Helpful Publications and Links

Maps and Directions -- Harvard Medical School and Longwood Medical Area

Assay Development

• General Assay Development -
  • Inglese, J., Johnson, R.L., Simeonov, A., Xia, M., Zheng, W., Austin, C.P, Auld, D.S. (2007) High-Throughput Screening Assays for the Identification of Chemical Probes. Nat. Chem Bio 2007 Aug;3(8): 466-479.
  • NIH Chemical Genetics Center (NCGC) Assay Guidance Manual
• Imaging -
  • Autofluorescence: Causes and Cures (PDF)
  • Review: (PDF) Billinton, N., Knight, A.W. (2001) Seeing the Wood through the Trees: A review of techniques for distinguishing green fluorescent protein from Endogenous Autofluorescence. Analytical Biochem 291, 2001 Mar 16; 175-197.
• Fluorescence Polarization -
  • Jameson, D.M, Croney, J.C.(2003) Fluorescence Polarization: Past, Present and Future. Comb Chem High Throughput Screen. 2003 May;6(3):167-73.
  • Burke, T.J., Loniello, K.R., Beebe, J.A., Ervin, K.M. (2003) Development and Application of Fluorescence Polarization Assays in Drug Discovery. Comb Chem High Throughput Screen. 2003 May;6(3):183-94.
  • Jameson, D.M., Seifried, S.E. (1999) Quantification of Protein-Protein Interactions Using Fluorescence Polarization. Methods. 1999 Oct;19(2):222-23.
• Assay Development for RNAi screens
  • Zhang, X.D., Heyse, J.F. (2009) Determination of sample size in genome-scale RNAi screens. Bioinformatics 25(7); 841-844.
    
    Good case study for optimizing transfection
  • Carralot, J.P., Kim, T.K., Lenseigne, B., Boese, A.S., Sommer, P., Genovesio, A., Brodin, P. (2009) Automated high-throughput siRNA transfection in raw 264.7 macrophates: a case study for optimizing procedure. J Biomol Screen. 2009 Feb;14(2):151-60.

Edge Effects

• Lundholt, B.K., Scudder, K.M., Pagliaro, L. (2003) A Simple Technique for Reducing Edge Effect in Cell-Based Assays. J. Biomol. Screen. 2003 Oct;8(5): 566-570).
• Tanner, A. Helpful Hints to Manage Edge Effect of Cultured Cells for High Throughput Screening. Corning Application Note (PDF).

Data Analysis

• Review: Malo, N., Hanley, J.A., Cerquozzi, S., Pelletier, J., Nadon, R. (2006) Statistical Practice in High-Throughput Screening Data Analysis. Nat. Biotechnol. 2006 Feb; 24(2): 167-175.
• Review: Birmingham, A., Selfors, L.M., Forster, T., Wrobel, D., Kennedy, C.J., Shanks, E., Santoyo-Lopez, J., Dunicann, D.J., Long, A., Kelleher, D., Smith, Q., Beijersbergen, R.L., Ghazal, P., Shamu, C.E. (2009) Statistical methods for analysis of high-throughput RNA interference screens. Nat Methods. 2009 Aug;6(8):569-75.
• B-score: Brideau, C., Gunter, B., Pikounis, B., Liaw, A. (2003) Improved Statistical Methods for Hit Selection in High-Throughput Screening. J. Biomol. Screen. 2003 Dec; 8(6): 634-647.
• Z-factor: Zhang, J.H., Chung, T.D., Oldenburg, K.R. (1999) A Simple Statistical Parameter for Use in Evaluation and Validation of High-Throughput Screening Assays. J. Biomol. Screen. 1999; 4(2):67-73.
• Weblink for open source software for dose-response curve fitting: http://ncgc.nih.gov/pub/openhts/curvefit/. Please contact Ajit Jadhav (ajadhav"AT"mail.nih.gov) with questions.
• Weblink for open source software and code from the NIH Chemical Genomics Center: http://ncgc.nih.gov/pub/openhts.

Reporting Screening Data

• Inglese, J., Shamu, C.E., Guy, R.K. (2007) Reporting Data from High-Throughput Screening of Small-Molecule Libraries. Nat. Chem. Biol. 2007 Aug;3(8):438-441.

Lab Automation

• Resource: LabAutopedia

Published Screens of Whole Genome siRNA Libraries from non-ICCBL Screeners

(see ICCBL RNAi Publications for additional published screens)

• Whitehurst, A.W., Bodemann, B.O, Cardenas, J., Ferguson, D., Girard, L., Peyton, M., Minna, J.D., Michnoff, C., Hao, W., Roth, M.G., Xie, X.J., White, M.A. (2007) Synthetic Lethal Screen Identification of Chemosensitizer Loci in Cancer Cells. Nature 2007 Apr. 12;446(7137):815-819
• Swanton, C., Marani, M., Pardo, O., Warne, P.H., Kelly, G., Sahai, E., Elustonodo, F., Chang, J., Temple, J., Ahmed, A.A., Brenton, J.D., Downward, J., Nicke, B. (2007) Regulators of Mitotic Arrest and Ceramide Metabolism are Determinants of Sensitivity to Paclitaxel and other Chemotherapeutic Drugs. Cancer Cell. 2007 Jun;11(6):498-512.
• Bushman, F., et al. (2009) Host cell factors in HIV replication: Meta-Analysis of Genome-Wide studies. PLoS Pathogens. 2009 May; 5(5): e1000437.