2009

J. Anderson and A. Papachristodoulou. (2009) On Validation and Invalidation of Biological Models. BMC Bioinformatics, 10:132.

E. August and A. Papachristodoulou. (2009) A new computational tool for establishing model parameter identifiability. Journal of Computational Biology. 16(6): 875-885.

E. August and A. Papachristodoulou. (2009) Efficient, sparse biological network determination. BMC Systems Biology, 3:25.

Balali-Mood, K., Bond, P.J. and Sansom, M.S.P. (2009) The interaction of monotopic membrane enzymes with a lipid bilayer: a coarse-grained MD simulation study. Biochem. (in press)

K. Burrage and G. Lythe (2009): Accurate stationary densities with partitioned numerical methods for stochastic differential Equations, SIAM J. Num. Anal., Vol. 47, No. 3, 1601–1618.

Chowdhury R, McDonough MA, Mecinovic J, Loenarz C, Flashman E, Hewitson KS, Domene C, Schofield CJ (2009) Structural Basis for Binding of Hypoxia-Inducible Factor to the Oxygen-Sensing Prolyl Hydroxylases Structure, 17, 981-989

Cox, K. & Sansom, M.S.P. (2009) One membrane protein, two structures and six environments: a comparative molecular dynamics simulation study of the bacterial outer membrane protein PagP. Molec. Memb. Biol. 26(4) 205-214

Csikász-Nagy A, Kapuy O, Tóth A, Pál C, Jensen LJ, Uhlmann F, Tyson JJ, Novák B. (2009): Cell cycle regulation by feed-forward loops coupling transcription and phosphorylation. Mol. Syst. Biol. 5: 236.

Daniels J-P, Kelly S, Wickstead B, Gull K (2009) Identification of a crenarchaeal orthologue of Elf1: implications for chromatin and transcription in Archaea. Biology Direct 4:24

Delalez N., Armitage J.P. (2009) Parts exchange: tuning the flagellar motor to fit the conditions. Mol Microbiol. 71(4) 807-10. Epub 2008 Dec 23.

Dobbie IM, Robson A, Delalez N, Leake MC (2009) Visualizing Single Molecular Complexes In Vivo Using Advanced Fluorescence Microscopy. J Vis Exp. 8:(31):1508. doi: 10.3791/1508.

Fenn DJ, Porter MA, McDonald M, Williams S, Johnson NF, Jones NS (2009) Dynamic communities in multichannel data Chaos, Vol. 19, No. 3: 03311

Hall, B.A. and Sansom, M.S.P. (2009) Coarse-Grained MD Simulations and Protein-Protein Interactions: The Cohesin-Dockerin System. J. Chem. Theor. Comput. 5: 2465-2471 http://pubs.acs.org/doi/abs/10.1021/ct900140w

Harding P.J., Attrill H., Boehringer J., Ross S., Wadhams G.H., Smith E., Armitage J.P., Watts A. (2009) Constitutive dimerization of the G-protein coupled receptor, neurotensin receptor 1, reconstituted into phospholipid bilayers. Biophys J. 96(3) 964-73.

Hardy, A. P., Prokes, I., Kelly, L., Campbell, I. D., Schofield, C. J. (2009) Asparaginyl beta-Hydroxylation of Proteins Containing Ankyrin Repeat Domains Influences Their Stability and Function. Journal of Molecular Biology 392(4) 994-1006

Ind, A. C., Porter, S.L., Brown, M.T., Byles, E.D., de Beyer, J., Godfrey, S.A. and Armitage, J.P. (2009) An inducible expression plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans : AEM 75(20): 6613-5

Kapuy, O., Barik, D., Sananes, M.R., Tyson, J.J. & Novák, B. (2009): Bistability by multiple phosphorylation of regulatory proteins. Prog Biophys Mol Biol. 100: 47-56.

Kapuy, O,, He, E., López-Avilés, S., Uhlmann, F., Tyson, J.J. & Novák, B. (2009): System-level feedbacks control cell cycle progression. http://www.ncbi.nlm.nih.gov/pubmed/19703449?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum FEBS Letters 583: 3992-3998.

Kelly L, McDonough MA, Coleman ML, Ratcliffe PJ. Schofield CJ. (2009) Asparagine beta-hydroxylation stabilizes the ankyrin repeat domain fold Molecular Biosystems 5, 52-58

Kelly S, Wickstead B, Gull, K. (2009) Archaeal phylogenomics provides evidence for a mesophilic origin of the Archaea and a thaumarchaeal origin for the eukaryotes. (submitted)

Klingelhoefer, J., Carpenter, T., and Sansom, M.S.P. (2009) Peptide nanopores and lipid bilayers: Interactions by coarse-grained molecular dynamics simulations. Biophys. J. (in press)

Lacomble S, Portman N, Gull K (2009) A Protein-Protein Interaction Map of the Trypanosoma brucei Paraflagellar Rod. PLoS ONE 4(11): e7685. doi:10.1371/journal.pone.0007685

Leake, M.C. (2009) Advanced fluorescence microscopy of single, living cells: using single cell proteomics to study native biochemistry one molecular at a time. Biophys. J. 96: 202a

I.M.M. van Leeuwen, G.R. Mirams, A. Walter, A. Fletcher, P. Murray, J.M. Osborne, S. Varma, S.J. Young, J. Cooper, J. Pitt--Francis, L. Momtahan, P. Pathmanathan, J.P. Whiteley, S.J. Chapman, D.J. Gavaghan, O.E. Jensen, J.R. King, P.K. Maini S.L. Waters and H.M. Byrne.(2009) An Integrative Computational Model for Intestinal Tissue Renewal. Cell Prolif. 42(5):617-36

Lewis ACF, Saeed R and Deane CM (2009) Predicting Protein-Protein Interactions in the Context of Protein Evolution Molecular BioSystems, DOI:10.1039/B916371A

Loenarz C, Mecinovic J, Chowdhury R, McNeill LA, Flashman E, Schofield CJ. (2009) Evidence for a Stereoelectronic Effect in Human Oxygen Sensing Angewandte Chemie-International Edition 48, 1784-1787

Loenarz C, Schofield CJ. (2009) Oxygenase Catalyzed 5-Methylcytosine Hydroxylation, Chemistry & Biology 16(16) 580-583

Lopez-Avilés, S., Kapuy, O., Novák, B. & Uhlmann, F. (2009): Irreversibility of mitotic exit is the consequence of systems level feedback. Nature 459: 592-595.

S. MacNamara and K. Burrage (2009): Krylov and steady-state techniques for the solution of the Chemical Master Equation for the Mitogen-activated protein kinase cascade, Numerical Algorithms, Vol. 51, Iss. 3, 281.

McGuinness, B.E., Anger, M., Kouznetsova, A., Gil-Bernabé, A.M.,Helmhart, W., Kudo, N.R., Wuensche, A., Taylor, S., Hoog, C, Novák, B. & Nasmyth, K. (2009): Regulation of APC/C activity in oocytes by a Bub1-dependent Spindle assembly checkpoint. Current Biology 19:369-380.

Mecinovic, J.; Chowdhury, R.; Flashman, E.; Schofield, C.J. (2009) Use of mass spectrometry to probe the nucleophilicity of cysteinyl residues of prolyl hydroxylase domain 2 Analytical Biochemistry 393(2) 215-221

D. Mortimer, K. Burrage, P. Dayan and G.J. Goodhill (2009): Optimizing chemotaxis by measuring unbound-bound transitions, Physica D: Nonlinear Phenomena, Vol 239, No 9, 477-484. doi:10.1016/ j.physd.2009.09.009 .

D. Mortimer, J. Feldner, T. Vaughan, I. Vetter, Z. Pujic, W.J. Rosoff, K. Burrage, P. Dayan, L.J. Richards and G.J. Goodhill (2009): A Bayesian model predicts the response of axons to molecular gradients, PNAS, June 23, Vol. 106, No. 25, 10296-10301.

P.J. Murray, C.M. Edwards, M.J. Tindall, P.K. Maini (2009) From a discrete to a continuum model of cell dynamics in one dimension. Phys Rev E 80(3 Pt 1):031912.

Nicolau D.V. Jr., Armitage, J.P. and Maini, P.K. (2009) Directional persistence and the optimality of run-and-tumble chemotaxis. Comp Biol Chem 33: 269-274

Pilizota T., Brown M.T., Leake M.C., Branch R.W., Berry R.M., Armitage J.P. (2009) A molecular brake, not a clutch, stops the Rhodobacter sphaeroides flagellar motor. Proc Natl Acad Sci USA. 106(28) 11582-7.

Plank M., Wadhams G.H. and Leake M.C. (2009) A novel millisecond time scale "slimfield" imaging technology for detecting, tracking and quantifying single fluorescent protein molecules for use in probing complex biological processes. Integr. Biol, 1(10):602-612.

Porter S.L., Brown M.T., Byles E.D., de Beyer J.A., Godfrey S.A., Armitage J.P. (2009) Inducible-expression plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans. Ind AC,  Appl Environ Microbiol. 75(20) 6613-5.

Portman N, Lacomble S, Thomas B, McKean PG, Gull K. (2009) Combining RNA interference mutants and comparative proteomics to identify protein components and dependences in a eukaryotic flagellum. J Biol Chem. Feb 27;284(9):5610-9.

Pongprayoon, P.; Beckstein, O.; Wee, C.L.; Sansom, M.S.P. (2009) Simulations of anion transport through OprP reveal the molecular basis for high affinity and selectivity for phosphate Proc Nat Acad Science USA 106(51) 21614-21618

E. Pueyo, Al. Corrias, D. Gavaghan, K. Burrage and B. Rodriguez (2009): Role of stochastic IKs gating kinetic in arrhythmogenesis, Heart Rhythm.

Gesine Reinert, David Chew, Fengzhu Sun, Michael S. Waterman, (2009), 'Alignment-Free Sequence Comparison (I): Statistics and Power' in Journal of Computational Biology, 16, 1-20

M. A. J. Roberts, E. August, A. Hamadeh, P. K. Maini, P. E. McSharry, J. P. Armitage and A. Papachristodoulou. (2009) A model invalidation-based approach for elucidating biological signalling pathways, applied to the chemotaxis pathway in R. Sphaeroides. BMC Systems Biology 3:105.

Robson, A, Tindall, M, Maini, P.K and Leake MC (2009) Developing statistical diagnostic tools for discriminating between diffusive modes of fluorescently tagged protein complexes in living cells for short duration trajectories. Biophys.J. 96 33a

Rosser, G, Delalez, N., Wadhams, GH, Armitage, JP and Leake, MC (2009) A discrete generalized model for dynamic turnover in molecular protein complexes. Biophys J 96: 325a

Satija, R, Novak, A, Miklos, I., Lyngso, R. and Hein J (2009) BigFoot: Bayesian alignment and phylogenetic footprinting for multiple sequences with MCMC. BMC Evol Biol 9: 217

Sekirnik, R.; Rose, N.R.; Thalhammer, A.; Seden, P.T.; Mecinovic, J.; Schofield, C.J. Inhibition of the histone lysine demethylase JMJD2A by ejection of structural Zn(II) (2009) Chemical Communications 42 6376-6378

Simonetta M, Manzoni R, Mosca R, Mapelli M, Massimiliano L, Vink M, Novák B, Musacchio A, Ciliberto A. (2009): The influence of catalysis on Mad2 activation dynamics. PLoS Biol. 7:e10.

Smith DMD, Onnela J-P, Jones NS (2009) Master-equation analysis of accelerating networks Phys. Rev. E 79, 056101

Staniczenko PPA, Lee CF, Jones NS (2009) Rapidly detecting disorder in rhythmic biological signals Phys. Rev. E 79, 011915

Stubbs, C.J.; Loenarz, C.; Mecinovic, J.; Yeoh, K.K.; Hindley, N.; Lienard, B.M.; Sobott, F.; Schofield, C.J.; Flashman, E. Application of a Proteolysis/Mass Spectrometry Method for Investigating the Effects of Inhibitors on Hydroxylase Structure Journal of Medicinal Chemistry 52(9) 2799-2805

Tai, K., Fowler, P., Mokrab, Y., Stansfeld, P. and Sansom, M.S.P. (2009) Molecular modelling and simulation studies of ion channel structures, dynamics and mechanisms. Invited chapter for Nano Cell Biology. (in press)

Tai, K., Haider, S., Grottesi, A. and Sansom, M.S.P. (2009) Ion channel gates: comparative analysis of energy barriers. Eur. Biophys. J. (in press) doi: 10.1007/s00249-008-0377-x

Tai, K., Stansfeld, P.J. & Sansom, M.S.P. (2009) Ion-blocking sites of the Kir2.1 channel revealed by multiscale modelling. Biochem. 48:8758-8763

Tindall M.J., Porter S.L., Wadhams G.H., Maini P.K. and Armitage J.P. (2009) Spatiotemporal modelling of CheY complexes in Escherichia coli chemotaxis. Prog. Biophys. Mol. Biol. 100(1-3):40-6.

Webby CJ, Wolf A, Gromak,N, Dreger M, Kramer H, Kessler B, Nielsen ML, Schmitz C, Butler DS,. Yates JR III,. Delahunty CM, Hahn P, Lengeling A, Mann M, Proudfoot NJ, Schofield CJ, Böttger A. (2009) Jmjd6 Catalyses Lysyl-Hydroxylation of U2AF65, a Protein Associated with RNA Splicing Science 325, 90-93.

Xue Q & Leake MC. (2009) A novel multiple particle tracking algorithm for noisy in vivo data by minimal path optimization within the spatio-temporal volume. Proc. IEEE Internat. Symp. Biomed. Imaging (ISBI): From Nano to Macro, In Press.

C.A. Yates, R. Erban, C. Escudero, I.D. Couzin, J. Buhl, I.G. Kevrekidis, P.K. Maini+, D.J.T. Sumpter. (2009) Inherent noise can facilitate coherence in collective swarm motion, PNAS, 106: 5464-5469