Senior Research Associate (Mathematical & Computational Biology):
Richard Dybowski is accepting applications for PhD students.
Richard Dybowski is available for consultancy.
Subject groups/Research projects
Departments and Institutes
A. Within-host dynamics of bacterial infections with respect to antibiotic intervention.
I am interested in mathematical and computational techniques that, in conjunction with observed data, reveal the dynamics of within-host infections caused by Salmonella enterica. Application of Bayesian inference is of particular interest in this regard, such as the use of nested sampling and approximate Bayesian computation. The intention is to extend the modelling process to include the known pharmacodynamics and pharmacokinetics of a range of antibiotics with respect to S. enterica in order to ascertain optimal antibiotic regimens. In this context, I am also looking at the potential of probabilistic programming.
B. Biological applications of deep learning.
Although the main focus of deep learning (DL) continues to be the automatic interpretation of images, DL has also started to be considered in other areas. Of particular interest to me is the potential of DL to the biological sciences. Recent developments by others in this field include applications to proteomics, genomics and neuroscience. And I am exploring the use of DL for the estimation of parameters for mathematical models of within-host infections.
C. Optimal experimental design.
We are designing computational packages to facilitate the integration of dynamic models and laboratory experiments in microbiology and infectious disease research. This includes the development of a toolbox that estimates the expected information from Bayesian experimental designs, which has implications to the philosophy of science.
D. Logics for clinical decision making.
I have a long-standing interest in the development of clinical diagnostic decision-support systems both via the use of machine-learning techniques (including deep learning) and through the use of formal methods for the fusion of knowledge with data for decision support (e.g., by means of probabilistic graphical models). I am currently focusing on a theoretical comparison of probabilistic logic and various alternative logics that have been proposed for clinical decision making, including possibility theory, Dempster-Shafer theory, and Jøsang's subjective logic.
Dybowski R., Restif O., Goupy A., Maskell D.J., Mastroeni P., Grant A.J. (2015) "Single passage in mouse organs enhances the survival and spread of Salmonella enterica", Journal of the Royal Society Interface 12:20150702.
Coward C., Restif O., Dybowski R., Grant A., Maskell D., Mastroeni P. (2014) "The effects of vaccination and immunity on bacterial infection dynamics in vivo". PLoS Pathogens, 10(9): e1004359.
Dybowski R., McKinley T.J., Mastroeni P., Restif, O. (2013) "Nested sampling for Bayesian model comparison in the context of Salmonella disease dynamics". PLoS One, 8(12): e82317.
Mahroo O.A., Dybowski R., Wong R., Williamson T.H. (2012) "Characteristics of rhegmatogenous retinal detachment in pseudophakic and phakic eyes". Eye, 26(8): 1114-1121
Farnaud S., Wang Z., Dybowski R., Evans R.W., Odell E.W. (2006) "Towards a tree-induction approach to antimicrobial activity analysis of cationic peptides". Biochemistry and Cell Biology, 84(3): 394.
Dybowski R., Roberts S. (2005) "An anthology of probabilistic models for medical informatics". In Husmeier D., Dybowski R., Roberts S. (eds.) Probabilistic Modeling in Bioinformatics and Medical Informatics. London: Springer Verlag, pp 297-349.
Dybowski, R., Weller P.R. (2001) "Prediction intervals for the visualization of incomplete datasets". Computational Statistics, 16(1): 25-41.
Dybowski, R., Roberts, S. (2001) "Confidence intervals and prediction intervals for feed-forward neural networks". In Dybowski R, Gant V. (eds.) Clinical Applications of Artificial Neural Networks. Cambridge: Cambridge University Press, pp 298-326.
Ramoni, M., Sebastiani, P., Dybowski, R. (2001) "Robust outcome prediction of intensive-care patients". Methods of Information in Medicine, 40(1): 39-45.
Dybowski, R. (1998) "Classification of incomplete feature vectors by radial basis function networks". Pattern Recognition Letters, 19: 1257-1264.
Husmeier D., Dybowski R., Roberts S. (eds.) Probabilistic Modeling in Bioinformatics and Medical Informatics. London: Springer Verlag, 2005.
Dybowski R., Gant V. (eds.) Clinical Applications of Artificial Neural Networks. Cambridge: Cambridge University Press, 2001.