(Q35455068)

8 August 2017

title

MysiRNA-designer: a workflow for efficient siRNA design (English)

1 reference

8 August 2017

0 references

1 reference

Mahmoud Elhefnawi

3

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Jonathan M. Garibaldi

object named as

Jonathan M Garibaldi

series ordinal

2

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author name string

Mohamed Mysara

series ordinal

1

1 reference

8 August 2017

language of work or name

English

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publication date

26 October 2011

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8 August 2017

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8 August 2017

volume

6

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8 August 2017

issue

10

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8 August 2017

page(s)

e25642

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Creative Commons Attribution 4.0 International

8 August 2017

copyright license

start time

26 October 2011

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Impact of target mRNA structure on siRNA silencing efficiency: A large-scale study

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Efficient siRNA selection using hybridization thermodynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Effect of target secondary structure on RNAi efficiency

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Molecular basis for target RNA recognition and cleavage by human RISC.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Comparison of approaches for rational siRNA design leading to a new efficient and transparent method

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

In silico selection of active siRNA.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Specific residues at every third position of siRNA shape its efficient RNAi activity

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

More complete gene silencing by fewer siRNAs: transparent optimized design and biophysical signature

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

An accurate and interpretable model for siRNA efficacy prediction

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

3' UTR seed matches, but not overall identity, are associated with RNAi off-targets

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Computational models with thermodynamic and composition features improve siRNA design

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Thermodynamics of RNA-RNA binding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Design of siRNAs producing unstructured guide-RNAs results in improved RNA interference efficiency.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Sfold web server for statistical folding and rational design of nucleic acids

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

An effective method for selecting siRNA target sequences in mammalian cells

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

siRNAs: applications in functional genomics and potential as therapeutics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

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

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: determinants of gene silencing for use in cell-based screens

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Rational siRNA design for RNA interference

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Asymmetry in the assembly of the RNAi enzyme complex

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Vienna RNA secondary structure server

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Structural variations and stabilising modifications of synthetic siRNAs in mammalian cells

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Expression profiling reveals off-target gene regulation by RNAi

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Specificity of short interfering RNA determined through gene expression signatures

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Tolerance for mutations and chemical modifications in a siRNA.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

Analysis of gene function in somatic mammalian cells using small interfering RNAs

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

An algorithm for selection of functional siRNA sequences.

12 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0025642

The impact of target site accessibility on the design of effective siRNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0025642

Experimental validation of the importance of seed complement frequency to siRNA specificity

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0025642

Designing optimal siRNA based on target site accessibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0025642

MysiRNA: improving siRNA efficacy prediction using a machine-learning model combining multi-tools and whole stacking energy (ΔG).

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3202522

A protocol for designing siRNAs with high functionality and specificity

26 September 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/22046244

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0025642

1 reference

8 August 2017

0 references

1 reference

8 August 2017

1 reference