Associate Professor Dov Stekel
Dr Dov Stekel,
Multidisciplinary Centre of Integrative Biology,
The University of Nottingham,
Sutton Bonington, LE12 5RD.
Phone: 0115 9516294
We use mathematical, computing and statistical techniques to build predictive models for biological systems, with the aims of best interpretation of experimental data, deepening our understanding of how biological systems work, and helping to inform the design of future experimental work. We use a wide variety of techniques, including differential equations, stochastic models, multi-scale models, artificial life, computer evolution, statistical analysis and bioinformatics analysis. We try, where possible, to work on projects with active collaborations with experimental biologists. We have a particular interest in the integration of experimental data, data quality and mechanistic hyptheses through the combined use of dynamical models with Bayesian inference. At the moment, many of the biological applications of our work are in microbiology, including pathogenic E. coli strains, bioluminescent reporters, the antibiotic-resistance bearing RK2 plasmids and the use of Biolog Phenotype arrays in brewing, bioenergy and food safety applications. However, we are happy to foster collaborations with scientists working in any area of biology, and this range of applications is reflected in our publications.
I am Associate Professor of Integrative Systems Biology at the Multidisciplinary Centre for Integrative Biology, School of Biosciences, University of Nottingham. I studied mathematics at Trinity College, Cambridge and for a D.Phil. at the Department of Zoology, University of Oxford, supervised by Martin Nowak. My D.Phil. topic was on mathematical modeling of T lymphocyte recirculation and virus dynamics. Following my D.Phil., I worked briefly with Boris Vojnovic at the Gray Laboratory, before taking a position in the Bioinformatics group at Glaxo Wellcome Research and Development (as it was), and then as Head of Bioinformatics at Ed Southern's microarray company, Oxford Gene Technology. I left OGT after receiving a commission from Cambridge University Press to write Microarray Bioinformatics, and worked as a free-lance bioinformatics consultant during that time. In 2004 I took the position as Lecturer in Bioinformatics at the School of Biosciences, University of Birmingham and in 2009 moved to the University of Nottingham to take my current post.
For more recent information about Dov Stekel's research and latest news, please click on the following website: Dov Stekel's Laboratory.
Group Members:
Dr Mudassar Iqbal
Dorota Herman
Richard Crossland
Selected publications:
Herbert, J.M.J., Stekel, D.J., Mura, M., Sychev, M. and Bicknell, R. 2011. Bioinformatic methods for finding differentially expressed genes in cDNA libraries, applied to the identification of tumour vascular targets. In Lu, C. et al., cDNA libraries: Methods and Applications, Methods in Molecular Biology 729. Springer.
Jenkins, D.J. and Stekel, D.J. 2010. De Novo Evolution of Complex, Global and Hierarchical Gene Regulatory Mechanisms. Journal of Molecular Evolution, 71: 128-40.
Salama, R.A. and Stekel, D.J. 2010. Inclusion of
neighboring base interdependencies substantially improves genome-wide
prokaryotic transcription factor binding site prediction. Nucleic Acids Research, 38: e135.
Jenkins, D.J. and Stekel, D.J. 2010. Stochasticity Versus Determinism: Consequences for Realistic Gene Regulatory Network Modelling and Evolution. Journal of Molecular Evolution, 70: 215-231.
Fernando, C.T., Goldstein, R.A., Husbands, P., Stekel, D.J. 2010. In silico biology. Pacific Symposium on Biocomputing, 477-80.
Gasson, P., Miller, R., Stekel, D.J. Whinder, F. and
Zieminska, Z. 2010. Wood identification of Dalbergia nigra (CITES
Appendix I) using quantitative wood anatomy, principal components
analysis and naive Bayes classification. Annals of botany, 105: 45-56.
Welham, P.A. and Stekel, D.J. 2009. Mathematical model of the Lux luminescence system in the terrestrial bacterium Photorabdus luminescens. Molecular Biosystems. 5: 68 - 76.
Ma, H., Hagen, F., Stekel, D.J., Johnston, S.A., Sionov, E.,
Falk, R., Polacheck, I., Boekhout, T. and May, R.C. 2009. The fatal
fungal outbreak on Vancouver Island is characterized by enhanced
intracellular parasitism driven by mitochondrial regulation. Proceedings
of the National Academy of Sciences of the United States of America,
106: 12980-5.
Chaudhuri, R.R., Peters, S.E., Pleasance, S.J., Northern, H.,
Willers, C., Paterson, G.K., Cone, D.B., Allen, A.G., Owen, P.J, Shalom,
G., Stekel. D.J., Charles, I.G. and Maskell, D.J. 2009. Comprehensive
identification of Salmonella enterica serovar typhimurium genes required
for infection of BALB/c mice. PLoS pathogens, 5: e1000529.
Leadbeater, B.S., Yu, Q., Kent, J. and Stekel, D.J. 2009.
Three-dimensional images of choanoflagellate loricae. Proceedings of the
Royal Society B: Biological Sciences, 276:3-11.
Jenkins, D.J. and Stekel, D.J. 2009. A new model for investigating the evolution of transcription control networks. Artificial Life. 15: 259-291.
Fernando, C.T., Liekens, A.M.L., Bingle, E.H., Beck, C., Lenser,
T., Stekel, D.J. and Rowe, J.E. 2008. Molecular circuits for associative
learning in single-celled organisms. J. Roy. Soc. Interface. 6: 463-469.
Leadbeater, B.S., Yu, Q., Kent, J. and Stekel, D.J. 2009. Three-dimensional images of choanoflagellate loricae. Proc Roy Soc B. 276: 3-11.
Jenkins, D.J. and Stekel, D.J. 2008. Effects of signalling on the evolution of gene regulatory networks. Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems. 289 - 296.
Herbert, J.M., Stekel, D.J., Sanderson, S., Heath, V.L.
and Bicknell, R. 2008. A novel method of differential gene expression
analysis using multiple cDNA libraries applied to the identification of
tumour endothelial genes. BMC Genomics. 9:153.
Stekel, D.J. and Jenkins, D.J. 2008. Strong negative self
regulation of prokaryotic transcription factors increases the intrinsic
noise of protein expression. BMC Systems Biology. 2:6.
Chaudhuri, R.R., Loman, N.J., Snyder, L.A., Bailey, C.M., Stekel, D.J. and Pallen, M.A. 2008. xBASE2: a comprehensive resource for comparative bacterial genomics. Nucleic Acids Research. 36:D543-6.
Bowles, E.J., Lee, J.H., Alberio, R., Lloyd, R.E., Stekel, D.J.,
Campbell, K.H., and St John,. J.C. 2007. Contrasting effects of in
vitro fertilization and nuclear transfer on the expression of mtDNA
replication factors. Genetics. 176: 1511-26.
Jones, B., Stekel, D.J., Rowe, J. and Fernando, C. 2007. Is there a Liquid State Machine in the Bacterium Escherichia Coli? Proceedings of the 2007 IEEE Symposium on Artificial Life (CI-Alife 2007). 187-191.
Stekel, D.J., Sarti, D., Trevino, V., Constantinidou, C.,
Hobman, J., Salmon, M., Buckley, C., Penn, C. and Falciani, F. 2005.
Analysis of Host-Pathogen response in infection using Error Model based
Gene Expression Microarray Experiments. Nucleic Acids Research. 33: e53.
Stekel, D.J., Git Y. and Falciani, F. 2000. The comparison of gene expression from multiple cDNA libraries. Genome Research. 10(12):2055-61.
Schettino, G., Folkard, M., Vojnovic, B., Michette, A.G., Stekel, D.J.,
Pfauntcsh, S.K., Prise, K.M. and Michael, B.D. 2000. The ultrasoft
X-ray microbeam: a subcellular probe of radiation response. Radiation Research. 153: 222-225.
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