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 Humans. Nature Ecology & Evolution, 4:156-168. (PMCID: PMC6961462).

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NCBI SRA PRJNA506245  |  NCBI GEO GSE135791

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).

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Mendeley Data  |  NCBI SRA PRJNA512481

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).

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NCBI SRA PRJNA495886  |  MassIVE Data Set MSV000083634

Chang, T.H., Mattei, E., Gainetdinov, I., Weng, Z., Zamore, P.D. (2019). Maelstrom Represses Canonical Polymerase II Transcription within Bi-direcional piRNA Clusters in Drosophila. Molecular Cell, 71:291-303. (PMCID: PMC6551610).

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NCBI BioProject Archive PRJNA448445  

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 Data. Nature Communications, 10:1-9. (PMCID: PMC6336789).

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Pipleline Code & User Manual  |  Dataset of Raw and Processed Images

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).

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NCBI SRA PRJNA421205

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).

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NCBI SRA SRP148742 

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).

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UMI Toolset  |  NCBI SRA PRJNA416930

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).

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NCBI GEO GSE89538

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).

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DDBJ/ENA/GenBank  |  NCBI SRA PRJNA336361

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. (2018). Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements. Nature Ecology & Evolution 2:174-181. (PMCID: PMC5732027).

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TE Annotation Source Code  |  TE Annotation  |  Virus identification & genome assembly source code  | 

GenBank Viral Contigs MG012486, MG012487 & MG012488  |  Python Script  | Gene expression analysis

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. (PMCID: PMC5068941).

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Fly Stocks  |  Plasmid pCFD4d  |  Plasmid pCFD4d-U6-1:white1-U6-3:white1  |  Plasmid pUC57-white[coffee]  

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). 

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NCBI GEO GSE79055

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 Mechanisms. Molecular Cell 59:819-830. (PMCID: PMC4560842).

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NCBI SRA SRP053028

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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Open Source project

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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NCBI SRA SRP045930 

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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NCBI SRA SRP043516

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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NCBI SRA SRP043482

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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NCBI SRA SRP037575

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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NCBI Traces Archive SRP030460

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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NCBI Traces Archive SRP024291

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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NCBI SRA SRP000409

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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Small RNA Libraries SRX337129

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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NCBI GEO GSE44690

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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NCBI GEO GSE35638

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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NCBI GEO GSE37443  |  NCBI SRA SRP014526

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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NCBI GEO GSE25971

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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NCBI GEO GSE31813  |  NCBI SRA SRP007937

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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NCBI Traces Archive SRP007101  |  NCBI GEO GSE30061  |  Detailed Trasposon Analysis

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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RNA Data Sets

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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NCBI GEO GSE25899

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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NCBI SRA GSE18806

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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NCBI SRA SRA10045, GSM278704 & GSE18806

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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NCBI GEO GSE17629

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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NCBI Trace Archives SRP000458  |  NCBI GEO GSE14370

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).

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NCBI GEO GSE14370

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).

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NCBI GEO GSE9389 & GPL6664

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

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NCBI GEO GSE9389

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 germline. Science 313:320-324.

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NCBI GEO GSE4932

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).

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NCBI GEO GSE5291

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 Humans. Nature Ecology & Evolution, 4:156-168. (PMCID: PMC6961462).

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NCBI GEO GSE5291