Amy A. Caudy

Lewis-Sigler Institute for Integrative Genomics

Princeton University

Princeton, New Jersey 08544; 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                                                                                          

      Watson School of Biological Sciences, Ph.D. student                                                                                          1999—2003

      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

      Craig S. Pikaard Laboratory: Enhancer and repressor domains in RNA Polymerase I transcription


      Ohio Wesleyan University          

      High School Research                                                                                                                                                1992—1995

      Gerald Goldstein Laboratory: Free Radical Damage to DNA and proteins



Watson School of Biological Sciences, Cold Spring Harbor Laboratory; Cold Spring Harbor, NY                 1999—2003

      Ph.D. 2003  Thesis title: “Mechanism and applications of RNA interference.”


Washington University; St. Louis, Missouri                                                                                                                1995—1999

      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).



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.