Masaru Tomita Institute for Advanced Biosciences Keio University Biography Publications Institution JoVE Articles Masaru Tomita has not added a biography. If you are Masaru Tomita and would like to personalize this page please email our Author Liaison for assistance. 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 タイトなアソシエーション転写プロモーター型とヒストン位置決め・改質のエピジェネティックな変化。 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 計算解析高屈曲、壊れやすい構造はヌクレオソーム DNA の示唆しています。 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 酵母のリン酸化プロテオームおよび蛋白質蛋白質の相互作用マップの統合的な機能です。 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 リン酸化ダイナミクスを用いてシグナル伝達ネットワークの系統的探索に向けて。 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 インシリコ リン酸化プロテオーム データの解析 Phosphosite 蓄積するリッチ取得豊かなプロセス上の進化を示唆しています。 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 生物の DNA の合成データを安定させます。 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 古細菌由来 TRNA 遺伝子の網羅的解析の TRNA イントロン順序サーモプロテウス目での急激な増加を明らかにします。 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 PLS20 枯草 168 の送りがな譲渡制限。 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 複数のイントロン膨らみヘリックスの膨らみを有する古細菌由来 TRNA をコードする遺伝子の in Silico スクリーニングのモチーフをスプライシングします。 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: ゲノム指紋スキャン用ハイブリッド法。 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 超低入力ヒトゲノム単一 Tardigrade の標本からのライブラリの準備 Yuki Yoshida1,2, Sayuri Konno1,3, Ryousuke Nishino1,3, Yumi Murai1,3, Masaru Tomita1,2,3, Kazuharu Arakawa1,2,3 1Institute for Advanced Biosciences, Keio University, 2Systems Biology Program, Graduate School of Media and Governance, Keio University, 3Faculty of Environment and Information Studies, Keio University JoVE 57615 Genetics
超低入力ヒトゲノム単一 Tardigrade の標本からのライブラリの準備 Yuki Yoshida1,2, Sayuri Konno1,3, Ryousuke Nishino1,3, Yumi Murai1,3, Masaru Tomita1,2,3, Kazuharu Arakawa1,2,3 1Institute for Advanced Biosciences, Keio University, 2Systems Biology Program, Graduate School of Media and Governance, Keio University, 3Faculty of Environment and Information Studies, Keio University JoVE 57615 Genetics