(Q33877367)

29 July 2017

Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana (English)

1 reference

29 July 2017

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1

1 reference

29 July 2017

2

Hadi Quesneville

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language of work or name

English

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publication date

23 June 2014

1 reference

29 July 2017

Nature Communications

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29 July 2017

5

1 reference

29 July 2017

4104

1 reference

Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International

29 July 2017

start time

23 June 2014

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

exact match

https://scigraph.springernature.com/pub.10.1038/ncomms5104

0 references

cites work

The Capsella rubella genome and the genomic consequences of rapid mating system evolution

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Genome-wide characterization of endogenous retroviruses in the bat Myotis lucifugus reveals recent and diverse infections

28 July 2018

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The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to access H1-containing heterochromatin

28 July 2018

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The Reference Genome of the Halophytic Plant Eutrema salsugineum

28 July 2018

1 reference

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Transposon variants and their effects on gene expression in Arabidopsis

28 July 2018

1 reference

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Comprehensive analysis of silencing mutants reveals complex regulation of the Arabidopsis methylome.

28 July 2018

1 reference

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The impact of transposable elements in environmental adaptation.

28 July 2018

1 reference

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Insights into salt tolerance from the genome of Thellungiella salsuginea

28 July 2018

1 reference

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Centromere-targeted de novo integrations of an LTR retrotransposon of Arabidopsis lyrata

28 July 2018

1 reference

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The Pfam protein families database

28 July 2018

1 reference

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S-MART, a software toolbox to aid RNA-Seq data analysis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

The genome of the mesopolyploid crop species Brassica rapa

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

The genome of the extremophile crucifer Thellungiella parvula

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Reference-guided assembly of four diverse Arabidopsis thaliana genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Genome-wide evidence for local DNA methylation spreading from small RNA-targeted sequences in Arabidopsis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

The Arabidopsis lyrata genome sequence and the basis of rapid genome size change

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Considering transposable element diversification in de novo annotation approaches

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Cabbage family affairs: the evolutionary history of Brassicaceae

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Epigenetic silencing of transposable elements: a trade-off between reduced transposition and deleterious effects on neighboring gene expression

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Comparative analysis of Alu repeats in primate genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

A probabilistic model of local sequence alignment that simplifies statistical significance estimation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Highly integrated single-base resolution maps of the epigenome in Arabidopsis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Evolution and control of imprinted FWA genes in the genus Arabidopsis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Evolutionary history of mammalian transposons determined by genome-wide defragmentation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Poorly known relatives of Arabidopsis thaliana.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Combined evidence annotation of transposable elements in genome sequences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Chromosome triplication found across the tribe Brassiceae.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Rapid recent growth and divergence of rice nuclear genomes

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Perspective: transposable elements, parasitic DNA, and genome evolution

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Initial sequencing and analysis of the human genome

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Stress and transposable elements: co-evolution or useful parasites?

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

The paleontology of intergene retrotransposons of maize

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Transposable elements as sources of variation in animals and plants

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

The repair of 5-methylcytosine deamination damage

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

DNA Methylation and Gene Function

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

CpG-rich islands and the function of DNA methylation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4090718

Selfish DNA: the ultimate parasite

28 July 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

PERSPECTIVE: TRANSPOSABLE ELEMENTS, PARASITIC DNA, AND GENOME EVOLUTION

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

RNA-directed de novo methylation of genomic sequences in plants.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

NERD, a plant-specific GW protein, defines an additional RNAi-dependent chromatin-based pathway in Arabidopsis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

The shrunken genome of Arabidopsis thaliana

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

Reconstructing de novo silencing of an active plant retrotransposon.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

21 January 2018

Phylogeny of Methylomes

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

Codon usage by transposable elements and their host genes in five species.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

The age of Alu subfamilies.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

The dynamic ups and downs of genome size evolution in Brassicaceae

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

Bursts of retrotransposition reproduced in Arabidopsis

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

Selective epigenetic control of retrotransposition in Arabidopsis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

Repbase Update, a database of eukaryotic repetitive elements

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

De novo identification of repeat families in large genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

EMBOSS: the European Molecular Biology Open Software Suite

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS5104

Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24954583

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Presidential address. Transposable elements, epigenetics, and genome evolution

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24954583

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1038/NCOMMS5104

1 reference

Dimensions Publication ID

29 July 2017

0 references

0 references

1 reference

29 July 2017

1 reference

PubMed ID

24954583