Student Publications

2001

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.

2002

 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.

2003

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.

2004

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.

2005

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.

2006

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.

2007

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.

2008

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.

Ewald, R.C., Van Keuren-Jensen, K.R., Aizenman, C.D., and Cline, H.T. 2008. Roles of NR2A and NR2B in the development of dendritic arbor morphology in vivo. J. Neurosci. 28: 850–861.

Finigan, P. and Martienssen, R.A. 2008. 

Nucleolar dominance and DNA methylation directed by small interfering RNA. Mol. Cell 32: 753-754.

Girard, A., and Hannon, G.J. 2008. Conserved themes in small-RNA-mediated transposon control. Trends Cell Biol. 18: 136–148.

Gruntman, E., Qi, Y., Slotkin, R.K., Roeder, T., Martienssen, R.A., Sachidanandam, R. 2008. Kismeth: analyzer of plant methylation states through bisulfite sequencing. BMC Bioinformatics 9:371–384.

Guo, M., Thomas, J., Collins, G., and Timmermans, M.C. 2008. Direct repression of KNOX loci by the ASYMMETRIC LEAVES1 complex of Arabidopsis. Plant Cell 20: 48–58.

Harvey, C.D., Ehrhardt, A.G., Cellurale, C., Zhong, H., Yasuda, R., Davis, R.J., and Svoboda, K. 2008. A genetically encoded fluorescent sensor of ERK activity. Proc. Natl. Acad. Sci U S A. 105: 19264-19269.

Harvey, C.D., Yasuda, R., Zhong, H., and Svoboda, K. 2008. The spread of Rasactivity triggered by activation of a single dendritic spine. Science 321:136-140.

Hromádka, T., DeWeese, M.R., and Zador, A.M. 2008. Sparse representation of sounds in the unanaesthetized auditory cortex. PLoS Biol. 6: e16.

Iijima, K., Chiang, H.C., Hearn, S.A., Hakker, I., Gatt, A., Shenton, C., Granger, L., Leung, A., Iijima-Ando, K., and Zhong, Y. 2008. Ab42 mutants with different aggregation profiles induce distinct pathologies in Drosophila. PLoS ONE 3: e1703.

Tam, O.H., Aravin, A.A., Stein, P., Girard, A., Murchison, E.P., Cheloufi, S., Hodges, E., Anger, M., Sachidanandam, R., Schultz, R.M., and Hannon, G.J. 2008. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature 453: 534–539.

Leung, A., Geng, F., Daulny, A., Collins, G., Guzzardo, P. and Tansey, W.P. 2008. Transcriptional control and the ubiquitin-proteasome system. Ernst Schering Found. Symp. Proc. 1:75-97.

Wilusz, J.E., Freier, S.M., and Spector, D.L. 2008. 3’ end processing of a long nuclear-retained non-coding RNA yields a tRNA-like cytoplasmic RNA. Cell 135: 919-932.

Wu, Y., Bolduc, F.V., Bell, K., Tully, T., Fang, Y., Sehgal, A., and Fischer, J.A. 2008. A Drosophila model for Angelman Syndrome. Proc. Natl. Acad. Sci. USA 105: 12399–12404.

Zhou, R., Hotta, I., Denli, A.M., Hong, P., Perrimon, N. and Hannon, G.J. 2008. Comparative analysis of Argonaute-dependent small RNA pathways in Drosophila. Mol. Cell 32:592-599.

2009

Asari, H., and Zador, A.M. 2009. Long-lasting context dependence constrains neural encoding models in rodent auditory cortex. J. Neurophysiol 102: 2638-2656.

Benitez-Alfonso, Y., Cilia, M., Roman, A.S., Thomas, C., Maule, A., Hearn, S. and Jackson, D. 2009. Control of Arabidopsis meristem development by thioredoxin-dependent regulation of intercellular transport. Proc. Natl. Acad. Sci.U S A 106: 3615-3620.

Blum, A.L., Li, W., Cressy, M. and Dubnau, J. 2009. Short- and long-term memory in Drosophila require cAMP signaling in distinct meuron types. Curr Biol. 19: 1341-1350.

Bolduc, F.V. and Tully, T. 2009. Fruit flies and intellectual disability. Fly 3:91-104.

Bric, A., Miething, C., Bialucha, C.U., Scuoppo, C., Zender, L., Krasnitz, A., Xuan, Z., Zuber, J., Wigler, M., Hicks, J., McCombie, R.W., Hemann, M.T., Hannon, G.J., Powers, S. and Lowe, S.W. 2009. Functional Identification of Tumor-Suppressor Genes through an In Vivo RNA Interference Screen in a Mouse Lymphoma Model. Cancer Cell 16:324-335.

Chitwood, D.H.,  Nogueira, F.T.S., Howell, M.D., Montgomery, T.A., Carrington,  J.C. and Timmermans, M.C.P. 2009. Pattern formation via small RNA mobility. Genes Dev. 23: 549-554.

Collins, G., Lipford, R., Deshaies, R. J., Tansey, W. P. Gal4 turnover and transcription activation. 2009. Nature 461: E7-E7.

Czech, B., Zhou, R., Erlich, Y., Brennecke, J., Binari, R., Villalta, C., Gordon, A., Perrimon, N., and Hannon, G.J. 2009. Hierarchical rules for Argonaute loading in Drosophila. Mol Cell 36: 445-456.

Couvillion, M.T., Lee, S.R., Hogstad, B., Malone, C.D., Tonkin, L.A., Sachidanandam, R., Hannon, G.J. and Collins, K. 2009. Sequence, biogenesis, and function of diverse small RNA classes bound to the Piwi family proteins of Tetrahymena thermophila. Genes Dev. 23: 2016-2032.

Erlich, Y., Chang, K., Gordon, A., Ronen, R., Navon, O., Rooks, M., and Hannon, G.J. 2009. DNA Sudoku--harnessing high-throughput sequencing for multiplexed specimen analysis. Genome Res. 9: 1243-1253.

Husbands, A.Y, Chitwood, D.H., Plavskin, Y. and Timmermans, M.C.P. 2009. Signals and prepatterns: new insights into organ polarity in plants. Genes Dev. 23: 1986-1997.

Kessels, H.W., Kopec, C.D., Klein, M.E., and Malinow, R. 2009. Roles of stargazin and phosphorylation in the control of AMPA receptor subcellular distribution. Nat Neurosci. 12: 888-896.

Lima, S.Q., Hromádka, T., Znamenskiy, P., and Zador, A.M. 2009. PINP: A New Method of Tagging Neuronal Populations for Identification during In Vivo Electrophysiological Recording. PLoS One 4: e6099.

Makino, H., and Malinow, R. 2009. AMPA Receptor incorporation into synapses during LTP: The role of lateral movement and exocytosis. Neuron 64: 381-390.

Malone, C.D. and Hannon, G.J. 2009. Small RNAs as guardians of the genome. Cell 136: 656-668.

Malone, C.D., Brennecke, J., Dus, M., Stark, A., McCombie, W.R., Sachidanandam, R., and Hannon, G.J. 2009. Specialized piRNA Pathways Act in Germline and Somatic Tissues of the Drosophila Ovary. Cell. 137: 522-535.

Nogueira, F.T., Chitwood, D.H., Madi, S., Ohtsu, K., Schnable, P.S., Scanlon, M.J., and Timmermans, M.C. 2009. Regulation of small RNA accumulation in the maize shoot apex. PLoS Genet. 1:e1000320.

Quirk, M.C., Sosulski, D.L., Feierstein, C.E., Uchida, N., and Mainen, Z.F. 2009. A defined network of fast-spiking interneurons in orbitofrontal cortex: responses to behavioral contingencies and ketamine administration. Front Syst Neurosci. 3:13.

Rechavi, O., Erlich, Y., Amram, H., Flomenblit, L., Karginov, F.V., Goldstein, I., Hannon, G.J. and Kloog, Y. 2009. Cell contact-dependent acquisition of cellular and viral nonautonomously encoded small RNAs. Genes Dev. 23: 1971-1979.

Sunwoo, H., Dinger, M.E., Wilusz, J.E., Amaral, P.P, Mattick, J.S. and Spector, D.L. 2009. MEN ϵ/β nuclear retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res. 19: 347-359.

Wilusz, J.E., Sunwoo, H. and Spector, D.L. 2009. Long noncoding RNAs: functional surprises from the RNA world. Genes Dev. 23: 1494-1504.

Zhao, R., Bodnar M.S., and Spector, D.L. 2009. Nuclear neighborhoods and gene expression. Curr. Opin. Genet. Dev. 19: 172-179.

Zuber, J., Radtke, I., Pardee, T.S., Zhao, Z., Rappaport, A.R., Luo, W., McCurrach, M.E., Yang, M-M., Dolan, M.E., Kogan, S.C., Downing, J.R., and Lowe, S.W. 2009. Mouse models of human AML accurately predict chemotherapy response. Genes Dev. 23: 877-889.

2010

Blum, A., and Dubnau, J.T. 2010. Parallel processing of olfactory memories in Drosophila. Fly (Austin): 4:163-166. 

Bolduc, F.V., Bell, K., Rosenfelt, C., Cox, H., and Tully, T. 2010. Fragile x mental retardation 1 and filamin a interact genetically in Drosophila long-term memory. Front Neural Circuits. 3: 22.

Chicas, A., Wang, X., Zhang, C., McCurrach, M., Zhao, Z., Mert, O., Dickins, R.A., Narita, M., Zhang, M., and Lowe, S.W. 2010. Dissecting the Unique Role of the Retinoblastoma Tumor Suppressor during Cellular Senescence. Cancer Cell 17: 311-414.

Chiu, S.L., and Cline, H.T. 2010. Insulin receptor signaling in the development of neuronal structure and function. Neural Dev. 5:7.

Collins, G.A., Gomez, T.A., Deshaies, R.J., and Tansey, W.P. 2010. Combined chemical and genetic approach to inhibit proteolysis by the proteasome. Yeast 27: 965-974.

Edvardson, S., Shaag, A., Zenvirt, S., Erlich, Y., Hannon, G.J., Shanske, A.L., Gomori, J.M., Ekstein, J., and Elpeleg, O. 2010. American Journal of Human Joubert Syndrome 2 (JBTS2) in Ashkenazi Jews Is Associated with a TMEM216 Mutation. Am. J. Hum. Genet. 86:93-7.

Egeblad, M., Nakasone, E.S., and Werb, Z. 2010. Tumors as organs: complex tissues that interface with the entire organism. Dev. Cell 18: 884-901.

Erlich, Y., Gordon, A., Brand, M., Hannon, G. J., and Mitra, P. P. 2010.  Compressed Genotyping. IEEE Transaction on Information Theory 56: 706-723.

Haase, A.D., Fenoglio, S., Muerdter, F., Guzzardo, P.M., Czech, B., Pappin, D.J., Chen, C., Gordon, A. and Hannon, G.J. 2010. Probing the initiation and effector phases of the somatic piRNA pathway in Drosophila.  Genes Dev. 24: 2499-2504.

Li, J., Wang, Y., Chiu, S.L., and Cline, H.T. 2010. Membrane targeted horseradish peroxidase as a marker for correlative fluorescence and electron microscopy studies. Front Neural Circuits 26: 6.

Malone, C.D., and Hannon, G.J. 2010. Molecular evolution of piRNA and transposon control pathways in Drosophila. Cold Spring Harb. Symp. Quant. Biol. 74: 225-234.

Mangone, M., Myers, M.P., and Herr, W. 2010. Role of the HCF-1 basic region in sustaining cell proliferation. PLoS One. 5: e9020.

Mavrakis, K.J., Wolfe, A.L., Oricchio, E., Palomero, T., de Keersmaecker, K., McJunkin, K., Zuber, J., James, T., Khan, A.A., Leslie, C.S., Parker, J.S., Paddison, P.J., Tam, W., Ferrando, A., and Wendel, H.G. 2010. Genome-wide RNA-mediated interference screen identifies miR-19 targets in Notch-induced T-cell acute lymphoblastic leukaemia. Nat. Cell Biol. 12: 372-379.

Pineau, P., Volinia, S., McJunkin, K., Marchio, A., Battiston, C., Terris, B., Mazzaferro, V., Lowe, S.W., Croce, C.M., and Dejean, A. 2010. miR-221 overexpression contributes to liver tumorigenesis. Proc. Natl. Acad. Sci. U S A. 107: 264-269.

Wei, W., Nguyen, L.N., Kessels, H.W., Hagiwara, H., Sisodia, S., and Malinow, R. 2010. Amyloid beta from axons and dendrites reduces local spine number and plasticity. Nat. Neurosci. 13: 190-196.

Wilusz, J.E., and Spector, D.L. 2010. An unexpected ending: noncanonical 3' end processing mechanisms. RNA. 16: 259-266.

Yao, Z., Fenoglio, S., Gao, D.C., Camiolo, M., Stiles, B., Lindsted, T., Schlederer, M., Johns, C., Altorki, N., Mittal, V., Kenner, L., and Sordella, R. 2010. TGF-{beta} IL-6 axis mediates selective and adaptive mechanisms of resistance to molecular targeted therapy in lung cancer. Proc Natl Acad Sci U S A. 107: 15535-15540.

                                                          2011

Calarco, J.P., and Martienssen, R.A. 2011. Genome reprogramming and small interfering RNA in the Arabidopsis germline. Curr. Opin. Genet. Dev. 21: 134–139. Review.

Chien, Y.*, Scuoppo, C.*, Wang, X., Fang, X., Balgley, B., Bolden, J.E., Premsrirut, P., Luo, W., Chicas, A., Lee, C.S., Kogan, S.C., and Lowe, S.W. 2011. Control of the senescence-associated secretory phenotype by NF-{kappa}B promotes senescence and enhances chemosensitivity. Genes Dev. 25: 2125–2136.

Clark, M.B., Amaral, P.P., Schlesinger, F.J., Dinger, M.E., Taft, R.J., Rinn, J.L., Ponting, C.P., Stadler, P.F., Morris, K.V., Morillon, A., Rozowsky, J.S., Gerstein, M.B., Wahlestedt, C., Hayashizaki, Y., Carninci, P., Gingeras, T.R., and Mattick, J.S. 2011. The reality of pervasive transcription. PLoS Biol. 9: e1000625. Review

Deng, X., Hiatt, J.B., Nguyen, D.K., Ercan, S., Sturgill, D., Hillier, L.W., Schlesinger, F., Davis, C.A., Reinke, V.J., Gingeras, T.R., Shendure, J., Waterston, R.H., Oliver, B., Lieb, J.D., and Disteche, C.M. 2011. Evidence for compensatory upregulation of expressed X-linked genes in mammals, Caenorhabditis elegans and Drosophila melanogaster. Nat Genet. 43: 1179-1185. 

Fellmann, C., Zuber, J., McJunkin, K., Chang, K., Malone, C.D., Dickins, R.A., Xu, Q., Hengartner, M.O., Elledge, S.J., Hannon, G.J., and Lowe, S.W. 2011. Functional identification of optimized RNAi triggers using a massively parallel sensor assay. Mol. Cell. 41: 733–746.

Honegger, K.S., Campbell, R.A., and Turner, G.C. 2011. Cellular-resolution population imaging reveals robust sparse coding in the Drosophila mushroom body. J. Neurosci. 31: 11772-11785.

Jiang, L.* Schlesinger, F*, Davis, C.A., Zhang, Y., Li, R., Salit, M., Gingeras, T.R., and Oliver, B. 2011. Synthetic spike-in standards for RNA-seq experiments. Genome Res. 21: 1543-1551.

Kopec, C.D., Bowers, A.C., Pai, S., and Brody, C.D. 2011. Semi-automated atlas-based analysis of brain histological sections. J. Neurosci. Methods 196: 12–19.

Leung, A., Cajigas, I., Jia, P., Ezhkova, E., Brickner, J.H., Zhao, Z., Geng, F., and Tansey, W.P. 2011. Histone H2B ubiquitylation and H3 lysine 4 methylation prevent ectopic silencing of euchromatic loci important for the cellular response to heat. Mol. Biol. Cell. 22: 2741-2753.

Makino, H., and Malinow, R. 2011. Compartmentalized versus global synaptic plasticity on dendrites controlled by experience. Neuron 72: 1001-1011.

McJunkin, K., Mazurek, A., Premsrirut, P.K., Zuber, J., Dow, L.E., Simon, J., Stillman, B., and Lowe, S.W. 2011. Reversible suppression of an essential gene in adult mice using transgenic RNA interference. Proc. Natl. Acad. Sci. U S A. 17: 7113-7118.

Pai, S., Erlich, J.C., Kopec, C., and Brody, C.D. 2011. Minimal impairment in a rat model of duration discrimination following excitotoxic lesions of primary auditory and prefrontal cortices. Front Syst. Neurosci. 5: 74.

Premsrirut, P.K., Dow, L.E., Kim, S.Y., Camiolo, M., Malone, C.D., Miething, C., Scuoppo, C., Zuber, J., Dickins, R.A., Kogan, S.C., Shroyer, K.R., Sordella, R., Hannon, G.J., and Lowe, S.W. 2011. A rapid and scalable system for studying gene function in mice using conditional RNA interference. Cell 145: 145–158.

Rangan, P., Malone, C.D., Navarro, C., Newbold, S.P., Hayes, P.S., Sachidanandam, R., Hannon, G.J., and Lehmann, R. 2011. piRNA Production Requires Heterochromatin Formation in Drosophila. Curr. Biol. 21: 1373-1379. 

Simpson, D.R., Yu, M., Zheng, S., Zhao, Z., Muthuswamy, S.K., and Tansey, W.P. 2011. Epithelial cell organization suppresses myc function by attenuating myc expression. Cancer Res. 71: 3822-3830. 

Sun, S., Zhang, Z., Fregoso, O., and Krainer, A.R. 2011. Mechanisms of activation and repression by the alternative splicing factors RBFOX1/2. RNA 18: 274-283.  

Wasik, K.A., and Rebbeck, C.A. 2011. Keystone Symposia 40th Season: MicroRNAs and Noncoding RNAs in Cancer. Cancer Res. 71: 6102–6105. Review

Varshney, L.R., Chen, B.L., Paniagua, E., Hall, D.H., and Chklovskii, D.B. 2011. Structural properties of the Caenorhabditis elegans neuronal network. PLoS Comput Biol. 7: e1001066.

Zamparini, A.L., Davis, M.Y., Malone, C.D., Vieira, E., Zavadil, J., Sachidanandam, R., Hannon, G.J., and Lehmann, R. 2011. Vreteno, a gonad-specific protein, is essential for germline development and primary piRNA biogenesis in Drosophila. Development 138: 4039-4050.

Zaratiegui, M., Castel, S.E., Irvine, D.V., Kloc, A., Ren, J., Li, F., de Castro, E., Marín, L., Chang, A.Y., Goto, D., Cande, W.Z., Antequera, F., Arcangioli, B., and Martienssen, R.A. 2011. RNAi promotes heterochromatic silencing through replication-coupled release of RNA Pol II. Nature 479: 135–138.

Zuber, J.*, Rappaport, A.R.*, Luo, W., Wang, E., Chen, C., Vaseva, A.V., Shi, J., Weissmueller, S., Taylor, M.J., Weissenboeck, M., Graeber, T.G., Kogan, S.C., Vakoc, C.R. and Lowe, S.W. 2011. An integrated approach to dissecting oncogene addiction implicates a Myb coordinated self-renewal program as essential for leukemia maintenance. Genes Dev. 25: 1628-1640.

Zuber, J., Shi, J., Wang, E., Rappaport, A.R., Herrmann, H., Sison, E.A., Magoon, D., Qi, J., Blatt, K., Wunderlich, M., Taylor, M.J., Johns, C., Chicas, A., Mulloy, J.C., Kogan, S.C., Brown, P., Valent, P., Bradner, J.E., Lowe, S.W., and Vakoc, C.R. 2011. RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia. Nature 478: 524–528.

2012

Aksoy, O., Chicas, A., Zheng, T., Zhao, Z., McCurrach, M., Wang, X. and Lowe, S.W. 2012. The atypical E2F family member E2F7 couples the p53 and Rb pathways during cellular senescence. Genes Dev. 26: 1546–1557.

Borges, F., Calarco, J.P., and Martienssen, R.A. 2012. Reprogramming the epigenome in Arabidopsis pollen. Cold Spring Harb Symp Quant Biol. 77: 1-5. Review.

Borges, F., Gardner, R., Lopes, T., Calarco, J.P., Boavida, L.C., Slotkin, R.K., Martienssen, R.A., and Becker, J.D. 2012. FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei. Plant Methods 8: 44.

Bergerson, R.J., Collier, L.S., Sarver, A.L., Been, R.A., Lugthart, S., Diers, M.D., Zuber, J., Rappaport, A.R., Nixon, M.J., Silverstein, K.A., Fan, D., Lamblin, A.F., Wolff, L., Kersey, J.H., Delwel, R., Lowe, S.W., O'Sullivan, M.G., Kogan, S.C., Adams, D.J., and Largaespada, D.A. 2012. An insertional mutagenesis screen identifies genes that cooperate with Mll-AF9 in a murine leukemogenesis model. Blood 19: 4512–4523. 

Calarco, J.P., Borges, F., Donoghue, M.T., Van Ex, F., Jullien, P.E., Lopes, T., Gardner, R., Berger, F., Feijó, J.A., Becker, J.D., and Martienssen, R.A. 2012. Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA. Cell 151: 194-205.

Calarco, J.P., and Martienssen, R.A. 2012. Imprinting: DNA methyltransferases illuminate reprogramming. Curr Biol. 22: R929-931.

Campbell, R.A.A.*, Honegger, K.S.*, Qin, H., Li, W., Demir, E., and Turner, G.C. 2013. Imaging a population code for odor identity in the Drosophila mushroom body. J Neurosci. 33: 10568-10581.

Chicas, A., Kapoor, A., Wang, X., Aksoy, O., Evertts, A.G., Zhang, M.Q., Garcia, B.A., Bernstein, E., and Lowe, S.W. 2012. H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence. Proc Natl Acad Sci U S A. 23: 8971–8976.

Djebali, S., Lagarde, J., Kapranov, P., Lacroix, V., Borel, C., Mudge, J.M., Howald, C., Foissac, S., Ucla, C., Chrast, J., Ribeca, P., Martin, D., Murray, R.R., Yang, X., Ghamsari, L., Lin, C., Bell, I., Dumais, E., Drenkow, J., Tress, M.L., Gelpí, J.L., Orozco, M., Valencia, A., van Berkum, N.L., Lajoie, B.R., Vidal, M., Stamatoyannopoulos, J., Batut, P., Dobin, A., Harrow, J., Hubbard, T., Dekker, J., Frankish, A., Salehi-Ashtiani, K., Reymond, A., Antonarakis, S.E., Guigó, R., and Gingeras, T.R. 2012. Evidence for transcript networks composed of chimeric RNAs in human cells. PLoS One 7: e28213. 

Dow, L.E., Premsrirut, P.K., Zuber, J., Fellmann, C., McJunkin, K., Miething, C., Park, Y., Dickins, R.A., Hannon, G.J., and Lowe, S.W. 2012. A pipeline for the generation of shRNA transgenic mice. Nat Protoc. 7: 374–393. 

Glaser, S.P., Lee, E.F., Trounson, E., Bouillet, P., Wei, A., Fairlie, W.D., Izon, D.J., Zuber, J., Rappaport, A.R., Herold, M.J., Alexander, W.S., Lowe, S.W., Robb, L., and Strasser, A. 2012. Anti-apoptotic Mcl-1 is essential for the development and sustained growth of acute myeloid leukemia. Genes Dev. 26: 120–125.

Iossifov, I., Ronemus, M., Levy, D., Wang, Z., Hakker, I., Rosenbaum, J., Yamrom, B., Lee, Y.,   Narzisi, G., Leotta, A., Kendall, J., Grabowska, E., Ma, B., Marks, S., Rodgers, L., Stepansky, A., Troge, J., Andrews, P., Bekritsky, M., Pradhan, K., Ghiban, E., Kramer, M., Parla, J.,  Demeter, R., Fulton, L.L., Fulton, R.S., Magrini, V.J., Ye, K., Darnell, J.C., Darnell, R.B., Mardis, E.R., Wilson, R.K., Schatz, M.C., McCombie, W.R., and Wigler, M. 2012. De novo gene disruptions in children on the autistic spectrum. Neuron 74: 285–299.

Nakasone, E.S., Askautrud, H.A., Kees, T., Park, J.H., Plaks, V., Ewald, A.J., Fein, M., Rasch, M.G., Tan, Y.X., Qiu, J., Park, J., Sinha, P., Bissell, M.J., Frengen, E., Werb, Z., and Egeblad, M. 2012. Imaging tumor-stroma interactions during chemotherapy reveals contributions of the microenvironment to resistance. Cancer Cell 21: 488–503.

Plavskin, Y., and Timmermans, M.C. 2012. Small RNA-regulated networks and the evolution of novel structures in plants. Cold Spring Harb Symp Quant Biol. 77: 221-233. Review.

Preall, J.B., Czech, B., Guzzardo, P.M., Muerdter, F., and Hannon, G.J. 2012. shutdown is a component of the Drosophila piRNA biogenesis machinery. RNA 18: 1446–1457.

Raposo, D., Sheppard, J.P., Schrater, P.R., Churchland, A.K. 2012. Multisensory decision-making in rats and humans. J. Neurosci. 32: 3726–3735.

Sanders, J.I., and Kepecs, A. 2012. Choice ball: a response interface for two-choice psychometric discrimination in head-fixed mice. J Neurophysiol. 108: 3416-3423.

Schlesinger, F., Smith, A.D., Gingeras, T.R., Hannon, G.J., and Hodges, E. 2013. De novo DNA demethylation and non-coding transcription define active intergenic regulatory elements. Genome Res. 23: 1601-1614.

Shi, J., Wang, E., Zuber, J., Rappaport, A., Taylor, M., Johns, C., Lowe, S.W., and Vakoc, C.R. 2012. The Polycomb complex PRC2 supports aberrant self-renewal in a mouse model of MLL-AF9;Nras(G12D) acute myeloid leukemia. Oncogene 32: 930-938.

Scuoppo, C., Miething, C., Lindqvist, L., Reyes, J., Ruse, C., Appelmann, I., Yoon, S., Krasnitz, A., Teruya-Feldstein, J., Pappin, D., Pelletier, J., and Lowe, S.W. 2012. A tumour suppressor network relying on the polyamine-hypusine axis. Nature 487: 244–248.

Tasdemir, N., and Lowe, S.W. 2013. Senescent cells spread the word: non-cell autonomous propagation of cellular senescence. EMBO J. 32: 1975-1976. Review.

Vagin, V.V., Yu, Y., Jankowska, A., Luo, Y., Wasik, K.A., Malone, C.D., Harrison, E., Rosebrock, A., Wakimoto, B.T., Fagegaltier, D., Muerdter, F., and Hannon, G.J. 2013. Minotaur is critical for primary piRNA biogenesis. RNA 19: 1064-1077.

Wang, Z., Chatterjee, D., Jeon, H.Y., Akerman, M., Vander Heiden, M.G., Cantley, L.C. and Krainer, A.R. 2011. Exon-centric regulation of pyruvate kinase M alternative splicing via mutually exclusive exons. J. Mol. Cell Biol. 4: 79–87.

Wang, Z., Jeon, H.Y., Rigo, F., Bennett, C.F. and Krainer, A.R. 2012. Manipulation of PK-M mutually exclusive alternative Splicing by antisense oligonucleotides. Open Biol. 2: 120133.

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* - Authors contributed equally to the work.

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