University of Dundee

Computational Biology 2017

Barton, D. L., Henkes, S., Weijer, C. J. and Sknepnek, R. (2017) Active Vertex Model for cell-resolution description of epithelial tissue mechanics. PLoS computational biology. 13, e1005569
d.o.i 10.1371/journal.pcbi.1005569
Pubmed: 5493290
PMC: 28665934

Bowick, M. J., Kosmrlj, A., Nelson, D. R. and Sknepnek, R. (2017) Non-Hookean statistical mechanics of clamped graphene ribbons. Physical Review B. 95d.o.i Artn 104109
10.1103/Physrevb.95.104109
PMC: ISI:000399205100002

Britto-Borges, T. and Barton, G. J. (2017) A study of the structural properties of sites modified by the O-linked 6-N-acetylglucosamine transferase. PloS one. 12, e0184405
d.o.i 10.1371/journal.pone.0184405
Pubmed: 5590929
PMC: 28886091

Carvalheda, C. A. and Pisliakov, A. V. (2017) On the role of subunit M in cytochrome cbb3 oxidase. Biochemical and biophysical research communications. 491, 47-52
d.o.i 10.1016/j.bbrc.2017.07.031
PMC: 28694191

Carvalheda, C. A. and Pisliakov, A. V. (2017) Insights into proton translocation in cbb3 oxidase from MD simulations. Biochimica et biophysica acta. 1858, 396-406
d.o.i 10.1016/j.bbabio.2017.02.013
PMC: 28259641

Chen, Z. H., Singh, R., Cole, C., Lawal, H. M., Schilde, C., Febrer, M., Barton, G. J. and Schaap, P. (2017) Adenylate cyclase A acting on PKA mediates induction of stalk formation by cyclic diguanylate at the Dictyostelium organizer. Proceedings of the National Academy of Sciences of the United States of America. 114, 516-521
d.o.i 10.1073/pnas.1608393114
Pubmed: 5255622
PMC: 28057864

Fitzpatrick, A. W. P., Llabres, S., Neuberger, A., Blaza, J. N., Bai, X. C., Okada, U., Murakami, S., van Veen, H. W., Zachariae, U., Scheres, S. H. W., Luisi, B. F. and Du, D. (2017) Structure of the MacAB-TolC ABC-type tripartite multidrug efflux pump. Nature microbiology. 2, 17070
d.o.i 10.1038/nmicrobiol.2017.70
Pubmed: 5447821
PMC: 28504659

Froussios, K., Mourão, K., Simpson, G. G., Barton, G. J. and Schurch, N. J. (2017) Identifying differential isoform abundance with RATs: a universal tool and a warning. bioRxivd.o.i 10.1101/132761

Glusman, G., Rose, P. W., Prlic, A., Dougherty, J., Duarte, J. M., Hoffman, A. S., Barton, G. J., Bendixen, E., Bergquist, T., Bock, C., Brunk, E., Buljan, M., Burley, S. K., Cai, B., Carter, H., Gao, J., Godzik, A., Heuer, M., Hicks, M., Hrabe, T., Karchin, R., Leman, J. K., Lane, L., Masica, D. L., Mooney, S. D., Moult, J., Omenn, G. S., Pearl, F., Pejaver, V., Reynolds, S. M., Rokem, A., Schwede, T., Song, S., Tilgner, H., Valasatava, Y., Zhang, Y. and Deutsch, E. W. (2017) Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework. Genome medicine. 9, 113
d.o.i 10.1186/s13073-017-0509-y
Pubmed: 5735928
PMC: 29254494

Krah, A. and Zachariae, U. (2017) Insights into the ion-coupling mechanism in the MATE transporter NorM-VC. Physical biology. 14, 045009
d.o.i 10.1088/1478-3975/aa5ee7
PMC: 28169223

Liu, D., Albergante, L. and Newman, T. J. (2017) Universal attenuators and their interactions with feedback loops in gene regulatory networks. Nucleic acids research. 45, 7078-7093
d.o.i 10.1093/nar/gkx485
Pubmed: 5499555
PMC: 28575450

Matoz-Fernandez, D. A., Martens, K., Sknepnek, R., Barrat, J. L. and Henkes, S. (2017) Cell division and death inhibit glassy behaviour of confluent tissues. Soft matter. 13, 3205-3212
d.o.i 10.1039/c6sm02580c
PMC: 28398448

Patwardhan, A., Brandt, R., Butcher, S. J., Collinson, L., Gault, D., Grunewald, K., Hecksel, C., Huiskonen, J. T., Iudin, A., Jones, M. L., Korir, P. K., Koster, A. J., Lagerstedt, I., Lawson, C. L., Mastronarde, D., McCormick, M., Parkinson, H., Rosenthal, P. B., Saalfeld, S., Saibil, H. R., Sarntivijai, S., Solanes Valero, I., Subramaniam, S., Swedlow, J. R., Tudose, I., Winn, M. and Kleywegt, G. J. (2017) Building bridges between cellular and molecular structural biology. eLife. 6d.o.i 10.7554/eLife.25835
Pubmed: 5524535
PMC: 28682240

Russell, E. R., Sknepnek, R. and Bowick, M. (2017) Stiffening thermal membranes by cutting. Physical Review E. 96d.o.i Artn 013002
10.1103/Physreve.96.013002
PMC: ISI:000405194200010

Schleicher, K., Porter, M., Ten Have, S., Sundaramoorthy, R., Porter, I. M. and Swedlow, J. R. (2017) The Ndc80 complex targets Bod1 to human mitotic kinetochores. Open biology. 7d.o.i 10.1098/rsob.170099
Pubmed: 5717335
PMC: 29142109

Singh, R., Lawal, H. M., Schilde, C., Glockner, G., Barton, G. J., Schaap, P. and Cole, C. (2017) Improved annotation with de novo transcriptome assembly in four social amoeba species. BMC genomics. 18, 120
d.o.i 10.1186/s12864-017-3505-0
Pubmed: 5282741
PMC: 28143409

Tamburrino, G., Llabres, S., Vickery, O. N., Pitt, S. J. and Zachariae, U. (2017) Modulation of the Neisseria gonorrhoeae drug efflux conduit MtrE. Scientific reports. 7, 17091
d.o.i 10.1038/s41598-017-16995-x
Pubmed: 5719041
PMC: 29213101

Williams, E., Moore, J., Li, S. W., Rustici, G., Tarkowska, A., Chessel, A., Leo, S., Antal, B., Ferguson, R. K., Sarkans, U., Brazma, A., Salas, R. E. C. and Swedlow, J. R. (2017) The Image Data Resource: A Bioimage Data Integration and Publication Platform. Nature methods. 14, 775-781
d.o.i 10.1038/nmeth.4326
Pubmed: 5536224
PMC: 28775673

Vickery, O. N., Carvalheda, C. A., Zaidi, S. A., Pisliakov, A. V., Katritch, V. and Zachariae, U. (2018) Intracellular Transfer of Na(+) in an Active-State G-Protein-Coupled Receptor. Structure. 26, 171-180 e172
d.o.i 10.1016/j.str.2017.11.013
PMC: 29249607

MacGowan, S. A., Madeira, F., Britto Borges, T., Schmittner, M. S., Cole, C. and Barton, G. J. (2017) Human Missense Variation is Constrained by Domain Structure and Highlights Functional and Pathogenic Residues. bioRxivd.o.i 10.1101/12705