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 from 2015 to present. For a full list of all publications from 2008 onward please visit our page on the School of Life Sciences website.

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  • 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

Di Santo, R., Bandau, S. and Stark, M. J. R.

A conserved and essential basic region mediates tRNA binding to the Elp1 subunit of the Saccharomyces cerevisiaeElongator complex

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Mol Microbiol. 2014;92(6):1227-42. doi: 10.1111/mmi.12624

PMID: 24750273 Abstract

Maculins, T., Carter, N., Dorval, T., Hudson, K., Nissink, J. W., Hay, R. T. and Alwan, H.

A Generic Platform for Cellular Screening Against Ubiquitin Ligases

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PMID: 26743172 Abstract

Gorski, J.J., Pathak, S., Panov, K., Kasciukovic, T., Panova, T., Russell, J. and Zomerdijk, J.C.B.M. (2007).

A novel TBP-associated factor of SL1 functions in RNA polymerase I transcription.

EMBO J. 26, 1560-1568

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

Ly T, Ahmad Y, Shlien A, Soroka D, Mills A, Emanuele MJ, Stratton MR, Lamond AI

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

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eLife. 2014;3:e01630. doi: 10.7554/eLife.0163

PMID: 24596151 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, 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

Raich, L., Borodkin, V., Fang, W., Castro-Lopez, J., van Aalten, D. M., Hurtado-Guerrero, R. and Rovira, C

A Trapped Covalent Intermediate of a Glycoside Hydrolase on the Pathway to Transglycosylation. Insights from Experiments and Quantum Mechanics/Molecular Mechanics Simulations.

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PMID: 26859322 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

Esmaeeli-Nieh, S., Fenckova, M., Porter, I. M., Motazacker, M. M., Nijhof, B., Castells-Nobau, A., Asztalos, Z., Weißmann, R., Behjati, F., Tzschach, A., Felbor, U., Scherthan, H., Sayfati, S. M., Ropers, H. H., Kahrizi, K., Najmabadi, H., Swedlow, J. R., Schenck, A. and Kuss, A. W

BOD1 Is Required for Cognitive Function in Humans and Drosophila

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PMID: 27166630 Abstract

Fernandez-Alonso, R., Davidson, L., Hukelmann, J., Zengerle, M., Prescott, A. R., Lamond, A. I., Ciulli, A., Sapkota, G. P. and Findlay, G. M

Brd4-Brd2 isoform switching coordinates pluripotent exit and Smad2-dependent lineage specification

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PMID: 28588073 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

Aregger, M., Kaskar, A., Varshney, D., Fernandez-Sanchez, M. E., Inesta-Vaquera, F. A., Weidlich, S. and Cowling, V. H

CDK1-Cyclin B1 Activates RNMT, Coordinating mRNA Cap Methylation with G1 Phase Transcription

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PMID: 26942677 Abstract

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

Cell cycle synchronization in Xenpous egg extracts.

PMID: 26254920 Abstract

Bremm, A., Moniz, S., Mader, J., Rocha, S., and Komander, D.

Cezanne (OTUD7B) regulates HIF-1alpha homeostasis in a proteasome-independent manner

EMBO Rep.15, 1268-1277.

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

Kirkwood, K.J., Ahmad, Y., Larance, M. and Lamond, A.I.

Characterization of native protein complexes and protein isoform variation using size-fractionation-based quantitative proteomics

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Mol Cell Proteomics. 2013;12(12):3851-73. doi: 10.1074/mcp.M113.032367

PMID: 24043423 Abstract

Alabert C and Groth A

Chromatin replication and epigenome maintenance

Nature Review Mol Cell Biol.13, 153-167.

Agostinho A, Meier B, Sonneville R, Jagut M, Woglar A, Blow J, Jantsch V, Gartner A.

Combinational regulation of meiotic holliday juntion resolution in C. elegans by HIM-6 (BLM) helicase, SLX-4, and the SLX-1, MUS-81 and XPF-1 nucleases.

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PLoS Genet. 2013;9(7):e1003591. doi: 10.1371/journal.pgen.1003591. PubMed PMID: 23901331; PubMed Central

PMID: 3715425 Abstract

Agostinho A, Meier B, Sonneville R, Jagut M, Woglar A, Blow J, Jantsch V, Gartner A.

Combinational regulation of meiotic holliday juntion resolution in C. elegans by HIM-6 (BLM) helicase, SLX-4, and the SLX-1, MUS-81 and XPF-1 nucleases.

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Molecular Cell (accepted for publication)

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

Offenburger, S. L., Bensaddek, D., Murillo, A. B., Lamond, A. I. and Gartner, A

Comparative genetic, proteomic and phosphoproteomic analysis of C. elegans embryos with a focus on ham-1/STOX and pig-1/MELK in dopaminergic neuron development

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PMID: 28659600 Abstract

Renshaw MJ, Ward JJ, Kanemaki M, Natsume K, Nedelec FJ & Tanaka TU

Condensins promote chromosome recoiling during early anaphase to complete sister chromatid separation

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Developmental Cell 19, (2) 232-24

PMID: 20708586 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

Alabert C, Bianco JN, Pasero P

Differential regulation of homologous recombination at DNA breaks and replication forks by the Mrc1 branch of the S-phase checkpoint.

EMBO J. 28, 1131-41.

Benatti, P., Belluti, S., Miotto, B., Neusiedler, J., Dolfini, D., Drac, M., Basile, V., Schwob, E., Mantovani, R., Blow, J. J. and Imbriano, C

Direct non transcriptional role of NF-Y in DNA replication

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PMID: 26732297 Abstract

Sherstnev, A., Duc, C., Cole, C., Zacharaki, V., Hornyik, C., Ozsolak, F., Milos, P.M., Barton G.J., and Simpson, G.G.

Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation.

Nat Struct Mol Biol, 2012. 19(8): p. 845-52.

Sherstnev, A., Duc, C., Cole, C., Zacharaki, V., Hornyik, C., Ozsolak, F., Milos, P. M., Barton, G. J**.and Simpson, G. G.

Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation.

Nature Structural & Molecular Biology 19: 845-852.

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

Ackermann, L., Schell, M., Pokrzywa, W., Kevei, E., Gartner, A. and Schumacher, B

E4 ligase-specific ubiquitination hubs coordinate DNA double-strand-break repair and apoptosis

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PMID: 27669035 Abstract

Makrantoni, V. and Stark, M. J. R.

Efficient chromosome bi-orientation and the tension checkpoint in Saccharomyces cerevisiae both require Bir1

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Molecular and Cellular Biology. 29, (16) 4552-4562

PMID: 19528231 Abstract

Ono, M., Yamada, K., Bensaddek, D., Afzal, V., Biddlestone, J., Ortmann, B., Mudie, S., Boivin, V., Scott, M. S., Rocha, S. and Lamond, A. I

Enhanced snoMEN Vectors Facilitate Establishment of GFP-HIF-1alpha Protein Replacement Human Cell Lines

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PMID: 27128805 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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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 differential gene expression analysis by RNA-seq on a 48 biological replicate experiment.

Birch, J.L., Tan, B.C.-M., Panov, K.I., Panova, T.B., Andersen, J.S., Owen-Hughes, T.A., Russell, J., Lee, S.-C. and Zomerdijk, J.C.B.M. (2009)

FACT facilitates chromatin transcription by RNA polymerases I and III.

EMBO J.28, 854-865.

Yamada, K., Ono, M., Bensaddek, D., Lamond, A.I. and Rocha, S.

FMN2 is a novel regulator of the cyclin-dependent kinase inhibitor p21

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Cell Cycle. 2013;12(15):2348-54. doi: 10.4161/cc.25511

PMID: 23839046 Abstract

Larance, M., Kirkwood, K. J., Tinti, M., Brenes Murillo, A., Ferguson, M. A. and Lamond, A. I

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

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PMID: 27114452 Abstract

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

Swamy, M., Pathak, S., Grzes, K. M., Damerow, S., Sinclair, L. V. and van Aalten, D. M.

Glucose and glutamine fuel protein O-GlcNAcylation to control T cell self-renewal and malignancy

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PMID: 27111141 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-1α restricts NF-κB-dependent gene expression to control innate immunity signals

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PMID: 25510503 Abstract

Dickerson, D., Gierlinski, M., Singh, V., Kitamura, E., Ball, G., Tanaka, T. U. and Owen-Hughes, T

High resolution imaging reveals heterogeneity in chromatin states between cells that is not inherited through cell division

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PMID: 27609610 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., Gierliński, 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?

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PMID: 27022035 Abstract

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

Shire, K., Wong, A. I., Tatham, M. H., Anderson, O. F., Ripsman, D., Gulstene, S., Moffat, J., Hay, R. T. and Frappier, L.

Identification of RNF168 as a PML nuclear body regulator

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PMID: 26675234 Abstract

Schurch, N.J., Cole, C., Sherstnev, A., Song, J., Duc, C., Storey, K.G., McLean, W.H., Brown, S.J., Simpson, G.G., and Barton, G.J.

Improved annotation of 3′ untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs.

PLoS One, 2014. 9(4): p. e94270.

Singh, R., Lawal, H. M., Schilde, C., Gloeckner, G., Barton, G. J., Schaap, P. and Cole, C

Improved Annotation with de novo Transcripome Assembly in Four Social Amoeba Species

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PMID: 28143409 Abstract

Falbo K*, Alabert C*, Katou Y§, Wu S, Han J, Wehr T, Xiao J, He X, Zhang Z, Shi Y, Shirahige K, Pasero P, Shen X

Involvement of a chromatin-remodelling complex in damage tolerance during DNA replication

Nat Struct Mol Biol.16, 1167-1172.

Teresa Pinto, A., Laranjeiro Pinto, M., Patricia Cardoso, A., Monteiro, C., Teixeira Pinto, M., Filipe Maia, A., Castro, P., Figueira, R., Monteiro, A., Marques, M., Mareel, M., Dos Santos, S. G., Seruca, R., Adolfo Barbosa, M., Rocha, S. and Jose Oliveira, M

Ionizing radiation modulates human macrophages towards a pro-inflammatory phenotype preserving their pro-invasive and pro-angiogenic capacities

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PMID: 26735768 Abstract

Gandhi, S. R., Gierlinski, M., Mino, A., Tanaka, K., Kitamura, E., Clayton, L. and Tanaka, T. U.

Kinetochore-dependent microtubule rescue ensures their efficient and sustained interactions in early mitosis

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Dev Cell, 21, 920-33

PMID: 22075150 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

Natsume T, Muller CA, Katou Y, Retkute R, Gierlinski M, Araki H, Blow JJ, Shirahige K, Nieduszynski CA, Tanaka TU

Kinetochores coordinate pericentromeric cohesion and early DNA replication by Cdc7-Dbf4 kinase recruitment

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Mol Cell. 2013;50(5):661-74. doi: 10.1016/j.molcel.2013.05.011

PMID: 23746350 Abstract

Kitamura E*, Tanaka K*, Komoto S*, Kitamura Y, Antony C & Tanaka TU

Kinetochores generate microtubules with distal plus ends: their roles and limited lifetime in mitosis

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Developmental Cell 18, (2) 248-259

PMID: 20159595 Abstract

Maure, J. F., Moser, S. C., Jaffray, E. G., A, F. A. and Hay, R. T

Loss of ubiquitin E2 Ube2w rescues hypersensitivity of Rnf4 mutant cells to DNA damage

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PMID: 27185577 Abstract

Narlikar GJ, Sundaramoorthy R, Owen-Hughes T

Mechanisms and functions of ATP-dependent chromatin-remodeling enzymes.

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Cell. 154, 490-503 doi. 10.1016/j.cell.2013.07.011

PMID: 23911317 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

Bensaddek, D., Narayan, V., Nicolas, A., Murillo, A. B., Gartner, A., Kenyon, C. J. 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

Varshney, D., Petit, A. P., Bueren-Calabuig, J. A., Jansen, C., Fletcher, D. A., Peggie, M., Weidlich, S., Scullion, P., Pisliakov, A. V. and Cowling, V. H

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, M. P. and Cowling, V. H

mRNA Cap Methylation in Pluripotency and Differentiation

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PMID: 27452456 Abstract

Harvald, E. B., Sprenger, R. R., Dall, K. B., Ejsing, C. S., Nielsen, R., Mandrup, S., Murillo, A. B., Larance, M., Gartner, A., Lamond, A. I. and Faergeman, N. J.

Multi-omics Analyses of Starvation Responses Reveal a Central Role for Lipoprotein Metabolism in Acute Starvation Survival in C. elegans

PMID: 28734827 Abstract

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

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

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PMID: 28604694 Abstract

Trapannone, R., Mariappa, D., Ferenbach, A. T. and van Aalten, D. M

Nucleocytoplasmic human O-GlcNAc transferase is sufficient for O-GlcNAcylation of mitochondrial proteins

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PMID: 27048592 Abstract

M. Schimpl, X. Zheng, V.S. Borodkin, D.E. Blair, A.T. Ferenbach, A.W. Schuettelkopf, I. Navratilova, T. Aristotelous, O. Albarbarawi, D.A. Robinson, M.A. MacNaughtan and D.M.F. van Aalten,

O-GlcNAc transferase invokes nucleotide sugar pyrophosphate participation in catalysis

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Nature Chem.Biol. (2012), 8, 969-974.

PMID: 23103942 Abstract

S. Pathak, V.S. Borodkin, O. Albarbarawi, D.G. Campbell, A. Ibrahim and D.M.F. van Aalten

O-GlcNAcylation of TAB1 modulates TAK1-mediated cytokine release

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MBO J. (2012), 31, 1394-1404.

PMID: 22307082 Abstract

Leigh, R., Gault, D., Linkert, M., Burel, J-M., Moore, J., Besson, S. and Swedlow, J.R.

OME Files – An open source reference library for the OME-XML metadata model and the OME-TIFF file format

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

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

PHD1 links cell cycle progression to oxygen sensing by hydroxylation of the centrossomal protein Cep192

Dev Cell.26, 381-392.

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

Makrantoni, V., Corbishley, S. J.,Rachidi, N.,Morrice, N. A., Robinson, D. A. and Stark, M. J. R.

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

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PLoS One. 2014;9(2):e89399. doi: 10.1371/journal.pone.0089399

PMID: 24558497 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

Kapuria, V., Rohrig, U. F., Bhuiyan, T., Borodkin, V. S., van Aalten, D. M., Zoete, V. and Herr, W

Proteolysis of HCF-1 by Ser/Thr glycosylation-incompetent O-GlcNAc transferase:UDP-GlcNAc complexes

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PMID: 27056667 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

Tammsalu T, Matic I, Jaffray EG, Ibrahim AF, Tatham MH, Hay RT

Proteome-wide identification of SUMO2 modification sites

View Publication

Sci Signal. 2014;7(323):rs2. doi: 10.1126/scisignal.2005146

PMID: 24782567 Abstract

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

Proteotoxic stress reprograms the chromatin landscape of SUMO modification.

View Publication

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

View Publication

PMID: 26223880 Abstract

Gonatopoulos-Pournatzis T, Dunn S, Bounds R, and Cowling VH

RAM/Fam103a1 is required for mRNA cap methylation

Molecular Cell 2011 Nov18;44(4):585-596

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

View Publication

PMID: 25922883 Abstract

Newman TJ, Mamun MA, Nieduszynski CA, Blow JJ

Replisome stall events have shaped the distribution of replication origins in the genomes of yeasts

View Publication

Nucleic Acids Res. 2013;41(21):9705-18. doi: 10.1093/nar/gkt728

PMID: 23963700 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

View Publication

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

View Publication

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.

View Publication

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.

View Publication

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.

View Publication

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

View Publication

PMID: 28332978 Abstract

Plechanovova, A., Jaffray, E.G., Tatham, M.H., Naismith, J.H., Hay, R.T.

Structure of RING E3 ligase and ubiquitin-loaded E2 primed for catalysis

Nature 469 (7414)

PMID: 22842904 Abstract

Rojas-Fernandez A, Plechanovova A, Hattersley N, Jaffray E, Tatham MH, Hay RT

SUMO chain-induced dimerization activates RNF4

View Publication

Mol Cell. 2014;53(6):880-92. doi: 10.1016/j.molcel.2014.02.031

PMID: 24656128 Abstract

Naidu, S., Friedrich, J.K., Russell, J. and Zomerdijk, J.C.B.M. (2011)

TAF1B is a TFIIB-like component of the basal transcription machinery for RNA Polymerase I.

Science333, 1640-1642.

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.

View Publication

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

View Publication

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

View Publication

PMID: 26237509 Abstract

Uthman, S., Bär, C., Scheidt, V., Liu, S., ten Have, S., Giorgini, F., Stark, M. J. R. and RaffaelSchaffrath, R.

The amidation step of diphthamidebiosynthesis in yeast requires DPH6, a gene identified through mining the DPH1-DPH5interaction network

View Publication

PLoS Genetics. doi. 10.1371/journal.pgen.1003334

PMID: 23468660 Abstract

AP Bailly, A Freeman, J Hall, AC Déclais, AAlpi, D Lilley, S Ahmed, A Gartner.

The Caenorhabtidis elegans homolog of Gen1/Yen1 resolvases links DNA damage signaling to DNA double-strand break repair.

View Publication

PLoS Genetics, 2010 Jul 15;6(7):e1001025

PMID: 20661466 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

View Publication

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

View Publication

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.

View Publication

PMID: 26551880 Abstract

Akay, A., Di Domenico, T., Suen, K. M., Nabih, A., Parada, G. E., Larance, M., Medhi, R., Berkyurek, A. C., Zhang, X., Wedeles, C. J., Rudolph, K. L. M., Engelhardt, J., Hemberg, M., Ma, P., Lamond, A. I., Claycomb, J. M. and Miska, E. A.

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription

View Publication

PMID: 28787591 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

View Publication

PMID: 27036862 Abstract

Williams, E., Moore, J., Li, S. W., Rustici, G., Tarkowska, A., Chessel, A., Leo, S., Antal, B., Ferguson, R. K., Sarkans, U., Brazma, A., Carazo-Salas, R. E. and Swedlow, J

The Image Data Resource: A Scalable Platform for Biological Image Data Access, Integration, and Dissemination

Maure, J. F., Komoto, S., Oku, Y., Mino, A., Pasqualato, S., Natsume, K., Clayton, L., Musacchio, A. and Tanaka, T. U.

The Ndc80 loop region facilitates formation of kinetochore attachment to the dynamic microtubule plus end

Current Biology 21, (13) 207-213

PMID: 21256019 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.

View Publication

PMID: 25867069 Abstract

Hong, Y., Sonneville, R., Agostinho, A., Meier, B., Wang, B., Blow, J. J. and 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.

View Publication

PMID: 27010650 Abstract

Hornyik, C., Terzi, L.C. and Simpson, G.G.(

The spen family protein, FPA, controls alternative cleavage and polyadenylation of RNA.

Developmental Cell 18: 203-213.

Tanaka TU, Clayton L, Natsume T.

Three wise centromere functions: see no error, hear no break, speak no delay

View Publication

EMBO Rep. 2013;14(12):1073-83. doi: 10.1038/embor.2013.181

PMID: 24232185 Abstract

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

Time-lapse imaging of nuclear bodies

PMID: 25555575 Abstract

Pelisch, F. and Hay, R. T

Tools to Study SUMO Conjugation in Caenorhabditis elegans

PMID: 27631810 Abstract

Ray, S., Panova, T., Miller, G., Volkov, A., Porter, A.C.G., Russell, J., Panov, K.I. and Zomerdijk, J.C.B.M. (2013)

Topoisomerase IIα promotes activation of RNA polymerase I transcription by facilitating pre-initiation complex formation.

Nature Commun.4, 1598-1609.

Duc, C., Sherstnev, A., Cole, C., Barton, G.J. and Simpson, G.G.

Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA

View Publication

PLOS Genetics 9: e1003867.

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.

View Publication

PMID: 25792596 Abstract

. Panov, K.I., Friedrich, J.K., Russell, J. and Zomerdijk, J.C.B.M.  (2006).

UBF activates RNA polymerase I transcription by stimulating promoter escape.

EMBO J. 25, 3310-3322.

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.

View Publication

PMID: 25489924 Abstract

Krupina, K., Kleiss, C., Metzger, T., Fournane, S., Schmucker, S., Hofmann, K., Fischer, B., Paul, N., Porter, I. M., Raffelsberger, W., Poch, O., Swedlow, J. R., Brino, L. and Sumara, I

Ubiquitin Receptor Protein UBASH3B Drives Aurora B Recruitment to Mitotic Microtubules

View Publication

PMID: 26766443 Abstract

Lachaud, C., Moreno, A., Marchesi, F., Toth, R., Blow, J. J. and Rouse, J

Ubiquitinated Fancd2 recruits Fan1 to stalled replication forks to prevent genome instability

View Publication

PMID: 26797144 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

View Publication

PMID: 28355556 Abstract

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

View Publication

PMID: 27516545 Abstract

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

View Publication

PMID: 25747390 Abstract

Poh, W.T., Singh Chadha, G., Gillespie, P.J., Kaldis, P. and Blow, J.J.

Xenopus Cdc7 executes its essential function early in S phase and is counteracted by checkpoint-regulated protein phosphatase 1

View Publication

Open biology. 2014;4:130138. doi: 10.1098/rsob.130138

PMID: 24403013 Abstract

Chadha, G. S., Gambus, A., Gillespie, P. J. and Blow, J. J

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

View Publication

PMID: 27327991 Abstract