University of Dundee

2019

 

Agger K, Nishimura K, Miyagi S, Messling J-E, Rasmussen KD, Helin K. 2019. The KDM4/JMJD2 histone demethylases are required for hematopoietic stem cell maintenance. Blood. https://doi.org/10.1182/blood.2019000855

Bailly AP, Perrin A, Serrano-Macia M, Maghames C, Leidecker O, Trauchessec H, Martinez-Chantar ML, Gartner A, Xirodimas DP. 2019. The Balance between Mono- and NEDD8-Chains Controlled by NEDP1 upon DNA Damage Is a Regulatory Module of the HSP70 ATPase Activity. Cell Reports. 29(1):212-224.e8.https://doi.org/10.1016/j.celrep.2019.08.070

Bensaddek D, Nicolas A, Lamond AI. 2019. Signal enhanced proteomics: a biological perspective on dissecting the functional organisation of cell proteomes. Current Opinion in Chemical Biology. 48:114-122. https://doi.org/10.1016/j.cbpa.2018.10.011

Berest I, Arnold C, Reyes-Palomares A, Palla G, Rasmussen KD, Giles H, Bruch P-M, Huber W, Dietrich S, Helin K, Zaugg JB. 2019. Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF. Cell Reports. 29(10):3147-3159.e12. https://doi.org/10.1016/j.celrep.2019.10.106

Besson S, Leigh R, Linkert M, Allan C, Burel J-M, Carroll M, Gault D, Gozim R, Li S, Lindner D, Moore J, Moore W, Walczysko P, Wong F, Swedlow J. 2019. Bringing Open Data to Whole Slide Imaging. Reyes-Aldasoro CC, Janowczyk A, Veta M, Bankhead P, Sirinukunwattana K, editors. In Digital Pathology: 15th European Congress, ECDP 2019, Warwick, UK, April 10–13, 2019, Proceedings. Switzerland: Springer . pp. 3-10. (Lecture Notes in Computer Science). https://doi.org/10.1007/978-3-030-23937-4_1

Blow JJ. 2019. Defects in the origin licensing checkpoint stresses cells exiting G0. Journal of Cell Biology. 218(7):2080-2081. https://doi.org/10.1083/jcb.201905181

Booth AJR, Yue Z, Eykelenboom JK, Stiff T, Luxton GWG, Hochegger H, Tanaka T. 2019. Contractile acto-myosin network on nuclear envelope remnants positions human chromosomes for mitosis. eLife. 8. https://doi.org/10.7554/eLife.46902

Branigan E, Plechanovová A, Hay RT. 2019. Methods to analyze STUbL activity. Hochstrasser M, editor. In Methods in Enzymology. Cambridge, MA: Elsevier. pp. 257-280. (Methods in Enzymology). https://doi.org/10.1016/bs.mie.2018.11.005

Brenes Murillo A, Lamond A. 2019. The Encyclopedia of Proteome Dynamics: The KinoViewer. Bioinformatics. 35(8):1441-1442. https://doi.org/10.1093/bioinformatics/bty823

Brenes Murillo A, Hukelmann J, Bensaddek D, Lamond A. 2019. Multi-batch TMT reveals false positives, batch effects and missing values. Molecular and Cellular Proteomics. https://doi.org/10.1074/mcp.RA119.001472

Bueren-Calabuig J, Bage M, Cowling V, Pisliakov A. 2019. Mechanism of allosteric activation of human mRNA cap methyltransferase (RNMT) by RAM: Insights from accelerated molecular dynamics simulations. Nucleic Acids Research. 47(16):8675-8692. https://doi.org/10.1093/nar/gkz613

Cowling V. 2019. CAPAM: the mRNA cap adenosine N6 methyltransferase. Trends in Biochemical Sciences. 44(3):183-185. https://doi.org/10.1016/j.tibs.2019.01.002

Dunn S, Lombardi O, Lukoszek R, Cowling V. 2019. Oncogenic PIK3CA mutations increase dependency on the mRNA cap methyltransferase, RNMT, in breast cancer cells. Open Biology. 9(4):1-15. https://doi.org/10.1098/rsob.190052

Elias MS, Wright SC, Remenyi J, Abbott JC, Bray SE, Cole C, Edwards S, Gierlinski M, Glok M, McGrath JA, Nicholson WV, Paternoster L, Prescott AR, Have ST, Whitfield PD, Lamond AI, Brown SJ. 2019. EMSY expression affects multiple components of the skin barrier with relevance to atopic dermatitis. Journal of Allergy and Clinical Immunology. 144(2):470-481. https://doi.org/10.1016/j.jaci.2019.05.024

Elias MS, Wright SC, Nicholson WV, Morrison KD, Prescott AR, Ten Have S, Whitfield PD, Lamond AI, Brown SJ. 2019. Functional and proteomic analysis of a full thickness filaggrin-deficient skin organoid model. Wellcome Open Research. 4:134. https://doi.org/10.12688/wellcomeopenres.15405.2

Eykelenboom J, Gierlinski M, Yue Z, Hegarat N, Pollard H, Fukagawa T, Hochegger H, Tanaka T. 2019. Live imaging of marked chromosome regions reveals their dynamic resolution and compaction in mitosis. Journal of Cell Biology. 218(5):1531-1552. https://doi.org/10.1083/jcb.201807125

Fang W, Sanz AB, Galan Bartual S, Wang B, Ferenbach A, Farkaš V, Hurtado-Guerrero R, Arroyo J, van Aalten D. 2019. Mechanisms of redundancy and specificity of the Aspergillus fumigatus Crh transglycosylases. Nature Communications. 10(1):1-10. https://doi.org/10.1038/s41467-019-09674-0

Farnaby W, Koegl M, Roy MJ, Whitworth C, Diers E, Trainor N, Zollman D, Steurer S, Karolyi-oezguer J, Riedmueller C, Gmaschitz T, Wachter J, Dank C, Galant M, Sharps B, Rumpel K, Traxler E, Gerstberger T, Schnitzer R, Petermann O, Greb P, Weinstabl H, Bader G, Zoephel A, Weiss-Puxbaum A, Ehrenhöfer-Wölfer K, Wöhrle S, Boehmelt G, Rinnenthal J, Arnhof H, Wiechens N, Wu M-Y, Owen-Hughes T, Ettmayer P, Pearson M, Mcconnell DB, Ciulli A. 2019. Publisher Correction: BAF complex vulnerabilities in cancer demonstrated via structure-based PROTAC design. Nature Chemical Biology. 15(8):846. https://doi.org/10.1038/s41589-019-0329-z

Flaus A, Owen-Hughes T. 2019. The Face of Chromatin Variants. Cell. 178(6):1284-1286. https://doi.org/10.1016/j.cell.2019.08.024

Froussios K, Schurch N, Mackinnon K, Gierlinski M, Duc C, Simpson G, Barton G. 2019. How well do RNA-Seq differential gene expression tools perform in a complex eukaryote? A case study in A. thaliana. Bioinformatics. https://doi.org/10.1093/bioinformatics/btz089

Froussios K, Mourao K, Simpson G, Barton G, Schurch N. 2019. Relative Abundance of Transcripts (RATs): Identifying differential isoform abundance from RNA-seq [version 1; referees: 1 approved, 2 approved with reservations]. F1000 Research. 8:1-20. https://doi.org/10.12688/f1000research.17916.1

Galloway A, Cowling V. 2019. mRNA cap regulation in mammalian cell function and fate. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1862(3):270-279. https://doi.org/10.1016/j.bbagrm.2018.09.011

García-Rodríguez LJ, Kasciukovic T, Denninger V, Tanaka T. 2019. Aurora B–INCENP localization at centromeres/inner kinetochores is required for chromosome bi-orientation in budding yeast. Current Biology. 29(9):1536-1544.e4. https://doi.org/10.1016/j.cub.2019.03.051

Gorelik A, Galan Bartual S, Borodkin V, Varghese J, Ferenbach A, van Aalten D. 2019. Genetic recoding to dissect the roles of site-specific protein O-GlcNAcylation. Nature Structural & Molecular Biology. 26(11):1071-1077. https://doi.org/10.1038/s41594-019-0325-8

Howden AJM, Hukelmann JL, Brenes A, Spinelli L, Sinclair LV, Lamond AI, Cantrell DA. 2019. Quantitative analysis of T cell proteomes and environmental sensors during T cell differentiation. Nature Immunology. 20(11):1542-1554. https://doi.org/10.1038/s41590-019-0495-x

Krutyhołowa R, Hammermeister A, Zabel R, Abdel-Fattah W, Reinhardt-Tews A, Helm M, Stark MJR, Breunig KD, Schaffrath R, Glatt S. 2019. Kti12, a PSTK-like tRNA dependent ATPase essential for tRNA modification by Elongator. Nucleic Acids Research. 47(9):4814-4830. https://doi.org/10.1093/nar/gkz190

Matera AG, Raimer AC, Schmidt CA, Kelly JA, Droby GN, Baillat D, Ten Have S, Lamond AI, Wagner EJ, Gray KM. 2019. Composition of the Survival Motor Neuron (SMN) complex in Drosophila melanogaster. G3 : Genes, Genomes, Genetics. 9(2):491-503. https://doi.org/10.1534/g3.118.200874

McGloin D, Swedlow J, Zdankowski P. 2019. Full volume super-resolution imaging of thick mitotic spindle using 3D AO STED microscope. Biomedical Optics Express. 10(4):1999-2009. https://doi.org/10.1364/BOE.10.001999

MacGowan S, Madeira F, Britto-Borges T, Warowny M, Drozdetskiy A, Procter J, Barton G. 2019. The Dundee Resource for Sequence Analysis and Structure Prediction. Protein Science. https://doi.org/10.1002/pro.3783

Mourão K, Schurch NJ, Lukoszek R, Froussios K, Mackinnon K, Duc C, Simpson G, Barton G. 2019. Detection and Mitigation of Spurious Antisense RNA-seq Reads with RoSA. F1000 Research. 8:1-7. https://doi.org/10.1101/425900, https://doi.org/10.12688/f1000research.18952.1

Muha V, Williamson R, Hills R, McNeilly A, McWilliams TG, Alonso J, Schimpl M, Leney AC, Heck AJR, Sutherland C, Read K, McCrimmon R, Brooks SP, van Aalten D. 2019. Loss of CRMP2 O-GlcNAcylation leads to reduced novel object recognition performance in mice. Open Biology. 9(11):1-15. https://doi.org/10.1098/rsob.190192

Pelisch F, Bel Borja L, Jaffray E, Hay R. 2019. Sumoylation regulates protein dynamics during meiotic chromosome segregation in C. elegans oocytes. Journal of Cell Science. 132. https://doi.org/10.1242/jcs.232330

Pinneh EC, Mina JG, Stark MJR, Lindell SD, Luemmen P, Knight MR, Steel PG, Denny PW. 2019. The identification of small molecule inhibitors of the plant inositol phosphorylceramide synthase which demonstrate herbicidal activity. Scientific Reports. 9:1-8. https://doi.org/10.1038/s41598-019-44544-1

Pravata V, Muha V, Gundogdu M, Ferenbach A, Kakade P, Vandadi V, Wilmes AC, Borodkin V, Joss S, Stavridis M, van Aalten D. 2019. Catalytic deficiency of O-GlcNAc transferase leads to X-linked intellectual disability. Proceedings of the National Academy of Sciences. 116(30):14961-14970. https://doi.org/10.1073/pnas.1900065116

Pravata VM, Gundogdu M, Bartual SG, Ferenbach AT, Stavridis M, Õunap K, Pajusalu S, Žordania R, Wojcik MH, van Aalten DMF. 2019. A missense mutation in the catalytic domain of O-GlcNAc transferase links perturbations in protein O-GlcNAcylation to X-linked intellectual disability. FEBS Letters. https://doi.org/10.1002/1873-3468.13640

Rabl J, Bunker RD, Schenk AD, Cavadini S, Gill ME, Abdulrahman W, Andrés-Pons A, Luijsterburg MS, Ibrahim AFM, Branigan E, Aguirre JD, Marceau AH, Guérillon C, Bouwmeester T, Hassiepen U, Peters AHFM, Renatus M, Gelman L, Rubin SM, Mailand N, van Attikum H, Hay RT, Thomä NH. 2019. Structural Basis of BRCC36 Function in DNA Repair and Immune Regulation. Molecular Cell. 75(3):483-497.e9. https://doi.org/10.1016/j.molcel.2019.06.002

Rasmussen KD, Berest I, Keβler S, Nishimura K, Simón-Carrasco L, Vassiliou GS, Pedersen MT, Christensen J, Zaugg JB, Helin K. 2019. TET2 binding to enhancers facilitates transcription factor recruitment in hematopoietic cells. Genome Research. 29(4):564-575. https://doi.org/10.1101/gr.239277.118

Schmidt N, Domingues P, Golebiowski F, Patzina C, Tatham MH, Hay RT, Hale BG. 2019. An influenza virus-triggered SUMO switch orchestrates co-opted endogenous retroviruses to stimulate host antiviral immunity. Proceedings of the National Academy of Sciences of the United States of America. 116(35):17399-17408. https://doi.org/10.1073/pnas.1907031116

Sinclair LV, Howden A, Brenes Murillo A, Spinelli L, Hukelmann J, Macintyre AN, Liu X, Thomson S, Taylor P, Rathmell JC, Locasale JW, Lamond A, Cantrell DA. 2019. Antigen receptor control of methionine metabolism in T cells. eLife. 8. https://doi.org/10.7554/eLife.44210

Tinti M, Güther MLS, Crozier TWM, Lamond AI, Ferguson MAJ. 2019. Proteome turnover in the bloodstream and procyclic forms of Trypanosoma brucei measured by quantitative proteomics. Wellcome Open Research. 4:1-27. https://doi.org/10.12688/wellcomeopenres.15421.1

Wang Y, Tatham MH, Schmidt-Heck W, Swann C, Singh-Dolt K, Meseguer-Ripolles J, Lucendo-Villarin B, Kunath T, Rudd TR, Smith AJH, Hengstler JG, Godoy P, Hay RT, Hay DC. 2019. Multiomics Analyses of HNF4α Protein Domain Function during Human Pluripotent Stem Cell Differentiation. iScience. 16:206-217. https://doi.org/10.1016/j.isci.2019.05.028

Winczura A, Appanah R, Tatham MH, Hay RT, De Piccoli G. 2019. The S phase checkpoint promotes the Smc5/6 complex dependent SUMOylation of Pol2, the catalytic subunit of DNA polymerase ε. PLoS Genetics. 15(11):1-26. https://doi.org/10.1371/journal.pgen.1008427

Zdańkowski P, Trusiak M, McGloin D, Swedlow JR. 2019. Numerically Enhanced Stimulated Emission Depletion Microscopy with Adaptive Optics for Deep-Tissue Super-Resolved Imaging. ACS Nano. https://doi.org/10.1021/acsnano.9b05891