Integrated siRNA design based on surveying of features associated with high RNAi effectiveness (Q33264731)

24 July 2017

title

Integrated siRNA design based on surveying of features associated with high RNAi effectiveness (English)

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24 July 2017

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Wuming Gong

1

1 reference

24 July 2017

Yongliang Ren

2

1 reference

24 July 2017

Qiqi Xu

3

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24 July 2017

Yejun Wang

4

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24 July 2017

Dong Lin

5

1 reference

24 July 2017

Haiyan Zhou

6

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24 July 2017

Tongbin Li

7

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24 July 2017

publication date

27 November 2006

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24 July 2017

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24 July 2017

volume

7

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24 July 2017

page(s)

516

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On the art of identifying effective and specific siRNAs

24 July 2017

cites work

1 reference

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

21 June 2018

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21 June 2018

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

21 June 2018

1 reference

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Local RNA target structure influences siRNA efficacy: a systematic global analysis

21 June 2018

1 reference

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Small interfering RNA-mediated Polo-like kinase 1 depletion preferentially reduces the survival of p53-defective, oncogenic transformed cells and inhibits tumor growth in animals

21 June 2018

1 reference

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RNA interference mediated in human primary cells via recombinant baculoviral vectors

21 June 2018

1 reference

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The energy profiling of short interfering RNAs is highly predictive of their activity.

21 June 2018

1 reference

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

21 June 2018

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siRNA Selection Server: an automated siRNA oligonucleotide prediction server

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

Improving the efficiency of RNA interference in mammals

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

The gene-silencing efficiency of siRNA is strongly dependent on the local structure of mRNA at the targeted region

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

Rational siRNA design for RNA interference

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

Functional siRNAs and miRNAs Exhibit Strand Bias

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

Asymmetry in the assembly of the RNAi enzyme complex

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

High-throughput selection of effective RNAi probes for gene silencing.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

siRNA function in RNAi: a chemical modification analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

Statistical significance for genomewide studies

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

Mfold web server for nucleic acid folding and hybridization prediction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

A lentivirus-based system to functionally silence genes in primary mammalian cells, stem cells and transgenic mice by RNA interference

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

Gene silencing in mammals by small interfering RNAs

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

Positional effects of short interfering RNAs targeting the human coagulation trigger Tissue Factor

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

RNA accessibility prediction: a theoretical approach is consistent with experimental studies in cell extracts

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

An RNA-directed nuclease mediates post-transcriptional gene silencing in Drosophila cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probability

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

Stability of RNA stem-loop structure and distribution of non-random structure in the human immunodeficiency virus (HIV-I).

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

Thermodynamic stability and statistical significance of potential stem-loop structures situated at the frameshift sites of retroviruses

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

siRecords: an extensive database of mammalian siRNAs with efficacy ratings.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

Sequence characteristics of functional siRNAs

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

A comparison of siRNA efficacy predictors.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

Filtering of ineffective siRNAs and improved siRNA design tool.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

How to design a highly effective siRNA.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

Improved and automated prediction of effective siRNA.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

OptiRNAi, an RNAi design tool.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

An algorithm for selection of functional siRNA sequences.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

Computer-aided search for effective antisense RNA target sequences of the human immunodeficiency virus type 1.

31 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1698580

WT1 and BCR-ABL specific small interfering RNA have additive effects in the induction of apoptosis in leukemic cells

31 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17129386

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17129386

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/17129386

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1186/1471-2105-7-516

1 reference

journals/bmcbi/GongRXWLZL06

24 July 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

24 July 2017

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