Student Publications


Bernstein, E., Caudy, A.A., Hammond, S.M., and Hannon, G.J. 2001. Role for a bidentate ribonuclease in the initiation step of RNA interference. Nature 409: 363–366.

Bernstein, E., Denli, A.M., and Hannon, G.J. 2001. The rest is silence. RNA 7: 1509–1521.

Hammond, S.M., Boettcher, S., Caudy, A.A., Kobayashi, R., and Hannon, G.J. 2001. Argonaute2, a link between genetic and biochemical analyses of RNAi. Science 293: 1146–1150.

Hammond, S.M., Caudy, A.A., and Hannon, G.J. 2001. Post-transcriptional gene silencing by double-stranded RNA. Nat. Rev. Genet. 2: 110–119.

Salghetti, S.E., Caudy, A.A., Chenoweth, J.G., and Tansey, W.P. 2001. Regulation of transcriptional activation domain function by ubiquitin. Science 293: 1651–1653.


 Bjerling, P., Silverstein, R.A., Thon, G., Caudy, A.A., Grewal, S., and Ekwall, K. 2002. Functional divergence between histone deacetylases in fission yeast by distinct cellular localization and in vivo specificity. Mol. Cell. Biol. 22: 2170–2181.

Caudy, A.A., Myers, M., Hannon, G.J., and Hammond, S.M. 2002. Fragile X-related protein and VIG associate with the RNA interference machinery. Genes Dev. 16: 2491–2496. 

Cilia, M.,* Cantrill, L.,* and Van Bel, A. 2002. Plasmodesma 2001: on safari through the symplast. Plant Cell 14: 7–10.

Ejkova, E., and Tansey, W.P. 2002. Old dogs and new tricks: meeting on mechanisms of eukaryotic transcription. EMBO Reports 3: 219–223.

Gendrel, A-V.,* Lippman, Z.,* Yordan, C., Colot, V., and Martienssen, R.A. 2002. Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1. Science 297: 1871–1873.

Hall, I. M.,* Shankaranarayana, G.D.,* Noma, K.,* Ayoub, N., Cohen, A., and Grewal, S.I. 2002. Establishment and maintenance of a heterochromatin domain. Science 297: 2232–2237.

Kim, J.Y., Yuan, Z., Cilia, M., Khalfan-Jagani, Z., and Jackson, D. 2002. Intercellular trafficking of a KNOTTED1 green fluorescent protein fusion in the leaf and shoot meristem of Arabidopsis. Proc. Natl. Acad. Sci. USA 99: 4103–4108.

Muratani, M.,* Gerlich, D.,* Janicki, S.M., M. Gebhard, Eils, R., and Spector, D.L. 2002. Metabolic-energy-dependent movement of PML bodies within the mammalian cell nucleus. Nat. Cell Biol. 4: 106–110.

Paddison, P. J., Caudy, A.A., Bernstein E., Hannon, G.J., and Conklin, D.S. 2002. Short hairpin RNAs (shRNAs) induce sequence-specific silencing in mammalian cells. Genes Dev. 16: 948–958.

Paddison, P. J.,* Caudy, A.A.,* and Hannon, G.J. 2002. Stable suppression of gene expression by RNAi in mammalian cells. Proc. Natl. Acad. Sci. USA 99: 1443–1448.

Paddison, P.J., and Hannon, G.J. 2002. RNA interference: the new somatic cell genetics? Cancer Cell 2: 17–23.

Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., and Lewis, S. 2002. The generic genome browser: a building block for a model organism system database. Genome Res. 12: 1599–1610.

Volpe, T.A., Kidner, C., Hall, I.M., G., Grewal, S.I., and Martienssen, R.A. 2002. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297: 1833–1837.


Bernstein, E., Kim, S.Y., Carmell, M.A, Murchison, E.P., Alcorn, H., Li, M.Z., Mills, A.A., Elledge, S.J., Anderson, K.V., and Hannon, G.J. 2003. Dicer is essential for mouse development. Nat. Genet. 35: 215–217.

Caudy, A.A.,. Ketting, R.F, Hammond, S.M., Denli, A.M., Bathoorn, A.M., Tops, B.B., Silva, J.M., Myers, M.M., Hannon, G.J., and Plasterk, R.H. 2003. A micrococcal nuclease homologue in RNAi effector complexes. Nature 425: 411–414.

Denli, A.M., and Hannon, G.J. 2003. RNAi: an ever growing puzzle. Trends Biochem Sci. 28: 196–201.

Dubnau, J., Chiang, A.S., Grady, L., Barditch, J., Gossweiler, S., McNeil, J., Smith, P., Bolduc, F., Scott, R., Certa, U., Broger, C., and Tully, T. 2003. The staufen/pumilio pathway is involved in Drosophila long-term memory. Curr. Biol. 13: 286–296.

Hall, I.M., and Grewal, S.I. 2003. Structure and function of heterochromatin: implications for epigenetic gene silencing and genome organization. In: RNAi: a guide to gene silencing (ed. G.J. Hannon), pp. 205–232. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.

Hall, I.M., Noma, K., and Grewal, S.I. 2003. RNA interference machinery regulates chromosome dynamics during mitosis and meiosis in fission yeast. Proc. Natl. Acad. Sci. USA 100: 193–198.

Healy, J., Thomas, E.E., Schwartz, J.T., and Wigler, M. 2003. Annotating large genomes with exact word matches. Genome Res. 13: 2306–2315.

Hemann, M.T., Fridman, J. S., Zilfou, J.T., Hernando, E., Paddison, P.J., Cordon-Cardo, C., Hannon, G.J., and Lowe, S.W. 2003. An epi-allelic series of p53 hypomorphs created by stable RNAi produces distinct tumor phenotypes in vivo. Nat. Genet. 33: 396–400.

Lippman, Z.,* May B.,* Yordan, C., Singer, T., and Martienssen, R.A. 2003. Distinct mechanisms determine transposon inheritance and methylation via small RNA and histone modification. PLoS Biol. 1: e67.

Muratani, M., and Tansey, W.P. 2003. How the ubiquitin-proteasome system controls transcription. Nat. Rev. Mol. Cell. Biol. 4: 192–201.

Paddison, P.J., and Hannon, G.J. 2003. siRNAs and shRNAs: Skeleton keys to the human genome. Curr. Opin. Mol. Ther. 5: 217–224.

Song, J.-J., Liu, J., Tolia, N.H., Schneiderman, J., Smith, S.K., Martienssen, R.A., Hannon, G.J., and Joshua-Tor, L. 2003. The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes. Nat. Struct. Biol. 10: 1026–1032.


Bastow, R., Mylne, J., Lister, C., Lippman, Z.B., Martienssen, R.A., and Dean, C. 2004. Vernalization requires epigenetic silencing of FLC by histone methylation. Nature 427: 164–­167.

Caudy, A.A., and Hannon, G.J. 2004. Induction and biochemical purification of RNA-induced silencing complex from Drosophila S2 cells. Methods Mol. Biol. 265: 59–72.

Chen, Z.J., Wang, J., Tian, L., Lee, H.S., Wang, J.J., Chen, M., Lee, J.J., Josefsson, C., Madlung, A., Watson, B., Lippman, Z., Vaughn, M., Pires, J.C., Colot, V., Doerge, R.W., Martienssen, R.A., Comai, L., and Osborn, T.C. 2004. The development of an Arabidopsis model system for genome-wide analysis of polyploidy effects. Biol. J. Linn. Soc. Lond. 82: 689–700.

Cilia, M.L., and Jackson, D. 2004. Plasmodesmata form and function. Curr. Opin. Cell Biol. 16: 500–506.

Cleary, M.A., Kilian, K., Wang, Y., Bradshaw, J., Cavet, G., Ge, W., Kulkarni, A., Paddison, P.J., Chang, K., Sheth, N., Leproust, E., Coffey, E.M., Burchard, J., McCombie, W.R., Linsley, P., and Hannon, G.J. 2004. Production of complex nucleic acid libraries using highly parallel in situ oligonucleotide synthesis. Nat. Methods 1: 241–248.

Denli, A.M., Tops, B.B., Plasterk, R.H., Ketting, R.F., and Hannon, G.J. 2004. Processing of primary microRNAs by the Microprocessor complex. Nature 432: 231–235.

Ezhkova, E., and Tansey, W.P. 2004. Proteasomal ATPases link ubiquitylation of histone H2B to methylation of histone H3. Mol. Cell 13: 435–442.

Hemann, M.T., Zilfou, J.T., Zhao, Z., Burgess, D.J., Hannon, G.J., and Lowe, S.W. 2004. Suppression of tumorigenesis by the p53 target PUMA. Proc. Natl. Acad. Sci. USA 101: 9333–9338.

Juarez, M.T., Kui, J.S., Thomas, J., Heller, B.A., and Timmermans, M.C. 2004. microRNA-mediated repression of rolled leaf1 specifies maize leaf polarity. Nature 428: 84–88.

Lippman, Z., Gendrel, A.V., Black, M., Vaughn, M.W., Dedhia, N., McCombie, W.R., Lavine, K., Mittal, V., May, B., Kasschau, K.D., Carrington, J.C., Doerge, R.W., Colot V., and Martienssen, R. 2004. Role of transposable elements in heterochromatin and epigenetic control. Nature 430: 471–476.

Lippman, Z.B., and Martienssen, R.M. 2004. The role of RNA interference in heterochromatic silencing. Nature 431: 364–370.

Liu, J., Carmell, M.A., Rivas, F.V., Marsden, C.G., Thomson, J.M.,Song, J.-J., Hammond, S.M., Joshua-Tor, L., and Hannon, G.J. 2004. Argonaute2 is the catalytic engine of mammalian RNAi. Science 305: 1437–1441.

Martienssen, R., Lippman, Z., May, B., Ronemus, M., and Vaughn, M. 2004. Transposons, tandem repeats, and the silencing of imprinted genes. Cold Spring Harbor Symp. Quant. Biol. 69: 1–10.

Murchison, E.P., and Hannon, G.J. 2004. miRNAs on the move: miRNA biogenesis and the RNAi machinery. Curr. Opin. Cell Biol. 16: 223–229.

Paddison, P.J., Caudy, A.A., Sachidanandam, R., and Hannon, G.J. 2004. Short hairpin activated gene silencing in mammalian cells. Methods Mol. Biol. 265: 85–100.

Paddison, P.J., Cleary, M., Silva, J.M., Chang, K., Sheth, N., Sachidanandam, R., and Hannon, G.J. 2004. Cloning of short hairpin RNAs for gene knockdown in mammalian cells. Nat. Methods 1: 163–167.

Paddison, P.J., Silva, J.M., Conklin, D.S., Schlabach, M., Li, M., Aruleba, S., Balija, V., O'Shaughnessy, A., Gnoj, L., Scobie, K., Chang, K., Westbrook, T., Cleary, M., Sachidanandam, R., McCombie, W.R., Elledge, S.J., and Hannon, G.J. 2004. A resource for large-scale RNA-interference-based screens in mammals. Nature 428: 427–431.

Song, J.-J., Smith, S.K., Hannon, G.J., and Joshua-Tor, L. 2004. Crystal structure of Argonaute and its implications for RISC slicer activity. Science 305: 1434–1437.

Thomas, E.E., Srebro, N., Sebat, J., Navin, N., Healy, J., Mishra, B., and Wigler, M. 2004. Distribution of short paired duplications in mammalian genomes. Proc. Natl. Acad. Sci. USA 101: 10349–10354.

Tian, G.W., Mohanty, A., Chary, S.N., Li, S., Paap, B., Drakakaki, G., Kopec, C.D., Li, J., Ehrhardt, D., Jackson, D., Rhee, S.Y., Raikhel, N.V., and Citovsky, V. 2004. High-throughput fluorescent tagging of full-length Arabidopsis gene products in planta. Plant Physiol. 135: 25–38.


Chan, N., Harris, T.W., Antoshechkin, I., Bastiani, C., Bieri, T., Blasiar, D., Bradnam, K., Canaran, P., Chan, J., Chen, C.K., Chen, W.J, Cunningham, F., Davis, P., Kenny, E., R. Kishore, D. Lawson, R. Lee, H., Muller, M., Nakamura, C., Pai, S., Ozersky, P., Petcherski, A., Roer, A., Sabo, A., Schwarz, E.M., Van Auken, K., Wang, Q., Durbin, R., Spieth, J., Sternberg, P.W, and Stein, L.D. 2005. WormBase: a comprehensive data resource for Caenorhabditis biology and genomics. Nucl. Acids Res. 33 (Database issue): D383–D389.

Chen, N., Pai, S., Zhao, Z., Mah, A., Newburry, R., Johnson, R.C., Altun, Z., Moerman, D.G, Baillie, D.L., and Stein, L. 2005. Identification of a nematode chemosensory gene family. Proc. Natl. Acad. Sci. USA 102: 145–141.

DeWeese, M.R., Hromádka, T., and Zador, A.M. 2005. Reliability and representational bandwidth in the auditory cortex. Neuron 48: 479–488.

Dickins, R.A., Hemann, M.T., Zilfou, J.T., Simpson, D.R., Ibarra, I., Hannon, G.J., and Lowe, S.W. 2005. Probing tumor phenotypes using stable and regulated synthetic micro RNA precursors. Nat. Genet. 37: 1289–1295.

Gendrel, A.-V., Lippman, Z., Martienssen, R., and Colot, V. 2005. Profiling histone modification patterns in plants using genomic tiling microarrays. Nat. Methods 2: 213–218.

Karpova, A.Y., Tervo, D.G.R., Gray, N.W., and Svoboda, K. 2005. Rapid and reversible chemical inactivation of synaptic transmission in genetically targeted neurons. Neuron 48: 727–735.

Lee, D., Ezhkova, E., Li, B., Pattenden, S.G., Tansey, W.P., and Workman, J.L. 2005. The proteasome regulatory particle alters the SAGA coactivator to enhance its interactions with transcriptional activators. Cell 123: 123–136.

Lippman, Z., Gendrel, A.-V., Colot, V., and Martienssen, R. 2005. Profiling DNA methylation patterns using genomic tiling microarrays. Nat. Methods 2: 219–224.

May, B.P., Lippman, Z.B., Fang, Y., Spector, D.L., and Martienssen, R.A. 2005. Differential regulation of strand-specific transcripts from Arabidopsis centromeric satellite repeats. PLoS Genet. 1: e79.

Muratani, M., Kung, C., and Tansey, W.P. 2005. The F-box protein Dsg1/Mdm30 is a transcriptional co-activator that stimulates Gal4 turnover and cotranscriptional mRNA processing. Cell 120: 887–899.

Murchison, E.P., Partridge, J.F., Tam, O.H., Cheloufi, S., and Hannon, G.J. 2005. Characterization of Dicer-deficient murine embryonic stem cells. Proc. Natl. Acad. Sci. USA 102: 12135–12140.

Qi, Y., Denli, A.M., and Hannon, G.J. 2005. Biochemical specialization within Arabidopsis RNA silencing pathways. Mol. Cell 19: 421–428.

Rivas, F.V., Tolia, N.H., Song, J.J., Aragon, J.P., Liu, J., Hannon, G.J., and Joshua-Tor, L. 2005. Purified Argonaute2 and an siRNA form recombinant human RISC. Nat. Struct. Mol. Biol. 12: 340–349.

Silva, J.M., Li, M.Z., Chang, K., Ge, W., Golding, M.C., Rickles, R.J., Siolas, D., Hu, G., Paddison, P.J., Schlabach, M.R., Sheth, N., Bradshaw, J., Burchard, J., Kulkarni, A., Cavet, G., Sachidanandam, R., McCombie, W.R., Cleary, M.A., Elledge, S.J., and Hannon, G.J. 2005. Second-generation shRNA libraries covering the mouse and human genomes. Nat. Genet. 37: 1281–1288.

Siolas D., C. Lerner, J. Burchard, Ge, W., Linsley, P.S., Paddison, P.J., Hannon, G.J. and M.A. Cleary. 2005. Synthetic shRNAs as potent RNAi triggers. Nat. Biotechnol. 23: 227–231.

Tolia, N.H., Enemark, E.J., Sim, B.K.L., and Joshua-Tor, L. 2005. Structural basis for the EBA-175 erythrocyte invasion pathway of the malaria parasite Plasmodium falciparum. Cell 122: 183–193.


Andl, T., Murchison, E.P., Liu, F., Zhang, Y. Yunta-Gonzalez, M., Tobias, J.W., Andl, C.D., Seykora, J.T., Hannon, G.J., and Miller, S.E. 2006. The miRNA-processing enzyme Dicer is essential for the morphogenesis and maintenance of hair follicles. Curr. Biol. 16: 1041–1049.

Aranda, V., Haire, T., Nolan, M.E., Calarco, J.P., Rosenberg, A.Z., Fawcett, J.P., Pawson, T., and Muthuswamy, S.K. 2006. Par6-aPKC uncouples ErbB2 induced disruption of polarized epithelial organization from proliferation control. Nat. Cell Biol. 11: 1235–1245.

Asari, H., Pearlmutter, B.A., and Zador, A.M. 2006. Sparse representations for the cocktail party problem. J. Neurosci. 26: 7477–7490.

Bestman, J.E., Ewald, R.C., Chiu, S.-L., and Cline, H.T. 2006. In vivo single-cell electroporation for transfer of DNA and macromolecules. Nat. Protoc. 1: 1268–1273.

Chen, B.L., Hall, D.H., and Chklovskii, D.B. 2006. Wiring optimization can relate neuronal structure and function. Proc. Natl. Acad. Sci. USA 103: 4723–4728.

Collins, G.A., and Tansey, W.P. 2006. The proteasome: a utility tool for transcription? Curr. Opin. Genet. Dev. 16: 197–202.

Ezhkova, E., and Tansey, W.P. 2006. Chromatin Immunoprecipitation to study protein-DNA interactions in budding yeast. Methods Mol. Biol. 313: 225–244.

Feierstein, C.E., Quirk, M.C., Uchida, N., Sosulski, D.L., and Mainen, Z.F. 2006. Representation of spatial goals in rat orbitofrontal cortex. Neuron 51: 495–507.

Girard, A., Sachidanandam, R., Hannon, G.J., and Carmell, M.A. 2006. A germline-specific class of small RNAs bind mammalian Piwi proteins. Nature 442: 199–202.

Hannon, G.J., Riva, F.V., Murchison, E.P., and Steitz, J.A. 2006. The expanding universe of noncoding RNAs. Cold Spring Harbor Symp. Quant. Biol. 7I: 551–564.

Irvine, D.V., Zaratiegui, M., Tolia, N.H., Goto, D.B., Chitwood, D.H., Vaughn, M.W., Joshua-Tor, L., and Martienssen, R.A. 2006. Argonaute slicing is required for heterochromatic silencing and spreading. Science 313: 1134–1137.

Kopec, C.D., Li, B., Wei, W., Boehm, J., and Malinow, R. 2006. Glutamate receptor exocytosis and spine enlargement during chemically induced long-term potentiation. J. Neurosci. 26: 2000–2009.

Kopec, C., and Malinow, R. 2006. Matter of size. Science 314: 1554–1555.

Locke, S.M., and Martienssen, R.A. 2006. Slicing and spreading of heterochromatic silencing by RNA interference. Cold Spring Harbor Symp. Quant. Biol. 7I: 497–503.

Nogueira, F.T.S., Sarkar, A.K., Chitwood, D.H., and Timmermans, M.C.P. 2006. Organ polarity in plants is specified through the opposing activity of two distinct small regulatory RNAs. Cold Spring Harbor Symp. Quant. Biol. 7I: 157–164.

Rial Verde, E.M., Lee-Osbourne, J., Worley, P.F., Malinow, R., and Cline, H.T. 2006. Increased expression of the immediate-early gene arc reduces AMPA receptor-mediated synaptic transmission. Neuron 52: 461–474.

Song, J.-J., and Joshua-Tor, L. 2006. Argonaute and RNA - getting into the groove. Curr. Opin. Struct. Biol. 16: 5–11.

Watabe-Uchida, M., John, K.A., Janas, J.A., Newey, S.E., and Van Aelst, L. 2006. The Rac activator DOCK7 regulates neuronal polarity through local phosphorylation of Stathmin/Op18. Neuron 51: 727–739.

Yasuda, R., Harvey, C.D., Zhong, H., Sobczyk, A., Van Aelst, L., and Svoboda, K. 2006. Supersensitive Ras activation in dendrites and spines revealed by two-photon fluorescence lifetime imaging. Nat. Neurosci. 9: 283–291.


Aravin, A.A., Sachidanandam, R., Girard, A., Fejes-Toth, K., and Hannon, G.J. 2007. Developmentally regulated piRNA clusters implicate MILI in transposon control. Science 316: 744–747.

Bish, R.A., and Myers, M.P. 2007. Werner Helicase-Interacting Protein 1 binds polyubiquitin via its zinc finger domain. J. Biol. Chem. 282: 23184–23193.

Brennecke, J., Aravin, A.A., Stark, A., Dus, M., Kellis, M., Sachidanandam, R., and Hannon, G.J. 2007. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128: 1089–1103.

Brower-Toland, B., Findley, S.D., Jiang, L., Liu, L., Yin, H., Dus, M., Zhou, P., Elgin, S.C., and Lin, H. 2007. Drosophila PIWI associates with chromatin and interacts directly with HP1a. Genes Dev. 21: 2300–2311.

Carmell, M.A., Girard, A., van de Kant, H.J.G., Bourc'his, D., Bestor, T.H., de Rooij, D.G., and Hannon, G.J. 2007. MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline. Dev. Cell 12: 503–514.

Chitwood, D.H., Guo, M., Nogueira, F.T.S., and Timmermans, M.C.P. 2007. Establishing leaf polarity: the role of small RNAs and positional signals in the shoot apex. Development 134: 813–823.

Chitwood, D.H., and Timmermans, M.C.P. 2007. Target mimics modulate miRNAs. Nat. Genet. 39: 935–936.

Dickins, R.A., McJunkin, K., Hernando, E. Premsrirut, P.K., Krizhanovsky, V., Burgess, D., Kim, S.Y., Cordon-Cardo, C., Zender, L., Hannon, G.J., and Lowe, S.W. 2007. Tissue-specific and reversible RNA interference in transgenic mice. Nat. Genet. 39: 914–921.

Harvey, C.D., and Svoboda, K. 2007. Locally dynamic synaptic learning rules in pyramidal neuron dendrites. Nature 450: 1195–1200.

Houwing, S., Kamminga, L.M., Berezikov, E., Cronembold, D., Girard, A., van den Elst, H., Filippov, D.V., Blaser, H., Raz, E., Moens, C.B., Plasterk, R.H.A., Hannon, G.J., Draper, B.W., and Ketting, R.F. 2007. A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in zebrafish. Cell 129: 69–82.

Hromádka, T., and Zador, A.M. 2007. Toward the mechanisms of auditory attention. Hear. Res. 229: 180–185.

Huber, D., Petreanu, L., Ghitani, N., Ranade, S., Hromádka, T., Mainen, Z., and Svoboda, K. 2007. Sparse optical microstimulation in barrel cortex drives learned behaviour in freely moving mice. Nature 451: 61–64.

Ibarra, I., Erlich, Y., Muthuswamy, S.K., Sachidanandam, R., and Hannon, G.J. 2007. A role for microRNAs in maintenance of mouse mammary epithelial progenitor cells. Genes Dev. 21: 3238–3243.

Kim, J., Inoue, K., Ishii, J., Vanti, W.B., Voronov, S.V., Murchison, E., Hannon, G., and Abeliovich, A. 2007. A microRNA feedback circuit in midbrain dopamine neurons Science 317: 1220–1224.

Kopec, C.D., Kessels, H.W.H.G., Bush, D.E.A., Cain, C.K., LeDoux, J.E., and Malinow, R. 2007. A robust automated method to analyze rodent motion during fear conditioning. Neuropharmacol. 52: 228–233.

Kopec, C.D., Real, E., Kessels, H.W., and Malinow, R. 2007. GluR1 links structural and functional plasticity at excitatory synapses. J. Neurosci. 27: 13706–13718.

Maximov, A., Pang, Z.P., Tervo, D.G., and Südhof, T.C. 2007. Monitoring synaptic transmission in primary neuronal cultures using local extracellular stimulation. J. Neurosci. Methods 161: 75–87.

Murchison, E.P., Stein, P., Xuan, Z., Pan, H., Zhang, M.Q., Schultz, R.M., and Hannon, G.J. 2007. Critical roles for Dicer in the female germline. Genes Dev. 21: 682–693.

Nogueira, F.T.S., Madi, S., Chitwood, D.H., Juarez, M.T., and Timmermans, M.C.P. 2007. Two small regulatory RNAs establish opposing fates of a developmental axis. Genes Dev. 21: 750–755.

Tervo, D., and Karpova, A.Y. 2007. Rapidly inducible, genetically targeted inactivation of neural and synaptic activity in vivo. Curr. Opin. Neurobiol. 5: 581–586.

Vaughn, M.W., Tanurdžić, M., Lippman, Z., Jiang, H., Carrasquillo, R., Rabinowicz, P.D., Dedhia, N., McCombie, W.R., Agier, N., Bulski, A., Colot, V., Doerge, R.W., and Martienssen, R.A. 2007. Epigenetic natural variation in Arabidopsis thaliana. PLoS Biol. 5: e174.


Benetti, R., Gonzalo, S., Jaco, I., Muñoz, P., Gonzalez, S., Schoeftner, S., Murchison, E., Andl, T., Chen, T., Klatt, P., Li, E., Serrano, M., Millar, S., Hannon, G., and Blasco, M.A. 2008. A mammalian micro RNA cluster controls DNA methylation and telomere recombination via Rbl2-dependent regulation of DNA methyltransferases. Nat. Struct. Mol. Bio. 15: 268–279.

Bish, R.A., Fregoso, O.I., Piccini, A., and Myers, M.P. 2008. Conjugation of Complex Polyubiquitin Chains to WRNIP1. J. Proteome Research. 7: 3481–3489.

Bolduc, F.V., Bell, K., Cox, H., Broadie, K.S., Tully, T. 2008. Excess protein synthesis in Drosophila fragile X mutants impairs long-term memory. Nat. Neurosci. 11:1143–1145.

Brennecke, J., * Malone, C.D.,* Aravin, A.A., Sachidanandam, R., Stark, A., and Hannon, G.J. 2008. An epigenetic role for maternally inherited piRNAs in transposon silencing. Science 322: 1387-1392.

Burgess, D.J., Doles, J., Zender, L., Xue, W., Ma, B., McCombie, W.R., Hannon, G.J., Lowe, S.W., and Hemann, M.T. 2008. Topoisomerase levels determine chemotherapy response in vitro and in vivo. Proc. Natl. Acad. Sci. USA 105: 9053–9058.

Chen, J.F., Murchison, E.P., Tang, R., Callis, T.E., Tatsuguchi, M., Deng, Z., Rojas, M., Hammond, S.M., Schneider, M.D., Selzman, C.H., Meissner, G., Patterson, C., Hannon. G.J., and Wang, D.Z. 2008. Targeted deletion of Dicer in the heart leads to dilated cardiomyopathy and heart failure. Proc. Natl. Acad. Sci. USA 6: 2111–2116.

Chiu, S.L., Chen, C.M. and Cline, H.T. 2008. Insulin receptor signaling regulates synapse number, dendritic plasticity, and circuit function in vivo. Neuron 58: 708–719.

Czech, B.,* Malone, C.D.,* Zhou, R., Stark, A., Schlingeheyde, C., Dus, M., Perrimon, N., Kellis, M., Wohlschlegel, J.A., Sachidanandam, R., Hannon, G.J. and Brennecke, J. 2008. An endogenous small interfering RNA pathway in Drosophila. Nature 453: 798–802.

Daulny, A., Geng, F., Muratani, M., Geisinger, J.M., Salghetti, S.E., and Tansey, W.P. 2008. Modulation of RNA polymerase II subunit composition by ubiquitylation. Proc. Natl. Acad. Sci. U S A. 50: 19649-19654.

Erlich, Y., Mitra, P.P., Delabastide, M., McCombie, W.R., and Hannon, G.J. 2008.  Alta-Cyclic: a self-optimizing base caller for next-generation sequencing. Nature Methods 5: 679–682.

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* - Authors contributed equally to the work.

........ - Watson School student