ArticleMolecular cell2014
A computational algorithm to predict shRNA potency.
Article in Molecular cell, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 69 papers.
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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.
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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.
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Who cites it
69 citing papers in PubMed.
- shRNAI: A deep neural network for the design of highly potent shRNAs.Molecular therapy. Nucleic acids · 2025Article
- Targeting the Eye: RNA-Based Therapies, Interferences, and Delivery Strategies.Pharmaceutics · 2025Review
- Gamma-retrovirus design for efficacious microRNA-mediated gene knock-down and protein co-expression without compromising titers.NAR molecular medicine · 2025Article
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- UTF1 Expression is Important for the Generation and Maintenance of Human iPSCs.Stem cell reviews and reports · 2025Article
- Regulation of synapse density by Pumilio RNA-binding proteins.Cell reports · 2024Article
- Design of antiviral AGO2-dependent short hairpin RNAs.Virologica Sinica · 2024Article
- RNA-binding protein PCBP2 regulates pancreatic β cell function and adaptation to glucose.The Journal of clinical investigation · 2024Article
- Efficacy and safety of a SOD1-targeting artificial miRNA delivered by AAV9 in mice are impacted by miRNA scaffold selection.Molecular therapy. Nucleic acids · 2023Article
- Efficient shRNA-based knockdown of multiple target genes for cell therapy using a chimeric miRNA cluster platform.Molecular therapy. Nucleic acids · 2023Article
- Article
- Partial gene suppression improves identification of cancer vulnerabilities when CRISPR-Cas9 knockout is pan-lethal.Genome biology · 2023Article
- Regulation of store-operated CaeLife · 2023Article
- Retinitis Pigmentosa: Novel Therapeutic Targets and Drug Development.Pharmaceutics · 2023Review
- Erythroid lineage-specific lentiviral RNAi vectors suitable for molecular functional studies and therapeutic applications.Scientific reports · 2022Article
- Pooled shRNA Library Screening to Identify Factors that Modulate a Drug Resistance Phenotype.Journal of visualized experiments : JoVE · 2022Article
- Secondary structure RNA elements control the cleavage activity of DICER.Nature communications · 2022Article
- miR-AB, a miRNA-based shRNA viral toolkit for multicolor-barcoded multiplex RNAi at a single-cell level.EMBO reports · 2022Article
- Perivascular tenascin C triggers sequential activation of macrophages and endothelial cells to generate a pro-metastatic vascular niche in the lungs.Nature cancer · 2022Article
- Identification of the global miR-130a targetome reveals a role for TBL1XR1 in hematopoietic stem cell self-renewal and t(8;21) AML.Cell reports · 2022Article
9 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
Abstract
The strength of conclusions drawn from RNAi-based studies is heavily influenced by the quality of tools used to elicit knockdown. Prior studies have developed algorithms to design siRNAs. However, to date, no established method has emerged to identify effective shRNAs, which have lower intracellular abundance than transfected siRNAs and undergo additional processing steps. We recently developed a multiplexed assay for identifying potent shRNAs and used this method to generate ∼250,000 shRNA efficacy data points. Using these data, we developed shERWOOD, an algorithm capable of predicting, for any shRNA, the likelihood that it will elicit potent target knockdown. Combined with additional shRNA design strategies, shERWOOD allows the ab initio identification of potent shRNAs that specifically target the majority of each gene's multiple transcripts. We validated the performance of our shRNA designs using several orthogonal strategies and constructed genome-wide collections of shRNAs for humans and mice based on our approach.
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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.