(Q39107523)

23 May 2018

title

RNAcompete methodology and application to determine sequence preferences of unconventional RNA-binding proteins (English)

1 reference

23 May 2018

Quaid D Morris

6

0 references

author name string

Debashish Ray

1

1 reference

23 May 2018

Kevin C H Ha

2

1 reference

23 May 2018

Kate Nie

3

1 reference

23 May 2018

Hong Zheng

4

1 reference

23 May 2018

Timothy R Hughes

5

1 reference

23 May 2018

language of work or name

1 reference

10 December 2016

1 reference

23 May 2018

published in

Methods

1 reference

23 May 2018

volume

118-119

1 reference

23 May 2018

page(s)

3-15

1 reference

23 May 2018

Cleavage factor Im (CFIm) as a regulator of alternative polyadenylation

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1 reference

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15 June 2018

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Recognition of distinct RNA motifs by the clustered CCCH zinc fingers of neuronal protein Unkempt

15 June 2018

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The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs

15 June 2018

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The Crystal Structure of the NHL Domain in Complex with RNA Reveals the Molecular Basis of Drosophila Brain-Tumor-Mediated Gene Regulation

15 June 2018

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High-throughput characterization of protein-RNA interactions

15 June 2018

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Eosinophilic myositis as first manifestation in a patient with type 2 myotonic dystrophy CCTG expansion mutation and rheumatoid arthritis

15 June 2018

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RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins

15 June 2018

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Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling

15 June 2018

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Quantitative analysis of RNA-protein interactions on a massively parallel array reveals biophysical and evolutionary landscapes

15 June 2018

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CNBP regulates wing development in Drosophila melanogaster by promoting IRES-dependent translation of dMyc

15 June 2018

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15 June 2018

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A compendium of RNA-binding motifs for decoding gene regulation.

15 June 2018

1 reference

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Structure of histone mRNA stem-loop, human stem-loop binding protein, and 3'hExo ternary complex

15 June 2018

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RRM-RNA recognition: NMR or crystallography…and new findings

15 June 2018

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Systematic reconstruction of RNA functional motifs with high-throughput microfluidics

15 June 2018

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Site identification in high-throughput RNA-protein interaction data

15 June 2018

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Cooperativity in RNA-protein interactions: global analysis of RNA binding specificity

15 June 2018

1 reference

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The mRNA-bound proteome and its global occupancy profile on protein-coding transcripts

15 June 2018

1 reference

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Insights into RNA biology from an atlas of mammalian mRNA-binding proteins

15 June 2018

1 reference

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HITS-CLIP: panoramic views of protein-RNA regulation in living cells

15 June 2018

1 reference

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RBPDB: a database of RNA-binding specificities

15 June 2018

1 reference

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Structural basis of UGUA recognition by the Nudix protein CFI(m)25 and implications for a regulatory role in mRNA 3' processing

15 June 2018

1 reference

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Expression, purification, and initial characterization of different domains of recombinant mouse 2',3'-cyclic nucleotide 3'-phosphodiesterase, an enigmatic enzyme from the myelin sheath.

15 June 2018

1 reference

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BEDTools: a flexible suite of utilities for comparing genomic features

15 June 2018

1 reference

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

The Sequence Alignment/Map format and SAMtools

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

Biopython: freely available Python tools for computational molecular biology and bioinformatics

15 June 2018

1 reference

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

RNA-binding proteins: modular design for efficient function

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities

15 June 2018

1 reference

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Sequence-specific binding of single-stranded RNA: is there a code for recognition?

15 June 2018

1 reference

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ROCR: visualizing classifier performance in R

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

Superior 5' homogeneity of RNA from ATP-initiated transcription under the T7 phi 2.5 promoter

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

A mechanism for the regulation of pre-mRNA 3' processing by human cleavage factor Im

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

CLIP identifies Nova-regulated RNA networks in the brain

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

LRP130, a pentatricopeptide motif protein with a noncanonical RNA-binding domain, is bound in vivo to mitochondrial and nuclear RNAs

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

Mouse genomics: making sense of the sequence

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

The protein that binds the 3' end of histone mRNA: a novel RNA-binding protein required for histone pre-mRNA processing

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

RNA recognition: towards identifying determinants of specificity

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

Brain tumor is a sequence-specific RNA-binding protein that directs maternal mRNA clearance during the Drosophila maternal-to-zygotic transition

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

A G-Rich Motif in the lncRNA Braveheart Interacts with a Zinc-Finger Transcription Factor to Specify the Cardiovascular Lineage.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

Paralogs hnRNP L and hnRNP LL exhibit overlapping but distinct RNA binding constraints

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

Dissecting CNBP, a zinc-finger protein required for neural crest development, in its structural and functional domains

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

Bioinformatic identification of candidate cis-regulatory elements involved in human mRNA polyadenylation

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

A census of human RNA-binding proteins

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5411283

10.1016/J.YMETH.2016.12.003

2 December 2018

Identifiers

DOI

1 reference

23 May 2018

PMC publication ID

5411283

1 reference

23 May 2018

PubMed publication ID

27956239

1 reference

23 May 2018