Gene Regulation and Expression

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2019

Reprogramming of Trypanosoma cruzi metabolism triggered by parasite interaction with the host cell extracellular matrix

Mattos, E. C., Canuto, G., Varón, N. C. M., Magalhães, R. D. M., Crozier, T. W. M., Lamont, D. J., Tavares, M. F. M., Colli, W., Ferguson, M. A. J. & Alves, M. J. M., 6 Feb 2019, In : PLoS Neglected Tropical Diseases. 13, 2, p. 1-27 27 p., e0007103.

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2 Citations (Scopus)
101 Downloads (Pure)

RNA-seq analysis of PHD and VHL inhibitors reveals differences and similarities to the hypoxia response

Frost, J., Ciulli, A. & Rocha, S., 29 Jan 2019, In : Wellcome Open Research. 4, p. 1-17 17 p., 17.

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SILAC-based quantitative proteomic analysis of Drosophila gastrula stage embryos mutant for fibroblast growth factor signalling

Beati, H., Langlands, A., ten Have, S. & Müller, H. -A. J., 24 Dec 2019, In : Fly. 19 p.

Research output: Contribution to journalArticle

Spatial-Stochastic modelling of synthetic gene regulatory networks

Macnamara, C. K., Mitchell, E. I. & Chaplain, M. A. J., 7 May 2019, In : Journal of Theoretical Biology. 468, p. 27-44 18 p.

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Structural Basis of BRCC36 Function in DNA Repair and Immune Regulation

Rabl, J., Bunker, R. D., Schenk, A. D., Cavadini, S., Gill, M. E., Abdulrahman, W., Andrés-Pons, A., Luijsterburg, M. S., Ibrahim, A. F. M., Branigan, E., Aguirre, J. D., Marceau, A. H., Guérillon, C., Bouwmeester, T., Hassiepen, U., Peters, A. H. F. M., Renatus, M., Gelman, L., Rubin, S. M., Mailand, N. & 3 others, van Attikum, H., Hay, R. T. & Thomä, N. H., 8 Aug 2019, In : Molecular Cell. 75, 3, p. 483-497.e9 15 p.

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Structure-Based Design of a Macrocyclic PROTAC

Testa, A., Hughes, S. J., Lucas, X., Wright, J. E. & Ciulli, A., 19 Nov 2019, In : Angewandte Chemie International Edition. 9 p.

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1 Citation (Scopus)
79 Downloads (Pure)

Ten quick tips for biocuration

Tang, Y. A., Pichler, K., Füllgrabe, A., Lomax, J., Malone, J., Munoz-Torres, M. C., Vasant, D. V., Williams, E. & Haendel, M., 2 May 2019, In : PLoS Computational Biology. 15, 5, p. 1-7 7 p., e1006906.

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TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells

Rasmussen, K. D., Berest, I., Keβler, S., Nishimura, K., Simón-Carrasco, L., Vassiliou, G. S., Pedersen, M. T., Christensen, J., Zaugg, J. B. & Helin, K., Apr 2019, In : Genome Research. 29, 4, p. 564-575 12 p.

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8 Citations (Scopus)
148 Downloads (Pure)

The Balance between Mono- and NEDD8-Chains Controlled by NEDP1 upon DNA Damage Is a Regulatory Module of the HSP70 ATPase Activity

Bailly, A. P., Perrin, A., Serrano-Macia, M., Maghames, C., Leidecker, O., Trauchessec, H., Martinez-Chantar, M. L., Gartner, A. & Xirodimas, D. P., 1 Oct 2019, In : Cell Reports. 29, 1, p. 212-224.e8 21 p.

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The Encyclopedia of Proteome Dynamics: The KinoViewer

Brenes Murillo, A. & Lamond, A., 15 Apr 2019, In : Bioinformatics. 35, 8, p. 1441-1442 2 p., bty823.

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2 Citations (Scopus)
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The Face of Chromatin Variants

Flaus, A. & Owen-Hughes, T., 5 Sep 2019, In : Cell. 178, 6, p. 1284-1286 3 p.

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The Identification of Potential Therapeutic Targets for Cutaneous Squamous Cell Carcinoma

McHugh, A., Fernandes, K., Chinner, N., Ibrahim, A. F. M., Garg, A. K., Boag, G., Hepburn, L. A., Proby, C. M., Leigh, I. M. & Saville, M. K., 6 Nov 2019, In : Journal of Investigative Dermatology. 17 p.

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The KDM4/JMJD2 histone demethylases are required for hematopoietic stem cell maintenance

Agger, K., Nishimura, K., Miyagi, S., Messling, J-E., Rasmussen, K. D. & Helin, K., 21 Aug 2019, In : Blood. 14 p.

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1 Citation (Scopus)
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The S phase checkpoint promotes the Smc5/6 complex dependent SUMOylation of Pol2, the catalytic subunit of DNA polymerase ε

Winczura, A., Appanah, R., Tatham, M. H., Hay, R. T. & De Piccoli, G., 25 Nov 2019, In : PLoS Genetics. 15, 11, p. 1-26 26 p., e1008427.

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2018

6-hydroxydopamine (6-OHDA) Oxidative Stress Assay for Observing Dopaminergic Neuron Loss in Caenorhabditis elegans

Offenburger, S-L. & Gartner, A., 20 Sep 2018, In : Bio-Protocol. 8, 18, 12 p., e3025.

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6-OHDA-induced dopaminergic neurodegeneration in Caenorhabditis elegans is promoted by the engulfment pathway and inhibited by the transthyretin-related protein TTR-33

Offenburger, S-L., Ho, X. Y., Tachie-Menson, T., Coakley, S., Hilliard, M. A. & Gartner, A., 18 Jan 2018, In : PLoS Genetics. 14, 1, p. 1-27 27 p., e1007125.

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2 Citations (Scopus)
187 Downloads (Pure)

A call for public archives for biological image data

Ellenberg, J., Swedlow, J. R., Barlow, M., Cook, C. E., Sarkans, U., Patwardhan, A., Brazma, A. & Birney, E., 30 Oct 2018, In : Nature Methods. 15, 11, p. 849-854 6 p.

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3 Citations (Scopus)
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Accurate Recycling of Parental Histones Reproduces the Histone Modification Landscape during DNA Replication

Reverón-Gómez, N., González-Aguilera, C., Stewart-Morgan, K. R., Petryk, N., Flury, V., Graziano, S., Johansen, J. V., Jakobsen, J. S., Alabert, C. & Groth, A., 18 Oct 2018, In : Molecular Cell. 72, 2, p. 239-249.e5

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24 Citations (Scopus)
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Activity-based E3 ligase profiling uncovers an E3 ligase with esterification activity

Pao, K-C., Wood, N. T., Knebel, A., Rafie, K., Stanley, M., Mabbitt, P. D., Sundaramoorthy, R., Hofmann, K., van Aalten, D. M. F. & Virdee, S., 11 Apr 2018, In : Nature. 556, 7701, p. 381-385 5 p.

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34 Citations (Scopus)
256 Downloads (Pure)

AKT overactivation can suppress DNA repair via p70S6 kinase-dependent downregulation of MRE11

Piscitello, D., Varshney, D., Lilla, S., Vizioli, M. G., Reid, C., Gorbunova, V., Seluanov, A., Gillespie, D. A. & Adams, P. D., 25 Jan 2018, In : Oncogene. 37, 4, p. 427-438 12 p.

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13 Citations (Scopus)
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Amino acid-dependent cMyc expression is essential for NK cell metabolic and functional responses in mice

Loftus, R. M., Assmann, N., Kedia-Mehta, N., O'Brien, K. L., Garcia, A., Gillespie, C., Hukelmann, J. L., Oefner, P. J., Lamond, A. I., Gardiner, C. M., Dettmer, K., Cantrell, D. A., Sinclair, L. V. & Finlay, D. K., 14 Jun 2018, In : Nature Communications. 9, 1, p. 1-15 15 p., 2341.

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29 Citations (Scopus)
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Analysis of novel missense ATR mutations reveals new splicing defects underlying Seckel Syndrome

Llorens-Agost, M., Luessing, J., van Beneden, A., Eykelenboom, J., O'Reilly, D., Bicknell, L. S., Reynolds, J. J., van Koegelenberg, M., Hurles, M. E., Brady, A. F., Jackson, A. P., Stewart, G. S. & Lowndes, N. F., Dec 2018, In : Human Mutation. 39, 12, p. 1847-1853 7 p.

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2 Citations (Scopus)
72 Downloads (Pure)

Computational Modelling of Cancer Development and Growth: Modelling at Multiple Scales and Multiscale Modelling

Szymańska, Z., Cytowski, M., Mitchell, E., Macnamara, C. K. & Chaplain, M., 1 May 2018, In : Bulletin of Mathematical Biology. 80, 5, p. 1366-1403 38 p.

Research output: Contribution to journalArticle

7 Citations (Scopus)

DHX15 regulates CMTR1-dependent gene expression and cell proliferation

Inesta-Vaquera, F., Chaugule, V. K., Galloway, A., Chandler, L., Rojas-Fernandez, A., Weidlich, S., Peggie, M. & Cowling, V., 18 Jun 2018, In : Life Science Alliance. 1, 3, 18 p., e201800092.

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9 Citations (Scopus)
127 Downloads (Pure)

E1B-55K-Mediated Regulation of RNF4 SUMO-Targeted Ubiquitin Ligase Promotes Human Adenovirus Gene Expression

Müncheberg, S., Hay, R. T., Ip, W. H., Meyer, T., Weiß, C., Brenke, J., Masser, S., Hadian, K., Dobner, T. & Schreiner, S., Jul 2018, In : Journal of Virology. 92, 13, 18 p., e00164-18.

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2 Citations (Scopus)
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Effects of hypo O-GlcNAcylation on Drosophila development

Mariappa, D. N., Ferenbach, A. & van Aalten, D. M. F., 11 May 2018, In : Journal of Biological Chemistry. 293, 19, p. 7209-7221 13 p.

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4 Citations (Scopus)
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Efficient Analysis of Mammalian Polysomes in cells and tissues using Ribo Mega-SEC

Yoshikawa, H., Larance, M., Harney, D. J., Sundaramoorthy, R., Ly, T., Owen-Hughes, T. & Lamond, A. I., 10 Aug 2018, In : eLife. 7, 7, p. 1-26 26 p., e36530.

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2 Citations (Scopus)
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Evidence for substrate assisted catalysis in N-acetylphosphoglucosamine mutase

Raimi, O. G., Hurtado Guerrero, R. & van Aalten, D. M. F., 16 Aug 2018, In : The Biochemical journal. 475, 15, p. 2547-2557 11 p.

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Expanded Interactome of the Intrinsically Disordered Protein Dss1

Schenstrøm, S. M., Rebula, C. A., Tatham, M. H., Hendus-Altenburger, R., Jourdain, I., Hay, R. T., Kragelund, B. B. & Hartmann-Petersen, R., 23 Oct 2018, In : Cell Reports. 25, 4, p. 862-870 9 p.

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1 Citation (Scopus)
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30 Citations (Scopus)
142 Downloads (Pure)

Histone H4K20 methylation mediated chromatin compaction threshold ensures genome integrity by limiting DNA replication licensing

Shoaib, M., Walter, D., Gillespie, P. J., Izard, F., Fahrenkrog, B., Lleres, D., Lerdrup, M., Johansen, J. V., Hansen, K., Julien, E., Blow, J. J. & Sørensen, C. S., 12 Sep 2018, In : Nature Communications. 9, 1, p. 1-11 11 p., 3704.

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3 Citations (Scopus)
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Identification of Elg1 interaction partners and effects on post-replication chromatin re-formation

Gali, V. K., Dickerson, D., Katou, Y., Fujiki, K., Shirahige, K., Owen-Hughes, T., Kubota, T. & Donaldson, A. D., Nov 2018, In : PLoS Genetics. 14, 11, p. 1-20 20 p., e1007783.

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2 Citations (Scopus)
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Inhibitors against Fungal Cell Wall Remodeling Enzymes

Delso, I., Valero-Gonzalez, J., Gomollón-Bel, F., Castro-López, J., Fang, W., Navratilova, I., van Aalten, D. M. F., Tejero, T., Merino, P. & Hurtado-Guerrero, R., 22 Jan 2018, In : ChemMedChem. 13, 2, p. 128-132 5 p.

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1 Citation (Scopus)
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Killing with proficiency: integrated post-translational regulation of an offensive Type VI secretion system

Ostrowski, A., Cianfanelli, F. R., Porter, M., Mariano, G., Peltier, J., Wong, J. J., Swedlow, J. R., Trost, M. & Coulthurst, S. J., 27 Jul 2018, In : PLoS Pathogens. 14, 7, p. 1-25 25 p., e1007230.

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8 Citations (Scopus)
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LEM-3 is a midbody-tethered DNA nuclease that resolves chromatin bridges during late mitosis

Hong, Y., Sonneville, R., Wang, B., Scheidt, V., Meier, B., Woglar, A., Demetriou, S., Labib, K., Jantsch, V. & Gartner, A., 20 Feb 2018, In : Nature Communications. 9, p. 1-11 11 p., 728.

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9 Citations (Scopus)
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Live-cell imaging of marked chromosome regions reveals dynamics of mitotic chromosome resolution and compaction

Eykelenboom, J. K., Gierlinski, M., Yue, Z., Hegarat, N., Pollard, H., Fukagawa, T., Hochegger, H. & Tanaka, T. U., 17 May 2018, In : BioRxiv. 53 p.

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Mechanism of activation of the BNLF2a immune evasion gene of Epstein-Barr virus by Zta

Almohammed, R., Osborn, K., Ramasubramanyan, S., Perez-Fernandez, I. B. N., Godfrey, A., Mancini, E. J. & Sinclair, A. J., 1 Jun 2018, In : Journal of General Virology. 99, 6, p. 805-817 13 p., 001056.

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Morphological and genetic characterisation of the root system architecture of selected barley recombinant chromosome substitution lines using an integrated phenotyping approach

Canto, C. D. L. F., Kalogiros, D. I., Ptashnyk, M., George, T. S., Waugh, R., Bengough, A. G., Russell, J. & Dupuy, L. X., 14 Jun 2018, In : Journal of Theoretical Biology. 447, p. 84-97 14 p.

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2 Citations (Scopus)
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mRNA cap methyltransferase, RNMT-RAM, promotes RNA pol II-dependent transcription

Varshney, D., Lombardi, O., Schweikert, G., Dunn, S., Suska, O. & Cowling, V., May 2018, In : Cell Reports. 23, 5, p. 1530-1542 13 p.

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7 Citations (Scopus)
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Mutational signatures of DNA mismatch repair deficiency in C. elegans and human cancers

Meier, B., Volkova, N. V., Hong, Y., Schofield, P., Campbell, P. J., Gerstung, M. & Gartner, A., May 2018, In : Genome Research. 28, 5, p. 666-675 10 p.

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15 Citations (Scopus)
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Mutations in Caenorhabditis elegans neuroligin-like glit-1, the apoptosis pathway and the calcium chaperone crt-1 increase dopaminergic neurodegeneration after 6-OHDA treatment

Offenburger, S-L., Jongsma, E. & Gartner, A., 18 Jan 2018, In : PLoS Genetics. 14, 1, p. 1-34 34 p., e1007106.

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6 Citations (Scopus)
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Myc activity is required for maintenance of the neuromesodermal progenitor signalling network and for segmentation clock gene oscillations in mouse

Mastromina, I., Verrier, L., Clara Silva, J., Storey, K. & Dale, J., 30 Jul 2018, In : Development. 145, 14, p. 1-14 14 p., dev161091.

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3 Citations (Scopus)
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O-GlcNAcase Fragment Discovery with Fluorescence Polarimetry

Borodkin, V. S., Rafie, K., Selvan, N., Aristotelous, T., Navratilova, I., Ferenbach, A. T. & Van Aalten, D. M. F., 18 May 2018, In : ACS Chemical Biology. 13, 5, p. 1353-1360 8 p.

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2 Citations (Scopus)
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PAWS1controls cytoskeletal dynamics and cell migration through association with the SH3 adaptor CD2AP

Cummins, T. D., Wu, K. Z. L., Bozatzi, P., Dingwell, K. S., Macartney, T. J., Wood, N. T., Varghese, J., Gourlay, R., Campbell, D. G., Prescott, A., Griffis, E., Smith, J. C. & Sapkota, G. P., 10 Jan 2018, In : Journal of Cell Science. 131, 1, p. 1-12 12 p., jcs202390.

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11 Citations (Scopus)
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Phosphorylation of Parkin at Serine65 is essential for its activation in vivo

McWilliams, T. G., Barini, E., Pohjolan-Pirhonen, R., Brooks, S. P., Singh, F., Burel, S., Balk, K., Kumar, A., Montava Garriga, L., Prescott, A., Hassoun, S. M., Mouton-Liger, F., Ball, G., Hills, R., Knebel, A., Ulusoy, A., Di Monte, D. A., Tamjar, J., Antico, O., Fears, K. & 11 others, Smith, L., Brambilla, R., Palin, E., Valori, M., Eerola-Rautio, J., Tienari, P., Corti, O., Dunnett, S. B., Ganley, I., Suomalainen, A. & Muqit, M., 7 Nov 2018, In : Open Biology. 8, 11, p. 1-18 18 p., 181108.

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15 Citations (Scopus)
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PIP30/FAM192A is a novel regulator of the nuclear proteasome activator PA28γ

Jonik-Nowak, B., Menneteau, T., Fesquet, D., Baldin, V., Bonne-Andrea, C., Méchali, F., Fabre, B., Boisguerin, P., de Rossi, S., Henriquet, C., Pugnière, M., Ducoux-Petit, M., Burlet-Schiltz, O., Lamond, A., Fort, P., Boulon, S., Bousquet, M-P. & Coux, O., 10 Jul 2018, In : Proceedings of the National Academy of Sciences of the United States of America. 115, 28, p. E6477-E6486 10 p., 201722299.

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6 Citations (Scopus)
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Positioning Europe for the EPITRANSCRIPTOMICS challenge

Jantsch, M., Quattrone, A., O'Connell, M., Helm, M., Frye, M., Macias-Gonzales, M., Ohman, M., Ameres, S., Willems, L., Fuks, F., Oulas, A., Vanacova, S., Nielsen, H., Bousquet-Antonelli, C., Motorin, Y., Roignant, J-Y., Balatsos, N., Dinnyes, A., Baranov, P., Kelly, V. & 40 others, Lamm, A., Rechavi, G., Pelizzola, M., Liepins, J., Holodnuka Kholodnyuk, I., Zammit, V., Ayers, D., Drablos, F., Dahl, J. A., Bujnicki, J., Jeronimo, C., Almeida, R., Neagu, M., Costache, M., Bankovic, J., Banovic, B., Kyselovic, J., Valor, L. M., Selbert, S., Pir, P., Demircan, T., Cowling, V., Schäfer, M., Rossmanith, W., Lafontaine, D., David, A., Carre, C., Lyko, F., Schaffrath, R., Schwartz, S., Verdel, A., Klungland, A., Purta, E., Timotijevic, G., Cardona, F., Davalos, A., Ballana, E., O Carroll, D., Ule, J. & Fray, R., 3 Jun 2018, In : RNA Biology. 15, 6, p. 829-831 8 p.

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6 Citations (Scopus)
133 Downloads (Pure)
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2 Citations (Scopus)
114 Downloads (Pure)