Masaru Tomita

Institute for Advanced Biosciences, Keio University

Research Area

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 11	2018

Other Publications

Article	Year
Introns and reading frames: correlation between splicing sites and their codon positions. Molecular biology and evolution\| PubMed ID: 8896374	1996
ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes. Journal of molecular evolution\| PubMed ID: 10441670	1999
Whole-cell simulation: a grand challenge of the 21st century. Trends in biotechnology\| PubMed ID: 11356281	2001
Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data. Genome research\| PubMed ID: 12176936	2002
Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome research\| PubMed ID: 12819127	2003
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\| PubMed ID: 15115438	2004
Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes. RNA (New York, N.Y.)\| PubMed ID: 15208437	2004
Comparative analysis of physical maps of four Bacillus subtilis (natto) genomes. Applied and environmental microbiology\| PubMed ID: 15466572	2004
Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7. Nucleic acids research\| PubMed ID: 15520465	2004
GC-compositional strand bias around transcription start sites in plants and fungi. BMC genomics\| PubMed ID: 15733327	2005
Dynamic simulation of red blood cell metabolism and its application to the analysis of a pathological condition. Theoretical biology & medical modelling\| PubMed ID: 15882454	2005
Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein. The Biochemical journal\| PubMed ID: 16176183	2006
Hybrid dynamic/static method for large-scale simulation of metabolism. Theoretical biology & medical modelling\| PubMed ID: 16202166	2005
A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks. BMC bioinformatics\| PubMed ID: 16351711	2005
A comprehensive software suite for the analysis of cDNAs. Genomics, proteomics & bioinformatics\| PubMed ID: 16487083	2005
Characteristics and clustering of human ribosomal protein genes. BMC genomics\| PubMed ID: 16504170	2006
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. BMC bioinformatics\| PubMed ID: 16553966	2006
Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome research\| PubMed ID: 16606699	2006
Parameter estimation for stiff equations of biosystems using radial basis function networks. BMC bioinformatics\| PubMed ID: 16643665	2006
Modeling Hsp70-mediated protein folding. Biophysical journal\| PubMed ID: 16648174	2006
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Molecular systems biology\| PubMed ID: 16738554	2006
A simplified method for power-law modelling of metabolic pathways from time-course data and steady-state flux profiles. Theoretical biology & medical modelling\| PubMed ID: 16846504	2006
HybGFS: a hybrid method for genome-fingerprint scanning. BMC bioinformatics\| PubMed ID: 17069662	2006
Role of phosphoenolpyruvate in the NADP-isocitrate dehydrogenase and isocitrate lyase reaction in Escherichia coli. Journal of bacteriology\| PubMed ID: 17142397	2007
MathDAMP: a package for differential analysis of metabolite profiles. BMC bioinformatics\| PubMed ID: 17166258	2006
Visualization of three-way comparisons of omics data. BMC bioinformatics\| PubMed ID: 17335588	2007
In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs. RNA (New York, N.Y.)\| PubMed ID: 17369313	2007
Distinguishing enzymes using metabolome data for the hybrid dynamic/static method. Theoretical biology & medical modelling\| PubMed ID: 17511884	2007
Restauro-G: a rapid genome re-annotation system for comparative genomics. Genomics, proteomics & bioinformatics\| PubMed ID: 17572364	2007
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\| PubMed ID: 17573465	2007
Indeterminacy of reverse engineering of Gene Regulatory Networks: the curse of gene elasticity. PloS one\| PubMed ID: 17593963	2007
Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes. BMC evolutionary biology\| PubMed ID: 17663799	2007
Sequential logic model deciphers dynamic transcriptional control of gene expressions. PloS one\| PubMed ID: 17712424	2007
Sequence evidence in the archaeal genomes that tRNAs emerged through the combination of ancestral genes as 5' and 3' tRNA halves. PloS one\| PubMed ID: 18286179	2008
Development of bottom-fermenting saccharomyces strains that produce high SO2 levels, using integrated metabolome and transcriptome analysis. Applied and environmental microbiology\| PubMed ID: 18310411	2008
Junction ribonuclease: a ribonuclease HII orthologue from Thermus thermophilus HB8 prefers the RNA-DNA junction to the RNA/DNA heteroduplex. The Biochemical journal\| PubMed ID: 18318663	2008
GANDivAWeb: a web server for detecting early folding units ("foldons") from protein 3D structures. BMC structural biology\| PubMed ID: 18325123	2008
Proteins as networks: usefulness of graph theory in protein science. Current protein & peptide science\| PubMed ID: 18336321	2008
Variation in the correlation of G + C composition with synonymous codon usage bias among bacteria. EURASIP journal on bioinformatics & systems biology\| PubMed ID: 18350114	2007
Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Molecular systems biology\| PubMed ID: 18463617	2008
Implications from a network-based topological analysis of ubiquitin unfolding simulations. PloS one\| PubMed ID: 18478068	2008
Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments. Bioinformatics (Oxford, England)\| PubMed ID: 18492686	2008
Time-resolved metabolomics reveals metabolic modulation in rice foliage. BMC systems biology\| PubMed ID: 18564421	2008
Versatile architecture of a bacterial aconitase B and its catalytic performance in the sequential reaction coupled with isocitrate dehydrogenase. Biochimica et biophysica acta\| PubMed ID: 18640291	2008
Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography. Journal of proteome research\| PubMed ID: 18767875	2008
Restriction on conjugational transfer of pLS20 in Bacillus subtilis 168. Bioscience, biotechnology, and biochemistry\| PubMed ID: 18776676	2008
Design of peptide inhibitors for the importin alpha/beta nuclear import pathway by activity-based profiling. Chemistry & biology\| PubMed ID: 18804031	2008
Nuclear export signal consensus sequences defined using a localization-based yeast selection system. Traffic (Copenhagen, Denmark)\| PubMed ID: 18817528	2008
Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales. Molecular biology and evolution\| PubMed ID: 18832079	2008
Signaling flux redistribution at toll-like receptor pathway junctions. PloS one\| PubMed ID: 18927610	2008
Junction ribonuclease activity specified in RNases HII/2. The FEBS journal\| PubMed ID: 18959768	2008
Six classes of nuclear localization signals specific to different binding grooves of importin alpha. The Journal of biological chemistry\| PubMed ID: 19001369	2009
Simulation of developmental changes in action potentials with ventricular cell models. Systems and synthetic biology\| PubMed ID: 19003434	2007
The Hsp70 chaperone system maintains high concentrations of active proteins and suppresses ATP consumption during heat shock. Systems and synthetic biology\| PubMed ID: 19003436	2007
Stabilizing synthetic data in the DNA of living organisms. Systems and synthetic biology\| PubMed ID: 19083123	2008
GeNESiS: gene network evolution simulation software. BMC bioinformatics\| PubMed ID: 19087333	2008
Cooperativity of two active sites in bacterial homodimeric aconitases. Biochemical and biophysical research communications\| PubMed ID: 19116142	2009
In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution. Molecular & cellular proteomics : MCP\| PubMed ID: 19136663	2009
Characterization of a heat-stable enzyme possessing GTP-dependent RNA ligase activity from a hyperthermophilic archaeon, Pyrococcus furiosus. RNA (New York, N.Y.)\| PubMed ID: 19155324	2009
Genome Projector: zoomable genome map with multiple views. BMC bioinformatics\| PubMed ID: 19166610	2009
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\| PubMed ID: 19190180	2009
Can complex cellular processes be governed by simple linear rules? Journal of bioinformatics and computational biology\| PubMed ID: 19226669	2009
Predicting novel features of toll-like receptor 3 signaling in macrophages. PloS one\| PubMed ID: 19252739	2009
Emergent genome-wide control in wildtype and genetically mutated lipopolysaccarides-stimulated macrophages. PloS one\| PubMed ID: 19300509	2009
Degradation of ppGpp by nudix pyrophosphatase modulates the transition of growth phase in the bacterium Thermus thermophilus. The Journal of biological chemistry\| PubMed ID: 19346251	2009
Chemical cleavage-assisted tryptic digestion for membrane proteome analysis. Journal of proteome research\| PubMed ID: 19348461	2009
Metabolite profiling reveals YihU as a novel hydroxybutyrate dehydrogenase for alternative succinic semialdehyde metabolism in Escherichia coli. The Journal of biological chemistry\| PubMed ID: 19372223	2009
Quantitative metabolome profiling of colon and stomach cancer microenvironment by capillary electrophoresis time-of-flight mass spectrometry. Cancer research\| PubMed ID: 19458066	2009
Selection effects on the positioning of genes and gene structures from the interplay of replication and transcription in bacterial genomes. Evolutionary bioinformatics online\| PubMed ID: 19461975	2007
The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection. Evolutionary bioinformatics online\| PubMed ID: 19461976	2007
Identification of DNA-dependent protein kinase as a cofactor for the forkhead transcription factor FoxA2. The Journal of biological chemistry\| PubMed ID: 19478084	2009
Measure of synonymous codon usage diversity among genes in bacteria. BMC bioinformatics\| PubMed ID: 19480720	2009
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\| PubMed ID: 19520826	2009
Metabolomic profiling of anionic metabolites by capillary electrophoresis mass spectrometry. Analytical chemistry\| PubMed ID: 19522513	2009
[Not Available]. Frontiers in neuroinformatics\| PubMed ID: 19543432	2009
In silico modeling and metabolome analysis of long-stored erythrocytes to improve blood storage methods. Journal of biotechnology\| PubMed ID: 19695295	2009
Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism. Molecular systems biology\| PubMed ID: 19756045	2009
A web server for interactive and zoomable Chaos Game Representation images. Source code for biology and medicine\| PubMed ID: 19761591	2009
Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants. Molecular & cellular proteomics : MCP\| PubMed ID: 19767571	2009
Disrupted tRNA gene diversity and possible evolutionary scenarios. Journal of molecular evolution\| PubMed ID: 19826747	2009
Recharacterization of Chlamydomonas reinhardtii and its relatives with new isolates from Japan. Journal of plant research\| PubMed ID: 19882207	2010
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. PloS one\| PubMed ID: 19907644	2009
Correlation between sensory evaluation scores of Japanese sake and metabolome profiles. Journal of agricultural and food chemistry\| PubMed ID: 19961224	2010
A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation. Systems and synthetic biology\| PubMed ID: 20012222	2010
Update on the Keio collection of Escherichia coli single-gene deletion mutants. Molecular systems biology\| PubMed ID: 20029369	2009
Quantitative analysis of replication-related mutation and selection pressures in bacterial chromosomes and plasmids using generalised GC skew index. BMC genomics\| PubMed ID: 20042086	2009
Characterization of RNase HII substrate recognition using RNase HII-argonaute chimaeric enzymes from Pyrococcus furiosus. The Biochemical journal\| PubMed ID: 20047562	2010
Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals. BMC genomics\| PubMed ID: 20144220	2010
Quantitative proteome and phosphoproteome analyses of cultured cells based on SILAC labeling without requirement of serum dialysis. Molecular bioSystems\| PubMed ID: 20174688	2010
A comprehensive resource of interacting protein regions for refining human transcription factor networks. PloS one\| PubMed ID: 20195357	2010
Computational prediction of nucleosome positioning by calculating the relative fragment frequency index of nucleosomal sequences. FEBS letters\| PubMed ID: 20206172	2010
Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics : Official journal of the Metabolomic Society\| PubMed ID: 20300169	2010
Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. BMC genomics\| PubMed ID: 20409305	2010
Unveiling cellular biochemical reactions via metabolomics-driven approaches. Current opinion in microbiology\| PubMed ID: 20430690	2010
Large-scale tRNA intron transposition in the archaeal order Thermoproteales represents a novel mechanism of intron gain. Molecular biology and evolution\| PubMed ID: 20430862	2010
G-language genome analysis environment with REST and SOAP web service interfaces. Nucleic acids research\| PubMed ID: 20439313	2010
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data. BMC bioinformatics\| PubMed ID: 20459641	2010
Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants. Plant physiology\| PubMed ID: 20466843	2010
Transcription-associated mutagenesis increases protein sequence diversity more effectively than does random mutagenesis in Escherichia coli. PloS one\| PubMed ID: 20479947	2010
Another origin of coloniality in volvocaleans: the phylogenetic position of Pyrobotrys arnoldi (Spondylomoraceae, Volvocales). The Journal of eukaryotic microbiology\| PubMed ID: 20553352	2010
Prediction of metabolite identity from accurate mass, migration time prediction and isotopic pattern information in CE-TOFMS data. Electrophoresis\| PubMed ID: 20568260	2010
Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions. BMC bioinformatics\| PubMed ID: 20584269	2010
Metabolomic profiles and sensory attributes of edamame under various storage duration and temperature conditions. Journal of agricultural and food chemistry\| PubMed ID: 20593783	2010
Chemical dephosphorylation for identification of multiply phosphorylated peptides and phosphorylation site determination. Rapid communications in mass spectrometry : RCM\| PubMed ID: 20623713	2010
A metabolic model of human erythrocytes: practical application of the E-Cell Simulation Environment. Journal of biomedicine & biotechnology\| PubMed ID: 20625505	2010
Collective dynamics of specific gene ensembles crucial for neutrophil differentiation: the existence of genome vehicles revealed. PloS one\| PubMed ID: 20725638	2010
An extreme thermophile, Thermus thermophilus, is a polyploid bacterium. Journal of bacteriology\| PubMed ID: 20729360	2010
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\| PubMed ID: 20730757	2010
Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes. BMC genomics\| PubMed ID: 21223577	2011
Integrative features of the yeast phosphoproteome and protein-protein interaction map. PLoS computational biology\| PubMed ID: 21298081	2011
Serum metabolomics reveals γ-glutamyl dipeptides as biomarkers for discrimination among different forms of liver disease. Journal of hepatology\| PubMed ID: 21334394	2011
Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA. Gene\| PubMed ID: 21338662	2011
OryzaPG-DB: rice proteome database based on shotgun proteogenomics. BMC plant biology\| PubMed ID: 21486466	2011
KBWS: an EMBOSS associated package for accessing bioinformatics web services. Source code for biology and medicine\| PubMed ID: 21529350	2011
Positive autoregulation delays the expression phase of mammalian clock gene Per2. PloS one\| PubMed ID: 21533189	2011
A screening system for artificial small RNAs that inhibit the growth of Escherichia coli. Journal of biochemistry\| PubMed ID: 21546360	2011
Redox regulation in respiring Saccharomyces cerevisiae. Biochimica et biophysica acta\| PubMed ID: 21549177	2011
Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes. BMC medical genomics\| PubMed ID: 21575255	2011
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\| PubMed ID: 21594678	2011
Metabolic flux analysis and visualization. Journal of proteome research\| PubMed ID: 21815690	2011
Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification. BMC genomics\| PubMed ID: 21846408	2011
Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. BMC genomics\| PubMed ID: 21864382	2011
A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic acids research\| PubMed ID: 21880595	2011
Microscale phosphoproteome analysis of 10,000 cells from human cancer cell lines. Analytical chemistry\| PubMed ID: 21888424	2011
Predicting the Kinetic Properties Associated with Redox Imbalance after Oxidative Crisis in G6PD-Deficient Erythrocytes: A Simulation Study. Advances in hematology\| PubMed ID: 21977034	2011
GTP-dependent RNA 3'-terminal phosphate cyclase from the hyperthermophilic archaeon Pyrococcus furiosus. Genes to cells : devoted to molecular & cellular mechanisms\| PubMed ID: 22074260	2011
MMMDB: Mouse Multiple Tissue Metabolome Database. Nucleic acids research\| PubMed ID: 22139941	2012
Metatranscriptomic analysis of microbes in an Oceanfront deep-subsurface hot spring reveals novel small RNAs and type-specific tRNA degradation. Applied and environmental microbiology\| PubMed ID: 22156430	2012
Time-structure of the yeast metabolism in vivo. Advances in experimental medicine and biology\| PubMed ID: 22161340	2012
Nematode-specific tRNAs that decode an alternative genetic code for leucine. Nucleic acids research\| PubMed ID: 22187151	2012
The third plasmid pVV8 from Thermus thermophilus HB8: isolation, characterization, and sequence determination. Extremophiles : life under extreme conditions\| PubMed ID: 22212656	2012
Changes in the charged metabolite and sugar profiles of pasteurized and unpasteurized Japanese sake with storage. Journal of agricultural and food chemistry\| PubMed ID: 22352923	2012
Enhancing apoptosis in TRAIL-resistant cancer cells using fundamental response rules. Scientific reports\| PubMed ID: 22355661	2011
Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption. PloS one\| PubMed ID: 22403667	2012
Muscle-specific knock-out of NUAK family SNF1-like kinase 1 (NUAK1) prevents high fat diet-induced glucose intolerance. The Journal of biological chemistry\| PubMed ID: 22418434	2012
Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis. Current bioinformatics\| PubMed ID: 22438836	2012
Validation of bacterial replication termination models using simulation of genomic mutations. PloS one\| PubMed ID: 22509315	2012
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\| PubMed ID: 22553167	2012
Cancer. Systems biology, metabolomics, and cancer metabolism. Science (New York, N.Y.)\| PubMed ID: 22628644	2012
The Rice Proteogenomics Database OryzaPG-DB: Development, Expansion, and New Features. Frontiers in plant science\| PubMed ID: 22639657	2012
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\| PubMed ID: 22686349	2012
Prediction of axillary lymph node metastasis in primary breast cancer patients using a decision tree-based model. BMC medical informatics and decision making\| PubMed ID: 22695278	2012
Rapid DNA, RNA and protein extraction protocols optimized for slow continuously growing yeast cultures. Yeast (Chichester, England)\| PubMed ID: 22763810	2012
Metabolic regulation analysis of wild-type and arcA mutant Escherichia coli under nitrate conditions using different levels of omics data. Molecular bioSystems\| PubMed ID: 22790675	2012
Metabolomic profiling rationalized pyruvate efficacy in cybrid cells harboring MELAS mitochondrial DNA mutations. Mitochondrion\| PubMed ID: 22884939	2012
Measures of compositional strand bias related to replication machinery and its applications. Current genomics\| PubMed ID: 22942671	2012
A yeast metabolite extraction protocol optimised for time-series analyses. PloS one\| PubMed ID: 22952947	2012
Temporal profiling of lapatinib-suppressed phosphorylation signals in EGFR/HER2 pathways. Molecular & cellular proteomics : MCP\| PubMed ID: 22964224	2012
Sheathless capillary electrophoresis-mass spectrometry with a high-sensitivity porous sprayer for cationic metabolome analysis. The Analyst\| PubMed ID: 23000847	2012
Metabolic profiling reveals new serum biomarkers for differentiating diabetic nephropathy. Analytical and bioanalytical chemistry\| PubMed ID: 23052862	2012
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, defi... Journal of biochemistry\| PubMed ID: 23055537	2012
Identification of a replication initiation protein of the pVV8 plasmid from Thermus thermophilus HB8. Extremophiles : life under extreme conditions\| PubMed ID: 23114983	2013
Is central dogma a global property of cellular information flow? Frontiers in physiology\| PubMed ID: 23189060	2012
A medium-chain fatty acid as an alternative energy source in mouse preimplantation development. Scientific reports\| PubMed ID: 23226596	2012
Comprehensive computational analysis of bacterial CRP/FNR superfamily and its target motifs reveals stepwise evolution of transcriptional networks. Genome biology and evolution\| PubMed ID: 23315382	2013
Metabolomic study of Chilean biomining bacteria Acidithiobacillus ferrooxidans strain Wenelen and Acidithiobacillus thiooxidans strain Licanantay. Metabolomics : Official journal of the Metabolomic Society\| PubMed ID: 23335869	2013
Computational analysis of associations between alternative splicing and histone modifications. FEBS letters\| PubMed ID: 23353998	2013
Merging multiple omics datasets in silico: statistical analyses and data interpretation. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 23417818	2013
Global microRNA elevation by inducible Exportin 5 regulates cell cycle entry. RNA (New York, N.Y.)\| PubMed ID: 23431327	2013
Metabolic and morphological changes of an oil accumulating trebouxiophycean alga in nitrogen-deficient conditions. Metabolomics : Official journal of the Metabolomic Society\| PubMed ID: 23463323	2013
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\| PubMed ID: 23523883	2013
Metabolomic profiling of lung and prostate tumor tissues by capillary electrophoresis time-of-flight mass spectrometry. Metabolomics : Official journal of the Metabolomic Society\| PubMed ID: 23543897	2013
Quantitative assay for TALEN activity at endogenous genomic loci. Biology open\| PubMed ID: 23616919	2013
Time-resolved metabolomics of a novel trebouxiophycean alga using (13)CO2 feeding. Journal of bioscience and bioengineering\| PubMed ID: 23706992	2013
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\| PubMed ID: 23760774	2013
Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients. Electrophoresis\| PubMed ID: 23857558	2013
GEMBASSY: an EMBOSS associated software package for comprehensive genome analyses. Source code for biology and medicine\| PubMed ID: 23987304	2013
A systems biology approach to suppress TNF-induced proinflammatory gene expressions. Cell communication and signaling : CCS\| PubMed ID: 24199619	2013
Dynamic simulation and metabolome analysis of long-term erythrocyte storage in adenine-guanosine solution. PloS one\| PubMed ID: 24205395	2013
Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells. Nature\| PubMed ID: 24226770	2013
Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol. Nature communications\| PubMed ID: 24481126	2014
Comparative metabolite profiling of foxglove aphids (Aulacorthum solani Kaltenbach) on leaves of resistant and susceptible soybean strains. Molecular bioSystems\| PubMed ID: 24514152	2014
Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness. PLoS biology\| PubMed ID: 24866127	2014
Undesigned selection for replication termination of bacterial chromosomes. Journal of molecular biology\| PubMed ID: 24946150	2014
Quantifying periodicity in omics data. Frontiers in cell and developmental biology\| PubMed ID: 25364747	2014
Transcriptome-wide variability in single embryonic development cells. Scientific reports\| PubMed ID: 25409746	2014
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\| PubMed ID: 25441083	2014
Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo. BMC genomics\| PubMed ID: 25512115	2014
Identification, expression, and molecular evolution of microRNAs in the "living fossil" Triops cancriformis (tadpole shrimp). RNA (New York, N.Y.)\| PubMed ID: 25525151	2015
Systems Biology Strategy Reveals PKCδ is Key for Sensitizing TRAIL-Resistant Human Fibrosarcoma. Frontiers in immunology\| PubMed ID: 25601862	2014
Analysis of genetic code ambiguity arising from nematode-specific misacylated tRNAs. PloS one\| PubMed ID: 25602944	2015
Organization and evolution of brain lipidome revealed by large-scale analysis of human, chimpanzee, macaque, and mouse tissues. Neuron\| PubMed ID: 25661180	2015
Effects of processing and storage conditions on charged metabolomic profiles in blood. Electrophoresis\| PubMed ID: 25820922	2015
Alteration of metabolomic profiles by titanium dioxide nanoparticles in human gingivitis model. Biomaterials\| PubMed ID: 25913073	2015
Method of preparing an equimolar DNA mixture for one-step DNA assembly of over 50 fragments. Scientific reports\| PubMed ID: 25990947	2015
Tracking global gene expression responses in T cell differentiation. Gene\| PubMed ID: 26028587	2015
Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes. PLoS computational biology\| PubMed ID: 26046580	2015
Precise mapping and dynamics of tRNA-derived fragments (tRFs) in the development of Triops cancriformis (tadpole shrimp). BMC genetics\| PubMed ID: 26168920	2015
Metabolomic alterations in human cancer cells by vitamin C-induced oxidative stress. Scientific reports\| PubMed ID: 26350063	2015
Metabolomic profiling reveals novel biomarkers of alcohol intake and alcohol-induced liver injury in community-dwelling men. Environmental health and preventive medicine\| PubMed ID: 26459263	2016
Expansion of Noncanonical V-Arm-Containing tRNAs in Eukaryotes. Molecular biology and evolution\| PubMed ID: 26545920	2016
Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly. Molecular ecology resources\| PubMed ID: 26561354	2016
Phylogenetic Position and Molecular Chronology of a Colonial Green Flagellate, Stephanosphaera pluvialis (Volvocales, Chlorophyceae), among Unicellular Algae. The Journal of eukaryotic microbiology\| PubMed ID: 26595722	2016
G-Links: a gene-centric link acquisition service. F1000Research\| PubMed ID: 26673001	2014
Curing the Megaplasmid pTT27 from Thermus thermophilus HB27 and Maintaining Exogenous Plasmids in the Plasmid-Free Strain. Applied and environmental microbiology\| PubMed ID: 26712540	2015
Conversion of graded phosphorylation into switch-like nuclear translocation via autoregulatory mechanisms in ERK signalling. Nature communications\| PubMed ID: 26786866	2016
The Consumption of Bicarbonate-Rich Mineral Water Improves Glycemic Control. Evidence-based complementary and alternative medicine : eCAM\| PubMed ID: 26798400	2015
Erratum to: Metabolomic profiling reveals novel biomarkers of alcohol intake and alcohol-induced liver injury in community-dwelling men. Environmental health and preventive medicine\| PubMed ID: 26898210	2016
De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions. BMC genomics\| PubMed ID: 26939900	2016
Taxonomic revision of oil-producing green algae, Chlorococcum oleofaciens (Volvocales, Chlorophyceae), and its relatives. Journal of phycology\| PubMed ID: 26986894	2015
Taxonomic revision of Chlamydomonas subg. Amphichloris (Volvocales, Chlorophyceae), with resurrection of the genus Dangeardinia and descriptions of Ixipapillifera gen. nov. and Rhysamphichlo... Journal of phycology\| PubMed ID: 27037593	2016
Profiling of plasma metabolites in postmenopausal women with metabolic syndrome. Menopause (New York, N.Y.)\| PubMed ID: 27070805	2016
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\| PubMed ID: 27118840	2016
Smad2/3 Proteins Are Required for Immobilization-induced Skeletal Muscle Atrophy. The Journal of biological chemistry\| PubMed ID: 27129272	2016
Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria. Genome announcements\| PubMed ID: 27151793	2016
Simultaneous analysis of consumer variables, acceptability and sensory characteristics of dry-cured ham. Meat science\| PubMed ID: 27343459	2016
Serum metabolome profiles characterized by patients with hepatocellular carcinoma associated with hepatitis B and C. World journal of gastroenterology\| PubMed ID: 27468212	2016
Genome sequencing of a single tardigrade Hypsibius dujardini individual. Scientific data\| PubMed ID: 27529330	2016
Identification of salivary metabolomic biomarkers for oral cancer screening. Scientific reports\| PubMed ID: 27539254	2016
Draft Genome Sequence of Arenibacter sp. Strain C-21, an Iodine-Accumulating Bacterium Isolated from Surface Marine Sediment. Genome announcements\| PubMed ID: 27738047	2016
Metabolic Profiling of Total Physical Activity and Sedentary Behavior in Community-Dwelling Men. PloS one\| PubMed ID: 27741291	2016
Morphology and phylogeny of a new wall-less freshwater volvocalean flagellate, Hapalochloris nozakii gen. et sp. nov. (Volvocales, Chlorophyceae). Journal of phycology\| PubMed ID: 27767210	2017
Metabolomic Profiling as a Possible Reverse Engineering Tool for Estimating Processing Conditions of Dry-Cured Hams. Journal of agricultural and food chemistry\| PubMed ID: 27951640	2017
Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth. RNA biology\| PubMed ID: 27981881	2017
A serum metabolomics-based profile in low bone mineral density postmenopausal women. Bone\| PubMed ID: 27989648	2017
Effect of timing of collection of salivary metabolomic biomarkers on oral cancer detection. Amino acids\| PubMed ID: 28101653	2017
Rearing and observation of immature stages of the hoverfly (Diptera, Syrphidae). Biodiversity data journal\| PubMed ID: 28174503	2016
Differential Binding of Three Major Human ADAR Isoforms to Coding and Long Non-Coding Transcripts. Genes\| PubMed ID: 28208661	2017
Synthetic Biomarker Design by Using Analyte-Responsive Acetaminophen. Chembiochem : a European journal of chemical biology\| PubMed ID: 28236354	2017
Developmental changes in the balance of glycolytic ATP production and oxidative phosphorylation in ventricular cells: A simulation study. Journal of theoretical biology\| PubMed ID: 28237394	2017
Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis. Scientific reports\| PubMed ID: 28272447	2017
Time resolved DNA occupancy dynamics during the respiratory oscillation uncover a global reset point in the yeast growth program. Microbial cell (Graz, Austria)\| PubMed ID: 28357254	2014
Serum Metabolomic Profiles for Human Pancreatic Cancer Discrimination. International journal of molecular sciences\| PubMed ID: 28375170	2017
Thymidine Catabolism as a Metabolic Strategy for Cancer Survival. Cell reports\| PubMed ID: 28514652	2017
Draft Genome Sequence of sp. A-2, an Iodide-Oxidizing Bacterium Isolated from Natural Gas Brine Water, Chiba, Japan. Journal of genomics\| PubMed ID: 28529651	2017
Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging. Molecular cell\| PubMed ID: 28712725	2017
Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus. PLoS biology\| PubMed ID: 28749982	2017
Effect of masticatory stimulation on the quantity and quality of saliva and the salivary metabolomic profile. PloS one\| PubMed ID: 28813487	2017
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\| PubMed ID: 28847964	2017
Effects of 3-styrylchromones on metabolic profiles and cell death in oral squamous cell carcinoma cells. Toxicology reports\| PubMed ID: 28962471	2015
An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus. Scientific reports\| PubMed ID: 28978920	2017
eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria. BMC genomics\| PubMed ID: 29029602	2017
Evolutionary Analysis of HIV-1 Pol Proteins Reveals Representative Residues for Viral Subtype Differentiation. Frontiers in microbiology\| PubMed ID: 29163435	2017
Comparative genomic analysis of ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan. Gut pathogens\| PubMed ID: 29213333	2017
The first high frequency of recombination-like conjugal transfer from an integrated origin of transfer sequence in Bacillus subtilis 168. Bioscience, biotechnology, and biochemistry\| PubMed ID: 29316866	2018
Reliability of plasma polar metabolite concentrations in a large-scale cohort study using capillary electrophoresis-mass spectrometry. PloS one\| PubMed ID: 29346414	2018
Systematic Analysis of the Binding Surfaces between tRNAs and Their Respective Aminoacyl tRNA Synthetase Based on Structural and Evolutionary Data. Frontiers in genetics\| PubMed ID: 29358943	2017
Elevated Polyamines in Saliva of Pancreatic Cancer. Cancers\| PubMed ID: 29401744	2018
Efficient delivery of large DNA from Escherichia coli to Synechococcus elongatus PCC7942 by broad-host-range conjugal plasmid pUB307. Journal of biochemistry\| PubMed ID: 29420737	2018
Human AK2 links intracellular bioenergetic redistribution to the fate of hematopoietic progenitors. Biochemical and biophysical research communications\| PubMed ID: 29462620	2018
Development of a sheathless CE-ESI-MS interface. Electrophoresis\| PubMed ID: 29493797	2018
Urinary Polyamine Biomarker Panels with Machine-Learning Differentiated Colorectal Cancers, Benign Disease, and Healthy Controls. International journal of molecular sciences\| PubMed ID: 29518931	2018
Thymidine catabolism promotes NADPH oxidase-derived reactive oxygen species (ROS) signalling in KB and yumoto cells. Scientific reports\| PubMed ID: 29713062	2018
Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells. ACS synthetic biology\| PubMed ID: 29786424	2018
Changes of liver metabolites following hepatectomy with ischemia reperfusion towards liver regeneration. Annals of gastroenterological surgery\| PubMed ID: 29863192	2018
Far rapid synthesis of giant DNA in the Bacillus subtilis genome by a conjugation transfer system. Scientific reports\| PubMed ID: 29884789	2018
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\| PubMed ID: 29950133	2018
MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data. BMC bioinformatics\| PubMed ID: 29954316	2018
Metabolomics-based profiles predictive of low bone mass in menopausal women. Bone reports\| PubMed ID: 29955645	2018
High-Quality Overlapping Paired-End Reads for the Detection of A-to-I Editing on Small RNA. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 29959681	2018