Staff Profile

Colin is the author of Efficient R Programming, published by O'Reilly Media and a DataCamp presenter. He has published over 80 peer-reviewed journal articles in applied and methodological statistics and successfully supervised 7 PhD students. His areas of expertise are high-performance statistical computing, bayesian statistics and stochastic kinetic modelling. Over the last few years, he has worked with numerous companies, including Shell, the NHS, MoD, and several Banks. He is also the CTO of Jumping Rivers. 

Google Scholar

Research Interests (Google Scholar)

• Parallel computing;
• Bayesian statistics;
• Moment closure;
• Stochastic kinetic models. 

• Articles

  • Rajgor AD, Kui C, McQueen A, Cowley J, Gillespie C, Mill A, Rushton S, Obara B, Bigirumurame T, Kallas K, O'Hara J, Aboagye E, Hamilton DW. CT-based radiomic markers are independent prognosticators of survival in advanced laryngeal cancer: A pilot study. Journal of Laryngology and Otology 2023, epub ahead of print.
  • Prangle D, Harbisher S, Gillespie CS. Bayesian Experimental Design Without Posterior Calculations: An Adversarial Approach. Bayesian Analysis 2023, 18(1), 133-163.
  • Fisher HF, Boys RJ, Gillespie CS, Proctor CJ, Golightly A. Parameter inference for a stochastic kinetic model of expanded polyglutamine proteins. Biometrics 2022, 78(3), 1195-1208.
  • Rajgor AD, Cowley J, Gillespie C, Lee CW, O'Hara J, Iqbal MS, Hamilton D. Outcomes of the contemporary management approach for locally advanced (T3-T4) laryngeal cancer: a retrospective cohort study. Authorea 2022.
  • Smith LP, Moodie SL, Bergmann FT, Gillespie C, Keating SM, Konig M, Myers CJ, Swat MJ, Wilkinson DJ, Hucka M. Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1. Journal of Integrative Bioinformatics 2020, 17(2-3), 20200018.
  • Gillespie CS, Golightly A. Guided proposals for efficient weighted stochastic simulation. Journal of Chemical Physics 2019, 150(22), 224103.
  • Matthews TJ, Borregaard MK, Gillespie CS, Rigal F, Ugland KI, Kruger RF, Marques R, Sadler JP, Borges PAV, Kubota Y, Whittaker RJ. Extension of the gambin model to multimodal species abundance distributions. Methods in Ecology and Evolution 2019, 10(3), 432-437.
  • Gillespie CS, Boys RJ. Efficient construction of Bayes optimal designs for stochastic process models. Statistics and Computing 2019, 29(4), 697-706.
  • Golightly A, Bradley E, Lowe T, Gillespie CS. Correlated pseudo-marginal schemes for time-discretised stochastic kinetic models. Computational Statistics and Data Analysis 2019, 136, 92-107.
  • Paish HL, Baldock TE, Gillespie CS, del Carpio Pons A, Mann DA, Deehan DJ, Borthwick LA, Kalson NS. Chronic, Active Inflammation in Patients with Failed Total Knee Replacements Undergoing Revision Surgery. Journal of Orthopaedic Research 2019, 37(11), 2316-2324.
  • Albanna A, Sim M, Hoskisson PA, Gillespie C, Rao CV, Aldridge PD. Driving the expression of the Salmonella enterica sv Typhimurium flagellum using flhDC from Escherichia coli results in key regulatory and cellular differences. Scientific Reports 2018, 8(1), 16705.
  • James K, Chipeta C, Parker A, Harding S, Cockell SJ, Gillespie CS, Hallinan J, Barone F, Bowman SJ, Ng W-F, Fisher BA, for the UK Primary Sjögren's Syndrome Registry. B-cell activity markers are associated with different disease activity domains in primary Sjögren's syndrome. Rheumatology 2018, 57(7), 1222-1227.
  • Boys RJ, Ainsworth HF, Gillespie CS. Bayesian inference for a partially observed birth-death process using data on proportions. Australian and New Zealand Journal of Statistics 2018, 60(2), 157-173.
  • Andreasson ASI, Borthwick LA, Gillespie C, Jiwa K, Scott J, Henderson P, Mayes J, Romano R, Roman M, Ali S, Fildes JE, Marczin N, Dark JH, Fisher AJ, on behalf of the DEVELOP-UK Investigators. The role of interleukin-1β as a predictive biomarker and potential therapeutic target during clinical ex vivo lung perfusion. Journal of Heart and Lung Transplantation 2017, 36(9), 985-995.
  • Andreasson ASI, Karamanou DM, Gillespie CS, Özalp F, Butt T, Hill P, Jiwa K, RWalden H, Green NJ, Borthwick LA, Clark SC, Pauli H, Gould KF, Corris PA, Ali S, Dark JH, Fisher AJ. Profiling inflammation and tissue injury markers in perfusate and bronchoalveolar lavage fluid during human ex vivo lung perfusion. European Journal of Cardio-thoracic Surgery 2017, 51(3), 577-586.
  • Sim M, Koirala S, Picton D, Strahl H, Hoskissin PA, Rao CV, Gillespie CS, Aldridge PD. Growth rate control of flagellar assembly in Escherichai coli strain RP437. Scientific Reports 2017, 7, 41189.
  • Gillespie CS. Estimating the number of casualties in the American Indian war: a Bayesian analysis using the power law distribution. Annals of Applied Statistics 2017, 11(4), 2357-2374.
  • Gillespie CS, Golightly A. Diagnostics for assessing the linear noise and moment closure approximations. Statistical Applications in Genetics and Molecular Biology 2016, 15(5), 363–379.
  • Borthwick LA, Suwara MI, Carnell SC, Green NJ, Mahida R, Dixon D, Gillespie CS, Cartwright TN, Horabin J, Walker A, Olin E, Rangar M, Gardner A, Mann J, Corris PA, Mann DA, Fisher AJ. Pseudomonas aeruginosa induced Airway Epithelial Injury Drives Fibroblast Activation: A Mechanism in Chronic Lung Allograft Dysfunction. American Journal of Transplantation 2016, 16(6), 1751-1765.
  • Owen J, Wilkinson DJ, Gillespie CS. Scalable inference for Markov processes with intractable likelihoods. Statistics and Computing 2015, 25(1), 145-156.
  • Owen J, Wilkinson DJ, Gillespie CS. Likelihood free inference for Markov processes: a comparison. Statistical Applications in Genetics and Molecular Biology 2015, 14(2), 189–209.
  • Gillespie CS. Fitting Heavy Tailed Distributions: The poweRlaw Package. Journal of Statistical Software 2015, 64(2).
  • James K, Al-Ali S, Tarn J, Cockell SJ, Gillespie CS, Hindmarsh V, Locke J, Mitchell S, Lendrem D, Bowman S, Price E, Pease CT, Emery P, Lanyon P, Hunter JA, Gupta M, Bombardieri M, Sutcliffe N, Pitzalis C, McLaren J, Cooper A, Regan M, Giles I, Isenberg D, Saravanan V, Coady D, Dasgupta B, McHugh N, Young-Min S, Moots R, Gendi N, Akil M, Griffiths B, The UK Primary Sjögren’s Syndrome registry, Wipat A, Newton J, Jones DE, Isaacs J, Hallinan J, Ng W-F. A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren’s Syndrome. PLoS ONE 2015, 10(12), e0143970.
  • Sherlock C, Golightly A, Gillespie CS. Bayesian inference for hybrid discrete-continuous stochastic kinetic models. Inverse Problems 2014, 30(11), 114005.
  • Milner P, Gillespie CS, Wilkinson DJ. Moment closure based parameter inference of stochastic kinetic models. Statistics and Computing 2013, 23(2), 287-295.
  • Gillespie CS. Stochastic simulation of chemically reacting systems using multi-core processors. Journal of Chemical Physics 2012, 136(1), 014101.
  • Bell MJ, Gillespie CS, Swan D, Lord P. An approach to describing and analysing bulk annotation quality: a case study using UniprotKB. Bioinformatics 2012, 28(18), i562-i568.
  • Lawless C, Jurk D, Gillespie CS, Shanley D, Saretzki G, von Zglinicki T, Passos JF. A Stochastic Step Model of Replicative Senescence Explains ROS Production Rate in Ageing Cell Populations. PLoS One 2012, 7(2), e32117.
  • Wockenforth R, Gillespie CS, Jaffray B. Survival of children following Nissen fundoplication. British Journal of Surgery 2011, 98(5), 680-685.
  • Caldwell GS, Fitzer S, Gillespie CS, Pickavance G, Turnbull E, Bentley MG. Ocean acidification takes sperm back in time. Invertebrate Reproduction and Development 2011, 55(4), 217-221.
  • Milner P, Gillespie CS, Wilkinson DJ. Moment closure approximations for stochastic kinetic models with rational rate laws. Mathematical Biosciences 2011, 231(2), 99-104.
  • Pohl S, Tu WY, Aldridge PD, Gillespie C, Hahne H, Mäder U, Read TD, Harwood CR. Combined proteomic and transcriptomic analysis of the response of Bacillus anthracis to oxidative stress. Proteomics 2011, 11(15), 3036-3055.
  • Lei G, Boys RJ, Gillespie CS, Greenall AJ, Wilkinson DJ. Bayesian inference for sparse VAR(1) models, with application to time course microarray data. Journal of Biometrics and Biostatistics 2011, 2(127).
  • Chen YH, Lawless C, Gillespie CS, Wu J, Boys RJ, Wilkinson DJ. CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models. Briefings in Bioinformatics 2010, 11(3), 278-289.
  • Gillespie CS, Golightly A. Bayesian inference for generalized stochastic population growth models with application to aphids. Journal of the Royal Statistical Society: Series C (Applied Statistics) 2010, 59(2), 341-357.
  • Gillespie CS, Lei G, Boys RJ, Greenall AJ, Wilkinson DJ. Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays. BMC Research Notes 2010, 3(81).
  • Hong M, Ryan KR, Arkwright P, Gennery A, Costigan C, Denning D, Cant AJ, Abinun M, Young DA, McConnell V, Spickett GP, Swan DC, Gillespie CS, Lilac D, Dominguez M. Pattern recognition receptor expression is not impaired in patients with chronic mucocutanous candidiasis with or without autoimmune polyendocrinopathy candidiasis ectodermal dystrophy. Clinical and Experimental Immunology 2009, 156(1), 40-51.
  • Gillespie CS. Moment-closure approximations for mass-action models. IET Systems Biology 2009, 3(1), 52-58.
  • Evans TW, Gillespie CS, Wilkinson DJ. The SBML discrete stochastic models test suite. Bioinformatics 2008, 24(2), 285-286.
  • Gillespie CS, Renshaw E. The evolution of a single-paired immigration death process. Journal of Physics A: Mathematical and Theoretical 2008, 41(35), -.
  • Lawson SEM, Gillespie C. Three dimensional customization: effect of statistical technique on HJC prediction equations in children. Journal of Biomechanics 2007, 40(s2), S321.
  • Proctor CJ, Lydall D, Boys RJ, Gillespie CS, Shanley D, Wilkinson DJ, Kirkwood TBL. Modelling the checkpoint response to telomere uncapping in budding yeast. Journal of the Royal Society Interface 2007, 4(12), 73-90.
  • Gillespie CS, Renshaw E. An improved saddlepoint approximation. Mathematical Biosciences 2007, 208(2), 359-374.
  • Gillespie C, Wilkinson D, Proctor CJ, Shanley D, Boys RJ, Kirkwood TBL. Tools for the SBML community. Bioinformatics 2006, 22(5), 628-629.
  • Gillespie CS, Wilkinson DJ, Shanley DP, Proctor CJ, Boys RJ, Kirkwood TBL. BASIS: an internet resource for network modelling. Journal of Integrative Bioinformatics 2006, 3(2), [12].
  • Gillespie CS, Renshaw E. The evolution of a batch-immigration death process subject to counts. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 2005, 461(2057), 1563-1581.
  • Proctor CJ, Soti C, Boys RJ, Gillespie CS, Shanley DP, Wilkinson DJ, Kirkwood TBL. Modelling the actions of chaperones and their role in ageing. Mechanisms of Ageing and Development 2005, 126(1), 119-131.
  • Gillespie C, Proctor CJ, Boys R, Shanley D, Wilkinson D, Kirkwood T. A mathematical model of ageing in yeast. Journal of Theoretical Biology 2004, 229(2), 189-196.

• Book Chapters

  • Cockell S, Bashton M, Gillespie CS. Bioconductor tools for microarray data analysis. In: Rueda, L, ed. Microarray Image and Data Analysis: Theory and Practice. Boca Raton: CRC Press, 2014.
  • Golighty A, Gillespie CS. Simulation of stochastic kinetic models. In: Schneider, M.V, ed. In-silico Systems Biology: A systems-based approach to understanding biological processes. Humana Press, 2013, pp.169-187.
  • Kirkwood TBL, Boys RJ, Gillespie CS, Proctor CJ, Shanley DP, Wilkinson DJ. Computer modeling in the study of aging. In: Masoro, E.J., Austad, S.N, ed. Handbook of The Biology of Aging. London, UK: Academic Press, 2006, pp.334-356.
  • Kirkwood TBL, Boys RJ, Gillespie CS, Proctor CJ, Shanley DP, Wilkinson DJ. Computer Modeling in the Study of Aging. In: Austad, S.N., Masoro, E.J, ed. Handbook of the Biology of Aging. Amsterdam; Boston: Academic Press, 2005, pp.334-359.

• Conference Proceedings (inc. Abstracts)

  • Andreasson A, Karamanou D, Gillespie C, Borthwick L, Jiwa K, Henderson P, Ozalp F, Butt T, Clark SC, Pauli H, Corris PA, Ali S, Dark JH, Fisher AJ. Treating Donor Lung Inflammation by Blocking Interleukin-1B-An In Vitro Therapy Testing Platform for Ex Vivo Lung Perfusion. In: International Society for Heart and Lung Transplantation 36th Annual Meeting and Scientific Sessions. 2016, Washington, DC: Elsevier.
  • Howard-Tripp N, Tarn J, Gillespie C, Lendrem D, Griffiths B, Bowman S, Ng WF, United Kingdom Primary Sjögren's Syndrome Registry. A Cytokine-Mediated Biological Basis for Fatigue in Primary Sjögren’s Syndrome. In: Rheumatology 2016. 2016, Glasgow: Oxford University Press.
  • James K, Cockell SJ, Gillespie CS, Assi LK, Bowman S, Griffiths B, Ng WF, UKPSSR. Serum Free Light Chains are Associated with Clinical Disease Activity of Primary Sjögren's Syndrome in the Cutaneous, Biological and Renal Domains. In: The 13th International Symposium on Sjögren's Syndrome. 2015, Bergen, Norway: Wiley-Blackwell.
  • Tarn J, Lendrem D, Gillespie C, Al-Ali S, Griffiths B, Bowman S, Ng WF, Uk Primary Sjogren's Syndrome Regi. Patient Sub-Phenotyping in Primary Sjogren's Syndrome. In: 13th International Symposium on Sjögren's Syndrome. 2015, Bergen, Norway: Wiley-Blackwell Publishing Ltd.
  • James K, Al-Ali S, Tarn J, Cockell SJ, Gillespie CS, Bowman S, Isaacs J, Jones DE, Newton J, Price E, Wipat A, Hallinan J, Ng WF, UKPSSR. Gene Set Enrichment Analysis Across Multiple Expression Studies Reveals a Core Subset of Primary Sjögren's Syndrome-Related Genes. In: The 13th International Symposium on Sjögren's Syndrome. 2015, Bergen, Norway: Wiley-Blackwell.
  • James K, Al-Ali S, Tarn J, Cockell SJ, Gillespie CS, Bowman S, Isaacs J, Jones DE, Newton J, Price E, Wipat A, Hallinan J, Ng WF, UKPSSR. A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren's Syndrome. In: The 13th International Symposium on Sjögren's Syndrome. 2015, Bergen, Norway: Wiley-Blackwell.
  • James K, Cockell SJ, Gillespie CS, Assi L, Bowman S, Griffiths B, Ng WF, UKPSSR. Baff and B2m, but not Free Light Chains, Correlate with Disease Activity in Primary Sjögren's Syndrome (PSS). In: Annual European Congress of Rheumatology. 2014, Paris, France: BMJ Group.
  • Gillespie CS, Golightly A. Bayesian inference for the chemical master equation using approximate models. In: 9th International Workshop on Computational Systems Biology (WCSB). 2012, Ulm, Germany.
  • Gillespie CS, Proctor CJ, Shanley DP, Wilkinson DJ, Boys RJ, Kirkwood TBL. Web-services for the biology community: the BASIS project. In: UK e-Science All Hands Meeting. 2005, Nottingham, UK.

• Editorial

  • Dall'Olio GM, Marino J, Schubert M, Keys KL, Stefan MI, Gillespie CS, Poulain P, Shameer K, Sugar R, Invergo BM, Jensen LJ, Bertranpetit J, Laayouni H. Ten Simple Rules for Getting Help from Online Scientific Communities. PLoS Computational Biology 2011, 7(9), e1002202.

• Report

  • Bell MJ, Gillespie CS, Swan D, Lord P. An approach to describing and analysing bulk biological annotation quality: A case study using UniProtKB. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2012. School of Computing Science Technical Report Series 1336.

• Reviews

  • Keating SM, Waltemath D, Konig M, Zhang F, Drager A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gomez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M, Adams RR, Allen NA, Angermann BR, Antoniotti M, Bader GD, Cerveny J, Courtot M, Cox CD, Dalle Pezze P, Demir E, Denney WS, Dharuri H, Dorier J, Drasdo D, Ebrahim A, Eichner J, Elf J, Endler L, Evelo CT, Flamm C, Fleming RMT, Frohlich M, Glont M, Goncalves E, Golebiewski M, Grabski H, Gutteridge A, Hachmeister D, Harris LA, Heavner BD, Henkel R, Hlavacek WS, Hu B, Hyduke DR, de Jong H, Juty N, Karp PD, Karr JR, Kell DB, Keller R, Kiselev I, Klamt S, Klipp E, Knupfer C, Kolpakov F, Krause F, Kutmon M, Laibe C, Lawless C, Li L, Loew LM, Machne R, Matsuoka Y, Mendes P, Mi H, Mittag F, Monteiro PT, Natarajan KN, Nielsen PMF, Nguyen T, Palmisano A, Pettit J-B, Pfau T, Phair RD, Radivoyevitch T, Rohwer JM, Ruebenacker OA, Saez-Rodriguez J, Scharm M, Schmidt H, Schreiber F, Schubert M, Schulte R, Sealfon SC, Smallbone K, Soliman S, Stefan MI, Sullivan DP, Takahashi K, Teusink B, Tolnay D, Vazirabad I, von Kamp A, Wittig U, Wrzodek C, Wrzodek F, Xenarios I, Zhukova A, Zucker J. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology 2020, 16(8), e9110.
  • Kirkwood TBL, Boys RJ, Gillespie CJ, Proctor CJ, Shanley DP, Wilkinson DJ. Towards an e-biology of ageing: Integrating theory and data. Nature Reviews Molecular Cell Biology 2003, 4(3), 243-249.