(Q42109376)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

title

Recurrent rewiring and emergence of RNA regulatory networks (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

main subject

recurrent neural network

1 reference

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

Christopher P Lapointe

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

author name string

Daniel Wilinski

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

Natascha Buter

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

Eric U Selker

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

Audrey P Gasch

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

Marvin Wickens

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

language of work or name

English

0 references

publication date

20 March 2017

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

Proceedings of the National Academy of Sciences of the United States of America

13 March 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

volume

114

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

issue

14

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

page(s)

E2816-E2825

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

Evolution and Biological Roles of Alternative 3'UTRs

13 March 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Evolutionary Conservation and Diversification of Puf RNA Binding Proteins and Their mRNA Targets

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Protein-RNA networks revealed through covalent RNA marks

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

RNA regulatory networks diversified through curvature of the PUF protein scaffold

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Glucose-Regulated Phosphorylation of the PUF Protein Puf3 Regulates the Translational Fate of Its Bound mRNAs and Association with RNA Granules

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Metabolic regulation in model ascomycetes--adjusting similar genomes to different lifestyles.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

The InterPro protein families database: the classification resource after 15 years

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Evolution of transcription factor binding in metazoans - mechanisms and functional implications

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Following gene duplication, paralog interference constrains transcriptional circuit evolution

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Correction: Evolutionary principles of modular gene regulation in yeasts

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Extensive rewiring and complex evolutionary dynamics in a C. elegans multiparameter transcription factor network

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Site identification in high-throughput RNA-protein interaction data

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Rewiring of posttranscriptional RNA regulons: Puf4p in fungi as an example

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Fast gapped-read alignment with Bowtie 2

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Roles of Puf proteins in mRNA degradation and translation

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

New genes in Drosophila quickly become essential

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

PUF proteins: repression, activation and mRNA localization

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

The landscape of C. elegans 3'UTRs

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Evolutionary tinkering with conserved components of a transcriptional regulatory network

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Genome-wide analysis of mRNA targets for Caenorhabditis elegans FBF, a conserved stem cell regulator

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

A 5' cytosine binding pocket in Puf3p specifies regulation of mitochondrial mRNAs

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

From elements to modules: regulatory evolution in Ascomycota fungi

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

The GAIT system: a gatekeeper of inflammatory gene expression.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Tools for fungal proteomics: multifunctional neurospora vectors for gene replacement, protein expression and protein purification

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Turning a hobby into a job: how duplicated genes find new functions

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Transcription factor substitution during the evolution of fungal ribosome regulation

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Basis of altered RNA-binding specificity by PUF proteins revealed by crystal structures of yeast Puf4p

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Natural history and evolutionary principles of gene duplication in fungi

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

RNA regulons: coordination of post-transcriptional events

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Transcriptional rewiring of fungal galactose-metabolism circuitry

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Frequent gain and loss of functional transcription factor binding sites

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Early diverging Ascomycota: phylogenetic divergence and related evolutionary enigmas

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Dating divergences in the Fungal Tree of Life: review and new analyses

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

PhyloGibbs: a Gibbs sampling motif finder that incorporates phylogeny

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

RNA-protein interactions in the yeast three-hybrid system: affinity, sensitivity, and enhanced library screening

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Conservation and evolution of cis-regulatory systems in ascomycete fungi

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Java Treeview--extensible visualization of microarray data

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

MUSCLE: multiple sequence alignment with high accuracy and high throughput

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Extensive association of functionally and cytotopically related mRNAs with Puf family RNA-binding proteins in yeast

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

CLIP identifies Nova-regulated RNA networks in the brain

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

The PUF family of RNA-binding proteins: does evolutionarily conserved structure equal conserved function?

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

DAVID: Database for Annotation, Visualization, and Integrated Discovery

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

The staufen/pumilio pathway is involved in Drosophila long-term memory.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Modular recognition of RNA by a human pumilio-homology domain

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

A three-hybrid system to detect RNA-protein interactions in vivo

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

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

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Evolution of alternative transcriptional circuits with identical logic

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

A single spacer nucleotide determines the specificities of two mRNA regulatory proteins.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5389312

Dkk2 has a role in terminal osteoblast differentiation and mineralized matrix formation

17 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1617777114

Rewiring of the Yeast Transcriptional Network Through the Evolution of Motif Usage

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1617777114

Determining the RNA specificity and targets of RNA-binding proteins using a three-hybrid system

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/28320951

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1073/PNAS.1617777114

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:28320951%20AND%20SRC:MED&resulttype=core&format=json

13 March 2020

PubMed publication ID

28320951

1 reference