A computational algorithm to predict shRNA potency. (Q38936797)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25435137%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

title

A computational algorithm to predict shRNA potency (English)

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23 February 2020

11

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23 February 2020

Xin Zhou

6

1 reference

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23 February 2020

Elvin Wagenblast

9

1 reference

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23 February 2020

Sun Kim

10

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23 February 2020

12

Gregory J Hannon

1 reference

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23 February 2020

author name string

Simon R V Knott

1

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23 February 2020

Ashley Maceli

2

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23 February 2020

Nicolas Erard

3

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23 February 2020

Kenneth Chang

4

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23 February 2020

Krista Marran

5

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23 February 2020

Assaf Gordon

7

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23 February 2020

Osama El Demerdash

8

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23 February 2020

publication date

26 November 2014

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23 February 2020

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23 February 2020

volume

56

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23 February 2020

issue

6

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23 February 2020

page(s)

796-807

1 reference

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Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous microRNA dysregulation

23 February 2020

cites work

1 reference

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An optimized microRNA backbone for effective single-copy RNAi

9 September 2017

1 reference

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Diversifying microRNA sequence and function

9 September 2017

1 reference

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Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing.

9 September 2017

1 reference

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Preparation of small RNA libraries for high-throughput sequencing.

9 September 2017

1 reference

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Optimized models for design of efficient miR30-based shRNAs

9 September 2017

1 reference

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Genetically defined subsets of human pancreatic cancer show unique in vitro chemosensitivity

9 September 2017

1 reference

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Structure of yeast Argonaute with guide RNA

9 September 2017

1 reference

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The Structure of Human Argonaute-2 in Complex with miR-20a

9 September 2017

1 reference

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High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing

9 September 2017

1 reference

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Functional identification of optimized RNAi triggers using a massively parallel sensor assay

9 September 2017

1 reference

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The terminal loop region controls microRNA processing by Drosha and Dicer

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Structural basis for 5'-nucleotide base-specific recognition of guide RNA by human AGO2

9 September 2017

1 reference

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A genome-wide RNAi screen identifies multiple synthetic lethal interactions with the Ras oncogene

9 September 2017

1 reference

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An oncogenomics-based in vivo RNAi screen identifies tumor suppressors in liver cancer

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Structure of the guide-strand-containing argonaute silencing complex

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Argonaute loading improves the 5' precision of both MicroRNAs and their miRNA* strands in flies.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

An accurate and interpretable model for siRNA efficacy prediction

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

A potential protein-RNA recognition event along the RISC-loading pathway from the structure of A. aeolicus Argonaute with externally bound siRNA.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Molecular basis for the recognition of primary microRNAs by the Drosha-DGCR8 complex

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Rethinking the microprocessor

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Second-generation shRNA libraries covering the mouse and human genomes

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Induction of stable RNA interference in mammalian cells

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Design of a genome-wide siRNA library using an artificial neural network

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Processing of primary microRNAs by the Microprocessor complex

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

A large-scale RNAi screen in human cells identifies new components of the p53 pathway

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

A resource for large-scale RNA-interference-based screens in mammals.

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Guidelines for the selection of highly effective siRNA sequences for mammalian and chick RNA interference

9 September 2017

1 reference

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Inducible, reversible, and stable RNA interference in mammalian cells

9 September 2017

1 reference

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Rational siRNA design for RNA interference

9 September 2017

1 reference

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Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

MicroRNAs modulate hematopoietic lineage differentiation

9 September 2017

1 reference

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Nuclear export of microRNA precursors

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Functional siRNAs and miRNAs Exhibit Strand Bias

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Asymmetry in the assembly of the RNAi enzyme complex

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

The nuclear RNase III Drosha initiates microRNA processing

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Systematic functional analysis of the Caenorhabditis elegans genome using RNAi

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Single-stranded antisense siRNAs guide target RNA cleavage in RNAi

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

A microRNA in a multiple-turnover RNAi enzyme complex

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

A system for stable expression of short interfering RNAs in mammalian cells

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Micro RNAs are complementary to 3' UTR sequence motifs that mediate negative post-transcriptional regulation

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Dicer functions in RNA interference and in synthesis of small RNA involved in developmental timing in C. elegans

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Argonaute2, a link between genetic and biochemical analyses of RNAi

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Duplexes of 21-nucleotide RNAs mediate RNA interference in cultured mammalian cells

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Specific and heritable genetic interference by double-stranded RNA in Arabidopsis thaliana

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Targeted mRNA degradation by double-stranded RNA in vitro

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Double-stranded RNA specifically disrupts gene expression during planarian regeneration

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Specific interference by ingested dsRNA

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

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

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

STK33 kinase activity is nonessential in KRAS-dependent cancer cells

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Synthetic lethal interaction between oncogenic KRAS dependency and STK33 suppression in human cancer cells

9 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Sequence requirements for micro RNA processing and function in human cells

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Heterogeneity of tumor cells from a single mouse mammary tumor

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Drosophila immunity: a large-scale in vivo RNAi screen identifies five serine proteases required for Toll activation

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

RNAi in human cells: basic structural and functional features of small interfering RNA.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

Selective reduction of dormant maternal mRNAs in mouse oocytes by RNA interference.

21 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4272634

10.1016/J.MOLCEL.2014.10.025

21 August 2018

Identifiers

DOI

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:25435137%20AND%20SRC:MED&resulttype=core&format=json

23 February 2020

1 reference

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23 February 2020

1 reference