University of Dundee

Computational Biology 2016

1. Wilson, N. J., Cole, C., Kroboth, K., Hunter, W. N., Mann, J. A., McLean, W. H. I., Kernland Lang, K., Beltraminelli, H., Sabroe, R. A., Tiffin, N., Sobey, G. J., Borradori, L., Simpson, E. and Smith, F. J. D. (2016) Mutations in POGLUT1 in Galli–Galli/Dowling–Degos disease. British Journal of Dermatology, n/a-n/a
DOI: 10.1111/bjd.14914

2. Wiechens, N., Singh, V., Gkikopoulos, T., Schofield, P., Rocha, S. and Owen-Hughes, T. (2016) The Chromatin Remodelling Enzymes SNF2H and SNF2L Position Nucleosomes adjacent to CTCF and Other Transcription Factors. PLoS genetics. 12, e1005940
DOI: 10.1371/journal.pgen.1005940

3. Ward, J., Cole, C., Febrer, M. and Barton, G. J. (2016) AlmostSignificant: simplifying quality control of high-throughput sequencing data. Bioinformatics
DOI: 10.1093/bioinformatics/btw559
PMID: 27559158

4. Vickery, O. N., Machtens, J. P. and Zachariae, U. (2016) Membrane potentials regulating GPCRs: insights from experiments and molecular dynamics simulations. Current opinion in pharmacology. 30, 44-50
DOI: 10.1016/j.coph.2016.06.011
PMCID: 5080454
PMID: 27474871

5. Vickery, O. N., Machtens, J. P., Tamburrino, G., Seeliger, D. and Zachariae, U. (2016) Structural Mechanisms of Voltage Sensing in G Protein-Coupled Receptors. Structure. 24, 997-1007
DOI: 10.1016/j.str.2016.04.007
PMCID: 4906246
PMID: 27210286

6. 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. (2016) Molecular basis of RNA guanine-7 methyltransferase (RNMT) activation by RAM. Nucleic acids research
DOI: 10.1093/nar/gkw637
PMID: 27422871

7. Singh, R., Lawal, H. M., Schilde, C., Gloeckner, G., Barton, G. J., Schaap, P. and Cole, C. (2016) Improved Annotation with de novo Transcriptome Assembly in Four Social Amoeba Species. bioRxiv
DOI: 10.1101/054536

8. 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. (2016) How many biological replicates are needed in an RNA-seq experiment and which differential expression tool should you use? Rna. 22, 839-851
DOI: 10.1261/rna.053959.115
PMCID: 4878611
PMID: 27022035

9. Ortmann, B., Bensaddek, D., Carvalhal, S., Moser, S. C., Mudie, S., Griffis, E. R., Swedlow, J. R., Lamond, A. I. and Rocha, S. (2016) CDK-dependent phosphorylation of PHD1 on serine 130 alters its substrate preference in cells. Journal of cell science. 129, 191-205
DOI: 10.1242/jcs.179911
PMCID: 4732302
PMID: 26644182

10. Moreno, A., Carrington, J. T., Albergante, L., Al Mamun, M., Haagensen, E. J., Komseli, E. S., Gorgoulis, V. G., Newman, T. J. and Blow, J. J. (2016) Unreplicated DNA remaining from unperturbed S phases passes through mitosis for resolution in daughter cells. Proceedings of the National Academy of Sciences of the United States of America. 113, E5757-5764
DOI: 10.1073/pnas.1603252113
PMCID: 5047195
PMID: 27516545

11. Li, S., Besson, S., Blackburn, C., Carroll, M., Ferguson, R. K., Flynn, H., Gillen, K., Leigh, R., Lindner, D., Linkert, M., Moore, W. J., Ramalingam, B., Rozbicki, E., Rustici, G., Tarkowska, A., Walczysko, P., Williams, E., Allan, C., Burel, J. M., Moore, J. and Swedlow, J. R. (2016) Metadata management for high content screening in OMERO. Methods. 96, 27-32
DOI: 10.1016/j.ymeth.2015.10.006
PMCID: 4773399
PMID: 26476368

12. Kutzner, C., Kopfer, D. A., Machtens, J. P., de Groot, B. L., Song, C. and Zachariae, U. (2016) Insights into the function of ion channels by computational electrophysiology simulations. Biochimica et biophysica acta
DOI: 10.1016/j.bbamem.2016.02.006
PMID: 26874204

13. 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. (2016) Ubiquitin Receptor Protein UBASH3B Drives Aurora B Recruitment to Mitotic Microtubules. Developmental cell. 36, 63-78
DOI: 10.1016/j.devcel.2015.12.017
PMID: 26766443

14. Kasparis, C., Reid, D., Wilson, N. J., Okur, V., Cole, C., Hansen, C. D., Bosse, K., Betz, R. C., Khan, M. and Smith, F. J. D. (2016) Isolated recessive nail dysplasia caused by FZD6 mutations: report of three families and review of the literature. Clinical and Experimental Dermatology. 41, 884-889
DOI: 10.1111/ced.12934

15. 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. (2016) BOD1 Is Required for Cognitive Function in Humans and Drosophila. PLoS genetics. 12, e1006022
DOI: 10.1371/journal.pgen.1006022
PMCID: 4864283
PMID: 27166630

16. Dickerson, D., Gierliński, M., Singh, V., Kitamura, E., Ball, G., Tanaka, T. U. and Owen-Hughes, T. (2016) High resolution imaging reveals heterogeneity in chromatin states between cells that is not inherited through cell division. BMC Cell Biology. 17, 33
DOI: 10.1186/s12860-016-0111-y

17. Baptista-Hon, D. T., Krah, A., Zachariae, U. and Hales, T. G. (2016) A role for loop G in the beta1 strand in GABAA receptor activation. The Journal of physiology. 594, 5555-5571
DOI: 10.1113/JP272463
PMCID: 5043033
PMID: 27195487

18. Allen, E. H. A., Courtney, D. G., Atkinson, S. D., Moore, J. E., Mairs, L., Poulsen, E. T., Schiroli, D., Maurizi, E., Cole, C., Hickerson, R. P., James, J., Murgatroyd, H., Smith, F. J. D., MacEwen, C., Enghild, J. J., Nesbit, M. A., Leslie Pedrioli, D. M., McLean, W. H. I. and Moore, C. B. T. (2016) Keratin 12 missense mutation induces the unfolded protein response and apoptosis in Meesmann epithelial corneal dystrophy. Human molecular genetics. 25, 1176-1191
DOI: 10.1093/hmg/ddw001
PMID: PMC4764196

19. Albergante, L., Liu, D., Palmer, S. and Newman, T. J. (2016) Insights into Biological Complexity from Simple Foundations. Advances in experimental medicine and biology. 915, 295-305
DOI: 10.1007/978-3-319-32189-9_18
PMID: 27193550

20. Al Mamun, M., Albergante, L., Moreno, A., Carrington, J. T., Blow, J. J. and Newman, T. J. (2016) Inevitability and containment of replication errors for eukaryotic genome lengths spanning megabase to gigabase. Proceedings of the National Academy of Sciences of the United States of America
DOI: 10.1073/pnas.1603241113
PMID: 27630194

21. Naeem, A. S., Tommasi, C., Cole, C., Brown, S. J., Zhu, Y., Way, B., Willis Owen, S. A. G., Moffatt, M., Cookson, W. O., Harper, J. I., Wl, D., Brown, S. J., Reinheckel, T. and O’Shaughnessy, R. F. L. An mTORC1/AKT1/Cathepsin H axis controls filaggrin expression and processing in skin, a novel mechanism for skin barrier disruption in Atopic Dermatitis. Journal of Allergy and Clinical Immunology
DOI: 10.1016/j.jaci.2016.09.052

22. Lovgren, M. L., McAleer, M. A., Irvine, A. D., Wilson, N. J., Tavadia, S., Schwartz, M. E., Cole, C., Sandilands, A., Smith, F. J. D. and Zamiri, M. Mutations in desmoglein-1 cause diverse inherited palmoplantar keratoderma phenotypes: Implications for genetic screening. British Journal of Dermatology, n/a-n/a
DOI: 10.1111/bjd.14973

23. Tatham, M. H., Cole, C., Scullion, P., Wilkie, R., Westwood, N. J., Stark, L. A. and Hay, R. T. (2016) A proteomic approach to analyse the aspirin-mediated lysine acetylome. Molecular & Cellular Proteomics
DOI: 10.1074/mcp.O116.065219