Selection of antisense oligonucleotides based on multiple predicted target mRNA structures

scientific article

Selection of antisense oligonucleotides based on multiple predicted target mRNA structures is …
instance of (P31):
scholarly articleQ13442814

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P8978DBLP publication IDjournals/bmcbi/BoLSSYW06
P6179Dimensions Publication ID1032389976
P356DOI10.1186/1471-2105-7-122
P932PMC publication ID1421440
P698PubMed publication ID16526963
P5875ResearchGate publication ID7251314

P50authorWenjie ShuQ54937138
Xiaochen BoQ89462087
P2093author name stringJing Yang
Shengqi Wang
Daochun Sun
Shaoke Lou
P2860cites workEfficient algorithms for folding and comparing nucleic acid sequencesQ40492309
An overview of progress in antisense therapeuticsQ40858877
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Computer-aided search for effective antisense RNA target sequences of the human immunodeficiency virus type 1.Q45773186
Predicting the efficacy of short oligonucleotides in antisense and RNAi experiments with boosted genetic programming.Q45966750
Computational antisense oligo prediction with a neural network modelQ48268825
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Training feedforward networks with the Marquardt algorithm.Q52219242
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Complete suboptimal folding of RNA and the stability of secondary structures.Q52222269
Overcoming multidrug resistance in human tumor cells using free and liposomally encapsulated antisense oligodeoxynucleotidesQ72211702
Targeting of antisense DNA: comparison of activity of anti-rabbit beta-globin oligodeoxyribonucleoside phosphorothioates with computer predictions of mRNA foldingQ72358554
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Computational approaches to the identification of ribozyme target sitesQ73469200
Mapping of RNA accessible sites for antisense experiments with oligonucleotide librariesQ74109346
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Prediction of antisense oligonucleotide efficacy by in vitro methodsQ77683916
Mfold web server for nucleic acid folding and hybridization predictionQ24498105
Predicting oligonucleotide affinity to nucleic acid targetsQ24539440
Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimizationQ24540294
Sfold web server for statistical folding and rational design of nucleic acidsQ24562042
Optimal computer folding of large RNA sequences using thermodynamics and auxiliary informationQ24602467
Profiled support vector machines for antisense oligonucleotide efficacy predictionQ24792682
Vienna RNA secondary structure serverQ28131816
Selecting effective antisense reagents on combinatorial oligonucleotide arraysQ28240424
The equilibrium partition function and base pair binding probabilities for RNA secondary structureQ28261689
The meaning and use of the area under a receiver operating characteristic (ROC) curveQ29547182
On finding all suboptimal foldings of an RNA moleculeQ29547627
Mapping of RNA accessible sites by extension of random oligonucleotide libraries with reverse transcriptase.Q30662658
mRNA accessible site tagging (MAST): a novel high throughput method for selecting effective antisense oligonucleotidesQ30961001
Antisense oligonucleotides: a systematic high-throughput approach to target validation and gene function determinationQ33771816
RNA secondary structure: physical and computational aspectsQ33934096
Selecting optimal antisense reagentsQ34062626
Thermodynamic and kinetic characterization of antisense oligodeoxynucleotide binding to a structured mRNAQ34179717
Antisense therapeutics: lessons from early clinical trialsQ34416864
A rapid in vitro method for obtaining RNA accessibility patterns for complementary DNA probes: correlation with an intracellular pattern and known RNA structuresQ34646063
Approaches for the sequence-specific knockdown of mRNA.Q35597089
Statistical prediction of single-stranded regions in RNA secondary structure and application to predicting effective antisense target sites and beyondQ38303734
Specific inhibition of expression of a human collagen gene (COL1A1) with modified antisense oligonucleotides. The most effective target sites are clustered in double-stranded regions of the predicted secondary structure for the mRNA.Q38304416
RNA accessibility prediction: a theoretical approach is consistent with experimental studies in cell extractsQ38311071
Effects of RNA secondary structure on cellular antisense activityQ38315200
Artificial neural network prediction of antisense oligodeoxynucleotide activityQ38362285
A theoretical approach to select effective antisense oligodeoxyribonucleotides at high statistical probabilityQ39729504
Thermodynamic criteria for high hit rate antisense oligonucleotide designQ39959025
Computation of statistical secondary structure of nucleic acidsQ40466347
P304page(s)122
P577publication date2006-03-09
P1433published inBMC BioinformaticsQ4835939
P1476titleSelection of antisense oligonucleotides based on multiple predicted target mRNA structures
P478volume7

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cites work (P2860)
Q36740097Fundamental differences in the equilibrium considerations for siRNA and antisense oligodeoxynucleotide design
Q33287053Identification of sequence motifs significantly associated with antisense activity
Q39001868In vitro and in vivo protection against enterovirus 71 by an antisense phosphorothioate oligonucleotide
Q55394821In vitro inhibition of porcine reproductive and respiratory syndrome virus replication by short antisense oligonucleotides with locked nucleic acid modification.
Q35743375Inhibition of porcine reproductive and respiratory syndrome virus replication in vitro using DNA-based short antisense oligonucleotides

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