2012

Anderson J., N. Strelkowa, G.-B. Stan, T. Douglas, J. Savulescu, M. Barahona and A. Papachristodoulou. (2012) Engineering and ethical perspectives in synthetic biology. EMBO Reports, 13(7) 584-590 doi: 10.1038/embor.2012.81

Brown M.T., Steel B.C., Silvestrin C., Wilkinson D. A., Delalez N. J., Lumb, C.N., Obara B., Armitage J.P. Berry R.M. (2012) Flagellar Hook Flexibility Is Essential for Bundle Formation in Swimming Escherichia coli Cells Journal Of Bacteriology 194(13) 3495-3501 DOI: 10.1128/JB.00209-12

Caldara M, Friedlander RS, Kavanaugh NL, Aizenberg K, Foster KR, Ribbeck K (2012) Mucin biopolymers prevent bacterial aggregation by retaining cells in the free-swimming state. Current Biology 22(24) 2325-2330, ISSN 0960-9822, 10.1016/j.cub.2012.10.028.

Collingridge P., and Kelly, S., (2012) MergeAlign: improving multiple sequence alignment performance by dynamic reconstruction of consensus multiple sequence alignments BMC Bioinformatics 13:117 doi:10.1186/1471-2105-13-117

Dunn S.J., Appleton P.L., Nelson S. A, Näthke I.S., Gavaghan D.J., Osborne J.M. (2012) A two-dimensional model of the colonic crypt accounting for the role of the basement membrane and pericryptal fibroblast sheath PLoS computational biology 8(5) e1002515 doi:10.1371/journal.pcbi.1002515

Dunn S.J., Fletcher A.G., Chapman S.J., Gavaghan D.J., Osborne J.M. (2012) Modelling the role of the basement membrane beneath a growing epithelial monolayer Journal Of Theoretical Biology 298 82-91 DOI: 10.1016/j.jtbi.2011.12.013

Fisher, D., Krasinska, L., Coudreuse, D. & Novák, B. (2012) Phosphorylation network dynamics in the control of cell cycle transitions. J Cell Sci. 125: 4703-4711. doi: 10.1242/jcs.106351

Foster KR, Bell T. (2012) Competition, not cooperation, dominates interactions among culturable microbial species. Current biology 22(19) 1845-50. doi: 10.1016/j.cub.2012.08.005.

Freire, P., Vinod, P.K. & Novak, B. (2012) Interplay of transcriptional and proteolytic regulation in driving robust cell cycle progression Mol Biosyst. 8: 863-870 DOI: 10.1039/c2mb05406j

Ge W, Wolf A, Feng T, Ho C-h, Sekirnik R, Zayer A, Granatino N, Cockman ME, Loenarz C, Loik ND, Hardy AP, Claridge TDW, Hamed RB, Chowdhury R, Gong L, Robinson CV, Trudgian DC, Jiang M, Mackeen  MM, McCullagh,JS, Gordiyenko Y, Thalhammer A, Yamamoto A, Yang M, Liu-Yi P, Zhang Z, Schmidt-Zachmann M, Kessler BM, Ratcliffe PJ, Preston GM, Coleman ML, Schofield CJ (2012) Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans. Nat Chem Biol, 8, 960-62. doi:10.1038/nchembio.1093

Gilmore S.J., B.L. Vaughan Jr, A. Madzvamuse, P.K. Maini, (2012) A mechanochemical model for striae distensae, Math Biosciences, 240, 141-147 http://dx.doi.org/10.1016/j.mbs.2012.06.007

Hall, B.A., Armitage, J.P. & Sansom, M.S.P. (2012) Mechanism of Bacterial Signal Transduction Revealed by Molecular Dynamics of Tsr Dimers and Trimers of Dimers in Lipid Vesicles. PLoS Comput Biol 8(9) e1002685. doi:10.1371/journal.pcbi.1002685

Heaton L.L.M., Lopez E., Maini P.K., Fricker M.D. and Jones N. S., (2012) Advection, diffusion and delivery over a network, Physical Review E, 86, 021905 DOI: 10.1103/PhysRevE.86.021905

Johnston I.G., Gaal B., das Neves R.P., Enver T., Iborra F.J. and Jones N.S. (2012) Mitochondrial Variability as a Source of Extrinsic Cellular Noise PLoS Computational Biology 8(3) e1002416. doi:10.1371/journal.pcbi.1002416

Kelly, S., Kramer, S., Schwede, A., Maini, P.K., Gull, K., and Carrington M. (2012) Genome organisation is a major component of gene expression control in response to stress and during the cell-division cycle in trypanosomes. OpenBiology 2(4) doi: 10.1098/rsob.120033

Klingbeil G., Erban R., Giles M., and Maini P.K. (2012) Fat versus thin threading approach on GPUs: application to stochastic simulation of chemical reactions, IEEE. T. Parall. Distr. 23 280-287 DOI. 10.1109/TPDS.2011.157.

Lewis A.C., Jones N.S., Porter M.A., Deane C.M. (2012) What Evidence Is There for the Homology of Protein-Protein Interactions, PloS Comp. Bio., 8(9), e1002645

Lu, L.X., Domingo-Sananes, M.R., Huzarska, M., Novak, B. & Gould, K.L. (2012) Multisite phosphoregulation of Cdc25 activity refines the mitotic entrance and exit switches. Proc Natl Acad Sci U S A. 109: 9899-9904.

Maini P.K., T.E. Woolley, R.E. Baker, E.A. Gaffney, S. Seirin Lee, (2012) Turingʼs model for biological pattern formation and the robustness problem, Interface Focus (2) 487–496 doi:10.1098/rsfs.2011.0113

Mantri M., Zhang Z., McDonough M.A., Schofield C.J. (2012) Autocatalysed oxidative modifications to 2-oxoglutarate dependent oxygenases Febs Journal279(9) 1563-1575   DOI: 10.1111/j.1742-4658.2012.08496.x

Martin N.K., Robey I.F., Gaffney E.A., Gillies R.J., Gatenby R.A., Maini P.K. (2012) Predicting the safety and efficacy of buffer therapy to raise tumour pHe: an integrative modelling study, British J. Cancer, 106, 1280-1287 doi: 10.1038/bjc.2012.58

McGillen J.B., N.K. Martin, I. Robey, E. Gaffney, P.K. Maini, (2012) Applications of mathematical analysis to tumour acidity modelling, RIMS Kokyuroku Bessatsu, B31, 31-59

Mirams G.R., A.G. Fletcher, P.K. Maini, H.M. Byrne, (2012) A theoretical investigation of the effect of proliferation and adhesion on monoclonal conversion in the colonic crypt, J. Theor. Biol., 312, 143-156  DOI: 10.1016/j.jtbi.2012.08.002

McLennan R., Dyson L., Prather K.W., Morrison J.A., Baker R.E., Maini P.K., Kulesa P.M., (2012) Multiscale mechanisms of cell migration during development: theory and experiment, Development. 139, 2935-2944 doi: 10.1242/dev.081471

Murray P.J., Edwards C.M., Tindall M.J., Maini P.K. (2012) Classifying general nonlinear force laws in cell-based models via the continuum limit, Phys. Rev. E., 85, 021921 DOI:10.1103/PhysRevE.85.021921

Murray P.J., P.K. Maini, M.V. Pilkis, C.-M. Chuong, R.E. Baker, (2012) Modelling Hair Follicle Growth Dynamics as an Excitable Medium. PLoS Comput Biol 8(12): e1002804. doi:10.1371/journal.pcbi.1002804

Münz M, Hein J, Biggin PC. (2012) The Role of Flexibility and Conformational Selection in the Binding Promiscuity of PDZ Domains. PLoS Comput Biol 8(11): e1002749. doi:10.1371/journal.pcbi.1002749

Obara B., Grau V., Fricker M. (2012) A BioImage Informatics Approach to Automatically Extract Complex Fungal Networks, Bioinformatics PubMed PMID: 22743223 doi: 10.1093/bioinformatics/bts364

Obara B., Fricker M., Gavaghan D., Grau V. (2012) Contrast-Independent Curvilinear Structure Detection in Biomedical Images. IEEE Transactions on Image Processing 21(5) 2572-2581 DOI: 10.1109/TIP.2012.2185938

Obara B., Fricker M., Grau V. (2012) Coherence enhancing diffusion filtering based on the Phase Congruency Tensor. Biomedical Imaging (ISBI), 9th IEEE International Symposium 202-205 doi: 10.1109/ISBI.2012.6235519

Okaz, E., Argüello-Miranda, O., Bogdanova, A., Vinod, P.K., Lipp, J.J., Markova, Z., Zagoriy, I., Novak, B. & Zachariae, W. (2012): Meiotic Prophase Requires Proteolysis of M Phase Regulators Mediated by the Meiosis-Specific APC/C(Ama1). Cell 151: 603-618. doi: 10.1016/j.cell.2012.08.044.

Onnela J.P., Fenn D.J., Reid S., Porter M.A., Mucha P.J., Fricker M.D. and Jones N.S. (2012) Taxonomies of Networks Phys. Rev. E arXiv:1006.5731

Pawelczyk S., Scott K.A., Hamer R., Blades G., Deane C.M. and Wadhams G.H. (2012) Predicting inter-species cross-talk in two-component signalling systems. PLoS ONE 7(5) e37737 doi:10.1371/journal.pone.0037737

Poon, S.K., Peacock, L., Gibson, W., Gull, K., and Kelly, S. (2012) A modular and optimised single marker system for generating Trypanosoma brucei cell lines expressing T7 RNA polymerase and the tetracycline repressor. OpenBiology 2(2) doi: 10.1098/rsob.110037

Prescott T. P. and A. Papachristodoulou (2012) Guaranteed error bounds for structured complexity reduction of biochemical networks. Journal of Theoretical Biology, 304:172-182, DOI: 10.1016/j.jtbi.2012.04.002

Rito T, Deane CM, Reinert G. (2012) The importance of age and high degree, in protein-protein interaction networks, J Comput Biol., 19(6), 785-95 doi:10.1089/cmb.2012.0054.

Roberts M.A.J., Wadhams G.H., Hadfield K.A., Tickner S.A., Armitage J.P. (2012) ParA-like protein uses nonspecific chromosomal DNA binding to partition protein complexes Proceedings Of The National Academy Of Sciences Of The United States Of America 109(17) 6698- 6703 DOI: 10.1073/pnas.1114000109

Schluter J, Foster KR. (2012) The evolution of mutualism in gut microbiota via host epithelial selection. PLoS Biology, 10(11): e1001424. doi:10.1371/journal.pbio.1001424

Schwarzländer M., Logan D.C., Johnston I.G., Jones N.S., Fricker M.D. and Sweetlove L.J., (2012) Pulsing of Membrane Potential in Individual Mitochondria: A Stress-Induced Mechanism to Regulate Respiratory Bioenergetics in Arabidopsis Plant Cell 24(3) 1188-201 PMID: 22395486

Smith A.M., R.E. Baker, D. Kay, P.K. Maini, (2012) Incorporating chemical signalling factors into cell-based models of growing epithelial tissues, J. Math. Biol., 65, 441-463 DOI 10.1007/s00285-011-0464-y

Sükösd Zs., B. Knudsen, J. W. J. Anderson, Á. Novák, J. Kjems and C. N. S. Pedersen (2012) Characterising RNA secondary structure space using information entropy. BMC Bioinformatics, 14(Suppl 2):S22, doi:10.1186/1471-2105-14-S2-S22.

Trichas G., Smith A.M., White N., Wilkins V., Watanabe T., Moore A., Joyce B., Sugnaseelan J., Rodriguez T.A., Kay D., Baker R.E., Maini P.K., Srinivas S. (2012) Multi-cellular rosettes in the mouse visceral endoderm facilitate the ordered migration of anterior visceral endoderm cells, PLoS Biology, 10(2) e1001256 (cover article) doi 10.1371/journal.pbio.1001256

Venkei, Z., Przewloka, M.R., Ladak, Y., Albadri, S., Sossick, A., Juhasz, G., Novak, B., Glover, D.M. (2012) Spatiotemporal dynamics of Spc105 regulates the assembly of the Drosophila kinetochore. Open Biol. 2: 110032 doi: 10.1098/rsob.110032

Verhaegen P.D.H.M., Van Marle J., Kuehne A., Schouten H.J., Gaffney E.A., Maini P.K., Middlekoop E., and Van Zuijlen P.P.M. (2012) Collagen bundle morphometry in skin & scar tissue: a novel distance mapping method provides superior measurements compared to Fourier analysis, J. Microsc. 245 82-89 doi: 10.1111/j.1365-2818.2011.03547.x

Vostrikov, V.V., Hall, B.A., Sansom, M.S.P. & Koeppe, R.E. (2012) Accommodation of a Central Arginine in a Transmembrane Peptide by Changing the Placement of Anchor Residues. J. Phys. Chem. B. 116: 12980–12990. DOI: 10.1021/jp308182b

Woolley T.E., R.E. Baker, E.A. Gaffney, P.K. Maini, S. Seirin Lee (2012) Effects of intrinsic stochasticity on delayed reaction-diffusion patterning systems, Phys Rev. E., 85(5), 051914, 1-14 DOI: 10.1103/PhysRevE.85.051914

Zhao, X., Harashima, H., Dissmeyer, N., Pusch, S., Weimer, A.K., Bramsiepe,  J., Bouyer, D., Rademacher, S., Nowack, M.K., Novak, B., Sprunck, S. &  Schnittger, A. (2012) A General G1/S-Phase Cell-Cycle Control Module in the Flowering Plant Arabidopsis thaliana. PLoS Genet 8(8): e1002847. doi:10.1371/journal.pgen.1002847