2011
Brown M.T., Delalez N. J., Armitage J.P. (2011) Protein dynamics and mechanisms controlling the rotational behaviour of the bacterial flagellar motor Current Opinion In Microbiology 14(6) 734-740 DOI 10.1016/j.mib.2011.09.009
Cho S-W, Kwak S, Woolley TE, Lee M-J, Kim E-J, Baker RE, Kim H-J, Shin J-S, Tickle C, Maini PK, Jung H-S (2011) Interactions between Shh, Sostdc1 and Wnt signaling and a new feedback loop for spatial patterning of the teeth. Development, 138: 1807-1816
Domingo-Sananes M.R., Kapuy O., Hunt T., Novak B. (2011) Switches and latches: a biochemical tug-of-war between the kinases and phosphatases that control mitosis. Philos Trans R Soc Lond B Biol Sci. 366 3584-3594 doi: 10.1098/rstb.2011.0087
Fletcher A.G, Mirams G.R, Murray P.J, Walter A, Kang J.-W, Cho K.H, Maini P.K, Byrne H.M (2011) Multiscale modeling of colonic crypts and early colorectal cancer. Multiscale Cancer Modeling CRC Press (eds. T.S. Deisboeck and G.S. Stamatakos) pp 111-134
Hall B.A., Armitage J.P., Sansom M.S.P. (2011) Transmembrane Helix Dynamics of Bacterial Chemoreceptors Supports a Piston Model of Signalling Plos Computational Biology 7 10 e1002204 10.1371/journal.pcbi.1002204
Hall, B.A.; Chetwynd, A.P.; Sansom, M.S.P. (2011) Exploring Peptide-Membrane Interactions with Coarse-Grained MD Simulations Biophysical Journal 100(8) 1940-1948
Hamadeh A, Roberts MA, August E, McSharry PE, Maini PK, Armitage JP, Papachristodoulou A. (2011) Feedback control architecture and the bacterial chemotaxis network PLoS Comput Biol.;7(5):e1001130.
Hamadeh A.O., August E., Roberts M.A.J., Maini P.K., Armitage J.P., Ingalls B.P., Papachristodoulou A. (2011) Feedback control architecture of the R. sphaeroides chemotaxis network. IEEE Conference on Decision and Control and European Control Conference 3014-3019
Hansen AS, Thalhammer A, El-Sagheer AH, Brown T, Schofield CJ (2011) Improved synthesis of 5-hydroxymethyl-2'-deoxycytidine phosphoramidite using a 2'-deoxyuridine to 2'-deoxycytidine conversion without temporary protecting groups. Bioorg Med Chem Lett.;21(4):1181-4.
He, E., Kapuy, O., Oliveira, R.A., Uhlmann, F., Tyson, J.J. & Novák, B. (2011): System-level feedbacks make the anaphase switch irreversible. Proc. Natl. Acad. Sci. USA. 108: 10016-10021.
Hillringhaus L., Yue W.W., Rose N.R., Ng S.S., Gileadi C., Loenarz C., Bello S.H., Bray J.E., Schofield C.J., Oppermann U. (2011) Structural and Evolutionary Basis for the Dual Substrate Selectivity of Human KDM4 Histone Demethylase Family The Journal of Biological Chemistry, 286, 41616-41625 PMID:21914792
Hunt T, Nasmyth K., Novák B. (2011) The cell cycle. Philos Trans R Soc Lond B Biol Sci. 366: 3494-3497 PubMed PMID: 22084376
Kelly S, Wickstead B, Gull K (2011) Archaeal phylogenomics provides evidence in support of a methanogenic origin of the Archaea and a thaumarchaeal origin for the eukaryotes. Proc Biol Sci;278(1708):1009-18.
Kelly, S, Wickstead, B, Maini, P.K, Gull, K. (2011) Ab initio identification of novel regulatory elements in the genome of Trypanosoma brucei by Bayesian inference on sequence segmentation PLoS ONE 6(10): e25666. doi:10.1371/journal.pone.0025666
Klingbeil G, Erban R, Giles M, Maini PK (2011) STOCHSIMGPU: Parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB. Bioinformatics.
Kojadinovic M, Sirinelli A, Wadhams GH, Armitage JP.(2011) New Motion Analysis System for Characterization of the Chemosensory Response Kinetics of Rhodobacter sphaeroides under Different Growth Conditions. Appl Environ Microbiol.;77(12):4082-8.
Korolev K.S., Xavier J.B., Nelson D.R., Foster K.R. (2011) A quantitative test of population genetics using spatio-genetic patterns in bacterial colonies, American Naturalist, 178: 538-552 DOI: 10.1086/661897
Koschwanez J., Foster K.R., Murray A.J. (2011) Sucrose utilization in budding yeast as a model for the origin of undifferentiated multicellularity. Plos Biology, Plos Biology, 9(8) e1001122.
Krasinska, L., Domingo-Sananes, M.R., Kapuy, O., Parisis, N., Harker, B., Moorhead, G., Rossignol, M., Novak, B. & Fisher, D. (2011) Protein phosphatase 2A controls the order and dynamics of cell cycle transitions. Molecular Cell 44: 437-450.
Krylova SM, Karkhanina AA, Musheev MU, Bagg EA, Schofield CJ, Krylov SN (2011) DNA aptamers as analytical tools for the quantitative analysis of DNA-dealkylating enzymes. Anal Biochem.
Krylova SM, Karkhanina AA, Musheev MU, Bagg EA, Schofield CJ, Krylov SN (2011) DNA aptamers as analytical tools for the quantitative analysis of DNA-dealkylating enzymes. Anal Biochem.
Little MA, Jones NS (2011) Generalized methods and solvers for noise removal from piecewise constant signals. I Background theory, Proceedings of the Royal Society A, 467(2135) 3088-3114
Little MA, Jones NS (2011) Generalized methods and solvers for noise removal from piecewise constant signals. II New methods, Proceedings of the Royal Society A, 467(2135) 3115-3140
Little MA, Steel BC, Bai F, Sowa Y, Bilyard T, Mueller DM, Berry RM, Jones NS (2011) Steps and bumps: precision extraction of discrete states of molecular machines using physically-based, high-throughput time series analysis. Accepted in Biophysical Journal
Liu F. and Burrage K. (2011) Novel techniques in parameter estimation for fractional dynamical models arising from biological systems, Computer and Mathematics with Application, 62, 822-833.
Loenarz C, Coleman ML, Boleininger A, Schierwater B, Holland PW, Ratcliffe PJ, Schofield CJ (2011) The hypoxia-inducible transcription factor pathway regulates oxygen sensing in the simplest animal, Trichoplax adhaerens. EMBO Rep.;12(1):63-70.
Loenarz C, Schofield CJ (2011) Physiological and biochemical aspects of hydroxylations and demethylations catalyzed by human 2-oxoglutarate oxygenases. Trends Biochem Sci.;36(1):7-18.
MacNamara S., Baker R.E., Maini P.K., (2011) Distinguishing graded & ultrasensitive signalling cascade kinetics by the shape of morphogen gradients in Drosophila, J. Theor. Biol., 285, 136-146
Martin NK, Gaffney EA, Gatenby RA, Gillies RJ, Robey IF, Maini PK (2011) A mathematical model of tumour and blood pHe regulation: The HCO(3)(-)/CO(2) buffering system. Math Biosci. 230(1):1-11.
Mitri S, Xavier J, Foster KR (2011) Social evolution in multispecies biofilms. Proceedings of the National Academy of Sciences, 108, 10839-46.
Moriya, H., Chino, A., Kapuy, O., Csikasz-Nagy, A. & Novak, B. (2011) Overexpression limits of fission yeast cell-cycle regulators in vivo and in silico. Molecular Systems Biology 7; 556; doi:10.1038/msb.2011.91
Murray P.J., Maini P.K., Baker R.E., (2011) The clockfront and wavefront model revisited, J. Theor. Biol., 283, 227-238
Murray PJ, Walter A, Fletcher AG, Edwards CM, Tindall MJ, Maini PK (2011) Comparing a discrete and continuum model of the intestinal crypt. Phys Biol.8(2):026011.
Obara B., Fricker M. , Lichius A, Read N., Gavaghan D., and Grau V. (2011) Analysis and understanding of fungal tip growth, European Conference on Mathematical and Theoretical Biology. Krakow, Poland
Perfahl H, Byrne HM, Chen T, Estrella V, Alarcon T, Lapin A, Gatenby RA, Gillies RJ, Lloyd MC, Maini PK, Reuss M, Owen MR (2011) Multiscale modelling of vascular tumour growth in 3D: the roles
of domain size and boundary conditions. PLoS ONE, 6(4), e14790 (17 pages)
Plikus MV, Baker RE, Chen C-C, Fare C, de la Cruz D, Andl T, Maini PK, Millar SE, Widelitz R, Chuong C-M (2011) Self-organizing and stochastic behaviors during the regeneration of hair stem cells. Science. 332: 586-589.
Porter SL, Wadhams GH, Armitage JP (2011) Signal processing in complex chemotaxis pathways. Nat Rev Microbiol. 2011 Mar;9(3):153-65. Epub 2011 Feb 1.
Porter SL, Wilkinson DA, Byles ED, Wadhams GH, Taylor S, Saunders NJ, Armitage JP. (2011) Genome Sequence of Rhodobacter sphaeroides strain WS8N. J Bacteriol. 193(15) 4027-4028
Rose, N.R.; McDonough, M.A.; King, O.N.F.; Kawamura, A.; Schofield, C.J. (2011) Inhibition of 2-oxoglutarate dependent oxygenases Chemical Society Reviews 40(8) 4364-4397
Rotili D, Altun M, Kawamura A, Wolf A, Fischer R, Leung IKH, Mackeen MM, Tian YM, Ratcliffe PJ, Mai A, Kessler BM, Schofield CJ, (2011) A Photoreactive Small-Molecule Probe for 2-Oxoglutarate Oxygenases; Chemistry & Biology, 18, 642-654
Rotili D, Altun M, Hamed RB, Loenarz C, Thalhammer A, Hopkinson RJ, Tian YM, Ratcliffe PJ, Mai A, Kessler BM, Schofield CJ (2011) Photoactivable peptides for identifying enzyme-substrate and protein-protein interactions. Chem Commun (Camb).;47(5):1488-90.
Schaller GE, Shiu SH, Armitage JP (2011)Two-component systems and their co-option for eukaryotic signal transduction Curr Biol.;21(9):R320-30.
Schofield JW, Gaffney EA, Gatenby RA, Maini PK (2011) Tumour angiogenesis: the gap between theory and experiments. J Theor Biol.;274(1):97-102.
Soto A.M., Sonnenschein C., Maini P.K. (2011) Systems biology and cancer [Editorial] Prog. Biophys. Mol. Bio., 106(2) 337-339 doi:10.1016/j.pbiomolbio.2011.07.009
Thalhammer A, Bencokova Z, Poole R, Loenarz C, Adam J, O'Flaherty L, Schödel J, Mole D, Giaslakiotis K, Schofield CJ, Hammond EM, Ratcliffe PJ, Pollard PJ. (2011) Human AlkB homologue 5 is a nuclear 2-oxoglutarate dependent oxygenase and a direct target of hypoxia-inducible factor 1α (HIF-1α). PLoS One ;6(1):e16210.
Thalhammer A, Hansen AS, El-Sagheer AH, Brown T, Schofield CJ (2011) Hydroxylation of methylated CpG dinucleotides reverses stabilisation of DNA duplexes by cytosine 5-methylation.. Chem Commun (Camb).
Thalhammer A, Mecinović J, Loenarz C, Tumber A, Rose NR, Heightman TD, Schofield CJ (2011) Inhibition of the histone demethylase JMJD2E by 3-substituted pyridine 2,4-dicarboxylates. Org Biomol Chem.;9(1):127-35.
Tyson JJ, Novak B (2011) Cell cycle: who turns the crank? Curr Biol ;21(5):R185-7.
Vinod PK, Freire P, Rattani A, Ciliberto A, Uhlmann F, Novak B (2011) Computational modelling of mitotic exit in budding yeast: the role of separase and Cdc14 endocycles J R Soc Interface. 8: 1128-1141 doi: 10.1098/rsif.2010.0649
Wee, C.L., Chetwynd, A.P. and Sansom M.S. (2011) Membrane insertion of a voltage sensor helix. Biophys. J. 100: 410–419.
Wheeler, R. J., Gluenz, E. and Gull, K. (2011) The cell cycle of Leishmania: morphogenetic events and their implications for parasite biology. Mol Microbiol. 79, 647-662
Wilkinson DA, Chacko SJ, Vénien-Bryan C, Wadhams GH, Armitage JP (2011) Regulation of flagella number by FliA and FlgM and the role in biofilm formation of Rhodobacter sphaeroides. J Bacteriol, 193(15), 4010-4014
Xue Q, Harriman O & Leake MC. Using bespoke fluorescence microscopy to study the soft condensed matter of living cells at the single molecule level. (2011) J. Phys: Conf Ser. 286 012001.
Yang M, Chowdhury R, Ge W, Hamed RB, McDonough MA, Claridge TD, Kessler BM, Cockman ME, Ratcliffe PJ, Schofield CJ. (2011) Factor-inhibiting hypoxia-inducible factor (FIH) catalyses the post-translational hydroxylation of histidinyl residues within ankyrin repeat domains. FEBS J. 278(7):1086-97. doi: 10.1111/j.1742-4658.2011.08022.x.
Yang M, Ge W, Chowdhury R, Claridge TD, Kramer HB, Schmierer B, McDonough MA, Gong L, Kessler BM, Ratcliffe PJ, Coleman ML, Schofield CJ (2011) Asparagine and aspartate hydroxylation of the cytoskeletal ankyrin family is catalyzed by factor-inhibiting hypoxia-inducible factor. J Biol Chem 286(9):7648-60.
Yates CA, Burrage K (2011) Look before you leap: A confidence-based method for selecting species criticality while avoiding negative populations in τ-leaping. J Chem Phys.;134(8):084109.
Zhang, T., Schmierer, B. & Novak B. (2011): Cell cycle commitment in budding yeast emerges from the cooperation of multiple bistable switches. Open Biology. 1, 110009 (doi: 10.1098/rsob.110009)