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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

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

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

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, 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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