Publikationen

• [ 2025 ]
• [ 2024 ]
• [ 2023 ]
• [ 2022 ]
• [ 2021 ]
• [ 2020 ]
• [ 2019 ]
• [ 2018 ]
• [ 2017 ]
• [ 2016 ]
• [ 2015 ]
• [ 2013 ]
• [ 2012 ]
• [ 2011 ]
• [ 2010 ]
• [ 2009 ]
• [ 2008 ]
• [ 2007 ]
• [ 2006 ]

• Eudenbach, M., Busam, J., Bouchard, C., Rossbach, O., Zarnack, K., & Bauer, U.-M. (2025). Assessment of PRMT6-dependent alternative splicing in pluripotent and differentiating NT2/D1 cells. Life Science Alliance, 8(4), e202402946-. https://doi.org/10.26508/lsa.202402946
• Northoff, B. H., Herbst, A., Wenk, C., Weindl, L., Gäbel, G., Brezski, A., Zarnack, K., Küpper, A., Dimmeler, S., Moretti, A., Laugwitz, K.-L., Engelhardt, S., Maegdefessel, L., Boon, R., Doppler, S., Dreßen, M., Lahm, H., Lange, R., Krane, M., … Teupser, D. (2025). CircRNAs increase during vascular cell differentiation and are biomarkers for vascular disease. Cardiovascular Research, cvaf013-. https://doi.org/10.1093/cvr/cvaf013
• Stoffel, N. K., Sankaranarayanan, S., Müntjes, K., Körtel, N., Busch, A., Zarnack, K., König, J., & Feldbrügge, M. (2025). Microbial iCLIP2: enhanced mapping of RNA-protein interaction by promoting protein and RNA stability. RNA (New York, N.Y.), 31(2), 258-272. https://doi.org/10.1261/rna.080193.124

• Lewinski, M., Brüggemann, M., Köster, T., Reichel, M., Bergelt, T., Meyer, K., König, J., Zarnack, K., & Staiger, D. (2024). Mapping protein-RNA binding in plants with individual-nucleotide-resolution UV cross-linking and immunoprecipitation (plant iCLIP2). Nature Protocols, 19(4), 1183-1234. https://doi.org/10.1038/s41596-023-00935-3
• Arnold, B., Riegger, R. J., Okuda, E. K., Slišković, I., Keller, M., Bakisoglu, C., McNicoll, F., Zarnack, K., & Müller-McNicoll, M. (2024). hGRAD: A versatile "one-fits-all" system to acutely deplete RNA binding proteins from condensates. The Journal of Cell Biology, 223(2), e202304030-. https://doi.org/10.1083/jcb.202304030
• Brezski, A., Murtagh, J., Schulz, M. H., & Zarnack, K. (2024). A systematic analysis of circRNAs in subnuclear compartments. RNA Biology, 21(1), 1-16. https://doi.org/10.1080/15476286.2024.2395718
• Rosenkranz, R. R. E., Vraggalas, S., Keller, M., Sankaranarayanan, S., McNicoll, F., Löchli, K., Bublak, D., Benhamed, M., Crespi, M., Berberich, T., Bazakos, C., Feldbrügge, M., Schleiff, E., Müller-McNicoll, M., Zarnack, K., & Fragkostefanakis, S. (2024). A plant-specific clade of serine/arginine-rich proteins regulates RNA splicing homeostasis and thermotolerance in tomato. Nucleic Acids Research, 52(19), 11466-11480. https://doi.org/10.1093/nar/gkae730
• Verheyden, N. A., Klostermann, M., Brüggemann, M., Steede, H. M., Scholz, A., Amr, S., Lichtenthaeler, C., Münch, C., Schmid, T., Zarnack, K., & Krueger, A. (2024). A high-resolution map of functional miR-181 response elements in the thymus reveals the role of coding sequence targeting and an alternative seed match. Nucleic Acids Research, 52(14), 8515-8533. https://doi.org/10.1093/nar/gkae416
• Lewinski, M., Steffen, A., Kachariya, N., Elgner, M., Schmal, C., Messini, N., Köster, T., Reichel, M., Sattler, M., Zarnack, K., & Staiger, D. (2024). Arabidopsis thaliana GLYCINE RICH RNA-BINDING PROTEIN 7 interaction with its iCLIP target LHCB1.1 correlates with changes in RNA stability and circadian oscillation. The Plant Journal : For Cell and Molecular Biology, 118(1), 203-224. https://doi.org/10.1111/tpj.16601
• Niedner-Boblenz, A., Monecke, T., Hennig, J., Klostermann, M., Hofweber, M., Davydova, E., Gerber, A. P., Anosova, I., Mayer, W., Müller, M., Heym, R. G., Janowski, R., Paillart, J.-C., Dormann, D., Zarnack, K., Sattler, M., & Niessing, D. (2024). Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation. Nucleic Acids Research, 52(22), 14205-14228. https://doi.org/10.1093/nar/gkae1107
• Pacholewska, A., Lienhard, M., Brüggemann, M., Hänel, H., Bilalli, L., Königs, A., Heß, F., Becker, K., Köhrer, K., Kaiser, J., Gohlke, H., Gattermann, N., Hallek, M., Herling, C. D., König, J., Grimm, C., Herwig, R., Zarnack, K., & Schweiger, M. R. (2024). Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations. Genome Research, 34(11), 1832-1848. https://doi.org/10.1101/gr.279327.124
• von Ehr, J., Oberstrass, L., Yazgan, E., Schnaubelt, L. I., Blümel, N., McNicoll, F., Weigand, J. E., Zarnack, K., Müller-McNicoll, M., Korn, S. M., & Schlundt, A. (2024). Arid5a uses disordered extensions of its core ARID domain for distinct DNA- and RNA-recognition and gene regulation. The Journal of Biological Chemistry, 300(7), 107457-107457. https://doi.org/10.1016/j.jbc.2024.107457
• Prieto-Garcia, C., Matkovic, V., Mosler, T., Li, C., Liang, J., Oo, J. A., Haidle, F., Mačinković, I., Cabrera-Orefice, A., Berkane, R., Giuliani, G., Xu, F., Jacomin, A.-C., Tomaskovic, I., Basoglu, M., Hoffmann, M. E., Rathore, R., Cetin, R., Boutguetait, D., … Dikic, I. (2024). Pathogenic proteotoxicity of cryptic splicing is alleviated by ubiquitination and ER-phagy. Science (New York, N.Y.), 386(6723), 768-776. https://doi.org/10.1126/science.adi5295
• Stoffel, N. K., Sankaranarayanan, S., Muentjes, K., Kortel, N., Busch, A., Zarnack, K., Konig, J., & Feldbrugge, M. (2024). Microbial iCLIP2: Enhanced mapping of RNA-Protein interaction by promoting protein and RNA stability. RNA (New York, N.Y.), rna.080193.124-. https://doi.org/10.1261/rna.080193.124
• Klostermann, M., & Zarnack, K. (2024). racoon_clip-a complete pipeline for single-nucleotide analyses of iCLIP and eCLIP data. Bioinformatics Advances, 4(1), vbae084-vbae084. https://doi.org/10.1093/bioadv/vbae084
• Zhou, Y., Ćorović, M., Hoch-Kraft, P., Meiser, N., Mesitov, M., Körtel, N., Back, H., Naarmann-de Vries, I. S., Katti, K., Obrdlík, A., Busch, A., Dieterich, C., Vaňáčová, Štěpánka, Hengesbach, M., Zarnack, K., & König, J. (2024). m6A sites in the coding region trigger translation-dependent mRNA decay. Molecular Cell, 84(23), 4576-4593.e12. https://doi.org/10.1016/j.molcel.2024.10.033
• Rajagopal, V., Seiler, J., Nasa, I., Cantarella, S., Theiss, J., Herget, F., Kaifer, B., Schneider, M., Helm, D., König, J., Zarnack, K., Diederichs, S., Kettenbach, A. N., & Caudron-Herger, M. (2024). An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions. BioRxiv : The Preprint Server for Biology, 2024.09.25.614981-. https://doi.org/10.1101/2024.09.25.614981

• Glaser, S. F., Brezski, A., Baumgarten, N., Klangwart, M., Heumüller, A. W., Maji, R. K., Leisegang, M. S., Guenther, S., Zehendner, C. M., John, D., Schulz, M. H., Zarnack, K., & Dimmeler, S. (2023). Circular RNA circPLOD2 regulates pericyte function by targeting the transcription factor KLF4. Cell Reports, 42(8), 112824-112824. https://doi.org/10.1016/j.celrep.2023.112824
• Sankaranarayanan, S., Haag, C., Petzsch, P., Köhrer, K., Matuszyńska, A., Zarnack, K., & Feldbrügge, M. (2023). The mRNA stability factor Khd4 defines a specific mRNA regulon for membrane trafficking in the pathogen Ustilago maydis. Proceedings of the National Academy of Sciences of the United States of America, 120(34), e2301731120-e2301731120. https://doi.org/10.1073/pnas.2301731120
• Ebersberger, S., Hipp, C., Mulorz, M. M., Buchbender, A., Hubrich, D., Kang, H.-S., Martínez-Lumbreras, S., Kristofori, P., Sutandy, F. X. R., Llacsahuanga Allcca, L., Schönfeld, J., Bakisoglu, C., Busch, A., Hänel, H., Tretow, K., Welzel, M., Di Liddo, A., Möckel, M. M., Zarnack, K., … König, J. (2023). FUBP1 is a general splicing factor facilitating 3’ splice site recognition and splicing of long introns. Molecular Cell, 83(15), 2653-2672.e15. https://doi.org/10.1016/j.molcel.2023.07.002
• Rücklé, C., Körtel, N., Basilicata, M. F., Busch, A., Zhou, Y., Hoch-Kraft, P., Tretow, K., Kielisch, F., Bertin, M., Pradhan, M., Musheev, M., Schweiger, S., Niehrs, C., Rausch, O., Zarnack, K., Keller Valsecchi, C. I., & König, J. (2023). RNA stability controlled by m(6)A methylation contributes to X-to-autosome dosage compensation in mammals. Nature Structural & Molecular Biology, 30(8), 1207-1215. https://doi.org/10.1038/s41594-023-00997-7
• Keil, P., Wulf, A., Kachariya, N., Reuscher, S., Hühn, K., Silbern, I., Altmüller, J., Keller, M., Stehle, R., Zarnack, K., Sattler, M., Urlaub, H., & Sträßer, K. (2023). Npl3 functions in mRNP assembly by recruitment of mRNP components to the transcription site and their transfer onto the mRNA. Nucleic Acids Research, 51(2), 831-851. https://doi.org/10.1093/nar/gkac1206
• Zarnack, K., & Eyras, E. (2023). ‘Artificial intelligence and machine learning in RNA biology’. Briefings in Bioinformatics, 24(6), Article 6. https://doi.org/10.1093/bib/bbad415
• Acera Mateos, P., Zhou, Y., Zarnack, K., & Eyras, E. (2023). Concepts and methods for transcriptome-wide prediction of chemical messenger RNA modifications with machine learning. Briefings in Bioinformatics, 24(3), bbad163-. https://doi.org/10.1093/bib/bbad163
• de Oliveira Freitas Machado, C., Schafranek, M., Brüggemann, M., Hernández Cañás, M. C., Keller, M., Di Liddo, A., Brezski, A., Blümel, N., Arnold, B., Bremm, A., Wittig, I., Jaé, N., McNicoll, F., Dimmeler, S., Zarnack, K., & Müller-McNicoll, M. (2023). Poison cassette exon splicing of SRSF6 regulates nuclear speckle dispersal and the response to hypoxia. Nucleic Acids Research, 51(2), 870-890. https://doi.org/10.1093/nar/gkac1225
• Molitor, L., Klostermann, M., Bacher, S., Merl-Pham, J., Spranger, N., Burczyk, S., Ketteler, C., Rusha, E., Tews, D., Pertek, A., Proske, M., Busch, A., Reschke, S., Feederle, R., Hauck, S. M., Blum, H., Drukker, M., Fischer-Posovszky, P., König, J., … Niessing, D. (2023). Depletion of the RNA-binding protein PURA triggers changes in posttranscriptional gene regulation and loss of P-bodies. Nucleic Acids Research, 51(3), 1297-1316. https://doi.org/10.1093/nar/gkac1237
• Fischer, S., Lichtenthaeler, C., Stepanenko, A., Heyl, F., Maticzka, D., Kemmerer, K., Klostermann, M., Backofen, R., Zarnack, K., & Weigand, J. E. (2023). Heterogenous nuclear ribonucleoprotein D-like controls endothelial cell functions. Biological Chemistry, 405(4), 229-239. https://doi.org/10.1515/hsz-2023-0254
• Bauer, R., Meyer, S. P., Raue, R., Palmer, M. A., Guerrero Ruiz, V. M., Cardamone, G., Rösser, S., Heffels, M., Roesmann, F., Wilhelm, A., Lütjohann, D., Zarnack, K., Fuhrmann, D. C., Widera, M., Schmid, T., & Brüne, B. (2023). Hypoxia-altered cholesterol homeostasis enhances the expression of interferon-stimulated genes upon SARS-CoV-2 infections in monocytes. Frontiers in Immunology, 14, 1121864-1121864. https://doi.org/10.3389/fimmu.2023.1121864

• Bauer, R., Meyer, S. P., Kloss, K. A., Guerrero Ruiz, V. M., Reuscher, S., Zhou, Y., Fuhrmann, D. C., Zarnack, K., Schmid, T., & Brüne, B. (2022). Functional RNA Dynamics Are Progressively Governed by RNA Destabilization during the Adaptation to Chronic Hypoxia. International Journal of Molecular Sciences, 23(10), 5824-. https://doi.org/10.3390/ijms23105824
• Jones, A. N., Graß, C., Meininger, I., Geerlof, A., Klostermann, M., Zarnack, K., Krappmann, D., & Sattler, M. (2022). Modulation of pre-mRNA structure by hnRNP proteins regulates alternative splicing of MALT1. Science Advances, 8(31), eabp9153-eabp9153. https://doi.org/10.1126/sciadv.abp9153
• Elwakeel, E., Brüggemann, M., Wagih, J., Lityagina, O., Elewa, M. A. F., Han, Y., Frömel, T., Popp, R., Nicolas, A. M., Schreiber, Y., Gradhand, E., Thomas, D., Nüsing, R., Steinmetz-Späh, J., Savai, R., Fokas, E., Fleming, I., Greten, F. R., Zarnack, K., … Weigert, A. (2022). Disruption of Prostaglandin E2 Signaling in Cancer-Associated Fibroblasts Limits Mammary Carcinoma Growth but Promotes Metastasis. Cancer Research, 82(7), 1380-1395. https://doi.org/10.1158/0008-5472.CAN-21-2116
• Cortés-López, M., Schulz, L., Enculescu, M., Paret, C., Spiekermann, B., Quesnel-Vallières, M., Torres-Diz, M., Unic, S., Busch, A., Orekhova, A., Kuban, M., Mesitov, M., Mulorz, M. M., Shraim, R., Kielisch, F., Faber, J., Barash, Y., Thomas-Tikhonenko, A., Zarnack, K., … König, J. (2022). High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance. Nature Communications, 13(1), 5570-5570. https://doi.org/10.1038/s41467-022-31818-y

• Körtel, N., Rücklé, C., Zhou, Y., Busch, A., Hoch-Kraft, P., Sutandy, F. X. R., Haase, J., Pradhan, M., Musheev, M., Ostareck, D., Ostareck-Lederer, A., Dieterich, C., Hüttelmaier, S., Niehrs, C., Rausch, O., Dominissini, D., König, J., & Zarnack, K. (2021). Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning. Nucleic Acids Research, 49(16), e92-e92. https://doi.org/10.1093/nar/gkab485
• Schwich, O. D., Blümel, N., Keller, M., Wegener, M., Setty, S. T., Brunstein, M. E., Poser, I., Mozos, I. R. D. L., Suess, B., Münch, C., McNicoll, F., Zarnack, K., & Müller-McNicoll, M. (2021). SRSF3 and SRSF7 modulate 3’UTR length through suppression or activation of proximal polyadenylation sites and regulation of CFIm levels. Genome Biology, 22(1), 82-82. https://doi.org/10.1186/s13059-021-02298-y
• Schulz, L., Torres-Diz, M., Cortés-López, M., Hayer, K. E., Asnani, M., Tasian, S. K., Barash, Y., Sotillo, E., Zarnack, K., König, J., & Thomas-Tikhonenko, A. (2021). Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts. Genome Biology, 22(1), 190-190. https://doi.org/10.1186/s13059-021-02411-1
• Koch, I., Andrade-Navarro, M., Schulz, M. H., & Zarnack, K. (2021). Bioinformatics in theory and application - highlights of the 36th German Conference on Bioinformatics. Biological Chemistry, 402(8), 869-870. https://doi.org/10.1515/hsz-2021-0298

• Busch, A., Brüggemann, M., Ebersberger, S., & Zarnack, K. (2020). iCLIP data analysis: A complete pipeline from sequencing reads to RBP binding sites. Methods (San Diego, Calif.), 178, 49-62. https://doi.org/10.1016/j.ymeth.2019.11.008
• Zarnack, K., Balasubramanian, S., Gantier, M. P., Kunetsky, V., Kracht, M., Schmitz, M. L., & Sträßer, K. (2020). Dynamic mRNP Remodeling in Response to Internal and External Stimuli. Biomolecules, 10(9), 1310-. https://doi.org/10.3390/biom10091310
• Enculescu, M., Braun, S., Thonta Setty, S., Busch, A., Zarnack, K., König, J., & Legewie, S. (2020). Exon Definition Facilitates Reliable Control of Alternative Splicing in the RON Proto-Oncogene. Biophysical Journal, 118(8), 2027-2041. https://doi.org/10.1016/j.bpj.2020.02.022
• Dold, A., Han, H., Liu, N., Hildebrandt, A., Brüggemann, M., Rücklé, C., Hänel, H., Busch, A., Beli, P., Zarnack, K., König, J., Roignant, J.-Y., & Lasko, P. (2020). Makorin 1 controls embryonic patterning by alleviating Bruno1-mediated repression of oskar translation. PLoS Genetics, 16(1), e1008581-e1008581. https://doi.org/10.1371/journal.pgen.1008581
• Fischer, S., Di Liddo, A., Taylor, K., Gerhardus, J. S., Sobczak, K., Zarnack, K., & Weigand, J. E. (2020). Muscleblind-like 2 controls the hypoxia response of cancer cells. RNA (New York, N.Y.), 26(5), 648-663. https://doi.org/10.1261/rna.073353.119
• Kang, H.-S., Sánchez-Rico, C., Ebersberger, S., Sutandy, F. X. R., Busch, A., Welte, T., Stehle, R., Hipp, C., Schulz, L., Buchbender, A., Zarnack, K., König, J., & Sattler, M. (2020). An autoinhibitory intramolecular interaction proof-reads RNA recognition by the essential splicing factor U2AF2. Proceedings of the National Academy of Sciences of the United States of America, 117(13), 7140-7149. https://doi.org/10.1073/pnas.1913483117
• Monzón-Casanova, E., Matheson, L. S., Tabbada, K., Zarnack, K., Smith, C. W., & Turner, M. (2020). Polypyrimidine tract-binding proteins are essential for B cell development. ELife, 9, e53557-. https://doi.org/10.7554/eLife.53557
• Alvelos, M. I., Brüggemann, M., Sutandy, F. R., Juan-Mateu, J., Colli, M. L., Busch, A., Lopes, M., Castela, Ângela, Aartsma-Rus, A., König, J., Zarnack, K., & Eizirik, D. L. (2020). The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells. Life Science Alliance, 4(3), e202000825-. https://doi.org/10.26508/lsa.202000825
• König, J., & Zarnack, K. (2020). High-throughput approaches in RNA biology. Methods (San Diego, Calif.), 178, 1-2. https://doi.org/10.1016/j.ymeth.2020.04.002

• Biol., T. C. (Ed.). (2019). Membrane-Associated RNA-Binding Proteins Orchestrate Organelle-Coupled Translation.
• Di Liddo, A., de Oliveira Freitas Machado, C., Fischer, S., Ebersberger, S., Heumüller, A. W., Weigand, J. E., Müller-McNicoll, M., & Zarnack, K. (2019). A combined computational pipeline to detect circular RNAs in human cancer cells under hypoxic stress. Journal of Molecular Cell Biology, 11(10), 829-844. https://doi.org/10.1093/jmcb/mjz094
• Elwakeel, E., Brüggemann, M., Fink, A. F., Schulz, M. H., Schmid, T., Savai, R., Brüne, B., Zarnack, K., & Weigert, A. (2019). Phenotypic Plasticity of Fibroblasts during Mammary Carcinoma Development. International Journal of Molecular Sciences, 20(18), Article 18. https://doi.org/10.3390/ijms20184438
• Scholz, A., Eggenhofer, F., Gelhausen, R., Grüning, B., Zarnack, K., Brüne, B., Backofen, R., & Schmid, T. (2019). uORF-Tools—Workflow for the determination of translation-regulatory upstream open reading frames. PLOS ONE, 14(9), 1-9. https://doi.org/10.1371/journal.pone.0222459
• Hildebrandt, A., Brüggemann, M., Rücklé, C., Boerner, S., Heidelberger, J. B., Busch, A., Hänel, H., Voigt, A., Möckel, M. M., Ebersberger, S., Scholz, A., Dold, A., Schmid, T., Ebersberger, I., Roignant, J.-Y., Zarnack, K., König, J., & Beli, P. (2019). The RNA-binding ubiquitin ligase MKRN1 functions in ribosome-associated quality control of poly(A) translation. Genome Biology, 20(1), 216-216. https://doi.org/10.1186/s13059-019-1814-0
• Olgeiser, L., Haag, C., Boerner, S., Ule, J., Busch, A., Koepke, J., König, J., Feldbrügge, M., & Zarnack, K. (2019). The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs. EMBO Reports, 20(1), e46588-. https://doi.org/10.15252/embr.201846588

• Zarnack, K., & Müller-McNicoll, M. (2018). High-Throughput Screens for cis-Acting RNA Sequence Elements That Promote Nuclear Retention. Biochemistry, 57(26), 3542-3543. https://doi.org/10.1021/acs.biochem.8b00479
• Sutandy, F. X. R., Ebersberger, S., Huang, L., Busch, A., Bach, M., Kang, H.-S., Fallmann, J., Maticzka, D., Backofen, R., Stadler, P. F., Zarnack, K., Sattler, M., Legewie, S., & König, J. (2018). In vitro iCLIP-based modeling uncovers how the splicing factor U2AF2 relies on regulation by cofactors. Genome Research, 28(5), 699-713. https://doi.org/10.1101/gr.229757.117
• Braun, S., Enculescu, M., Setty, S. T., Cortés-López, M., de Almeida, B. P., Sutandy, F. X. R., Schulz, L., Busch, A., Seiler, M., Ebersberger, S., Barbosa-Morais, N. L., Legewie, S., König, J., & Zarnack, K. (2018). Decoding a cancer-relevant splicing decision in the RON proto-oncogene using high-throughput mutagenesis. Nature Communications, 9(1), 3315-3315. https://doi.org/10.1038/s41467-018-05748-7

• Hildebrandt, A., Alanis-Lobato, G., Voigt, A., Zarnack, K., Andrade-Navarro, M. A., Beli, P., & König, J. (2017). Interaction profiling of RNA-binding ubiquitin ligases reveals a link between posttranscriptional regulation and the ubiquitin system. Scientific Reports, 7(1), 16582-16582. https://doi.org/10.1038/s41598-017-16695-6
• Dixit, S., Müller-McNicoll, M., David, V., Zarnack, K., Ule, J., Hashimi, H., & Lukeš, J. (2017). Differential Binding of Mitochondrial Transcripts by MRB8170 and MRB4160 Regulates Distinct Editing Fates of Mitochondrial mRNA in Trypanosomes. MBio, 8(1), e02288-16. https://doi.org/10.1128/mBio.02288-16
• Haberman, N., Huppertz, I., Attig, J., König, J., Wang, Z., Hauer, C., Hentze, M. W., Kulozik, A. E., Le Hir, H., Curk, T., Sibley, C. R., Zarnack, K., & Ule, J. (2017). Insights into the design and interpretation of iCLIP experiments. Genome Biology, 18(1), 7-7. https://doi.org/10.1186/s13059-016-1130-x
• Botti, V., McNicoll, F., Steiner, M. C., Richter, F. M., Solovyeva, A., Wegener, M., Schwich, O. D., Poser, I., Zarnack, K., Wittig, I., Neugebauer, K. M., & Müller-McNicoll, M. (2017). Cellular differentiation state modulates the mRNA export activity of SR proteins. The Journal of Cell Biology, 216(7), 1993-2009. https://doi.org/10.1083/jcb.201610051

• Murn, J., Teplova, M., Zarnack, K., Shi, Y., & Patel, D. J. (2016). Recognition of distinct RNA motifs by the clustered CCCH zinc fingers of neuronal protein Unkempt. Nature Structural & Molecular Biology, 23(1), 16-23. https://doi.org/10.1038/nsmb.3140
• Müller-McNicoll, M., Botti, V., de Jesus Domingues, A. M., Brandl, H., Schwich, O. D., Steiner, M. C., Curk, T., Poser, I., Zarnack, K., & Neugebauer, K. M. (2016). SR proteins are NXF1 adaptors that link alternative RNA processing to mRNA export. Genes & Development, 30(5), 553-566. https://doi.org/10.1101/gad.276477.115
• Attig, J., Ruiz de Los Mozos, I., Haberman, N., Wang, Z., Emmett, W., Zarnack, K., König, J., & Ule, J. (2016). Splicing repression allows the gradual emergence of new Alu-exons in primate evolution. ELife, 5, e19545-. https://doi.org/10.7554/eLife.19545

• Murn, J., Zarnack, K., Yang, Y. J., Durak, O., Murphy, E. A., Cheloufi, S., Gonzalez, D. M., Teplova, M., Curk, T., Zuber, J., Patel, D. J., Ule, J., Luscombe, N. M., Tsai, L.-H., Walsh, C. A., & Shi, Y. (2015). Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. Genes & Development, 29(5), 501-512. https://doi.org/10.1101/gad.258483.115
• Diaz-Muñoz, M. D., Bell, S. E., Fairfax, K., Monzon-Casanova, E., Cunningham, A. F., Gonzalez-Porta, M., Andrews, S. R., Bunik, V. I., Zarnack, K., Curk, T., Heggermont, W. A., Heymans, S., Gibson, G. E., Kontoyiannis, D. L., Ule, J., & Turner, M. (2015). The RNA-binding protein HuR is essential for the B cell antibody response. Nature Immunology, 16(4), 415-425. https://doi.org/10.1038/ni.3115
• Tajnik, M., Vigilante, A., Braun, S., Hänel, H., Luscombe, N. M., Ule, J., Zarnack, K., & König, J. (2015). Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. Nucleic Acids Research, 43(21), 10492-10505. https://doi.org/10.1093/nar/gkv956

• Zarnack, K., König, J., Tajnik, M., Martincorena, I., Eustermann, S., Stévant, I., Reyes, A., Anders, S., Luscombe, N. M., & Ule, J. (2013). Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell, 152(3), 453-466. https://doi.org/10.1016/j.cell.2012.12.023

• König, J., Zarnack, K., Luscombe, N. M., & Ule, J. (2012). Protein-RNA interactions: new genomic technologies and perspectives. Nature Reviews. Genetics, 13(2), 77-83. https://doi.org/10.1038/nrg3141

• Koepke, J., Kaffarnik, F., Haag, C., Zarnack, K., Luscombe, N. M., König, J., Ule, J., Kellner, R., Begerow, D., & Feldbrügge, M. (2011). The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1. Molecular & Cellular Proteomics : MCP, 10(12), M111.011213-M111.011213. https://doi.org/10.1074/mcp.M111.011213
• Konig, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D. J., Luscombe, N. M., & Ule, J. (2011). iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. Journal of Visualized Experiments : JoVE, 50, 2638-. https://doi.org/10.3791/2638
• Tollervey, J. R., Wang, Z., Hortobágyi, T., Witten, J. T., Zarnack, K., Kayikci, M., Clark, T. A., Schweitzer, A. C., Rot, G., Curk, T., Zupan, B., Rogelj, B., Shaw, C. E., & Ule, J. (2011). Analysis of alternative splicing associated with aging and neurodegeneration in the human brain. Genome Research, 21(10), 1572-1582. https://doi.org/10.1101/gr.122226.111

• Zarnack, K., & Feldbrügge, M. (2010). Microtubule-dependent mRNA transport in fungi. Eukaryotic Cell, 9(7), 982-990. https://doi.org/10.1128/EC.00030-10
• Wang, Z., Kayikci, M., Briese, M., Zarnack, K., Luscombe, N. M., Rot, G., Zupan, B., Curk, T., & Ule, J. (2010). iCLIP predicts the dual splicing effects of TIA-RNA interactions. PLoS Biology, 8(10), e1000530-e1000530. https://doi.org/10.1371/journal.pbio.1000530
• König, J., Zarnack, K., Rot, G., Curk, T., Kayikci, M., Zupan, B., Turner, D. J., Luscombe, N. M., & Ule, J. (2010). iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nature Structural & Molecular Biology, 17(7), 909-915. https://doi.org/10.1038/nsmb.1838

• König, J., Baumann, S., Koepke, J., Pohlmann, T., Zarnack, K., & Feldbrügge, M. (2009). The fungal RNA-binding protein Rrm4 mediates long-distance transport of ubi1 and rho3 mRNAs. The EMBO Journal, 28(13), 1855-1866. https://doi.org/10.1038/emboj.2009.145
• Vollmeister, E., Haag, C., Zarnack, K., Baumann, S., König, J., Mannhaupt, G., & Feldbrügge, M. (2009). Tandem KH domains of Khd4 recognize AUACCC and are essential for regulation of morphology as well as pathogenicity in Ustilago maydis. RNA (New York, N.Y.), 15(12), 2206-2218. https://doi.org/10.1261/rna.1817609

• Feldbrügge, M., Zarnack, K., Vollmeister, E., Baumann, S., Koepke, J., König, J., Münsterkötter, M., & Mannhaupt, G. (2008). The posttranscriptional machinery of Ustilago maydis. Fungal Genetics and Biology : FG & B, 45 Suppl 1, S40-S46. https://doi.org/10.1016/j.fgb.2008.03.013
• Zarnack, K., Eichhorn, H., Kahmann, R., & Feldbrügge, M. (2008). Pheromone-regulated target genes respond differentially to MAPK phosphorylation of transcription factor Prf1. Molecular Microbiology, 69(4), 1041-1053. https://doi.org/10.1111/j.1365-2958.2008.06345.x

• Zarnack, K., & Feldbrügge, M. (2007). mRNA trafficking in fungi. Molecular Genetics and Genomics : MGG, 278(4), 347-359. https://doi.org/10.1007/s00438-007-0271-8

• Zarnack, K., Maurer, S., Kaffarnik, F., Ladendorf, O., Brachmann, A., Kämper, J., & Feldbrügge, M. (2006). Tetracycline-regulated gene expression in the pathogen Ustilago maydis. Fungal Genetics and Biology : FG & B, 43(11), 727-738. https://doi.org/10.1016/j.fgb.2006.05.006