(Q42006136)

15 October 2017

Coevolution in RNA molecules driven by selective constraints: evidence from 5S rRNA. (English)

1 reference

15 October 2017

0 references

Nan Cheng

1

1 reference

15 October 2017

Yuanhui Mao

series ordinal

2

1 reference

15 October 2017

Youyi Shi

series ordinal

3

1 reference

15 October 2017

Shiheng Tao

series ordinal

4

1 reference

15 October 2017

language of work or name

English

0 references

publication date

4 September 2012

1 reference

15 October 2017

1 reference

15 October 2017

7

1 reference

15 October 2017

e44376

1 reference

15 October 2017

9

1 reference

Creative Commons Attribution 4.0 International

15 October 2017

start time

4 September 2012

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Detecting coevolving positions in a molecule: why and how to account for phylogeny

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Biological significance of 5S rRNA import into human mitochondria: role of ribosomal protein MRP-L18

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

The evolution of the phage shock protein response system: interplay between protein function, genomic organization, and system function

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Coevolution within a transcriptional network by compensatory trans and cis mutations.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Accelerated evolution of CES7, a gene encoding a novel major urinary protein in the cat family

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Genome evolution and adaptation in a long-term experiment with Escherichia coli

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Specific features of 5S rRNA structure - its interactions with macromolecules and possible functions.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

5 June 2018

The Vienna RNA websuite

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

jModelTest: phylogenetic model averaging

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Co-evolutionary rates of functionally related yeast genes.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Two distinct structural elements of 5S rRNA are needed for its import into human mitochondria

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

High-confidence prediction of global interactomes based on genome-wide coevolutionary networks

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Structural basis for the coevolution of a viral RNA–protein complex

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Detecting groups of coevolving positions in a molecule: a clustering approach

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Detecting coevolution in and among protein domains

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Changes in the conformation of 5S rRNA cause alterations in principal functions of the ribosomal nanomachine

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

PAML 4: phylogenetic analysis by maximum likelihood

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

The delayed rise of present-day mammals

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Identification and classification of conserved RNA secondary structures in the human genome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

A novel method for detecting intramolecular coevolution: adding a further dimension to selective constraints analyses.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Predicting functional gene links from phylogenetic-statistical analyses of whole genomes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Functional genomic analysis of the rates of protein evolution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Phylogeny of gamma-proteobacteria: resolution of one branch of the universal tree?

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Quantifying modularity in the evolution of biomolecular systems

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Compensatory evolution of a precursor messenger RNA secondary structure in the Drosophila melanogaster Adh gene

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

MrBayes 3: Bayesian phylogenetic inference under mixed models

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Vienna RNA secondary structure server

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

5 S rRNA: structure and interactions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Complementary advantageous substitutions in the evolution of an antiviral RNase of higher primates

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

5S Ribosomal RNA Database

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

RNA sequence evolution with secondary structure constraints: comparison of substitution rate models using maximum-likelihood methods.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Exploring a phylogenetic approach for the detection of correlated substitutions in proteins.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Comparative sequence analysis and patterns of covariation in RNA secondary structures

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Episodic adaptive evolution of primate lysozymes.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Compensatory evolution in mitochondrial tRNAs navigates valleys of low fitness

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Single-nucleotide mutation rate increases close to insertions/deletions in eukaryotes.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Mutual information without the influence of phylogeny or entropy dramatically improves residue contact prediction.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Prediction of functional specificity determinants from protein sequences using log-likelihood ratios.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Using information theory to search for co-evolving residues in 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=3433437

Detecting coevolving amino acid sites using Bayesian mutational mapping

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

A model-based approach for detecting coevolving positions in a molecule.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Mutual information in protein multiple sequence alignments reveals two classes of coevolving positions.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Use of logic relationships to decipher protein network organization

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Mechanisms and convergence of compensatory evolution in mammalian mitochondrial tRNAs

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Compensated deleterious mutations in insect genomes

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Identification of functional links between genes using phylogenetic profiles.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Using multiple interdependency to separate functional from phylogenetic correlations in protein alignments

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Phylogenetically enhanced statistical tools for RNA structure prediction.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

The coordinated evolution of yeast proteins is constrained by functional modularity

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3433437

Base Pairing Constraints Drive Structural Epistasis in Ribosomal RNA Sequences

2 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22973441

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Exploiting the co-evolution of interacting proteins to discover interaction specificity

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22973441

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Detecting the coevolution of biosequences--an example of RNA interaction prediction

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22973441

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0044376

1 reference

15 October 2017

0 references

1 reference

15 October 2017

1 reference