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Breadcrumb Jernej Ule Ule lab RNA Networks Laboratory : Publications Lab contentLab contentIn this section Overview Areas of interest Publications Members Vacancies Genes in the brain are very long and can be transcribed into diverse RNAs. Toggle to view hero caption PublicationsYear published2024 (2)2023 (15)2022 (9)2021 (16)2020 (6)2019 (10)2018 (13)2017 (7)2015 (1) Facet Year publishedResearch topicsGene Expression (79)Genetics & Genomics (79)Biochemistry & Proteomics (78)Neurosciences (78)Stem Cells (78)Tumour Biology (27)Cell Biology (15)Chemical Biology & High Throughput (10)Model Organisms (6)Cell Cycle & Chromosomes (5)Genome Integrity & Repair (5)Structural Biology & Biophysics (5)Synthetic Biology (5)Metabolism (4)Signalling & Oncogenes (4)Developmental Biology (3)Human Biology & Physiology (3)Immunology (3)Infectious Disease (3)Imaging (2)Microfabrication & Bioengineering (2) (-)Computational & Systems Biology (79) Facet Research topicsPublication typeJournal article (79)Primary research (62)Review (10)Commentary (3)Method (3)Editorial (1) Facet Publication typeJournalMolecular Cell (9)Nature Communications (8)Nucleic Acids Research (6)Genome Biology (5)Nature (4)Cell Reports (3)eLife (3)International Journal of Molecular Sciences (3)Brain (2)Cell (2)EMBO Journal (2)EMBO Reports (2)Nature Reviews Methods Primers (2)Nature Structural and Molecular Biology (2)RNA Biology (2)The EMBO Journal (2)Wellcome Open Research (2)Annual Review of Biomedical Data Science (1)BioEssays (1)Cell Death & Differentiation (1)Cold Spring Harbor Perspectives in Biology (1)Developmental Cell (1)Frontiers in Genetics (1)Frontiers in Immunology (1)Genome Research (1)Journal of Biological Chemistry (1)Life Science Alliance (1)Molecular Systems Biology (1)Molecular Therapy - Nucleic Acids (1)Nature Ecology & Evolution (1)Nature Protocols (1)Nature Reviews Molecular Cell Biology (1)Neuron (1)RNA (1)Science advances (1)Science Translational Medicine (1)The Lancet (1) Facet Journal Publications Displaying 1 - 20 of 79Last updated : 16 April 2024 02:37 Interrogation of RNA-protein interaction dynamics in bacterial growth Authors (11) Mie Monti Reyme Herman Leonardo ManciniCharlotte Capitanchik Karen Davey Charlotte S DawsonJernej Ule Gavin H Thomas Anne E Willis Kathryn S Lilley Eneko Villanueva Molecular Systems Biology Published 26 March 2024 Crick labsJernej UleFull details Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD Authors (51) Sahba Seddighi Yue A Qi Anna-Leigh BrownOscar Wilkins Colleen Bereda Cedric Belair[...] Nicholas T Seyfried Manolis Maragkakis Leonard PetrucelliPietro Fratta Michael E Ward Science Translational Medicine Published 14 February 2024 Crick labsJernej UlePietro FrattaFull details Subcytoplasmic location of translation controls protein output Authors (9) Ellen L Horste Mervin M Fansler Ting Cai Xiuzhen Chen Sibylle Mitschka Gang ZhenFlora LeeJernej Ule Christine Mayr Molecular Cell Published 21 December 2023 Crick labsJernej UleFull details Transcriptome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides Authors (14) Rubika BalendraIgor Ruiz De Los Mozos Hana M Odeh Idoia Glaria Carmelo Milioto Katherine M Wilson[...] Stephen MartinRickie Patani James ShorterJernej Ule Adrian M Isaacs Life Science Alliance Published 1 September 2023 Crick labs/ facilitiesJernej UleRickie PataniStructural BiologyHigh Throughput ScreeningFull details Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning Authors (10) Marc Horlacher Nils Wagner Lambert Moyon Klara Kuret Nicolas Goedert Marco SalvatoreJernej Ule Julien Gagneur Ole Winther Annalisa Marsico Genome Biology Published 4 August 2023 Crick labsJernej UleFull details Control of protein synthesis through mRNA pseudouridylation by dyskerin Authors (10) Chiara Pederiva Davide M Trevisan Dimitra Peirasmaki Shan Chen Sharon A Savage Ola LarssonJernej Ule Laura Baranello Federico Agostini Marianne Farnebo Science advances Published 28 July 2023 Crick labs/ facilitiesJernej UleAdvanced SequencingFull details ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins Authors (18) Aina Maria Mas Enrique Goñi Igor Ruiz de los Mozos Aida Arcas Luisa Statello Jovanna González[...] Shou WagaJernej Ule Eli Rothenberg María Gómez Maite Huarte Nature Communications Published 24 July 2023 Crick labsJernej UleFull details Nucleocytoplasmic mRNA redistribution accompanies RNA binding protein mislocalization in ALS motor neurons and is restored by VCP ATPase inhibition Authors (10)Oliver ZiffJasmine HarleyYiran WangJacob NeevesGiulia Tyzack Fairouz IbrahimMark SkehelAnob ChakrabartiGavin KellyRickie Patani Neuron Published 4 October 2023 Crick labs/ facilitiesJernej UleRickie PataniProteomicsBioinformatics and BiostatisticsFull details The paralogues MAGOH and MAGOHB are oncogenic factors in high-grade gliomas and safeguard the splicing of cell division and cell cycle genes Authors (15) Rodrigo AS Barreiro Gabriela DA Guardia Fabiana M Meliso Xiufen Lei Wei-Qing Li Andre Savio[...] Mei Qiao Lorea BlazquezJernej Ule Luiz OF Penalva Pedro AF Galante RNA Biology Published 9 June 2023 Crick labsJernej UleFull details HNRNPH1 regulates the neuroprotective cold-shock protein RBM3 expression through poison exon exclusion Authors (15) Julie Qiaojin Lin Deepak Khuperkar Sofia Pavlou Stanislaw Makarchuk Nikolaos PatikasFlora Lee[...] Joshua L FreemanJernej Ule Emmanouil Metzakopian Marc-David Ruepp Giovanna R Mallucci The EMBO Journal Published 17 July 2023 Crick labsJernej UleFull details Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology Authors (14)Oliver ZiffJacob NeevesJamie MitchellGiulia Tyzack Carlos Martinez-Ruiz Raphaelle Luisier[...]Simon Boulton Ammar Al-ChalabiGavin Kelly Jack HumphreyRickie Patani Nature Communications Published 20 April 2023 Crick labs/ facilitiesJernej UleRickie PataniSimon BoultonBioinformatics and BiostatisticsScientific computingFull details Looping in on splicing: CRIC-seq uncovers PTBP1's long-range RNA regulatory rules Authors (3) Ira Alexandra Iosub Tajda KlobučarJernej Ule Molecular Cell Published 20 April 2023 Crick labsJernej UleNicholas LuscombeFull details An ERK1/2-driven RNA-binding switch in nucleolin drives ribosome biogenesis and pancreatic tumorigenesis downstream of RAS oncogene Authors (10) Muhammad S Azman Emilie L Alard Martin Dodel Federica CapraroRupert Faraway Maria Dermit Wanling Fan Alina ChakrabortyJernej Ule Faraz K Mardakheh The EMBO Journal Published 1 June 2023 Crick labsJernej UleFull details A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3' UTR structure to RNA metabolism Authors (5)Anob Chakrabarti Ira A IosubFlora LeeJernej UleNicholas Luscombe Nucleic Acids Research Published 8 May 2023 Crick labsJernej UleNicholas LuscombeFull details clipplotr - a comparative visualization and analysis tool for CLIP data Authors (4)Anob ChakrabartiCharlotte CapitanchikJernej UleNicholas Luscombe RNA Published 1 June 2023 Crick labsJernej UleNicholas LuscombeFull details Lactate exposure shapes the metabolic and transcriptomic profile of CD8+ T cells Authors (9) Laura Barbieri Pedro VeliçaPaulo Gameiro Pedro P Cunha Iosifina P Foskolou Eric Rullman David Bargiela Randall S Johnson Helene Rundqvist Frontiers in Immunology Published 27 February 2023 Crick labsJernej UleFull details RNA polymerase II-associated proteins reveal pathways affected in VCP-related amyotrophic lateral sclerosis Authors (5)Mahmoud-Reza Rafiee Sara Rohban Karen DaveyJernej UleNicholas Luscombe Brain Published 1 June 2023 Crick labsJernej UleNicholas LuscombeFull details N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast Authors (18) Radhika A VarierTheodora SideriCharlotte CapitanchikZornitsa ManovaEnrica CalvaniAlice Rossi[...] Michiel VermeulenMarkus RalserJernej UleNicholas LuscombeFolkert Van Werven eLife Published 24 November 2022 Crick labs/ facilitiesFolkert van WervenJernej UleMarkus RalserNicholas LuscombeProteomicsMetabolomicsBioinformatics and BiostatisticsFermentationAdvanced SequencingFull details Cell-specific bioorthogonal tagging of glycoproteins Authors (31)Anna CioceBea CalleTatiana Rizou Sarah C LoweryVicky Bridgeman Keira E Mahoney[...] Stuart M Haslam Sabine L Flitsch Stacy A MalakerIlaria MalanchiBen Schumann Nature Communications Published 25 October 2022 Crick labs/ facilitiesJernej UleBen SchumannIlaria MalanchiLuiz Pedro CarvalhoStructural BiologyProteomicsBioinformatics and BiostatisticsLight MicroscopyCell ServicesBiological Research FacilityAdvanced SequencingFull details CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1 Authors (15) Milan Hluchý Pavla GajduškováIgor Ruiz De Los Mozos Michal Rájecký Michael Kluge Benedict-Tilman Berger[...] Zbyněk Zdráhal Stefan Knapp Kamil Paruch Caroline C Friedel Dalibor Blazek Nature Published 22 September 2022 Crick labsJernej UleFull details Pagination Current page 1 Page 2 Page 3 Page 4 Next page Next Last page Last Share the page Share on Twitter 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Interrogation of RNA-protein interaction dynamics in bacterial growth Authors (11) Mie Monti Reyme Herman Leonardo ManciniCharlotte Capitanchik Karen Davey Charlotte S DawsonJernej Ule Gavin H Thomas Anne E Willis Kathryn S Lilley Eneko Villanueva Molecular Systems Biology Published 26 March 2024 Crick labsJernej UleFull details
Mis-spliced transcripts generate de novo proteins in TDP-43-related ALS/FTD Authors (51) Sahba Seddighi Yue A Qi Anna-Leigh BrownOscar Wilkins Colleen Bereda Cedric Belair[...] Nicholas T Seyfried Manolis Maragkakis Leonard PetrucelliPietro Fratta Michael E Ward Science Translational Medicine Published 14 February 2024 Crick labsJernej UlePietro FrattaFull details
Subcytoplasmic location of translation controls protein output Authors (9) Ellen L Horste Mervin M Fansler Ting Cai Xiuzhen Chen Sibylle Mitschka Gang ZhenFlora LeeJernej Ule Christine Mayr Molecular Cell Published 21 December 2023 Crick labsJernej UleFull details
Transcriptome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides Authors (14) Rubika BalendraIgor Ruiz De Los Mozos Hana M Odeh Idoia Glaria Carmelo Milioto Katherine M Wilson[...] Stephen MartinRickie Patani James ShorterJernej Ule Adrian M Isaacs Life Science Alliance Published 1 September 2023 Crick labs/ facilitiesJernej UleRickie PataniStructural BiologyHigh Throughput ScreeningFull details
Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning Authors (10) Marc Horlacher Nils Wagner Lambert Moyon Klara Kuret Nicolas Goedert Marco SalvatoreJernej Ule Julien Gagneur Ole Winther Annalisa Marsico Genome Biology Published 4 August 2023 Crick labsJernej UleFull details
Control of protein synthesis through mRNA pseudouridylation by dyskerin Authors (10) Chiara Pederiva Davide M Trevisan Dimitra Peirasmaki Shan Chen Sharon A Savage Ola LarssonJernej Ule Laura Baranello Federico Agostini Marianne Farnebo Science advances Published 28 July 2023 Crick labs/ facilitiesJernej UleAdvanced SequencingFull details
ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins Authors (18) Aina Maria Mas Enrique Goñi Igor Ruiz de los Mozos Aida Arcas Luisa Statello Jovanna González[...] Shou WagaJernej Ule Eli Rothenberg María Gómez Maite Huarte Nature Communications Published 24 July 2023 Crick labsJernej UleFull details
Nucleocytoplasmic mRNA redistribution accompanies RNA binding protein mislocalization in ALS motor neurons and is restored by VCP ATPase inhibition Authors (10)Oliver ZiffJasmine HarleyYiran WangJacob NeevesGiulia Tyzack Fairouz IbrahimMark SkehelAnob ChakrabartiGavin KellyRickie Patani Neuron Published 4 October 2023 Crick labs/ facilitiesJernej UleRickie PataniProteomicsBioinformatics and BiostatisticsFull details
The paralogues MAGOH and MAGOHB are oncogenic factors in high-grade gliomas and safeguard the splicing of cell division and cell cycle genes Authors (15) Rodrigo AS Barreiro Gabriela DA Guardia Fabiana M Meliso Xiufen Lei Wei-Qing Li Andre Savio[...] Mei Qiao Lorea BlazquezJernej Ule Luiz OF Penalva Pedro AF Galante RNA Biology Published 9 June 2023 Crick labsJernej UleFull details
HNRNPH1 regulates the neuroprotective cold-shock protein RBM3 expression through poison exon exclusion Authors (15) Julie Qiaojin Lin Deepak Khuperkar Sofia Pavlou Stanislaw Makarchuk Nikolaos PatikasFlora Lee[...] Joshua L FreemanJernej Ule Emmanouil Metzakopian Marc-David Ruepp Giovanna R Mallucci The EMBO Journal Published 17 July 2023 Crick labsJernej UleFull details
Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology Authors (14)Oliver ZiffJacob NeevesJamie MitchellGiulia Tyzack Carlos Martinez-Ruiz Raphaelle Luisier[...]Simon Boulton Ammar Al-ChalabiGavin Kelly Jack HumphreyRickie Patani Nature Communications Published 20 April 2023 Crick labs/ facilitiesJernej UleRickie PataniSimon BoultonBioinformatics and BiostatisticsScientific computingFull details
Looping in on splicing: CRIC-seq uncovers PTBP1's long-range RNA regulatory rules Authors (3) Ira Alexandra Iosub Tajda KlobučarJernej Ule Molecular Cell Published 20 April 2023 Crick labsJernej UleNicholas LuscombeFull details
An ERK1/2-driven RNA-binding switch in nucleolin drives ribosome biogenesis and pancreatic tumorigenesis downstream of RAS oncogene Authors (10) Muhammad S Azman Emilie L Alard Martin Dodel Federica CapraroRupert Faraway Maria Dermit Wanling Fan Alina ChakrabortyJernej Ule Faraz K Mardakheh The EMBO Journal Published 1 June 2023 Crick labsJernej UleFull details
A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3' UTR structure to RNA metabolism Authors (5)Anob Chakrabarti Ira A IosubFlora LeeJernej UleNicholas Luscombe Nucleic Acids Research Published 8 May 2023 Crick labsJernej UleNicholas LuscombeFull details
clipplotr - a comparative visualization and analysis tool for CLIP data Authors (4)Anob ChakrabartiCharlotte CapitanchikJernej UleNicholas Luscombe RNA Published 1 June 2023 Crick labsJernej UleNicholas LuscombeFull details
Lactate exposure shapes the metabolic and transcriptomic profile of CD8+ T cells Authors (9) Laura Barbieri Pedro VeliçaPaulo Gameiro Pedro P Cunha Iosifina P Foskolou Eric Rullman David Bargiela Randall S Johnson Helene Rundqvist Frontiers in Immunology Published 27 February 2023 Crick labsJernej UleFull details
RNA polymerase II-associated proteins reveal pathways affected in VCP-related amyotrophic lateral sclerosis Authors (5)Mahmoud-Reza Rafiee Sara Rohban Karen DaveyJernej UleNicholas Luscombe Brain Published 1 June 2023 Crick labsJernej UleNicholas LuscombeFull details
N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast Authors (18) Radhika A VarierTheodora SideriCharlotte CapitanchikZornitsa ManovaEnrica CalvaniAlice Rossi[...] Michiel VermeulenMarkus RalserJernej UleNicholas LuscombeFolkert Van Werven eLife Published 24 November 2022 Crick labs/ facilitiesFolkert van WervenJernej UleMarkus RalserNicholas LuscombeProteomicsMetabolomicsBioinformatics and BiostatisticsFermentationAdvanced SequencingFull details
Cell-specific bioorthogonal tagging of glycoproteins Authors (31)Anna CioceBea CalleTatiana Rizou Sarah C LoweryVicky Bridgeman Keira E Mahoney[...] Stuart M Haslam Sabine L Flitsch Stacy A MalakerIlaria MalanchiBen Schumann Nature Communications Published 25 October 2022 Crick labs/ facilitiesJernej UleBen SchumannIlaria MalanchiLuiz Pedro CarvalhoStructural BiologyProteomicsBioinformatics and BiostatisticsLight MicroscopyCell ServicesBiological Research FacilityAdvanced SequencingFull details
CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1 Authors (15) Milan Hluchý Pavla GajduškováIgor Ruiz De Los Mozos Michal Rájecký Michael Kluge Benedict-Tilman Berger[...] Zbyněk Zdráhal Stefan Knapp Kamil Paruch Caroline C Friedel Dalibor Blazek Nature Published 22 September 2022 Crick labsJernej UleFull details
