2022

Weaver, Liam, Das, Anup, Saffaran, Sina, Yehya, Nadir, Chikhani, Marc, Scott, Timothy E., Laffey, John G., Hardman, Jonathan G., Camporota, Luigi and Bates, Declan G. (2022) Optimising respiratory support for early COVID-19 pneumonia : a computational modelling study. British Journal of Anaesthesia, 128 (6). pp. 1052-1058. doi:10.1016/j.bja.2022.02.037 (In Press)

Mistry, Sonal, Das, Anup, Saffaran, Sina, Yehya, Nadir, Scott, Timothy E., Chikhani, Marc, Laffey, John G., Hardman, Jonathan G., Camporota, Luigi and Bates, Declan G. (2022) Validation of at-the-bedside formulae for estimating ventilator driving pressure during airway pressure release ventilation using computer simulation. Respiratory Research, 23 (1). 101. doi:10.1186/s12931-022-01985-z

Hannon, David M., Mistry, Sonal, Das, Anup, Saffaran, Sina, Laffey, John G., Brook, Bindi S., Hardman, Jonathan G. and Bates, Declan G. (2022) Modeling mechanical ventilation in silico—potential and pitfalls. Seminars in Respiratory and Critical Care Medicine . doi:10.1055/s-0042-1744446 (In Press)

Foo, Mathias, Akman, Ozgur E. and Bates, Declan G. (2022) Restoring circadian gene profiles in clock networks using synthetic feedback control. npj Systems Biology and Applications, 8 . 7. doi:10.1038/s41540-022-00216-x

Montefusco, Francesco, Procopio, Anna, Bates, Declan G., Amato, Francesco and Cosentino, Carlo (2022) Scalable reverse‐engineering of gene regulatory networks from time‐course measurements. International Journal of Robust and Nonlinear Control . doi:10.1002/rnc.6044 (In Press)

Mistry, Sonal, Das, Anup, Hardman, Jonathan G., Bates, Declan G. and Scott, Timothy E. (2022) Pre-hospital continuous positive airway pressure after blast lung injury and hypovolaemic shock : a modelling study. British Journal of Anaesthesia, 128 (2). E151-E157. doi:10.1016/j.bja.2021.10.012

2020

Paulino, Nuno M.G., Foo, Mathias, de Greef, Tom F.A., Kim, Jongmin and Bates, Declan G. (2020) Minimally complex nucleic acid feedback control systems for first experimental implementations. IFAC-PapersOnLine, 53 (2). pp. 16745-16752. doi:10.1016/j.ifacol.2020.12.1135

2019

Saffaran, Sina, Das, Anup, Hardman, Jonathan G., Yehya, Nadir and Bates, Declan (2019) High-fidelity computational simulation to refine strategies for lung-protective ventilation in paediatric acute respiratory distress syndrome. Intensive Care Medicine, 45 . pp. 1055-1057. doi:10.1007/s00134-019-05559-4

Paulino, Nuno M.G., Foo, Mathias, Kim, Jongmin and Bates, Declan G. (2019) Robustness analysis of a nucleic acid controller for a dynamic biomolecular process using the structured singular value. Journal of Process Control, 78 . pp. 34-44. doi:10.1016/j.jprocont.2019.02.009

Foo, Mathias, Kim, Jongrae and Bates, Declan (2019) Modelling and control of gene regulatory networks for perturbation mitigation. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 16 (2). pp. 583-595. doi:10.1109/TCBB.2017.2771775

Das, Anup, Camporota, Luigi, Hardman, Jonathan G. and Bates, Declan G. (2019) What links ventilator driving pressure with survival in the acute respiratory distress syndrome? A computational study. Respiratory Research, 20 (1). doi:10.1186/s12931-019-0990-5

2018

Darlington, Alexander P.S. and Bates, Declan G. (2018) On the design of integral translational resource allocation controllers for synthetic cellular circuitry. In: 2018 IEEE Conference on Decision and Control (CDC) pp. 1104-1109. doi:10.1109/CDC.2018.8618723

Laviola, Marianna, Das, Anup, Bates, Declan G. and Hardman, Jonathan G. (2018) Computational modelling of oxygen insufflation during apnoea in obesity. European Respiratory Journal . PA2320. doi:10.1183/13993003.congress-2018.PA2320

Darlington, Alexander P. S., Kim, Juhyun, Jiménez, José I. and Bates, Declan G. (2018) Engineering Translational Resource Allocation Controllers: Mechanistic Models, Design Guidelines, and Potential Biological Implementations. ACS Synthetic Biology, 7 (11). pp. 2485-2496. doi:10.1021/acssynbio.8b00029

Swiney, Lauren, Bates, Declan G. and Coley, John D. (2018) Cognitive Constraints Shape Public Debate on the Risks of Synthetic Biology. Trends in Biotechnology, 36 (12). pp. 1199-1201. doi:10.1016/j.tibtech.2018.09.002

Darlington, Alexander P. S., Kim, Jongrae and Bates, Declan G. (2018) Robustness Analysis of a Synthetic Translational Resource Allocation Controller. IEEE Control Systems Letters, 3 (2). pp. 266-271. doi:10.1109/LCSYS.2018.2867368

Haque, Mainul, Das, Anup, Scott, Timothy E., Bates, Declan and Hardman, J. G. (2018) Primary blast lung injury simulator : a new computerised model. Journal of the Royal Army Medical Corps . doi:10.1136/jramc-2018-000989

Saffaran, Sina, Wang, Wenfei, Das, Anup, Schmitt, Walter, Becker-Pelster, Eva-Maria, Hardman, Jonathan G., Weimann, Gerrit and Bates, Declan (2018) Inhaled sGC modulator can lower PH in patients with COPD without deteriorating oxygenation. CPT: pharmacometrics & systems pharmacology, 7 (8). pp. 491-498. doi:10.1002/psp4.12308

Foo, Mathias, Gherman, Iulia, Zhang, Peijun, Bates, Declan G. and Denby, Katherine J. (2018) A Framework for 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

Foo, Mathias, Gherman, Iulia, Zhang, Peijun, Bates, Declan G. and Denby, Katherine J. (2018) A framework for engineering stress resilient plants using genetic feedback control and regulatory network rewiring. ACS Synthetic Biology . doi:10.1021/acssynbio.8b00037

Kim, Jongrae, Foo, Mathias and Bates, Declan G. (2018) Computationally efficient modelling of stochastic spatio-temporal dynamics in biomolecular networks. Scientific Reports, 8 (1). 3498. doi:10.1038/s41598-018-21826-8

Darlington, Alexander P. S., Kim, Juhyun, Jiménez, José I. and Bates, Declan (2018) Dynamic allocation of orthogonal ribosomes facilitates uncoupling of co-expressed genes. Nature Communications, 9 (1). 695. doi:10.1038/s41467-018-02898-6

2017

Bowyer, Jack E., LC. de los Santos, Emmanuel, Styles, Kathryn, Fullwood, Alex, Corre, Christophe and Bates, Declan (2017) Modeling the architecture of the regulatory system controlling methylenomycin production in Streptomyces coelicolor. Journal of Biological Engineering, 11 (1). 30. doi:10.1186/s13036-017-0071-6

Alawo, Deborah O. A., Tahir, Tariq A., Fischer, Marlies, Bates, Declan, Amirova, Svetlana R. and Brindle, Nicholas P. J. (2017) Regulation of angiopoietin signalling by soluble Tie2 ectodomain and engineered ligand trap. Scientific Reports, 7 (1). 3658. doi:10.1038/s41598-017-03981-6

Bowyer, Jack E., Hsiao, Victoria, Wong, Wilson W. and Bates, Declan (2017) Mechanistic modelling of a recombinase-based two-input temporal logic gate. Engineering Biology, 1 (1). pp. 40-50. doi:10.1049/enb.2017.0006

Foo, Mathias, Kim, Jongrae, Sawlekar, Rucha and Bates, Declan (2017) Design of an embedded inverse-feedforward biomolecular tracking controller for enzymatic reaction processes. Computers & Chemical Engineering, 99 . pp. 145-157. doi:10.1016/j.compchemeng.2017.01.027

Das, Anup, Haque, Mainul, Chikhani, Marc, Cole, Oana, Wang, Wenfei, Hardman, Jonathan G. and Bates, Declan (2017) Hemodynamic effects of lung recruitment maneuvers in acute respiratory distress syndrome. BMC Pulmonary Medicine, 17 . 34. doi:10.1186/s12890-017-0369-7

Foo, Mathias, Sawlekar, Rucha, Kim, J., Bates, Declan, Stan, Guy-Bart and Kulkarni, Vishwesh V. (2017) Biomolecular implementation of nonlinear system theoretic operators. In: European Control Conference 2016, Aalborg, Denmark, 29 Jun-1 Jul 2016. Published in: 2016 European Control Conference (ECC) ISBN 9781509025923. doi:10.1109/ECC.2016.7810556

Du Lac, Melchior, Scarpelli, Andrew H., Younger, Andrew K. D., Bates, Declan and Leonard, Joshua N. (2017) Predicting the dynamics and heterogeneity of genomic DNA content within bacterial populations across variable growth regimes. ACS Synthetic Biology, 6 (7). pp. 1131-1139. doi:10.1021/acssynbio.5b00217

2016

Foo, Mathias, Jongrae, Kim, Jongmin, Kim and Bates, Declan (2016) Proportional-integral degradation (PI-Deg) control allows accurate tracking of biomolecular concentrations with fewer chemical reactions. IEEE Life Sciences Letters . doi:10.1109/LLS.2016.2644652

Chikhani, M., Das, Anup, Haque, M., Wang, Wenfei, Bates, Declan G. and Hardman, J. G. (2016) High PEEP in acute respiratory distress syndrome: quantitative evaluation between improved arterial oxygenation and decreased oxygen delivery. British Journal of Anaesthesia, 117 (5). pp. 650-658. doi:10.1093/bja/aew314

Chikhani, M., Das, Anup, Haque, M., Wang, Wenjie , Bates, Declan and Hardman, J. G. (2016) High PEEP in ARDS : quantitative evaluation between improved oxygenation and decreased oxygen delivery. British Journal of Anaesthesia, 117 (5). pp. 650-658. doi:10.1093/bja/aew314

Foo, Mathias, Sawlekar, Rucha, Kulkarni, Vishwesh V. and Bates, Declan (2016) Biologically inspired design of feedback control systems implemented using DNA strand displacement reactions. In: 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Orlando, Florida, 16-20 Aug 2016. Published in: 2016 IEEE 38th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC) ISSN 1558-4615.

Foo, Mathias, Sawlekar, Rucha and Bates, Declan (2016) Exploiting the dynamic properties of covalent modification cycle for the design of synthetic analog biomolecular circuitry. Journal of Biological Engineering, 10 (15).

Montefusco, Francesco, Akman, Ozgur E., Soyer, Orkun S. and Bates, Declan (2016) Ultrasensitive negative feedback control : a natural approach for the design of synthetic controllers. PLoS One, 11 (8). e0161605. doi:10.1371/journal.pone.0161605

Sawlekar, Rucha, Montefusco, Francesco, Kulkarni, Vishwesh V. and Bates, Declan (2016) Implementing nonlinear feedback controllers using DNA strand displacement reactions. IEEE Transactions on NanoBioscience, 15 (5). 443 -454. doi:10.1109/TNB.2016.2560764

Bowyer, Jack E., Zhao, Jia, Subsoontorn, Pakpoom, Wong, Wilson, Rosser, Susan and Bates, Declan (2016) Mechanistic modeling of a rewritable recombinase addressable data module. IEEE Transactions on Biomedical Circuits and Systems, 10 (6). pp. 1161-1170. doi:10.1109/TBCAS.2016.2526668

Sawlekar, Rucha, Montefusco, Francesco, Kulkarni, Vishwesh V. and Bates, Declan (2016) Implementing nonlinear feedback controllers using DNA strand displacement reactions. IEEE Transactions on NanoBioscience, 15 (5). pp. 443-454. doi:DOI: 10.1109/TNB.2016.2560764

Steinacher, Arno, Bates, Declan, Akman, Ozgur E. and Soyer, Orkun S. (2016) Nonlinear dynamics in gene regulation promote robustness and evolvability of gene expression levels. PLoS One, 11 (4). e0153295. doi:10.1371/journal.pone.0153295

2015

Sawlekar, Rucha, Montefusco, Francesco, Kulkarni, Vishwesh V. and Bates, Declan (2015) Biomolecular implementation of a quasi sliding mode feedback controller based on DNA strand displacement reactions. In: 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), Milan, Italy, August 25-29, 2015. Published in: Proceedings of the 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society pp. 949-952. ISSN DOI: 10.1109/EMBC.2015.7318520.

Das, Anup, Cole, Oana, Chikhani, Marc, Wang, Wenfei, Ali, Tayyba, Haque, Mainul, Bates, Declan and Hardman, Jonathan G. (2015) Evaluation of lung recruitment maneuvers in acute respiratory distress syndrome using computer simulation. Critical Care, Volume 19 (Number 1). Article number 8. doi:10.1186/s13054-014-0723-6