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List of works by Jernej Ule

'Oming in on RNA-protein interactions

scientific article published on 31 January 2014

'Read-through marking' reveals differential nucleotide composition of read-through and truncated cDNAs in iCLIP

article

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

scientific article published on 9 October 2014

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

scientific article published on 26 November 2021

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

scientific article published on 11 September 2014

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

scientific article published in August 2017

A systems view of spliceosomal assembly and branchpoints with iCLIP

A systems view of spliceosomal assembly and branchpoints with iCLIP

scientific article published on 30 September 2019

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

scientific article

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

scientific article published on 22 October 2012

Advances in CLIP Technologies for Studies of Protein-RNA Interactions

scientific article published in February 2018

Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution

scientific article published on 01 October 2019

Alu elements: at the crossroads between disease and evolution

scientific article

An RNA map predicting Nova-dependent splicing regulation

scientific article

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

scientific article

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

scientific article (publication date: 23 January 2012)

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

scientific article

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

scientific article published on 08 July 2020

CDK11 is required for transcription of replication-dependent histone genes

scientific article published on 04 May 2020

CELF4 regulates translation and local abundance of a vast set of mRNAs, including genes associated with regulation of synaptic function

scientific article

CLIP identifies Nova-regulated RNA networks in the brain

scientific article (publication date: 14 November 2003)

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

scientific article

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

scientific article

CLIPing the brain: studies of protein-RNA interactions important for neurodegenerative disorders

scientific article published on 10 April 2013

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

scientific article

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

scientific article published on 27 February 2011

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

scientific article

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

scientific article published on 16 June 2016

Cholinergic regulation of striatal Nova mRNAs

scientific article published on 12 May 2010

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

scientific article published on 01 December 2021

Common molecular pathways mediate long-term potentiation of synaptic excitation and slow synaptic inhibition.

scientific article published in October 2005

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

scientific article

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

scientific article

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

scientific article published on 07 February 2014

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

scientific article published on 23 October 2020

Data Science Issues in Understanding Protein-RNA Interactions

scholarly article published 25 October 2017

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

scientific article

Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements

scientific article published on January 2013

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

scientific article published on 16 March 2021

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

scientific article published on 15 August 2017

Evolution of Nova-dependent splicing regulation in the brain

scientific article

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing

scientific article published in November 2018

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

scientific article published on 01 November 2019

Flow: a web platform and open database to analyse, store, curate and share bioinformatics data at scale

scientific article published on 29 August 2023

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

scientific article published on January 2007

Gene regulation via protein–RNA interactions

article

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

scientific article published on 01 February 2019

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

scientific article published on 17 June 2015

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

scientific article

Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing

scientific article published on 02 August 2018

Hexanucleotide repeats in ALS/FTD form length-dependent RNA foci, sequester RNA binding proteins, and are neurotoxic

scientific article

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

scientific article

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

scientific article published in December 2009

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

scientific article published in January 2017

Insights into the design and interpretation of iCLIP experiments

scientific article published on 16 January 2017

Integrative analysis of higher-order transcriptome organisation and RNA condensation principles

scientific article published on 16 October 2024

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

scientific article

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

scientific article published on 22 May 2018

Jernej Ule: an RNA runaway success. Interview by Ruth Williams

scientific article published on February 2008

Lessons from non-canonical splicing

scientific article published on 31 May 2016

MIR-NATs repress MAPT translation and aid proteostasis in neurodegeneration

scientific article published on 19 May 2021

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

scientific article published on January 2017

Matrin3: connecting gene expression with the nuclear matrix

scientific article

Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling

scientific article published in 2021

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

scientific article

NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs

scientific article

Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability

scientific article

No way out: when RNA elements promote nuclear retention

scientific article published on 27 February 2018

Nova regulates brain-specific splicing to shape the synapse

scientific article

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

scientific article published on 19 January 2015

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins

scientific article published on 18 January 2016

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

scientific article published on 26 February 2019

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

Perturbation of chromatin structure globally affects localization and recruitment of splicing factors

scientific article

Poised PABP-RNA hubs implement signal-dependent mRNA decay in development

scientific article published in September 2024

Poised PABP-RNA hubs implement signal-dependent mRNA decay in development

scientific article published on 7 August 2023

Positioning Europe for the EPITRANSCRIPTOMICS challenge.

scientific article published on 19 April 2018

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

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

scientific article

Promiscuous RNA binding ensures effective encapsidation of APOBEC3 proteins by HIV-1.

scientific article

Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing

scientific article

RNA binding proteins and the regulation of neuronal synaptic plasticity.

scientific article

RNA modifications detection by comparative Nanopore direct RNA sequencing

scientific article published on 10 December 2021

RNA regulation and modular control of the neuronal synapse

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

scientific article

RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing

scientific article

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

scientific article

Recursive splicing in long vertebrate genes

scientific article

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

scientific article

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

scientific article published on 21 September 2015

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

scientific article

Regulatory feedback from nascent RNA to chromatin and transcription

scientific article published on 8 March 2017

Requirement of heterogeneous nuclear ribonucleoprotein C for BRCA gene expression and homologous recombination

scientific article

Ribonucleoprotein complexes in neurologic diseases

scientific article published on 27 October 2008

SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements.

scientific article

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

scientific article published on 25 October 2011

Sixty years of genome biology

scientific article published on 25 April 2013

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

scientific article published on January 2014

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

scientific article

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

scientific article published on 23 February 2022

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

scientific article

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

scientific article

The Future of Cross-Linking and Immunoprecipitation (CLIP)

scientific article published on 01 August 2018

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

scientific article

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

scientific article

The RNA-binding protein HuR is essential for the B cell antibody response.

scientific article published on 23 February 2015

The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1

scientific article

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

scientific article published on 28 February 2018

The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila

scientific article published on 01 July 2019

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

scientific article published on 17 June 2016

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

scientific article published on 6 November 2014

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

scientific article published on July 17, 2012

The interaction of PRC2 with RNA or chromatin is mutually antagonistic

scientific article published on 9 May 2016

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

scientific article published on 14 December 2018

The origin of neural microexons

scientific article published on 01 April 2019

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

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

scientific article published on 13 September 2017

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

scientific article

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

scientific article published on 10 May 2022

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

scientific article published on 07 June 2021

Understanding splicing regulation through RNA splicing maps

scientific article published on 12 January 2011

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

scientific article

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

scientific article published on 05 January 2012

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

scientific article published on 29 October 2013

Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis

scientific article published on 01 September 2019

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

scientific article published on 28 August 2012

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

scientific article

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

scientific article published on 22 December 2015

iCLIP predicts the dual splicing effects of TIA-RNA interactions.

scientific article

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

scientific article

iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution.

scientific article

iCLIP: protein-RNA interactions at nucleotide resolution

scientific article

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

scientific article published on 05 March 2021

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