐tandem mass spectrometry (2004) (119)
Organization and Evolution of Brain Lipidome Revealed by Large-Scale Analysis of Human, Chimpanzee, Macaque, and Mouse Tissues (2015) (118)
Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column. (2008) (117)
Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non‐pathogenic Pseudomonas species (2009) (115)
A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription (2003) (105)
Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography. (2008) (105)
Identification and expression analysis of putative mRNA‐like non‐coding RNA in Drosophila (2005) (105)
KEGG-Based Pathway Visualization Tool for Complex Omics Data (2005) (104)
Metabolomic alterations in human cancer cells by vitamin C-induced oxidative stress (2015) (103)
Base editors for simultaneous introduction of C-to-T and A-to-G mutations (2020) (102)
13C‐metabolic flux analysis for batch culture of Escherichia coli and its pyk and pgi gene knockout mutants based on mass isotopomer distribution of intracellular metabolites (2010) (102)
Permuted tRNA Genes Expressed via a Circular RNA Intermediate in Cyanidioschyzon merolae (2007) (100)
Toward large-scale modeling of the microbial cell for computer simulation. (2004) (98)
Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination. (1998) (98)
Capillary electrophoresis‐mass spectrometry‐based metabolome analysis of serum and saliva from neurodegenerative dementia patients (2013) (98)
Pathway Projector: Web-Based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API (2009) (95)
G-language Genome Analysis Environment: a workbench for nucleotide sequence data mining (2003) (94)
Proteins as networks: usefulness of graph theory in protein science. (2008) (93)
An Extreme Thermophile, Thermus thermophilus, Is a Polyploid Bacterium (2010) (92)
Non-targeted metabolite profiling in activated macrophage secretion (2012) (89)
A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation (2009) (88)
Analysis of nucleotides by pressure-assisted capillary electrophoresis-mass spectrometry using silanol mask technique. (2007) (87)
Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol (2014) (83)
Analysis of base-pairing potentials between 16S rRNA and 5' UTR for translation initiation in various prokaryotes (1999) (83)
GC-compositional strand bias around transcription start sites in plants and fungi (2005) (83)
A new role for expressed pseudogenes as ncRNA: regulation of mRNA stability of its homologous coding gene (2004) (82)
On dynamics of overlapping genes in bacterial genomes. (2003) (82)
Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea (2009) (80)
Metabolomics approach for enzyme discovery. (2006) (80)
Exceptional Evolutionary Divergence of Human Muscle and Brain Metabolomes Parallels Human Cognitive and Physical Uniqueness (2014) (80)
Bioinformatic analysis of post‐transcriptional regulation by uORF in human and mouse (2007) (79)
Computational Challenges in Cell Simulation: A Software Engineering Approach (2002) (77)
Systems Biology, Metabolomics, and Cancer Metabolism (2012) (75)
Metabolomic profiling reveals novel biomarkers of alcohol intake and alcohol-induced liver injury in community-dwelling men (2015) (75)
Alignment‐Based Approach for Durable Data Storage into Living Organisms (2007) (74)
De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions (2016) (72)
OryzaPG-DB: Rice Proteome Database based on Shotgun Proteogenomics (2011) (72)
Metabolic and morphological changes of an oil accumulating trebouxiophycean alga in nitrogen-deficient conditions (2012) (71)
Evaluation of metabolic alteration in transgenic rice overexpressing dihydroflavonol-4-reductase. (2006) (71)
Roles of Hemoglobin Allostery in Hypoxia-induced Metabolic Alterations in Erythrocytes (2007) (71)
Direct measurement of isotopomer of intracellular metabolites using capillary electrophoresis time-of-flight mass spectrometry for efficient metabolic flux analysis. (2007) (69)
Physiological and environmental parameters associated with mass spectrometry-based salivary metabolomic profiles (2012) (67)
Characteristics and clustering of human ribosomal protein genes (2006) (67)
Transcriptome-wide Variability in Single Embryonic Development Cells (2014) (66)
Redox regulation in respiring Saccharomyces cerevisiae. (2011) (66)
Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes (2011) (66)
Prediction of metabolite identity from accurate mass, migration time prediction and isotopic pattern information in CE‐TOFMS data (2010) (65)
Metabolite Profiling Reveals YihU as a Novel Hydroxybutyrate Dehydrogenase for Alternative Succinic Semialdehyde Metabolism in Escherichia coli* (2009) (65)
Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes. (2004) (65)
Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales. (2008) (65)
Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli (2011) (64)
Reverse engineering of biochemical equations from time-course data by means of genetic programming. (2005) (64)
Microscale phosphoproteome analysis of 10,000 cells from human cancer cell lines. (2011) (63)
Global microRNA elevation by inducible Exportin 5 regulates cell cycle entry. (2013) (63)
Effects of processing and storage conditions on charged metabolomic profiles in blood (2015) (62)
A Comprehensive Resource of Interacting Protein Regions for Refining Human Transcription Factor Networks (2010) (62)
Simulation study of methemoglobin reduction in erythrocytes (2007) (62)
Time-resolved metabolomics reveals metabolic modulation in rice foliage (2008) (61)
Metabolomic profiles and sensory attributes of edamame under various storage duration and temperature conditions. (2010) (61)
Degradation of ppGpp by Nudix Pyrophosphatase Modulates the Transition of Growth Phase in the Bacterium Thermus thermophilus* (2009) (60)
On biased distribution of introns in various eukaryotes. (2002) (60)
Correlation between sensory evaluation scores of Japanese sake and metabolome profiles. (2010) (60)
Comparative study of overlapping genes in the genomes of Mycoplasma genitalium and Mycoplasma pneumoniae. (1999) (59)
Development of Bottom-Fermenting Saccharomyces Strains That Produce High SO2 Levels, Using Integrated Metabolome and Transcriptome Analysis (2008) (59)
A Mathematical Model for the Kai-Protein–Based Chemical Oscillator and Clock Gene Expression Rhythms in Cyanobacteria (2007) (58)
Orb-weaving spider Araneus ventricosus genome elucidates the spidroin gene catalogue (2019) (58)
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 (2005) (57)
Sheathless capillary electrophoresis-mass spectrometry with a high-sensitivity porous sprayer for cationic metabolome analysis. (2012) (54)
Integrative Features of the Yeast Phosphoproteome and Protein–Protein Interaction Map (2011) (54)
Signaling Flux Redistribution at Toll-Like Receptor Pathway Junctions (2008) (53)
Recharacterization of Chlamydomonas reinhardtii and its relatives with new isolates from Japan (2009) (53)
Characterization of the aryl hydrocarbon receptor repressor gene and association of its Pro185Ala polymorphism with micropenis. (2002) (53)
A general computational model of mitochondrial metabolism in a whole organelle scale (2004) (51)
Genome Projector: zoomable genome map with multiple views (2009) (51)
Alteration of metabolomic profiles by titanium dioxide nanoparticles in human gingivitis model. (2015) (51)
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes (2006) (50)
Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7. (2004) (50)
MMMDB: Mouse Multiple Tissue Metabolome Database (2011) (50)
In silico modeling and metabolome analysis of long-stored erythrocytes to improve blood storage methods. (2009) (50)
Conversion of graded phosphorylation into switch-like nuclear translocation via autoregulatory mechanisms in ERK signalling (2016) (50)
SPLITS: A New Program for Predicting Split and Intron-Containing tRNA Genes at the Genome Level (2006) (50)
The Consumption of Bicarbonate-Rich Mineral Water Improves Glycemic Control (2015) (49)
Elevated Polyamines in Saliva of Pancreatic Cancer (2018) (49)
Computational analysis of microRNA targets in Caenorhabditis elegans. (2006) (49)
Indeterminacy of Reverse Engineering of Gene Regulatory Networks: The Curse of Gene Elasticity (2007) (48)
Changes in the charged metabolite and sugar profiles of pasteurized and unpasteurized Japanese sake with storage. (2012) (48)
Comparative expression analysis uncovers novel features of endogenous antisense transcription. (2008) (48)
Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition (2005) (47)
Emergent Genome-Wide Control in Wildtype and Genetically Mutated Lipopolysaccarides-Stimulated Macrophages (2009) (47)
In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs. (2007) (47)
Reliability of plasma polar metabolite concentrations in a large-scale cohort study using capillary electrophoresis-mass spectrometry (2018) (46)
Metabolic Profiling of Total Physical Activity and Sedentary Behavior in Community-Dwelling Men (2016) (46)
Prediction of liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome using artificial neural networks. (2006) (46)
Smad2/3 Proteins Are Required for Immobilization-induced Skeletal Muscle Atrophy* (2016) (46)
Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo (2014) (46)
Temporal Profiling of Lapatinib-suppressed Phosphorylation Signals in EGFR/HER2 Pathways* (2012) (46)
Large-scale prediction of cationic metabolite identity and migration time in capillary electrophoresis mass spectrometry using artificial neural networks. (2005) (45)
Inhibitory effect of phosphoenolpyruvate on glycolytic enzymes in Escherichia coli. (2007) (45)
Computational analysis of microRNA‐mediated antiviral defense in humans (2007) (45)
Complete genome sequence and comparative analysis of Shewanella violacea, a psychrophilic and piezophilic bacterium from deep sea floor sediments. (2010) (45)
Position‐specific expression of Hox genes along the gastrointestinal tract (2004) (44)
Genome sequencing of a single tardigrade Hypsibius dujardini individual (2016) (44)
Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model. (2006) (44)
Differential metabolomics software for capillary electrophoresis-mass spectrometry data analysis (2010) (44)
Modeling Hsp70-mediated protein folding. (2006) (43)
Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves (2008) (43)
Effects of 3-styrylchromones on metabolic profiles and cell death in oral squamous cell carcinoma cells (2015) (42)
Dynamic simulation of an in vitro multi‐enzyme system (2007) (42)
Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes (2007) (42)
Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions (2010) (41)
Metabolomics: the frontier of systems biology (2005) (41)
Construction of a Biological Tissue Model Based on a Single-Cell Model: A Computer Simulation of Metabolic Heterogeneity in the Liver Lobule (2008) (41)
Identification of the first archaeal Type 1 RNase H gene from Halobacterium sp. NRC-1: archaeal RNase HI can cleave an RNA-DNA junction. (2004) (41)
Salivary metabolomics with alternative decision tree-based machine learning methods for breast cancer discrimination (2019) (41)
Local and global responses in complex gene regulation networks (2009) (40)
A serum metabolomics-based profile in low bone mineral density postmenopausal women. (2017) (40)
Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data. (2012) (40)
Prediction of axillary lymph node metastasis in primary breast cancer patients using a decision tree-based model (2012) (39)
Correlation between sequence conservation of the 5' untranslated region and codon usage bias in Mus musculus genes. (2001) (38)
Urinary Polyamine Biomarker Panels with Machine-Learning Differentiated Colorectal Cancers, Benign Disease, and Healthy Controls (2018) (38)
Thymidine Catabolism as a Metabolic Strategy for Cancer Survival. (2017) (37)
Hybrid dynamic/static method for large-scale simulation of metabolism (2005) (37)
Dynamic Simulation and Metabolome Analysis of Long-Term Erythrocyte Storage in Adenine–Guanosine Solution (2013) (37)
A Yeast Metabolite Extraction Protocol Optimised for Time-Series Analyses (2012) (37)
Quantitative assay for TALEN activity at endogenous genomic loci (2013) (37)
Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns (2010) (37)
In Silico Analysis of Phosphoproteome Data Suggests a Rich-get-richer Process of Phosphosite Accumulation over Evolution*S (2009) (36)
Metabolomic study of Chilean biomining bacteria Acidithiobacillus ferrooxidans strain Wenelen and Acidithiobacillus thiooxidans strain Licanantay (2012) (36)
The GC Skew Index: A Measure of Genomic Compositional Asymmetry and the Degree of Replicational Selection (2007) (36)
Correlation Between Shine–Dalgarno Sequence Conservation and Codon Usage of Bacterial Genes (2001) (36)
Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals (2010) (36)
Informatics for peptide retention properties in proteomic LC‐MS (2008) (35)
Comparative analysis of cis-encoded antisense RNAs in eukaryotes. (2007) (34)
A Metabologenomic Approach Reveals Changes in the Intestinal Environment of Mice Fed on American Diet (2018) (34)
Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress. (2020) (34)
Gene expression waves (2007) (34)
Kinetic simulation of signal transduction system in hippocampal long-term potentiation with dynamic modeling of protein phosphatase 2A (2003) (34)
Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly (2016) (34)
G-language System as a platform for large-scale analysis of high-throughput omics data (2006) (34)
Cooperative regulation for Okazaki fragment processing by RNase HII and FEN-1 purified from a hyperthermophilic archaeon, Pyrococcus furiosus. (2003) (33)
Profiling of plasma metabolites in postmenopausal women with metabolic syndrome (2016) (33)
Metabolomic profiling of the response of susceptible and resistant soybean strains to foxglove aphid, Aulacorthum solani Kaltenbach. (2013) (33)
Metabolomics Platform with Capillary Electrophoresis Coupled with High-Resolution Mass Spectrometry for Plasma Analysis. (2018) (33)
Predicting Novel Features of Toll-Like Receptor 3 Signaling in Macrophages (2009) (33)
Effect of masticatory stimulation on the quantity and quality of saliva and the salivary metabolomic profile (2017) (32)
Predictive value of CD24 and CD44 for neoadjuvant chemotherapy response and prognosis in primary breast cancer patients. (2010) (32)
Is central dogma a global property of cellular information flow? (2012) (32)
A problem in multivariate analysis of codon usage data and a possible solution (2005) (32)
Comprehensive Computational Analysis of Bacterial CRP/FNR Superfamily and Its Target Motifs Reveals Stepwise Evolution of Transcriptional Networks (2013) (32)
Disrupted tRNA Gene Diversity and Possible Evolutionary Scenarios (2009) (32)
Stabilizing synthetic data in the DNA of living organisms (2008) (31)
Computational methods for microRNA target prediction. (2007) (30)
Characterization of the Splice Sites in Gt-ag and Gc-ag Introns in Higher Eukaryotes Using Full-length Cdnas (2004) (30)
Comparative Analysis of Physical Maps of Four Bacillus subtilis (natto) Genomes (2004) (30)
Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics (2012) (30)
Enhancing apoptosis in TRAIL-resistant cancer cells using fundamental response rules (2011) (29)
A Metabolic Model of Human Erythrocytes: Practical Application of the E-Cell Simulation Environment (2010) (29)
Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index (2009) (29)
Metabolomics-based profiles predictive of low bone mass in menopausal women (2018) (29)
Muscle-specific Knock-out of NUAK Family SNF1-like Kinase 1 (NUAK1) Prevents High Fat Diet-induced Glucose Intolerance* (2012) (29)
Multicomponent nature underlies the extraordinary mechanical properties of spider dragline silk (2021) (29)
Metabolome profiling of various seaweed species discriminates between brown, red, and green algae (2019) (29)
Large-scale tRNA intron transposition in the archaeal order Thermoproteales represents a novel mechanism of intron gain. (2010) (28)
Unveiling cellular biochemical reactions via metabolomics-driven approaches. (2010) (28)
Development of a sheathless CE‐ESI‐MS interface (2018) (28)
Application of capillary electrophoresis‐mass spectrometry to synthetic in vitro glycolysis studies (2004) (28)
A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity (2011) (28)
Differential Binding of Three Major Human ADAR Isoforms to Coding and Long Non-Coding Transcripts (2017) (27)
A systems biology approach to suppress TNF-induced proinflammatory gene expressions (2013) (27)
Collective Dynamics of Specific Gene Ensembles Crucial for Neutrophil Differentiation: The Existence of Genome Vehicles Revealed (2010) (27)
Metabolic flux analysis and visualization. (2011) (27)
Effect of storage conditions on salivary polyamines quantified via liquid chromatography-mass spectrometry (2018) (27)
Erratum: Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells (2014) (27)
Chemical cleavage-assisted tryptic digestion for membrane proteome analysis. (2009) (27)
Computational Analysis of Stop Codon Readthrough in D.melanogaster (2003) (27)
Parameter estimation for stiff equations of biosystems using radial basis function networks (2006) (27)
Computational analysis suggests that alternative first exons are involved in tissue-specific transcription in rice (Oryza sativa) (2005) (26)
Development of quantitative method for determination of γ-glutamyl peptides by capillary electrophoresis tandem mass spectrometry: an efficient approach avoiding matrix effect. (2014) (26)
Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells. (2018) (26)
A medium-chain fatty acid as an alternative energy source in mouse preimplantation development (2012) (26)
Taxonomic revision of oil‐producing green algae, Chlorococcum oleofaciens (Volvocales, Chlorophyceae), and its relatives (2015) (26)
Taxonomic revision of Chlamydomonas subg. Amphichloris (Volvocales, Chlorophyceae), with resurrection of the genus Dangeardinia and descriptions of Ixipapillifera gen. nov. and Rhysamphichloris gen. nov. (2016) (26)
Time-structure of the yeast metabolism in vivo. (2012) (26)
Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data. (2002) (26)
Network scaling invariants help to elucidate basic topological principles of proteins. (2007) (26)
Effects of inter-day and intra-day variation on salivary metabolomic profiles. (2019) (25)
Can Complex Cellular Processes be Governed by Simple Linear Rules? (2009) (25)
ApA Dinucleotide Periodicity in Prokaryote, Eukaryote, and Organelle Genomes (1999) (25)
The 'weighted sum of relative entropy': a new index for synonymous codon usage bias. (2004) (24)
Serum Metabolomic Profiles for Human Pancreatic Cancer Discrimination (2017) (24)
Cutibacterium acnes (Propionibacterium acnes) 16S rRNA Genotyping of Microbial Samples from Possessions Contributes to Owner Identification (2019) (24)
Identification, expression, and molecular evolution of microRNAs in the “living fossil” Triops cancriformis (tadpole shrimp) (2015) (24)
Changes of metabolic profiles in an oral squamous cell carcinoma cell line induced by eugenol. (2013) (23)
Mice carrying a human GLUD2 gene recapitulate aspects of human transcriptome and metabolome development (2016) (23)
Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes (2015) (23)
Complete mutation analysis panel of the 39 human HOX genes. (2001) (23)
Precise mapping and dynamics of tRNA-derived fragments (tRFs) in the development of Triops cancriformis (tadpole shrimp) (2015) (23)
Profiling of the charged metabolites of traditional herbal medicines using capillary electrophoresis time-of-flight mass spectrometry (2012) (22)
Interaction Generality, a Measurement to Assess the Reliability of a Protein-Protein Interaction (2002) (22)
Computational analysis of associations between alternative splicing and histone modifications (2013) (22)
Model-based definition of population heterogeneity and its effects on metabolism in sporulating Bacillus subtilis. (2007) (22)
All systems go: launching cell simulation fueled by integrated experimental biology data. (2005) (22)
Metabolomic Profiling as a Possible Reverse Engineering Tool for Estimating Processing Conditions of Dry-Cured Hams. (2017) (22)
A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles (2006) (22)
The third plasmid pVV8 from Thermus thermophilus HB8: isolation, characterization, and sequence determination (2012) (22)
Multi-faceted integrated omics analysis revealed parsley (Petroselinum crispum) as a novel dietary intervention in dextran sodium sulphate induced colitic mice (2014) (22)
Preferential usage of some minor codons in bacteria. (2001) (21)
Association between dyslipidemia and plasma levels of branched-chain amino acids in the Japanese population without diabetes mellitus. (2019) (21)
Merging multiple omics datasets in silico: statistical analyses and data interpretation. (2013) (21)
Polymer entrapment in polymerized silicate for preparing highly stable capillary coatings for CE and CE-MS. (2007) (21)
Proteome-Wide Prediction of Novel DNA/RNA-Binding Proteins Using Amino Acid Composition and Periodicity in the Hyperthermophilic Archaeon Pyrococcus furiosus (2007) (21)
Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs (Proceedings of the National Academy of Sciences of the United States of America (2009) 106, (10171-10176) DOI: 10.1073/pnas.0900604106) (2009) (21)
Rapid DNA, RNA and protein extraction protocols optimized for slow continuously growing yeast cultures (2012) (21)
Multi-Omics Data-Driven Systems Biology of E. coli (2009) (21)
Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis (2017) (20)
Junction ribonuclease activity specified in RNases HII/2 (2008) (20)
The Rice Proteogenomics Database OryzaPG-DB: Development, Expansion, and New Features (2012) (20)
The role of Staphylococcal enterotoxin in atopic keratoconjunctivitis and corneal ulceration (2012) (20)
Computational Genome Analysis Using The G-language System (2008) (20)
Metabolomic profiling rationalized pyruvate efficacy in cybrid cells harboring MELAS mitochondrial DNA mutations. (2012) (20)
Quantitative proteome and phosphoproteome analyses of cultured cells based on SILAC labeling without requirement of serum dialysis. (2010) (20)
Implications from a Network-Based Topological Analysis of Ubiquitin Unfolding Simulations (2008) (20)
Junction ribonuclease: a ribonuclease HII orthologue from Thermus thermophilus HB8 prefers the RNA-DNA junction to the RNA/DNA heteroduplex. (2008) (19)
Sustained MAPK activation is dependent on continual NGF receptor regeneration (2004) (19)
Dynamics of serum metabolites in patients with chronic hepatitis C receiving pegylated interferon plus ribavirin: a metabolomics analysis. (2013) (19)
Simulation of developmental changes in action potentials with ventricular cell models (2006) (19)
Predictions of the pathological response to neoadjuvant chemotherapy in patients with primary breast cancer using a data mining technique (2012) (19)
A novel mechanism regulates H2S and SO2 production in Saccharomyces cerevisiae (2011) (19)
Comprehensive sequence analysis of translation termination sites in various eukaryotes. (2002) (19)
Measure of synonymous codon usage diversity among genes in bacteria (2009) (19)
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data (2010) (18)
Computer analyses of complete genomes suggest that some archaebacteria employ both eukaryotic and eubacterial mechanisms in translation initiation. (1999) (18)
On Negative Selection Against ATG Triplets Near Start Codons in Eukaryotic and Prokaryotic Genomes (1999) (18)
Method of preparing an equimolar DNA mixture for one-step DNA assembly of over 50 fragments (2015) (18)
Reconsidering plasmid maintenance factors for computational plasmid design (2018) (18)
Sensory properties and metabolomic profiles of dry-cured ham during the ripening process. (2020) (18)
Role of Phosphoenolpyruvate in the NADP-Isocitrate Dehydrogenase and Isocitrate Lyase Reaction in Escherichia coli (2006) (18)
A Metabolomic-Based Evaluation of the Role of Commensal Microbiota throughout the Gastrointestinal Tract in Mice (2018) (18)
Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments (2008) (17)
Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus. (2009) (17)
Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification (2011) (17)
Onco-proteogenomics: a novel approach to identify cancer-specific mutations combining proteomics and transcriptome deep sequencing (2010) (17)
Metatranscriptomic Analysis of Microbes in an Oceanfront Deep-Subsurface Hot Spring Reveals Novel Small RNAs and Type-Specific tRNA Degradation (2011) (17)
MEGU: Pathway Mapping Web-Service Based on KEGG and SVG (2006) (16)
The bagworm genome reveals a unique fibroin gene that provides high tensile strength (2019) (16)
G-language genome analysis environment with REST and SOAP web service interfaces (2010) (16)
Towards Computer Aided Design (CAD) of Useful Microorganisms (2001) (16)
TGF-β-dependent reprogramming of amino acid metabolism induces epithelial–mesenchymal transition in non-small cell lung cancers (2021) (16)
Tracking global gene expression responses in T cell differentiation. (2015) (16)
Validation of Bacterial Replication Termination Models Using Simulation of Genomic Mutations (2012) (16)
Measures of Compositional Strand Bias Related to Replication Machinery and its Applications (2012) (16)
The dynamics of cellular energetics during continuous yeast culture (2013) (16)
Noise‐reduction filtering for accurate detection of replication termini in bacterial genomes (2007) (15)
Causal analysis of CpG suppression in the Mycoplasma genome. (2000) (15)
Reprogramming of glutamine metabolism via glutamine synthetase silencing induces cisplatin resistance in A2780 ovarian cancer cells (2021) (15)
Phylogenetic position of a rare loricated green alga, Cephalomonas granulata N. L. Higinb. (Volvocales, Chlorophyceae) (2010) (15)
Spidroin profiling of cribellate spiders provides insight into the evolution of spider prey capture strategies (2020) (15)
Metabolomic profiling of sodium fluoride-induced cytotoxicity in an oral squamous cell carcinoma cell line (2014) (15)
Mass Spectrometry-compatible Subcellular Fractionation for Proteomics. (2020) (15)
Drying and extraction effects on three edible brown seaweeds for metabolomics (2018) (15)
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. (2012) (15)
Validating the significance of genomic properties of Chi sites from the distribution of all octamers in Escherichia coli. (2007) (15)
Another Origin of Coloniality in Volvocaleans: The Phylogenetic Position of Pyrobotrys Arnoldi (Spondylomoraceae, Volvocales) (2010) (15)
Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein. (2006) (15)
Nematode-specific tRNAs that decode an alternative genetic code for leucine (2011) (14)
Alteration of fatty acid chain length of Chlamydomonas reinhardtii by simultaneous expression of medium‐chain‐specific thioesterase and acyl carrier protein (2017) (14)
Chemical dephosphorylation for identification of multiply phosphorylated peptides and phosphorylation site determination. (2010) (14)
Metabolomic Analysis of Small Extracellular Vesicles Derived from Pancreatic Cancer Cells Cultured under Normoxia and Hypoxia (2021) (14)
Accelerated Laboratory Evolution Reveals the Influence of Replication on the GC Skew in Escherichia coli (2018) (14)
Pathway Finding from Given Time-Courses Using Genetic Algorithm (2001) (14)
Computational prediction of nucleosome positioning by calculating the relative fragment frequency index of nucleosomal sequences (2010) (14)
Detection of Rap1A as a yessotoxin binding protein from blood cell membranes. (2010) (14)
Far rapid synthesis of giant DNA in the Bacillus subtilis genome by a conjugation transfer system (2018) (13)
Distributed Cell Biology Simulations with E-Cell System (2004) (13)
Systems Biology Strategy Reveals PKCδ is Key for Sensitizing TRAIL-Resistant Human Fibrosarcoma (2015) (13)
Comparative metabolite profiling of foxglove aphids (Aulacorthum solani Kaltenbach) on leaves of resistant and susceptible soybean strains. (2014) (13)
Serum metabolome profiles characterized by patients with hepatocellular carcinoma associated with hepatitis B and C. (2016) (13)
Human AK2 links intracellular bioenergetic redistribution to the fate of hematopoietic progenitors. (2018) (13)
Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program (2014) (13)
Time-resolved metabolomics of a novel trebouxiophycean alga using (13)CO2 feeding. (2013) (12)
Microelectrospray interface with coaxial sheath flow for high-resolution capillary electrophoresis/mass spectrometry separation. (2007) (12)
A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks (2005) (12)
Characterization of RNase HII substrate recognition using RNase HII-argonaute chimaeric enzymes from Pyrococcus furiosus. (2010) (12)
GeNESiS: gene network evolution simulation software (2008) (12)
GEMBASSY: an EMBOSS associated software package for comprehensive genome analyses (2013) (12)
Positive Autoregulation Delays the Expression Phase of Mammalian Clock Gene Per2 (2011) (12)
Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions (2007) (12)
The SCO2299 gene from Streptomyces coelicolor A3(2) encodes a bifunctional enzyme consisting of an RNase H domain and an acid phosphatase domain (2005) (11)
Curing the Megaplasmid pTT27 from Thermus thermophilus HB27 and Maintaining Exogenous Plasmids in the Plasmid-Free Strain (2015) (11)
Thymidine catabolism promotes NADPH oxidase-derived reactive oxygen species (ROS) signalling in KB and yumoto cells (2018) (11)
Multiomics study of a heterotardigrade, Echinisicus testudo, suggests the possibility of convergent evolution of abundant heat-soluble proteins in Tardigrada (2021) (11)
Evolutionary Analysis of HIV-1 Pol Proteins Reveals Representative Residues for Viral Subtype Differentiation (2017) (11)
Restriction on Conjugational Transfer of pLS20 in Bacillus subtilis 168 (2008) (11)
Cerebral hyperemia and ischemia, from the standpoint of cerebral blood volume : proceedings of the statellite symposium, Brain Section, Fourth World Congress for Microcirculation, Osaka, Japan, 1-2 August 1987 (1988) (11)
Identification of DNA-dependent Protein Kinase as a Cofactor for the Forkhead Transcription Factor FoxA2* (2009) (11)
Genome‐wide screening of dioxin‐responsive genes in fetal brain: bioinformatic and experimental approaches (2006) (11)
Conjugational transfer system to shuttle giant DNA cloned by Bacillus subtilis genome (BGM) vector. (2007) (11)
Systematic Analysis of the Binding Surfaces between tRNAs and Their Respective Aminoacyl tRNA Synthetase Based on Structural and Evolutionary Data (2017) (11)
The use of a double coaxial electrospray ionization sprayer improves the peak resolutions of anionic metabolites in capillary ion chromatography-mass spectrometry. (2020) (10)
Base-pairing probability in the microRNA stem region affects the binding and editing specificity of human A-to-I editing enzymes ADAR1-p110 and ADAR2 (2018) (10)
Undesigned selection for replication termination of bacterial chromosomes. (2014) (10)
Comparison of the transcriptomes of two tardigrades with different hatching coordination (2019) (10)
Distinguishing enzymes using metabolome data for the hybrid dynamic/static method (2007) (10)
Computational assessment of insulin secretion and insulin sensitivity from 2-h oral glucose tolerance tests for clinical use for type 2 diabetes (2011) (10)
Comparative analysis of base correlations in 5' untranslated regions of various species. (2006) (10)
Relationship between Standard Uptake Values of Positron Emission Tomography/Computed Tomography and Salivary Metabolites in Oral Cancer: A Pilot Study (2020) (10)
Quantifying periodicity in omics data (2014) (10)
Stage‐specific expression of Caenorhabditis elegans ribonuclease H1 enzymes with different substrate specificities and bivalent cation requirements (2006) (10)
Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System (2009) (10)
Evolution of gene regulatory networks: Robustness as an emergent property of evolution (2008) (10)
Cooperativity of two active sites in bacterial homodimeric aconitases. (2009) (10)
Network Features and Pathway Analyses of a Signal Transduction Cascade (2008) (10)
Gene expression emPAI Calc — for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry (2010) (10)
Over-representation of Chi sequences caused by di-codon increase in Escherichia coli K-12. (2006) (10)
Metabolome analysis and metabolic simulation (2005) (9)
Effect of blanching on the concentration of metabolites in two parts of Undaria pinnatifida, Wakame (leaf) and Mekabu (sporophyll) (2020) (9)
Phylogenetic Position and Molecular Chronology of a Colonial Green Flagellate, Stephanosphaera pluvialis (Volvocales, Chlorophyceae), among Unicellular Algae (2016) (9)
Effects of feed crops and boiling on chicken egg yolk and white determined by a metabolome analysis. (2020) (9)
On the interplay of gene positioning and the role of rho‐independent terminators in Escherichia coli (2006) (9)
Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics (2007) (9)
A Metabolomic Profile Predictive of New Osteoporosis or Sarcopenia Development (2021) (9)
Visualization of three-way comparisons of omics data (2007) (9)
Physical laws shape biology. (2013) (9)
Expansion of Noncanonical V-Arm-Containing tRNAs in Eukaryotes. (2016) (9)
P-BOSS: a new filtering method for treasure hunting in metabolomics. (2007) (9)
Transcription-Associated Mutagenesis Increases Protein Sequence Diversity More Effectively than Does Random Mutagenesis in Escherichia coli (2010) (9)
Pre‐treatment with D942, a furancarboxylic acid derivative, increases desiccation tolerance in an anhydrobiotic tardigrade Hypsibius exemplaris (2020) (9)
Fast and global detection of periodic sequence repeats in large genomic resources (2018) (9)
Comprehensive Dipeptide Profiling and Quantitation by Capillary Electrophoresis and Liquid Chromatography Coupled with Tandem Mass Spectrometry. (2020) (9)
Genomic Heterogeneity in a Natural Archaeal Population Suggests a Model of tRNA Gene Disruption (2012) (9)
Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias among Bacteria (2007) (8)
Serum glycerophosphate levels are increased in Japanese men with type 2 diabetes. (2012) (8)
Contribution of quantitative changes in individual ionic current systems to the embryonic development of ventricular myocytes: a simulation study (2013) (8)
Effect of aging on psychological stress-induced increases in noradrenaline release in the rat anterior hypothalamus: an in vivo microdialysis study (1997) (8)
Changes of liver metabolites following hepatectomy with ischemia reperfusion towards liver regeneration (2018) (8)
Characteristic Sequence Pattern in the 5- to 20-bp Upstream Region of Primate Alu Elements (2000) (8)
Simultaneous analysis of consumer variables, acceptability and sensory characteristics of dry-cured ham. (2016) (8)
A screening system for artificial small RNAs that inhibit the growth of Escherichia coli. (2011) (8)
Charged metabolite biomarkers of food intake assessed via plasma metabolomics in a population-based observational study in Japan (2021) (8)
Selection Effects on the Positioning of Genes and Gene Structures from the Interplay of Replication and Transcription in Bacterial Genomes (2007) (8)
Does the Gut Microbiota Modulate Host Physiology through Polymicrobial Biofilms? (2020) (8)
MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data (2018) (8)
Predicting the Kinetic Properties Associated with Redox Imbalance after Oxidative Crisis in G6PD-Deficient Erythrocytes: A Simulation Study (2011) (7)
Comparative Study of Translation Termination Sites and Release Factors (RF1 and RF2) in Procaryotes (2003) (7)
Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth (2016) (7)
High-Quality Overlapping Paired-End Reads for the Detection of A-to-I Editing on Small RNA. (2018) (7)
Analysis of Genetic Code Ambiguity Arising from Nematode-Specific Misacylated tRNAs (2015) (7)
Parameter Estimation Mechanism of E-CELL Simulation Environment (1999) (7)
Improved taxon sampling and multigene phylogeny of unicellular chlamydomonads closely related to the colonial volvocalean lineage Tetrabaenaceae-Goniaceae-Volvocaceae (Volvocales, Chlorophyceae). (2019) (7)
Hybridization between Japanese and North American Chlamydomonas reinhardtii (Volvocales, Chlorophyceae) (2014) (7)
Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria (2016) (7)
Computer analysis of potential stem structures of rRNA operons in various procaryote genomes. (2000) (7)
AMPK activity is required for the induction of anhydrobiosis in a tardigrade Hypsibius exemplaris, and its potential up‐regulator is PP2A (2019) (7)
Correlation-centred variable selection of a gene expression signature to predict breast cancer metastasis (2020) (7)
Comprehensive Dipeptide Analysis Revealed Cancer-Specific Profile in the Liver of Patients with Hepatocellular Carcinoma and Hepatitis (2020) (7)
The bagworm genome reveals a unique fibroin gene that provides high tensile strength (2019) (7)
A single CRISPR base editor to induce simultaneous C-to-T and A-to-G mutations (2019) (7)
Regulation of cerebral microcirculation--update. (2000) (7)
Ultralow Input Genome Sequencing Library Preparation from a Single Tardigrade Specimen. (2018) (6)
The Salivary Gland and Systemic Health: Towards the Creation of Salivary Gland and Health Medicine (2011) (6)
Manufacturing of Biomimetic Silicone Rubber Films for Experimental Fluid Mechanics: 3D Printed Shark Skin Molds (2019) (6)
A Generic Software Platform for Brain-inspired Cognitive Computing (2015) (6)
Xanthurenic Acid Is the Main Pigment of Trichonephila clavata Gold Dragline Silk (2021) (6)
Versatile architecture of a bacterial aconitase B and its catalytic performance in the sequential reaction coupled with isocitrate dehydrogenase. (2008) (6)
KBWS: an EMBOSS associated package for accessing bioinformatics web services (2011) (6)
Genomic Analysis of Pseudomonas sp. Strain SCT, an Iodate-Reducing Bacterium Isolated from Marine Sediment, Reveals a Possible Use for Bioremediation (2019) (6)
Volvulina compacta (Volvocaceae, Chlorophyceae), new to Japan, and its phylogenetic position (2010) (5)
Chlorogonium complexum sp. nov. (Volvocales, Chlorophyceae), and morphological evolution of Chlorogonium (2010) (5)
Reshuffling of the Bacillus subtilis 168 genome by multifold inversion. (2007) (5)
Metabolic Characterization of Antifolate Responsiveness and Non-responsiveness in Malignant Pleural Mesothelioma Cells (2018) (5)
The complete mitochondrial genome of Eumeta variegata (Lepidoptera: Psychidae) (2018) (5)
Corrigendum to “On dynamics of overlapping genes in bacterial genomes” [Gene 323 (2003) 181–187] (2004) (5)
Computer Simulation of Human Erythrocyte using the E-CELL system (1999) (5)
Design and Development of Software Environment for Whole-Cell Simulation (2001) (5)
E. coli metabolomics: Capturing the complexity of a "simple" model (2007) (5)
Developmental changes in the balance of glycolytic ATP production and oxidative phosphorylation in ventricular cells: A simulation study. (2017) (5)
Comparative genomics of Bacteria commonly identified in the built environment (2019) (5)
Chlamydomonas neoplanoconvexa nom. nov. and its unique phylogenetic position within Volvocales (Chlorophyceae) (2011) (5)
A web server for interactive and zoomable Chaos Game Representation images (2009) (5)
Quality Assessment of Untargeted Analytical Data in a Large-Scale Metabolomic Study (2021) (5)
Comparative Study of Circadian Oscillatory Network Models of Drosophila (2008) (5)
E-CELL Project Overview:Towards Integrative Simulation of Cellular Processes (1998) (5)
Modeling of Human Red Blood Cell Using the E-CELL Simulation System (1998) (5)
Taxonomic Reassessment of Strains formerly Classified as Chloromonas insignis (Volvocales, Chlorophyceae) and Description of Gloeomonas anomalipyrenoides sp. nov. (2015) (5)
E-Cell System Version 3: A Software Platform for Integrative Computational Biology (2003) (5)
Light Microscopy and Phylogenetic Analyses of Chlamydomonas Species (Volvocales, Chlorophyceae). II. Molecular Phylogeny, Secondary Structure of ITS-2, Cell Morphology, and Nomenclature of Microglena opisthopyren, and M. media, comb. nov. (2014) (5)
Urinary Metabolome Analyses of Patients with Acute Kidney Injury Using Capillary Electrophoresis-Mass Spectrometry (2021) (5)
Comparison of metabolite production capability indices generated by network analysis methods (2008) (5)
Salivary metabolomics with machine learning for colorectal cancer detection (2022) (4)
The first high frequency of recombination-like conjugal transfer from an integrated origin of transfer sequence in Bacillus subtilis 168 (2018) (4)
GTP‐dependent RNA 3′‐terminal phosphate cyclase from the hyperthermophilic archaeon Pyrococcus furiosus (2011) (4)
Generic Gene Expression System for Modeling Complex Gene Regulation Network Using E-CELL System (1999) (4)
Pilot study of changes in salivary metabolic profiles induced by template therapy. (2012) (4)
Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA. (2011) (4)
Beta-galactosidase-responsive synthetic biomarker for targeted tumor detection. (2018) (4)
eXpanda: An Integrated Platform for Network Analysis and Visualization (2007) (4)
Metabolomics: A new omics technology for traditional herbal medicine analysis (2012) (4)
Reliability of urinary charged metabolite concentrations in a large-scale cohort study using capillary electrophoresis-mass spectrometry (2020) (4)
In silico diagnosis of inherently inhibited gene expression focusing on initial codon combinations. (2005) (4)
Inferring rules of Escherichia coli translational efficiency using an artificial neural network (2007) (4)
Rearing and observation of immature stages of the hoverfly Microdon katsurai (Diptera, Syrphidae) (2016) (4)
Algebraic Method for the Analysis of Signaling Crosstalk (2008) (4)
Conjunctival Injection Reduction in Patients with Atopic Keratoconjunctivitis Due to Synergic Effect of Bovine Enteric-Coated Lactoferrin in 0.1% Tacrolimus Ophthalmic Suspension (2020) (4)
Microglena redcarensis sp. nov. (Volvocales, Chlorophyceae), a brackish water chlamydomonad with contractile vacuoles (2018) (4)
Robust effects of Tsr-CheBp and CheA-CheYp affinity in bacterial chemotaxis (2007) (4)
Perioperative serum and urine metabolome analyses in patients with hepatocellular carcinoma undergoing partial hepatectomy. (2019) (4)
Chlorococcum turfosum comb. nov. (Volvocales, Chlorophyceae) and visualization of chimeric sequences (2019) (4)
The Hsp70 chaperone system maintains high concentrations of active proteins and suppresses ATP consumption during heat shock (2007) (3)
Large-Scale Molecular Evolutionary Analysis Uncovers a Variety of Polynucleotide Kinase Clp1 Family Proteins in the Three Domains of Life (2019) (3)
A simple method to provide a shuttling plasmid for delivery to other host ascertained by prolonged stability of extracellular plasmid DNA released from Escherichia coli K12 endA mutant, deficient in major endonuclease. (2012) (3)
eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria (2017) (3)
Erratum to: Metabolomic profiling reveals novel biomarkers of alcohol intake and alcohol-induced liver injury in community-dwelling men (2016) (3)
Morphology and phylogeny of a new wall‐less freshwater volvocalean flagellate, Hapalochloris nozakii gen. et sp. nov. (Volvocales, Chlorophyceae) (2017) (3)
Comparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan (2017) (3)
Upregulation of Thymidylate Synthase Induces Pemetrexed Resistance in Malignant Pleural Mesothelioma (2021) (3)
GANDivAWeb: A web server for detecting early folding units ("foldons") from protein 3D structures (2008) (3)
GPAC: Benchmarking the Sensitivity of Genome Informatics Analysis to Genome Annotation Completeness (2006) (3)
BriCA: A Modular Software Platform for Whole Brain Architecture (2016) (3)
Draft Genome Sequence of Geobacter sp. Strain SVR, Isolated from Antimony Mine Soil (2020) (3)
OP9 Predictive value of CD24 and CD44 for response to neoadjuvant chemotherapy and prognosis in patients with primary breast cancer (2011) (3)
Erratum: Gene expression waves. Cell cycle independent collective dynamics in cultured cells (FEBS Journal (2007) 274 (2878-2886)) (2007) (3)
Quantitative and Molecular Similarity Analyses of the Metabolites of Cold- and Hot-Natured Chinese Herbs (2021) (2)
Efficient delivery of large DNA from Escherichia coli to Synechococcus elongatus PCC7942 by broad-host-range conjugal plasmid pUB307 (2018) (2)
Multivariate Time Series Analysis of Metabolic Network Using the E-CELL Simulation System (1998) (2)
Proteins as networks (2007) (2)
Multiomics study of a heterotardigrade, Echinisicus testudo, suggests convergent evolution of anhydrobiosis-related proteins in Tardigrada (2020) (2)
Quantitative Modeling of Mitochondrial Energy Metabolism Using E-CELL Simulation Environment (2000) (2)
A novel Mn-dependent peroxidase contributes to tardigrade anhydrobiosis (2020) (2)
A Comprehensive Software Suite for the Analysis of cDNAs (2016) (2)
Identification of a replication initiation protein of the pVV8 plasmid from Thermus thermophilus HB8 (2012) (2)
Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades (2022) (2)
An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus (2017) (2)
Draft Genome Sequence of Arenibacter sp. Strain C-21, an Iodine-Accumulating Bacterium Isolated from Surface Marine Sediment (2016) (2)
RNA sequencing data for gamma radiation response in the extremotolerant tardigrade Ramazzottius varieornatus (2021) (2)
Evolution of Overlapping Genes: Comparative Genomics of Mycoplasma genitalium and Mycoplasma pneumoniae (1998) (2)
Light Microscopy and Phylogenetic Analyses of Chlamydomonas Species (Volvocales, Chlorophyceae). : I. Chlamydomonas pseudomacrostigma and Chlamydomonas media (2012) (2)
Modeling of Transcription and DNA Replication Using the E-CELL Simulation System (1998) (2)
Distinct Expansion of Group II Introns During Evolution of Prokaryotes and Possible Factors Involved in Its Regulation (2022) (2)
Microcirculatory stasis in the brain : proceedings of the Symposium on Microcirculatory Stasis in the Brain, Tokyo, May 20-21, 1993 (1993) (2)
Features of smaller ribosomes in candidate phyla radiation (CPR) bacteria revealed with a molecular evolutionary analysis (2022) (2)
Synthetic Biomarker Design by Using Analyte‐Responsive Acetaminophen (2017) (2)
Modeling of Signal Transduction for Bacterial Chemotaxis Using the E-CELL Simulation System (1998) (2)
[E-Cell simulation system and its application to the modeling of circadian rhythm]. (2003) (2)
Modeling Photorespiration Pathway through E-CELL (2001) (2)
Modeling Theory and Software Architecture of the E-CELL Simulation System (1998) (2)
Cinnamon bark extract suppresses metastatic dissemination of cancer cells through inhibition of glycolytic metabolism (2021) (2)
Development of Titania Particles Used for Phosphopeptide Enrichment in Mass Spectrometry-Based Phosphoproteomics (2010) (2)
A Simulation Model of Diabetes Using E-Cell System (2001) (2)
Stable and efficient delivery of DNA to Bacillus subtilis (natto) using pLS20 conjugational transfer plasmids (2019) (2)
In Silico Models for Metabolic Systems Engineering (2010) (2)
Complete Genome Sequence of Arthrobacter sp. Strain MN05-02, a UV-Resistant Bacterium from a Manganese Deposit in the Sonoran Desert (2019) (2)
Draft Genome Sequences of Enterococcus faecalis Strains Isolated from Healthy Japanese Individuals (2019) (1)
Cyanidioschyzon merolaeRNA Intermediate in Permuted tRNA Genes Expressed via a Circular (2009) (1)
964 Multiple Salivary Biomarkers for Pancreatic Cancer Detection (2009) (1)
Differences of Translation Termination Sites Among the Three Stop Codons (1999) (1)
Automatic Transformation of Kinetic Equations into S-System and GMA Forms (2002) (1)
Salivary metabolomics for oral cancer detection (2011) (1)
G-Links: a gene-centric link acquisition service. (2014) (1)
Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes (2011) (1)
Perspective in the Evolution of Human MicroRNAs : Copy Number Expansion and Acquisition of Target Gene Specialization(WHAT IS LIFE? THE NEXT 100 YEARS OF YUKAWA'S DREAM) (2008) (1)
High quality genome assembly of the anhydrobiotic midge provides insights on a single chromosome-based emergence of extreme desiccation tolerance (2022) (1)
Metabolome analysis and systems biology (2008) (1)
Distribution Analysis of the Oligonucleotide around 5' Splice Sites in H. sapiens, M. musculus, D. melanogaster and A. thaliana pre-mRNAs (2002) (1)
Kinetic Modelling of Energy Metabolism in Mitochondria (1999) (1)
Multiresolution Analysis Uncovers Hidden Conservation of Properties in Structurally and Functionally Similar Proteins (2006) (1)
E‐Cell: Computer Simulation of the Cell (2012) (1)
Draft Genome Sequence of Roseovarius sp. A-2, an Iodide-Oxidizing Bacterium Isolated from Natural Gas Brine Water, Chiba, Japan (2017) (1)
Brain activation and CBF control : proceedings of the Satellite meeting on Brain Activation and Cerebral Blood Flow Control, held in Tokyo, Japan 5-8 June 2001 (2002) (1)
Distribution Analysis of 5' Splice Site-Like Sequences in Human and Mouse pre-mRNAs (2001) (1)
E-Cell System (2013) (1)
Publisher Correction: Base editors for simultaneous introduction of C-to-T and A-to-G mutations (2020) (1)
Longitudinal Analyses Reveal That Aging-related Alterations in the Intestinal Environment Lead to Gut Dysbiosis With the Potential to Induce Obesity (2020) (1)
Hsp70-Mediated Protein Refolding in E-Cell (2013) (1)
Towards Simulation of Whole Metabolic Pathways in Human Erythrocyte (2001) (1)
Construction of a Simulation Model of Diabetes for Pathophysiological Analysis Using E-Cell System (2002) (1)
Integrated omics profiling of dextran sodium sulfate-induced colitic mice supplemented with Wolfberry (Lycium barbarum). (2020) (1)
Toward Computer Simulation of the Whole Cell (2002) (1)
Integrative modeling of gene expression and metabolism with E-CELL System (2002) (1)
G-Links: a gene-centric link acquisition service (2014) (1)
HybGFS: a hybrid method for genome-fingerprint scanning (2006) (1)
Identification of Non-Coding RNAs in the Escherichia coli Genome Using Sequence Specificity Index (SSI) (2003) (1)
Prediction of Biochemical Reactions Using Genetic Programming (2003) (1)
Computer Modeling of Photosynthesis Using the E-CELL System (2000) (1)
Correction: Charged metabolite biomarkers of food intake assessed via plasma metabolomics in a population-based observational study in Japan (2021) (1)
Neuron Report Organization and Evolution of Brain Lipidome Revealed by Large-Scale Analysis of Human , Chimpanzee , Macaque , andMouse Tissues (2015) (1)
Emergence of macroscopic simplicity from the Tumor Necrosis Factor-alpha signaling dynamics (2011) (1)
Estimation of Genetic Networks of the Circadian Rhythm in Cyanobacterium Using the E-CELL System (2001) (1)
Machine learning methods with salivary metabolomics for breast cancer detection. (2019) (1)
A New Method for Characterizing Functionally-Unknown Proteins Using Specific Amino Acid Frequency and Periodicity at the Proteome Level (2003) (1)
Multiomics study of a heterotardigrade, Echinisicus testudo, suggests the possibility of convergent evolution of abundant heat-soluble proteins in Tardigrada (2021) (0)
Strand-specific Single-stranded DNA Sequencing (4S-seq) of E. coli genomes. (2019) (0)
Protein analysis of dragline spider silk (2016) (0)
In silico models for metabolic systems (2009) (0)
Comparative genome analysis of Bifidobacterium longum strains isolated from different individuals (2017) (0)
Evolutionary analysis of HIV-1 pol proteins reveals critical residues for virus subtype differentiation (2017) (0)
Evolutionary analysis of antisense protein gene in HIV-1 using sequence similarity network (2017) (0)
Discovery of novel biomarkers by metabolome analysis using pre- and post-surgery serum samples and surgical tissue from hepatocellular carcinoma patients (2016) (0)
Computational in Cell Simulation: A Software Engineering Approach (2002) (0)
Stem Loop Structures in the B . subtilis Genome and Their Roles in the Transcription Machinery (2000) (0)
Genome sequencing and assembly of the extremophile tardigrade Hypsibius dujardini (2016) (0)
Statistical Analysis of Gene Expression in Innate Immune Responses: Dynamic Interactions between MicroRNA and Signaling Molecules (2007) (0)
An Electrophysiological Simulation Model of the Myocardial Cell Using E-CELL System (2001) (0)
Mathematical Analysis of Metabolic Networks Using the E-CELL Simulation Environment (1999) (0)
Integrated omics profiling of dextran sodium sulfate-induced colitic mice supplemented with Wolfberry (Lycium barbarum) (2020) (0)
Distinct Expansion of Group II Introns Depends on the Type of Intron-encoded Protein and Genomic Signatures in Prokaryotes (2021) (0)
Computer Analyses of Site-Specific Variabilities in Human Alu Sequences (1996) (0)
[Computer models of plant metabolism]. (2003) (0)
Nobuyoshi Ishii , to PerturbationsE . coliResponse of Multiple High-Throughput Analyses Monitor the (2010) (0)
Salivary Metabolomic Profiles for Oral, Breastand Pancreatic Cancer Detection (2010) (0)
Metabolomic analysis of cancer cell-derived extracellular vesicles (2019) (0)
Genomic Analysis of Rhodococcus sp. Br-6, a Bromate Reducing Bacterium Isolated From Soil in Chiba, Japan (2018) (0)
Finding Biological Roles of Averaging Effect of Large Numbers: The Existence of Genome Vehicles Guiding Cell Fate Decision (2011) (0)
Transcriptomic analysis of the extremotolerant tardigrade Ramazzottius varieornatus after heat shock using RNA-Seq (2015) (0)
On Correlation between G+C Contents and Intron Lengths: Longer Introns Tend to be More A+T Rich (1996) (0)
Modeling and simulation of developmental changes in contractile apparatus of ventricular cells (2015) (0)
1299Association between environmental cadmium exposure and plasma and urinary metabolite profiles in Japanese cohort study (2021) (0)
Modeling of Hsp70-Mediated Protein Refolding (2013) (0)
Next-generation sequencing and machine learning-based in silico proteomics (2017) (0)
Simulation of developmental changes in energy metabolism between fetal and adult ventricular cells (2013) (0)
AOSOP16 DEVELOPMENT OF WEB TOOLS TO PREDICT PATHOLOGICAL RESPONSE TO NEOADJUVANT CHEMOTHERAPY AND AXILLARY LYMPH NODE METASTASIS IN BREAST CANCER PATIENTS (2013) (0)
On Low Frequency of CpG Dinucleotides in Bacterial Genomes (1998) (0)
CpG Dinucleotide Distribution and DNA Methylation (1996) (0)
Contribution of developmental changes in energy metabolism to excitation-contraction coupling of a ventricular cell: A simulation study (2014) (0)
Comparison of the transcriptomes of two tardigrades with different hatching coordination (2019) (0)
Pathological Analyses of Enzyme Deficiency in Human Erythrocyte Using E-CELL System (1999) (0)
Computational Analysis of χ Sequences (1999) (0)
Towards Kinetic Modeling of DNA Replication Using the E-CELL System (1999) (0)
A method for estimation of enzyme kinetics in metabolic pathways using GMA (2004) (0)
Tear Metabolome Analysis in Atopic Keratoconjunctivitis (2009) (0)
3.Systems biology assessment of binary mixture effects in the social amoeba Dictyostelium discoideum (2010) (0)
Polarity protein SCRIB interacts with SLC3A2 to regulate proliferation and tamoxifen resistance in ER+ breast cancer (2022) (0)
Genetic vehicle comprising majority of lowly expressed genes guides cell fate decision (2010) (0)
Metabolomics: A new paradigm for cancer biomarker discovery (2011) (0)
Quantitative analysis of synonymous codon usage bias (2004) (0)
Identifying Potential Regulatory Sequences of Alternative Splicing (2003) (0)
Microarray Visualization System on the G-Language GAE (2003) (0)
Computational Analysis of the Strand Bias of the Chi Sequences and Other Oligonucleotides in Bacterial Genomes (2000) (0)
Technologies to dissect cell lineages of dynamic cell progression in complex systems (2017) (0)
Development of Dual Stable Isotope Labeling by Amino Acids in Cell Culture and Application to Quantitative Proteomics (2010) (0)
Proposition of cortical connectivity between 30 cytoarchitectural areas of human cerebral cortex (2000) (0)
Large-scale molecular evolutionary analysis of the Clp1 polynucleotide kinase family that is involved in pre-tRNA splicing (2017) (0)
Identification of Attenuators of Transcriptional Termination: Implications for RNA Regulation in Escherichia coli (2022) (0)
Integrated Distributed Computing Environment on the G-Language GAE v. 2 (2003) (0)
E-Cell IDE: An Integrated modeling and simulation environment for systems-biology (2009) (0)
Modeling a Complex Gene Regulation Network Using the E-CELL System (2000) (0)
Spider and bagworm moth genomes reveal the diversity of silk protein motifs and its mechanical properties (2019) (0)
On Periodicity of Adenine-Adenine Dinucleotides in Bacterial Genomes (1998) (0)
Sequence analysis of antisense protein gene during SIV and HIV evolution (2016) (0)
Establishment and mathematical modeling of a positive feedback genetic circuit on yeast (2017) (0)
Abstract P1-01-21: Predicting Risk of Axillary Lymph Node Metastasis: A Novel, Decision Tree-Based Approach That Can Handle Incomplete Datasets (2010) (0)
Pathway Projector : an Interactive Pathway Browser with Zoomable User Interface (2009) (0)
Perturbation of intraparenchymal arterioles during K + -induced cortical spreading depression in cats (2005) (0)
Genome-wide analysis of histone modification patterns in human (2011) (0)
Metabolome Analysis of Colon Tumor Tissues by Capillary Electrophoresis Time-of-Flight Mass Spectrometer (2009) (0)
Brain Poster Session: Spreading Depression (2009) (0)
[Not Available]. (2009) (0)
Next-generation Integrated Simulation Technique : Development of a Modeling and Simulation Environment for Systems Biology (2007) (0)
Time-series transcriptomic screening of factors contributing to the cross-tolerance to UV radiation and anhydrobiosis in tardigrades (2022) (0)
Computer Analyses of Overlapping Genes in Mycoplasma Genitalium (1996) (0)
Metabolomic Characterization of Escherichia coli K-12 Adaptation to Glycerol (2007) (0)
The Effects of the Expression of Cancer Stem Cell Marker LGR5 by PERK activation (2015) (0)
In Silico Simulation Represents Adenoviral Gene Knockdown of Myocardial Ventricular Cell (2003) (0)
eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria (2017) (0)
Computer Analyses of Translation Initiation Sites in Complete Genomes (1997) (0)
Signaling Flux Redistribution concept can switch survival to apoptosis in cancer cells (2010) (0)
Statistical Characterization of Transcription Start Sites in Plant Genomes (2005) (0)
Transcriptome analysis to elucidate the implication of tun state in tardigrades (2017) (0)
Predicting human cortical connectivity for language areas using the Conel database (1999) (0)
2P-239 Macroscopic Relationships between Protein Phosphorylation and Physical Interaction(Bioinformatics:Functional genomics,The 47th Annual Meeting of the Biophysical Society of Japan) (2009) (0)
Sequence Analysis of Short Tandem Repeats in the Genomes of H. influenzae and M. genitalium (1996) (0)
Salivary metabolomics with artificial intelligence-based methods for breast cancer detection and subtype prediction (2020) (0)
Drying and extraction effects on three edible brown seaweeds for metabolomics (2018) (0)
Sensitivity analysis of ectopic electrical activity in the pulmonary vein myocardium (2015) (0)
E-CELL2: E-CELL Simulation System for Windows (2002) (0)
Seeking after the molecular mechanism of web-building behaviour manipulation by spider-ectoparasitoids: RNA-seq analysis of both spider and parasitoid (2017) (0)
2PS044 Live cell imaging of the growth factor-induced nuclear translocation of ERK in PC12 cells(The 50th Annual Meeting of the Biophysical Society of Japan) (2012) (0)
Correlation between Sequence Conservation of 5' UTR and Codon Usage Bias (2000) (0)
Computer Analysis of Base Pairing Free-Energy between Shine-Dalgarno Sequence and 16S rRNA in Various Procaryotes (1998) (0)
Hao1 Is Not a Pathogenic Factor for Ectopic Ossifications but Functions to Regulate the TCA Cycle In Vivo (2022) (0)
Brain Poster Session: Experimental Cerebral Ischemia—Blood Flow and Metabolism (2009) (0)
Expression Frequency of the Human Immunoglobulin γ Light Chain Genes and the Roles of Their Recombination Signal and Spacer Sequences (1998) (0)
Metabolite changes during overwintering of red turnip (cv. Atsumi-kabu) bulbs. (2017) (0)
Meta-analysis of transcriptional regulatory networks for lipid metabolism in neural cells from schizophrenia patients based on an open-source intelligence approach (2021) (0)
Chapter seven Integrating genome and metabolome toward whole cell modeling with the E-cell system (2004) (0)
E-CELL: towards computer simulation of the whole cell (2002) (0)
Do heat shock proteins contribute to desiccation tolerance in tardigrades (2017) (0)
Inferring History of Genomic Duplication Using Subclassified Alu Elements (1996) (0)
Computer Analyses of Nucleotide Patterns around Start Codons (1996) (0)
Tomita On Negative Selection Against ATG Triplets Near Start Codons in Archaebacterial Genomes (2000) (0)
G-Language Genome Analysis Environment (2001) (0)
Differential gene expression analysis of Euglena gracilis chloroplast deleted mutant (2017) (0)
involved in tissue-specific transcription in rice (Oryza sativa) (2005) (0)
G-Language Genome Analysis Environment Version 2 (2003) (0)
Molecular evolution of Clp1 kinase that involved in pre-tRNA processing and its related enzymes (2016) (0)
E-Neuron Project: (2001) (0)
The Genome-Based E-CELL Modeling (GEM) System (2005) (0)
Molecular evidence of chemical disguise by the socially parasitic spiny ant Polyrhachis lamellidens (Hymenoptera: Formicidae) when invading a host colony (2022) (0)
Simulation study on the balance of glycolytic ATP production and oxidative phosphorylation in embryonic and adult ventricular cells (2016) (0)
Elucidation of the mechanisms of rice bran supplementation on the suppression of colitis development (2016) (0)
Sequence Patterns Observed in 5′ Flanking Regions of Primate Alu Elements (1999) (0)
Estimating cortical network model of developing human cerebral cortex (2001) (0)
Comparative genomic analysis of the genus Rhodococcus including Rhodococcus equi and its sister group Rhodococcus sp. Br-6, a bromate reducing bacterium isolated from soil in Chiba, Japan. (2017) (0)
Abstract 1442: Novel linkage of thymidine catabolism and the glycolytic pathway in human cancer cells (2018) (0)
Special RECOMB 2002 Issue (2004) (0)
Simulation of Human Erythrocyte (2013) (0)
2 dimensional visualization of RNA-protein binding regions and its application (2015) (0)
Large Scale Analysis of Transcriptional and Translational Control Mechanism in Human Ribosomal Proteins (2003) (0)
Second Virtual Conference on Genomics and Bioinformatics: Invited Speakers and Invited Discussion Leaders Remarking Notes (2003) (0)
Metabolomic analysis of culture media by CE-TOF/MS suggests a medium-chain fatty acid as an alternative energy source of mouse preimplantation embryos (2013) (0)
A Diabetes Model by the E-CELL system: (2001) (0)
Comparison and Characterization of Proteomes in the Three Domains of Life Using 2D Correlation Analysis(WHAT IS LIFE? THE NEXT 100 YEARS OF YUKAWA'S DREAM) (2008) (0)
Light Microscopy and Phylogenetic Analyses of Chlamydbmonas Species (Volvocales, Chlorophyceaej. I. Chlamydomonas pseudomacrostigma and (2014) (0)
Nature Butyrate Supplementary Information (2013) (0)
Comparative genomics of Bacteria commonly identified in the built environment (2019) (0)
Large-scale comparative analysis of spider fibroin genes using multi-omics approaches (2017) (0)
Towards high-resolution whole cell lineage tracing of mammalian development using genome editing and evolving DNA barcode technology (2017) (0)
Evaluation of the effects of age and diet on the gut ecosystem via multiple omics (2013) (0)
Electrophysiological Simulation of Myocardial Cell Using E-CELL System (2002) (0)
Phylogenomic analysis of spider silk genes (2016) (0)
[Refinement of genome-wide data]. (2004) (0)
2TP4-06 Macroscopic Relationships between Protein Phosphorylation and Physical Interaction(The 47th Annual Meeting of the Biophysical Society of Japan) (2009) (0)
Metabolomic Biomarkers of Daily Alcohol Intake and Alcohol-Induced Hepatopathy in Community-Dwelling Adults: Tsuruoka Metabolomic Cohort Study, Japan. (2014) (0)
Metabolome analysis reveals the relationship between polyamine metabolism and innate immune responses in murine macrophages (2016) (0)
A Simulation Model of Cardiovascular System for Diabetes Pathophysiological Model Using E-Cell System (2002) (0)
An investigation on the anti-obeisty mechanism of silkworm intake by use of metabolome analysis. (2017) (0)
An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus (2017) (0)
Analysis of Translation Initiation Sites in the Complete Genome of Mycoplasma genitalium Suggests That This Bacterium Uses Alternative Signal for Translation Initiation (1998) (0)
Characterization and evolution of the binding surface between tRNA and its aminoacyl-tRNA synthetase (2016) (0)
Computer Simulation of Enzyme Deficiency in Human Erythrocyte Using the E-Cell System (2000) (0)
Computer simulation of cellular metabolism and its application to medicine(EDUCATIONAL LECTURE) (2002) (0)
Building Working Cells in Computer : -Computer Simulation of the Cell Based on Genome Information- (2000) (0)
Translational Efficiency Prediction Using Structural Learning Method (2003) (0)
Integrative Modeling of Mitochondrial Metabolism (2000) (0)
Metabolomics Society’s annual Metabolomics publication awards (2013) (0)
Collective fluctuations guiding global biological responses (2013) (0)
Personal identification using skin bacterial genotype (2016) (0)
Diversification of Polynucleotide Kinase Clp1 Family Proteins and Their Possible Origins in Eukaryotic Evolution (2023) (0)
Computer Simulation of Glycolysis in Pancreatic β-Cells Using the E-CELL System (2000) (0)
Computer Analysis of Hairpins at Transcription Termination Sites in Procaryote Genomes (1997) (0)
Heterogeneity in Synonymous Codon Usage among Genes of Diverse Bacterial Genomes (2003) (0)
Cooperative regulation of pre-16S rRNA processing by archaeal proteins, Pf -Nob1 and Pf -Dim2 (2016) (0)
Modeling Environment for Large-Scale Models Using the E-CELL System (2001) (0)
Comprehensive analysis of stress responsive peptides (2016) (0)
Model Construction of the Energy Metabolism Pathway in Myocardial Cell (2003) (0)
A mathematical model of stochastic phenotype of an engineered cell (2017) (0)
Comparative genomics of two tardigrades (2017) (0)
Identification of a replication initiation protein of the pVV8 plasmid from Thermus thermophilus HB8 (2012) (0)
Skin microbiome alteration in chronic pyoderma patients with antibiotics treatment (2017) (0)
Rare sugar, D-psicose suppresses high-fat diet-induced obesity through gut microbiota alteration (2018) (0)
Combination of quantitative changes in ionic components to enhance the contractile force during T-tubule development (2016) (0)
Global landscape of periodically patterned DNA elements in prokaryotic and eukaryotic genomes (2017) (0)
Genome Analysis Workshop: a Personal Genomics Class at Keio SFC (2014) (0)
Automatic Generation of Cell-Wide Pathway Model from Complete Genome (2003) (0)
MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data (2018) (0)
E-CELL Simulation Environment Version 3: System Architecture of Simulation Engine (2001) (0)
Extraction of high molecular weight sericin from the silk glands of Bombyx mori (2017) (0)
Supplemental Figure 4. Simulated membrane potentials for 32 combinations using the Luo–Rudy model. (2013) (0)
An interaction knowledgebase for biomolecular modeling (2006) (0)
Temporal phosphoproteomic analysis of VEGF-A signaling in HUVECs: an insight into early signaling events associated with angiogenesis. (2023) (0)
Development of the Bacteria Analysis System on G-Language Genome Analysis Environment (2001) (0)
Comprehensive comparison and evolutionary analysis of group II introns in Bacteria (2017) (0)
iDMET: network-based approach for integrating differential analysis of cancer metabolomics (2022) (0)
Convergent evolution of anhydrobiosis-related proteins in Tardigrades suggested by multi-oimcs analysis of Echiniscus testudo (2019) (0)
Elucidation of the pathogenic mechanisms of chronic pyoderma via skin microbiome analysis (2017) (0)
2P024 Structural analysis of aconitase B and isocitrate dehydrogenase in solution(Proteins-structure and structure-function relationship,Poster Presentations) (2007) (0)
Computational Analysis of X Sequences (1999) (0)
Reproductive toxicology. 9-Aminoacridine hydrochloride. (1997) (0)
Analysis of Amino Acid Substitution Rate in Proteins between Hyperthermophilic and Mesophilic Organisms Using Complete Genome Data (2001) (0)
Sequence similarity network analysis reveals both RNase H domain and reverse transcriptase connection domain on HIV-1 pol protein are important for virus subtype differentiation (2016) (0)
Development of Comparative Genome Analysis System (COMGA) on the G-Language Genome Analysis Environment (2002) (0)
E-CELL Project: Towards Whole Cell Simulation (2001) (0)
Development and Implementation of the G-Language Genome Analysis Environment Version 2 (2002) (0)
MON-PP050: Perioperative Serum and Urine Metabolome Analysis in Patients with Hepatocellular Carcinoma (2015) (0)
Elevated polyamines in saliva of pancreatic cancer 2 (2018) (0)
Cancer metabolomics: Toward the development of novel anticancer therapeutics targeting the energy metabolism in tumor microenvironment (2008) (0)
Elucidation of behavioral significance about mounting behavior through multi-omics analysis of temporary social parasitic ant, Polyrhachis lamellidens (Hymenoptera: Formicidae) (2017) (0)
Corrigendum (2007) (0)
S2I3 E-CELL Project : Towards Whole Cell Simulation (2002) (0)
Pluripotent stem cell models of reticular dysgenesis as a tool for elucidating the potential role of intracellular bioenergetic systems on controlling the fate of hematopoietic progenitors (2015) (0)
Gene Knockout and Metabolome Analysis of SLC22A4 (2010) (0)
Development of Chi Sequence Analysis System on the G-Language Genome Analysis Environment (2002) (0)
Stable mutants of restriction-deficient/modification-proficient Bacillus subtilis 168: Hub strains for giant DNA engineering. (2019) (0)
Correlation Analysis between tRNA Composition and Codon Usage Using Diversity and Equitability Index (2002) (0)
Additional file 2: Table S2. of eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria (2017) (0)
The third plasmid pVV8 from Thermus thermophilus HB8: isolation, characterization, and sequence determination (2012) (0)
E-cell project: towards computer modeling of the whole cell (2000) (0)
Draft Genome Sequences of Bifidobacterium animalis Consecutively Isolated from Healthy Japanese Individuals (2020) (0)
On Base-Pairing Potential Between 16 S rRNA and 5 ’ UTR in Archaebacterial Genomes (2000) (0)
Electronic Cell Environments: Combining Gene, Protein, and Metabolic Networks (2006) (0)
Computer Simulation of the Asymmetric Cell Division in Early Development of C. elegans Embryo Using E-CELL System (2001) (0)

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