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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 AGO2. Molecular Cell, 75:741-755. (PMCID:PMC6823844).

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 Mitochondria. Molecular Cell, 74:982-995. (PMCID: PMC6636356).

Jouravleva, K., Zamore, P.D. (2019). MicroRNAs Tame CRISPR-Cas9. Nature Cell Biology, 21:416-417.

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)

Özata, D.M., Gainetdinov, I., Zoch, A., O'Carroll, D., Zamore P.D. (2019). PIWI-interacting RNAs: small RNAs with big functions. Nature 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 melanogaster. Molecular Cell, 73:291-303. (NIHMSID: NIHMS1511579).

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 Animals. Molecular 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 Mice. Nature Biotechnology 36:839-842. (PMCID: PMC6126964).

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 identifiers. BMC 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 vivo. Nucleic Acid Research 46:2185-2196. (PMCID: PMC5861422).

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 biology. eLife 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 rAAVs. Molecular 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 elements. Nature Ecology & Evolution 2:174-181. (*equal contributors) (PMCID: PMC5732027). 

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 pseudouridine. Scientific Reports 7:969-982. (PMCID: PMC5430550).

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-conversion. Genes, Genomes, Genetics 6:3197-3206. (PMC: PMCID5068941)

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 metabolism. Nature Immunology 17:677-686. (PMCID: PMC4873392).

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).

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).

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).

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).

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).

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).

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).

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).

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).

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).

Broderick, J., and Zamore P.D. (2014). Preview. Competitive endogenous RNAs cannot alter microRNA Function in vivo. Molecular 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 biogenesis. Cell 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).

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).

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).

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).

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).

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).

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).

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).

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

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).

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).

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).

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 21:1878-1887. (PMCID: PMC3236499).

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 silencing. RNA 17:1858-1869. (PMCID: PMC3185918).

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).

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).

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).

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).

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).

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).

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).

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).

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

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).

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).

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).

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).

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).