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Gainetdinov I, Vega-Badillo J, Cecchini K, Bagci A, Colpan C, De D, Bailey S, Arif A, Wu PH, MacRae IJ, Zamore PD. (2023). Relaxed targeting rules help PIWI proteins silence transposons. Nature, 7969:394-402. (PMCID: PMC10338343).

Cecchini, K., Biasini, A., Yu, T., Säflund, M., Mou, H., Arif, A., Eghbali, A., Colpan, C., Gainetdinov, I., de Rooij, D.G., Weng, Z., Zamore, P.D., Özata, D.M. (2023). The transcription factor TCFL5 responds to A-MYB to elaborate the male meiotic program in mice. Reproduction 165:183-196 (PMCID: PMC9812935).

Yu, T., Biasini, A., Cecchini, K., Saflund, M., Mou, H., Arif, A., Eghbali, A., de Rooij, D., Weng, Z., Zamore, P.D., Ozata, D.M. (2023). A-MYB/TCFL5 regulatory architecture ensures the production of pachytene piRNAs in placental mammalsRNA 29:30–43 (PMCID: PMC9808571).

Jouravleva, K., Golovenko, D., Demo, G., Dutcher, R.C., Tanaka Hall, T.M., Zamore, P.D., Korostelev, A.A. (2022). Structural basis of microRNA biogenesis by Dicer-1 and its partner protein Loqs-PB. Molecular Cell, 82:4049-4063 (PMCID: PMC9637774)


Arif, A., Bailey, S., Izumi, N., Anzelon, T.A., Ozata, D.M., Andersson, C., Gainetdinov, I., MacRae, I.J., Tomari, Y., Zamore, P.D. (2022). GTSF1 accelerates target RNA cleavage by PIWI-clade Argonaute proteins. Nature, 608:618-625 (PMCID: PMC9385479).


Chen, Z., Devi, G., Arif, A., Zamore, P., Sontheimer, E., Watts, J. (2022). Tetrazine-Ligated CRISPR sgRNAs for Efficient Genome Editing. ACS Chemical Biology, 17:1045-1050 (PMCID: PMC9127786).

Ober-Reynolds, B., Becker, W.R., Jouravleva, K., Jolly, S.M., Zamore, P.D., Greenleaf, W.J. (2022). High-throughput biochemical profiling reveals functional adaptation of a bacterial Argonaute. Molecular Cell, 82:1-14 (PMCID: PMC9158488).


Jouravleva, K, Vega-Badillo, J., Zamore, P.D. (2022). Principles and pitfalls of high-throughput analysis of microRNA-binding thermodynamics and kinetics by RNA Bind-n-Seq. Cell Reports Methods, 2:100185 (PMCID: PMC9017153).

Wu, P.-H., Zamore, P.D. (2021). Defining the functions of PIWI-interacting RNAsNature Reviews Molecular Cell Biology 1-2.

Wu, P.-H., Zamore, P.D. (2021). To Degrade a microRNA, Destroy its Argonaute ProteinMolecular Cell 81:223-225.

Yu, T., Fan, K., Özata, D.M., Zhang, G., Theurkauf, W.E., Zamore, P.D., Weng, Z. (2021). Long First Exons and Epigenetic Marks Distinguish Conserved Pachytene piRNA Clusters from Other Mammalian Genes. Nature Communications 12:73.


Gainetdinov, I., Colpan, C., Cecchini, K., Albosta, P., Jouravleva, K., Vega-Badillo, J., Lee, Y., Özata, D.M., Zamore, P.D. (2021) Terminal Modification, Sequence, and Length Determines piRNA Stability in Animals. Mol Cell 81:4826-4842.

Jolly, S.M., Gainetdinov, I., Jouravleva, K., Zhang, H., Strittmatter, L., Bailey, S.M., Hendricks, G.M., Dhabaria, A., Ueberheide, B., Zamore, P.D. Thermus thermophilus Argonaute Functions in the Completion of DNA Replication. (2020). Cell 182:1545-1559. (PMCID: PMC7502556). 

Wu, P.-H., Fu, Y., Cecchini, K., Özata, D.M., Arif, A., Yu, T., Colpan, C., Gainetdinov, I., Weng, Z., *Zamore, P.D. (2020). The Evolutionarily Conserved piRNA-Producing Locus pi6 is Required for Male Mouse FertilityNature Genetics 52:738-739. (PMCID: PMC7383350)

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Xie, J., Tai, PWL., Brown, A., Gong, S., Zhu, S., Wang, Y., Li, C., Colpan, C., Su, Q., He., R., Ma, H., Li, J., Ye, H., Ko, J., Zamore, P.D., Gao, G. (2020). Effective and Accurate Gene Silencing by a Recombinant AAV-Compatible MicroRNA ScaffoldMolecular Therapy 28:422-430. (PMCID: PMC7001000).

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Özata, D.M., Yu, T., Mou, H., Gainetdinov, I., Colpan, C., Cecchini, K., Kaymaz, Y., Wu, P.-X., Fan, K., Kucukural, A., Weng, Z., Zamore, P.D. (2019). Evolutionarily Conserved Pachytene piRNA Loci are Highly Divergent among Modern HumansNature Ecology & Evolution4:156-168. (PMCID: PMC6961462).

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Becker W.R., Ober-Reynolds, B., Jouravleva, K., Jolly, S.M., Zamore, P.D., Greenleaf, W.J. (2019). High-Throughput Analysis Reveals Rules for Target RNA Binding and Cleavage by AGO2Molecular Cell75:741-755. (PMCID:PMC6823844).

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Ge, D.T., Wang, W., Tipping, C., Gainetdinov, I., Weng, Z., Zamore, P.D. (2019). The RNA-binding ATPase, Armitage, Couples piRNA Amplification in Nuage to Phased piRNA Production on MitochondriaMolecular Cell74:982-995. (PMCID: PMC6636356).

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Jouravleva, K., Zamore, P.D. (2019). MicroRNAs Tame CRISPR-Cas9Nature Cell Biology21:416-417.

Smith, C.S., Jouravleva, K., Huisman, M., Jolly, S.M., Zamore, P.D., Grunwald, D. (2019). An Automated Bayesian Pipeline for Rapid Analysis of Single-Molecule Binding DataNature Communications10:1-9 (PMCID: PMC6336789)

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Özata, D.M., Gainetdinov, I., Zoch, A., O'Carroll, D., Zamore P.D. (2019). PIWI-interacting RNAs: small RNAs with big functionsNature Reviews Genetics 20:89-108

Chang, T.H., Mattei, E., Gainetdinov, I., Weng, Z., Zamore, P.D. (2019). Maelstrom Represses Canonical Polymerase II Transcription within Bi-directional piRNA Clusters in Drosophila melanogasterMolecular Cell73:291-303. (PMCID: PMC6551610).

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Gainetdinov, I., Colpan, C., Arif, A., Cecchini, K., Zamore, P.D. (2018). A Single Mechanism of Biogenesis, Initiated and Directed by PIWI Proteins, Explains piRNA Production in Most AnimalsMolecular Cell 71:775-790. (PMCID: PMC6130920).


Wang, D., Li, J., Song, CQ., Tran, K., Mou, H., Wu, P.H., Pai, P.W.L., Mendonca, C.A., Ren, L., Wang, B.Y., Su, Q., Gessler, D.J., Zamore, P.D., Xue, W., Gao, G. (2018). Cas9-Mediated Allelic Exchange Repairs Compound Heterozygous Recessive Mutations in MiceNature Biotechnology 36:839-842. (PMCID: PMC6126964).

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Fu, Y., Wu, P.H., Beane, T., Zamore, P.D., Weng, Z. (2018). Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiersBMC Genomics 19:531 (PMCID: PMC6044086).

Hassler, M.R., Turanov, A.A., Alterman, J.F., Haraszti, R.A., Coles, A.H., Osborn, M.F., Echeverria, D., Nikan, M., Salomon, W.E., Roux, L., Godinho, B.M.D.C., Davis, S.M., Morrissey, D.V., Zamore, P.D., Karumanchi, S.A., Moore, M.J., Aronin, N., Khvorova. (2018). Comparison of partially and fully chemically-modified siRNA in conjugate-mediated delivery in vivoNucleic Acid Research 46:2185-2196. (PMCID: PMC5861422).

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Fu, Y., Yang, Y., Zhang, H., Farley, G., Wang, J., Quarles, K.A., Weng, Z., Zamore, P.D. (2018). The genome of the Hi5 germ cell line from Trichoplusia ni, an agricultural pest and novel model for small RNA biologyeLife 7:1-41. (PMCID: PMC5844692).

Lu, Y., Tai, P.W.L., Ai, J., Gessler, D.J., Su, Q., Yao, X., Zheng, Q., Zamore, P.D., Xu, X., Gao, G. (2018). Transcriptome Profiling of Neovascularized Corneas Reveals miR-204 as a Multi-target Biotherapy Deliverable by rAAVsMolecular Therapy Nucleic Acids 10:349-360. (PMCID: PMC5862543).

Lewis, S.H., Quarles, K.A., Yang, Y., Tanguy, M., Frézal, L., Smith, S.A., Sharma, P.P., Cordaux, R., Gilbert, C., Giraud, I., Collins, D.H., *Zamore, P.D., *Miska, E.A., *Sarkies, P., *Jiggins, F.M. (2017). Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elementsNature Ecology & Evolution 2:174-181. (*equal contributors) (PMCID: PMC5732027). 

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Zamore, P.D., (2017). Rhino gives voice to silent chromatin. Nature 549:38-39.

Koh, C.S., Madireddy, R., Beane, T.J., Zamore, P.D., Korostelev, A.A. (2017). Small methyltransferase RlmH assembles a composite active site to methylate a ribosomal pseudouridineScientific Reports 7:969-982. (PMCID: PMC5430550).

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Ge, D.T., Tipping, C., Brodsky, M.H., Zamore, P.D. (2016). Rapid screening for CRISPR-directed editing of the Drosophila genome using white co-conversionGenes, Genomes, Genetics 6:3197-3206. (PMC: PMCID5068941)

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Ouimet, M., Koster, S., Sakowski, E., Ramkhelawon, B., van Solingen, C., Oldebeken, S., Karunakaran, D., Portal-Celhay, C., Sheedy, F.J., Ray, T.D., Cecchini, K., Zamore, P.D., Yaner, K.J., Marcel, Y.L., Philips J.A., and Moore, K.J. (2016). Mycobacterium tuberculosis induces the miR-33 locus to reprogram autophagy and host lipid metabolismNature Immunology 17:677-686. (PMCID: PMC4873392).

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Ouimet, M., Ediriweera, H.N., Gundra, U.M., Sheedy, F.J., Ramkhelawon, B., Hutchison, S.B., Rinehold, K., van Solingen, C., Fullerton, M.D., Cecchini, K., Rayner, K.J., Steinberg, G.R., Zamore, P.D., Fisher, E.A., Loke, P., and Moore, K.J. (2015). MicroRNA-33-dependent regulation of macrophage metabolism directs immune cell polarization in atherosclerosisJournal of Clinical Investigation 125:4334-4348. (PMCID: PMC4665799).

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Wang, W., Han, B.W., Tipping, C., Ge, D.T., Zhang, Z., Weng, Z., Zamore, P.D. (2015). Slicing and Binding by Ago3 or Aub Trigger Piwi-bound piRNA Production By Distinct MechanismsMolecular Cell 59:819-830. (PMCID: PMC4560842).

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Salomon, W.E., Jolly, S.M., Moore, M.J., Zamore, P.D., Serebrov, V. (2015). Single-Molecule imaging reveals that Argonaute reshapes the binding properties of its nucleic acid guidesCell 162:84-95. (PMCID: PMC4503223).

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Chou, M.T., Han, B.W., Hsiao, C.P., Zamore, P.D., Weng, Z., Hung, J.H. (2015). Tailor: a computational framework for detecting non-templated tailing of small silencing RNAs. Nucleic Acids Research 43:1-9. (PMCID: PMC4632877).

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Han, B.W., Wang, W., Li, C., Weng, Z., Zamore, P.D. (2015). Noncoding RNA. piRNA-guided transposon cleavage initiates Zucchini-dependent, phased piRNA production. Science 348:817-821. (PMCID: PMC4545291).

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Roy, C.K., Olson, S., Graveley, B.R., Zamore, P.D., Moore, M.J. (2015). Assessing long-distance RNA sequence connectivity via RNA-templated DNA-DNA ligation. eLife 13:1-21. (PMCID: PMC4442144).

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Marinov, G.K., Wang, J., Handler, D., Wold, B.J., Weng, Z., Hannon, G.J., Aravin, A.A., Zamore, P.D., Brennecke, J., Toth, K,F. (2015). Pitfalls of Mapping High-throughput Sequencing Data to Repetitive Sequences: Piwi’s Genomic Targets Still Not Identified. Developmental Cell 32:765-771. (PMCID: PMC4494788).

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Han, B.W., Wang, W., Zamore, P.D., Weng, Z. (2015). piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing. Bioinformatics 31:593-595. (PMCID: PMC4325541).

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Babcock, G.J., Iyer, S., Smith, H.L., Wang, Y., Rowley, K., Ambrosino, D.M., Zamore, P.D., Pierce, B.G., Molrine, D.C., Weng, Z. (2014). High-throughput sequencing analysis of post-liver transplantation HCV E2 glycoprotein evolution in the presence and absence of neutralizing monoclonal antibody. PLoS ONE 23:e100325. (PMCID: PMC4067308).

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Wang, W., Yoshikawa, M., Han, B.W., Izumi, N., Tomari, Y., Weng, Z., Zamore, P.D. (2014). The initial uridine of primary piRNAs does not create the tenth adenine that is the hallmark of secondary piRNAs. Molecular Cell 56:708-716. (PMCID: PMC4337030).

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Han, B.W., and Zamore P.D. (2014). Primer. piRNAs. Current Biology 24:R730-R733.

Zhang, Z., Wang, J., Schultz, N., Zhang, F., Parhad, S.S., Tu, S., Vreven, T., Zamore, P.D., Weng, Z., Theurkauf, W.E. (2014). The HP1 homolog Rhino anchors a nuclear complex that suppresses piRNA precursor splicing. Cell 157:1353-1363. (PMCID: PMC4167631).

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Broderick, J., and Zamore P.D. (2014). Preview. Competitive endogenous RNAs cannot alter microRNA Function in vivoMolecular Cell 54:711-713.

Fukunaga, R., and Zamore, P.D. (2014). A universal small molecule, Inorganic phosphate, restricts the substrate specificity of Dicer-2 in small RNA biogenesisCell Cycle 13:1671-1676. (PMCID: PMC4111713).

Zhang, Z., Koppetsch, B.S., Wang, J., Tipping, C., Weng, Z., Theurkauf, W.E., Zamore, P.D. (2014). Antisense piRNA amplification, but not piRNA production or nuage assembly, requires the Tudor-domain protein Qin. EMBO Journal 33:536-539. (PMCID: PMC3989648).

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Moran, Y., Fredman, D., Praher, D., Li, X.Z., Wee, L.M., Rentzsch, F., Zamore, P.D., Technau, U., Seitz, H. (2014). Cnidarian microRNAs frequently regulate targets by cleavage. Genome Research 24:651-663. (PMCID:PMC3975064).

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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. (PMCID: PMC3989643).

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Chung, R.T., Gordon, F.D., Curry, M.P., Schiano, T.D., Emre, S., Corey, K., Markmann, J., Hertl, M., Pomposelli, J.J., Pomfret, E.A., Florman, S., Schilsky, M., Broering, T.J., Finberg, R.W., Szabo, G., Zamore, P.D., Khettry, U., Babcock, G.J., Ambrosino, D.M., Leav, B., Leney, M., Smith, H.L., Molrine, D.C. (2013). Human Monoclonal Antibody MBL-HCV1 Delays HCV Viral Rebound Following Liver Transplantation: A Randomized Controlled Study. American Journal of Transplantation 13:1047-1054. (PMCID: PMC3618536).


Ameres, S.L., and Zamore, P.D. (2013). Diversifying microRNA sequence and function. Nature Reviews Molecular & Cellular Biology 14:475-488.

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., and 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. (PMCID: PMC3671569).

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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).

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Liu, W., Chaurette, J., Pfister, E.L., Kennington, L.A., Chase, K.O., Bullock, J., Vonsattel, J.P., Faull, R.L., MacDonald, D., DiFiglia, M., Zamore, P.D., Aronin, N. (2013). Increased Steady-State Mutant Huntingtin mRNA in Huntington’s Disease Brain. Journal of Huntington’s Disease 2:491-500.


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 3:1-9 (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).

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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).

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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).

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Zamore, P.D. (2012). RNA: methods and protocols - a new seriesSilence 3:1. (PMCID: PMC3420260).

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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 rAAV vectors. Nature Methods 9:403-409. (PMCID: PMC3420816).

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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 Liver miRNA Profiles. Molecular Therapy 20:590-600. (PMCID: PMC3293602).

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Fukunaga, R., and Zamore, P.D. (2012). “Loquacious, a Dicer Partner Protein, Functions in Both the MicroRNA and siRNA Pathways” in Eukaryotic RNases and Their Partners in RNA Degradation and Biogenesis, Part B. Guo, F., Chanfreau, G., and Tamanoi, F., eds. The Enzymes 32:37-68.

Li, C., and Zamore, P.D. (2012). “RNA Interference and Small RNA Analysis,” in Molecular Cloning: A Laboratory Manual (Fourth Edition), Green, M.R., and Sambrook, J., eds. (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY), pp. 1415-1480.


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

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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).

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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 21:1878-1887. (PMCID: PMC3236499).

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

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

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).

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Zamore, P.D., and Ma, S. (2011). Isolation of Drosophila melanogaster Testes. JoVE 51:e2641. (PMCID: PMC3197105).

Broderick, J.A., and Zamore, P.D. (2011). microRNA Therapeutics. Gene Therapy 18:1104-1110. (PMCID: PMC3237828).

Cenik, E.S., Fukunaga, R., Lu, G., Dutcher, R., Wang, Y., Tanaka Hall, T.M., 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).

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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., 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).

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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., Gao, G. (2011). MicroRNA-regulated, systemically delivered rAAV9: a step closer to CNS-restricted transgene expressionMolecular Therapy 19:526-535. (PMCID: PMC3048189).

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Ameres, S.L., Hung, J.H., Xu, J., Weng, Z., 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).

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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., Rando, O.J. (2010). Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell 143:1084-96. (PMCID: PMC3039484).

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

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

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

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

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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., Zamore, P.D. (2009). Collapse of germline piRNAs in the absence of Argonaute3 reveals somatic piRNAs in flies. Cell 132:509-521. (PMCID: PMC2768572).

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

Supplemental Material

Pfister, E.L., Kennington, L., Straubhaar, J., Wagh, S., Liu, W., DiFiglia, M., Landwehrmeyer, B., Vonsattel, J.-P., Zamore, P.D., 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).

Supplemental Material


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. Nature Reviews Genetics 10:94-108. (PMCID: PMC2724769).


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

Supplemental Material

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).

Supplemental Material

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

Supplemental Material

Seitz, H., Ghildiyal, M., 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).

Supplemental Material

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

Supplemental Material

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

Supplemental Material

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

Supplemental Material

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

Supplemental Material

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., Zamore, P.D. (2006). “Measuring the rates of transcriptional elongation in the female Drosophila melanogaster germline 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., 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., 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.

Supplemental Material

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

Supplemental Material


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

Du, T., and Zamore, P.D. (2005). microPrimer: The biogenesis and function of microRNADevelopment 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). microRNA Biogenesis: Drosha cant cut it without a partnerCurrent Biology 15:R61-R64.


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

Mallory, A.C., Reinhart, B.J., Jones-Rhoades, M.W., Tang, G., Zamore, P.D., *Barton, K.,* Bartel, D.P. (2004). MicroRNA control of PHABULOSA in leaf development: importance of pairing to the microRNA 5 regionEMBO Journal 16:3356-3364. (PMCID: PMC514513).


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


Sigova, A., Rhind, N., Zamore, P.D. (2004). A single Argonaute protein mediates both transcriptional and post-transcriptional silencing in Schizosaccharomyces pombeGenes & Development 8:2359-2367. (PMCID: PMC522986).

Supplemental Material

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

Supplementary Material


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

Supplemental Material

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

Supplemental Material

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

Supplemental Material

Zamore, P.D. (2004). Plant RNAi: How a viral silencing suppressor inactivates siRNACurrent Biology 14:R198-R200.


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

Supplemental Material

Ding, H., Schwarz, D.S., Keene, A., Affar, E., Fenton, L., Shi, Y., Zamore, P.D., Xu, Z. (2003). Selective silencing by RNAi of a dominant allele that causes amyotrophic lateral sclerosis. Aging Cell 2:209-217. 


Tang, G., Reinhardt, B.J., Bartel, D.P., Zamore, P.D. (2003). A Biochemical Framework for RNA Silencing in PlantsGenes & 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 plantsMethods in Molecular Biology (Humana) 257:223-44.


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


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


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


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


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

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


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


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


Feldbrügge, M., Arizti, P., Sullivan, M.L., Zamore, P.D., Belasco, J.G., *Green, P.J. (2002). Comparative analysis of the plant mRNA-destabilizing element, DST, in mammalian and tobacco cellsPlant Molecular Biology 49:215-223.


Nykänen, A., Haley, B., Zamore, P.D. (2001). ATP requirements and small interfering RNA structure in the RNA interference pathwayCell 107:309-321.


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

Supplemental Material

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


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


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


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


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



*Tuschl, T.†, *Zamore, P.D.†, Lehmann, R., *Bartel, D.P., Sharp, P.A. (1999). Targeted mRNA degradation by double-stranded RNA in vitroGenes & Development 13:3191-3197 (†equal contributors). (PMCID: PMC317199).


Zamore, P.D., Bartel, D.P., Lehmann, R., *Williamson, J.R. (1999). The PUMILIO-RNA interaction: A single RNA-binding domain monomer recognizes a bipartite target sequenceBiochemistry 38:596-604.


Zamore, P.D., Williamson, J.R., *Lehmann, R. (1997). The Pumilio protein binds RNA through a conserved domain that defines a new class of RNA-binding proteinsRNA 3:1421-1433. (PMCID: PMC1369583).


Curtis, D., Treiber, D.K., Tao, F., Zamore, P.D., Williamson, J.R., *Lehmann, R. (1997). A CCHC metal-binding domain in Nanos essential for translational regulationEMBO Journal 16:834-843. (PMCID: PMC1169684).


Zamore, P.D., and Lehmann, R. (1996). Drosophila development: homeodomains and translational controlCurrent Biology 7:773-775.


Curtis, D., Lehmann, R., Zamore, P.D. (1995). Translational regulation in developmentCell 81:171-178.


Lee, C-G., Zamore, P.D., Green, M.R., Hurwitz, J. (1993). RNA annealing activity is intrinsically associated with U2AF. Journal of Biological Chemistry 268:13472-13478.


Valcarçel, J., Singh, R., Zamore, P.D., Green, M.R. (1993). The protein Sex Lethal antagonizes the splicing factor USAF to regulate alternative splicing of transformer pre-mRNANature 362:171-175.


Zhang, M,† Zamore, P.D.†, Carmo-Fonseca, M., Lamond, A.I., Green, M.R. (1992). Cloning and intracellular localization of the U2 small nuclear ribonucleoprotein auxiliary factor small subunit. Proceedings of the National Academy of Sciences, USA 89:8769-8773 (†equal contributors). (PMCID: PMC50002).


Zamore, P.D., Patton, J.G., Green, M.R. (1992). Cloning and domain structure of the mammalian splicing factor U2AFNature 355:609-614.


Zamore, P.D. and Green, M.R. (1991). Biochemical characterization of U2 snRNP auxiliary factor: an essential pre-mRNA splicing factor with a novel intranuclear distributionEMBO Journal 10:207-214. (PMCID: PMC452631).


Carmo-Fonseca, M., Tollervey, D., Pepperkok, R., Barabino, S.M.L., Merdes, A., Brunner, C., Zamore, P.D., Green, M.R., Hurt, E.,

Lamond, A.I. (1991). Mammalian nuclei contain foci which are highly enriched in components of the pre-mRNA splicing machineryEMBO Journal 10:195-206. (PMCID: PMC452630).


Zamore, P.D., Zapp, M.L., Green, M.R. (1990). Gene expression. RNA binding: βs and basicsNature 348:485-486.



Zamore, P.D., and Green, M.R. (1989). Identification, purification, and biochemical characterization of U2 small nuclear ribonucleoprotein auxiliary factorProceedings of the National Academy of Sciences, USA 86:9243-9247. (PMCID: PMC298470).


Ruskin, B.R., Zamore, P.D., Green, M.R. (1988). A factor, U2AF, is required for U2 snRNP binding and splicing complex assemblyCell 52:207-219.


Blacklow, S.C., Raines, R.T., Lim, W.A., Zamore, P.D., *Knowles, J.R. (1988). Triosephosphate isomerase catalysis is diffusion controlledBiochemistry 27:1158-1167.


Ruskin, B.R., Bindereif, A., Nelson, K., Pikielny, C., Zamore, P.D., Green, M.R. (1987). Biochemical mechanisms of mammalian pre-mRNA splicingMolecular Biology Reports 12:201.

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