Helpful Publications and Links
Assay Development
Alpha Screen
- AlphaLISA Assay Development Guide [Internet]. Working Paper; Publisher's Version.
Assay Development for RNAi Screens
- Determination of sample size in genome-scale RNAi screens. Bioinformatics 2009;25(7):841-4..
Case Study for Optimizing Transfection
- Automated high-throughput siRNA transfection in raw 264.7 macrophates: a case study for optimizing procedure. J Biomol Screen 2009;14(2):151-60..
Cell Death Assays
- Guidelines for the use and interpretation of assays for monitoring cell death in higher eukaryotes. Cell Death Differ 2009;16(8):1093-107.
- Cell death assays for drug discovery. Nat Rev Drug Discov 2011;10(3):221-37..
Edge Effects
- A Simple Technique for Reducing Edge Effect in Cell-Based Assays. J Biomol Screen 2003;8(5):566-570..
- Helpful Hints to Manage Edge Effect of Cultured Cells for High Throughput Screening. Corning Application Note Working Paper;.
Fluorescence Polarization
- Fluorescence Polarization: Past, Present and Future. Comb Chem High Throughput Screen 2003;6(3):167-73..
- Development and Application of Fluorescence Polarization Assays in Drug Discovery. Comb Chem High Throughput Screen 2003;6(3):183-94..
- Quantification of Protein-Protein Interactions Using Fluorescence Polarization [Internet]. Methods 1999;19(2):222-23. Publisher's Version.
- Fluorescence Polarization (FP) Assays for Monitoring Peptide-Protein or Nucleic Acid-Protein Binding. Current Protocols in Chemical Biology 2009;1(1):1-15..
General Assay Development
- Assay Guidance Manual. NCATS; 2004.
- High-Throughput Screening Assays for the Identification of Chemical Probes. Nat Chem Bio 2007;3(8):466-479..
Imaging
- Autofluorescence: Causes and Cures. Wright Cell Imaging Facility 2004;
- Seeing the Wood through the Trees: A review of techniques for distinguishing green fluorescent protein from Endogenous Autofluorescence. Analytical Biochem 2001;291:175-197..
Luciferase
Data Analysis
Reviews
- Statistical practice in high-throughput screening data analysis. Nat Biotechnol 2006;24(2):167-75..
- Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods 2009;6(8):569-75..
- Reporting data from high-throughput screening of small-molecule libraries. Nat Chem Biol 2007;3(8):438-41..
- NoiseMaker: simulated screens for statistical assessment. Bioinformatics 2010;26(19):2484-5..
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B-score
- Improved statistical methods for hit selection in high-throughput screening. J Biomol Screen 2003;8(6):634-47..
Z-factor
How differences within cell population can impact RNAi screen results
- Single-cell analysis of population context advances RNAi screening at multiple levels. Mol Syst Biol 2012;8:579..
Weblink for open source software for dose-response curve fitting
- Weblink for open source software for dose-response curve fitting. 2005;
Please contact Ajit Jadhav with questions
Genome RNAi
- Genome RNAi. 2005;
A database containing phenotypes from RNAi screens in Drosophila and humans that is maintained by a research group at DKFZ, the German Cancer Research Center. Within GenomeRNAi, you have the ability to search the database by screens or for a particular gene of interest. Information from other RNAi screens may be useful during data analysis.
Frontiers in RNAi
RNAi Off Target Effects
Review
- Vigilance and Validation: Keys to Success in RNAi Screening. ACS Chem Biol 2011;6(1):47-60..
GESS
- A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens. 2012;Feb 19; 9(4):363-6..
- Online GESS: prediction of miRNA-like off-target effects in large-scale RNAi screen data by seed region analysis. BMC Bioinformatics 2014;Jun 17;(15):192..
- Online GESS. 2014;
Haystack
. - Haystack Analysis Web Server. 2012;
C911
- C911: A bench-level control for sequence specific siRNA off-target effects. PLoS One 2012;7(12):e51942..
- C911 Calculator. 2012;
Pan-Assay Interference Compounds (PAINS)
- Learning from our mistakes: the 'unknown knowns' in fragment screening. Bioorg Med Chem Lett 2013;23(10):2844-52..
- Chemistry: Chemical con artists foil drug discovery. Nature 2014;513(7519):481-3..
- Feeling Nature's PAINS: Natural Products, Natural Product Drugs, and Pan Assay Interference Compounds (PAINS). J Nat Prod 2016;79(3):616-628..