Published in RNA on July 01, 2004
Protein modularity of alternatively spliced exons is associated with tissue-specific regulation of alternative splicing. PLoS Genet (2005) 2.63
Sequence conservation, relative isoform frequencies, and nonsense-mediated decay in evolutionarily conserved alternative splicing. Proc Natl Acad Sci U S A (2005) 1.93
Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences. Proc Natl Acad Sci U S A (2005) 1.88
Distribution of SR protein exonic splicing enhancer motifs in human protein-coding genes. Nucleic Acids Res (2005) 1.70
Regulation of alternative splicing by the core spliceosomal machinery. Genes Dev (2011) 1.60
Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. Mol Cell (2013) 1.56
Characteristics and regulatory elements defining constitutive splicing and different modes of alternative splicing in human and mouse. RNA (2005) 1.28
DEDB: a database of Drosophila melanogaster exons in splicing graph form. BMC Bioinformatics (2004) 1.20
A novel intronic cis element, ISE/ISS-3, regulates rat fibroblast growth factor receptor 2 splicing through activation of an upstream exon and repression of a downstream exon containing a noncanonical branch point sequence. Mol Cell Biol (2005) 1.19
Positive selection acting on splicing motifs reflects compensatory evolution. Genome Res (2008) 1.18
Where do introns come from? PLoS Biol (2008) 1.10
The effect of intron length on exon creation ratios during the evolution of mammalian genomes. RNA (2008) 1.07
Solution conformation and thermodynamic characteristics of RNA binding by the splicing factor U2AF65. J Biol Chem (2008) 1.03
Exon creation and establishment in human genes. Genome Biol (2008) 0.98
Widespread recognition of 5' splice sites by noncanonical base-pairing to U1 snRNA involving bulged nucleotides. Genes Dev (2012) 0.98
Differentiated evolutionary rates in alternative exons and the implications for splicing regulation. BMC Evol Biol (2006) 0.93
Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3. BMC Genet (2009) 0.92
Alternative approach to a heavy weight problem. Genome Res (2007) 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
U2AF65 adapts to diverse pre-mRNA splice sites through conformational selection of specific and promiscuous RNA recognition motifs. Nucleic Acids Res (2013) 0.88
Fast splice site detection using information content and feature reduction. BMC Bioinformatics (2008) 0.86
COMIT: identification of noncoding motifs under selection in coding sequences. Genome Biol (2009) 0.85
A DNA damage signal activates and derepresses exon inclusion in Drosophila TAF1 alternative splicing. RNA (2008) 0.83
Evolutionary divergence of exon flanks: a dissection of mutability and selection. Genetics (2006) 0.80
Prediction of alternatively skipped exons and splicing enhancers from exon junction arrays. BMC Genomics (2008) 0.78
Comparative component analysis of exons with different splicing frequencies. PLoS One (2009) 0.75
regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution. Hum Genet (2017) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47
A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res (1998) 22.69
Predictive identification of exonic splicing enhancers in human genes. Science (2002) 16.86
Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science (2003) 16.49
RNA splice junctions of different classes of eukaryotes: sequence statistics and functional implications in gene expression. Nucleic Acids Res (1987) 14.53
A genomic view of alternative splicing. Nat Genet (2002) 12.62
Sorting out the complexity of SR protein functions. RNA (2000) 9.25
Frequent alternative splicing of human genes. Genome Res (1999) 6.68
Functional annotation of a full-length Arabidopsis cDNA collection. Science (2002) 6.15
Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss. Nat Genet (2003) 6.09
Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1. Nat Genet (2002) 5.80
Information content of individual genetic sequences. J Theor Biol (1997) 5.62
Features of spliceosome evolution and function inferred from an analysis of the information at human splice sites. J Mol Biol (1992) 5.38
A computational analysis of sequence features involved in recognition of short introns. Proc Natl Acad Sci U S A (2001) 4.68
The human splicing factors ASF/SF2 and SC35 possess distinct, functionally significant RNA binding specificities. EMBO J (1995) 4.66
Discovery of regulatory elements by a computational method for phylogenetic footprinting. Genome Res (2002) 4.25
How prevalent is functional alternative splicing in the human genome? Trends Genet (2004) 3.81
A Drosophila full-length cDNA resource. Genome Biol (2002) 3.67
Alternative mRNA splicing. Annu Rev Cell Biol (1992) 2.74
New type of disease causing mutations: the example of the composite exonic regulatory elements of splicing in CFTR exon 12. Hum Mol Genet (2003) 2.60
Human Tra2 proteins are sequence-specific activators of pre-mRNA splicing. Cell (1998) 2.25
Factors influencing the identification of transcription factor binding sites by cross-species comparison. Genome Res (2002) 2.01
A novel algorithm for computational identification of contaminated EST libraries. Nucleic Acids Res (2003) 1.96
The Plasma Membrane H+-ATPase (A Highly Regulated Enzyme with Multiple Physiological Functions). Plant Physiol (1995) 1.83
Gene number. What if there are only 30,000 human genes? Science (2001) 1.83
Splice variation in mouse full-length cDNAs identified by mapping to the mouse genome. Genome Res (2002) 1.78
Molecular biology and evolution. Can genes explain biological complexity? Science (2001) 1.71
The human XPC DNA repair gene: arrangement, splice site information content and influence of a single nucleotide polymorphism in a splice acceptor site on alternative splicing and function. Nucleic Acids Res (2002) 1.58
A sequence compilation and comparison of exons that are alternatively spliced in neurons. Nucleic Acids Res (1994) 1.50
Similar splice-site mutations of the ATP7A gene lead to different phenotypes: classical Menkes disease or occipital horn syndrome. Am J Hum Genet (2000) 1.40
Factors affecting authentic 5' splice site selection in plant nuclei. Mol Cell Biol (1993) 1.26
Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data. Genome Res (2002) 1.11
Using information content and base frequencies to distinguish mutations from genetic polymorphisms in splice junction recognition sites. Hum Mutat (1995) 1.10
Introns and reading frames: correlation between splicing sites and their codon positions. Mol Biol Evol (1996) 1.09
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
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
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
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
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 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
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
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
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
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
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
Emergent genome-wide control in wildtype and genetically mutated lipopolysaccarides-stimulated macrophages. PLoS One (2009) 1.04
A novel three-unit tRNA splicing endonuclease found in ultrasmall Archaea possesses broad substrate specificity. Nucleic Acids Res (2011) 1.04
Informatics for peptide retention properties in proteomic LC-MS. Proteomics (2008) 1.03
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
Characteristics and clustering of human ribosomal protein genes. BMC Genomics (2006) 1.03
The GC skew index: a measure of genomic compositional asymmetry and the degree of replicational selection. Evol Bioinform Online (2007) 1.02
Position-specific expression of Hox genes along the gastrointestinal tract. Congenit Anom (Kyoto) (2004) 1.02
Evolution of ribonuclease H genes in prokaryotes to avoid inheritance of redundant genes. BMC Evol Biol (2007) 1.01
Computational analysis of microRNA-mediated antiviral defense in humans. FEBS Lett (2007) 1.01
Alignment-based approach for durable data storage into living organisms. Biotechnol Prog (2007) 1.00
Gene expression waves. Cell cycle independent collective dynamics in cultured cells. FEBS J (2007) 1.00
Computational analysis of microRNA targets in Caenorhabditis elegans. Gene (2005) 1.00
Metabolite profiling reveals YihU as a novel hydroxybutyrate dehydrogenase for alternative succinic semialdehyde metabolism in Escherichia coli. J Biol Chem (2009) 1.00
Inhibitory effect of phosphoenolpyruvate on glycolytic enzymes in Escherichia coli. Res Microbiol (2006) 0.99
Cooperative regulation for Okazaki fragment processing by RNase HII and FEN-1 purified from a hyperthermophilic archaeon, Pyrococcus furiosus. Biochem Biophys Res Commun (2003) 0.99
Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography. J Proteome Res (2008) 0.99
Comparative analysis of cis-encoded antisense RNAs in eukaryotes. Gene (2006) 0.98
Comprehensive prediction of chromosome dimer resolution sites in bacterial genomes. BMC Genomics (2011) 0.97
Time-resolved metabolomics reveals metabolic modulation in rice foliage. BMC Syst Biol (2008) 0.97
A problem in multivariate analysis of codon usage data and a possible solution. FEBS Lett (2005) 0.97
Evaluation of metabolic alteration in transgenic rice overexpressing dihydroflavonol-4-reductase. Ann Bot (2006) 0.97
Core promoter structure and genomic context reflect histone 3 lysine 9 acetylation patterns. BMC Genomics (2010) 0.96
Proteins as networks: usefulness of graph theory in protein science. Curr Protein Pept Sci (2008) 0.96