Institute for Advanced Biosciences,
Systems Biology Program,
Graduate School of Media and Governance,
Faculty of Environment and Information Studies,
Systems Biology Program, Graduate School of Media and Governance
Masaru Tomita has not added Biography.
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Introns and reading frames: correlation between splicing sites and their codon positions.
Molecular biology and evolution Nov, 1996 | Pubmed ID: 8896374
ApA dinucleotide periodicity in prokaryote, eukaryote, and organelle genomes.
Journal of molecular evolution Aug, 1999 | Pubmed ID: 10441670
Whole-cell simulation: a grand challenge of the 21st century.
Trends in biotechnology Jun, 2001 | Pubmed ID: 11356281
Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data.
Genome research Aug, 2002 | Pubmed ID: 12176936
Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection.
Genome research Jun, 2003 | Pubmed ID: 12819127
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
Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes.
RNA (New York, N.Y.) Jul, 2004 | Pubmed ID: 15208437
Comparative analysis of physical maps of four Bacillus subtilis (natto) genomes.
Applied and environmental microbiology Oct, 2004 | Pubmed ID: 15466572
Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7.
Nucleic acids research , 2004 | Pubmed ID: 15520465
GC-compositional strand bias around transcription start sites in plants and fungi.
BMC genomics Feb, 2005 | Pubmed ID: 15733327
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
Archaeal Pyrococcus furiosus thymidylate synthase 1 is an RNA-binding protein.
The Biochemical journal Jan, 2006 | Pubmed ID: 16176183
Hybrid dynamic/static method for large-scale simulation of metabolism.
Theoretical biology & medical modelling Oct, 2005 | Pubmed ID: 16202166
A microarray data-based semi-kinetic method for predicting quantitative dynamics of genetic networks.
BMC bioinformatics Dec, 2005 | Pubmed ID: 16351711
A comprehensive software suite for the analysis of cDNAs.
Genomics, proteomics & bioinformatics Aug, 2005 | Pubmed ID: 16487083
Characteristics and clustering of human ribosomal protein genes.
BMC genomics Feb, 2006 | Pubmed ID: 16504170
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes.
BMC bioinformatics Mar, 2006 | Pubmed ID: 16553966
Large-scale identification of protein-protein interaction of Escherichia coli K-12.
Genome research May, 2006 | Pubmed ID: 16606699
Parameter estimation for stiff equations of biosystems using radial basis function networks.
BMC bioinformatics Apr, 2006 | Pubmed ID: 16643665
Modeling Hsp70-mediated protein folding.
Biophysical journal Jul, 2006 | Pubmed ID: 16648174
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection.
Molecular systems biology , 2006 | Pubmed ID: 16738554
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
HybGFS: a hybrid method for genome-fingerprint scanning.
BMC bioinformatics , 2006 | Pubmed ID: 17069662
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
Visualization of three-way comparisons of omics data.
BMC bioinformatics , 2007 | Pubmed ID: 17335588
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
Distinguishing enzymes using metabolome data for the hybrid dynamic/static method.
Theoretical biology & medical modelling May, 2007 | Pubmed ID: 17511884
Restauro-G: a rapid genome re-annotation system for comparative genomics.
Genomics, proteomics & bioinformatics Feb, 2007 | Pubmed ID: 17572364
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
Indeterminacy of reverse engineering of Gene Regulatory Networks: the curse of gene elasticity.
PloS one Jun, 2007 | Pubmed ID: 17593963
Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes.
BMC evolutionary biology Jul, 2007 | Pubmed ID: 17663799
Sequential logic model deciphers dynamic transcriptional control of gene expressions.
PloS one Aug, 2007 | Pubmed ID: 17712424
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
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
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
GANDivAWeb: a web server for detecting early folding units ("foldons") from protein 3D structures.
BMC structural biology Mar, 2008 | Pubmed ID: 18325123
Proteins as networks: usefulness of graph theory in protein science.
Current protein & peptide science Feb, 2008 | Pubmed ID: 18336321
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
Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis.
Molecular systems biology , 2008 | Pubmed ID: 18463617
Implications from a network-based topological analysis of ubiquitin unfolding simulations.
PloS one May, 2008 | Pubmed ID: 18478068
Aligning LC peaks by converting gradient retention times to retention index of peptides in proteomic experiments.
Bioinformatics (Oxford, England) Jul, 2008 | Pubmed ID: 18492686
Time-resolved metabolomics reveals metabolic modulation in rice foliage.
BMC systems biology Jun, 2008 | Pubmed ID: 18564421
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
Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.
Journal of proteome research Oct, 2008 | Pubmed ID: 18767875
Restriction on conjugational transfer of pLS20 in Bacillus subtilis 168.
Bioscience, biotechnology, and biochemistry Sep, 2008 | Pubmed ID: 18776676
Design of peptide inhibitors for the importin alpha/beta nuclear import pathway by activity-based profiling.
Chemistry & biology Sep, 2008 | Pubmed ID: 18804031
Nuclear export signal consensus sequences defined using a localization-based yeast selection system.
Traffic (Copenhagen, Denmark) Dec, 2008 | Pubmed ID: 18817528
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
Signaling flux redistribution at toll-like receptor pathway junctions.
PloS one , 2008 | Pubmed ID: 18927610
Junction ribonuclease activity specified in RNases HII/2.
The FEBS journal Nov, 2008 | Pubmed ID: 18959768
Six classes of nuclear localization signals specific to different binding grooves of importin alpha.
The Journal of biological chemistry Jan, 2009 | Pubmed ID: 19001369
Simulation of developmental changes in action potentials with ventricular cell models.
Systems and synthetic biology Mar, 2007 | Pubmed ID: 19003434
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
Stabilizing synthetic data in the DNA of living organisms.
Systems and synthetic biology Jun, 2008 | Pubmed ID: 19083123
GeNESiS: gene network evolution simulation software.
BMC bioinformatics Dec, 2008 | Pubmed ID: 19087333
Cooperativity of two active sites in bacterial homodimeric aconitases.
Biochemical and biophysical research communications Feb, 2009 | Pubmed ID: 19116142
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
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
Genome Projector: zoomable genome map with multiple views.
BMC bioinformatics Jan, 2009 | Pubmed ID: 19166610
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
Can complex cellular processes be governed by simple linear rules?
Journal of bioinformatics and computational biology Feb, 2009 | Pubmed ID: 19226669
Predicting novel features of toll-like receptor 3 signaling in macrophages.
PloS one , 2009 | Pubmed ID: 19252739
Emergent genome-wide control in wildtype and genetically mutated lipopolysaccarides-stimulated macrophages.
PloS one , 2009 | Pubmed ID: 19300509
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
Chemical cleavage-assisted tryptic digestion for membrane proteome analysis.
Journal of proteome research Jun, 2009 | Pubmed ID: 19348461
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
Quantitative metabolome profiling of colon and stomach cancer microenvironment by capillary electrophoresis time-of-flight mass spectrometry.
Cancer research Jun, 2009 | Pubmed ID: 19458066
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 GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection.
Evolutionary bioinformatics online Sep, 2007 | Pubmed ID: 19461976
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
Measure of synonymous codon usage diversity among genes in bacteria.
BMC bioinformatics Jun, 2009 | Pubmed ID: 19480720
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
Metabolomic profiling of anionic metabolites by capillary electrophoresis mass spectrometry.
Analytical chemistry Aug, 2009 | Pubmed ID: 19522513
[Not Available].
Frontiers in neuroinformatics , 2009 | Pubmed ID: 19543432
In silico modeling and metabolome analysis of long-stored erythrocytes to improve blood storage methods.
Journal of biotechnology Nov, 2009 | Pubmed ID: 19695295
Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism.
Molecular systems biology , 2009 | Pubmed ID: 19756045
A web server for interactive and zoomable Chaos Game Representation images.
Source code for biology and medicine Sep, 2009 | Pubmed ID: 19761591
Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants.
Molecular & cellular proteomics : MCP Dec, 2009 | Pubmed ID: 19767571
Disrupted tRNA gene diversity and possible evolutionary scenarios.
Journal of molecular evolution Nov, 2009 | Pubmed ID: 19826747
Recharacterization of Chlamydomonas reinhardtii and its relatives with new isolates from Japan.
Journal of plant research Jan, 2010 | Pubmed ID: 19882207
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.
PloS one Nov, 2009 | Pubmed ID: 19907644
Correlation between sensory evaluation scores of Japanese sake and metabolome profiles.
Journal of agricultural and food chemistry Jan, 2010 | Pubmed ID: 19961224
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
Update on the Keio collection of Escherichia coli single-gene deletion mutants.
Molecular systems biology , 2009 | Pubmed ID: 20029369
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
Characterization of RNase HII substrate recognition using RNase HII-argonaute chimaeric enzymes from Pyrococcus furiosus.
The Biochemical journal Feb, 2010 | Pubmed ID: 20047562
Computational prediction and experimental validation of evolutionarily conserved microRNA target genes in bilaterian animals.
BMC genomics Feb, 2010 | Pubmed ID: 20144220
Quantitative proteome and phosphoproteome analyses of cultured cells based on SILAC labeling without requirement of serum dialysis.
Molecular bioSystems Mar, 2010 | Pubmed ID: 20174688
A comprehensive resource of interacting protein regions for refining human transcription factor networks.
PloS one Feb, 2010 | Pubmed ID: 20195357
Computational prediction of nucleosome positioning by calculating the relative fragment frequency index of nucleosomal sequences.
FEBS letters Apr, 2010 | Pubmed ID: 20206172
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
Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns.
BMC genomics Apr, 2010 | Pubmed ID: 20409305
Unveiling cellular biochemical reactions via metabolomics-driven approaches.
Current opinion in microbiology Jun, 2010 | Pubmed ID: 20430690
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
G-language genome analysis environment with REST and SOAP web service interfaces.
Nucleic acids research Jul, 2010 | Pubmed ID: 20439313
Towards the systematic discovery of signal transduction networks using phosphorylation dynamics data.
BMC bioinformatics , 2010 | Pubmed ID: 20459641
Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants.
Plant physiology Jul, 2010 | Pubmed ID: 20466843
Transcription-associated mutagenesis increases protein sequence diversity more effectively than does random mutagenesis in Escherichia coli.
PloS one May, 2010 | Pubmed ID: 20479947
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
Prediction of metabolite identity from accurate mass, migration time prediction and isotopic pattern information in CE-TOFMS data.
Electrophoresis Jul, 2010 | Pubmed ID: 20568260
Protein complex prediction via verifying and reconstructing the topology of domain-domain interactions.
BMC bioinformatics Jun, 2010 | Pubmed ID: 20584269
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
Chemical dephosphorylation for identification of multiply phosphorylated peptides and phosphorylation site determination.
Rapid communications in mass spectrometry : RCM Aug, 2010 | Pubmed ID: 20623713
A metabolic model of human erythrocytes: practical application of the E-Cell Simulation Environment.
Journal of biomedicine & biotechnology , 2010 | Pubmed ID: 20625505
Collective dynamics of specific gene ensembles crucial for neutrophil differentiation: the existence of genome vehicles revealed.
PloS one Aug, 2010 | Pubmed ID: 20725638
An extreme thermophile, Thermus thermophilus, is a polyploid bacterium.
Journal of bacteriology Oct, 2010 | Pubmed ID: 20729360
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
Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes.
BMC genomics Jan, 2011 | Pubmed ID: 21223577
Integrative features of the yeast phosphoproteome and protein-protein interaction map.
PLoS computational biology , 2011 | Pubmed ID: 21298081
Serum metabolomics reveals γ-glutamyl dipeptides as biomarkers for discrimination among different forms of liver disease.
Journal of hepatology Oct, 2011 | Pubmed ID: 21334394
Computational analysis suggests a highly bendable, fragile structure for nucleosomal DNA.
Gene May, 2011 | Pubmed ID: 21338662
OryzaPG-DB: rice proteome database based on shotgun proteogenomics.
BMC plant biology Apr, 2011 | Pubmed ID: 21486466
KBWS: an EMBOSS associated package for accessing bioinformatics web services.
Source code for biology and medicine Apr, 2011 | Pubmed ID: 21529350
Positive autoregulation delays the expression phase of mammalian clock gene Per2.
PloS one Apr, 2011 | Pubmed ID: 21533189
A screening system for artificial small RNAs that inhibit the growth of Escherichia coli.
Journal of biochemistry Sep, 2011 | Pubmed ID: 21546360
Redox regulation in respiring Saccharomyces cerevisiae.
Biochimica et biophysica acta Oct, 2011 | Pubmed ID: 21549177
Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes.
BMC medical genomics May, 2011 | Pubmed ID: 21575255
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
Metabolic flux analysis and visualization.
Journal of proteome research Aug, 2011 | Pubmed ID: 21815690
Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification.
BMC genomics , 2011 | Pubmed ID: 21846408
Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli.
BMC genomics Aug, 2011 | Pubmed ID: 21864382
A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity.
Nucleic acids research Dec, 2011 | Pubmed ID: 21880595
Microscale phosphoproteome analysis of 10,000 cells from human cancer cell lines.
Analytical chemistry Oct, 2011 | Pubmed ID: 21888424
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
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
MMMDB: Mouse Multiple Tissue Metabolome Database.
Nucleic acids research Jan, 2012 | Pubmed ID: 22139941
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
Time-structure of the yeast metabolism in vivo.
Advances in experimental medicine and biology , 2012 | Pubmed ID: 22161340
Nematode-specific tRNAs that decode an alternative genetic code for leucine.
Nucleic acids research Apr, 2012 | Pubmed ID: 22187151
The third plasmid pVV8 from Thermus thermophilus HB8: isolation, characterization, and sequence determination.
Extremophiles : life under extreme conditions Mar, 2012 | Pubmed ID: 22212656
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
Enhancing apoptosis in TRAIL-resistant cancer cells using fundamental response rules.
Scientific reports , 2011 | Pubmed ID: 22355661
Genomic heterogeneity in a natural archaeal population suggests a model of tRNA gene disruption.
PloS one , 2012 | Pubmed ID: 22403667
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
Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis.
Current bioinformatics Mar, 2012 | Pubmed ID: 22438836
Validation of bacterial replication termination models using simulation of genomic mutations.
PloS one , 2012 | Pubmed ID: 22509315
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
Cancer. Systems biology, metabolomics, and cancer metabolism.
Science (New York, N.Y.) May, 2012 | Pubmed ID: 22628644
The Rice Proteogenomics Database OryzaPG-DB: Development, Expansion, and New Features.
Frontiers in plant science , 2012 | Pubmed ID: 22639657
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
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
Rapid DNA, RNA and protein extraction protocols optimized for slow continuously growing yeast cultures.
Yeast (Chichester, England) Aug, 2012 | Pubmed ID: 22763810
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
Metabolomic profiling rationalized pyruvate efficacy in cybrid cells harboring MELAS mitochondrial DNA mutations.
Mitochondrion Nov, 2012 | Pubmed ID: 22884939
Measures of compositional strand bias related to replication machinery and its applications.
Current genomics Mar, 2012 | Pubmed ID: 22942671
A yeast metabolite extraction protocol optimised for time-series analyses.
PloS one , 2012 | Pubmed ID: 22952947
Temporal profiling of lapatinib-suppressed phosphorylation signals in EGFR/HER2 pathways.
Molecular & cellular proteomics : MCP Dec, 2012 | Pubmed ID: 22964224
Sheathless capillary electrophoresis-mass spectrometry with a high-sensitivity porous sprayer for cationic metabolome analysis.
The Analyst Nov, 2012 | Pubmed ID: 23000847
Metabolic profiling reveals new serum biomarkers for differentiating diabetic nephropathy.
Analytical and bioanalytical chemistry Dec, 2012 | Pubmed ID: 23052862
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
Identification of a replication initiation protein of the pVV8 plasmid from Thermus thermophilus HB8.
Extremophiles : life under extreme conditions Jan, 2013 | Pubmed ID: 23114983
Is central dogma a global property of cellular information flow?
Frontiers in physiology , 2012 | Pubmed ID: 23189060
A medium-chain fatty acid as an alternative energy source in mouse preimplantation development.
Scientific reports , 2012 | Pubmed ID: 23226596
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
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
Computational analysis of associations between alternative splicing and histone modifications.
FEBS letters Mar, 2013 | Pubmed ID: 23353998
Merging multiple omics datasets in silico: statistical analyses and data interpretation.
Methods in molecular biology (Clifton, N.J.) , 2013 | Pubmed ID: 23417818
Global microRNA elevation by inducible Exportin 5 regulates cell cycle entry.
RNA (New York, N.Y.) Apr, 2013 | Pubmed ID: 23431327
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
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
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
Quantitative assay for TALEN activity at endogenous genomic loci.
Biology open Apr, 2013 | Pubmed ID: 23616919
Time-resolved metabolomics of a novel trebouxiophycean alga using (13)CO2 feeding.
Journal of bioscience and bioengineering Sep, 2013 | Pubmed ID: 23706992
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
Capillary electrophoresis-mass spectrometry-based metabolome analysis of serum and saliva from neurodegenerative dementia patients.
Electrophoresis Oct, 2013 | Pubmed ID: 23857558
GEMBASSY: an EMBOSS associated software package for comprehensive genome analyses.
Source code for biology and medicine Aug, 2013 | Pubmed ID: 23987304
A systems biology approach to suppress TNF-induced proinflammatory gene expressions.
Cell communication and signaling : CCS Nov, 2013 | Pubmed ID: 24199619
Dynamic simulation and metabolome analysis of long-term erythrocyte storage in adenine-guanosine solution.
PloS one , 2013 | Pubmed ID: 24205395
Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells.
Nature Dec, 2013 | Pubmed ID: 24226770
Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol.
Nature communications , 2014 | Pubmed ID: 24481126
Comparative metabolite profiling of foxglove aphids (Aulacorthum solani Kaltenbach) on leaves of resistant and susceptible soybean strains.
Molecular bioSystems Apr, 2014 | Pubmed ID: 24514152
Exceptional evolutionary divergence of human muscle and brain metabolomes parallels human cognitive and physical uniqueness.
PLoS biology May, 2014 | Pubmed ID: 24866127
Undesigned selection for replication termination of bacterial chromosomes.
Journal of molecular biology Aug, 2014 | Pubmed ID: 24946150
Quantifying periodicity in omics data.
Frontiers in cell and developmental biology , 2014 | Pubmed ID: 25364747
Transcriptome-wide variability in single embryonic development cells.
Scientific reports Nov, 2014 | Pubmed ID: 25409746
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
Effect of codon adaptation on codon-level and gene-level translation efficiency in vivo.
BMC genomics Dec, 2014 | Pubmed ID: 25512115
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
Systems Biology Strategy Reveals PKCδ is Key for Sensitizing TRAIL-Resistant Human Fibrosarcoma.
Frontiers in immunology , 2014 | Pubmed ID: 25601862
Analysis of genetic code ambiguity arising from nematode-specific misacylated tRNAs.
PloS one , 2015 | Pubmed ID: 25602944
Organization and evolution of brain lipidome revealed by large-scale analysis of human, chimpanzee, macaque, and mouse tissues.
Neuron Feb, 2015 | Pubmed ID: 25661180
Effects of processing and storage conditions on charged metabolomic profiles in blood.
Electrophoresis Sep, 2015 | Pubmed ID: 25820922
Alteration of metabolomic profiles by titanium dioxide nanoparticles in human gingivitis model.
Biomaterials Jul, 2015 | Pubmed ID: 25913073
Method of preparing an equimolar DNA mixture for one-step DNA assembly of over 50 fragments.
Scientific reports May, 2015 | Pubmed ID: 25990947
Tracking global gene expression responses in T cell differentiation.
Gene Sep, 2015 | Pubmed ID: 26028587
Particle Simulation of Oxidation Induced Band 3 Clustering in Human Erythrocytes.
PLoS computational biology Jun, 2015 | Pubmed ID: 26046580
Precise mapping and dynamics of tRNA-derived fragments (tRFs) in the development of Triops cancriformis (tadpole shrimp).
BMC genetics Jul, 2015 | Pubmed ID: 26168920
Metabolomic alterations in human cancer cells by vitamin C-induced oxidative stress.
Scientific reports Sep, 2015 | Pubmed ID: 26350063
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
Expansion of Noncanonical V-Arm-Containing tRNAs in Eukaryotes.
Molecular biology and evolution Feb, 2016 | Pubmed ID: 26545920
Evaluation of the impact of RNA preservation methods of spiders for de novo transcriptome assembly.
Molecular ecology resources May, 2016 | Pubmed ID: 26561354
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
G-Links: a gene-centric link acquisition service.
F1000Research , 2014 | Pubmed ID: 26673001
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
Conversion of graded phosphorylation into switch-like nuclear translocation via autoregulatory mechanisms in ERK signalling.
Nature communications Jan, 2016 | Pubmed ID: 26786866
The Consumption of Bicarbonate-Rich Mineral Water Improves Glycemic Control.
Evidence-based complementary and alternative medicine : eCAM , 2015 | Pubmed ID: 26798400
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
De novo assembly and comparative transcriptome analysis of Euglena gracilis in response to anaerobic conditions.
BMC genomics Mar, 2016 | Pubmed ID: 26939900
Taxonomic revision of oil-producing green algae, Chlorococcum oleofaciens (Volvocales, Chlorophyceae), and its relatives.
Journal of phycology Oct, 2015 | Pubmed ID: 26986894
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
Profiling of plasma metabolites in postmenopausal women with metabolic syndrome.
Menopause (New York, N.Y.) 07, 2016 | Pubmed ID: 27070805
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
Smad2/3 Proteins Are Required for Immobilization-induced Skeletal Muscle Atrophy.
The Journal of biological chemistry Jun, 2016 | Pubmed ID: 27129272
Draft Genome Sequences of 37 Salmonella enterica Strains Isolated from Poultry Sources in Nigeria.
Genome announcements May, 2016 | Pubmed ID: 27151793
Simultaneous analysis of consumer variables, acceptability and sensory characteristics of dry-cured ham.
Meat science Nov, 2016 | Pubmed ID: 27343459
Serum metabolome profiles characterized by patients with hepatocellular carcinoma associated with hepatitis B and C.
World journal of gastroenterology Jul, 2016 | Pubmed ID: 27468212
Genome sequencing of a single tardigrade Hypsibius dujardini individual.
Scientific data 08, 2016 | Pubmed ID: 27529330
Identification of salivary metabolomic biomarkers for oral cancer screening.
Scientific reports 08, 2016 | Pubmed ID: 27539254
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
Metabolic Profiling of Total Physical Activity and Sedentary Behavior in Community-Dwelling Men.
PloS one , 2016 | Pubmed ID: 27741291
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
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
Systematic characterization of artificial small RNA-mediated inhibition of Escherichia coli growth.
RNA biology 02, 2017 | Pubmed ID: 27981881
A serum metabolomics-based profile in low bone mineral density postmenopausal women.
Bone 02, 2017 | Pubmed ID: 27989648
Effect of timing of collection of salivary metabolomic biomarkers on oral cancer detection.
Amino acids 04, 2017 | Pubmed ID: 28101653
Rearing and observation of immature stages of the hoverfly (Diptera, Syrphidae).
Biodiversity data journal , 2016 | Pubmed ID: 28174503
Differential Binding of Three Major Human ADAR Isoforms to Coding and Long Non-Coding Transcripts.
Genes Feb, 2017 | Pubmed ID: 28208661
Synthetic Biomarker Design by Using Analyte-Responsive Acetaminophen.
Chembiochem : a European journal of chemical biology 05, 2017 | Pubmed ID: 28236354
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
Eggshell membrane powder ameliorates intestinal inflammation by facilitating the restitution of epithelial injury and alleviating microbial dysbiosis.
Scientific reports Mar, 2017 | Pubmed ID: 28272447
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
Serum Metabolomic Profiles for Human Pancreatic Cancer Discrimination.
International journal of molecular sciences Apr, 2017 | Pubmed ID: 28375170
Thymidine Catabolism as a Metabolic Strategy for Cancer Survival.
Cell reports 05, 2017 | Pubmed ID: 28514652
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
Dynamic Organization of Chromatin Domains Revealed by Super-Resolution Live-Cell Imaging.
Molecular cell Jul, 2017 | Pubmed ID: 28712725
Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus.
PLoS biology Jul, 2017 | Pubmed ID: 28749982
Effect of masticatory stimulation on the quantity and quality of saliva and the salivary metabolomic profile.
PloS one , 2017 | Pubmed ID: 28813487
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
Effects of 3-styrylchromones on metabolic profiles and cell death in oral squamous cell carcinoma cells.
Toxicology reports , 2015 | Pubmed ID: 28962471
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
eRP arrangement: a strategy for assembled genomic contig rearrangement based on replication profiling in bacteria.
BMC genomics Oct, 2017 | Pubmed ID: 29029602
Evolutionary Analysis of HIV-1 Pol Proteins Reveals Representative Residues for Viral Subtype Differentiation.
Frontiers in microbiology , 2017 | Pubmed ID: 29163435
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
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
Reliability of plasma polar metabolite concentrations in a large-scale cohort study using capillary electrophoresis-mass spectrometry.
PloS one , 2018 | Pubmed ID: 29346414
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
Elevated Polyamines in Saliva of Pancreatic Cancer.
Cancers Feb, 2018 | Pubmed ID: 29401744
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
Human AK2 links intracellular bioenergetic redistribution to the fate of hematopoietic progenitors.
Biochemical and biophysical research communications 03, 2018 | Pubmed ID: 29462620
Development of a sheathless CE-ESI-MS interface.
Electrophoresis Jun, 2018 | Pubmed ID: 29493797
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
Thymidine catabolism promotes NADPH oxidase-derived reactive oxygen species (ROS) signalling in KB and yumoto cells.
Scientific reports Apr, 2018 | Pubmed ID: 29713062
Tuning Gene Activity by Inducible and Targeted Regulation of Gene Expression in Minimal Bacterial Cells.
ACS synthetic biology Jun, 2018 | Pubmed ID: 29786424
Changes of liver metabolites following hepatectomy with ischemia reperfusion towards liver regeneration.
Annals of gastroenterological surgery May, 2018 | Pubmed ID: 29863192
Far rapid synthesis of giant DNA in the Bacillus subtilis genome by a conjugation transfer system.
Scientific reports Jun, 2018 | Pubmed ID: 29884789
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
MICOP: Maximal information coefficient-based oscillation prediction to detect biological rhythms in proteomics data.
BMC bioinformatics Jun, 2018 | Pubmed ID: 29954316
Metabolomics-based profiles predictive of low bone mass in menopausal women.
Bone reports Dec, 2018 | Pubmed ID: 29955645
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
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