The Library
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Number of items: 48.
2023
Montefusco, Francesco, Procopio, Anna, Bates, Declan G., Amato, Francesco and Cosentino, Carlo (2023) Scalable reverseβengineering of gene regulatory networks from timeβcourse measurements. International Journal of Robust and Nonlinear Control, 33 (9). pp. 5023-5038. doi:10.1002/rnc.6044 ISSN 1049-8923.
Daudre-Vignier, Clara, Bates, Declan G., Scott, Timothy E., Hardman, Jonathan G. and Laviola, Marianna (2023) Evaluating current guidelines for cardiopulmonary resuscitation using an integrated computational model of the cardiopulmonary system. Resuscitation, 186 . 109758. doi:10.1016/j.resuscitation.2023.109758 ISSN 0300-9572.
Paulino, Nuno M. G., Foo, Mathias, de Greef, Tom F. A., Kim, Jongmin and Bates, Declan G. (2023) A theoretical framework for implementable nucleic acids feedback systems. Bioengineering, 10 (4). 466. doi:10.3390/bioengineering10040466 ISSN 2306-5354.
2022
Kwok, T'ng Chang, Henry, Caroline, Saffaran, Sina, Meeus, Marisse, Bates, Declan G., Van Laere, David, Boylan, Geraldine, Boardman, James P. and Sharkey, Don (2022) Application and potential of artificial intelligence in neonatal medicine. Seminars in Fetal and Neonatal Medicine, 27 (5). 101346. doi:10.1016/j.siny.2022.101346 ISSN 1744-165X.
Weaver, Liam, Saffaran, Sina, Chikhani, Marc, Laffey, John G., Scott, Tim E., Camporota, Luigi, Hardman, Jonathan G. and Bates, Declan G. (2022) Why reduced inspiratory pressure could determine success of non-invasive ventilation in acute hypoxic respiratory failure. In: 2022 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Glasgow, Scotland, United Kingdom, 11-15 Jul 2022 ISBN 9781728127828. doi:10.1109/embc48229.2022.9871901 ISSN 2694-0604.
Mistry, Sonal, Brook, Bindi S., Saffaran, Sina, Chikhani, Marc, Hannon, David M., Laffey, John G., Scott, Tim E., Camporota, Luigi, Hardman, Jonathan G. and Bates, Declan G. (2022) A computational cardiopulmonary physiology simulator accurately predicts individual patient responses to changes in mechanical ventilator settings. In: 2022 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), Glasgow, Scotland, United Kingdom, 11-15 Jul 2022 ISBN 9781728127828. doi:10.1109/embc48229.2022.9871182 ISSN 2694-0604.
Darlington, Alexander P. S. and Bates, Declan G. (2022) Performance and robustness analysis of control strategies for ameliorating cellular host-circuit interactions. In: 2022 European Control Conference (ECC), London, United Kingdom, 12-15 Jul 2022. Published in: 2022 European Control Conference (ECC) doi:10.23919/ecc55457.2022.9837985 ISSN 9783907144077.
Legon, Laurence, Corre, Christophe, Bates, Declan G. and Mannan, Ahmad A. (2022) gcFront : a tool for determining a Pareto front of growth-coupled cell factory designs. Bioinformatics, 38 (14). pp. 3657-3659. doi:10.1093/bioinformatics/btac376 ISSN 1460-2059.
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 ISSN 0007-0912.
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 ISSN 1465-993X.
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 silicoβpotential and pitfalls. Seminars in Respiratory and Critical Care Medicine, 43 (3). pp. 335-345. doi:10.1055/s-0042-1744446 ISSN 1098-9048.
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 ISSN 2056-7189.
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 ISSN 0007-0912.
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 ISSN 2405-8963.
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 ISSN 0342-4642.
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 ISSN 09591524.
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 ISSN 1545-5963.
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 ISSN 1465-993X.
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 ISSN 0903-1936.
Darlington, Alexander P. S., Kim, Juhyun, JimΓ©nez, JosΓ© 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 ISSN 2161-5063.
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 ISSN 0167-7799.
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 ISSN 2475-1456.
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 ISSN 0035-8665.
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 ISSN 2163-8306.
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 ISSN 2161-5063.
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 ISSN 2161-5063.
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 ISSN 2045-2322.
Darlington, Alexander P. S., Kim, Juhyun, JimΓ©nez, JosΓ© 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 ISSN 2041-1723.
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 ISSN 1754-1611.
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 ISSN 2045-2322.
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 ISSN 2398-6182.
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 ISSN 0098-1354.
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 ISSN 1471-2466.
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 ISSN 2161-5063.
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 ISSN 2332-7685.
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 ISSN 0007-0912.
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 ISSN 0007-0912.
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). ISSN 1754-1611.
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 ISSN 1932-6203.
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 ISSN 1536-1241.
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 ISSN 1940-9990.
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:10.1109/TNB.2016.2560764 ISSN 1536-1241.
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 ISSN 1932-6203.
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 ISSN 1466-609X.
This list was generated on Sat Apr 20 03:58:52 2024 BST.