(Q41961524)

14 October 2017

PAREsnip: a tool for rapid genome-wide discovery of small RNA/target interactions evidenced through degradome sequencing (English)

1 reference

14 October 2017

2

1 reference

14 October 2017

Matthew B Stocks

4

0 references

Hugh C Woolfenden

object named as

Hugh C Woolfenden

3

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Gyorgy Szittya

object named as

Gyorgy Szittya

5

0 references

Tamas Dalmay

object named as

Tamas Dalmay

6

0 references

author name string

Leighton Folkes

1

1 reference

PMCID

3401462

14 October 2017

Vincent Moulton

7

1 reference

14 October 2017

29 March 2012

1 reference

14 October 2017

Nucleic Acids Research

1 reference

14 October 2017

40

1 reference

14 October 2017

13

1 reference

14 October 2017

e103

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

14 October 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

SoMART: a web server for plant miRNA, tasiRNA and target gene analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

SeqTar: an effective method for identifying microRNA guided cleavage sites from degradome of polyadenylated transcripts in plants

5 June 2018

1 reference

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The International Nucleotide Sequence Database Collaboration

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Small RNA discovery and characterisation in eukaryotes using high-throughput approaches

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Global analysis of the mammalian RNA degradome reveals widespread miRNA-dependent and miRNA-independent endonucleolytic cleavage

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

MicroRNA activity in the Arabidopsis male germline.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

NCBI GEO: archive for functional genomics data sets--10 years on

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

miRBase: integrating microRNA annotation and deep-sequencing data

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

siRNAs from miRNA sites mediate DNA methylation of target genes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Diverse endonucleolytic cleavage sites in the mammalian transcriptome depend upon microRNAs, Drosha, and additional nucleases

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Identification of grapevine microRNAs and their targets using high-throughput sequencing and degradome analysis

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Transcriptome-wide identification of microRNA targets in rice

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

MicroRNA and tasiRNA diversity in mature pollen of Arabidopsis thaliana

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Sequencing technologies - the next generation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Uncovering small RNA-mediated responses to phosphate deficiency in Arabidopsis by deep sequencing

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Computational and analytical framework for small RNA profiling by high-throughput sequencing

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

AGO1-miR173 complex initiates phased siRNA formation in plants

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Next-generation DNA sequencing

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

uShuffle: a useful tool for shuffling biological sequences while preserving the k-let counts

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Update of ASRP: the Arabidopsis Small RNA Project database

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

The Arabidopsis Information Resource (TAIR): gene structure and function annotation.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Specialization and evolution of endogenous small RNA pathways

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

The diversity of RNA silencing pathways in plants

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

miRU: an automated plant miRNA target prediction server

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

microRNA-directed phasing during trans-acting siRNA biogenesis in plants

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Rfam: annotating non-coding RNAs in complete genomes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

The role of RNA interference in heterochromatic silencing

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Regulation of flowering time and floral organ identity by a MicroRNA and its APETALA2-like target genes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Role for a bidentate ribonuclease in the initiation step of RNA interference

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

TAPIR, a web server for the prediction of plant microRNA targets, including target mimics.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

A toolkit for analysing large-scale plant small RNA datasets.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

PatMaN: rapid alignment of short sequences to large databases

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3401462

Specific Effects of MicroRNAs on the Plant Transcriptome

18 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKS277

21 January 2018

Identifiers

DOI

10.1093/NAR/GKS277

1 reference

14 October 2017

1 reference

14 October 2017

1 reference

PMCID

3401462