Amy A. Caudy
Lewis-Sigler Institute for Integrative Genomics
Princeton University
Princeton, New Jersey 08544
acaudy@princeton.edu; 609-258-8877
Research Experience
Princeton University
Lewis-Sigler Institute for Integrative Genomics, Lewis-Sigler Fellow 2005—present
Regulation of mitochondrial compartment and mitochondrial DNA copy number
Washington University School of Medicine
Department of Internal Medicine, Postdoctoral Fellow 2003—2005
John P.Atkinson Laboratory: Membrane Regulators of Complement Activation
Cold Spring Harbor Laboratory
Gregory J. Hannon Laboratory: Mechanisms of RNA interference (thesis laboratory)
Shiv I. S. Grewal Laboratory: Clr-6, a histone deacetylase important for chromatin condensation (rotation)
William P. Tansey Laboratory: Regulation of transcriptional activation via ubiquitination (rotation)
Washington University
Undergraduate Research 1995—1999
Education
Ph.D. 2003 Thesis title: “Mechanism and applications of RNA interference.”
B.A. 1999 Summa Cum Laude
Refereed Publications
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.
Salghetti SE, Caudy AA, Chenoweth JG, Tansey WP. Regulation of transcriptional activation domain function by ubiquitin. Science. 2001 Aug 31; 293(5535): 1651-3.
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. 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 1 Feb 2007 119(2): p. 482.
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).
Reviews
Hammond SM, Caudy AA, Hannon GJ. Post-transcriptional gene silencing by double-stranded RNA. Nat Rev Genet. 2001 Feb; 2(2): 110-9.
Books and Book Chapters
Watson JD, Caudy AA, Myers RM, Witkowski J. Recombinant DNA: Genes and Genomes – A Short Course. Third Edition. W.H. Freeman. 2007.
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.
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.
Honors and Fellowships
Helen Hay Whitney Postdoctoral Fellowship (declined to accept Lewis-Sigler Fellowship), 2005.
Ruth Kirschstein NIH Postdoctoral Fellowship, NIAID, 2005.
Harold M. Weintraub Graduate Student Award. 2003.
Howard Hughes Medical Institute Predoctoral Fellow. 1999-2003.
Phi Beta Kappa. 1999.
George A. and Marjorie H. Anderson Fellow of the Watson School of Biological Sciences. 1999-2003.
Barry Goldwater Scholar: fellowship for undergraduate research. 1997-1999.
Arthur Holly Compton Full-Tuition Fellowship, Washington University. 1995-1999.
International Science and Engineering Fair–Second Grand Award in Microbiology. 1995.