2010
Agarwal S, Deane CM, Porter MA, Jones NS (2010) Revisiting date and party hubs: novel approaches to role assignment in protein interaction networks. PLoS Comput Biol.;6(6) :e1000817.
Armitage JP, Berry RM (2010) Time for bacteria to slow down Cell, 141(1):24-6.
Bai F, Branch RW, Nicolau DV Jr, Pilizota T, Steel BC, Maini PK, Berry RM (2010) Conformational spread as a mechanism for cooperativity in the bacterial flagellar switch. Science.;327(5966):685-9.
Barik D, Baumann WT, Paul MR, Novak B, Tyson JJ (2010) A model of yeast cell-cycle regulation based on multisite phosphorylation. Mol Syst Biol;6:405.
Bell, CH, Porter, SL, Strawson, A, Stuart, DI & Armitage, JP (2010) Using structural information to change the phosphotransfer specificity of a Two-Component chemotaxis signalling complex PLoS Biology 8(2): e1000306. doi:10.1371/journal.pbio.1000306
Chetwynd, A.P., Wee, C.L., Hall, B.A., and Sansom M.S. (2010) The energetics of transmembrane helix insertion into a lipid bilayer. Biophys. J. 99 2534–2540
Cominetti O, Matzavinos A, Samarasinghe S, Kulasiri D, Liu S, Maini PK, Erban R (2010) DifFUZZY@ A fuzzy clustering algorithm for complex data sets. Int. J. of Comput. Intelligence in Bioinformatics and Systems Biology. 1(4): 402-417.
Delalez NJ, Wadhams GH, Rosser G, Xue Q, Brown MT, Dobbie IM, Berry RM, Leake MC, Armitage JP. (2010) Signal-dependent turnover of the bacterial flagellar switch protein FliM PNAS, 107(25):11347-51.
Di Garbo A, Johnston MD, Chapman SJ, Maini PK (2010) Variable renewal rate and growth properties of cell populations in colon crypts. Phys Rev E Stat Nonlin Soft Matter Phys.;81(6 Pt 1):061909.
Dissmeyer N, Weimer AK, Veylder LD, Novak B, Schnittger A. (2010) The regulatory network of cell-cycle progression is fundamentally different in plants versus yeast or metazoans. Plant Signal Behav. ;5(12)
Domingo-Sananes MR, Novak B. (2010) Different effects of redundant feedback loops on a bistable switch. Chaos.;20(4):045120.
Escudero C, Yates CA, Buhl J, Couzin ID, Erban R, Kevrekidis IG, Maini PK (2010) Ergodic directional switching in mobile insect groups. Phys Rev E Stat Nonlin Soft Matter Phys.;82(1 Pt 1):011926.
Flashman E, Davies SL, Yeoh KK, Schofield CJ (2010) Investigating the dependence of the hypoxia-inducible factor hydroxylases (factor inhibiting HIF and prolyl hydroxylase domain 2) on ascorbate and other reducing agents. Biochem J.;427(1):135-42.
Flashman E, Hoffart LM, Hamed RB, Bollinger JM Jr, Krebs C, Schofield CJ (2010) Evidence for the slow reaction of hypoxia-inducible factor prolyl hydroxylase 2 with oxygen.. FEBS J.;277(19):4089-99. doi: 10.1111/j.1742-4658.2010.07804.x..
Hahn P, Wegener I, Burrells A, Böse J, Wolf A, Erck C, Butler D, Schofield CJ, Böttger A, Lengeling A (2010) Analysis of Jmjd6 cellular localization and testing for its involvement in histone demethylation. PLoS One;5(10):e13769.
Hamer, R., Chen, P-Y, Armitage, J.P., Reinert, G. and Deane, C.M. (2010) Deciphering chemotaxis pathways using cross species comparisons BMC Sys Biol, 4:3
Hamer, R., Lui, Q., Armitage, J.P., Reinert, G. and Deane, C.M. (2010) i-Patch: Inter-Protein contact prediction using local network information. Proteins 78(13): 2781-97.
Heaton LL, López E, Maini PK, Fricker MD, Jones NS (2010) Growth-induced mass flows in fungal networks.Proc Biol Sci.;277(1698):3265-74.
Illingworth CJ, Loenarz C, Schofield CJ, Domene C (2010) Chemical basis for the selectivity of the von Hippel Lindau tumor suppressor pVHL for prolyl-hydroxylated HIF-1alpha. Biochemistry ;49(32):6936-44.
Iqbal A, Arunlanantham H, Brown T Jr, Chowdhury R, Clifton IJ, Kershaw NJ, Hewitson KS, McDonough MA, Schofield CJ. (2010) Crystallographic and mass spectrometric analyses of a tandem GNAT protein from the clavulanic acid biosynthesis pathway. Proteins;78(6):1398-407.
Johnston MD, Maini PK, Jonathan Chapman S, Edwards CM, Bodmer WF (2010) On the proportion of cancer stem cells in a tumour..J Theor Biol.;266(4):708-11.
King ON, Li XS, Sakurai M, Kawamura A, Rose NR, Ng SS, Quinn AM, Rai G, Mott BT, Beswick P, Klose RJ, Oppermann U, Jadhav A, Heightman TD, Maloney DJ, Schofield CJ, Simeonov A. (2010) Quantitative high-throughput screening identifies 8-hydroxyquinolines as cell-active histone demethylase inhibitors. PLoS One.;5(11):e15535.
Kvilekval K, Fedorov D, Obara B, Singh AK, and Manjunath BS. Bisque: A Platform for Bioimage Analysis and Management. (2010) Bioinformatics 26.4; 544–552
Leung IK, Krojer TJ, Kochan GT, Henry L, von Delft F, Claridge TD, Oppermann U, McDonough MA, Schofield CJ (2010) Structural and mechanistic studies on γ-butyrobetaine hydroxylase. Chem Biol.;17(12):1316-24.
Lewis AC, Jones NS, Porter MA, Deane CM (2010) The function of communities in protein interaction networks at multiple scales. BMC Syst Biol. 4 100.
Loenarz, C.; Ge, W.; Coleman, M.L.; Rose, N.R.; Cooper, C.D.O.; Klose, R.J.; Ratcliffe, P.J.; Schofield, C.J. PHF8, a gene associated with cleft lip/palate and mental retardation, encodes for an N(epsilon)-dimethyl lysine demethylase Human Molecular Genetics 19(2) 217-222
Mackeen MM, Kramer HB, Chang KH, Coleman ML, Hopkinson RJ, Schofield CJ, Kessler BM (2010) Small-molecule-based inhibition of histone demethylation in cells assessed by quantitative mass spectrometry. J Proteome Res. ;9(8):4082-92.
Mackenzie AK, Valegård K, Iqbal A, Caines ME, Kershaw NJ, Jensen SE, Schofield CJ, Andersson I (2010) Crystal structures of an oligopeptide-binding protein from the biosynthetic pathway of the beta-lactamase inhibitor clavulanic acid.. J Mol Biol.;396(2):332-44.
Madzvamuse A, Gaffney EA, Maini PK (2010) Stability analysis of non-autonomous reaction-diffusion systems: the effects of growing domains. J Math Biol. ;61(1):133-64.
Mantri M, Krojer T, Bagg EA, Webby CJ, Butler DS, Kochan G, Kavanagh KL, Oppermann U, McDonough MA, Schofield CJ (2010) Crystal structure of the 2-oxoglutarate- and Fe(II)-dependent lysyl hydroxylase JMJD6.. J Mol Biol.401(2):211-22.
Martin NK, Gaffney EA, Gatenby RA, Maini PK (2010) Leaky vessels as a potential source of stromal acidification in tumours..J Theor Biol;267(3):454-60.
Martin NK, Gaffney EA, Gatenby RA, Maini PK.(2010) Tumour-stromal interactions in acid-mediated invasion: a mathematical model. J Theor Biol.;267(3):461-70.
McDonough MA, Loenarz C, Chowdhury R, Clifton IJ, Schofield CJ (2010) Structural studies on human 2-oxoglutarate dependent oxygenases.. Curr Opin Struct Biol. ;20(6):659-72.
Mélykúti.B, Papachristodoulou. A, August. E and El-Samad.H. (2010) Discriminating between rival biochemical network models: three approaches to optimal experiment design. BMC Systems Biology.
Munz, M, Lyngso, R, Hein, J and Biggin, PC (2010) Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity. BMC Bioinformatics 11:188.
Murray PJ, Kang JW, Mirams GR, Shin SY, Byrne HM, Maini PK, Cho KH (2010) Modelling spatially regulated beta-catenin dynamics and invasion in intestinal crypts..Biophys J.;99(3):716-25.
Nagel S, Talbot NP, Mecinović J, Smith TG, Buchan AM, Schofield CJ (2010) Therapeutic manipulation of the HIF hydroxylases. Antioxid Redox Signal.;12(4):481-501.
Neves R, Jones NS, Andreu L, Gupta R, Enver T, Iborra F (2010) Connecting Variability in Global transcription Rate to Mitochondrial Variability. PLoS Biology 8(12) :e1000560
Novák B, Kapuy O, Domingo-Sananes MR, Tyson JJ (2010) Regulated protein kinases and phosphatases in cell cycle decisions. Curr Opin Cell Biol. ;22(6):801-8. Epub 2010 Aug 2.
Novák B, Vinod PK, Freire P, Kapuy O. (2010) Systems-level feedback in cell-cycle control. Biochem Soc Trans. 2010 Oct;38(5):1242-6. Review. Erratum in: Biochem Soc Trans.;38(6):1723.
Obara B, Veeman M, Choi JH, Smith W, and Manjunath BS. (2010) Segmentation of ascidian notochord cells in DIC timelapse images. Microscopy Research and Technique. doi: 10.1002/jemt.20950
Osborne JM, Walter A, Kershaw SK, Mirams GR, Fletcher AG, Pathmanathan P, Gavaghan D, Jensen OE, Maini PK, Byrne HM (2010) A hybrid approach to multi-scale modelling of cancer. Philos Transact A Math Phys Eng Sci;368(1930):5013-28.
Piedrahita D, Hernandez I, Lopez-Tobon A, Alzate D, LaFerla F, Davidson B, Fedorov D, Obara B, Manjunath BS, Kosik K, Gallego-Gomez JC, and Cardona-Gomez GP. (2010) Silencing of CDK5 reduces neurofibrillary tangles in transgenic Alzheimers mice. The Journal of Neuroscience 30.42;13966–13976
Pires das Neves R, Jones NS, Andreu L, Gupta R, EnverbT, Iborra FJ (2010) Connecting Variability in Global Transcription Rate to Mitochondrial Variability - PLoS Biology 8(12): e1000560.
Psachoulia E, Marshall DP, Sansom MS (2010) Molecular dynamics simulations of the dimerization of transmembrane alpha-helices.Acc Chem Res.;43(3):388-96.
Rito T, Wang Z, Deane CM, Reinert G. (2010) How threshold behaviour affects the use of subgraphs for network comparison. Bioinformatics;26(18):i611-7.
Roberts, MAJ, Papachristoudoulou, A, and Armitage, JP (2010) Adaptation and control circuits in bacterial chemotaxis. Trans Biochem Soc 38(5):1265-9
Rodriguez B, Burrage K, Gavaghan D, Grau V, Kohl P, Noble D. (2010) The systems biology approach to drug development: application to toxicity assessment of cardiac drugs. D.Clin Pharmacol Ther.;88(1):130-4.
Roodbarkelari F, Bramsiepe J, Weinl C, Marquardt S, Novák B, Jakoby MJ, Lechner E, Genschik P, Schnittger A. (2010) Cullin 4-ring finger-ligase plays a key role in the control of endoreplication cycles in Arabidopsis trichomes. Proc Natl Acad Sci U S A.;107(34):15275-80.
Rose NR, McDonough MA, King ON, Kawamura A, Schofield CJ (2010) Inhibition of 2-oxoglutarate dependent oxygenases.. Chem Soc Rev.
Rose NR, Woon EC, Kingham GL, King ON, Mecinović J, Clifton IJ, Ng SS, Talib-Hardy J, Oppermann U, McDonough MA, Schofield CJ (2010) Selective inhibitors of the JMJD2 histone demethylases: combined nondenaturing mass spectrometric screening and crystallographic approaches.. J Med Chem.;53(4):1810-8.
Ryan, RP, McCarthy, Y, Andrade, M, Farah, CS, Armitage, JP & Dow, JM (2010) Physical interactions between HD-GYP and GGDEF domain proteins mediate virulence-related signaling in Xanthomonas campestris, PNAS 107(13):5989-94.
Schmierer B, Novák B, Schofield CJ (2010) Hypoxia-dependent sequestration of an oxygen sensor by a widespread structural motif can shape the hypoxic response--a predictive kinetic model.. BMC Syst Biol.;4:139.
Scott, KA, Porter,SL, Bagg, EAL, Hamer,R, Hill, JL, Wilkinson, D and Armitage, JP (2010) Specificity of localization and phosphotransfer in the CheA proteins of Rhodobacter sphaeroides. Mol Micro 76(2):318-30
Sekirnik R, Rose NR, Mecinović J, Schofield CJ (2010) 2-Oxoglutarate oxygenases are inhibited by a range of transition metals. Metallomics;2(6):397-9.
Smallbone K, Maini PK, Gatenby RA (2010) Episodic, transient systemic acidosis delays evolution of the malignant phenotype: Possible mechanism for cancer prevention by increased physical activity..Biol Direct.;5:22.
Sourjik V, Armitage JP (2010) Spatial organization in bacterial chemotaxis. EMBO J, 29(16) 2724-33.
Stamper IJ, Owen MR, Maini PK, Byrne HM (2010) Oscillatory dynamics in a model of vascular tumour growth--implications for chemotherapy. Biol Direct.;5:27.
Staniczenko PP, Lewis O, Jones NS, Reed-Tsochas F (2010) Structural dynamics and robustness of food webs. Ecology Letters vol 13 p891+
Tindall MJ, Porter,SL, P.K. Maini, and Armitage, JP (2010) Modeling chemotaxis eveals the role of reversed phosphotransfer and a bi-functional kinase-phosphatase. PLoS Comput Biol, 6(8). pii: e1000896.
Tyson JJ, Novák B (2010) Functional motifs in biochemical reaction networks. Annu Rev Phys Chem.;61:219-40.
Vohra S, Hall BA, Holdbrook DA, Khalid S, Biggin PC (2010) Bookshelf: a simple curation system for the storage of biomolecular simulation data. Database (Oxford);2010:baq033.
Wee CL, Gavaghan D, Sansom MS (2010) Interactions between a voltage sensor and a toxin via multiscale simulations..Biophys J.;98(8):1558-65.
Wolkenhauer.O, Auffray. C, Baltrusch. S, Bluthgen. N, Byrne. H, Cascante.M , Ciliberto. A, Dale. T, Drasdo. D, Fell. D, Ferrell. J, Gallahan. D, Gatenby. R, Guenther. U, Herzel. H, Junghanss. C, Kunz. M, Laplace. F, van Leeuwen. I, Lenormand. P, Levi. F, Linnebacher. M, Lowengrub. J, Maini. P.K, Marcus. F, Malik. A, Rateitschak. K, Sansom. O, Schafer. R, Schurrle. K, Sers. C, Schnell. S, Harms. B, Shibata. D, Tyson. J, Vera. J, White. M, Zhivotovsky. B, Jaster.R. (2010) Systems biologists seek fuller integration of systems biology approaches in new cancer research programs. Cancer Research 70(1):12-3.
Woolley TE, Baker RE, Maini PK, Aragón JL, Barrio RA (2010) Analysis of stationary droplets in a generic Turing reaction-diffusion system. Phys Rev E Stat Nonlin Soft Matter Phys;82(5 Pt 1):051929.
Yates CA, Baker RE, Erban R, Maini PK (2010) Refining self-propelled particle models for collective behaviour. Canadian Applied Mathematics Quarterly 18: 299-349.
Yue WW, Hozjan V, Ge W, Loenarz C, Cooper CD, Schofield CJ, Kavanagh KL, Oppermann U, McDonough MA. (2010) Crystal structure of the PHF8 Jumonji domain, an Nepsilon-methyl lysine demethylase. FEBS Lett.;584(4):825-30.
Zhai ZY, Ku SY, Luan YH, Reinert G, Waterman MS, Sun FZ (2010) The Power of Detecting Enriched Patterns: An HMM Approach. Journal of Computational Biology, in press.