Helpful Publications and Links
Assay Development
PerkinElmer. AlphaLISA Assay Development Guide [Internet]. Working Paper; Publisher's Version
Zhang XD, Heyse JF. Determination of sample size in genome-scale RNAi screens. Bioinformatics 2009;25(7):841-4.
Carralot JP, Kim TK, Lenseigne B, Boese AS, Sommer P, Genovesio A, Brodin P. Automated high-throughput siRNA transfection in raw 264.7 macrophates: a case study for optimizing procedure. J Biomol Screen 2009;14(2):151-60.
Galluzi L, Aaronson SA, Abrams J, Alnemri ES, Andrews DW, et al. Guidelines for the use and interpretation of assays for monitoring cell death in higher eukaryotes. Cell Death Differ 2009;16(8):1093-107.
Kepp O, Galluzi L, Lipinski M, Yuan J, Kroemer G. Cell death assays for drug discovery. Nat Rev Drug Discov 2011;10(3):221-37.
Lundholt BK, Scudder KM, Pagliaro L. A Simple Technique for Reducing Edge Effect in Cell-Based Assays. J Biomol Screen 2003;8(5):566-570.
Tanner A. Helpful Hints to Manage Edge Effect of Cultured Cells for High Throughput Screening. Corning Application Note Working Paper;
Jameson DM, Croney JC. Fluorescence Polarization: Past, Present and Future. Comb Chem High Throughput Screen 2003;6(3):167-73.
Burke TJ, Loniello KR, Beebe JA, Ervin KM. Development and Application of Fluorescence Polarization Assays in Drug Discovery. Comb Chem High Throughput Screen 2003;6(3):183-94.
Jameson DM, Seifried SE. Quantification of Protein-Protein Interactions Using Fluorescence Polarization [Internet]. Methods 1999;19(2):222-23. Publisher's Version
Moerke NJ. Fluorescence Polarization (FP) Assays for Monitoring Peptide-Protein or Nucleic Acid-Protein Binding. Current Protocols in Chemical Biology 2009;1(1):1-15.
Sittampalam GS, Weidner J, et al. Assay Guidance Manual. NCATS; 2004.
Inglese J, Johnson RL, Simeonov A, Xia M, Zheng W, Austin CP, Auld DS. High-Throughput Screening Assays for the Identification of Chemical Probes. Nat Chem Bio 2007;3(8):466-479.
Autofluorescence: Causes and Cures. Wright Cell Imaging Facility 2004;
Billington N, Knight AW. Seeing the Wood through the Trees: A review of techniques for distinguishing green fluorescent protein from Endogenous Autofluorescence. Analytical Biochem 2001;291:175-197.
Thorn N, Shen M, Lea WA, Simeonov A, Lovell S, Auld DS, Inglese J. Firefly luciferase in chemical biology: a compendium of inhibitors, mechanistic evaluation of chemotypes, and suggested use as a reporter. . Chem Biol 2012;19(8):1060-72.
Data Analysis
Malo N, Hanley JA, Cerquozzi S, Pelletier J, Nadon R. Statistical practice in high-throughput screening data analysis. Nat Biotechnol 2006;24(2):167-75.
Birmingham A, Selfors LM, Forster T, Wrobel D, Kennedy CJ, Shanks E, Santoyo-Lopez J, Dunican DJ, Long A, Kelleher D, Smith Q, Beijersbergen RL, Ghazal P, Shamu CE. Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods 2009;6(8):569-75.
Inglese J, Shamu CE, Guy KR. Reporting data from high-throughput screening of small-molecule libraries. Nat Chem Biol 2007;3(8):438-41.
Kwan P, Birmingham A. NoiseMaker: simulated screens for statistical assessment. Bioinformatics 2010;26(19):2484-5.
Hutz JE, Nelson T, Wu H, McAllister G, Moutsatsos I, Jaeger SA, Bandyopadhyay S, Nigsch F, Cornett B, Jenkins JL, Selinger DW. The multidimensional perturbation value: a single metric to measure similarity and activity of treatments in high-throughput multidimensional screens. J Biomol Screen 2013;18(4):367-77.
Brideau C, Gunter B, Pikounis B, Liaw A. Improved statistical methods for hit selection in high-throughput screening. J Biomol Screen 2003;8(6):634-47.
Zhang J, Chung T, Oldenburg KR. A simple statistical parameter for use in evaluation and validation of high throughput screening assays. [Internet]. 1999; J Biomol Screen. 1999;4(2):67-73.
Snijder B, Sacher R, Rämö P, Liberali P, Mench K, Wolfrum N, Burleigh L, Scott CC, Verheije MH, Mercer J, Moese S, Heger T, Theusner K, Jurgeit A, Lamparter D, Balistreri G, Schelhaas M, De Haan CAM, Marjomäki V, Hyypiä T, Rottier PJM, Sodeik B, Marsh M, Gruenberg J, Amara A, Greber U, Helenius A, Pelkmans L. 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. 2005;
Please contact Ajit Jadhav with questions
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.
Schmidt EE, Bano MS, Smith JA, Birmingham A, Boutros M, Shamu CE. Public repositories for RNAi screening data [Internet]. 2014; Frontiers in RNAi. eBook; eISBN:978-1-60805-940-9 Chapter 3 Pages 40-57
RNAi Off Target Effects
Sigoillot FD, King RW. Vigilance and Validation: Keys to Success in RNAi Screening. ACS Chem Biol 2011;6(1):47-60.
Sigoillot FD, Lyman S, Huckins JF, Adamson B, Chung E, Quattrochi B, King RW. A bioinformatics method identifies prominent off-targeted transcripts in RNAi screens. 2012;Feb 19; 9(4):363-6.
Yilmazel B, Hu Y, Sigoillot F, Smith JA, Shamu CE, Perrimon N, Mohr SE. 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;
Buehler E, Khan AA, Marine S, Rajaram M, Bahl A, Burchard J, Ferrer M. siRNA off-target effects in genome-wide screens identify signaling pathway members. Sci Rep 2012;2(428)
Haystack Analysis Web Server. 2012;
Buehler E, Chen Y-C, Martin ST. 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)
Davis BJ, Erlanson DA. Learning from our mistakes: the 'unknown knowns' in fragment screening. Bioorg Med Chem Lett 2013;23(10):2844-52.
Baell J, Walters MA. Chemistry: Chemical con artists foil drug discovery. Nature 2014;513(7519):481-3.
Baell J. Feeling Nature's PAINS: Natural Products, Natural Product Drugs, and Pan Assay Interference Compounds (PAINS). J Nat Prod 2016;79(3):616-628.
Lab Automation
LabAutoPedia. 2015;
Johnston SJ, Shamu SE, Smith JA. Automation considerations for RNAi library formatting and high throughput transfection [Internet]. 2014; Frontiers in RNAi. eBook, eISBN:978-1-60805-940-9. Chapter 2 Pages 21-39.