Attig J, Mozos I, Haberman N, Wang Z, Emmett W, Zarnack K, König J# and Ule J# (2016). Splicing repression allows the gradual emergence of new Alu-exons in primate evolution. eLife, 5, e19545 (#indicates joint correspondence)

Sutandy FX*, Hildebrandt A* and König J (2016). Profiling the binding sites of RNA-binding proteins with nucleotide resolution using iCLIP. Methods Mol Biol, 1358, 175-195 (*indicates joint contribution)

Coelho MB, Attig J, Bellora N, König J, Hallegger M, Kayikci M, Eyras E, Ule J and Smith CW (2015). Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB. EMBO J, 34, 653-668

Tajnik M, Vigilante A, Braun S, Hanel H, Luscombe NM, Ule J, Zarnack K and König J (2015). Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. Nucleic Acids Res, 43, 10492-10505

Baumann S, König J, Koepke J and Feldbrügge M (2014). Endosomal transport of septin mRNA and protein indicates local translation on endosomes and is required for correct septin filamentation. EMBO Rep, 15, 94-102

Huppertz I, Attig J, D'Ambrogio A, Easton LE, Sibley CR, Sugimoto Y, Tajnik M, König J# and Ule J# (2014). iCLIP: protein-RNA interactions at nucleotide resolution. Methods, 653, 274-287 (#indicates joint correspondence)

Rossbach O, Hung LH, Khrameeva E, Schreiner S, König J, Curk T, Zupan B, Ule J, Gelfand MS and Bindereif A (2014). Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L. RNA Biol, 11, 146-155

Anantha RW, Alcivar AL, Ma J, Cai H, Simhadri S, Ule J, König J and Xia B (2013). Requirement of Heterogeneous Nuclear Ribonucleoprotein C for BRCA Gene Expression and Homologous Recombination. PLoS One, 8, e61368

Zarnack K*, König J*, Tajnik M, Martincorena I, Eustermann S, Stévant I, Reyes A, Anders S, Luscombe NM and Ule J (2013). Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements. Cell, 152, 453-466 (*indicates joint contribution)

König J, McGlincy NJ and Ule J (2012). Global analysis of protein-RNA interactions with single-nucleotide resolution using iCLIP. Handbook of RNA Biochemistry, Wiley-Blackwell-VCH. Bindereif A, Hartmann R, Schön A and Westhof E (Eds.)

König J, McGlincy NJ and Ule J (2012). Analysis of protein-RNA interactions with single-nucleotide resolution using iCLIP and Next Generation Sequencing. In: Tag-based Approaches for Next Generation Sequencing, Wiley-Blackwell-VCH. Kahl G, Harbers M (Eds.)

König J, Zarnack K, Luscombe NM and Ule J (2012). Protein-RNA interactions: new genomic technologies and perspectives. Nat Rev Genet, 13, 77-83

Sugimoto Y, König J, Hussain S, Zupan B, Curk T, Frye M and Ule J (2012). Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biol, 13, R67

Koepke J, Kaffarnik F, Haag C, Zarnack K, Luscombe NM, König J, Ule J, Kellner R, Begerow D and Feldbrügge M (2011). The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1. Mol Cell Proteomics, 10, M111.011213

König J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM and Ule J (2011). iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J Vis Exp, doi: 10.3791/2638

Tollervey JR, Curk T, Rogelj B, Briese M, Cereda M, Kayikci M, König J, Hortobágyi T, Nishimura AL, Zupunski V, Patani R, Chandran S, Rot G, Zupan B, Shaw CE and Ule J (2011). Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nat Neurosci, 14, 452-458

König J*, Zarnack K*, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM and Ule J (2010). iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution. Nat Struct Mol Biol, 17, 909-915 (*indicates joint contribution)

König J*, Baumann S*, Koepke J, Pohlmann T, Zarnack K and Feldbrügge M (2009).The fungal RNA-binding protein Rrm4 mediates long-distance transport of ubi1 and rho3 mRNAs. EMBO J, 13, 1855-1866 (*indicates joint contribution)

Vollmeister E, Haag C, Zarnack K, Baumann S, König J, Mannhaupt G and 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, 13, 2206-2218

Feldbrügge M, Zarnack K, Vollmeister E, Baumann S, Koepke J, König J, Münsterkötter M and Mannhaupt G (2008). The posttranscriptional machinery of Ustilago maydis. Fungal Genet Biol, 45, S40-S46

König J*, Julius C*, Baumann S, Homann M, Göringer HU, Feldbrügge M (2007). Combining SELEX and the yeast three-hybrid system for the in vivo selection and classification of RNA aptamers. RNA, 13, 614-622  (*indicates joint contribution)

Becht P*, König J* and Feldbrügge M (2006). The RNA-binding protein Rrm4 is essential for polarity in Ustilago maydis and shuttles along microtubules. J Cell Sci, 119, 4964-4973 (*indicates joint contribution)

Brachmann A*, König J* , Julius C and Feldbrügge M (2004). A reverse genetic approach for generating gene replacement mutants in Ustilago maydis. Mol Genet Genomics, 272, 212-226 (*indicates joint contribution)