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Stark, A., Brennecke, J., Russell, RB., Cohen, SM. (2003). Identification of Drosophila MicroRNA targets. PLoS Biol. 1(3):E60

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

Brennecke, J., Cohen, SM. (2003). Towards a complete description of the microRNA complement of animal genomes. Genome Biol. 4(9):228

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

Brennecke, J., Stark, A., Russell, RB., Cohen, SM. (2005). Principles of microRNA-target recognition. PLoS Biol. 3(3):e85

Brennecke, J., Stark, A., Cohen, SM. (2005). Not miR-ly muscular: microRNAs and muscle development. Genes Dev. 19(19):2261-4

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

Cohen, SM., Brennecke, J. (2006). Developmental biology. Mixed messages in early development. Science. 312(5770):65-6

Rehwinkel, J., Natalin, P., Stark, A (...) 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

Cohen, SM., Brennecke, J., Stark, A. (2006). Denoising feedback loops by thresholding--a new role for microRNAs. Genes Dev. 20(20):2769-72

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

Brennecke, J., Aravin, AA., Stark, A (...) Sachidanandam, R., Hannon, GJ. (2007). Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell. 128(6):1089-103

Stark, A., Lin, MF., Kheradpour, P (...) Gelbart, WM., Kellis, M. (2007). Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature. 450(7167):219-32

Stark, A., Kheradpour, P., Parts, L (...) Hannon, GJ., Kellis, M. (2007). Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes. Genome Res. 17(12):1865-79

Brennecke, J., Malone, CD., Aravin, AA (...) Stark, A., Hannon, GJ. (2008). An epigenetic role for maternally inherited piRNAs in transposon silencing. Science. 322(5906):1387-92

Czech, B., Malone, CD., Zhou, R (...) Hannon, GJ., Brennecke, J. (2008). An endogenous small interfering RNA pathway in Drosophila. Nature. 453(7196):798-802

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

Stark, A., Bushati, N., Jan, CH (...) Cohen, SM., Kellis, M. (2008). A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev. 22(1):8-13

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

Olson, AJ., Brennecke, J., Aravin, AA., Hannon, GJ., Sachidanandam, R. (2008). Analysis of large-scale sequencing of small RNAs. Pac Symp Biocomput. :126-36

Malone, CD., Brennecke, J., Dus, M (...) Sachidanandam, R., Hannon, GJ. (2009). Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary. Cell. 137(3):522-35

Zhou, R., Czech, B., Brennecke, J (...) Perrimon, N., Hannon, GJ. (2009). Processing of Drosophila endo-siRNAs depends on a specific Loquacious isoform. RNA. 15(10):1886-95

Czech, B., Zhou, R., Erlich, Y (...) Perrimon, N., Hannon, GJ. (2009). Hierarchical rules for Argonaute loading in Drosophila. Mol Cell. 36(3):445-56

Senti, KA., Brennecke, J. (2010). The piRNA pathway: a fly's perspective on the guardian of the genome. Trends Genet. 26(12):499-509

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

Handler, D., Olivieri, D., Novatchkova, M (...) 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

Ni, JQ., Zhou, R., Czech, B (...) Hannon, GJ., Perrimon, N. (2011). A genome-scale shRNA resource for transgenic RNAi in Drosophila. Nat Methods. 8(5):405-7

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

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

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

Handler, D., Meixner, K., Pizka, M (...) Gruber, FS., Brennecke, J. (2013). The genetic makeup of the Drosophila piRNA pathway. Mol Cell. 50(5):762-77

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

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):1364-1379

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

Mohn, F., Handler, D., Brennecke, J. (2015). Noncoding RNA. piRNA-guided slicing specifies transcripts for Zucchini-dependent, phased piRNA biogenesis. Science. 348(6236):812-817

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

Marinov, GK., Wang, J., Handler, D (...) 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

Sienski, G., Batki, J., Senti, KA (...) Meixner, K., Brennecke, J. (2015). Silencio/CG9754 connects the Piwi-piRNA complex to the cellular heterochromatin machinery. Genes Dev. 29(21):2258-71

Hayashi, R., Schnabl, J., Handler, D (...) Ameres, SL., Brennecke, J. (2016). Genetic and mechanistic diversity of piRNA 3'-end formation. Nature. 539(7630):588-592

Andersen, PR., Tirian, L., Vunjak, M., Brennecke, J. (2017). A heterochromatin-dependent transcription machinery drives piRNA expression. Nature. 549(7670):54-59

ElMaghraby, MF., Andersen, PR., Pühringer, F (...) Tirian, L., Brennecke, J. (2019). A Heterochromatin-Specific RNA Export Pathway Facilitates piRNA Production. Cell. 178(4):964-979.e20

Batki, J., Schnabl, J., Wang, J (...) Patel, DJ., Brennecke, J. (2019). The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation. Nat Struct Mol Biol. 26(8):720-731

Xie, W., Sowemimo, I., Hayashi, R (...) Ameres, SL., Patel, DJ. (2020). Structure-function analysis of microRNA 3'-end trimming by Nibbler. Proc Natl Acad Sci U S A. 117(48):30370-30379

Grentzinger, T., Oberlin, S., Schott, G (...) Brennecke, J., Voinnet, O. (2020). A universal method for the rapid isolation of all known classes of functional silencing small RNAs. Nucleic Acids Res. 48(14):e79

Pühringer, T., Hohmann, U., Fin, L (...) Brennecke, J., Plaschka, C. (2020). Structure of the human core transcription-export complex reveals a hub for multivalent interactions. Elife. 9

Schnabl, J., Wang, J., Hohmann, U (...) Patel, DJ., Brennecke, J. (2021). Molecular principles of Piwi-mediated cotranscriptional silencing through the dimeric SFiNX complex. Genes Dev. 35(5-6):392-409

Kellner MJ, Matl M, Ross JJ, Schnabl J, Handler D, Heinen R, Schaeffer J, Hufnagl P, Indra A, Dekens MPS, Fritsche-Polanz R, Födinger M, Zuber J, Vienna Covid-19 Detection Initiative (VCDI), Allerberger F, Pauli A, Brennecke J (2021). Head-to-head comparison of direct-input RT-PCR and RT-LAMP against RT-qPCR on extracted RNA for rapid SARS-CoV-2 diagnostics. medRxiv. 2021.01.19.21250079

ElMaghraby, MF., Tirian, L., Senti, KA., Meixner, K., Brennecke, J. (2021). A genetic toolkit for studying transposon control in the Drosophila melanogaster ovary. Genetics.

Kellner, MJ., Ross, JJ., Schnabl, J (...) Pauli, A., Brennecke, J. (2022). A Rapid, Highly Sensitive and Open-Access SARS-CoV-2 Detection Assay for Laboratory and Home Testing. Front Mol Biosci. 9:801309

Andreev, VI., Yu, C., Wang, J (...) Patel, DJ., Brennecke, J. (2022). Panoramix SUMOylation on chromatin connects the piRNA pathway to the cellular heterochromatin machinery. Nat Struct Mol Biol. 29(2):130-142

Baumgartner, L., Handler, D., Platzer, SW (...) Duchek, P., Brennecke, J. (2022). The <i>Drosophila</i> ZAD zinc finger protein Kipferl guides Rhino to piRNA clusters. Elife. 11

L Baumgartner, JJ Ipsaro, U Hohmann, D Handler, A Schleiffer, P Duchek, J Brennecke (2023). Evolutionary adaptation of the chromodomain of the HP1-protein Rhino allows the integration of chromatin and DNA sequence signals BioRxiv.

Yelagandula, R., Stecher, K., Novatchkova, M (...) Brennecke, J., Bell, O. (2023). ZFP462 safeguards neural lineage specification by targeting G9A/GLP-mediated heterochromatin to silence enhancers. Nat Cell Biol.

Pliota, P., Marvanova, H., Koreshova, A (...) Ben-David, E., Burga, A. (2024). Selfish conflict underlies RNA-mediated parent-of-origin effects. Nature.