University of Dundee

Computational Biology 2015

1. Brandani, G. B., Schor, M., Morris, R., Stanley-Wall, N., MacPhee, C. E., Marenduzzo, D. and Zachariae, U. (2015) The Bacterial Hydrophobin BslA is a Switchable Ellipsoidal Janus Nanocolloid. Langmuir : 31, 11558-11563
DOI:10.1021/acs.langmuir.5b02347
PMID: 26378478

2. Bromley, K. M., Morris, R. J., Hobley, L., Brandani, G., Gillespie, R. M., McCluskey, M., Zachariae, U., Marenduzzo, D., Stanley-Wall, N. R. and MacPhee, C. E. (2015) Interfacial self-assembly of a bacterial hydrophobin. Proceedings of the National Academy of Sciences of the United States of America. 112, 5419-5424
DOI:10.1073/pnas.1419016112
PMCID: 4418867
PMID: 25870300

3. 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. (2015) Publishing and sharing multi-dimensional image data with OMERO. Mammalian genome : official journal of the International Mammalian Genome Society. 26, 441-447
DOI: 10.1007/s00335-015-9587-6
PMCID: 4602067
PMID: 26223880

4. Drozdetskiy, A., Cole, C., Procter, J. and Barton, G. J. (2015) JPred4: a protein secondary structure prediction server. Nucleic acids research. 43, W389-394
DOI: 10.1093/nar/gkv332
PMCID: 4489285
PMID: 25883141

5. 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. (2015) Statistical models for RNA-seq data derived from a two-condition 48-replicate experiment. Bioinformatics. 31, 3625-3630
DOI: 10.1093/bioinformatics/btv425
PMID: 26206307

6. 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. (2015) Metadata management for high content screening in OMERO. Methods
DOI: 10.1016/j.ymeth.2015.10.006
PMID: 26476368

7. Machtens, J. P., Kortzak, D., Lansche, C., Leinenweber, A., Kilian, P., Begemann, B., Zachariae, U., Ewers, D., de Groot, B. L., Briones, R. and Fahlke, C. (2015) Mechanisms of anion conduction by coupled glutamate transporters. Cell. 160, 542-553
DOI: 10.1016/j.cell.2014.12.035
PMID: 25635461

8. Madeira, F., Tinti, M., Murugesan, G., Berrett, E., Stafford, M., Toth, R., Cole, C., MacKintosh, C. and Barton, G. J. (2015) 14-3-3-Pred: improved methods to predict 14-3-3-binding phosphopeptides. Bioinformatics. 31, 2276-2283
DOI: 10.1093/bioinformatics/btv133
PMCID: 4495292
PMID: 25735772

9. Ortmann, B., Bensaddek, D., Carvalhal, S., Moser, S. C., Mudie, S., Griffis, E. R., Swedlow, J. R., Lamond, A. I. and Rocha, S. (2015) CDK dependent phosphorylation of PHD1 on Serine 130 determines specificity in substrate targeting in cells. Journal of cell science  
DOI: 10.1242/jcs.179911
PMID: 26644182

10. Pumroy, R. A., Ke, S., Hart, D. J., Zachariae, U. and Cingolani, G. (2015) Molecular determinants for nuclear import of influenza A PB2 by importin alpha isoforms 3 and 7. Structure. 23, 374-384
DOI: 10.1016/j.str.2014.11.015
PMCID: 4346194
PMID: 25599645

11. Rose, A. S., Zachariae, U., Grubmuller, H., Hofmann, K. P., Scheerer, P. and Hildebrand, P. W. (2015) Role of Structural Dynamics at the Receptor G Protein Interface for Signal Transduction. PloS one. 10, e0143399
DOI: 10.1371/journal.pone.0143399
PMCID: 4659624
PMID: 26606751
12. Seifert, A., Schofield, P., Barton, G. J. and Hay, R. T. (2015) Proteotoxic stress reprograms the chromatin landscape of SUMO modification. Science signaling. 8, rs7
DOI: 10.1126/scisignal.aaa2213
PMID: 26152697

13. Sknepnek, R. and Henkes, S. (2015) Active swarms on a sphere. Physical review. E, Statistical, nonlinear, and soft matter physics. 91, 022306
DOI: 10.1103/PhysRevE.91.022306
PMID: 25768504

14. Wan, D., Bowick, M. J. and Sknepnek, R. (2015) Effects of scars on icosahedral crystalline shell stability under external pressure. Physical review. E, Statistical, nonlinear, and soft matter physics. 91, 033205
DOI: 10.1103/PhysRevE.91.033205
PMID: 25871236

15. Zhang, T., Sknepnek, R., Bowick, M. J. and Schwarz, J. M. (2015) On the modeling of endocytosis in yeast. Biophysical journal. 108, 508-519
DOI: 10.1016/j.bpj.2014.11.3481
PMCID: 4317554
PMID: 25650919