Masaru Tomita

Introns and reading frames: correlation between splicing sites and their codon positions.

ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes.

Whole-cell simulation: a grand challenge of the 21st century.

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

Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection.

Identification of the first archaeal Type 1 RNase H gene from Halobacterium sp. NRC-1: archaeal RNase HI can cleave an RNA-DNA junction.

Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes.

Comparative analysis of physical maps of four Bacillus subtilis (natto) genomes.

Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7.

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

Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition.

Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein.

Hybrid dynamic/static method for large-scale simulation of metabolism.

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

A comprehensive software suite for the analysis of cDNAs.

Characteristics and clustering of human ribosomal protein genes.

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

Large-scale identification of protein-protein interaction of Escherichia coli K-12.

Parameter estimation for stiff equations of biosystems using radial basis function networks.

Modeling Hsp70-mediated protein folding.

Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.

A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles.

HybGFS: a hybrid method for genome-fingerprint scanning.

Role of phosphoenolpyruvate in the NADP-isocitrate dehydrogenase and isocitrate lyase reaction in Escherichia coli.

MathDAMP: a package for differential analysis of metabolite profiles.

Visualization of three-way comparisons of omics data.

In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs.

Distinguishing enzymes using metabolome data for the hybrid dynamic/static method.

Restauro-G: a rapid genome re-annotation system for comparative genomics.

Proteome-wide prediction of novel DNA/RNA-binding proteins using amino acid composition and periodicity in the hyperthermophilic archaeon Pyrococcus furiosus.

Indeterminacy of reverse engineering of Gene Regulatory Networks: the curse of gene elasticity.

Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes.

Sequential logic model deciphers dynamic transcriptional control of gene expressions.

Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5' and 3' tRNA halves.

Development of bottom-fermenting saccharomyces strains that produce high SO2 levels, using integrated metabolome and transcriptome analysis.

Junction ribonuclease: a ribonuclease HII orthologue from Thermus thermophilus HB8 prefers the RNA-DNA junction to the RNA/DNA heteroduplex.

GANDivAWeb: a web server for detecting early folding units ("foldons") from protein 3D structures.

Proteins as networks: usefulness of graph theory in protein science.

Variation in the correlation of G + C composition with synonymous codon usage bias among bacteria.

Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis.

Implications from a network-based topological analysis of ubiquitin unfolding simulations.

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

Time-resolved metabolomics reveals metabolic modulation in rice foliage.

Versatile architecture of a bacterial aconitase B and its catalytic performance in the sequential reaction coupled with isocitrate dehydrogenase.

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

Restriction on conjugational transfer of pLS20 in Bacillus subtilis 168.

Design of peptide inhibitors for the importin alpha/beta nuclear import pathway by activity-based profiling.

Nuclear export signal consensus sequences defined using a localization-based yeast selection system.

Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales.

Signaling flux redistribution at toll-like receptor pathway junctions.

Junction ribonuclease activity specified in RNases HII/2.

Six classes of nuclear localization signals specific to different binding grooves of importin alpha.

Simulation of developmental changes in action potentials with ventricular cell models.

The Hsp70 chaperone system maintains high concentrations of active proteins and suppresses ATP consumption during heat shock.

Stabilizing synthetic data in the DNA of living organisms.

GeNESiS: gene network evolution simulation software.

Cooperativity of two active sites in bacterial homodimeric aconitases.

In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution.

Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus.

Genome Projector: zoomable genome map with multiple views.

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

Can complex cellular processes be governed by simple linear rules?

Predicting novel features of toll-like receptor 3 signaling in macrophages.

Emergent genome-wide control in wildtype and genetically mutated lipopolysaccarides-stimulated macrophages.

Degradation of ppGpp by nudix pyrophosphatase modulates the transition of growth phase in the bacterium Thermus thermophilus.

Chemical cleavage-assisted tryptic digestion for membrane proteome analysis.

Metabolite profiling reveals YihU as a novel hydroxybutyrate dehydrogenase for alternative succinic semialdehyde metabolism in Escherichia coli.

Quantitative metabolome profiling of colon and stomach cancer microenvironment by capillary electrophoresis time-of-flight mass spectrometry.

Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes.

The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection.

Identification of DNA-dependent protein kinase as a cofactor for the forkhead transcription factor FoxA2.

Measure of synonymous codon usage diversity among genes in bacteria.

Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs.

Metabolomic profiling of anionic metabolites by capillary electrophoresis mass spectrometry.

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

Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism.

A web server for interactive and zoomable Chaos Game Representation images.

Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants.

Disrupted tRNA gene diversity and possible evolutionary scenarios.

Recharacterization of Chlamydomonas reinhardtii and its relatives with new isolates from Japan.

Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

Correlation between sensory evaluation scores of Japanese sake and metabolome profiles.

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

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

Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index.

Characterization of RNase HII substrate recognition using RNase HII-argonaute chimaeric enzymes from Pyrococcus furiosus.

Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals.

Quantitative proteome and phosphoproteome analyses of cultured cells based on SILAC labeling without requirement of serum dialysis.

A comprehensive resource of interacting protein regions for refining human transcription factor networks.

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

Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles.

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

Unveiling cellular biochemical reactions via metabolomics-driven approaches.

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

G-language genome analysis environment with REST and SOAP web service interfaces.

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

Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants.

Transcription-associated mutagenesis increases protein sequence diversity more effectively than does random mutagenesis in Escherichia coli.

Another origin of coloniality in volvocaleans: the phylogenetic position of Pyrobotrys arnoldi (Spondylomoraceae, Volvocales).

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

Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions.

Metabolomic profiles and sensory attributes of edamame under various storage duration and temperature conditions.

Chemical dephosphorylation for identification of multiply phosphorylated peptides and phosphorylation site determination.

A metabolic model of human erythrocytes: practical application of the E-Cell Simulation Environment.

Collective dynamics of specific gene ensembles crucial for neutrophil differentiation: the existence of genome vehicles revealed.

An extreme thermophile, Thermus thermophilus, is a polyploid bacterium.

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.

Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes.

Integrative features of the yeast phosphoproteome and protein-protein interaction map.

Serum metabolomics reveals γ-glutamyl dipeptides as biomarkers for discrimination among different forms of liver disease.

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

OryzaPG-DB: rice proteome database based on shotgun proteogenomics.

KBWS: an EMBOSS associated package for accessing bioinformatics web services.

Positive autoregulation delays the expression phase of mammalian clock gene Per2.

A screening system for artificial small RNAs that inhibit the growth of Escherichia coli.

Redox regulation in respiring Saccharomyces cerevisiae.

Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes.

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

Metabolic flux analysis and visualization.

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

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

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

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

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

GTP-dependent RNA 3'-terminal phosphate cyclase from the hyperthermophilic archaeon Pyrococcus furiosus.

MMMDB: Mouse Multiple Tissue Metabolome Database.

Metatranscriptomic analysis of microbes in an Oceanfront deep-subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation.

Time-structure of the yeast metabolism in vivo.

Nematode-specific tRNAs that decode an alternative genetic code for leucine.

The third plasmid pVV8 from Thermus thermophilus HB8: isolation, characterization, and sequence determination.

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

Enhancing apoptosis in TRAIL-resistant cancer cells using fundamental response rules.

Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption.

Muscle-specific knock-out of NUAK family SNF1-like kinase 1 (NUAK1) prevents high fat diet-induced glucose intolerance.

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

Validation of bacterial replication termination models using simulation of genomic mutations.

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.

Cancer. Systems biology, metabolomics, and cancer metabolism.

The Rice Proteogenomics Database OryzaPG-DB: Development, Expansion, and New Features.

Mass spectrum sequential subtraction speeds up searching large peptide MS/MS spectra datasets against large nucleotide databases for proteogenomics.

Prediction of axillary lymph node metastasis in primary breast cancer patients using a decision tree-based model.

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

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

Metabolomic profiling rationalized pyruvate efficacy in cybrid cells harboring MELAS mitochondrial DNA mutations.

Measures of compositional strand bias related to replication machinery and its applications.

A yeast metabolite extraction protocol optimised for time-series analyses.

Temporal profiling of lapatinib-suppressed phosphorylation signals in EGFR/HER2 pathways.

Sheathless capillary electrophoresis-mass spectrometry with a high-sensitivity porous sprayer for cationic metabolome analysis.

Metabolic profiling reveals new serum biomarkers for differentiating diabetic nephropathy.

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.

Identification of a replication initiation protein of the pVV8 plasmid from Thermus thermophilus HB8.

Is central dogma a global property of cellular information flow?

A medium-chain fatty acid as an alternative energy source in mouse preimplantation development.

Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks.

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

Computational analysis of associations between alternative splicing and histone modifications.

Merging multiple omics datasets in silico: statistical analyses and data interpretation.

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

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

Metabolomic profiling of the response of susceptible and resistant soybean strains to foxglove aphid, Aulacorthum solani Kaltenbach.

Metabolomic profiling of lung and prostate tumor tissues by capillary electrophoresis time-of-flight mass spectrometry.

Quantitative assay for TALEN activity at endogenous genomic loci.

Time-resolved metabolomics of a novel trebouxiophycean alga using (13)CO2 feeding.

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

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

GEMBASSY: an EMBOSS associated software package for comprehensive genome analyses.

A systems biology approach to suppress TNF-induced proinflammatory gene expressions.

Dynamic simulation and metabolome analysis of long-term erythrocyte storage in adenine-guanosine solution.

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells.

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

Comparative metabolite profiling of foxglove aphids (Aulacorthum solani Kaltenbach) on leaves of resistant and susceptible soybean strains.

Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness.

Undesigned selection for replication termination of bacterial chromosomes.

Quantifying periodicity in omics data.

Transcriptome-wide variability in single embryonic development cells.

Development of quantitative method for determination of γ-glutamyl peptides by capillary electrophoresis tandem mass spectrometry: an efficient approach avoiding matrix effect.

Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo.

Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp).

Systems Biology Strategy Reveals PKCδ is Key for Sensitizing TRAIL-Resistant Human Fibrosarcoma.

Analysis of genetic code ambiguity arising from nematode-specific misacylated tRNAs.

Organization and evolution of brain lipidome revealed by large-scale analysis of human, chimpanzee, macaque, and mouse tissues.

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

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

Method of preparing an equimolar DNA mixture for one-step DNA assembly of over 50 fragments.

Tracking global gene expression responses in T cell differentiation.

Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes.

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

Metabolomic alterations in human cancer cells by vitamin C-induced oxidative stress.

Metabolomic profiling reveals novel biomarkers of alcohol intake and alcohol-induced liver injury in community-dwelling men.

Expansion of Noncanonical V-Arm-Containing tRNAs in Eukaryotes.

Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly.

Phylogenetic Position and Molecular Chronology of a Colonial Green Flagellate, Stephanosphaera pluvialis (Volvocales, Chlorophyceae), among Unicellular Algae.

G-Links: a gene-centric link acquisition service.

Curing the Megaplasmid pTT27 from Thermus thermophilus HB27 and Maintaining Exogenous Plasmids in the Plasmid-Free Strain.

Conversion of graded phosphorylation into switch-like nuclear translocation via autoregulatory mechanisms in ERK signalling.

The Consumption of Bicarbonate-Rich Mineral Water Improves Glycemic Control.

Erratum to: Metabolomic profiling reveals novel biomarkers of alcohol intake and alcohol-induced liver injury in community-dwelling men.

De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions.

Taxonomic revision of oil-producing green algae, Chlorococcum oleofaciens (Volvocales, Chlorophyceae), and its relatives.

Taxonomic revision of Chlamydomonas subg. Amphichloris (Volvocales, Chlorophyceae), with resurrection of the genus Dangeardinia and descriptions of Ixipapillifera gen. nov. and Rhysamphichloris gen. nov.

Profiling of plasma metabolites in postmenopausal women with metabolic syndrome.

Mice carrying a human GLUD2 gene recapitulate aspects of human transcriptome and metabolome development.

Smad2/3 Proteins Are Required for Immobilization-induced Skeletal Muscle Atrophy.

Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria.

Simultaneous analysis of consumer variables, acceptability and sensory characteristics of dry-cured ham.

Serum metabolome profiles characterized by patients with hepatocellular carcinoma associated with hepatitis B and C.

Genome sequencing of a single tardigrade Hypsibius dujardini individual.

Identification of salivary metabolomic biomarkers for oral cancer screening.

Draft Genome Sequence of Arenibacter sp. Strain C-21, an Iodine-Accumulating Bacterium Isolated from Surface Marine Sediment.

Metabolic Profiling of Total Physical Activity and Sedentary Behavior in Community-Dwelling Men.

Morphology and phylogeny of a new wall-less freshwater volvocalean flagellate, Hapalochloris nozakii gen. et sp. nov. (Volvocales, Chlorophyceae).

Metabolomic Profiling as a Possible Reverse Engineering Tool for Estimating Processing Conditions of Dry-Cured Hams.

Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth.

A serum metabolomics-based profile in low bone mineral density postmenopausal women.

Effect of timing of collection of salivary metabolomic biomarkers on oral cancer detection.

Rearing and observation of immature stages of the hoverfly (Diptera, Syrphidae).

Differential Binding of Three Major Human ADAR Isoforms to Coding and Long Non-Coding Transcripts.

Synthetic Biomarker Design by Using Analyte-Responsive Acetaminophen.

Developmental changes in the balance of glycolytic ATP production and oxidative phosphorylation in ventricular cells: A simulation study.

Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis.

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

Serum Metabolomic Profiles for Human Pancreatic Cancer Discrimination.

Thymidine Catabolism as a Metabolic Strategy for Cancer Survival.

Draft Genome Sequence of sp. A-2, an Iodide-Oxidizing Bacterium Isolated from Natural Gas Brine Water, Chiba, Japan.

Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging.

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus.

Effect of masticatory stimulation on the quantity and quality of saliva and the salivary metabolomic profile.

Global metabolic reprogramming of colorectal cancer occurs at adenoma stage and is induced by MYC.

Effects of 3-styrylchromones on metabolic profiles and cell death in oral squamous cell carcinoma cells.

An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus.

eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria.

Evolutionary Analysis of HIV-1 Pol Proteins Reveals Representative Residues for Viral Subtype Differentiation.

Comparative genomic analysis of ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan.

The first high frequency of recombination-like conjugal transfer from an integrated origin of transfer sequence in Bacillus subtilis 168.

Reliability of plasma polar metabolite concentrations in a large-scale cohort study using capillary electrophoresis-mass spectrometry.

Systematic Analysis of the Binding Surfaces between tRNAs and Their Respective Aminoacyl tRNA Synthetase Based on Structural and Evolutionary Data.

Elevated Polyamines in Saliva of Pancreatic Cancer.

Efficient delivery of large DNA from Escherichia coli to Synechococcus elongatus PCC7942 by broad-host-range conjugal plasmid pUB307.

Human AK2 links intracellular bioenergetic redistribution to the fate of hematopoietic progenitors.

Development of a sheathless CE-ESI-MS interface.

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

Thymidine catabolism promotes NADPH oxidase-derived reactive oxygen species (ROS) signalling in KB and yumoto cells.

Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells.

Changes of liver metabolites following hepatectomy with ischemia reperfusion towards liver regeneration.

Far rapid synthesis of giant DNA in the Bacillus subtilis genome by a conjugation transfer system.

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.

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

Metabolomics-based profiles predictive of low bone mass in menopausal women.

High-Quality Overlapping Paired-End Reads for the Detection of A-to-I Editing on Small RNA.