Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data (Q31116138)

14 October 2017

Learning to Predict miRNA-mRNA Interactions from AGO CLIP Sequencing and CLASH Data (English)

1 reference

14 October 2017

Yuheng Lu

1

1 reference

PMCID

4954643

14 October 2017

Christina S Leslie

series ordinal

2

1 reference

PMCID

4954643

14 October 2017

language of work or name

1 reference

20 July 2016

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PLOS Computational Biology

14 October 2017

1 reference

14 October 2017

12

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14 October 2017

7

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14 October 2017

e1005026

1 reference

Creative Commons Attribution 4.0 International

14 October 2017

start time

20 July 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Improving microRNA target prediction by modeling with unambiguously identified microRNA-target pairs from CLIP-ligation studies

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

miRNA-target chimeras reveal miRNA 3'-end pairing as a major determinant of Argonaute target specificity

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Predicting effective microRNA target sites in mammalian mRNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

A Single miRNA-mRNA Interaction Affects the Immune Response in a Context- and Cell-Type-Specific Manner

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Accurate transcriptome-wide prediction of microRNA targets and small interfering RNA off-targets with MIRZA-G.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Unambiguous identification of miRNA:target site interactions by different types of ligation reactions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Widespread context dependency of microRNA-mediated regulation

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Identifying mRNA sequence elements for target recognition by human Argonaute proteins

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Global analyses of the effect of different cellular contexts on microRNA targeting

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Advancing the functional utility of PAR-CLIP by quantifying background binding to mRNAs and lncRNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Ubiquitously transcribed genes use alternative polyadenylation to achieve tissue-specific expression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

MicroRNA target site identification by integrating sequence and binding information

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

CLIP-based prediction of mammalian microRNA binding sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

A quantitative atlas of polyadenylation in five mammals

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Pumilio facilitates miRNA regulation of the E2F3 oncogene

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

An alternative mode of microRNA target recognition

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

A Pumilio-induced RNA structure switch in p27-3' UTR controls miR-221 and miR-222 accessibility

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Regulation of mRNA translation and stability by microRNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Fast and accurate long-read alignment with Burrows-Wheeler transform

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Widespread changes in protein synthesis induced by microRNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

The impact of microRNAs on protein output

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

POIMs: positional oligomer importance matrices--understanding support vector machine-based signal detectors

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

RNA-binding protein Dnd1 inhibits microRNA access to target mRNA

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Determinants of targeting by endogenous and exogenous microRNAs and siRNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

MicroRNA targeting specificity in mammals: determinants beyond seed pairing

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

The Caenorhabditis elegans pumilio homolog, puf-9, is required for the 3'UTR-mediated repression of the let-7 microRNA target gene, hbl-1

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Transcripts targeted by the microRNA-16 family cooperatively regulate cell cycle progression

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

Functional microRNA targets in protein coding sequences

21 June 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1005026

A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1005026

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

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1005026

Corrigendum to "Quantifying the strength of miRNA-target interactions" [Methods (2015) 90-99].

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4954643

10.1371/JOURNAL.PCBI.1005026

25 November 2018

Identifiers

DOI

1 reference

14 October 2017

journals/ploscb/LuL16

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

14 October 2017

1 reference

PMCID

4954643