Publications

Papers (2024).

Aperiodic 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. Journal article.

Optimising the tumour elimination pay-off in cancer therapy. Nigel J. Burroughs, Mathilde L.C. Leuridan. IET Control Theory & Applications. 18, 1621–1637 (2024).. Journal article.

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. PLoS Comp Biology, 18(12): e1010765, 2022.
Evidence for a HURP/EB free mixed-nucleotide zone in kinetochore-microtubules. Cédric Castrogiovanni, Alessio V. Inchingolo, Jonathan U. Harrison, Damian Dudka, Onur Sen, Nigel J. Burroughs, Andrew D. McAinsh & Patrick Meraldi. Nature Communications, 13 (2022) 4704. Open access.
Kinetochore tracking in 3D from lattice light-sheet imaging data with KiT. Jonathan U. Harrison, Onur Sen, Andrew D. McAinsh and Nigel J. Burroughs. Bioinformatics 38 (2022), 3315–3317.

Submitted.

Tension-clock control of human mitotic chromosome oscillations. Nigel J. Burroughs, Andrew D. McAinsh. On ArXiv 2022.
Computational modelling and near-complete tracking reveal how chromosome segregation is coordinated in space and time. Jonathan U. Harrison†*, Onur Sen†, Andrew D. McAinsh, Nigel J. Burroughs*. BioRxiv 2021.

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*. Dev Cell 56 (2021) 3082–3099.
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*. STAR Protocols (2021) 2,100774. Open access.
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. Open access MBC.

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. Open access.

Computational modelling predicts substantial carbon assimilation gains for C₃ plants with a single-celled C₄ biochemical pump. Ivan Juri ́c, Julian M. Hibberd, Mike Blatt, Nigel J. Burroughs. PLOS computational Biology (2019), 15(9): e1007373. Open Access. WRAP.

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. Mol. Biol. Cell. 2019, 30(8):933-941.
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. Nucleic Acids Research. 2019, 47:2229–2243.

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. Nature Nanotechnology 2018, 13:386–91. WRAP depository

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. 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.

Actomyosin Ring Formation and Tension Generation in Eukaryotic Cytokinesis. Thomas H. Cheffings, Nigel J. Burroughs, Mohan K. Balasubramania. Current Biology, 2016, 26; R719–R737.

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.
A Hidden Markov Model for Detecting Confinement in Single-Particle Tracking Trajectories. Paddy J. Slator, Nigel J. Burroughs
Biophys J. 2018 Nov 6; 115(9): 1741–1754.

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 Grønlund, 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. Open Access
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. Open access.

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. Applied Mathematics and Information Sciences, An international journal. 9 (2015) 1-11.To appear.
Error correction and diversity analysis of population mixtures determined by NGS. Graham R. Wood, Nigel J. Burroughs, David J. Evans, Eugene V. Ryabov. 2014. PeerJ 2:e645 http://dx.doi.org/10.7717/peerj.645Link opens in a new window.

Correcting for link loss in causal network inference caused by regulator interference. 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. Open Access.
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. Open access.
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. Open Access.
Metabolic Switches and Adaptations Deduced from the Proteomes of Streptomyces coelicolor Wild Type and phoP Mutant Grown in Batch Culture. 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).
Semi-automated Acanthamoeba polyphaga detection and computation of Salmonella typhimurium concentration in spatio-temporal images. 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.
Loss of the SPHF Homologue Slr1768 leads to a Catastrophic Failure in the Maintenance of Thylakoid Membranes in Synechocystis sp. 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. PLoS Comp. Biol. 2011, 7(8): e1002076. doi:10.1371/journal.pcbi.1002076.
Springs, clutches and motors: driving forward kinetochore mechanism by modelling. Elina Vladimirou, Ed Harry, Nigel Burroughs, Andrew D. McAinsh. Chromosome Research 2011 Apr;19(3):409-21. via PUBMED.
Inferring the time-invariant topology of a non-linear sparse gene regulatory network using fully Bayesian spline autoregression. Edward R. Morrissey, Miguel A Juarez, Katherine J Denby, Nigel J Burroughs. Biostatistics, (2011) 12(4): 682-694.
Recombinants between Deformed wing virus and Varroa destructor virus-1 may prevail in Varroa destructor-infested honeybee colonies. Moore, J., Jironkin, A., Chandler, D., Burroughs, N., Evans, D.J. and Ryabov, E. J. Gen. Virol. 92 (2011), 156-161.
Matched sizes of activating and inhibitory receptor/ligand pairs are required for optimal signal integration by human Natural Killer cells. 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.
On reverse engineering gene interaction networks using time course data with repeated measurements. E.R. Morrissey, MA. Juárez, KJ Denby, NJ Burroughs. Bioinformatics, 2010, 26;2305--12.
The dynamic architecture of the metabolic switch in Streptomyces coelicolor. Nieselt, et al. BMC Genomics 11 (2010) 10.

An improved strip FRAP method for estimating diffusion coefficients: correcting for the degree of photobleaching. 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

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

Nonequilibrium-Driven Motion in Actin Networks: Comet Tails and Moving Beads. Physical Review Letters. 98, 2007, (issue 23) 238302. N. J. Burroughs and D. Marenduzzo.

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.