(Q34099016)

31 July 2017

Modes of gene duplication contribute differently to genetic novelty and redundancy, but show parallels across divergent angiosperms (English)

1 reference

31 July 2017

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1 reference

3

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31 July 2017

5

1 reference

31 July 2017

Yupeng Wang

1

0 references

Andrew H Paterson

series ordinal

7

object named as

Andrew H Paterson

1 reference

31 July 2017

Xiyin Wang

2

1 reference

31 July 2017

Xu Tan

series ordinal

4

1 reference

31 July 2017

F Alex Feltus

series ordinal

6

1 reference

31 July 2017

language of work or name

English

0 references

publication date

2 December 2011

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31 July 2017

1 reference

31 July 2017

6

1 reference

31 July 2017

12

1 reference

31 July 2017

e28150

1 reference

Creative Commons Attribution 4.0 International

31 July 2017

start time

2 December 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Genetic interactions reveal the evolutionary trajectories of duplicate genes

1 reference

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Comparison of computational models for assessing conservation of gene expression across species

5 July 2018

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Transposed genes in Arabidopsis are often associated with flanking repeats

5 July 2018

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Insights from the comparison of plant genome sequences

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Conservation and divergence of methylation patterning in plants and animals

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Contrasting genetic paths to morphological and physiological evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Need-based up-regulation of protein levels in response to deletion of their duplicate genes

5 July 2018

1 reference

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Angiosperm genome comparisons reveal early polyploidy in the monocot lineage

5 July 2018

1 reference

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The cytochrome p450 homepage.

5 July 2018

1 reference

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A comprehensive analysis of gene expression evolution between humans and mice.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

The frequency of polyploid speciation in vascular plants

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Bias in plant gene content following different sorts of duplication: tandem, whole-genome, segmental, or by transposition

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Expression pattern divergence of duplicated genes in rice

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Evolution of gene function and regulatory control after whole-genome duplication: comparative analyses in vertebrates.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

The Sorghum bicolor genome and the diversification of grasses

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Duplicate genes increase expression diversity in closely related species and allopolyploids

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

arrayQualityMetrics--a bioconductor package for quality assessment of microarray data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

RNA-based gene duplication: mechanistic and evolutionary insights

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Many or most genes in Arabidopsis transposed after the origin of the order Brassicales

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Computational analysis of constraints on noncoding regions, coding regions and gene expression in relation to Plasmodium phenotypic diversity

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Genome duplication and the origin of the vertebrate skeleton.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Pervasive and persistent redundancy among duplicated genes in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Null mutations in human and mouse orthologs frequently result in different phenotypes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Preferential protection of protein interaction network hubs in yeast: evolved functionality of genetic redundancy

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Extensive concerted evolution of rice paralogs and the road to regaining independence

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in Arabidopsis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Increased glycolytic flux as an outcome of whole-genome duplication in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Comparative analysis indicates regulatory neofunctionalization of yeast duplicates

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

TimeTree: a public knowledge-base of divergence times among organisms

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Many gene and domain families have convergent fates following independent whole-genome duplication events in Arabidopsis, Oryza, Saccharomyces and Tetraodon

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Unequal genetic redundancies in Arabidopsis--a neglected phenomenon?

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

An analysis of intra array repeats: the good, the bad and the non informative

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Influence of metabolic network structure and function on enzyme evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Mechanisms of genomic rearrangements and gene expression changes in plant polyploids

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

A global definition of expression context is conserved between orthologs, but does not correlate with sequence conservation

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Epigenetics and plant evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Novel patterns of gene expression in polyploid plants

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Modeling gene and genome duplications in eukaryotes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Evolution of DNA sequence nonhomologies among maize inbreds

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Conservation, diversification and expansion of C2H2 zinc finger proteins in the Arabidopsis thaliana genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Functional divergence of duplicated genes formed by polyploidy during Arabidopsis evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Dosage sensitivity and the evolution of gene families in yeast

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Role of duplicate genes in genetic robustness against null mutations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Rapid divergence in expression between duplicate genes inferred from microarray data

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Gene loss, silencing and activation in a newly synthesized wheat allotetraploid.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Sequence elimination and cytosine methylation are rapid and reproducible responses of the genome to wide hybridization and allopolyploidy in wheat

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Allopolyploidy-induced rapid genome evolution in the wheat (Aegilops-Triticum) group

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Protein-coding genes are epigenetically regulated in Arabidopsis polyploids

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

The evolutionary fate and consequences of duplicate genes

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Preservation of duplicate genes by complementary, degenerative mutations

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Cytochrome P450 superfamily in Arabidopsis thaliana: isolation of cDNAs, differential expression, and RFLP mapping of multiple cytochromes P450.

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Dispersed repetitive DNA has spread to new genomes since polyploid formation in cotton

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Molecular evidence for an ancient duplication of the entire yeast genome

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Transcriptional analysis of nucleolar dominance in polyploid plants: biased expression/silencing of progenitor rRNA genes is developmentally regulated in Brassica

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Rapid genome change in synthetic polyploids of Brassica and its implications for polyploid evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Retroposons--seeds of evolution

5 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3229532

Seventy million years of concerted evolution of a homoeologous chromosome pair, in parallel, in major Poaceae lineages

5 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028150

Phenotypic instability and rapid gene silencing in newly formed arabidopsis allotetraploids.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028150

Epigenetic silencing may aid evolution by gene duplication

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028150

Not Born Equal: Increased Rate Asymmetry in Relocated and Retrotransposed Rodent Gene Duplicates

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028150

Divergence in Expression between Duplicated Genes in Arabidopsis

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028150

Pack-MULE transposable elements mediate gene evolution in plants

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028150

The evolution of functionally novel proteins after gene duplication.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028150

Synteny and Collinearity in Plant Genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028150

Duplicate genes increase gene expression diversity within and between species.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028150

Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028150

Microarray-based analysis of gene expression in very large gene families: the cytochrome P450 gene superfamily of Arabidopsis thaliana.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028150

The Arabidopsis co-expression tool (ACT): a WWW-based tool and database for microarray-based gene expression analysis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028150

Evolutionary conservation of expression profiles between human and mouse orthologous genes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0028150

Transcriptional activation of retrotransposons alters the expression of adjacent genes in wheat

21 January 2018

1 reference

12 December 2020

Evolution of duplicate genes in a tetraploid animal, Xenopus laevis

1 reference

12 December 2020

1 reference

12 December 2020

Exposing the fitness contribution of duplicated genes

1 reference

12 December 2020

Nonlinear effects in macromolecular assembly and dosage sensitivity

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0028150

Identifiers

DOI

1 reference

31 July 2017

0 references

1 reference

31 July 2017

1 reference