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ShortStack: comprehensive annotation and quantification of small RNA genes
scientific article published on 22 April 2013
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scholarly article
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Europe PubMed Central
PMCID
3683909
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17 August 2017
title
ShortStack: comprehensive annotation and quantification of small RNA genes
(English)
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Europe PubMed Central
PMCID
3683909
retrieved
17 August 2017
author name string
Michael J Axtell
series ordinal
1
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Europe PubMed Central
PMCID
3683909
retrieved
17 August 2017
language of work or name
English
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publication date
22 April 2013
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Europe PubMed Central
PMCID
3683909
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17 August 2017
published in
RNA
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PMCID
3683909
retrieved
17 August 2017
volume
19
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Europe PubMed Central
PMCID
3683909
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17 August 2017
issue
6
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Europe PubMed Central
PMCID
3683909
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17 August 2017
page(s)
740-751
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Europe PubMed Central
PMCID
3683909
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17 August 2017
cites work
The role of long non-coding RNA in transcriptional gene silencing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Repeat associated small RNAs vary among parents and following hybridization in maize
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Reducing ligation bias of small RNAs in libraries for next generation sequencing
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
The helicase and RNaseIIIa domains of Arabidopsis Dicer-Like1 modulate catalytic parameters during microRNA biogenesis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
MicroRNAs and their isomiRs function cooperatively to target common biological pathways
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Identifying small interfering RNA loci from high-throughput sequencing data
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Uniting germline and stem cells: the function of Piwi proteins and the piRNA pathway in diverse organisms
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Identification and remediation of biases in the activity of RNA ligases in small-RNA deep sequencing.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
piRNA profiling during specific stages of mouse spermatogenesis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Arabidopsis Argonaute 2 regulates innate immunity via miRNA393(∗)-mediated silencing of a Golgi-localized SNARE gene, MEMB12
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Evolution and functional diversification of MIRNA genes
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Widespread regulatory activity of vertebrate microRNA* species
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Multiple distinct small RNAs originate from the same microRNA precursors
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Unique functionality of 22-nt miRNAs in triggering RDR6-dependent siRNA biogenesis from target transcripts in Arabidopsis
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
An endogenous, systemic RNAi pathway in plants
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Finding sRNA generative locales from high-throughput sequencing data with NiBLS.
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Establishing, maintaining and modifying DNA methylation patterns in plants and animals
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
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1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Rice MicroRNA effector complexes and targets
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
Widespread shortening of 3'UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
29 September 2017
The Sequence Alignment/Map format and SAMtools
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
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RNA-mediated chromatin-based silencing in plants
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
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Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
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An endogenous small interfering RNA pathway in Drosophila
1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
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1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
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1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
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1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
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1 reference
stated in
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reference URL
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retrieved
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1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
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1 reference
stated in
PubMed Central
reference URL
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retrieved
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1 reference
stated in
PubMed Central
reference URL
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retrieved
29 September 2017
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1 reference
stated in
PubMed Central
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retrieved
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1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
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1 reference
stated in
PubMed Central
reference URL
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retrieved
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1 reference
stated in
PubMed Central
reference URL
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retrieved
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1 reference
stated in
PubMed Central
reference URL
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retrieved
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1 reference
stated in
PubMed Central
reference URL
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retrieved
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1 reference
stated in
PubMed Central
reference URL
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retrieved
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1 reference
stated in
PubMed Central
reference URL
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retrieved
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1 reference
stated in
PubMed Central
reference URL
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retrieved
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1 reference
stated in
PubMed Central
reference URL
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retrieved
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1 reference
stated in
PubMed Central
reference URL
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retrieved
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1 reference
stated in
PubMed Central
reference URL
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retrieved
4 September 2018
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1 reference
stated in
PubMed Central
reference URL
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3683909
retrieved
20 October 2018
Identifiers
DOI
10.1261/RNA.035279.112
1 reference
stated in
Europe PubMed Central
PMCID
3683909
retrieved
17 August 2017
PMCID
3683909
1 reference
stated in
Europe PubMed Central
PMCID
3683909
retrieved
17 August 2017
PubMed ID
23610128
1 reference
stated in
Europe PubMed Central
PMCID
3683909
retrieved
17 August 2017
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