Browse by UCL people
Group by: Type | Date
Number of items: 86.
2026
Abouward, Reem;
Abdelhafid, Alya Masoud;
Wilkins, Oscar G;
Lee, Song-Yi;
Ibrahim, Fairouz;
Skehel, Mark;
Ting, Alice;
... Schiavo, Giampietro; + view all
(2026)
LAMP1 and LAMP2A localise to axonal organelles with distinct motility dynamics and partially overlapping molecular signatures in human neurons.
Journal of Cell Science
, Article jcs.264466. 10.1242/jcs.264466.
(In press).
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2024
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Seddighi, Sahba;
Qi, Yue A;
Brown, Anna-Leigh;
Wilkins, Oscar G;
Bereda, Colleen;
Belair, Cedric;
Zhang, Yong-Jie;
... Ward, Michael E; + view all
(2024)
Mis-spliced transcripts generate de novo proteins in TDP-43–related ALS/FTD.
Science Translational Medicine
, 16
(734)
10.1126/scitranslmed.adg7162.
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Wilkins, Oscar G;
Chien, Max ZYJ;
Wlaschin, Josette J;
Barattucci, Simone;
Harley, Peter;
Mattedi, Francesca;
Mehta, Puja R;
... Fratta, Pietro; + view all
(2024)
Creation of de novo cryptic splicing for ALS and FTD precision medicine.
Science
, 386
(6717)
pp. 61-69.
10.1126/science.adk2539.
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2023
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Azman, Muhammad S;
Alard, Emilie L;
Dodel, Martin;
Capraro, Federica;
Faraway, Rupert;
Dermit, Maria;
Fan, Wanling;
... Mardakheh, Faraz K; + view all
(2023)
An ERK1/2-driven RNA-binding switch in nucleolin drives ribosome biogenesis and pancreatic tumorigenesis downstream of RAS oncogene.
The EMBO Journal
, 42
(11)
, Article e110902. 10.15252/embj.2022110902.
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Balendra, Rubika;
Ruiz de Los Mozos, Igor;
Odeh, Hana M;
Glaria, Idoia;
Milioto, Carmelo;
Wilson, Katherine M;
Ule, Agnieszka M;
... Isaacs, Adrian M; + view all
(2023)
Transcriptome-wide RNA binding analysis of C9orf72 poly(PR) dipeptides.
Life Science Alliance
, 6
(9)
, Article e202201824. 10.26508/lsa.202201824.
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Barreiro, RAS;
Guardia, GDA;
Meliso, FM;
Lei, X;
Li, WQ;
Savio, A;
Fellermeyer, M;
... Galante, PAF; + view all
(2023)
The paralogues MAGOH and MAGOHB are oncogenic factors in high-grade gliomas and safeguard the splicing of cell division and cell cycle genes.
RNA Biology
, 20
(1)
pp. 311-322.
10.1080/15476286.2023.2221511.
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Chakrabarti, Anob M;
Capitanchik, Charlotte;
Ule, Jernej;
Luscombe, Nicholas M;
(2023)
clipplotr - a comparative visualisation and analysis tool for CLIP data.
RNA
10.1261/rna.079326.122.
(In press).
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Chakrabarti, Anob M;
Iosub, Ira A;
Lee, Flora CY;
Ule, Jernej;
Luscombe, Nicholas M;
(2023)
A computationally-enhanced hiCLIP atlas reveals Staufen1-RNA binding features and links 3′ UTR structure to RNA metabolism.
Nucleic Acids Research
, Article gkad221. 10.1093/nar/gkad221.
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Rafiee, Mahmoud-Reza;
Rohban, Sara;
Davey, Karen;
Ule, Jernej;
Luscombe, Nicholas M;
(2023)
RNA polymerase II-associated proteins reveal pathways affected in VCP-related amyotrophic lateral sclerosis.
Brain
, 146
(6)
pp. 2547-2556.
10.1093/brain/awad046.
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2022
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Alkan, Ferhat;
Wilkins, Oscar G;
Hernandez-Perez, Santiago;
Ramalho, Sofia;
Silva, Joana;
Ule, Jernej;
Faller, William J;
(2022)
Identifying ribosome heterogeneity using ribosome profiling.
Nucleic Acids Research
, 50
(16)
, Article e95. 10.1093/nar/gkac484.
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Brown, Anna-Leigh;
Wilkins, Oscar G;
Keuss, Matthew J;
Hill, Sarah E;
Zanovello, Matteo;
Lee, Weaverly Colleen;
Bampton, Alexander;
... Fratta, Pietro; + view all
(2022)
TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A.
Nature
, 603
pp. 131-137.
10.1038/s41586-022-04436-3.
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Hluchy, Milan;
Gajduskova, Pavla;
Ruiz de los Mozos, Igor;
Rajecky, Michal;
Kluge, Michael;
Berger, Benedict-Tilman;
Slaba, Zuzana;
... Blazek, Dalibor; + view all
(2022)
CDK11 regulates pre-mRNA splicing by phosphorylation ofSF3B1.
Nature
, 609
(7928)
pp. 829-834.
10.1038/s41586-022-05204-z.
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Iles, Jason;
Zmuidinaite, Raminta;
Sadee, Christoph;
Gardiner, Anna;
Lacey, Jonathan;
Harding, Stephen;
Ule, Jernej;
... Iles, Ray K; + view all
(2022)
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.
International Journal of Molecular Sciences
, 23
(8)
, Article 4126. 10.3390/ijms23084126.
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Kuret, Klara;
Amalietti, Aram Gustav;
Jones, D Marc;
Capitanchik, Charlotte;
Ule, Jernej;
(2022)
Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP.
Genome Biology
, 23
, Article 191. 10.1186/s13059-022-02755-2.
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Rovira, Eric;
Moreno, Beatriz;
Razquin, Nerea;
Hjerpe, Roland;
Gonzalez-Lopez, Monika;
Barrio, Rosa;
de los Mozos, Igor Ruiz;
... Fortes, Puri; + view all
(2022)
U1A is a positive regulator of the expression of heterologous and cellular genes involved in cell proliferation and migration.
Molecular Therapy - Nucleic Acids
, 28
pp. 831-846.
10.1016/j.omtn.2022.05.023.
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Varier, Radhika A;
Sideri, Theodora;
Capitanchik, Charlotte;
Manova, Zornitsa;
Calvani, Enrica;
Rossi, Alice;
Edupuganti, Raghu R;
... van Werven, Folkert J; + view all
(2022)
N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast.
eLife
, 11
, Article e84034. 10.7554/eLife.84034.
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2021
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Agostini, F;
Zagalak, J;
Attig, J;
Ule, J;
Luscombe, NM;
(2021)
Intergenic RNA mainly derives from nascent transcripts of known genes.
Genome Biology
, 22
(1)
, Article 136. 10.1186/s13059-021-02350-x.
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Fernández‐moya, SM;
Ehses, J;
Bauer, KE;
Schieweck, R;
Chakrabarti, AM;
Lee, FCY;
Illig, C;
... Kiebler, MA; + view all
(2021)
RGS4 RNA secondary structure mediates Staufen2 RNP assembly in Neurons.
International Journal of Molecular Sciences
, 22
(23)
, Article 13021. 10.3390/ijms222313021.
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Gameiro, PA;
Encheva, V;
Dos Santos, MS;
MacRae, JI;
Ule, J;
(2021)
Metabolic turnover and dynamics of modified ribonucleosides by ¹³C labeling.
Journal of Biological Chemistry
, Article 101294. 10.1016/j.jbc.2021.101294.
(In press).
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Gong, C;
Krupka, JA;
Gao, J;
Grigoropoulos, NF;
Giotopoulos, G;
Asby, R;
Screen, M;
... Hodson, DJ; + view all
(2021)
Sequential inverse dysregulation of the RNA helicases DDX3X and DDX3Y facilitates MYC-driven lymphomagenesis.
Molecular Cell
, 81
(19)
4059-4075.e11.
10.1016/j.molcel.2021.07.041.
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Hafner, M;
Katsantoni, M;
Köster, T;
Marks, J;
Mukherjee, J;
Staiger, D;
Ule, J;
(2021)
CLIP and complementary methods.
Nature Reviews Methods Primers
, 1
(1)
, Article 20. 10.1038/s43586-021-00018-1.
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Hallegger, M;
Chakrabarti, A;
Lee, F;
Amalietti, A;
Kuret, K;
Huppertz, I;
Luscombe, N;
(2021)
TDP-43 condensation properties specify its RNA binding and regulation.
Cell
10.1016/j.cell.2021.07.018.
(In press).
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Hellewell, J;
Russell, TW;
SAFER Investigators and Field Study Team, ,;
Crick COVID-19 Consortium, ,;
CMMID COVID-19 working group, ,;
Beale, R;
Kelly, G;
... Kucharski, AJ; + view all
(2021)
Estimating the effectiveness of routine asymptomatic PCR testing at different frequencies for the detection of SARS-CoV-2 infections.
BMC Medicine
, 19
(1)
, Article 106. 10.1186/s12916-021-01982-x.
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Leger, A;
Amaral, PP;
Pandolfini, L;
Capitanchik, C;
Capraro, F;
Miano, V;
Migliori, V;
... Kouzarides, T; + view all
(2021)
RNA modifications detection by comparative Nanopore direct RNA sequencing.
Nature Communications
, 12
, Article 7198. 10.1038/s41467-021-27393-3.
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Martini, S;
Davis, K;
Faraway, R;
Elze, L;
Lockwood, N;
Jones, A;
Xie, X;
... Parker, PJ; + view all
(2021)
A genetically-encoded crosslinker screen identifies SERBP1 as a PKCε substrate influencing translation and cell division.
Nature Communications
, 12
(1)
, Article 6934. 10.1038/s41467-021-27189-5.
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Rafiee, M-R;
Zagalak, JA;
Sidorov, S;
Steinhauser, S;
Davey, K;
Ule, J;
Luscombe, NM;
(2021)
Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs.
Nucleic Acids Research
10.1093/nar/gkab1180.
(In press).
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Simone, R;
Javad, F;
Emmett, W;
Wilkins, OG;
Almeida, FL;
Barahona-Torres, N;
Zareba-Paslawska, J;
... De Silva, R; + view all
(2021)
MIR-NATs repress MAPT translation and aid proteostasis in neurodegeneration.
Nature
, 594
pp. 117-123.
10.1038/s41586-021-03556-6.
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Strittmatter, LM;
Capitanchik, C;
Newman, AJ;
Hallegger, M;
Norman, CM;
Fica, SM;
Oubridge, C;
... Nagai, K; + view all
(2021)
psiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation.
Nature Communications
, 12
, Article 1488. 10.1038/s41467-021-21745-9.
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Wei, G;
Almeida, M;
Pintacuda, G;
Coker, H;
Bowness, JS;
Ule, J;
Brockdorff, N;
(2021)
Acute depletion of METTL3 implicates N6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome.
Genome Research
10.1101/gr.271635.120.
(In press).
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Wilkins, O;
Capitanchik, C;
Luscombe, N;
Ule, J;
(2021)
Ultraplex- A rapid, flexible, all-in-one fastq demultiplexer [version 1; peer review- 1 approved].
Wellcome Open Research
, 6
, Article 141. 10.12688/wellcomeopenres.16791.1.
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2020
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Capitanchik, C;
Toolan-Kerr, P;
Luscombe, NM;
Ule, J;
(2020)
How Do You Identify m⁶ A Methylation in Transcriptomes at High Resolution? A Comparison of Recent Datasets.
Frontiers in Genetics
, 11
, Article 398. 10.3389/fgene.2020.00398.
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Dermit, M;
Dodel, M;
Lee, FCY;
Azman, MS;
Schwenzer, H;
Jones, JL;
Blagden, SP;
... Mardakheh, FK; + view all
(2020)
Subcellular mRNA Localization Regulates Ribosome Biogenesis in Migrating Cells.
Developmental Cell
, 55
(3)
298-313.e10.
10.1016/j.devcel.2020.10.006.
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Gajduskova, P;
Ruiz de los Mozos, I;
Rajecky, M;
Hluchy, M;
Ule, J;
Blazek, D;
(2020)
CDK11 is required for transcription of replication-dependent histone genes.
Nature Structural and Molecular Biology
, 27
pp. 500-510.
10.1038/s41594-020-0406-8.
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Rundqvist, H;
Veliça, P;
Barbieri, L;
Gameiro, PA;
Bargiela, D;
Gojkovic, M;
Mijwel, S;
... Johnson, RS; + view all
(2020)
Cytotoxic T-cells mediate exercise-induced reductions in tumor growth.
eLife
, 9
, Article e59996. 10.7554/eLife.59996.
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Ule, J;
(2020)
Open access, open data and peer review.
Genome Biology
, 21
(1)
, Article 86. 10.1186/s13059-020-02005-3.
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2019
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Attig, J;
Ule, J;
(2019)
Genomic Accumulation of Retrotransposons Was Facilitated by Repressive RNA-Binding Proteins: A Hypothesis.
Bioessays
, Article e1800132. 10.1002/bies.201800132.
(In press).
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Briese, M;
Haberman, N;
Sibley, CR;
Faraway, R;
Elser, AS;
Chakrabarti, AM;
Wang, Z;
... Ule, J; + view all
(2019)
A systems view of spliceosomal assembly and branchpoints with iCLIP.
Nature Structural and Molecular Biology
, 26
(10)
pp. 930-940.
10.1038/s41594-019-0300-4.
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Bugai, A;
Quaresma, AJC;
Friedel, CC;
Lenasi, T;
Düster, R;
Sibley, CR;
Fujinaga, K;
... Barborič, M; + view all
(2019)
P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress.
Molecular Cell
, 74
10.1016/j.molcel.2019.01.033.
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Carter, J-M;
Emmett, W;
Mozos, IR;
Kotter, A;
Helm, M;
Ule, J;
Hussain, S;
(2019)
FICC-Seq: a method for enzyme-specified profiling of methyl-5-uridine in cellular RNA.
Nucleic Acids Research
, 47
(19)
p. 113.
10.1093/nar/gkz658.
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Castelo-Szekely, V;
De Matos, M;
Tusup, M;
Pascolo, S;
Ule, J;
Gatfield, D;
(2019)
Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock.
Nucleic Acids Research
, 47
(10)
pp. 5193-5209.
10.1093/nar/gkz261.
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Faraway, R;
Ule, J;
(2019)
The origin of neural microexons.
Nature Ecology & Evolution
, 3
pp. 526-527.
10.1038/s41559-019-0818-1.
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Modic, M;
Grosch, M;
Rot, G;
Schirge, S;
Lepko, T;
Yamazaki, T;
Lee, FCY;
... Drukker, M; + view all
(2019)
Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition.
Molecular Cell
, 74
(5)
pp. 951-956.
10.1016/j.molcel.2019.03.041.
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Obrdlik, A;
Lin, G;
Haberman, N;
Ule, J;
Ephrussi, A;
(2019)
The Transcriptome-wide Landscape and Modalities of EJC Binding in Adult Drosophila.
Cell Reports
, 28
(5)
1219-1236.e11.
10.1016/j.celrep.2019.06.088.
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Olgeiser, L;
Haag, C;
Boerner, S;
Ule, J;
Busch, A;
Koepke, J;
König, J;
... Zarnack, K; + view all
(2019)
The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs.
EMBO Reports
, 20
(1)
, Article e46588. 10.15252/embr.201846588.
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Tyzack, GE;
Luisier, R;
Taha, DM;
Neeves, J;
Modic, M;
Mitchell, JS;
Meyer, I;
... Patani, R; + view all
(2019)
Widespread FUS mislocalization is a molecular hallmark of amyotrophic lateral sclerosis.
Brain
10.1093/brain/awz217.
(In press).
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Ule, J;
Blencowe, BJ;
(2019)
Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution.
Molecular Cell
, 76
(2)
pp. 329-345.
10.1016/j.molcel.2019.09.017.
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2018
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Agostini, F;
Ule, J;
Zagalak, JA;
(2018)
No way out: when RNA elements promote nuclear retention.
EMBO Journal
, 37
(6)
, Article e99123. 10.15252/embj.201899123.
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Attig, J;
Agostini, F;
Gooding, C;
Chakrabarti, AM;
Singh, A;
Haberman, N;
Zagalak, JA;
... Ule, J; + view all
(2018)
Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing.
Cell
, 174
(5)
1067-1081.e17.
10.1016/j.cell.2018.07.001.
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Bertero, A;
Brown, S;
Madrigal, P;
Osnato, A;
Ortmann, D;
Yiangou, L;
Kadiwala, J;
... Vallier, L; + view all
(2018)
The SMAD2/3 interactome reveals that TGF beta controls m(6)A mRNA methylation in pluripotency.
Nature
, 555
(7695)
pp. 256-259.
10.1038/nature25784.
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Blazquez, L;
Emmett, W;
Faraway, R;
Pineda, JMB;
Bajew, S;
Gohr, A;
Haberman, N;
... Ule, J; + view all
(2018)
Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing.
Molecular Cell
, 72
(3)
496-509.e9.
10.1016/j.molcel.2018.09.033.
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Bugai, A;
Quaresma, AJC;
Friedel, C;
Lenasi, V;
Sibley, C;
Kukanja, P;
Fujinaga, K;
... Barboric, M; + view all
(2018)
P-TEFb activation by RBM7 shapes a pro-survival transcriptional response to genotoxic stress.
bioRxiv: Cold Spring Harbor, NY, USA.
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Chakrabarti, A;
Haberman, N;
Praznik, A;
Luscombe, N;
Ule, J;
(2018)
Data Science Issues in Understanding Protein-RNA Interactions.
Annual Review of Biomedical Data Science
, 1
pp. 235-261.
10.1146/annurev-biodatasci-080917-013525.
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Do, DV;
Strauss, B;
Cukuroglu, E;
Macaulay, I;
Wee, KB;
Hu, TX;
Igor, RDLM;
... Surani, MA; + view all
(2018)
SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements.
Cell Discovery
, 4
, Article 33. 10.1038/s41421-018-0032-3.
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Huppertz, I;
Haberman, N;
Ule, J;
(2018)
‘Read–through marking’ reveals differential nucleotide composition of read-through and truncated cDNAs in iCLIP.
Wellcome Open Research
, 3
, Article 77. 10.12688/wellcomeopenres.14663.1.
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Jantsch, M;
Quattrone, A;
O'Connell, M;
Helm, M;
Frye, M;
Macias-Gonzales, M;
Ohman, M;
... Fray, R; + view all
(2018)
Positioning Europe for the EPITRANSCRIPTOMICS challenge.
RNA Biology
, 15
(6)
pp. 829-831.
10.1080/15476286.2018.1460996.
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Lee, FCY;
Ule, J;
(2018)
Advances in CLIP Technologies for Studies of Protein-RNA Interactions.
Molecular Cell
, 69
(3)
pp. 354-369.
10.1016/j.molcel.2018.01.005.
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Luisier, R;
Tyzack, GE;
Hall, CE;
Mitchell, JS;
Devine, H;
Taha, DM;
Malik, B;
... Patani, R; + view all
(2018)
Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS.
Nature Communications
, 9
, Article 2010. 10.1038/s41467-018-04373-8.
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Ule, J;
Hwang, H-W;
Darnell, RB;
(2018)
The Future of Cross-Linking and Immunoprecipitation (CLIP).
Cold Spring Harbor Perspectives in Biology
, 10
(8)
, Article a032243. 10.1101/cshperspect.a032243.
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2017
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Diaz-Munoz, MD;
Kiselev, VY;
Le Novere, N;
Curk, T;
Ule, J;
Turner, M;
(2017)
Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells.
Nature Communications
, 8
, Article 530. 10.1038/s41467-017-00454-2.
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Dixit, S;
Müller-McNicoll, M;
David, V;
Zarnack, K;
Ule, J;
Hashimi, H;
Lukeš, J;
(2017)
Differential Binding of Mitochondrial Transcripts by MRB8170 and MRB4160 Regulates Distinct Editing Fates of Mitochondrial mRNA in Trypanosomes.
MBio
, 8
(1)
, Article e02288-16. 10.1128/mBio.02288-16.
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George, H;
Ule, J;
Hussain, S;
(2017)
Illustrating the Epitranscriptome at Nucleotide Resolution Using Methylation-iCLIP (miCLIP).
Methods in Molecular Biology
, 1562
pp. 91-106.
10.1007/978-1-4939-6807-7_7.
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Haberman, N;
Huppertz, I;
Attig, J;
König, J;
Wang, Z;
Hauer, C;
Hentze, MW;
... Ule, J; + view all
(2017)
Erratum to: Insights into the design and interpretation of iCLIP experiments.
[Corrigendum].
Genome Biology
, 18
(1)
, Article 154. 10.1186/s13059-017-1294-z.
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Haberman, N;
Huppertz, I;
Attig, J;
König, J;
Wang, Z;
Hauer, C;
Hentze, MW;
... Ule, J; + view all
(2017)
Insights into the design and interpretation of iCLIP experiments.
Genome Biology
, 18
, Article 7. 10.1186/s13059-016-1130-x.
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Hall, CE;
Yao, Z;
Choi, M;
Tyzack, GE;
Serio, A;
Luisier, R;
Harley, J;
... Patani, R; + view all
(2017)
Progressive Motor Neuron Pathology and the Role of Astrocytes in a Human Stem Cell Model of VCP-Related ALS.
Cell Reports
, 19
(9)
pp. 1739-1749.
10.1016/j.celrep.2017.05.024.
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Kolisnyk, B;
Al-Onaizi, M;
Soreq, L;
Barbash, S;
Bekenstein, U;
Haberman, N;
Hanin, G;
... Prado, MAM; + view all
(2017)
Cholinergic Surveillance over Hippocampal RNA Metabolism and Alzheimer's-Like Pathology.
Cerebral Cortex
, 27
(7)
pp. 3553-3567.
10.1093/cercor/bhw177.
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Ottens, F;
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