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Gene Regulation & Expression

  1. The chromatin remodelling enzymes SNF2H and SNF2L position nucleosomes adjacent to CTCF and other transcription

    Wiechens, N., Singh, V., Gkikopoulos, T., Schofield, P., Rocha, S. & Owen-Hughes, T. 28 Mar 2016 In : PLoS Genetics.

    Research output: Contribution to journalArticle

  2. Metadata management for high content screening in OMERO

    Li, S. , Besson, S. , Blackburn, C. , Carroll, M. , Ferguson, R. K. , Flynn, H. , Gillen, K. , Leigh, R. , Lindner, D. , Linkert, M. , Moore, W. J. , Ramalingam, B. , Rozbicki, E. , Rustici, G. , Tarkowska, A. , Walczysko, P. , Williams, E. , Allan, C. , Burel, J. M. & 2 others Moore, J. & Swedlow, J. R. 1 Mar 2016 In : Methods. p. 27-32

    Research output: Contribution to journalArticle

  3. CDK-dependent phosphorylation of PHD1 on serine 130 alters its substrate preference in cells

    Ortmann, B., Bensaddek, D., Carvalhal, S., Moser, S. C., Mudie, S., Griffis, E. R., Swedlow, J. R., Lamond, A. I. & Rocha, S. Jan 2016 In : Journal of Cell Science. 129, 1, p. 191-205 15 p.

    Research output: Contribution to journalArticle

  4. 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. 2016 In : Oncogene. 35, p. 69-82 14 p.

    Research output: Contribution to journalArticle

  5. 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. 2016 In : Oncogene. 35, p. 415-426 12 p.

    Research output: Contribution to journalArticle

  6. The nucleoporin ALADIN regulates Aurora A localization to ensure robust mitotic spindle formation

    Carvalhal, S., Abreu Ribeiro, S., Arocena, M., Kasciukovic, T., Temme, A., Koehler, K., Huebner, A. & Griffis, E. R. 1 Oct 2015 In : Molecular Biology of the Cell. 26, 19, p. 3424-3438 15 p.

    Research output: Contribution to journalArticle

  7. Screen for multi-SUMO-binding proteins reveals a multi-SIM-binding mechanism for recruitment of the transcriptional regulator ZMYM2 to chromatin

    Aguilar-Martinez, E., Chen, X., Webber, A., Mould, A. P., Seifert, A., Hay, R. T. & Sharrocks, A. D. 1 Sep 2015 In : Proceedings of the National Academy of Sciences of the United States of America. 112, 35, p. E4854-E4863 10 p.

    Research output: Contribution to journalArticle

  8. Cezanne regulates E2F1-dependent HIF2α expression

    Moniz, S., Bandarra, D., Biddlestone, J., Campbell, K. J., Komander, D., Bremm, A. & Rocha, S. 15 Aug 2015 In : Journal of Cell Science. 128, 16, p. 3082-3093 12 p., JOCES/2015/168864

    Research output: Contribution to journalArticle

  9. Discovery of an unconventional centromere in budding yeast redefines evolution of point centromeres

    Kobayashi, N., Suzuki, Y., Schoenfeld, L., Müller, C., Nieduszynski, C., Wolfe, K. & Tanaka, T. 3 Aug 2015 In : Current Biology. 25, 15, p. 2026-2033 8 p.

    Research output: Contribution to journalArticle

  10. Structural basis for the RING catalyzed synthesis of K63 linked ubiquitin chains

    Branigan, E., Plechanovova, A., Jaffray, E. G., Naismith, J. H. & Hay, R. T. Aug 2015 In : Nature Structural & Molecular Biology. 22, 8, p. 597-602 6 p.

    Research output: Contribution to journalArticle

  11. Both Chromosome Decondensation and Condensation Are Dependent on DNA Replication in C.elegans Embryos

    Sonneville, R., Craig, G., Labib, K., Gartner, A. & Blow, J. J. 21 Jul 2015 In : Cell Reports. 12, 3, p. 405-417 13 p.

    Research output: Contribution to journalArticle

  12. Proteotoxic stress reprograms the chromatin landscape of SUMO modification

    Seifert, A., Schofield, P., Barton, G. & Hay, R. 7 Jul 2015 In : Science Signaling. 8, 384, p. rs7 14 p.

    Research output: Contribution to journalArticle

  13. Global proteomics analysis of the response to starvation in C. elegans

    Larance, M., Pourkarimi, E., Wang, B., Brenes Murillo, A., Kent, R., Lamond, A. I. & Gartner, A. 1 Jul 2015 In : Molecular & Cellular Proteomics. 14, 7, p. 1989-2001 13 p.

    Research output: Contribution to journalArticle

  14. Maintenance of distinct melanocyte populations in the interfollicular epidermis

    Glover, J. D., Knolle, S., Wells, K. L., Liu, D., Jackson, I. J., Mort, R. L. & Headon, D. J. 1 Jul 2015 In : Pigment Cell and Melanoma Research. 28, 4, p. 476-480 5 p.

    Research output: Contribution to journalArticle

  15. Multidimentional proteomics for cell biology

    Larance, M. & Lamond, A. I. May 2015 In : Nature Reviews Molecular Cell Biology. 16, 5, p. 269-280 12 p.

    Research output: Contribution to journalArticle

  16. Rapid generation of endogenously driven transcriptional reporters in cells through CRISPR/Cas9

    Rojas-Fernandez, A., Herhaus, L., Macartney, T., Lachaud, C., Hay, R. T. & Sapkota, G. P. 29 Apr 2015 In : Scientific Reports. 5, 6 p., 9811

    Research output: Contribution to journalArticle

  17. HIF-1α, a novel piece in the NF-κB puzzle

    Bandarra, D. & Rocha, S. 28 Apr 2015 In : Infammation and Cell Signaling. 2, 1, 4 p., e792

    Research output: Contribution to journalArticle

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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. & 43 others Ramakrishna, M., 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

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

    Forsberg, N. E. G., Russell, J., Macaulay, M., Leino, M. W. & Hagenblad, J. Feb 2015 In : Heredity. 114, 2, p. 195-206

    Research output: Contribution to journalArticle

  25. 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

  26. 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

  27. 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

  28. Embracing the chaos of behavioral proteomics: a comment on Valcu and Kempenaers

    Bailey, N. W. & Ly, T. 2015 In : Behavioral Ecology. 26, 1, p. 18-19 2 p.

    Research output: Contribution to journalComment/debate

  29. NF-κB and HIF crosstalk in immune responses

    D'Ignazio, L., Bandarra, D. & Rocha, S. 2015 In : FEBS Journal. 12 p.

    Research output: Contribution to journalArticle

  30. 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.). Bellingham: SPIE-International Society for Optical Engineering, 941307. (Proceedings of SPIE; vol. 9413)

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

  31. 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

  32. Identification of small molecule inhibitors of pre-mRNA splicing

    Pawellek, A., McElroy, S., Samatov, T., Mitchell, L., Woodland, A., Ryder, U., Gray, D., Lührmann, R. & Lamond, A. I. 12 Dec 2014 In : Journal of Biological Chemistry. 289, 50, p. 34683-34698 16 p.

    Research output: Contribution to journalArticle

  33. 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

  34. 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

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

    Bremm, A., Moniz, S., Mader, J., Rocha, S. & Komander, D. 1 Dec 2014 In : EMBO Reports. 15, 12, p. 1268-1277 10 p.

    Research output: Contribution to journalArticle

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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. & 9 others Imrie, H., 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 journalLetter

  42. 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

  43. 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

  44. 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

  45. 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

  46. 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

  47. 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. & 5 others Sanz-García, E., Subramaniam, S., Verkade, P., Swedlow, J. R. & Kleywegt, G. J. 7 Oct 2014 In : Nature Structural & Molecular Biology. 21, 10, p. 841-845 5 p.

    Research output: Contribution to journalComment/debate

  48. 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

  49. 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

  50. Cell cycle progression in response to oxygen levels

    Ortmann, B., Druker, J. & Rocha, S. Sep 2014 In : Cellular and Molecular Life Sciences. 71, 18, p. 3569-3582 14 p.

    Research output: Contribution to journalArticle

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