(Q41338193)

29 September 2017

title

Coordinated rates of evolution between interacting plastid and nuclear genes in Geraniaceae (English)

1 reference

29 September 2017

Geraniaceae

1 reference

Jin Zhang

1

1 reference

29 September 2017

Tracey A Ruhlman

2

1 reference

29 September 2017

Jamal Sabir

3

1 reference

29 September 2017

J Chris Blazier

4

1 reference

29 September 2017

Robert K Jansen

5

1 reference

29 September 2017

publication date

27 February 2015

1 reference

29 September 2017

1 reference

29 September 2017

volume

27

1 reference

29 September 2017

issue

3

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29 September 2017

page(s)

563-573

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Protein-protein interaction detection: methods and analysis

29 September 2017

cites work

1 reference

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29 August 2018

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Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes

29 August 2018

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Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates

29 August 2018

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Mitochondrial-nuclear interactions: compensatory evolution or variable functional constraint among vertebrate oxidative phosphorylation genes?

29 August 2018

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29 August 2018

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29 August 2018

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29 August 2018

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Evidence for compensatory evolution of ribosomal proteins in response to rapid divergence of mitochondrial rRNA.

29 August 2018

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Phylogeny, rate variation, and genome size evolution of Pelargonium (Geraniaceae).

29 August 2018

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Evolutionary rate covariation reveals shared functionality and coexpression of genes

29 August 2018

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29 August 2018

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Mitochondrial-nuclear interactions and accelerated compensatory evolution: evidence from the primate cytochrome C oxidase complex.

29 August 2018

1 reference

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Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae).

29 August 2018

1 reference

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29 August 2018

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29 August 2018

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29 August 2018

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Identification of shared single copy nuclear genes in Arabidopsis, Populus, Vitis and Oryza and their phylogenetic utility across various taxonomic levels

29 August 2018

1 reference

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A novel method to detect proteins evolving at correlated rates: identifying new functional relationships between coevolving proteins

29 August 2018

1 reference

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Biparental inheritance of plastidial and mitochondrial DNA and hybrid variegation in Pelargonium

29 August 2018

1 reference

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29 August 2018

1 reference

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Virus-host coevolution: common patterns of nucleotide motif usage in Flaviviridae and their hosts

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Protein co-evolution, co-adaptation and interactions

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Coordinated evolution of the hepatitis C virus

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

The complete nucleotide sequences of the 5 genetically distinct plastid genomes of Oenothera, subsection Oenothera: II. A microevolutionary view using bioinformatics and formal genetic data

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

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

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Detecting coevolution in and among protein domains

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Clustal W and Clustal X version 2.0

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

PAML 4: phylogenetic analysis by maximum likelihood

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

The Complete Chloroplast Genome Sequence of Pelargonium x hortorum: Organization and Evolution of the Largest and Most Highly Rearranged Chloroplast Genome of Land Plants

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

A hybrid micro-macroevolutionary approach to gene tree reconstruction.

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Specific function of a plastid sigma factor for ndhF gene transcription

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Plastid RNA polymerases, promoters, and transcription regulators in higher plants

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Assessing protein co-evolution in the context of the tree of life assists in the prediction of the interactome.

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Structure, function, and evolution of transient and obligate protein-protein interactions

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

The inference of protein-protein interactions by co-evolutionary analysis is improved by excluding the information about the phylogenetic relationships

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

SPACE: a suite of tools for protein structure prediction and analysis based on complementarity and environment.

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Pigment deficiency in nightshade/tobacco cybrids is caused by the failure to edit the plastid ATPase alpha-subunit mRNA.

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Comparative analysis of the Saccharomyces cerevisiae and Caenorhabditis elegans protein interaction networks

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

HyPhy: hypothesis testing using phylogenies

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Gene expression intensity shapes evolutionary rates of the proteins encoded by the vertebrate genome

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Coevolution of gene expression among interacting proteins

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

MUSCLE: multiple sequence alignment with high accuracy and high throughput

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Preferential duplication of conserved proteins in eukaryotic genomes

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Evolution of interacting proteins in the mitochondrial electron transport system in a marine copepod

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Positive selection and subfunctionalization of duplicated CCT chaperonin subunits

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Characterization of two chloroplast RNA polymerase sigma factors from Zea mays: photoregulation and differential expression

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

How frequent are correlated changes in families of protein sequences?

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Compensating changes in protein multiple sequence alignments

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

The coordinated evolution of yeast proteins is constrained by functional modularity

29 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4558654

Plastid signals remodel light signaling networks and are essential for efficient chloroplast biogenesis in Arabidopsis

2 December 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25724640

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Preferential duplication in the sparse part of yeast protein interaction network

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25724640

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

The role of chloroplastic NAD(P)H dehydrogenase in photoprotection

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/25724640

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1105/TPC.114.134353

1 reference

29 September 2017

0 references

1 reference