• publications

Publications, talks and posters

Many publications, talks and posters have arisen directly or indirectly from the CaliBayes project, as follows.

Published work

• Milner, P., Gillespie, C. S., Wilkinson, D. J. (2011) Moment closure approximations for stochastic kinetic models with rational rate laws, Mathematical Biosciences, in press.

• Wilkinson, D. J. (2011) Stochastic dynamical systems, in Handbook of Statistical Systems Biology, Wiley, in press.

• Wilkinson, D. J. (2011) Parameter inference for stochastic kinetic models of bacterial gene regulation: a Bayesian approach to systems biology (with discussion), in J.-M. Bernardo et al (eds) Bayesian Statistics 9, OUP, in press.

• Chen, Y., Lawless, C., Gillespie, C.S., Wu, J., Boys, R.J., Wilkinson, D.J. (2010) CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models, Briefings in Bioinformatics, 11(3), 278-289.

• Golightly, A., Wilkinson, D. J. (2010) Markov chain Monte Carlo algorithms for SDE parameter estimation, in N. D. Lawrence et al (eds), Learning and Inference for Computational Systems Biology, MIT Press, pp.253-275.

• Henderson, D. A., Boys, R. J., Proctor, C. J., Wilkinson, D. J. (2010) Linking systems biology models to data: a stochastic kinetic model of p53 oscillations, A. O'Hagan and M. West (eds.) Handbook of Applied Bayesian Analysis, Oxford University Press, pp. 155-87.

• Henderson, D. A., Boys, R. J., Wilkinson, D. J. (2010) Bayesian calibration of a stochastic kinetic computer model using multiple data sources, Biometrics, 66, 249-56.

• Wilkinson, D. J. (2009) Stochastic modelling for quantitative description of heterogeneous biological systems, Nature Reviews Genetics, 10(2):122-133.

• Henderson, D. A., Boys, R. J., Krishnan, K. J., Lawless, C., Wilkinson, D. J. (2009) Bayesian emulation and calibration of a stochastic computer model of mitochondrial DNA deletions in substantia nigra neurons, Journal of the American Statistical Association, 104, 76-87.

• Hucka, M., Hoops, S., Keating, S., Le Novere, N., Sahle, S., and Wilkinson, D. J. (2008) Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions. Nature Precedings doi:10.1038/npre.2008.2715.1

• Boys, R. J., Wilkinson, D. J., Kirkwood, T. B. L. (2008) Bayesian inference for a discretely observed stochastic kinetic model, Statistics and Computing, 18(2):125-135.

• Evans, T. W., Gillespie, C. S., Wilkinson, D. J. (2008) The SBML discrete stochastic models test suite, Bioinformatics, 24:285-286 DSMTS website.

• Golightly, A., Wilkinson, D. J. (2008) Bayesian inference for nonlinear multivariate diffusion models observed with error, Computational Statistics and Data Analysis, 52(3):1674-1693.

• Wilkinson, D. J. (2007) Bayesian methods in bioinformatics and computational systems biology, Briefings in Bioinformatics, 8(2), 109-116.

• Golightly, A., Wilkinson, D. J. (2006) Bayesian sequential inference for nonlinear multivariate diffusions, Statistics and Computing, 16:323-338.

• Wilkinson, D. J. (2006) Stochastic modelling for systems biology, Boca Raton, Florida: Chapman and Hall/CRC Press.

• Golightly, A., Wilkinson, D. J. (2006) Bayesian sequential inference for stochastic kinetic biochemical network models, Journal of Computational Biology, 13(3):838-851.

• Golightly, A., Wilkinson, D. J. (2005) Bayesian inference for stochastic kinetic models using a diffusion approximation, Biometrics, 61(3):781-788.

Talks and Posters

• D. J. Wilkinson (December 2010): Math-Bio-Medicine (MBM) Seminar, Leeds.

• R. J. Boys (November 2010): Department of Statistics, University College Dublin, Inference for a stochastic kinetic model of p53 oscillations.

• R. J. Boys (October 2010): Department of Probability and Statistics, Sheffield University, Inference for a stochastic kinetic model of p53 oscillations.

• R. J. Boys (October 2010): Department of Statistics, University of Warwick, Inference for a stochastic kinetic model of p53 oscillations.

• D. J. Wilkinson (October 2010): Noise in Life 2010, Benasque, Spain.
• D. J. Wilkinson (October 2010): Workshop on Advanced Modelling and Simulation Techniques, Edinburgh.
• D. J. Wilkinson (October 2010): ICSB 2010, Edinburgh.

• R. J. Boys (September 2010): 6th International Workshop on Computation of Biochemical Pathways and Genetic Networks, Heidelberg, Germany, Linking systems biology models to data: a stochastic kinetic model of p53 oscillations.

• D. J. Wilkinson (September 2010): Duke statistics seminar, Durham, NC, USA.
• D. J. Wilkinson (August 2010): IMS 2010 Annual Meeting, Gothenburg, Sweden.
• D. J. Wilkinson (July 2010): Uncertainty in Computer Models 2010, Sheffield.
• D. J. Wilkinson (June 2010): Bayesian Statistics 9, Valencia, Spain.

• R. J. Boys (May 2010): Workshop on Statistical Modelling - Challenges in Health, Centre of Statistics and Applications, Lisbon, Portugal, Linking systems biology models to data: a stochastic kinetic model of p53 oscillations. * D. J. Wilkinson (February 2010): Heriot-Watt statistics seminar, Edinburgh

• D. J. Wilkinson (January 2010): BIRS Workshop on Multiscale stochastic modelling of cell dynamics, Banff, Canada
• D. J. Wilkinson (November 2009): Statistics seminar, Southampton
• D. J. Wilkinson (August 2009): SAMSI Workshop on Stochastic Dynamics, RTP, NC, USA.

• R. J. Boys (July 2009): MMBNOTT/MRM Summer School, Centre for Mathematical Medicine and Biology, University of Nottingham, Bayesian emulation and calibration of stochastic biological simulators.

• C. S. Gillespie, R.J. Boys, J. Chen, D. A. Henderson, T.B.L. Kirkwood, D.J. Wilkinson and J. Wu (July 2009). StoMP 2009, Noisy Bugs: modelling and microbiology, Edinburgh, CaliBayes: Integration of Grid-based post-genomic data resources through Bayesian calibration of biological simulators.

• D. J. Wilkinson (June 2009): Challenges in Scientific Computing, Warwick.
• D. J. Wilkinson (May 2009): Workshop on Statistical Bioinformatics and Stochastic Systems Biology, Newcastle.
• D. J. Wilkinson (May 2009): BBSRC Mathematical Biology Workshop, Warwick.

• D. J. Wilkinson (January 2009): Statistical Methods for Post Genomic Data 2009, Paris, France. Bayesian inference for biochemical network dynamics.

• D. J. Wilkinson (December 2008): New technologies for Protein Analysis, London.

• D. J. Wilkinson (November 2008): Joint RSS Local Group/Medical Section meeting, Leeds. Bayesian inference for stochastic models of intra-cellular reaction networks.

• R. J. Boys (November 2008): Institute of Mathematics and Statistics, University of Kent, Bayesian calibration of biological simulators.

• R. J. Boys (November 2008): Department of Mathematics, University of St Andrews, Bayesian calibration of biological simulators.

• R. J. Boys (October 2008): Fall Conference on Statistics in Biology, Iowa State University (USA), Bayesian emulation and calibration of stochastic biological simulators.

• J. Wu, R.J. Boys, T.B.L. Kirkwood and D.J. Wilkinson (September 2008): UK e-Science All Hands Meeting, Edinburgh, CaliBayes: Integration of Grid-based post-genomic data resources through Bayesian calibration of biological simulators (Poster)

• J. Wu, R.J. Boys, T.B.L. Kirkwood and D.J. Wilkinson (August 2008): The 9th International Conference on Systems Biology, Gothenburg (Sweden), CaliBayes: Integration of Grid-based post-genomic data resources through Bayesian calibration of biological simulators (Poster)

• D.A. Henderson, R.J. Boys, K.J. Krishnan, C. Lawless and D.J. Wilkinson (July 2008): The 9th ISBA World Meeting, Hamilton Island (Australia), Bayesian Emulation and Calibration of a Stochastic Computer Model of Mitochondrial DNA Deletions in Substantia Nigra Neurons (Poster)

• D. J. Wilkinson (June 2008): Workshop on Computational Systems Biology (WCSB) 2008 Keynote lecture, Leipzig, Germany. Bayesian inference for stochastic models of intracellular reaction networks.

• D. J. Wilkinson (May 2008): IMA (Institute for Mathematics and its Applications) workshop on Stochastic Models for Intracellular Reaction Networks, Minnesota (USA). Bayesian inference for stochastic intracellular reaction network models.

• D. J. Wilkinson (April 2008): INI/CRiSM Workshop on Bayesian Analysis of High Dimensional Data, Warwick. High-throughput data for systems biology modelling.

• R. J. Boys (March 2008): Department of Mathematical Sciences, University of Durham, Bayesian calibration of biological simulators.

• D. J. Wilkinson (January 2008): OCISB (Oxford Centre for Integrative Systems Biology) launch meeting - Visions for Systems Biology, Oxford.

• D. J. Wilkinson (October 2007): Systems Biology seminar, Warwick. The chemical Langevin equation: bridging the gap between descriptive and mechanistic stochastic models in Systems Biology.

• D. J. Wilkinson (April 2007): NIEHS (National Institute of Environmental Health Sciencs) Biostatistics seminar, Research Triangle Park, North Carolina (USA).

• W. E.Wolski, D. A.Henderson, R. J.Boys, T. B. L.Kirkwood and D. J. Wilkinson (April 2007): Workshop on Statistical Bioinformatics and Systems Biology, Newcastle University, CaliBayes: Integration of GRID-based simulation and data resources for Bayesian calibration of biological models (Poster).

• D. A. Henderson (March 2007): SAMSI Parameter estimation working group, Research Triangle Park, North Carolina (USA), An overview of CaliBayes: Bayesian calibration of biological models.

• D. A. Henderson, W. E. Wolski, R. J. Boys, D. J. Wilkinson, T. B. L. Kirkwood, C. Lawless and K.J. Krishnan (March 2007): SAMSI Biosystems Modelling Workshop, North Carolina (USA), Bayesian modelling of mtDNA deletions in substantia nigra neurons (Poster).

• D. J. Wilkinson (March 2007): SAMSI Undergraduate workshop on complex computer models, Research Triangle Park, North Carolina (USA).

• D. J. Wilkinson (November 2006): INI (Isaac Newton Institute) workshop on Recent Advances in Monte Carlo Based Inference, Cambridge. Bayesian inference for nonlinear multivariate diffusion processes.

• R. J. Boys (September 2006): 3me cycle de la Suisse Romande en statistique et probabilite applique, Ovronnaz (Switzerland), Topics in Stochastic Systems Biology.

• D. J. Wilkinson (September 2006): SAMSI (Statistical and Applied Mathematical Sciences Institute) Complex Computer Models kickoff workshop, Research Triangle Park, North Carolina (USA). Tutorial on (Computational Systems) Biological Models.

• D. J. Wilkinson (August 2006): Joint Statistical Meetings (JSM) 06, Seattle (USA).

• R. J. Boys (July 2006): The 23rd International Biometric Conference, Montreal (Canada), Discussant in session on Innovative Bayesian Computation for Biometrical applications.

• D. J. Wilkinson (June 2006): European Bioinformatics Institute (EBI) Industry Club meeting on Systems Biology, Cambridge.

• D. A. Henderson, W. E. Wolski, R. J. Boys, T. B. L. Kirkwood and D. J. Wilkinson (June 2006): The 8th Valencia International Meeting, Benidorm (Spain), Bayesian calibration of biological simulation models (Poster).

• D. J. Wilkinson (January 2006): EURANDOM workshop on Statistics for Biological Networks, Eindhoven (Netherlands).
• D. J. Wilkinson (September 2005): Imperial Genomics Workshop, London.

• R. J. Boys, D. A. Henderson, T. B. L. Kirkwood, D. J. Wilkinson and W. E. Wolski (July 2005): Bioinformatics and Systems Biology Conference, Edinburgh, (Poster;Abstract in BMC Bioinformatics, 6(Suppl 3), 14).

• D. J. Wilkinson, T. B. L. Kirkwood and R. J. Boys (November 2004): BBSRC Grantholders' Meeting, Edinburgh, CaliBayes: Integration of GRID-based post-genomic data resources through Bayesian calibration of biological simulators (Poster).

Technical reports and software documentation

• See the Documentation page for details.