Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes (Q28710416)

object named as

Thomas Wicker

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author name string

Konstantinos Kritsas

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Samuel E Wuest

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Daniel Hupalo

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Andrew D Kern

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

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language of work or name

English

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publication date

December 2012

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2455-66

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cites work

1 reference

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Transposed genes in Arabidopsis are often associated with flanking repeats

17 March 2017

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Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements

17 March 2017

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Genome sequencing and analysis of the model grass Brachypodium distachyon

17 March 2017

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17 March 2017

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The genome of the cucumber, Cucumis sativus L

17 March 2017

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PMRD: plant microRNA database

17 March 2017

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Plants with double genomes might have had a better chance to survive the Cretaceous-Tertiary extinction event

17 March 2017

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Ultraconserved elements: analyses of dosage sensitivity, motifs and boundaries

17 March 2017

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Ultraconservation identifies a small subset of extremely constrained developmental enhancers

17 March 2017

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Deletion of ultraconserved elements yields viable mice

17 March 2017

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PAML 4: phylogenetic analysis by maximum likelihood

17 March 2017

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The Genome of Black Cottonwood, Populus trichocarpa (Torr. & Gray)

17 March 2017

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A genomic code for nucleosome positioning

17 March 2017

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Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data

17 March 2017

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Functional evolution of a cis-regulatory module

17 March 2017

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Highly conserved non-coding sequences are associated with vertebrate development

17 March 2017

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Ultraconserved Elements in the Human Genome

17 March 2017

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A molecular timeline for the origin of photosynthetic eukaryotes

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Darwin's abominable mystery: Insights from a supertree of the angiosperms

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

DNA binding sites: representation and discovery

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Dating of the human-ape splitting by a molecular clock of mitochondrial DNA

17 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Stomatal size in fossil plants: evidence for polyploidy in majority of angiosperms

17 March 2017

1 reference

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

7 April 2017

1 reference

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Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

In vivo enhancer analysis of human conserved non-coding sequences

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Long identical multispecies elements in plant and animal genomes

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Thousands of cis-regulatory sequence combinations are shared by Arabidopsis and poplar

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

DNA methylation in higher plants: past, present and future.

3 June 2018

1 reference

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Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Patching gaps in plant genomes results in gene movement and erosion of colinearity

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Insights from the comparison of plant genome sequences

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Global analysis of gene activity during Arabidopsis seed development and identification of seed-specific transcription factors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Arabidopsis female gametophyte gene expression map reveals similarities between plant and animal gametes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Chromatin 'programming' by sequence--is there more to the nucleosome code than %GC?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Early evolution of conserved regulatory sequences associated with development in vertebrates

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Pan-vertebrate conserved non-coding sequences associated with developmental regulation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Correcting the site frequency spectrum for divergence-based ascertainment

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Gene expression map of the Arabidopsis shoot apical meristem stem cell niche

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Conserved noncoding sequences (CNSs) in higher plants

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Structural relationships between highly conserved elements and genes in vertebrate genomes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Human genome ultraconserved elements are ultraselected

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Recombination and linkage disequilibrium in Arabidopsis thaliana.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Ultraconserved non-coding sequence element controls a subset of spatiotemporal GLI3 expression

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

The strength of selection on ultraconserved elements in the human genome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Transcriptional profile of the Arabidopsis root quiescent center

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

In vivo characterization of a vertebrate ultraconserved enhancer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Close split of sorghum and maize genome progenitors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Conserved noncoding sequences in the grasses

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Utility and distribution of conserved noncoding sequences in the grasses

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Evidence for stabilizing selection in a eukaryotic enhancer element.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Whole-genome sequencing of multiple Arabidopsis thaliana populations.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Large number of ultraconserved elements were already present in the jawed vertebrate ancestor

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

The words of the regulatory code are arranged in a variable manner in highly conserved enhancers.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Genome-wide high-resolution mapping of exosome substrates reveals hidden features in the Arabidopsis transcriptome

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Large-Scale Appearance of Ultraconserved Elements in Tetrapod Genomes and Slowdown of the Molecular Clock

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Comparison of orthologous loci from small grass genomes Brachypodium and rice: implications for wheat genomics and grass genome annotation

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Conserved noncoding sequences are selectively constrained and not mutation cold spots

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Striking nucleotide frequency pattern at the borders of highly conserved vertebrate non-coding sequences

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Comparing the linkage maps of the close relatives Arabidopsis lyrata and A. thaliana

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Conserved Noncoding Sequences among Cultivated Cereal Genomes Identify Candidate Regulatory Sequence Elements and Patterns of Promoter Evolution[W]

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Numerous potentially functional but non-genic conserved sequences on human chromosome 21

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Rates of nucleotide substitution in angiosperm mitochondrial DNA sequences and dates of divergence between Brassica and other angiosperm lineages

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3514675

Ultraconserved elements between the genomes of the plants Arabidopsis thaliana and rice

27 November 2018

1 reference

12 December 2020

Consensus features of microsatellite distribution: microsatellite contents are universally correlated with recombination rates and are preferentially depressed by centromeres in multicellular eukaryotic genomes

1 reference

12 December 2020

AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks

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12 December 2020

Conservation of Endo16 expression in sea urchins despite evolutionary divergence in both cis and trans-acting components of transcriptional regulation

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12 December 2020

Identifiers

DOI

10.1101/GR.129346.111

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PubMed publication ID

22987666

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