| Year |
Citation |
Score |
| 2024 |
Monti M, Herman R, Mancini L, Capitanchik C, Davey K, Dawson CS, Ule J, Thomas GH, Willis AE, Lilley KS, Villanueva E. Interrogation of RNA-protein interaction dynamics in bacterial growth. Molecular Systems Biology. PMID 38531971 DOI: 10.1038/s44320-024-00031-y |
0.418 |
|
| 2023 |
West C, Capitanchik C, Cheshire C, Luscombe NM, Chakrabarti A, Ule J. nf-core/clipseq - a robust Nextflow pipeline for comprehensive CLIP data analysis. Wellcome Open Research. 8: 286. PMID 37829674 DOI: 10.12688/wellcomeopenres.19453.1 |
0.739 |
|
| 2023 |
Horlacher M, Wagner N, Moyon L, Kuret K, Goedert N, Salvatore M, Ule J, Gagneur J, Winther O, Marsico A. Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning. Genome Biology. 24: 180. PMID 37542318 DOI: 10.1186/s13059-023-03015-7 |
0.381 |
|
| 2023 |
Pederiva C, Trevisan DM, Peirasmaki D, Chen S, Savage SA, Larsson O, Ule J, Baranello L, Agostini F, Farnebo M. Control of protein synthesis through mRNA pseudouridylation by dyskerin. Science Advances. 9: eadg1805. PMID 37506213 DOI: 10.1126/sciadv.adg1805 |
0.351 |
|
| 2023 |
Mas AM, Goñi E, Ruiz de Los Mozos I, Arcas A, Statello L, González J, Blázquez L, Lee WTC, Gupta D, Sejas Á, Hoshina S, Armaos A, Tartaglia GG, Waga S, Ule J, et al. ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins. Nature Communications. 14: 4447. PMID 37488096 DOI: 10.1038/s41467-023-40105-3 |
0.483 |
|
| 2023 |
Balendra R, Ruiz de Los Mozos I, Odeh HM, Glaria I, Milioto C, Wilson KM, Ule AM, Hallegger M, Masino L, Martin S, Patani R, Shorter J, Ule J, Isaacs AM. Transcriptome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides. Life Science Alliance. 6. PMID 37438085 DOI: 10.26508/lsa.202201824 |
0.469 |
|
| 2023 |
Lin JQ, Khuperkar D, Pavlou S, Makarchuk S, Patikas N, Lee FC, Zbiegly JM, Kang J, Field SF, Bailey DM, Freeman JL, Ule J, Metzakopian E, Ruepp MD, Mallucci GR. HNRNPH1 regulates the neuroprotective cold-shock protein RBM3 expression through poison exon exclusion. The Embo Journal. e113168. PMID 37248947 DOI: 10.15252/embj.2022113168 |
0.381 |
|
| 2023 |
Chakrabarti AM, Haberman N, Praznik A, Luscombe NM, Ule J. Data Science Issues in Studying Protein-RNA Interactions with CLIP Technologies. Annual Review of Biomedical Data Science. 1: 235-261. PMID 37123514 DOI: 10.1146/annurev-biodatasci-080917-013525 |
0.523 |
|
| 2023 |
Iosub IA, Klobučar T, Ule J. Looping in on splicing: CRIC-seq uncovers PTBP1's long-range RNA regulatory rules. Molecular Cell. 83: 1206-1207. PMID 37084712 DOI: 10.1016/j.molcel.2023.03.020 |
0.469 |
|
| 2023 |
Azman MS, Alard EL, Dodel M, Capraro F, Faraway R, Dermit M, Fan W, Chakraborty A, Ule J, Mardakheh FK. An ERK1/2-driven RNA-binding switch in nucleolin drives ribosome biogenesis and pancreatic tumorigenesis downstream of RAS oncogene. The Embo Journal. e110902. PMID 37039106 DOI: 10.15252/embj.2022110902 |
0.341 |
|
| 2023 |
Chakrabarti AM, Iosub IA, Lee FCY, Ule J, Luscombe NM. A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3' UTR structure to RNA metabolism. Nucleic Acids Research. PMID 37013995 DOI: 10.1093/nar/gkad221 |
0.516 |
|
| 2023 |
Chakrabarti AM, Capitanchik C, Ule J, Luscombe NM. clipplotr - a comparative visualisation and analysis tool for CLIP data. Rna (New York, N.Y.). PMID 36894192 DOI: 10.1261/rna.079326.122 |
0.743 |
|
| 2023 |
Rafiee MR, Rohban S, Davey K, Ule J, Luscombe NM. RNA polymerase II-associated proteins reveal pathways affected in VCP-related amyotrophic lateral sclerosis. Brain : a Journal of Neurology. PMID 36789492 DOI: 10.1093/brain/awad046 |
0.348 |
|
| 2022 |
Varier RA, Sideri T, Capitanchik C, Manova Z, Calvani E, Rossi A, Edupuganti RR, Ensinck I, Chan VWC, Patel H, Kirkpatrick J, Faull P, Snijders AP, Vermeulen M, Ralser M, ... Ule J, et al. -methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast. Elife. 11. PMID 36422864 DOI: 10.7554/eLife.84034 |
0.747 |
|
| 2022 |
Hluchý M, Gajdušková P, Ruiz de Los Mozos I, Rájecký M, Kluge M, Berger BT, Slabá Z, Potěšil D, Weiß E, Ule J, Zdráhal Z, Knapp S, Paruch K, Friedel CC, Blazek D. CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1. Nature. 609: 829-834. PMID 36104565 DOI: 10.1038/s41586-022-05204-z |
0.306 |
|
| 2022 |
Kuret K, Amalietti AG, Jones DM, Capitanchik C, Ule J. Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP. Genome Biology. 23: 191. PMID 36085079 DOI: 10.1186/s13059-022-02755-2 |
0.79 |
|
| 2022 |
Alkan F, Wilkins OG, Hernández-Pérez S, Ramalho S, Silva J, Ule J, Faller WJ. Identifying ribosome heterogeneity using ribosome profiling. Nucleic Acids Research. PMID 35687114 DOI: 10.1093/nar/gkac484 |
0.33 |
|
| 2021 |
Leger A, Amaral PP, Pandolfini L, Capitanchik C, Capraro F, Miano V, Migliori V, Toolan-Kerr P, Sideri T, Enright AJ, Tzelepis K, van Werven FJ, Luscombe NM, Barbieri I, Ule J, et al. RNA modifications detection by comparative Nanopore direct RNA sequencing. Nature Communications. 12: 7198. PMID 34893601 DOI: 10.1038/s41467-021-27393-3 |
0.783 |
|
| 2021 |
Fernández-Moya SM, Ehses J, Bauer KE, Schieweck R, Chakrabarti AM, Lee FCY, Illig C, Luscombe NM, Harner M, Ule J, Kiebler MA. RNA Secondary Structure Mediates Staufen2 RNP Assembly in Neurons. International Journal of Molecular Sciences. 22. PMID 34884825 DOI: 10.3390/ijms222313021 |
0.507 |
|
| 2021 |
Rafiee MR, Zagalak JA, Sidorov S, Steinhauser S, Davey K, Ule J, Luscombe NM. Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs. Nucleic Acids Research. 49: 13092-13107. PMID 34871434 DOI: 10.1093/nar/gkab1180 |
0.357 |
|
| 2021 |
Gameiro PA, Encheva V, Dos Santos MS, MacRae JI, Ule J. Metabolic turnover and dynamics of modified ribonucleosides by C labeling. The Journal of Biological Chemistry. 297: 101294. PMID 34634303 DOI: 10.1016/j.jbc.2021.101294 |
0.421 |
|
| 2021 |
Gong C, Krupka JA, Gao J, Grigoropoulos NF, Giotopoulos G, Asby R, Screen M, Usheva Z, Cucco F, Barrans S, Painter D, Zaini NBM, Haupl B, Bornelöv S, Ruiz De Los Mozos I, ... ... Ule J, et al. Sequential inverse dysregulation of the RNA helicases DDX3X and DDX3Y facilitates MYC-driven lymphomagenesis. Molecular Cell. PMID 34437837 DOI: 10.1016/j.molcel.2021.07.041 |
0.329 |
|
| 2021 |
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, ... ... Ule J, et al. TDP-43 condensation properties specify its RNA-binding and regulatory repertoire. Cell. PMID 34380047 DOI: 10.1016/j.cell.2021.07.018 |
0.5 |
|
| 2021 |
Wilkins OG, Capitanchik C, Luscombe NM, Ule J. Ultraplex: A rapid, flexible, all-in-one fastq demultiplexer. Wellcome Open Research. 6: 141. PMID 34286104 DOI: 10.12688/wellcomeopenres.16791.1 |
0.702 |
|
| 2021 |
Wei G, Almeida M, Pintacuda G, Coker H, Bowness JS, Ule J, Brockdorff N. Acute depletion of METTL3 implicates -methyladenosine in alternative intron/exon inclusion in the nascent transcriptome. Genome Research. 31: 1395-1408. PMID 34131006 DOI: 10.1101/gr.271635.120 |
0.467 |
|
| 2021 |
Agostini F, Zagalak J, Attig J, Ule J, Luscombe NM. Intergenic RNA mainly derives from nascent transcripts of known genes. Genome Biology. 22: 136. PMID 33952325 DOI: 10.1186/s13059-021-02350-x |
0.406 |
|
| 2021 |
Strittmatter LM, Capitanchik C, Newman AJ, Hallegger M, Norman CM, Fica SM, Oubridge C, Luscombe NM, Ule J, Nagai K. psiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation. Nature Communications. 12: 1488. PMID 33674615 DOI: 10.1038/s41467-021-21745-9 |
0.781 |
|
| 2020 |
Capitanchik C, Toolan-Kerr P, Luscombe NM, Ule J. How Do You Identify m6 A Methylation in Transcriptomes at High Resolution? A Comparison of Recent Datasets. Frontiers in Genetics. 11: 398. PMID 32508872 DOI: 10.3389/Fgene.2020.00398 |
0.761 |
|
| 2019 |
Ule J, Blencowe BJ. Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution. Molecular Cell. 76: 329-345. PMID 31626751 DOI: 10.1016/j.molcel.2019.09.017 |
0.396 |
|
| 2019 |
Briese 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, ... ... Ule J, et al. A systems view of spliceosomal assembly and branchpoints with iCLIP. Nature Structural & Molecular Biology. PMID 31570875 DOI: 10.1038/S41594-019-0300-4 |
0.476 |
|
| 2019 |
Skalska L, Beltran-Nebot M, Ule J, Jenner RG. Author Correction: Regulatory feedback from nascent RNA to chromatin and transcription. Nature Reviews. Molecular Cell Biology. 20: 715. PMID 31506602 DOI: 10.1038/s41580-019-0174-7 |
0.372 |
|
| 2019 |
Tyzack GE, Luisier R, Taha DM, Neeves J, Modic M, Mitchell JS, Meyer I, Greensmith L, Newcombe J, Ule J, Luscombe NM, Patani R. Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis. Brain : a Journal of Neurology. PMID 31368485 DOI: 10.1093/Brain/Awz217 |
0.308 |
|
| 2019 |
Obrdlik A, Lin G, Haberman N, Ule J, Ephrussi A. The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila. Cell Reports. 28: 1219-1236.e11. PMID 31365866 DOI: 10.1016/j.celrep.2019.06.088 |
0.476 |
|
| 2019 |
Carter JM, Emmett W, Mozos IR, Kotter A, Helm M, Ule J, Hussain S. FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA. Nucleic Acids Research. PMID 31361898 DOI: 10.1093/nar/gkz658 |
0.431 |
|
| 2019 |
Modic M, Grosch M, Rot G, Schirge S, Lepko T, Yamazaki T, Lee FCY, Rusha E, Shaposhnikov D, Palo M, Merl-Pham J, Cacchiarelli D, Rogelj B, Hauck SM, von Mering C, ... ... Ule J, et al. Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition. Molecular Cell. PMID 31047794 DOI: 10.1016/J.Molcel.2019.03.041 |
0.337 |
|
| 2019 |
Bugai A, Quaresma AJC, Friedel CC, Lenasi T, Düster R, Sibley CR, Fujinaga K, Kukanja P, Hennig T, Blasius M, Geyer M, Ule J, Dölken L, Barborič M. P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress Molecular Cell. 74: 254. PMID 30824372 DOI: 10.1016/J.Molcel.2019.01.033 |
0.331 |
|
| 2019 |
Attig J, Ule J. Genomic Accumulation of Retrotransposons Was Facilitated by Repressive RNA-Binding Proteins: A Hypothesis. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 41: e1800132. PMID 30706962 DOI: 10.1002/bies.201800132 |
0.469 |
|
| 2019 |
Olgeiser L, Haag C, Boerner S, Ule J, Busch A, Koepke J, König J, Feldbrügge M, Zarnack K. The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs. Embo Reports. 20. PMID 30552148 DOI: 10.15252/embr.201846588 |
0.304 |
|
| 2018 |
Attig J, Agostini F, Gooding C, Chakrabarti AM, Singh A, Haberman N, Zagalak JA, Emmett W, Smith CWJ, Luscombe NM, Ule J. Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing. Cell. PMID 30078707 DOI: 10.1016/j.cell.2018.07.001 |
0.408 |
|
| 2018 |
Ule J, Hwang HW, Darnell RB. The Future of Cross-Linking and Immunoprecipitation (CLIP). Cold Spring Harbor Perspectives in Biology. 10. PMID 30068528 DOI: 10.1101/Cshperspect.A032243 |
0.655 |
|
| 2018 |
Huppertz I, Haberman N, Ule J. 'Read-through marking' reveals differential nucleotide composition of read-through and truncated cDNAs in iCLIP. Wellcome Open Research. 3: 77. PMID 30057947 DOI: 10.12688/wellcomeopenres.14663.1 |
0.409 |
|
| 2018 |
Agostini F, Ule J, Zagalak JA. No way out: when RNA elements promote nuclear retention. The Embo Journal. PMID 29487065 DOI: 10.15252/embj.201899123 |
0.403 |
|
| 2018 |
Lee FCY, Ule J. Advances in CLIP Technologies for Studies of Protein-RNA Interactions. Molecular Cell. 69: 354-369. PMID 29395060 DOI: 10.1016/j.molcel.2018.01.005 |
0.53 |
|
| 2017 |
Díaz-Muñoz MD, Kiselev VY, Novère NL, Curk T, Ule J, Turner M. Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells. Nature Communications. 8: 530. PMID 28904350 DOI: 10.1038/S41467-017-00454-2 |
0.306 |
|
| 2017 |
Rot G, Wang Z, Huppertz I, Modic M, Lenče T, Hallegger M, Haberman N, Curk T, von Mering C, Ule J. High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43. Cell Reports. 19: 1056-1067. PMID 28467899 DOI: 10.1016/J.Celrep.2017.04.028 |
0.498 |
|
| 2017 |
Skalska L, Beltran-Nebot M, Ule J, Jenner RG. Regulatory feedback from nascent RNA to chromatin and transcription. Nature Reviews. Molecular Cell Biology. 18: 331-337. PMID 28270684 DOI: 10.1038/nrm.2017.12 |
0.474 |
|
| 2017 |
Sugimoto Y, Chakrabarti AM, Luscombe NM, Ule J. Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein. Nature Protocols. 12: 611-637. PMID 28230851 DOI: 10.1038/nprot.2016.188 |
0.521 |
|
| 2017 |
Dixit S, Müller-McNicoll M, David V, Zarnack K, Ule J, Hashimi H, Lukeš J. Differential Binding of Mitochondrial Transcripts by MRB8170 and MRB4160 Regulates Distinct Editing Fates of Mitochondrial mRNA in Trypanosomes. Mbio. 8. PMID 28143982 DOI: 10.1128/mBio.02288-16 |
0.462 |
|
| 2017 |
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. Insights into the design and interpretation of iCLIP experiments. Genome Biology. 18: 7. PMID 28093074 DOI: 10.1186/S13059-016-1130-X |
0.45 |
|
| 2016 |
Llorian M, Gooding C, Bellora N, Hallegger M, Buckroyd A, Wang X, Rajgor D, Kayikci M, Feltham J, Ule J, Eyras E, Smith CW. The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators. Nucleic Acids Research. PMID 27317697 DOI: 10.1093/nar/gkw560 |
0.304 |
|
| 2016 |
Sibley CR, Blazquez L, Ule J. Lessons from non-canonical splicing. Nature Reviews. Genetics. 17: 407-421. PMID 27240813 DOI: 10.1038/nrg.2016.46 |
0.341 |
|
| 2016 |
Beltran M, Yates CM, Skalska L, Dawson M, Reis FP, Viiri K, Fisher CL, Sibley CR, Foster BM, Bartke T, Ule J, Jenner RG. The interaction of PRC2 with RNA or chromatin is mutually antagonistic. Genome Research. PMID 27197219 DOI: 10.1101/gr.197632.115 |
0.49 |
|
| 2016 |
Coelho MB, Attig J, Ule J, Smith CW. Matrin3: connecting gene expression with the nuclear matrix. Wiley Interdisciplinary Reviews. Rna. PMID 26813864 DOI: 10.1002/wrna.1336 |
0.368 |
|
| 2016 |
Stražar M, Žitnik M, Zupan B, Ule J, Curk T. Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins. Bioinformatics (Oxford, England). 32: 1527-35. PMID 26787667 DOI: 10.1093/bioinformatics/btw003 |
0.515 |
|
| 2015 |
Rivers C, Idris J, Scott H, Rogers M, Lee YB, Gaunt J, Phylactou L, Curk T, Campbell C, Ule J, Norman M, Uney JB. iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function. Bmc Biology. 13: 111. PMID 26694817 DOI: 10.1186/S12915-015-0220-7 |
0.432 |
|
| 2015 |
Wickramasinghe VO, Gonzàlez-Porta M, Perera D, Bartolozzi AR, Sibley CR, Hallegger M, Ule J, Marioni JC, Venkitaraman AR. Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength. Genome Biology. 16: 201. PMID 26392272 DOI: 10.1186/s13059-015-0749-3 |
0.343 |
|
| 2015 |
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, et al. The RNA-binding protein Musashi1 is a central regulator of adhesion pathways in glioblastoma. Molecular and Cellular Biology. PMID 26100017 DOI: 10.1128/MCB.00410-15 |
0.428 |
|
| 2015 |
Sugimoto Y, Vigilante A, Darbo E, Zirra A, Militti C, D'Ambrogio A, Luscombe NM, Ule J. hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1. Nature. 519: 491-4. PMID 25799984 DOI: 10.1038/nature14280 |
0.464 |
|
| 2015 |
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, et al. Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt. Genes & Development. 29: 501-12. PMID 25737280 DOI: 10.1101/Gad.258483.115 |
0.404 |
|
| 2015 |
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, et al. The RNA-binding protein HuR is essential for the B cell antibody response. Nature Immunology. 16: 415-25. PMID 25706746 DOI: 10.1038/Ni.3115 |
0.412 |
|
| 2015 |
Coelho MB, Attig J, Bellora N, König J, Hallegger M, Kayikci M, Eyras E, Ule J, Smith CW. Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB. The Embo Journal. 34: 653-68. PMID 25599992 DOI: 10.15252/embj.201489852 |
0.416 |
|
| 2015 |
Apolonia L, Schulz R, Curk T, Rocha P, Swanson CM, Schaller T, Ule J, Malim MH. Promiscuous RNA binding ensures effective encapsidation of APOBEC3 proteins by HIV-1. Plos Pathogens. 11: e1004609. PMID 25590131 DOI: 10.1371/Journal.Ppat.1004609 |
0.412 |
|
| 2014 |
Machyna M, Kehr S, Straube K, Kappei D, Buchholz F, Butter F, Ule J, Hertel J, Stadler PF, Neugebauer KM. The coilin interactome identifies hundreds of small noncoding RNAs that traffic through Cajal bodies. Molecular Cell. 56: 389-99. PMID 25514182 DOI: 10.1016/J.Molcel.2014.10.004 |
0.481 |
|
| 2014 |
Chan SL, Huppertz I, Yao C, Weng L, Moresco JJ, Yates JR, Ule J, Manley JL, Shi Y. CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3' processing. Genes & Development. 28: 2370-80. PMID 25301780 DOI: 10.1101/Gad.250993.114 |
0.392 |
|
| 2014 |
Singh RK, Xia Z, Bland CS, Kalsotra A, Scavuzzo MA, Curk T, Ule J, Li W, Cooper TA. Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis. Molecular Cell. 55: 592-603. PMID 25087874 DOI: 10.1016/J.Molcel.2014.06.035 |
0.452 |
|
| 2014 |
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, ... ... Ule J, et al. Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders. The Embo Journal. 33: 2020-39. PMID 25063673 DOI: 10.15252/Embj.201489282 |
0.394 |
|
| 2014 |
Rossbach O, Hung LH, Khrameeva E, Schreiner S, König J, Curk T, Zupan B, Ule J, Gelfand MS, Bindereif A. Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L. Rna Biology. 11: 146-55. PMID 24526010 DOI: 10.4161/rna.27991 |
0.338 |
|
| 2014 |
Rinn JL, Ule J. 'Oming in on RNA-protein interactions. Genome Biology. 15: 401. PMID 24485348 DOI: 10.1186/gb4158 |
0.435 |
|
| 2014 |
Cereda M, Pozzoli U, Rot G, Juvan P, Schweitzer A, Clark T, Ule J. RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing. Genome Biology. 15: R20. PMID 24485098 DOI: 10.1186/Gb-2014-15-1-R20 |
0.499 |
|
| 2014 |
Huppertz I, Attig J, D'Ambrogio A, Easton LE, Sibley CR, Sugimoto Y, Tajnik M, König J, Ule J. iCLIP: protein-RNA interactions at nucleotide resolution. Methods (San Diego, Calif.). 65: 274-87. PMID 24184352 DOI: 10.1016/j.ymeth.2013.10.011 |
0.519 |
|
| 2013 |
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, et al. Hexanucleotide repeats in ALS/FTD form length-dependent RNA foci, sequester RNA binding proteins, and are neurotoxic. Cell Reports. 5: 1178-86. PMID 24290757 DOI: 10.1016/J.Celrep.2013.10.049 |
0.468 |
|
| 2013 |
Lukavsky PJ, Daujotyte D, Tollervey JR, Ule J, Stuani C, Buratti E, Baralle FE, Damberger FF, Allain FH. Molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43. Nature Structural & Molecular Biology. 20: 1443-9. PMID 24240615 DOI: 10.1038/Nsmb.2698 |
0.495 |
|
| 2013 |
Kiebler MA, Scheiffele P, Ule J. What, where, and when: the importance of post-transcriptional regulation in the brain. Frontiers in Neuroscience. 7: 192. PMID 24194693 DOI: 10.3389/fnins.2013.00192 |
0.411 |
|
| 2013 |
Hussain S, Sajini AA, Blanco S, Dietmann S, Lombard P, Sugimoto Y, Paramor M, Gleeson JG, Odom DT, Ule J, Frye M. NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs. Cell Reports. 4: 255-61. PMID 23871666 DOI: 10.1016/J.Celrep.2013.06.029 |
0.46 |
|
| 2013 |
Modic M, Ule J, Sibley CR. CLIPing the brain: studies of protein-RNA interactions important for neurodegenerative disorders. Molecular and Cellular Neurosciences. 56: 429-35. PMID 23583633 DOI: 10.1016/j.mcn.2013.04.002 |
0.497 |
|
| 2012 |
Wagnon JL, Briese M, Sun W, Mahaffey CL, Curk T, Rot G, Ule J, Frankel WN. CELF4 regulates translation and local abundance of a vast set of mRNAs, including genes associated with regulation of synaptic function. Plos Genetics. 8: e1003067. PMID 23209433 DOI: 10.1371/Journal.Pgen.1003067 |
0.348 |
|
| 2012 |
Schor IE, Llères D, Risso GJ, Pawellek A, Ule J, Lamond AI, Kornblihtt AR. Perturbation of chromatin structure globally affects localization and recruitment of splicing factors. Plos One. 7: e48084. PMID 23152763 DOI: 10.1371/journal.pone.0048084 |
0.33 |
|
| 2012 |
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. Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability. Neuron. 75: 1067-80. PMID 22998874 DOI: 10.1016/J.Neuron.2012.07.009 |
0.569 |
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| 2012 |
Rogelj B, Easton LE, Bogu GK, Stanton LW, Rot G, Curk T, Zupan B, Sugimoto Y, Modic M, Haberman N, Tollervey J, Fujii R, Takumi T, Shaw CE, Ule J. Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain. Scientific Reports. 2: 603. PMID 22934129 DOI: 10.1038/Srep00603 |
0.474 |
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| 2012 |
Sugimoto Y, König J, Hussain S, Zupan B, Curk T, Frye M, Ule J. Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions. Genome Biology. 13: R67. PMID 22863408 DOI: 10.1186/gb-2012-13-8-r67 |
0.494 |
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| 2012 |
Änkö ML, Müller-McNicoll M, Brandl H, Curk T, Gorup C, Henry I, Ule J, Neugebauer KM. The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes. Genome Biology. 13: R17. PMID 22436691 DOI: 10.1186/gb-2012-13-3-r17 |
0.499 |
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| 2012 |
Patani R, Sibley CR, Chandran S, Ule J. Using human pluripotent stem cells to study post-transcriptional mechanisms of neurodegenerative diseases. Brain Research. 1462: 129-38. PMID 22285437 DOI: 10.1016/j.brainres.2011.12.057 |
0.38 |
|
| 2011 |
König J, Zarnack K, Luscombe NM, Ule J. Protein-RNA interactions: new genomic technologies and perspectives. Nature Reviews. Genetics. 13: 77-83. PMID 22251872 DOI: 10.1038/nrg3141 |
0.532 |
|
| 2011 |
Koepke J, Kaffarnik F, Haag C, Zarnack K, Luscombe NM, König J, Ule J, Kellner R, Begerow D, Feldbrügge M. The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1. Molecular & Cellular Proteomics : McP. 10: M111.011213. PMID 21808052 DOI: 10.1074/mcp.M111.011213 |
0.305 |
|
| 2011 |
Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, Turner DJ, Luscombe NM, Ule J. iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. Journal of Visualized Experiments : Jove. PMID 21559008 DOI: 10.3791/2638 |
0.546 |
|
| 2011 |
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, ... Ule J, et al. Characterizing the RNA targets and position-dependent splicing regulation by TDP-43. Nature Neuroscience. 14: 452-8. PMID 21358640 DOI: 10.1038/Nn.2778 |
0.498 |
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| 2011 |
Witten JT, Ule J. Understanding splicing regulation through RNA splicing maps. Trends in Genetics : Tig. 27: 89-97. PMID 21232811 DOI: 10.1016/J.Tig.2010.12.001 |
0.47 |
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| 2011 |
Ayala YM, De Conti L, Avendaño-Vázquez SE, Dhir A, Romano M, D'Ambrogio A, Tollervey J, Ule J, Baralle M, Buratti E, Baralle FE. TDP-43 regulates its mRNA levels through a negative feedback loop. The Embo Journal. 30: 277-88. PMID 21131904 DOI: 10.1038/Emboj.2010.310 |
0.419 |
|
| 2010 |
Wang Z, Kayikci M, Briese M, Zarnack K, Luscombe NM, Rot G, Zupan B, Curk T, Ule J. iCLIP predicts the dual splicing effects of TIA-RNA interactions. Plos Biology. 8: e1000530. PMID 21048981 DOI: 10.1371/Journal.Pbio.1000530 |
0.47 |
|
| 2010 |
Racca C, Gardiol A, Eom T, Ule J, Triller A, Darnell RB. The Neuronal Splicing Factor Nova Co-Localizes with Target RNAs in the Dendrite. Frontiers in Neural Circuits. 4: 5. PMID 20407637 DOI: 10.3389/Neuro.04.005.2010 |
0.639 |
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| 2010 |
Ule J. High-throughput sequencing methods to study neuronal RNA-protein interactions. Biochemical Society Transactions. 37: 1278-80. PMID 19909262 DOI: 10.1042/BST0371278 |
0.418 |
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| 2009 |
Wang Z, Tollervey J, Briese M, Turner D, Ule J. CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo. Methods (San Diego, Calif.). 48: 287-93. PMID 19272451 DOI: 10.1016/j.ymeth.2009.02.021 |
0.506 |
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| 2008 |
Licatalosi DD, Mele A, Fak JJ, Ule J, Kayikci M, Chi SW, Clark TA, Schweitzer AC, Blume JE, Wang X, Darnell JC, Darnell RB. HITS-CLIP yields genome-wide insights into brain alternative RNA processing. Nature. 456: 464-9. PMID 18978773 DOI: 10.1038/nature07488 |
0.676 |
|
| 2008 |
Ule J. Ribonucleoprotein complexes in neurologic diseases. Current Opinion in Neurobiology. 18: 516-23. PMID 18929657 DOI: 10.1016/j.conb.2008.09.018 |
0.491 |
|
| 2008 |
Ule J. Jernej Ule: an RNA runaway success. Interview by Ruth Williams. The Journal of Cell Biology. 180: 448-9. PMID 18268098 DOI: 10.1083/jcb.1803pi |
0.445 |
|
| 2007 |
Ule J, Darnell RB. Functional and mechanistic insights from genome-wide studies of splicing regulation in the brain. Advances in Experimental Medicine and Biology. 623: 148-60. PMID 18380345 |
0.643 |
|
| 2007 |
Jelen N, Ule J, Zivin M, Darnell RB. Evolution of Nova-dependent splicing regulation in the brain. Plos Genetics. 3: 1838-47. PMID 17937501 DOI: 10.1371/journal.pgen.0030173 |
0.547 |
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| 2006 |
Ule J, Stefani G, Mele A, Ruggiu M, Wang X, Taneri B, Gaasterland T, Blencowe BJ, Darnell RB. An RNA map predicting Nova-dependent splicing regulation. Nature. 444: 580-6. PMID 17065982 DOI: 10.1038/Nature05304 |
0.709 |
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| 2006 |
Ule J, Darnell RB. RNA binding proteins and the regulation of neuronal synaptic plasticity. Current Opinion in Neurobiology. 16: 102-10. PMID 16418001 DOI: 10.1016/j.conb.2006.01.003 |
0.606 |
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| 2005 |
Ule J, Jensen K, Mele A, Darnell RB. CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods (San Diego, Calif.). 37: 376-86. PMID 16314267 DOI: 10.1016/j.ymeth.2005.07.018 |
0.641 |
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| 2005 |
Huang CS, Shi SH, Ule J, Ruggiu M, Barker LA, Darnell RB, Jan YN, Jan LY. Common molecular pathways mediate long-term potentiation of synaptic excitation and slow synaptic inhibition. Cell. 123: 105-18. PMID 16213216 DOI: 10.1016/J.Cell.2005.07.033 |
0.45 |
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| 2005 |
Ule J, Ule A, Spencer J, Williams A, Hu JS, Cline M, Wang H, Clark T, Fraser C, Ruggiu M, Zeeberg BR, Kane D, Weinstein JN, Blume J, Darnell RB. Nova regulates brain-specific splicing to shape the synapse. Nature Genetics. 37: 844-52. PMID 16041372 DOI: 10.1038/Ng1610 |
0.616 |
|
| 2003 |
Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, Darnell RB. CLIP identifies Nova-regulated RNA networks in the brain. Science (New York, N.Y.). 302: 1212-5. PMID 14615540 DOI: 10.1126/science.1090095 |
0.64 |
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