Published in Nucleic Acids Res on April 12, 2010
A dual platform approach to transcript discovery for the planarian Schmidtea mediterranea to establish RNAseq for stem cell and regeneration biology. PLoS One (2010) 1.16
Steroid receptor RNA activator protein binds to and counteracts SRA RNA-mediated activation of MyoD and muscle differentiation. Nucleic Acids Res (2010) 1.05
Correcting for differential transcript coverage reveals a strong relationship between alternative splicing and organism complexity. Mol Biol Evol (2014) 1.00
Dynamic usage of alternative splicing exons during mouse retina development. Nucleic Acids Res (2011) 0.97
Regulation of alternative splicing by the circadian clock and food related cues. Genome Biol (2012) 0.97
The Tpr protein regulates export of mRNAs with retained introns that traffic through the Nxf1 pathway. RNA (2011) 0.97
Low Dose Iron Treatments Induce a DNA Damage Response in Human Endothelial Cells within Minutes. PLoS One (2016) 0.91
ExoLocator--an online view into genetic makeup of vertebrate proteins. Nucleic Acids Res (2013) 0.80
JuncDB: an exon-exon junction database. Nucleic Acids Res (2015) 0.80
Evolutionary Character of Alternative Splicing in Plants. Bioinform Biol Insights (2016) 0.80
Evolution of gene structural complexity: an alternative-splicing-based model accounts for intron-containing retrogenes. Plant Physiol (2014) 0.80
Comparative analyses between retained introns and constitutively spliced introns in Arabidopsis thaliana using random forest and support vector machine. PLoS One (2014) 0.77
The dynamics of the alternatively spliced NOL7 gene products and role in nucleolar architecture. Nucleus (2011) 0.75
Alternative splicing affects the targeting sequence of peroxisome proteins in Arabidopsis. Plant Cell Rep (2017) 0.75
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
WebLogo: a sequence logo generator. Genome Res (2004) 59.58
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res (2006) 48.10
A greedy algorithm for aligning DNA sequences. J Comput Biol (2000) 47.89
miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res (2006) 39.25
The transcriptional landscape of the mammalian genome. Science (2005) 37.63
PatternHunter: faster and more sensitive homology search. Bioinformatics (2002) 35.65
Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods (2008) 31.04
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (2008) 29.99
Initial sequence of the chimpanzee genome and comparison with the human genome. Nature (2005) 25.67
The UCSC Table Browser data retrieval tool. Nucleic Acids Res (2004) 25.12
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet (2008) 24.51
Repbase Update, a database of eukaryotic repetitive elements. Cytogenet Genome Res (2005) 23.41
The UCSC Genome Browser Database: 2008 update. Nucleic Acids Res (2007) 23.13
Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res (2006) 20.92
RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
GenBank. Nucleic Acids Res (2007) 16.92
Genome-wide survey of human alternative pre-mRNA splicing with exon junction microarrays. Science (2003) 16.80
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol (2008) 13.96
Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol (2005) 13.21
A genomic view of alternative splicing. Nat Genet (2002) 12.62
Ensembl 2006. Nucleic Acids Res (2006) 11.66
Alternative splicing: new insights from global analyses. Cell (2006) 10.31
Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proc Natl Acad Sci U S A (2002) 10.28
Molecular phylogenetics and the origins of placental mammals. Nature (2001) 8.42
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res (2004) 8.35
Splicing in disease: disruption of the splicing code and the decoding machinery. Nat Rev Genet (2007) 7.42
Alternative splicing and genome complexity. Nat Genet (2001) 7.30
Patterns of variant polyadenylation signal usage in human genes. Genome Res (2000) 6.09
Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet (2007) 5.75
Lineage-specific biology revealed by a finished genome assembly of the mouse. PLoS Biol (2009) 5.45
snoRNA-LBME-db, a comprehensive database of human H/ACA and C/D box snoRNAs. Nucleic Acids Res (2006) 4.80
Genomewide comparative analysis of alternative splicing in plants. Proc Natl Acad Sci U S A (2006) 4.51
General and specific functions of exonic splicing silencers in splicing control. Mol Cell (2006) 3.76
Different levels of alternative splicing among eukaryotes. Nucleic Acids Res (2006) 3.07
Alternative splicing and RNA selection pressure--evolutionary consequences for eukaryotic genomes. Nat Rev Genet (2006) 3.00
Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach. BMC Genomics (2006) 2.98
Regulation of gene expression by alternative untranslated regions. Trends Genet (2006) 2.95
Selecting for functional alternative splices in ESTs. Genome Res (2002) 2.90
Nuclear mRNA export: insights from virology. Trends Biochem Sci (2003) 2.79
Intron retention is a major phenomenon in alternative splicing in Arabidopsis. Plant J (2004) 2.42
Alternative splicing of the Robo3 axon guidance receptor governs the midline switch from attraction to repulsion. Neuron (2008) 2.33
Genome-wide analysis of alternative pre-mRNA splicing in Arabidopsis thaliana based on full-length cDNA sequences. Nucleic Acids Res (2004) 2.19
Detection and evaluation of intron retention events in the human transcriptome. RNA (2004) 2.18
Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotes. Genome Res (2007) 1.86
Mining ChIP-chip data for transcription factor and cofactor binding sites. Bioinformatics (2005) 1.81
The ASAP II database: analysis and comparative genomics of alternative splicing in 15 animal species. Nucleic Acids Res (2006) 1.80
The coupling of alternative splicing and nonsense-mediated mRNA decay. Adv Exp Med Biol (2007) 1.77
An intron with a constitutive transport element is retained in a Tap messenger RNA. Nature (2006) 1.65
Patterns and rates of intron divergence between humans and chimpanzees. Genome Biol (2007) 1.61
Estimating rates of alternative splicing in mammals and invertebrates. Nat Genet (2004) 1.57
A phylogenomic study of human, dog, and mouse. PLoS Comput Biol (2006) 1.49
DBTSS provides a tissue specific dynamic view of Transcription Start Sites. Nucleic Acids Res (2009) 1.36
Intronic Alus influence alternative splicing. PLoS Genet (2008) 1.35
Extragenic accumulation of RNA polymerase II enhances transcription by RNA polymerase III. PLoS Genet (2007) 1.34
In vivo requirement of the small subunit of U2AF for recognition of a weak 3' splice site. Mol Cell Biol (2006) 1.33
Alternative splicing of intron 3 of the serine/arginine-rich protein 9G8 gene. Identification of flanking exonic splicing enhancers and involvement of 9G8 as a trans-acting factor. J Biol Chem (2000) 1.30
Comparative cross-species alternative splicing in plants. Plant Physiol (2007) 1.21
A new advance in alternative splicing databases: from catalogue to detailed analysis of regulation of expression and function of human alternative splicing variants. BMC Bioinformatics (2007) 1.21
Cytoplasmic BK(Ca) channel intron-containing mRNAs contribute to the intrinsic excitability of hippocampal neurons. Proc Natl Acad Sci U S A (2008) 1.20
Multifactorial interplay controls the splicing profile of Alu-derived exons. Mol Cell Biol (2008) 1.12
The Wilms' tumor 1 (WT1) gene (+KTS isoform) functions with a CTE to enhance translation from an unspliced RNA with a retained intron. Genes Dev (2006) 1.11
Intron retention generates a novel Id3 isoform that inhibits vascular lesion formation. J Biol Chem (2004) 1.10
Complex splicing control of the human Thrombopoietin gene by intronic G runs. Nucleic Acids Res (2006) 1.09
An apparent pseudo-exon acts both as an alternative exon that leads to nonsense-mediated decay and as a zero-length exon. Mol Cell Biol (2006) 1.07
Developmental regulation of a proinsulin messenger RNA generated by intron retention. EMBO Rep (2005) 1.06
A profile of alternative RNA splicing and transcript variation of CACNA1H, a human T-channel gene candidate for idiopathic generalized epilepsies. Hum Mol Genet (2006) 1.06
Conserved introns reveal novel transcripts in Drosophila melanogaster. Genome Res (2009) 1.01
Endothelial cell processing and alternatively spliced transcripts of factor VIII: potential implications for coagulation cascades and pulmonary hypertension. PLoS One (2010) 0.97
Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs. Nucleic Acids Res (2008) 0.97
Diversity of human U2AF splicing factors. FEBS J (2006) 0.96
Tandem insertions of Alu elements. Cytogenet Genome Res (2005) 0.88
DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation. Cell (2009) 3.66
Dynamic association of RNA-editing enzymes with the nucleolus. J Cell Sci (2003) 2.14
Intracellular macromolecular mobility measured by fluorescence recovery after photobleaching with confocal laser scanning microscopes. Mol Biol Cell (2004) 2.10
Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36. Nat Struct Mol Biol (2011) 1.85
The emerging role of splicing factors in cancer. EMBO Rep (2008) 1.83
The intranuclear mobility of messenger RNA binding proteins is ATP dependent and temperature sensitive. J Cell Biol (2002) 1.68
Chemical chaperones reduce endoplasmic reticulum stress and prevent mutant HFE aggregate formation. J Biol Chem (2007) 1.55
Macromolecular mobility inside the cell nucleus. Trends Cell Biol (2002) 1.53
Tissue-specific splicing factor gene expression signatures. Nucleic Acids Res (2008) 1.49
Genome-wide identification of functionally distinct subsets of cellular mRNAs associated with two nucleocytoplasmic-shuttling mammalian splicing factors. Genome Biol (2006) 1.49
RNA interference knockdown of hU2AF35 impairs cell cycle progression and modulates alternative splicing of Cdc25 transcripts. Mol Biol Cell (2006) 1.49
Clastosome: a subtype of nuclear body enriched in 19S and 20S proteasomes, ubiquitin, and protein substrates of proteasome. Mol Biol Cell (2002) 1.38
In vivo recruitment of exon junction complex proteins to transcription sites in mammalian cell nuclei. RNA (2004) 1.35
Protein phosphatase 1 binds to the RNA recognition motif of several splicing factors and regulates alternative pre-mRNA processing. Hum Mol Genet (2007) 1.33
In vivo requirement of the small subunit of U2AF for recognition of a weak 3' splice site. Mol Cell Biol (2006) 1.33
SUMO-1 modification alters ADAR1 editing activity. Mol Biol Cell (2005) 1.32
The spliceosome: a self-organized macromolecular machine in the nucleus? Trends Cell Biol (2009) 1.29
Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansion. Genome Res (2005) 1.28
A reaction-diffusion model to study RNA motion by quantitative fluorescence recovery after photobleaching. Biophys J (2007) 1.27
The CTD role in cotranscriptional RNA processing and surveillance. FEBS Lett (2008) 1.27
CPEB1 coordinates alternative 3'-UTR formation with translational regulation. Nature (2013) 1.23
Alternative splicing microarrays reveal functional expression of neuron-specific regulators in Hodgkin lymphoma cells. J Biol Chem (2004) 1.22
Data integration gets 'Sloppy'. Nat Biotechnol (2006) 1.17
Spliceosome assembly is coupled to RNA polymerase II dynamics at the 3' end of human genes. Nat Struct Mol Biol (2011) 1.15
A stochastic view of spliceosome assembly and recycling in the nucleus. PLoS Comput Biol (2007) 1.15
Expression of the human RNA-binding protein HuR in Trypanosoma brucei increases the abundance of mRNAs containing AU-rich regulatory elements. Nucleic Acids Res (2002) 1.15
In vivo aggregation properties of the nuclear poly(A)-binding protein PABPN1. RNA (2005) 1.13
Depletion of the yeast nuclear exosome subunit Rrp6 results in accumulation of polyadenylated RNAs in a discrete domain within the nucleolus. Mol Cell Biol (2007) 1.12
Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription. Nucleic Acids Res (2013) 1.12
A link between nuclear RNA surveillance, the human exosome and RNA polymerase II transcriptional termination. Nucleic Acids Res (2010) 1.10
Splicing- and cleavage-independent requirement of RNA polymerase II CTD for mRNA release from the transcription site. J Cell Biol (2007) 1.09
Oculopharyngeal muscular dystrophy-like nuclear inclusions are present in normal magnocellular neurosecretory neurons of the hypothalamus. Hum Mol Genet (2004) 1.03
Diversity of vertebrate splicing factor U2AF35: identification of alternatively spliced U2AF1 mRNAS. J Biol Chem (2004) 1.03
Design principles of interconnections between chromatin and pre-mRNA splicing. Trends Biochem Sci (2012) 1.03
Dynamic transitions in RNA polymerase II density profiles during transcription termination. Genome Res (2012) 1.02
Hepatitis delta virus ribonucleoproteins shuttle between the nucleus and the cytoplasm. RNA (2002) 1.02
Splicing factors SF1 and U2AF associate in extraspliceosomal complexes. Mol Cell Biol (2008) 1.00
Stimulation of an unfolded protein response impairs MHC class I expression. J Immunol (2007) 0.99
Live-cell visualization of pre-mRNA splicing with single-molecule sensitivity. Cell Rep (2013) 0.98
Diversity of human U2AF splicing factors. FEBS J (2006) 0.96
Studies on the role of NonA in mRNA biogenesis. Exp Cell Res (2006) 0.88
Trypanosoma brucei histone H1 inhibits RNA polymerase I transcription and is important for parasite fitness in vivo. Mol Microbiol (2014) 0.87
Hsp70 chaperones and type I PRMTs are sequestered at intranuclear inclusions caused by polyalanine expansions in PABPN1. PLoS One (2009) 0.87
Photobleaching microscopy reveals the dynamics of mRNA-binding proteins inside live cell nuclei. Prog Mol Subcell Biol (2004) 0.86
Abundance of the largest subunit of RNA polymerase II in the nucleus is regulated by nucleo-cytoplasmic shuttling. Exp Cell Res (2006) 0.86
Regulation of adenovirus alternative RNA splicing correlates with a reorganization of splicing factors in the nucleus. Exp Cell Res (2003) 0.81
Inactivation of cleavage factor I components Rna14p and Rna15p induces sequestration of small nucleolar ribonucleoproteins at discrete sites in the nucleus. Mol Biol Cell (2008) 0.81
Cotranscriptional RNA checkpoints. Epigenomics (2010) 0.79
Frontiers in fluorescence microscopy. Int J Dev Biol (2009) 0.79
Differential isoform expression and interaction with the P32 regulatory protein controls the subcellular localization of the splicing factor U2AF26. J Biol Chem (2008) 0.78
N-glycosylation is important for the correct intracellular localization of HFE and its ability to decrease cell surface transferrin binding. FEBS J (2010) 0.77
Alternative splicing and cancer. J Nucleic Acids (2012) 0.77
A single RNA recognition motif in splicing factor ASF/SF2 directs it to nuclear sites of adenovirus transcription. J Gen Virol (2004) 0.77