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Gene Regulation and Expression

  1. Dose-dependent Effects of Allopurinol on Human Foreskin Fibroblast Cell and Human Umbilical Vein Endothelial Cell under Hypoxia

    Sun, Y., George, J. & Rocha, S. 1 Apr 2015 In : PLoS ONE. 10, 4, 12 p.e0123649

    Research output: Contribution to journalArticle

  2. Dose-Dependent Effects of Allopurinol on Human Foreskin Fibroblast Cells and Human Umbilical Vein Endothelial Cells under Hypoxia

    Sun, Y., George, J. & Rocha, S. 1 Apr 2015 In : PLoS ONE. 10, 4, 12 p.e0123649

    Research output: Contribution to journalArticle

  3. The role of hypoxia in inflammatory disease (Review)

    Biddlestone, J., Bandarra, D. & Rocha, S. 1 Apr 2015 In : International Journal of Molecular Medicine. 35, 4, p. 859-869 11 p.

    Research output: Contribution to journalArticle

  4. Kinetochore-microtubule error correction is driven by differentially regulated interaction modes

    Kalantzaki, M., Kitamura, E., Zhang, T., Mino, A., Novák , B. & Tanaka, T. U. Apr 2015 In : Nature Cell Biology. 17, 4, p. 421-433 13 p.

    Research output: Contribution to journalArticle

  5. Ubiquitin-C-terminal hydrolases cleave isopeptide and peptide-linked ubiquitin from structured proteins but do not edit ubiquitin homopolymers

    Bett, J. S., Ritorto, M. S., Ewan, R., Jaffray, E. G., Virdee, S., Chin, J. W., Knebel, A., Kurz, T., Trost, M., Tatham, M. H. & Hay, R. T. 15 Mar 2015 In : Biochemical Journal. 466, 3, p. 489-498 10 p.

    Research output: Contribution to journalArticle

  6. Erratum: dynamic SUMO modification regulates mitotic chromosome assembly and cell cycle progression in Caenorhabditis elegans

    Pelisch, F., Sonneville, R., Pourkarimi, E., Agostinho, A., Blow, J. J., Gartner, A. & Hay, R. T. 12 Feb 2015 In : Nature Communications. 6, 6352

    Research output: Contribution to journalArticle

  7. Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra-hypermutated cancers

    Shlien, A. , Campbell, B. B. , De Borja, R. , Alexandrov, L. B. , Merico, D. , Wedge, D. , Van Loo, P. , Tarpey, P. S. , Coupland, P. , Behjati, S. , Pollett, A. , Lipman, T. , Heidari, A. , Deshmukh, S. , Avitzur, N. , Meier, B. , Gerstung, M. , Hong, Y. , Merino, D. M. , Ramakrishna, M. & 42 others Remke, M., Arnold, R., Panigrahi, G. B., Thakkar, N. P., Hodel, K. P., Henninger, E. E., Göksenin, A. Y., Bakry, D., Charames, G. S., Druker, H., Lerner-Ellis, J., Mistry, M., Dvir, R., Grant, R., Elhasid, R., Farah, R., Taylor, G. P., Nathan, P. C., Alexander, S., Ben-Shachar, S., Ling, S. C., Gallinger, S., Constantini, S., Dirks, P., Huang, A., Scherer, S. W., Grundy, R. G., Durno, C., Aronson, M., Gartner, A., Meyn, M. S., Taylor, M. D., Pursell, Z. F., Pearson, C. E., Malkin, D., Futreal, P. A., Stratton, M. R., Bouffet, E., Hawkins, C., Campbell, P. J., Tabori, U. & for the Biallelic Mismatch Repair Deficiency Consortium 2 Feb 2015 In : Nature Genetics. 47, 3, p. 257-262 6 p.

    Research output: Contribution to journalLetter

  8. HIF-1α restricts NF-κB-dependent gene expression to control innate immunity signals

    Bandarra, D., Biddlestone, J., Mudie, S., Müller, H. -A. J. & Rocha, S. Feb 2015 In : Disease Models & Mechanisms. 8, 2, p. 169-181 13 p.

    Research output: Contribution to journalArticle

  9. Phosphorylation of Elp1 by Hrr25 Is Required for Elongator-Dependent tRNA Modification in Yeast

    Abdel-Fattah, W., Jablonowski, D., Di Santo, R., Thüring, K. L., Scheidt, V., Hammermeister, A., ten Have, S., Helm, M., Schaffrath, R. & Stark, M. J. R. 8 Jan 2015 In : PLoS Genetics. 11, 1, 16 p.e1004931

    Research output: Contribution to journalArticle

  10. Proteomic analysis of the response to cell cycle arrests in human myeloid leukemia cells

    Ly, T., Endo, A. & Lamond, A. I. 2 Jan 2015 In : eLife. 2015, 4, 15 p.e04534

    Research output: Contribution to journalArticle

  11. OMERO and Bio-Formats 5: Flexible Access to Large Bioimaging Datasets at Scale

    Moore, J., Linkert, M., Blackburn, C., Carroll, M., Ferguson, G., Flynn, H., Gillen, K., Leigh, R., Li, S., Lindner, D., Moore, W., Patterson, A., Pindelski, B., Ramalingam, B., Rozbicki, E., Tarkowska, A., Walczysko, P., Allan, C., Burel, J-M. & Swedlow, J. R. 2015 Medical Imaging 2015: Image Processing. Ourselin, S. & Styner, M. A. (eds.). SPIE-International Society for Optical Engineering, (Proceedings of SPIE; vol. 9413)

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  12. PML isoforms IV and V contribute to adenovirus-mediated oncogenic transformation by functionally inhibiting the tumor-suppressor p53

    Wimmer, P., Berscheminski, J., Blanchette, P., Groitl, P., Branton, P. E., Hay, R. T., Dobner, T. & Schreiner, S. 2015 In : Oncogene. 14 p.

    Research output: Contribution to journalArticle

  13. The NEDD8 inhibitor MLN4924 increases the size of the nucleolus and activates p53 through the ribosomal-Mdm2 pathway

    Bailly, A., Perrin, A., Bou Malhab, L. J., Pion, E., Larance, M., Nagala, M., Smith, P., O'Donohue, M-F., Gleizes, P-E., Zomerdijk, J., Lamond, A. I. & Xirodimas, D. P. 2015 In : Oncogene. 12 p.

    Research output: Contribution to journalArticle

  14. PITX1, a specificity determinant in the HIF-1α-mediated transcriptional response to hypoxia

    Mudie, S., Bandarra, D., Batie, M., Biddlestone, J., Moniz, S., Ortmann, B., Shmakova, A. & Rocha, S. 15 Dec 2014 In : Cell Cycle. 13, 24, p. 3878-3891 14 p.

    Research output: Contribution to journalArticle

  15. Dynamic SUMO modification regulates mitotic chromosome assembly and cell cycle progression in Caenorhabditis elegans

    Pelisch, F., Sonneville, R., Pourkarimi, E., Agostinho, A., Blow, J. J., Gartner, A. & Hay, R. T. 5 Dec 2014 In : Nature Communications. 5, 12 p.5485

    Research output: Contribution to journalArticle

  16. Tetraspanin (TSP-17) Protects Dopaminergic Neurons against 6-OHDA-Induced Neurodegeneration in C. elegans

    Masoudi, N., Ibanez-Cruceyra, P., Offenburger, S-L., Holmes, A. & Gartner, A. 4 Dec 2014 In : PLoS Genetics. 10, 12, 15 p.e1004767

    Research output: Contribution to journalArticle

  17. FMDV replicons encoding green fluorescent protein are replication competent

    Tulloch, F., Pathania, U., Luke, G. A., Nicholson, J., Stonehouse, N. J., Rowlands, D. J., Jackson, T., Tuthill, T., Haas, J., Lamond, A. I. & Ryan, M. D. 1 Dec 2014 In : Journal of Virological Methods. 209, p. 35-40 6 p.

    Research output: Contribution to journalArticle

  18. Cezanne (OTUD7B) regulates HIF-1α homeostasis in a proteasome-independent manner

    Bremm, A., Moniz, S., Mader, J., Rocha, S. & Komander, D. Dec 2014 In : EMBO Reports. 15, 12, p. 1268-1277 10 p.

    Research output: Contribution to journalArticle

  19. GEN1 from a thermophilic fungus is functionally closely similar to non-eukaryotic junction-resolving enzymes

    Freeman, A. D. J., Liu, Y., Déclais, A-C., Gartner, A. & Lilley, D. M. J. Dec 2014 In : Journal of Molecular Biology. 426, 24, p. 3946-3959 14 p.

    Research output: Contribution to journalArticle

  20. Modelling multi-protein complexes using PELDOR distance measurements for rigid body minimisation experiments using XPLOR-NIH

    Hammond, C. M., Owen-Hughes, T. & Norman, D. G. Dec 2014 In : Methods (San Diego, Calif.). 70, 2-3, p. 139-153 15 p.

    Research output: Contribution to journalArticle

  21. Proteomic and 3D structure analyses highlight the C/D box snoRNP assembly mechanism and its control

    Bizarro, J., Charron, C., Boulon, S., Westman, B., Pradet-Balade, B., Vandermoere, F., Chagot, M-E., Hallais, M., Ahmad, Y., Leonhardt, H., Lamond, A., Manival, X., Branlant, C., Charpentier, B., Verheggen, C. & Bertrand, E. 24 Nov 2014 In : Journal of Cell Biology. 207, 4, p. 463-480 18 p.

    Research output: Contribution to journalArticle

  22. Having a direct look: analysis of DNA damage and repair mechanisms by next generation sequencing

    Meier, B. & Gartner, A. 15 Nov 2014 In : Experimental Cell Research. 329, 1, p. 35-41 7 p.

    Research output: Contribution to journalArticle

  23. Piezo1 integration of vascular architecture with physiological force

    Li, J. , Hou, B. , Tumova, S. , Muraki, K. , Bruns, A. , Ludlow, M. J. , Sedo, A. , Hyman, A. J. , McKeown, L. , Young, R. S. , Yuldasheva, N. Y. , Majeed, Y. , Wilson, L. A. , Rode, B. , Bailey, M. A. , Kim, H. R. , Fu, Z. , Carter, D. A. L. , Bilton, J. , Imrie, H. & 8 others Ajuh, P., Dear, T. N., Cubbon, R. M., Kearney, M. T., Prasad, K. R., Evans, P. C., Ainscough, J. F. X. & Beech, D. J. 13 Nov 2014 In : Nature. 515, 7526, p. 279-82 4 p.

    Research output: Contribution to journalArticle

  24. Dss1 is a 26S proteasome ubiquitin receptor

    Paraskevopoulos, K., Kriegenburg, F., Tatham, M. H., Rösner, H. I., Medina, B., Larsen, I. B., Brandstrup, R., Hardwick, K. G., Hay, R. T., Kragelund, B. B., Hartmann-Petersen, R. & Gordon, C. 6 Nov 2014 In : Molecular Cell. 56, 3, p. 453-461 9 p.

    Research output: Contribution to journalArticle

  25. Monitoring Keap1-Nrf2 interactions in single live cells

    Baird, L., Swift, S., Llères, D. & Dinkova-Kostova, A. T. 1 Nov 2014 In : Biotechnology Advances. 32, 6, p. 1133-1144 12 p.

    Research output: Contribution to journalArticle

  26. The spatial effect of protein deuteration on nitroxide spin-label relaxation: implications for EPR distance measurement

    El Mkami, H., Ward, R., Bowman, A., Owen-Hughes, T. & Norman, D. G. Nov 2014 In : Journal of Magnetic Resonance . 248, p. 36-41 6 p.

    Research output: Contribution to journalArticle

  27. Prohibitin is required for transcriptional repression by the WT1-BASP1 complex

    Toska, E., Shandilya, J., Goodfellow, S. J., Medler, K. F. & Roberts, S. G. E. 23 Oct 2014 In : Oncogene. 33, 43, p. 5100-5108 9 p.

    Research output: Contribution to journalArticle

  28. Stochasticity in the symmetric division of plant cells: when the exceptions are the rule

    Besson, S. & Dumais, J. 9 Oct 2014 In : Frontiers in Plant Science. 5, October, p. 538

    Research output: Contribution to journalArticle

  29. A 3D cellular context for the macromolecular world

    Patwardhan, A. , Ashton, A. , Brandt, R. , Butcher, S. , Carzaniga, R. , Chiu, W. , Collinson, L. , Doux, P. , Duke, E. , Ellisman, M. H. , Franken, E. , Grünewald, K. , Heriche, J-K. , Koster, A. , Kühlbrandt, W. , Lagerstedt, I. , Larabell, C. , Lawson, C. L. , Saibil, H. R. , Sanz-García, E. & 4 others Subramaniam, S., Verkade, P., Swedlow, J. R. & Kleywegt, G. J. Oct 2014 In : Nature Structural & Molecular Biology. 21, 10, p. 841-845 5 p.

    Research output: Contribution to journalComment/debate

  30. Farmers without borders-genetic structuring in century old barley (Hordeum vulgare)

    Forsberg, N. E. G., Russell, J., Macaulay, M., Leino, M. W. & Hagenblad, J. 17 Sep 2014 In : Heredity.

    Research output: Contribution to journalArticle

  31. Chromatin and oxygen sensing in the context of JmjC histone demethylases

    Shmakova, A., Batie, M., Druker, J. & Rocha, S. 15 Sep 2014 In : Biochemical Journal. 462, 3, p. 385-395 11 p.

    Research output: Contribution to journalArticle

  32. Buffered Qualitative Stability explains the robustness and evolvability of transcriptional networks

    Albergante, L., Blow, J. J. & Newman, T. J. 2 Sep 2014 In : eLife. 3, 28 p.e02863

    Research output: Contribution to journalArticle

  33. Sumoylation controls host anti-bacterial response to the gut invasive pathogen Shigella flexneri

    Fritah, S., Lhocine, N., Golebiowski, F., Mounier, J., Andrieux, A., Jouvion, G., Hay, R. T., Sansonetti, P. & Dejean, A. Sep 2014 In : EMBO Reports. 15, 9, p. 965-972 8 p.

    Research output: Contribution to journalArticle

  34. Family-wide analysis of poly(ADP-ribose) polymerase activity

    Vyas, S., Matic, I., Uchima, L., Rood, J., Zaja, R., Hay, R. T., Ahel, I. & Chang, P. 21 Jul 2014 In : Nature Communications. 5, 13 p.4426

    Research output: Contribution to journalArticle

  35. The contribution of dormant origins to genome stability: from cell biology to human genetics

    Alver, R. C., Chadha, G. S. & Blow, J. J. Jul 2014 In : DNA Repair. 19, p. 182-189 8 p.

    Research output: Contribution to journalArticle

  36. Structural insight into SUMO chain recognition and manipulation by the ubiquitin ligase RNF4

    Xu, Y., Plechanovová, A., Simpson, P., Marchant, J., Leidecker, O., Kraatz, S., Hay, R. T. & Matthews, S. J. 27 Jun 2014 In : Nature Communications. 5, 12 p.4217

    Research output: Contribution to journalArticle

  37. A dynamic microtubule cytoskeleton directs medial actomyosin function during tube formation

    Booth, A. J. R., Blanchard, G. B., Adams, R. J. & Röper, K. 9 Jun 2014 In : Developmental Cell. 29, 5, p. 562-576 15 p.

    Research output: Contribution to journalArticle

  38. A conserved and essential basic region mediates tRNA binding to the Elp1 subunit of the Saccharomyces cerevisiae Elongator complex

    Di Santo, R., Bandau, S. & Stark, M. J. R. Jun 2014 In : Molecular Microbiology. 92, 6, p. 1227-1242 16 p.

    Research output: Contribution to journalArticle

  39. Sp100 isoform-specific regulation of human adenovirus 5 gene expression

    Berscheminski, J., Wimmer, P., Brun, J., Ip, W. H., Groitl, P., Horlacher, T., Jaffray, E., Hay, R. T., Dobner, T. & Schreiner, S. Jun 2014 In : Journal of Virology. 88, 11, p. 6076-6092 17 p.

    Research output: Contribution to journalArticle

  40. The essential roles of cytidine diphosphate-diacylglycerol synthase in bloodstream form Trypanosoma brucei

    Lilley, A. C., Major, L., Young, S., Stark, M. J. R. & Smith, T. K. May 2014 In : Molecular Microbiology. 92, 3, p. 453-470 18 p.

    Research output: Contribution to journalArticle

  41. Proteome-wide identification of SUMO2 modification sites

    Tammsalu, T., Matic, I., Jaffray, E. G., Ibrahim, A. F. M., Tatham, M. H. & Hay, R. T. 29 Apr 2014 In : Science Signaling. 7, 323, 10 p.rs2

    Research output: Contribution to journalArticle

  42. E3 ubiquitin ligase HOIP attenuates apoptotic cell death induced by cisplatin

    MacKay, C., Carroll, E., Ibrahim, A. F. M., Garg, A., Inman, G. J., Hay, R. T. & Alpi, A. F. 15 Apr 2014 In : Cancer Research. 74, 8, p. 2246-2257 12 p.

    Research output: Contribution to journalArticle

  43. A perspective on proteomics in cell biology

    Ahmad, Y. & Lamond, A. I. Apr 2014 In : Trends in Cell Biology. 24, 4, p. 257-264 8 p.

    Research output: Contribution to journalScientific review

  44. Acetylation of histone H3 at lysine 64 regulates nucleosome dynamics and facilitates transcription

    Di Cerbo, V., Mohn, F., Ryan, D. P., Montellier, E., Kacem, S., Tropberger, P., Kallis, E., Holzner, M., Hoerner, L., Feldmann, A., Richter, F. M., Bannister, A. J., Mittler, G., Michaelis, J., Khochbin, S., Feil, R., Schuebeler, D., Owen-Hughes, T., Daujat, S. & Schneider, R. 25 Mar 2014 In : eLife. 3, e01632

    Research output: Contribution to journalArticle

  45. NDK-1, the homolog of NM23-H1/H2 regulates cell migration and apoptotic engulfment in C. elegans

    Fancsalszky, L., Monostori, E., Farkas, Z., Pourkarimi, E., Masoudi, N., Hargitai, B., Bosnar, M. H., Deželjin, M., Zsákai, A., Vellai, T., Mehta, A. & Takács-Vellai, K. 21 Mar 2014 In : PLoS ONE. 9, 3, 12 p.e92687

    Research output: Contribution to journalArticle

  46. SUMO chain-induced dimerization activates RNF4

    Rojas-Fernandez, A., Plechanovová, A., Hattersley, N., Jaffray, E., Tatham, M. H. & Hay, R. T. 20 Mar 2014 In : Molecular Cell. 53, 6, p. 880-92 13 p.

    Research output: Contribution to journalArticle

  47. Near real-time processing of proteomics data using Hadoop.

    Hillman, C., Ahmad, Y., Whitehorn, M. & Cobley, A. 14 Mar 2014 In : Big Data. 2, 1, p. 44-49 5 p.

    Research output: Contribution to journalArticle

  48. A role for the Cajal-body-associated SUMO isopeptidase USPL1 in snRNA transcription mediated by RNA polymerase II

    Hutten, S., Chachami, G., Winter, U., Melchior, F. & Lamond, A. I. 1 Mar 2014 In : Journal of Cell Science. 127, 5, p. 1065-1078 14 p.

    Research output: Contribution to journalArticle

  49. Phosphorylation of Sli15 by Ipl1 is important for proper CPC localization and chromosome stability in Saccharomyces cerevisiae

    Makrantoni, V., Corbishley, S., Rachidi, N., Morrice, N. A., Robinson, D. A. & Stark, M. J. R. 18 Feb 2014 In : PLoS ONE. 9, 2, 15 p.e89399

    Research output: Contribution to journalArticle

  50. PML isoforms in response to arsenic: high-resolution analysis of PML body structure and degradation

    Hands, K. J., Cuchet-Lourenco, D., Everett, R. D. & Hay, R. T. 15 Jan 2014 In : Journal of Cell Science. 127, 2, p. 365-375 11 p.

    Research output: Contribution to journalArticle

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