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Declan Bates


Recent Research Grants

  • Synthetic Integrons for Continuous Directed Evolution of Complex Genetic Ensembles, EPSRC/NSF, (with Dr. Susan Rosser, University of Glasgow, Prof. Paul Freemont, Imperial College London, Prof. Anne Osbourn, John Innes Centre, Prof. Joshua Leonard, Northwestern University, USA and Prof. Jay Keasling, University of Berkeley, USA) 2010-2012.
  • Integrated Cardiopulmonary Modelling for the Investigation of the Management of Disturbed Tissue Perfusion, MRC, (with Dr. Jonathan Hardman and Dr. Iain Moppett, University of Nottingham), 2011-2012
  • Post-Transcriptional Feedback Control of Polyamine Metabolism in Yeast: An Integrated Modelling and Experimental Investigation, BBSRC, (with Dr. Ian Stansfield, University of Aberdeen), 2008-2011.
  • Preventing Ventilator Associated Lung Injury using Feedback Control Engineering, EPSRC, (with Dr. Jonathan Hardman, University of Nottingham), 2008-2011

Selected Publications

  • L. Salerno, C. Cosentino, A. Merola, D.G. Bates and F. Amato, “Validation of a model of the GAL regulatory system via robustness analysis of its bistability characteristics”, BMC Systems Biology, 17;7(1):39, 2013.
  • A.Das, P.P. Menon, J. Hardman and D.G. Bates, “Optimization of Ventilation Settings for Pulmonary Disease States”, IEEE Transactions on Biomedical Engineering, 60(6):1599-607, 2013.
  • F. Montefusco, A. Steinacher, O. Akman, D.G. Bates and O.S. Soyer, “On the Role of Ultrasensitivity in Biomolecular Control Systems”, Invited Session on Control Theory for Synthetic Biology, in Proceedings of the IEEE Conference on Decision and Control, Hawaii, 2012C.
  • Cosentino, L. Salerno, A. Passanti, A. Merola, D.G. Bates, F. Amato, “Structural bistability of the GAL regulatory network and characterization of its domains of attraction”, Journal of Computational Biology, 19(2):148-62, 2012.
  • C. Cosentino and D.G. Bates, Feedback Control in Systems Biology, CRC Press (Taylor & Francis), 2012
  • F. Montefusco, C. Cosentino, F. Amato and D.G. Bates, “Reverse-Engineering Biological InteractionNetworks from Noisy Data using Regularized Least Squares and Instrumental Variables”, Proceedings of the joint IEEE Conference on Decision and Control / European Control Conference, Orlando, Florida, 2011
  • N. Kotov, D.G. Bates et al, “Computational modelling elucidates the mechanism of ciliary regulation in health and disease”, BMC Systems Biology 5:143, 2011
  • D.G. Bates and C. Cosentino, “Validation and Invalidation of Systems Biology Models using Robustness Analysis”, IET Systems Biology, 5(4)229-244, 2011.
  • F. Montefusco, C. Cosentino and D.G. Bates, “Introduction to network reconstruction methods based on dynamical systems theory”, in Handbook of Statistical Systems Biology, M. Stumpf, D.J. Balding, M. Girolami (Eds.), Wiley, 2011.
  • C. Rato, S. Amirova, D.G. Bates, I. Stansfield and H.M. Wallace, “Translational recoding as a feedback controller: systems approaches reveal polyamine-specific effects on the antizyme ribosomal frameshift”, Nucleic Acids Research, doi:10.1093/nar/gkq1349, 2011.
  • A. Das, Z. Gao, P.P. Menon, J. Hardman and D.G. Bates, “A Systems Engineering approach to validation of a pulmonary physiology simulator for clinical applications”, Journal of The Royal Society Interface, doi: 10.1098/rsif.2010.0224, 2011.
  • N.V. Valeyev, D.G. Bates, Y. Umezawa, A.N. Gizatullina, N.V. Kotov, “Systems Biology of Cell Behaviour”, in Systems Biology in Drug Discovery and Development: Methods and Protocols, Methods in Molecular Biology Series, Springer Verlag, 2010.
  • J. Kim, P. Heslop-Harrison, I. Postlethwaite and D. G. Bates, “Structural adaptation and robustness of Dictyostelium ligand-receptor kinetics for low and high ligand concentration”, International Journal of Robust and Nonlinear Control, Special Issue: Focus on Robustness in Systems Biology: Methods and Applications, 20(9): 1047-1058, 2010.
  • J.-S. Kim, N. V. Valeyev, I. Postlethwaite, P. Heslop-Harrison, K.-W. Cho and D. G. Bates, “Analysis and Extension of a Biochemical Network Model Using Robust Control Theory”, International Journal of Robust and Nonlinear Control, Special Issue: Focus on Robustness in Systems Biology: Methods and Applications, 20(9): 1017-1026, 2010
  • C.-Y. Dong, T.-W. Yoon, D. G. Bates and K.-H. Cho, “Identification of Feedback Loops Embedded in Cellular Circuits by Investigating Non-Causal Impulse Response Components”, Journal of Mathematical Biology, DOI: 10.1007/s00285-009-0263-x, 2009.
  • N. V. Valeyev, J.-S. Kim, P. Heslop-Harrison, I. Postlethwaite, N. Kotov and D. G. Bates, “Computational Modelling Suggests Dynamic Interactions between Ca2+, IP3 and G Protein-Coupled Modules are Key to Achieving Robust Dictyostelium Aggregation”, Molecular BioSystems, Vol. 5, 612-628, 2009.
  • N. V. Valeyev, N. Kotov, P. Heslop-Harrison, I. Postlethwaite and D. G. Bates, “Crosstalk between G-protein and Ca2+ pathways switches intracellular cAMP levels”, Molecular BioSystems, Vol. 5(1), 2008.
  • J. Kim, D. G. Bates and I. Postlethwaite, “Evaluation of Stochastic Effects on Biomolecular Networks using the Generalised Nyquist Stability Criterion”, IEEE Transactions on Automatic Control, Vol. 53(8), 2008.
  • N. V. Valeyev, D. G. Bates, P. Heslop-Harrison, I. Postlethwaite and N. Kotov, “Elucidating Mechanisms of Calcium-Dependent Calmodulin Regulation using Structural Systems Biology”, BMC Systems Biology, Vol. 2(48), 2008.