(Q33592928)

English

Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes

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scholarly article

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Europe PubMed Central

PubMed publication ID

28 July 2017

Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes (English)

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

1 reference

based on heuristic

inferred from title

whole genome sequencing

1 reference

based on heuristic

inferred from title

author name string

Casey R Richardson

1

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Qing-Jun Luo

2

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Viktoria Gontcharova

3

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Ying-Wen Jiang

4

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Manoj Samanta

5

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

Eunseog Youn

6

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Europe PubMed Central

PubMed publication ID

28 July 2017

Christopher D Rock

7

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Europe PubMed Central

PubMed publication ID

28 July 2017

language of work or name

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publication date

26 May 2010

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Europe PubMed Central

PubMed publication ID

28 July 2017

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

5

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

5

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

e10710

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Europe PubMed Central

PubMed publication ID

28 July 2017

copyright license

Creative Commons Attribution 4.0 International

26 May 2010

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April 2022 Public Data File from Crossref

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Small RNAs - secrets and surprises of the genome

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A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

What is a support vector machine?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

The TIGR Rice Genome Annotation Resource: improvements and new features

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

RNA polymerase III transcribes human microRNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

A two-hit trigger for siRNA biogenesis in plants

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Rice embryogenic calli express a unique set of microRNAs, suggesting regulatory roles of microRNAs in plant post-embryogenic development

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Comprehensive identification of Drosophila dorsal-ventral patterning genes using a whole-genome tiling array.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Complex Loci in human and mouse genomes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

A high-resolution map of transcription in the yeast genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Antisense transcription in the mammalian transcriptome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Expression of Arabidopsis MIRNA genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

miRU: an automated plant miRNA target prediction server

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

DINAMelt web server for nucleic acid melting prediction

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Computational prediction of miRNAs in Arabidopsis thaliana

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

MicroRNA binding sites in Arabidopsis class III HD-ZIP mRNAs are required for methylation of the template chromosome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Computational identification of plant microRNAs and their targets, including a stress-induced miRNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

MicroRNA-directed cleavage of HOXB8 mRNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Empirical analysis of transcriptional activity in the Arabidopsis genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Experimental RNomics: identification of 140 candidates for small non-messenger RNAs in the plant Arabidopsis thaliana

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Influence of cytokinins on the expression of phosphate starvation responsive genes in Arabidopsis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Isolation and analysis of cDNA within a 300 kb Arabidopsis thaliana genomic region located around the 100 map unit of chromosome 1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Sequence analysis of a 40-kb Arabidopsis thaliana genomic region located at the top of chromosome 1.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

Basic local alignment search tool

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

21 June 2018

MicroRNA-targeted and small interfering RNA-mediated mRNA degradation is regulated by argonaute, dicer, and RNA-dependent RNA polymerase in Arabidopsis.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Noncoding RNA for CR20, a cytokinin-repressed gene of cucumber

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

The down-regulation of Mt4-like genes by phosphate fertilization occurs systemically and involves phosphate translocation to the shoots

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Distinct expression patterns of natural antisense transcripts in Arabidopsis

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Transcriptome-wide analysis of uncapped mRNAs in Arabidopsis reveals regulation of mRNA degradation

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Retrotransposons and siRNA have a role in the evolution of desiccation tolerance leading to resurrection of the plant Craterostigma plantagineum

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

A cluster of disease resistance genes in Arabidopsis is coordinately regulated by transcriptional activation and RNA silencing

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Identification of microRNA regulatory modules in Arabidopsis via a probabilistic graphical model

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Conservation and divergence of plant microRNA genes.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Expansion mechanisms and functional annotations of hypothetical genes in the rice genome.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Criteria for annotation of plant MicroRNAs

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Arabidopsis FIERY1, XRN2, and XRN3 are endogenous RNA silencing suppressors

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

A link between RNA metabolism and silencing affecting Arabidopsis development.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Identification of cold-inducible microRNAs in plants by transcriptome analysis.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Whole-genome microarray in Arabidopsis facilitates global analysis of retained introns.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

C. elegans ORFeome version 1.1: experimental verification of the genome annotation and resource for proteome-scale protein expression.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Selective epigenetic control of retrotransposition in Arabidopsis.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Bursts of retrotransposition reproduced in Arabidopsis

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Experimental RNomics

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Genome-wide transcription analyses in rice using tiling microarrays

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Uniparental expression of PolIV-dependent siRNAs in developing endosperm of Arabidopsis

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

DNA methylation mediated by a microRNA pathway

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2877095

30 October 2018

Genome-wide analysis of the RNA-DEPENDENT RNA POLYMERASE6/DICER-LIKE4 pathway in Arabidopsis reveals dependency on miRNA- and tasiRNA-directed targeting

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0010710

21 January 2018

Orphan transcripts in Arabidopsis thaliana: identification of several hundred previously unrecognized genes

1 reference

https://pubmed.ncbi.nlm.nih.gov/20520764

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Riboactivators: transcription activation by noncoding RNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/20520764

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The epigenetic landscape of plants

1 reference

https://pubmed.ncbi.nlm.nih.gov/20520764

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identification of the candidate genes regulated by RNA-directed DNA methylation in Arabidopsis

1 reference

https://pubmed.ncbi.nlm.nih.gov/20520764

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1371/JOURNAL.PONE.0010710

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

2010PLoSO...510710R

0 references

PMC publication ID

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

PubMed publication ID

1 reference

Europe PubMed Central

PubMed publication ID

28 July 2017

ResearchGate publication ID

0 references

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