2008
Amiri, S., Shimomura, M., Vijayan, R., Nishiwaki, H., Akamatsu, M., Matsuda, K., Jones, A.K., Sansom, M.S.P., Biggin, P.C., and Sattelle, D.B. (2008) The role of Leu118 of loop E in agonist binding to the α7 nicotinic acetylcholine receptor. Mol. Pharmacol. 73:1659-1667
M. Barrio, K. Burrage, P. Burrage, A. Leier, T. Márquez Lago (2008): Computational Approaches for Modeling Intrinsic Noise and Delays in Genetic Regulatory Networks, to appear in Computational Methodologies in Gene Regulatory Networks.
Berry, R.M. and Armitage J.P. (2008) How bacteria change gear. Science (perspective) 320:1599-1600
Bond, P.J., Parton, D.L., Clark, J.F., and Sansom, M.S.P. (2008) Coarse-grained simulations of the membrane-active antimicrobial peptide maculatin 1.1. Biophys. J. 95:3802-3815
Bond, P.J., Wee C.L. and Sansom, M.S.P. (2008) Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer. Biochem. 47:11321–11331
K. Burrage, I. Lenane and G. Lythe (2008): Numerical methods for second order stochastic equations, SIAM Journal of Scientific Computing, 29, 1, 245-264.
Carpenter, T., Bond, P.J., Khalid, S. and Sansom, M.S.P. (2008) Self-assembly of a simple membrane protein: coarse-grained molecular dynamics simulations of the influenza M2 channel Biophys. J. 95:3790-3801
C-M. Chen, F. Liu and K. Burrage (2008): Finite difference method and a new Fourier analysis for the Fractional Reaction-Diffusion Equation, Applied Mathematics and Computation, Vol. 198, No. 2, 754-769.
Chen, M., Khalid, M., Sansom, M.S.P. and Bayley, H. (2008) OmpG: engineering a quiet pore for biosensing Proc. Natl. Acad. Sci. USA. 105:6272-6277
Chen P-Y, Deane CM, Reinert G (2008) Predicting and Validating Protein Interactions Using Network Structure. PLoS Comput Biol 4(7):
Chetwynd, A.P., Scott, K.A., Mokrab, Y. and Sansom, M.S.P. (2008) CGDB: a database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations. Mol. Memb. Biol. 25:662-669
Chowdhury, R.; Hardy, A.; Schofield, C.J. (2008) The human oxygen sensing machinery and its manipulation Chemical Society Reviews 37(7) 1308-1319
Cox, K., Bond, P.J., Grottesi, A., Baaden, M. and Sansom, M.S.P. (2008) Outer membrane proteins: comparing X-ray and NMR structures by MD simulations in lipid bilayers. Eur. Biophys. J. 37:131-141
Csikász-Nagy, Győrffy, B., Alt, W., Tyson, J.J. & Novák, B. (2008): Spatial controls for growth zone formation during the fission yeast cell cycle. Yeast 25:59-69.
Delalez, N. and Armitage, J.P. (2008) Parts exchange: tuning the flagellar motor to fit the conditions. Mol.Microbiol. (pub online Dec 23rd)
D’Rozario, R. and Sansom, M.S.P. (2008) Helix dynamics in a membrane transport protein: comparative simulations of the glycerol-3-phosphate transporter GlpT and its constituent helices Molec. Memb. Biol. 25:571-583
Fowler, P.F., Tai, K. and Sansom, M.S.P. (2008) The selectivity of K+ ion channels: testing the hypotheses Biophys. J. 95:5062-5072
Flashman, E., Bagg, E. A. L., Chowdhury, R., Mecinovic, J., Loenarz, C., McDonough, M. A., Hewitson, K. S., Schofield, C. J. (2008) Kinetic rationale for selectivity toward N- and C-terminal oxygen-dependent degradation domain substrates mediated by a loop region of hypoxia-inducible factor prolyl hydroxylases. Journal of Biological Chemistry 283(7) 3808-3815
Johnston, J.M., Khalid, S., and Sansom, M.S.P. (2008) Conformational dynamics of the mitochondrial ADP/ATP carrier: A simulation study. Mol. Memb. Biol. 25:506-517
Jones, N.S. (2008) Using the memories of multiscale machines to characterize complex systems Physical review letters 100(20) 208702
Khalid, S., Bond, P.J., Holyoake, J., Hawtin, R.W. and Sansom, M.S.P. (2008) DNA and lipid bilayers: self assembly and insertion. J. Roy. Soc. Interface 5:S241-S250
Khalid, S., Holyoake, J., and Sansom, M.S.P. (2008) Molecular dynamics studies of membrane proteins: outer membrane proteins and transporters. Biophysical Analysis of Membrane Proteins: Investigating Structure and Function. Ed. E. Pebay-Peyroula. Publ. Wiley pp. 161-185
Labro, A.J., Grottesi, A., Sansom, M.S.P., Raes, A.L. and Snyders, D.J. (2008) A Kv channel with an altered activation gate sequence displays both ‘fast’ and ‘slow’ activation kinetics Amer. J. Physiol. Cell Physiol. 294:C1476-C1484
Labro, A.J., Raes, A.L., Grottesi, A., Van Hoorick, D., Sansom, M.S.P. and Snyders, D.J. (2008) Kv channel gating requires a compatible S4-S5 linker and bottom part of S6, constrained by non-interacting residues. J. Gen. Physiol. 132:667-680
Leake, M.J., Wadhams, G.H. and Armitage, J.P. (2008) Parts exchange: why molecular machines are like used cars. 55:33-39.
A. Leier, T. T. Marquez-Lago, and K.Burrage (2008): Generalized binomial Tau-leap method for biochemical kinetics incorporating both delay and intrinsic noise, Journal of Chemical Physics 128, 205107.
Lenn T, Leake MC & Mullineaux CW. (2008) In vivo clustering and dynamics of cytochrome bd complexes in the Escherichia coli plasma membrane. Mol. Microbiol. 70, 1397-1407.
Lienard, B.M.; Conejo-Garcia, A.; Stolze, I.; Loenarz, C.; Oldham, N.J.; Ratcliffe, P.J.; Schofield, C.J. (2008) Evaluation of aspirin metabolites as inhibitors of hypoxia-inducible factor hydroxylases Chemical Communications 47 6393-6395
Lindahl, E. and Sansom, M.S.P. (2008) Membrane proteins: molecular dynamics simulations Curr. Opin. Struct. Biol. 18:425-431
Loenarz, C.; Schofield, C.J. (2008) Expanding chemical biology of 2-oxoglutarate oxygenases Nature Chemical Biology 4(3) 152-156
MacNamara S., Bersani A.M., Burrage K., & Sidje R.B. (2008) Stochastic chemical kinetics and the total quasi-steady-state assumption: application to the stochastic simulation algorithm and chemical master equation, Journal of Chemical Physics, 129(9):095105.
S. McNamara, K. Burrage and R. B. Sidje (2008): Application of the Strang splitting to the chemical master equation for simulating biochemical kinetics, International Journal of Computational Science, Ed. K. K. Lai, Vol. 2, No. 3, 402-421.
S.MacNamara, K. Burrage and R. B. Sidje (2008): Multiscale modeling of chemical kinetics via the master equation, SIAM J. Multiscale Modelling and Simulation Multiscale, Vol. 6, No. 4, 1146-1168.
Miklos, I., Novak, A., Dombai, B. & Hein, J. (2008) How reliably can we predict the reliability of protein structure predictions? BMC Bioinformatics9, 137
Miklos, I., Novak, A., Satija, R., Lyngsø R. & Hein , J. (2008) Stochastic Models of Sequence Evolution including Insertion-Deletion events. Statistical Methods in Medical Research (in press)
Nicolau, D.V. Jr., Armitage, J.P. and Maini, P.K. (2008) In silico evolution of chemotactic swimming (PLoS ONE, in revision)
D. V. Nicolau Jr., K. Burrage, D. V. Nicolau, P. K. Maini (2008): ‘Extremotaxis’: Computing with a bacterial-inspired algorithm, BioSystems, Vol. 94, Issues 1-2, October-November 2008, 47-54.
Novak, A., Miklos, I., Lyngsø, R. & Hein, J. (2008) StatAlign: An extendable software package for joint Bayesian estimation of alignments and evolutionary trees. Bioinformatics Advance Access. Published 27 August. Associate Editor, Prof Martin Bishop
Novak, B.; Tyson J.J. (2008) Design principles of biochemical oscillators Nature Reviews Molecular Cell Biology 9(12) 981-991
J. Pitt--Francis, M.O. Bernabeu, J. Cooper, A. Garny, L. Momtahan, J.M. Osborne, P. Pathmanathan, B. Rodriguez, J.P. Whiteley, D.J. Gavaghan (2008) Chaste: using agile programming techniques to develop computational biology software. Phil. Trans. R. Soc. A, 366:3111--3136
Pollard PJ, Loenarz C, Mole DR, McDonough, MA, Gleadle JM, Schofield CJ, Ratcliffe PJ (2008) Regulation of Jumonji-domain-containing histone demethylases by hypoxia-inducible factor (HIF)-1 alpha Biochemical Journal 416: 387-394
Porter, S.L., Roberts, M.A.J., Manning, C. and Armitage, J.P. (2008) A bifunctional kinase-phosphatase in bacterial chemotaxis PNAS 2008 Nov 25;105(47):18531-6. Epub 2008 Nov 19.
Porter, S.L., Wadhams, G.H. and Armitage, J.P. (2008) Rhodobacter sphaeroides: Complexity in chemotactic signaling. Trends in Microbiol 16:251-260
Portman,N, Lacomble, S, Thomas, B, McKean, P.G. and Gull, K. (2008) Combining RNA Interference mutants and comparative proteomics to identify protein components and dependencies in a Eukaryotic Flagellum. The Journal of Biological Chemistry
Psachoulia, E., Fowler, P.F., Bond, P.J., and Sansom, M.S.P. (2008) Helix-helix interactions in membrane proteins: coarse grained simulations of glycophorin helix dimerization. Biochem. 47:10503-105012
Psachoulia, E., and Sansom, M.S.P. (2008) PH domain interactions with PIP2 and membranes: characterization via MD simulations. Biochem. 47:4211-4220
Rodrigues, M.L., Scott, K.A., Sansom, M.S.P., Pereira, I.A.C., and Archer, M. (2008) Quinol oxidation by cytochromes c: structural characterization of the menaquinol binding site of NrfHA J. Mol. Biol. 381:341-350
Rose, N.R.; Ng, S.S.; Mecinovic, J.; Lienard, B.M.R.; Bello, S.H.; Sun, Z.; McDonough, M.A.; Oppermann, U.; Schofield, C.J. (2008) Inhibitor Scaffolds for 2-Oxoglutarate-Dependent Histone Lysine Demethylases Journal of Medicinal Chemistry 51(22) 7053-7056
T. Rudge and K. Burrage (2008): Effects of intrinsic and extrinsic noise can accelerate and stabilise juxtacrine pattern formation, Bulletin of Mathematical Biology, Vol. 70, No. 4, 971-991.
Sabouri-Ghomi, M., Ciliberto, A. Kar, S., Novák, B. & Tyson, J.J. (2008): Antagonism and bistability in protein interaction networks. J Theor Biol. 250: 209-218.
Sansom, M.S.P., Scott, K.A. and Bond, P.J. (2008) Coarse grained simulation: a high throughput computational approach to membrane proteins Biochem. Soc. Transac. 36:27-32
Satija, R., Novak, A., Miklos, A., Lyngsø, R. & Hein, J. (2008) BiGFoot: Baysian alignment and phylogenetic footprinting for multiple sequences with MCMC. Submitted to BMC Bioinformatics
Satija, R.,Pachter, L. & Hein, J. (2008) Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinformatics 24, 1236-1242
Scott, K.A., Bond, P.J., Ivetac, A., Chetwynd, A.P., Khalid, S., and Sansom, M.S.P. (2008) Coarse-grained MD simulations of membrane protein/bilayer self assembly. Structure 16:621-630
Sherwood, P., Brooks, B.R. and Sansom, M.S.P. (2008) Multiscale methods for molecular simulation. Curr. Opin. Struct. Biol. 18:630-640
Stansfeld, P.J., Grottesi, A., Sands, Z.A., Sansom, M.S.P., Gedeck, P., Gosling, M., Cox, B., Stanfield, P.R., Mitcheson, J.S., and Sutcliffe, M.J. (2008) Insight into the mechanism of inactivation and pH sensitivity in potassium channels from molecular dynamics simulations. Biochem. 47:7414-7422.
Sun, Y., McKeever, S., Balali-Mood, K. and Sansom, M.S.P. (2008) Integrating multi-level molecular simulations across heterogeneous resources In Proceedings of the 8th IEEE/ACM International Conference on Grid Computing (Grid 2007) pp. 161-168. Austin, Texas.
Tindall, M.J., Maini, P.K., Armitage, J.P., Singleton, C. And Mason, A. (2008) Intracellular signalling during bacterial chemotaxis SEB. Exp. Biol. Ser 61: 161-174
Tindall, M.J., Maini, P.K., Porter, S.L. and Armitage J.P. (2008) Overview of mathematical approaches used to model bacterial chemotaxis II: Bacterial populations. Bulletin of Mathematical Biology 70: 1570-1607
Tindall, M.J., Porter, S.L., Maini, P.K., Gaglia, G. and Armitage, J.P. (2008) Overview of mathematical approaches used to model bacterial chemotaxis I: The single cell. Bulletin of Mathematical Biology 70: 1525-1569
Tyson, J.J. & Novák, B. (2008) : Temporal organization of the cell cycle. Current Biology 18: R759-R768.
Novák, B. & Tyson, J.J. (2008): Design principles of biochemical oscillators. Nature Reviews Molecular Cell Biology 9: 981-991.
Vaccaro, L. and Sansom, M.S.P. (2008) Gating at both ends and breathing in the middle: conformational dynamics of TolC. Biophys. J. 95:5681-5691
Wallace, E.J. and Sansom, M.S.P. (2008) Blocking of carbon nanotube based nanoinjectors by lipids: a simulation study. Nano Letters. 8:2751-2756
Wee, C.L., Balali-Mood, K., Gavaghan, D. and Sansom, M.S.P. (2008) The interaction of phospholipase A2 with a phospholipid bilayer: coarse-grained molecular dynamics simulations Biophys. J. 95: 1649-1657
Wee, C.L., Gavaghan, D. and Sansom, M.S.P. (2008) Bilayer deformation and free energy of interaction of a Kv channel gating modifier toxin. Biophys. J. 95:3816-3826
Wee, C.L., Sansom, M.S.P., Reich, S. and Akhmatskaya, E. (2008) Improved sampling for simulations of interfacial membrane proteins: application of Generalized Shadowing Hybrid Monte Carlo to a peptide toxin/bilayer system. J. Phys. Chem. B. 112:5710-5717