Referred Publications:

• Salghetti SE, Caudy AA, Chenoweth JG, Tansey WP. Regulation of transcriptional activation domain function by ubiquitin. Science. 2001 Aug 31; 293(5535): 1651-3.
• Bernstein E, Caudy AA, Hammond SM, Hannon GJ. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature. 2001 Jan 18; 409(6818): 363-6.
• Hammond SM, Caudy AA, Hannon GJ. Post-transcriptional gene silencing by double-stranded RNA. Nat Rev Genet. 2001 Feb; 2(2): 110-9.
• Hammond SM, Boettcher S, Caudy AA, Kobayashi R, Hannon GJ. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science. 2001 Aug 10; 293(5532): 1146-50.
• Bjerling P, Silverstein RA, Thon G, Caudy A, Grewal S, Ekwall K. Functional divergence between histone deacetylases in fission yeast by distinct cellular localization and in vivo specificity. Mol Cell Biol. 2002 Apr; 22(7): 2170-81.
• Paddison PJ^*, Caudy AA^*, Hannon GJ. Stable suppression of gene expression by RNAi in mammalian cells. Proc Natl Acad Sci U S A. 2002 Feb 5; 99(3): 1443-8. ^* Shared first authorship.
• Paddison PJ, Caudy AA, Bernstein E, Hannon GJ, Conklin DS. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 2002 Apr 15; 16(8): 948-58.
• Caudy AA, Pikaard CS. Xenopus Ribosomal RNA Gene Intergenic Spacer Elements Conferring Transcriptional Enhancement and Nucleolar Dominance-like Competition in Oocytes. J Biol Chem. 2002 Aug 30; 277(35): 31577-84.
• Caudy AA, Myers MP, Hannon GJ, Hammond SM. Fragile X-Related protein and VIG associate with the RNA interference machinery. Genes Dev. 2002 Oct 1; 16(19): 2491-6.
• Caudy AA, Ketting RF, Hammond SM, Denli AM, Bathoorn AMP, Tops BBJ, Silva JM, Myers MP, Hannon GJ, Plasterk RHA. A micrococcal nuclease homolog in RNAi effector complexes.  Nature. 2003 Sep 25;425(6956):411-4.
• Fremeaux-Bacchi V, Moulton EA, Kavanagh D, Dragon-Durey M, Blouin J, Caudy A, Arzouk N, Cleper R, Francois M, Guest G, Pourrat J, Seligman R, Fridman WH, Loirat C, and Atkinson JP. Genetic and Functional Analyses of Membrane Cofactor Protein (CD46) Mutations in Atypical Hemolytic Uremic Syndrome.  J. Am. Soc. Nephrol. 2006;  17(7): p. 2017-2025
• Haynes KA, Caudy AA, Collins L, Elgin SC. Genetic and Functional Analyses of Membrane Cofactor Protein (CD46) Element 1360 and RNAi Components Contribute to HP1-Dependent Silencing of a Pericentric Reporter.  Curr Biol. 2006 Nov 21;16(22):2222-7.
• Caudy AA, Reddy ST, Chatila T, Atkinson JP, Verbsky JW. CD25 deficiency causes an immune dysregulation, polyendocrinopathy, enteropathy, X-linked-like syndrome, and defective IL-10 expression from CD4 lymphocytes. J Allergy Clin Immunol. 2007 Feb;119(2):482-7. Epub 2006 Dec 27.
• Yuanfang Guan1, Chad L Myers, David C Hess, Zafer Barutcuoglu, Amy A Caudy and Olga G Troyanskaya. Predicting gene function in a hierarchical context with an ensemble of classifiers. Genome Biology 2008, 9(Suppl 1):S3doi:10.1186/gb-2008-9-s1-s3
• EM Airoldi, C Huttenhower, D Gresham, C Lu, AA Caudy, MJ Dunham, JR Broach, D Botstein, and OG Troyanskaya. Predicting cellular growth from gene expression signatures. PLoS Comput Biol 1 Jan 2009 5(1): p. e1000257
• MA Hibbs, CL Myers, C Huttenhower, DC Hess, K Li, AA Caudy, and OG Troyanskaya. Directing experimental biology: a case study in mitochondrial biogenesis. PLoS Comput Biol 1 Mar 2009 5(3): p. e1000322.
• DC Hess, CL Myers, C Huttenhower, MA Hibbs, AP Hayes, J Paw, JJ Clore, RM Mendoza, BS Luis, C Nislow, G Giaever, M Costanzo, OG Troyanskaya, and AA Caudy. Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis. PLoS Genet 1 Mar 2009 5(3): p. e1000407.
• Joshua S Bloom, Zia Khan, Leonid Kruglyak, Mona Singh and Amy A Caudy. Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays. BMC Genomics 2009, 10:221 (12 May 2009).

Book Chapters

• Caudy AA, Hannon GJ. Induction and Biochemical Purification of RISC from Drosophila S2 Cells. Methods Mol Biol. 2004;265:59-72.
• Paddison PJ, Caudy AA, Sachidanandam R, Hannon GJ. Short Hairpin Activated Gene Silencing in Mammalian Cells. Methods Mol Biol. 2004;265:85-100.
• 
  James Watson, Jan Witkowski, Myers Richard, Amy Caudy. Recombinant DNA: Genes and Genomics: A short Course (Paperback).  Published by W.H. Freeman on Dec.15, 2006. now available on Amazon.com 

Meeting Abstracts

• Weitz DP, Caudy AA. Identification of Pathways Regulating Mitochondrial Number in Saccharomyces cerevisiae. Keystone Symposium on Metabolomics: Bioenergetics to Apoptosis.  April, 2006.
• Paddison PJ, Caudy AA, Hannon GJ. Stable suppression of gene expression by RNAi in mammalian cells. Keystone Symposium on RNA Interference, Taos, New Mexico.  Poster presentation. February, 2002.