Source: http://gre.dundee.ac.uk/publications/
Timestamp: 2019-04-23 00:53:00+00:00

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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.
14-3-3-Pred: Improved methods to predict 14-3-3-binding phosphopeptides.
6-hydroxydopamine (6-OHDA) Oxidative Stress Assay for Observing Dopaminergic Neuron Loss in Caenorhabditis elegans.
6-OHDA-induced dopaminergic neurodegeneration in Caenorhabditis elegans is promoted by the engulfment pathway and inhibited by the transthyretin-related protein TTR-33.
Makrantoni V, Ciesiolka A, Lawless C, Fernius J, Marston A, Lydall D, Stark MJR.
Maculins, T., Carter, N., Dorval, T., Hudson, K., Nissink, J. W., Hay, R. T. and Alwan, H.
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.
A Trapped Covalent Intermediate of a Glycoside Hydrolase on the Pathway to Transglycosylation. Insights from Experiments and Quantum Mechanics/Molecular Mechanics Simulations.
Ward, J., Cole, C., Febrer, M. and Barton, G.
Amino acid-dependent cMyc expression is essential for NK cell metabolic and functional responses in mice.
An evolutionarily conserved ribosome-rescue pathway maintains epidermal homeostasis.
Analysis of the SUM02 proteome during HSV-1 infection.
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.
Biochemical and Structural Properties of Fungal Holliday Junction-Resolving Enzymes.
Lombardi, O., Varshney, D., Phillips, N. M. and Cowling, V. H.
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.
Cell cycle synchronization in Xenpous egg extracts.
Bremm, A., Moniz, S., Mader, J., Rocha, S., and Komander, D.
Kirkwood, K.J., Ahmad, Y., Larance, M. and Lamond, A.I.
Nature Review Mol Cell Biol.13, 153-167.
Chromatin Replication and Histone Dynamics.
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.
Combined hereditary and somatic mutations of replication error repair genes result in rapid onset of ultra hypermutated cancers.
Composition of the Survival Motor Neuron (SMN) complex in Drosophila melanogaster.
DHX15 regulates CMTR1-dependent gene expression and cell proliferation.
Differential regulation of homologous recombination at DNA breaks and replication forks by the Mrc1 branch of the S-phase checkpoint.
Sherstnev, A., Duc, C., Cole, C., Zacharaki, V., Hornyik, C., Ozsolak, F., Milos, P.M., Barton G.J., and Simpson, G.G.
Nat Struct Mol Biol, 2012. 19(8): p. 845-52.
Pelisch, F*; Pozzi, B; Risso, G; Muñoz, M; and Srebrow, A*. *co–corresponding authors.
E1B-55K mediated regulation of RNF4 STUbL promotes HAdV gene expression.
Effects of hypo O-GlcNAcylation on Drosophila development.
Efficient Analysis of Mammalian Polysomes in cells and tissues using Ribo Mega-SEC.
Evaluating the use of HILIC in large-scale, multi dimensional proeromics: Horses for courses?
Evaluation of tools for differential gene expression analysis by RNA-seq on a 48 biological replicate experiment.
Evidence for substrate assisted catalysis in N-acetylphosphoglucosamine mutase.
Expanded Interactome of the Intrinsically Disordered Protein Dss1.
FACT facilitates chromatin transcription by RNA polymerases I and III.
Yamada, K., Ono, M., Bensaddek, D., Lamond, A.I. and Rocha, S.
Global Proteomics analysis of the response to starvation in C. elegans.
Swamy, M., Pathak, S., Grzes, K. M., Damerow, S., Sinclair, L. V. and van Aalten, D. M.
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.
Identification of Elg1 interaction partners and effects on post-replication chromatin re-formation.
Shire, K., Wong, A. I., Tatham, M. H., Anderson, O. F., Ripsman, D., Gulstene, S., Moffat, J., Hay, R. T. and Frappier, L.
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.
Inhibitors against Fungal Cell Wall Remodeling Enzymes.
Nat Struct Mol Biol.16, 1167-1172.
JPred4: a protein secondary structure prediction server.
Killing with proficiency: integrated post-translational regulation of an offensive Type VI secretion system.
LEM-3 is a midbody-tethered DNA nuclease that resolves chromatin bridges during late mitosis.
Loss of TET2 in hematopoietic cells leads to DNA hypermethylation of active enhancers and induction of leukemogenesis.
Yue, Z., Komoto, S., Gierlinski, M., Pasquali, D., Kitamura, E. and Tanaka, T. U.
mRNA cap methyltransferase, RNMT-RAM, promotes RNA pol II-dependent transcription.
mRNA cap regulation in mammalian cell function and fate.
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.
Mutational signatures of DNA mismatch repair deficiency in and human cancers.
Mutations in Caenorhabditis elegans neuroligin-like glit-1, the apoptosis pathway and the calcium chaperone crt-1 increase dopaminergic neurodegeneration after 6-OHDA treatment.
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.
Nature Chem.Biol. (2012), 8, 969-974.
O-GlcNAcase Fragment Discovery with Fluorescence Polarimetry.
MBO J. (2012), 31, 1394-1404.
Leigh, R., Gault, D., Linkert, M., Burel, J-M., Moore, J., Besson, S. and Swedlow, J.R.
Moser, S.C., Bensaddek, D., Ortmann, B., Mudie, S., Blow, J.J., Lamond, A.I., Swedlow, J.R., and Rocha, S.
PIP30/FAM192A is a novel regulator of the nuclear proteasome activator PA28γ.
Wimmer,P., Berscheminski, J., Blanchette, P., Groitl, P., Branton, P.E. Hay, R.T. Dobner, T. and Schreiner, S.
Positioning Europe for the EPITRANSCRIPTOMICS challenge.
Proteomic analysis of the cell cycle of procylic form Trypanosoma brucei.
Proteotoxic stress reprograms the chromatin landscape of SUMO modification.
Publisher Correction: Image Data Resource: a bioimage data integration and publication platform.
RNF12 X-linked intellectual disability mutations disrupt E3 ligase activity and neural differentiation.
Self-oligomerization regulates stability of survival motor neuron protein isoforms by sequestering an SCFSlmb degron.
Signal enhanced proteomics: a biological perspective on dissecting the functional organisation of cell proteomes.
Single cell tuning of Myc expression by antigen receptor signal strength and interleukin 2 in T lymphocytes.
Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment.
Structural basis for the RING-catalysed synthesis of K63-linked ubiquitin chains.
Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome.
TAF1B is a TFIIB-like component of the basal transcription machinery for RNA Polymerase I.
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.
The Anthelmintic Drug Niclosamide and Its Analogues Activate the Parkinson’s Disease Associated Protein Kinase PINK1.
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.
Wiechens, N., Singh, V., Gkikopoulos, T., Schofield, P., Rocha, S. and Owen-Hughes, T.
The conserved LEM-3/Ankle1 nuclease is involved in the combinatorial regulation of meiotic recombination repair and chromosome segregation in Caenorhabditis elegans.
Kapuria V, Röhrig UF, Waridel P, Lammers F, Borodkin VS, van Aalten DMF, Zoete V, Herr W.
The conserved threonine-rich region of the HCF-1PRO repeat activates promiscuous OGT: UDP-GlcNAc glycosylation and proteolysis activities.
The cytotoxic T cell proteome and its shaping by mammalian target of rapamycin.
The Encyclopedia of Proteome Dynamics – A big data ecosystem for (prote)omics. Nucleic Acids Research.
The Encyclopedia of Proteome Dynamics: The KinoViewer.
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 miR-144/451 locus is required for erythroid homeostasis.
The mRNA cap methyltransferase gene TbCMT1 is not essential in vitro but is a virulence factor in vivo for bloodstream form Trypanosoma brucei.
The NEDD8 inhibitor MLN4924 increases the size of the nucleous and activates p53 through the ribolsomal-Mdm2 pathway.
The O-GlcNAc Transferase Intellectual Disability Mutation L254F Distorts the TPR Helix.
The SMC-5/6 Complex and the HIM-6 (BLM) helicase synergistically promote meiotic recombination intermediate processing and chromosome maturation during Caenorhabditis elegans meiosis.
Topoisomerase IIα promotes activation of RNA polymerase I transcription by facilitating pre-initiation complex formation.
. 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.
Ubiquitin C-terminal hydrolases cleave isopeptide and peptide-linked ubiquitin from structured proteins but do not edit ubiquitin homopolymers.
UDP-GlcNAc Analogues as Inhibitors of O-GlcNAc Transferase (OGT): Spectroscopic, Computational, and Biological Studies.
Judes, A., Ebert, F., Bar, C., Thuring, K. L., Harrer, A., Klassen, R., Helm, M., Stark, M. J. and Schaffrath, R.
Mehlgarten C, Prochaska H, Hammermeister A, Abdel-Fattah W, Wagner M, Krutyhołowa R, Jun SE, Kim GT, Glatt S, Breunig KD, Stark MJR, Schaffrath R.
O’Donoghue SI, Baldi BF, Clark SJ, Darling AE, Hogan JM, Kaur S, Maier-Hein L, McCarthy DJ, Moore W, Stenau E, Swedlow J, Vuong J, Procter J.

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