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Publications as a corresponding or first author


*Co-first or co-corresponding authors are marked by a star.

Method papers

Reviews

Book contributions

Other research publications


  • Beltran M, Yates CM, Skalska L, Dawson M, Reis FP, Viiri K, Fisher CL, Sibley CR, Foster BM, Bartke T, Ule J, Jenner RG. (2016) The interaction of PRC2 with RNA or chromatin is mutually antagonistic. Genome Res. 2016 Jul;26(7):896-907.
  • Llorian M, Gooding C, Bellora N, Hallegger M, Buckroyd A, Wang X, Rajgor D, Kayikci M, Feltham J, Ule J, Eyras E, Smith CW. (2016) The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators. Nucleic Acids Res. Jun 17. pii: gkw560.
  • Kolisnyk B, Al-Onaizi M, Soreq L, Barbash S, Bekenstein U, Haberman N, Hanin G, Kish MT, Souza da Silva J, Fahnestock M, Ule J, Soreq H, Prado VF, Prado MA. (2016) Cholinergic Surveillance over Hippocampal RNA Metabolism and Alzheimer's-Like Pathology. Cereb Cortex. Jun 16.
  • Coelho MB, Attig J, Ule J, Smith CW. (2016) Matrin3: connecting gene expression with the nuclear matrix. Wiley Interdiscip Rev RNA. Jun 16. pii: bhw177
  • Stražar M, Žitnik M, Zupan B, Ule J, Curk T. (2016) Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins. Bioinformatics. May 15;32(10):1527-35
  • Rivers C, Idris J, Scott H, Rogers M, Lee YB, Gaunt J, Phylactou L, Curk T, Campbell C, Ule J, Norman M, Uney JB (2015) iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function. BMC Biol. Dec 22;13(1):111
  • Tajnik M, Vigilante A, Braun S, Hänel H, Luscombe NM, Ule J, Zarnack K, König J. (2015) Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends. Nucleic Acids Res. Sep 22.
  • Wickramasinghe VO, Gonzàlez-Porta M, Perera D, Bartolozzi AR, Sibley CR, Hallegger M, Ule J, Marioni JC, Venkitaraman AR. (2015) Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength. Genome Biol. Sep 21;16(1):201.
  • Uren PJ, Vo DT, Rosa de Araujo P, Pötschke R, Burns SC, Bahrami-Samani E, Qiao M, de Sousa Abreu R, Nakaya HI, Correa BR, Kühnöl C, Ule J, Martindale JL, Abdelmohsen K, Gorospe M, Smith AD, Penalva LO. (2015) The RNA-binding protein Musashi1 is a central regulator of adhesion pathways in glioblastoma. Mol Cell Biol. Jun 22
  • Mirtschink P, Krishnan J, Grimm F, Sarre A, Hörl M, Kayikci M, Fankhauser N, Christinat Y, Cortijo C, Feehan O, Vukolic A, Sossalla S, Stehr SN, Ule J, Zamboni N, Pedrazzini T, Krek W. (2015) HIF-driven SF3B1 induces KHK-C to enforce fructolysis and heart disease. Nature. 2015 Jun 17
  • Murn J, Zarnack K, Yang YJ, Durak O, Murphy EA, Cheloufi S, Gonzalez DM, Teplova M, Curk T, Zuber J, Patel DJ, Ule J, Luscombe NM, Tsai LH, Walsh CA, Shi Y. (2015) Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. Genes Dev. 2015 Mar 1;29(5):501-12.
  • Diaz-Muñoz MD, Bell SE, Fairfax K, Monzon-Casanova E, Cunningham AF, Gonzalez-Porta M, Andrews SR, Bunik VI, Zarnack K, Curk T, Heggermont WA, Heymans S, Gibson GE, Kontoyiannis DL, Ule J, Turner M. (2015) The RNA-binding protein HuR is essential for the B cell antibody response. Nat Immunol. Feb 23.
  • Coelho MB, Attig J, Bellora N, König J, Hallegger M, Kayikci M, Eyras E, Ule J, Smith CW. (2015) Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB. EMBO J. Jan 19. pii: e201489852.
  • Apolonia L, Schulz R, Curk T, Rocha P, Swanson CM, Schaller T, Ule J, Malim MH. (2015) Promiscuous RNA Binding Ensures Effective Encapsidation of APOBEC3 Proteins by HIV-1. PLoS Pathog. Jan 15;11(1):e1004609. doi: 10.1371/journal.ppat.1004609
  • Huo Q, Kayikci M, Odermatt P, Meyer K, Michels O, Saxena S, Ule J, Schümperli D. (2014) Splicing changes in SMA mouse motoneurons and SMN-depleted neuroblastoma cells: Evidence for involvement of splicing regulatory proteins. RNA Biol. Nov 2;11(11):1430-47. doi: 10.1080/15476286.2014.996494.
  • Machyna M, Kehr S, Straube K, Kappei D, Buchholz F, Butter F, Ule J, Hertel J, Stadler PF, Neugebauer KM. (2014) The Coilin Interactome Identifies Hundreds of Small Noncoding RNAs that Traffic through Cajal Bodies. Mol Cell. Nov 6;56(3):389-399.
  • Boehm V, Haberman N, Ottens F, Ule J, Gehring NH. (2014) 3' UTR Length and Messenger Ribonucleoprotein Composition Determine Endocleavage Efficiencies at Termination Codons. Cell Rep. Oct 7. pii: S2211-1247(14)00780-3.
  • Chan SL, Huppertz I, Yao C, Weng L, Moresco JJ, Yates JR 3rd, Ule J, Manley JL, Shi Y. (2014) CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3' processing. Genes Dev. Oct 9. pii: gad.250993.114.
  • Raj B, Irimia M, Braunschweig U, Sterne-Weiler T, O'Hanlon D, Lin ZY, Chen GI, Easton LE, Ule J, Gingras AC, Eyras E, Blencowe BJ. (2014) A Global Regulatory Mechanism for Activating an Exon Network Required for Neurogenesis. Mol Cell. Sep 9
  • Singh RK, Xia Z, Bland CS, Kalsotra A, Scavuzzo MA, Curk T, Ule J, Li W, Cooper TA. (2014) Rbfox2-Coordinated Alternative Splicing of Mef2d and Rock2 Controls Myoblast Fusion during Myogenesis. Mol Cell. Aug 21;55(4):592-603
  • Blanco S, Dietmann S, Flores JV, Hussain S, Kutter C, Humphreys P, Lukk M, Lombard P, Treps L, Popis M, Kellner S, Hölter SM, Garrett L, Wurst W, Becker L, Klopstock T, Fuchs H, Gailus-Durner V, Hrabĕ de Angelis M, Káradóttir RT, Helm M, Ule J, Gleeson JG, Odom DT, Frye M. (2014) Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders. EMBO J. Jul 25. pii: e201489282.
  • Rossbach O, Hung LH, Khrameeva E, Schreiner S, König J, Curk T, Zupan B, Ule J, Gelfand MS, Bindereif A. (2014) Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L. RNA Biol. Feb;11(2):146-55.
  • Lee YB, Chen HJ, Peres JN, Gomez-Deza J, Attig J, Stalekar M, Troakes C, Nishimura AL, Scotter EL, Vance C, Adachi Y, Sardone V, Miller JW, Smith BN, Gallo JM, Ule J, Hirth F, Rogelj B, Houart C, Shaw CE. (2013) Hexanucleotide Repeats in ALS/FTD Form Length-Dependent RNA Foci, Sequester RNA Binding Proteins, and Are Neurotoxic. Cell Rep. Dec 12;5(5):1178-86.
  • Lukavsky PJ, Daujotyte D, Tollervey JR, Ule J, Stuani C, Buratti E, Baralle FE, Damberger FF, Allain FH. (2013) Molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43. Nat Struct Mol Biol. Nov 17.
  • Doolittle WF, Fraser P, Gerstein MB, Graveley BR, Henikoff S, Huttenhower C, Oshlack A, Ponting CP, Rinn JL, Schatz MC, Ule J, Weigel D, Weinstock GM. (2013) Sixty years of genome biology. Genome Biol. 2013 Apr 25;14(4):113.
  • Anantha RW, Alcivar AL, Ma J, Cai H, Simhadri S, Ule J, König J, Xia B. (2013) Requirement of heterogeneous nuclear ribonucleoprotein C for BRCA gene expression and homologous recombination. PLoS One. 2013 Apr 9;8(4):e61368
  • Schor IE, Llères D, Risso GJ, Pawellek A, Ule J, Lamond AI, Kornblihtt AR. (2012) Perturbation of chromatin structure globally affects localization and recruitment of splicing factors. PLoS One. 2012;7(11):e48084
  • Wagnon JL*, Briese M*, Sun W, Mahaffey CL, Li Y, Curk T, Rot G, Lin DT, Ule J, Frankel WN (2012) CELF4 Regulates Translation and Local Abundance of a Vast Set of mRNAs, Including Genes Associated with Regulation of Synaptic Function. PLOS Genet, Nov;8(11)
  • Sun W, Wagnon JL, Mahaffey CL, Briese M, Ule J, Frankel WN (2012) Aberrant Nav1.6 Activity in the Complex Seizure Disorder of Celf4 Mutant Mice. J. Physiol, 2012 Oct 22.
  • Ince-Dunn G, Okano HJ, Jensen KB, Park WY, Zhong R, Ule J, Mele A, Fak JJ, Yang C, Zhang C, Yoo J, Herre M, Okano H, Noebels JL, Darnell RB. (2012) Neuronal Elav-like (Hu) Proteins Regulate RNA Splicing and Abundance to Control Glutamate Levels and Neuronal Excitability. Neuron. Sep 20;75(6):1067-80
  • Pradeepa MM, Sutherland HG, Ule J, Grimes GR, Bickmore WA. (2012) Psip1/Ledgf p52 Binds Methylated Histone H3K36 and Splicing Factors and Contributes to the Regulation of Alternative Splicing. PLoS Genet. 2012 May;8(5):e1002717.
  • Ankö ML, Müller-McNicoll M, Brandl H, Curk T, Gorup C, Henry I, Ule J, Neugebauer KM. (2012) The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes. Genome Biol. Mar 21;13(3).
  • Léveillé N, Elkon R, Davalos V, Manoharan V, Hollingworth D, Oude Vrielink J, le Sage C, Melo CA, Horlings HM, Wesseling J, Ule J, Esteller M, Ramos A, Agami R. (2011) Selective inhibition of microRNA accessibility by RBM38 is required for p53 activity. Nat Commun. Oct 25;2:513.
  • Koepke J, Kaffarnik F, Haag C, Zarnack K, Luscombe NM, König J, Ule J, Kellner R, Begerow D, Feldbrügge M. (2011) The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1. Mol Cell Proteomics. Dec;10(12):M111.011213.
  • Blazek D, Kohoutek J, Bartholomeeusen K, Johansen E, Hulinkova P, Luo Z, Cimermancic P, Ule J, Peterlin BM. (2011) The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes. Genes Dev. Oct 15;25(20):2158-72.
  • Jelen N, Ule J, Zivin M. (2010) Cholinergic regulation of striatal Nova mRNAs. Neuroscience. Aug 25;169(2):619-27.
  • Huang SC, Shi SH, Ule J, Ruggiu M., Barker L, Darnell RB, Nung Jan Y, and Jan LY (2005) Long-term potentiation of slow synaptic inhibition requires Nova-2 and NMDA receptor activity. Cell. Oct 7;123(1):105-118.
  • Liu F, Ma XH, Ule J, Bibb JA, Nishi A, DeMaggio AJ, Yan Z, Nairn AC, Greengard P. (2001) Regulation of cyclin-dependent kinase 5 and casein kinase 1 by metabotropic glutamate receptors. Proc Natl Acad Sci U S A. Sep 25;98(20):11062-8.
  • Bibb JA, Nishi A, O'Callaghan JP, Ule J, Lan M, Snyder GL, Horiuchi A, Saito T, Hisanaga S, Czernik AJ, Nairn AC, Greengard P. (2001) Phosphorylation of protein phosphatase inhibitor-1 by Cdk5. J Biol Chem. Apr 27;276(17):14490-7.