J. Ule

发表

HITS-CLIP yields genome-wide insights into brain alternative RNA processing

Tyson A. Clark, D. Licatalosi, A. Mele, 2008, Nature.

Protein–RNA interactions: new genomic technologies and perspectives

J. Ule, N. Luscombe, J. König, 2012, Nature Reviews Genetics.

An RNA map predicting Nova-dependent splicing regulation

B. Blencowe, A. Mele, J. Ule, 2006, Nature.

Nova regulates brain-specific splicing to shape the synapse

Tyson A. Clark, J. Ule, J. Blume, 2005, Nature Genetics.

iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution

J. Ule, M. Kayikci, B. Zupan, 2010, Nature Structural &Molecular Biology.

CLIP: a method for identifying protein-RNA interaction sites in living cells.

Jernej Ule, Robert B Darnell, A. Mele, 2005, Methods.

CLIP Identifies Nova-Regulated RNA Networks in the Brain

Jernej Ule, A. Mele, J. Ule, 2003, Science.

Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution.

B. Blencowe, J. Ule, 2019, Molecular cell.

Lessons from non-canonical splicing

Christopher R. Sibley, J. Ule, L. Blazquez, 2016, Nature Reviews Genetics.

How Do You Identify m6 A Methylation in Transcriptomes at High Resolution? A Comparison of Recent Datasets

J. Ule, N. Luscombe, Charlotte Capitanchik, 2020, Frontiers in Genetics.

Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock

J. Ule, D. Gatfield, V. Castelo-Szekely, 2018, bioRxiv.

The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes

Jernej Ule, Tomaz Curk, Ian Henry, 2012, Genome Biology.

A global regulatory mechanism for activating an exon network required for neurogenesis.

Jernej Ule, Anne-Claude Gingras, Zhen-Yuan Lin, 2014, Molecular cell.

Understanding splicing regulation through RNA splicing maps

Jernej Ule, J. Ule, Joshua T Witten, 2011, Trends in genetics : TIG.

Analysis of alternative splicing associated with aging and neurodegeneration in the human brain.

Tomaž Curk, Jernej Ule, Blaž Zupan, 2011, Genome research.

The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes.

Jernej Ule, Peter Cimermancic, Jiri Kohoutek, 2011, Genes & development.

NSun2-Mediated Cytosine-5 Methylation of Vault Noncoding RNA Determines Its Processing into Regulatory Small RNAs

Jernej Ule, Michaela Frye, Duncan T. Odom, 2013, Cell reports.

Characterizing the RNA targets and position-dependent splicing regulation by TDP-43.

J. Ule, M. Kayikci, T. Hortobágyi, 2011, Nature neuroscience.

A systems view of spliceosomal assembly and branchpoints with iCLIP

Christopher R. Sibley, J. Ule, N. Luscombe, 2018, bioRxiv.

Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS

J. Ule, N. Luscombe, L. Greensmith, 2018, Nature Communications.

Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements

Julian König, Nicholas M. Luscombe, Jernej Ule, 2013, Cell.

Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain

Nejc Haberman, Tomaž Curk, Jernej Ule, 2012, Scientific Reports.

iCLIP Predicts the Dual Splicing Effects of TIA-RNA Interactions

Michael Briese, Nicholas M. Luscombe, Tomaž Curk, 2010, PLoS biology.

TDP‐43 regulates its mRNA levels through a negative feedback loop

Jernej Ule, Andrea D'Ambrogio, Marco Baralle, 2011, The EMBO journal.

RNA-Binding Protein Musashi1 Is a Central Regulator of Adhesion Pathways in Glioblastoma

J. Ule, Kotb Abdelmohsen, M. Gorospe, 2015, Molecular and Cellular Biology.

CELF4 Regulates Translation and Local Abundance of a Vast Set of mRNAs, Including Genes Associated with Regulation of Synaptic Function

Jacy L. Wagnon, C. Mahaffey, J. Ule, 2012, PLoS genetics.

Regulation of alternative splicing by the circadian clock and food related cues

Nicholas J. McGlincy, J. Ule, E. Maywood, 2012, Genome Biology.

Cholinergic Surveillance over Hippocampal RNA Metabolism and Alzheimer's-Like Pathology

J. Ule, H. Soreq, U. Bekenstein, 2016, Cerebral cortex.

Scalable and robust SARS-CoV-2 testing in an academic center

Robert L. Goldstone, James M. A. Turner, J. Ule, 2020, Nature Biotechnology.

iDiscover – an intelligent assistant for integrative analysis of transcriptome data

Tomaž Curk, Jernej Ule, Blaž Zupan, 2011 .

The SMAD 2 / 3 interactome reveals that TGF β controls m 6 A 1 mRNA methylation in pluripotency 2 3

J. Ule, H. Stunnenberg, N. Hubner, 2018 .

Title : HIF-driven SF 3 B 1 induces KHK-C to enforce fructolysis and heart disease

J. Ule, M. Kayikci, Nicola Zamboni, 2022 .

Hexanucleotide Repeats in ALS/FTD Form Length-Dependent RNA Foci, Sequester RNA Binding Proteins, and Are Neurotoxic

J. Ule, C. Shaw, C. Troakes, 2013, Cell reports.

A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3′ UTR structure to RNA metabolism

J. Ule, N. Luscombe, I. Iosub, 2022, bioRxiv.

Major Shifts in Glial Regional Identity Are a Transcriptional Hallmark of Human Brain Aging

J. Ule, M. Cookson, J. Hardy, 2017, Cell reports.

Explorer Psip 1 / Ledgf p 52 Binds Methylated Histone H 3 K 36 and Splicing Factors and Contributes to the Regulation of Alternative Splicing

J. Ule, W. Bickmore, G. Grimes, 2012 .

Characterizing the RNA targets and position-dependent splicing regulation by TDP-43.

J. Ule, M. Kayikci, T. Hortobágyi, 2011, Nature neuroscience.

The RNA-Binding Protein Rrm4 is Essential for Efficient Secretion of Endochitinase Cts1□S

J. Ule, N. Luscombe, J. Koepke, 2011 .

The coilin interactome identifies hundreds of small noncoding RNAs that traffic through Cajal bodies.

P. Stadler, J. Ule, Jana Hertel, 2014, Molecular cell.

Insights into the design and interpretation of iCLIP experiments

Nejc Haberman, Christopher R. Sibley, Julian König, 2017, Genome Biology.

Erratum to: Insights into the design and interpretation of iCLIP experiments

Christopher R. Sibley, J. Ule, M. Hentze, 2017, Genome Biology.

Title: Metabolic turnover and dynamics of RNA modifications by 13 C labelling

J. Ule, R. Johnson, J. MacRae, 2022 .

The greatest catch: big game fishing for mRNA-bound proteins

Christopher R. Sibley, J. Ule, J. Attig, 2012, Genome Biology.

The Future of CLIP

J. Ule, R. Darnell, Hun-Way Hwang, 2018 .

Edinburgh Research Explorer P-TEFb activation by RBM7 shapes a pro-survival transcriptional response to genotoxic stress

Christopher R. Sibley, J. Ule, T. Hennig, 2019 .

Genomic Accumulation of Retrotransposons Was Facilitated by Repressive RNA‐Binding Proteins: A Hypothesis

J. Ule, J. Attig, 2019, BioEssays : news and reviews in molecular, cellular and developmental biology.

Progressive Motor Neuron Pathology and the Role of Astrocytes in a Human Stem Cell Model of VCP-Related ALS

Christopher R. Sibley, J. Ule, N. Luscombe, 2017, Cell reports.

3' UTR length and messenger ribonucleoprotein composition determine endocleavage efficiencies at termination codons.

J. Ule, N. Gehring, Niels H. Gehring, 2014, Cell reports.

Neuronal Elav-like (Hu) Proteins Regulate RNA Splicing and Abundance to Control Glutamate Levels and Neuronal Excitability

A. Mele, J. Fak, J. Ule, 2012, Neuron.

Common Molecular Pathways Mediate Long-Term Potentiation of Synaptic Excitation and Slow Synaptic Inhibition

J. Ule, R. Darnell, Y. Jan, 2005, Cell.

CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1

J. Ule, S. Knapp, C. Friedel, 2022, Nature.

Subcellular mRNA Localization Regulates Ribosome Biogenesis in Migrating Cells

J. Ule, M. Dermit, S. Blagden, 2019, bioRxiv.

Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends

J. Ule, N. Luscombe, J. König, 2015, Nucleic acids research.

Identifying ribosome heterogeneity using ribosome profiling

J. Ule, W. Faller, Ferhat Alkan, 2022, Nucleic acids research.

Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning

J. Ule, J. Gagneur, O. Winther, 2022, bioRxiv.

Genome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides

J. Ule, M. Hallegger, J. Shorter, 2022, bioRxiv.

The paralogues MAGOH and MAGOHB are oncogenic factors in high-grade gliomas and safeguard the splicing of cell division and cell cycle genes

Gabriela D. A. Guardia, J. Ule, Xiu-fen Lei, 2022, bioRxiv.

Metabolic turnover and dynamics of RNA modifications by 13C labelling

J. Ule, R. Johnson, P. Gameiro, 2021 .

Subcytoplasmic location of translation controls protein output

J. Ule, C. Mayr, Xiuzhen Chen, 2023, bioRxiv.

Regulatory feedback from nascent RNA to chromatin and transcription

Richard G. Jenner, J. Ule, Lenka Skalska, 2017, Nature Reviews Molecular Cell Biology.

The interaction of PRC2 with RNA or chromatin is mutually antagonistic

Christopher R. Sibley, Richard G. Jenner, J. Ule, 2016, Genome research.

Cholinergic regulation of striatal Nova mRNAs

J. Ule, M. Živin, N. Jelen, 2010, Neuroscience.

Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections

Robert L. Goldstone, Naomi R. Waterlow, Quentin J. Leclerc, 2020, BMC Medicine.

Regulation of alternative splicing by the circadian clock and food related cues

Nicholas J. McGlincy, J. Ule, E. Maywood, 2012, Genome Biology.

TDP-43 condensation properties specify its RNA-binding and regulatory repertoire

Nicolas L. Fawzi, J. Ule, N. Luscombe, 2021, Cell.

CLIP and complementary methods

Jernej Ule, Mihaela Zavolan, Dorothee Staiger, 2021, Nature Reviews Methods Primers.

Cytotoxic T-cells mediate exercise-induced reductions in tumor growth

J. Ule, R. Johnson, P. Gameiro, 2020, eLife.

Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions

Julian König, Tomaž Curk, Jernej Ule, 2012, Genome Biology.

Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders

Jernej Ule, Michaela Frye, Wolfgang Wurst, 2014, The EMBO journal.

Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L

Julian König, Tomaž Curk, Jernej Ule, 2014, RNA biology.

Acute depletion of METTL3 implicates N6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome

J. Ule, N. Brockdorff, G. Pintacuda, 2021, Genome research.

Splicing repression allows the gradual emergence of new Alu-exons in primate evolution

J. Ule, J. König, W. Emmett, 2016, eLife.

The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators

J. Ule, M. Kayikci, E. Eyras, 2016, Nucleic acids research.

THE FUNCTIONS OF GLYCINE ‐ RICH REGIONS IN TDP ‐ 43 , FUS AND RELATED RNA ‐ BINDING PROTEINS

J. Ule, C. Shaw, B. Rogelj, 2011 .

An RNA-binding switch drives ribosome biogenesis and tumorigenesis downstream of RAS oncogene

J. Ule, M. Dermit, Martin Dodel, 2021, bioRxiv.

Perturbation of Chromatin Structure Globally Affects Localization and Recruitment of Splicing Factors

J. Ule, I. Schor, A. Kornblihtt, 2012, PloS one.

University of Dundee Perturbation of Chromatin Structure Globally Affects Localization and Recruitment of Splicing Factors Schor,

J. Ule, I. Schor, A. Kornblihtt, 2012 .

Characterising the RNA targets and position-dependent splicing regulation by TDP-43; implications for neurodegenerative diseases

J. Ule, M. Kayikci, T. Hortobágyi, 2011, Nature Neuroscience.

iCLIP: Protein–RNA interactions at nucleotide resolution

Christopher R. Sibley, Julian König, Jernej Ule, 2014, Methods.

Frontiers in Neural Circuits Neural Circuits

J. Ule, R. Darnell, A. Triller, 2022 .

Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells

Manuel D. Díaz-Muñoz, J. Ule, Tomaž Curk, 2017, Nature Communications.

RNA modifications detection by comparative Nanopore direct RNA sequencing

Anton J. Enright, Nicholas M. Luscombe, Jernej Ule, 2019, Nature Communications.

Sixty years of genome biology

J. Rinn, M. Schatz, M. Gerstein, 2013, Genome Biology.

'genes in Pieces': Introns Sixty Years of Genome Biology * and George M Weinstock O P I N I O N

J. Rinn, M. Schatz, M. Gerstein, 2022 .

Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing

J. Ule, N. Luscombe, C. Gooding, 2018, Cell.

Advances in CLIP Technologies for Studies of Protein-RNA Interactions.

Jernej Ule, J. Ule, Flora C Y Lee, 2018, Molecular cell.

The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency

Jernej Ule, Juned Kadiwala, Ludovic Vallier, 2018, Nature.

Illustrating the Epitranscriptome at Nucleotide Resolution Using Methylation-iCLIP (miCLIP).

J. Ule, S. Hussain, Harry George, 2017, Methods in molecular biology.

HIF-driven SF3B1 induces KHK-C to enforce fructolysis and heart disease

J. Ule, M. Kayikci, Nicola Zamboni, 2015, Nature.

Evolution of Nova-Dependent Splicing Regulation in the Brain

J. Ule, R. Darnell, M. Živin, 2007, PLoS genetics.

Selective inhibition of microRNA accessibility by RBM38 is required for p53 activity

J. Ule, M. Esteller, R. Elkon, 2011, Nature communications.

Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis.

Jernej Ule, Tomaz Curk, Auinash Kalsotra, 2014, Molecular cell.

The Future of Cross-Linking and Immunoprecipitation (CLIP).

J. Ule, R. Darnell, Hun-Way Hwang, 2018, Cold Spring Harbor perspectives in biology.

NSUN 2-mediated cytosine-5 RNA methylation

J. Ule, H. Fuchs, D. Odom, 2014 .

Psip1/Ledgf p52 Binds Methylated Histone H3K36 and Splicing Factors and Contributes to the Regulation of Alternative Splicing

Jernej Ule, Wendy A. Bickmore, J. Ule, 2012, PLoS genetics.

Using human pluripotent stem cells to study post-transcriptional mechanisms of neurodegenerative diseases

Christopher R. Sibley, J. Ule, S. Chandran, 2012, Brain Research.

Requirement of Heterogeneous Nuclear Ribonucleoprotein C for BRCA Gene Expression and Homologous Recombination

J. Ule, J. König, Jianglin Ma, 2013, PloS one.

CDK11 is required for transcription of replication-dependent histone genes

J. Ule, D. Blazek, Igor Ruiz de los Mozos, 2020, Nature Structural & Molecular Biology.

Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis

J. Ule, N. Luscombe, L. Greensmith, 2019, Brain : a journal of neurology.

Widespread FUS mislocalization is a molecular hallmark of ALS

J. Ule, N. Luscombe, L. Greensmith, 2019, bioRxiv.

Post-transcriptional remodelling is temporally deregulated during motor neurogenesis in human ALS models

J. Ule, N. Luscombe, Raphaëlle Luisier, 2017, bioRxiv.

CLIPing the brain: Studies of protein–RNA interactions important for neurodegenerative disorders☆☆☆

Christopher R. Sibley, J. Ule, Miha Modic, 2013, Molecular and Cellular Neuroscience.

TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A

Anna L. Brown, J. Ule, O. Rozenblatt-Rosen, 2022, Nature.

Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP

J. Ule, Charlotte Capitanchik, Klara Kuret, 2021, Genome Biology.

Common ALS/FTD risk variants in UNC13A exacerbate its cryptic splicing and loss upon TDP-43 mislocalization

Anna L. Brown, J. Ule, T. Raj, 2021, bioRxiv.

A systems view of spliceosomal assembly and branchpoints with iCLIP

Christopher R. Sibley, Andrea S. Elser, J. Ule, 2019, Nature Structural & Molecular Biology.

The Transcriptome-wide L andscape and Modalities of EJC Binding in Adult Drosophila Graphical

J. Ule, A. Ephrussi, Gen Lin, 2019 .

The transcriptome-wide landscape and modalities of EJC binding in adult Drosophila

J. Ule, A. Ephrussi, Gen Lin, 2018, bioRxiv.

High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43

J. Ule, M. Hallegger, Tomaž Curk, 2017, Cell reports.

Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein

J. Ule, N. Luscombe, A. Chakrabarti, 2017, Nature Protocols.

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins

Marinka Zitnik, Blaz Zupan, Jernej Ule, 2016, Bioinform..

iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function

J. Ule, Tomaž Curk, M. Rogers, 2015, BMC Biology.

RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing

Tyson A. Clark, J. Ule, A. Schweitzer, 2014, Genome Biology.

Molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43

J. Ule, F. Damberger, E. Buratti, 2013, Nature Structural &Molecular Biology.

Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling

J. Ule, P. Gameiro, J. MacRae, 2021, bioRxiv.

Promiscuous RNA Binding Ensures Effective Encapsidation of APOBEC3 Proteins by HIV-1

J. Ule, M. Malim, Tomaž Curk, 2015, PLoS pathogens.

Functional and mechanistic insights from genome-wide studies of splicing regulation in the brain.

J. Ule, R. Darnell, 2007, Advances in experimental medicine and biology.

Splicing changes in SMA mouse motoneurons and SMN-depleted neuroblastoma cells: Evidence for involvement of splicing regulatory proteins

J. Ule, M. Kayikci, S. Saxena, 2014, RNA biology.

RNA binding proteins and the regulation of neuronal synaptic plasticity

J. Ule, R. Darnell, 2006, Current Opinion in Neurobiology.

Epiblast morphogenesis is controlled by selective mRNA decay triggered by LIN28A relocation

J. Ule, N. Luscombe, H. Leonhardt, 2021, bioRxiv.

P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress

Christopher R. Sibley, J. Ule, T. Hennig, 2018, bioRxiv.

psiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation

J. Ule, N. Luscombe, C. Oubridge, 2020, bioRxiv.

Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5′ splice site strength

Christopher R. Sibley, J. Ule, J. Marioni, 2015, Genome Biology.

A genetically-encoded crosslinker screen identifies SERBP1 as a PKCε substrate influencing translation and cell division

J. Ule, P. Parker, D. Mann, 2021, Nature Communications.

The RNA-binding protein HuR (Elavl1) is essential for the B cell antibody response

Tomaž Curk, Jernej Ule, Kathi Zarnack, 2015, Nature Immunology.

U1A is a positive regulator of the expression of heterologous and cellular genes involved in cell proliferation and migration

J. Ule, Roland Hjerpe, N. Razquin, 2022, Molecular therapy. Nucleic acids.

Recursive splicing in long vertebrate genes

Michael Briese, Nejc Haberman, Christopher R. Sibley, 2015, Nature.

CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3′ processing

John R Yates, Jernej Ule, Lingjie Weng, 2014, Genes & development.

Pandemic peak SARS-CoV-2 infection and seroconversion rates in London frontline health-care workers

Robert L. Goldstone, James M. A. Turner, J. Ule, 2020, The Lancet.

Matrin3: connecting gene expression with the nuclear matrix

J. Ule, Christopher W. J. Smith, J. Attig, 2016, Wiley interdisciplinary reviews. RNA.

Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB

J. Ule, M. Kayikci, E. Eyras, 2015, The EMBO journal.

Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition

D. Cacchiarelli, J. Ule, C. von Mering, 2019, Molecular cell.

Human Integrator provides a quality checkpoint during elongation to facilitate RNA polymerase II processivity

J. Ule, N. Luscombe, M. Rafiee, 2023, bioRxiv.

Subcytoplasmic location of translation controls protein output

J. Ule, C. Mayr, Xiuzhen Chen, 2023, bioRxiv.

A systems view of spliceosomal assembly and branchpoints with iCLIP

Christopher R. Sibley, Andrea S. Elser, J. Ule, 2019, Nature Structural & Molecular Biology.

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing

Nejc Haberman, Christopher R. Sibley, Rupert Faraway, 2018, Molecular cell.

HNRNPH1 regulates the neuroprotective cold‐shock protein RBM3 expression through poison exon exclusion

J. Ule, E. Metzakopian, M. Ruepp, 2022, bioRxiv.

Data Science Issues in Studying Protein-RNA Interactions with CLIP Technologies.

Nejc Haberman, Anob M. Chakrabarti, Nicholas M. Luscombe, 2018, Annual review of biomedical data science.

Gene regulation via protein–RNA interactions

J. Ule, 2014 .

Ribonucleoprotein complexes in neurologic diseases

J. Ule, 2008, Current Opinion in Neurobiology.

The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs

J. Ule, J. Koepke, J. König, 2018, bioRxiv.

Aberrant sodium channel activity in the complex seizure disorder of Celf4 mutant mice

Jacy L. Wagnon, C. Mahaffey, J. Ule, 2013, The Journal of physiology.

FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA

Jernej Ule, Mark Helm, Annika Kotter, 2019, Nucleic acids research.

clipplotr—a comparative visualization and analysis tool for CLIP data

J. Ule, N. Luscombe, Charlotte Capitanchik, 2021, bioRxiv.

ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins

J. Ule, Maite Huarte, G. Tartaglia, 2023, bioRxiv.

RGS4 RNA Secondary Structure Mediates Staufen2 RNP Assembly in Neurons

J. Ule, N. Luscombe, M. Kiebler, 2021, International journal of molecular sciences.

Data Science Issues in Understanding Protein-RNA Interactions

Nejc Haberman, Anob M. Chakrabarti, Nicholas M. Luscombe, 2017, bioRxiv.

CPSF 30 and Wdr 33 directly bind to AAUAAA in mammalian mRNA 3 9 processing

J. Ule, J. Yates, Lingjie Weng, 2014 .

No way out: when RNA elements promote nuclear retention

J. Ule, F. Agostini, Julian A Zagalak, 2018, The EMBO journal.

MIR-NATs repress MAPT translation and aid proteostasis in neurodegeneration

J. Ule, P. Svenningsson, J. Hardy, 2021, Nature.

Global Analysis of Protein-RNA Interactions with Single-Nucleotide Resolution Using iCLIP

Julian König, Jernej Ule, Nicholas J. McGlincy, 2014 .

Analysis of Protein–RNA Interactions with Single‐Nucleotide Resolution Using iCLIP and Next‐Generation Sequencing

Julian König, Jernej Ule, Nicholas J. McGlincy, 2012 .

The RNA-Binding Protein Rrm4 is Essential for Efficient Secretion of Endochitinase Cts1

J. Ule, N. Luscombe, J. Koepke, 2011, Molecular & Cellular Proteomics.

for efficient secretion of endochitinase Cts1

J. Ule, J. Koepke, J. König, 2011 .

Sequential inverse dysregulation of the RNA helicases DDX3X and DDX3Y facilitates MYC-driven lymphomagenesis.

J. Ule, S. Barrans, D. Painter, 2021, Molecular cell.

Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt

C. Walsh, J. Ule, L. Tsai, 2015, Genes & development.

Acute depletion of METTL3 identifies a role for N6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome

J. Ule, N. Brockdorff, G. Pintacuda, 2020, bioRxiv.

Sequential Inverse Dysregulation of the RNA Helicases DDX3X and DDX3Y Facilitates MYC-Driven Lymphomagenesis

J. Ule, S. Barrans, D. Painter, 2020 .

An improved iCLIP protocol

Christopher R. Sibley, J. Ule, J. König, 2021, bioRxiv.

Transcript-specific characteristics determine the contribution of endo- and exonucleolytic decay pathways during the degradation of nonsense-mediated decay substrates

Christopher R. Sibley, J. Ule, Niels H. Gehring, 2017, RNA.

iCLIP - Transcriptome-wide Mapping of Protein-RNA Interactions with Individual Nucleotide Resolution

Blaz Zupan, Nicholas M. Luscombe, Jernej Ule, 2011, Journal of visualized experiments : JoVE.

A retained intron in the 3′‐UTR of Calm3 mRNA mediates its Staufen2‐ and activity‐dependent localization to neuronal dendrites

Jernej Ule, J. Ule, M. Kiebler, 2017, EMBO reports.

University of Birmingham The RNA-binding protein HuR is essential for the B cell antibody response

Kathi, Manuel D. Díaz-Muñoz, J. Ule, 2016 .

Differential Binding of Mitochondrial Transcripts by MRB8170 and MRB4160 Regulates Distinct Editing Fates of Mitochondrial mRNA in Trypanosomes

J. Ule, H. Hashimi, J. Lukeš, 2017, mBio.

N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast

J. Ule, N. Luscombe, M. Vermeulen, 2022, eLife.

m6A reader Pho92 is recruited co-transcriptionally and couples translation efficacy to mRNA decay to promote meiotic fitness in yeast

J. Ule, N. Luscombe, M. Vermeulen, 2022, bioRxiv.

Lactate potentiates differentiation and expansion of cytotoxic T cells

J. Ule, R. Johnson, P. Veliça, 2019, bioRxiv.

Positioning Europe for the EPITRANSCRIPTOMICS challenge

Ayelet T. Lamm, Stefan L Ameres, J. Ule, 2018, RNA biology.

SPACE exploration of RNA-binding proteins as major chromatin components

J. Ule, Luscombe, M. Rafiee, 2021 .

Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs

J. Ule, N. Luscombe, Sebastian Steinhauser, 2020, bioRxiv.

SARS-CoV-2 Spike Protein Binding of Glycated Serum Albumin—Its Potential Role in the Pathogenesis of the COVID-19 Clinical Syndromes and Bias towards Individuals with Pre-Diabetes/Type 2 Diabetes and Metabolic Diseases

J. Ule, J. Heeney, H. Baxendale, 2022, International journal of molecular sciences.

SARS-CoV-2 Spike protein binding of glycated serum albumin - its potential role in the pathogenesis of the COVID-19 clinical syndromes and bias towards individuals with pre-diabetes/type 2 diabetes & metabolic diseases.

J. Ule, J. Lacey, R. Iles, 2021, medRxiv.

CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo.

J. Ule, D. Turner, James R. Tollervey, 2009, Methods.

Protein–RNA interactions: new genomic technologies and perspectives

Julian König, Nicholas M. Luscombe, Jernej Ule, 2012, Nature Reviews Genetics.

'Oming in on RNA–protein interactions

Jernej Ule, John L Rinn, J. Rinn, 2014, Genome Biology.

THEME 2 GENETICS AND GENOMICS GEN-01 Genetic analysis using a gene panel in a cohort of 282 Spanish patients with ALS

J. Ule, T. Raj, J. Newcombe, 2022 .

Phosphorylation of Protein Phosphatase Inhibitor-1 by Cdk5*

P. Greengard, J. Ule, A. Nairn, 2001, The Journal of Biological Chemistry.

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1

Jernej Ule, Nicholas M Luscombe, Andrea D’Ambrogio, 2015, Nature.

Regulation of cyclin-dependent kinase 5 and casein kinase 1 by metabotropic glutamate receptors

P. Greengard, J. Ule, A. Nairn, 2001, Proceedings of the National Academy of Sciences of the United States of America.

SPACE exploration of chromatin proteome to reveal associated RNA-binding proteins

J. Ule, N. Luscombe, M. Rafiee, 2020 .

Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells

Manuel D. Díaz-Muñoz, J. Ule, N. L. Le Novère, 2017, Nature Communications.

What, where, and when: the importance of post-transcriptional regulation in the brain

Jernej Ule, Michael A. Kiebler, J. Ule, 2013, Front. Neurosci..

Publisher Correction: A systems view of spliceosomal assembly and branchpoints with iCLIP

Christopher R. Sibley, Andrea S. Elser, J. Ule, 2021, Nature Structural & Molecular Biology.

Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS

J. Ule, N. Luscombe, L. Greensmith, 2018, Nature Communications.

Open access, open data and peer review

J. Ule, 2020, Genome Biology.

Abundant capped RNAs are derived from mRNA cleavage at 3’UTR G-Quadruplexes

Christopher R. Sibley, J. Ule, Piero Carninci, 2023, bioRxiv.

Ribocutter: Cas9-mediated rRNA depletion from multiplexed Ribo-seq libraries

J. Ule, O. Wilkins, 2021, bioRxiv.

iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function

Mark F. Rogers, J. Ule, Tomaž Curk, 2015, BMC Biology.

RNA polymerase II-associated proteins reveal pathways affected in neural precursors with VCP mutation

J. Ule, N. Luscombe, M. Rafiee, 2023 .

Abundant capped RNAs are derived from mRNA cleavage at 3’UTR G-Quadruplexes

Christopher R. Sibley, J. Ule, Piero Carninci, 2023, bioRxiv.

Transcriptome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides

J. Ule, J. Shorter, A. Isaacs, 2023, Life Science Alliance.

Control of protein synthesis through mRNA pseudouridylation by dyskerin

J. Ule, S. Savage, Laura Baranello, 2023, Science advances.

An ERK1/2‐driven RNA‐binding switch in nucleolin drives ribosome biogenesis and pancreatic tumorigenesis downstream of RAS oncogene

J. Ule, M. Dermit, Martin Dodel, 2023, The EMBO journal.

Interrogation of RNA-protein interaction dynamics in bacterial growth

G. H. Thomas, J. Ule, K. Lilley, 2023, bioRxiv.

RNA polymerase II-associated proteins reveal pathways affected in VCP-related amyotrophic lateral sclerosis

J. Ule, N. Luscombe, M. Rafiee, 2023, Brain : a journal of neurology.

Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5′ splice site strength

Christopher R. Sibley, J. Ule, J. Marioni, 2015, Genome Biology.

Ultraplex: A rapid, flexible, all-in-one fastq demultiplexer

J. Ule, N. Luscombe, Charlotte Capitanchik, 2021, Wellcome open research.

The Neuronal Splicing Factor Nova Co-Localizes with Target RNAs in the Dendrite

J. Ule, R. Darnell, A. Triller, 2009, Front. Neural Circuits.

The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes

J. Ule, Tomaž Curk, K. Neugebauer, 2012, Genome Biology.

Subcytoplasmic location of translation controls protein output

J. Ule, C. Mayr, Xiuzhen Chen, 2023, bioRxiv.

Alu elements: at the crossroads between disease and evolution

J. Ule, 2013, Biochemical Society transactions.

Mutual homeostasis of charged proteins

Stefan L Ameres, J. Ule, I. Iosub, 2023, bioRxiv.

High-throughput sequencing methods to study neuronal RNA-protein interactions.

J. Ule, 2009, Biochemical Society transactions.

The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes

J. Ule, Tomaž Curk, K. Neugebauer, 2012, Genome Biology.

The Future of Cross-Linking and Immunoprecipitation (CLIP).

J. Ule, R. Darnell, Hun-Way Hwang, 2018, Cold Spring Harbor perspectives in biology.

Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein

J. Ule, N. Luscombe, A. Chakrabarti, 2017, Nature Protocols.

iCLIP: Protein–RNA interactions at nucleotide resolution

Christopher R. Sibley, J. Ule, J. König, 2014, Methods.

CLIP: construction of cDNA libraries for high-throughput sequencing from RNAs cross-linked to proteins in vivo.

J. Ule, D. Turner, James R. Tollervey, 2009, Methods.

Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition

D. Cacchiarelli, J. Ule, C. von Mering, 2019, Molecular cell.

Theme 02 - GENETICS AND GENOMICS

J. Ule, T. Raj, J. Newcombe, 2021, Amyotrophic lateral sclerosis & frontotemporal degeneration.

The coilin interactome identifies hundreds of small noncoding RNAs that traffic through Cajal bodies.

P. Stadler, J. Ule, Jana Hertel, 2014, Molecular cell.

Riboseq-flow: A streamlined, reliable pipeline for ribosome profiling data analysis and quality control

J. Ule, I. Iosub, O. Wilkins, 2024, Wellcome Open Research.

The interaction of PRC2 with RNA or chromatin is mutually antagonistic

Christopher R. Sibley, Richard G. Jenner, J. Ule, 2016, Genome research.

Opus: University of Bath Online Publication Store Analysis of Clip and Iclip Methods for Nucleotide-resolution Studies of Protein-rna Interactions

J. Ule, B. Zupan, J. König, 2022 .

Opus: University of Bath Online Publication Store Aberrant Methylation of Trnas Links Cellular Stress to Neuro-developmental Disorders

J. Ule, D. Odom, C. Kutter, 2022 .

Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis.

J. Ule, T. Cooper, Tomaž Curk, 2014, Molecular cell.

The impact of IDR phosphorylation on the RNA binding profiles of proteins.

J. Ule, Miha Modic, Maksimiljan Adamek, 2024, Trends in genetics : TIG.

Mis-spliced transcripts generate de novo proteins in TDP-43–related ALS/FTD

J. Ule, N. Staff, L. Petrucelli, 2024, Science Translational Medicine.