MREdictor: a two-step dynamic interaction model that accounts for mRNA accessibility and Pumilio binding accurately predicts microRNA targets (Q42047792)

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English	MREdictor: a two-step dynamic interaction model that accounts for mRNA accessibility and Pumilio binding accurately predicts microRNA targets	scientific article

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scholarly article

1 reference

Europe PubMed Central

15 October 2017

MREdictor: a two-step dynamic interaction model that accounts for mRNA accessibility and Pumilio binding accurately predicts microRNA targets (English)

1 reference

Europe PubMed Central

15 October 2017

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based on heuristic

inferred from title

object named as

Francesco Neri

2

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Salvatore Oliviero

object named as

Salvatore Oliviero

4

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author name string

Danny Incarnato

1

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Europe PubMed Central

15 October 2017

Daniela Diamanti

3

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Europe PubMed Central

15 October 2017

language of work or name

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based on heuristic

inferred from title

publication date

17 July 2013

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Europe PubMed Central

15 October 2017

Nucleic Acids Research

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Europe PubMed Central

15 October 2017

41

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Europe PubMed Central

15 October 2017

18

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Europe PubMed Central

15 October 2017

8421-8433

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Europe PubMed Central

15 October 2017

copyright license

Creative Commons Attribution-NonCommercial 3.0 Unported

4 October 2016

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April 2022 Public Data File from Crossref

copyright status

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Human Pumilio proteins recruit multiple deadenylases to efficiently repress messenger RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Pumilio facilitates miRNA regulation of the E2F3 oncogene

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

A conserved PUF-Ago-eEF1A complex attenuates translation elongation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

TarBase 6.0: capturing the exponential growth of miRNA targets with experimental support

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

ViennaRNA Package 2.0

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

MultiMiTar: a novel multi objective optimization based miRNA-target prediction method

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

The conformation of microRNA seed regions in native microRNPs is prearranged for presentation to mRNA targets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

miRBase: integrating microRNA annotation and deep-sequencing data

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5 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Digital genome-wide ncRNA expression, including SnoRNAs, across 11 human tissues using polyA-neutral amplification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Expanding the microRNA targeting code: functional sites with centered pairing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

TargetSpy: a supervised machine learning approach for microRNA target prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Structural basis for 5'-nucleotide base-specific recognition of guide RNA by human AGO2

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

UTRdb and UTRsite (RELEASE 2010): a collection of sequences and regulatory motifs of the untranslated regions of eukaryotic mRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Revisiting the principles of microRNA target recognition and mode of action

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

miRecords: an integrated resource for microRNA-target interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Most mammalian mRNAs are conserved targets of microRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Comparative analysis of mRNA targets for human PUF-family proteins suggests extensive interaction with the miRNA regulatory system

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Structure of the guide-strand-containing argonaute silencing complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Identification of synaptic targets of Drosophila pumilio

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

The effect of central loops in miRNA:MRE duplexes on the efficiency of miRNA-mediated gene regulation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

RNA-binding protein Dnd1 inhibits microRNA access to target mRNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

The role of site accessibility in microRNA target recognition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

MicroRNA targeting specificity in mammals: determinants beyond seed pairing

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

MEME: discovering and analyzing DNA and protein sequence motifs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Relief of microRNA-mediated translational repression in human cells subjected to stress

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Regulation by let-7 and lin-4 miRNAs results in target mRNA degradation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Principles of microRNA-target recognition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Identification and characterization of RNA sequences to which human PUMILIO-2 (PUM2) and deleted in Azoospermia-like (DAZL) bind

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

MicroRNA targets in Drosophila

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Prediction of mammalian microRNA targets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

A PUF family portrait: 3'UTR regulation as a way of life

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

PUM2, a novel murine puf protein, and its consensus RNA-binding site

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

A bulged lin-4/lin-14 RNA duplex is sufficient for Caenorhabditis elegans lin-14 temporal gradient formation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

5 June 2018

Target-align: a tool for plant microRNA target identification

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

17 August 2018

TargetMiner: microRNA target prediction with systematic identification of tissue-specific negative examples.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

17 August 2018

Prediction of both conserved and nonconserved microRNA targets in animals.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

17 August 2018

Potent effect of target structure on microRNA function.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

17 August 2018

The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794589

17 August 2018

Target accessibility dictates the potency of human RISC

1 reference

https://pubmed.ncbi.nlm.nih.gov/23863844

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Perfect seed pairing is not a generally reliable predictor for miRNA-target interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/23863844

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1093/NAR/GKT629

1 reference

Europe PubMed Central

15 October 2017

1 reference

Europe PubMed Central

15 October 2017

1 reference

Europe PubMed Central

15 October 2017

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