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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 (3)2023 (15)2022 (9)2021 (16)2020 (6)2019 (10)2018 (13)2017 (7)2015 (3)2013 (1) Facet Year publishedResearch topicsGenetics & Genomics (80)Biochemistry & Proteomics (79)Computational & Systems Biology (79)Gene Expression (79)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)Developmental Biology (4)Metabolism (4)Signalling & Oncogenes (4)Human Biology & Physiology (3)Immunology (3)Infectious Disease (3)Imaging (2)Microfabrication & Bioengineering (2) Facet Research topicsPublication typeJournal article (83)Primary research (66)Review (10)Commentary (3)Method (3)Editorial (1) Facet Publication typeJournalMolecular Cell (9)Nature Communications (8)Nucleic Acids Research (6)Genome Biology (5)Nature (5)Cell (3)Cell Reports (3)eLife (3)International Journal of Molecular Sciences (3)Brain (2)EMBO Journal (2)EMBO Reports (2)Nature Reviews Methods Primers (2)Nature Structural and Molecular Biology (2)RNA Biology (2)Science advances (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)Genes & Development (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 Translational Medicine (1)The Lancet (1) Facet Journal Publications Displaying 41 - 60 of 83Last updated : 19 April 2024 02:05 psiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation Authors (10) Lisa StrittmatterCharlotte Capitanchik Andrew NewmanMartina Hallegger Christine Norman Sebastian Fica Chris OubridgeNicholas LuscombeJernej Ule Kiyoshi Nagai Nature Communications Published 5 March 2021 Crick labsJernej UleNicholas LuscombeFull details CLIP and complementary methods Authors (8) Markus Hafner Maria Katsantoni Tino Köster James MarksJoyita Mukherjee Dorothee StaigerJernej Ule Mihaela Zavolan Nature Reviews Methods Primers Published 4 March 2021 Crick labsJernej UleFull details CLIP and complimentary methods Authors (8) Markus Hafner Maria Katsantoni Tino Köster James MarksJoyita Mukherjee Dorothee StaigerJernej Ule Mihaela Zavolan Nature Reviews Methods Primers Published 4 March 2021 Crick labsJernej UleFull details Subcellular mRNA localization regulates ribosome biogenesis in migrating cells Authors (9) Maria Dermit Martin DodelFlora Lee Muhammad S Azman Hagen Schwenzer J Louise Jones Sarah P BlagdenJernej Ule Faraz K Mardakheh Developmental Cell Published 9 November 2020 Crick labs/ facilitiesJernej UleAdvanced SequencingFull details Cytotoxic T-cells mediate exercise-induced reductions in tumor growth Authors (13) Helene Rundqvist Pedro Veliça Laura BarbieriPaulo Gameiro David Bargiela Milos Gojkovic[...] David Wulliman Emil AhlstedtJernej Ule Arne Östman Randall S Johnson eLife Published 23 October 2020 Crick labs/ facilitiesJernej UleMetabolomicsFull details Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers Authors (341) Catherine F Houlihan Nina Vora Thomas Byrne Dan LewerGavin Kelly Judith Heaney[...] Andrew Hayward Richard Gilson Gavin KellyFiona Roberts Emine Hatipoglu The Lancet Published 25 July 2020 Crick labs/ facilitiesAndreas WackKaren VousdenJernej UleJames TurnerMoritz TreeckCharles SwantonAdam SaterialeErik SahaiCaetano Reis e SousaPeter RatcliffeLucia Prieto-GodinoVenizelos PapayannopoulosAnne O’GarraPaul NurseGeorge KassiotisMaximiliano GutierrezSonia GandhiSteve GamblinPeter Cherepanov Luiz Pedro CarvalhoDominique BonnetMike BlackmanRupert BealeWorldwide Influenza CentreStructural BiologyMetabolomicsHuman Embryonic Stem CellHigh Throughput ScreeningGenetic Modification ServiceFlow CytometryFermentationExperimental HistopathologyElectron MicroscopyCell ServicesBiological Research FacilityBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details How do you identify m6 A methylation in transcriptomes at high resolution? A comparison of recent datasets Authors (4)Charlotte CapitanchikPatrick Toolan-KerrNicholas LuscombeJernej Ule Frontiers in Genetics Published 20 May 2020 Crick labsJernej UleNicholas LuscombeFull details CDK11 is required for transcription of replication-dependent histone genes Authors (6) Pavla GajduškováIgor Ruiz De Los Mozos Michal Rájecký Milan HluchýJernej Ule Dalibor Blazek Nature Structural and Molecular Biology Published 4 May 2020 Crick labsJernej UleFull details Open access, open data and peer review Authors (1)Jernej Ule Genome Biology Published 4 May 2020 Crick labsJernej UleFull details Alternative splicing regulatory networks: Functions, mechanisms, and evolution Authors (2)Jernej Ule Benjamin J Blencowe Molecular Cell Published 17 October 2019 Crick labsJernej UleFull details A systems view of spliceosomal assembly and branchpoints with iCLIP Authors (17) Michael Briese Nejc Haberman Christopher R SibleyRupert FarawayAndrea ElserAnob Chakrabarti[...] Luciano Saieva Livio Pellizzoni Christopher WJ Smith Tomaž CurkJernej Ule Nature Structural and Molecular Biology Published 30 September 2019 Crick labsJernej UleNicholas LuscombeFull details Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis Authors (12)Giulia Tyzack Raphaelle LuisierDoaa TahaJacob NeevesMiha ModicJamie Mitchell[...] Linda Greensmith Jia NewcombeJernej UleNicholas LuscombeRickie Patani Brain Published 1 September 2019 Crick labsJernej UleRickie PataniNicholas LuscombeFull details FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA Authors (7) Jean-Michel Carter Warren Emmett Igor RDL Mozos Annika Kotter Mark HelmJernej Ule Shobbir Hussain Nucleic Acids Research Published 4 November 2019 Crick labsJernej UleFull details The transcriptome-wide landscape and modalities of EJC binding in adult Drosophila Authors (5) Ales Obrdlik Gen Lin Nejc HabermanJernej Ule Anne Ephrussi Cell Reports Published 30 July 2019 Crick labsJernej UleFull details Cross-regulation between TDP-43 and paraspeckles promotes pluripotency-differentiation transition Authors (20)Miha Modic Markus Grosch Gregor Rot Silvia Schirge Tjasa Lepko Tomohiro Yamazaki[...] Alexander Meissner Heiko Lickert Tetsuro HiroseJernej Ule Micha Drukker Molecular Cell Published 6 June 2019 Crick labsJernej UleFull details Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock Authors (6) Violeta Castelo-Szekely Mara De Matos Marina Tusup Steve PascoloJernej Ule David Gatfield Nucleic Acids Research Published 4 June 2019 Crick labsJernej UleFull details The origin of neural microexons Authors (2) Rupert FarawayJernej Ule Nature Ecology & Evolution Published 4 March 2019 Crick labsJernej UleFull details P-TEFb activation by RBM7 shapes a pro-survival transcriptional response to genotoxic stress Authors (14) Andrii Bugai Alexandre JC Quaresma Caroline C Friedel Tina Lenasi Robert Düster Christopher R Sibley[...] Melanie Blasius Matthias GeyerJernej Ule Lars Dölken Matjaž Barborič Molecular Cell Published 18 April 2019 Crick labsJernej UleFull details Genomic accumulation of retrotransposons was facilitated by repressive RNA-binding proteins: A hypothesis Authors (2)Jan AttigJernej Ule BioEssays Published 1 February 2019 Crick labsJernej UleFull details The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs Authors (9) Lilli Olgeiser Carl Haag Susan BoernerJernej Ule Anke Busch Janine Koepke Julian König Michael Feldbrügge Kathi Zarnack EMBO Reports Published 1 January 2019 Crick labsJernej UleFull details Pagination First page First Previous page Previous Page 1 Page 2 Current page 3 Page 4 Page 5 Next page Next Last page Last Share the page Share on Twitter Share on Facebook Share on LinkedIn Share on Email
psiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation Authors (10) Lisa StrittmatterCharlotte Capitanchik Andrew NewmanMartina Hallegger Christine Norman Sebastian Fica Chris OubridgeNicholas LuscombeJernej Ule Kiyoshi Nagai Nature Communications Published 5 March 2021 Crick labsJernej UleNicholas LuscombeFull details
CLIP and complementary methods Authors (8) Markus Hafner Maria Katsantoni Tino Köster James MarksJoyita Mukherjee Dorothee StaigerJernej Ule Mihaela Zavolan Nature Reviews Methods Primers Published 4 March 2021 Crick labsJernej UleFull details
CLIP and complimentary methods Authors (8) Markus Hafner Maria Katsantoni Tino Köster James MarksJoyita Mukherjee Dorothee StaigerJernej Ule Mihaela Zavolan Nature Reviews Methods Primers Published 4 March 2021 Crick labsJernej UleFull details
Subcellular mRNA localization regulates ribosome biogenesis in migrating cells Authors (9) Maria Dermit Martin DodelFlora Lee Muhammad S Azman Hagen Schwenzer J Louise Jones Sarah P BlagdenJernej Ule Faraz K Mardakheh Developmental Cell Published 9 November 2020 Crick labs/ facilitiesJernej UleAdvanced SequencingFull details
Cytotoxic T-cells mediate exercise-induced reductions in tumor growth Authors (13) Helene Rundqvist Pedro Veliça Laura BarbieriPaulo Gameiro David Bargiela Milos Gojkovic[...] David Wulliman Emil AhlstedtJernej Ule Arne Östman Randall S Johnson eLife Published 23 October 2020 Crick labs/ facilitiesJernej UleMetabolomicsFull details
Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers Authors (341) Catherine F Houlihan Nina Vora Thomas Byrne Dan LewerGavin Kelly Judith Heaney[...] Andrew Hayward Richard Gilson Gavin KellyFiona Roberts Emine Hatipoglu The Lancet Published 25 July 2020 Crick labs/ facilitiesAndreas WackKaren VousdenJernej UleJames TurnerMoritz TreeckCharles SwantonAdam SaterialeErik SahaiCaetano Reis e SousaPeter RatcliffeLucia Prieto-GodinoVenizelos PapayannopoulosAnne O’GarraPaul NurseGeorge KassiotisMaximiliano GutierrezSonia GandhiSteve GamblinPeter Cherepanov Luiz Pedro CarvalhoDominique BonnetMike BlackmanRupert BealeWorldwide Influenza CentreStructural BiologyMetabolomicsHuman Embryonic Stem CellHigh Throughput ScreeningGenetic Modification ServiceFlow CytometryFermentationExperimental HistopathologyElectron MicroscopyCell ServicesBiological Research FacilityBioinformatics and BiostatisticsAdvanced SequencingScientific computingFull details
How do you identify m6 A methylation in transcriptomes at high resolution? A comparison of recent datasets Authors (4)Charlotte CapitanchikPatrick Toolan-KerrNicholas LuscombeJernej Ule Frontiers in Genetics Published 20 May 2020 Crick labsJernej UleNicholas LuscombeFull details
CDK11 is required for transcription of replication-dependent histone genes Authors (6) Pavla GajduškováIgor Ruiz De Los Mozos Michal Rájecký Milan HluchýJernej Ule Dalibor Blazek Nature Structural and Molecular Biology Published 4 May 2020 Crick labsJernej UleFull details
Open access, open data and peer review Authors (1)Jernej Ule Genome Biology Published 4 May 2020 Crick labsJernej UleFull details
Alternative splicing regulatory networks: Functions, mechanisms, and evolution Authors (2)Jernej Ule Benjamin J Blencowe Molecular Cell Published 17 October 2019 Crick labsJernej UleFull details
A systems view of spliceosomal assembly and branchpoints with iCLIP Authors (17) Michael Briese Nejc Haberman Christopher R SibleyRupert FarawayAndrea ElserAnob Chakrabarti[...] Luciano Saieva Livio Pellizzoni Christopher WJ Smith Tomaž CurkJernej Ule Nature Structural and Molecular Biology Published 30 September 2019 Crick labsJernej UleNicholas LuscombeFull details
Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis Authors (12)Giulia Tyzack Raphaelle LuisierDoaa TahaJacob NeevesMiha ModicJamie Mitchell[...] Linda Greensmith Jia NewcombeJernej UleNicholas LuscombeRickie Patani Brain Published 1 September 2019 Crick labsJernej UleRickie PataniNicholas LuscombeFull details
FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA Authors (7) Jean-Michel Carter Warren Emmett Igor RDL Mozos Annika Kotter Mark HelmJernej Ule Shobbir Hussain Nucleic Acids Research Published 4 November 2019 Crick labsJernej UleFull details
The transcriptome-wide landscape and modalities of EJC binding in adult Drosophila Authors (5) Ales Obrdlik Gen Lin Nejc HabermanJernej Ule Anne Ephrussi Cell Reports Published 30 July 2019 Crick labsJernej UleFull details
Cross-regulation between TDP-43 and paraspeckles promotes pluripotency-differentiation transition Authors (20)Miha Modic Markus Grosch Gregor Rot Silvia Schirge Tjasa Lepko Tomohiro Yamazaki[...] Alexander Meissner Heiko Lickert Tetsuro HiroseJernej Ule Micha Drukker Molecular Cell Published 6 June 2019 Crick labsJernej UleFull details
Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock Authors (6) Violeta Castelo-Szekely Mara De Matos Marina Tusup Steve PascoloJernej Ule David Gatfield Nucleic Acids Research Published 4 June 2019 Crick labsJernej UleFull details
The origin of neural microexons Authors (2) Rupert FarawayJernej Ule Nature Ecology & Evolution Published 4 March 2019 Crick labsJernej UleFull details
P-TEFb activation by RBM7 shapes a pro-survival transcriptional response to genotoxic stress Authors (14) Andrii Bugai Alexandre JC Quaresma Caroline C Friedel Tina Lenasi Robert Düster Christopher R Sibley[...] Melanie Blasius Matthias GeyerJernej Ule Lars Dölken Matjaž Barborič Molecular Cell Published 18 April 2019 Crick labsJernej UleFull details
Genomic accumulation of retrotransposons was facilitated by repressive RNA-binding proteins: A hypothesis Authors (2)Jan AttigJernej Ule BioEssays Published 1 February 2019 Crick labsJernej UleFull details
The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs Authors (9) Lilli Olgeiser Carl Haag Susan BoernerJernej Ule Anke Busch Janine Koepke Julian König Michael Feldbrügge Kathi Zarnack EMBO Reports Published 1 January 2019 Crick labsJernej UleFull details
