Global pairwise RNA interaction landscapes reveal core features of protein recognition. (Q55397375)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

title

Global pairwise RNA interaction landscapes reveal core features of protein recognition (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

author

José Alberto De la Paz

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Faruck Morcos

6

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Zachary T Campbell

7

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

author name string

Qin Zhou

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Nikesh Kunder

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Alexandra E Lasley

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

Vandita D Bhat

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

language of work or name

English

0 references

publication date

28 June 2018

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

published in

Nature Communications

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

volume

9

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

page(s)

2511

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

issue

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

Creative Commons Attribution 4.0 International

3 April 2020

copyright license

start time

28 June 2018

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

exact match

https://scigraph.springernature.com/pub.10.1038/s41467-018-04729-0

0 references

cites work

Revealing protein networks and gene-drug connectivity in cancer from direct information.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

High-throughput biochemical profiling reveals sequence determinants of dCas9 off-target binding and unbinding

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Optimization of RNA 3D structure prediction using evolutionary restraints of nucleotide-nucleotide interactions from direct coupling analysis.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Mutation effects predicted from sequence co-variation

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Simultaneous identification of specifically interacting paralogs and interprotein contacts by direct coupling analysis.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Integrated analysis of RNA-binding protein complexes using in vitro selection and high-throughput sequencing and sequence specificity landscapes (SEQRS).

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Advances in the characterization of RNA-binding proteins

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

3D RNA and Functional Interactions from Evolutionary Couplings

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Epistasis in protein evolution

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

DNA-dependent formation of transcription factor pairs alters their binding specificity

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Coevolutionary Landscape Inference and the Context-Dependence of Mutations in Beta-Lactamase TEM-1.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Direct-Coupling Analysis of nucleotide coevolution facilitates RNA secondary and tertiary structure prediction

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Specificity and nonspecificity in RNA-protein interactions

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

TUT7 controls the fate of precursor microRNAs by using three different uridylation mechanisms

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

The Clothes Make the mRNA: Past and Present Trends in mRNP Fashion

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

RNA aptamers as genetic control devices: the potential of riboswitches as synthetic elements for regulating gene expression

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Probing RNA-protein networks: biochemistry meets genomics

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Coevolutionary information, protein folding landscapes, and the thermodynamics of natural selection

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Insights into RNA structure and function from genome-wide studies

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

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

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

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

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Methods for comprehensive experimental identification of RNA-protein interactions

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Coevolutionary signals across protein lineages help capture multiple protein conformations.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Hidden specificity in an apparently nonspecific RNA-binding protein

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

The nucleic acid-binding domain and translational repression activity of a Xenopus terminal uridylyl transferase.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

How cells get the message: dynamic assembly and function of mRNA-protein complexes

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

SeqFold: genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

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

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Identification of a conserved interface between PUF and CPEB proteins

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Cofactor binding evokes latent differences in DNA binding specificity between Hox proteins

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Direct-coupling analysis of residue coevolution captures native contacts across many protein families

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Genome-wide binding map of the HIV-1 Tat protein to the human genome

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

RNA structure and the mechanisms of alternative splicing.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

FragSeq: transcriptome-wide RNA structure probing using high-throughput sequencing

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Genome-wide measurement of RNA secondary structure in yeast

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Specificity landscapes of DNA binding molecules elucidate biological function

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

High-resolution protein complexes from integrating genomic information with molecular simulation

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Role of RNA structure in regulating pre-mRNA splicing

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

10 July 2018

The centrality of RNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Identification of direct residue contacts in protein-protein interaction by message passing

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Bacteriophage P22 antitermination boxB sequence requirements are complex and overlap with those of lambda

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

CSI-Tree: a regression tree approach for modeling binding properties of DNA-binding molecules based on cognate site identification (CSI) data

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Arginine-rich motifs present multiple interfaces for specific binding by RNA.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Regulation of translation via mRNA structure in prokaryotes and eukaryotes

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

The HIV-1 Tat transactivator protein: a therapeutic target?

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Binding of Tat to TAR and recruitment of positive transcription elongation factor b occur independently in bovine immunodeficiency virus

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Antitermination in bacteriophage lambda. The structure of the N36 peptide-boxB RNA complex

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Altering the context of an RNA bulge switches the binding specificities of two viral Tat proteins

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Solution structure of P22 transcriptional antitermination N peptide-boxB RNA complex

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Analysis of bacteriophage N protein and peptide binding to boxB RNA using polyacrylamide gel coelectrophoresis (PACE).

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

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

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Solution structure of a bovine immunodeficiency virus Tat-TAR peptide-RNA complex

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Use of the ‘Perceptron’ algorithm to distinguish translational initiation sites inE. coli

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

A method for measuring the non-random bias of a codon usage table

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

lambda N antitermination system: functional analysis of phage interactions with the host NusA protein.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

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

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Purification of RNA and RNA-protein complexes by an R17 coat protein affinity method

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

In vitro selection of RNA molecules that bind specific ligands

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Architecture and dynamics of overlapped RNA regulatory networks.

10 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Comprehensive and quantitative mapping of RNA-protein interactions across a transcribed eukaryotic genome

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Global analysis of RNA secondary structure in two metazoans.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

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

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Binding specificity and mRNA targets of a C. elegans PUF protein, FBF-1.

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Translation driven by an eIF4G core domain in vivo

12 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=6023938

Antitermination in bacteriophage λ

12 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FS41467-018-04729-0

inferred from DOI database lookup

7 January 2021

based on heuristic

A direct approach to false discovery rates

1 reference

Crossref

https://api.crossref.org/works/10.1038%2FS41467-018-04729-0

inferred from DOI database lookup

7 January 2021

based on heuristic

Identifiers

DOI

10.1038/S41467-018-04729-0

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

3 April 2020

ADS bibcode

2018NatCo...9.2511Z

0 references

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:29955037%20AND%20SRC:MED&resulttype=core&format=json

3 April 2020

1 reference