Section14:References

From Assay Guidance Wiki

Publications:

1. Bartz SR, Zhang Z, Burchard J, Imakura M, Martin M, Palmieri A, Needham R, Guo J, Gordon M, Chung N, Warrener P, Jackson AL, Carleton M, Oatley M, Locco L, Fantini F, Smith T, Kunapuli P, Ferrer M, Strulovici B, Friend SH and Linsley PS. (2006). siRNA screens reveal enhanced cisplatin cytotoxicity in tumor cells having both BRCA network and TP53 distruptions. Molecular and Cellular Biology 26(24): 9377–9386.
2. Bland JM and Altaman DG. (1986). Statistical methods for assessing agreement between two methods of clinical measurement. Lancet I: 307-310.
3. Boutros M, Bras LP and Huber W. (2006). Analysis of cell-based RNAi screens. Genome Biology 7: R66.
4. Brideau C, Gunter B, Pikounis B and Liaw A. (2003). Improved statistical methods for hit selection in high-throughput screening. Journal of Biomolecular Screening 8(6): 634-647.
5. Chatterjee-Kishore M. (2006). From genome to phenome--RNAi library screening and hit characterization using signaling pathway analysis. Current Opinion in Drug Discovery & Development 9(2):231-239.
6. Echeverri CJ, Beachy PA, Baum B, Boutros M, Buchholz F, Chanda SK, Downward J, Ellenberg J, Fraser AG, Hacohen N, Hahn WC, Jackson AL, Kiger A, Linsley PS, Lum L, Ma Y, Mathey-Prevot B, Root DE, Sabatini DM, Taipale J, Perrimon N, and Bernards R. (2006). Minimizing the risk of reporting false positives in large-scale RNAi screens. Nature Methods 3(10):777-779.
7. Echeverri CJ and Perrimon N. (2006). High-throughput RNAi screening in cultured cells: a user's guide. Nature Review Genetics 7(5):373-384.
8. Fuchs F and Boutros M. (2006). Cellular phenotyping by RNAi. Briefings in Functional Genomics and Proteomics 5(1):52-56.
9. Lin, LI. (1989). A concordance correlation coefficient to evaluate reproducibility. Biometrics 45: 255-268.
10. Lin, LI. (2000). A note on the concordance correlation coefficient. Biometrics 56: 324-325.
11. Moffat J and Sabatini DM. (2006). Building mammalian signaling pathways with RNAi screens. Nature Reviews Molecular Cell Biology 7(3):177-187.
12. Naldini L, Blömer U, Gage FH, Trono D, and Verma IM. (1996). Efficient transfer, integration, and sustained long-term expression of the transgene in adult rat brains injected with a lentiviral vector. PNAS 93: 11382-11388.
13. Root DE, Hacohen N, Hahn WC, Lander ES, and Sabatini DM. (2006). Genome-scale loss-of-function screening with a lentiviral RNAi library. Nature Methods 3(9):715-719.
14. Sachse C, Krausz E, Kronke A, Hannus M, Walsh A, Grabner A, Ovcharenko D, Dorris D, Trudel C, Sonnichsen B, and Echeverri CJ. (2005). High-throughput RNA interference strategies for target discovery and validation by using synthetic short interfering RNAs: functional genomics investigations of biological pathways. Methods in Enzymology 392: 242-277.
15. Willingham AT, Deveraux QL, Hampton GM, and Aza-Blanc P. (2004). RNAi and HTS: exploring cancer by systematic loss-of-function. Oncogene 23(51):8392-8400.
16. Yee J, Miyanohara A, LaPorte P, Bouic K, Burns JC, and Friedmann T. (1994). A General Method for the Generation of High-Titer, Pantropic Retroviral Vectors: Highly Efficient Infection of Primary Hepatocytes. PNAS 91, 9564-9568.
17. Zufferey R, Nagy D, Mandel RJ, Naldini L, and Trono D. (1997). Multiply attenuated lentiviral vector achieves efficient gene delivery in vivo. Nature Biotechnology 15, 871 - 875.
18. Brideau C., Gunter B., Pikounis B. and Liaw A. (2003). Improved statistical methods for hit selection in high-throughput screening. Journal of Biomolecular Screening 8, 634-647.
19. Gunter B., Brideau C., Pikounis B. and Liaw A. (2003). Statistical and graphical methods for quality control determination of high-throughput screening data. Journal of Biomolecular Screening 8, 624-633.
20. Iversen PW., Eastwood BJ., Sittampalam S. and Cox KL. (2006). A comparison of assay performance measures in screening assays: signal window, Z' factor and assay variability ratio. Journal of Biomolecular Screening 11, 1-6.
21. Malo N., Hanley JA., Cerquozzi S., Pelletier J. and Naddon R. (2006). Statistical practice in high-throughput screening data analysis. Nature Biotechnology 24, 167-175.
22. Epping MT, Wang L, Plumb JA, Lieb M, Gronemeyer H, Brown R, Bernards R.A functional genetic screen identifies retinoic acid signaling as a target of histone deacetylase inhibitors.Proc Natl Acad Sci U S A. 2007 Nov 6;104(45):17777-82. Epub 2007 Oct 29.
23. Berns K, Horlings HM, Hennessy BT, Madiredjo M, Hijmans EM, Beelen K, Linn SC, Gonzalez-Angulo AM, Stemke-Hale K, Hauptmann M, Beijersbergen RL, Mills GB, van de Vijver MJ, Bernards R.A functional genetic approach identifies the PI3K pathway as a major determinant of trastuzumab resistance in breast cancer.Cancer Cell. 2007 Oct;12(4):395-402.
24. Whitehurst AW, Bodemann BO, Cardenas J, Ferguson D, Girard L, Peyton M, Minna JD, Michnoff C, Hao W, Roth MG, Xie XJ, White MA.Synthetic lethal screen identification of chemosensitizer loci in cancer cells.Nature. 2007 Apr 12;446(7137):815-9.
25. Brummelkamp TR, Fabius AW, Mullenders J, Madiredjo M, Velds A, Kerkhoven RM, Bernards R, Beijersbergen RL.An shRNA barcode screen provides insight into cancer cell vulnerability to MDM2 inhibitors.Nat Chem Biol. 2006 Apr;2(4):202-6. Epub 2006 Feb 13.
26. Eggert US, Kiger AA, Richter C, Perlman ZE, Perrimon N, Mitchison TJ, Field CM.Parallel chemical genetic and genome-wide RNAi screens identify cytokinesis inhibitors and targets.PLoS Biol. 2004 Dec;2(12):e379. Epub 2004 Oct 5.

Web sites:

1. Minimum Information About an RNAi Experiment (MIARE) - http://miare.sourceforge.net/HomePage
2. GraphPad Prism Manual - http://www.broad.mit.edu/genome_bio/trc/publicProtocols.html