Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency (Q39981882)

16 September 2017

Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency (English)

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16 September 2017

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Jochen W Klingelhoefer

series ordinal

1

1 reference

16 September 2017

Loukas Moutsianas

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2

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16 September 2017

Chris Holmes

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3

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16 September 2017

6 May 2009

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16 September 2017

language of work or name

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1 reference

16 September 2017

25

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16 September 2017

13

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16 September 2017

1594-1601

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Structure of an argonaute silencing complex with a seed-containing guide DNA and target RNA duplex

16 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Efficient siRNA selection using hybridization thermodynamics

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Effect of target secondary structure on RNAi efficiency

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Improving model predictions for RNA interference activities that use support vector machine regression by combining and filtering features

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

An accurate and interpretable model for siRNA efficacy prediction

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Rational design and rapid screening of antisense oligonucleotides for prokaryotic gene modulation

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

On the art of identifying effective and specific siRNAs

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Efficient prediction of siRNAs with siRNArules 1.0: an open-source JAVA approach to siRNA algorithms

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Off-target effects by siRNA can induce toxic phenotype

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Computational models with thermodynamic and composition features improve siRNA design

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Cleavage of the siRNA passenger strand during RISC assembly in human cells

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Relative gene-silencing efficiencies of small interfering RNAs targeting sense and antisense transcripts from the same genetic locus

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Efficient RNA interference depends on global context of the target sequence: quantitative analysis of silencing efficiency using Eulerian graph representation of siRNA.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Rational siRNA design for RNA interference

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Nonspecific, concentration-dependent stimulation and repression of mammalian gene expression by small interfering RNAs (siRNAs).

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Functional siRNAs and miRNAs Exhibit Strand Bias

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Expression profiling reveals off-target gene regulation by RNAi

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Specificity of short interfering RNA determined through gene expression signatures

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

siRNAs generated by recombinant human Dicer induce specific and significant but target site-independent gene silencing in human cells

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

siRecords: a database of mammalian RNAi experiments and efficacies

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

siDRM: an effective and generally applicable online siRNA design tool

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

siRNA becomes smart and intelligent.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Sequence characteristics of functional siRNAs

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Prediction of siRNA functionality using generalized string kernel and support vector machine

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Small interfering RNA molecules as potential anti-human rhinovirus agents: in vitro potency, specificity, and mechanism

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

Identification of Modulators of TRAIL-Induced Apoptosis via RNAi-Based Phenotypic Screening

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2940241

ODNBase--a web database for antisense oligonucleotide effectiveness studies. Oligodeoxynucleotides

20 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19420052

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Noise amidst the silence: off-target effects of siRNAs?

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/19420052

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIOINFORMATICS/BTP284

1 reference

journals/bioinformatics/KlingelhoeferMH09

16 September 2017

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

16 September 2017

PubMed publication ID

19420052

1 reference