OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics (Q36749348)

16 August 2017

OligoWalk: an online siRNA design tool utilizing hybridization thermodynamics (English)

1 reference

16 August 2017

0 references

0 references

Zhi John Lu

1

1 reference

PMCID

2447759

16 August 2017

David H Mathews

series ordinal

2

1 reference

PMCID

2447759

16 August 2017

language of work or name

English

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publication date

19 May 2008

1 reference

16 August 2017

Nucleic Acids Research

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16 August 2017

36

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16 August 2017

W104-8

1 reference

16 August 2017

Web Server issue

1 reference

Efficient siRNA selection using hybridization thermodynamics

16 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

A set of nearest neighbor parameters for predicting the enthalpy change of RNA secondary structure formation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

Computational models with thermodynamic and composition features improve siRNA design

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

siRNA target site secondary structure predictions using local stable substructures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

siRNA Selection Server: an automated siRNA oligonucleotide prediction server

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

Rational siRNA design for RNA interference

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

Approaches for the sequence-specific knockdown of mRNA.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

Functional siRNAs and miRNAs Exhibit Strand Bias

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

Asymmetry in the assembly of the RNAi enzyme complex

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

The activity of siRNA in mammalian cells is related to structural target accessibility: a comparison with antisense oligonucleotides

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

Sequence, chemical, and structural variation of small interfering RNAs and short hairpin RNAs and the effect on mammalian gene silencing

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

Effects of RNA secondary structure on cellular antisense activity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

Predicting oligonucleotide affinity to nucleic acid targets

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

On finding all suboptimal foldings of an RNA molecule

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

A comparison of siRNA efficacy predictors.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

An algorithm for selection of functional siRNA sequences.

5 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2447759

Improving specificity of DNA hybridization-based methods

5 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKN250

The efficacy of small interfering RNAs targeted to the type 1 insulin-like growth factor receptor (IGF1R) is influenced by secondary structure in the IGF1R transcript

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18490376

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKN250

1 reference

16 August 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

16 August 2017

1 reference

PMCID

2447759