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Professor Declan Bates

Professor of Bioengineering

 

Co-Director, ESPRC/BBSRC Warwick Integrative Synthetic Biology Centre (WISB)

Co-Director (Warwick), EPSRC/BBSRC Centre for Doctoral Training in Synthetic Biology

Co-Director, Interdisciplinary Collaboration in Systems Medicine

School of Engineering
University of Warwick
Coventry
CV4 7AL, UK

Room: D220
Phone: +44 (0)24 765 23142

D dot Bates at warwick dot ac dot uk

Full CV

 

News | Research Interests | Teaching | Publications | Research Grants | Profile

News

  • August 2019: Congratulations to Alex who has been awarded a BBSRC Flexible Talent Mobility Account Innovation Fellowship to work with Ingenza on potential commercial applications of his research.
  • July 2019: Excellent visit with Prof. John Laffey and his team at the NUI Galway Curam Research Centre on Medical Devices and the Intensive Care Unit at Galway University Hospital.
  • March 2019: Follow-up article on our Intensive Care Medicine article in the Science page of the Irish Times.
  • March 2019: Congratulations to Alex who has won the inaugural Faculty Post-Doctoral Research Prize for Engineering.
  • February 2019: News story on our research in the Irish Times.
  • February 2019: Our first paper with Dr. Nadir Yehya of the Children's Hospital of Philadelphia is published in the leading journal in the field of Intensive Care Medicine! Read the University press release on this research here.
  • October 2018: Very honoured to speak at the 8th Hedenstierna Laboratory Master Class Symposium in Uppsala University, Sweden, on our work on physiological modelling for intensive care and anaesthesia.
  • October 2018: New paper in Trends in Biotechnology with WISB Research Fellow Lauren Swiney looking at ways in which cognitive biases shape public perceptions of Synthetic Biology.
  • August 2018: Nuno and Alex will both be presenting their work at a special invited session on Biomolecular Computing and Feedback Systems at the upcoming IEEE CDC in Miami in December.
  • August 2018: Anup's new paper is published in the Journal of the Royal Army Medical Corps!
  • June 2018: Warwick University press release on Iulia's ACS Synthetic Biology paper.
  • May 2018: Congratulations to Alex, who has passed his PhD viva subject to minor corrections, and has already started as a PDRA in the group. Also welcome to Dr. Ahmad Mannan, who joins the group as a WISB PDRA. We expect great things!
  • May 2018: Congratulations to Iulia, whose paper with Mathias "A Framework for Engineering Stress Resilient Plants using Genetic Feedback Control and Regulatory Network Rewiring" has just been published in ACS Synthetic Biology!
  • April 2018: Congratulations to Mathias, who has taken up a lecturing position at Coventry University.
  • March 2018: Warwick University press release on Alex's Nature Comms paper.
  • December 2017: Congratulations to Alex, whose paper with our collaborators from the Jimenez lab has been accepted for publication in Nature Communications!
  • November 2017: Congratulations to Melchior, who has passed his PhD viva subject to minor corrections.
  • September 2017: Excellent talks and fun times at WISB's International Workshop in Venice.
  • July 2017: A three year PDRA position funded by the Leverhulme Trust is now available in our group to conduct research on the control of chemical reaction networks. For more details and to apply, click here.
  • July 2017: Jack's new paper with Victoria Hsiao (Caltech) and Wilson Wong (Boston University) on modelling recombinase-based temporal logic gates is published in the inaugural issue of IET Engineering Biology.
  • May 2017: A pre-print of Alex's new paper on cellular resource allocation controllers is now on bioRXiv and is in the top 5% of all research outputs ever tracked by Altmetric.
  • March 2017: Very much looking forward to starting our new £1.4M EPSRC project on “Personalised Simulation Technologies for Optimising Treatment in the Intensive Care Unit: Realising Industrial and Medical Applications”, in collaboration with our industrial and academic partners Prof. Jonathan Hardman, University of Nottingham, and Dr. Luigi Camporota, King’s College London.
  • January 2017: A nice "Crystal Ball" essay in Microbial Biotechnology from our collaborator Dr. Jose Jimenez of the University of Surrey on the future role of modelling in biology.
  • December 2016: Congratulations to Emzo de los Santos who has been awarded a four-year Research Career Development Fellowship from WISB. We expect great things!
  • November 2016: Anup's new paper with Marc Chikhani and Jon Hardman from the University of Nottingham is published in the world's leading journal in the field of Anaesthesiology.
  • October 2016: Bon voyage to Rucha Sawlekar who has submitted her PhD thesis exactly 3 years after joining the group and is now departing to take up a PDRA position with Jorge Goncalves' group in Luxembourg. All the best Rucha and we will miss you!
  • September 2016: After a heroic amount of work by Melchior du Lac, our new paper with the Leonard Lab on "Predicting the dynamics and heterogeneity of genomic DNA content within bacterial populations across variable growth regimes" has been accepted for publication in an upcoming special issue of ACS Synthetic Biology on bio-design automation. Congratulations Mel!
  • June 2016: Press release from the University of Nottingham about our new EPSRC Healthcare Grand Challenges Network on Closed Loop Control Systems for Optimisation of Treatment

Research Interests

  • Systems Medicine
    • Pulmonary and cardiovascular pathophysiology

    • Mechanical ventilation of critically ill patients

    • Personalised simulation and control technologies for the Intensive Care Unit

  • Synthetic Biology
    • Systems and control theory for synthetic biology

    • Modelling and simulation frameworks for robust model-based design of synthetic biological systems

    • Design of synthetic circuits using recombinases and DNA-based chemistry

For papers and research grants related to my previous research on Aerospace Control, click here


Teaching


Recent Publications

  • M. Foo, D.G. Bates and O.A. Akman, "A simplified modelling framework facilitates more complex representations of plant circadian clocks", submitted, 2019.
  • J.E. Bowyer, D. Chakravarti, W.W. Wong and D.G. Bates, "Mechanistic modelling of tyrosine recombination reveals key parameters determining the performance of a CAR T cell switching circuit", submitted, 2019.
  • N.M.G. Paulino, M. Foo, J. Kim and D.G. Bates, "On nucleic acid feedback controllers", submitted, 2019. Preprint pdf available on arXiv.
  • A.P.S. Darlington and D.G. Bates, "Combining transcriptional and translational resource allocation controllers for synthetic circuits", to appear in the proceedings of the 58th IEEE Conference on Decision and Control, Nice, France, 2019.
  • N.M.G. Paulino, M. Foo, J. Kim and D.G. Bates, "PID and state feedback controllers using DNA strand displacement reactions", to appear in the proceedings of the 58th IEEE Conference on Decision and Control, Nice, France, 2019 and IEEE Control Systems Letters, 3(4) pp. 805-810, 2019. pdf
  • M. Haque, T.E. Scott, A. Das, I. Cliff, D.G. Bates and J.G. Hardman, "Efficacy of continuous positive airway pressure (CPAP) in casualties suffering from primary blast lung injury: A modeling study", in the proceedings of the 41st IEEE Engineering in Biology and Medicine Conference, Berlin, 2019. pdf
  • M. Laviola, C. Niklas, A. Das, D.G. Bates and J.G. Hardman, "High oxygen fraction during airway opening is key to effective airway rescue in obese subjects", in the proceedings of the 41st IEEE Engineering in Biology and Medicine Conference, Berlin, 2019. pdf
  • N.M.G. Paulino, J. Kim, M. Foo, D.G. Bates, "Robustness analysis of a nucleic acid controller for a dynamic biomolecular process using the structured singular value", Journal of Process Control, Vol. 78C, pp. 34-44, 2019. pdf
  • S. Saffaran, A. Das, J.G. Hardman, N. Yehya and D.G. Bates, "High-fidelity Computational Simulation to Refine Strategies for Lung-Protective Ventilation in Paediatric Acute Respiratory Distress Syndrome", Intensive Care Medicine, https://doi.org/10.1007/s00134-019-05559-4, 2019. pdf  supplemental file
  • A. Das, L. Camporota, J.G. Hardman and D.G. Bates, "What links ventilator driving pressure with survival in the acute respiratory distress syndrome? A computational study", Respiratory Research, 20:29, DOI: https://doi.org/10.1186/s12931-019-0990-5, 2019. pdf
  • M. Laviola, A. Das, M. Chikhani, D.G. Bates and J.G. Hardman, "Computer simulation clarifies mechanisms of carbon dioxide clearance during apnoea", British Journal of Anaesthesia, https://doi.org/10.1016/j.bja.2018.11.012, 2019. pdf
  • A.P.S. Darlington, J. Kim and D.G. Bates, "Robustness Analysis of a Synthetic Translational Resource Allocation Controller", IEEE Control Systems Letters (Special Issue on Control and Network Theory for Biological Systems), Vol 3(2), DOI: 10.1109/LCSYS.2018.2867368, 2019. pdf SM
  • L. Swiney, D.G. Bates and J. Coley, "Cognitive constraints shape public debate on the risks of synthetic biology", Trends in Biotechnology, DOI:https://doi.org/10.1016/j.tibtech.2018.09.0022018, 2018. pdf
  • N.M.G. Paulino, M. Foo, J. Kim and D.G. Bates, "Uncertainty Modelling and Stability Robustness Analysis of Nucleic Acid-Based Feedback Control Systems", in the proceedings of the 57th IEEE Conference on Decision and Control, (Invited Session on Biomolecular Computing and Feedback Systems ), Miami Beach, FL, USA, 2018. pdf
  • A.P.S. Darlington and D.G. Bates, "On the design of integral translational resource allocation controllers for synthetic cellular circuitry", in the proceedings of the 57th IEEE Conference on Decision and Control, (Invited Session on Biomolecular Computing and Feedback Systems ), Miami Beach, FL, USA, 2018. pdf
  • A.P.S. Darlington, J. Kim, J.I. Jimenez, and D.G. Bates, "Engineering Translational Resource Allocation Controllers: Mechanistic Models, Design Guidelines, and Potential Biological Implementations", ACS Synthetic Biology, DOI: 10.1021/acssynbio.8b00029, 2018. pdf
  • M. Haque, A. Das, T.E. Scott, D.G. Bates, and J.G. Hardman, "The primary blast lung injury simulator: A new computerised model", Journal of the Royal Army Medical Corps, DOI: 10.1136/jramc-2018-000989, 2018. pdf
  • S. Saffaran, W. Wang, A. Das, W. Schmitt, J.G. Hardman, G. Weimann and D.G. Bates, "An inhaled sGC modulator can lower PH in COPD patients without deteriorating oxygenation", CPT Pharmacometrics & Systems Pharmacology, DOI: 10.1002/psp4.12308, 2018. pdf
  • M. Foo, I. Gherman, P. Zhang, D.G. Bates and K. Denby, "Engineering Stress Resilient Plants using Genetic Feedback Control and Regulatory Network Rewiring", ACS Synthetic Biology, 7 (6), pp 1553–1564, DOI: 10.1021/acssynbio.8b00037, 2018. pdf
  • J. Kim, M. Foo, and D.G. Bates, "Computationally Efficient Modelling of Stochastic Spatio-Temporal Dynamics in Biomolecular Networks", Scientific Reports 8:3498, DOI:10.1038/s41598-018-21826-8, 2018. pdf
  • A.P.S. Darlington, J. Kim, J.I. Jimenez, and D.G. Bates, "Dynamic Allocation Of Orthogonal Ribosomes Facilitates Uncoupling Of Co-Expressed Genes", Nature Communications, 9:695, DOI: 10.1038/s41467-018-02898-62018, 2018. pdf
  • M. Foo, J. Kim, and D.G. Bates, "Modelling and Control of Gene Regulatory Networks for Perturbation Mitigation", IEEE/ACM Transactions on Computational Biology and Bioinformatics, DOI: 10.1109/TCBB.2017.2771775, 2017. pdf
  • J.E. Bowyer, E.L.C. de los Santos, K.M. Styles, C. Corre and D.G. Bates, "Modeling the Architecture of the Regulatory System Controlling Methylenomycin Production in Streptomyces coelicolor", Journal of Biological Engineering, 11:30, DOI: 10.1186/s13036-017-0071-6, 2017. pdf
  • D.O.A. Alowa, T.A. Tahir, M. Fischer, D.G. Bates, S. Amirova and N.P.J. Brindle, "Regulation of Angiopoietin Signalling by Endogenous Soluble Tie2 Ectodomain and Engineered Ligand Trap", Scientific Reports, 7:3658, DOI: 10.1038/s41598-017-03981-6, 2017. pdf
  • J.E. Bowyer, V. Hsiao, W.W. Wong and D.G. Bates, "Mechanistic modelling of a recombinase-based two-input temporal logic gate", IET Engineering Biology, 2017. pdf
  • M. Laviola, A. Das, M. Chikhani, D.G. Bates and J.G. Hardman "Investigating the effect of cardiac oscillations and deadspace gas mixing during apnea using computational simulation", in proceedings of the 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, JeJu Island, S. Korea, 2017.
  • S. Saffaran, A. Das, J.G. Hardman, N. Yehya, and D.G. Bates, "Development and Validation of a Computational Simulator for Pediatric ARDS Patients", in proceedings of the 39th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, JeJu Island, S. Korea, 2017.
  • M. Foo, I. Gherman, K. Denby and D.G. Bates, "Control Strategies for Mitigating the Effect of External Perturbations on Gene Regulatory Networks", in proceedings of the 20th World Congress of the International Federation of Automatic Control (IFAC), Toulouse, 2017.
  • M. Foo, J. Kim and D.G. Bates, "System identification of gene regulatory networks for perturbation mitigation via feedback control", in proceedings of the 14th IEEE International Conference on Networking, Sensing and Control, Calabria, 2017.
  • A. Das, M. Haque, M. Chikhani, O. Cole, W. Wang, J.G. Hardman and D.G. Bates, "Hemodynamic effects of lung recruitment maneuvers in acute respiratory distress syndrome", BMC Pulmonary Medicine, 17:34,

    DOI: 10.1186/s12890-017-0369-7, 2017. pdf

  • M. Foo, J. Kim, R. Sawlekar and D.G. Bates, "Embedded inverse-feedforward tracking control of enzymatic reaction processes", Computers & Chemical Engineering, 99, 145–157, DOI: 10.1016/j.compchemeng.2017.01.027, 2017. pdf
  • M. Foo, J. Kim, J. Kim and D.G. Bates, "Proportional-Integral Degradation (PI-Deg) control allows accurate tracking of biomolecular concentrations with fewer chemical reactions", IEEE Life Sciences Letters, 2(4), DOI: 10.1109/LLS.2016.2644652, 2016. pdf
  • M. Foo, R. Sawlekar and D.G. Bates, "Exploiting the dynamic properties of covalent modification cycles for the design of synthetic analog circuitry", Journal of Biological Engineering, 10:15, DOI: 10.1186/s13036-016-0036-1, 2016. pdf
  • M. Chikhani, A. Das, M. Haque, W. Wang, D.G. Bates, and J.G. Hardman, "High PEEP in ARDS: evaluating the trade-off between improved oxygenation and decreased oxygen delivery", British Journal of Anaesthesia, 117 (5): 650–8 (2016) DOI: 10.1093/bja/aew314, 2016. pdf
  • J. Bowyer, V. Hsiao and D.G. Bates, "Development and Experimental Validation of a Mechanistic Model of a Recombinase-Based Temporal Logic Gate", in proceedings of the 12th IEEE Biomedical Circuits and Systems Conference, Shanghai, 2016. pdf
  • R. Sawlekar, M. Foo and D.G. Bates, "Robustness Analysis of DNA-based Biomolecular Feedback Controllers to Parametric and Time Delay Uncertainties", in proceedings of the 12th IEEE Biomedical Circuits and Systems Conference, Shanghai, 2016. pdf
  • M. du Lac, A. Scarpelli, A.K.D. Younger, D.G Bates and J. Leonard, "Predicting the dynamics and heterogeneity of genomic DNA content within bacterial populations across variable growth regimes", ACS Synthetic Biology, Special Issue on Bio-Design Automation, DOI: 10.1021/acssynbio.5b00217, 2016. pdf
  • M. Bilotta, C. Cosentino, A. Merola, D.G. Bates and F. Amato, "Zero-Retroactivity Subtraction Module for Embedded Feedback Control of Chemical Reaction Networks", in proceedings of the 6th IFAC Conference on Foundations of Systems Biology in Engineering, Magdeburg, 2016. pdf
  • F. Montefusco, O. Akman, O. Soyer and D.G. Bates, "Ultrasensitive Negative Feedback Control: A Natural Approach for the Design of Synthetic Controllers", PloS One 11(8):e0161605, doi:10.1371/journal.pone.0161605, 2016. pdf
  • M. Foo, R. Sawlekar, V.V. Kulkarni and D.G. Bates, "Biologically inspired design of feedback control systems implemented using DNA strand displacement reactions", in proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Orlando, 2016. pdf
  • A. Darlington and D.G. Bates, "Host-aware modelling of a synthetic genetic oscillator", in proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Orlando, 2016. pdf
  • A. Das, M. Haque, M. Chikhani, W. Wang, J.G. Hardman and D.G. Bates, "Creating Virtual ARDS Patients", in proceedings of the 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Orlando, 2016. pdf
  • M. Foo, R. Sawlekar, J. Kim, G.-B. Stan, D.G. Bates and V.V. Kulkarni, "On the biomolecular implementation of nonlinear system theoretic operators", in the Proceedings of the European Control Conference, Aalborg, 2016. pdf
  • R. Sawlekar, F. Montefusco, V.V. Kulkarni and D.G. Bates, "Implementing Nonlinear Feedback Controllers using DNA Strand Displacement Reactions", IEEE Transactions on NanoBioscience, DOI: 10.1109/TNB.2016.2560764, 2016. pdf
  • J. Bowyer, J. Zhao, P. Subsoontorn, W. Wong, S. Rosser and D.G. Bates, "Mechanistic Modeling of a Rewritable Recombinase Addressable Data Module", IEEE Transactions on Biomedical Circuits and Systems, 10(6), 1161-1170, DOI: 10.1109/TBCAS.2016.2526668, 2016. pdf
  • A. Steinacher, D.G. Bates, O. Akman and O. Soyer, "Nonlinear Dynamics in Gene Regulation Promote Robustness and Evolvability of Gene Expression Levels", PLoS ONE 11(4): e0153295. doi:10.1371/journal.pone.0153295, 2016. pdf
  • W. Wang, A. Das, O. Cole, M. Chikhani, J.G. Hardman and D.G. Bates, "Computational simulation indicates that moderately high frequency ventilation can allow safe reduction of tidal volumes and airway pressures in ARDS patients", Intensive Care Medicine Experimental 3(1), 1-12, 2015. pdf
  • R. Sawlekar, F. Montefusco, V.V. Kulkarni and D. G. Bates, "Biomolecular Implementation of a Quasi Sliding Mode Feedback Controller based on DNA Strand Displacement Reactions", in Proceedings of the 37th IEEE Engineering in Medicine and Biology Conference, Milano, 2015. pdf
  • J. Bowyer, J. Zhao, S. Rosser, S. Colloms and D.G. Bates, "Development and Experimental Validation of a Mechanistic Model of in vitro DNA Recombination", in Proceedings of the 37th IEEE Engineering in Medicine and Biology Conference, Milano, 2015. pdf
  • A. Das, M. Haque, M. Chikhani, W. Wang, T. Ali, O. Cole, J.G. Hardman and D.G. Bates, "Development of an Integrated Model of Cardiovascular and Pulmonary Physiology for the Evaluation of Mechanical Ventilation Strategies", in Proceedings of the 37th IEEE Engineering in Medicine and Biology Conference, Milano, 2015. pdf
  • M. Bilotta, C. Cosentino, D.G. Bates and F. Amato, "Retroactivity Analysis of a Chemical Reaction Network Module for the Subtraction of Molecular Fluxes", in Proceedings of the 37th IEEE Engineering in Medicine and Biology Conference, Milano, 2015. pdf
  • A. Das, O. Cole, M. Chikhani, W. Wang, T. Ali, M. Haque, J.G. Hardman and D.G. Bates, "Evaluation of lung recruitment maneuvers in Acute Respiratory Distress Syndrome using computer simulation", Critical Care, 19:8, doi:10.1186/s13054-014-0723-62014, 2015. pdf
  • W. Wang, P.P. Menon, D.G. Bates, S. Ciabuschi, N.M. Gomes Paulino, E. Di Sotto, A. Bidaux, A. Kron, S. Salehi, S. Bennani, "Verification and Validation Framework for Autonomous Rendezvous Systems in the Terminal Phase", AIAA Journal of Spacecraft and Rockets, doi: 10.2514/1.A32531, 2014. pdf
  • W. Wang, A. Das, T. Ali, O. Cole, M. Chikhani, M. Haque, J.G. Hardman and D.G. Bates, "Can computer simulators accurately represent the pathophysiology of individual COPD patients?", Intensive Care Medicine Experimental, 2:23, doi:10.1186/s40635-014-0023-02014, 2014. pdf
  • F. Montefusco, O.E. Akman, O.S. Soyer, and D.G. Bates, "Modelling and Analysis of Feedback Control Mechanisms Underlying Osmoregulation in Yeast", in A Systems Theoretic Approach to Systems and Synthetic Biology, Editors: V.V. Kulkarni, G.-B. Stan and K. Raman, 2014. pdf
  • J. Kim, M. Kishida and D.G. Bates, "State bounds estimation for nonlinear systems using mu-analysis", in Proceedings of the 19th World Congress of the International Federation of Automatic Control, Cape Town, South Africa. August 24-29, 2014. pdf
  • 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. pdf
  • 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. pdf
  • 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, 2012. pdf
  • C. 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. pdf
  • C. Cosentino and D.G. Bates, Feedback Control in Systems Biology, CRC Press (Taylor & Francis), 2011.
  • F. Montefusco, C. Cosentino, F. Amato and D.G. Bates, “Reverse-Engineering Biological Interaction Networks 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. pdf
  • 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. pdf
  • D.G. Bates and C. Cosentino, “Validation and Invalidation of Systems Biology Models using Robustness Analysis”, IET Systems Biology, 5(4)229-244, 2011. pdf
  • 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. pdf
  • 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. pdf
  • 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. pdf
  • 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. pdf
  • 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. pdf
  • 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. pdf
  • 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. pdf
  • 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. pdf
  • 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. pdf

Current/Recent Research Grants

  • £145K, Towards a Comprehensive Theory of Feedback Control for Chemical Reaction Networks, Leverhulme Trust, 2018-2021
  • £59.7K, Investigation of Closed-Loop Ventilation Strategies for Neonatal ICU Patients using Computational Simulation, EPSRC Healthcare Technologies Network Plus Feasibility Study, (with Prof. Don Sharkey and Prof. Jonathan Hardman, University of Nottingham), 2018-2019
  • £1.1M, Personalised Simulation Technologies for Optimising Treatment in the Intensive Care Unit: Realising Industrial and Medical Applications, EPSRC, with Prof. Jonathan Hardman, University of Nottingham, and Dr. Luigi Camporota, King’s College London, 2017-2021
  • £298K/$665K, Rewritable Biocomputers in Mammalian Cells, BBSRC/NSF, (with Prof. Wilson Wong, University of Boston), 2017-2020
  • £634K, Closed Loop Control Systems for Optimisation of Treatment, EPSRC Healthcare Technologies Network Plus Grant, (with Prof. Steve Morgan and Prof. Jonathan Hardman, University of Nottingham, and Prof. Helen Byrne, University of Oxford), 2016-2019
  • £220K, Development of a Computational Simulator, Bayer Healthcare, Commercial Research Contract, 2015-2017
  • £12.4M, Warwick Integrative Synthetic Biology Centre, BBSRC/EPSRC, (with Prof. John McCarthy and Prof. Orkun Soyer, University of Warwick), 2015-2020
  • £4.7M, Centre for Doctoral Training in Synthetic Biology, EPSRC/BBSRC, (with Prof. Antonis Papachristodoulou, Prof. Andrew Tuberfield, Prof. Judy Armitage, University of Oxford, Prof. Claire Grierson, Prof. Dek Wolfson, University of Bristol, Prof. Orkun Soyer, University of Warwick), 2014-2022.
  • £1.4M, Exploiting the Syntegron Technology Platform for Assembly and Optimisation of Complex Genetic Ensembles, EPSRC/NSF, (with Prof. 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) 2013-2016.
  • £650K, Integrated Cardiopulmonary Modelling for the Investigation of the Management of Disturbed Tissue Perfusion, MRC, (with Prof. Jonathan Hardman and Dr. Iain Moppett, University of Nottingham), 2012-2015.
  • £4M, Engineering Synthetic Microbial Communities for Biomethane Production, BBSRC sLOLA, (with Prof. Orkun Soyer, School of Life Sciences, University of Warwick, Prof. Richard Titball, Prof. David Studholme and Prof. Angus Buckling, University of Exeter, Prof. Russell Davenport, Prof. Jan Dolfing and Prof. Tom Curtis, University of Newcastle, David Campbell Stuckey, Imperial College London, Prof. David Swarbreck, TGAC), 2013-2018.
  • £425K, Development, Validation and Application of Population-Based Pulmonary Disease Models using Robustness Analysis and Ensemble Forecasting, EPSRC, (with Prof. Jonathan Hardman, Queen’s Medical Centre, University of Nottingham), 2011-2014.
  • £417K, Evolving Controllers and Controlling Evolution, EPSRC (with Prof. Orkun Soyer, School of Life Sciences, University of Warwick), 2011-2014.
  • £1.4M, 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.
  • £586, 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.
  • £432K, Preventing Ventilator Associated Lung Injury using Feedback Control Engineering, EPSRC, (with Dr. Jonathan Hardman, University of Nottingham), 2008-2011.

Profile

Declan Bates is Professor of Bioengineering in the School of Engineering at the University of Warwick. He is Co-Director of the BBSRC/EPSRC Warwick Integrative Synthetic Biology Centre (WISB), and Co-Director at Warwick of the EPSRC/BBSRC Oxford-Warwick-Bristol Centre for Doctoral Training in Synthetic Biology.

Prof. Bates was born in Clonmel, Co. Tipperary, Ireland in 1970 and educated at Powerstown National School and the High School, Clonmel. He received a B.Eng degree in Electronic Engineering and a Ph.D. degree in Robust Control Theory from the School of Electronic Engineering, Dublin City University, Ireland, in 1992 and 1996 respectively. On completing his PhD he joined the Control and Instrumentation Research Group led by Prof. Ian Postlethwaite in the Department of Engineering at Leicester University, where he worked as a post-doctoral research associate, lecturer, and senior lecturer, before being appointed to a Personal Chair in Control Engineering, aged 38. In 2010 he was appointed Professor of Biological Systems Engineering in the College of Engineering, Mathematics and Physical Sciences of the University of Exeter and in 2013 he moved to the University of Warwick as Professor of Bioengineering.

His early research applied design and analysis methods from robust control theory to a range of aersopace systems, including gas-turbine engines (with Alstom Power) and large passenger aircraft (with Airbus). Between 2007 and 2012 his group participated in nine international research projects funded by the European Space Agency. Working with industrial partners including GMV, Deimos Space, Alenia Thales and Astrium, these projects developed advanced verification and validation methods for applications ranging from hypersonic re-entry vehicles, launch vehicles, flexible satellites and autonomous rendezvous systems. His current research is focussed on the modelling, analysis, design and control of complex biological and medical systems. In 2006, he was awarded an EPSRC Discipline Hopping Research Fellowship with Prof. Jonathan Hardman of the Queen's Medical Centre of the University of Nottingham to pursue research on the Control Engineering/Life Sciences Interface - his collaborative work with Prof. Hardman has been continuously funded by EPSRC, MRC and industry since that time.

He has served on numerous research grant review panels in the UK and internationally, including on BBSRC's Engineering and Biological Systems Research Committee, and subsequently BBSRC's Research Committee C on Technology and Methodological Development (2007 to 2010), on MRC's Systems immunology of the Human Life Course Review Panel (2013), as a member of EPSRC's Peer Review College (2013 to present), as a member, Co-Chair and subsequently Chair of the Research Grants Review Committee of the International Human Frontier Science Program (2009 to 2014), as Chair of the HFSP review committee for Career Development Awards (2016 to 2019), on the international ERA-NET Synthetic Biology Expert Evaluation Panel (2014), on the Technology and Production Sciences - Biomedical Engineering Panel of the Independent Research Fund Denmark (2019), and the French National Research Agency "Mathématiques et sciences du numérique pour la biologie et la santé" committee (2019).

He is the co-author (with Carlo Cosentino) of Feedback Control in Systems Biology, published by Taylor & Francis. From 2016 to 2019 he acted as external examiner for the M.Res. Degree in Systems and Synthetic Biology at Imperial College London, and is currently external examiner for the Electrical & Electronic Engineering B.Eng Degree programme at Technological University Dublin. He has authored more than 200 peer reviewed research publications and obtained funding in excess of £10M from EPSRC, BBSRC, MRC, The Leverhulme Trust, ESA and industry.

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Postdoctoral Research Associates:

Dr. Anup Das

Dr. Ahmad Mannan

Dr. Jack Bowyer

Dr. Alexander Darlington

Dr. Emzo de los Santos (WISB Research Career Development Fellow)


PhD students:

Sina Saffaran

Nuno Paulino

Alexandros Constantinou

Laurence Legon

 

Book

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Alumni:

Dr. Prathyush Menon

Dr. Jongrae Kim

Dr. Zhiwei Gao

Dr. Francesco Montefusco

Dr. Rucha Sawlekar

Dr. Mathias Foo