Published in Dev Growth Differ on October 01, 2004
Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway. Biochem J (2005) 1.70
Akt versus p53 in a network of oncogenes and tumor suppressor genes regulating cell survival and death. Biophys J (2006) 1.20
Kinetic analysis of neurotrophin-3-mediated differentiation of embryonic stem cells into neurons. Tissue Eng Part A (2009) 0.76
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol (2006) 40.15
Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science (2007) 5.87
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
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
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
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
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
Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci U S A (2014) 1.91
Space in systems biology of signaling pathways--towards intracellular molecular crowding in silico. FEBS Lett (2005) 1.87
Genome Projector: zoomable genome map with multiple views. BMC Bioinformatics (2009) 1.73
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
Validation of the Japanese version of the Roland-Morris Disability Questionnaire. J Orthop Sci (2003) 1.58
Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API. PLoS One (2009) 1.57
An anatomic study of the sacral hiatus: a basis for successful caudal epidural block. Clin J Pain (2003) 1.52
Systematic phenome analysis of Escherichia coli multiple-knockout mutants reveals hidden reactions in central carbon metabolism. Mol Syst Biol (2009) 1.52
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
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
JOA back pain evaluation questionnaire: initial report. J Orthop Sci (2007) 1.40
Identification and expression analysis of putative mRNA-like non-coding RNA in Drosophila. Genes Cells (2005) 1.36
Nuclear export signal consensus sequences defined using a localization-based yeast selection system. Traffic (2008) 1.36
Comprehensive analysis of archaeal tRNA genes reveals rapid increase of tRNA introns in the order thermoproteales. Mol Biol Evol (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
Experimental spinal stenosis: relationship between degree of cauda equina compression, neuropathology, and pain. Spine (Phila Pa 1976) (2004) 1.31
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
The histologic effects of pulsed and continuous radiofrequency lesions at 42 degrees C to rat dorsal root ganglion and sciatic nerve. Spine (Phila Pa 1976) (2005) 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
Development of a clinical diagnosis support tool to identify patients with lumbar spinal stenosis. Eur Spine J (2007) 1.30
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
Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J (2014) 1.22
Transcriptome sequences resolve deep relationships of the grape family. PLoS One (2013) 1.22
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
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
Mycobacterium bovis BCG vertebral osteomyelitis after intravesical BCG therapy, diagnosed by PCR-based genomic deletion analysis. J Clin Microbiol (2007) 1.17
A comprehensive resource of interacting protein regions for refining human transcription factor networks. PLoS One (2010) 1.17
In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs. RNA (2007) 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
The sequence and analysis of a Chinese pig genome. Gigascience (2012) 1.15
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
Predictive value of self-reported patient information for the identification of lumbar spinal stenosis. Fam Pract (2008) 1.13
Reverse engineering of biochemical equations from time-course data by means of genetic programming. Biosystems (2004) 1.13
Inhibition of p38 MAP kinase activity enhances axonal regeneration. Exp Neurol (2003) 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
Inflammatory cytokines released from the facet joint tissue in degenerative lumbar spinal disorders. Spine (Phila Pa 1976) (2004) 1.11
Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data. Genome Res (2002) 1.11
Japanese Orthopaedic Association Cervical Myelopathy Evaluation Questionnaire: part 3. Determination of reliability. J Orthop Sci (2007) 1.10
Pressure-assisted capillary electrophoresis electrospray ionization mass spectrometry for analysis of multivalent anions. Anal Chem (2002) 1.09
Automated phosphoproteome analysis for cultured cancer cells by two-dimensional nanoLC-MS using a calcined titania/C18 biphasic column. Anal Sci (2008) 1.08
Tri-split tRNA is a transfer RNA made from 3 transcripts that provides insight into the evolution of fragmented tRNAs in archaea. Proc Natl Acad Sci U S A (2009) 1.07
Indeterminacy of reverse engineering of Gene Regulatory Networks: the curse of gene elasticity. PLoS One (2007) 1.07
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. Biotechnol Prog (2010) 1.06
Prediction of non-coding and antisense RNA genes in Escherichia coli with Gapped Markov Model. Gene (2006) 1.05
Infliximab attenuates immunoreactivity of brain-derived neurotrophic factor in a rat model of herniated nucleus pulposus. Spine (Phila Pa 1976) (2004) 1.04
A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic Acids Res (2011) 1.04
Emergent genome-wide control in wildtype and genetically mutated lipopolysaccarides-stimulated macrophages. PLoS One (2009) 1.04
Prediction of liquid chromatographic retention times of peptides generated by protease digestion of the Escherichia coli proteome using artificial neural networks. J Proteome Res (2006) 1.03
Informatics for peptide retention properties in proteomic LC-MS. Proteomics (2008) 1.03
Characteristics and clustering of human ribosomal protein genes. BMC Genomics (2006) 1.03
Position-specific expression of Hox genes along the gastrointestinal tract. Congenit Anom (Kyoto) (2004) 1.02
The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection. Evol Bioinform Online (2007) 1.02