Publications

(2016)
 
Hayashi, R., Schnabl, J., Handler, D., Mohn, F., Ameres, SL., Brennecke, J. (2016). Genetic and mechanistic diversity of piRNA 3'-end formation. Nature. 539(7630):588-592 (abstract)
 
(2015)
 
Marinov, GK., Wang, J., Handler, D., Wold, BJ., Weng, Z., Hannon, GJ., Aravin, AA., Zamore, PD., Brennecke, J., Toth, KF. (2015). Pitfalls of mapping high-throughput sequencing data to repetitive sequences: Piwi's genomic targets still not identified. Dev Cell. 32(6):765-71 (abstract)
 
Mohn, F., Handler, D., Brennecke, J. (2015). Noncoding RNA. piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis. Science. 348(6236):812-7 (abstract)
 
Senti, KA., Jurczak, D., Sachidanandam, R., Brennecke, J. (2015). piRNA-guided slicing of transposon transcripts enforces their transcriptional silencing via specifying the nuclear piRNA repertoire. Genes Dev. 29(16):1747-62 (abstract)
 
Sienski, G., Batki, J., Senti, KA., Dönertas, D., Tirian, L., Meixner, K., Brennecke, J. (2015). Silencio/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery. Genes Dev. 29(21):2258-71 (abstract)
 
(2014)
 
Hayashi, R., Handler, D., Ish-Horowicz, D., Brennecke, J. (2014). The exon junction complex is required for definition and excision of neighboring introns in Drosophila. Genes Dev. 28(16):1772-85 (abstract)
 
Mohn, F., Sienski, G., Handler, D., Brennecke, J. (2014). The rhino-deadlock-cutoff complex licenses noncanonical transcription of dual-strand piRNA clusters in Drosophila. Cell. 157(6):1364-79 (abstract)
 
(2013)
 
Dönertas, D., Sienski, G., Brennecke, J. (2013). Drosophila Gtsf1 is an essential component of the Piwi-mediated transcriptional silencing complex. Genes Dev. 27(15):1693-705 (abstract)
 
Handler, D., Meixner, K., Pizka, M., Lauss, K., Schmied, C., Gruber, FS., Brennecke, J. (2013). The genetic makeup of the Drosophila piRNA pathway. Mol Cell. 50(5):762-77 (abstract)
 
(2012)
 
Malone, C., Brennecke, J., Czech, B., Aravin, A., Hannon, GJ. (2012). Preparation of small RNA libraries for high-throughput sequencing. Cold Spring Harb Protoc. 2012(10):1067-77 (abstract)
 
Olivieri, D., Senti, KA., Subramanian, S., Sachidanandam, R., Brennecke, J. (2012). The cochaperone shutdown defines a group of biogenesis factors essential for all piRNA populations in Drosophila. Mol Cell. 47(6):954-69 (abstract)
 
Sienski, G., Dönertas, D., Brennecke, J. (2012). Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. Cell. 151(5):964-80 (abstract)
 
(2011)
 
Handler, D., Olivieri, D., Novatchkova, M., Gruber, FS., Meixner, K., Mechtler, K., Stark, A., Sachidanandam, R., Brennecke, J. (2011). A systematic analysis of Drosophila TUDOR domain-containing proteins identifies Vreteno and the Tdrd12 family as essential primary piRNA pathway factors. EMBO J. 30(19):3977-93 (abstract)
 
Ni, JQ., Zhou, R., Czech, B., Liu, LP., Holderbaum, L., Yang-Zhou, D., Shim, HS., Tao, R., Handler, D., Karpowicz, P., Binari, R., Booker, M., Brennecke, J., Perkins, LA., Hannon, GJ., Perrimon, N. (2011). A genome-scale shRNA resource for transgenic RNAi in Drosophila. Nat Methods. 8(5):405-7 (abstract)
 
(2010)
 
Olivieri, D., Sykora, MM., Sachidanandam, R., Mechtler, K., Brennecke, J. (2010). An in vivo RNAi assay identifies major genetic and cellular requirements for primary piRNA biogenesis in Drosophila. EMBO J. 29(19):3301-17 (abstract)
 
Senti, KA., Brennecke, J. (2010). The piRNA pathway: a fly's perspective on the guardian of the genome. Trends Genet. 26(12):499-509 (abstract)
 
(2009)
 
Czech, B., Zhou, R., Erlich, Y., Brennecke, J., Binari, R., Villalta, C., Gordon, A., Perrimon, N., Hannon, GJ. (2009). Hierarchical rules for Argonaute loading in Drosophila. Mol Cell. 36(3):445-56 (abstract)
 
Malone, CD., Brennecke, J., Dus, M., Stark, A., McCombie, WR., Sachidanandam, R., Hannon, GJ. (2009). Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell. 137(3):522-35 (abstract)
 
Zhou, R., Czech, B., Brennecke, J., Sachidanandam, R., Wohlschlegel, JA., Perrimon, N., Hannon, GJ. (2009). Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform. RNA. 15(10):1886-95 (abstract)
 
(2008)
 
Brennecke, J., Malone, CD., Aravin, AA., Sachidanandam, R., Stark, A., Hannon, GJ. (2008). An epigenetic role for maternally inherited piRNAs in transposon silencing. Science. 322(5906):1387-92 (abstract)
 
Bushati, N., Stark, A., Brennecke, J., Cohen, SM. (2008). Temporal reciprocity of miRNAs and their targets during the maternal-to-zygotic transition in Drosophila. Curr Biol. 18(7):501-6 (abstract)
 
Czech, B., Malone, CD., Zhou, R., Stark, A., Schlingeheyde, C., Dus, M., Perrimon, N., Kellis, M., Wohlschlegel, JA., Sachidanandam, R., Hannon, GJ., Brennecke, J. (2008). An endogenous small interfering RNA pathway in Drosophila. Nature. 453(7196):798-802 (abstract)
 
Müller, MS., Brennecke, JF., Porter, ET., Ottinger, MA., Anderson, DJ. (2008). Perinatal androgens and adult behavior vary with nestling social system in siblicidal boobies. PLoS One. 3(6):e2460 (abstract)
 
Olson, AJ., Brennecke, J., Aravin, AA., Hannon, GJ., Sachidanandam, R. (2008). Analysis of large-scale sequencing of small RNAs. Pac Symp Biocomput. :126-36 (abstract)
 
Stark, A., Bushati, N., Jan, CH., Kheradpour, P., Hodges, E., Brennecke, J., Bartel, DP., Cohen, SM., Kellis, M. (2008). A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev. 22(1):8-13 (abstract)
 
(2007)
 
Aravin, AA., Hannon, GJ., Brennecke, J. (2007). The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science. 318(5851):761-4 (abstract)
 
Brennecke, J., Aravin, AA., Stark, A., Dus, M., Kellis, M., Sachidanandam, R., Hannon, GJ. (2007). Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell. 128(6):1089-103 (abstract)
 
Stark, A., Kheradpour, P., Parts, L., Brennecke, J., Hodges, E., Hannon, GJ., Kellis, M. (2007). Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res. 17(12):1865-79 (abstract)
 
Stark, A., Lin, MF., Kheradpour, P., Pedersen, JS., Parts, L., Carlson, JW., Crosby, MA., Rasmussen, MD., Roy, S., Deoras, AN., Ruby, JG., Brennecke, J., Hodges, E., Hinrichs, AS., Caspi, A., Paten, B., Park, SW., Han, MV., Maeder, ML., Polansky, BJ., Robson, BE., Aerts, S., van Helden, J., Hassan, B., Gilbert, DG., Eastman, DA., Rice, M., Weir, M., Hahn, MW., Park, Y., Dewey, CN., Pachter, L., Kent, WJ., Haussler, D., Lai, EC., Bartel, DP., Hannon, GJ., Kaufman, TC., Eisen, MB., Clark, AG., Smith, D., Celniker, SE., Gelbart, WM., Kellis, M. (2007). Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450(7167):219-32 (abstract)
 
(2006)
 
Cohen, SM., Brennecke, J. (2006). Developmental biology. Mixed messages in early development. Science. 312(5770):65-6 (abstract)
 
Cohen, SM., Brennecke, J., Stark, A. (2006). Denoising feedback loops by thresholding--a new role for microRNAs. Genes Dev. 20(20):2769-72 (abstract)
 
Rehwinkel, J., Natalin, P., Stark, A., Brennecke, J., Cohen, SM., Izaurralde, E. (2006). Genome-wide analysis of mRNAs regulated by Drosha and Argonaute proteins in Drosophila melanogaster. Mol Cell Biol. 26(8):2965-75 (abstract)
 
(2005)
 
Brennecke, J., Stark, A., Cohen, SM. (2005). Not miR-ly muscular: microRNAs and muscle development. Genes Dev. 19(19):2261-4 (abstract)
 
Brennecke, J., Stark, A., Russell, RB., Cohen, SM. (2005). Principles of microRNA-target recognition. PLoS Biol. 3(3):e85 (abstract)
 
Stark, A., Brennecke, J., Bushati, N., Russell, RB., Cohen, SM. (2005). Animal MicroRNAs confer robustness to gene expression and have a significant impact on 3'UTR evolution. Cell. 123(6):1133-46 (abstract)
 
(2004)
 
Güttinger, S., Mühlhäusser, P., Koller-Eichhorn, R., Brennecke, J., Kutay, U. (2004). Transportin2 functions as importin and mediates nuclear import of HuR. Proc Natl Acad Sci U S A. 101(9):2918-23 (abstract)
 
(2003)
 
Brennecke, J., Cohen, SM. (2003). Towards a complete description of the microRNA complement of animal genomes. Genome Biol. 4(9):228 (abstract)
 
Brennecke, J., Hipfner, DR., Stark, A., Russell, RB., Cohen, SM. (2003). bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila. Cell. 113(1):25-36 (abstract)
 
Stark, A., Brennecke, J., Russell, RB., Cohen, SM. (2003). Identification of Drosophila MicroRNA targets. PLoS Biol. 1(3):E60 (abstract)
 
(2002)
 
Gritzan, U., Weiss, C., Brennecke, J., Bohmann, D. (2002). Transrepression of AP-1 by nuclear receptors in Drosophila. Mech Dev. 115(1-2):91-100 (abstract)
 

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