CoMPLEX Publications

In this section you can find the publications of current CoMPLEX students by intake year.

2004 intake

Tak C Fung

Seymour, R. M., G. Knight and T. Fung. 2010. Conditions for global dynamic stability of a class of resource-bounded model ecosystems. Bulletin of Mathematical Biology 72: 1971-2003.

Fung, T., R. M. Seymour and C. R. Johnson. 2011. Alternative stable states and phase shifts in coral reefs under anthropogenic stress. Ecology 92: 967-982.

Melbourne-Thomas, J., C. R. Johnson, T. Fung, R. M. Seymour, L. M. Chérubin, J. E. Arias-González and E. A. Fulton. 2011. Regional-scale scenario modeling for coral reefs: a decision support tool to inform management of a complex system. Ecological Applications 21: 1380-1398.

Fung, T., R. M. Seymour and C. R. Johnson. 2013. Warning signals of regime shifts as intrinsic properties of endogenous dynamics. The American Naturalist 182: 208-222.

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2005 intake

Nuno Rocha Nene

Nene, N.R.,Zaikin, A. Decision making in noisy bistable systems with time-dependent asymmetry. (PRE, in press)

Nene, N. R., Zaikin, A. (2012) Interplay between path and speed in decision making by high-dimensional stochastic gene regulatory networks. PLoS ONE 7(7): e40085.

E. Ullner, S. Ares, L.G. Morelli, A.C. Oates, F. Julicher, E. Nicola , R. Heussen, D. Whitmore, K. Blyuss, M. Fryett, A. Zakharova, A. Koseska, N.R. Nene, and A. Zaikin. (2012) Noise and oscillations in biological systems: multidisciplinary approach between experimental biology, theoretical modelling and synthetic biology. Int. J. Mod. Phys. B 26, 1246009 (2012).

Nene, N.R., Garca-Ojalvo, J., Zaikin, A. (2012) Speed-Dependent Cellular Decision         Making in Nonequilibrium Genetic Circuits. PLoS ONE 7(3): e32779.

N.R. Nene, A. Zaikin. Gene regulatory network attractor selection and cell fate decision: insights into cancer multi-targeting. Proceedings of the BIOSIGNAL 2010 conference. 14th – 16th July 2010 Berlin, Germany.

Samantha Lee

Caldwell M, Del Linz SJ, Smart TG, Moss GW.   (2nd Author).  (2012) Method for estimating the tip geometry of scanning ion conductance microscope pipets.

Anal Chem. 2012 Nov 6;84(21):8980-4. doi: 10.1021/ac301851n. Epub 2012 Oct 19.

Andrew Rider Rider AT, McOwan PW, Johnston A. (2009) Motion-induced position shifts in global dynamic Gabor arrays.
J Vis. 2009 Dec 8;9(13):8.1-8. doi: 10.1167/9.13.8.
David Wright

S. K. Sadiq, D. W. Wright, O. A. Kenway, P. V. Coveney, (2010). Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases. Journal of Chemical Information and Modeling, 50, 890-905, (2010).

R. S. Saksena, B. Boghosian, L. Fazendeiro, O. A. Kenway, S. Manos, M. D. Mazzeo, S. K. Sadiq, J. L. Suter, D. Wright, and P. V. Coveney, (2009). Real Science at the Petascale. Philosophical Transactions of the Royal Society A, 367, (1897), 2557-2571, (2009).

S. K. Sadiq, D. Wright, S. J. Watson, S. J. Zasada, I. Stoica, Ileana, and P. V. Coveney. (2008). Automated Molecular Simulation-Based Binding Affinity Calculator for Ligand-Bound HIV-1 Proteases.  Journal of Chemical Information and Modeling, 48, (9), 1909-1919, (2008)

Lisa Willis

Willis, L., Alarcon, T., Elia, G., Jones, L.J., Wright, N., Tomlinson, I.M.P., Graham, T.A., & Page, K.M. (2010) Breast cancer dormancy can be maintained by small numbers of micrometastases.  Cancer Research 70(11).

Willis, L., Page, K.M., Broomhead, D.S. & Cox, E.J. (2010) Discrete free-boundary reaction-diffusion model of diatom pore occlusions. Plant Ecology and Evolution 143(3): 297--306.

Pollard, P., Deheragoda, M., Segditsas, S., Lewis, A., Rowan, A., Howarth, K., Willis, L., Nye, E., McCart, A., Mandir, N., Silver, A., Goodlad, R., Stamp, G., Cockman, M., East, P., Spencer-Dene, B., Poulsom, R., Wright, N., Tomlinson, I.M.P. (2009) The APC1322T mouse develops severe polyposis associated with submaximal nuclear beta-catenin expression. Gastroenterology 136(7): 2204--2213.

Justin Chumbley

Chumbley J, Worsley K, Flandin G, Friston K.  (2010)

Topological FDR for neuroimaging. Neuroimage. 2010 Feb 15;49(4):3057-64. doi: 10.1016/j.neuroimage.2009.10.090. Epub 2009 Nov 24.

Chumbley JR, Friston KJ. (2009) False discovery rate revisited: FDR and topological inference using Gaussian random fields. Neuroimage. 2009 Jan 1;44(1):62-70. doi: 10.1016/j.neuroimage.2008.05.021. Epub 2008 May 23.

Chumbley JR, Dolan R, Friston KJ (2008) Attractor models of working memory and their modulation by reward. Biological Cybernetics 98(1): 11-18.

Chumbley JR, Friston KJ, Fearn T, Kiebel S (2007) A rejection metropolis hastings alorigthm for bayesian inference on dynamic causal models. Neuroimage 38: 478–487.

Thomas Sumner Bogle, I.D.L., Allen, R., Sumner, T. (2010) The role of computer aided process engineering in physiology and clinical medicine. Computers and Chemical Engineering, 34(5), 763-769.
Alexander Stewart A. J. Stewart, R. M. Seymour, and A. Pomiankowski. (2009) Degree dependence in rates of transcrip- tion factor evolution explains the unusual structure of transcription networks. Proceedings of the Royal Society B: Biological Sciences, 276(1666):2493–2501, 2009. 10.1098/rspb.2009.0210 AJ. Stewart, T. L. Parsons and J. B. Plotkin. (2012) Environmental robustness and the adaptability of populations. Evolution. 2012 May;66(5):1598-612. Stewart AJ, Seymour RM, Pomiankowski A, Reuter M. (2013) Under-dominance constrains the evolution of negative autoregulation in diploids. PLoS Comput Biol. 2013 Mar;9(3):e1002992.
Michael Cohen

Cohen, M., Baum, B and M. Miodownik, M. (2010) The importance of structured noise in the generation of self-organising tissue patterns through contact-mediated cell-cell signaling. Journal of the Royal Society Interface, Published Online, Nov 17. 

Cohen, M. and Georgiou M., Stevenson, N.L., Miodownik, M. and Baum, B. (2010). Dynamic filopodia transmit intermittent Delta-Notch signaling to drive pattern refinement during lateral inhibition. Developmental Cell, vol. 19, pp. 78-89.  

Cohen, M., Miodownik, M. and Baum, B. (2008). Measuring the robustness of a developmental system based on sequential growth rules. Artificial Life XI: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems, pp. 118-125

Irenjeet Bains

I. Bains, R. Thiebaut, A.J. Yates, and R. Callard. Oct 2009. Quantifying thymic export: combining models of naive T cell proliferation and TCR excision circle dynamics gives an explicit measure of thymic output. J Immunol 183: 4329–36.

I. Bains, R. Antia, R. Callard, and A.J. Yates. May 2009. Quantifying the development of the peripheral naive CD4+ T-cell pool in humans. Blood 113:5480–5487.

Remigio Picone

Picone Remigio, Ren X, Clarke J D W, McKendry R. A, Baum B. (2010). A Polarised Population of Dynamic Microtubules Mediates Homeostatic Length Control in Animal Cells. Plos Biology 8: e1000542.

Tao Liu, Jennifer L. Rohn, Remigio Picone, Patricia Kunda, and Buzz Baum (2010). Tao-1 is a negative regulator of microtubule plus-end growth. J Cell Sci 123: 2708-2716.

Picone Remigio, Ren X, Clarke J D W, McKendry R. BioPatterning. (June 2012)

Encyclopedia of Nanotechnology, 1st Edition, Springer-Verlag, ISBN: 978-90-481-9752-1

Lancaster OM, Le Berre M, Dimitracopoulos A, Bonazzi D, Zlotek-Zlotkiewicz E, Picone R, Duke T, Piel M, Baum B. (2013) Mitotic rounding alters cell geometry to ensure efficient bipolar spindle formation. Dev Cell. 2013 May 13;25(3):270-83. 

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2006 intake

Matthew Caldwell

Nanoscale live-cell imaging using hopping probe ion conductance microscopy Novak et al, Nature Methods 2009, Apr; 6(4):279-81

Caldwell M, Del Linz SJ, Smart TG, Moss GW (2012)

Method for estimating the tip geometry of scanning ion conductance microscope pipets. Anal Chem. 2012 Nov 6;84(21)

Yoana Dimitrova Dimitrova YD, McOwan P, Johnston A, 2010, Lightness estimation errors in a 3D context. J Vis August 2, 2010 10(7): 453; doi:10.1167/10.7.453.

Gleeson P, Crook S, Cannon RC, Hines ML, Billings GO, Farinella M, Morse TM, Davison AP, Ray S, Bhalla US, Barnes SR, Dimitrova YD, R. Angus Silver A, 2010, “NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail”, PLoS Comput Biol 6(6): e1000815.
Ben Hall Ben Hall, Alan Johnston and John Shawe-Taylor, NIPS Workshop Paper, 2007, kCCA Audio Visual Speech Recognition.
Ed Long E. Long, B. Henderson and A. Zaikin. In silico analysis of microdomain-mediated trimer formation in the T cell membrane. From the issue entitled "The Dynamics of Nonlinear Stochastic Systems”
James Muir Muir J, Arancibia-Carcamo IL, MacAskill AF, Smith KR, Griffin LD, Kittler JT.NMDA receptors regulate GABAA receptor lateral mobility and clustering at inhibitory synapses through serine 327 on the γ2 subunit. Proc Natl Acad Sci U S A. 2010 Sep 21;107(38):16679-84. Epub 2010 Sep 7.

Arancibia-Cárcamo IL, Yuen EY, Muir J, Lumb MJ, Michels G, Saliba RS, Smart TG, Yan Z, Kittler JT, Moss SJ.Ubiquitin-dependent lysosomal targeting of GABA(A) receptors regulates neuronal inhibition. Proc Natl Acad Sci U S A. 2009 Oct 13;106(41):17552-7. Epub 2009 Oct 6.

Macaskill AF, Rinholm JE, Twelvetrees AE, Arancibia-Carcamo IL, Muir J, Fransson A, Aspenstrom P, Attwell D, Kittler JT. Miro1 is a calcium sensor for glutamate receptor-dependent localization of mitochondria at synapses. Neuron. 2009 Feb 26;61(4):541-55.
Andy Newell

A.J. Newell, L. D. Griffin, R. M. Morgan, and P. A. Bull, “Texture-based estimation of physical characteristics of sand grains,” in Proceedings of the International Conference on Digital Image Computing: Techniques and Applications Sydney, pp. 504–509, 2010.

Newell, A. J., Morgan, R. M., Griffin, L. D., Bull, P. A., Marshall, J.R. and Graham, G. Automated texture recognition of quartz sand grains for forensic applications Journal of Forensic Sciences

A. J. Newell. What should we be comparing for writer identification? To appear in Proceedings of the International Conference on Document Analysis and Recognition (ICDAR), 2013

L. D. Griffin, H. M. Wahab & A. J. Newell. Distributional learning of appearance. PLOS One 2013 8(2):e58074 (2013)

A. J. Newell and L.D. Griffin. Natural image character recognition using oriented Basic Image Features. In Proceedings of the International Conference on Digital Image Computing: Techniques and Applications (DICTA) 2011 p. 191-196

A. D. F. Clarke, F. Halley, A. J. Newell, L. D. Griffin, and M. J. Chantler. (2011) Perceptual similarity: A texture challenge. In Proceedings of the British Machine Vision Conference (BMVC) 2011 p. 52-58

A. J. Newell and L.D. Griffin. (2011) Multiscale histogram of oriented gradient descriptors for robust character recognition. In Proceedings of the International Conference on Document Analysis and Recognition (ICDAR), 2011 p. 1085-1089

Sam Tazzyman S.J. Tazzyman, T. Pizzari, R.M. Seymour and A. Pomiankowski, "The Evolution of Continuous Variation in Ejaculate Expenditure Strategy"; American Naturalist 174(2009), E71-E82.

S.J. Tazzyman and Y. Iwasa, "Sexual selection can increase the effect of random genetic drift - a quantitative genetic model of polymorphism in Oophaga pumilio, the strawberry poison-dart frog"; Evolution 64(2010), 1719-1728

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2007 intake

Maqsood Ahmed

M. Ahmed, G. Hamilton and A. Seifalian “Viscoelastic behaviour of a small calibre vascular graft made from a POSS-nanocomposite” Conf Proc IEEE Eng Med Biol Soc, 2010, pp 251-254.

M. Desai, M. Ahmed, Z. You, G. Hamilton, A. Seifalian, “An aortic model for the physiological assessment of endovascular stent-grafts”, Annals of Vascular Surgery, in press. Paper: M. Ahmed, L. Yildrimer, A. Khademhosseini, A. Seifalian., Nanostructured Materials for Cardiovascular Tissue Engineering., Journal of Nanoscience and Nanotechnology, accepted for publication – in press.

M. Ahmed and A. Seifalian, “Organs from Nanomaterials” in Handbook of Nanophysics: Nanomedicine and Nanorobotics, CRC Press, 2010, Chapter 19

M. Ahmed, L. Yildrimer, A. Khademhosseini, A. Seifalian., J Nanosci Nanotechnol.

Nanostructured materials for cardiovascular tissue engineering. 2012 Jun;12(6):4775-85.

Arturo Araujo Araujo, A., Bentley, P. J. and Baum, B. (2010) Modelling the Role of Aneuploidy in Tumour Evolution. In Proc of 12th International Conference on the Synthesis and Simulation of Living Systems. Odense, Denmark, 19-23 August 2010. MIT Press.

Araujo, A., Bentley, P. J. and Baum, B. (2010) Modelling the Role of Chromosome Missegregation in Cancer Therapies. Extended Abstract in 3rd Complex Systems Modelling and Simulation Workshop, 12th International Conference on the Synthesis and Simulation of Living Systems.
Victoria Harris Victoria Harris, Martin Edwards and Sofia C.Olhede; Multidecadal Atlantic Climate Variability and it's Impact on Marine Pelagic Communities. TBA, 2013 (in revision).
Gwenan Knight

Seymour RM, Knight G, Fung T. Bull Math Biol. 2010 Nov;72(8):1971-2003. Epub 2010 Mar 3. Conditions for global dynamic stability of a class of resource-bounded model ecosystems.

Knight GM, Budd EL, Lindsay JA. (2013) Large mobile genetic elements carrying resistance genes that do not confer a fitness burden in healthcare-associated methicillin-resistant Staphylococcus aureus (HA-MRSA). Microbiology. 2013 May 31.

Garnett JP, Baker EH, Naik S, Lindsay JA, Knight GM, Gill S, Tregoning JS, Baines DL. (2013)Metformin reduces airway glucose permeability and hyperglycaemia-induced Staphylococcus aureus load independently of effects on blood glucose.

Thorax. 2013 May 24. doi: 10.1136 Lindsay JA, Knight GM, Budd EL, McCarthy AJ. (2012)

Shuffling of mobile genetic elements (MGEs) in successful healthcare-associated MRSA (HA-MRSA). Mob Genet Elements. 2012 Sep 1;2(5):239-243.

Knight GM, Budd EL, Whitney L, Thornley A, Al-Ghusein H, Planche T, Lindsay JA. (2012) Shift in dominant hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA) clones over time, Journal of Antimicrobial Chemotherapy Vol.67 Iss 10 (

Julia Krupic

Krupic J, Burgess N, O'Keefe J. (2012) Neural representations of location composed of spatially periodic bands. Science. 2012 Aug 17;337(6096):853-7.

Schultz SR, Kitamura K, Post-Uiterweer A, Krupic J, Häusser M. (2009) Spatial pattern coding of sensory information by climbing fiber-evoked calcium signals in networks of neighboring cerebellar Purkinje cells. J Neurosci. 2009 Jun 24;29(25):8005-15.

Kevin Lau Lau, K. D.; Diaz, V.; Scambler, P. & Burriesci, G. Mitral valve dynamics in structural and fluid-structure interaction models. Med Eng Phys, 2010, 32, 1057-1064
Lorette Noiret

Wright, G., Noiret, L., Olde Damink, S. W. M. and Jalan, R. (2011), Interorgan ammonia metabolism in liver failure: the basis of current and future therapies. Liver International, 31: 163–175. doi: 10.1111/j.1478-3231.2010.02302.x

Jover-Cobos M, Noiret L, Sharifi Y, Jalan R. (2013) Ornithine phenylacetate revisited. Metab Brain Dis. 2013 Jun;28(2):327-31.

Johannes Riegler

J. Riegler, J. A. Wells, P. G. Kyrtatos, A. N. Price, Q. A. Pankhurst and M. F. Lythgoe, "Targeted magnetic delivery and tracking of cells using a magnetic resonance imaging system," Biomaterials 31, 5366-5371 (2010).

J. Riegler, B. Allain, R. J. Cook, M. F. Lythgoe and Q. A. Pankhurst, "Magnetically assisted delivery of cells using a magnetic resonance imaging system," Journal of Physics D: Applied Physics 44, 055001-055011 (2011).

J. Riegler, K. K. Cheung, Y. F. Man, J. O. Cleary, A. N. Price and M. F. Lythgoe, "Comparison of segmentation methods for MRI measurement of cardiac function in rats," Journal of Magnetic Resonance Imaging 32, 869-877 (2010). S. Bollini, M. Pozzobon, M. Nobles,

J. Riegler, X. Dong, M. Piccoli, A. Chiavegato, A. Price, M. Ghionzoli, K. Cheung, A. Cabrelle, P. O. Mahoney, E. Cozzi, S. Sartore, A. Tinker, M. Lythgoe and P. De Coppi, "In Vitro and In Vivo Cardiomyogenic Differentiation of Amniotic Fluid Stem Cells," Stem Cell Reviews and Reports 1-17 (2010).

A. N. Price, K. K. Cheung, J. O. Cleary, A. E. Campbell, J. Riegler and M. F. Lythgoe, "Cardiovascular Magnetic Resonance Imaging in Experimental Models," The Open Cardiovascular Medicine Journal 278-292 (2010).

Evans MA, Smart N, Dubé KN, Bollini S, Clark JE, Evans HG, Taams LS, Richardson R, Lévesque M, Martin P, Mills K, Riegler J, Price AN, Lythgoe MF, Riley PR. (2013) Thymosin β4-sulfoxide attenuates inflammatory cell infiltration and promotes cardiac wound healing. Nat Commun. 2013 Jul 2;4:2081.

Watkins-Chow DE, Cooke J, Pidsley R, Edwards A, Slotkin R, Leeds KE, Mullen R, Baxter LL, Campbell TG, Salzer MC, Biondini L, Gibney G, Phan Dinh Tuy F, Chelly J, Morris HD, Riegler J, Lythgoe MF, Arkell RM, Loreni F, Flint J, Pavan WJ, Keays DA. (2013)

Mutation of the diamond-blackfan anemia gene Rps7 in mouse results in morphological and neuroanatomical phenotypes. PLoS Genet. 2013;9(1):e1003094.

Riegler J, Liew A, Hynes SO, Ortega D, O'Brien T, Day RM, Richards T, Sharif F, Pankhurst QA, Lythgoe MF. (2013)

Superparamagnetic iron oxide nanoparticle targeting of MSCs in vascular injury. Biomaterials. 2013 Mar;34(8):1987-94.

Smart N, Bollini S, Dubé KN, Vieira JM, Zhou B, Riegler J, Price AN, Lythgoe MF, Davidson S, Yellon D, Pu WT, Riley PR (2012) Myocardial regeneration: expanding the repertoire of thymosin β4 in the ischemic heart. Ann N Y Acad Sci. 2012 Oct;1269:92-101.

Treiber CD, Salzer MC, Riegler J, Edelman N, Sugar C, Breuss M, Pichler P, Cadiou H, Saunders M, Lythgoe M, Shaw J, Keays DA. (2012)

Clusters of iron-rich cells in the upper beak of pigeons are macrophages not magnetosensitive neurons. Nature. 2012 Apr 11;484(7394):367-70.

Totonelli G, Maghsoudlou P, Garriboli M, Riegler J, Orlando G, Burns AJ, Sebire NJ, Smith VV, Fishman JM, Ghionzoli M, Turmaine M, Birchall MA, Atala A, Soker S, Lythgoe MF, Seifalian A, Pierro A, Eaton S, De Coppi P. (2012)

A rat decellularized small bowel scaffold that preserves villus-crypt architecture for intestinal regeneration. Biomaterials. 2012 Apr;33(12):3401-10.

Duffy BA, Choy M, Riegler J, Wells JA, Anthony DC, Scott RC, Lythgoe MF. (2012)

Imaging seizure-induced inflammation using an antibody targeted iron oxide contrast agent. Neuroimage. 2012 Apr 2;60(2):1149-55. doi: 10.1016/j.neuroimage.2012.01.048.

Riegler J, Lau KD, Garcia-Prieto A, Price AN, Richards T, Pankhurst QA, Lythgoe MF. (2011)

Magnetic cell delivery for peripheral arterial disease: A theoretical framework. Med Phys. 2011 Jul;38(7):3932-43.

Smart N, Bollini S, Dubé KN, Vieira JM, Zhou B, Davidson S, Yellon D, Riegler J, Price AN, Lythgoe MF, Pu WT, Riley PR (2011) De novo cardiomyocytes from within the activated adult heart after injury. Nature. 2011 Jun 8;474(7353):640-4.

Bollini S, Cheung KK, Riegler J, Dong X, Smart N, Ghionzoli M, Loukogeorgakis SP, Maghsoudlou P, Dubé KN, Riley PR, Lythgoe MF, De Coppi P. (2011)

Amniotic fluid stem cells are cardioprotective following acute myocardial infarction. Stem Cells Dev. 2011 Nov;20(11):1985-94.

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2008 intake

Tom Blacker

Nicolaou, N., Marsh, R. J., Blacker, T., Armoogum, D. A., Bain, A. J.; Time-resolved fluorescence and FCS studies of dye-doped DNA, Nanophotonic Materials VI, SPIE 7393, 2009.

Blacker, T.S., Marsh, R.J., Duchen, M.R., and Bain, A.J. (2013). Activated barrier crossing dynamics in the non-radiative decay of NADH and NADPH. Chemical Physics:

Anton Flügge Flügge, Anton J., Sofia C. Olhede, and David J. Murrell. 2012. The memory of spatial patterns: changes in local abundance and aggregation in a tropical forest. Ecology 93:1540–1549.
Jack Honeysett

Honeysett J. E., Stride E. & Leung T. Feasibility study of non-invasive oxygenation measurement in a deep blood vessel using acousto-optics and microbubbles. Advances in Experimental Medicine and Biology (in press).

Honeysett J., Stride E. & Leung T. Monte Carlo simulations of acousto-optics with microbubbles. Proceedings of SPIE 7564, 75640K(2010)

Leung TS, Honeysett JE, Stride E, Deng J. (2013) Light propagation in a turbid medium with insonified microbubbles. J Biomed Opt. 2013 Jan;18(1):15002

Caroline Hartley

C. Hartley, L. Berthouze, S.R.Mathieson, G.B.Boylan, J.M.Rennie, N. Marlow and S.F.Farmer. (2012) Long-range temporal correlations in the EEG bursts of human preterm babies. (2012) PLoS One. 7(2): e31543.

T.J.Taylor, C. Hartley, P.L. Simon, I.Z. Kiss and L. Berthouze . (2013) Identification of criticality in neuronal avalanches: I. A theoretical investigation of the non-driven case. The Journal of Mathematical Neuroscience 2013

C. Hartley, T.J. Taylor, I.Z. Kiss, S.F. Farmer and L. Berthouze. (2013) Identification of criticality in neuronal avalanches: II. A theoretical and empirical investigation of the driven case. The Journal of Mathematical Neuroscience 2013

C. Hartley, S.F. Farmer and L. Berthouze (2013) Long-range temporal correlations leads to small-world connectivity in an activity-dependent neuronal network. The Journal of Mathematical Neuroscience 2013

Joanna Lewis

Lewis J, Walker AS, Castro H, De Rossi A, Gibb DM, Giaquinto C, Klein N, Callard R. (2012) Age and CD4 count at initiation of antiretroviral therapy in HIV-infected children: effects on long-term T-cell reconstitution. J Infect Dis. 2012 Feb 15;205(4):548-56.

Lewis J, Walker AS, Klein N, Callard R.  (2012) CD31+ cell percentage correlation with speed of CD4+ T-cell count recovery in HIV-infected adults is reversed in children: higher thymic output may be responsible. Clin Infect Dis. 2012 Jul;55(2):304-7; author reply 307.

Tracy Moroz

Kolyva C, Tachtsidis I, Ghosh A, Moroz T, Cooper CE, Smith M, Elwell CE. (2012)

Systematic investigation of changes in oxidized cerebral cytochrome c oxidase concentration during frontal lobe activation in healthy adults.

Biomed Opt Express. 2012 Oct 1;3(10):2550-66. doi: 10.1364/BOE.3.002550. Epub 2012 Sep 14.

Rong Z, Banaji M, Moroz T, Cooper CE. (2013) Can mitochondrial cytochrome oxidase mediate hypoxic vasodilation via nitric oxide metabolism? Adv Exp Med Biol. 2013;765:231-8.

Moroz T, Banaji M, Robertson NJ, Cooper CE, Tachtsidis I. (2012)

Computational modelling of the piglet brain to simulate near-infrared spectroscopy and magnetic resonance spectroscopy data collected during oxygen deprivation.

J R Soc Interface. 2012 Jul 7;9(72):1499-509.

Tracy Moroz, Murad Banaji, Martin Tisdall, Chirs E. Cooper, Clare E. Elwell, and Ilias Tachtsidis. Development of a model to aid NIRS data interpretation: Results from a hypercapnia study in healthy adults. Advances in Experimental Medicine and Biology series. (accepted for publication January 2011)

Fran Norris

Cleary JO, Wiseman FK, Norris FC, Price AN, Choy M, Tybulewicz VL, Ordidge RJ, Brandner S, Fisher EM, Lythgoe MF. Structural correlates of active-staining following magnetic resonance microscopy in the mouse brain. 2011 Jun 1;56(3):974-83. Epub 2011 Feb 16.

Cleary JO, Modat M, Norris FC, Price AN, Jayakody SA, Martinez-Barbera JP, Greene ND, Hawkes DJ, Ordidge RJ, Scambler PJ, Ourselin S, Lythgoe MF. Magnetic resonance virtual histology for embryos: 3D atlases for automated high-throughput phenotyping. 2011 Jan 15;54(2):769-78. Epub 2010 Jul 23.

Martin O’Reily O’Reilly, M.; Roth, A.; Häusser, M. & Griffin, L.D. (2011). A circle-based method for detection of neural fibre cross-sections in classically stained 2D electron micrographs. Sixth international workshop on Microscopic Image Analysis with Applications in Biology (MIAAB), Heidelberg (accepted for oral presentation).
Mae Woods Carmona-Fontaine C, Theveneau E, Tzekou A, Tada M, Woods M, Page KM, Parsons M, Lambris JD, Mayor R. (2011) Complement fragment C3a controls mutual cell attraction during collective cell migration. Dev Cell. 2011 Dec 13;21(6):1026-37. 

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2009 intake

Joe Bailey
Leung G, Knott P, Bailey J, Kendon V. Coined quantum walks on percolation graphs. New Journal of Physics. 2010;12(12):123018. December 20, 2010.
Zena Hadjivasiliou Hadjivasiliou Z, Pomiankowski A, Seymour RM, Lane N. (2012) Selection for mitonuclear co-adaptation could favour the evolution of two sexes. Proc Biol Sci. 2012 May 7;279(1734):1865-72. 
Nicolas Jaccard

Nicolas Szita, Karen Polizzi, Nicolas Jaccard and Frank Baganz. Microfluidic approaches for systems and synthetic biology. Current Opinion in Biotechnology, Volume 21, Issue 4, August 2010, Pages 517-523

Reichen M, Macown RJ, Jaccard N, Super A, Ruban L, Griffin LD, Veraitch FS, Szita N. Microfabricated modular scale-down device for regenerative medicine process development. PLoS One. 2012;7(12):e52246.

Mirna Kovacevic  Bains RK, Kovacevic M, Plaster CA, Tarekegn A, Bekele E, Bradman NN, Thomas MG. Molecular diversity and population structure at the Cytochrome P450 3A5 gene in Africa.  BMC Genetics 14:34. 
Donal O’Donoghue O'Donoghue DL, Dua V, Moss GW, Vergani P. (2013) Increased apical Na+ permeability in cystic fibrosis is supported by a quantitative model of epithelial ion transport.  J Physiol. 2013 Jul 8.
Niclas Thomas

Thomas N, Heather J, Ndifon W, Shawe-Taylor J, Chain B. (2013) Decombinator: a tool for fast, efficient gene assignment in T-cell receptor sequences using a finite state machine. Bioinformatics. 2013 Mar 1;29(5):542-50.

Niclas Thomas, Lenka Matejovicova, Wichat Srikusalanukul, John Shawe-Taylor, Benny Chain (2012)

Directional Migration of Recirculating Lymphocytes through Lymph Nodes via Random Walks.  PLoS One. 2012;7(9):e45262.

James West

West, J., Lacasa, L., Severini, S. & Teschendorff. (2012) Approximate entropy of network parameters. Phys. Rev. E 85, 046111 (2012)

West J, Bianconi G, Severini S, Teschendorff AE. (2012) Differential network entropy reveals cancer system hallmarks. Sci Rep. 2012;2:802.

Matthias Lechner, Tim Fenton, James West, Gareth Wilson, Andrew Feber, Stephen Henderson, Christina Thirlwell,Harpreet K Dibra, Amrita Jay, Lee Butcher, Ankur R Chakravarthy, Fiona Gratrix, Nirali Patel, Francis Vaz, Paul O'Flynn, Nicholas Kalavrezos, Andrew E Teschendorff, Chris Boshoff and Stephan Beck. (2013) Identification and functional validation of HPV-mediated hypermethylation in head and neck squamous cell carcinoma. Genome Medicine 2013, 5:15

West, J., Beck, S., Wang, X. & Teschendorff, A.E. An integrative network algorithm identifies age-associated differential methylation interactome hotspots targeting stem-cell differentiation pathways. Sci. Rep. 3, 1630; 

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2010 intake

Thomas Bartlett

Bartlett, T. E., Olhede, S. C., & Zaikin, A. (2014). A DNA Methylation Network Interaction Measure, and Detection of Network Oncomarkers. PLOS ONE9(1), e84573. (link)

Bartlett, T. E., Zaikin, A., Olhede, S. C., West, J., Teschendorff, A. E., & Widschwendter, M. (2013). Corruption of the intra-gene DNA methylation architecture is a hallmark of cancer. PloS one8(7), e68285. (link)

Siân Culley R. Marsh, S. Culley, and A. Bain. Low power super resolution fluorescence microscopy by lifetime modification and image reconstruction. Opt. Express 22, 12327-12338 (2014). 
Michael Epstein Plagnol V, Curtis J, Epstein M, Mok KY, Stebbings E, Grigoriadou S, Wood NW, Hambleton S, Burns SO,Thrasher AJ, Kumararatne D, Doffinger R, Nejentsev S. (2012). A robust model for read count data in exome sequencing experiments and implications for copy number variant calling. Bioinformatics 28(21): 2747-54.
Manos Protonotarios
Protonotarios ED, Baum B, Johnston A, Hunter GL, Griffin LD. (2014). An absolute interval scale of order for point patterns. J R Soc Interface 11(99): 2014034.(link)
Thomas Roberts Roberts T, Griffin H, McOwan P W, Johnston A. (2011). Judging political affiliation from faces of UK MPs. Perception 40(8) 949 – 952.
Rob Stanley Chalabi, Z., Ferguson, E., Stanley, R., & Briend, A. (2014). A probabilistic model to evaluate population dietary recommendations. British Journal of Nutrition, 1-8. (link)
Bartlomiej (Bartek) Tomickzek Laussmann MA, Passante E, Hellwig CT, Tomiczek B, Flanagan L, Prehn JH, Huber HJ, Rehm M. (2012) Proteasome inhibition can impair caspase-8 activation upon submaximal stimulation of apoptotic tumor necrosis factor-related apoptosis inducing ligand (TRAIL) signaling. J Biol Chem. 287(18)

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2011 intake

Chris Barnerji

Banerji CRS, Mansour T, Severini S. (2014). A notion of graph likelihood and an infinite monkey theorem. Journal of Physics A: Mathematical and Theoretical47(3): 035101. (link)

Banerji CRS, Severini S, Teschendorff AE. (2013). Network transfer entropy and metric space for causality inference. Physical Review E87(5): 052814. (link)

Banerji CRS, Miranda-Saavedra D, Severini S, Widschwendter M, Enver T, Zhou JX, Teschendorff AE. (2013). Cellular network entropy as the energy potential in Waddington's differentiation landscape. Scientific reports3. (link)

Nargess Khalilgharibi Harris AR, Bellis J, Khalilgharibi N, Wyatt T, Baum B, Kabla AJ, Charras GT. (2013). Generating suspended cell monolayers for mechanobiological studies. Nature protocols8(12): 2516-2530. (link)
Víctor Sojo Sojo V, Pomiankowski A, Lane N. (2014). A Bioenergetic Basis for Membrane Divergence in Archaea and Bacteria. PLoS Biology, 12(8): e1001926. (link)
Tom Wyatt Harris AR, Bellis J, Khalilgharibi N, Wyatt T, Baum B, Kabla AJ, Charras GT. (2013). Generating suspended cell monolayers for mechanobiological studies. Nature protocols8(12): 2516-2530. (link)

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2012 intake

Matthew Topping Simoni, A., Wolfgang, W., Topping, M. P., Kavlie, R. G., Stanewsky, R., & Albert, J. T. (2014). A Mechanosensory Pathway to the Drosophila Circadian Clock. Science343(6170), 525-528. (link)

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2013 intake

Nils Gustafsson Maurer, S. P., Cade, N. I., Bohner, G., Gustafsson, N., Boutant, E., & Surrey, T. (2014). EB1 Accelerates Two Conformational Transitions Important for Microtubule Maturation and Dynamics. Current Biology24(4), 372-384. (link)

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