Gene Regulation and Expression

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2015

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.

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6 Citations (Scopus)
136 Downloads (Pure)
1 Citation (Scopus)

Evaluating the use of HILIC in large-scale, multi dimensional proteomics: horses for courses?

Bensaddek, D., Nicolas, A. & Lamond, A. I., 30 Nov 2015, In : International Journal of Mass Spectrometry. 391, p. 105-114 10 p.

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5 Citations (Scopus)
159 Downloads (Pure)

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

13 Citations (Scopus)

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.

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23 Citations (Scopus)
175 Downloads (Pure)

Global Reprogramming of Host SUMOylation during Influenza Virus Infection

Domingues, P., Golebiowski, F., Tatham, M. H., Lopes, A. M., Taggart, A., Hay, R. T. & Hale, B. G., 17 Nov 2015, In : Cell Reports. 13, 7, p. 1467-1480 14 p.

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28 Citations (Scopus)
155 Downloads (Pure)

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.

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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.

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39 Citations (Scopus)

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.

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31 Citations (Scopus)
281 Downloads (Pure)

Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis

Rasmussen, K. D., Jia, G., Johansen, J. V., Pedersen, M. T., Rapin, N., Bagger, F. O., Porse, B. T., Bernard, O. A., Christensen, J. & Helin, K., 1 May 2015, In : Genes and Development. 29, 9, p. 910-922 13 p.

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116 Citations (Scopus)
82 Downloads (Pure)

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.

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17 Citations (Scopus)

Mio depletion links mTOR regulation to Aurora A and Plk1 activation at mitotic centrosomes

Platani, M., Trinkle-Mulcahy, L., Porter, M., Jeyaprakash, A. A. & Earnshaw, W. C., 6 Jul 2015, In : Journal of Cell Biology. 210, 1, p. 45-62 18 p.

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8 Citations (Scopus)

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.

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211 Citations (Scopus)
289 Downloads (Pure)

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.

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24 Citations (Scopus)

Proteome-wide identification of SUMO modification sites by mass spectrometry

Tammsalu, T., Matic, I., Jaffray, E. G., Ibrahim, A. F. M., Tatham, M. H. & Hay, R. T., Sep 2015, In : Nature Protocols. 10, 9, p. 1374-1388 15 p.

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26 Citations (Scopus)

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, p. 1-15 15 p., e04534.

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22 Citations (Scopus)
139 Downloads (Pure)

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.

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36 Citations (Scopus)
221 Downloads (Pure)

Publishing and sharing multi-dimensional image data with OMERO

Burel, J-M., Besson, S., Blackburn, C., Carroll, M., Ferguson, R., Flynn, H., Gillen, K., Leigh, R., Li, S., Lindner, D., Linkert, M., Moore, W. J., Ramalingam, B., Rozbicki, E., Tarkowska, A., Walczysko, P., Allan, C., Moore, J. & Swedlow, J. R., Oct 2015, In : Mammalian Genome : Official Journal of the International Mammalian Genome Society. 26, 9, p. 441-447 7 p.

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9 Citations (Scopus)
184 Downloads (Pure)

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.

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23 Citations (Scopus)
255 Downloads (Pure)

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

18 Citations (Scopus)

Single cell tuning of Myc expression by antigen receptor signal strength and interleukin-2 in T lymphocytes

Preston, G. C., Sinclair, L. V., Kaskar, A., Hukelmann, J. L., Navarro, M., Ferrero, I., MacDonald, H. R., Cowling, V. H. & Cantrell, D. A., 4 Aug 2015, In : EMBO Journal. 34, 15, p. 2008-2024 17 p.

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Open Access
59 Citations (Scopus)

Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment

Gierlinski, M., Cole, C., Schofield, P., Schurch, N. J., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G., Owen-Hughes, T., Blaxter, M. & Barton, G. J., 15 Nov 2015, In : Bioinformatics. 31, 22, p. 3625-3630 6 p.

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34 Citations (Scopus)
170 Downloads (Pure)

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.

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53 Citations (Scopus)
160 Downloads (Pure)

Targeted knock-down of miR21 primary transcripts using snoMEN vectors induces apoptosis in human cancer cell lines

Ono, M., Ono, K., Avolio, F., Afzal, V., Bensaddek, D. & Lamond, A. I., 25 Sep 2015, In : PLoS ONE. 10, 9, 22 p., e0138668.

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8 Citations (Scopus)
401 Downloads (Pure)

Targeting of SUMO substrates to a Cdc48-Ufd1-Npl4 segregase and STUbL pathway in fission yeast

Køhler, J. B., Tammsalu, T., Jørgensen, M. M., Steen, N., Hay, R. T. & Thon, G., 2015, In : Nature Communications. 6, p. 1-14 14 p., 8827.

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14 Citations (Scopus)
126 Downloads (Pure)

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.

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15 Citations (Scopus)
208 Downloads (Pure)

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.

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75 Citations (Scopus)

Two distinct modes for propagation of histone PTMs across the cell cycle

Alabert, C., Barth, T. K., Reverón-Gómez, N., Sidoli, S., Schmidt, A., Jensen, O., Imhof, A. & Groth, A., 15 Mar 2015, In : Genes and Development. 29, 6, p. 585-590 6 p.

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149 Citations (Scopus)
109 Downloads (Pure)

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.

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17 Citations (Scopus)

Urmylation and tRNA thiolation functions of ubiquitin-like Uba4·Urm1 systems are conserved from yeast to man

Jüdes, A., Ebert, F., Bär, C., Thüring, K. L., Harrer, A., Klassen, R., Helm, M., Stark, M. J. R. & Schaffrath, R., 2 Apr 2015, In : FEBS Letters. 589, 8, p. 904-909 6 p.

Research output: Contribution to journalArticle

16 Citations (Scopus)

Visualization of the Serratia type VI secretion system reveals unprovoked attacks and dynamic assembly

Gerc, A. J., Diepold, A., Trunk, K., Porter, M., Rickman, C., Armitage, J. P., Stanley-Wall, N. R. & Coulthurst, S. J., 29 Sep 2015, In : Cell Reports. 12, 12, p. 2131-2142 12 p.

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36 Citations (Scopus)
243 Downloads (Pure)
2014

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.

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58 Citations (Scopus)
359 Downloads (Pure)

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.

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15 Citations (Scopus)
173 Downloads (Pure)

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.

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40 Citations (Scopus)
171 Downloads (Pure)

Analysis of Global RNA Synthesis at the Single Cell Level following Hypoxia

Biddlestone, J., Druker, J., Shmakova, A., Ferguson, G., Swedlow, J. R. & Rocha, S., 13 May 2014, In : JoVE: Journal of Visualized Experiments. 87, 7 p., e51420.

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2 Citations (Scopus)
159 Downloads (Pure)

ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome

Tinti, M., Madeira, F., Murugesan, G., Hoxhaj, G., Toth, R. & Mackintosh, C., 2014, In : Database: the Journal of Biological Databases and Curation. 2014, 15 p., bat085.

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28 Citations (Scopus)
196 Downloads (Pure)

A proteomic chronology of gene expression through the cell cycle in human myeloid leukemia cells

Ly, T., Ahmad, Y., Shlien, A., Soroka, D., Mills, A., Emanuele, M. J., Stratton, M. R. & Lamond, A. I., 4 Mar 2014, In : eLife. 2014, 3, e01630.

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73 Citations (Scopus)
117 Downloads (Pure)

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.

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28 Citations (Scopus)
212 Downloads (Pure)
Open Access
38 Citations (Scopus)

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, p. 1-28 28 p., e02863.

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16 Citations (Scopus)
177 Downloads (Pure)

C. elegans whole genome sequencing reveals mutational signatures related to carcinogens and DNA repair deficiency.

Meier, B., Cooke, S. L., Weiss, J., Bailly, A. P., Alexandrov, L. B., Marshall, J., Raine, K., Maddison, M., Anderson, E., Stratton, M. R., Gartner, A. & Campbell, P. J., 2014, In : Genome Research. 24, p. 1624-1636 14 p.

Research output: Contribution to journalArticle

Open Access
86 Citations (Scopus)

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.

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38 Citations (Scopus)

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.

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43 Citations (Scopus)
71 Downloads (Pure)

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.

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48 Citations (Scopus)
176 Downloads (Pure)

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.

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48 Citations (Scopus)
148 Downloads (Pure)
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27 Citations (Scopus)

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

Open Access
36 Citations (Scopus)

Erythropoietin guides multipotent hematopoietic progenitor cells toward an erythroid fate

Grover, A., Mancini, E., Moore, S., Mead, A. J., Atkinson, D., Rasmussen, K. D., O'Carroll, D., Jacobsen, S. E. W. & Nerlov, C., 10 Feb 2014, In : Journal of Experimental Medicine. 211, 2, p. 181-188 8 p.

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73 Citations (Scopus)
115 Downloads (Pure)

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

Open Access
182 Citations (Scopus)

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.

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13 Citations (Scopus)
129 Downloads (Pure)