Kevin Burrage

Professor Kevin Burrage

Professor in Computational Systems Biology

Wolfson Building, Parks Road, Oxford OX1 3QD

Interests

Professional and Social Background

I am a Federation Fellow of the Australian Research Council (2003-2008). Until the end of 2007 I was also Professor of Computational Mathematics at the University of Queensland and Director of the Advanced Computational Modelling Centre. I was also founding CEO of the Queensland Parallel Supercomputing foundation (now QCIF). In Australia I am now Professor of Computational Mathematics at the Queensland University of Technology and Adjunct Professor at the Institute for Molecular Bioscience at the University for Queensland.
I share my time between Brisbane and Oxford.

I joined Oxford University in early 2008 and am now Professor of Computational Systems Biology at the Department of Computer Science, University of Oxford and the Oxford Centre for Integrative Systems Biology.
I am also a supernumerary fellow of New College at Oxford University.

I am married to Pamela and we have two children at Queensland doing the Medical program.

Contact Details

UK:Email: kevin.burrage@cs.ox.ac.uk
UK: Phone: +44 01865 283568
Aus: Email: kevin.burrage@gmail.com

Academic Interests
I have general interests in

Computational Mathematics
Computational and Systems Biology
Stochastic modelling for the Life Sciences
Multiscale modelling and simulation

Links to research partners at the University of Queensland

Computational and Systems Biology
Within Systems Biology, I work on

Monte Carlo modelling of chemical kinetics on the plasma membrane;
Genetic regulatory models incorporating noise and delays with applications to tHes 1 and Her 1/7;
Spatial cellular models and particularly granular transport of insulin in the pancreatic Beta cell;
Multiscale models incorporating noise at many different temporal and spatial scales;
Construction and analysis of interaction networks;
The role of small numbers of protein in immunological applications.

Selected Publications
Here is some recent work that I have done in Systems Biology: Reprints can be got from me via email.

S.MacNamara , K. Burrage and R. B. Sidje (2008): Multiscale modeling of chemical kinetics via the master equation, to appear in SIAM J. Multiscale Modelling and Simulation Multiscale Modeling & Simulation (Vol.6, No.4).
K. Burrage, I. Lenane and G. Lythe (2008): Numerical methods for second order stochastic equations, SIAM Journal of Scientific Computing, 29, 1, 245-264.
T. Marquez-Lago, K. Burrage (2007): Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics, J. Chem. Phys, 127, 1.
J. Song, K. Burrage (2007): Predicting disulfide connectivity from protein sequence using multiple sequence feature vectors and secondary structure, Bioinformatics.
K. Burrage, J. Hancock, A. Leier, D. V. Nicolau, Jr. (2007): Modelling and simulation techniques for Membrane Biology, Briefings in Bioinformatics, 8(4): 234-244, July 2007.
D. V. Nicolau Jr., J. F. Hancock, and K. Burrage (2007): Sources of Anomalous Diffusion on Cell Membranes: A Monte Carlo Study, Biophysics Journal 92:1975-1987.
F. Liu, P. Zhuang, V. Anh, I. Turner and K. Burrage (2007): Stability and Convergence of an Implicit Method for the Space-Time Fractional Advection-Diffusion Equation, Journal of Applied Mathematics and Computation.
C-M. Chen, F. Liu and K. Burrage (2007): Finite difference method and a new Fourier analysis for the Fractional Reaction-Diffusion Equation, Journal of Applied Mathematics and Computation.
D. Nicolau Jr, K. Burrage, R. G. Parton and J. Hancock (2006): Optimal microdomain characteristics for nano-scale protein-protein interactions, Molecular and Cellular Biology, January 2006, Vol. 26, No. 1, p. 313-323.
T. Tian and K.Burrage (2006): Stochastic models for regulatory networks of the genetic toggle switch, PNAS, Vol. 103, No. 22, 8372-8377.
M. Barrio, K. Burrage, A. Leier and T. Tian (2006): Oscillatory Regulation of Hes1: Discrete Stochastic Delay Modelling and Simulation, PLOS Computational Biology, September 2006, Volume 2, Issue 9.
T. Tian, S. Xu, J. Gao and Kevin Burrage (2006): Simulated maximum likelihood method for estimating kinetic rates in gene expression, Bioinformatics, 2006; doi: 10.1093/bioinformatics/btl552.
K. Burrage, L. Hood and M. A. Ragan (2006): Advanced computing for systems biology, Briefings in Bioinformatics, 7: 390-398.
J. Song, K. Burrage, Z. Yuan and T. Huber (2006), Prediction of cis/trans isomerization in proteins using psi-BLAST profiles and secondary structure information, BMC Bioinformatics, March 9, 7:124.
J. Song, M. Wang and K. Burrage (2006): Exploring synonymous codon usage preferences of disulfide-bonded and non-disulfide bonded cysteines in the E. coli Genome, J Theor Biol., Jan 18, 2006.
J. Song, and K. Burrage (2006): Predicting residue-wise contact orders in proteins by support vector regression, BMC Bioinformatics, 7:425, doi:10.1186/1471-2105-7-425.
T. Tian, K.Burrage, P. M. Burrage and M. Carletti (2006): Stochastic Delay Differential Equations for Genetic Regulatory Networks, Special Issue of J. Comp and Applied Maths, doi:10.1016/j.cam.2006.02.063.
K. Burrage, P. Burrage, D. J. Higham, P. E. Kloeden, E.Platen (2006): Comments on Numerical methods for stochastic differential equations: a correction and a warning, Physical Review E, 74, 068701.
T. Tian and K. Burrage (2004): Bistability and switching in the lysis lsogeny genetic regulatory network of Bacteriophage lambda, Journal of Theoretical Biology, 227, 229-237.
M. Carletti, K. Burrage and P.M. Burrage (2004): Numerical simulation of stochastic ordinary differential equations in biomathematical modeling, Mathematics and Computers in Simulation, 64, 271-277.
K. Burrage and T. Tian (2004): Poisson Runge-Kutta methods for Chemical Reaction Systems, in Advances in Scientific Computing and Applications, Y.Lu W. Sun and T. Tang eds, Science Press, Beijing/New York, 82-96.
K. Burrage, T. Tian and P. Burrage (2004): A multi-scaled approach for Chemical Reaction Systems Modelling Cellular and Tissue Function in Prog. Biophys. Mol. Biol, Vol. 85, Issue 2-3, 217-234.
N. Hamilton, K. Burrage, M. Ragan and T. Huber (2004): Protein contact prediction using patterns of correlation, Proteins: Structure, Function and Bioinformatics, 56, 679-684.
T. E. Turner, S. Schnell and K. Burrage (2004): Stochastic modelling of intracellular reactions, Computational Biology and Chemistry, 28, 3, 165-178.
T. Tian and K. Burrage (2004): Binomial leap methods for simulating stochastic chemical kinetics, J.Chem. Phys., 121, 10356-10364.
L.Croft, S. Schandoff, F. Clark, K. Burrage, P. Actander and J.S. Mattick (2000): ISIS the intron information system reveals the frequency of alternative splicing in the human genome, Nature Genetics, 24(4), 340-1.