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Publications

Cytoskeleton - modelling, mechanics, imaging, reverse engineering

Kinetochore swivel: a new conformational degree of freedom.

  • Human kinetochores are swivel joints that mediate microtubule attachments. Chris A Smith, Andrew D McAinsh and Nigel J Burroughs. eLife 2016. eLife 2016;5:e16159.

Kinetochore dynamics during cell division - Reverse engineering spatial biological systems. Here we use reverse engineering techniques (MCMC) to fit models of kinetochore oscillations to individual sister pair trajectories. The following papers examine our initial data set of 1000 trajectories in HeLA cells.

  • Super-resolution kinetochore tracking reveals the mechanisms of human sister kinetochore directional switching. Nigel J. Burroughs*, Edward F. Harry* and Andrew D. McAinsh. eLife 2015, eLife 2015;10.7554/eLife.09500: PDF.
  • Inferring the Forces Controlling Metaphase Kinetochore Oscillations by Reverse Engineering System Dynamics. Jonathan W. Armond, Edward F. Harry, Andrew D. McAinsh, Nigel J. Burroughs, PLOS Comp. Biol. 2015, DOI: 10.1371/journal.pcbi.1004607. Open access.
  • SOFTWARE: KiT: A MATLAB package for kinetochore tracking. Jonathan W. Armond, Elina Vladimirou, Andrew D. McAinsh and Nigel J. Burroughs. Bioinformatics, 2016. 32(12):1917-9. Open access.

A related paper on quantifying EB proteins at kinetochores.

  • Probing microtubule polymerisation state at single kinetochores during metaphase chromosome motion. Jonathan W. Armond, Elina Vladimirou, Muriel Erent, Andrew D. McAinsh, Nigel J. Burroughs. JCS 2015: doi: 10.1242/jcs.168682. Open Access.

Review of actomyosin ring mechanics.

Single particle tracking using hidden Markov Models. We develop a number of models of heterogeneity of molecule movement in membranes and develop algorithms (MCMC) to fit to trajectory data. Includes model discrimination.

  • Detection of Diffusion Heterogeneity in Single Particle Tracking Trajectories using a Hidden Markov Model with Measurement Noise Propagation. Paddy J. Slator, Christopher W. Cairo, Nigel J. Burroughs. PLOS ONE 2015: 10.1371/journal.pone.0140759.
  • Papers in preparation.


Photosynthesis modelling

Size matters for single-cell C4 photosynthesis in Bienertia. Ivan Juric, Vinicio Gonzalez-Perez, Julian M. Hibberd, Gerald Edwards, Nigel Burroughs.
Journal of Experimental Botany. 2016; 68(2): 255--267. doi: 10.1093/jxb/erw374. Open Access.

Bacteria - modelling, imaging, omics analysis.

  • Regulation of Gene Expression During Electron Acceptor Limitation and Bacterial Nanowire Formation in Shewanella oneidensis MR-1. Sarah E Barchinger, Sahand Pirbadian, Christine Sambles, Carol S Baker, Kar Man Leung, Nigel J Burroughs, Mohamed Y El-Naggar, John H Golbeck. Appl Environ Microbiol 2016 Jun 24, 82(17);5428--5443. Open Access.

Protein localisation in cyanobacteria. We demonstrate dynamic spatial localisation of a number of proteins in synechocystis using image processing techniques.

  • Sub-cellular location of FtsH proteases in the cyanobacterium Synechocystis sp. PCC 6803 suggests localised PSII repair zones in the thylakoid membranes. Sacharz J, Bryan SJ, Yu J, Burroughs NJ, Spence EM, Nixon PJ, Mullineaux CW. Mol. Micro. (2015). doi: 10.1111/mmi.12940. [Epub ahead of print]
  • Localisation and interactions of the Vipp1 protein in cyanobacteria. Samantha J. Bryan*, Nigel J. Burroughs*, Dmitriy Shevela, Jianfeng Yu, Eva Rupprecht, Lu-Ning Liu, Giulia Mastroianni, Quan Xue, Isabel Llorente-Garcia, Mark C. Leake, Lutz A. Eichacker, Dirk Schneider, Peter J. Nixon and Conrad W. Mullineaux. 2014. Mol. Micro. 94 (5): 1179-1195.
  • Solar powered biohydrogen production requires specific localization of the hydrogenase. Nigel J Burroughs, Marko Boehm, Carrie Eckert, Giulia Mastroianni, Edward M Spence, Jianfeng Yu, Peter J Nixon, Jens Appel, Conrad W Mullineaux and Samantha J Bryan. Energy and Environmental Science 2014, , DOI: 10.1039/C4EE02502D.

Earlier publications (network inference, omics analysis (bee virus DWV, streptomyces), theoretical immunology).

  • Transformation from Spots to Waves in a Model of Actin Pattern Formation. Stephen Whitelam, Till Bretschneider, and Nigel J. Burroughs. PRL. 102, 2009, 198103.

  • The expression of recombinant genes in Escherichia coli can be strongly stimulated at the transcript production level by mutating the DNA-region corresponding to the 5’-untranslated part of mRNA. Laila Berg, Rahmi Lale, Ingrid Bakke, N.J. Burroughs and Svein Valla. Microbial Biotechnology. 2 (2009) 379--389.

  • Evidence for the intense exchange of MazG in marine cyanophages by horizontal gene transfer. Michael J. Bryan, Nigel J. Burroughs, Edward M. Spence, Martha R. J. Clokie, Nicholas H. Mann and Samantha J. Bryan. PLOS ONE. 3(4): e2048. doi:10.1371/journal.pone.0002048

  • Stochasticity and spatial heterogeneity in TCR activation. NJ Burroughs and PA van der Merwe.
    Immunological Reviews, (2007), 216: 69-80.

  • Close contact fluctuations: the seeding of signalling domains in the immunological synapse.
    A.K. Chattopadhyay and N.J. Burroughs. EPL. 77, (2007), 48003

  • A Markov Chain Monte Carlo Method for Estimating Population Mixing Using Y-chromosome Markers:
    Mixing of the Han People in China. H. Jow, W. Amos, H. Luo, Y. Zhang and N. J. Burroughs. Annals of Human Genetics (2007) 71,407-420.

  • Ligand detection and discrimination by spatial relocalisation: a kinase-phosphatase segregation model of TCR activation. NJ. Burroughs, Z. Lazic, PA van der Merwe. (2006) BJ, 91: 1619-1629.

  • T cell activation: a queueing theory analysis at low agonist density. Janak Wedagedera and N.J. Burroughs. (2006) BJ, 91: 1604-1618.

  • Regulatory T cell adjustment of quorum growth thresholds and the control of local immune responses. [PDF]
    N.J. Burroughs, Bruno Miguel Paz Mendes de Oliveira, Alberto Adrego Pinto. (2006) JTB. 241: 134-141.

  • Growth of a semi-flexible polymer close to a fluctuating obstacle: application to cytoskeletal actin fibers and testing of rachet models. NJ. Burroughs and D. Marenduzzo. J. Phys: Condens. matter. (2006). 18:S357-S374.

  • Three dimensional dynamic Monte-Carlo simulations of polymer ratchets.
    NJ. Burroughs and D. Marenduzzo. Journal of Chemical Physics. 23, 174908 (2005). [PDF]

  • Discriminating self from nonself with short peptides from large proteomes. N.J. Burroughs, Can Kesmir and Rob de Boer. (2004). Immunogenetics. 56, 311--320.

  • Interactions between Salmonella typhimurium and Acanthamoeba polyphaga, and observation of a new mode of intracellular growth within contractile vacuoles. William H Gaze, Nigel Burroughs, Maurice P Gallagher and Elizabeth MH Wellington. Microbial. Ecol. 46 (2003) 358--369.

  • Perturbation theory analysis of competition in a heterogeneous population.
    C. Utzny and NJ Burroughs. Physica D 175 (2003) 109--126.

  • Interface accumulation of receptor/ligand couples in lymphocyte activation: Methods, mechanisms and significance. Immunological Reviews, 189 (2002) 64-83. C. Wulfing, I. Tskvitaria-Fuller, N.J. Burroughs, M.D. Sjaastad, J. Klem and J.D. Schatzle.

  • Differential segregation in a cell:cell contact interface - the formation of the immunological synapse. Biophysical Journal, 83 (2002), 1784-1796. N.J. Burroughs and C. Wulfing.

  • Quantifying the strength of ligand antagonism in TCR triggering. Bulletin of Mathematical Biology, 64 (2002) 781-808. H.A. van den Berg, N.J. Burroughs & D.A. Rand.

  • TCR dynamics on the surface of living T cells. Int. Imm. 13 (2001) 1525-1532 Benoit Favier, N.J. Burroughs, Lucy Wedderburn, Salvatore Valitutti.

  • Long-term stability of Diverse Immunological Memory. Utzny C. and Burroughs N.J. Journal of Theortical Biology, 211 (2001) 393-402.

  • Stability of a diverse immunological memory is determined by T-cell population dynamics. Utzny, C. & Burroughs, NJ. Bulletin in Mathematical Biology, 63 (2001), 685-713.

  • A reliable and safe T cell repertoire based on low-affinity T cell receptors. J. Theor. Bio. 209; (2001) 465-486. H. van den Berg, D.A. Rand and NJ Burroughs. PDF

  • Mathematical Analysis of Growth and Interaction Dynamics of Streptomycetes and a Bacteriophage in Soil . Applied & Environmental Microbiology, 66 (2000), 3868-3877. N.J. Burroughs, P. Marsh, E.M.H. Wellington.

  • Defective Deletion Mutant Amplification. Journal of Theoretical Biology, 206 (2000) 449-464. N.J. Burroughs and B. McLeod

  • Significance testing of clinical data using virus dynamics models and MCMC. Proceedings of the Royal Society, B266; (1999), 2359-2366. N.J. Burroughs, D. Mutimer, D. Pillay.

  • Markov Chain Monte Carlo Analysis of Human Y Chromosome Microsatellites. Proceedings of the National Academy of Sciences, USA 96; (1999) 11916-11921. G. Cooper , N.J. Burroughs, D.A. Rand, D.C. Rubinsztein, W. Amos.

  • Dynamics of T-cell Antagonism : Enhanced Viral Diversity and Survival. Proceedings of the Royal Society: Biological Sciences (1998) 265, 529-535. N.J. Burroughs, D.A. Rand.