Identification of RNA-protein interaction networks using PAR-CLIP (Q27023093)

5

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Markus Hafner

2

0 references

Manuel Ascano

1

object named as

Manuel Ascano

1 reference

Pavol Cekan

3

1 reference

Stefanie Gerstberger

4

1 reference

language of work or name

1 reference

2012

1 reference

Wiley interdisciplinary reviews. RNA

published in

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volume

3

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issue

2

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page(s)

159-77

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Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data

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CLIPZ: a database and analysis environment for experimentally determined binding sites of RNA-binding proteins

21 March 2017

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starBase: a database for exploring microRNA-mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

21 March 2017

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iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

21 March 2017

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Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP

21 March 2017

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Comprehensive discovery of endogenous Argonaute binding sites in Caenorhabditis elegans

21 March 2017

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The Pfam protein families database

21 March 2017

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Rapid and systematic analysis of the RNA recognition specificities of RNA-binding proteins

21 March 2017

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Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps

21 March 2017

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Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling

21 March 2017

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An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells

21 March 2017

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Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Targeted deletion reveals essential and overlapping functions of the miR-17 through 92 family of miRNA clusters

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Phosphorylation of HuR by Chk2 regulates SIRT1 expression

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny

21 March 2017

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Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Mfold web server for nucleic acid folding and hybridization prediction

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Identification and cDNA cloning of a novel RNA-binding protein that interacts with the cyclic nucleotide-responsive sequence in the Type-1 plasminogen activator inhibitor mRNA

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

JAZ requires the double-stranded RNA-binding zinc finger motifs for nuclear localization

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

The spinal muscular atrophy disease gene product, SMN, and its associated protein SIP1 are in a complex with spliceosomal snRNP proteins

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

The neuronal RNA binding protein Nova-1 recognizes specific RNA targets in vitro and in vivo

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

hTAF(II)68, a novel RNA/ssDNA-binding protein with homology to the pro-oncoproteins TLS/FUS and EWS is associated with both TFIID and RNA polymerase II

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

RNA sequence analysis using covariance models

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Identification of a putative RNA helicase (HRH1), a human homolog of yeast Prp22

21 March 2017

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hnRNP G: sequence and characterization of a glycosylated RNA-binding protein

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Identifying protein-binding sites from unaligned DNA fragments

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Mammalian microRNAs predominantly act to decrease target mRNA levels

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing

21 March 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Systematic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

CLIP identifies Nova-regulated RNA networks in the brain

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Functional and molecular characterization of nucleobase transport by recombinant human and rat equilibrative nucleoside transporters 1 and 2. Chimeric constructs reveal a role for the ENT2 helix 5-6 region in nucleobase translocation

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Identification of neuronal RNA targets of TDP-43-containing ribonucleoprotein complexes

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Prp43 bound at different sites on the pre-rRNA performs distinct functions in ribosome synthesis

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

The cold shock domain protein LIN-28 controls developmental timing in C. elegans and is regulated by the lin-4 RNA

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Novel proteins with binding specificity for DNA CTG repeats and RNA CUG repeats: implications for myotonic dystrophy

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

The pre-mRNA binding K protein contains a novel evolutionarily conserved motif

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Rapid insulin-stimulated accumulation of an mRNA encoding a proline-rich protein

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

A growth factor-inducible nuclear protein with a novel cysteine/histidine repetitive sequence

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Genome-wide identification of polycomb-associated RNAs by RIP-seq

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Zcchc11-dependent uridylation of microRNA directs cytokine expression

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

21 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Pfam: a comprehensive database of protein domain families based on seed alignments

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

RNA targets of wild-type and mutant FET family proteins

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Reversible inhibition of PSD-95 mRNA translation by miR-125a, FMRP phosphorylation, and mGluR signaling

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

The impact of miRNA target sites in coding sequences and in 3'UTRs

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

The prospects for designer single-stranded RNA-binding proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Genome-wide identification of Ago2 binding sites from mouse embryonic stem cells with and without mature microRNAs.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

TDP-43 regulates its mRNA levels through a negative feedback loop

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

iCLIP predicts the dual splicing effects of TIA-RNA interactions.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Systematic analysis of posttranscriptional gene expression

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Feed-forward regulation of a cell fate determinant by an RNA-binding protein generates asymmetry in yeast

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

A role for a bacterial ortholog of the Ro autoantigen in starvation-induced rRNA degradation

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Evidence-ranked motif identification

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

RNA gain-of-function in spinocerebellar ataxia type 8.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

MIWI-independent small RNAs (MSY-RNAs) bind to the RNA-binding protein, MSY2, in male germ cells

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Molecular characterization of human Argonaute-containing ribonucleoprotein complexes and their bound target mRNAs

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Identification of nuclear and cytoplasmic mRNA targets for the shuttling protein SF2/ASF

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Target RNA motif and target mRNAs of the Quaking STAR protein

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Nova regulates brain-specific splicing to shape the synapse

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Casein kinase II phosphorylates the fragile X mental retardation protein and modulates its biological properties

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

A two-tracked approach to analyze RNA-protein crosslinking sites in native, nonlabeled small nuclear ribonucleoprotein particles

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Characterization of Sm-like proteins in yeast and their association with U6 snRNA

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

High yield photocrosslinking of a 5-iodocytidine (IC) substituted RNA to its associated protein

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Hel-N1: an autoimmune RNA-binding protein with specificity for 3' uridylate-rich untranslated regions of growth factor mRNAs

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Photocrosslinking of 5-iodouracil-substituted RNA and DNA to proteins

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Site-specific crosslinking of 4-thiouridine-modified human tRNA(3Lys) to reverse transcriptase from human immunodeficiency virus type I.

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

staufen, a gene required to localize maternal RNAs in the Drosophila egg

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

TU-tagging: cell type-specific RNA isolation from intact complex tissues

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

High-resolution gene expression profiling for simultaneous kinetic parameter analysis of RNA synthesis and decay

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

mRNAs associated with the Sam68 RNA binding protein

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Thionucleobases as intrinsic photoaffinity probes of nucleic acid structure and nucleic acid-protein interactions.

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

4-Thiouridine photosensitized RNA-protein crosslinking in mammalian cells

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

Incorporation of 6-Thioguanosine and 4-Thiouridine into RNA. Application to Isolation of Newly Synthesised RNA by Affinity Chromatography

31 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3711140

G-patch: a new conserved domain in eukaryotic RNA-processing proteins and type D retroviral polyproteins

31 May 2018

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Novel eIF4G domain homologues linking mRNA translation with nonsense-mediated mRNA decay

21 January 2018

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Developmental roles and molecular characterization of a Drosophila homologue of Arabidopsis Argonaute1, the founder of a novel gene superfamily.

21 January 2018

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Genome-wide studies reveal that Lin28 enhances the translation of genes important for growth and survival of human embryonic stem cells.

21 January 2018

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Transcriptome-wide analysis of regulatory interactions of the RNA-binding protein HuR.

21 January 2018

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A quantitative analysis of CLIP methods for identifying binding sites of RNA-binding proteins

21 January 2018

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Site-specific crosslinking of human microRNPs to RNA targets

21 January 2018

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GIMSAN: a Gibbs motif finder with significance analysis.

21 January 2018

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An algorithm for finding signals of unknown length in DNA sequences

21 January 2018

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Intra-RNA and RNA-protein cross-linking techniques in Escherichia coli ribosomes

21 January 2018

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12 December 2020

The U5 and U6 small nuclear RNAs as active site components of the spliceosome

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12 December 2020

Biosynthetic labeling of RNA with uracil phosphoribosyltransferase allows cell-specific microarray analysis of mRNA synthesis and decay

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12 December 2020

The multifunctional RNA-binding protein hnRNP A1 is required for processing of miR-18a

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12 December 2020

RNA under attack: cellular handling of RNA damage

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12 December 2020

Nucleoprotein photo-cross-linking using halopyrimidine-substituted RNAs

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12 December 2020

Identifiers

DOI

10.1002/WRNA.1103

1 reference

1751334

1751334

1 reference

1 reference

1 reference