ArticleNucleic acids research2007
Thermodynamic instability of siRNA duplex is a prerequisite for dependable prediction of siRNA activities.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 77 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
77 citing papers in PubMed.
- Characterization of a novel long noncoding RNA, SCAL1, induced by cigarette smoke and elevated in lung cancer cell lines.American journal of respiratory cell and molecular biology · 2013Trial
- From rules to foundation models: a comprehensive review of machine learning approaches for siRNA design.NAR genomics and bioinformatics · 2026Review
- Staple oligomers induce a stable RNA G-quadruplex structure for protein translation inhibition in therapeutics.Nature biomedical engineering · 2026Article
- Strategic Computational Design of siRNA Molecules Targeting Structural Genes of SARS-CoV-2.Applied biochemistry and biotechnology · 2026Article
- Synthetic Biology of Plants and Microbes for Agriculture, Environment, and Future Applications.Chemical reviews · 2026Review
- SiaRNA: a siamese neural network with bidirectional cross-attention for pairwise siRNA-mRNA efficacy prediction.Frontiers in bioinformatics · 2026Article
- The Rieske iron-sulfur protein is a primary target of molecular hydrogen.Redox biology · 2025Article
- Exploitation of Biocomputational Approaches for siRNA-Mediated Gene Silencing of HPV: A Novel Therapeutic Strategy for Cervical Cancer.Cancer reports (Hoboken, N.J.) · 2025Article
- Designing siRNAs against non-structural genes of all serotypes of Dengue virus using RNAi technology - A computational investigation.Journal, genetic engineering & biotechnology · 2025Article
- Design, pharmacology, and toxicology of a novel chemically modified siRNA targeting hepatic angiotensinogen.Molecular therapy. Nucleic acids · 2025Article
- In Silico and In Vitro development of novel small interfering RNAs (siRNAs) to inhibit SARS-CoV-2.Computational and structural biotechnology journal · 2025Article
- siRNAEfficacyDB: An experimentally supported small interfering RNA efficacy database.IET systems biology · 2024Article
- OligoFormer: an accurate and robust prediction method for siRNA design.Bioinformatics (Oxford, England) · 2024Article
- siRNADiscovery: a graph neural network for siRNA efficacy prediction via deep RNA sequence analysis.Briefings in bioinformatics · 2024Article
- Design of antiviral AGO2-dependent short hairpin RNAs.Virologica Sinica · 2024Article
- RNAi-based drug design: considerations and future directions.Nature reviews. Drug discovery · 2024Review
- The chromatin-associated lncREST ensures effective replication stress response by promoting the assembly of fork signaling factors.Nature communications · 2024Article
- An ncRNA transcriptomics-based approach to design siRNA molecules against SARS-CoV-2 double membrane vesicle formation and accessory genes.BMC infectious diseases · 2023Article
- Gene silencing of Helicobacter pylori through newly designed siRNA convenes the treatment of gastric cancer.Cancer medicine · 2023Article
- Frizzled2 receives WntA signaling during butterfly wing pattern formation.Development (Cambridge, England) · 2023Article
17 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We developed a simple algorithm, i-Score (inhibitory-Score), to predict active siRNAs by applying a linear regression model to 2431 siRNAs. Our algorithm is exclusively comprised of nucleotide (nt) preferences at each position, and no other parameters are taken into account. Using a validation dataset comprised of 419 siRNAs, we found that the prediction accuracy of i-Score is as good as those of s-Biopredsi, ThermoComposition21 and DSIR, which employ a neural network model or more parameters in a linear regression model. Reynolds and Katoh also predict active siRNAs efficiently, but the numbers of siRNAs predicted to be active are less than one-eighth of that of i-Score. We additionally found that exclusion of thermostable siRNAs, whose whole stacking energy (DeltaG) is less than -34.6 kcal/mol, improves the prediction accuracy in i-Score, s-Biopredsi, ThermoComposition21 and DSIR. We also developed a universal target vector, pSELL, with which we can assay an siRNA activity of any sequence in either the sense or antisense direction. We assayed 86 siRNAs in HEK293 cells using pSELL, and validated applicability of i-Score and the whole DeltaG value in designing siRNAs.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.