Transcriptome-wide identification of RNA binding sites by CLIP-seq (Q44809252)

6 December 2017

Transcriptome-wide identification of RNA binding sites by CLIP-seq (English)

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6 December 2017

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Valentine Murigneux

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6 December 2017

Jérôme Saulière

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2

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6 December 2017

Hugues Roest Crollius

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3

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6 December 2017

Hervé Le Hir

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4

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6 December 2017

30 March 2013

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6 December 2017

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6 December 2017

63

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6 December 2017

1

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6 December 2017

32-40

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Pre-mRNA processing reaches back to transcription and ahead to translation

6 December 2017

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Protein-RNA interactions: new genomic technologies and perspectives

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

CLIP identifies Nova-regulated RNA networks in the brain

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Transcriptome-wide analysis of protein-RNA interactions using high-throughput sequencing.

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

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

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

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

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

CLIP-seq of eIF4AIII reveals transcriptome-wide mapping of the human exon junction complex

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Structural insights into the exon junction complex

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

FMRP stalls ribosomal translocation on mRNAs linked to synaptic function and autism

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Quality control and preprocessing of metagenomic datasets

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

ESTclean: a cleaning tool for next-gen transcriptome shotgun sequencing

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Manipulation of FASTQ data with Galaxy

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

AdapterRemoval: easy cleaning of next-generation sequencing reads

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

RobiNA: a user-friendly, integrated software solution for RNA-Seq-based transcriptomics

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

CLIP: a method for identifying protein-RNA interaction sites in living cells

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

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

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Fast and SNP-tolerant detection of complex variants and splicing in short reads

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Fast and accurate short read alignment with Burrows-Wheeler transform

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Fast mapping of short sequences with mismatches, insertions and deletions using index structures

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

TopHat: discovering splice junctions with RNA-Seq

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

MapSplice: accurate mapping of RNA-seq reads for splice junction discovery.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Fast gapped-read alignment with Bowtie 2

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Alternative expression analysis by RNA sequencing

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

The Sequence Alignment/Map format and SAMtools

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Repetitive DNA and next-generation sequencing: computational challenges and solutions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

BEDTools: a flexible suite of utilities for comparing genomic features

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

The Ensembl Web site: mechanics of a genome browser

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Integrative genomics viewer

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Pyicos: a versatile toolkit for the analysis of high-throughput sequencing data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Site identification in high-throughput RNA-protein interaction data

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

LIN28A is a suppressor of ER-associated translation in embryonic stem cells

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Position-dependent FUS-RNA interactions regulate alternative splicing events and transcriptions

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Nuclear matrix factor hnRNP U/SAF-A exerts a global control of alternative splicing by regulating U2 snRNP maturation.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Gene ontology: tool for the unification of biology

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

DAVID: Database for Annotation, Visualization, and Integrated Discovery

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

GOstat: find statistically overrepresented Gene Ontologies within a group of genes

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Distribution and characterization of regulatory elements in the human genome

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

The cellular EJC interactome reveals higher-order mRNP structure and an EJC-SR protein nexus

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

An RNA map predicting Nova-dependent splicing regulation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Understanding splicing regulation through RNA splicing maps

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

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

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Computational definition of sequence motifs governing constitutive exon splicing.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Finding DNA regulatory motifs within unaligned noncoding sequences clustered by whole-genome mRNA quantitation

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

Regulatory sequence analysis tools

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

The value of position-specific priors in motif discovery using MEME.

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

UNAFold: software for nucleic acid folding and hybridization

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

CONTRAfold: RNA secondary structure prediction without physics-based models

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

RNA targets of wild-type and mutant FET family proteins

7 January 2021

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https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

LIN28 binds messenger RNAs at GGAGA motifs and regulates splicing factor abundance

7 January 2021

1 reference

https://api.crossref.org/works/10.1016%2FJ.YMETH.2013.03.022

10.1016/J.YMETH.2013.03.022

7 January 2021

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DOI

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release_eymvz7ftcvdsbclrzafc3hqcd4

6 December 2017

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Fatcat

https://api.fatcat.wiki/v0/release/eymvz7ftcvdsbclrzafc3hqcd4

mapped directly with Wikidata item

24 November 2022

based on heuristic

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