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Genes in the brain are very long and can be transcribed into diverse RNAs. Toggle to view hero caption Jernej Ule : Publications Lab MenuLab Menu Overview Areas of interest View more Back RNP assembly RNP function RNP evolution RNPs in disease RNPs in Development Publications Members Vacancies Breadcrumb Home Research Labs Jernej Ule Publications PublicationsJournalMolecular Cell (5)Cell Reports (3)Nucleic Acids Research (3)Cell (2)EMBO Journal (2)EMBO Reports (2)Genome Biology (2)Nature (2)Nature Communications (2)Nature Structural and Molecular Biology (2)Annual Review of Biomedical Data Science (1)BioEssays (1)Brain (1)Cold Spring Harbor Perspectives in Biology (1)eLife (1)Genes & Development (1)Nature Ecology & Evolution (1)Nature Protocols (1)Nature Reviews Molecular Cell Biology (1)RNA Biology (1)Wellcome Open Research (1)Publication typeJournal article (36)Primary research (24)Review (7)Commentary (2)Method (2)Editorial (1)Research topicsBiochemistry & Proteomics (33)Computational & Systems Biology (33)Gene Expression (33)Genetics & Genomics (33)Neurosciences (33)Stem Cells (33)Tumour Biology (9)Cell Biology (4)Year published2020 (2)2019 (10)2018 (13)2017 (7)2015 (3)2013 (1) Publications Displaying 1 - 20 of 36Last updated : 03 June 2020 03:51 CDK11 is required for transcription of replication-dependent histone genes Authors Pavla GajduškováIgor Ruiz De Los Mozos Michal Rájecký Milan HluchýJernej Ule Dalibor Blazek Journal Nature Structural and Molecular Biology Publication date 4 May 2020 Crick labsJernej UleFull details Open access, open data and peer review AuthorsJernej Ule Journal Genome Biology Publication date 4 May 2020 Crick labsJernej UleFull details Alternative splicing regulatory networks: Functions, mechanisms, and evolution AuthorsJernej Ule Benjamin J Blencowe Journal Molecular Cell Publication date 17 October 2019 Crick labsJernej UleFull details A systems view of spliceosomal assembly and branchpoints with iCLIP Authorstotal 17 Michael Briese Nejc Haberman Christopher R SibleyRupert FarawayAndrea ElserAnob Chakrabarti[...] Luciano Saieva Livio Pellizzoni Christopher WJ Smith Tomaž CurkJernej Ule Journal Nature Structural and Molecular Biology Publication date 30 September 2019 Crick labsNicholas LuscombeJernej UleFull details Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis Authorstotal 12Giulia Tyzack Raphaelle LuisierDoaa TahaJacob NeevesMiha ModicJamie Mitchell[...] Linda Greensmith Jia NewcombeJernej UleNicholas LuscombeRickie Patani Journal Brain Publication date 1 September 2019 Crick labsNicholas LuscombeJernej UleRickie PataniFull details FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA Authors Jean-Michel Carter Warren Emmett Igor RDL Mozos Annika Kotter Mark HelmJernej Ule Shobbir Hussain Journal Nucleic Acids Research Publication date 4 November 2019 Crick labsJernej UleFull details The transcriptome-wide landscape and modalities of EJC binding in adult Drosophila Authors Ales Obrdlik Gen Lin Nejc HabermanJernej Ule Anne Ephrussi Journal Cell Reports Publication date 30 July 2019 Crick labsJernej UleFull details Cross-regulation between TDP-43 and paraspeckles promotes pluripotency-differentiation transition Authorstotal 20Miha Modic Markus Grosch Gregor Rot Silvia Schirge Tjasa Lepko Tomohiro Yamazaki[...] Alexander Meissner Heiko Lickert Tetsuro HiroseJernej Ule Micha Drukker Journal Molecular Cell Publication date 6 June 2019 Crick labsJernej UleFull details P-TEFb activation by RBM7 shapes a pro-survival transcriptional response to genotoxic stress Authorstotal 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 Journal Molecular Cell Publication date 18 April 2019 Crick labsJernej UleFull details Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock Authors Violeta Castelo-Szekely Mara De Matos Marina Tusup Steve PascoloJernej Ule David Gatfield Journal Nucleic Acids Research Publication date 4 June 2019 Crick labsJernej UleFull details The origin of neural microexons Authors Rupert FarawayJernej Ule Journal Nature Ecology & Evolution Publication date 4 March 2019 Crick labsJernej UleFull details Genomic accumulation of retrotransposons was facilitated by repressive RNA-binding proteins: A hypothesis AuthorsJernej Ule Journal BioEssays Publication date 1 February 2019 Crick labsJernej UleFull details The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs Authors Lilli Olgeiser Carl Haag Susan BoernerJernej Ule Anke Busch Janine Koepke Julian König Michael Feldbrügge Kathi Zarnack Journal EMBO Reports Publication date 14 December 2018 Crick labsJernej UleFull details Exon junction complex shapes the transcriptome by repressing recursive splicing Authors Lorea Blazquez Warren Emmett Rupert Faraway Jose Mario Bello Pineda Simon Bajew Andre Gohr Nejc Haberman Christopher R Sibley Robert K Bradley Manuel IrimiaJernej Ule Journal Molecular Cell Publication date 1 November 2018 Crick labs/ facilitiesJernej UleCell ServicesGenomics/Equipment ParkFull details Heteromeric RNP assembly at LINEs controls lineage-specific RNA processing AuthorsJan Attig Federico Agostini Clare Gooding Anob M Chakrabarti Aarti Singh Nejc HabermanJulian Zagalak Warren Emmett Christopher WJ SmithNicholas LuscombeJernej Ule Journal Cell Publication date 2 August 2018 Crick labsNicholas LuscombeJernej UleFull details The future of cross-lnking and imunoprecipitation (CLIP) AuthorsJernej Ule Hun-Way Hwang Robert B Darnell Journal Cold Spring Harbor Perspectives in Biology Publication date 1 August 2018 Crick labsJernej UleFull details Data science issues in studying protein–RNA interactions with CLIP technologies Authors Anob M Chakrabarti Nejc Haberman Arne PraznikNicholas LuscombeJernej Ule Journal Annual Review of Biomedical Data Science Publication date 1 July 2018 Crick labsNicholas LuscombeJernej UleFull details Read-through marking' reveals differential nucleotide composition of read-through and truncated cDNAs in iCLIP Authors Ina Huppertz Nejc HabermanJernej Ule Journal Wellcome Open Research Publication date 22 June 2018 Crick labsJernej UleFull details Mice with endogenous TDP-43 mutations exhibit gain of splicing function and characteristics of amyotrophic lateral sclerosis Authorstotal 42 Pietro Fratta Prasanth Sivakumar Jack Humphrey Kitty Lo Thomas Ricketts Hugo Oliveira[...] Linda Greensmith Emanuele Buratti Vincent Plagnol Elizabeth MC Fisher Abraham Acevedo-Arozena Journal EMBO Journal Publication date 1 June 2018 Crick labsJernej UleFull details Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS Authorstotal 13 Raphaelle Luisier Giulia E Tyzack Claire E HallJamie Mitchell Helen DevineDoaa Taha[...] Linda Greensmith Jia NewcombeJernej UleNicholas LuscombeRickie Patani Journal Nature Communications Publication date 22 May 2018 Crick labsNicholas LuscombeJernej UleRickie PataniFull details Pagination Current page 1 Page 2 Next page Next Last page Last Share the page Share on Twitter Share on Facebook Share on LinkedIn Share on Email
CDK11 is required for transcription of replication-dependent histone genes Authors Pavla GajduškováIgor Ruiz De Los Mozos Michal Rájecký Milan HluchýJernej Ule Dalibor Blazek Journal Nature Structural and Molecular Biology Publication date 4 May 2020 Crick labsJernej UleFull details
Open access, open data and peer review AuthorsJernej Ule Journal Genome Biology Publication date 4 May 2020 Crick labsJernej UleFull details
Alternative splicing regulatory networks: Functions, mechanisms, and evolution AuthorsJernej Ule Benjamin J Blencowe Journal Molecular Cell Publication date 17 October 2019 Crick labsJernej UleFull details
A systems view of spliceosomal assembly and branchpoints with iCLIP Authorstotal 17 Michael Briese Nejc Haberman Christopher R SibleyRupert FarawayAndrea ElserAnob Chakrabarti[...] Luciano Saieva Livio Pellizzoni Christopher WJ Smith Tomaž CurkJernej Ule Journal Nature Structural and Molecular Biology Publication date 30 September 2019 Crick labsNicholas LuscombeJernej UleFull details
Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis Authorstotal 12Giulia Tyzack Raphaelle LuisierDoaa TahaJacob NeevesMiha ModicJamie Mitchell[...] Linda Greensmith Jia NewcombeJernej UleNicholas LuscombeRickie Patani Journal Brain Publication date 1 September 2019 Crick labsNicholas LuscombeJernej UleRickie PataniFull details
FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA Authors Jean-Michel Carter Warren Emmett Igor RDL Mozos Annika Kotter Mark HelmJernej Ule Shobbir Hussain Journal Nucleic Acids Research Publication date 4 November 2019 Crick labsJernej UleFull details
The transcriptome-wide landscape and modalities of EJC binding in adult Drosophila Authors Ales Obrdlik Gen Lin Nejc HabermanJernej Ule Anne Ephrussi Journal Cell Reports Publication date 30 July 2019 Crick labsJernej UleFull details
Cross-regulation between TDP-43 and paraspeckles promotes pluripotency-differentiation transition Authorstotal 20Miha Modic Markus Grosch Gregor Rot Silvia Schirge Tjasa Lepko Tomohiro Yamazaki[...] Alexander Meissner Heiko Lickert Tetsuro HiroseJernej Ule Micha Drukker Journal Molecular Cell Publication date 6 June 2019 Crick labsJernej UleFull details
P-TEFb activation by RBM7 shapes a pro-survival transcriptional response to genotoxic stress Authorstotal 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 Journal Molecular Cell Publication date 18 April 2019 Crick labsJernej UleFull details
Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock Authors Violeta Castelo-Szekely Mara De Matos Marina Tusup Steve PascoloJernej Ule David Gatfield Journal Nucleic Acids Research Publication date 4 June 2019 Crick labsJernej UleFull details
The origin of neural microexons Authors Rupert FarawayJernej Ule Journal Nature Ecology & Evolution Publication date 4 March 2019 Crick labsJernej UleFull details
Genomic accumulation of retrotransposons was facilitated by repressive RNA-binding proteins: A hypothesis AuthorsJernej Ule Journal BioEssays Publication date 1 February 2019 Crick labsJernej UleFull details
The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs Authors Lilli Olgeiser Carl Haag Susan BoernerJernej Ule Anke Busch Janine Koepke Julian König Michael Feldbrügge Kathi Zarnack Journal EMBO Reports Publication date 14 December 2018 Crick labsJernej UleFull details
Exon junction complex shapes the transcriptome by repressing recursive splicing Authors Lorea Blazquez Warren Emmett Rupert Faraway Jose Mario Bello Pineda Simon Bajew Andre Gohr Nejc Haberman Christopher R Sibley Robert K Bradley Manuel IrimiaJernej Ule Journal Molecular Cell Publication date 1 November 2018 Crick labs/ facilitiesJernej UleCell ServicesGenomics/Equipment ParkFull details
Heteromeric RNP assembly at LINEs controls lineage-specific RNA processing AuthorsJan Attig Federico Agostini Clare Gooding Anob M Chakrabarti Aarti Singh Nejc HabermanJulian Zagalak Warren Emmett Christopher WJ SmithNicholas LuscombeJernej Ule Journal Cell Publication date 2 August 2018 Crick labsNicholas LuscombeJernej UleFull details
The future of cross-lnking and imunoprecipitation (CLIP) AuthorsJernej Ule Hun-Way Hwang Robert B Darnell Journal Cold Spring Harbor Perspectives in Biology Publication date 1 August 2018 Crick labsJernej UleFull details
Data science issues in studying protein–RNA interactions with CLIP technologies Authors Anob M Chakrabarti Nejc Haberman Arne PraznikNicholas LuscombeJernej Ule Journal Annual Review of Biomedical Data Science Publication date 1 July 2018 Crick labsNicholas LuscombeJernej UleFull details
Read-through marking' reveals differential nucleotide composition of read-through and truncated cDNAs in iCLIP Authors Ina Huppertz Nejc HabermanJernej Ule Journal Wellcome Open Research Publication date 22 June 2018 Crick labsJernej UleFull details
Mice with endogenous TDP-43 mutations exhibit gain of splicing function and characteristics of amyotrophic lateral sclerosis Authorstotal 42 Pietro Fratta Prasanth Sivakumar Jack Humphrey Kitty Lo Thomas Ricketts Hugo Oliveira[...] Linda Greensmith Emanuele Buratti Vincent Plagnol Elizabeth MC Fisher Abraham Acevedo-Arozena Journal EMBO Journal Publication date 1 June 2018 Crick labsJernej UleFull details
Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS Authorstotal 13 Raphaelle Luisier Giulia E Tyzack Claire E HallJamie Mitchell Helen DevineDoaa Taha[...] Linda Greensmith Jia NewcombeJernej UleNicholas LuscombeRickie Patani Journal Nature Communications Publication date 22 May 2018 Crick labsNicholas LuscombeJernej UleRickie PataniFull details
