(Q43954038)

28 November 2017

title

Characteristics and significance of intergenic polyadenylated RNA transcription in Arabidopsis (English)

1 reference

28 November 2017

9

1 reference

28 November 2017

Piyada Juntawong

6

0 references

Gaurav D Moghe

object named as

Gaurav D Moghe

1

0 references

Julia Bailey-Serres

object named as

Julia Bailey-Serres

8

0 references

Federica Brandizzi

7

object named as

Federica Brandizzi

1 reference

28 November 2017

2

Melissa D Lehti-Shiu

1 reference

28 November 2017

Alex E Seddon

3

1 reference

28 November 2017

Shan Yin

4

1 reference

28 November 2017

Yani Chen

5

1 reference

28 November 2017

language of work or name

English

0 references

publication date

6 November 2012

1 reference

28 November 2017

number of pages

15

1 reference

based on heuristic

inferred from page(s)

published in

Plant Physiology

1 reference

28 November 2017

volume

161

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28 November 2017

issue

1

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28 November 2017

page(s)

210-224

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Creative Commons Attribution 4.0 International

28 November 2017

copyright license

start time

27 January 2021

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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Landscape of transcription in human cells

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27 August 2018

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The reality of pervasive transcription

27 August 2018

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Comparative network analysis reveals that tissue specificity and gene function are important factors influencing the mode of expression evolution in Arabidopsis and rice.

27 August 2018

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

27 August 2018

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Vernalization-mediated epigenetic silencing by a long intronic noncoding RNA.

27 August 2018

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Cell-type specific analysis of translating RNAs in developing flowers reveals new levels of control

27 August 2018

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27 August 2018

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Intergenic and repeat transcription in human, chimpanzee and macaque brains measured by RNA-Seq

27 August 2018

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Comparison and calibration of transcriptome data from RNA-Seq and tiling arrays

27 August 2018

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Most "dark matter" transcripts are associated with known genes

27 August 2018

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Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

27 August 2018

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sORF finder: a program package to identify small open reading frames with high coding potential

27 August 2018

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Genome-wide mapping of alternative splicing in Arabidopsis thaliana

27 August 2018

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Pervasive transcription of the eukaryotic genome: functional indices and conceptual implications

27 August 2018

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Digital transcriptome profiling using selective hexamer priming for cDNA synthesis

27 August 2018

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Getting the message across: cytoplasmic ribonucleoprotein complexes

27 August 2018

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Conserved introns reveal novel transcripts in Drosophila melanogaster

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

The genetic signatures of noncoding RNAs

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Evolutionary genomics and the reach of selection

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

TopHat: discovering splice junctions with RNA-Seq

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Evolution and functions of long noncoding RNAs

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Long non-coding RNAs: insights into functions

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Bidirectional promoters generate pervasive transcription in yeast

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Discovery and revision of Arabidopsis genes by proteogenomics

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Differentiating protein-coding and noncoding RNA: challenges and ambiguities

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Application of a translational profiling approach for the comparative analysis of CNS cell types

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Selective mRNA translation coordinates energetic and metabolic adjustments to cellular oxygen deprivation and reoxygenation in Arabidopsis thaliana

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Arabidopsis transcriptome analysis under drought, cold, high-salinity and ABA treatment conditions using a tiling array

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

A link between RNA metabolism and silencing affecting Arabidopsis development.

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

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

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Analysis of CATMA transcriptome data identifies hundreds of novel functional genes and improves gene models in the Arabidopsis genome

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

RNA maps reveal new RNA classes and a possible function for pervasive transcription

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Rapid, transient expression of fluorescent fusion proteins in tobacco plants and generation of stably transformed plants.

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

PAML 4: phylogenetic analysis by maximum likelihood

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

A large number of novel coding small open reading frames in the intergenic regions of the Arabidopsis thaliana genome are transcribed and/or under purifying selection

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Global identification and characterization of transcriptionally active regions in the rice genome

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Transcriptional noise and the fidelity of initiation by RNA polymerase II.

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

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

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Doubling genome size without polyploidization: dynamics of retrotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Differential lineage-specific amplification of transposable elements is responsible for genome size variation in Gossypium

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

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

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Distinguishing protein-coding from non-coding RNAs through support vector machines

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

A high-resolution map of transcription in the yeast genome

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

The transcriptional landscape of the mammalian genome

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

A gene expression map of Arabidopsis thaliana development

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

GMAP: a genomic mapping and alignment program for mRNA and EST sequences

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Global identification of human transcribed sequences with genome tiling arrays

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

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

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Intron retention is a major phenomenon in alternative splicing in Arabidopsis.

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Common pattern of evolution of gene expression level and protein sequence in Drosophila

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Empirical analysis of transcriptional activity in the Arabidopsis genome

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Regulation of translational initiation in plants.

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

The K(A)/K(S) ratio test for assessing the protein-coding potential of genomic regions: an empirical and simulation study

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Small open reading frames: beautiful needles in the haystack.

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

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

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome

27 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3532253

A gateway cloning vector set for high-throughput functional analysis of genes in planta

29 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23132786

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Mouse transcriptome: neutral evolution of 'non-coding' complementary DNAs

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23132786

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1104/PP.112.205245

1 reference

28 November 2017

0 references

1 reference