Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments. (Q34662492)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21356093%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

review article

1 reference

title

Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21356093%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

0 references

1 reference

3

1 reference

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23 January 2020

Matthew R Willmann

series ordinal

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21356093%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

author name string

Kevin P McCormick

series ordinal

1

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23 January 2020

publication date

28 February 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21356093%20AND%20SRC:MED&resulttype=core&format=json

Silence: a journal of RNA regulation

23 January 2020

published in

1 reference

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23 January 2020

volume

2

1 reference

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23 January 2020

issue

1

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23 January 2020

page(s)

2

1 reference

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describes a project that uses

23 January 2020

edgeR

object named as

edgeR

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

exact match

https://scigraph.springernature.com/pub.10.1186/1758-907x-2-2

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7 July 2018

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7 July 2018

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Genome-wide measurement of RNA secondary structure in yeast

7 July 2018

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22-Nucleotide RNAs trigger secondary siRNA biogenesis in plants

7 July 2018

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siRNAs from miRNA sites mediate DNA methylation of target genes

7 July 2018

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

7 July 2018

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Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens

7 July 2018

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Highly-multiplexed barcode sequencing: an efficient method for parallel analysis of pooled samples

7 July 2018

1 reference

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Modeling non-uniformity in short-read rates in RNA-Seq data

7 July 2018

1 reference

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A comparison of massively parallel nucleotide sequencing with oligonucleotide microarrays for global transcription profiling

7 July 2018

1 reference

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

7 July 2018

1 reference

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A scaling normalization method for differential expression analysis of RNA-seq data

7 July 2018

1 reference

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Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments

7 July 2018

1 reference

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FRT-seq: amplification-free, strand-specific transcriptome sequencing

7 July 2018

1 reference

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Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries

7 July 2018

1 reference

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RNA-Seq gene expression estimation with read mapping uncertainty

7 July 2018

1 reference

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A novel class of small RNAs: tRNA-derived RNA fragments (tRFs).

7 July 2018

1 reference

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edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

7 July 2018

1 reference

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Calibration of microarray gene-expression data

7 July 2018

1 reference

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Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Genome-wide analysis of small RNA and novel MicroRNA discovery in human acute lymphoblastic leukemia based on extensive sequencing approach

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Direct multiplex sequencing (DMPS)--a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Quantification of the yeast transcriptome by single-molecule sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Comparative study on ChIP-seq data: normalization and binding pattern characterization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Bioinformatics analysis suggests base modifications of tRNAs and miRNAs in Arabidopsis thaliana

7 July 2018

1 reference

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

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

7 July 2018

1 reference

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Comparison of Affymetrix data normalization methods using 6,926 experiments across five array generations

7 July 2018

1 reference

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Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Comparing platforms for C. elegans mutant identification using high-throughput whole-genome sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Global rank-invariant set normalization (GRSN) to reduce systematic distortions in microarray data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Small RNAs with 5'-polyphosphate termini associate with a Piwi-related protein and regulate gene expression in the single-celled eukaryote Entamoeba histolytica

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Real-time DNA sequencing from single polymerase molecules

7 July 2018

1 reference

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The diploid genome sequence of an Asian individual

7 July 2018

1 reference

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Accurate whole human genome sequencing using reversible terminator chemistry

7 July 2018

1 reference

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Removal of AU bias from microarray mRNA expression data enhances computational identification of active microRNAs

7 July 2018

1 reference

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Identification of genetic variants using bar-coded multiplexed sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

7 July 2018

1 reference

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tRNA cleavage is a conserved response to oxidative stress in eukaryotes

7 July 2018

1 reference

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Characterization of unique small RNA populations from rice grain

7 July 2018

1 reference

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A comparison of global gene expression measurement technologies in Arabidopsis thaliana

7 July 2018

1 reference

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A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome

7 July 2018

1 reference

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Capped small RNAs and MOV10 in human hepatitis delta virus replication

7 July 2018

1 reference

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RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

7 July 2018

1 reference

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

7 July 2018

1 reference

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Mapping and quantifying mammalian transcriptomes by RNA-Seq

7 July 2018

1 reference

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A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

7 July 2018

1 reference

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

7 July 2018

1 reference

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An endogenous small interfering RNA pathway in Drosophila

7 July 2018

1 reference

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The transcriptional landscape of the yeast genome defined by RNA sequencing

7 July 2018

1 reference

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Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing

7 July 2018

1 reference

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The complete genome of an individual by massively parallel DNA sequencing

7 July 2018

1 reference

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Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

7 July 2018

1 reference

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Single-molecule DNA sequencing of a viral genome

7 July 2018

1 reference

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The growing catalog of small RNAs and their association with distinct Argonaute/Piwi family members

7 July 2018

1 reference

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Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Parallel tagged sequencing on the 454 platform

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

SOAP: short oligonucleotide alignment program

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

A comparison of background correction methods for two-colour microarrays

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Targeted high-throughput sequencing of tagged nucleic acid samples

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Polony multiplex analysis of gene expression (PMAGE) in mouse hypertrophic cardiomyopathy

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Comparison of hybridization-based and sequencing-based gene expression technologies on biological replicates.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Assessing the need for sequence-based normalization in tiling microarray experiments

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Genome-wide profiling and analysis of Arabidopsis siRNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Effect of various normalization methods on Applied Biosystems expression array system data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

RETRACTED: Secondary siRNAs result from unprimed RNA synthesis and form a distinct class

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Distinct populations of primary and secondary effectors during RNAi in C. elegans

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Multiplex sequencing of paired-end ditags (MS-PET): a strategy for the ultra-high-throughput analysis of transcriptomes and genomes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

A distinct small RNA pathway silences selfish genetic elements in the germline

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Characterization of the piRNA Complex from Rat Testes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

A novel class of small RNAs in mouse spermatogenic cells

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Identification and characterization of two novel classes of small RNAs in the mouse germline: retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

A novel class of small RNAs bind to MILI protein in mouse testes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

A germline-specific class of small RNAs binds mammalian Piwi proteins

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

How to decide? Different methods of calculating gene expression from short oligonucleotide array data will give different results

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Interacting endogenous and exogenous RNAi pathways in Caenorhabditis elegans

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2' OH of the 3' terminal nucleotide

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Functional proteomics reveals the biochemical niche of C. elegans DCR-1 in multiple small-RNA-mediated pathways

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Comparison of algorithms for the analysis of Affymetrix microarray data as evaluated by co-expression of genes in known operons

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Extensive 3' modification of plant small RNAs is modulated by helper component-proteinase expression

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Elucidation of the small RNA component of the transcriptome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Accurate multiplex polony sequencing of an evolved bacterial genome

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Genome sequencing in microfabricated high-density picolitre reactors

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Housekeeping genes in cancer: normalization of array data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Human mitochondrial tRNAMet is exported to the cytoplasm and associates with the Argonaute 2 protein

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Methylation as a crucial step in plant microRNA biogenesis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Empirical evaluation of data transformations and ranking statistics for microarray analysis.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

A novel design of whole-genome microarray probes for Saccharomyces cerevisiae which minimizes cross-hybridization

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Exploration, normalization, and summaries of high density oligonucleotide array probe level data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

A comparison of normalization methods for high density oligonucleotide array data based on variance and bias

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

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

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Two classes of short interfering RNA in RNA silencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Small RNAs correspond to centromere heterochromatic repeats

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

A variance-stabilizing transformation for gene-expression microarray data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Variance stabilization applied to microarray data calibration and to the quantification of differential expression

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

A microRNA in a multiple-turnover RNAi enzyme complex

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Endogenous and silencing-associated small RNAs in plants

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Normalizing DNA microarray data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Correcting for signal saturation errors in the analysis of microarray data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data

7 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

7 July 2018

https://api.crossref.org/works/10.1186%2F1758-907X-2-2

Control genes and variability: absence of ubiquitous reference transcripts in diverse mammalian expression studies

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

On the role of RNA amplification in dsRNA-triggered gene silencing

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

An extensive class of small RNAs in Caenorhabditis elegans

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Identification of novel genes coding for small expressed RNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Issues in cDNA microarray analysis: quality filtering, channel normalization, models of variations and assessment of gene effects

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

RNA interference is mediated by 21- and 22-nucleotide RNAs

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Analyzing high-density oligonucleotide gene expression array data

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Transcriptional silencing and promoter methylation triggered by double-stranded RNA

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Control selection for RNA quantitation

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Gene expression analysis by massively parallel signature sequencing (MPSS) on microbead arrays

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Housekeeping genes as internal standards: use and limits

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

A species of small antisense RNA in posttranscriptional gene silencing in plants

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Incorporation of terminal phosphorothioates into oligonucleotides.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

The significance of digital gene expression profiles

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Classical and novel approaches to the detection and localization of the numerous modified nucleotides in eukaryotic ribosomal RNA.

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Enzymatic oligoribonucleotide synthesis with T4 RNA ligase

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Addition of mononucleotides to oligoribonucleotide acceptors with T4 RNA ligase

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Joining of ribooligonucleotides with T4 RNA ligase and identification of the oligonucleotide-adenylate intermediate

7 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

A link between RNA metabolism and silencing affecting Arabidopsis development.

7 July 2018

1 reference

https://api.crossref.org/works/10.1186%2F1758-907X-2-2

Comparison of Affymetrix GeneChip expression measures.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1758-907X-2-2

Spreading of RNA targeting and DNA methylation in RNA silencing requires transcription of the target gene and a putative RNA-dependent RNA polymerase

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1758-907X-2-2

Processing of naturally occurring sense/antisense transcripts of the vertebrate Slc34a gene into short RNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1758-907X-2-2

Limitations and possibilities of small RNA digital gene expression profiling.

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1758-907X-2-2

Detecting heteroplasmy from high-throughput sequencing of complete human mitochondrial DNA genomes

21 January 2018

1 reference

https://api.crossref.org/works/10.1186%2F1758-907X-2-2

Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3055805

Erratum: Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster

26 October 2018

1 reference

12 December 2020

The effect of acceptor oligoribonucleotide sequence on the T4 RNA ligase reaction

1 reference

12 December 2020

Determinants of sensitivity and specificity in spotted DNA microarrays with unmodified oligonucleotides

1 reference

12 December 2020

Direct comparison of GeneChip and SAGE on the quantitative accuracy in transcript profiling analysis

1 reference

12 December 2020

Donor activation in the T4 RNA ligase reaction

1 reference

12 December 2020

Identifiers

DOI

10.1186/1758-907X-2-2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21356093%20AND%20SRC:MED&resulttype=core&format=json

Dimensions Publication ID

23 January 2020

0 references

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21356093%20AND%20SRC:MED&resulttype=core&format=json

23 January 2020

1 reference