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shERWOOD-UltramiR shRNA

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  1. Knott et al., 2014. A computational algorithm to predict shRNA potency. Volume 56, Issue 6, 18 December 2014, Pages 796–807.
  2. Auyeung, V.C., I. Ulitsky, S.E. McGeary, and D.P. Bartel. (2013). Beyond Secondary Structure: Primary-Sequence Determinants License Pri-miRNA Hairpins for Processing. Cell 152(4):844-858.
  3. Fellmann, C. et al., (2011). Functional identification of optimized RNAi triggers using a massively parallel sensor assay. Mol Cell. 18; 41(6):733-46.
  4. Baek, S.T. et al. (2014). Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous microRNA dysregulation. Neuron 18; 82, 1255–1262.
  5. Castanotto, D. et al. (2007). Combinatorial delivery of small interfering RNAs reduces RNAi efficacy by selective incorporation into RISC. Nucleic Acids Res. 35(15):5154-64.
  6. Grimm, D. et al., (2006). Fatality in mice due to oversaturation of cellular microRNA/short hairpin RNA pathways. Nature 441, 537-541.
  7. McBride, J. L. et al., (2008). Artificial miRNAs mitigate shRNA-mediated toxicity in the brain: Implications for the therapeutic development of RNAi. PNAS 105; 15, 5868-5873
  8. Beer, S. et al., (2010). Low-level shRNA Cytotoxicity can contribute to MYC-induced hepatocellular carcinoma in adult mice. Mol Ther 18(1):161-170.
  9. Pan, Q. et al., (2011). Disturbance of the microRNA pathway by commonly used lentiviral shRNA libraries limits the application for screening host factors involved in hepatitis C virus infection. FEBS Lett. 6;585(7):1025-1030.
  10. Huesken, D., et al. (2005). Design of a genome-wide siRNA library using an artificial neural network. Nat. Biotechnol. 23(8), 995–1001.
  11. Vert, J.P., et al., (2006). An accurate and interpretable model for siRNA efficacy prediction. BMC Bioinformatics 7, 520.
  12. Li, L., et al., (2007). Defining the optimal parameters for hairpin-based knockdown constructs. RNA 13(10), 1765–1774.
  13. Bassik, M.C., et al., (2009). Rapid creation and quantitative monitoring of high coverage shRNA libraries. Nat. Methods 6, 443–445.
  14. Castanotto, D (2011). Sensor and Sensitivity: A Screen for Elite shRNAs. Molecular Therapy 19, 5, 823-825.
  15. Moffat, J. et al, (2006). A Lentiviral RNAi Library for Human and Mouse Genes Applied to an Arrayed Viral High-Content Screen. Cell, 124(6): 1283-1298.
  16. Silva, J.M. et al. (2005). Second-generation shRNA libraries covering the mouse and human genomes. Nat Genet 37, 1281-1288.
  17. Boden, D. et al, (2004). Enhanced gene silencing of HIV-1 specific siRNA using microRNA designed hairpins. Nucleic Acids Res 32(3): 1154-1158.