Comparison of approaches for rational siRNA design leading to a new efficient and transparent method (Q35829289)

10 August 2017

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

1 reference

10 August 2017

0 references

Svetlana A. Shabalina

object named as

Svetlana A Shabalina

8

0 references

John F Atkins

object named as

John F Atkins

7

0 references

author name string

Olga Matveeva

1

1 reference

10 August 2017

Yury Nechipurenko

2

1 reference

10 August 2017

Leo Rossi

3

1 reference

10 August 2017

Barry Moore

4

1 reference

10 August 2017

Pål Saetrom

5

1 reference

10 August 2017

Aleksey Y Ogurtsov

6

1 reference

10 August 2017

language of work or name

English

0 references

publication date

10 April 2007

1 reference

10 August 2017

Nucleic Acids Research

1 reference

10 August 2017

35

1 reference

10 August 2017

8

1 reference

10 August 2017

e63

1 reference

An accurate and interpretable model for siRNA efficacy prediction

10 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Competition for RISC binding predicts in vitro potency of siRNA.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Analysis of internal loops within the RNA secondary structure in almost quadratic time

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Computational models with thermodynamic and composition features improve siRNA design

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Small interfering RNAs containing full 2'-O-methylribonucleotide-modified sense strands display Argonaute2/eIF2C2-dependent activity

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Identification and characterization of small RNAs involved in RNA silencing

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Prediction of siRNA knockdown efficiency using artificial neural network models

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

E-RNAi: a web application to design optimized RNAi constructs

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

The contributions of dsRNA structure to Dicer specificity and efficiency

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

siRNA Selection Server: an automated siRNA oligonucleotide prediction server

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

siDirect: highly effective, target-specific siRNA design software for mammalian RNA interference

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

DEQOR: a web-based tool for the design and quality control of siRNAs

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

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

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Rational siRNA design for RNA interference

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Functional siRNAs and miRNAs Exhibit Strand Bias

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Asymmetry in the assembly of the RNAi enzyme complex

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Thermodynamic parameters for DNA sequences with dangling ends

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Predicting oligonucleotide affinity to nucleic acid targets

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Sequence characteristics of functional siRNAs

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Highly specific and accurate selection of siRNAs for high-throughput functional assays

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

A comparison of siRNA efficacy predictors.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Filtering of ineffective siRNAs and improved siRNA design tool.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Improved and automated prediction of effective siRNA.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

An algorithm for selection of functional siRNA sequences.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Statistical comparison of two ROC-curve estimates obtained from partially-paired datasets.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1885645

Free energy lights the path toward more effective RNAi

24 September 2018

1 reference

12 December 2020

Gene specific siRNA selector

1 reference

12 December 2020

A Web-based design center for vector-based siRNA and siRNA cassette

1 reference

12 December 2020

Picking a winner: new mechanistic insights into the design of effective siRNAs

1 reference

12 December 2020

Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes

1 reference

12 December 2020

Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKM088

1 reference

10 August 2017

1 reference

10 August 2017

PubMed publication ID

17426130

1 reference