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The Zeeman Institute

Publications

Papers (2026).

  • Bayesian data driven modelling of kinetochore dynamics: space-time organisation of the human metaphase plate. Koki et al. PLOS Comp. Biology. .

Papers (2025).

  • Optimal Control and Tumour Elimination by Maximisation of Patient Life Expectancy. Byron D. E. Tzamarias, Annabelle Ballesta, Nigel John Burroughs . Mathematics 2025, 13(19), 3080.

  • Hierarchical Latent Space Clustering for Synthetic Cell Images. Bacon et al. IEEE International Symposium on Biomedical Imaging, Housten, Texas, 14-17 Apr 2025.

  • Fertility, time to pregnancy, and pregnancy outcomes among women with recurrent miscarriages in the UK: a prospective observational longitudinal study. Constandina Koki, Rebecca Shields, Rebecca Sweetman, James Boyle, Omar Khan, Sarah N Lim Choi Keung, Theodoros N Arvanitis, Adam J Devall, Nigel John Burroughs, Siobhan Quenby. .

BioRxiv papers

  • Single kinetochores execute an ordered series of molecular events as the Spindle Assembly Checkpoint is silenced. Conway et al. .
  • Attenuation of mosaic aneuploidy and erroneous first mitotic division of human embryos. Currie et al. .

  • Bayesian data driven modelling of kinetochore dynamics: space-time organisation of the human metaphase plate. Koki et al. .

Papers (2024).

  • Optimal Chronotherapy in Simple Compartment Tumour Growth Models Under Circadian Drug Toxicity Conditions. Byron D. E. Tzamarias, Annabelle Ballesta, Nigel John Burroughs . Mathematics 2024, 12(22), 3516. .
  • Optimising the tumour elimination pay-off in cancer therapy. Nigel J. Burroughs, Mathilde L.C. Leuridan. IET Control Theory & Applications. 18, 1621–1637 (2024).. .

 

Papers (2022).

  • Bayesian inference of multi-point macromolecular architecture mixtures at nanometre resolution. Peter Embacher, Tsvetelina E Germanova, Emanuele Roscioli, Andrew D McAinsh, Nigel J Burroughs. .
  • Evidence for a HURP/EB free mixed-nucleotide zone in kinetochore-microtubules. C茅dric Castrogiovanni, Alessio V. Inchingolo, Jonathan U. Harrison, Damian Dudka, Onur Sen, Nigel J. Burroughs, Andrew D. McAinsh & Patrick Meraldi. .

  • Kinetochore tracking in 3D from lattice light-sheet imaging data with KiT. Jonathan U. Harrison, Onur Sen, Andrew D. McAinsh and Nigel J. Burroughs.

Submitted.

  • Tension-clock control of human mitotic chromosome oscillations. Nigel J. Burroughs, Andrew D. McAinsh. On 2022.
  • Computational modelling and near-complete tracking reveal how chromosome segregation is coordinated in space and time. Jonathan U. Harrison鈥�*, Onur Sen鈥�, Andrew D. McAinsh, Nigel J. Burroughs*. .

Papers (2021).

  • Kinetochore life histories reveal an Aurora B dependent error correction mechanism in anaphase. Onur Sen+, Jonathan U. Harrison+, Nigel J. Burroughs*, and Andrew D.McAinsh*. .

  • Subcellular Euclidean distance measurements with Multicolor Fluorescence localization imaging in cultured cells. Tsvetelina E. Germanova*, Emanuele Roscioli, Jonathan U. Harrison, Andrew D. McAinsh and Nigel J. Burroughs*.

  • Time varying mobility and turnover of actomyosin ring components during cytokinesis in Schizosaccharomyces pombi. Anton Kamnev, Saravanan Palani, Paola Zambon, Tom Cheffings, Nigel Burroughs and Mohan K. Balasubramanian. Mol. Biol. Cell. 32 (2021):237-246.

Papers (2019,2020)

  • Ensemble-level organization of human kinetochores and evidence for distinct tension and attachment sensors. Emanuele Roscioli, Tsvetelina E. Germanova, Christopher A. Smith, Peter A. Embacher, Muriel Erent, Amelia I. Thompson, Nigel J. Burroughs, and Andrew D. McAinsh. Cell Reports 31(4), (2020), 107535. .
  • Computational modelling predicts substantial carbon assimilation gains for C鈧� plants with a single-celled C鈧� biochemical pump. Ivan Juri 虂c, Julian M. Hibberd, Mike Blatt, Nigel J. Burroughs. PLOS computational Biology (2019), 15(9): e1007373. . .

  • Actin turnover ensures uniform tension distribution during cytokinetic actomyosin ring contraction. Thomas H. Cheffings, Nigel J. Burroughs, and Mohan K. Balasubramanian. Molecular Biology of the Cell.

  • Bayesian inference of origin firing time distributions, origin interference and licencing probabilities from Next Generation Sequencing data. Alina Bazarova, Conrad A Nieduszynski, Ildem Akerman, Nigel J Burroughs. .

2018 and earlier, by topic

Cytoskeleton - modelling, mechanics, imaging, reverse engineering

Microtubule structure

  • Kinesin expands and stabilizes the GDP-microtubule lattice. R. Peet, Nigel J Burroughs, Robert A. Cross. .

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. doi:10.7554/eLife.16159.

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: .
  • 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, 11(11): e1004607. DOI: 10.1371/journal.pcbi.1004607. .
  • 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. .

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. .

Review of actomyosin ring mechanics.

  • Actomyosin Ring Formation and Tension Generation in Eukaryotic Cytokinesis. Thomas H. Cheffings, Nigel J. Burroughs, Mohan K. Balasubramania. .

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. .
  • A Hidden Markov Model for Detecting Confinement in Single-Particle Tracking Trajectories. Paddy J. Slator, Nigel J. Burroughs
    .

 

Plants: Photosynthesis modelling and gene networks

  • Root architecture shaping by the environment is orchestrated by dynamic gene expression in space and time. Liam Walker, Clare Boddington, Dafyd Jenkins, Ying Wang, Jesper T Gr酶nlund, Jo Hulsmans, Sanjeev Kumar, Dhaval Patel, Jonathan D Moore, Anthony Carter, Siva Samavedam, Giovanni Bomono, David S Hersh, Gloria M Coruzzi, Nigel J Burroughs, Miriam L Gifford. Plant Cell. 2017; 29, 2393–2412.
  • 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. .

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.

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).

  • Approximate equilibria for a T cell and Treg model. Bruno M. P. M. Oliveira, Isabel P. Figueiredo, Nigel J. Burroughs, Alberto A. Pinto. 9 (2015) 1-11.To appear.
  • Error correction and diversity analysis of population mixtures determined by NGS. Graham R. Wood鈥�, Nigel J. Burroughs, David J. Evans, Eugene V. Ryabov. 2014. .

  • . Ying Wang, Christopher A. Penfold, David A. Hodgson, Miriam L. Gifford and Nigel J. Burroughs. Bioinformatics, 2014; 30 (19): 2779-2786.
    doi: 10.1093/bioinformatics/btu388. .

  • A Virulent Strain of Deformed Wing Virus (DWV) of Honeybees (Apis mellifera) Prevails after Varroa destructor-Mediated, or In Vitro, Transmission. Eugene V. Ryabov, Graham R. Wood, Jessica M. Fannon, Jonathan D. Moore, James C. Bull, Dave Chandler, Andrew Mead, Nigel Burroughs, & David J. Evans. PLoS Pathogens, 10(6): e1004230. doi:10.1371/journal.ppat.1004230. .

  • MosaicSolver: a tool for determining recombinants of viral genomes from pileup data. Graham R. Wood, Eugene V. Ryabov, Jessica M. Fannon, Jonathan D. Moore, David J. Evans and Nigel Burroughs. NAR (2014) 15; 42(16): e123.

  • Extracting regulator activity profiles by integration of de novo motifs and expression data: characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor. Iqbal M., Mast Y., Amin R., Hodgson D. A., The STREAM Consortium , Wohlleben W., Burroughs N. J. NAR (2012) 40: 5227–5239. .
  • . Thomas, L (Thomas, Louise); Hodgson, DA (Hodgson, David A.); Wentzel, A (Wentzel, Alexander); Nieselt, K (Nieselt, Kay); Ellingsen, TE (Ellingsen, Trond E.); Moore, J (Moore, Jonathan); Morrissey, ER (Morrissey, Edward R.); Legaie, R (Legaie, Roxane); Wohlleben, W (Wohlleben, Wolfgang); Rodriguez-Garcia, A (Rodriguez-Garcia, Antonio); Martin, JF (Martin, Juan F.); Burroughs, NJ (Burroughs, Nigel J.); Wellington, EMH (Wellington, Elizabeth M. H.); Smith, MCM. Molecular and Cellular Proteomics. 11 (2012).
  • . Tsibidis, GD (Tsibidis, George D.); Burroughs, NJ (Burroughs, Nigel J.); Gaze, W (Gaze, William); Wellington, EMH (Wellington, Elizabeth M. H.). MICRON 42 (2011) 911-920.

  • . PCC 6803. Samantha J. Bryan, Nigel J Burroughs, Carol Evered, Joanna Sacharz, Anja Nenninger, Conrad W Mullineaux and Edward M. Spence. PLoS ONE 6(5): e19625. doi:10.1371/journal.pone.0019625. Open Access. IF 4.35.

  • Boltzmann energy-based image analysis demonstrates that extracellular domain size differences explain protein segregation at immune synapses. Nigel J. Burroughs, Karsten Kohler, Vladimir Miloserdov, Michael L. Dustin, P. Anton van der Merwe, Daniel M Davis. .
  • Springs, clutches and motors: driving forward kinetochore mechanism by modelling. Elina Vladimirou, Ed Harry, Nigel Burroughs, Andrew D. McAinsh. . .
  • . Edward R. Morrissey, Miguel A Juarez, Katherine J Denby, Nigel J Burroughs. Biostatistics, (2011) 12(4): 682-694.

  • . Moore, J., Jironkin, A., Chandler, D., Burroughs, N., Evans, D.J. and Ryabov, E. J. Gen. Virol. 92 (2011), 156-161.

  • . Karsten Kohler, Shiqiu Xiong, Joanna Brzostek, Maryam Mehrabi, Philipp Eissmann, Alice Harrison, Shaun-Paul Cordoba, Stephane Oddos, Vladimir Miloserdov, Keith Gould, Nigel J. Burroughs, P. Anton van der Merwe, Daniel M. Davis. PLoS ONE 5(11): e15374. doi:10.1371/journal.pone.0015374.

  • . E.R. Morrissey, MA. Ju谩rez, KJ Denby, NJ Burroughs. Bioinformatics, 2010, 26;2305--12.

  • . Nieselt, et al. BMC Genomics 11 (2010) 10.

  • . J. Yang, K. Kohler, D.M. Davis, N.J. Burroughs. J. Microscopy 2009, 238; 240-253. doi:10.1111/j.1365-2818.2009.03347.x

  • . 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鈥�-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

  • Nonequilibrium-Driven Motion in Actin Networks: Comet Tails and Moving Beads. . N. J. Burroughs and D. Marenduzzo.

  • Stochasticity and spatial heterogeneity in TCR activation. NJ Burroughs and PA van der Merwe.

  • 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. []
    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). []

  • 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.

  • 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.

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