Masaru Tomita

Publications

• High-Quality Overlapping Paired-End Reads for the Detection of A-to-I Editing on Small RNA
  Methods in Molecular Biology (Clifton, N.J.). 2018  |   Pubmed ID: 29959681
• Metabolomics-based Profiles Predictive of Low Bone Mass in Menopausal Women
  Bone Reports. Dec, 2018  |   Pubmed ID: 29955645
• MICOP: Maximal Information Coefficient-based Oscillation Prediction to Detect Biological Rhythms in Proteomics Data
  BMC Bioinformatics. Jun, 2018  |   Pubmed ID: 29954316
• 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
  RNA Biology. Jun, 2018  |   Pubmed ID: 29950133
• Far Rapid Synthesis of Giant DNA in the Bacillus Subtilis Genome by a Conjugation Transfer System
  Scientific Reports. Jun, 2018  |   Pubmed ID: 29884789
• Changes of Liver Metabolites Following Hepatectomy with Ischemia Reperfusion Towards Liver Regeneration
  Annals of Gastroenterological Surgery. May, 2018  |   Pubmed ID: 29863192
• Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells
  ACS Synthetic Biology. Jun, 2018  |   Pubmed ID: 29786424
• Thymidine Catabolism Promotes NADPH Oxidase-derived Reactive Oxygen Species (ROS) Signalling in KB and Yumoto Cells
  Scientific Reports. Apr, 2018  |   Pubmed ID: 29713062
• Urinary Polyamine Biomarker Panels with Machine-Learning Differentiated Colorectal Cancers, Benign Disease, and Healthy Controls
  International Journal of Molecular Sciences. Mar, 2018  |   Pubmed ID: 29518931
• Development of a Sheathless CE-ESI-MS Interface
  Electrophoresis. Jun, 2018  |   Pubmed ID: 29493797
• Human AK2 Links Intracellular Bioenergetic Redistribution to the Fate of Hematopoietic Progenitors
  Biochemical and Biophysical Research Communications. 03, 2018  |   Pubmed ID: 29462620
• Efficient Delivery of Large DNA from Escherichia Coli to Synechococcus Elongatus PCC7942 by Broad-host-range Conjugal Plasmid PUB307
  Journal of Biochemistry. Jul, 2018  |   Pubmed ID: 29420737
• Elevated Polyamines in Saliva of Pancreatic Cancer
  Cancers. Feb, 2018  |   Pubmed ID: 29401744
• Reliability of Plasma Polar Metabolite Concentrations in a Large-scale Cohort Study Using Capillary Electrophoresis-mass Spectrometry
  PloS One. 2018  |   Pubmed ID: 29346414
• The First High Frequency of Recombination-like Conjugal Transfer from an Integrated Origin of Transfer Sequence in Bacillus Subtilis 168
  Bioscience, Biotechnology, and Biochemistry. Feb, 2018  |   Pubmed ID: 29316866
• Systematic Analysis of the Binding Surfaces Between TRNAs and Their Respective Aminoacyl TRNA Synthetase Based on Structural and Evolutionary Data
  Frontiers in Genetics. 2017  |   Pubmed ID: 29358943
• Comparative Genomic Analysis of Ribotype 027 Strains Including the Newly Sequenced Strain NCKUH-21 Isolated from a Patient in Taiwan
  Gut Pathogens. 2017  |   Pubmed ID: 29213333
• Evolutionary Analysis of HIV-1 Pol Proteins Reveals Representative Residues for Viral Subtype Differentiation
  Frontiers in Microbiology. 2017  |   Pubmed ID: 29163435
• ERP Arrangement: a Strategy for Assembled Genomic Contig Rearrangement Based on Replication Profiling in Bacteria
  BMC Genomics. Oct, 2017  |   Pubmed ID: 29029602
• An Archaeal RNA Binding Protein, FAU-1, is a Novel Ribonuclease Related to RRNA Stability in Pyrococcus and Thermococcus
  Scientific Reports. Oct, 2017  |   Pubmed ID: 28978920
• Global Metabolic Reprogramming of Colorectal Cancer Occurs at Adenoma Stage and is Induced by MYC
  Proceedings of the National Academy of Sciences of the United States of America. 09, 2017  |   Pubmed ID: 28847964
• Effect of Masticatory Stimulation on the Quantity and Quality of Saliva and the Salivary Metabolomic Profile
  PloS One. 2017  |   Pubmed ID: 28813487
• Comparative Genomics of the Tardigrades Hypsibius Dujardini and Ramazzottius Varieornatus
  PLoS Biology. Jul, 2017  |   Pubmed ID: 28749982
• Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging
  Molecular Cell. Jul, 2017  |   Pubmed ID: 28712725
• Draft Genome Sequence of Sp. A-2, an Iodide-Oxidizing Bacterium Isolated from Natural Gas Brine Water, Chiba, Japan
  Journal of Genomics. 2017  |   Pubmed ID: 28529651
• Thymidine Catabolism As a Metabolic Strategy for Cancer Survival
  Cell Reports. 05, 2017  |   Pubmed ID: 28514652
• Serum Metabolomic Profiles for Human Pancreatic Cancer Discrimination
  International Journal of Molecular Sciences. Apr, 2017  |   Pubmed ID: 28375170
• Eggshell Membrane Powder Ameliorates Intestinal Inflammation by Facilitating the Restitution of Epithelial Injury and Alleviating Microbial Dysbiosis
  Scientific Reports. Mar, 2017  |   Pubmed ID: 28272447
• Developmental Changes in the Balance of Glycolytic ATP Production and Oxidative Phosphorylation in Ventricular Cells: A Simulation Study
  Journal of Theoretical Biology. Apr, 2017  |   Pubmed ID: 28237394
• Synthetic Biomarker Design by Using Analyte-Responsive Acetaminophen
  Chembiochem : a European Journal of Chemical Biology. 05, 2017  |   Pubmed ID: 28236354
• Differential Binding of Three Major Human ADAR Isoforms to Coding and Long Non-Coding Transcripts
  Genes. Feb, 2017  |   Pubmed ID: 28208661
• Effect of Timing of Collection of Salivary Metabolomic Biomarkers on Oral Cancer Detection
  Amino Acids. 04, 2017  |   Pubmed ID: 28101653
• A Serum Metabolomics-based Profile in Low Bone Mineral Density Postmenopausal Women
  Bone. 02, 2017  |   Pubmed ID: 27989648
• Systematic Characterization of Artificial Small RNA-mediated Inhibition of Escherichia Coli Growth
  RNA Biology. 02, 2017  |   Pubmed ID: 27981881
• Metabolomic Profiling As a Possible Reverse Engineering Tool for Estimating Processing Conditions of Dry-Cured Hams
  Journal of Agricultural and Food Chemistry. Jan, 2017  |   Pubmed ID: 27951640
• Morphology and Phylogeny of a New Wall-less Freshwater Volvocalean Flagellate, Hapalochloris Nozakii Gen. Et Sp. Nov. (Volvocales, Chlorophyceae)
  Journal of Phycology. Feb, 2017  |   Pubmed ID: 27767210
• Rearing and Observation of Immature Stages of the Hoverfly (Diptera, Syrphidae)
  Biodiversity Data Journal. 2016  |   Pubmed ID: 28174503
• Metabolic Profiling of Total Physical Activity and Sedentary Behavior in Community-Dwelling Men
  PloS One. 2016  |   Pubmed ID: 27741291
• Draft Genome Sequence of Arenibacter Sp. Strain C-21, an Iodine-Accumulating Bacterium Isolated from Surface Marine Sediment
  Genome Announcements. Oct, 2016  |   Pubmed ID: 27738047
• Identification of Salivary Metabolomic Biomarkers for Oral Cancer Screening
  Scientific Reports. 08, 2016  |   Pubmed ID: 27539254
• Genome Sequencing of a Single Tardigrade Hypsibius Dujardini Individual
  Scientific Data. 08, 2016  |   Pubmed ID: 27529330
• Serum Metabolome Profiles Characterized by Patients with Hepatocellular Carcinoma Associated with Hepatitis B and C
  World Journal of Gastroenterology. Jul, 2016  |   Pubmed ID: 27468212
• Simultaneous Analysis of Consumer Variables, Acceptability and Sensory Characteristics of Dry-cured Ham
  Meat Science. Nov, 2016  |   Pubmed ID: 27343459
• Draft Genome Sequences of 37 Salmonella Enterica Strains Isolated from Poultry Sources in Nigeria
  Genome Announcements. May, 2016  |   Pubmed ID: 27151793
• Smad2/3 Proteins Are Required for Immobilization-induced Skeletal Muscle Atrophy
  The Journal of Biological Chemistry. Jun, 2016  |   Pubmed ID: 27129272
• Mice Carrying a Human GLUD2 Gene Recapitulate Aspects of Human Transcriptome and Metabolome Development
  Proceedings of the National Academy of Sciences of the United States of America. May, 2016  |   Pubmed ID: 27118840
• Profiling of Plasma Metabolites in Postmenopausal Women with Metabolic Syndrome
  Menopause (New York, N.Y.). 07, 2016  |   Pubmed ID: 27070805
• Taxonomic Revision of Chlamydomonas Subg. Amphichloris (Volvocales, Chlorophyceae), with Resurrection of the Genus Dangeardinia and Descriptions of Ixipapillifera Gen. Nov. and Rhysamphichloris Gen. Nov
  Journal of Phycology. Apr, 2016  |   Pubmed ID: 27037593
• De Novo Assembly and Comparative Transcriptome Analysis of Euglena Gracilis in Response to Anaerobic Conditions
  BMC Genomics. Mar, 2016  |   Pubmed ID: 26939900
• Erratum To: Metabolomic Profiling Reveals Novel Biomarkers of Alcohol Intake and Alcohol-induced Liver Injury in Community-dwelling Men
  Environmental Health and Preventive Medicine. Jul, 2016  |   Pubmed ID: 26898210
• Conversion of Graded Phosphorylation into Switch-like Nuclear Translocation Via Autoregulatory Mechanisms in ERK Signalling
  Nature Communications. Jan, 2016  |   Pubmed ID: 26786866
• Phylogenetic Position and Molecular Chronology of a Colonial Green Flagellate, Stephanosphaera Pluvialis (Volvocales, Chlorophyceae), Among Unicellular Algae
  The Journal of Eukaryotic Microbiology. 05, 2016  |   Pubmed ID: 26595722
• Evaluation of the Impact of RNA Preservation Methods of Spiders for De Novo Transcriptome Assembly
  Molecular Ecology Resources. May, 2016  |   Pubmed ID: 26561354
• Expansion of Noncanonical V-Arm-Containing TRNAs in Eukaryotes
  Molecular Biology and Evolution. Feb, 2016  |   Pubmed ID: 26545920
• Metabolomic Profiling Reveals Novel Biomarkers of Alcohol Intake and Alcohol-induced Liver Injury in Community-dwelling Men
  Environmental Health and Preventive Medicine. Jan, 2016  |   Pubmed ID: 26459263
• Effects of 3-styrylchromones on Metabolic Profiles and Cell Death in Oral Squamous Cell Carcinoma Cells
  Toxicology Reports. 2015  |   Pubmed ID: 28962471
• Taxonomic Revision of Oil-producing Green Algae, Chlorococcum Oleofaciens (Volvocales, Chlorophyceae), and Its Relatives
  Journal of Phycology. Oct, 2015  |   Pubmed ID: 26986894
• The Consumption of Bicarbonate-Rich Mineral Water Improves Glycemic Control
  Evidence-based Complementary and Alternative Medicine : ECAM. 2015  |   Pubmed ID: 26798400
• Curing the Megaplasmid PTT27 from Thermus Thermophilus HB27 and Maintaining Exogenous Plasmids in the Plasmid-Free Strain
  Applied and Environmental Microbiology. Dec, 2015  |   Pubmed ID: 26712540
• Metabolomic Alterations in Human Cancer Cells by Vitamin C-induced Oxidative Stress
  Scientific Reports. Sep, 2015  |   Pubmed ID: 26350063
• Precise Mapping and Dynamics of TRNA-derived Fragments (tRFs) in the Development of Triops Cancriformis (tadpole Shrimp)
  BMC Genetics. Jul, 2015  |   Pubmed ID: 26168920
• Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes
  PLoS Computational Biology. Jun, 2015  |   Pubmed ID: 26046580
• Tracking Global Gene Expression Responses in T Cell Differentiation
  Gene. Sep, 2015  |   Pubmed ID: 26028587
• Method of Preparing an Equimolar DNA Mixture for One-step DNA Assembly of over 50 Fragments
  Scientific Reports. May, 2015  |   Pubmed ID: 25990947
• Alteration of Metabolomic Profiles by Titanium Dioxide Nanoparticles in Human Gingivitis Model
  Biomaterials. Jul, 2015  |   Pubmed ID: 25913073
• Effects of Processing and Storage Conditions on Charged Metabolomic Profiles in Blood
  Electrophoresis. Sep, 2015  |   Pubmed ID: 25820922
• Organization and Evolution of Brain Lipidome Revealed by Large-scale Analysis of Human, Chimpanzee, Macaque, and Mouse Tissues
  Neuron. Feb, 2015  |   Pubmed ID: 25661180
• Analysis of Genetic Code Ambiguity Arising from Nematode-specific Misacylated TRNAs
  PloS One. 2015  |   Pubmed ID: 25602944
• Identification, Expression, and Molecular Evolution of MicroRNAs in the "living Fossil" Triops Cancriformis (tadpole Shrimp)
  RNA (New York, N.Y.). Feb, 2015  |   Pubmed ID: 25525151
• Time Resolved DNA Occupancy Dynamics During the Respiratory Oscillation Uncover a Global Reset Point in the Yeast Growth Program
  Microbial Cell (Graz, Austria). Sep, 2014  |   Pubmed ID: 28357254
• G-Links: a Gene-centric Link Acquisition Service
  F1000Research. 2014  |   Pubmed ID: 26673001
• Systems Biology Strategy Reveals PKCδ is Key for Sensitizing TRAIL-Resistant Human Fibrosarcoma
  Frontiers in Immunology. 2014  |   Pubmed ID: 25601862
• Effect of Codon Adaptation on Codon-level and Gene-level Translation Efficiency in Vivo
  BMC Genomics. Dec, 2014  |   Pubmed ID: 25512115
• Development of Quantitative Method for Determination of γ-glutamyl Peptides by Capillary Electrophoresis Tandem Mass Spectrometry: an Efficient Approach Avoiding Matrix Effect
  Journal of Chromatography. A. Nov, 2014  |   Pubmed ID: 25441083
• Transcriptome-wide Variability in Single Embryonic Development Cells
  Scientific Reports. Nov, 2014  |   Pubmed ID: 25409746
• Quantifying Periodicity in Omics Data
  Frontiers in Cell and Developmental Biology. 2014  |   Pubmed ID: 25364747
• Undesigned Selection for Replication Termination of Bacterial Chromosomes
  Journal of Molecular Biology. Aug, 2014  |   Pubmed ID: 24946150
• Exceptional Evolutionary Divergence of Human Muscle and Brain Metabolomes Parallels Human Cognitive and Physical Uniqueness
  PLoS Biology. May, 2014  |   Pubmed ID: 24866127
• Comparative Metabolite Profiling of Foxglove Aphids (Aulacorthum Solani Kaltenbach) on Leaves of Resistant and Susceptible Soybean Strains
  Molecular BioSystems. Apr, 2014  |   Pubmed ID: 24514152
• Global Metabolic Network Reorganization by Adaptive Mutations Allows Fast Growth of Escherichia Coli on Glycerol
  Nature Communications. 2014  |   Pubmed ID: 24481126
• Commensal Microbe-derived Butyrate Induces the Differentiation of Colonic Regulatory T Cells
  Nature. Dec, 2013  |   Pubmed ID: 24226770
• Dynamic Simulation and Metabolome Analysis of Long-term Erythrocyte Storage in Adenine-guanosine Solution
  PloS One. 2013  |   Pubmed ID: 24205395
• A Systems Biology Approach to Suppress TNF-induced Proinflammatory Gene Expressions
  Cell Communication and Signaling : CCS. Nov, 2013  |   Pubmed ID: 24199619
• GEMBASSY: an EMBOSS Associated Software Package for Comprehensive Genome Analyses
  Source Code for Biology and Medicine. Aug, 2013  |   Pubmed ID: 23987304
• Capillary Electrophoresis-mass Spectrometry-based Metabolome Analysis of Serum and Saliva from Neurodegenerative Dementia Patients
  Electrophoresis. Oct, 2013  |   Pubmed ID: 23857558
• Contribution of Quantitative Changes in Individual Ionic Current Systems to the Embryonic Development of Ventricular Myocytes: a Simulation Study
  The Journal of Physiological Sciences : JPS. Sep, 2013  |   Pubmed ID: 23760774
• Time-resolved Metabolomics of a Novel Trebouxiophycean Alga Using (13)CO2 Feeding
  Journal of Bioscience and Bioengineering. Sep, 2013  |   Pubmed ID: 23706992
• Quantitative Assay for TALEN Activity at Endogenous Genomic Loci
  Biology Open. Apr, 2013  |   Pubmed ID: 23616919
• Metabolomic Profiling of Lung and Prostate Tumor Tissues by Capillary Electrophoresis Time-of-flight Mass Spectrometry
  Metabolomics : Official Journal of the Metabolomic Society. Apr, 2013  |   Pubmed ID: 23543897
• Metabolomic Profiling of the Response of Susceptible and Resistant Soybean Strains to Foxglove Aphid, Aulacorthum Solani Kaltenbach
  Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences. Apr, 2013  |   Pubmed ID: 23523883
• Metabolic and Morphological Changes of an Oil Accumulating Trebouxiophycean Alga in Nitrogen-deficient Conditions
  Metabolomics : Official Journal of the Metabolomic Society. Mar, 2013  |   Pubmed ID: 23463323
• Global MicroRNA Elevation by Inducible Exportin 5 Regulates Cell Cycle Entry
  RNA (New York, N.Y.). Apr, 2013  |   Pubmed ID: 23431327
• Merging Multiple Omics Datasets in Silico: Statistical Analyses and Data Interpretation
  Methods in Molecular Biology (Clifton, N.J.). 2013  |   Pubmed ID: 23417818
• Computational Analysis of Associations Between Alternative Splicing and Histone Modifications
  FEBS Letters. Mar, 2013  |   Pubmed ID: 23353998
• Metabolomic Study of Chilean Biomining Bacteria Acidithiobacillus Ferrooxidans Strain Wenelen and Acidithiobacillus Thiooxidans Strain Licanantay
  Metabolomics : Official Journal of the Metabolomic Society. Feb, 2013  |   Pubmed ID: 23335869
• Comprehensive Computational Analysis of Bacterial CRP/FNR Superfamily and Its Target Motifs Reveals Stepwise Evolution of Transcriptional Networks
  Genome Biology and Evolution. 2013  |   Pubmed ID: 23315382
• Identification of a Replication Initiation Protein of the PVV8 Plasmid from Thermus Thermophilus HB8
  Extremophiles : Life Under Extreme Conditions. Jan, 2013  |   Pubmed ID: 23114983
• A Medium-chain Fatty Acid As an Alternative Energy Source in Mouse Preimplantation Development
  Scientific Reports. 2012  |   Pubmed ID: 23226596
• Is Central Dogma a Global Property of Cellular Information Flow?
  Frontiers in Physiology. 2012  |   Pubmed ID: 23189060
• 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
  Journal of Biochemistry. Dec, 2012  |   Pubmed ID: 23055537
• Metabolic Profiling Reveals New Serum Biomarkers for Differentiating Diabetic Nephropathy
  Analytical and Bioanalytical Chemistry. Dec, 2012  |   Pubmed ID: 23052862
• Sheathless Capillary Electrophoresis-mass Spectrometry with a High-sensitivity Porous Sprayer for Cationic Metabolome Analysis
  The Analyst. Nov, 2012  |   Pubmed ID: 23000847
• Temporal Profiling of Lapatinib-suppressed Phosphorylation Signals in EGFR/HER2 Pathways
  Molecular & Cellular Proteomics : MCP. Dec, 2012  |   Pubmed ID: 22964224
• A Yeast Metabolite Extraction Protocol Optimised for Time-series Analyses
  PloS One. 2012  |   Pubmed ID: 22952947
• Measures of Compositional Strand Bias Related to Replication Machinery and Its Applications
  Current Genomics. Mar, 2012  |   Pubmed ID: 22942671
• Metabolomic Profiling Rationalized Pyruvate Efficacy in Cybrid Cells Harboring MELAS Mitochondrial DNA Mutations
  Mitochondrion. Nov, 2012  |   Pubmed ID: 22884939
• Metabolic Regulation Analysis of Wild-type and ArcA Mutant Escherichia Coli Under Nitrate Conditions Using Different Levels of Omics Data
  Molecular BioSystems. Oct, 2012  |   Pubmed ID: 22790675
• Rapid DNA, RNA and Protein Extraction Protocols Optimized for Slow Continuously Growing Yeast Cultures
  Yeast (Chichester, England). Aug, 2012  |   Pubmed ID: 22763810
• Prediction of Axillary Lymph Node Metastasis in Primary Breast Cancer Patients Using a Decision Tree-based Model
  BMC Medical Informatics and Decision Making. Jun, 2012  |   Pubmed ID: 22695278
• Mass Spectrum Sequential Subtraction Speeds Up Searching Large Peptide MS/MS Spectra Datasets Against Large Nucleotide Databases for Proteogenomics
  Genes to Cells : Devoted to Molecular & Cellular Mechanisms. Aug, 2012  |   Pubmed ID: 22686349
• The Rice Proteogenomics Database OryzaPG-DB: Development, Expansion, and New Features
  Frontiers in Plant Science. 2012  |   Pubmed ID: 22639657
• Cancer. Systems Biology, Metabolomics, and Cancer Metabolism
  Science (New York, N.Y.). May, 2012  |   Pubmed ID: 22628644
• 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
  Biotechnology Journal. Jul, 2012  |   Pubmed ID: 22553167
• Validation of Bacterial Replication Termination Models Using Simulation of Genomic Mutations
  PloS One. 2012  |   Pubmed ID: 22509315
• Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis
  Current Bioinformatics. Mar, 2012  |   Pubmed ID: 22438836
• Muscle-specific Knock-out of NUAK Family SNF1-like Kinase 1 (NUAK1) Prevents High Fat Diet-induced Glucose Intolerance
  The Journal of Biological Chemistry. May, 2012  |   Pubmed ID: 22418434
• Genomic Heterogeneity in a Natural Archaeal Population Suggests a Model of TRNA Gene Disruption
  PloS One. 2012  |   Pubmed ID: 22403667
• Changes in the Charged Metabolite and Sugar Profiles of Pasteurized and Unpasteurized Japanese Sake with Storage
  Journal of Agricultural and Food Chemistry. Mar, 2012  |   Pubmed ID: 22352923
• The Third Plasmid PVV8 from Thermus Thermophilus HB8: Isolation, Characterization, and Sequence Determination
  Extremophiles : Life Under Extreme Conditions. Mar, 2012  |   Pubmed ID: 22212656
• Nematode-specific TRNAs That Decode an Alternative Genetic Code for Leucine
  Nucleic Acids Research. Apr, 2012  |   Pubmed ID: 22187151
• Time-structure of the Yeast Metabolism in Vivo
  Advances in Experimental Medicine and Biology. 2012  |   Pubmed ID: 22161340
• Metatranscriptomic Analysis of Microbes in an Oceanfront Deep-subsurface Hot Spring Reveals Novel Small RNAs and Type-specific TRNA Degradation
  Applied and Environmental Microbiology. Feb, 2012  |   Pubmed ID: 22156430
• MMMDB: Mouse Multiple Tissue Metabolome Database
  Nucleic Acids Research. Jan, 2012  |   Pubmed ID: 22139941
• Enhancing Apoptosis in TRAIL-resistant Cancer Cells Using Fundamental Response Rules
  Scientific Reports. 2011  |   Pubmed ID: 22355661
• GTP-dependent RNA 3'-terminal Phosphate Cyclase from the Hyperthermophilic Archaeon Pyrococcus Furiosus
  Genes to Cells : Devoted to Molecular & Cellular Mechanisms. Dec, 2011  |   Pubmed ID: 22074260
• Predicting the Kinetic Properties Associated with Redox Imbalance After Oxidative Crisis in G6PD-Deficient Erythrocytes: A Simulation Study
  Advances in Hematology. 2011  |   Pubmed ID: 21977034
• Microscale Phosphoproteome Analysis of 10,000 Cells from Human Cancer Cell Lines
  Analytical Chemistry. Oct, 2011  |   Pubmed ID: 21888424
• A Novel Three-unit TRNA Splicing Endonuclease Found in Ultrasmall Archaea Possesses Broad Substrate Specificity
  Nucleic Acids Research. Dec, 2011  |   Pubmed ID: 21880595
• Deep Sequencing Reveals As-yet-undiscovered Small RNAs in Escherichia Coli
  BMC Genomics. Aug, 2011  |   Pubmed ID: 21864382
• Tight Associations Between Transcription Promoter Type and Epigenetic Variation in Histone Positioning and Modification
  BMC Genomics. 2011  |   Pubmed ID: 21846408
• Metabolic Flux Analysis and Visualization
  Journal of Proteome Research. Aug, 2011  |   Pubmed ID: 21815690
• Computational Assessment of Insulin Secretion and Insulin Sensitivity from 2-h Oral Glucose Tolerance Tests for Clinical Use for Type 2 Diabetes
  The Journal of Physiological Sciences : JPS. Jul, 2011  |   Pubmed ID: 21594678
• Comprehensive Expressional Analyses of Antisense Transcripts in Colon Cancer Tissues Using Artificial Antisense Probes
  BMC Medical Genomics. May, 2011  |   Pubmed ID: 21575255
• Redox Regulation in Respiring Saccharomyces Cerevisiae
  Biochimica Et Biophysica Acta. Oct, 2011  |   Pubmed ID: 21549177
• A Screening System for Artificial Small RNAs That Inhibit the Growth of Escherichia Coli
  Journal of Biochemistry. Sep, 2011  |   Pubmed ID: 21546360
• Positive Autoregulation Delays the Expression Phase of Mammalian Clock Gene Per2
  PloS One. Apr, 2011  |   Pubmed ID: 21533189
• KBWS: an EMBOSS Associated Package for Accessing Bioinformatics Web Services
  Source Code for Biology and Medicine. Apr, 2011  |   Pubmed ID: 21529350
• OryzaPG-DB: Rice Proteome Database Based on Shotgun Proteogenomics
  BMC Plant Biology. Apr, 2011  |   Pubmed ID: 21486466
• Computational Analysis Suggests a Highly Bendable, Fragile Structure for Nucleosomal DNA
  Gene. May, 2011  |   Pubmed ID: 21338662
• Serum Metabolomics Reveals γ-glutamyl Dipeptides As Biomarkers for Discrimination Among Different Forms of Liver Disease
  Journal of Hepatology. Oct, 2011  |   Pubmed ID: 21334394
• Integrative Features of the Yeast Phosphoproteome and Protein-protein Interaction Map
  PLoS Computational Biology. 2011  |   Pubmed ID: 21298081
• Comprehensive Prediction of Chromosome Dimer Resolution Sites in Bacterial Genomes
  BMC Genomics. Jan, 2011  |   Pubmed ID: 21223577
• 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
  Biotechnology Progress. Jul-Aug, 2010  |   Pubmed ID: 20730757
• An Extreme Thermophile, Thermus Thermophilus, is a Polyploid Bacterium
  Journal of Bacteriology. Oct, 2010  |   Pubmed ID: 20729360
• Collective Dynamics of Specific Gene Ensembles Crucial for Neutrophil Differentiation: the Existence of Genome Vehicles Revealed
  PloS One. Aug, 2010  |   Pubmed ID: 20725638
• A Metabolic Model of Human Erythrocytes: Practical Application of the E-Cell Simulation Environment
  Journal of Biomedicine & Biotechnology. 2010  |   Pubmed ID: 20625505
• Chemical Dephosphorylation for Identification of Multiply Phosphorylated Peptides and Phosphorylation Site Determination
  Rapid Communications in Mass Spectrometry : RCM. Aug, 2010  |   Pubmed ID: 20623713
• Metabolomic Profiles and Sensory Attributes of Edamame Under Various Storage Duration and Temperature Conditions
  Journal of Agricultural and Food Chemistry. Jul, 2010  |   Pubmed ID: 20593783
• Protein Complex Prediction Via Verifying and Reconstructing the Topology of Domain-domain Interactions
  BMC Bioinformatics. Jun, 2010  |   Pubmed ID: 20584269
• Prediction of Metabolite Identity from Accurate Mass, Migration Time Prediction and Isotopic Pattern Information in CE-TOFMS Data
  Electrophoresis. Jul, 2010  |   Pubmed ID: 20568260
• Another Origin of Coloniality in Volvocaleans: the Phylogenetic Position of Pyrobotrys Arnoldi (Spondylomoraceae, Volvocales)
  The Journal of Eukaryotic Microbiology. Jul-Aug, 2010  |   Pubmed ID: 20553352
• Transcription-associated Mutagenesis Increases Protein Sequence Diversity More Effectively Than Does Random Mutagenesis in Escherichia Coli
  PloS One. May, 2010  |   Pubmed ID: 20479947
• Large-scale Comparative Phosphoproteomics Identifies Conserved Phosphorylation Sites in Plants
  Plant Physiology. Jul, 2010  |   Pubmed ID: 20466843
• Towards the Systematic Discovery of Signal Transduction Networks Using Phosphorylation Dynamics Data
  BMC Bioinformatics. 2010  |   Pubmed ID: 20459641
• G-language Genome Analysis Environment with REST and SOAP Web Service Interfaces
  Nucleic Acids Research. Jul, 2010  |   Pubmed ID: 20439313
• Large-scale TRNA Intron Transposition in the Archaeal Order Thermoproteales Represents a Novel Mechanism of Intron Gain
  Molecular Biology and Evolution. Oct, 2010  |   Pubmed ID: 20430862
• Unveiling Cellular Biochemical Reactions Via Metabolomics-driven Approaches
  Current Opinion in Microbiology. Jun, 2010  |   Pubmed ID: 20430690
• Core Promoter Structure and Genomic Context Reflect Histone 3 Lysine 9 Acetylation Patterns
  BMC Genomics. Apr, 2010  |   Pubmed ID: 20409305
• Capillary Electrophoresis Mass Spectrometry-based Saliva Metabolomics Identified Oral, Breast and Pancreatic Cancer-specific Profiles
  Metabolomics : Official Journal of the Metabolomic Society. Mar, 2010  |   Pubmed ID: 20300169
• Computational Prediction of Nucleosome Positioning by Calculating the Relative Fragment Frequency Index of Nucleosomal Sequences
  FEBS Letters. Apr, 2010  |   Pubmed ID: 20206172
• A Comprehensive Resource of Interacting Protein Regions for Refining Human Transcription Factor Networks
  PloS One. Feb, 2010  |   Pubmed ID: 20195357
• Quantitative Proteome and Phosphoproteome Analyses of Cultured Cells Based on SILAC Labeling Without Requirement of Serum Dialysis
  Molecular BioSystems. Mar, 2010  |   Pubmed ID: 20174688
• Computational Prediction and Experimental Validation of Evolutionarily Conserved MicroRNA Target Genes in Bilaterian Animals
  BMC Genomics. Feb, 2010  |   Pubmed ID: 20144220
• Characterization of RNase HII Substrate Recognition Using RNase HII-argonaute Chimaeric Enzymes from Pyrococcus Furiosus
  The Biochemical Journal. Feb, 2010  |   Pubmed ID: 20047562
• A New Multicompartmental Reaction-diffusion Modeling Method Links Transient Membrane Attachment of E. Coli MinE to E-ring Formation
  Systems and Synthetic Biology. Mar, 2010  |   Pubmed ID: 20012222
• Correlation Between Sensory Evaluation Scores of Japanese Sake and Metabolome Profiles
  Journal of Agricultural and Food Chemistry. Jan, 2010  |   Pubmed ID: 19961224
• Recharacterization of Chlamydomonas Reinhardtii and Its Relatives with New Isolates from Japan
  Journal of Plant Research. Jan, 2010  |   Pubmed ID: 19882207
• Quantitative Analysis of Replication-related Mutation and Selection Pressures in Bacterial Chromosomes and Plasmids Using Generalised GC Skew Index
  BMC Genomics. Dec, 2009  |   Pubmed ID: 20042086
• Update on the Keio Collection of Escherichia Coli Single-gene Deletion Mutants
  Molecular Systems Biology. 2009  |   Pubmed ID: 20029369
• Pathway Projector: Web-based Zoomable Pathway Browser Using KEGG Atlas and Google Maps API
  PloS One. Nov, 2009  |   Pubmed ID: 19907644
• Disrupted TRNA Gene Diversity and Possible Evolutionary Scenarios
  Journal of Molecular Evolution. Nov, 2009  |   Pubmed ID: 19826747
• Unbiased Quantitation of Escherichia Coli Membrane Proteome Using Phase Transfer Surfactants
  Molecular & Cellular Proteomics : MCP. Dec, 2009  |   Pubmed ID: 19767571
• A Web Server for Interactive and Zoomable Chaos Game Representation Images
  Source Code for Biology and Medicine. Sep, 2009  |   Pubmed ID: 19761591
• Systematic Phenome Analysis of Escherichia Coli Multiple-knockout Mutants Reveals Hidden Reactions in Central Carbon Metabolism
  Molecular Systems Biology. 2009  |   Pubmed ID: 19756045
• In Silico Modeling and Metabolome Analysis of Long-stored Erythrocytes to Improve Blood Storage Methods
  Journal of Biotechnology. Nov, 2009  |   Pubmed ID: 19695295
• [Not Available]
  Frontiers in Neuroinformatics. 2009  |   Pubmed ID: 19543432
• Metabolomic Profiling of Anionic Metabolites by Capillary Electrophoresis Mass Spectrometry
  Analytical Chemistry. Aug, 2009  |   Pubmed ID: 19522513
• 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. Jun, 2009  |   Pubmed ID: 19520826
• Measure of Synonymous Codon Usage Diversity Among Genes in Bacteria
  BMC Bioinformatics. Jun, 2009  |   Pubmed ID: 19480720
• Identification of DNA-dependent Protein Kinase As a Cofactor for the Forkhead Transcription Factor FoxA2
  The Journal of Biological Chemistry. Jul, 2009  |   Pubmed ID: 19478084
• Quantitative Metabolome Profiling of Colon and Stomach Cancer Microenvironment by Capillary Electrophoresis Time-of-flight Mass Spectrometry
  Cancer Research. Jun, 2009  |   Pubmed ID: 19458066
• Metabolite Profiling Reveals YihU As a Novel Hydroxybutyrate Dehydrogenase for Alternative Succinic Semialdehyde Metabolism in Escherichia Coli
  The Journal of Biological Chemistry. Jun, 2009  |   Pubmed ID: 19372223
• Chemical Cleavage-assisted Tryptic Digestion for Membrane Proteome Analysis
  Journal of Proteome Research. Jun, 2009  |   Pubmed ID: 19348461
• Degradation of PpGpp by Nudix Pyrophosphatase Modulates the Transition of Growth Phase in the Bacterium Thermus Thermophilus
  The Journal of Biological Chemistry. Jun, 2009  |   Pubmed ID: 19346251
• Emergent Genome-wide Control in Wildtype and Genetically Mutated Lipopolysaccarides-stimulated Macrophages
  PloS One. 2009  |   Pubmed ID: 19300509
• Predicting Novel Features of Toll-like Receptor 3 Signaling in Macrophages
  PloS One. 2009  |   Pubmed ID: 19252739
• Can Complex Cellular Processes Be Governed by Simple Linear Rules?
  Journal of Bioinformatics and Computational Biology. Feb, 2009  |   Pubmed ID: 19226669
• Tri-split TRNA is a Transfer RNA Made from 3 Transcripts That Provides Insight into the Evolution of Fragmented TRNAs in Archaea
  Proceedings of the National Academy of Sciences of the United States of America. Feb, 2009  |   Pubmed ID: 19190180
• Genome Projector: Zoomable Genome Map with Multiple Views
  BMC Bioinformatics. Jan, 2009  |   Pubmed ID: 19166610
• Characterization of a Heat-stable Enzyme Possessing GTP-dependent RNA Ligase Activity from a Hyperthermophilic Archaeon, Pyrococcus Furiosus
  RNA (New York, N.Y.). Mar, 2009  |   Pubmed ID: 19155324
• In Silico Analysis of Phosphoproteome Data Suggests a Rich-get-richer Process of Phosphosite Accumulation over Evolution
  Molecular & Cellular Proteomics : MCP. May, 2009  |   Pubmed ID: 19136663
• Cooperativity of Two Active Sites in Bacterial Homodimeric Aconitases
  Biochemical and Biophysical Research Communications. Feb, 2009  |   Pubmed ID: 19116142
• Six Classes of Nuclear Localization Signals Specific to Different Binding Grooves of Importin Alpha
  The Journal of Biological Chemistry. Jan, 2009  |   Pubmed ID: 19001369
• GeNESiS: Gene Network Evolution Simulation Software
  BMC Bioinformatics. Dec, 2008  |   Pubmed ID: 19087333
• Stabilizing Synthetic Data in the DNA of Living Organisms
  Systems and Synthetic Biology. Jun, 2008  |   Pubmed ID: 19083123
• Junction Ribonuclease Activity Specified in RNases HII/2
  The FEBS Journal. Nov, 2008  |   Pubmed ID: 18959768
• Signaling Flux Redistribution at Toll-like Receptor Pathway Junctions
  PloS One. 2008  |   Pubmed ID: 18927610
• Comprehensive Analysis of Archaeal TRNA Genes Reveals Rapid Increase of TRNA Introns in the Order Thermoproteales
  Molecular Biology and Evolution. Dec, 2008  |   Pubmed ID: 18832079
• Nuclear Export Signal Consensus Sequences Defined Using a Localization-based Yeast Selection System
  Traffic (Copenhagen, Denmark). Dec, 2008  |   Pubmed ID: 18817528
• Design of Peptide Inhibitors for the Importin Alpha/beta Nuclear Import Pathway by Activity-based Profiling
  Chemistry & Biology. Sep, 2008  |   Pubmed ID: 18804031
• Restriction on Conjugational Transfer of PLS20 in Bacillus Subtilis 168
  Bioscience, Biotechnology, and Biochemistry. Sep, 2008  |   Pubmed ID: 18776676
• Successive and Selective Release of Phosphorylated Peptides Captured by Hydroxy Acid-modified Metal Oxide Chromatography
  Journal of Proteome Research. Oct, 2008  |   Pubmed ID: 18767875
• Versatile Architecture of a Bacterial Aconitase B and Its Catalytic Performance in the Sequential Reaction Coupled with Isocitrate Dehydrogenase
  Biochimica Et Biophysica Acta. Nov, 2008  |   Pubmed ID: 18640291
• Time-resolved Metabolomics Reveals Metabolic Modulation in Rice Foliage
  BMC Systems Biology. Jun, 2008  |   Pubmed ID: 18564421
• Aligning LC Peaks by Converting Gradient Retention Times to Retention Index of Peptides in Proteomic Experiments
  Bioinformatics (Oxford, England). Jul, 2008  |   Pubmed ID: 18492686
• Implications from a Network-based Topological Analysis of Ubiquitin Unfolding Simulations
  PloS One. May, 2008  |   Pubmed ID: 18478068
• Large-scale Phosphorylation Mapping Reveals the Extent of Tyrosine Phosphorylation in Arabidopsis
  Molecular Systems Biology. 2008  |   Pubmed ID: 18463617
• Proteins As Networks: Usefulness of Graph Theory in Protein Science
  Current Protein & Peptide Science. Feb, 2008  |   Pubmed ID: 18336321
• GANDivAWeb: a Web Server for Detecting Early Folding Units ("foldons") from Protein 3D Structures
  BMC Structural Biology. Mar, 2008  |   Pubmed ID: 18325123
• Junction Ribonuclease: a Ribonuclease HII Orthologue from Thermus Thermophilus HB8 Prefers the RNA-DNA Junction to the RNA/DNA Heteroduplex
  The Biochemical Journal. Jun, 2008  |   Pubmed ID: 18318663
• Development of Bottom-fermenting Saccharomyces Strains That Produce High SO2 Levels, Using Integrated Metabolome and Transcriptome Analysis
  Applied and Environmental Microbiology. May, 2008  |   Pubmed ID: 18310411
• Sequence Evidence in the Archaeal Genomes That TRNAs Emerged Through the Combination of Ancestral Genes As 5' and 3' TRNA Halves
  PloS One. Feb, 2008  |   Pubmed ID: 18286179
• The GC Skew Index: a Measure of Genomic Compositional Asymmetry and the Degree of Replicational Selection
  Evolutionary Bioinformatics Online. Sep, 2007  |   Pubmed ID: 19461976
• Selection Effects on the Positioning of Genes and Gene Structures from the Interplay of Replication and Transcription in Bacterial Genomes
  Evolutionary Bioinformatics Online. Oct, 2007  |   Pubmed ID: 19461975
• The Hsp70 Chaperone System Maintains High Concentrations of Active Proteins and Suppresses ATP Consumption During Heat Shock
  Systems and Synthetic Biology. Mar, 2007  |   Pubmed ID: 19003436
• Simulation of Developmental Changes in Action Potentials with Ventricular Cell Models
  Systems and Synthetic Biology. Mar, 2007  |   Pubmed ID: 19003434
• Variation in the Correlation of G + C Composition with Synonymous Codon Usage Bias Among Bacteria
  EURASIP Journal on Bioinformatics & Systems Biology. 2007  |   Pubmed ID: 18350114
• Sequential Logic Model Deciphers Dynamic Transcriptional Control of Gene Expressions
  PloS One. Aug, 2007  |   Pubmed ID: 17712424
• Evolution of Ribonuclease H Genes in Prokaryotes to Avoid Inheritance of Redundant Genes
  BMC Evolutionary Biology. Jul, 2007  |   Pubmed ID: 17663799
• Indeterminacy of Reverse Engineering of Gene Regulatory Networks: the Curse of Gene Elasticity
  PloS One. Jun, 2007  |   Pubmed ID: 17593963
• Proteome-wide Prediction of Novel DNA/RNA-binding Proteins Using Amino Acid Composition and Periodicity in the Hyperthermophilic Archaeon Pyrococcus Furiosus
  DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes. Jun, 2007  |   Pubmed ID: 17573465
• Restauro-G: a Rapid Genome Re-annotation System for Comparative Genomics
  Genomics, Proteomics & Bioinformatics. Feb, 2007  |   Pubmed ID: 17572364
• Distinguishing Enzymes Using Metabolome Data for the Hybrid Dynamic/static Method
  Theoretical Biology & Medical Modelling. May, 2007  |   Pubmed ID: 17511884
• In Silico Screening of Archaeal TRNA-encoding Genes Having Multiple Introns with Bulge-helix-bulge Splicing Motifs
  RNA (New York, N.Y.). May, 2007  |   Pubmed ID: 17369313
• Visualization of Three-way Comparisons of Omics Data
  BMC Bioinformatics. 2007  |   Pubmed ID: 17335588
• Role of Phosphoenolpyruvate in the NADP-isocitrate Dehydrogenase and Isocitrate Lyase Reaction in Escherichia Coli
  Journal of Bacteriology. Feb, 2007  |   Pubmed ID: 17142397
• MathDAMP: a Package for Differential Analysis of Metabolite Profiles
  BMC Bioinformatics. 2006  |   Pubmed ID: 17166258
• HybGFS: a Hybrid Method for Genome-fingerprint Scanning
  BMC Bioinformatics. 2006  |   Pubmed ID: 17069662
• A Simplified Method for Power-law Modelling of Metabolic Pathways from Time-course Data and Steady-state Flux Profiles
  Theoretical Biology & Medical Modelling. Jul, 2006  |   Pubmed ID: 16846504
• Construction of Escherichia Coli K-12 In-frame, Single-gene Knockout Mutants: the Keio Collection
  Molecular Systems Biology. 2006  |   Pubmed ID: 16738554
• Modeling Hsp70-mediated Protein Folding
  Biophysical Journal. Jul, 2006  |   Pubmed ID: 16648174
• Parameter Estimation for Stiff Equations of Biosystems Using Radial Basis Function Networks
  BMC Bioinformatics. Apr, 2006  |   Pubmed ID: 16643665
• Large-scale Identification of Protein-protein Interaction of Escherichia Coli K-12
  Genome Research. May, 2006  |   Pubmed ID: 16606699
• GEM System: Automatic Prototyping of Cell-wide Metabolic Pathway Models from Genomes
  BMC Bioinformatics. Mar, 2006  |   Pubmed ID: 16553966
• Characteristics and Clustering of Human Ribosomal Protein Genes
  BMC Genomics. Feb, 2006  |   Pubmed ID: 16504170
• Archaeal Pyrococcus Furiosus Thymidylate Synthase 1 is an RNA-binding Protein
  The Biochemical Journal. Jan, 2006  |   Pubmed ID: 16176183
• A Comprehensive Software Suite for the Analysis of CDNAs
  Genomics, Proteomics & Bioinformatics. Aug, 2005  |   Pubmed ID: 16487083
• A Microarray Data-based Semi-kinetic Method for Predicting Quantitative Dynamics of Genetic Networks
  BMC Bioinformatics. Dec, 2005  |   Pubmed ID: 16351711
• Hybrid Dynamic/static Method for Large-scale Simulation of Metabolism
  Theoretical Biology & Medical Modelling. Oct, 2005  |   Pubmed ID: 16202166
• Dynamic Simulation of Red Blood Cell Metabolism and Its Application to the Analysis of a Pathological Condition
  Theoretical Biology & Medical Modelling. May, 2005  |   Pubmed ID: 15882454
• GC-compositional Strand Bias Around Transcription Start Sites in Plants and Fungi
  BMC Genomics. Feb, 2005  |   Pubmed ID: 15733327
• Cleavage of Double-stranded RNA by RNase HI from a Thermoacidophilic Archaeon, Sulfolobus Tokodaii 7
  Nucleic Acids Research. 2004  |   Pubmed ID: 15520465
• Comparative Analysis of Physical Maps of Four Bacillus Subtilis (natto) Genomes
  Applied and Environmental Microbiology. Oct, 2004  |   Pubmed ID: 15466572
• Computational Comparative Analyses of Alternative Splicing Regulation Using Full-length CDNA of Various Eukaryotes
  RNA (New York, N.Y.). Jul, 2004  |   Pubmed ID: 15208437
• Identification of the First Archaeal Type 1 RNase H Gene from Halobacterium Sp. NRC-1: Archaeal RNase HI Can Cleave an RNA-DNA Junction
  The Biochemical Journal. Aug, 2004  |   Pubmed ID: 15115438
• Identification of Putative Noncoding RNAs Among the RIKEN Mouse Full-length CDNA Collection
  Genome Research. Jun, 2003  |   Pubmed ID: 12819127
• Inferring Alternative Splicing Patterns in Mouse from a Full-length CDNA Library and Microarray Data
  Genome Research. Aug, 2002  |   Pubmed ID: 12176936
• Whole-cell Simulation: a Grand Challenge of the 21st Century
  Trends in Biotechnology. Jun, 2001  |   Pubmed ID: 11356281
• ApA Dinucleotide Periodicity in Prokaryote, Eukaryote, and Organelle Genomes
  Journal of Molecular Evolution. Aug, 1999  |   Pubmed ID: 10441670
• Introns and Reading Frames: Correlation Between Splicing Sites and Their Codon Positions
  Molecular Biology and Evolution. Nov, 1996  |   Pubmed ID: 8896374