RNA motifs: prediction of multivalent RNA motifs that control alternative splicing, HiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1,Ĭereda M, Pozzoli U, Rot G, Juvan P, Schweitzer A, Clark T, Ule J. Sugimoto Y, Vigilante A, Darbo E, Zirra A, Militti C, D’Ambrogio A, Luscombe N*, Ule J* (2105) Recursive splicing in long vertebrate genes, Sibley RC, Emmett W, Blazquez L, Faro A, Haberman N, Briese M, Trabzuni D, Ryten M, Hardy J, UK Brain Expression Consortium, Modic M, Curk T, Wilson SW, Plagnol V*, Ule J* (2105) Splicing repression allows the gradual emergence of new Alu-exons in primate evolution. Insights into the design and interpretation of iCLIP experiments,Īttig J, Ruiz de Los Mozos I, Haberman N, Wang Z, Emmett W, Zarnack K, König J*, Ule J* (2016) Haberman N, Huppertz I, Attig J, König J, Wang Z, Hauer C, Hentze MW, Kulozik AE, Le Hir H, Curk T, Sibley CR, Zarnack K*, Ule J* (2017) Major shifts in glial regional identity are a transcriptional hallmark of human brain aging, Cookson, Colin Smith, Mina Ryten, Rickie Patani*, Jernej Ule* (2017) Lilach Soreq, UK Brain Expression Consortium, North American Brain Expression Consortium, Jamie Rose, Eyal Soreq, John Hardy, Daniah Trabzuni, Mark R. High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43, Cell Reports. Rot G*, Wang Z, Huppertz I, Modic M, Lenče T, Hallegger M, Haberman N, Curk T, von Mering C, Ule J*. Heteromeric RNP assembly at LINEs controls lineage-specific RNA processing,
Jan Attig*, Federico Agostini, Clare Gooding, Anob M Chakrabarti, Julian A Zagalak, Aarti Singh, Nejc Haberman, Warren Emmett, Christopher WJ Smith, Nicholas M Luscombe, Jernej Ule* (2018) Lorea Blazquez*, Warren Emmett, Rupert Faraway, Simon Bajew, Andre Gohr, Nejc Haberman, Christopher R Sibley, Manuel Irimia, Jernej Ule* (2018)Įxon junction complex shapes the transcriptome by repressing recursive splicing, Hauck, Christian von Mering, Alexander Meissner, Tetsuro Hirose, Jernej Ule*, Micha Drukker* (2019)Ĭross-regulation between TDP-43 and paraspeckles promotes pluripotency-differentiation transition, Miha Modic, Markus Grosch, Gregor Rot, Tjasa Lepko, Tomohiro Yamazaki, Dmitry Shaposhnikov, Davide Cacchiarelli, Ejona Rusha, Boris Rogelj, Stefanie M. (2019)Ī systems view of spliceosomal assembly and branchpoints with iCLIP. PsiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation.īriese M, Haberman N, Sibley CR, Faraway R, Elser AS, Chakrabarti AM, Wang Z, König J, Perera D, Wickramasinghe VO, Venkitaraman AR, Luscombe NM, Saieva L, Pellizzoni L, Smith CWJ, Curk T, Ule J. Strittmatter LM, Capitanchik C, Newman AJ, Hallegger M, Norman CM, Fica SM, Oubridge C, Luscombe NM, Ule J, Nagai K. (2021) Ultraplex: A rapid, flexible, all-in-one fastq demultiplexer. Wilkins OG, Capitanchik C, Luscombe NM, Ule J. Hallegger M*, Chakrabarti AM, Lee FCY, Lee BL, Amalietti AG, Odeh HM, Copley KE, Rubien JD, Portz B, Kuret K, Huppertz I, Rau F, Patani R, Fawzi NL, Shorter J, Luscombe NM, Ule J.* (2021) TDP-43 condensation properties specify its RNA-binding and regulatory repertoire. Gameiro PA*, Encheva V, Dos Santos MS, MacRae JI, Ule J* (2021) Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling. Rafiee MR*, Zagalak JA, Sidorov S, Steinhauser S, Davey K, Ule J*, Luscombe NM* (2021) Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs. (2022) Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP. Kuret K, Amalietti AG, Jones DM, Capitanchik C, Ule J. *Co-corresponding authors are marked by a star.
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