Published in Chembiochem on October 04, 2004
Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Mol Cell (2011) 4.29
Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins. Nat Biotechnol (2009) 3.44
Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol Biol (2006) 2.74
The favorable IFNL3 genotype escapes mRNA decay mediated by AU-rich elements and hepatitis C virus-induced microRNAs. Nat Immunol (2013) 2.60
Genome-wide analysis of mRNA decay rates and their determinants in Arabidopsis thaliana. Plant Cell (2007) 2.51
Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements. Cell Mol Life Sci (2012) 1.96
Pre-mRNA secondary structures influence exon recognition. PLoS Genet (2007) 1.92
Predicting in vivo binding sites of RNA-binding proteins using mRNA secondary structure. RNA (2010) 1.87
RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins. PLoS Comput Biol (2010) 1.78
The rough endoplasmatic reticulum is a central nucleation site of siRNA-mediated RNA silencing. EMBO J (2013) 1.68
HuR protein attenuates miRNA-mediated repression by promoting miRISC dissociation from the target RNA. Nucleic Acids Res (2012) 1.58
AREsite: a database for the comprehensive investigation of AU-rich elements. Nucleic Acids Res (2010) 1.58
Post-transcriptional control during chronic inflammation and cancer: a focus on AU-rich elements. Cell Mol Life Sci (2010) 1.58
The mRNA stability factor HuR inhibits microRNA-16 targeting of COX-2. Mol Cancer Res (2011) 1.56
Using RNA secondary structures to guide sequence motif finding towards single-stranded regions. Nucleic Acids Res (2006) 1.55
Specific protein domains mediate cooperative assembly of HuR oligomers on AU-rich mRNA-destabilizing sequences. J Biol Chem (2007) 1.41
The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels. PLoS Genet (2012) 1.25
p38alpha stabilizes interleukin-6 mRNA via multiple AU-rich elements. J Biol Chem (2007) 1.21
RNA-binding protein HuR mediates cytoprotection through stimulation of XIAP translation. Oncogene (2010) 1.17
Noncoding RNA and its associated proteins as regulatory elements of the immune system. Nat Immunol (2014) 1.15
Global target mRNA specification and regulation by the RNA-binding protein ZFP36. Genome Biol (2014) 1.15
A hairpin-like structure within an AU-rich mRNA-destabilizing element regulates trans-factor binding selectivity and mRNA decay kinetics. J Biol Chem (2005) 1.14
The RNA binding protein HuR differentially regulates unique subsets of mRNAs in estrogen receptor negative and estrogen receptor positive breast cancer. BMC Cancer (2010) 1.10
Fast prediction of RNA-RNA interaction. Algorithms Mol Biol (2010) 1.04
Finding the target sites of RNA-binding proteins. Wiley Interdiscip Rev RNA (2013) 0.99
Overexpression of the RNA binding protein HuR impairs tumor growth in triple negative breast cancer associated with deficient angiogenesis. Cell Cycle (2010) 0.98
Detecting non-coding selective pressure in coding regions. BMC Evol Biol (2007) 0.98
cAMP-dependent posttranscriptional regulation of steroidogenic acute regulatory (STAR) protein by the zinc finger protein ZFP36L1/TIS11b. Mol Endocrinol (2009) 0.95
High-resolution flow cytometry: a suitable tool for monitoring aneuploid prostate cancer cells after TMZ and TMZ-BioShuttle treatment. Int J Med Sci (2009) 0.92
A novel high throughput biochemical assay to evaluate the HuR protein-RNA complex formation. PLoS One (2013) 0.92
Open reading frames provide a rich pool of potential natural antisense transcripts in fungal genomes. Nucleic Acids Res (2005) 0.91
Comparative 3'UTR analysis allows identification of regulatory clusters that drive Eph/ephrin expression in cancer cell lines. PLoS One (2008) 0.87
ElrA binding to the 3'UTR of cyclin E1 mRNA requires polyadenylation elements. Nucleic Acids Res (2007) 0.83
Post-transcriptional regulation of interferons and their signaling pathways. J Interferon Cytokine Res (2014) 0.82
A deep learning framework for modeling structural features of RNA-binding protein targets. Nucleic Acids Res (2015) 0.80
Regulation of the mRNA half-life in breast cancer. World J Clin Oncol (2014) 0.80
C. elegans RNA-binding protein GLD-1 recognizes its multiple targets using sequence, context, and structural information to repress translation. Worm (2013) 0.80
Conditional knockout of the RNA-binding protein HuR in CD4⁺ T cells reveals a gene dosage effect on cytokine production. Mol Med (2014) 0.80
cAMP stimulation of StAR expression and cholesterol metabolism is modulated by co-expression of labile suppressors of transcription and mRNA turnover. Mol Cell Endocrinol (2010) 0.79
Modeling the combined effect of RNA-binding proteins and microRNAs in post-transcriptional regulation. Nucleic Acids Res (2016) 0.79
RNA Structures as Mediators of Neurological Diseases and as Drug Targets. Neuron (2015) 0.79
The RNA binding protein HuR does not interact directly with HIV-1 reverse transcriptase and does not affect reverse transcription in vitro. Retrovirology (2010) 0.79
RNA binding proteins as regulators of immune cell biology. Clin Exp Immunol (2015) 0.77
Variation among rainbow trout (Oncorhynchus mykiss) estrogen receptor isoform 3' untranslated regions and the effect of 17beta-estradiol on mRNA stability in hepatocyte culture. DNA Cell Biol (2010) 0.77
Bioinformatic identification of novel elements potentially involved in messenger RNA fate control during spermatogenesis. Biol Reprod (2012) 0.77
Quantifying RNA binding sites transcriptome-wide using DO-RIP-seq. RNA (2016) 0.77
The functional consequences of relative substrate specificity in complex biochemical systems. Front Genet (2011) 0.76
hnRNPs and ELAVL1 cooperate with uORFs to inhibit protein translation. Nucleic Acids Res (2016) 0.75
Competing Repressive Factors Control Bone Morphogenetic Protein 2 (BMP2) in Mesenchymal Cells. J Cell Biochem (2016) 0.75
Re-evaluating Strategies to Define the Immunoregulatory Roles of miRNAs. Trends Immunol (2017) 0.75
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59
Structure and mechanism of the glycerol-3-phosphate transporter from Escherichia coli. Science (2003) 7.96
The primary transcriptome of the major human pathogen Helicobacter pylori. Nature (2010) 7.70
Deep-sea oil plume enriches indigenous oil-degrading bacteria. Science (2010) 6.73
Interleukin-6 dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer. Blood (2007) 5.14
Fast mapping of short sequences with mismatches, insertions and deletions using index structures. PLoS Comput Biol (2009) 4.24
Thermodynamics of RNA-RNA binding. Bioinformatics (2006) 3.10
Genetic evidence for three unique components in primary cell-wall cellulose synthase complexes in Arabidopsis. Proc Natl Acad Sci U S A (2007) 2.72
Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69
Polycomb complexes act redundantly to repress genomic repeats and genes. Genes Dev (2010) 2.63
The distal V(H) gene cluster of the Igh locus contains distinct regulatory elements with Pax5 transcription factor-dependent activity in pro-B cells. Immunity (2011) 2.41
Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharification. Bioresour Technol (2009) 2.32
Wapl is an essential regulator of chromatin structure and chromosome segregation. Nature (2013) 1.92
A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection. Genome Biol (2014) 1.60
Deep-sea bacteria enriched by oil and dispersant from the Deepwater Horizon spill. Environ Microbiol (2012) 1.58
Plant cell walls throughout evolution: towards a molecular understanding of their design principles. J Exp Bot (2009) 1.57
An RNA-Seq strategy to detect the complete coding and non-coding transcriptome including full-length imprinted macro ncRNAs. PLoS One (2011) 1.53
Three-dimensional crystallization of the Escherichia coli glycerol-3-phosphate transporter: a member of the major facilitator superfamily. Protein Sci (2003) 1.52
The B-cell identity factor Pax5 regulates distinct transcriptional programmes in early and late B lymphopoiesis. EMBO J (2012) 1.50
Molecular architecture of the chick vestibular hair bundle. Nat Neurosci (2013) 1.43
Twist1-induced dissemination preserves epithelial identity and requires E-cadherin. J Cell Biol (2014) 1.42
High-pressure freezing, cellular tomography, and structural cell biology. Biotechniques (2006) 1.41
Structural and biophysical characterization of the EphB4*ephrinB2 protein-protein interaction and receptor specificity. J Biol Chem (2006) 1.40
Pseudomonas aeruginosa forms biofilms in acute infection independent of cell-to-cell signaling. Infect Immun (2007) 1.39
RNAs everywhere: genome-wide annotation of structured RNAs. J Exp Zool B Mol Dev Evol (2007) 1.38
Identification and mechanistic characterization of low-molecular-weight inhibitors for HuR. Nat Chem Biol (2007) 1.36
Mammary collective cell migration involves transient loss of epithelial features and individual cell migration within the epithelium. J Cell Sci (2012) 1.32
Evolution of vault RNAs. Mol Biol Evol (2009) 1.31
The cooperative activities of CSLD2, CSLD3, and CSLD5 are required for normal Arabidopsis development. Mol Plant (2011) 1.30
Natural acidophilic biofilm communities reflect distinct organismal and functional organization. ISME J (2008) 1.27
Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis. Plant Physiol (2012) 1.26
Single bead labeling method for combining confocal fluorescence on-bead screening and solution validation of tagged one-bead one-compound libraries. Chem Biol (2009) 1.24
Mutations in UDP-Glucose:sterol glucosyltransferase in Arabidopsis cause transparent testa phenotype and suberization defect in seeds. Plant Physiol (2009) 1.22
The transcription factor Pax5 regulates its target genes by recruiting chromatin-modifying proteins in committed B cells. EMBO J (2011) 1.22
Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools. Microbiology (2008) 1.21
Perivascular-resident macrophage-like melanocytes in the inner ear are essential for the integrity of the intrastrial fluid-blood barrier. Proc Natl Acad Sci U S A (2012) 1.18
Engineering secondary cell wall deposition in plants. Plant Biotechnol J (2012) 1.18
The effect of RNA secondary structures on RNA-ligand binding and the modifier RNA mechanism: a quantitative model. Gene (2005) 1.17
Computational RNomics of drosophilids. BMC Genomics (2007) 1.15
Loss of Cellulose synthase-like F6 function affects mixed-linkage glucan deposition, cell wall mechanical properties, and defense responses in vegetative tissues of rice. Plant Physiol (2012) 1.12
The role of bacterial outer membrane vesicles for intra- and interspecies delivery. Environ Microbiol (2012) 1.12
Essential role of EBF1 in the generation and function of distinct mature B cell types. J Exp Med (2012) 1.12
Volumetric feature extraction and visualization of tomographic molecular imaging. J Struct Biol (2003) 1.11
Electron tomography, three-dimensional Fourier analysis and colour prediction of a three-dimensional amorphous biophotonic nanostructure. J R Soc Interface (2009) 1.11
Bacterial social networks: structure and composition of Myxococcus xanthus outer membrane vesicle chains. Environ Microbiol (2013) 1.09
Three-dimensional macromolecular organization of cryofixed Myxococcus xanthus biofilms as revealed by electron microscopic tomography. J Bacteriol (2009) 1.07
Percutaneous absorption of drugs used in atopic eczema: pimecrolimus permeates less through skin than corticosteroids and tacrolimus. Int J Pharm (2004) 1.07
Surface multiheme c-type cytochromes from Thermincola potens and implications for respiratory metal reduction by Gram-positive bacteria. Proc Natl Acad Sci U S A (2012) 1.04
HLA-DRB1*0401 and HLA-DRB1*0408 are strongly associated with the development of antibodies against interferon-beta therapy in multiple sclerosis. Am J Hum Genet (2008) 0.98
Assessing the function of human UNC-93B in Toll-like receptor signaling and major histocompatibility complex II response. Hum Immunol (2007) 0.98
SURFCOMP: a novel graph-based approach to molecular surface comparison. J Chem Inf Comput Sci (2004) 0.96
Subcellular localization of ceramide kinase and ceramide kinase-like protein requires interplay of their Pleckstrin Homology domain-containing N-terminal regions together with C-terminal domains. Biochim Biophys Acta (2009) 0.95
CD31, EDNRB and TSPAN7 are promising prognostic markers in clear-cell renal cell carcinoma revealed by genome-wide expression analyses of primary tumors and metastases. Int J Cancer (2012) 0.94
Identification of a small molecule inhibitor of importin β mediated nuclear import by confocal on-bead screening of tagged one-bead one-compound libraries. ACS Chem Biol (2010) 0.93
Three Novel Rice Genes Closely Related to the Arabidopsis IRX9, IRX9L, and IRX14 Genes and Their Roles in Xylan Biosynthesis. Front Plant Sci (2013) 0.92
Survey of renewable chemicals produced from lignocellulosic biomass during ionic liquid pretreatment. Biotechnol Biofuels (2013) 0.91
Covalent fluorescence labeling of His-tagged proteins on the surface of living cells. Chembiochem (2008) 0.89
Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs. Genome Biol (2014) 0.88
Terminal adenosyl transferase activity of posttranscriptional regulator HuR revealed by confocal on-bead screening. J Mol Biol (2008) 0.88
The x-ray crystal structure of the first RNA recognition motif and site-directed mutagenesis suggest a possible HuR redox sensing mechanism. J Mol Biol (2010) 0.88
The chemical hunt for the identification of drugable targets. Curr Opin Chem Biol (2004) 0.88
Activation-induced cytidine deaminase (AID)-associated multigene signature to assess impact of AID in etiology of diseases with inflammatory component. PLoS One (2011) 0.87
ACF7 is a hair-bundle antecedent, positioned to integrate cuticular plate actin and somatic tubulin. J Neurosci (2014) 0.86
Understanding changes in lignin of Panicum virgatum and Eucalyptus globulus as a function of ionic liquid pretreatment. Bioresour Technol (2012) 0.86
Community dynamics of cellulose-adapted thermophilic bacterial consortia. Environ Microbiol (2013) 0.86
Effects of ceramide-1-phosphate on cultured cells: dependence on dodecane in the vehicle. J Lipid Res (2006) 0.85
Computational discovery of human coding and non-coding transcripts with conserved splice sites. Bioinformatics (2011) 0.85
Inactivation of OsIRX10 leads to decreased xylan content in rice culm cell walls and improved biomass saccharification. Mol Plant (2012) 0.85
A highly potent and cellularly active beta-peptidic inhibitor of the p53/hDM2 interaction. Chembiochem (2009) 0.85
Isolation and culture of endothelial cells, pericytes and perivascular resident macrophage-like melanocytes from the young mouse ear. Nat Protoc (2013) 0.85
Confocal nanoscanning, bead picking (CONA): PickoScreen microscopes for automated and quantitative screening of one-bead one-compound libraries. J Comb Chem (2009) 0.85
Beyond dimerization: a membrane-dependent activation model for interleukin-4 receptor-mediated signalling. J Mol Biol (2006) 0.84
Biofilms: structures that may facilitate cell-cell interactions. ISME J (2010) 0.83
A direct way of redox sensing. RNA Biol (2011) 0.83
Control of sulfidogenesis through bio-oxidation of H2S coupled to (per)chlorate reduction. Environ Microbiol Rep (2014) 0.83
Electron tomography: a 3D view of the subcellular world. Anal Chem (2007) 0.83
On-bead screens sample narrower affinity ranges of protein-ligand interactions compared to equivalent solution assays. Chemphyschem (2012) 0.83
Correlative microscopy for phylogenetic and ultrastructural characterization of microbial communities. Environ Microbiol Rep (2011) 0.82
Single-bead, single-molecule, single-cell fluorescence: technologies for drug screening and target validation. Ann N Y Acad Sci (2008) 0.82
Duplicated RNA genes in teleost fish genomes. J Bioinform Comput Biol (2008) 0.81
Detection of differentially expressed segments in tiling array data. Bioinformatics (2012) 0.81
A critical beta6-beta7 loop in the pleckstrin homology domain of ceramide kinase. Biochem J (2006) 0.81
High-throughput enzymatic hydrolysis of lignocellulosic biomass via in-situ regeneration. Bioresour Technol (2010) 0.80
A first glimpse at the genome of the Baikalian amphipod Eulimnogammarus verrucosus. J Exp Zool B Mol Dev Evol (2014) 0.80
Ablation of the regulatory IE1 protein of murine cytomegalovirus alters in vivo pro-inflammatory TNF-alpha production during acute infection. PLoS Pathog (2012) 0.79
High-throughput chemical screening for antivirulence developmental phenotypes in Trypanosoma brucei. Eukaryot Cell (2014) 0.78
A conserved cysteine motif essential for ceramide kinase function. Biochimie (2008) 0.78
NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences. Genomics (2008) 0.78
Towards mimicking short linear peptide motifs: identification of new mixed α,β-peptidomimetic ligands for SLAM-Associated Protein (SAP) by confocal on-bead screening. J Chem Biol (2012) 0.77
Ceramide kinase profiling by mass spectrometry reveals a conserved phosphorylation pattern downstream of the catalytic site. J Proteome Res (2010) 0.77
Intergenic Polycomb target sites are dynamically marked by non-coding transcription during lineage commitment. RNA Biol (2012) 0.76
Analyzing the performance of conformational search programs on compound databases. J Mol Graph Model (2006) 0.76