Published in Anal Sci on January 01, 2008
BUB1 and BUBR1: multifaceted kinases of the cell cycle. Trends Biochem Sci (2010) 1.99
GSK3beta phosphorylation modulates CLASP-microtubule association and lamella microtubule attachment. J Cell Biol (2009) 1.95
Regulation of mTOR complex 1 (mTORC1) by raptor Ser863 and multisite phosphorylation. J Biol Chem (2009) 1.53
Mammalian peroxisomal ABC transporters: from endogenous substrates to pathology and clinical significance. Br J Pharmacol (2011) 1.13
UBXN7 docks on neddylated cullin complexes using its UIM motif and causes HIF1α accumulation. BMC Biol (2012) 1.10
Ser/Thr/Tyr protein phosphorylation in the archaeon Halobacterium salinarum--a representative of the third domain of life. PLoS One (2009) 1.10
Defining the molecular basis of BubR1 kinetochore interactions and APC/C-CDC20 inhibition. J Biol Chem (2010) 1.08
Cardiac mitochondrial matrix and respiratory complex protein phosphorylation. Am J Physiol Heart Circ Physiol (2012) 1.01
PTMs in conversation: activity and function of deubiquitinating enzymes regulated via post-translational modifications. Cell Biochem Biophys (2011) 1.00
Enrichment techniques employed in phosphoproteomics. Amino Acids (2011) 0.99
Partners and post-translational modifications of nuclear lamins. Chromosoma (2013) 0.97
Identification of PTPsigma as an autophagic phosphatase. J Cell Sci (2011) 0.95
The enzymes of human diphosphoinositol polyphosphate metabolism. FEBS J (2013) 0.92
In silico analysis of phosphoproteome data suggests a rich-get-richer process of phosphosite accumulation over evolution. Mol Cell Proteomics (2009) 0.91
DEAD-box helicases: posttranslational regulation and function. Biochem Biophys Res Commun (2010) 0.89
Identification of Myb-binding protein 1A (MYBBP1A) as a novel substrate for aurora B kinase. J Biol Chem (2010) 0.89
Molecular characterization, expression analysis, and role of ALDH3B1 in the cellular protection against oxidative stress. Free Radic Biol Med (2010) 0.87
Regulation of ABC transporter function via phosphorylation by protein kinases. Curr Pharm Biotechnol (2011) 0.86
Structural biology of DNA repair: spatial organisation of the multicomponent complexes of nonhomologous end joining. J Nucleic Acids (2010) 0.84
The identification of raptor as a substrate for p44/42 MAPK. Endocrinology (2011) 0.83
Novel Ser/Thr protein phosphatase 5 (PP5) regulated targets during DNA damage identified by proteomics analysis. J Proteome Res (2010) 0.82
ERK crosstalks with 4EBP1 to activate cyclin D1 translation during quinol-thioether-induced tuberous sclerosis renal cell carcinoma. Toxicol Sci (2011) 0.81
Cell cycle-regulated protein abundance changes in synchronously proliferating HeLa cells include regulation of pre-mRNA splicing proteins. PLoS One (2013) 0.81
Insulin-stimulated phosphorylation of protein phosphatase 1 regulatory subunit 12B revealed by HPLC-ESI-MS/MS. Proteome Sci (2012) 0.79
Protein kinase Cα phosphorylates a novel argininosuccinate synthase site at serine 328 during calcium-dependent stimulation of endothelial nitric-oxide synthase in vascular endothelial cells. J Biol Chem (2012) 0.79
Systems Proteomics View of the Endogenous Human Claudin Protein Family. J Proteome Res (2016) 0.79
A bird's-eye view of post-translational modifications in the spliceosome and their roles in spliceosome dynamics. Mol Biosyst (2010) 0.78
Akt Phosphorylates Wnt Coactivator and Chromatin Effector Pygo2 at Serine 48 to Antagonize Its Ubiquitin/Proteasome-mediated Degradation. J Biol Chem (2015) 0.76
Quantitative analysis of global phosphorylation changes with high-resolution tandem mass spectrometry and stable isotopic labeling. Methods (2013) 0.75
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol (2006) 40.15
Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal Chem (2003) 13.58
Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc (2007) 10.71
Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science (2007) 5.87
Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry. Nature (2002) 5.48
Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell (2005) 4.78
Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. J Proteome Res (2003) 4.36
Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res (2006) 4.25
Splicing factor SF3b as a target of the antitumor natural product pladienolide. Nat Chem Biol (2007) 3.97
Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs. Proc Natl Acad Sci U S A (2009) 3.64
Quantitative metabolome profiling of colon and stomach cancer microenvironment by capillary electrophoresis time-of-flight mass spectrometry. Cancer Res (2009) 3.50
Type 2C protein phosphatases directly regulate abscisic acid-activated protein kinases in Arabidopsis. Proc Natl Acad Sci U S A (2009) 3.28
Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumption. J Biol Chem (2006) 3.23
Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res (2003) 2.63
PINK1-mediated phosphorylation of the Parkin ubiquitin-like domain primes mitochondrial translocation of Parkin and regulates mitophagy. Sci Rep (2012) 2.60
Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics (2003) 2.57
Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Mol Syst Biol (2008) 2.49
Six classes of nuclear localization signals specific to different binding grooves of importin alpha. J Biol Chem (2008) 2.26
Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol Syst Biol (2009) 2.11
Capillary electrophoresis mass spectrometry-based saliva metabolomics identified oral, breast and pancreatic cancer-specific profiles. Metabolomics (2009) 2.03
Simultaneous determination of anionic intermediates for Bacillus subtilis metabolic pathways by capillary electrophoresis electrospray ionization mass spectrometry. Anal Chem (2002) 2.00
Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics. Nat Protoc (2011) 1.99
Permuted tRNA genes expressed via a circular RNA intermediate in Cyanidioschyzon merolae. Science (2007) 1.98
Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications. Mol Cell Proteomics (2007) 1.95
Large-scale comparative phosphoproteomics identifies conserved phosphorylation sites in plants. Plant Physiol (2010) 1.93
Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico. FEBS Lett (2005) 1.87
Quantitative mouse brain proteomics using culture-derived isotope tags as internal standards. Nat Biotechnol (2005) 1.76
Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics (2009) 1.73
LGI1 and LGI4 bind to ADAM22, ADAM23 and ADAM11. Int J Biol Sci (2008) 1.72
MathDAMP: a package for differential analysis of metabolite profiles. BMC Bioinformatics (2006) 1.68
Visualization of three-way comparisons of omics data. BMC Bioinformatics (2007) 1.66
On dynamics of overlapping genes in bacterial genomes. Gene (2003) 1.65
Phase transfer surfactant-aided trypsin digestion for membrane proteome analysis. J Proteome Res (2008) 1.64
KEGG-based pathway visualization tool for complex omics data. In Silico Biol (2005) 1.64
Simultaneous determination of the main metabolites in rice leaves using capillary electrophoresis mass spectrometry and capillary electrophoresis diode array detection. Plant J (2004) 1.63
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. PLoS One (2009) 1.57
Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism. Mol Syst Biol (2009) 1.52
Genetics and phosphoproteomics reveal a protein phosphorylation network in the abscisic acid signaling pathway in Arabidopsis thaliana. Sci Signal (2013) 1.51
A multi-algorithm, multi-timescale method for cell simulation. Bioinformatics (2004) 1.48
Complete mutation analysis panel of the 39 human HOX genes. Teratology (2002) 1.47
MEGU: pathway mapping web-service based on KEGG and SVG. In Silico Biol (2006) 1.44
emPAI Calc--for the estimation of protein abundance from large-scale identification data by liquid chromatography-tandem mass spectrometry. Bioinformatics (2009) 1.43
A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. FEBS Lett (2003) 1.42
A systematic survey of in vivo obligate chaperonin-dependent substrates. EMBO J (2010) 1.41
Depiction of metabolome changes in histidine-starved Escherichia coli by CE-TOFMS. Mol Biosyst (2007) 1.41
Metabolomic profiling of anionic metabolites by capillary electrophoresis mass spectrometry. Anal Chem (2009) 1.40
Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila. Genes Cells (2005) 1.36
Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales. Mol Biol Evol (2008) 1.36
Nuclear export signal consensus sequences defined using a localization-based yeast selection system. Traffic (2008) 1.36
SPLITS: a new program for predicting split and intron-containing tRNA genes at the genome level. In Silico Biol (2006) 1.33
Computational comparative analyses of alternative splicing regulation using full-length cDNA of various eukaryotes. RNA (2004) 1.33
Computational methods for microRNA target prediction. Methods Enzymol (2007) 1.32
Bioinformatics Tools for Mass Spectroscopy-Based Metabolomic Data Processing and Analysis. Curr Bioinform (2012) 1.31
Serum metabolomics reveals γ-glutamyl dipeptides as biomarkers for discrimination among different forms of liver disease. J Hepatol (2011) 1.30
Design of peptide inhibitors for the importin alpha/beta nuclear import pathway by activity-based profiling. Chem Biol (2008) 1.30
Unbiased quantitation of Escherichia coli membrane proteome using phase transfer surfactants. Mol Cell Proteomics (2009) 1.30
Efficient in-gel digestion procedure using 5-cyclohexyl-1-pentyl-beta-D-maltoside as an additive for gel-based membrane proteomics. Rapid Commun Mass Spectrom (2004) 1.27
mTORC1 is essential for leukemia propagation but not stem cell self-renewal. J Clin Invest (2012) 1.27
A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation. Syst Synth Biol (2009) 1.26
GC-compositional strand bias around transcription start sites in plants and fungi. BMC Genomics (2005) 1.25
Metabolomic anatomy of an animal model revealing homeostatic imbalances in dyslipidaemia. Mol Biosyst (2011) 1.24
Roles of hemoglobin Allostery in hypoxia-induced metabolic alterations in erythrocytes: simulation and its verification by metabolome analysis. J Biol Chem (2007) 1.24
Quantitative assay for TALEN activity at endogenous genomic loci. Biol Open (2013) 1.22
An extreme thermophile, Thermus thermophilus, is a polyploid bacterium. J Bacteriol (2010) 1.22
A protein associated with toll-like receptor 4 (PRAT4A) regulates cell surface expression of TLR4. J Immunol (2006) 1.21
Transcriptional regulation by Pol II(G) involving mediator and competitive interactions of Gdown1 and TFIIF with Pol II. Mol Cell (2012) 1.18
Personalized medicine and proteomics: lessons from non-small cell lung cancer. J Proteome Res (2007) 1.18
Comparative expression analysis uncovers novel features of endogenous antisense transcription. Hum Mol Genet (2008) 1.18
GEM System: automatic prototyping of cell-wide metabolic pathway models from genomes. BMC Bioinformatics (2006) 1.18
One-dimensional capillary liquid chromatographic separation coupled with tandem mass spectrometry unveils the Escherichia coli proteome on a microarray scale. Anal Chem (2010) 1.18
Metabolomic profiling of lung and prostate tumor tissues by capillary electrophoresis time-of-flight mass spectrometry. Metabolomics (2012) 1.17
In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs. RNA (2007) 1.17
A comprehensive resource of interacting protein regions for refining human transcription factor networks. PLoS One (2010) 1.17
Metabolomics approach for enzyme discovery. J Proteome Res (2006) 1.16
A new role for expressed pseudogenes as ncRNA: regulation of mRNA stability of its homologous coding gene. J Mol Med (Berl) (2004) 1.16
Deep sequencing reveals as-yet-undiscovered small RNAs in Escherichia coli. BMC Genomics (2011) 1.16
Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non-pathogenic Pseudomonas species. Proteomics (2009) 1.15
Bioinformatic analysis of post-transcriptional regulation by uORF in human and mouse. FEBS Lett (2007) 1.14
Reverse engineering of biochemical equations from time-course data by means of genetic programming. Biosystems (2004) 1.13
Signaling flux redistribution at toll-like receptor pathway junctions. PLoS One (2008) 1.12
A mathematical model for the Kai-protein-based chemical oscillator and clock gene expression rhythms in cyanobacteria. J Biol Rhythms (2007) 1.12
Cleavage of double-stranded RNA by RNase HI from a thermoacidophilic archaeon, Sulfolobus tokodaii 7. Nucleic Acids Res (2004) 1.12
Analysis of nucleotides by pressure-assisted capillary electrophoresis-mass spectrometry using silanol mask technique. J Chromatogr A (2007) 1.12
Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data. Genome Res (2002) 1.11
Pressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anions. Anal Chem (2002) 1.09