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Publications

2000 |2001 | 2002 | 2003 | 2004 | 2005 | 2006 | 2007 |2008 |2009 | 2010 | 2011 |2012 | 20132014 |

Fukunaga, R., Colpan, C., Han, B.W., Zamore, P.D. (2014). Inorganic phosphate blocks binding of pre-miRNA to Dicer-2 via its PAZ domain. EMBO Journal, 33, 371-384.

Li, X.Z., Roy, C.K., Moore, M.J., Zamore, P.D. (2013). Defining piRNA Primary Transcripts. Cell Cycle, 12, 1657-1658.

Ge, D.T., Zamore, P.D. (2013). Small RNA-Directed Silencing: The Fly Finds Its Inner Fission Yeast? Current Biology, 23, R318-R320.

Li, X.Z., Roy, C.K., Dong, X., Bolcun-Filas, E., Wang, J., Han, B.W., Xu, J., Moore, M.J., Schimenti, J.C., Weng, Z., Zamore, P.D. (2013). An Ancient Transcription Factor Initiates the Burst of piRNA Production During Early Meiosis in Mouse Testes. Molecular Cell, 50, 67-81. (NIHMSID:NIHMS469552).

  • Supplemental Materials can be found here.

Flores-Jasso, C.F., Salomon, W,E., Zamore, P.D. (2013). Rapid and specific purification of Argonaute-small RNA complexes from crude cell lysates. RNA, 19, 271-279. (PMCID:PMC3543083).

  • Supplemental Materials can be found here.

Zhang, Z., Theurkauf, W.E., Weng, Z., Zamore, P.D. (2012). Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection. Silence 3, 9. (PMCID:PMC3552703).

Zhang F., Wang J., Xu J., Zhang Z., Koppetsch B.S., Schultz N., Vreven T., Meignin C., Davis I., Zamore P.D., Weng Z., Theurkauf W.E. (2012). UAP56 Couples piRNA Clusters to the Perinuclear Transposon Silencing Machinery. Cell 151, 871-884. (PMCID:PMC3499805).

  • Supplemental Material can be found here.

Wee, L.M., Flores-Jasso, C.F., Salomon, W,E., Zamore, P.D. (2012). Argonaute Divides Its RNA Guide Into Domains with Distinct Functions and RNA-Binding Properties. Cell 151, 1055-1067. (PMCID:PMC3595543).

  • Supplemental Material can be found here.

Fukunaga, R., Han, B.W., Hung, J.H., Xu, J., Weng, Z., Zamore, P.D. (2012). Dicer Partner Proteins Tune the Length of Mature miRNAs in Flies and Mammals. Cell 151, 533-546. (PMCID:PMC3609031).

  • Supplemental Material can be found here.

Xie, J., Ameres, S.L., Friedline, R., Hung, J.-H., Zhang, Y., Xie, Q., Zhong, L., Zhang, H., Su, Q., He, R., Li, M., Mu, X., Broderick, J.A., Li, C., Kim, J., Weng, Z., Flotte, T.R., Zamore, P.D., Gao, G. (2012). Long-term, efficient inhibition of miRNA function in mice using Tough Decoys delivered by Adeno-associated virus vectors. Nature Methods, 9, 403-409. (PMCID:PMC3420816).

Mueller C., Tang Q., Gruntman A., Blomenkamp K., Teckman J., Song L., Zamore P.D., Flotte T.R. (2012). Sustained miRNA-mediated Knockdown of Mutant AAT with Simultaneous Augmentation of Wild-type AAT has Minimal Effect on Global War Liver miRNA Profiles. Molecular Therapy, Jan 17, 1-11. (PMCID:PMC3293602).

Khurana, J.S., Wang, J., Xu, J., Koppetsch, B., Thomson, T., Nowosielska, A., Li, C., Zamore, P.D., Weng, Z., and Theurkauf, W.E. (2011). Adaptation to transposon invasion in Drosophila melanogaster. Cell 137, 1551-1563. (PMCID:PMC3246748).

Zhang, Z., Xu, J., Koppetsch, B.S., Wang, J., Tipping, C., Ma, S., Weng, Z., Theurkauf, W.E., Zamore, P.D. (2011). Heterotypic piRNA Ping-Pong Requires Qin, a Protein with Both E3-ligase and Tudor Domains. Molecular Cell 44, 572-584. (PMCID:PMC3236501).

Han, B.W., Hung, J.H., Weng, Z., Zamore. P.D., Ameres, S.L. (2011). The 3'-to-5' Exoribonuclease Nibbler Shapes the 3' Ends of MicroRNAs Bound to Drosophila Argonaute1. Current Biology, 21, 1-10. (PMCID:PMC3236499).

Seitz, H., Tushir, J.S., Zamore, P.D. (2011). A 5′ uridine amplifies miRNA/miRNA* asymmetry in Drosophila by promoting RISC formation. Silence 2, 1-10. (PMCID:PMC3127740).

Broderick, J.A., Salomon, W.E., Ryder, S.P., Aronin, N., and Zamore, P.D. (2011). Argonaute protein identity and pairing geometry determine cooperativity in mammalian RNA silencing. RNA 17, 1858-1869. (PMCID:PMC3185918).

  • Supplemental Material can be downloaded here.

Cenik, E.S., Fukunaga, R., Lu, G., Dutcher, R., Wang, Y., Tanaka Hall, T.M., and Zamore, P.D. (2011). Phosphate and R2D2 Restrict the Substrate Specificity of Dicer-2, an ATP-Driven Ribonuclease. Molecular Cell 42, 172-184. (PMCID:PMC3115569).

Berezikov E., Robine N., Samsonova A., Westholm J.O., Naqvi A., Hung J.H., Okamura K., Dai Q., Bortolamiol-Becet D., Martin R., Zhao Y., Zamore P.D., Hannon G.J., Marra M.A., Weng Z., Perrimon N., and Lai E.C. (2011). Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence.Genome Research 21, 203-15. (PMCID:PMC3032924).

  •  Supplemental material for this article can be found here.

Xie, J., Xie, Q., Zhang, H., Ameres, S.L., Hung, J.-H., Su, Q., He, R., Mu, X., Ahmed, S., Park, S., Kato, H., Li, C., Mueller, C., Mello, C.C., Weng, Z., Flotte, T.R., Zamore. P.D., and Gao, G. (2011). MicroRNA-regulated, systemically delivered rAAV9: a step closer to CNS-restricted transgene expression. Molecular Therapy 19(3): 526-535.  (PMCID:PMC3048189).

Ameres S.L., Hung J.H., Xu J., Weng Z., and Zamore P.D. (2011). Target RNA-directed tailing and trimming purifies the sorting of endo-siRNAs between the two Drosophila Argonaute proteins. RNA 17, 54-63. (PMCID:PMC3004066).

  •  Supplemental material for this article can be found here.

Zamore, P.D., and Ma, S. (2011). Isolation of Drosophila melanogaster Testes. JoVE e2641.

Cenik, E.S., and Zamore, P.D. (2011). Quick guide: Argonaute proteins. Current Biology 21(12), R446-449.

Broderick, J.A., and Zamore, P.D. (2011).microRNA Therapeutics. Gene Therapy, April 28, 1-7.

Carone B.R., Fauquier L., Habib N., Shea J.M., Hart C.E., Li R., Bock C., Li C., Gu H., Zamore P.D., Meissner A., Weng Z., Hofmann H.A., Friedman N., and Rando O.J. (2010). Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell 143, 1084-96. (PMCID: PMC3039484).

Ameres, S.L., Horwich, M.D., Hung, J., Xu, J., Ghildiyal, M., Weng, Z., and Zamore, P.D. (2010). Target RNA-directed trimming and tailing of small silencing RNAs. Science 328, 1534-1539.(PMCID: PMC2902985).

  •  Supplemental material for this article can be found here.

Ghildiyal, M., Xu, J., Seitz, H., Weng, Z., and Zamore, P.D. (2010). Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway. RNA 16, 43-56.(PMCID: PMC2802036).

  •  Supplemental material for this article can be found here.

Zamore, P.D. (2010). Somatic piRNA biogenesis. EMBO J 29, 3219-3221. (PMCID: PMC2957218).

Baulcombe, D.C., Zamore, P.D. (2010). Welcome to Science. Silence 1(1). (PMCID:PMC2835995).

Kadener, S., Menet, J.S., Sugino, K., Horwich, M.D., Weissbein, U., Nawathean, P., Vagin, V.V., Zamore, P.D., Nelson, S.B., and Rosbash, M. (2009). A role for microRNAs in the Drosophila circadian clock. Genes & Development 23, 2179-2191. (PMCID: PMC2751990).

Klattenhoff, C., X, H., Li, C., Lee, S., Xu, J., Khurana, J., Schultz, N., Koppetsch, B.S., Nowosielska, A., Seitz, H., Zamore, P.D., Weng, Z., and Theurkauf, W.E. (2009). The Drosophila HP1 homologue Rhino is required for transposon silencing and piRNA production by dual strand clusters. Cell 138, 1137-1149. (PMCID:PMC2770713).

Li, C., Vagin, V.V., Lee, S., Xu, J., Ma, S., Xi, H., Seitz, H., Horwich, M.D., Syrzycka, M., Honda, B.M., Kittler, E.L.W., Zapp, M.L., Klattenhoff, C., Schulz, N., Theurkauf, W.E., Weng, Z., and Zamore, P.D. (2009). Collapse of germ-line piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 132, 509-521. (PMCID: PMC2768572).

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Pfister, E.L., Kennington, L., Straubhaar, J., Wagh, S., Liu, W., DiFiglia, M., Landwehrmeyer, B., Vonsattel, J.-P., Zamore, P.D., and Aronin, N. (2009). Five siRNAs targeting three SNPs in Huntingtin may provide therapy for three-quarters of Huntington’s disease patients. Current Biology 19, 774-778. (PMCID: PMC2746439).

Pfister E.L., and Zamore P.D. (2009). Huntington’s disease: Silencing a brutal killer. Experimental Neurology 220, 226-229. (PMCID:PMC2805437).

Tushir, J.S., Zamore, P.D., and Zhang, Z. (2009). SnapShot: Mouse piRNAs, PIWI Proteins and the Ping-Pong Cycle. Cell 139, 830.e1.

Tushir, J.S., Zamore, P.D., and Zhang, Z. (2009). SnapShot: Fly piRNAs, PIWI Proteins, and the Ping-Pong Cycle. Cell 139, 634.e1.

Izaurralde E., Zamore P.D., Editors (2009). Nucleus and Gene Expression. Current Opinion in Cell Biology 21, 331-334.

Barringhaus, K.G., and Zamore, P.D. (2009). Basic Science for Clinicians: MicroRNAs: Regulating a Change of Heart. Circulation 119, 2217-2224. (PMCID: PMC2724766).

Zamore, P.D. (2009). Collaborative Excellence. Worcester Medicine 73, 14–15.

Ghildiyal, M., and Zamore, P. D. (2009). Small silencing RNAs: an expanding universe. Nat Rev Genet 10, 94-108. (PMCID: PMC2724769).

Liu, W., Kennington, W.A., Rosas, H. D., Hersch, S., Cha, J.-H., Zamore, P.D., and Aronin, N. (2008). Linking SNP identity to CAG repeat length in Huntington’s Disease patients. Nature Methods 5, 951-953. (PMCID: PMC2587014).

Horwich, M.D., and Zamore, P.D. (2008). Design and Delivery of Antisense Oligonucleotides to Block microRNA Function in Cultured Drosophila and Human Cells. Nature Protocols 3, 1537-1549. (PMCID: PMC2559958).

Ghildiyal, M., Seitz, H., Horwich, M.D., Li, C., Du, T., Lee, S, Xu, J., Kittler, E.L.W., Zapp, M.L., Weng, Z., and Zamore, P.D. (2008). Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells. Science 320, 1077-1081. (PMCID: PMC2953241).

Seitz, H., Ghildiyal, M., and Zamore, P.D. (2008). Argonaute loading contributes to the precision of the 5´ ends of both microRNAs and their miRNA* strands in flies. Current Biology 18, 147-151. (PMCID: PMC2854039).

DiFiglia, M., Sena-Esteves, M., Chase, K., Sapp, E., Pfister, E., Sass, M., Yoder, J., Reeves, P., Pandey, R.K., Rajeev, K.G., Manoharan, M., Sah, D.W.Y., Zamore, P.D., and Aronin, N. (2007). Therapeutic silencing of mutant huntingtin with siRNA attenuates striatal and cortical neuropathology and behavioral deficits. PNAS 104, 17204-17209. (PMCID: PMC2040405).

Tomari, Y., Du, T., and Zamore, P.D. (2007). Sorting of Drosophila small silencing RNAs. Cell 130, 299-308. (PMCID: PMC2841505).

Förstemann, K., Horwich, M.D., Wee, L.-M., Tomari, Y., and Zamore, P.D. (2007). Drosophila microRNAs are sorted into functionally distinct Argonaute protein complexes after their production by Dicer-1. Cell 130, 287-297. (PMCID: PMC2686109).

Horwich, M.D., Li, C., Matranga, C., Vagin, V., Farley, G., Wang, P., and Zamore, P.D. (2007). The Drosophila RNA Methyltransferase, DmHen1, Modifies Germline piRNAs and Single-Stranded siRNAs in RISC. Current Biology 17, 1265-72.

Matranga, C., and Zamore P.D. (2007). Primer: Small Silencing RNAs. Current Biology 17, R789-93.

Du, T., and Zamore, P.D. (2007). Beginning to understand microRNA function. Cell Research 8, 661-663.

Zamore, P.D. (2007). RNA Silencing: Genomic defence with a slice of pi. Nature 446, 864-865.

Sigova, A., Vagin, V., and Zamore, P.D. (2006). Measuring the rates of transcriptional elongation in the female Drosophila melanogaster germ line by nuclear run-on,’ in Regulatory RNAs. 71st Cold Spring Harbor Symposia on Quantitative Biology 71, 335-41.

Schwarz, D.S., Ding, H., Kennington, L., Moore, J.T., Schelter, J., Burchard, J., Linsley, P.S., Aronin, N., Xu, Z., and Zamore, P.D. (2006). Designing siRNA that distinguish between genes that differ by a single nucleotide. PLoS Genetics 2, e140. (PMCID: PMC1560399).

Vagin, V.V., Sigova, A., Li, C., Seitz, H., Gvozdev, V., and Zamore, P.D. (2006). A distinct small RNA pathway silences selfish genetic elements in the germ line. Science 313, 320-324.

Zamore, P.D. (2006). RNA interference: big applause for silencing in Stockholm. Cell 127,1083-6.

Seitz H, and Zamore, PD. (2006). Rethinking the microprocessor. Cell 2, 827-829.

Matranga, C., Tomari, Y., Shin, C. Bartel, D.P., Zamore, P.D. (2005). Passenger-Strand Cleavage Facilitates Assembly of siRNA into Ago2-Containing RNAi Enzyme Complexes. Cell 123, 607-20.

Förstemann, K., Tomari, Y., Du, T., Vagin, V.V., Denli, A.M., Bratu, D.P., Klattenhoff, C., Theurkauf, W.E., and Zamore, P.D. (2005). Normal microRNA maturation by Dicer-1 and germ-line stem cell maintenance requires the double-stranded RNA-binding domain protein, Loquacious. PLoS Biology 3, e236. (PMCID: PMC1141267).

Matranga , C., and Zamore, P.D. (2005). Plant RNAi interference in vitro,’ in Epigenetics. 69th Cold Spring Harbor Symposium on Quantitative Biology 69, 403-8.

Du, T., and Zamore, P.D. (2005). microPrimer: The biogenesis and function of microRNA. Development 132, 4645-5.

Zamore, P.D., and Haley, B. (2005). Ribognome: The Big World of Small RNAs. Science 309, 1519-1524.

Tomari, Y., and Zamore, P.D. (2005). Perspective: machines for RNAi. Genes & Development 19: 517-529.

Tomari, Y., and Zamore, P.D. (2005). microRNA Biogenesis: Drosha can’t cut it without a partner. Current Biology 15, R61-R64.

Tomari, Y., Matranga, C., Haley, B., Martinez, N., and Zamore, P.D. (2004). A protein sensor for siRNA asymmetry. Science 306,1377-80.

Sigova, A., Rhind, N., and Zamore, P.D. (2004). A single Argonaute protein mediates both transcriptional and post-transcriptional silencing in Schizosaccharomyces pombe. Genes & Development 8, 2359-67. (PMCID: PMC522986).

Haley, B., and Zamore, P.D. (2004). Kinetic analysis of the RNAi enzyme complex. Nature Structural & Molecular Biology 11, 599-606.

Tomari, Y., Du, T., Haley, B. Schwarz, D.S., Bennett, R. Cook, H.A., Koppetsch, B.S., Theurkauf, W.E., and Zamore, P.D. (2004). RISC assembly defects in the Drosophila RNAi mutant armitage. Cell 116, 831-841.

Schwarz, D.S., Tomari, Y., and Zamore, P. D. (2004). The RNA-induced silencing complex is a Mg2+-dependent endonuclease. Current Biology 14, 787-791.

Hutvágner, G., Simard, M.J., Mello, C.C., and Zamore, P.D. (2004). Sequence-specific inhibition of small RNA function. PLoS Biology 2, 465-475. (PMCID: PMC350664).

Zamore, P.D. (2004). Plant RNAi: How the silencing suppressor p19 inactivates siRNA. Current Biology 14, R198-R200.

Schwarz, D.S., Hutvágner, G., Du, T., Xu, Z., Aronin, N., and Zamore, P.D. (2003). Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199-208.

Ding, H., Schwarz, D.S., Keene, A., Affar, E., Fenton, L., Shi, Y., Zamore, P.D., and Xu, Z. (2003). Selective silencing by RNAi of a dominant, disease-causing ALS allele. Aging Cell 2, 209-217.

Tang, G., Reinhardt, B.J., Bartel, D.P., and Zamore, P.D. (2003). A Biochemical Framework for RNA Silencing in Plants. Genes & Development 17, 49-63. (PMCID: PMC195971).

Hannon, G.J. and Zamore, P.D. (2003). Small RNAs, Big Biology: Biochemical Studies of RNA Interference. In RNAi: A Guide To Gene Silencing, G. J. Hannon, ed. (Cold Spring Harbor, NY, Cold Spring Harbor Laboratory Press), pp. 87-108.

Tang, G., and Zamore, P.D.(2003). Biochemical dissection of RNA silencing in plants. Methods in Molecular Biology (Humana) 257, 223-44.

Haley, B., Tang, Guiliang, and Zamore, P.D. (2003). In vitro analysis of RNA interference in Drosophila melanogaster. Methods 30, 330-336.

Zamore, P.D. and Aronin, N. (2003). siRNA knocks down hepatitis.Nature Medicine 9, 266-267.

Zamore, P.D. (2002).Viewpoint: Ancient pathways programmed by small RNAs. Science 296, 1265-1269.

Schwarz, D., Hutvágner, G., Haley, B., and Zamore, P.D. (2002). Evidence that siRNAs function as guides, not primers, in the Drosophila and human RNAi pathways. Molecular Cell 10, 537-548.

Hutvágner, G., and Zamore, P.D. (2002). A microRNA in a multiple-turnover RNAi enzyme complex. Science 297, 2056-2060.

Wang, X., McLachlan, J., Zamore, P.D., and Hall, T.M.T. (2002). Modular recognition of RNA by a human Pumilio-homology domain. Cell 110, 501-512.

Schwarz, D. and Zamore, P.D. (2002). Review: Why do miRNAs live in the miRNP? Genes and Development 16, 1025-31.

Hutvágner, G. and Zamore, P.D. (2002). RNAi: Nature abhors a double-strand. Current Opinion in Genetics and Development 12, 225-232.

Nykänen, A., Haley, B., and Zamore, P.D. (2001).ATP requirements and siRNA structure in the RNA interference pathway. Cell 107, 309-321.

Hutvágner, G., McLachlan, J., Pasquinelli, A. E., Bálint, É., Tuschl, T., and Zamore, P. D. (2001). A cellular function for the RNA-interference enzyme Dicer in the maturation of the let-7 small temporal RNA. Science 293, 834-838.

Wang, X., Zamore, P.D., and Hall, T.M.T. (2001). Crystal structure of a Pumilio-homology domain. Molecular Cell 7, 855-865.

Zamore, P.D. (2001). Preview. Thirty-three years later, a glimpse at the ribonuclease III active site. Molecular Cell 8, 1158-1160. >

Zamore, P.D. (2001). RNA interference: listening to the sound of silence. Nature Structural Biology 8, 746-750.

Zamore, P.D., Tuschl, T., Sharp, P.A., and Bartel, D.P. (2000).RNAi: double-stranded RNA directs the ATP-dependent cleavage of mRNA at 21 to 23 nucleotide intervals. Cell 101, 25-33.

Sharp, P.A. and Zamore, P.D. (2000). Perspective: Molecular Biology. RNA interference. Science 287, 2431-2433.