Search Publications

For the most up to date information on articles, books, conference papers and other research outputs, please check the Gene Regulations and Expression page on the University of Dundee Discovery Research Portal.

Below is a list of Featured Publications. For a full list of all publications please visit our page on the School of Life Sciences website.

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  • 2017
  • 2016
  • 2015

Madeira, F., Tinti, M., Murugesan, G., Berrett, E., Stafford, M., Toth, R., Cole, C., MacKintosh, C. and Barton, G. J

14-3-3-Pred: Improved methods to predict 14-3-3-binding phosphopeptides.

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PMID: 25735772 Abstract

Tatham, M. H., Cole, C., Scullion, P., Wilkie, R., Westwood, N. J., Stark, L. A. and Hay, R. T

A Proteomic Approach to Analyze the Aspirin-mediated Lysine Acetylome. Molecular & cellular proteomics

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PMID: 27913581 Abstract

Aguilar-Martinez, E., Chen, X., Webber, A., Mould, A. P., Seifert, A., Hay, R. T. and Sharrocks, A. D

A screen for multi-SUMO binding proteins reveals a multi-SIM binding mechanism for reruitment of ZMYM2 to chromatin

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PMID: 26283374 Abstract

Pelisch F, Tammsalu T, Wang B, Jaffray EG, Gartner A, Hay RT

A SUMO-Dependent Protein Network Regulates Chromosome Congression During Oocyte Meiosis.

Molecular Cell (accepted for publication)

Pelisch, F., Tammsalu, T., Wang, B., Jaffray, E. G., Gartner, A. and Hay, R. T

A SUMO-Dependent Protein Network Regulates Chromosome Congression during Oocyte Meiosis. Molecular cell

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PMID: 27939944 Abstract

Ward, J., Cole, C., Febrer, M. and Barton, G.

Almost Significant: simplifying quality control of high-throughput sequencing data

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PMID: 27559158 Abstract

Masuzzo, P., Martens, L., Cell Migration Workshop, P., Ampe, C., Anderson, K. I., Barry, J., De Wever, O., Debeir, O., Decaestecker, C., Dolznig, H., Friedl, P., Gaggioli, C., Geiger, B., Goldberg, I. G., Horn, E., Horwitz, R., Kam, Z., Le Devedec, S. E., Vignjevic, D. M., Moore, J., Olivo-Marin, J. C., Sahai, E., Sansone, S. A., Sanz-Moreno, V., Stromblad, S., Swedlow, J., Textor, J., Van Troys, M. and Zantl, R

An open data ecosystem for cell migration research.

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PMID: 25484346 Abstract

Sloan, E., Tatham, M. H., Groslambert, M., Glass, M., Orr, A., Hay, R. T. and Everett, R. D

Analysis of the SUM02 proteome during HSV-1 infection.

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PMID: 26200910 Abstract

Gonzalez, A. E., Munoz, V. C., Cavieres, V. A., Bustamante, H. A., Cornejo, V. H., Januario, Y. C., Gonzalez, I., Hetz, C., daSilva, L. L., Rojas-Fernandez, A., Hay, R. T., Mardones, G. A. and Burgos, P. V.

Autophagosomes cooperate in the degradation of intracellular C-terminal fragments of the amyloid precursor protein via the MVB/lysosomal pathway

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PMID: 28254759 Abstract

Meier B, Cooke SL, Weiss J, Bailly AP, Alexandrov LB, Marshall J, Raine K, Maddison M, Anderson E, Stratton MR, Gartner A*, Campbell PJ.

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

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Genome research. 2014. doi: 10.1101/gr.175547.114. [Epub ahead of print] *Co-corresponding author

PMID: 4199376 Abstract

Ortmann, B., Bensaddek, D., Carvalhal, S., Moser, S. C., Mudie, S., Griffis, E. R., Swedlow, J. R., Lamond, A. I., and Rocha, S.

CDK dependent phosphorylation of PHD1 on Serine 130 determines specificity in substrate targeting in cells

J. Cell Sci. 129, 191-205

Aregger M, Kaskar A, Fernandez-Sanchez ME, Simone Weidlich S and Cowling VH 

CDK1-cyclinB activates RNMT co-ordinating mRNA cap methylation with G1 phase transcription

Mol Cell. 2016 Mar 3;61(5):734-46. doi: 10.1016/j.molcel.2016.02.008

Gillespie, P.J., Neusiedler, J., Creavin, K. and Blow, J.J

Cell cycle synchronization in Xenpous egg extracts.

PMID: 26254920 Abstract

Moniz, S., Bandarra, D., Biddlestone, J., Campbell, K. J., Komander, D., Bremm, A. and Rocha, S

Cezanne regulates E2F1-dependent HIF-2alpha expression

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PMID: 26148512 Abstract

Moniz, S., Bandarra, D., Biddlestone, J., Campbell, K.J., Komander, D., Bremm, A., and Rocha, S.

Cezanne regulates E2F1-dependent HIF-2alpha expression

J Cell Sci. 128.3082-3093 doi: 10.1242/jcs.168864

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., Remke, M., Arnold, R., Panigrahi, G. B., Thakkar, N. P., Hodel, K. P., Henninger, E. E., Goksenin, 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. and Biallelic Mismatch Repair Deficiency, C

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

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PMID: 25642631 Abstract

Kilpinen, H., Goncalves, A., Leha, A., Afzal, V., Alasoo, K., Ashford, S., Bala, S., Bensaddek, D., Casale, F. P., Culley, O. J., Danecek, P., Faulconbridge, A., Harrison, P. W., Kathuria, A., McCarthy, D., McCarthy, S. A., Meleckyte, R., Memari, Y., Moens, N., Soares, F., Mann, A., Streeter, I., Agu, C. A., Alderton, A., Nelson, R., Harper, S., Patel, M., White, A., Patel, S. R., Clarke, L., Halai, R., Kirton, C. M., Kolb-Kokocinski, A., Beales, P., Birney, E., Danovi, D., Lamond, A. I., Ouwehand, W. H., Vallier, L., Watt, F. M., Durbin, R., Stegle, O. and Gaffney, D. J

Common genetic variation drives molecular heterogeneity in human iPSCs

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PMID: 28489815 Abstract

Liu, Y., Freeman, A. D., Declais, A. C., Wilson, T. J., Gartner, A. and Lilley, D. M

Crystal structure of a eukaryotic GEN1 resolving enzyme bound to DNA

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PMID: 26686639 Abstract

Sonneville, R., Moreno, S. P., Knebel, A., Johnson, C., Hastie, C. J., Gartner, A., Gambus, A. and Labib, K

CUL-2LRR-1 and UBXN-3 drive replisome disassembly during DNA replication termination and mitosis. Nature cell biology

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PMID: 28368371 Abstract

Vikram Narayan, Tony Ly, EhsanPourkarimi, Alejandro Brenes Murillo, Anton Gartner*, Angus I Lamond* and Cynthia Kenyon*

Deep proteome analysis identifies new age-related processes in C. elegans

Cell Systems 2016 Jul 20. pii: S2405-4712(16)30216-2. doi: 10.1016 *Co-senior authors

Kobayashi, N., Suzuki, Y., Schoenfeld, L. W., Muller, C. A., Nieduszynski, C., Wolfe, K. H. and Tanaka, T. U

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

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PMID: 26166782 Abstract

Sun, Y., George, J. and Rocha, S

Dose-dependent effects of allopurinol on human foreskin fibroblast cells and human umbilical vein endothelial cells under hypoxia

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PMID: 25830774 Abstract

Mariappa, D., Zheng, X., Schimpl, M., Raimi, O., Ferenbach, A.T., Mueller, H.A.J. and van Aalten ,D.M.F

Dual functionality of O-GlcNAc transferase is required for Drosophila development

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PMID: 26674417 Abstract

Fennessy, R.T., and Owen-Hughes, T.

Establishment of a promoter-based chromatin architecture on recently replicated DNA can accommodate variable inter-nucleosome spacing

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Nucleic Acids Research doi 10.1093/nar/gkw331

PMID: 27106059 Abstract

Bensaddek, D., Nicolas, A. and Lamond, A. I

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

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PMID: 26869852 Abstract

Schurch, N.J., Schofield, P., Gierlinski, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G.G., Owen-Huges, T., Blaxter, M. and Barton, G.J

Evaluation of tools for differntial gene expression analysis by RNA-seq on a 48 biolgocal replicate experiment.

Larance M, Kirkwood KJ, Tinti M, Murillo AB, Ferguson MA. and Lamond AI

Global Membrane Protein Interactome Analysis using In vivo Crosslinking and MS-based Protein Correlation Profiling

Molecular & Cellular Proteomics, mcp. O115.055467.

Domingues, P., Golebiowski, F., Tatham, M. H., Lopes, A. M., Taggart, A., Hay, R. T. and Hale, B. G

Global Reprogramming of Host SUMOylation during Influenza Virus Infection

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PMID: 26549460 Abstract

GWAS for executive function and processing speed suggests involvement of the CADM2 gene

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PMID: 25869804 Abstract

Bandarra, D., Biddlestone, J., Mudie, S., Muller, H. A., and Rocha, S.

HIF-1alpha restricts NF-kappaB-dependent gene expression to control innate immunity signals

Disease models & mchanisms. 8 169-181doi: 10.1242/dmm.017285

PMID: 4314782 Abstract

Bandarra, D., Biddlestone, J., Mudie, S., Muller, H.A. and Rocha, S

HIF-1alpha restricts NF-kappaB-dependent gene expression to control innate immunity signals.

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PMID: 25510503 Abstract

Bandarra, D., Biddlestone, J., Mudie, S., Muller, H. A. and Rocha, S

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

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PMID: 25510503 Abstract

Hauer, M. H., Seeber, A., Singh, V., Thierry, R., Sack, R., Amitai, A., Kryzhanovska, M., Eglinger, J., Holcman, D., Owen-Hughes, T. and Gasser, S. M

Histone degradation in response to DNA damage enhances chromatin dynamics and recombination rates

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PMID: 28067915 Abstract

Schurch, N.J., Schofield, P., Gierlinski, M., Cole, C., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G.G., Owen-Hughes, T., Blaxter, M., and Barton, G.J.

How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use?

RNA, 2016.

Young, D. F., Andrejeva, J., Li, X., Inesta-Vaquera, F., Dong, C., Cowling, V. H., Goodbourn, S. and Randall, R. E.

Human IFIT1 Inhibits mRNA Translation of Rubulaviruses but Not Other Members of the Paramyxoviridae Family.

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PMID: 27512068 Abstract

Hiraga, S. I., Ly, T., Garzon, J., Horejsi, Z., Ohkubo, Y. N., Endo, A., Obuse, C., Boulton, S. J., Lamond, A. I. and Donaldson, A. D

Human RIF1 and protein phosphatase 1 stimulate DNA replication origin licensing but suppress origin activation

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PMID: 28077461 Abstract

Kalantzaki, M., Kitamura, E., Zhang, T., Mino, A., Novak, B. and Tanaka, T. U

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

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PMID: 25751138 Abstract

Yue, Z., Komoto, S., Gierlinski, M., Pasquali, D., Kitamura, E. and Tanaka, T. U.

Mechanisms mitigating problems with multiple kinetochores on one microtubule in early mitosis

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PMID: 28546446 Abstract

Bennsaddek, D., Narayan, V., Nicolas, A., Brenes Murillo, A., Gartner, A., Kenyon, C. and Lamond, A.I.

Micro-proteomics with iterative data analysis: proteome analysis in C.elegans at the single worm level.

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PMID: 26552604 Abstract

Bensaddek D, Narayan V, Nicolas A, Murillo AB, Gartner A, Kenyon CJ, Lamond AI

Micro‐proteomics with iterative data analysis: Proteome analysis in C. elegans at the single worm level

Proteomics. 2016, 16 (3), 381-392

Varshney D, Petit A, Juan Bueren-Calabuig J, Jansen C, Peggie M, Piskialov A and Cowling VH

Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM

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PMID: 27422871 Abstract

Vasileva, V., Gierlinski, M., Yue, Z., O’Reilly, N., Kitamura, E. and Tanaka, T. U

Molecular mechanisms facilitating the initial kinetochore encounter with spindle microtubules

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PMID: 28446512 Abstract

Grasso L, Suska O, Davidson L, Gonatopoulos-Pournatzis T, Williamson R, Wasmus L, Wiedlich S, Peggie M, Stavridis MP and Cowling VH

mRNA cap methylation in pluripotency and differentiation

Cell Rep. 2016 Aug 2;16(5):1352-65. doi: 10.1016/j.celrep.2016.06.089 Epub 2016 Jul 21

PMID: 27452456 Abstract

Alabert C, Bukowski-Wills JC, Lee SB, Kustatscher G, Nakamura K, Alves FDL, Menard P, Mejlvang J, Rappsilber J, Groth A

Nascent chromatin capture (NCC) proteomics characterize chromatin dynamics during DNA replication and identify new replication factors.

Nat Cell Biol.3, 281-93.

N. Selvan, R. Williamson, D. Mariappa, D.G. Campbell, R. Gourlay, A.T. Ferenbach, T. Aristotelous, I. Hopkins-Navratilova, M. Trost and Daan M. F. van Aalten

Native enrichment of the Drosophila O-GlcNAc proteome reveals candidate conveyors of the supersex combs phenotype

Nature Chem.Biol. (2017), in press.

Moore, J., Linkert, M., Blackburn, C., Carroll, M., Ferguson, R.K., Flynn, H., Gilen, K., Leigh, R., Li, S.,, Lindner, D., Moore, W.J. Patterson, A.J. Pindelski, B., Ramalingham, B., Rozbicki, E., Tarkowska, A., Walczyko, P., Allan, C., Burel, J-M. and Swedlow, J

OMERO and Bio-Formats 5: flexible access to large bioimaging datasets at scale

Abdel-Fattah, W., Jablonowski, D., Di Santo, R., Thuring, K. L., Scheidt, V., Hammermeister, A., Ten Have, S., Helm, M., Schaffrath, R. and Stark, M. J.

Phosphorylation of Elp1 by Hrr25 is required for Elongator-dependent tRNA modification in yeast

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PMID: 25569479 Abstract

Wimmer,P., Berscheminski, J., Blanchette, P., Groitl, P., Branton, P.E. Hay, R.T. Dobner, T. and Schreiner, S.

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

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PMID: 25772236 Abstract

Tammsalu, T., Matic, I., Jaffray, E. G., Ibrahim, A. F., Tatham, M. H. and Hay, R. T

Proteome-wide identification of SUMO modification sites by mass spectrometry

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PMID: 26292070 Abstract

Seifert, A., Schofield, P., Barton, G. J. and Hay, R. T

Proteotoxic stress reprograms the chromatin landscape of SUMO modification.

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PMID: 26152697 Abstract

Burel, J. M., Besson, S., Blackburn, C., Carroll, M., Ferguson, R. K., 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. and Swedlow, J. R

Publishing and sharing multi-dimensional image data with OMERO

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PMID: 26223880 Abstract

Rojas-Fernandez, A., Herhaus, L., Macartney, T., Lachaud, C., Hay, R. T. and Sapkota, G. P

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

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PMID: 25922883 Abstract

Alver, R. C., Chadha, G. S., Gillespie, P. J. and Blow, J. J

Reversal of DDK-Mediated MCM Phosphorylation by Rif1-PP1 Regulates Replication Initiation and Replisome Stability Independently of ATR/Chk1

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PMID: 28273463 Abstract

Varshney, D., Vavrova-Anderson, J., Oler, A. J., Cowling, V. H., Cairns, B. R. and White, R. J

SINE transcription by RNA polymerase III is suppressed by histone methylation but not by DNA methylation

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PMID: 25798578 Abstract

Preston, G. C., Sinclair, L. V., Kaskar, A., Hukelmann, J. L., Navarro, M. N., Ferrero, I., MacDonald, H. R., Cowling, V. H. and Cantrell, D. A

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

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PMID: 26136212 Abstract

Gierlinski, M., Cole, C., Schofield, P., Schurch, N. J., Sherstnev, A., Singh, V., Wrobel, N., Gharbi, K., Simpson, G., Owen-Hughes, T., Blaxter, M. and Barton, G. J

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

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PMID: 26206307 Abstract

Branigan, E., Plechanovova, A., Jaffray, E. G., Naismith, J. H. and Hay, R. T

Structural basis for the RING-catalysed synthesis of K63-linked ubiquitin chains.

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PMID: 26148049 Abstract

Sundaramoorthy, R., Hughes, A. L., Singh, V., Wiechens, N., Ryan, D. P., El-Mkami, H., Petoukhov, M., Svergun, D. I., Treutlein, B., Quack, S., Fischer, M., Michaelis, J., Bottcher, B., Norman, D. G. and Owen-Hughes, T

Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes

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PMID: 28332978 Abstract

Ono, M., Yamada, K., Ono, K., Avolio, F., Afzal, V., Bensaddek, D and Lamond, A.I.

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

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PMID: 26405811 Abstract

Kohler, J. B., Tammsalu, T., Jorgensen, M. M., Steen, N., Hay, R. T. and Thon, G

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

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PMID: 26537787 Abstract

Pathak, S., Alonso, J., Schimpl, M., Rafie, K., Blair D.E., Borodkin, V.S., Schuettelkopf, A.W., Albarbarawi, O and van Aalten, D.M.F

The active site of O-GlcNAc transferase imposes constraints on substrate sequence

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PMID: 26237509 Abstract

Endo, A., Ly, T., Pippa, R., Bensaddek, D., Nicolas, A. and Lamond, A. I

The Chromatin Assembly Factor Complex 1 (CAF1) and 5-Azacytidine (5-AzaC) Affect Cell Motility in Src-transformed Human Epithelial Cells

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PMID: 27872192 Abstract

Wiechens, N., Singh, V., Gkikopoulos, T., Schofield, P., Rocha, S. and Owen-Hughes, T.

The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors

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PMID: 27019336 Abstract

Wiechens, N., Singh, V., Gkikopoulos, T., Schofield, P., Rocha, S., and Owen-Hughes, T.

The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors.

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PlosGenetics  12doi ARTN e1005940 10.1371/journal.pgen.1005940

PMID: 27019336 Abstract

Hukelmann, J.L., Anderson, K.E., Sinclair, L.V., Katarzyna, M.G., Brenes Murillo, A., Hawkins, P.T., Stephens, L.R. Lamond, A.I. and Cantrell, D.A

The cytotoxic T cell proteome and its shaping by mammalian target of rapamycin.

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PMID: 26551880 Abstract

Hammond, C.M., Sundaramoorthy, R., Larance, M., Lamond, A., Stevens, M.A., El-Mkami, H., Norman, D.G., and Owen-Hughes, T.

The histone chaperone Vps75 forms multiple oligomeric assemblies capable of mediating exchange between histone H3–H4 tetramers and Asf1–H3–H4 complexes

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Nucleic Acids Research doi 10.1093/nar/gkw209

PMID: 27036862 Abstract

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. and Xirodimas, D. P

The NEDD8 inhibitor MLN4924 increases the size of the nucleous and activates p53 through the ribolsomal-Mdm2 pathway.

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PMID: 25867069 Abstract

Hong Y, Sonneville R, Agostinho A, Meier B, Wang B, Blow JJ, Gartner A

The SMC-5/6 Complex and the HIM-6 (BLM) helicase synergistically promote meiotic recombination intermediate processing and chromosome maturation during Caenorhabditis elegans meiosis.

PLoS Genet. 2016 Mar 24;12(3):e1005872

Hutten, S., Swift, S. and Lamond, A. I

Time-lapse imaging of nuclear bodies

PMID: 25555575 Abstract

Alabert C*, Barth TK*, Reverón-Gómez N, Sidoli S, Schmidt A, Jensen ON, Imhof A and Groth A

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

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PMID: 25792596 Abstract

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. and Hay, R. T

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

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PMID: 25489924 Abstract

Maric, M., Mukherjee, P., Tatham, M. H., Hay, R. and Labib, K

Ufd1-Npl4 Recruit Cdc48 for Disassembly of Ubiquitylated CMG Helicase at the End of Chromosome Replication

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PMID: 28355556 Abstract

Moreno, A., Carrington, J.T., Albergante, L.,Al Mamum, M., Haagensen, E.J., Komseli, E.-S., Gourgolis, V.G., Newman, T.J. and Blow, J.J

Unreplicated DNA remaining from unperturbed S phases passes through mitosis for resolution in daughter cells

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Proc Natl AcadSci USA 113, E5757-64

Judes, A., Ebert, F., Bar, C., Thuring, K. L., Harrer, A., Klassen, R., Helm, M., Stark, M. J. and Schaffrath, R.

Urmylation and tRNA thiolation functions of ubiquitin-like Uba4Urm1 systems are conserved from yeast to man

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PMID: 25747390 Abstract

Singh Chadha, G. and Blow, J.J.

Xenopus Mcm10 is a CDK-substrate required for replication fork stability

Cell Cycle 15, 2183–2195