Published in Nat Struct Mol Biol on July 04, 2010
Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat Neurosci (2011) 5.24
Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability. Mol Cell (2011) 4.29
Counting absolute numbers of molecules using unique molecular identifiers. Nat Methods (2011) 4.18
Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet (2014) 3.52
Functional consequences of developmentally regulated alternative splicing. Nat Rev Genet (2011) 3.27
Transcriptome-wide regulation of pre-mRNA splicing and mRNA localization by muscleblind proteins. Cell (2012) 3.20
Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol (2011) 3.18
Landscape and variation of RNA secondary structure across the human transcriptome. Nature (2014) 3.01
Protein-RNA interactions: new genomic technologies and perspectives. Nat Rev Genet (2012) 2.80
Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. Cell Rep (2012) 2.76
Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell (2013) 2.67
Complexity of the alternative splicing landscape in plants. Plant Cell (2013) 2.62
HITS-CLIP: panoramic views of protein-RNA regulation in living cells. Wiley Interdiscip Rev RNA (2010) 2.59
Conservation of an RNA regulatory map between Drosophila and mammals. Genome Res (2010) 2.43
iCLIP predicts the dual splicing effects of TIA-RNA interactions. PLoS Biol (2010) 2.39
The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes. Genes Dev (2011) 2.24
The dynamic epitranscriptome: N6-methyladenosine and gene expression control. Nat Rev Mol Cell Biol (2014) 2.19
Context-dependent control of alternative splicing by RNA-binding proteins. Nat Rev Genet (2014) 2.17
The RNA-binding protein repertoire of embryonic stem cells. Nat Struct Mol Biol (2013) 2.12
Understanding splicing regulation through RNA splicing maps. Trends Genet (2011) 2.12
The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain. Nat Genet (2011) 2.10
N(6)-methyladenosine-dependent RNA structural switches regulate RNA-protein interactions. Nature (2015) 2.09
Function of alternative splicing. Gene (2012) 2.00
Noncoding RNA and Polycomb recruitment. RNA (2013) 2.00
Tandem stem-loops in roX RNAs act together to mediate X chromosome dosage compensation in Drosophila. Mol Cell (2013) 1.99
CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins. Nucleic Acids Res (2010) 1.88
Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biol (2012) 1.85
Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS Genet (2012) 1.82
The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes. Genome Biol (2012) 1.82
DGCR8 HITS-CLIP reveals novel functions for the Microprocessor. Nat Struct Mol Biol (2012) 1.81
FTO-dependent demethylation of N6-methyladenosine regulates mRNA splicing and is required for adipogenesis. Cell Res (2014) 1.80
iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J Vis Exp (2011) 1.80
HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. Cell Rep (2014) 1.78
RNA templating the epigenome: long noncoding RNAs as molecular scaffolds. Epigenetics (2011) 1.75
Alternative polyadenylation: new insights from global analyses. RNA (2012) 1.72
Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res (2010) 1.71
Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain. Genes Dev (2012) 1.70
RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins. Mol Cell (2014) 1.68
How cells get the message: dynamic assembly and function of mRNA-protein complexes. Nat Rev Genet (2013) 1.67
Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes. Proc Natl Acad Sci U S A (2011) 1.64
Identification of RNA-protein interaction networks using PAR-CLIP. Wiley Interdiscip Rev RNA (2011) 1.61
iCLIP: protein-RNA interactions at nucleotide resolution. Methods (2013) 1.61
Intronic RNAs mediate EZH2 regulation of epigenetic targets. Nat Struct Mol Biol (2012) 1.56
Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain. Sci Rep (2012) 1.54
Transcriptome-wide analyses of CstF64-RNA interactions in global regulation of mRNA alternative polyadenylation. Proc Natl Acad Sci U S A (2012) 1.54
Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges. Nat Struct Mol Biol (2013) 1.49
NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Rep (2013) 1.48
Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. Nat Methods (2015) 1.47
In vivo and transcriptome-wide identification of RNA binding protein target sites. Mol Cell (2011) 1.47
Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. Mol Cell (2014) 1.46
Protein-RNA networks revealed through covalent RNA marks. Nat Methods (2015) 1.44
Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. Nat Rev Genet (2014) 1.44
Regulation of transcription by long noncoding RNAs. Annu Rev Genet (2014) 1.43
Site identification in high-throughput RNA-protein interaction data. Bioinformatics (2012) 1.43
hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1. Nature (2015) 1.42
Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. Nat Protoc (2014) 1.41
RNA mis-splicing in disease. Nat Rev Genet (2015) 1.41
Insights into the design and interpretation of iCLIP experiments. Genome Biol (2017) 1.40
MicroRNA target prediction using thermodynamic and sequence curves. BMC Genomics (2015) 1.39
Analysis of alternative splicing associated with aging and neurodegeneration in the human brain. Genome Res (2011) 1.35
HNRNPA2B1 Is a Mediator of m(6)A-Dependent Nuclear RNA Processing Events. Cell (2015) 1.34
ChIP-nexus enables improved detection of in vivo transcription factor binding footprints. Nat Biotechnol (2015) 1.32
A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation. Genes Dev (2015) 1.31
RNA protein interaction in neurons. Annu Rev Neurosci (2013) 1.31
PAR-CLIP data indicate that Nrd1-Nab3-dependent transcription termination regulates expression of hundreds of protein coding genes in yeast. Genome Biol (2014) 1.30
Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP). Nat Methods (2016) 1.29
Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability. Neuron (2012) 1.27
Translation-dependent displacement of UPF1 from coding sequences causes its enrichment in 3' UTRs. Nat Struct Mol Biol (2013) 1.26
Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs. Genome Biol (2014) 1.24
Genomic analyses of the RNA-binding protein Hu antigen R (HuR) identify a complex network of target genes and novel characteristics of its binding sites. J Biol Chem (2011) 1.24
Selective inhibition of microRNA accessibility by RBM38 is required for p53 activity. Nat Commun (2011) 1.20
Library construction for next-generation sequencing: overviews and challenges. Biotechniques (2014) 1.20
Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo. Nat Struct Mol Biol (2012) 1.20
Rbfox2 controls autoregulation in RNA-binding protein networks. Genes Dev (2014) 1.18
N6-methyladenosine–encoded epitranscriptomics. Nat Struct Mol Biol (2016) 1.17
Methods for comprehensive experimental identification of RNA-protein interactions. Genome Biol (2014) 1.16
Long non-coding RNA and alternative splicing modulations in Parkinson's leukocytes identified by RNA sequencing. PLoS Comput Biol (2014) 1.15
Motif-based analysis of large nucleotide data sets using MEME-ChIP. Nat Protoc (2014) 1.15
Networking in a global world: establishing functional connections between neural splicing regulators and their target transcripts. RNA (2011) 1.14
Deciphering the role of RNA-binding proteins in the post-transcriptional control of gene expression. Brief Funct Genomics (2010) 1.14
Dissecting noncoding and pathogen RNA-protein interactomes. RNA (2014) 1.12
GraphProt: modeling binding preferences of RNA-binding proteins. Genome Biol (2014) 1.12
Cytoplasmic RNA-binding proteins and the control of complex brain function. Cold Spring Harb Perspect Biol (2012) 1.12
Characterizing 5-methylcytosine in the mammalian epitranscriptome. Genome Biol (2013) 1.11
Two new and distinct roles for Drosophila Argonaute-2 in the nucleus: alternative pre-mRNA splicing and transcriptional repression. Genes Dev (2013) 1.10
De novo prediction of PTBP1 binding and splicing targets reveals unexpected features of its RNA recognition and function. PLoS Comput Biol (2014) 1.08
Translational control by 3'-UTR-binding proteins. Brief Funct Genomics (2012) 1.08
Specificity and nonspecificity in RNA-protein interactions. Nat Rev Mol Cell Biol (2015) 1.08
Long noncoding RNAs in cancer: mechanisms of action and technological advancements. Mol Cancer (2016) 1.08
Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome. Nat Chem Biol (2015) 1.07
CELF4 regulates translation and local abundance of a vast set of mRNAs, including genes associated with regulation of synaptic function. PLoS Genet (2012) 1.07
m(6)A RNA methylation promotes XIST-mediated transcriptional repression. Nature (2016) 1.06
CLIPdb: a CLIP-seq database for protein-RNA interactions. BMC Genomics (2015) 1.05
The RNAissance family: SR proteins as multifaceted regulators of gene expression. Wiley Interdiscip Rev RNA (2014) 1.05
The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion. Annu Rev Biochem (2015) 1.04
RBPmap: a web server for mapping binding sites of RNA-binding proteins. Nucleic Acids Res (2014) 1.04
Suppression of artifacts and barcode bias in high-throughput transcriptome analyses utilizing template switching. Nucleic Acids Res (2012) 1.04
PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis. Genome Biol (2014) 1.03
RNA-binding proteins in neurodegeneration: Seq and you shall receive. Trends Neurosci (2015) 1.03
Emerging roles for the Ro 60-kDa autoantigen in noncoding RNA metabolism. Wiley Interdiscip Rev RNA (2011) 1.02
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
WebLogo: a sequence logo generator. Genome Res (2004) 59.58
Ensembl 2009. Nucleic Acids Res (2008) 25.38
HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature (2008) 14.17
The spliceosome: design principles of a dynamic RNP machine. Cell (2009) 12.82
CLIP identifies Nova-regulated RNA networks in the brain. Science (2003) 8.88
Expansion of the eukaryotic proteome by alternative splicing. Nature (2010) 8.84
An RNA map predicting Nova-dependent splicing regulation. Nature (2006) 7.63
Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches. Nat Rev Mol Cell Biol (2009) 7.11
Nova regulates brain-specific splicing to shape the synapse. Nat Genet (2005) 6.58
An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells. Nat Struct Mol Biol (2009) 6.37
CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods (2005) 6.26
Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins. Science (1995) 5.97
Heterogeneous nuclear ribonucleoproteins: role in RNA splicing. Science (1986) 5.52
Identification and characterization of the packaging proteins of core 40S hnRNP particles. Cell (1977) 5.50
Structure of PTB bound to RNA: specific binding and implications for splicing regulation. Science (2005) 5.14
Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping. Mol Cell (2009) 4.71
Mechanisms of fidelity in pre-mRNA splicing. Curr Opin Cell Biol (2000) 2.66
Interaction of the RNA-binding domain of the hnRNP C proteins with RNA. EMBO J (1992) 2.26
The determinants of RNA-binding specificity of the heterogeneous nuclear ribonucleoprotein C proteins. J Biol Chem (1994) 2.02
Smooth muscle-specific switching of alpha-tropomyosin mutually exclusive exon selection by specific inhibition of the strong default exon. EMBO J (1994) 1.91
Heterogeneous nuclear ribonucleoprotein C modulates translation of c-myc mRNA in a cell cycle phase-dependent manner. Mol Cell Biol (2003) 1.82
Nucleolin and heterogeneous nuclear ribonucleoprotein C proteins specifically interact with the 3'-untranslated region of amyloid protein precursor mRNA. J Biol Chem (1995) 1.72
A two-tracked approach to analyze RNA-protein crosslinking sites in native, nonlabeled small nuclear ribonucleoprotein particles. Methods (2002) 1.61
Laser cross-linking of nucleic acids to proteins. Methodology and first applications to the phage T4 DNA replication system. J Biol Chem (1986) 1.54
Arrangement of 30S heterogeneous nuclear ribonucleoprotein on polyoma virus late nuclear transcripts. Mol Cell Biol (1981) 1.47
Independent deposition of heterogeneous nuclear ribonucleoproteins and small nuclear ribonucleoprotein particles at sites of transcription. Proc Natl Acad Sci U S A (1992) 1.40
The C proteins of HeLa 40S nuclear ribonucleoprotein particles exist as anisotropic tetramers of (C1)3 C2. Mol Cell Biol (1989) 1.31
The C-protein tetramer binds 230 to 240 nucleotides of pre-mRNA and nucleates the assembly of 40S heterogeneous nuclear ribonucleoprotein particles. Mol Cell Biol (1994) 1.25
A major determinant of hnRNP C protein binding to RNA is a novel bZIP-like RNA binding domain. RNA (1996) 1.19
Proteins C1 and C2 of heterogeneous nuclear ribonucleoprotein complexes bind RNA in a highly cooperative fashion: support for their contiguous deposition on pre-mRNA during transcription. Biochemistry (1996) 1.07
Solution structure of the symmetric coiled coil tetramer formed by the oligomerization domain of hnRNP C: implications for biological function. J Mol Biol (2005) 1.05
Mutational definition of RNA-binding and protein-protein interaction domains of heterogeneous nuclear RNP C1. J Biol Chem (2000) 1.02
Laser cross-linking of proteins to nucleic acids. I. Examining physical parameters of protein-nucleic acid complexes. J Biol Chem (1993) 0.98
Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet (2008) 43.63
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72
A large genome center's improvements to the Illumina sequencing system. Nat Methods (2008) 15.56
HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature (2008) 14.17
Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes. Nat Methods (2009) 10.41
A census of human transcription factors: function, expression and evolution. Nat Rev Genet (2009) 9.19
Target-enrichment strategies for next-generation sequencing. Nat Methods (2010) 8.78
The transcriptional activity of human Chromosome 22. Genes Dev (2003) 6.82
Neuronal MeCP2 is expressed at near histone-octamer levels and globally alters the chromatin state. Mol Cell (2010) 5.43
Annotation transfer between genomes: protein-protein interologs and protein-DNA regulogs. Genome Res (2004) 5.26
Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat Neurosci (2011) 5.24
DNA-binding specificities of human transcription factors. Cell (2013) 5.14
CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature (2010) 4.86
Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol (2004) 4.48
Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing. Nature (2012) 4.37
Simultaneous assay of every Salmonella Typhi gene using one million transposon mutants. Genome Res (2009) 4.12
Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12
High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res (2011) 4.09
Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A (2003) 3.89
FRT-seq: amplification-free, strand-specific transcriptome sequencing. Nat Methods (2010) 3.55
Mutation spectrum revealed by breakpoint sequencing of human germline CNVs. Nat Genet (2010) 3.52
Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res (2010) 3.46
GATA-1 binding sites mapped in the beta-globin locus by using mammalian chIp-chip analysis. Proc Natl Acad Sci U S A (2002) 3.41
Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet (2010) 3.38
Complex transcriptional circuitry at the G1/S transition in Saccharomyces cerevisiae. Genes Dev (2002) 3.27
CEP152 is a genome maintenance protein disrupted in Seckel syndrome. Nat Genet (2010) 3.25
Genome-wide analysis reveals MOF as a key regulator of dosage compensation and gene expression in Drosophila. Cell (2008) 3.18
TDP-43 regulates its mRNA levels through a negative feedback loop. EMBO J (2010) 2.90
Molecular fossils in the human genome: identification and analysis of the pseudogenes in chromosomes 21 and 22. Genome Res (2002) 2.89
Protein-RNA interactions: new genomic technologies and perspectives. Nat Rev Genet (2012) 2.80
Predictive data mining in clinical medicine: current issues and guidelines. Int J Med Inform (2006) 2.78
Drosophila dosage compensation involves enhanced Pol II recruitment to male X-linked promoters. Science (2012) 2.75
dictyBase--a Dictyostelium bioinformatics resource update. Nucleic Acids Res (2008) 2.75
Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell (2013) 2.67
Epistasis analysis with global transcriptional phenotypes. Nat Genet (2005) 2.67
High-throughput decoding of antitrypanosomal drug efficacy and resistance. Nature (2012) 2.55
Gene loops enhance transcriptional directionality. Science (2012) 2.50
Complete genome sequence of uropathogenic Proteus mirabilis, a master of both adherence and motility. J Bacteriol (2008) 2.47
iCLIP predicts the dual splicing effects of TIA-RNA interactions. PLoS Biol (2010) 2.39
Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet (2003) 2.38
Comprehensive analysis of combinatorial regulation using the transcriptional regulatory network of yeast. J Mol Biol (2006) 2.36
CREB binds to multiple loci on human chromosome 22. Mol Cell Biol (2004) 2.28
The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes. Genes Dev (2011) 2.24
Optimizing Illumina next-generation sequencing library preparation for extremely AT-biased genomes. BMC Genomics (2012) 2.20
A simple method for directional transcriptome sequencing using Illumina technology. Nucleic Acids Res (2009) 2.19
Conserved developmental transcriptomes in evolutionarily divergent species. Genome Biol (2010) 2.16
Understanding splicing regulation through RNA splicing maps. Trends Genet (2011) 2.12
Nuclear pore proteins nup153 and megator define transcriptionally active regions in the Drosophila genome. PLoS Genet (2010) 1.94
The GENCODE exome: sequencing the complete human exome. Eur J Hum Genet (2011) 1.88
Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biol (2012) 1.85
Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing. PLoS Genet (2012) 1.82
The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes. Genome Biol (2012) 1.82
iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J Vis Exp (2011) 1.80
Polymorphic members of the lag gene family mediate kin discrimination in Dictyostelium. Curr Biol (2009) 1.77
Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli. Nucleic Acids Res (2010) 1.71
The nonspecific lethal complex is a transcriptional regulator in Drosophila. Mol Cell (2010) 1.68
Evidence of non-random mutation rates suggests an evolutionary risk management strategy. Nature (2012) 1.56
Bacterial discrimination by dictyostelid amoebae reveals the complexity of ancient interspecies interactions. Curr Biol (2013) 1.56
Prediction of regulatory networks: genome-wide identification of transcription factor targets from gene expression data. Bioinformatics (2003) 1.55
Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain. Sci Rep (2012) 1.54
CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo. Methods (2009) 1.53
Mobilization of giant piggyBac transposons in the mouse genome. Nucleic Acids Res (2011) 1.49
Predictive model for estimating risk of crush syndrome: a data mining approach. J Trauma (2007) 1.48
NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Rep (2013) 1.48
Whole genome sequencing highlights genetic changes associated with laboratory domestication of C. elegans. PLoS One (2010) 1.44
Genetic basis of Y-linked hearing impairment. Am J Hum Genet (2013) 1.42
Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes. Nucleic Acids Res (2002) 1.40
Microarray data mining with visual programming. Bioinformatics (2004) 1.40
Structural variation on the short arm of the human Y chromosome: recurrent multigene deletions encompassing Amelogenin Y. Hum Mol Genet (2006) 1.36
Common molecular pathways mediate long-term potentiation of synaptic excitation and slow synaptic inhibition. Cell (2005) 1.36
Improved protocols for the illumina genome analyzer sequencing system. Curr Protoc Hum Genet (2009) 1.36
Comprehensive reanalysis of transcription factor knockout expression data in Saccharomyces cerevisiae reveals many new targets. Nucleic Acids Res (2010) 1.35
Analysis of alternative splicing associated with aging and neurodegeneration in the human brain. Genome Res (2011) 1.35